Align Enoyl-CoA hydratase; EC 4.2.1.17 (characterized, see rationale)
to candidate WP_068169371.1 HTA01S_RS08655 enoyl-CoA hydratase
Query= uniprot:A0A2Z5MCI7 (262 letters) >NCBI__GCF_001592305.1:WP_068169371.1 Length = 259 Score = 263 bits (673), Expect = 2e-75 Identities = 134/246 (54%), Positives = 178/246 (72%) Query: 16 TLVLTLSNPGARNALHPDMYAAGIEALDSVERDPSIRAVVITGADNFFCAGGNLNRLLEN 75 T+VLT+SNP RNAL PD+YAAG+EAL+ E +P +R+VVITG N FCAGGNL RL++N Sbjct: 13 TMVLTISNPEHRNALGPDLYAAGVEALNVAENNPEVRSVVITGEGNHFCAGGNLQRLMDN 72 Query: 76 RAKDPSVQAQSIDLLAEWISALRLSSKPVIAAVDGAAAGAGFSLALACDLIVAADDAKFV 135 R + P VQ QS++ L WI +R SKPV+AAV+G+ AGAGFSLALACDL+VAA ++ FV Sbjct: 73 RQQPPEVQTQSVEGLHNWIETIRAFSKPVVAAVEGSCAGAGFSLALACDLVVAAHNSVFV 132 Query: 136 MSYARVGLTPDGGGSWFLAQALPRQLATEVLIEGKPIGAARLHELGVVNKLTKPGTARDA 195 M+Y+ VGL+PDGG +W L +ALPR A ++L+ G+ I A RL +LGV+N+++ G + + Sbjct: 133 MAYSNVGLSPDGGATWSLMRALPRATALQLLMGGERISAERLQQLGVINQVSALGESLND 192 Query: 196 AVAWADELGKISPNSVARIKTLVCAAGTQPLSEHLVAERDNFVASLHHREGLEGISAFLE 255 A+A + L +PN++A IK L A T L L AERD+FV +LHH EGI+AFLE Sbjct: 193 ALALCERLNTRAPNALASIKELANEAMTGSLHAQLGAERDHFVRNLHHANAGEGIAAFLE 252 Query: 256 KRAPVY 261 KR Y Sbjct: 253 KRRANY 258 Lambda K H 0.317 0.132 0.377 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: 194 Number of extensions: 3 Number of successful extensions: 1 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: 262 Length of database: 259 Length adjustment: 25 Effective length of query: 237 Effective length of database: 234 Effective search space: 55458 Effective search space used: 55458 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.
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:
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