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_068172592.1 HTA01S_RS13945 3-hydroxyacyl-CoA dehydrogenase
Query= BRENDA::A4YDS4 (651 letters) >NCBI__GCF_001592305.1:WP_068172592.1 Length = 702 Score = 176 bits (447), Expect = 2e-48 Identities = 128/406 (31%), Positives = 211/406 (51%), Gaps = 40/406 (9%) Query: 3 VTVIGSGVMGHGIAELAAIAGNEVWMNDISTEILQQAMERIKWSLSKLRESGSLKEGVEQ 62 V VIG+G MG GI AG V + ++ + L + + I+ + + G LK + Sbjct: 304 VAVIGAGTMGGGITMNFLNAGIPVKVLEMKQDALDRGVATIRKNYEAQVKKGKLKADKYE 363 Query: 63 VLARIHPETDQAQALKGSDFVIEAVKEDLELKRTIFRNAEAHASPSAVLATNTSSLPISE 122 + T + +D VIEAV E++ +K +F+ + P A+LA+NTS+L +++ Sbjct: 364 QRMSLLSTTLSYDDIGLADLVIEAVFEEIGVKEAVFKELDRVMKPGAILASNTSTLDVNK 423 Query: 123 IASVLKSPQRVVGMHFFNPPVLMPLVEIVRGKDTSDEVVKTTAEMAKSMNKETIVVKDVP 182 IAS + PQ VVG+HFF+P +M L+E+VRG+ T+ +V+ T +AK + K +V Sbjct: 424 IASFTQRPQDVVGLHFFSPANVMKLLEVVRGEKTAKDVMATVMTVAKKIKKTAVVSGVCD 483 Query: 183 GFFVNRVLLRIMEAGCYLVEKGIASIQEVDSSAIEELGFPMGVFLLADYTGLDIGYSVWK 242 GF NR++ + G +L+++G + ++VD A+E+ G MG F + D G DIG+++ K Sbjct: 484 GFIGNRMIEQYGRQGGFLLDEG-CTPEQVD-KAMEKFGMAMGPFRMGDLAGNDIGWAIRK 541 Query: 243 AVTARGFKAFP----CSSTEKLVSQGKLGVKSGSGYYQYPSPGKFVRPTLPSTS------ 292 R ++ P + + L +G+ G K+G+G+Y Y PGK R +P+ Sbjct: 542 ----RRYQEKPDMKYSKTADLLCEKGRFGQKTGAGWYDY-VPGK--RDAIPNAEVVQMIE 594 Query: 293 ---KKLG------------RYLISPAVNEVSYLLREGIVGK-DDAEKGCVLGLGLP---K 333 K LG + L+ VNE +++L EGI K D + + G G P Sbjct: 595 DHRKALGITPRKISDEEIVQRLVFSLVNEAAHILEEGIANKASDIDVVYIFGYGFPVYRG 654 Query: 334 GILSYADEIGIDVVVNTLEEMRQTSGMD--HYSPDPLLLSMVKEGK 377 G L+YA+E+G+ VV ++ + D + P PLL + +EGK Sbjct: 655 GPLNYANEVGLFNVVQAMKRFAKNPLDDAKFWQPAPLLARLAEEGK 700 Score = 114 bits (285), Expect = 1e-29 Identities = 71/201 (35%), Positives = 104/201 (51%), Gaps = 10/201 (4%) Query: 398 TIVVRVEPPLAWIVLNRPTRYNAINGDMIREINQALDSLEEREDVRVIAITGQGRVFSAG 457 T +V +A I LN P N + + I L+ E V+ I +TG G+ FS G Sbjct: 2 TAEYQVHGDVAVITLNNPP-VNGLGLSTRQAITAGLEKAEADPAVKAIVLTGAGKAFSGG 60 Query: 458 ADVTEFGSLTPVKAMIASRKFHEVFMKIQFLTKPVIAVINGLALGGGMELALSADFRVAS 517 AD+ EFGS I V + ++ +KPV+A ++ + +GGG+ELAL A +R+A+ Sbjct: 61 ADIREFGS----PKAIQEPNLLSVILAVENTSKPVVAAVHSVCMGGGLELALGAHYRIAA 116 Query: 518 KTAEMGQPEINLGLIPGGGGTQRLSRLSG-RKGLELVLTGRRVKAEEAYRLG----IVEF 572 + PE+ LGLIPG GGTQRL R+ G L ++++G VK+E +L + Sbjct: 117 PGCNVALPEVKLGLIPGAGGTQRLPRVLGVEAALNMIVSGEPVKSEMLAQLPGQKLFDKL 176 Query: 573 LAEPEELESEVRKLANAIAEK 593 A PE L E A +A K Sbjct: 177 AASPESLAEEALAFAREVAAK 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: 932 Number of extensions: 62 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 651 Length of database: 702 Length adjustment: 39 Effective length of query: 612 Effective length of database: 663 Effective search space: 405756 Effective search space used: 405756 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