GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braF in Azospirillum thiophilum BV-S

Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_167543410.1 AL072_RS29550 ABC transporter ATP-binding protein

Query= uniprot:Q1MCU2
         (292 letters)



>NCBI__GCF_001305595.1:WP_167543410.1
          Length = 303

 Score =  355 bits (911), Expect = e-103
 Identities = 177/268 (66%), Positives = 216/268 (80%), Gaps = 5/268 (1%)

Query: 14  LLKVEHLSMKFGGLMAINDFSFEAKRGDITALIGPNGAGKTTVFNCITGFYKPTMGMITF 73
           LL VEHL+M+FGGL+A ND SFEA+ G+ITALIGPNGAGKTT+FNC+TGFY PT+G +  
Sbjct: 11  LLTVEHLTMRFGGLVANNDVSFEARAGEITALIGPNGAGKTTLFNCVTGFYTPTVGRLCL 70

Query: 74  NQKSGKQYLLERLPDFRITKEARVARTFQNIRLFSGLTVLENLLVAQHNKLMKASGYTIL 133
               G+++LLER+P +RI + A VARTFQNIRLF G++VLENL+VAQHNKLM+AS + I 
Sbjct: 71  RHPEGREFLLERMPGYRIAQLAGVARTFQNIRLFGGMSVLENLIVAQHNKLMRASSFAIG 130

Query: 134 GLIGVGPYKREAAEAIELARFWLEKADLIDRADDPAGDLPYGAQRRLEIARAMCTGPELL 193
           GL+G+  Y+R   EA+ELA++WLE+  L + AD  AG+LPYGAQRRLEIARAMCT P LL
Sbjct: 131 GLLGLPSYRRAEHEAVELAKYWLERVRLTEFADWEAGNLPYGAQRRLEIARAMCTEPVLL 190

Query: 194 CLDEPAAGLNPRESATLNALL---KSIRAETG--TSILLIEHDMSVVMEISDHVVVLEYG 248
           CLDEPAAGLNPRES  L  +L   + +R   G  T +LLIEHDMSVVM ISDHVVVL+YG
Sbjct: 191 CLDEPAAGLNPRESGELAEILTFIRDVRTPQGHRTGVLLIEHDMSVVMRISDHVVVLDYG 250

Query: 249 QKISDGTPDHVKNDPRVIAAYLGVEDEE 276
           +KISDG P+HVKNDP VI AYLG +++E
Sbjct: 251 RKISDGDPEHVKNDPAVIRAYLGEDEDE 278


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: 303
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: 292
Length of database: 303
Length adjustment: 26
Effective length of query: 266
Effective length of database: 277
Effective search space:    73682
Effective search space used:    73682
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: 48 (23.1 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