GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AZOBR_RS08250 in Acidovorax sp. GW101-3H11

Align Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate Ac3H11_1936 Branched-chain amino acid transport ATP-binding protein LivF (TC 3.A.1.4.1)

Query= uniprot:G8ALJ1
         (236 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_1936
          Length = 272

 Score =  212 bits (540), Expect = 5e-60
 Identities = 110/233 (47%), Positives = 156/233 (66%), Gaps = 1/233 (0%)

Query: 1   MLKVSGVHTFYGAIEALKGVDIEIGAGEIVSLIGANGAGKSTLLMTICGSPRARMGRITF 60
           +L++  V + YG I+A++GV +++  GEI +++G+NGAGK+T+L TI G    R G I F
Sbjct: 20  LLRLQNVESAYGPIKAIRGVSLQVRRGEIAAVLGSNGAGKTTILKTISGIIDPRKGSIEF 79

Query: 61  EGQDITQMPTYELVRLGIAQSPEGRRIFPRMSVLENLQMGSIT-AKPGSFANELERVLTL 119
           +GQDIT      +VR G+   PEGR +FP +SV +NL MG+ T A     A ++E V   
Sbjct: 80  QGQDITARDPAAIVRRGLMHVPEGREVFPLLSVRDNLLMGAYTRADKDGVARDIETVFGY 139

Query: 120 FPRLKERISQRAGTMSGGEQQMLAIGRALMSQPRLLLLDEPSLGLAPLVVKQIFQAVKDI 179
           FP LKER +Q AG +SGG+QQMLAI RALM+ P L+LLDEPSLGL+P + K+IF+ V  I
Sbjct: 140 FPILKERAAQDAGLLSGGQQQMLAISRALMAAPELILLDEPSLGLSPKLTKEIFEIVVRI 199

Query: 180 NREQKMTVFMVEQNAFHALKLAHRGYVMVNGKVTMSGTGAELLANEEVRSAYL 232
           NRE+  T+ +VEQNA  AL  +  GYV+ NG++ M  +   L   ++++  YL
Sbjct: 200 NRERGTTILLVEQNANMALNASDYGYVLENGRIVMEDSCERLREKDDIKEFYL 252


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: 170
Number of extensions: 6
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: 272
Length adjustment: 24
Effective length of query: 212
Effective length of database: 248
Effective search space:    52576
Effective search space used:    52576
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