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 BWI76_RS13125 BWI76_RS13125 3-hydroxyacyl-CoA dehydrogenase
Query= BRENDA::A4YDS4 (651 letters) >FitnessBrowser__Koxy:BWI76_RS13125 Length = 473 Score = 182 bits (461), Expect = 4e-50 Identities = 122/364 (33%), Positives = 189/364 (51%), Gaps = 17/364 (4%) Query: 3 VTVIGSGVMGHGIAELAAIAGNEVWMNDISTEILQQAMERIKWSLSKLRESGSLK-EGVE 61 V VIGSG MG GIAE+AA AG+ V + DI+ E + +A++ I+ L+ G L E + Sbjct: 8 VAVIGSGTMGAGIAEVAAAAGHPVLIFDIAPEAVVRAIDGIRQRLASRVSRGKLATEQAD 67 Query: 62 QVLARIHPETDQAQALKGSDFVIEAVKEDLELKRTIFRNAEAHASPSAVLATNTSSLPIS 121 +LAR+ P + + L + +IEA E LE+K+ +F A SPS +L +NTSS+ I+ Sbjct: 68 ALLARLVPAAELSN-LADAQLIIEAASERLEVKKALFEQLAAICSPSTLLVSNTSSISIT 126 Query: 122 EIASVLKSPQRVVGMHFFNPPVLMPLVEIVRGKDTSDEVVKTTAEMAKSMNKETIVVKDV 181 IA+ +K P+RV G+HFFNP +M LVE+V G TS EVV+ + K+ + + Sbjct: 127 AIAAGIKHPERVAGLHFFNPAPVMKLVEVVSGLATSTEVVEQLCQWVSDWGKQPVRCRST 186 Query: 182 PGFFVNRVLLRIMEAGCYLVEKGIASIQEVDSSAIEELGFPMGVFLLADYTGLDIGYSVW 241 PGF VNRV +E+ +A+ + +D++ + GFPMG L D G D+ + Sbjct: 187 PGFIVNRVARPFYAEAWRALEEQVAAPEVIDAALRDGGGFPMGPLALTDLIGQDVNF--- 243 Query: 242 KAVTARGFKAF-------PCSSTEKLVSQGKLGVKSGSGYYQYPSPGKFVRPTLPSTSKK 294 AVT F A P ++L G+LG KSG G Y++P+ + R ++++ Sbjct: 244 -AVTCSVFNACWQDRRYQPSLLQQELALAGRLGKKSGQGVYRWPAEAQPERALAAVSAER 302 Query: 295 LGRYLISPAVNEVSYLLREGIVGKDDAEKGCVLGLGLPKGILSYADEIGIDVVVNTLEEM 354 + + V E+ +L G E L L + ++ Y G VV+ + E Sbjct: 303 AAKRIKRDVVTELDEILLLETTG----ETALALSLQHGRPVVVYDHCAGDTVVLASAETT 358 Query: 355 RQTS 358 Q + Sbjct: 359 SQAA 362 Score = 41.6 bits (96), Expect = 8e-08 Identities = 20/70 (28%), Positives = 38/70 (54%) Query: 300 ISPAVNEVSYLLREGIVGKDDAEKGCVLGLGLPKGILSYADEIGIDVVVNTLEEMRQTSG 359 ++ VNE L++G+ +D + LG+ P+G L++ + +G V+ LE +++ G Sbjct: 392 VAMLVNEALDALQKGVASAEDIDTAMRLGVNYPRGPLAWGESLGWGRVLRLLENLQRHYG 451 Query: 360 MDHYSPDPLL 369 + Y P LL Sbjct: 452 EERYRPCSLL 461 Score = 37.4 bits (85), Expect = 2e-06 Identities = 33/133 (24%), Positives = 51/133 (38%), Gaps = 11/133 (8%) Query: 302 PAVNEVSYLLREGIVGKDDAEKGCVLGLGLPKGILSYADEIGIDVVVNTLEEMRQTSGMD 361 P E L E + + + G G P G L+ D IG DV + D Sbjct: 197 PFYAEAWRALEEQVAAPEVIDAALRDGGGFPMGPLALTDLIGQDVNFAVTCSVFNACWQD 256 Query: 362 H-YSPDPLLLSMVKEGKLGRKSGQGFHTYAHEEAKYSTIVVRVEPPLAWIVLNRPTRYNA 420 Y P L + G+LG+KSGQG + + E +P A ++ Sbjct: 257 RRYQPSLLQQELALAGRLGKKSGQGVYRWPAE----------AQPERALAAVSAERAAKR 306 Query: 421 INGDMIREINQAL 433 I D++ E+++ L Sbjct: 307 IKRDVVTELDEIL 319 Score = 34.3 bits (77), Expect = 1e-05 Identities = 16/77 (20%), Positives = 35/77 (45%) Query: 148 VEIVRGKDTSDEVVKTTAEMAKSMNKETIVVKDVPGFFVNRVLLRIMEAGCYLVEKGIAS 207 V + + TS + K+ + + D PG V R + ++ ++KG+AS Sbjct: 350 VVLASAETTSQAATDKATFYFQQQGKKVLQIADYPGLLVWRTVAMLVNEALDALQKGVAS 409 Query: 208 IQEVDSSAIEELGFPMG 224 +++D++ + +P G Sbjct: 410 AEDIDTAMRLGVNYPRG 426 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: 582 Number of extensions: 26 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 4 Number of HSP's successfully gapped: 4 Length of query: 651 Length of database: 473 Length adjustment: 36 Effective length of query: 615 Effective length of database: 437 Effective search space: 268755 Effective search space used: 268755 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: 53 (25.0 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