GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galdh in Nocardiopsis gilva YIM 90087

Align L-arabinose 1-dehydrogenase; D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate WP_017618015.1 CDO52_RS17480 3-oxoacyl-[acyl-carrier-protein] reductase

Query= reanno::BFirm:BPHYT_RS16920
         (266 letters)



>NCBI__GCF_002263495.1:WP_017618015.1
          Length = 234

 Score =  113 bits (282), Expect = 4e-30
 Identities = 75/242 (30%), Positives = 117/242 (48%), Gaps = 13/242 (5%)

Query: 23  VDRTVLITGGATGIGASFVEHFAAQGARVAFFDIDASAGEALADELGDSKHKPLFLSCDL 82
           + RT L+TGG+ GIG +     A  G  VA   +   +GE      G        + CD+
Sbjct: 1   MSRTALVTGGSRGIGLAIARELATAGDDVA---VTYRSGEPPEGLFG--------VHCDI 49

Query: 83  TDIDALQKAIADVKAALGPIQVLVNNAANDKRHTIGEVTRESFDAGIAVNIRHQFFAAQA 142
           TD  A+  A   V+   GP++VLV NA   K   +  ++ E F + +  N+   F  A+ 
Sbjct: 50  TDTAAVDAAFKQVEDTYGPVEVLVANAGVTKDQLLALMSEEDFSSVLDTNLTGAFRVAKR 109

Query: 143 VMEDMKAANSGSIINLGSISWMLKNGGYPVYVMSKSAVQGLTRGLARDLGHFNIRVNTLV 202
            +  M     G II + S+  +L +GG   Y  SK+ + G  R LAR+LG  NI VN + 
Sbjct: 110 AVRGMMRKRGGRIILISSVVGLLGSGGQANYAASKAGLVGFGRSLARELGSRNITVNVVA 169

Query: 203 PGWVMTEKQKRLWLDDAGRRSIKEGQCIDAELEPADLARMALFLAADDSRMITAQDIVVD 262
           PG++ T+      L +  +  IK+   +       ++A+   FL+++D+  IT   I VD
Sbjct: 170 PGFIETDMTAE--LPEERQTEIKKNVPLARYGSVEEIAKTVRFLSSEDAAYITGAVIPVD 227

Query: 263 GG 264
           GG
Sbjct: 228 GG 229


Lambda     K      H
   0.320    0.134    0.388 

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: 134
Number of extensions: 5
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: 266
Length of database: 234
Length adjustment: 24
Effective length of query: 242
Effective length of database: 210
Effective search space:    50820
Effective search space used:    50820
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 Sep 24 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