GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadB in Pseudomonas litoralis 2SM5

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 WP_090271901.1 BLU11_RS02515 3-hydroxyacyl-CoA dehydrogenase

Query= BRENDA::Q99714
         (261 letters)



>NCBI__GCF_900105005.1:WP_090271901.1
          Length = 255

 Score =  259 bits (662), Expect = 4e-74
 Identities = 138/248 (55%), Positives = 173/248 (69%), Gaps = 2/248 (0%)

Query: 12  VAVITGGASGLGLATAERLVGQGASAVLLDLPNSGGEAQAKKLGNNCVFAPADVTSEKDV 71
           + +ITGGASGLG ATA  LV  GA   L+DL  S  + +  +LG N     AD+  E+  
Sbjct: 7   IFMITGGASGLGAATAALLVEAGARVALIDLNESALQQRVAELGENARGYAADIADEQQA 66

Query: 72  QTALALAKGKFGRVDVAVNCAGIAVASKTYNLKKGQTHTLEDFQRVLDVNLMGTFNVIRL 131
             A+A A+  FG++   +NCAGIA   K   L +   H L  F R L VNL+GTFN++RL
Sbjct: 67  AEAIAAARRDFGQLHGLINCAGIAPGEKI--LGRNGPHGLASFDRALRVNLLGTFNMLRL 124

Query: 132 VAGEMGQNEPDQGGQRGVIINTASVAAFEGQVGQAAYSASKGGIVGMTLPIARDLAPIGI 191
            A  M + EPD+ G+RGVIINTASVAA++GQ+GQ AY+ASKGG+V MTLP AR+LA  GI
Sbjct: 125 AAEVMAEGEPDEQGERGVIINTASVAAYDGQIGQVAYAASKGGVVSMTLPAARELARHGI 184

Query: 192 RVMTIAPGLFGTPLLTSLPEKVCNFLASQVPFPSRLGDPAEYAHLVQAIIENPFLNGEVI 251
           RVMTIAPG+F TP++  + ++V + LA  VPFP RLG P EYA LV+ IIENP LNGEVI
Sbjct: 185 RVMTIAPGIFETPMMAGMTQQVRDSLAKDVPFPPRLGLPEEYAALVRHIIENPMLNGEVI 244

Query: 252 RLDGAIRM 259
           RLDGA+RM
Sbjct: 245 RLDGALRM 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: 223
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 24 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