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 Alpha-glucosidase (EC 3.2.1.20) (characterized)
to candidate 5209418 Shew_1889 alpha amylase, catalytic region (RefSeq)

Query= reanno::ANA3:7025148
         (540 letters)



>FitnessBrowser__PV4:5209418
          Length = 541

 Score =  875 bits (2261), Expect = 0.0
 Identities = 411/538 (76%), Positives = 457/538 (84%), Gaps = 2/538 (0%)

Query: 1   MSELTWWRGAVIYQIYPRSLLDTNGDGVGDLRGIITKLDYIASLNVDAIWISPFFKSPMA 60
           M++L+WWRGAVIYQIYPRSL+D+NGDGVGDL+GII+KLDYIASLNVDAIWISPFFKSPM 
Sbjct: 1   MNQLSWWRGAVIYQIYPRSLMDSNGDGVGDLQGIISKLDYIASLNVDAIWISPFFKSPMK 60

Query: 61  DFGYDISDYREVDPLFGTMQDFDELIEKAHQRGIKVIIDQVLSHTSDQHAWFCESRESRT 120
           DFGYDISDYR +DPLFGTM DFDELI+KAH  GIKVIIDQVLSHTSDQHAWF ESR+SR 
Sbjct: 61  DFGYDISDYRAIDPLFGTMADFDELIDKAHGLGIKVIIDQVLSHTSDQHAWFSESRQSRD 120

Query: 121 NPKADWYVWAEPKEDGTAPNNWLAIFGGCAWEWEPRRQQYYLHNFLRSQPDINFHNPDVR 180
           N K DWYVWA+P  DGTAPNNWLAIFGGCAWEWEPRRQQYYLHNFL SQPD+NFHNPDVR
Sbjct: 121 NAKQDWYVWADPNPDGTAPNNWLAIFGGCAWEWEPRRQQYYLHNFLTSQPDLNFHNPDVR 180

Query: 181 QAVLDNVEFWLKKGVDGFRLDAITFCYHDEQLRDNPPKPKDKRQGRGFSEDNPYAYQYHY 240
           QAVLDNV+FWL KGVDGFRLDAITFCYHDEQLRDNPPKP+DKRQGRGFSEDNPYAYQYHY
Sbjct: 181 QAVLDNVKFWLDKGVDGFRLDAITFCYHDEQLRDNPPKPEDKRQGRGFSEDNPYAYQYHY 240

Query: 241 YNNDRPQTILFIEELRQLINRYPGAVTLGEVSAEDSLAVMAAYTKGEDRLHMAYSFELLT 300
           YNN RPQT+ FIEELR LIN+YPG VTLGEVS+EDSLA MA YT+G+DRLHMAYSFELLT
Sbjct: 241 YNNTRPQTVGFIEELRALINQYPGVVTLGEVSSEDSLATMAEYTQGDDRLHMAYSFELLT 300

Query: 301 DDYSAAYIRQTVEALEASIGDGWPCWAIGNHDAQRVASRWGRGKQTSDMVKMLNAMVNSL 360
           DD+S AYIR TVEALE SIGDGWPCWAIGNHD QRVA+RWGR    SDM KMLNAM+ SL
Sbjct: 301 DDFSPAYIRHTVEALEQSIGDGWPCWAIGNHDVQRVATRWGRDAFNSDMAKMLNAMLCSL 360

Query: 361 RGSVCSYQGEELGLTEAPIEYHELQDPFGKTFWPMFKGRDGCRTPMPWEQNADFSGFSQV 420
           RGSVCSYQGEELGL E  I Y +LQDPFG TFWPMFKGRDGCRTPMPW  +A+ +GFS  
Sbjct: 361 RGSVCSYQGEELGLGEVEIAYEQLQDPFGITFWPMFKGRDGCRTPMPWRHDANHAGFSDN 420

Query: 421 TPWLPIAQAHRALAVDVQEADSQSMLHGYRQFLAWRKGYPALVEGEIEFLDAPEPLLVFV 480
           TPWLP+   H+A+AVDVQEA+ +S+L+ YR  LAWRK +P LV G+I+F+++ + LLVF 
Sbjct: 421 TPWLPVPADHKAVAVDVQEANPESILNHYRHMLAWRKLHPILVTGDIKFIESTDALLVFE 480

Query: 481 RTSGEQKLLVCFNLQDTEQALSLDALSIQ--QEITGHGLKTAQRIADTLTFSAYACFY 536
           R  GEQ LLV FNL    Q+ SL  L  +    + GHGL  A+   D + F  + CFY
Sbjct: 481 RRLGEQTLLVAFNLSGQPQSFSLAGLGDKALSPLEGHGLPKAELKGDLVQFDGFGCFY 538


Lambda     K      H
   0.320    0.137    0.436 

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: 1123
Number of extensions: 36
Number of successful extensions: 2
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: 540
Length of database: 541
Length adjustment: 35
Effective length of query: 505
Effective length of database: 506
Effective search space:   255530
Effective search space used:   255530
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 52 (24.6 bits)

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

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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