GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kgtP in Sphingomonas koreensis DSMZ 15582

Align Alpha-ketoglutarate permease, MFS superfamily (characterized)
to candidate Ga0059261_3091 Ga0059261_3091 Sugar (and other) transporter

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



>FitnessBrowser__Korea:Ga0059261_3091
          Length = 430

 Score =  569 bits (1467), Expect = e-167
 Identities = 276/424 (65%), Positives = 331/424 (78%), Gaps = 2/424 (0%)

Query: 18  EKTTASRIKSIFSGSVGNMVEWYDWYVYAAFSLYFAKAFFPKGDTTAQLLNTAAIFAVGF 77
           E  T  R+KSI  GS GN+VEWYDWY YAAF+LYFA  FFPKGD T QLLNTAA+FAVGF
Sbjct: 7   EAGTRQRLKSILGGSAGNLVEWYDWYAYAAFTLYFAPHFFPKGDQTTQLLNTAAVFAVGF 66

Query: 78  LMRPIGGWLMGLYADRAGRKAALMASVYLMCFGSLIIALSPGYETIGVGAPILLVFARLL 137
           LMRPIGGWLMG+YAD+ GRKA L  SV LMC GSL+IA++PGYETIG  AP LLVFARL+
Sbjct: 67  LMRPIGGWLMGVYADKYGRKAGLTLSVSLMCAGSLLIAVTPGYETIGALAPALLVFARLM 126

Query: 138 QGLSVGGEYGTSATYLSEMATKERRGFFSSFQYVTLISGQLIALGVLIVLQQTLTTEQLY 197
           QGLS+GGEYG SATYLSEMA ++RRGFFSSFQYVTLISGQLIALGVL++LQ +++   L 
Sbjct: 127 QGLSIGGEYGASATYLSEMAGRKRRGFFSSFQYVTLISGQLIALGVLLILQASMSEAALE 186

Query: 198 DWGWRIPFAIGALCAIVALYLRRGMEETESF--AKKEKSKESAMRTLLRHPKELMTVVGL 255
            WGWRIPF IG   A++  +LRRG+ ET+SF  AK E  K  A+  L  HP E + V+ L
Sbjct: 187 SWGWRIPFFIGGALAVIVFWLRRGLSETQSFENAKAEGRKTGALALLREHPGEFLLVMAL 246

Query: 256 TMGGTLAFYTYTTYMQKYLVNTVGMSISDSTTISAATLFLFMCLQPIIGGLSDKVGRRPI 315
           T GGTLAFY Y+ Y+QK+LVNT G     ++ I+AA LF+FMC+QP+ G LSD++GR+P+
Sbjct: 247 TAGGTLAFYAYSIYLQKFLVNTSGFDRETASEINAAALFVFMCIQPLAGALSDRIGRKPL 306

Query: 316 LIAFGILGTLFTVPILTTLHTIQTWWGAFFLIMAALIIVSGYTSINAVVKAELFPTEIRA 375
           +I FG+LG L T PI T L  + + W AF L++ AL+IV+GYTSINAVVKAELFP  IR 
Sbjct: 307 MIGFGVLGVLCTYPIFTALEQVSSAWAAFGLMLGALVIVTGYTSINAVVKAELFPAHIRT 366

Query: 376 LGVGLPYALTVSIFGGTAEYIALWFKSIGMETGYYWYVTACIAVSLLVYVTMKDTRKHSR 435
           LGV LPYAL  +IFGGTAEY+ALWFK  GME G+YWYVT  I +SL+VY+ M+DTR HS+
Sbjct: 367 LGVALPYALANAIFGGTAEYVALWFKDQGMERGFYWYVTGMIGISLIVYLRMRDTRTHSK 426

Query: 436 IETD 439
           I  D
Sbjct: 427 ILED 430


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: 699
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: 430
Length adjustment: 32
Effective length of query: 407
Effective length of database: 398
Effective search space:   161986
Effective search space used:   161986
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