GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kgtP in Kocuria flava HO-9041

Align alpha-ketoglutarate permease (MHS family) (characterized)
to candidate WP_058859649.1 AS188_RS01290 MFS transporter

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



>NCBI__GCF_001482365.1:WP_058859649.1
          Length = 449

 Score =  226 bits (576), Expect = 1e-63
 Identities = 141/415 (33%), Positives = 215/415 (51%), Gaps = 17/415 (4%)

Query: 26  KSIFSGSVGNMVEWYDWYVYAAFSLYFAKVFFPKGDTTAQLLNTAAIFAVGFLMRPIGGW 85
           +++ + ++GN  EW+D+ VYA   +Y  + FFP    T   L+T   FA  FL+RP+GG 
Sbjct: 19  RAVAASAIGNATEWFDYGVYAVSVVYITQNFFPGEYGTILALST---FAFSFLVRPLGGL 75

Query: 86  LMGLYADRAGRKRALMASVYLMCFGSLIIALSPSYETIGVGAPILLVFARLLQGLSVGGE 145
             G   DR GRKR L  ++ LM   +  I L P+ ETIG+ APILL+  R +QG S GGE
Sbjct: 76  FWGPLGDRLGRKRILALTIILMAGATFCIGLLPTVETIGIAAPILLILLRAVQGFSTGGE 135

Query: 146 YGTSATYLSEMATKERRGFFSSFQYVTLISGQLIALGVLIVL--QQFLTTEQLYAWGWRI 203
           YG +AT+++E A  +RRGF  SF     ++G   ALG LIVL  +  L  + +  WGWRI
Sbjct: 136 YGGAATFMAEYAPDKRRGFLGSFLEFGTLAG--FALGSLIVLLGEVVLGNDAMSEWGWRI 193

Query: 204 PFAIGALCAVVALYLRRGMEETESFTKKEKSKES------AMRTLL-RHPKELMTVVGLT 256
           PF +     +V LYLR  + ++  F + E+S  +      A++ L+ R+ + ++ + GL 
Sbjct: 194 PFLLAGPMGLVGLYLRSRLADSPVFQELEESGHTESSAGMALKDLVTRYWRPMLIMTGLV 253

Query: 257 MGGTLAFYTYTTYMQKYLVNTVGMSISDSTTISAATLFLFMCLQPVIGGLSDKIGRRPIL 316
           +   +  YT  +YM  YL    GM+     TI     F  M + P  G LSD++GR+P+ 
Sbjct: 254 IALNVVNYTLLSYMPTYLEGQTGMANRTVLTIMFVAQFAMMLVIPFAGALSDRVGRKPMW 313

Query: 317 IAFGILGTLFTVPILTTLHTIQTWWGAFFLIMAALIIVSGYTSINAVVKAELFPTEIRAL 376
               ++G       +  L     WW      +  L+ +    +I+A   A +FPT++R  
Sbjct: 314 YT-SLIGLFVLAIPMYMLMANGFWWALLGFAVLGLLYIPQLATISATFPA-MFPTQVRYA 371

Query: 377 GVGLPYALTVSIFGGTAEYI-ALWFKSIGMETGYYWYVTACIAVSLLVYITMKDT 430
           G  + Y L  ++FGGTA         + G      +Y+ A   V L+    MK+T
Sbjct: 372 GFAITYNLATAVFGGTAPLANEALIGATGNPLVPAFYMMAACVVGLVAVRAMKET 426


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: 579
Number of extensions: 34
Number of successful extensions: 5
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: 449
Length adjustment: 32
Effective length of query: 407
Effective length of database: 417
Effective search space:   169719
Effective search space used:   169719
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 24 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