GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Pedo557:CA265_RS22390
          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:

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