GapMind for catabolism of small carbon sources

 

Alignments for a candidate for cbtF in Flavobacterium beibuense F44-8

Align CbtF, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate WP_035131541.1 Q763_RS04180 ABC transporter ATP-binding protein

Query= TCDB::Q97VF4
         (324 letters)



>NCBI__GCF_000769915.1:WP_035131541.1
          Length = 562

 Score =  166 bits (420), Expect = 1e-45
 Identities = 94/263 (35%), Positives = 154/263 (58%), Gaps = 9/263 (3%)

Query: 3   LMELKGVSVIFEDKVGLFKKR-KFYALKDVSLSMNQGDLLIVLGESGAGKTTLGRVIVGL 61
           L+E+  V   +    GLF +  KF A+ +VS  + +G+ L ++GESG GK+TLG  I+ L
Sbjct: 304 LLEVINVEKEYVSSSGLFGRDVKFKAVNNVSFKIYEGETLGLVGESGCGKSTLGNAILQL 363

Query: 62  QKPTSGEVVYDGYNIWKNKRKIFKKYRKDVQLIPQDPYSTLPFNKTVEEILVAPILRWEK 121
            K T+G ++Y G ++ K      ++ RK++Q+I QDPYS+L    TV + ++ P+     
Sbjct: 364 DKATAGSILYKGQDLTKLSASAIRELRKEIQIIFQDPYSSLNPRITVGKAIMEPMKVHGL 423

Query: 122 INKD-ELRKRLINLLELVKLTPAEEFLGKYPHQLSGGQKQRLSIARSLSVNPRIIVADEP 180
              D E R++ I +L+ V L   EE   +YPH+ SGGQ+QR+ IAR++++ P++IV DE 
Sbjct: 424 YKNDRERREKTIEILKRVGL--GEEHFNRYPHEFSGGQRQRVGIARTIALQPKLIVCDES 481

Query: 181 VTMVDASLRIGILNTLAEIKNRLNLTMVFITHDIPIARYFYHLFDKGNTIVMFAGRIVER 240
           V+ +D S++  +LN L E+K     T +FI+HD+ + +Y          +VM  G+I E 
Sbjct: 482 VSALDISVQAQVLNLLNELKENFGFTYIFISHDLAVVKYM-----SDQVLVMNKGQIEEM 536

Query: 241 ADLEEILKDPLHPYTNDLIKLTP 263
            + + + + P   YT  LI+  P
Sbjct: 537 NEADALYEHPEKEYTKKLIEAIP 559



 Score =  137 bits (345), Expect = 6e-37
 Identities = 81/253 (32%), Positives = 143/253 (56%), Gaps = 19/253 (7%)

Query: 30  DVSLSMNQGDLLIVLGESGAGKTTLGRVIVGLQ-----KPTSGEVVYDGYNIWKNKRKIF 84
           D + ++ Q ++L ++GESG+GK+     ++GL      + T G + ++G +I +   +  
Sbjct: 27  DSTFTLEQNEILGIVGESGSGKSVTSLAVMGLLPKGILQVTQGSIAFEGRDISQLTTREM 86

Query: 85  KKYR-KDVQLIPQDPYSTL-PFNKT---VEEILVAPILRWEKINKDELRKRLINLLELVK 139
           +  R  D+ +I Q+P S+L P  K    VEEI          ++K E++  +++L E VK
Sbjct: 87  RNIRGNDIAMIFQEPMSSLNPSLKCGYQVEEIFK----EHTSLSKREIKATVLSLFEKVK 142

Query: 140 LTPAEEFLGKYPHQLSGGQKQRLSIARSLSVNPRIIVADEPVTMVDASLRIGILNTLAEI 199
           L   E+   +YPH++SGGQKQR+ IA +++  P+I++ADEP T +D +++  I+  L E+
Sbjct: 143 LPNPEKIYNRYPHEISGGQKQRVMIAMAIACKPKILIADEPTTALDVTVQKEIILLLKEL 202

Query: 200 KNRLNLTMVFITHDIPIARYFYHLFDKGNTIVMFAGRIVERADLEEILKDPLHPYTNDLI 259
           +    ++++FI+HD+ +             +VM+ G IVE+    EI ++P H YT  LI
Sbjct: 203 QQETKMSIIFISHDLSLVSEI-----ANRVLVMYKGNIVEQGVATEIFENPKHTYTKALI 257

Query: 260 KLTPSIDNLYKEI 272
              PS+D   K +
Sbjct: 258 NSRPSLDVRLKRL 270


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: 492
Number of extensions: 25
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 324
Length of database: 562
Length adjustment: 32
Effective length of query: 292
Effective length of database: 530
Effective search space:   154760
Effective search space used:   154760
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: 51 (24.3 bits)

This GapMind analysis is from Sep 24 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