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 GFF4159 HP15_4099 branched-chain amino acid ABC transporter, ATP-binding protein

Query= uniprot:G8ALJ1
         (236 letters)



>FitnessBrowser__Marino:GFF4159
          Length = 269

 Score =  197 bits (501), Expect = 2e-55
 Identities = 108/243 (44%), Positives = 156/243 (64%), Gaps = 8/243 (3%)

Query: 1   MLKVSGVHTFYG-AIEALKGVDIEIGAGEIVSLIGANGAGKSTLLMTICGSPRARMGRIT 59
           +L++  +   Y  +++ L+G+ + +  G IV+L+G+NGAGKST L ++ G      G +T
Sbjct: 4   LLEIDNIEVVYNKSVQVLRGLSLRVPKGAIVALLGSNGAGKSTTLKSVSGLLTLEDGEVT 63

Query: 60  -----FEGQDITQMPTYELVRLGIAQSPEGRRIFPRMSVLENLQMGS--ITAKPGSFANE 112
                F G+D+  +P   LVR G+    EGRR+F  ++V ENL   +  ++    S ++ 
Sbjct: 64  AGEVRFRGKDVKGVPPERLVRDGLFHVMEGRRVFEDLTVEENLIAATYALSGSKPSLSDS 123

Query: 113 LERVLTLFPRLKERISQRAGTMSGGEQQMLAIGRALMSQPRLLLLDEPSLGLAPLVVKQI 172
            E V   FPRLKER  Q AG +SGGEQQMLA+GRAL++QP L++LDEPSLGLAPL+V++I
Sbjct: 124 YELVYNYFPRLKERRKQLAGYLSGGEQQMLALGRALIAQPDLIMLDEPSLGLAPLLVEEI 183

Query: 173 FQAVKDINREQKMTVFMVEQNAFHALKLAHRGYVMVNGKVTMSGTGAELLANEEVRSAYL 232
           F  V  INREQ   + +VEQNA  +L +A  GY+M NGK+ + G   +L ANE+V+  YL
Sbjct: 184 FTIVARINREQGTAILLVEQNAAVSLAIASYGYIMENGKIVIDGPADKLTANEDVQEFYL 243

Query: 233 EGG 235
             G
Sbjct: 244 GVG 246


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: 200
Number of extensions: 9
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: 269
Length adjustment: 24
Effective length of query: 212
Effective length of database: 245
Effective search space:    51940
Effective search space used:    51940
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