Alignments for a candidate for glpV in Dinoroseobacter shibae DFL-12

GapMind for catabolism of small carbon sources

Alignments for a candidate for glpV in Dinoroseobacter shibae DFL-12

Align GlpV, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate 3609744 Dshi_3127 extracellular solute-binding protein family 1 (RefSeq)

Query= TCDB::G3LHZ3
         (569 letters)



>FitnessBrowser__Dino:3609744
          Length = 579

 Score =  716 bits (1849), Expect = 0.0
 Identities = 353/573 (61%), Positives = 427/573 (74%), Gaps = 16/573 (2%)

Query: 5   AGLLLAMTASAYAGMDEAKTFLDKEVGDLSTLPRADQEKEMQWFVDAAKPFAGMDIKVVS 64
           AG ++A  + A A    A+ ++D+E    STL + +Q +EM+WF+ AA+PFAGM+I V+S
Sbjct: 11  AGAVIAGQSGAMADEAAAQRWIDEEFQP-STLSKEEQLEEMRWFIQAAEPFAGMEINVLS 69

Query: 65  ETITTHEYESKVLAPAFTAITGIKITHDLIGEGDVVEKLQTQMQSGENIYDAYINDSDLI 124
           E I TH YES+VL  AF  ITGIK+ H ++GEG+VV+ +QTQMQ+G N+YD Y+NDSDLI
Sbjct: 70  EGIPTHSYESEVLTRAFEEITGIKVNHQILGEGEVVQAVQTQMQTGRNLYDGYVNDSDLI 129

Query: 125 GTHWRYQQARSLTDWMANEGKDVTNPGLDIDDFIGKSFTTAPDGKLYQLPDQQFANLYWF 184
           GTH R Q A +LT+ MA +    T+P LD++DF+G  FTT PDG LYQLPDQQFANLYWF
Sbjct: 130 GTHSRLQLAYNLTEQMAGDWAATTSPTLDLEDFMGIQFTTGPDGNLYQLPDQQFANLYWF 189

Query: 185 RYDWFNDEKNKADFKAKYGYDLGVPVNWSAYEDIAEFFTG--REIDGKKVFGHMDYGKKD 242
           R DWF+DE NKA FK KYGY+LGVPVNWSAYEDIAEFFT   +EIDG +++GHMDYGK+ 
Sbjct: 190 RKDWFDDEANKAAFKEKYGYELGVPVNWSAYEDIAEFFTNDVQEIDGVRIYGHMDYGKRA 249

Query: 243 PSLGWRFTDAWLSMAGNGDKGIPNGKPVDEWGIKVDENS-RPVGSCVARGGDTNGPAAVY 301
           P LGWR TDAWLSMAG GD G PNG PVDEWGI+++  +  PVG+ V RGG  NGPAAVY
Sbjct: 250 PDLGWRMTDAWLSMAGAGDVGEPNGVPVDEWGIRMEAGTCNPVGASVTRGGAANGPAAVY 309

Query: 302 SIQKYLDWMKAYAPAAAQGMTFSESGPVPSQGEVAQQMFTYTAFTADFVK---EGLPVVN 358
           +I+K+ +W++ YAP  A    F +S P  SQG VAQQ+F YTAFTAD VK   EG   V+
Sbjct: 310 AIRKWDEWLRNYAPPGAASYDFYQSLPALSQGNVAQQIFWYTAFTADMVKPKSEGNNTVD 369

Query: 359 ADGTPKWRFAPSPHGVYWKDGMKLGYQDAGSWTLMKSTPDDRAKAAWLYAQFVTSKTVDV 418
            DG P WR APSPHG YW +G K+GYQD GSWT +KSTP DRA+AAWLYAQFVTSKTVDV
Sbjct: 370 DDGNPLWRMAPSPHGPYWTEGQKVGYQDVGSWTFLKSTPSDRAQAAWLYAQFVTSKTVDV 429

Query: 419 KKSHMGLTFIRQSTLDHKSFTDRAPKLGGLIEFYRSPARLQWSPTGTNVPDYPKLAQLWW 478
           KKSH+GLTFIR S++ H+SFT+RAPKLGGL+EFYRSP R  WSPTG NVPDYPKLAQ+WW
Sbjct: 430 KKSHVGLTFIRDSSVRHESFTERAPKLGGLVEFYRSPDRTAWSPTGINVPDYPKLAQIWW 489

Query: 479 QAIGDASSGAKTAQEAMDSLCSEQEKVLQRL----ERAKVQGDIGPKLAEEHDLAYWNAD 534
           Q IGD +SGA T QEAMD L  E +  + R+    E A V G  GP+L EE D  YW + 
Sbjct: 490 QQIGDVNSGAFTPQEAMDRLAEEMDITMARMQQADEAAGVYGGCGPRLNEERDAEYWFSQ 549

Query: 535 AVKNGNLAPQLKIENEKDKPVTVNYDELVKSWQ 567
                  +P+ K+ NEK +  TVNYDELV  WQ
Sbjct: 550 PG-----SPKPKLANEKPQGETVNYDELVARWQ 577


Lambda     K      H
   0.315    0.132    0.409 

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: 1246
Number of extensions: 48
Number of successful extensions: 6
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: 569
Length of database: 579
Length adjustment: 36
Effective length of query: 533
Effective length of database: 543
Effective search space:   289419
Effective search space used:   289419
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 (21.5 bits)
S2: 53 (25.0 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