GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadB in Pseudomonas fluorescens FW300-N2E3

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 AO353_25690 AO353_25690 3-hydroxy-2-methylbutyryl-CoA dehydrogenase

Query= BRENDA::Q99714
         (261 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_25690
          Length = 253

 Score =  258 bits (658), Expect = 1e-73
 Identities = 137/252 (54%), Positives = 178/252 (70%), Gaps = 4/252 (1%)

Query: 8   VKGLVAVITGGASGLGLATAERLVGQGASAVLLDLPNSGGEAQAKKLGNNCVFAPADVTS 67
           ++  V ++TGGASGLG ATAE LVG GA  +L+DL      AQAK+LG +CV A  D++ 
Sbjct: 3   IENKVFLVTGGASGLGAATAEMLVGAGAKVMLVDLNAEAVAAQAKRLGAHCVVA--DISQ 60

Query: 68  EKDVQTALALAKGKFGRVDVAVNCAGIAVASKTYNLKKGQTHTLEDFQRVLDVNLMGTFN 127
           E   + A+  A   FG +   VNCAG+    K   L K   H L  F +V++VNL+G+FN
Sbjct: 61  EAAAEAAVQAAVAAFGGLHGLVNCAGVVRGEKI--LGKNGPHALASFSQVINVNLIGSFN 118

Query: 128 VIRLVAGEMGQNEPDQGGQRGVIINTASVAAFEGQVGQAAYSASKGGIVGMTLPIARDLA 187
           ++RL A  + + E ++ G+RGVIINTASVAAF+GQ+GQAAY+ASKG I  +TLP AR+LA
Sbjct: 119 MLRLAAAAIAETEANEDGERGVIINTASVAAFDGQIGQAAYAASKGAIASLTLPAARELA 178

Query: 188 PIGIRVMTIAPGLFGTPLLTSLPEKVCNFLASQVPFPSRLGDPAEYAHLVQAIIENPFLN 247
             GIRVMTIAPG+F TP++  + ++V + LA+ VPFP RLG P EYA LV+ IIEN  LN
Sbjct: 179 RYGIRVMTIAPGIFETPMMAGMTQEVRDSLAAGVPFPPRLGKPVEYAALVRHIIENSMLN 238

Query: 248 GEVIRLDGAIRM 259
           GEVIRLDGA+RM
Sbjct: 239 GEVIRLDGALRM 250


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: 215
Number of extensions: 6
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: 261
Length of database: 253
Length adjustment: 24
Effective length of query: 237
Effective length of database: 229
Effective search space:    54273
Effective search space used:    54273
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