GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AZOBR_RS08250 in Pantoea rwandensis LMG 26275

Align Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate WP_084935579.1 HA51_RS15825 ABC transporter ATP-binding protein

Query= uniprot:G8ALJ1
         (236 letters)



>NCBI__GCF_002095475.1:WP_084935579.1
          Length = 249

 Score =  263 bits (671), Expect = 3e-75
 Identities = 141/234 (60%), Positives = 171/234 (73%), Gaps = 1/234 (0%)

Query: 1   MLKVSGVHTFYGAIEALKGVDIEIGAGEIVSLIGANGAGKSTLLMTICGSPRARMGRITF 60
           ML    V  FYG ++ALK V + +  GE V+LIGANGAGKSTLLM+I G PR   G I  
Sbjct: 5   MLSFEQVDVFYGPVQALKQVSLTVNQGETVALIGANGAGKSTLLMSIFGQPRIASGDIRL 64

Query: 61  EGQDITQMPTYELVRLGIAQSPEGRRIFPRMSVLENLQMGSITAKPGSFANELERVLTLF 120
            G+ I    T+ +   GIAQ+PEGRRIFP M+V ENL MG+I         + ER+  LF
Sbjct: 65  RGESIGHRSTHFIAASGIAQAPEGRRIFPDMTVEENLLMGTIAVGERHVKEDKERMYQLF 124

Query: 121 PRLKERISQRAGTMSGGEQQMLAIGRALMSQPRLLLLDEPSLGLAPLVVKQIFQAVKDIN 180
           PRL ER  QRA T+SGGEQQMLAI RALMS+P+LLLLDEPSLGLAP+VVKQIF  ++++ 
Sbjct: 125 PRLLERRKQRAMTLSGGEQQMLAIARALMSRPKLLLLDEPSLGLAPIVVKQIFNILRELT 184

Query: 181 REQKMTVFMVEQNAFHALKLAHRGYVMVNGKVTMSGTGAELLANEEVRSAYLEG 234
            +Q MT+F+VEQNA HAL+LA RGYVMVNG++ +SG G ELL N+EVRSAYL G
Sbjct: 185 -QQGMTLFLVEQNARHALQLADRGYVMVNGEIKLSGRGEELLNNDEVRSAYLGG 237


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: 210
Number of extensions: 7
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: 249
Length adjustment: 23
Effective length of query: 213
Effective length of database: 226
Effective search space:    48138
Effective search space used:    48138
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 24 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