GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kgtP in Burkholderia phytofirmans PsJN

Align Alpha-ketoglutarate permease, MFS superfamily (characterized)
to candidate BPHYT_RS27905 BPHYT_RS27905 MFS transporter

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



>FitnessBrowser__BFirm:BPHYT_RS27905
          Length = 435

 Score =  458 bits (1178), Expect = e-133
 Identities = 229/432 (53%), Positives = 307/432 (71%), Gaps = 5/432 (1%)

Query: 1   MDNSQTLPLGSAAVPAKEKTTASRIKSIFSGSVGNMVEWYDWYVYAAFSLYFAKAFFPKG 60
           M  +    L +A  P + +   S ++SI  GS+GN++EWYD++VY  FS++FA +FFP+ 
Sbjct: 1   MHETTPAELDAATRPLRRR---SALRSIAGGSIGNLIEWYDFHVYTTFSIFFAASFFPRE 57

Query: 61  DTTAQLLNTAAIFAVGFLMRPIGGWLMGLYADRAGRKAALMASVYLMCFGSLIIALSPGY 120
           + T QLL+TAAIFA+GFL+RP+G WL+GLYADR GR++AL  SV LMC GSL I L P Y
Sbjct: 58  NRTIQLLSTAAIFAIGFLLRPVGSWLIGLYADRRGRRSALTLSVILMCAGSLAIGLCPTY 117

Query: 121 ETIGVGAPILLVFARLLQGLSVGGEYGTSATYLSEMATKERRGFFSSFQYVTLISGQLIA 180
             IG+ AP++L+ ARL+QG S+GGEYG S+ YLSE+A    RGF+SSF YVTLI GQL+A
Sbjct: 118 PQIGMAAPLVLLLARLVQGFSLGGEYGASSVYLSEIARPGHRGFYSSFHYVTLILGQLLA 177

Query: 181 LGVLIVLQQTLTTEQLYDWGWRIPFAIGALCAIVALYLRRGMEETESF-AKKEKSKESAM 239
             V +VLQ  +   +L DWGWR+PF  GA  A+VA ++RR ++ET  F A  EK K    
Sbjct: 178 TLVQVVLQALIPRAELIDWGWRVPFITGAALALVAWWVRRNIDETPDFRALDEKDKRGVS 237

Query: 240 RTLLR-HPKELMTVVGLTMGGTLAFYTYTTYMQKYLVNTVGMSISDSTTISAATLFLFMC 298
            + LR H + ++ V GLT GGTLAF+TYT YM  YLVNTVG+S   S  +S +TL LFM 
Sbjct: 238 LSALREHWRPVLLVFGLTTGGTLAFFTYTVYMHNYLVNTVGLSAQTSAWLSLSTLTLFMV 297

Query: 299 LQPIIGGLSDKVGRRPILIAFGILGTLFTVPILTTLHTIQTWWGAFFLIMAALIIVSGYT 358
           +QP  G LSD++GRRP+L+ FGI GT  T P+LT L    +   AF L+  AL+IVSGYT
Sbjct: 298 VQPFFGALSDRIGRRPLLLWFGIGGTFGTWPLLTALAHTHSATTAFLLLALALMIVSGYT 357

Query: 359 SINAVVKAELFPTEIRALGVGLPYALTVSIFGGTAEYIALWFKSIGMETGYYWYVTACIA 418
           S+ +V+KA+LFP  +RALGVG+PYA+  ++FGGTA Y  LWFKSIG E+G+Y Y +ACI 
Sbjct: 358 SVCSVMKAQLFPARLRALGVGVPYAIATAVFGGTASYAGLWFKSIGHESGFYLYASACIG 417

Query: 419 VSLLVYVTMKDT 430
            +L+  ++++ +
Sbjct: 418 CTLIATLSLRSS 429


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: 647
Number of extensions: 39
Number of successful extensions: 2
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: 435
Length adjustment: 32
Effective length of query: 407
Effective length of database: 403
Effective search space:   164021
Effective search space used:   164021
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