GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bgtA in Sulfurivirga caldicuralii DSM 17737

Align BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized)
to candidate WP_074200832.1 BUQ81_RS02650 lipoprotein-releasing ABC transporter ATP-binding protein LolD

Query= TCDB::P73721
         (252 letters)



>NCBI__GCF_900141795.1:WP_074200832.1
          Length = 227

 Score =  120 bits (301), Expect = 2e-32
 Identities = 76/207 (36%), Positives = 121/207 (58%), Gaps = 6/207 (2%)

Query: 23  VLRGVTGEIYPKDVISIIGPSGCGKSTFLRCLNRLEPISGGRLEVAGVDLSGAKIDQKHL 82
           VL+GV+  ++ ++ ++I+G SG GKST L  L  L+  + G + + G   S  K+ +   
Sbjct: 24  VLKGVSLILHRRERVAIVGSSGSGKSTLLHLLGGLDRPTDGEVLLLGQPFS--KLGEAAR 81

Query: 83  RQLRVR-VGMVFQHFNLFPHLTVLQNLLLAPRKVLRIPMAEAKDRALTYLDKVGLGTKAD 141
            +LR R +G V+Q  +L P LT  +N+++ P  + R   A A+D+AL  LD VGL  +  
Sbjct: 82  GRLRNRHMGFVYQFHHLLPELTAEENVMM-PLLIRRESEATARDKALALLDAVGLSRRTA 140

Query: 142 NYPDQLSGGQKQRVAIARGLCMKPEILLFDEPTSALDPELVGEVLNVMKQLAEE-GMTMA 200
           + P +LSGG++QRVA+AR L  +P+ +L DEPT  LD     +VL++M  L +  G  + 
Sbjct: 141 HKPSELSGGERQRVALARALVTEPDCVLADEPTGNLDSRSAEQVLSLMDDLNQRFGTALL 200

Query: 201 VVTHEMQFAREVSNRVFFFNQGIIEEE 227
           VVTH++  A  + +R      G+I  E
Sbjct: 201 VVTHDVNIAARM-DRTLTLRDGMIRVE 226


Lambda     K      H
   0.321    0.139    0.397 

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: 124
Number of extensions: 7
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: 252
Length of database: 227
Length adjustment: 23
Effective length of query: 229
Effective length of database: 204
Effective search space:    46716
Effective search space used:    46716
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 (21.9 bits)
S2: 46 (22.3 bits)

This GapMind analysis is from Apr 09 2024. 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