GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braF in Methanosarcina acetivorans C2A

Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_011022097.1 MA_RS10955 daunorubicin resistance protein DrrA family ABC transporter ATP-binding protein

Query= uniprot:Q1MCU2
         (292 letters)



>NCBI__GCF_000007345.1:WP_011022097.1
          Length = 267

 Score =  106 bits (265), Expect = 5e-28
 Identities = 77/247 (31%), Positives = 118/247 (47%), Gaps = 36/247 (14%)

Query: 14  LLKVEHLSMKFGGLMAINDFSFEAKRGDITALIGPNGAGKTTVFNCITGFYKPTMGMITF 73
           +L V+ L+ KF  L A+   SF+ + G I A +GPNGAGK+T    +T   +PT G I  
Sbjct: 4   ILSVKSLTKKFDDLTAVKGISFDVETGSIFAFLGPNGAGKSTTIKMLTTVLRPTSGEILI 63

Query: 74  NQKSGKQYLLERLPDFRITKEARVART-----FQNIRLFSGLTVLENLLVAQHNKLMKAS 128
           N              +   KE   AR+     FQ+  L S LT  EN+   +++ ++   
Sbjct: 64  N-------------GYNALKEQDKARSSFGIVFQDYSLDSELTAYENM---EYHSVI--- 104

Query: 129 GYTILGLIGVGPYKREAAEAIELARFWLEKADLIDRADDPAGDLPYGAQRRLEIARAMCT 188
                       YK   AE  E  +  LE   L +R +D       G +RRLEIARA+  
Sbjct: 105 ------------YKVPKAEREERIKTALEIVGLWNRRNDLVKKYSGGMKRRLEIARALVH 152

Query: 189 GPELLCLDEPAAGLNPRESATLNALLKSIRAETGTSILLIEHDMSVVMEISDHVVVLEYG 248
            P++L LDEP  GL+P+   ++   +K +  E   +I L  H M     ++D + ++++G
Sbjct: 153 YPKVLFLDEPTVGLDPQTRMSIWNHIKRLNEERKMTIFLTTHYMDEAEAMADKIAIIDHG 212

Query: 249 QKISDGT 255
           + I  GT
Sbjct: 213 KIIESGT 219


Lambda     K      H
   0.318    0.136    0.386 

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: 154
Number of extensions: 8
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: 292
Length of database: 267
Length adjustment: 26
Effective length of query: 266
Effective length of database: 241
Effective search space:    64106
Effective search space used:    64106
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Apr 09 2024. 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