GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadB in Pseudomonas putida KT2440

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 PP_2214 PP_2214 3-hydroxyacyl-CoA dehydrogenase type-2

Query= BRENDA::Q99714
         (261 letters)



>FitnessBrowser__Putida:PP_2214
          Length = 255

 Score =  253 bits (647), Expect = 2e-72
 Identities = 133/246 (54%), Positives = 175/246 (71%), Gaps = 2/246 (0%)

Query: 14  VITGGASGLGLATAERLVGQGASAVLLDLPNSGGEAQAKKLGNNCVFAPADVTSEKDVQT 73
           +++G ASGLG ATA+ LV  GA  +L+DL     EA+A++LG+N  FA AD++ E+  Q+
Sbjct: 9   IVSGAASGLGAATAQMLVEAGAKVMLVDLNAQAVEAKARELGDNARFAVADISDEQAAQS 68

Query: 74  ALALAKGKFGRVDVAVNCAGIAVASKTYNLKKGQTHTLEDFQRVLDVNLMGTFNVIRLVA 133
           A+  A   FG +   VNCAGI  A K   L K   H L  F +V++VNL+G+FN++RL A
Sbjct: 69  AVDAAVSAFGSLHGLVNCAGIVGAEKV--LGKQGPHGLASFAKVINVNLIGSFNLLRLAA 126

Query: 134 GEMGQNEPDQGGQRGVIINTASVAAFEGQVGQAAYSASKGGIVGMTLPIARDLAPIGIRV 193
             M +   D+ G+RGVIINTAS+AA++GQ+GQAAY+ASKG I  +TLP AR+LA  GIRV
Sbjct: 127 AAMAEGAADESGERGVIINTASIAAYDGQIGQAAYAASKGAIASLTLPAARELARFGIRV 186

Query: 194 MTIAPGLFGTPLLTSLPEKVCNFLASQVPFPSRLGDPAEYAHLVQAIIENPFLNGEVIRL 253
           MTIAPG+F TP++  + ++V   LA+ VPFP RLG P EYA L + IIEN  LNGEVIRL
Sbjct: 187 MTIAPGIFETPMMAGMSDEVRASLAAGVPFPPRLGRPQEYAALARHIIENSMLNGEVIRL 246

Query: 254 DGAIRM 259
           DGA+RM
Sbjct: 247 DGALRM 252


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: 199
Number of extensions: 3
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: 255
Length adjustment: 24
Effective length of query: 237
Effective length of database: 231
Effective search space:    54747
Effective search space used:    54747
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