GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ivdG in Pseudomonas fluorescens GW456-L13

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 PfGW456L13_2522 3-oxoacyl-[acyl-carrier protein] reductase (EC 1.1.1.100)

Query= BRENDA::Q99714
         (261 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2522
          Length = 248

 Score =  117 bits (294), Expect = 2e-31
 Identities = 88/248 (35%), Positives = 123/248 (49%), Gaps = 24/248 (9%)

Query: 12  VAVITGGASGLGLATAERLVGQGASAVLLDLPNSGGEAQAKKLGNNCVFAPADVTSEKDV 71
           VAV+TGGASG+GLA   R   +GA  + LD+    G A A   G   +F   DV  E  V
Sbjct: 8   VAVVTGGASGIGLACVRRFSAEGAQVIGLDI----GSAPADFPG---LFMTLDVRDEAQV 60

Query: 72  QTALALAKGKFGRVDVAVNCAGIAVASKTYNLKKGQTHTLEDFQRVLDVNLMGTFNVIRL 131
           Q  +     +FGR+DV VN AG+A              T  ++QRV+D+NL G+    + 
Sbjct: 61  QQVMQEVISRFGRIDVLVNAAGVADQGSVTQT------TTANWQRVMDINLTGSMLTSKY 114

Query: 132 VAGEMGQNEPDQGGQRGVIINTASVAAFEGQVGQAAYSASKGGIVGMTLPIARDLAPIGI 191
               M +       + G IIN  S+   +G  G  AY+ SKGGI  +T  +A D     I
Sbjct: 115 ALASMVEQ------RNGSIINVGSIFGLQGCDGNVAYNVSKGGINQLTRSMAIDYGYANI 168

Query: 192 RVMTIAPGLFGTPLLTSLPEKVC--NFLASQVPFPSRLGDPAEYAH--LVQAIIENPFLN 247
           RV  + PGL  TP+ + + +      F ASQ    +R G P E A+  L  A  E  F++
Sbjct: 169 RVNGLCPGLIETPMTSMVRDNDAFHAFFASQ-HMLNRSGQPEEVANVALFLASDEASFVS 227

Query: 248 GEVIRLDG 255
           G++I +DG
Sbjct: 228 GQMIAVDG 235


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: 158
Number of extensions: 12
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: 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.

Links

Downloads

Related tools

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