Alignments for a candidate for cbtF in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Alignments for a candidate for cbtF in Pseudomonas putida KT2440

Align CbtF, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate PP_4453 PP_4453 glutathione ABC transporter ATP-binding subunit

Query= TCDB::Q97VF4
         (324 letters)



>FitnessBrowser__Putida:PP_4453
          Length = 610

 Score =  165 bits (417), Expect = 3e-45
 Identities = 105/293 (35%), Positives = 165/293 (56%), Gaps = 21/293 (7%)

Query: 3   LMELKGVSVIFEDKVGLFKK--RKFYALKDVSLSMNQGDLLIVLGESGAGKTTLGRVIVG 60
           L+E+ G++  F+ + G FK+   + +A+++VS +++QG+ L ++GESG GK+T GR+I G
Sbjct: 308 LLEVSGLTTRFDVRSGFFKRVTGRVHAVENVSFNLSQGETLAIVGESGCGKSTTGRLITG 367

Query: 61  LQKPTSGEVVYDGYNIWKNKRKIFKKYRKDVQLIPQDPYSTLPFNKTVEEILVAPILRWE 120
           L  PT G V  +G  +        ++ RK +Q++ QDPYS+L   +TV + ++ P+    
Sbjct: 368 LLDPTHGSVKLEGVEL--GSITPMERARK-IQMVFQDPYSSLNPRQTVAQSIIEPLRVHG 424

Query: 121 KINKDELRKRLINLLELVKLTPAEEFLGKYPHQLSGGQKQRLSIARSLSVNPRIIVADEP 180
             +     +  I LL  V L PA+    + PH+ SGGQ+QR+ IAR+L++ P  IVADE 
Sbjct: 425 LYDAKRCEEVAIELLVKVGL-PADA-AWRLPHEFSGGQRQRVCIARALALRPGTIVADEA 482

Query: 181 VTMVDASLRIGILNTLAEIKNRLNLTMVFITHDIPIARYFYHLFDKGNTIVMFAGRIVER 240
           V+ +D S+++ I+N L E++  L L  +FI+HD+ +     H        VM+ G IVE 
Sbjct: 483 VSALDVSVKVQIVNLLLELQQELGLGFIFISHDMAVVERVSH-----RVAVMYMGEIVEI 537

Query: 241 ADLEEILKDPLHPYTNDLIKLTPSIDNLYKEINVKINYERVEKGCPYRLRCPF 293
                I  DP HPYT  LI   P  D   K++      +RV  G    LR P+
Sbjct: 538 GPRAAIFNDPKHPYTRRLIDAVPIPDPARKQV------QRVSAG---TLRTPY 581



 Score =  132 bits (333), Expect = 2e-35
 Identities = 85/312 (27%), Positives = 157/312 (50%), Gaps = 16/312 (5%)

Query: 3   LMELKGVSVIFEDKVGLFKKRKFYALKDVSLSMNQGDLLIVLGESGAGKTTLGRVIVGL- 61
           ++E+ G++V F    G         +KD+S  + +G+ L ++GESG+GK+     I+GL 
Sbjct: 12  VLEVTGLNVAFRRGGGWSP-----VVKDLSFRVARGETLAIVGESGSGKSVSAMSILGLL 66

Query: 62  ---QKPTSGEVVYDGYNIWKNKRKIFKKYRKD-VQLIPQDPYSTLPFNKTVEEILVAPIL 117
                  +G +   G  +           R + + +I Q+P ++L    T+ E +  P+ 
Sbjct: 67  PANTSQVTGSIRLQGQELLCLPEPEMADIRGNRIAMIFQEPMTSLNPVMTIGEQIAEPLR 126

Query: 118 RWEKINKDELRKRLINLLELVKLTPAEEFLGKYPHQLSGGQKQRLSIARSLSVNPRIIVA 177
               ++  + ++  + L+E V++  A+E    YPHQ SGG +QR+ IA +L+ NP +++A
Sbjct: 127 LHRGLDATQAKEEALKLMERVRIPAAQERYDDYPHQFSGGMRQRVMIAMALACNPAVLIA 186

Query: 178 DEPVTMVDASLRIGILNTLAEIKNRLNLTMVFITHDIPIARYFYHLFDKGNTIVMFAGRI 237
           DEP T +D +++  IL  + E++ + ++ +VFITHD+ +            T+VM+ G +
Sbjct: 187 DEPTTALDVTIQAQILELIKELQAQEHMAVVFITHDMGVVAQI-----ADRTLVMYRGDL 241

Query: 238 VERADLEEILKDPLHPYTNDLIKLTPSIDNLYKEINVKINYERVEKGCPYRLRCPFAMDI 297
           VE A   EI   P  PYT  L+   P + ++  E + K  +   +      +  P   D 
Sbjct: 242 VETASTSEIFSAPQKPYTKALLSAVPELGSMAAEPSPK-PFPIYDMAAGSNVPAPEMKDS 300

Query: 298 CKNEEPKLFKYS 309
            ++ +P L + S
Sbjct: 301 VRHTKPYLLEVS 312


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: 508
Number of extensions: 21
Number of successful extensions: 8
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: 610
Length adjustment: 32
Effective length of query: 292
Effective length of database: 578
Effective search space:   168776
Effective search space used:   168776
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