GapMind for catabolism of small carbon sources

 

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

Align Aconitate isomerase; AI; EC 5.3.3.7 (uncharacterized)
to candidate Ac3H11_1182 Hypothetical ABC transport system, periplasmic component

Query= curated2:A0A0A1H8I4
         (262 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_1182
          Length = 233

 Score =  135 bits (339), Expect = 1e-36
 Identities = 92/236 (38%), Positives = 132/236 (55%), Gaps = 8/236 (3%)

Query: 26  VTTLTVLSSGGIMGT---IREVAPAYEKATGVKLDIAAAPSMGDTPQAIPNRLARNEPAD 82
           +TT T+L     M T   + ++  AY  A+  +       S+G    A   R+A  E  D
Sbjct: 1   MTTATLLRGISSMATRQVLADLTAAYA-ASAAEAGTVQIESVGGVDAA--KRVAAGEVFD 57

Query: 83  VVLMVGSALDKLVASGQVAKDSRVDLGQSFIAMAVRQGAPKPDISNMDAFKQTLEKAQSV 142
           VV++   A+DKL+A+G +   S+VD   S +A+AV  GAP PD+S+ DA    +  A S+
Sbjct: 58  VVILASDAIDKLLAAGHLLPGSKVDWVHSGVAVAVPAGAPLPDLSSEDAVHSAVLAAPSI 117

Query: 143 AYSDSASGVYLSRILFPRMQLDKSFMAK-ARMIPAEPVGAVVARGEAQLGFQQLSELKAV 201
           + S   SGV L++ LF R  + +    +  +  P  PVG++VA+GE  LGFQQLSEL  V
Sbjct: 118 SLSTGPSGVALAK-LFERWGIAEQIAPRMVQAPPGVPVGSLVAKGEVALGFQQLSELLHV 176

Query: 202 PGIDIVGLIPDQAQKMTLYSGAMVSKSQHPEAARALLQYLASKDAAKAIEDSGLKP 257
            GI IVG +P   Q  T +S  +   SQ  +AAR+LL YLAS  AA+A +  G+ P
Sbjct: 177 QGIQIVGPLPPAIQITTTFSAGVGVHSQQADAARSLLAYLASPAAAEAKQKQGMTP 232


Lambda     K      H
   0.316    0.130    0.354 

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: 142
Number of extensions: 6
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: 262
Length of database: 233
Length adjustment: 24
Effective length of query: 238
Effective length of database: 209
Effective search space:    49742
Effective search space used:    49742
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 (21.6 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