GapMind for catabolism of small carbon sources

 

Alignments for a candidate for scrK in Pseudomonas fluorescens GW456-L13

Align Fructokinase (EC 2.7.1.4) (characterized)
to candidate PfGW456L13_3036 Fructokinase (EC 2.7.1.4)

Query= reanno::pseudo13_GW456_L13:PfGW456L13_3036
         (314 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3036
          Length = 314

 Score =  624 bits (1608), Expect = 0.0
 Identities = 314/314 (100%), Positives = 314/314 (100%)

Query: 1   MYLVCGEALFDFFSENDASGLASKVNFKAIAGGSPFNVAVGLRRLGVDAALLAGLSTDYL 60
           MYLVCGEALFDFFSENDASGLASKVNFKAIAGGSPFNVAVGLRRLGVDAALLAGLSTDYL
Sbjct: 1   MYLVCGEALFDFFSENDASGLASKVNFKAIAGGSPFNVAVGLRRLGVDAALLAGLSTDYL 60

Query: 61  GRRLLQVLQDEGVCLDYLLEFAAPTTLAMVAVGANGSPQYSFRGEGCADRQLQAEHLPTL 120
           GRRLLQVLQDEGVCLDYLLEFAAPTTLAMVAVGANGSPQYSFRGEGCADRQLQAEHLPTL
Sbjct: 61  GRRLLQVLQDEGVCLDYLLEFAAPTTLAMVAVGANGSPQYSFRGEGCADRQLQAEHLPTL 120

Query: 121 GPEVRGLHIGSFSLVVQPIADTLLALVRRESGKRLISLDPNVRLNPEPDIDLWRKRVATL 180
           GPEVRGLHIGSFSLVVQPIADTLLALVRRESGKRLISLDPNVRLNPEPDIDLWRKRVATL
Sbjct: 121 GPEVRGLHIGSFSLVVQPIADTLLALVRRESGKRLISLDPNVRLNPEPDIDLWRKRVATL 180

Query: 181 VELADLIKVSDEDLHLLYPDQDPAQVIEGWLQHRCQLVFLTRGGEGATVFSRAHGSWSAP 240
           VELADLIKVSDEDLHLLYPDQDPAQVIEGWLQHRCQLVFLTRGGEGATVFSRAHGSWSAP
Sbjct: 181 VELADLIKVSDEDLHLLYPDQDPAQVIEGWLQHRCQLVFLTRGGEGATVFSRAHGSWSAP 240

Query: 241 ACSVKIADTVGAGDTFQAALITWLTEQQLDSVEGVKQLGREQIDRMLKFAVRAAALTCSK 300
           ACSVKIADTVGAGDTFQAALITWLTEQQLDSVEGVKQLGREQIDRMLKFAVRAAALTCSK
Sbjct: 241 ACSVKIADTVGAGDTFQAALITWLTEQQLDSVEGVKQLGREQIDRMLKFAVRAAALTCSK 300

Query: 301 TGPDLPYRKQLDLR 314
           TGPDLPYRKQLDLR
Sbjct: 301 TGPDLPYRKQLDLR 314


Lambda     K      H
   0.321    0.138    0.410 

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: 510
Number of extensions: 5
Number of successful extensions: 1
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: 314
Length of database: 314
Length adjustment: 27
Effective length of query: 287
Effective length of database: 287
Effective search space:    82369
Effective search space used:    82369
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 (21.9 bits)
S2: 48 (23.1 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