GapMind for catabolism of small carbon sources

 

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

Align Putative TRAP dicarboxylate transporter, DctM subunit (characterized, see rationale)
to candidate 3609946 Dshi_3328 TRAP dicarboxylate transporter, DctM subunit (RefSeq)

Query= uniprot:Q88NP0
         (426 letters)



>FitnessBrowser__Dino:3609946
          Length = 426

 Score =  301 bits (772), Expect = 2e-86
 Identities = 166/423 (39%), Positives = 263/423 (62%), Gaps = 5/423 (1%)

Query: 1   MEAFILLGSFIVLILIGMPVAYALGLSALIGAWWID--IPLQAMMIQVASGVNKFSLLAI 58
           M  F +  + + +I + +P+A AL +SA++G   ++    L  + + + +G  KFSL+AI
Sbjct: 1   MLMFGIFVAMVAMICLNIPIAVALAVSAILGLLVMEGTSSLVTVALDMYNGSTKFSLIAI 60

Query: 59  PFFVLAGAIMAEGGMSRRLVAFAGVLVGFVRGGLSLVNIMASTFFGAISGSSVADTASVG 118
           P FVLAGAIM  GG++ RL+ F   ++GFVRGGL+ VNI  S FF  ISGS+VAD A++G
Sbjct: 61  PMFVLAGAIMNAGGITDRLINFVTCIIGFVRGGLAHVNIGVSLFFAEISGSAVADVAAMG 120

Query: 119 SVLIPEMERKGYPREFSTAVTVSGSVQALLTPPSHNSVLYSLAAGGTVSIASLFMAGIMP 178
           SV+IP+M+++GY   FS AVT S +  A++ PPS   +LY+ +A   VS+  LF+AGI+P
Sbjct: 121 SVMIPQMKKRGYSGAFSAAVTSSSASLAIIIPPSIPMILYATSA--NVSVEQLFVAGIVP 178

Query: 179 GLLLSAVMMGLCLIFAKKRNYPKGEVIPLREALKIAGEALWGLMAMVIILGGILSGVFTA 238
           GL+ +A +MG+  +FA++ + P+ E    R   +   +AL      VIILGGI  G  TA
Sbjct: 179 GLMGAAGLMGVAYVFARRYDLPREEAFSGRRLWETFIDALPTFALPVIILGGIFGGFVTA 238

Query: 239 TESAAVAVVWSFFVTMFIYRDYKWRDLPKLMHRTVRTISIVMILIGFAASFGYVMTLMQI 298
           TE+A +AV+ +  V+++ YR      L   M       ++VM+L+  +   G  +T  Q+
Sbjct: 239 TEAAGLAVLAAILVSLY-YRQVNLGRLKSAMLDGGMQTAVVMVLVAASVVMGGFLTRAQV 297

Query: 299 PSKITTAFLTLSDNRYVILMCINFMLMLLGTVMDMAPLILILTPILLPVITGIGVDPVHF 358
           P +I    L ++DN++VIL+ +NF  +++G  +  A  I+++ PI++P+I    ++P+HF
Sbjct: 298 PQEIAQNILEITDNKWVILLILNFFFLIIGFFLHSAAAIILVVPIVIPLIVAADINPIHF 357

Query: 359 GMIMLVNLGIGLITPPVGAVLFVGSAIGKVSIESTVKALMPFYLALFLVLMAVTYIPAIS 418
           G+++ +NL IG  TPPV +VL    A+ + +I    K  + F L L  VL+  TYIP+I 
Sbjct: 358 GLVVTLNLAIGQQTPPVASVLITACAVARANIWEVSKVNIWFILVLLTVLLMCTYIPSIP 417

Query: 419 LWL 421
           L+L
Sbjct: 418 LFL 420


Lambda     K      H
   0.329    0.142    0.418 

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: 555
Number of extensions: 23
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: 426
Length of database: 426
Length adjustment: 32
Effective length of query: 394
Effective length of database: 394
Effective search space:   155236
Effective search space used:   155236
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 (21.8 bits)
S2: 51 (24.3 bits)

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

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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:

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:

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:

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:

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