GapMind for catabolism of small carbon sources

 

Aligments for a candidate for scrK in Pseudomonas fluorescens FW300-N1B4

Align Fructokinase (EC 2.7.1.4) (characterized)
to candidate Pf1N1B4_4844 Fructokinase (EC 2.7.1.4)

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



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4844 Fructokinase (EC
           2.7.1.4)
          Length = 312

 Score =  556 bits (1433), Expect = e-163
 Identities = 277/311 (89%), Positives = 293/311 (94%)

Query: 1   MYLVCGEALFDFFSENDASGLASKVNFKAIAGGSPFNVAVGLRRLGVDAALLAGLSTDYL 60
           MYLVCGEALFDFFSE+DASGLASKVNFKAIAGGSPFNVAVGLRRLGVDAAL  GLSTDYL
Sbjct: 1   MYLVCGEALFDFFSEDDASGLASKVNFKAIAGGSPFNVAVGLRRLGVDAALFGGLSTDYL 60

Query: 61  GRRLLQVLQDEGVCLDYLLEFAAPTTLAMVAVGANGSPQYSFRGEGCADRQLQAEHLPTL 120
           GRRL QVLQDEGV  DYL++FAAPTTLAMVAVGANGSP YSFRGEGCADRQL   HLP L
Sbjct: 61  GRRLQQVLQDEGVRPDYLVDFAAPTTLAMVAVGANGSPHYSFRGEGCADRQLSLAHLPEL 120

Query: 121 GPEVRGLHIGSFSLVVQPIADTLLALVRRESGKRLISLDPNVRLNPEPDIDLWRKRVATL 180
           GPEVRGLH+GSFSLVVQPIADTLLALV+RESGKRLISLDPNVRLNPEP+I+LWR R+A L
Sbjct: 121 GPEVRGLHVGSFSLVVQPIADTLLALVQRESGKRLISLDPNVRLNPEPNIELWRSRIAKL 180

Query: 181 VELADLIKVSDEDLHLLYPDQDPAQVIEGWLQHRCQLVFLTRGGEGATVFSRAHGSWSAP 240
           VELADLIKVSDEDL LLYP+QDP +VIEGWL+HRCQLVFLTRGGEGATVFSRAHG+WS P
Sbjct: 181 VELADLIKVSDEDLSLLYPEQDPQRVIEGWLEHRCQLVFLTRGGEGATVFSRAHGTWSVP 240

Query: 241 ACSVKIADTVGAGDTFQAALITWLTEQQLDSVEGVKQLGREQIDRMLKFAVRAAALTCSK 300
           ACSVKIADTVGAGDTFQAALITWLTEQQLDSVEG++QL REQID ML+FAV AAALTCSK
Sbjct: 241 ACSVKIADTVGAGDTFQAALITWLTEQQLDSVEGLQQLSREQIDAMLRFAVSAAALTCSK 300

Query: 301 TGPDLPYRKQL 311
           TGPDLPYR+QL
Sbjct: 301 TGPDLPYRRQL 311


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: 453
Number of extensions: 9
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: 312
Length adjustment: 27
Effective length of query: 287
Effective length of database: 285
Effective search space:    81795
Effective search space used:    81795
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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