Alignments for a candidate for susB in Shewanella loihica PV-4

GapMind for catabolism of small carbon sources

Alignments for a candidate for susB in Shewanella loihica PV-4

Align α-glucosidase (YgjK;EcYgjK;b3080) (EC 3.2.1.20|3.2.1.84) (characterized)
to candidate 5211333 Shew_3745 glycoside hydrolase family protein (RefSeq)

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



>FitnessBrowser__PV4:5211333
          Length = 738

 Score =  447 bits (1150), Expect = e-130
 Identities = 282/787 (35%), Positives = 409/787 (51%), Gaps = 84/787 (10%)

Query: 10  VTCALLISF-SAHAANADNYKNVINRTGAPQYMKDYDYDDHQRFNP-FFDLGAWHGHLLP 67
           ++ +LL S  S   A A  Y++++N  G P  M+  D   +      + D GAWHG  LP
Sbjct: 15  LSLSLLCSLPSVSVAQASEYRDLLNYRGTPSNMEQRDPQGNLTIPAVYMDQGAWHGFHLP 74

Query: 68  DGPNTMGGFPGVALLTEEYINFMASNFDRLTVW--QDGKKVDFT----LEAYSIPGALVQ 121
           D P   GGF G   + +EY   ++ +  +L ++  + G+ VD      +E YS P  LVQ
Sbjct: 75  DSPAYYGGFTGPLFIAQEYSLHLSDSLQKLQLFSGESGQSVDLAKAEQVEIYSEPWGLVQ 134

Query: 122 KLTAKDVQVEMTLRFATPRTSLLETKIT--SNKPLD--LVWDGELLEKLEAKEGKPLSDK 177
           +   KD+++  TL ++  RT+++ T++   S+KP    L W G         +   L DK
Sbjct: 135 RFRFKDLELSTTLEYSDNRTAIVSTRLINLSDKPGSWRLSWSGSPFATHPKLKQYRLVDK 194

Query: 178 TIAGEYPDYQRKISATRDGLKVTFGKVRATWDLLTSGESEYQVHKSLPVQTEINGNRFTS 237
            +  E            D +   F  +  TW +    ++ Y++     V   + G +   
Sbjct: 195 RLLSE------------DAVTWQFTPIDQTWQMQLD-DASYRLAFEQAVTLSVEGPQ--G 239

Query: 238 KAHINGSTTLYTTYSHLL-TAQEVSKEQMQIRDILARPAFYLTA----SQQRWEEYLKKG 292
               +G  TL    + +L  A +    Q++ R         +TA    ++ RW++ L K 
Sbjct: 240 YRADSGLLTLAPGEATVLRAAHQYFHTQVEARHAAKLDWPTVTAKLAVNRSRWQQRLDK- 298

Query: 293 LTNPDATPEQTRVAVKAIETLNGNWRSPGGAVKFNTVTPSVTGRWFSGNQTWPWDTWKQA 352
           L      P + R+A K++ TL  NWRSP GA+  + VTPSVT +WF+G   W WD+WKQA
Sbjct: 299 LVRGGELPAR-RLAAKSMMTLLHNWRSPAGALLHDAVTPSVTYKWFNG--VWAWDSWKQA 355

Query: 353 FAMAHFNPDIAKENIRAVFSWQIQPGDSVRPQDVGFVPDLIAWNLSPERGGDGGNWNERN 412
            A+A F+  +A+ N+ A+F +Q    D +RP+D G +PD I +N    RGG GGNWNERN
Sbjct: 356 VALAQFDVALAELNVLAMFDYQFDAKDPLRPEDAGNLPDAIFYNPDASRGGKGGNWNERN 415

Query: 413 TKPSLAAWSVMEVYNVTQDKTWVAEMYPKLVAYHDWWLRNRDHNGNGVPEYGATRDKAHN 472
            KP LAAW+V ++Y  +QDK  +  +YPKLVAYH+WW RNRDHN NG+ EYGA R   H 
Sbjct: 416 GKPPLAAWAVWQIYQQSQDKALITRLYPKLVAYHEWWYRNRDHNHNGLAEYGANRHPRHG 475

Query: 473 TESGEMLFTVKKGDKEETQSGLNNYARVVEKGQYDSLEIPAQVAASWESGRDDAAVFGFI 532
            E G           E  + G  +   V+E             AA+WESG D+A  F   
Sbjct: 476 -EPG-----------EPGEPGEPDREAVIE-------------AAAWESGMDNAPRFDMG 510

Query: 533 DKEQLDKYVANGGKRSDWTVKFAENRSQDGTLLGYSLLQESVDQASYMYSDNHYLAEMAT 592
           D+ Q+                  EN    G LLGYS+ QESVD  SY+Y++  YLA+MA 
Sbjct: 511 DELQV-----------------LENYDAKGRLLGYSISQESVDLNSYLYAEKGYLAQMAE 553

Query: 593 ILGKPEEAKRYRQLAQQLADYINTCMFDPTTQFYYDVRIEDKPLANGCAGKPIVERGKGP 652
           +L    EA  +R+ A +L   I +  FD  + F+YD R+       G   + ++  GKG 
Sbjct: 554 LLDLDSEAAVWREQAARLGQLIRSEFFDEESGFFYDRRLA------GERSRLMIAEGKGV 607

Query: 653 EGWSPLFNGAATQANADAVVKVMLDPKEFNTFVPLGTAALTNPAFGADIYWRGRVWVDQF 712
           EGW PL+ GAA+QA A+ ++   L+   F T +P  T +  N AF    YWRG VW+DQ 
Sbjct: 608 EGWLPLWAGAASQAQAEQMIATQLNASNFGTKLPFPTVSADNSAFAPRRYWRGPVWLDQA 667

Query: 713 WFGLKGMERYGYRDDALKLADTFFRHAKGLTADGPIQENYNPLTGAQQGAPNFSWSAAHL 772
            FGL+G+ RYG+ + A +LA      A G+  DGPI+ENY+PLTG      NFSWSA+ L
Sbjct: 668 LFGLQGVSRYGHDELARRLATRLVNEADGVLGDGPIRENYDPLTGDGLHCTNFSWSASVL 727

Query: 773 YMLYNDF 779
            ++Y  +
Sbjct: 728 LLIYRSW 734


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: 1767
Number of extensions: 89
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 783
Length of database: 738
Length adjustment: 40
Effective length of query: 743
Effective length of database: 698
Effective search space:   518614
Effective search space used:   518614
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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Protein sequences (fasta format)
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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