GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcV in Dinoroseobacter shibae DFL-12

Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate 3607124 Dshi_0546 ABC transporter related (RefSeq)

Query= BRENDA::Q97UY8
         (353 letters)



>FitnessBrowser__Dino:3607124
          Length = 338

 Score =  189 bits (481), Expect = 7e-53
 Identities = 107/288 (37%), Positives = 170/288 (59%), Gaps = 18/288 (6%)

Query: 1   MVRIIVKNVSKVFKKGKVVALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTG 60
           M  I +  ++K +  G   AL ++N++IE+GE    +GPSG GK+T +R +AGL+  S+G
Sbjct: 1   MAGIKIDKINKFY--GTTQALFDINLDIEDGEFVVFVGPSGCGKSTLLRTLAGLEGVSSG 58

Query: 61  ELYFDDRLVASNGKLIVPPEDRKIGMVFQTWALYPNLTAFENIAFPLTNMKMSKEEIRKR 120
            +    R V +     V P DR + MVFQ++ALYP++T  EN+ F +       +  ++R
Sbjct: 59  RIEIGGRDVTT-----VEPADRDLAMVFQSYALYPHMTVRENMEFGMKVNGFEPDLRKER 113

Query: 121 VEEVAKILDIHHVLNHFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDSAR 180
           + E A++L +   L+  P +LSGGQ+QRVA+ RA+VK+PS+ L DEP SNLDA++R   R
Sbjct: 114 IAEAARVLQLEDYLDRKPGQLSGGQRQRVAIGRAIVKNPSVFLFDEPLSNLDAKLRVQMR 173

Query: 181 ALVKEVQSRLGVTLLVVSHDPADIFAIADRVGVLVKGKLVQVGKPEDLYDNPVSIQVASL 240
             ++ +  +LG T++ V+HD  +   +AD++ VL +G++ QVG P DLY  P S  VA  
Sbjct: 174 VELEGLHKQLGATMIYVTHDQVEAMTMADKIVVLNRGRIEQVGSPMDLYHKPNSRFVAEF 233

Query: 241 IGE--INELEGKVTNEGVVIGSLRFPVSVSSDRAIIGIRPEDVKLSKD 286
           IG   +N     V  +          +S+ +  A +G RPE +++  D
Sbjct: 234 IGSPAMNVFSSDVGLQ---------DISLDASAAFVGCRPEHIEIVPD 272


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: 252
Number of extensions: 15
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: 338
Length adjustment: 29
Effective length of query: 324
Effective length of database: 309
Effective search space:   100116
Effective search space used:   100116
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