GapMind for catabolism of small carbon sources

 

Alignments for a candidate for scrK in Pseudomonas simiae WCS417

Align fructokinase; EC 2.7.1.4 (characterized)
to candidate GFF2464 PS417_12565 2-dehydro-3-deoxygluconokinase

Query= CharProtDB::CH_012664
         (307 letters)



>FitnessBrowser__WCS417:GFF2464
          Length = 313

 Score = 99.0 bits (245), Expect = 1e-25
 Identities = 87/280 (31%), Positives = 127/280 (45%), Gaps = 13/280 (4%)

Query: 29  GAPANVAVGIARLGGTSGFIGRVGDDPFGALMQRTLLTEGVDITYLKQDEWHRTSTVLVD 88
           GA +NVA+G++RLG    ++ RVG+D  G  +  TL  EG+D  ++  D  H T   L  
Sbjct: 36  GADSNVAIGLSRLGFKVAWLSRVGNDSLGRFVVDTLTQEGLDCRHVAVDPAHPTGFQLKS 95

Query: 89  LNDQG-ERSFTFMVRPSADLFLETTDL-PCWRHGEWLHLCSI--ALSAEPSRTSAFTAMT 144
             + G +    +  + SA   L    + P       LH   I  ALS E +R  +   MT
Sbjct: 96  REETGDDPQVEYFRKGSAASHLSIAAISPALLQARHLHATGIPPALS-EATRELSVELMT 154

Query: 145 AIRHAGGFVSFDPNIREDLWQDEHLLRLCLRQALQLADVVKLSEEEWRLISGKTQNDRDI 204
            +R AG  VSFDPN+R  LW ++  +   +     LAD V     E R ++G   +  DI
Sbjct: 155 QMRKAGRSVSFDPNLRPSLWANQQTMIREINALAGLADWVLPGLGEGRQLTG-FDDPADI 213

Query: 205 CALAKEYEIAMLLVTKGAEGVVVCYRGQVHHFAGMSVN-CVDSTGAGDAFVAGLLTGLSS 263
            A   +     + +  G +G            A + V+  VD+ GAGD F  G+++ L  
Sbjct: 214 AAFYLDQGAEAVAIKLGPDGAYYRTHLDQGFVAAVRVDKVVDTVGAGDGFAVGMISALLE 273

Query: 264 TGLSTDEREMRRIIDLAQRCGALAVTAKGAMTALPCRQEL 303
             LS  E   R         G+ AV ++G M  LP R EL
Sbjct: 274 -NLSFPEAVQR-----GNWIGSRAVQSRGDMEGLPARSEL 307


Lambda     K      H
   0.321    0.136    0.415 

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: 226
Number of extensions: 11
Number of successful extensions: 3
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: 307
Length of database: 313
Length adjustment: 27
Effective length of query: 280
Effective length of database: 286
Effective search space:    80080
Effective search space used:    80080
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