GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natA in Klebsiella michiganensis M5al

Align NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate BWI76_RS25260 BWI76_RS25260 ABC transporter ATP-binding protein

Query= TCDB::Q55164
         (267 letters)



>FitnessBrowser__Koxy:BWI76_RS25260
          Length = 241

 Score =  149 bits (376), Expect = 5e-41
 Identities = 85/248 (34%), Positives = 134/248 (54%), Gaps = 14/248 (5%)

Query: 19  LLAQGLSKSFGGLRAVDHADIVVKEGSITGLIGPNGAGKTTLFNLLSNFIRPDQGEVLFN 78
           L A+ L+K++ G R V+   + V  G I GL+GPNGAGKTT F ++   +  D G ++ +
Sbjct: 4   LTAKNLAKAYKGRRVVEDVSLTVNSGEIVGLLGPNGAGKTTTFYMVVGIVPRDAGNIIID 63

Query: 79  GDSIGQLAPHQIALRGSVRTFQVAKVLSRLTVLENMLLADQHQTGEKFLPRLINFRRVQK 138
            + I  L  H  A RG     Q A +  RL+V +N++   Q +          +    Q+
Sbjct: 64  DEDISLLPLHARARRGIGYLPQEASIFRRLSVYDNLMAVLQIRD---------DLSNEQR 114

Query: 139 EERANREKAMAMLESVGLGAKAQDYAGALSGGQRKLLEMARALMSNPKLILLDEPAAGVN 198
           E+RA       ++E   +         ALSGG+R+ +E+ARAL +NPK ILLDEP AGV+
Sbjct: 115 EDRAKE-----LMEEFHIEHLRDSLGQALSGGERRRVEIARALAANPKFILLDEPFAGVD 169

Query: 199 PTLIGQICEHIVNWNRQGITFLVIEHNMDVIMTLCHHVWVLAEGRNLADGTPEQIQSDPR 258
           P  +  I   I +    G+  L+ +HN+   + +C   +++++G  +A GTP+QI  D +
Sbjct: 170 PISVIDIKRIIEHLRDSGLGVLITDHNVRETLAVCERAYIVSQGHLIAHGTPQQILEDEQ 229

Query: 259 VLEAYLGD 266
           V   YLG+
Sbjct: 230 VKRVYLGE 237


Lambda     K      H
   0.319    0.136    0.389 

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: 6
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: 267
Length of database: 241
Length adjustment: 24
Effective length of query: 243
Effective length of database: 217
Effective search space:    52731
Effective search space used:    52731
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 (21.7 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