GapMind for catabolism of small carbon sources

 

Alignments for a candidate for cbtF in Shewanella sp. ANA-3

Align CbtF, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate 7025948 Shewana3_3096 spermidine/putrescine ABC transporter ATPase subunit (RefSeq)

Query= TCDB::Q97VF4
         (324 letters)



>FitnessBrowser__ANA3:7025948
          Length = 378

 Score =  124 bits (312), Expect = 3e-33
 Identities = 72/211 (34%), Positives = 127/211 (60%), Gaps = 20/211 (9%)

Query: 3   LMELKGVSVIFEDKVGLFKKRKFYALKDVSLSMNQGDLLIVLGESGAGKTTLGRVIVGLQ 62
           L++++ VS +F+D           A+ DVSL++N+G++  +LG SG+GK+TL R++ G +
Sbjct: 20  LLKIERVSKLFDD---------VRAVDDVSLTINKGEIFALLGGSGSGKSTLLRMLAGFE 70

Query: 63  KPTSGEVVYDGYNIWKNKRKIFKKYRKDVQLIPQDPYSTLPFNKTVEEILVAPILRWEKI 122
           +PTSG +  DG +I          Y + + ++ Q  Y+  P     + I     L+ +K+
Sbjct: 71  RPTSGRIFLDGEDITD-----LPPYERPINMMFQS-YALFPHMTVAQNIAFG--LKQDKL 122

Query: 123 NKDELRKRLINLLELVKLTPAEEFLGKYPHQLSGGQKQRLSIARSLSVNPRIIVADEPVT 182
            K E+ +R+  +L+LV +   E++  + PHQLSGGQ+QR+++ARSL+  P++++ DEP+ 
Sbjct: 123 PKAEIEQRVQEMLKLVHM---EQYGKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMG 179

Query: 183 MVDASLRIGILNTLAEIKNRLNLTMVFITHD 213
            +D  LR  +   + EI  R+ +T V +THD
Sbjct: 180 ALDKKLRTQMQLEVVEILERVGVTCVMVTHD 210


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: 253
Number of extensions: 12
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: 378
Length adjustment: 29
Effective length of query: 295
Effective length of database: 349
Effective search space:   102955
Effective search space used:   102955
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 17 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