GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natA in Pseudomonas putida KT2440

Align NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate PP_2748 PP_2748 putative Branched-chain amino acid ABC transporter, ATP-binding protein

Query= TCDB::Q55164
         (267 letters)



>FitnessBrowser__Putida:PP_2748
          Length = 266

 Score =  165 bits (418), Expect = 8e-46
 Identities = 99/266 (37%), Positives = 153/266 (57%), Gaps = 5/266 (1%)

Query: 1   MSDRITPAENLGSPESSLLLAQGLSKSFGGLRAVDHADIVVKEGSITGLIGPNGAGKTTL 60
           M+ RI+ A  +    S+LL  + +S SF G++A+      V+ G I  LIGPNGAGK++L
Sbjct: 1   MAARISGARGM----SALLEVRNVSLSFKGVKAISDLSFSVRRGEICALIGPNGAGKSSL 56

Query: 61  FNLLSNFIRPDQGEVLFNGDSIGQLAPHQIALRGSVRTFQVAKVLSRLTVLENMLLADQH 120
            N+L+   R D G++ F  + + +  P Q A  G  RTFQ   +  +++VL+N+L     
Sbjct: 57  LNILNGVYRADAGQLFFATEPLRRPHPLQAARLGIGRTFQNNALFKKMSVLDNLLTGLSR 116

Query: 121 QTGEKFLPRLINFRRVQKEERANREKAMAMLESVGLGAKAQDYAGALSGGQRKLLEMARA 180
                FL + +   R ++E RA  E+A  +L  + L        G+L+ G +K +E+ RA
Sbjct: 117 FQRSYFLEQALGLPRARREARAFAERAEQVLAFLELQPWRDVAVGSLAYGLQKRVELGRA 176

Query: 181 LMSNPKLILLDEPAAGVNPTLIGQICEHIVNWNRQ-GITFLVIEHNMDVIMTLCHHVWVL 239
           L++ P L+LLDEP AG+N      +   I + NR  G T ++IEH++ V+M L  HV VL
Sbjct: 177 LIAQPTLLLLDEPMAGMNAEEKQDMSRFIADINRDLGTTVILIEHDIQVVMGLSSHVVVL 236

Query: 240 AEGRNLADGTPEQIQSDPRVLEAYLG 265
             GR + DGTP ++Q++P V+ AYLG
Sbjct: 237 DYGRKVGDGTPAEVQANPDVIAAYLG 262


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: 170
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: 266
Length adjustment: 25
Effective length of query: 242
Effective length of database: 241
Effective search space:    58322
Effective search space used:    58322
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