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) >FitnessBrowser__pseudo3_N2E3:AO353_01155 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:
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