GapMind for catabolism of small carbon sources

 

Alignments for a candidate for cbtF in Pseudomonas fluorescens FW300-N2C3

Align CbtF, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate AO356_07275 AO356_07275 peptide ABC transporter ATP-binding protein

Query= TCDB::Q97VF4
         (324 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_07275
          Length = 326

 Score =  184 bits (467), Expect = 3e-51
 Identities = 107/309 (34%), Positives = 173/309 (55%), Gaps = 14/309 (4%)

Query: 13  FEDKVGLFKKRKFY-ALKDVSLSMNQGDLLIVLGESGAGKTTLGRVIVGLQKPTSGEVVY 71
           +E   G+FK      AL  VS  +  G  L V+GESG GK+TL R +  +++P+SG +  
Sbjct: 14  YEVSRGMFKGHATVRALNGVSFELEAGKTLAVVGESGCGKSTLARALTLIEEPSSGSLKI 73

Query: 72  DGYNIWKNKRKIFKKYRKDVQLIPQDPYSTLPFNKTVEEILVAPILRWEKINKDELRKRL 131
            G  +    +   K+ RKDVQ++ Q PY++L   + + + L  P+L    ++  E R+++
Sbjct: 74  AGQEVTGANKAERKQLRKDVQMVFQSPYASLNPRQKIGDQLAEPLLINTNLSATERREKV 133

Query: 132 INLLELVKLTPAEEFLGKYPHQLSGGQKQRLSIARSLSVNPRIIVADEPVTMVDASLRIG 191
             +++ V L P  E   +YPH  SGGQ+QR+++AR++ + P+++VADEP + +D S++  
Sbjct: 134 QAMMKQVGLRP--EHYQRYPHMFSGGQRQRIALARAMMLQPKVLVADEPTSALDVSIQAQ 191

Query: 192 ILNTLAEIKNRLNLTMVFITHDIPIARYFYHLFDKGNTIVMFAGRIVERADLEEILKDPL 251
           +LN   +++   N   VFI+H++ + +   H+ D  + +VM+ GR VE    E I   PL
Sbjct: 192 VLNLFMDLQQEFNTAYVFISHNLAVVQ---HVAD--DVMVMYLGRPVEMGPNESIYSRPL 246

Query: 252 HPYTNDLIKLTPSIDNLYKEINVKI-----NYERVEKGCPYRLRCPFAMDICKNEEPKLF 306
           HPYT  L+  TP+I     +  +KI     N      GC +  RCP+A + CK EEP L 
Sbjct: 247 HPYTQALLSATPTIHPDPNKPKIKIVGELPNPLNPPSGCAFHKRCPYATERCKTEEPALR 306

Query: 307 KYSHE-VAC 314
              +  VAC
Sbjct: 307 PLDNRLVAC 315


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: 271
Number of extensions: 15
Number of successful extensions: 4
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: 326
Length adjustment: 28
Effective length of query: 296
Effective length of database: 298
Effective search space:    88208
Effective search space used:    88208
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 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