GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaH in Kocuria flava HO-9041

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_058857332.1 AS188_RS01360 SDR family NAD(P)-dependent oxidoreductase

Query= BRENDA::Q99714
         (261 letters)



>NCBI__GCF_001482365.1:WP_058857332.1
          Length = 252

 Score =  220 bits (560), Expect = 3e-62
 Identities = 126/250 (50%), Positives = 163/250 (65%), Gaps = 7/250 (2%)

Query: 13  AVITGGASGLGLATAERLVGQGASAVLLDLPNSGGEAQAKKLGNNCVFAPADVTSEKDVQ 72
           A++TG ASGLG ATA  L G+G     LDLP +   A          +APADVT    V 
Sbjct: 8   ALVTGAASGLGAATAAMLAGRGVRVTGLDLPAALERAPDVP---GVRYAPADVTDRAAVA 64

Query: 73  TALALAKGKFGRVDVAVNCAGIAVASKTYNLKKGQTHTLEDFQRVLDVNLMGTFNVIRLV 132
            A+  A G+ G +   VNCAGIA +++   L +G  H LE F+ VL VNL+GTF V+ L 
Sbjct: 65  AAVETAAGQ-GPLRTVVNCAGIAPSARV--LGRGGVHDLELFETVLRVNLLGTFTVLALA 121

Query: 133 AGEMGQNEP-DQGGQRGVIINTASVAAFEGQVGQAAYSASKGGIVGMTLPIARDLAPIGI 191
           A  +   +P D  GQRG+++NTASVAAFEGQVGQAAY+ASKGG+  + L  ARDLA  GI
Sbjct: 122 AEHIAATDPVDDDGQRGLVVNTASVAAFEGQVGQAAYAASKGGVHSLGLTAARDLASAGI 181

Query: 192 RVMTIAPGLFGTPLLTSLPEKVCNFLASQVPFPSRLGDPAEYAHLVQAIIENPFLNGEVI 251
           RV TIAPG+  TP+L ++ ++    LA+ VPFP RLG P E+A LV A ++N +LNG  +
Sbjct: 182 RVNTIAPGVVETPMLATVSDEFRAGLAAGVPFPRRLGRPGEFAQLVAAFLDNDYLNGTTV 241

Query: 252 RLDGAIRMQP 261
           R+DGA+RM P
Sbjct: 242 RMDGALRMAP 251


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: 204
Number of extensions: 9
Number of successful extensions: 5
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: 252
Length adjustment: 24
Effective length of query: 237
Effective length of database: 228
Effective search space:    54036
Effective search space used:    54036
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