Align 3-hydroxybutyryl-CoA dehydrogenase (EC 1.1.1.157); 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); short-chain-enoyl-CoA hydratase (EC 4.2.1.150) (characterized)
to candidate WP_084198499.1 C0029_RS14200 3-hydroxyacyl-CoA dehydrogenase
Query= BRENDA::A4YDS4 (651 letters) >NCBI__GCF_002869505.1:WP_084198499.1 Length = 718 Score = 171 bits (433), Expect = 1e-46 Identities = 124/400 (31%), Positives = 190/400 (47%), Gaps = 30/400 (7%) Query: 2 KVTVIGSGVMGHGIAELAAIAGNEVWMNDISTEILQQAMERIKWSLSKLRESGSLKEGVE 61 K+ ++G+GVMG GIA AA G V + D++ E + + K R ++ E Sbjct: 322 KLGILGAGVMGAGIAFNAAKVGMNVVLKDLTQENADKGKAYAASACEKSRRID--EQQAE 379 Query: 62 QVLARIHPETDQAQALKGSDFVIEAVKEDLELKRTIFRNAEAHASPSAVLATNTSSLPIS 121 ++L RI P D A L D VIEAV E+ ++K + R EA AV A+NTS+LPI+ Sbjct: 380 EILGRIQPTADVAD-LADCDLVIEAVFENRDVKAAVTRETEAVLGEQAVFASNTSALPIT 438 Query: 122 EIASVLKSPQRVVGMHFFNPPVLMPLVEIVRGKDTSDEVVKTTAEMAKSMNKETIVVKDV 181 E+A PQ +GMHFF+P MPLVEI+ G+ TSDE + ++A+ M K+ IVVKD Sbjct: 439 ELAQASVRPQNFIGMHFFSPAERMPLVEIITGEQTSDECLAWAFDLAQKMGKKPIVVKDA 498 Query: 182 PGFFVNRVLLRIMEAGCYLVEKGIASIQEVDSSAIEELGFPMGVFLLADYTGLDIGYSVW 241 PGFF RV+ + + G ++ +G+ + +A G PMG D L+ Y Sbjct: 499 PGFFTTRVIGQTITQGQRMLAEGVNPALIENGAAFN--GSPMGPLETLDTISLETAYHAA 556 Query: 242 KA----VTARGFKAFPCSSTE----KLVSQGKLGVKSGSGYYQYPSPGKFVR--PTLPST 291 ARG + P + +E + ++G G+G+Y Y GK V L + Sbjct: 557 NQQRVDAEARGEQVEPSAESEVIRIMVEEAERVGQAKGAGFYDYDDNGKKVATWAGLKAL 616 Query: 292 SKKLG-----------RYLISPAVNEVSYLLREGIVGKDDAEKGCVLGLGLPK---GILS 337 K G R L S + + + + D G ++G+G P G+ Sbjct: 617 FAKDGYKDVPYQDVKDRLLFSQVLEAIRIMEEGVLTSVGDGNIGSIMGIGFPPHTGGVYQ 676 Query: 338 YADEIGIDVVVNTLEEMRQTSGMDHYSPDPLLLSMVKEGK 377 + G+ + +E+ G + + P LLL M +G+ Sbjct: 677 CVNAYGVQAFADRAKELAAAYG-EAFEPPQLLLDMAADGR 715 Score = 77.8 bits (190), Expect = 2e-18 Identities = 57/172 (33%), Positives = 91/172 (52%), Gaps = 12/172 (6%) Query: 419 NAINGDMIREINQALDSLEERED-VRVIAI-TGQGRVFSAGADVTEFGSLTPVKAMIASR 476 N + + + +ALD LE D ++ + I +G+ F AG D+T + + Sbjct: 26 NVMGEEYAEAMPKALDELEAMGDELKGLYIRSGKPGQFFAGGDITMMLEMDLNPSQEERE 85 Query: 477 KFH-------EVFMKIQFLTKPVIAVINGLALGGGMELALSADFRVA--SKTAEMGQPEI 527 + H E +I+ L PV ING ALGGG E+AL+ +R+A S ++G PE Sbjct: 86 EMHRGLLDAKEPLARIERLGVPVAVGINGPALGGGYEIALACHYRIAMDSPKVKVGLPEA 145 Query: 528 NLGLIPGGGGTQRLSRLSG-RKGLELVLTGRRVKAEEAYRLGIVEFLAEPEE 578 LGL+PG GG R++R+ G ++ L L+ G+++ A +A G++ LA EE Sbjct: 146 MLGLLPGAGGIVRMTRMLGMQEALGLISQGKQLVAAKALEKGLIHELAADEE 197 Lambda K H 0.316 0.134 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: 1040 Number of extensions: 54 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 651 Length of database: 718 Length adjustment: 39 Effective length of query: 612 Effective length of database: 679 Effective search space: 415548 Effective search space used: 415548 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 (21.6 bits) S2: 54 (25.4 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