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_3200 Amino acid ABC transporter permease protein

Query= uniprot:Q31RN8
         (261 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_3200
          Length = 604

 Score =  248 bits (634), Expect = 2e-70
 Identities = 140/276 (50%), Positives = 181/276 (65%), Gaps = 23/276 (8%)

Query: 8   PEPVTAIASAPETM------------IYAEGVEKWYGNQFQALCGVSLTVQRGEVVVMMG 55
           P PV   A AP  +            +   GV K YG   + L  V+LTV  G V V++G
Sbjct: 330 PGPVVPAAPAPVAVPRWTGALNRGGEVTIHGVSKRYG-ALEVLKDVTLTVLPGSVTVILG 388

Query: 56  PSGSGKSTFLRTLNALESHQRGEIWIEGHRLSHDR----------RDIATIRQEVGMVFQ 105
           PSGSGKST LR++N LE    G I I+G  + + +           DI   R +VGMVFQ
Sbjct: 389 PSGSGKSTLLRSINHLERVDGGFIAIDGELIGYRQDADALYELGENDILKRRVDVGMVFQ 448

Query: 106 QFNLFPHLTVLQNLMLAPVQVRRWPVAQAEATARQLLERVRIAEQADKYPGQLSGGQQQR 165
            FNLFPHLTVL+N++ APV VR+   A+AEA A +LL RV ++++A  YP QLSGGQQQR
Sbjct: 449 NFNLFPHLTVLENIVEAPVTVRKLARAEAEALALELLARVGLSDKAHSYPRQLSGGQQQR 508

Query: 166 VAIARALAMQPRILLFDEPTSALDPEMVREVLDVMRDLASEGMTMLVATHEVGFAREVAD 225
           VAIARALA++P++LLFDEPTSALDPE+V EVLDV+++LA  G T+++ THE+GFAREVAD
Sbjct: 509 VAIARALALKPKVLLFDEPTSALDPELVGEVLDVIKELARTGTTLVIVTHEIGFAREVAD 568

Query: 226 RVVLMADGQIVEEAPPDRFFTAPQSDRAKQFLAQIL 261
            VV M  G++VE   P + F+ P   R   FLA++L
Sbjct: 569 TVVFMEQGRVVETGTPAKVFSQPDHPRTAAFLAKVL 604


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: 369
Number of extensions: 19
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: 604
Length adjustment: 31
Effective length of query: 230
Effective length of database: 573
Effective search space:   131790
Effective search space used:   131790
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: 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:

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