GapMind for catabolism of small carbon sources

 

Alignments for a candidate for BPHYT_RS24010 in Acidovorax sp. GW101-3H11

Align Polar amino acid ABC transporter, inner membrane subunit (characterized, see rationale)
to candidate Ac3H11_4900 Putative amino acid ABC transporter, permease protein

Query= uniprot:B2TBJ8
         (250 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_4900
          Length = 217

 Score =  124 bits (312), Expect = 1e-33
 Identities = 77/221 (34%), Positives = 120/221 (54%), Gaps = 9/221 (4%)

Query: 8   LFDTIKQLLAAVPTTLGLFFCSLILGGLLSLVIVTMRVSPHWLPNRFARAYILVFRGSPL 67
           L+D ++ LL A   T+ L   + I GGL+ L+++ +R+S     +R   AY+ VF+G+PL
Sbjct: 6   LWDILRNLLLAARWTVSLSLIAFIGGGLVGLLLLVLRLSKVRGVDRAVGAYVQVFQGTPL 65

Query: 68  LIQMFLVYYGMGQFGVIRESFLWPVLREPYMCAVLSLALCTAGYTAEIIRGGLMAVPVGQ 127
           L+Q+FL Y+G+  FG+            P+  A ++L L T+ Y  EI RG + ++P GQ
Sbjct: 66  LMQLFLAYFGIALFGI---------KTSPWTAAAVALTLYTSAYLTEIWRGCVASIPKGQ 116

Query: 128 IEAGYSIGLSGFALLRRVIGPIALRQCLPAYSTEAVLLVKSTALASLVTVWEVTGVAQQI 187
            EA  S+  +    LR V+ P ALR  +P      V ++K TALAS++   E+T     I
Sbjct: 117 WEAAQSLAFNFGEQLRHVVLPQALRIAVPPTVGFLVQVIKGTALASVIGFVELTKAGSMI 176

Query: 188 IQQTYRTTEVFICAALIYLFLNFVIVRLLGMLETRLSRHLR 228
              TY+   V+ C AL+Y  L F +  +   LE +L  + R
Sbjct: 177 SNATYKPFLVYACVALLYFVLCFPVSLVAQSLERKLHGNRR 217


Lambda     K      H
   0.331    0.143    0.431 

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: 125
Number of extensions: 7
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: 250
Length of database: 217
Length adjustment: 23
Effective length of query: 227
Effective length of database: 194
Effective search space:    44038
Effective search space used:    44038
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 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