GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__BFirm:BPHYT_RS25415
          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 (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