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SAS results for UniProt accession no. P45686

Sequence annotated by structure

Key:
Sec. struc: By homology
  Helix Strand  
Residue contacts:   to ligand
Active sites:   (from PDB SITE records)

Secondary structure shown in red comes from a homologous protein structure which is at least 30% sequence identical to the target protein and has an alignment overlap of at least 80 residues or at least three-quarters of the length of the target sequence (whichever overlap is the larger).

Click on annotated residues to get source(s) of each annotation.

 

FASTA alignment for UniProt accession no. P45686 - coloured by no. of contacts to ligand

Below are the FASTA results from a search of the sequence of UniProt accession no. P45686 against all protein sequences in the PDB. Identical sequences are grouped together and represented by a single 'consensus' sequence (asterisked) onto which all relevant annotations are mapped. The number of sequences represented by each consensus sequence is shown by the '×n' on the right of the alignment. Use the box below to modify the annotations shown on the alignment. At the bottom of the page are given the FASTA stats for all the sequences. There you can exclude any sequences from the alignment.

Struct

FASTA

The search returned 36 unique sequences (including 7 consensus sequences) giving 58 sequence matches in all. The 26 sequences excluded from the alignment are listed at the end.

Modify alignment: Annotate by:
  Number:  
  Show secondary structure: Yes No  


                1         2         3         4         5         6     
       12345678901234567890123456789012345678901234567890123456789012345   Protein name
       ---------+---------+---------+---------+---------+---------+-----   ------------
P45686 maemqdykqslkyetfsylppmnaeriraqikyaiaqgwspgie----hv--------e-----v   Ribulose bisphosphate carboxylase small chain  ...
1svd:M --EMQDYKQSLKYETFSYLPPMNAERIRAQIKYAIAQGWSPGIE----HV--------E-----V   The structure of halothiobacillus neapolitanus rubisco
2ybv:B -----tlpkerryetfsylpplsdaqiarqiqyaidqgyhpcve----fn--------e-----t   Structure of rubisco from thermosynechococcus elongatus
1uzh:C -MMVWTPVNNKMFETFSYLPPLTDEQIAAQVDYIVANGWIPCLE----FA--------E-----H   A chimeric chlamydomonas, synechococcus rubisco enzyme
3zxw:B ----------------sylpplsdaqiarqiqyaidqgyhpcve----fn--------e-----t   Structure of activated rubisco from thermosynechococcus  ...
1rsc:M --smktlpkerrfetfsylpplsdrqiaaqieymieqgfhplie----fn--------e-----h   Structure of an effector induced inactivated state of  ...
1rbl:M --smktlpkerrfetfsylpplsdrqiaaqieymieqgfhplie----fn--------e-----h   Structure determination and refinement of ribulose 1,5  ...
1bxn:I --------mritqgtfsflpeltdeqitkqleyclnqgwavgle----yt--------d-----d   The crystal structure of rubisco from alcaligenes eutrophus  ...
1bwv:S --------vritqgtfsflpdltdeqikkqidymiskklaigie----yt--------n-----d   Activated ribulose 1,5-bisphosphate carboxylase/oxygenase  ...
1iwa:B --------mritqgtfsflpdltdeqikkqidymiskklaigie----yt--------n-----d   Rubisco from galdieria partita
4f0h:B*--------MRITQGTFSFLPDLTDEQIKKQIDYMISKKLAIGIE----YT--------N-----D×3 Unactivated rubisco with oxygen bound
1gk8:I -XMVWTPVNNKMFETFSYLPPLTDEQIAAQVDYIVANGWIPCLE----FA--------E-----A   Rubisco from chlamydomonas reinhardtii
1ir2:I -xmvwtpvnnkmfetfsylpplsdeqiaaqvdyivangwipcle----fa--------esdkayv   Crystal structure of activated ribulose-1,5-bisphosphate  ...
1uw9:C*-MMVWTPVNNKMFETFSYLPPLTDEQIAAQVDYIVANGWIPCLE----FA--------E-----A×2 L290f-a222t chlamydomonas rubisco mutant
2v63:I*-XMVWTPVNNKMFETFSYLPPLTDEQIAAQVDYIVANGWIPCLE----FA--------E-----A×7 Crystal structure of rubisco from chlamydomonas reinhardtii  ...
1bur:S -mqvwpilgmkkyetlsylppltteqllaevnyllvnnwipcle----f---------e-----v   Ribulose 1,5-bisphosphate carboxylase/oxygenase complexed  ...
1ej7:S*-mqvwppinkkkyetlsylpdlsqeqllseveyllkngwvpclefetehg--------f-----v×4 Crystal structure of unactivated tobacco rubisco with bound  ...
1uzd:C -MMVWTPVNNKMFETFSYLPPLTDEQIAAQVDYIVANGWIPCLE----FATDHGFVYRE-----H   Chlamydomonas,spinach chimeric rubisco
4rub:S -mqvwppinkkkyetlsylpdlsqeqllseveyllkngwvpclefetehg--------f-----v   A crystal form of ribulose-1,5-bisphosphate  ...
3axk:S xmqvwpiegikkfetlsylppltvedllkqieyllrskwvpcle----fs--------k-----v   Structure of rice rubisco in complex with NADP(h)
1wdd:S -xqvwpiegikkfetlsylppltvedllkqieyllrskwvpcle----fs--------k-----v   Crystal structure of activated rice rubisco complexed with  ...

                                         1         1         1         1
           7         8         9         0         1         2         3
       67890123456789012345678901234567890123456789012345678901234567890   Protein name
       ----+---------+---------+---------+---------+---------+---------+   ------------
P45686 -----knsm------------------n------q--------ywymwklpffgeqnvdnvlaei   Ribulose bisphosphate carboxylase small chain  ...
1svd:M -----KNSM------------------N------Q--------YWYMWKLPFFGEQNVDNVLAEI   The structure of halothiobacillus neapolitanus rubisco
2ybv:B -----snae------------------i------r--------ywtmwklplfnctnaqdvlnev   Structure of rubisco from thermosynechococcus elongatus
1uzh:C -----SNPE------------------E------F--------YWTMWKLPMFGCRDPMQVLREI   A chimeric chlamydomonas, synechococcus rubisco enzyme
3zxw:B -----snae------------------i------r--------ywtmwklplfnctnaqdvlnev   Structure of activated rubisco from thermosynechococcus  ...
1rsc:M -----snpe------------------e------f--------ywtmwklplfdckspqqvldev   Structure of an effector induced inactivated state of  ...
1rbl:M -----snpe------------------e------f--------ywtmwklplfacaapqqvldev   Structure determination and refinement of ribulose 1,5  ...
1bxn:I -----phpr------------------n------t--------ywemfglpmfdlrdaagilmei   The crystal structure of rubisco from alcaligenes eutrophus  ...
1bwv:S -----ihpr------------------n------a--------yweiwglplfdvtdpaavlfei   Activated ribulose 1,5-bisphosphate carboxylase/oxygenase  ...
1iwa:B -----ihpr------------------n------a--------yweiwglplfdvtdpaavlfei   Rubisco from galdieria partita
4f0h:B*-----IHPR------------------N------S--------FWEMWGLPLFEVTDPAPVLFEI×3 Unactivated rubisco with oxygen bound
1gk8:I -----DKAYVSNESAIRFGSVSCLYYDN------R--------YWTMWKLPMFGCRDPMQVLREI   Rubisco from chlamydomonas reinhardtii
1ir2:I -----snesairfgsvsclyyd-----n------r--------ywtmwklpmfgcrdpmqvlrei   Crystal structure of activated ribulose-1,5-bisphosphate  ...
1uw9:C*-----DKAYVSNESAIRFGSVSCLYYDN------R--------YWTMWKLPMFGCRDPMQVLREI×2 L290f-a222t chlamydomonas rubisco mutant
2v63:I*-----DKAYVSNESAIRFGSVSCLYYDN------R--------YWTMWKLPMFGCRDPMQVLREI×7 Crystal structure of rubisco from chlamydomonas reinhardtii  ...
1bur:S -----kdgfvyrehlkspgyyd-----g------r--------ywtmwklpmfgctdpaqvlnel   Ribulose 1,5-bisphosphate carboxylase/oxygenase complexed  ...
1ej7:S*-----yren------------------n------kspgyydgrywtmwklpmfgctdatqvlaev×4 Crystal structure of unactivated tobacco rubisco with bound  ...
1uzd:C -----HNSP------------------GYYDG--R--------YWTMWKLPMFGCRDPMQVLREI   Chlamydomonas,spinach chimeric rubisco
4rub:S -----yren------------------n------kspgyydgrywtmwklpmfgctdatqvlaev   A crystal form of ribulose-1,5-bisphosphate  ...
3axk:S gfvyrenhr------------------spgyydgr--------ywtmwklpmfgctdatqvlkel   Structure of rice rubisco in complex with NADP(h)
1wdd:S gfvyrenhr------------------spgyydgr--------ywtmwklpmfgctdatqvlkel   Crystal structure of activated rice rubisco complexed with  ...

