GapMind for catabolism of small carbon sources

 

Alignments for a candidate for frcA in Shewanella loihica PV-4

Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate 5210976 Shew_3402 ABC transporter-related protein (RefSeq)

Query= SwissProt::Q9F9B0
         (260 letters)



>FitnessBrowser__PV4:5210976
          Length = 322

 Score =  104 bits (259), Expect = 3e-27
 Identities = 70/226 (30%), Positives = 126/226 (55%), Gaps = 17/226 (7%)

Query: 5   PILTARGLVKRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEIR 64
           PI++  G+ KRY +V+AL+R DF+L+PGE++ + G NGAGK++++K I G +   +G+++
Sbjct: 9   PIVSLSGVAKRYAKVSALERIDFELFPGEVMGLFGHNGAGKTTIMKLILGIIPASDGQVK 68

Query: 65  LEGKPIQFRSPMEARQAGIETVYQNLALSPALSIADNMFLGREIRKPGIMGKWFRSLDRA 124
           + G+    +   EAR+  +  + +N++    L+       GRE+       ++F  L   
Sbjct: 69  VFGQDPLSKQAFEARKQ-VGYLPENVSFYDQLT-------GREVL------RYFARL--K 112

Query: 125 AMEKQARAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAALGV 184
           ++ KQA  +L E   +T   +++ V+T S G RQ + +A+A     K++++DEPT  L  
Sbjct: 113 SVPKQAIEQLLEQVGLT-HAMDRQVKTYSKGMRQRLGLAQAFLGSPKLLLLDEPTVGLDP 171

Query: 185 KESRRVLELILDVRRRGLPIVLISHNMPHVFEVADRIHIHRLGRRL 230
             ++     +  ++  G  I+L SH +P V +  DR  I   GR L
Sbjct: 172 IATQEFYASVDKLKSEGASIILCSHVLPGVEQHIDRALIISGGRLL 217


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: 177
Number of extensions: 7
Number of successful extensions: 2
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: 322
Length adjustment: 26
Effective length of query: 234
Effective length of database: 296
Effective search space:    69264
Effective search space used:    69264
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