GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AZOBR_RS08245 in Desulfovibrio vulgaris Hildenborough

Align Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate 209489 DVU0550 high-affinity branched-chain amino acid ABC transporter, ATP binding protein

Query= uniprot:G8ALJ0
         (294 letters)



>MicrobesOnline__882:209489
          Length = 262

 Score =  226 bits (576), Expect = 4e-64
 Identities = 129/264 (48%), Positives = 174/264 (65%), Gaps = 10/264 (3%)

Query: 11  LLTVEHLTMRFGGLVAVNDVSFSANNGEITAIIGPNGAGKTTLFNCITGFYTPTVGRLTL 70
           +L V  ++  FGGL A+N+V    + GEI A+IGPNGAGKTT FNCITG Y PT G + +
Sbjct: 4   VLDVRSISKNFGGLRALNEVDLRVDAGEIVALIGPNGAGKTTFFNCITGIYVPTEGEVVV 63

Query: 71  RHADGKEFLLERMPGYRISQ--KASVARTFQNIRLFGGMSVLENLIVAQHNKLIRASGFS 128
                +     R+ G + +Q  +  +ARTFQNIRLF  M+VLEN+++  H +    SG  
Sbjct: 64  TRPGSEPV---RVNGQKPNQVTELGMARTFQNIRLFQNMTVLENVMIGCHCRT--RSG-- 116

Query: 129 IAGLLGLPSYTR-TEREAVDLAKYWLDRVRLLEFADWEAGNLPYGAQRRLEIARAMCTEP 187
           I G L   + TR  E+E +D +   L  V L +    +A NLPYGAQRRLEIARA+ T P
Sbjct: 117 ILGALLRDAKTRGEEQEIIDKSYELLKSVHLQQHYKEQARNLPYGAQRRLEIARALATNP 176

Query: 188 VMLCLDEPAAGLNPRESGELADLLTYIRDEHKIGVLLIEHDMSVVMTISDHVVVLDYGRK 247
            +L LDEPAAG+NP+E+ EL  L+  IR+   + VLLIEHDM++VM++SD + V++YG K
Sbjct: 177 FLLLLDEPAAGMNPQETLELKGLVLEIRERLNLSVLLIEHDMNMVMSLSDRIYVMEYGSK 236

Query: 248 ISDGDPAFVKNDPAVIRAYLGEEE 271
           I++G P  V  +P VI+AYLGEEE
Sbjct: 237 IAEGTPEEVSRNPRVIKAYLGEEE 260


Lambda     K      H
   0.319    0.137    0.397 

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: 197
Number of extensions: 5
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: 294
Length of database: 262
Length adjustment: 25
Effective length of query: 269
Effective length of database: 237
Effective search space:    63753
Effective search space used:    63753
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 (21.8 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