Align 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) (characterized)
to candidate N515DRAFT_0416 N515DRAFT_0416 3-hydroxyacyl-CoA dehydrogenase / enoyl-CoA hydratase / 3-hydroxybutyryl-CoA epimerase
Query= BRENDA::P34439 (298 letters) >FitnessBrowser__Dyella79:N515DRAFT_0416 Length = 686 Score = 177 bits (448), Expect = 8e-49 Identities = 122/292 (41%), Positives = 160/292 (54%), Gaps = 23/292 (7%) Query: 11 IRNVAIVGSGQMGSGIAQVTASSGFNVMLADVNKK----ALDRAMKAISQSVTHLSKKQK 66 I +V +VG+G MG IA A GF V L D K ALDRA +A+ + KK K Sbjct: 308 IEHVHVVGAGVMGGDIAAWAAFKGFQVTLQDREMKFIQPALDRA-RALYE------KKLK 360 Query: 67 GTDKEKSDFVTLTMSRIKTCNNVSTAVADADLIIEAAIENIDLKRGIFAQIEQSCKKDSI 126 +K V T R++ + VA ADL IEA EN + K+ ++A IE + D I Sbjct: 361 TPEK-----VEETARRLRA-DVEGKGVAAADLAIEAIFENAEAKQALYASIEPQFQADEI 414 Query: 127 LTTNTSSFLLEDVAKGLQDKTRFGGLHFFNPVPVMKLLEVIRSDDTSDETYATLIKFGTA 186 L TNTSS L+++ +GL+ RF GLHFFNPV M L+EV+R D E + F A Sbjct: 415 LATNTSSIPLDELRRGLKAPQRFLGLHFFNPVAQMPLVEVVRHDGLDPEVEKRALAFCKA 474 Query: 187 VGKTTVACKDSPGFIVNRLLIPYFFEAARMYERGDASMTDIDEAMKLGAGHPMGPFELAD 246 +GK VA K +PGF+VNR+L+PY EA R+Y G EA K G PMGP ELAD Sbjct: 475 IGKLPVAVKGTPGFLVNRILMPYLLEAIRLYNEGVPGPVLDKEAKKFGM--PMGPIELAD 532 Query: 247 YIGLDTVKFVMDGWAAKYPEVQLFEASPLVDKLVAEGKLGRKTGDGFYSYKK 298 +GLD V A P + L E P ++ +A GK G+K G GFY +++ Sbjct: 533 TVGLDVCASVGKELA---PFLGL-ELPPGIEDKLAAGKRGKKDGQGFYVWQE 580 Lambda K H 0.318 0.133 0.376 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: 422 Number of extensions: 17 Number of successful extensions: 4 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: 298 Length of database: 686 Length adjustment: 33 Effective length of query: 265 Effective length of database: 653 Effective search space: 173045 Effective search space used: 173045 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: 51 (24.3 bits)
This GapMind analysis is from Sep 17 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