GapMind for catabolism of small carbon sources

 

Alignments for a candidate for cbtF in Phaeobacter inhibens BS107

Align CbtF, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate GFF3630 PGA1_262p00340 oligopeptide ABC transporter, ATP binding protein

Query= TCDB::Q97VF4
         (324 letters)



>FitnessBrowser__Phaeo:GFF3630
          Length = 332

 Score =  199 bits (507), Expect = 6e-56
 Identities = 121/337 (35%), Positives = 196/337 (58%), Gaps = 26/337 (7%)

Query: 3   LMELKGVSVIFE---DKVGLFKK---RKFYALKDVSLSMNQGDLLIVLGESGAGKTTLGR 56
           +ME+  +S+ F+     V + +K   R   AL  VSL++ +G+ L V+GESG GK+TL R
Sbjct: 5   VMEIDDLSLTFQLPRSLVDVIRKQPGRAVRALNGVSLALQKGETLGVVGESGCGKSTLAR 64

Query: 57  VIVGLQKPTSGEVVYDGYNIWKNKRKIFKKYRKDVQLIPQDPYSTLPFNKTVEEILVAPI 116
            IV L +P  G + + G +I+    +  + Y + VQ++ QDPYS+L    T  +IL   +
Sbjct: 65  CIVRLYQPQGGSIRHHGQDIFAEGARRDRSYNRRVQMMFQDPYSSLNPRMTCGQILSEAL 124

Query: 117 LRWEKINKDELRKRLINLLELVKLTPAEEFLGKYPHQLSGGQKQRLSIARSLSVNPRIIV 176
              +    DE+  R+  LLELV+L PA+    K PH+ SGGQ+QR++IAR+L+V P +++
Sbjct: 125 HVHKMRPADEIPARVEELLELVRL-PADA-AQKLPHEFSGGQRQRIAIARALAVEPEVLI 182

Query: 177 ADEPVTMVDASLRIGILNTLAEIKNRLNLTMVFITHDIPIARYFYHLFDKGNTIVMFAGR 236
           ADE V+ +D S++  ++N L E++ +L+LT++F+ HD+ + R+  H        V++ GR
Sbjct: 183 ADELVSALDVSVQAQVVNLLLELQEQLDLTILFVAHDLRLVRHVSH-----RVAVIYLGR 237

Query: 237 IVERADLEEILKDPLHPYTNDLIKLTPSID--------NLYKEINVKINYERVEKGCPYR 288
           IVE  D E +  +P HPY+  L+   PS+D         L  E+   +N   V  GCP+ 
Sbjct: 238 IVEIGDSETLFANPAHPYSQALLSAAPSLDPDDTGDAIRLEGELPSPLN---VPPGCPFH 294

Query: 289 LRCPFAMDICKNEEPKLFKYSH--EVACFLYGKVGES 323
           +RC  A D+C+ + P+L       EVAC L  ++ ++
Sbjct: 295 VRCAHAADVCRRDVPRLRPLGDRGEVACHLAEEISQN 331


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: 283
Number of extensions: 13
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: 332
Length adjustment: 28
Effective length of query: 296
Effective length of database: 304
Effective search space:    89984
Effective search space used:    89984
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