GapMind for catabolism of small carbon sources

 

Aligments for a candidate for cbtF in Pseudomonas fluorescens FW300-N2E2

Align CbtF, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate Pf6N2E2_3314 Dipeptide transport ATP-binding protein DppF (TC 3.A.1.5.2)

Query= TCDB::Q97VF4
         (324 letters)



>lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3314 Dipeptide transport
           ATP-binding protein DppF (TC 3.A.1.5.2)
          Length = 326

 Score =  184 bits (468), Expect = 2e-51
 Identities = 107/309 (34%), Positives = 174/309 (56%), Gaps = 14/309 (4%)

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

Query: 72  DGYNIWKNKRKIFKKYRKDVQLIPQDPYSTLPFNKTVEEILVAPILRWEKINKDELRKRL 131
            G  +    +   K+ RKDVQ++ Q PY++L   + + + L  P+L   K++  E R+++
Sbjct: 74  AGQEVAGANKAERKQLRKDVQMVFQSPYASLNPRQKIGDQLAEPLLINTKLSATERREKV 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: 270
Number of extensions: 16
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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