Alignments for a candidate for susB in Shewanella amazonensis SB2B

GapMind for catabolism of small carbon sources

Alignments for a candidate for susB in Shewanella amazonensis SB2B

Align α-glucosidase (YgjK;EcYgjK;b3080) (EC 3.2.1.20|3.2.1.84) (characterized)
to candidate 6939533 Sama_3625 cell wall surface anchor family protein (RefSeq)

Query= CAZy::AAA57881.1
         (783 letters)



>FitnessBrowser__SB2B:6939533
          Length = 717

 Score =  454 bits (1169), Expect = e-132
 Identities = 276/741 (37%), Positives = 390/741 (52%), Gaps = 99/741 (13%)

Query: 55  FFDLGAWHGHLLPDGPNTMGGFPGVALLTEEYINFMASNFDRLTVWQDGKKVDFT-LEAY 113
           + D GAWHG  LPD  +  G FPG  ++ +EY   +++  + +++ +D K ++   L+  
Sbjct: 42  YTDRGAWHGFHLPDERHA-GSFPGPLIIAQEYSLHLSAAMEAVSIGRDEKPLEQAELQTQ 100

Query: 114 SIPGALVQKLTAKDVQVEMTLRFATPRTSLLETKI--TSNKP--LDLVWDGELLEKLEAK 169
           S+P  L Q+L+    ++EM+L +   RT+++ TK+  TS +P  L L W G      +  
Sbjct: 101 SLPWGLFQRLSWPGTELEMSLSYFNNRTAIVTTKVRNTSGEPQTLTLEWHGA---PFDTH 157

Query: 170 EGKPLSDKTIAGEYPDYQRKISATRDGLKVTFGKVRATWDLLTSG-----------ESEY 218
             +PL+        P  Q+  S  R  L  +    R TW+ L  G           E+  
Sbjct: 158 NSQPLTLS------PQLQKTASGPR--LSWSMLPARDTWNRLIDGASYRLDFEGEREARL 209

Query: 219 QVHKSLPVQTEINGNRFTSKAHINGSTTLYTTYSHLLTAQEVSKEQMQIRDILARPAFYL 278
           +  K   V+T++      S+ +        T +S+  T QE S       D+   PA  L
Sbjct: 210 EADKGYVVKTDVYLGPGESREY-------RTAHSYFHTEQEASAGHFLWADVA--PA--L 258

Query: 279 TASQQRWEEYLKKGLTNPDATPEQTRVAVKAIETLNGNWRSPGGAVKFNTVTPSVTGRWF 338
           +A++ RW+    + + + D T +  R A KA+ TL  NWRS  GA++ + VTPS+T +WF
Sbjct: 259 SANRTRWQHRFDQLVASGDPTLD--RAAAKAVMTLAHNWRSAAGALQRDAVTPSITYKWF 316

Query: 339 SGNQTWPWDTWKQAFAMAHFNPDIAKENIRAVFSWQIQPGDSVRPQDVGFVPDLIAWNLS 398
           +G   W WD+WKQA A+A F+  +AK N+ A+F +Q    D VRPQD G +PD I +N  
Sbjct: 317 NG--VWAWDSWKQAVALARFDTLLAKSNVEAMFDYQFGADDPVRPQDAGNLPDAIFYNPG 374

Query: 399 PERGGDGGNWNERNTKPSLAAWSVMEVYNVTQDKTWVAEMYPKLVAYHDWWLRNRDHNGN 458
           PERGGDGGNWNERN KP LAAW+V E++    D  ++  MYPKLVAYH WW RNRDHNGN
Sbjct: 375 PERGGDGGNWNERNGKPPLAAWAVWEIHAHAPDLDFIKRMYPKLVAYHSWWYRNRDHNGN 434

Query: 459 GVPEYGATRDKAHNTESGEMLFTVKKGDKEETQSGLNNYARVVEKGQYDSLEIPAQVAAS 518
           G+ EYGA    AH                     G  N   ++E             AA+
Sbjct: 435 GLAEYGANVHPAH------------------VHDGKANPKAILE-------------AAA 463

Query: 519 WESGRDDAAVFGFIDKEQLDKYVANGGKRSDWTVKFAENRSQDGTLLGYSLLQESVDQAS 578
           WESG D+A  F   D                 T+   ENR+ DG LLGYSL QESVD  +
Sbjct: 464 WESGMDNAPRFDARD-----------------TLNVLENRTADGRLLGYSLSQESVDLNA 506

Query: 579 YMYSDNHYLAEMATILGKPEEAKRYRQLAQQLADYINTCMFDPTTQFYYDVRIEDKPLAN 638
           Y+Y++   LA++A  LG  E AK +R+ A  L   I   M+D +T F+YD+        +
Sbjct: 507 YLYAEKRLLAKLADALGDEEHAKSWRRDADNLGKLIREQMWDESTGFFYDL--------D 558

Query: 639 GCAGKPIVERGKGPEGWSPLFNGAATQANADAVVKVMLDPKEFNTFVPLGTAALTNPAFG 698
              GKP++  GKG EGW PL+ G ATQ  A+ ++   L    F T +P  T +  NPAF 
Sbjct: 559 SLTGKPLLGSGKGVEGWIPLWAGVATQQQAEVMIGRQLSAGTFGTPIPFPTVSADNPAFA 618

Query: 699 ADIYWRGRVWVDQFWFGLKGMERYGYRDDALKLADTFFRHAKGLTADGPIQENYNPLTGA 758
            + YWRG VW+DQ +F L G+ERYG +  A  LA   F   +G+    PI+ENY PLTG 
Sbjct: 619 PNKYWRGPVWLDQLYFALAGLERYGAQQQAKTLARRLFTRGEGILGQSPIRENYQPLTGE 678

Query: 759 QQGAPNFSWSAAHLYMLYNDF 779
              A NFSWSA+ + + +  +
Sbjct: 679 GLHATNFSWSASVILLAHQQW 699


Lambda     K      H
   0.316    0.133    0.413 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 1793
Number of extensions: 108
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 783
Length of database: 717
Length adjustment: 40
Effective length of query: 743
Effective length of database: 677
Effective search space:   503011
Effective search space used:   503011
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 55 (25.8 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for catabolism of small carbon sources