GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_1692 in Burkholderia phytofirmans PsJN

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate BPHYT_RS19445 BPHYT_RS19445 metal-dependent hydrolase

Query= uniprot:A0A165KC78
         (242 letters)



>FitnessBrowser__BFirm:BPHYT_RS19445
          Length = 254

 Score =  214 bits (546), Expect = 1e-60
 Identities = 113/239 (47%), Positives = 160/239 (66%), Gaps = 7/239 (2%)

Query: 9   LLQVKGLKVAYGGIQAVKGVDFEVREGELVSLIGSNGAGKTTTMKAITGTLSMND---GN 65
           +L V GL V YG ++A+ G   +VR G++VS+IG NGAGK+T + AI G L       G 
Sbjct: 11  ILDVDGLSVRYGKVEALHGAAIKVRPGQIVSVIGPNGAGKSTLLNAIMGALPTTGHAKGA 70

Query: 66  IEYLGKSIKGKGAWDLVKEGLVMVPEGRGVFARMTITENLQMGAYIRKDKAG---ILADI 122
           + Y G+ +        V  G+ +VPE R +FA MT+ +NL +GAY RK +AG    L  +
Sbjct: 71  VLYQGEDVSAVPVEKRVARGMCLVPEKRELFASMTVEDNLVLGAYRRK-RAGERNFLDQL 129

Query: 123 EKMFTIFPRLRERKDQLAGTMSGGEQQMLAMGRALMSQPKVLLLDEPSMGLSPIMVDKIF 182
           E +FT+FPRLRER+ Q AGT+SGGE+QMLA+GRALM +P +L+LDEPS+GL+P++V +IF
Sbjct: 130 EPVFTLFPRLRERRKQAAGTLSGGERQMLAVGRALMGKPDLLMLDEPSLGLAPLIVKEIF 189

Query: 183 EVVRDVYALGVTIVLVEQNASRALAIADRGYVMESGLITMTGPGQQLLNDPKVRAAYLG 241
            ++  +   GV  +L+EQNA  AL I+D GYV+E+G + + GP   L  +P+V   YLG
Sbjct: 190 HIISALRQTGVATLLIEQNARAALQISDYGYVLETGELALEGPAADLAQNPRVIETYLG 248


Lambda     K      H
   0.317    0.136    0.373 

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: 159
Number of extensions: 3
Number of successful extensions: 3
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: 242
Length of database: 254
Length adjustment: 24
Effective length of query: 218
Effective length of database: 230
Effective search space:    50140
Effective search space used:    50140
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 46 (22.3 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