GapMind for catabolism of small carbon sources

 

Aligments for a candidate for braF in Bacteroides thetaiotaomicron VPI-5482

Align NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate 353166 BT3640 lipoprotein releasing system ATP-binding protein (NCBI ptt file)

Query= TCDB::Q55164
         (267 letters)



>lcl|FitnessBrowser__Btheta:353166 BT3640 lipoprotein releasing
           system ATP-binding protein (NCBI ptt file)
          Length = 218

 Score = 95.9 bits (237), Expect = 6e-25
 Identities = 58/212 (27%), Positives = 111/212 (52%), Gaps = 19/212 (8%)

Query: 18  LLLAQGLSKSFGGLRAVDHADIVVKEGSITGLIGPNGAGKTTLFNLLSNFIRPDQGEVLF 77
           ++  +G++KSFG L+ +   D+ + +G I  ++GP+GAGKTTL  ++     PD G V  
Sbjct: 1   MIKLEGITKSFGSLQVLKGIDLEINKGEIVSIVGPSGAGKTTLLQIMGTLDEPDAGTVAI 60

Query: 78  NGDSIGQLAPHQIAL---RGSVRTFQVAKVLSRLTVLENMLLADQHQTGEKFLPRLINFR 134
           +G  + ++   +++    +     FQ  ++L   T LEN++           +P  I   
Sbjct: 61  DGTVVSRMKEKELSAFRNKNIGFVFQFHQLLPEFTALENVM-----------IPAFI--- 106

Query: 135 RVQKEERANREKAMAMLESVGLGAKAQDYAGALSGGQRKLLEMARALMSNPKLILLDEPA 194
                 +   E+AM +L  +GL  +A      LSGG+++ + +ARAL+++P +IL DEP+
Sbjct: 107 -AGVSSKEANERAMEILAFMGLTDRASHKPNELSGGEKQRVAVARALINHPAVILADEPS 165

Query: 195 AGVNPTLIGQICEHIVNW-NRQGITFLVIEHN 225
             ++      + +   +  +R G TF+++ H+
Sbjct: 166 GSLDTHNKEDLHQLFFDLRDRLGQTFVIVTHD 197


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: 123
Number of extensions: 4
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: 218
Length adjustment: 23
Effective length of query: 244
Effective length of database: 195
Effective search space:    47580
Effective search space used:    47580
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: 46 (22.3 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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