GapMind for catabolism of small carbon sources

 

Aligments for a candidate for ivdG in Burkholderia phytofirmans PsJN

Align GDP-6-deoxy-D-talose 4-dehydrogenase (EC 1.1.1.135); 3-hydroxy-2-methylbutyryl-CoA dehydrogenase (EC 1.1.1.178) (characterized)
to candidate BPHYT_RS25415 BPHYT_RS25415 3-hydroxy-2-methylbutyryl-CoA dehydrogenase

Query= BRENDA::Q99714
         (261 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS25415 BPHYT_RS25415
           3-hydroxy-2-methylbutyryl-CoA dehydrogenase
          Length = 248

 Score =  211 bits (536), Expect = 2e-59
 Identities = 122/252 (48%), Positives = 163/252 (64%), Gaps = 5/252 (1%)

Query: 7   SVKGLVAVITGGASGLGLATAERLVGQGASAVLLDLPNSGGEAQAKKLGNNCVFAPADVT 66
           +++  VA++TG ASGLGLAT + L   GA  V  DL  +  +   + LG +      DV+
Sbjct: 2   NLQNKVAIVTGAASGLGLATCKGLAAAGAMVVGFDLDQARLD---EALGADMQGLAVDVS 58

Query: 67  SEKDVQTALALAKGKFGRVDVAVNCAGIAVASKTYNLKKGQTHTLEDFQRVLDVNLMGTF 126
           +E  V++ +       GRV VAVNCAGI    KT  L KGQ    + + RVL VNL GTF
Sbjct: 59  NESSVKSGIDAVVAMHGRVHVAVNCAGILGPCKT--LSKGQLFPSDLWNRVLGVNLTGTF 116

Query: 127 NVIRLVAGEMGQNEPDQGGQRGVIINTASVAAFEGQVGQAAYSASKGGIVGMTLPIARDL 186
           NVIR  A  M  N+P++ G+RGVIINT+S AA  GQ+GQAAYSASK G++GMTLPIARDL
Sbjct: 117 NVIRHAALVMSANDPEETGERGVIINTSSGAARAGQMGQAAYSASKAGVIGMTLPIARDL 176

Query: 187 APIGIRVMTIAPGLFGTPLLTSLPEKVCNFLASQVPFPSRLGDPAEYAHLVQAIIENPFL 246
           A  GIRV++IAPGLF + +   +P+KV + L  ++ FP R+G   E+A LV+ I+EN +L
Sbjct: 177 AEHGIRVVSIAPGLFESGMSAGMPQKVSDSLIEKMLFPRRMGKAEEFAGLVRHIVENAYL 236

Query: 247 NGEVIRLDGAIR 258
           N   I +D  +R
Sbjct: 237 NAMTIDIDCGMR 248


Lambda     K      H
   0.318    0.135    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: 190
Number of extensions: 6
Number of successful extensions: 2
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: 261
Length of database: 248
Length adjustment: 24
Effective length of query: 237
Effective length of database: 224
Effective search space:    53088
Effective search space used:    53088
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 (21.7 bits)
S2: 47 (22.7 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 preprint 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