GapMind for catabolism of small carbon sources

 

Alignments for a candidate for frcA in Caulobacter crescentus NA1000

Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate CCNA_01670 CCNA_01670 sulfate transport ATP-binding protein cysA

Query= SwissProt::Q9F9B0
         (260 letters)



>FitnessBrowser__Caulo:CCNA_01670
          Length = 339

 Score =  114 bits (286), Expect = 2e-30
 Identities = 77/247 (31%), Positives = 134/247 (54%), Gaps = 18/247 (7%)

Query: 7   LTARGLVKRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEIRLE 66
           +  R + K++GR  AL++ D ++  GE+LA++G +G+GK+++++ I+G   PD G++  +
Sbjct: 3   IAIRSVEKQFGRYPALNKVDLEIADGELLALLGPSGSGKTTLLRTIAGLEFPDAGQVLFD 62

Query: 67  GKPIQFRSPMEARQAGIETVYQNLALSPALSIADNMFLGREIRKPGIMGKWFRSLDRAAM 126
           G+ + + S   AR+ G   V+Q  AL   +++A N+  G ++RK    GK     D+ + 
Sbjct: 63  GQDVTYAS-AAARRVGF--VFQQYALFKHMTVAKNIAFGLDVRK----GK-----DKPSK 110

Query: 127 EKQARAKLSELGLMTIQNI-NQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAALGV- 184
            + AR     L L+ ++ +  +    LSGGQRQ VA++RA A    V+++DEP  AL   
Sbjct: 111 AEIARRVEELLKLVELEGLGGRYPSQLSGGQRQRVALSRALAVQPSVLLLDEPFGALDAT 170

Query: 185 --KESRRVLELILDVRRRGLPIVLISHNMPHVFEVADRIHIHRLGRRLCVINPKDYTMSD 242
             K  RR L  + D    G+  + ++H+     E+ADR+ I   GR   +  P     + 
Sbjct: 171 VRKSLRRELRRVHDA--TGVTTIFVTHDQEEALELADRVAILNNGRIEQIGTPDQVHDAP 228

Query: 243 AVAFMTG 249
             AF+ G
Sbjct: 229 ETAFVCG 235


Lambda     K      H
   0.321    0.136    0.383 

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: 171
Number of extensions: 7
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: 260
Length of database: 339
Length adjustment: 26
Effective length of query: 234
Effective length of database: 313
Effective search space:    73242
Effective search space used:    73242
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:

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