GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bgtA in Acidovorax sp. GW101-3H11

Align ATPase (characterized, see rationale)
to candidate Ac3H11_4899 ABC transporter ATP-binding protein

Query= uniprot:Q31RN8
         (261 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_4899
          Length = 264

 Score =  240 bits (613), Expect = 2e-68
 Identities = 130/257 (50%), Positives = 174/257 (67%), Gaps = 9/257 (3%)

Query: 12  TAIASAPETMIYAE-------GVEKWYGNQFQALCGVSLTVQRGEVVVMMGPSGSGKSTF 64
           T +A A + ++  E        + K YG+  + L G+ L VQRGEV+ ++G SGSGKST 
Sbjct: 7   TTLAPAHDGIVVGEPPIVDITALRKSYGSN-EVLKGIDLKVQRGEVIAIIGKSGSGKSTL 65

Query: 65  LRTLNALESHQRGEIWIEGHRLSHDRRD-IATIRQEVGMVFQQFNLFPHLTVLQNLMLAP 123
           LR +N LE  Q G + + G +L HD    +  +RQ+VGM+FQ FNLFPHL+V +N+MLAP
Sbjct: 66  LRCVNGLEEFQEGALSVNGKKLLHDSPTAMRELRQQVGMIFQSFNLFPHLSVGRNIMLAP 125

Query: 124 VQVRRWPVAQAEATARQLLERVRIAEQADKYPGQLSGGQQQRVAIARALAMQPRILLFDE 183
             V+      AE  AR+LLERV +AE+ D  P QLSGGQQQRVAIARALAM+P++LL DE
Sbjct: 126 TLVKARDAKTAETQARKLLERVGLAEKFDAMPDQLSGGQQQRVAIARALAMEPQVLLCDE 185

Query: 184 PTSALDPEMVREVLDVMRDLASEGMTMLVATHEVGFAREVADRVVLMADGQIVEEAPPDR 243
            TSALDPE+V EVL V+  LA EGMT+++ THE+ FAR+V DRV+ M  G++ E+  P  
Sbjct: 186 ITSALDPELVGEVLRVVESLAQEGMTLMMVTHEMAFARKVGDRVIFMHQGRVHEQGTPAA 245

Query: 244 FFTAPQSDRAKQFLAQI 260
            F  PQ+   +QFL+ +
Sbjct: 246 LFGNPQTPELQQFLSSL 262


Lambda     K      H
   0.321    0.134    0.387 

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: 211
Number of extensions: 5
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: 261
Length of database: 264
Length adjustment: 25
Effective length of query: 236
Effective length of database: 239
Effective search space:    56404
Effective search space used:    56404
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 47 (22.7 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