GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AZOBR_RS08250 in Shewanella sp. ANA-3

Align Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate 7023443 Shewana3_0673 ABC transporter related (RefSeq)

Query= uniprot:G8ALJ1
         (236 letters)



>FitnessBrowser__ANA3:7023443
          Length = 243

 Score =  118 bits (295), Expect = 1e-31
 Identities = 72/234 (30%), Positives = 123/234 (52%), Gaps = 5/234 (2%)

Query: 2   LKVSGVHTFYGAIEALKGVDIEIGAGEIVSLIGANGAGKSTLLMTICGSPRARMGRITFE 61
           LK   +   Y + + +K V + +  G++V L+G NGAGK+T    + G  ++  G I  +
Sbjct: 6   LKAQNLAKSYKSRQVVKDVSLTVKTGQVVGLLGPNGAGKTTTFYMVVGLVKSDKGHIFID 65

Query: 62  GQDITQMPTYELVRLGIAQSPEGRRIFPRMSVLENLQMGSITAKP---GSFANELERVLT 118
             D+T  P +   R GI   P+   IF +++V +N+     T K         ELE +L 
Sbjct: 66  DDDLTADPMHLRARKGIGYLPQEASIFRKLTVHDNIMAVLQTRKELNRDQREEELEHLLE 125

Query: 119 LFPRLKERISQRAGTMSGGEQQMLAIGRALMSQPRLLLLDEPSLGLAPLVVKQIFQAVKD 178
            F     R SQ   ++SGGE++ + I RAL + P+ +LLDEP  G+ P+ V  I + ++ 
Sbjct: 126 EFHITHIRDSQ-GMSLSGGERRRVEIARALAANPKFILLDEPFAGVDPISVIDIKKIIEQ 184

Query: 179 INREQKMTVFMVEQNAFHALKLAHRGYVMVNGKVTMSGTGAELLANEEVRSAYL 232
           + + + + V + + N    L +    Y++ +G +   GT AE+L N++VR+ YL
Sbjct: 185 L-KSRGLGVLITDHNVRETLDVCEHAYIVSHGNLIAEGTPAEILDNQQVRAVYL 237


Lambda     K      H
   0.320    0.136    0.377 

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: 107
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: 236
Length of database: 243
Length adjustment: 23
Effective length of query: 213
Effective length of database: 220
Effective search space:    46860
Effective search space used:    46860
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: 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