GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natA in Pseudomonas stutzeri RCH2

Align NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate GFF1056 Psest_1089 ABC-type branched-chain amino acid transport systems, ATPase component

Query= TCDB::Q55164
         (267 letters)



>FitnessBrowser__psRCH2:GFF1056
          Length = 258

 Score =  178 bits (451), Expect = 1e-49
 Identities = 99/248 (39%), Positives = 151/248 (60%), Gaps = 6/248 (2%)

Query: 18  LLLAQGLSKSFGGLRAVDHADIVVKEGSITGLIGPNGAGKTTLFNLLSNFIRPDQGEVLF 77
           +L  +GL+K F G  AVD  D+ V++G I  LIGPNGAGKTT+FNLL+ F+ P +GE+L+
Sbjct: 6   VLETRGLTKEFRGFTAVDSVDLKVRQGHIHALIGPNGAGKTTVFNLLTKFLTPTRGEILY 65

Query: 78  NGDSIGQLAPHQIALRGSVRTFQVAKVLSRLTVLENMLLADQHQTGEKFLPRLINFRRVQ 137
            G +I  +  ++IA  G VR+FQ++ V   ++VLEN+ +A Q + G  F     +F R +
Sbjct: 66  RGKNITSMKANEIARLGLVRSFQISAVFGHMSVLENVRVALQQKMGNSF-----HFWRSE 120

Query: 138 KEERANREKAMAMLESVGLGAKAQDYAGALSGGQRKLLEMARALMSNPKLILLDEPAAGV 197
           +  R   ++ M +L  V L + AQ  A  L  G+++ LE+A  L  +P ++LLDEP  G+
Sbjct: 121 RSLRELDDQVMQLLAEVDLQSFAQTLAVELPYGRKRALELATTLALDPFVLLLDEPTQGM 180

Query: 198 NPTLIGQICEHIVNWNRQGITFLVIEHNMDVIMTLCHHVWVLAEGRNLADGTPEQIQSDP 257
               +  + E +V       T L++EHN+ V+  LC  + VLA G  LA+G  E + ++P
Sbjct: 181 GSEDVDMVVE-LVRKAAANRTVLMVEHNLSVVSRLCDRITVLARGSVLAEGDYESVSANP 239

Query: 258 RVLEAYLG 265
           +V EAYLG
Sbjct: 240 QVREAYLG 247


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: 158
Number of extensions: 10
Number of successful extensions: 3
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: 258
Length adjustment: 25
Effective length of query: 242
Effective length of database: 233
Effective search space:    56386
Effective search space used:    56386
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