GapMind for catabolism of small carbon sources

 

Aligments for a candidate for dctM in Desulfovibrio vulgaris Miyazaki F

Align Alr3027 protein, component of The 2-oxo monocarboxylate transporter (Pernil et al., 2010). Transports pyruvate which is inhibited by various 2-ketoacids (characterized)
to candidate 8501407 DvMF_2137 TRAP dicarboxylate transporter, DctM subunit (RefSeq)

Query= TCDB::Q8YSQ7
         (445 letters)



>lcl|FitnessBrowser__Miya:8501407 DvMF_2137 TRAP dicarboxylate
           transporter, DctM subunit (RefSeq)
          Length = 427

 Score =  192 bits (488), Expect = 2e-53
 Identities = 140/442 (31%), Positives = 223/442 (50%), Gaps = 27/442 (6%)

Query: 8   LGPVMFAGALVLLSSGYPVAFSLGGVAILFGLLGIGLGVFDPIFLTAM--PQRIFGIMAN 65
           +G ++F G ++L +   PVA +LGG A    +L  GL +  P+ L  M   QR++    +
Sbjct: 2   VGLILFGGMVLLFALNAPVAVALGGAAFA-AVLAKGLTM--PVGLEPMLAVQRLYAGADS 58

Query: 66  YTLLAIPYFIFMGAMLEKSGIAERLLETMGILLGRLRGGLALAVVLVGALLAATTGVVAA 125
           + LLA+P F+  G ++   GI+ R++     L+G L GGLA   V+     A  +G  AA
Sbjct: 59  FPLLAVPLFMLAGELMSAGGISRRIVALADALVGHLPGGLAAVSVVSAMFFAGVSGSAAA 118

Query: 126 TVVAMGLISLPIMLRYGYNKELATGVIAASGTLGQIIPPSVVLVVLGDQLGISVGDLFIG 185
              A+G I +P M+R GY   LA  V AA G +G IIPPS+ ++V G   G S+G LF G
Sbjct: 119 DTAAVGSILIPAMIRRGYPAPLAGAVQAAGGCIGVIIPPSIPMIVFGALTGASIGRLFAG 178

Query: 186 SVIPGLMMASAFALHVLIVAFIRPDV------APALPAQVREIGGKALGKRVIQVMIPPL 239
            V+PGL+M ++     ++ A     V      A AL   +R  G  ALG   I       
Sbjct: 179 GVLPGLLMGASLVALCVVEARRTGRVPERRFDARALWPAIRS-GAWALGAPAI------- 230

Query: 240 ILILLVLGSIFFGFATPTEAGAVGCAGAIALAA-ANGQFTLESLRQVCDTTLRITSMVVF 298
                +LG+I  G AT TE+ A+  A A+ +   A+ +     L ++       +++V+ 
Sbjct: 231 -----ILGTIIGGVATATESAAMAVAYALPVGLYAHRELRWRDLPRLALCAGVTSAVVML 285

Query: 299 ILIGSTAFSLVFRGLNGDQFMFDVLANLPGGKIGFLFVSMTTVFLLGFFIDFFEIAFIVI 358
           I+  ++ F  V       Q +   + +L G +I  L +    + ++G F++      + +
Sbjct: 286 IIAAASLFGWVMALERLPQAIAAWMLSLSGDRIVLLLLVNLLLLVVGAFLETTAAILLFV 345

Query: 359 PLFVPVAQKLGIDLVWYGVILGANLQTSFLTPPFGFALFYLRGVAPPEVTTSDIYRGVIP 418
           P+ VP+   LGIDLV  GVI+  NL    LTPP G  L     +A   +  S I R ++P
Sbjct: 346 PVLVPLLPALGIDLVHLGVIVVVNLAIGMLTPPLGVCLVVSCSIA--RIPLSAISRAIVP 403

Query: 419 FILLQLLVLLLIIIFPGIVSFL 440
            +++ ++ LLL+  FP +V +L
Sbjct: 404 MLVVLIVDLLLVTFFPPLVLWL 425


Lambda     K      H
   0.331    0.149    0.437 

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: 429
Number of extensions: 31
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: 445
Length of database: 427
Length adjustment: 32
Effective length of query: 413
Effective length of database: 395
Effective search space:   163135
Effective search space used:   163135
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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