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_011782207.1 MVAN_RS25460 3-hydroxyacyl-CoA dehydrogenase
Query= BRENDA::A4YDS4 (651 letters) >NCBI__GCF_000015305.1:WP_011782207.1 Length = 719 Score = 166 bits (420), Expect = 3e-45 Identities = 130/405 (32%), Positives = 204/405 (50%), Gaps = 42/405 (10%) Query: 2 KVTVIGSGVMGHGIAELAAIAGNEVWMNDISTEILQQAMERIKWSLSKLRESG-SLKEGV 60 K+ V+G+G+MG GIA ++A AG +V + D++ E Q+ + +K E G + KE Sbjct: 322 KIGVLGAGMMGAGIAYVSAKAGYDVVLKDVTLEAAQKGKAYSEKIEAKALERGRTTKEKS 381 Query: 61 EQVLARIHPETDQAQALKGSDFVIEAVKEDLELKRTIFRNAEAHASPSAVLATNTSSLPI 120 + +LARI P D A LKG DFVIEAV E+ ELK +F+ E P+A+L +NTS+LPI Sbjct: 382 DALLARITPTADAAD-LKGVDFVIEAVFENQELKHKVFQEIEDIVEPNALLGSNTSTLPI 440 Query: 121 SEIASVLKSPQRVVGMHFFNPPVLMPLVEIVRGKDTSDEVVKTTAEMAKSMNKETIVVKD 180 + +A+ +K + +G+HFF+P MPLVEI++G+ TSDE + + ++ K IVV D Sbjct: 441 TGLATGVKRQEDFIGIHFFSPVDKMPLVEIIKGEKTSDEALARVFDYTLAIGKTPIVVND 500 Query: 181 VPGFFVNRVLLRIMEAGCYLVEKGI--ASIQEVDSSAIEELGFPMGVFLLADYTGLD--- 235 GFF +RV+ + ++ +G+ ASI++ S A G+P L+D L+ Sbjct: 501 SRGFFTSRVIGTFVNEALAMLGEGVPAASIEQAGSQA----GYPAAPLQLSDELNLELMQ 556 Query: 236 -IGYSVWKAVTARG--FKAFPCS-STEKLVSQGKLGVKSGSGYYQYP------------- 278 I KA A G ++ P K++ G+ G+G+Y Y Sbjct: 557 KIANETRKATEAAGGTYEPHPAELVVNKMIEIGRPSRLKGAGFYSYIDGKRVGLWEGLAE 616 Query: 279 --SPGKFVRPTLPSTSKKLGRYLISPAVNEVSYLLREGIV-GKDDAEKGCVLGLGLP--- 332 G P + R L + A+ E L EG++ DA G ++G+G P Sbjct: 617 TFGAGSGHGPATMPLQDMIDRMLFAEAL-ETQKCLDEGVLTSTADANIGSIMGIGYPPYT 675 Query: 333 ----KGILSYADEIGI--DVVVNTLEEMRQTSGMDHYSPDPLLLS 371 + I+ Y E+G+ D V +E+ G + ++P L S Sbjct: 676 GGSAQFIVGYQGELGVGKDAFVARAKELAAKYG-ERFNPPASLTS 719 Score = 91.7 bits (226), Expect = 1e-22 Identities = 61/178 (34%), Positives = 97/178 (54%), Gaps = 15/178 (8%) Query: 410 IVLNRPT-RYNAINGDMIREINQALDSL-EEREDVRVIAITGQGRVFSAGADVTEFGSLT 467 + L+ PT N +N ++ A++ L E+E + + I + F AG D+ ++ Sbjct: 18 LTLDDPTGSANVMNEHYKESMHNAVEKLVAEKESITGVVIASAKKTFFAGGDLKGMMNVG 77 Query: 468 PVKAMIASRKFHEV------FMKIQFLTKPVIAVINGLALGGGMELALSADFRVASKT-- 519 P A + F EV K++ L KPV+A ING ALGGG+E+AL+ R+A+ T Sbjct: 78 PDNA---AESFAEVEFIKADLRKLETLGKPVVAAINGAALGGGLEIALACHHRIAADTKG 134 Query: 520 AEMGQPEINLGLIPGGGGTQRLSRLSG--RKGLELVLTGRRVKAEEAYRLGIVEFLAE 575 +G PE+ LGL+PGGGG R R+ G + +E++ G R K +A +G+V+ L + Sbjct: 135 VVIGLPEVTLGLLPGGGGVARTVRMFGIQKAFMEILSQGTRFKPGKALEIGLVDRLVQ 192 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: 1048 Number of extensions: 63 Number of successful extensions: 3 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: 719 Length adjustment: 39 Effective length of query: 612 Effective length of database: 680 Effective search space: 416160 Effective search space used: 416160 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