GapMind for catabolism of small carbon sources

 

Alignments for a candidate for cbtF in Pseudomonas stutzeri RCH2

Align CbtF, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate GFF4241 Psest_4314 ABC-type metal ion transport system, ATPase component

Query= TCDB::Q97VF4
         (324 letters)



>FitnessBrowser__psRCH2:GFF4241
          Length = 335

 Score =  128 bits (321), Expect = 2e-34
 Identities = 83/240 (34%), Positives = 134/240 (55%), Gaps = 10/240 (4%)

Query: 27  ALKDVSLSMNQGDLLIVLGESGAGKTTLGRVIVGLQKPTSGEVVYDGYNIWKNKRKIFKK 86
           AL+   L +  G++  ++G SGAGK+TL R+I  L++P+ G ++ +G ++        ++
Sbjct: 20  ALQPTQLEIASGEVFGLIGHSGAGKSTLLRLINRLEEPSGGRILVNGEDVTALDADGLRR 79

Query: 87  YRKDVQLIPQDPYSTLPFNKTVEEILVAPILRWEKINKDELRKRLINLLELVKLTPAEEF 146
           +R+ V +I Q  +  L  +KTV + +  P+      ++ E+  R+  LLE V L   +E 
Sbjct: 80  FRQRVGMIFQ--HFNLLMSKTVADNVAMPLRLAGIRSRREIDARVAALLERVGL---KEH 134

Query: 147 LGKYPHQLSGGQKQRLSIARSLSVNPRIIVADEPVTMVDASLRIGILNTLAEIKNRLNLT 206
             KYP QLSGGQKQR+ IAR+L+  P I++ DE  + +D      +L  LAEI   L LT
Sbjct: 135 ARKYPAQLSGGQKQRVGIARALATEPSILLCDEATSALDPQTTASVLQLLAEINRELKLT 194

Query: 207 MVFITHDIPIARYFYHLFDKGNTIVMFAGRIVERADLEEILKDPLHPYTNDLIKLTPSID 266
           +V ITH++ + R    + D+    VM AG IVE+  + E+   P HP T   +    ++D
Sbjct: 195 IVLITHEMDVIR---RVCDR--VAVMDAGAIVEQGPVTEVFLHPKHPTTQRFVLEDEAMD 249


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: 261
Number of extensions: 11
Number of successful extensions: 3
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: 335
Length adjustment: 28
Effective length of query: 296
Effective length of database: 307
Effective search space:    90872
Effective search space used:    90872
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