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 PP_2136 PP_2136 enoyl-CoA hydratase/3-hydroxyacyl-CoA dehydrogenase
Query= BRENDA::A4YDS4 (651 letters) >FitnessBrowser__Putida:PP_2136 Length = 715 Score = 188 bits (478), Expect = 6e-52 Identities = 134/402 (33%), Positives = 194/402 (48%), Gaps = 32/402 (7%) Query: 2 KVTVIGSGVMGHGIAELAAIAGNEVWMNDISTEILQQAMERIKWSLSKLRESGSLKEG-V 60 + V+G+G+MG GIA +A+ G + M DI E +Q + L E G L + Sbjct: 316 QAAVLGAGIMGGGIAYQSAVKGTPILMKDIREEAIQLGLNEASKLLGNRVEKGRLTPAKM 375 Query: 61 EQVLARIHPETDQAQALKGSDFVIEAVKEDLELKRTIFRNAEAHASPSAVLATNTSSLPI 120 + L I P D V+EAV E+ ++K+ + E A+LA+NTS++ I Sbjct: 376 AEALNAIRPTLSYGD-FANVDIVVEAVVENPKVKQAVLAEVEGQVKDDAILASNTSTISI 434 Query: 121 SEIASVLKSPQRVVGMHFFNPPVLMPLVEIVRGKDTSDEVVKTTAEMAKSMNKETIVVKD 180 + +A LK P+ VGMHFFNP +MPLVE++RG+ +SD V TT AK M K IVV D Sbjct: 435 NLLAKALKRPENFVGMHFFNPVHMMPLVEVIRGEKSSDVAVATTVAYAKKMGKNPIVVND 494 Query: 181 VPGFFVNRVLLRIMEAGCYLVEKGIASIQEVDSSAIEELGFPMGVFLLADYTGLDIGYSV 240 PGF VNRVL LV G+ ++ +D +E+ G+PMG L D G+D G+ Sbjct: 495 CPGFLVNRVLFPYFGGFAKLVSAGVDFVR-ID-KVMEKFGWPMGPAYLMDVVGIDTGHH- 551 Query: 241 WKAVTARGF----KAFPCSSTEKLVSQGKLGVKSGSGYYQYPS-----PGKFVRPTL--- 288 + V A GF K S+ + L +LG K+G G+Y Y + P K T+ Sbjct: 552 GRDVMAEGFPDRMKDERRSAVDALYEANRLGQKNGKGFYAYETDKRGKPKKVFDATVLDV 611 Query: 289 ---------PSTSKKLGRYLISPAVNEVSYLLREGIV-GKDDAEKGCVLGLGLPK---GI 335 T + + +++ P E L +GIV +A+ G V G+G P G Sbjct: 612 LKPIVFEQREVTDEDIINWMMVPLCLETVRCLEDGIVETAAEADMGLVYGIGFPPFRGGA 671 Query: 336 LSYADEIGIDVVVNTLEEMRQTSGMDHYSPDPLLLSMVKEGK 377 L Y D IG+ V ++ + Y P L M K G+ Sbjct: 672 LRYIDSIGVAEFVALADQYADLGPL--YHPTAKLREMAKNGQ 711 Score = 112 bits (280), Expect = 6e-29 Identities = 61/165 (36%), Positives = 96/165 (58%), Gaps = 4/165 (2%) Query: 419 NAINGDMIREINQALDSLEEREDVRVIAITGQGRVFSAGADVTEFGS---LTPVKAMIAS 475 N N + E+ QA+D++ V+ + + VF GAD+TEF L + + + Sbjct: 30 NKFNRLTLNELRQAVDAIRADASVKGVIVRSGKDVFIVGADITEFVDNFKLPEAELVAGN 89 Query: 476 RKFHEVFMKIQFLTKPVIAVINGLALGGGMELALSADFRVASKTAEMGQPEINLGLIPGG 535 + + +F + L P +A ING+ALGGG+E+ L+AD+RV S +A +G PE+ LG+ PG Sbjct: 90 LEANRIFNAFEDLEVPTVAAINGIALGGGLEMCLAADYRVMSTSARIGLPEVKLGIYPGF 149 Query: 536 GGTQRLSRLSGR-KGLELVLTGRRVKAEEAYRLGIVEFLAEPEEL 579 GGT RL RL G +E + G+ +AE+A ++G V+ + PE L Sbjct: 150 GGTVRLPRLIGSDNAIEWIAAGKENRAEDALKVGAVDAVVAPELL 194 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: 1027 Number of extensions: 64 Number of successful extensions: 8 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