GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braG in Desulfovibrio vulgaris Hildenborough

Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate 207079 DVU1627 ABC transporter, ATP-binding protein

Query= uniprot:Q1MCU3
         (247 letters)



>MicrobesOnline__882:207079
          Length = 241

 Score =  129 bits (323), Expect = 7e-35
 Identities = 81/235 (34%), Positives = 125/235 (53%), Gaps = 6/235 (2%)

Query: 11  LLQVNGVETYYGNIRALAGVDVHVNKGEIVSLIGANGAGKSTLMMTICGSPQARTGSVVF 70
           +LQ   +   +G    + GV V V +GEIV L+G NGAGK+T    + G  +   G V  
Sbjct: 4   VLQGEDLRKRFGQREVVRGVSVSVQQGEIVGLLGPNGAGKTTTFYMLTGIIKPTAGIVRL 63

Query: 71  EGRDITRMPTHEIARLRIAQSPEGRRIFPRMTVLENLQM---GAGLDNLKHFAEDVEKIF 127
           +G+DI   P HE AR+ ++  P+   +F R+TV ENL++     GL   +   E  E + 
Sbjct: 64  DGQDIADWPLHERARVGLSYLPQESSVFKRLTVRENLEIILEHTGLPAARQ-KERAEALM 122

Query: 128 TLFPRLKERHAQRGGTLSGGEQQMLSIGRALMARPKLLLLDEPSLGLAPLIVKGIFEAIR 187
             F  +    + R   LSGGE++ L I R ++  PK +LLDEP  G+ PL V  I   IR
Sbjct: 123 ADF-GIAHLASSRAMHLSGGERRRLEIARCMIREPKFVLLDEPFAGIDPLAVGDIQGLIR 181

Query: 188 KLNEAEGLTVFLVEQNAFAALRLSHRAYVMVNGKVTMSGSGKELLANPEVRAAYL 242
           KL +  G+ V + + N    L +  RAY++  G+V + G+ + ++ + + R  YL
Sbjct: 182 KLRD-RGIGVLISDHNVRETLTICDRAYLVHQGQVILDGTPEHIVGDEQARLVYL 235


Lambda     K      H
   0.320    0.137    0.387 

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: 157
Number of extensions: 6
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: 247
Length of database: 241
Length adjustment: 24
Effective length of query: 223
Effective length of database: 217
Effective search space:    48391
Effective search space used:    48391
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.

Links

Downloads

Related tools

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