GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AZOBR_RS08250 in Shewanella amazonensis SB2B

Align Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate 6937163 Sama_1333 lipoprotein releasing system ATP-binding protein LolD (RefSeq)

Query= uniprot:G8ALJ1
         (236 letters)



>FitnessBrowser__SB2B:6937163
          Length = 229

 Score = 87.4 bits (215), Expect = 2e-22
 Identities = 73/232 (31%), Positives = 116/232 (50%), Gaps = 22/232 (9%)

Query: 1   MLKVSGVHTFY--GAIEA--LKGVDIEIGAGEIVSLIGANGAGKSTLLMTICGSPRARMG 56
           +LKV  V   Y  G +E   L GVD+ +  GE ++++G +G+GKSTLL  +    +   G
Sbjct: 5   LLKVENVSKTYREGKLETQVLCGVDLSVYRGEQLAIVGGSGSGKSTLLHIMGSLDKPTSG 64

Query: 57  RITFEGQDITQMPTYELVRLGIAQSP---EGRRIFPRMSVLENLQMGSITA---KPGSFA 110
           ++  EG+D+  +      ++  A      +   + P  S LEN+ M +  A   K  +F 
Sbjct: 65  KVLLEGEDLYSLSAARQAQIRNASLGFIYQFHHLLPEFSALENVAMPARIAGVDKKTAFG 124

Query: 111 NE---LERVLTLFPRLKERISQRAGTMSGGEQQMLAIGRALMSQPRLLLLDEPSLGLAPL 167
                LERV      L  R+S     +SGGE+Q +AI RAL++QPRL+L DEP+  L   
Sbjct: 125 RAEALLERV-----GLSHRLSHAPSELSGGERQRVAIARALINQPRLVLADEPTGNLDAA 179

Query: 168 VVKQIFQAVKDINREQKMTVFMVEQNAFHALKLAHRGYVMVNGKVTMSGTGA 219
             + ++  ++++   Q  T F+V  +         R   M +GK+T   TGA
Sbjct: 180 SGEAVYALIREL-AAQLGTAFVVVTHDNALAARMDRQLSMKSGKLT---TGA 227


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: 132
Number of extensions: 8
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: 236
Length of database: 229
Length adjustment: 23
Effective length of query: 213
Effective length of database: 206
Effective search space:    43878
Effective search space used:    43878
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