                1         1         1         1         1         1     
                4         5         6         7         8         9     
       12345678901234567890123456789012345678901234567890123456789012345   Protein name
       ---------+---------+---------+---------+---------+---------+-----   ------------
P45686 eacrsaypthqvklvaydny--aqslglafvvyrgn-----------------------------   Ribulose bisphosphate carboxylase small chain  ...
1svd:M EACRSAYPTHQVKLVAYDNY--AQSLGLAFVVYRGN-----------------------------   The structure of halothiobacillus neapolitanus rubisco
2ybv:B qqcrseypncfirvvafdni--kqcqvmsfivykp------------------------------   Structure of rubisco from thermosynechococcus elongatus
1uzh:C VACTKAFPDAYVRLVAFDNQ--KQVQIMGFLVQRPKTARDFQPANKRSV----------------   A chimeric chlamydomonas, synechococcus rubisco enzyme
3zxw:B qqcrseypncfirvvafdni--kqcqvmsfivykp------------------------------   Structure of activated rubisco from thermosynechococcus  ...
1rsc:M recrseygdcyirvagfdni--kecqtvsfivhrpgr----------------------------   Structure of an effector induced inactivated state of  ...
1rbl:M recrseygdcyirvagfdni--kecqtssfivhrpgr----------------------------   Structure determination and refinement of ribulose 1,5  ...
1bxn:I nnarntfpnhyirvtafdsthtvesvvmsfivnrpadepgfrlvrqeepgrtlrysiesya----   The crystal structure of rubisco from alcaligenes eutrophus  ...
1bwv:S nacrkarsnfyikvvgfssvrgiestiisfivnrpkhepgfnlmrqedksrsikytihsyesykp   Activated ribulose 1,5-bisphosphate carboxylase/oxygenase  ...
1iwa:B nacrkarsnfyikvvgfssvrgiestiisfivnrpkhepgfnlmrqedksrsikytihsyesykp   Rubisco from galdieria partita
4f0h:B*NACRKAKSNFYIKVVGFSSERGIESTIISFIVNRPKHEPGFNLIRQEDKSRSIKYSIQAYETYKP×3 Unactivated rubisco with oxygen bound
1gk8:I VACTKAFPDAYVRLVAFDNQ--KQVQIMGFLVQR-------------------------------   Rubisco from chlamydomonas reinhardtii
1ir2:I vactkafpdayvrlvafdnq--kqvqimgflvqrpksardwqpankrs-----------------   Crystal structure of activated ribulose-1,5-bisphosphate  ...
1uw9:C*VACTKAFPDAYVRLVAFDNQ--KQVQIMGFLVQRPKSARDWQPANKRSV----------------×2 L290f-a222t chlamydomonas rubisco mutant
2v63:I*VACTKAFPDAYVRLVAFDNQ--KQVQIMGFLVQRPKTARDFQPANKRS-----------------×7 Crystal structure of rubisco from chlamydomonas reinhardtii  ...
1bur:S eeckkaypdafiriigfdnk--rqvqcisfiaykpagy---------------------------   Ribulose 1,5-bisphosphate carboxylase/oxygenase complexed  ...
1ej7:S*eeakkaypqawiriigfdnv--rqvqcisfiaykpegy---------------------------×4 Crystal structure of unactivated tobacco rubisco with bound  ...
1uzd:C VACTKAFPDAYVRLVAFDNQ--KQVQIMGFLVQRPKQPANKRSV---------------------   Chlamydomonas,spinach chimeric rubisco
4rub:S geakkaypqawiriigfdnv--rqvqcisfiaykpegy---------------------------   A crystal form of ribulose-1,5-bisphosphate  ...
3axk:S eeakkaypdafvriigfdnv--rqvqcisfiaykp------------------------------   Structure of rice rubisco in complex with NADP(h)
1wdd:S eeakkaypdafvriigfdnv--rqvqlisfiaykppg----------------------------   Crystal structure of activated rice rubisco complexed with  ...

