GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AZOBR_RS08250 in Marinobacter adhaerens HP15

Align Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate GFF2759 HP15_2703 branched-chain amino acid ABC transporter ATP-binding protein

Query= uniprot:G8ALJ1
         (236 letters)



>FitnessBrowser__Marino:GFF2759
          Length = 454

 Score =  246 bits (628), Expect = 5e-70
 Identities = 130/233 (55%), Positives = 173/233 (74%), Gaps = 2/233 (0%)

Query: 1   MLKVSGVHTFYGAIEALKGVDIEIGAGEIVSLIGANGAGKSTLLMTICGSPRARMGRITF 60
           ML + G+ T YG IE L  VDI I +GEIVSL+GANGAGKSTLLMTI G      G ITF
Sbjct: 221 MLSIKGLVTSYGQIEVLHDVDIHINSGEIVSLVGANGAGKSTLLMTISGLQPTDRGAITF 280

Query: 61  EGQDITQMPTYELVRLGIAQSPEGRRIFPRMSVLENLQMGSIT-AKPGSFANELERVLTL 119
           EG+D++++   + V  GI Q PEGR++F  +SV +NL +G+ T  K     ++LER+ T 
Sbjct: 281 EGKDLSKITADQRVADGIVQVPEGRQVFKDLSVHDNLLLGAYTRGKTPEVMDDLERMYTK 340

Query: 120 FPRLKERISQRAGTMSGGEQQMLAIGRALMSQPRLLLLDEPSLGLAPLVVKQIFQAVKDI 179
           FP L+++    AG +SGG+QQMLA+GRALM++PRLLLLDEPS+GLAPL++++IF  VK++
Sbjct: 341 FPILRQKRHNLAGELSGGQQQMLAMGRALMAKPRLLLLDEPSMGLAPLIIEEIFNIVKEL 400

Query: 180 NREQKMTVFMVEQNAFHALKLAHRGYVMVNGKVTMSGTGAELLANEEVRSAYL 232
            +E+ +T+F+VEQNA  AL LA RGYV+  GKV + GTG ELL+NE+VR AYL
Sbjct: 401 -KEEGITIFLVEQNASQALALADRGYVLETGKVVIEGTGRELLSNEKVREAYL 452


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: 274
Number of extensions: 15
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: 454
Length adjustment: 28
Effective length of query: 208
Effective length of database: 426
Effective search space:    88608
Effective search space used:    88608
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: 48 (23.1 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