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 Pf6N2E2_1850 Enoyl-CoA hydratase [isoleucine degradation] (EC 4.2.1.17) / 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) / 3-hydroxybutyryl-CoA epimerase (EC 5.1.2.3)
Query= BRENDA::A4YDS4 (651 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1850 Length = 715 Score = 194 bits (492), Expect = 2e-53 Identities = 130/398 (32%), Positives = 206/398 (51%), Gaps = 26/398 (6%) Query: 2 KVTVIGSGVMGHGIAELAAIAGNEVWMNDISTEILQQAMERIKWSLSKLRESGSLKEG-V 60 K+ +IG+G+MG+GIA ++A G EV + D+S E ++ ++ LSK G L E Sbjct: 319 KLGIIGAGMMGNGIAHVSAKVGIEVMLLDVSLEAAERGKANVEKLLSKTVSQGRLSEAKK 378 Query: 61 EQVLARIHPETDQAQALKGSDFVIEAVKEDLELKRTIFRNAEAHASPSAVLATNTSSLPI 120 +++LA I P D A L+G DFV+EAV E ++LK + + AEA SAV TNTS+LPI Sbjct: 379 DEILALIKPTVDYAD-LQGVDFVVEAVFESVDLKGKVTQQAEAQLPESAVFGTNTSTLPI 437 Query: 121 SEIASVLKSPQRVVGMHFFNPPVLMPLVEIVRGKDTSDEVVKTTAEMAKSMNKETIVVKD 180 S +A+ K P +G+HFF+P MPLVEI+ G+ TSD + + A+ + K IVV D Sbjct: 438 SLLANASKRPANFIGIHFFSPVERMPLVEIICGEQTSDAALAKAFDFARQIGKTAIVVND 497 Query: 181 VPGFFVNRVLLRIMEAGCYLVEKGIASIQEVDSSAIEELGFPMGVFLLADYTGLDIGYSV 240 GFF +R + GC L+++G+ + +D+ +++G P+G + D L++ V Sbjct: 498 SLGFFTSRTFGSYFDEGCKLLQEGVDPLL-IDNLG-KQIGMPVGPLTVLDEVSLELMRKV 555 Query: 241 WKAVTARGFKAFPCSSTEK-------LVSQGKLGVKSGSGYYQYPSPGK----------F 283 + G A ++ + + G G G+Y YP G+ F Sbjct: 556 NETQKEMGVFATVFDNSHSDAVGNILIKEYNRPGRHYGGGFYDYPEGGEKTIWPGLYELF 615 Query: 284 VRPTLPSTSKKLGRYLISPAVNEVSYLLREGIV-GKDDAEKGCVLGLGLPK---GILSYA 339 VRP + + + L+ V E L+EG++ D G +LG+G P G L + Sbjct: 616 VRPEVVLPVEDIKERLLFRQVIEAVKCLQEGVLRSVADGNVGSILGIGAPTWTGGFLQFV 675 Query: 340 DEIGIDVVVNTLEEMRQTSGMDHYSPDPLLLSMVKEGK 377 + G++ V E+ QT G + ++P LLL +G+ Sbjct: 676 NGYGVERFVQRARELAQTYG-ERFTPPVLLLEKAAKGE 712 Score = 92.8 bits (229), Expect = 5e-23 Identities = 60/172 (34%), Positives = 88/172 (51%), Gaps = 6/172 (3%) Query: 410 IVLNRPTRYNAINGDMIREINQALDSLEEREDVRVIAITGQGRVFSAGADVTEFGSLTPV 469 + ++ P NA+N + ++ LE+ + + I F AG D+ E P Sbjct: 16 VTMDMPGPVNAMNQLYRETMAATVNRLEQENGLTGVVIASAKSTFFAGGDLNELTDFKPG 75 Query: 470 KAMIASRKFHEV---FMKIQFLTKPVIAVINGLALGGGMELALSADFRVA--SKTAEMGQ 524 K +++ L PV+A ING ALGGG E+AL+ ++RV S A +G Sbjct: 76 DEADFQAKIELTKNDLRRLERLPVPVVAAINGAALGGGFEIALACNYRVLLNSPAAVVGL 135 Query: 525 PEINLGLIPGGGGTQRL-SRLSGRKGLELVLTGRRVKAEEAYRLGIVEFLAE 575 PE++LGL+PGGGG RL L + L L+L G+R+K EA LG+V L E Sbjct: 136 PEVSLGLLPGGGGIVRLVHHLGLERALPLLLEGKRMKPAEALALGLVNELIE 187 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: 1003 Number of extensions: 55 Number of successful extensions: 9 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: 715 Length adjustment: 39 Effective length of query: 612 Effective length of database: 676 Effective search space: 413712 Effective search space used: 413712 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