           2
           0
       67890                                                               Protein name
       ----+                                                               ------------
P45686 -----                                                               Ribulose bisphosphate carboxylase small chain  ...
1svd:M -----                                                               The structure of halothiobacillus neapolitanus rubisco
2ybv:B -----                                                               Structure of rubisco from thermosynechococcus elongatus
1uzh:C -----                                                               A chimeric chlamydomonas, synechococcus rubisco enzyme
3zxw:B -----                                                               Structure of activated rubisco from thermosynechococcus  ...
1rsc:M -----                                                               Structure of an effector induced inactivated state of  ...
1rbl:M -----                                                               Structure determination and refinement of ribulose 1,5  ...
1bxn:I -----                                                               The crystal structure of rubisco from alcaligenes eutrophus  ...
1bwv:S edery                                                               Activated ribulose 1,5-bisphosphate carboxylase/oxygenase  ...
1iwa:B edery                                                               Rubisco from galdieria partita
4f0h:B*EDQRY                                                            ×3 Unactivated rubisco with oxygen bound
1gk8:I -----                                                               Rubisco from chlamydomonas reinhardtii
1ir2:I -----                                                               Crystal structure of activated ribulose-1,5-bisphosphate  ...
1uw9:C*-----                                                            ×2 L290f-a222t chlamydomonas rubisco mutant
2v63:I*-----                                                            ×7 Crystal structure of rubisco from chlamydomonas reinhardtii  ...
1bur:S -----                                                               Ribulose 1,5-bisphosphate carboxylase/oxygenase complexed  ...
1ej7:S*-----                                                            ×4 Crystal structure of unactivated tobacco rubisco with bound  ...
1uzd:C -----                                                               Chlamydomonas,spinach chimeric rubisco
4rub:S -----                                                               A crystal form of ribulose-1,5-bisphosphate  ...
3axk:S -----                                                               Structure of rice rubisco in complex with NADP(h)
1wdd:S -----                                                               Crystal structure of activated rice rubisco complexed with  ...

Residue colours: black = 0, purple = 1, blue = 2, green = 3, orange = 4, red = 5 or more contacts.

Sequence listing

The listing below shows the FASTA statistics for the PDB entries that matched UniProt accession no. P45686. Ditto marks indicate identical sequences represented by a single representative sequence in the alignment above. The representative is asterisked and the names of all its duplicate sequences are indented to the right.

Structures whose names are given in purple are those that are annotated above. The parameters defining which sequences can transfer their annotations are shown at the bottom of the page where they can be altered and the alignment regenerated.

Use the checkboxes to the left of the PDB codes to exclude any sequences from the alignment (or to add back any sequences in the Excluded list). Then click the SELECT button at the bottom of the page to redisplay the alignment.

