GapMind for catabolism of small carbon sources

 

Alignments for a candidate for cbtF in Methanococcus aeolicus Nankai-3

Align CbtF, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate WP_011972867.1 MAEO_RS00720 ATP-binding cassette domain-containing protein

Query= TCDB::Q97VF4
         (324 letters)



>NCBI__GCF_000017185.1:WP_011972867.1
          Length = 281

 Score = 98.6 bits (244), Expect = 2e-25
 Identities = 72/224 (32%), Positives = 121/224 (54%), Gaps = 14/224 (6%)

Query: 27  ALKDVSLSMNQGDLLIVLGESGAGKTTLGRVIVGLQKPTSGEVVYDGYNIWKNKRKIFKK 86
           AL   ++S+ +GD++ +LG +GAGK+TL     G+ KP SG+++  G  I K   K   +
Sbjct: 19  ALDRANISVEKGDMVALLGPNGAGKSTLFLHFNGILKPKSGKILLKGAPI-KYDAKSLME 77

Query: 87  YRKDVQLIPQDPYSTLPFNKTVEEILVAPILRWEKINKDELRKRLINLLELVKLTPAEEF 146
            RK V ++ Q+    L      +++   P+    K  ++E+ KR+   L+ V +   E F
Sbjct: 78  VRKTVGIVFQNSDDQLFAPTVKQDVAFGPLNLGLK--EEEVEKRVKEALKEVGM---EGF 132

Query: 147 LGKYPHQLSGGQKQRLSIARSLSVNPRIIVADEPVTMVDASLRIGILNTLAEIKNRLNLT 206
             K PH LSGGQK+R++IA  L+++P I+V DEP   +D      I+  L ++ N+  +T
Sbjct: 133 ENKPPHHLSGGQKKRVAIAGILAMHPEIMVLDEPTAGLDPMGASKIMKLLYKL-NKEGIT 191

Query: 207 MVFITHDIPIAR-YFYHLFDKGNTIVMFAGRIVERADLEEILKD 249
           ++  THD+ +   Y   +F  G T      +IV+   +EE+  D
Sbjct: 192 IIISTHDVDLVPIYANKIFVMGKT------KIVKSGTVEEVFSD 229


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: 225
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: 324
Length of database: 281
Length adjustment: 27
Effective length of query: 297
Effective length of database: 254
Effective search space:    75438
Effective search space used:    75438
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: 48 (23.1 bits)

This GapMind analysis is from Apr 09 2024. 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