GapMind for catabolism of small carbon sources

 

Aligments for a candidate for Ac3H11_1694 in Burkholderia phytofirmans PsJN

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate BPHYT_RS31745 BPHYT_RS31745 ABC transporter ATP-binding protein

Query= uniprot:A0A165KER0
         (358 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS31745 BPHYT_RS31745 ABC
           transporter ATP-binding protein
          Length = 389

 Score =  426 bits (1096), Expect = e-124
 Identities = 216/342 (63%), Positives = 264/342 (77%), Gaps = 3/342 (0%)

Query: 12  AVALLVLPLIL-QSFGNAWVRIADLALLYVLLALGLNIVVGYAGLLDLGYVAFYAVGAYL 70
           A+ +  LPL++  + GN  VR+ D A+LYV+LALGLNIVVG+AGLLDLGY+AFYAVGAY 
Sbjct: 30  AIGVTALPLLIGAAAGNYGVRVLDFAMLYVMLALGLNIVVGFAGLLDLGYIAFYAVGAYT 89

Query: 71  FALMASPHLADNFAAFAAMFPNGLHTSLWIVIPVAALLAAFFGAMLGAPTLKLRGDYLAI 130
            AL+ SPHLA +F     M+P+G H   W V+PVA +LAA  G  LGAPTL+LRGDYLAI
Sbjct: 90  AALLTSPHLAAHFEWIGHMWPSGFHAPYWFVMPVAMVLAAIAGICLGAPTLRLRGDYLAI 149

Query: 131 VTLGFGEIIRIFLNNLDHPVNLTNGPKGLGQIDSVKVFGLDLGKRLEVFGFDINSVTLYY 190
           VTLGFGEI+RIF+NNLD PVN+TNGP+G+  +  V V G +L +     GF   +V +YY
Sbjct: 150 VTLGFGEIVRIFMNNLDRPVNITNGPQGITGVAPVTVAGFNLSETHAFLGFQFTTVYMYY 209

Query: 191 YLFLVLVVVSVIICYRLQDSRIGRAWMAIREDEIAAKAMGINTRNMKLLAFGMGASFGGV 250
           Y+F++  ++ V +C RLQ SRIGRAW AIREDEIAAKAMGINTRN+KLLAF MGASFGG+
Sbjct: 210 YVFVLCSLLVVWVCTRLQHSRIGRAWAAIREDEIAAKAMGINTRNVKLLAFAMGASFGGL 269

Query: 251 SGAMFGAFQGFVSPESFSLMESVMIVAMVVLGGIGHIPGVILGAVLLSALPEVLRYVAGP 310
           SGAMF  FQGFVSPESF+L ESV ++A VVLGG+GHIPGVI GAVLL+ LPE+LR    P
Sbjct: 270 SGAMFAGFQGFVSPESFTLWESVTVLACVVLGGMGHIPGVIFGAVLLAILPEILRSTMTP 329

Query: 311 LQAMTDGR--LDSAILRQLLIALAMIIIMLLRPRGLWPSPEH 350
           LQ    G   +D+ ++RQLL  LAM+IIML RP GLWP+P+H
Sbjct: 330 LQNAIFGHVIVDTEVIRQLLYGLAMVIIMLRRPEGLWPAPKH 371


Lambda     K      H
   0.328    0.144    0.430 

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: 435
Number of extensions: 15
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 358
Length of database: 389
Length adjustment: 30
Effective length of query: 328
Effective length of database: 359
Effective search space:   117752
Effective search space used:   117752
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: 50 (23.9 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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