Aligned sequences

  Smith-
Waterman
score
%-tage
identity
a.a.
overlap
Seq
len
z-score E-
value
  PDB
code
Protein name
1. - - - 110 - - P45686 Ribulose bisphosphate carboxylase small chain OS=Halothiobacillus neapolitanus (strain ATCC 23641 / c2) GN=cbbS PE=1 SV=1
2. 739 100.0% 108 108 969.2 5.2e-47 1svd:M The structure of halothiobacillus neapolitanus rubisco
3. 340 47.4% 97 104 453.1 2.9e-18 2ybv:B Structure of rubisco from thermosynechococcus elongatus
4. 322 49.0% 96 122 428.7 6.5e-17 1uzh:C A chimeric chlamydomonas, synechococcus rubisco enzyme
5. 310 45.7% 92 93 415.1 3.8e-16 3zxw:B Structure of activated rubisco from thermosynechococcus elon complexed with 2-carboxyarabinitol-1,5-diphosphate
6. 294 40.0% 105 109 393.3 6.2e-15 1rsc:M Structure of an effector induced inactivated state of ribulo bisphosphate carboxylase(slash)oxygenase: the binary comple enzyme and xylulose bisphosphate
7. 286 40.0% 105 109 382.9 2.3e-14 1rbl:M Structure determination and refinement of ribulose 1,5 bisph carboxylase(slash)oxygenase from synechococcus pcc6301
8. 247 34.4% 96 129 331.2 1.8e-11 1bxn:I The crystal structure of rubisco from alcaligenes eutrophus angstroms.
9. 216 36.5% 96 138 290.7 3.2e-09 1bwv:S Activated ribulose 1,5-bisphosphate carboxylase/oxygenase (r complexed with the reaction intermediate analogue 2-carboxy 1,5-bisphosphate
10. 216 36.5% 96 138 290.7 3.2e-09 1iwa:B Rubisco from galdieria partita
11. 213 36.5% 96 138 286.8 5.3e-09 4f0h:B * Unactivated rubisco with oxygen bound
12. " " " " " "  = 4f0k:B *
Unactivated rubisco with magnesium and carbon dioxide bound
13. " " " " " "  = 4f0m:B *
Unactivated rubisco with magnesium and a water molecule boun
14. 288 41.2% 114 125 258.9 1.9e-07 1gk8:I Rubisco from chlamydomonas reinhardtii
15. 288 43.0% 114 139 258.2 2.1e-07 1ir2:I Crystal structure of activated ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisco) from green alga, chlamydomo reinhardtii complexed with 2-carboxyarabinitol-1,5-bisphosp cabp)
16. 288 41.2% 114 140 258.2 2.1e-07 1uw9:C * L290f-a222t chlamydomonas rubisco mutant
17. " " " " " "  = 1uwa:C *
L290f mutant rubisco from chlamydomonas
18. 288 41.2% 114 139 258.2 2.1e-07 2v63:I * Crystal structure of rubisco from chlamydomonas reinhardtii with a large-subunit v331a mutation
19. " " " " " "  = 2v67:I *
Crystal structure of chlamydomonas reinhardtii rubisco with a large-subunit supressor mutation t342i
20. " " " " " "  = 2v68:I *
Crystal structure of chlamydomonas reinhardtii rubisco with large-subunit mutations v331a, t342i
21. " " " " " "  = 2v69:I *
Crystal structure of chlamydomonas reinhardtii rubisco with a large-subunit mutation d473e
22. " " " " " "  = 2v6a:I *
Crystal structure of chlamydomonas reinhardtii rubisco with large-subunit mutations v331a, g344s
23. " " " " " "  = 2vdh:I *
Crystal structure of chlamydomonas reinhardtii rubisco with a large-subunit c172s mutation
24. " " " " " "  = 2vdi:I *
Crystal structure of chlamydomonas reinhardtii rubisco with a large-subunit c192s mutation
25. 271 36.4% 110 123 251.4 4.9e-07 1bur:S Ribulose 1,5-bisphosphate carboxylase/oxygenase complexed with carbon dioxide, mg==2+== and 2-carboxyarabinitol-1,5-bisphosphate
26. 263 35.8% 109 123 250.1 5.8e-07 1ej7:S * Crystal structure of unactivated tobacco rubisco with bound ions
27. " " " " " "  = 1rlc:S *
Crystal structure of the unactivated ribulose 1, 5-bisphosph carboxylase(slash)oxygenase complexed with a transition sta 2-carboxy-d-arabinitol 1,5-bisphosphate
28. " " " " " "  = 1rld:S *
Solid-state phase transition in the crystal structure of rib biphosphate carboxylase(slash)oxygenase
29. " " " " " "  = 3rub:S *
Crystal structure of the unactivated form of ribulose-1,5-bi carboxylase(slash)oxygenase from tobacco refined at 2.0-ang resolution
30. 288 44.4% 108 129 249.7 6.1e-07 1uzd:C Chlamydomonas,spinach chimeric rubisco
31. 254 34.9% 109 123 238.4 2.6e-06 4rub:S A crystal form of ribulose-1,5-bisphosphate carboxylase(slas oxygenase from nicotiana tabacum in the activated state
32. 251 36.1% 108 120 237.2 3e-06 3axk:S Structure of rice rubisco in complex with NADP(h)
33. 250 36.1% 108 121 235.9 3.6e-06 1wdd:S Crystal structure of activated rice rubisco complexed with 2 carboxyarabinitol-1,5-bisphosphate

