GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braF in Klebsiella michiganensis M5al

Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate BWI76_RS15325 BWI76_RS15325 ABC transporter ATP-binding protein

Query= uniprot:Q1MCU2
         (292 letters)



>FitnessBrowser__Koxy:BWI76_RS15325
          Length = 265

 Score =  124 bits (311), Expect = 2e-33
 Identities = 87/261 (33%), Positives = 135/261 (51%), Gaps = 19/261 (7%)

Query: 12  DTLLKVEHLSMKFGGLMAINDFSFEAKRGDITALIGPNGAGKTTVFNCITGFYKPTMGMI 71
           D +L++E +++ F G  A+ + S +   G++  +IGPNGAGKTT+ + ITG  +P  G  
Sbjct: 22  DPVLQLEEINVNFDGFQALTNLSLQIGVGELRCVIGPNGAGKTTLMDVITGKTRPQSGRA 81

Query: 72  TFNQKSGKQYLLERLPDFRITKEARVARTFQNIRLFSGLTVLENL-LVAQHNKLMKASGY 130
            ++Q       L  L    I ++  + R FQ   +F  LTV ENL L  + +K + AS  
Sbjct: 82  LYDQSVD----LTTLDPIAIARQG-IGRKFQKPTVFEALTVAENLELAMKGDKSVWASLR 136

Query: 131 TILGLIGVGPYKREAAEAIELARFWLEKADLIDRADDPAGDLPYGAQRRLEIARAMCTGP 190
             L            +E + L R   E+         PAG L +G ++ LEI   +   P
Sbjct: 137 ARLN----SEQADRISETLRLLRLEGERY-------RPAGLLSHGQKQFLEIGMLLVQEP 185

Query: 191 ELLCLDEPAAGLNPRESATLNALLKSIRAETGTSILLIEHDMSVVMEISDHVVVLEYGQK 250
            LL LDEPAAG+   E+     L +++  +   S++++EHDM  V  I+D V VL  GQ 
Sbjct: 186 HLLLLDEPAAGMTDAETEYTAELFRTLAGQ--HSLMVVEHDMGFVETIADRVTVLHQGQV 243

Query: 251 ISDGTPDHVKNDPRVIAAYLG 271
           +++G+   VK + +VI  YLG
Sbjct: 244 LAEGSLREVKANEQVIEVYLG 264


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: 164
Number of extensions: 7
Number of successful extensions: 4
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: 265
Length adjustment: 25
Effective length of query: 267
Effective length of database: 240
Effective search space:    64080
Effective search space used:    64080
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 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 (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