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_036260031.1 DL86_RS07960 3-hydroxyacyl-CoA dehydrogenase NAD-binding domain-containing protein
Query= BRENDA::A4YDS4 (651 letters) >NCBI__GCF_000746085.1:WP_036260031.1 Length = 736 Score = 164 bits (414), Expect = 2e-44 Identities = 129/401 (32%), Positives = 197/401 (49%), Gaps = 38/401 (9%) Query: 2 KVTVIGSGVMGHGIAELAAIAGNEVWMNDISTEILQQAM----ERIKWSLSKLRESGSLK 57 +V ++G+G MG GIA + A AG E + D + + I + K R G+ K Sbjct: 329 RVGILGAGFMGAGIAYVTAGAGMEGVLIDRDQASADKGKAFCDQLISSQVLKGRAKGADK 388 Query: 58 EGVEQVLARIHPETDQAQALKGSDFVIEAVKEDLELKRTIFRNAEAHASPSAVLATNTSS 117 E + L RI D L G++ VIEAV ED +K R A A P A+ A+NTS+ Sbjct: 389 EAL---LGRIKTSADYND-LAGAELVIEAVFEDRTVKAEATRKARAAIGPDAIFASNTST 444 Query: 118 LPISEIASVLKSPQRVVGMHFFNPPVLMPLVEIVRGKDTSDEVVKTTAEMAKSMNKETIV 177 LPI +A +P+ +G+HFF+P M LVE++ G T D + T + +++ K IV Sbjct: 445 LPIGSLAEADSAPENFIGVHFFSPVEKMLLVEVILGAKTGDRALATALDYVRAIKKTPIV 504 Query: 178 VKDVPGFFVNRVLLRIMEAGCYLVEKGI--ASIQEVDSSAIEELGFPMGVFLLADYTGLD 235 V D GFF NR + + G ++ +G A I+ + A G P+G L D GLD Sbjct: 505 VNDARGFFANRCVGNYIREGHLMLLEGAPPAMIENIAKMA----GMPVGPLALNDEVGLD 560 Query: 236 IGYSVWKAVTARGFKAFPCSSTEKL-----VSQGKLGVKSGSGYYQYPSPG-KFVRPTLP 289 + + +A A + E+L V G+LG K+G G+Y YPS G K + P L Sbjct: 561 LALKILEATKQDLGGAAIDLNQERLLKGLVVEHGRLGRKNGKGFYDYPSQGAKSLWPGLA 620 Query: 290 S------------TSKKLGRYLISPAVNEVSYLLREGIV-GKDDAEKGCVLGLGLPK--- 333 + ++ R+L+ A+ E + + EG+V +A+ G ++G G Sbjct: 621 ALQPTKCDPDAIDIAEFKHRFLVVQAL-EAARAIEEGVVTDPREADVGSIIGFGFAPFTG 679 Query: 334 GILSYADEIGIDVVVNTLEEMRQTSGMDHYSPDPLLLSMVK 374 G+LSY D +G V + +RQT G + +SP +L+ M K Sbjct: 680 GVLSYIDGMGAANFVVLCDRLRQTYG-ERFSPPQILIDMAK 719 Score = 85.1 bits (209), Expect = 1e-20 Identities = 60/196 (30%), Positives = 95/196 (48%), Gaps = 20/196 (10%) Query: 407 LAWIVLNRPTRYNAINGDMIREINQALDSLEEREDVRVIAITGQGRVFSAGADVTEFGSL 466 L W + R N I +I E+ Q +D + + IT + FS GAD++ G+ Sbjct: 18 LTWDMAGRSM--NVITPQVIDELEQVIDHVGAEAAITGCVITSGKQTFSGGADLSMLGAA 75 Query: 467 TPVKAMI--------ASRKFHE-------VFMKIQFLTKPVIAVINGLALGGGMELALSA 511 A+R F E V+ K++ KP A ING+ LGG ELAL+ Sbjct: 76 AADYQTARQEKGEEEAARLFFESARRLSLVYRKLETCGKPFAAAINGVCLGGAFELALAC 135 Query: 512 DFRVAS--KTAEMGQPEINLGLIPGGGGTQRLSRLSGR-KGLELVLTGRRVKAEEAYRLG 568 +RV + A +G PEI +GL PG GGTQR++RL L+++ G +++ + A + Sbjct: 136 HYRVVADDDKARVGLPEIKVGLFPGAGGTQRVARLMHTGDALQMLFKGEQIRPKAAKTMN 195 Query: 569 IVEFLAEPEELESEVR 584 +V +A E+ + + Sbjct: 196 LVHDVAPLGEIVGKAK 211 Score = 47.4 bits (111), Expect = 2e-09 Identities = 26/69 (37%), Positives = 41/69 (59%), Gaps = 3/69 (4%) Query: 330 GLPKGILSYADEIGIDVVVNTLEEMRQTSG---MDHYSPDPLLLSMVKEGKLGRKSGQGF 386 G+P G L+ DE+G+D+ + LE +Q G +D L +V+ G+LGRK+G+GF Sbjct: 545 GMPVGPLALNDEVGLDLALKILEATKQDLGGAAIDLNQERLLKGLVVEHGRLGRKNGKGF 604 Query: 387 HTYAHEEAK 395 + Y + AK Sbjct: 605 YDYPSQGAK 613 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: 979 Number of extensions: 47 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: 736 Length adjustment: 39 Effective length of query: 612 Effective length of database: 697 Effective search space: 426564 Effective search space used: 426564 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 Apr 09 2024. 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