GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcV in Pseudomonas simiae WCS417

Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate GFF5028 PS417_25760 spermidine/putrescine ABC transporter ATP-binding protein

Query= BRENDA::Q97UY8
         (353 letters)



>FitnessBrowser__WCS417:GFF5028
          Length = 370

 Score =  203 bits (517), Expect = 5e-57
 Identities = 116/325 (35%), Positives = 185/325 (56%), Gaps = 20/325 (6%)

Query: 2   VRIIVKNVSKVFKKGKVVALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTGE 61
           V +  + V K +  G+ + + ++N+ I  GE   +LGPSG+GKTT + ++AG + P+ GE
Sbjct: 9   VLVSFRGVQKSYD-GENLIVKDLNLEIRKGEFLTLLGPSGSGKTTSLMMLAGFETPTAGE 67

Query: 62  LYFDDRLVASNGKLIVPPEDRKIGMVFQTWALYPNLTAFENIAFPLTNMKMSKEEIRKRV 121
           +    R + +     VPP  R IGMVFQ +AL+P++T  EN+AFPL+   +SK +I +RV
Sbjct: 68  IQLAGRSINN-----VPPHKRDIGMVFQNYALFPHMTVAENLAFPLSVRALSKTDISERV 122

Query: 122 EEVAKILDIHHVLNHFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDSARA 181
           + V  ++ +      +P +LSGGQQQRVALARALV +P L+L+DEP   LD ++R+  + 
Sbjct: 123 KRVLSMVQLDAFAQRYPAQLSGGQQQRVALARALVFEPQLVLMDEPLGALDKQLREHMQM 182

Query: 182 LVKEVQSRLGVTLLVVSHDPADIFAIADRVGVLVKGKLVQVGKPEDLYDNPVSIQVASLI 241
            +K +  RLGVT++ V+HD  +   ++DRV V  +G++ Q+  P  LY+ P +  VA+ I
Sbjct: 183 EIKHLHQRLGVTVVYVTHDQGEALTMSDRVAVFHQGEIQQIAAPRTLYEEPKNTFVANFI 242

Query: 242 GEINELEGKVTN-----------EGVVIGSLRFPVSVSSDRAIIGIRPEDVKLSKDVIKD 290
           GE N L G++ +            G  + +L   V        + +RPE V L+      
Sbjct: 243 GENNRLNGRLHSHSGERCVVELARGEKVEALAVNVGQVGGPVTLSVRPERVSLNG---SS 299

Query: 291 DSWILVGKGKVKVIGYQGGLFRITI 315
           +S +    G+V    Y G   R+ +
Sbjct: 300 ESCVNRFSGRVAEFIYLGDHVRVRL 324


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: 313
Number of extensions: 12
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: 370
Length adjustment: 29
Effective length of query: 324
Effective length of database: 341
Effective search space:   110484
Effective search space used:   110484
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