Align cyclohexa-1,5-dienecarbonyl-CoA hydratase (EC 4.2.1.100) (characterized)
to candidate Ga0059261_0837 Ga0059261_0837 3-hydroxyacyl-CoA dehydrogenase
Query= BRENDA::O87873 (258 letters) >FitnessBrowser__Korea:Ga0059261_0837 Length = 676 Score = 85.5 bits (210), Expect = 3e-21 Identities = 66/217 (30%), Positives = 97/217 (44%), Gaps = 17/217 (7%) Query: 13 ERDGSLLRLRLARPKANIVDAAMIAAMRQALGEHLQAPALRAVLLDAEGPHFSFGASVDE 72 ER G +L + P N + AA+ + A+ E +L+A ++ +G F GA + E Sbjct: 8 ERQGDILVITSNNPPVNALGAAVRQGLDAAIKELAGDDSLKAAVIRCDGRTFFAGADITE 67 Query: 73 HMPDQCAQMLKSLHGLVREMLDSPVPILVALRGQCLGGGLEVAAAGNLLFAAPDAKFGQP 132 L L L+ S P++ A+ G LGGG EVA A + A P AKFG P Sbjct: 68 FGKPMQEPSLPVLVDLIEA---SEKPVVAAVHGTALGGGCEVALACHYRIAVPSAKFGLP 124 Query: 133 EIRLGVFAPAASCLLPPRVGQA-CAEDLLWSGRSIDGAEGHRIGLIDVLAEDPEAAALRW 191 E++LG+ A PRVG A +L G + + GL+D LA + Sbjct: 125 EVKLGILPGAGGTQRLPRVGGVEFALELATKGDPVSASAAKDAGLVDRLAGEDS------ 178 Query: 192 FDEHIARLSASSLRFAVRAARCDSVPRIKQKLDTVEA 228 L+A ++ +A A +PR +K TVEA Sbjct: 179 -------LTADAIAYANEIAAARPLPRTSEKPVTVEA 208 Lambda K H 0.321 0.135 0.402 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: 352 Number of extensions: 13 Number of successful extensions: 2 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: 258 Length of database: 676 Length adjustment: 31 Effective length of query: 227 Effective length of database: 645 Effective search space: 146415 Effective search space used: 146415 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 (21.9 bits) S2: 50 (23.9 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