GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braC in Desulfovibrio vulgaris Miyazaki F

Align Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein (characterized)
to candidate 8501892 DvMF_2607 Extracellular ligand-binding receptor (RefSeq)

Query= SwissProt::P21175
         (373 letters)



>FitnessBrowser__Miya:8501892
          Length = 372

 Score =  240 bits (613), Expect = 4e-68
 Identities = 134/364 (36%), Positives = 203/364 (55%), Gaps = 4/364 (1%)

Query: 1   MKKGTQRLSRLFAAMAIAGFASYSMAADTIKIALAGPVTGPVAQYGDMQRAGALMAIEQI 60
           M+KG      L A +A+A  A  + AADTIK  +AG  +G +A YG      A +  + I
Sbjct: 1   MRKGW--FKGLVAGLAVAVMACPAFAADTIKFGVAGAHSGDLASYGLPTVNAAKLVAKMI 58

Query: 61  NKAGGVNGAQLEGVIYDDACDPKQAVAVANKVVNDGVKFVVGHVCSSSTQPATDIYEDEG 120
           N  GGV G Q+E +  DD C P+ A   A K+V+DG   V+GH+CS +T+ A  IY++  
Sbjct: 59  NAKGGVLGKQVEVIPQDDQCKPELATNAATKLVSDGANVVLGHICSGATKAALPIYKEAN 118

Query: 121 VLMITPSATAPEITSRG-YKLIFRTIGLDNMQGPVAGKFIAERYKDKTIAVLHDKQQYGE 179
           +++++PSAT P +T  G Y   FRTI  D+ Q  +   F  ++   K IAVLHDK  YG+
Sbjct: 119 IVLMSPSATNPALTQSGDYPNFFRTIASDDQQAKLGVDFTIDKLGKKKIAVLHDKGDYGK 178

Query: 180 GIATEVKKTVEDAGI-KVAVFEGLNAGDKDFNALISKLKKAGVQFVYFGGYHPEMGLLLR 238
           G A   K+ VE +G   V +FEG+  G  D++A++ K++ +G + V FGGYHPE   +++
Sbjct: 179 GYAEYAKQFVEQSGKGTVVLFEGVTPGAVDYSAVVQKIRNSGAEAVMFGGYHPEASKIVQ 238

Query: 239 QAKQAGLDARFMGPEGVGNSEITAIAGDASEGMLATLPRAFEQDPKNKALIDAFKAKNQD 298
           Q ++  +D  F+  +GV +     +AG  +EG+ A+  +     P  K  I+A   +   
Sbjct: 239 QLRKKRMDLPFVSDDGVKDDTFIKVAGKDAEGVYASSSKDVSALPLYKEAIEAHVKEFGA 298

Query: 299 PSGIFVLPAYSAVTVIAKGIEKAGEADPEKVAEALRANTFETPTGNLGFDEKGDLKNFDF 358
             G F   AY+A   +   IEKAG  D  K+  ALR    ET  G + FD++GD +   F
Sbjct: 299 EPGAFYKEAYAASLALLNAIEKAGSTDSAKIMNALRTEFVETSVGKIKFDKRGDAEGVGF 358

Query: 359 TVYE 362
           ++Y+
Sbjct: 359 SMYQ 362


Lambda     K      H
   0.316    0.133    0.377 

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: 354
Number of extensions: 17
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: 373
Length of database: 372
Length adjustment: 30
Effective length of query: 343
Effective length of database: 342
Effective search space:   117306
Effective search space used:   117306
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 50 (23.9 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