Number of sequences: 33

Excluded sequences

  Smith-
Waterman
score
%-tage
identity
a.a.
overlap
Seq
len
z-score E-
value
  PDB
code
Protein name
1. 250 36.1% 108 122 235.8 3.6e-06 3axm:S Structure of rice rubisco in complex with 6pg
2. 246 33.6% 113 122 231.9 6e-06 1ir1:S Crystal structure of spinach ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisco) complexed with co2, mg2+ an carboxyarabinitol-1,5-bisphosphate
3. 262 35.5% 110 123 228.1 9.8e-06 8rub:S Lyase(carbon-carbon)
4. 243 33.0% 109 123 226.8 1.2e-05 1aa1:S * Activated spinach rubisco in complex with the product 3- phosphoglycerate
5. " " " " " "  = 1aus:S *
Activated unliganded spinach rubisco
6. " " " " " "  = 1rbo:S *
Spinach rubisco in complex with the inhibitor 2-carboxyarabi diphosphate
7. " " " " " "  = 1rco:S *
Spinach rubisco in complex with the inhibitor d-xylulose-2, 2-diol-1,5-bisphosphate
8. " " " " " "  = 1rcx:S *
Non-activated spinach rubisco in complex with its substrate ribulose-1,5-bisphosphate
9. " " " " " "  = 1rxo:S *
Activated spinach rubisco in complex with its substrate ribu bisphosphate and calcium
10. " " " " " "  = 1upm:C *
Activated spinach rubisco complexed with 2-carboxyarabinitol 2 bisphosphat and ca2+.
11. " " " " " "  = 1upp:I *
Spinach rubisco in complex with 2-carboxyarabinitol 2 bisphosphate and calcium.
12. " " " " " "  = 8ruc:I *
Activated spinach rubisco complexed with 2-carboxyarabinitol bisphosphate
13. 241 32.1% 109 123 224.2 1.6e-05 4mkv:S Structure of pisum sativum rubisco with aba
14. 223 30.3% 109 123 200.9 0.00032 4hhh:S Structure of pisum sativum rubisco
15. 84 28.0% 50 76 124.1 6.1 3u2b:C Structure of the sox4 hmg domain bound to DNA
16. 86 25.0% 100 348 115.9 17 3r2u:A 2.1 angstrom resolution crystal structure of metallo-beta-la from staphylococcus aureus subsp. Aureus col
17. 82 28.1% 64 239 113.4 24 1zgm:A * Crystal structure of putative glutathione s-transferase (15162326) from agrobacterium tumefaciens at 2.25 a resolution
18. " " " " " "  = 2fno:A *
Crystal structure of a glutathione s-transferase (atu5508) f agrobacterium tumefaciens str. C58 at 2.00 a resolution
19. 77 36.1% 36 99 113.1 25 4e5x:G Crystal structure of a complex between the human adenovirus 19k protein and mhc class i molecule hla-a2/tax
20. 73 38.5% 52 60 111.5 31 3pnw:C Crystal structure of the tudor domain of human tdrd3 in comp an anti-tdrd3 fab
21. 84 35.8% 53 488 110.9 33 3vue:A * Crystal structure of rice granule bound starch synthase i ca domain
22. " " " " " "  = 3vuf:A *
Crystal structure of rice granule bound starch synthase i ca domain in complex with adp
23. 84 32.9% 73 550 110.1 37 1jkh:A Crystal structure of y181c mutant HIV-1 reverse transcriptas complex with dmp-266(efavirenz)
24. 83 33.8% 71 540 108.9 42 1dtt:A Crystal structure of HIV-1 reverse transcriptase in complex with pett-2 (pett130a94)
25. 83 33.8% 71 545 108.9 43 1s1x:A Crystal structure of v108i mutant HIV-1 reverse transcriptase in complex with nevirapine
26. 84 28.2% 71 734 108.1 47 4l79:A Crystal structure of nucleotide-free myosin 1b residues 1-72 bound calmodulin

Number of sequences: 26

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Annotation parameters

The parameters below were used in determining which structural annotations could be transferred on to the target sequence. You can change the parameters and regenerate the SAS alignments and annotation by pressing the Rerun button.

Min. seq. identity:   Min. seq. overlap   Max. E-value

  spacer

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