GapMind for catabolism of small carbon sources

 

Aligments for a candidate for AZOBR_RS08250 in Bacteroides thetaiotaomicron VPI-5482

Align Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate 353166 BT3640 lipoprotein releasing system ATP-binding protein (NCBI ptt file)

Query= uniprot:G8ALJ1
         (236 letters)



>lcl|FitnessBrowser__Btheta:353166 BT3640 lipoprotein releasing
           system ATP-binding protein (NCBI ptt file)
          Length = 218

 Score =  105 bits (261), Expect = 9e-28
 Identities = 67/216 (31%), Positives = 115/216 (53%), Gaps = 5/216 (2%)

Query: 1   MLKVSGVHTFYGAIEALKGVDIEIGAGEIVSLIGANGAGKSTLLMTICGSPRARMGRITF 60
           M+K+ G+   +G+++ LKG+D+EI  GEIVS++G +GAGK+TLL  +        G +  
Sbjct: 1   MIKLEGITKSFGSLQVLKGIDLEINKGEIVSIVGPSGAGKTTLLQIMGTLDEPDAGTVAI 60

Query: 61  EGQDITQMPTYELVRL---GIAQSPEGRRIFPRMSVLENLQMGSITAKPGS-FANELERV 116
           +G  +++M   EL       I    +  ++ P  + LEN+ + +  A   S  ANE    
Sbjct: 61  DGTVVSRMKEKELSAFRNKNIGFVFQFHQLLPEFTALENVMIPAFIAGVSSKEANERAME 120

Query: 117 LTLFPRLKERISQRAGTMSGGEQQMLAIGRALMSQPRLLLLDEPSLGLAPLVVKQIFQAV 176
           +  F  L +R S +   +SGGE+Q +A+ RAL++ P ++L DEPS  L     + + Q  
Sbjct: 121 ILAFMGLTDRASHKPNELSGGEKQRVAVARALINHPAVILADEPSGSLDTHNKEDLHQLF 180

Query: 177 KDINREQKMTVFMVEQNAFHALKLAHRGYVMVNGKV 212
            D+ R++    F++  +     K+  R   MV+G +
Sbjct: 181 FDL-RDRLGQTFVIVTHDEGLAKITDRTVHMVDGTI 215


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: 113
Number of extensions: 4
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: 218
Length adjustment: 22
Effective length of query: 214
Effective length of database: 196
Effective search space:    41944
Effective search space used:    41944
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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