GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Btheta:353166
          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.

Links

Downloads

Related tools

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