Alignments for a candidate for Dshi_1194 in Dinoroseobacter shibae DFL-12

GapMind for catabolism of small carbon sources

Alignments for a candidate for Dshi_1194 in Dinoroseobacter shibae DFL-12

Align TRAP transporter, 4TM/12TM fusion protein (characterized, see rationale)
to candidate 3608896 Dshi_2287 TRAP transporter, 4TM/12TM fusion protein (RefSeq)

Query= uniprot:E4PQE4
         (729 letters)



>FitnessBrowser__Dino:3608896
          Length = 639

 Score =  307 bits (787), Expect = 9e-88
 Identities = 167/453 (36%), Positives = 264/453 (58%), Gaps = 5/453 (1%)

Query: 212 AAIAGTALIMELTRRVAGMALVIIGLVFLAYVFAGPYLPGFLGYPGLSVQRFFSQV-YTD 270
           A +AG   ++ L  RV G +L I+    + Y F GPYLP  + + G+ +  F     Y+ 
Sbjct: 108 AGLAGVFTVIVLAARVWGRSLAILAGALILYAFGGPYLPNAVAHFGVGLGDFVQITWYSF 167

Query: 271 AGILGPTTAVSSTYIILFIIFAAFLQSSKVGDYFVNFAFAAAGRSRGGPAKVSIFASGLM 330
            G+ G  T + ++ +++F+I  A LQ +  G+  +  + A  GR RGG A  +I AS + 
Sbjct: 168 DGVFGRMTGLVASNLLIFLILGAVLQQTGAGESLIRLSTALLGRVRGGGAHAAIAASAVF 227

Query: 331 GMINGTSAGNVVSTGSLTIPLMKKVGYSKQSAGAVEAAASTGGQIMPPIMGAGAFIMAEI 390
           GM+NG+ A N+  TG  TIP++K+ G+S + AGAVEAAAS+GGQ+ PPIM A  F+MA++
Sbjct: 228 GMMNGSVAANIAGTGVFTIPMIKRQGFSSRFAGAVEAAASSGGQLTPPIMAATVFVMADL 287

Query: 391 TGIPYTEIAIAAIIPAILYFASVYFMVDFEAAKTGMRGMREDELPKL--RTMMKQCYLFV 448
            G+P   +  AA +PA+  +  ++  V  EA +  +R +  +++PKL  +  ++   + V
Sbjct: 288 VGLPLLMVIAAAALPALFKYLGLFAQVYVEALRLDIRPLAAEDIPKLTRQDWLQSALVLV 347

Query: 449 PIIILIVALFMGYSVIRAGTLATVSAAVVSWLSPNKMGLR--HILQALEIASYMAIQIIV 506
           P+ +L++A   G S   AG   T++A V   +   ++  +   I  AL      + +I++
Sbjct: 348 PLAVLMIAFLSGSSPAMAGLAGTIAALVTGLVLTPQLRQQPIRIWWALCAGGLASARILL 407

Query: 507 VCAAAGVIVGVISLTGVGARFSVLLLDVAATSQLLALIFAMFISILLGMGMPTTAAYAVA 566
             A  G+++ V++ TG+  RF+V L +V      LAL+ AM  +++LGMG+PT  AY + 
Sbjct: 408 SVAVIGIVLAVVNETGIAIRFAVALSEVGDAYLPLALLMAMLGALVLGMGLPTLPAYLIV 467

Query: 567 ASVVAPGLVQLGIEPLTAHFFVFYFAVVSAITPPVALASYAAAGISGANAMETSVASFRI 626
           A ++ P L++ G+ PL AH FV YFAV S+I PP+A   + AA I+GA+A+  S  + RI
Sbjct: 468 AIMIVPTLIEAGVLPLAAHMFVLYFAVFSSIMPPIAYGCFVAAPIAGADALRISFTALRI 527

Query: 627 GIAAFIVPFMFFYNGALLMEAGWFEIARALVTA 659
            I   IVPF F Y  +LL+ AG F  A  L TA
Sbjct: 528 SIVGLIVPFAFVYAPSLLLVAGSFSWAELLTTA 560


Lambda     K      H
   0.327    0.139    0.410 

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: 1247
Number of extensions: 63
Number of successful extensions: 3
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: 729
Length of database: 639
Length adjustment: 39
Effective length of query: 690
Effective length of database: 600
Effective search space:   414000
Effective search space used:   414000
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 54 (25.4 bits)

This GapMind analysis is from Apr 09 2024. 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 2024 update 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