GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcV in Desulfovibrio vulgaris Miyazaki F

Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate 8500849 DvMF_1587 ABC transporter related (RefSeq)

Query= BRENDA::Q97UY8
         (353 letters)



>FitnessBrowser__Miya:8500849
          Length = 366

 Score =  184 bits (467), Expect = 3e-51
 Identities = 107/293 (36%), Positives = 168/293 (57%), Gaps = 11/293 (3%)

Query: 1   MVRIIVKNVSKVFKKGKVVALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTG 60
           M  I +  + K +  G    LD +++ + +GE F +LGPSG GKT  +R+IAG + P  G
Sbjct: 1   MADITLAGIGKAY--GAHAVLDGLSLTVNHGECFTLLGPSGCGKTVLLRLIAGFETPDAG 58

Query: 61  ELYFDDRLV--ASNGKLIVPPEDRKIGMVFQTWALYPNLTAFENIAFPLTNMKMSKEEIR 118
            +      V  A  G   VPP+ R +G+VFQ +A++P+++  +NI +PL    +   E  
Sbjct: 59  TISIGGEPVSDAVTGDC-VPPDARDLGVVFQDYAVWPHMSVADNIGYPLKLAGLPAAERT 117

Query: 119 KRVEEVAKILDIHHVLNHFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDS 178
           ++V E  +++++  + N  P +LSGGQQQRVALARALV  PSL+LLDEP  NLDA +R+ 
Sbjct: 118 RQVLETVEMVNLTGLENRMPSQLSGGQQQRVALARALVGRPSLMLLDEPLCNLDANLREE 177

Query: 179 ARALVKEVQSRLGVTLLVVSHDPADIFAIADRVGVL-VKGKLVQVGKPEDLYDNPVSIQV 237
            R  +KE+Q  LG+T+L V+HD     AI+DR+ ++   G + QVG P ++++ P    V
Sbjct: 178 MRFEIKELQRTLGITILYVTHDQEIALAISDRLAIMDHAGAIRQVGTPWEIFERPADEFV 237

Query: 238 ASLIGEINELEGKVTNEGVVIGSLRFPV-----SVSSDRAIIGIRPEDVKLSK 285
              +G  N L  +     ++      PV        ++  + G RP DV+L++
Sbjct: 238 FRFMGVANFLPARRRGMAMLAAGGEQPVPWGLPDGDAEHWMAGFRPSDVRLAR 290


Lambda     K      H
   0.319    0.139    0.390 

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: 267
Number of extensions: 10
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: 353
Length of database: 366
Length adjustment: 29
Effective length of query: 324
Effective length of database: 337
Effective search space:   109188
Effective search space used:   109188
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 (21.7 bits)
S2: 49 (23.5 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