GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kgtP in Cupriavidus basilensis 4G11

Align alpha-ketoglutarate permease (MHS family) (characterized)
to candidate RR42_RS19610 RR42_RS19610 MFS transporter

Query= reanno::pseudo5_N2C3_1:AO356_17790
         (439 letters)



>FitnessBrowser__Cup4G11:RR42_RS19610
          Length = 432

 Score =  269 bits (687), Expect = 1e-76
 Identities = 156/422 (36%), Positives = 239/422 (56%), Gaps = 12/422 (2%)

Query: 18  ERTTASRIKSIFSGSVGNMVEWYDWYVYAAFSLYFAKVFFPKGDTTAQLLNTAAIFAVGF 77
           E + A R K+I + ++GN +EW+D+ VY+ F+L  AK+FFP G+     L T A F VGF
Sbjct: 6   EISKAQRRKAILAATIGNGLEWFDFTVYSFFALIIAKLFFPTGNDLTSFLLTVATFGVGF 65

Query: 78  LMRPIGGWLMGLYADRAGRKRALMASVYLMCFGSLIIALSPSYETIGVGAPILLVFARLL 137
            MRP+G  ++G+YADR GRK AL  ++ +M  G+ II L+P+Y +IG+ AP L+V ARL+
Sbjct: 66  FMRPVGAIVLGVYADRVGRKAALTLTILMMALGTAIIGLAPTYSSIGLWAPALIVLARLI 125

Query: 138 QGLSVGGEYGTSATYLSEMATKERRGFFSSFQYVTL-ISGQL-IALGVLIVLQQFLTTEQ 195
           QG S GGE G +  +L E A  E RG ++S+Q  +  IS  L  A+G L++    L  EQ
Sbjct: 126 QGFSAGGEVGGATAFLIEHAPDEERGAYASWQQASQGISFMLGAAMGALVI--NGLEPEQ 183

Query: 196 LYAWGWRIPFAIGALCAVVALYLRRGMEETESFTKK------EKSKESAMRTLLR-HPKE 248
           + AWGWRIPF  G L   V +Y+R  +EE  +F  +       K K S +  +LR HP+E
Sbjct: 184 IDAWGWRIPFLFGLLIGPVGMYIRSHLEEPPAFEARRAERAASKVKFSPLTQVLRDHPRE 243

Query: 249 LMTVVGLTMGGTLAFYTYTTYMQKYLVNTVGMSISDSTTISAATLFLFMCLQPVIGGLSD 308
           ++  +G+T+  T+  Y    YM  Y    +G+ +  +   +A    + + L P++G LSD
Sbjct: 244 VLAGLGVTILWTVCTYVLVFYMPSYAKQQLGLPLGATFQSTALCGAIILVLCPLMGMLSD 303

Query: 309 KIGRRPILIAFGILGTLFTVPILTTLHTIQTWWGAFFLIMAALIIVSGYTSINAVVKAEL 368
           ++GR+ +L    ++  +   P+   L+   T      + +   I+++ +T     V AE 
Sbjct: 304 RVGRKRMLGTVALIIGVLAYPLFHWLNVSPTTQTLLMVQVILGILLAAFTGPAPAVLAEQ 363

Query: 369 FPTEIRALGVGLPYALTVSIFGGTAEYIALW-FKSIGMETGYYWYVTACIAVSLLVYITM 427
           FPTE+R+ G+ L Y   V+IFGG A  I  W   S G +    +YV A  A+S +  + M
Sbjct: 364 FPTEVRSTGLSLAYNFAVTIFGGFAPLIVTWLIASSGSKLAPAYYVIAAAAISFVALLFM 423

Query: 428 KD 429
            D
Sbjct: 424 HD 425


Lambda     K      H
   0.326    0.138    0.416 

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: 530
Number of extensions: 30
Number of successful extensions: 4
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: 439
Length of database: 432
Length adjustment: 32
Effective length of query: 407
Effective length of database: 400
Effective search space:   162800
Effective search space used:   162800
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 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