GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AZOBR_RS08250 in Pseudomonas stutzeri RCH2

Align Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate GFF1275 Psest_1308 ABC-type branched-chain amino acid transport systems, ATPase component

Query= uniprot:G8ALJ1
         (236 letters)



>FitnessBrowser__psRCH2:GFF1275
          Length = 233

 Score =  270 bits (689), Expect = 2e-77
 Identities = 137/234 (58%), Positives = 176/234 (75%), Gaps = 1/234 (0%)

Query: 1   MLKVSGVHTFYGAIEALKGVDIEIGAGEIVSLIGANGAGKSTLLMTICGSPRARMGRITF 60
           ML    V TFYG I+AL  +++++  GEIV+LIGANGAGKSTLLMT+CGSP+A  G I F
Sbjct: 1   MLTFENVSTFYGKIQALHDINVQVEQGEIVTLIGANGAGKSTLLMTLCGSPQAASGSIRF 60

Query: 61  EGQDITQMPTYELVRLGIAQSPEGRRIFPRMSVLENLQMGSITAKPGSFANELERVLTLF 120
           +G+++    T +++R  IA  PEGRRIF R++V ENL MG        F  +L++VL LF
Sbjct: 61  QGEELVGRQTCDIMRKAIAVVPEGRRIFARLTVEENLSMGGFFTGKTDFQEQLDKVLGLF 120

Query: 121 PRLKERISQRAGTMSGGEQQMLAIGRALMSQPRLLLLDEPSLGLAPLVVKQIFQAVKDIN 180
           PRLKER  QR GTMSGGEQQMLAI RALMS+P+LLLLDEPSLGLAP++++QIF+ ++ + 
Sbjct: 121 PRLKERYQQRGGTMSGGEQQMLAIARALMSKPKLLLLDEPSLGLAPIIIQQIFEIIEQL- 179

Query: 181 REQKMTVFMVEQNAFHALKLAHRGYVMVNGKVTMSGTGAELLANEEVRSAYLEG 234
           RE  +TVF+VEQNA  ALKLA RGYV+ NG + M G+G +LL + +VR AYL G
Sbjct: 180 REDGVTVFLVEQNANQALKLADRGYVLENGHIVMQGSGEDLLTDPKVRDAYLGG 233


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: 205
Number of extensions: 9
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: 233
Length adjustment: 23
Effective length of query: 213
Effective length of database: 210
Effective search space:    44730
Effective search space used:    44730
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