GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braG in Dethiosulfovibrio salsuginis USBA 82

Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_085544129.1 B9Y55_RS04285 ABC transporter ATP-binding protein

Query= uniprot:Q1MCU3
         (247 letters)



>NCBI__GCF_900177735.1:WP_085544129.1
          Length = 262

 Score =  124 bits (311), Expect = 2e-33
 Identities = 79/248 (31%), Positives = 127/248 (51%), Gaps = 16/248 (6%)

Query: 11  LLQVNGVETYYGNIRALAGVDVHVNKGEIVSLIGANGAGKSTLMMTICGSPQARTGSVVF 70
           +L    +   +G + A++   + + +  IV LIG NGAGK+T    I G  +   GSV F
Sbjct: 7   ILDAANLTMRFGGVTAVSDFSMAIQENRIVGLIGPNGAGKTTSFNMITGYYRPTEGSVSF 66

Query: 71  EGRDITRMPTHEIARLRIAQSPEGRRIFPRMTVLENLQMGAGLD----------NLKHFA 120
            G+DIT +  H++ R+ +A++ +  R+F   TVLEN+ +GA +           NL  F 
Sbjct: 67  SGQDITGLAPHKVCRMGVARTFQNIRLFKNETVLENVMIGAHIRQKSRWWQAPLNLPSFN 126

Query: 121 EDVEKIFTLFPRLKER---HA---QRGGTLSGGEQQMLSIGRALMARPKLLLLDEPSLGL 174
           ++  ++      L ER   H    +R  +L  G+Q+ L I RAL   P  LLLDEP+ G+
Sbjct: 127 KEEREVRDKAMELLERVDLHTVANERSESLPYGQQRRLEIARALATEPSFLLLDEPAAGM 186

Query: 175 APLIVKGIFEAIRKLNEAEGLTVFLVEQNAFAALRLSHRAYVMVNGKVTMSGSGKELLAN 234
            P     +   IR+L +   LT+ L+E +    + +    +V+  GK+   G+ KE+  +
Sbjct: 187 NPEESHVLMTFIRRLRDEFNLTILLIEHDMKVVMGVCEHIWVLDYGKLIAQGNPKEIQGD 246

Query: 235 PEVRAAYL 242
           P V  AYL
Sbjct: 247 PRVIEAYL 254


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: 148
Number of extensions: 5
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: 247
Length of database: 262
Length adjustment: 24
Effective length of query: 223
Effective length of database: 238
Effective search space:    53074
Effective search space used:    53074
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: 47 (22.7 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