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 AO353_01155 AO353_01155 3-hydroxyacyl-CoA dehydrogenase
Query= BRENDA::A4YDS4 (651 letters) >lcl|FitnessBrowser__pseudo3_N2E3:AO353_01155 AO353_01155 3-hydroxyacyl-CoA dehydrogenase Length = 714 Score = 155 bits (393), Expect = 5e-42 Identities = 122/400 (30%), Positives = 195/400 (48%), Gaps = 27/400 (6%) Query: 2 KVTVIGSGVMGHGIAELAAIAGNEVWMNDISTEILQQAMERIKWSLSKLRESGSLKEGV- 60 K+ V+G+G+MG GIA ++A+AG +V + DI+ ++ L K G L Sbjct: 318 KLGVLGAGMMGAGIAYVSAVAGIDVVLKDINLAAAEKGKAHSAALLDKKVARGQLSAAQR 377 Query: 61 EQVLARIHPETDQAQALKGSDFVIEAVKEDLELKRTIFRNAEAHASPSAVLATNTSSLPI 120 + LARI ++Q L G D +IEAV ED ELK + A+ AV+A+NTS+LPI Sbjct: 378 DATLARIKT-SEQGADLAGCDLIIEAVFEDRELKARVSSAAQKVVGADAVIASNTSTLPI 436 Query: 121 SEIASVLKSPQRVVGMHFFNPPVLMPLVEIVRGKDTSDEVVKTTAEMAKSMNKETIVVKD 180 S +A+ + + +G+HFF+P MPLVEI++G +TSDE + + + K IVV D Sbjct: 437 SGLATAVPDQSKFIGLHFFSPVDKMPLVEIIKGVNTSDETLARGFDFVLQIKKTPIVVND 496 Query: 181 VPGFFVNRVLLRIMEAGCYLVEKGIASIQEVDSSAIEELGFPMGVFLLADYTGLD----I 236 GFF +RV G ++ +GI S +++ A + G P+G ++D L I Sbjct: 497 SRGFFTSRVFGTFTNEGIAMLGEGI-SAPMIETEA-RKAGMPIGPLAISDEVSLSLMSHI 554 Query: 237 GYSVWKAVTARG--FKAFPCSSTEKLVSQ--GKLGVKSGSGYYQYPSPG-KFVRPTLPST 291 K + A G A P + L+ + G +G G+Y+YP+ G K + P L + Sbjct: 555 RQQAAKDLQAEGKPLPAHPAFAVIDLLLNECQRPGKAAGGGFYEYPAGGQKHLWPELKTR 614 Query: 292 SKKL----------GRYLISPAVNEVSYLLREGIVGKDDAEKGCVLGLGLPK---GILSY 338 +K R L A+ V + ++ DA G + G+G G L + Sbjct: 615 FEKADGQISPQDVRDRLLFVQAIETVRCVEEGVLLSTADANIGSIFGIGFAAWTGGALQF 674 Query: 339 ADEIGIDVVVNTLEEMRQTSGMDHYSPDPLLLSMVKEGKL 378 ++ G+ V + + + G + ++P LLL +G L Sbjct: 675 INQYGVKDFVARAQYLAEQYG-ERFTPPALLLEKAAKGAL 713 Score = 91.7 bits (226), Expect = 1e-22 Identities = 55/158 (34%), Positives = 94/158 (59%), Gaps = 15/158 (9%) Query: 438 EREDVRVIAITGQGRVFSAGADVTEFGSLTPVKAMIASRKFHEVFM-------KIQFLTK 490 +++ + + IT + F AG D+ E + +A + F+++ + ++ L K Sbjct: 47 DKDSITGVIITSAKKTFFAGGDLNELIKVGKSQA----KAFYDMVLLLKAQLRTLETLGK 102 Query: 491 PVIAVINGLALGGGMELALSADFRVA--SKTAEMGQPEINLGLIPGGGGTQRLSRLSG-R 547 PV+A ING ALGGG E+ L+ RVA + + ++G PE+ LGL+PGGGG R+ RL G Sbjct: 103 PVVAAINGAALGGGWEICLACHHRVALDNPSVQIGLPEVTLGLLPGGGGVVRMVRLLGLE 162 Query: 548 KGLELVLTGRRVKAEEAYRLGIV-EFLAEPEELESEVR 584 K L +L G++V++++A + G+V E A+ +EL ++ R Sbjct: 163 KALPYLLEGKKVRSQQALQAGLVDELAADRDELLAKAR 200 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: 937 Number of extensions: 52 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: 714 Length adjustment: 39 Effective length of query: 612 Effective length of database: 675 Effective search space: 413100 Effective search space used: 413100 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 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.
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