GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natF in Desulfovibrio vulgaris Miyazaki F

Align Extracellular solute-binding protein, family 3 (characterized, see rationale)
to candidate 8502446 DvMF_3152 extracellular solute-binding protein family 3 (RefSeq)

Query= uniprot:Q31RP1
         (359 letters)



>FitnessBrowser__Miya:8502446
          Length = 271

 Score =  120 bits (301), Expect = 4e-32
 Identities = 76/240 (31%), Positives = 121/240 (50%), Gaps = 13/240 (5%)

Query: 23  LCFLPLAACRSLGGNETESNSRLNQVQARGKLLCGVEGRLPGFSFLDSQGNYS-GLDVDI 81
           L  L +A C  L G    +  ++  ++ARG L+CGV+     F ++D Q     G D+DI
Sbjct: 4   LVLLAVALCVVLTGTMAHAG-KIEDIKARGALVCGVKDSTVPFGYIDEQSKQIVGFDIDI 62

Query: 82  CKAIAAALFNDPKAIEYRSLDSVERFPALASGEVDLLSRNTTWTLSRDAKGGNNLEFAPT 141
           CKA+A  L      +E +++ S  R P L  G VD+++   T    RD    + ++F+ T
Sbjct: 63  CKAVADKL---GVKLELKTVTSATRIPMLTQGSVDMVAATMTHKFERD----DVIDFSIT 115

Query: 142 TFYDGQGLMVRRNSGIQSLQDFQGKSICVETGTTSELNLADTMRELGVQYQEIKFPNSDA 201
            F DGQ L+V++  G++S  D +GK +    G+TSE N+     E  V    + F     
Sbjct: 116 YFMDGQKLLVKKGGGVKSAADLKGKKVATAKGSTSEKNIKAAQPEATV----VSFDEYPQ 171

Query: 202 NYAAYAQGRCEGVTSDRSQLAARRTTLSDADQHQLLDAVISKEPLSPATLNNDSPWFDVV 261
            + A  QG+ E VT+D + L   R +  + D+ +++   IS EP       NDS + D+V
Sbjct: 172 AFLALKQGKAEAVTTDSTILLGLRNSDPEPDKWEIVGDYISPEPYGLGLAENDSKFRDLV 231


Lambda     K      H
   0.317    0.134    0.391 

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: 207
Number of extensions: 11
Number of successful extensions: 5
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: 359
Length of database: 271
Length adjustment: 27
Effective length of query: 332
Effective length of database: 244
Effective search space:    81008
Effective search space used:    81008
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: 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