GapMind for catabolism of small carbon sources

 

Aligments for a candidate for kgtP in Pedobacter sp. GW460-11-11-14-LB5

Align Alpha-ketoglutarate permease, MFS superfamily (characterized)
to candidate CA265_RS22390 CA265_RS22390 alpha-ketoglutarate transporter

Query= reanno::pseudo3_N2E3:AO353_03810
         (439 letters)



>lcl|FitnessBrowser__Pedo557:CA265_RS22390 CA265_RS22390
           alpha-ketoglutarate transporter
          Length = 428

 Score =  562 bits (1448), Expect = e-165
 Identities = 275/421 (65%), Positives = 339/421 (80%), Gaps = 2/421 (0%)

Query: 19  KTTASRIKSIFSGSVGNMVEWYDWYVYAAFSLYFAKAFFPKGDTTAQLLNTAAIFAVGFL 78
           K    R+KSIF GSVGN+VEWYDWY Y+AF+LYF+ AFFP  + TAQLL+TA IFAVGFL
Sbjct: 7   KDVEYRLKSIFGGSVGNLVEWYDWYTYSAFALYFSPAFFPNSNPTAQLLDTAGIFAVGFL 66

Query: 79  MRPIGGWLMGLYADRAGRKAALMASVYLMCFGSLIIALSPGYETIGVGAPILLVFARLLQ 138
           MRPIGGWL G  AD+ GRK ++  SV +M  GSLII L+PGY+ IG+ AP+LL+FARL+Q
Sbjct: 67  MRPIGGWLFGSIADKLGRKRSMTLSVLIMAIGSLIIGLTPGYKQIGIAAPLLLIFARLIQ 126

Query: 139 GLSVGGEYGTSATYLSEMATKERRGFFSSFQYVTLISGQLIALGVLIVLQQ-TLTTEQLY 197
           GLS GGEYGTSATYLSEMATK+ RGF+SSFQYVTLI GQL+ALG+ ++LQ   LT  +L+
Sbjct: 127 GLSTGGEYGTSATYLSEMATKKHRGFYSSFQYVTLIGGQLLALGIQLILQNWLLTPAELH 186

Query: 198 DWGWRIPFAIGALCAIVALYLRRGMEETESF-AKKEKSKESAMRTLLRHPKELMTVVGLT 256
           +WGWRIPF IGA+ + +ALYLRR ++ET +F +K    K+  +  L+++PKE+ TVVGLT
Sbjct: 187 EWGWRIPFFIGAILSFIALYLRRHIDETSAFKSKNTADKKGGIAVLMKYPKEVFTVVGLT 246

Query: 257 MGGTLAFYTYTTYMQKYLVNTVGMSISDSTTISAATLFLFMCLQPIIGGLSDKVGRRPIL 316
           +GGT+AFYT++TYMQK+LVNTV +S   STT+S  +L +F+ LQP+ G LSDK+GR+P+L
Sbjct: 247 LGGTIAFYTFSTYMQKFLVNTVHLSKETSTTLSFISLLVFVVLQPLFGLLSDKIGRKPLL 306

Query: 317 IAFGILGTLFTVPILTTLHTIQTWWGAFFLIMAALIIVSGYTSINAVVKAELFPTEIRAL 376
           I FG+LGTL T PILT L         F L++ ALIIVSGYTSINAVVKAELFP EIRAL
Sbjct: 307 IGFGVLGTLCTYPILTGLAGESNTTIIFLLMIGALIIVSGYTSINAVVKAELFPAEIRAL 366

Query: 377 GVGLPYALTVSIFGGTAEYIALWFKSIGMETGYYWYVTACIAVSLLVYVTMKDTRKHSRI 436
           GVGLPYALTV+IFGGTAEY ALWFK+IG E  +YWYVT CI +SL++Y TMKDT+ HS+I
Sbjct: 367 GVGLPYALTVAIFGGTAEYFALWFKNIGHENYFYWYVTGCILISLILYTTMKDTKHHSKI 426

Query: 437 E 437
           E
Sbjct: 427 E 427


Lambda     K      H
   0.325    0.138    0.414 

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: 726
Number of extensions: 44
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: 428
Length adjustment: 32
Effective length of query: 407
Effective length of database: 396
Effective search space:   161172
Effective search space used:   161172
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 (21.6 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, 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