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 N515DRAFT_0416 N515DRAFT_0416 3-hydroxyacyl-CoA dehydrogenase / enoyl-CoA hydratase / 3-hydroxybutyryl-CoA epimerase
Query= BRENDA::A4YDS4 (651 letters) >FitnessBrowser__Dyella79:N515DRAFT_0416 Length = 686 Score = 175 bits (444), Expect = 5e-48 Identities = 121/370 (32%), Positives = 184/370 (49%), Gaps = 16/370 (4%) Query: 3 VTVIGSGVMGHGIAELAAIAGNEVWMNDISTEILQQAMERIKWSLSKLRESGSLKEGVEQ 62 V V+G+GVMG IA AA G +V + D + +Q A++R + K ++ E VE+ Sbjct: 311 VHVVGAGVMGGDIAAWAAFKGFQVTLQDREMKFIQPALDRARALYEKKLKT---PEKVEE 367 Query: 63 VLARIHPETDQAQALKGSDFVIEAVKEDLELKRTIFRNAEAHASPSAVLATNTSSLPISE 122 R+ + + + + +D IEA+ E+ E K+ ++ + E +LATNTSS+P+ E Sbjct: 368 TARRLRADVE-GKGVAAADLAIEAIFENAEAKQALYASIEPQFQADEILATNTSSIPLDE 426 Query: 123 IASVLKSPQRVVGMHFFNPPVLMPLVEIVRGKDTSDEVVKTTAEMAKSMNKETIVVKDVP 182 + LK+PQR +G+HFFNP MPLVE+VR EV K K++ K + VK P Sbjct: 427 LRRGLKAPQRFLGLHFFNPVAQMPLVEVVRHDGLDPEVEKRALAFCKAIGKLPVAVKGTP 486 Query: 183 GFFVNRVLLRIMEAGCYLVEKGIASIQEVDSSAIEELGFPMGVFLLADYTGLDIGYSVWK 242 GF VNR+L+ + L +G+ V ++ G PMG LAD GLD+ SV K Sbjct: 487 GFLVNRILMPYLLEAIRLYNEGVPG--PVLDKEAKKFGMPMGPIELADTVGLDVCASVGK 544 Query: 243 AVTARGFKAFPCSSTEKLVSQGKLGVKSGSGYYQYPSPGKFVRPTLP---STSKKLGRYL 299 + P +KL + GK G K G G+Y + GK +P + + L + Sbjct: 545 ELAPFLGLELPPGIEDKLAA-GKRGKKDGQGFYVW-QEGKPQKPEVDPDYAVPADLQERM 602 Query: 300 ISPAVNEVSYLLREGIVGKDD-AEKGCVLGLGLPK---GILSYADEIGIDVVVNTLEEMR 355 + P VNE L +G+V D + G + G G G + Y G V+ LE + Sbjct: 603 LLPMVNEAVACLADGVVDDADLLDAGVIFGTGFAPFRGGPIQYVRSEGAAVIKGKLERLA 662 Query: 356 QTSGMDHYSP 365 Q G + ++P Sbjct: 663 QRHG-ERFTP 671 Score = 94.0 bits (232), Expect = 2e-23 Identities = 59/172 (34%), Positives = 94/172 (54%), Gaps = 4/172 (2%) Query: 419 NAINGDMIREINQALDSLEEREDVRVIAITGQGRVFSAGADVTEFGSLTPVKAMIAS-RK 477 NA++ +++ E+ Q ++ L + V+ + + F+ GAD+ EF ++ + Sbjct: 32 NALSREVLDELGQIVERLSIEKPAGVLIHSAKPGGFAVGADIKEFVEYARDGTVLQNIEN 91 Query: 478 FHEVFMKIQFLTKPVIAVINGLALGGGMELALSADFRVAS--KTAEMGQPEINLGLIPGG 535 VF + L P +A I+G +GGG EL L+ R+A+ + +G PE+ LG+ PG Sbjct: 92 GQRVFESLARLPCPTVAAIHGACMGGGTELVLACRQRIAADDEKTRIGLPEVMLGIHPGW 151 Query: 536 GGTQRLSRLSGR-KGLELVLTGRRVKAEEAYRLGIVEFLAEPEELESEVRKL 586 GGT RL RL G L ++LTG+ + A A LG+V+ LA P EL +E R L Sbjct: 152 GGTARLPRLIGALDALPVMLTGKALSARRAAALGVVDRLAPPNELLAEARAL 203 Score = 41.2 bits (95), Expect = 2e-07 Identities = 27/94 (28%), Positives = 47/94 (50%), Gaps = 11/94 (11%) Query: 299 LISPAVNEVSYLLREGIVGK---DDAEKGCVLGLGLPKGILSYADEIGIDVVVNTLEEMR 355 ++ P + E L EG+ G +A+K G+P G + AD +G+DV + +E+ Sbjct: 493 ILMPYLLEAIRLYNEGVPGPVLDKEAKK-----FGMPMGPIELADTVGLDVCASVGKELA 547 Query: 356 QTSGMDHYSPDPLLLSMVKEGKLGRKSGQGFHTY 389 G++ P + + GK G+K GQGF+ + Sbjct: 548 PFLGLEL---PPGIEDKLAAGKRGKKDGQGFYVW 578 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: 962 Number of extensions: 57 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: 3 Length of query: 651 Length of database: 686 Length adjustment: 38 Effective length of query: 613 Effective length of database: 648 Effective search space: 397224 Effective search space used: 397224 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