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 8499890 DvMF_0655 ABC transporter related (RefSeq)

Query= BRENDA::Q97UY8
         (353 letters)



>FitnessBrowser__Miya:8499890
          Length = 350

 Score =  192 bits (488), Expect = 1e-53
 Identities = 111/290 (38%), Positives = 173/290 (59%), Gaps = 17/290 (5%)

Query: 1   MVRIIVKNVSKVFKKGKVVALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTG 60
           M  I + NVS+ +  G V A+D+V+  +E G    +LGPSG GK+T +R+IAGL+  ++G
Sbjct: 1   MSAIQLLNVSRHW--GDVRAVDDVSFEVEQGTMLVLLGPSGCGKSTTLRLIAGLESVTSG 58

Query: 61  ELYFDDRLVASNGKLIVPPEDRKIGMVFQTWALYPNLTAFENIAFPLTNMKMSKEEIRKR 120
            +   +R V       +PP  R++ MVFQ++AL+P+LT  ENI F LT  K+ + E  KR
Sbjct: 59  RIMIGERDVTH-----LPPAQRQLAMVFQSYALFPHLTVRENILFGLTVRKVPEAEREKR 113

Query: 121 VEEVAKILDIHHVLNHFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDSAR 180
           +     IL +  +L   P ELSGGQQQRVAL RALV + ++ L+DEP SNLDA++R   R
Sbjct: 114 LTRAVDILGLSALLQRKPGELSGGQQQRVALGRALVAEAAVCLMDEPLSNLDAKLRHEMR 173

Query: 181 ALVKEVQSRLGVTLLVVSHDPADIFAIADRVGVLVKGKLVQVGKPEDLYDNPVSIQVASL 240
             ++ +Q  LG+T++ V+HD  +  ++ADR+ ++  G++VQ   P +LY  P +    + 
Sbjct: 174 REIRALQQTLGMTMVYVTHDQTEAMSMADRIILMQGGRIVQNATPSELYSRPATTFAGNF 233

Query: 241 IG-------EINELEGKVTNEGVVIGSLRFPVSVSSDRAIIGIRPEDVKL 283
           IG        +++  G V   G   G++     V S   ++GIRPE +++
Sbjct: 234 IGTPPMNLVRLDDARGSVCVAGSRSGTVSV---VDSADYVLGIRPEHIRI 280


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: 278
Number of extensions: 11
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: 350
Length adjustment: 29
Effective length of query: 324
Effective length of database: 321
Effective search space:   104004
Effective search space used:   104004
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