GapMind for catabolism of small carbon sources

 

Alignments for a candidate for cbtF in Bacteroides clarus YIT 12056

Align CbtF, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate WP_039950239.1 BUB52_RS11690 glycine betaine/L-proline ABC transporter ATP-binding protein

Query= TCDB::Q97VF4
         (324 letters)



>NCBI__GCF_900129655.1:WP_039950239.1
          Length = 408

 Score =  119 bits (297), Expect = 2e-31
 Identities = 75/235 (31%), Positives = 137/235 (58%), Gaps = 12/235 (5%)

Query: 27  ALKDVSLSMNQGDLLIVLGESGAGKTTLGRVIVGLQKPTSGEVVYDGYNIWK-NKRKIFK 85
           A+KD +LS+N+G++ +++G SG+GK+TL R I  L +PTSGE++ +  +I K +K+++ +
Sbjct: 42  AVKDANLSINEGEIFVIMGLSGSGKSTLLRCINRLIRPTSGEIIINETDISKASKQELLQ 101

Query: 86  KYRKDVQLIPQDPYSTLPFNKTVEEILVAPILRWEKINKDELRKRLINLLELVKLTPAEE 145
             RK++ ++ Q  +  LP    +  I     L  + + K E  K+ +  ++ V L   E 
Sbjct: 102 IRRKELAMVFQH-FGLLPHRSVLHNIAFG--LELQGVKKREREKKAMECMQQVGLKGYEN 158

Query: 146 FLGKYPHQLSGGQKQRLSIARSLSVNPRIIVADEPVTMVDASLRIGILNTLAEIKNRLNL 205
              +   QLSGG +QR+ +AR+L+ NP +++ DE  + +D  +R+ + + L  +++++  
Sbjct: 159 ---QMVGQLSGGMQQRVGLARALANNPEVLLMDEAFSALDPLIRVQMQDELLTLQSKMKK 215

Query: 206 TMVFITHDIPIARYFYHLFDKGNTIVMFAGRIVERADLEEILKDPLHPYTNDLIK 260
           T+VFITHD+  A     L D+    +M  G IV+    EEIL +P + Y    ++
Sbjct: 216 TIVFITHDLNEA---IKLGDR--IAIMKDGEIVQTGTSEEILTEPANAYVERFVE 265


Lambda     K      H
   0.321    0.141    0.410 

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: 301
Number of extensions: 14
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: 324
Length of database: 408
Length adjustment: 29
Effective length of query: 295
Effective length of database: 379
Effective search space:   111805
Effective search space used:   111805
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 (21.8 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 24 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