GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcV in Pseudomonas putida KT2440

Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate PP_0411 PP_0411 Polyamine ABC transporter, ATP-binding protein

Query= BRENDA::Q97UY8
         (353 letters)



>FitnessBrowser__Putida:PP_0411
          Length = 374

 Score =  207 bits (526), Expect = 5e-58
 Identities = 114/311 (36%), Positives = 181/311 (58%), Gaps = 19/311 (6%)

Query: 16  GKVVALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTGELYFDDRLVASNGKL 75
           G+ + + ++N++I  GE   +LGPSG+GKTT + ++AG + P+ GE+    R + +    
Sbjct: 26  GESLIVKDLNLDIRKGEFLTLLGPSGSGKTTSLMMLAGFETPTAGEIQLGGRSINN---- 81

Query: 76  IVPPEDRKIGMVFQTWALYPNLTAFENIAFPLTNMKMSKEEIRKRVEEVAKILDIHHVLN 135
            VPP  R IGMVFQ +AL+P++T  EN+AFPLT   +SK +I +RV+ V  ++ +     
Sbjct: 82  -VPPHKRDIGMVFQNYALFPHMTVAENLAFPLTVRNLSKTDISERVKRVLNMVQLDAFAK 140

Query: 136 HFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDSARALVKEVQSRLGVTLL 195
            +P +LSGGQQQRVALARALV +P L+L+DEP   LD ++R+  +  +K +  RLGVT++
Sbjct: 141 RYPGQLSGGQQQRVALARALVFEPQLVLMDEPLGALDKQLREHMQMEIKHIHQRLGVTVV 200

Query: 196 VVSHDPADIFAIADRVGVLVKGKLVQVGKPEDLYDNPVSIQVASLIGEINELEGKV---- 251
            V+HD  +   ++DRV V  +G++ Q+  P  LY+ P +  VA+ IGE N + G +    
Sbjct: 201 YVTHDQGEALTMSDRVAVFHQGEIQQIADPRTLYEEPCNTFVANFIGENNRISGTLLASD 260

Query: 252 -------TNEGVVIGSLRFPVSVSSDRAIIGIRPEDVKLSKDVIKDDSWILVGKGKVKVI 304
                     G  + +L   V  + +   + IRPE V+L+      +S +    G+V   
Sbjct: 261 GKRCQVQLPRGERVEALAVNVGQAGEPVTLSIRPERVRLNG---HSESCVNRFSGRVAEF 317

Query: 305 GYQGGLFRITI 315
            Y G   R+ +
Sbjct: 318 IYLGDHVRVRL 328


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: 322
Number of extensions: 10
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: 374
Length adjustment: 29
Effective length of query: 324
Effective length of database: 345
Effective search space:   111780
Effective search space used:   111780
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