GapMind for catabolism of small carbon sources

 

Alignments for a candidate for CCNA_00435 in Pedobacter sp. GW460-11-11-14-LB5

Align Amino acid transporter (characterized, see rationale)
to candidate CA265_RS17395 CA265_RS17395 amino acid transporter

Query= uniprot:A0A0H3C3Q5
         (483 letters)



>FitnessBrowser__Pedo557:CA265_RS17395
          Length = 483

 Score =  325 bits (834), Expect = 2e-93
 Identities = 179/483 (37%), Positives = 276/483 (57%), Gaps = 21/483 (4%)

Query: 14  RKAIDTITAGHADSHQ--LKKTLSWPHLVALGVGAIVGTGIYTLTGVGAGL-AGPGVILS 70
           +K+I +I A   +S +  LK+TL   +L+ +GVG  +G G++++TG+ A   +GP V LS
Sbjct: 2   KKSIASIVAEANESGEGSLKRTLGPINLILIGVGLTLGAGLFSITGLAAANHSGPAVTLS 61

Query: 71  FLIAGAVCACAALCYAELSTMIPASGSAYTYSYAAMGEPVAWFVGWSLILEYTLVCAAVA 130
           F+IA   C  AALCYAE ++MIP +GSAYTYSYA MGE  AW +GW L+LEY++ CA VA
Sbjct: 62  FVIAALGCGFAALCYAEFASMIPVAGSAYTYSYATMGELFAWIIGWDLVLEYSVGCATVA 121

Query: 131 VGWSAHAHGLFKM--IGFPDALLAGPHQ----------GGLINMPAVFISMAVAGLLALG 178
           + WS +         I  P  L   P +           G+IN+PA  + + +  +L  G
Sbjct: 122 ISWSQYLTKFLASLHIYLPPQLTLSPFETAKLADGSTVNGIINIPAALVVVLMTAILIRG 181

Query: 179 TRESATVNMVLVFVKIIALIVFVVLCLPAFNLAHFTPFMPNGFQAHVPEGAAADAAKVGV 238
           T+ SA VN ++VF+K+  ++VF+ L     + A++ P++P         G        GV
Sbjct: 182 TKGSAIVNGIIVFLKVGVVLVFIALGWQYIDPANYHPYIPEN------TGTFGQFGWSGV 235

Query: 239 MAAASLIFFAFYGFDAVSTAAEETKNPKRDLTIGIVGSMAVCTAIYMIVAAVSIGASRTE 298
           +  A L+FF F GFDAV+ +A+ETKNP RDL IGI+GS+ VCT ++ +   V  G +  +
Sbjct: 236 LRGAGLVFFVFIGFDAVAASAQETKNPARDLPIGIIGSLLVCTVLFGLFGHVMTGLANYK 295

Query: 299 VFSKSEAPLVFILESLNHGKIAQLVALAAVIALPTVILAFMYGQSRIFFVMARDGLLPRA 358
            F+ S AP+   +E   +  ++Q + LA +I   +VIL  +  QSR+F+ +++DGLLP+ 
Sbjct: 296 EFANSGAPVAIAIEKTPYAWLSQAIILAILIGYTSVILIDLMAQSRMFYSISKDGLLPKM 355

Query: 359 LSKVNAKTGTPVMMTLLTGVLAAVISGLLSLKDIAELANAGTLWAFIAVGASVILLRLRE 418
            S V+AK  TP    ++  V   + +  + +  + E+ + GTL AF+ V   +++LR   
Sbjct: 356 FSDVHAKFKTPYKSNIILCVFIGLFAAFVPMNVVGEMTSIGTLLAFLMVCVGILILRKTN 415

Query: 419 PNRPRVFSTPLWPIVAPAGILGCLYLFLSLPGKTQLYFLYAHLIGAVVYLAYGMRKSVLA 478
           P   R F  P  P++   GIL C+ + + LP +T L      +IG  +Y  YG + S L 
Sbjct: 416 PEAKRPFKVPFVPLIPILGILTCIAMMVFLPWETWLRLAVWLIIGLAIYFWYGKKNSKLK 475

Query: 479 QQE 481
            QE
Sbjct: 476 AQE 478


Lambda     K      H
   0.326    0.138    0.415 

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: 665
Number of extensions: 47
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: 483
Length of database: 483
Length adjustment: 34
Effective length of query: 449
Effective length of database: 449
Effective search space:   201601
Effective search space used:   201601
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 52 (24.6 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