Alignments for a candidate for cbtF in Dechlorosoma suillum PS

GapMind for catabolism of small carbon sources

Alignments for a candidate for cbtF in Dechlorosoma suillum PS

Align CbtF, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate Dsui_2799 Dsui_2799 oligopeptide/dipeptide ABC transporter, ATP-binding protein

Query= TCDB::Q97VF4
         (324 letters)



>FitnessBrowser__PS:Dsui_2799
          Length = 670

 Score =  177 bits (450), Expect = 5e-49
 Identities = 112/309 (36%), Positives = 173/309 (55%), Gaps = 16/309 (5%)

Query: 3   LMELKGVSVIFEDKVGLFKKRKFY--ALKDVSLSMNQGDLLIVLGESGAGKTTLGRVIVG 60
           L+ +  + V F  + GLFK+   +  A+  VSL + +G  L ++GESG GKTT G+ ++ 
Sbjct: 351 LLAVGELKVHFPIRKGLFKRTVGHVKAVDGVSLELQRGRTLALVGESGCGKTTAGKAVLR 410

Query: 61  LQKPTSGEVVYDGYNIWKNKRKIFKKYRKDVQLIPQDPYSTLPFNKTVEEILVAPILRWE 120
           L  P +G V  DG  +     +  K  R+ +Q++ QDP+++L    TV EI+   +    
Sbjct: 411 LL-PATGSVRLDGRELLGLPERELKPLRRRMQMVFQDPFASLNPRLTVGEIIEEGMTALR 469

Query: 121 -KINKDELRKRLINLLELVKLTPAEEFLGKYPHQLSGGQKQRLSIARSLSVNPRIIVADE 179
              ++DE R  L  LLE V L PAE  LG+YPH+ SGGQ+QR++IAR+L+V P ++V DE
Sbjct: 470 VAASRDERRAALAALLESVGL-PAEA-LGRYPHEFSGGQRQRIAIARALAVQPELLVCDE 527

Query: 180 PVTMVDASLRIGILNTLAEIKNRLNLTMVFITHDIPIARYFYHLFDKGNTIVMFAGRIVE 239
           P + +D S++  ILN L  ++  L L  +FITH+  +  Y  H     +  VM+ GRIVE
Sbjct: 528 PTSALDVSVQAQILNLLRRLQEELGLAYLFITHNFAVVEYLAH-----DVAVMYLGRIVE 582

Query: 240 RADLEEILKDPLHPYTNDLIKLTPSIDNLYKEINVKINYE-----RVEKGCPYRLRCPFA 294
           +  ++++L  P HPYT  L+   P      +   V++  E     R  +GC +  RC  A
Sbjct: 583 QGPVQQVLAAPCHPYTRALLSAVPEPRLAGQREMVRLPGETPSPARPPQGCHFHPRCAQA 642

Query: 295 MDICKNEEP 303
            + C+ E P
Sbjct: 643 SERCRQEYP 651



 Score =  130 bits (328), Expect = 7e-35
 Identities = 93/303 (30%), Positives = 143/303 (47%), Gaps = 16/303 (5%)

Query: 23  RKFYALKDVSLSMNQGDLLIVLGESGAGKTT----LGRVIVGLQKPTSGEVVYDGYNIWK 78
           R   A+  VS ++  G+   +LGESG GK+     L R++    +   GEV  +G  I  
Sbjct: 19  RVLTAVDGVSFAVAPGETFALLGESGCGKSATALALLRLLPNAGRIQGGEVWLEGEEILA 78

Query: 79  NKRKIFKKYRKDVQ-LIPQDPYSTLPFNKTVEEILVAPILRWEKINKDELRKRLINLLEL 137
                 +  R     +I Q+P ++L    T+   +   + R   +  +  R+  + LL  
Sbjct: 79  LPEAAMRDRRGSAAAMIFQEPATSLNPVLTIGRQIGESLERHRGMKGEAARREALALLTA 138

Query: 138 VKLTPAEEFLGKYPHQLSGGQKQRLSIARSLSVNPRIIVADEPVTMVDASLRIGILNTLA 197
           V +   E  L +YP QLSGG KQR  IA +L+  PR+++ADEP T +D +++  IL+ LA
Sbjct: 139 VGIADPERRLEEYPFQLSGGMKQRAMIAIALAGEPRLLIADEPTTALDVTIQAQILDLLA 198

Query: 198 EIKNRLNLTMVFITHDIPIARYFYHLFDKGNTIVMFAGRIVERADLEEILKDPLHPYTND 257
            ++    + M+ ITHD+ +     H        VM+AG IVE A  +E    P HPYT  
Sbjct: 199 RLQAERAMGMLLITHDLGVVARSAH-----RVGVMYAGEIVETAPRQEFFASPRHPYTQK 253

Query: 258 LIKLTPSIDNLYKEI----NVKINYERVEKGCPYRLRCPFAMDICKNEEP--KLFKYSHE 311
           L    P +     ++            +  GC +  RCP AMD C+ E P     +  H+
Sbjct: 254 LFAALPDLGQRGAQLATIPGQVPGLAAMPAGCRFAPRCPVAMDRCRLESPGWTELEAGHQ 313

Query: 312 VAC 314
           V C
Sbjct: 314 VRC 316


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: 546
Number of extensions: 27
Number of successful extensions: 9
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 324
Length of database: 670
Length adjustment: 33
Effective length of query: 291
Effective length of database: 637
Effective search space:   185367
Effective search space used:   185367
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: 51 (24.3 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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources