GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hpcD in Methylocapsa aurea KYG

Align 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized)
to candidate WP_036263857.1 DL86_RS15400 enoyl-CoA hydratase/isomerase family protein

Query= BRENDA::A4YI89
         (259 letters)



>NCBI__GCF_000746085.1:WP_036263857.1
          Length = 259

 Score =  125 bits (314), Expect = 9e-34
 Identities = 85/262 (32%), Positives = 132/262 (50%), Gaps = 13/262 (4%)

Query: 4   ETIETKKEGNLFWITLNRPDKLNALNAKLLEELDRAVSQAESDPEIRVIIITGKG-KAFC 62
           E +  K E  +  +  NRP   NAL + + E L    ++ ++DP I+V+I+TG G +AF 
Sbjct: 3   EDLLFKVEAGIAQVVFNRPRTRNALTSGMYEGLAAICAKVDADPAIKVLILTGAGDQAFA 62

Query: 63  AGADITQFNQL-TPAEAWKFSKKGREIMDKIEALSKPTIAMINGYALGGGLELALACDIR 121
           +G DI +F Q  +P +   +  +    +  +E     TIA I G   GGG  +A  CD+R
Sbjct: 63  SGTDIAEFRQFASPDDVLAYEARIEAALSALERCRASTIAAIAGVCTGGGAMIAACCDLR 122

Query: 122 IAAEEAQLGLP-EINLGIYPGYGGTQRLTRVIGKGRALEMMMTGDRIPGKDAEKYGLVNR 180
           I   E +LG+P    LG         RL  +IG  R  ++++T   +  K+A   GL+N 
Sbjct: 123 IGEPETKLGMPIARTLGNCLSMSNYARLAGLIGPARVKDLILTARLVGAKEAIAMGLLNE 182

Query: 181 VV-PLANLEQETRKLAEKIAKKSPISLALIKEVVNRGLDSPLLSGLALESVGWGVV---F 236
            V     L      L  ++A  +P+SL   KE + R      + G A +S    +V   +
Sbjct: 183 AVDQTKELLPRAHDLGRRVAGHAPLSLRATKEALLR------MRGQAPQSAAEDLVLMCY 236

Query: 237 STEDKKEGVSAFLEKREPTFKG 258
            +ED +EGV+AFLEKR P ++G
Sbjct: 237 LSEDFREGVAAFLEKRSPRWRG 258


Lambda     K      H
   0.315    0.135    0.382 

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: 120
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: 259
Length of database: 259
Length adjustment: 24
Effective length of query: 235
Effective length of database: 235
Effective search space:    55225
Effective search space used:    55225
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: 42 (22.0 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Apr 09 2024. 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