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

GapMind for catabolism of small carbon sources

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

Align Homogentisate 1,2-dioxygenase (EC 1.13.11.5) (characterized)
to candidate 5209701 Shew_2154 homogentisate 1,2-dioxygenase (RefSeq)

Query= reanno::MR1:201124
         (386 letters)



>FitnessBrowser__PV4:5209701
          Length = 386

 Score =  729 bits (1882), Expect = 0.0
 Identities = 330/386 (85%), Positives = 366/386 (94%)

Query: 1   MPFYVKQGQVPHKRHIAFEKENGELYREELFSTHGFSNIYSNKYHHNMPTKALEVAPYRL 60
           MPFYV+QG++PHKRHI F+KENGELYREELFSTHGFSNIYSNKYHHNMPTKALEV+P+ +
Sbjct: 1   MPFYVRQGEIPHKRHITFKKENGELYREELFSTHGFSNIYSNKYHHNMPTKALEVSPFEV 60

Query: 61  GHGAHWEDSLVQNYKLDSRSADREGNFFSARNKIFYNNDVAIYTAKVTQDTAEFYRNAYA 120
            HG  W+D+L+QNYKLD++ ADREGNF+SARNKIF+NNDVA+Y+AKVT+ T EFYRNAYA
Sbjct: 61  NHGQTWQDTLIQNYKLDAKLADREGNFYSARNKIFFNNDVAMYSAKVTEATEEFYRNAYA 120

Query: 121 DEVVFVHEGEGTLYSEYGTLEIKKWDYLVIPRGTTHQLKFNNYSNVRLFVIEAFSMVEVP 180
           DEV+FVHEG+G LYSEYG L++KKWDYLVIPRGTT+QLKF++YS VRLFVIEAFSMVEVP
Sbjct: 121 DEVIFVHEGQGKLYSEYGVLDVKKWDYLVIPRGTTYQLKFDDYSQVRLFVIEAFSMVEVP 180

Query: 181 KHCRNEYGQLLESAPYCERDLRTPILQAAVVERGAFPLVCKFGDKYQLTTLEWHPFDLVG 240
           KH RNEYGQLLESAPYCERD+R P LQ AVVE+GAFPLVCKFGDKYQLT LEWHPFDLVG
Sbjct: 181 KHFRNEYGQLLESAPYCERDIRVPSLQEAVVEKGAFPLVCKFGDKYQLTQLEWHPFDLVG 240

Query: 241 WDGCVYPWAFNITEYAPKVGKIHLPPSDHLVFTAHNFVVCNFVPRPYDFHERAIPAPYYH 300
           WDGCVYPWAFNI +YAPKVG+IHLPPSDHLVFTAHNFV+CNFVPRPYDFH ++IPAPYYH
Sbjct: 241 WDGCVYPWAFNIQDYAPKVGQIHLPPSDHLVFTAHNFVICNFVPRPYDFHPQSIPAPYYH 300

Query: 301 NNIDSDEVLYYVDGDFMSRTGIEAGYITLHQKGVAHGPQPGRTEASIGKKETYEYAVMVD 360
           NNIDSDEVLYYVDGDFMSRTGIEAGY+TLHQKGV HGPQPGRTEAS+GKKETYEYAVMVD
Sbjct: 301 NNIDSDEVLYYVDGDFMSRTGIEAGYMTLHQKGVPHGPQPGRTEASVGKKETYEYAVMVD 360

Query: 361 TFAPLKLTEHVQHCMSKDYNRSWLEN 386
           TFAPL+LT+HVQ CMSKDYNRSWLE+
Sbjct: 361 TFAPLQLTQHVQGCMSKDYNRSWLED 386


Lambda     K      H
   0.321    0.137    0.435 

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: 749
Number of extensions: 26
Number of successful extensions: 1
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: 386
Length of database: 386
Length adjustment: 30
Effective length of query: 356
Effective length of database: 356
Effective search space:   126736
Effective search space used:   126736
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: 50 (23.9 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