GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natA in Pedobacter sp. GW460-11-11-14-LB5

Align NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate CA265_RS23135 CA265_RS23135 ABC transporter ATP-binding protein

Query= TCDB::Q55164
         (267 letters)



>FitnessBrowser__Pedo557:CA265_RS23135
          Length = 302

 Score = 89.0 bits (219), Expect = 1e-22
 Identities = 72/232 (31%), Positives = 110/232 (47%), Gaps = 22/232 (9%)

Query: 23  GLSKSFGGLRAVDHADIVVKEGSITGLIGPNGAGKTTLFNLLSNFIRPDQGEVLFNGDSI 82
           GL+ +FG    V    + V +GSI G +GPNGAGKTT   +L N ++    +V   G  I
Sbjct: 10  GLNFNFGNQVIVKDLSLQVPKGSIYGFLGPNGAGKTTTIKILLNLLKSPSDQVFIFGKEI 69

Query: 83  GQLAPHQIALRGSVRTFQVAKVLSRLTVLENMLLADQHQTGEKFLPRLINFRRVQKEERA 142
                ++IA             L R+  L        H TG++ L        ++K    
Sbjct: 70  NS---NRIA------------TLKRIGALVEQPAIYGHLTGKENLINRCILLGIKK---- 110

Query: 143 NREKAMAMLESVGLGAKAQDYAGALSGGQRKLLEMARALMSNPKLILLDEPAAGVNPTLI 202
              KA  ML  VGL   A   A   S G ++ L +A+AL+S+P+L+LLDEP  G++P  I
Sbjct: 111 --NKADEMLALVGLTEAANKKANKYSLGMKQRLGIAQALISDPELLLLDEPTNGLDPNGI 168

Query: 203 GQICEHIVNW-NRQGITFLVIEHNMDVIMTLCHHVWVLAEGRNLADGTPEQI 253
            +I   +++   +   T LV  H +  I     HV ++ +G+ L  GT  ++
Sbjct: 169 IEIRNLMIDLATKHQKTILVSSHLLAEIERTATHVGIINKGQLLFQGTINEL 220


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: 147
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: 267
Length of database: 302
Length adjustment: 26
Effective length of query: 241
Effective length of database: 276
Effective search space:    66516
Effective search space used:    66516
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