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 3608624 Dshi_2017 ABC transporter related (RefSeq)

Query= BRENDA::Q97UY8
         (353 letters)



>FitnessBrowser__Dino:3608624
          Length = 333

 Score =  196 bits (498), Expect = 7e-55
 Identities = 115/286 (40%), Positives = 168/286 (58%), Gaps = 22/286 (7%)

Query: 1   MVRIIVKNVSKVFKKGKVVALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTG 60
           M  + + NV K F  GK   +  V+I++  GE   I+GPSG GK+T +R++AGL+  S+G
Sbjct: 1   MATLTLDNVKKSF--GKTDVIHGVSIDVTEGEFIVIVGPSGCGKSTLLRMVAGLETVSSG 58

Query: 61  ELYFDDRLVASNGKLIVPPEDRKIGMVFQTWALYPNLTAFENIAFPLTNMKMSKEEIRKR 120
           E+  D R+V +     + P DR I MVFQ +ALYP+++ F+N+A+ L   K+ K EI  R
Sbjct: 59  EVRIDGRVVNT-----LEPMDRDIAMVFQNYALYPHMSVFDNMAYGLKIAKVPKAEIADR 113

Query: 121 VEEVAKILDIHHVLNHFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDSAR 180
           V   AK+L +   L   P+ELSGGQ+QRVA+ RA+V+ P++ L DEP SNLDA++R   R
Sbjct: 114 VAVAAKLLQLEPYLGRKPKELSGGQRQRVAMGRAIVRKPAVFLFDEPLSNLDAKLRVQMR 173

Query: 181 ALVKEVQSRLGVTLLVVSHDPADIFAIADRVGVLVKGKLVQVGKPEDLYDNPVSIQVASL 240
             +K +Q  LGVT L V+HD  +   +ADR+ V+  G   Q+G P ++Y NP +  VA  
Sbjct: 174 LEIKALQRELGVTSLYVTHDQVEAMTLADRMIVMNGGVADQIGAPLEVYANPQTAFVAGF 233

Query: 241 IGE--INELEGKVTNEGVVIGSLRFPVSVSSDRAIIGIRPEDVKLS 284
           IG    N L   +   G        P         +GIRPE ++++
Sbjct: 234 IGSPPTNFLPADMVRAG--------PAGQQ-----VGIRPEHLRVA 266


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: 255
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: 333
Length adjustment: 29
Effective length of query: 324
Effective length of database: 304
Effective search space:    98496
Effective search space used:    98496
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