GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4844
          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:

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