GapMind for catabolism of small carbon sources

 

Alignments for a candidate for scrK in Paraburkholderia bryophila 376MFSha3.1

Align fructokinase (EC 2.7.1.4) (characterized)
to candidate H281DRAFT_00856 H281DRAFT_00856 2-keto-3-deoxygluconate kinase

Query= BRENDA::Q42645
         (331 letters)



>FitnessBrowser__Burk376:H281DRAFT_00856
          Length = 311

 Score =  132 bits (333), Expect = 9e-36
 Identities = 96/312 (30%), Positives = 153/312 (49%), Gaps = 16/312 (5%)

Query: 10  SKELVVSFGEMLIDFVPTSSGVSLAEAPGFLKAPGGAPANVAIAVSRLGGNAAFVGKLGD 69
           +K  +++ GE +I+F       S  + P +L+  GG  +N  IA +R G    FV  +G 
Sbjct: 7   AKPEILALGEAMIEF-----NQSAKDEPNYLQGFGGDTSNFCIAAARQGARTGFVSAVGA 61

Query: 70  DEFGHMLAGILKKNGVSADGLSFDKGARTALAFVTLKSDGEREFMFYRNPSADMLLTPDE 129
           D FG +L  + ++  V    +  D  A T + FV+   DG   F + R  SA     P +
Sbjct: 62  DHFGRLLIDLWEREQVDTALVRVDPHASTGVYFVSHGPDG-HAFDYLRAGSAASRYAPRD 120

Query: 130 LNLDLIRSAKVFHYGSIRLIVE-PCRSAHLKAMEEAKKAGALLSYDPNLRLPLWPSAEEA 188
           L LD I +AKV H   I L +      A L+A+  A+  G  +S+D NLRL LWP    A
Sbjct: 121 LPLDAIAAAKVIHLSGISLAISLSACDAALEAITHARANGVQVSFDTNLRLKLWP-LNRA 179

Query: 189 REQIMSIWDKAEVIKVSDNELEFLTGNSTIDDATAMSLWHPNLKLLLVTLGDQGCRYYTK 248
           R  ++    + ++   S +++  LTG +  D+     L H   +++ + LG +G    T 
Sbjct: 180 RAVMLEAIRQTDICLPSWDDVTELTGLTGRDEIVDFLLSH-GPRVVALKLGKEGSYIATP 238

Query: 249 NFKGSLDGFKVNAVDTTGAGDSFVGALLNKIVDDHSIIEDESRLKEVLKFANACGAITTT 308
           + +  + G  VNAVD TGAGD F GA + ++V+            E  ++AN   A++T 
Sbjct: 239 DERRVVPGHVVNAVDATGAGDCFGGAFIARLVEGDDPF-------EAARYANVAAALSTQ 291

Query: 309 KKGAIPALPTVA 320
             GA+  +P+ A
Sbjct: 292 GYGAVAPIPSRA 303


Lambda     K      H
   0.316    0.134    0.385 

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: 244
Number of extensions: 17
Number of successful extensions: 4
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: 331
Length of database: 311
Length adjustment: 28
Effective length of query: 303
Effective length of database: 283
Effective search space:    85749
Effective search space used:    85749
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 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