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 8500851 DvMF_1589 ABC transporter related (RefSeq)

Query= BRENDA::Q97UY8
         (353 letters)



>FitnessBrowser__Miya:8500851
          Length = 354

 Score =  206 bits (523), Expect = 1e-57
 Identities = 119/296 (40%), Positives = 179/296 (60%), Gaps = 15/296 (5%)

Query: 2   VRIIVKNVSKVFKKGKVVALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTGE 61
           VR++  NV+K F  G V A+D++N+ I  GE F +LGPSG GKTT +R++AG +    GE
Sbjct: 4   VRLV--NVTKRF--GGVTAVDSLNLEIGRGECFSMLGPSGCGKTTTLRMVAGFEDLDDGE 59

Query: 62  LYFDDRLV-ASNGKLIVPPEDRKIGMVFQTWALYPNLTAFENIAFPLTNMKMSKEEIRKR 120
           ++  DRL+ A      +PPE R  GMVFQ +A++P+L+ +EN+AFPL   ++S  EI +R
Sbjct: 60  IHVGDRLLSARRNNYYLPPEKRDFGMVFQAFAVWPHLSVYENVAFPLRIRRLSAAEIDRR 119

Query: 121 VEEVAKILDIHHVLNHFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDSAR 180
             E      +  V    P +LSGG +QRVALARAL  +P ++LLDEP S+LD  +R+  R
Sbjct: 120 TREALHHTSLADVAQKSPDDLSGGGKQRVALARALAINPDVMLLDEPLSSLDPHLREEMR 179

Query: 181 ALVKEVQSRLGVTLLVVSHDPADIFAIADRVGVLVKGKLVQVGKPEDLYDNPVSIQVASL 240
             +K++Q   G ++L V+HD ++  A++DR+ V+  G + QVG P D+Y NP +  V   
Sbjct: 180 FEIKDLQRTFGFSILYVTHDQSEAMALSDRIMVMRNGVVQQVGTPLDVYTNPANSFVFGF 239

Query: 241 IGEINELEGKVTNEGVVI---GSLRFPVS-------VSSDRAIIGIRPEDVKLSKD 286
           IG  N L+  +T EG+V    G  R   +       VS+ RA +  RP ++  + +
Sbjct: 240 IGLSNFLDVNLTPEGLVRVNGGDARVTPATPPSARLVSAGRAALASRPSEIDFTAE 295


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: 295
Number of extensions: 9
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: 354
Length adjustment: 29
Effective length of query: 324
Effective length of database: 325
Effective search space:   105300
Effective search space used:   105300
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