GapMind for catabolism of small carbon sources

 

Alignments for a candidate for LRA1 in Paucidesulfovibrio gracilis DSM 16080

Align NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized)
to candidate WP_078715956.1 B5D49_RS01965 3-oxoacyl-[acyl-carrier-protein] reductase

Query= metacyc::MONOMER-16230
         (256 letters)



>NCBI__GCF_900167125.1:WP_078715956.1
          Length = 247

 Score =  148 bits (373), Expect = 1e-40
 Identities = 96/250 (38%), Positives = 138/250 (55%), Gaps = 6/250 (2%)

Query: 4   IDKTVIVTGASRGIGRAAARECARQGARVVIGHSGSDEGRAGALSLAEEIAAFGGTAIAV 63
           +    +VTG SRGIGRA A   A  G  V + +    E    A ++ + IA  GGTA AV
Sbjct: 4   LPNVALVTGGSRGIGRACAERLAADGFEVWLTYVSKPEA---AETVVQTIADAGGTARAV 60

Query: 64  GADAADLDSGEKLVAAAVEAFGSVDVLVNNAGICPFHSFLDMPRELYLKTVGTNLNGAYF 123
             D++D ++        ++    +  LVNNAGI      + M  E +   +  NL GA+ 
Sbjct: 61  QLDSSDREAVASFFKDEIKGKVHLAALVNNAGITRDGLLIRMKPEDWDSVLDINLTGAFS 120

Query: 124 TVQAAARRMKEQGRGGAIIAVSSISALVGGAMQTHYTPTKAGLLSLMQSCAIALGPYGIR 183
            +Q AA+ M  Q RGG+II +SS+   +G A Q +Y   KAGL+ L ++ A  L   G+R
Sbjct: 121 CLQEAAKIMARQ-RGGSIINISSVVGQMGNAGQANYVAAKAGLIGLTKAAARELAGRGVR 179

Query: 184 CNAVLPGTIATDINKEDLSDLEKRERMTSRVPLGRLGEPDDLAGPIVFLASDMARYVTGA 243
            NAV PG I TD+ K DL + +  E M + +PL RLG P D+A  + FLA + A Y+TG 
Sbjct: 180 VNAVAPGFIETDMTK-DLPE-KTVESMKTMIPLSRLGSPGDIAAAVSFLAGNGAGYITGQ 237

Query: 244 SLLVDGGLFV 253
            L V+GG+++
Sbjct: 238 VLAVNGGMYM 247


Lambda     K      H
   0.319    0.136    0.383 

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: 173
Number of extensions: 7
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: 256
Length of database: 247
Length adjustment: 24
Effective length of query: 232
Effective length of database: 223
Effective search space:    51736
Effective search space used:    51736
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 46 (22.3 bits)

This GapMind analysis is from Apr 09 2024. 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