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 8501226 DvMF_1960 putrescine/spermidine ABC transporter ATPase protein (RefSeq)

Query= BRENDA::Q97UY8
         (353 letters)



>FitnessBrowser__Miya:8501226
          Length = 399

 Score =  211 bits (537), Expect = 3e-59
 Identities = 102/250 (40%), Positives = 173/250 (69%), Gaps = 11/250 (4%)

Query: 4   IIVKNVSKVFKKGKVVALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTGELY 63
           I ++ V+K F+    VALD++++ I NGE   +LGPSG GKTT +R+++G + P++GE  
Sbjct: 8   IELRGVTKTFED--TVALDSIDLTIRNGEFLTLLGPSGCGKTTILRLVSGFEQPTSGE-- 63

Query: 64  FDDRLVASNGKLI--VPPEDRKIGMVFQTWALYPNLTAFENIAFPLTNMKMSKEEIRKRV 121
                V  NG+++  VPPE R++  VFQ +AL+P++T  +N+AF L    ++ +E  +RV
Sbjct: 64  -----VRINGQVVNRVPPEQRQVNTVFQNYALFPHMTVRDNVAFGLKMQGVAADETARRV 118

Query: 122 EEVAKILDIHHVLNHFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDSARA 181
            +  +++ + +  +  PR+LSGGQQQRVA+ARA++ +P +LLLDEPFS LD ++R   + 
Sbjct: 119 LDALRMVHLENFADRKPRQLSGGQQQRVAIARAVINNPLVLLLDEPFSALDFKLRKQMQL 178

Query: 182 LVKEVQSRLGVTLLVVSHDPADIFAIADRVGVLVKGKLVQVGKPEDLYDNPVSIQVASLI 241
            +K +Q +LG+T + V+HD  + FA++DRV V+ +G++ Q+G P+++Y+ P ++ VA  +
Sbjct: 179 EIKHLQRQLGITFVFVTHDQEEAFAMSDRVVVMNEGRIEQIGAPKEIYEEPANMYVARFV 238

Query: 242 GEINELEGKV 251
           G+IN L G++
Sbjct: 239 GDINALPGRI 248


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: 340
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: 399
Length adjustment: 30
Effective length of query: 323
Effective length of database: 369
Effective search space:   119187
Effective search space used:   119187
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: 50 (23.9 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