GapMind for catabolism of small carbon sources

 

Alignments for a candidate for cbtD in Flavobacterium sp. LM5

Align CbtD, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate WP_024981457.1 BXU11_RS04345 ATP-binding cassette domain-containing protein

Query= TCDB::Q97VF5
         (362 letters)



>NCBI__GCF_002017945.1:WP_024981457.1
          Length = 253

 Score =  103 bits (258), Expect = 4e-27
 Identities = 81/256 (31%), Positives = 134/256 (52%), Gaps = 18/256 (7%)

Query: 45  ILEVHNLNVIYDEGNSRIIKAVNDVSFGVEKGEILGIIGESGSGKTTLISAILRAIRPPG 104
           ++E+ N+   +  G+S+++K V+ +    E G+   IIG+SGSGKT L+ ++L    P  
Sbjct: 1   MIEIKNIEKSF--GSSKVLKGVSCL---FEAGKTNLIIGQSGSGKTVLLKSLLGIHSPE- 54

Query: 105 KIISGKVIFNGMDIFSMTIDEFRKLLWKDISYVPQASQNALNPVLPISEI--FYHEAISH 162
               G + F+G  I+S  + E ++ L  +I  V Q S  AL   + ++E   F  +  +H
Sbjct: 55  ---VGTISFDGR-IYSDLLPEEKRELRTEIGMVFQGS--ALFDSMTVAENVGFPLKMFTH 108

Query: 163 GEADKKRVIERASELLKLVGLDPARVLKMYPFQLSGGMKQRVMIALSLLLNPKLILMDEP 222
               + R  +R   +LK V L  A   K  P ++SGGM++RV IA +++ NPK +  DEP
Sbjct: 109 NSPSETR--DRVDFVLKRVNLIDAH--KKLPSEISGGMQKRVAIARAIVNNPKYLFCDEP 164

Query: 223 TSALDMLNQELLLKLIKNINQEMGVTIVYVTHDILNIAQIANRLLVMYKGYVMEEGKTEE 282
            S LD     ++  LIK I +E  +T V  THD+ ++ +I   +L +  G    +G  EE
Sbjct: 165 NSGLDPNTSTIIDNLIKEITEEYNITTVINTHDMNSVMEIGENILFLKNGIKEWQGTKEE 224

Query: 283 IIKSPLNPYTSLLVSS 298
           I ++        + SS
Sbjct: 225 IFRTDNQAIVDFVYSS 240


Lambda     K      H
   0.319    0.138    0.391 

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: 183
Number of extensions: 6
Number of successful extensions: 1
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: 362
Length of database: 253
Length adjustment: 27
Effective length of query: 335
Effective length of database: 226
Effective search space:    75710
Effective search space used:    75710
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 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