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 3607421 Dshi_0835 3-hydroxyacyl-CoA dehydrogenase NAD-binding (RefSeq)
Query= BRENDA::A4YDS4 (651 letters) >FitnessBrowser__Dino:3607421 Length = 737 Score = 177 bits (448), Expect = 2e-48 Identities = 127/400 (31%), Positives = 203/400 (50%), Gaps = 32/400 (8%) Query: 2 KVTVIGSGVMGHGIAELAAIAGNEVWMNDISTEILQQAMERIKWSLSKLRESGSLKEGV- 60 KV ++G+G+MG GIA ++A AG EV + D + Q++ +R K + + + G ++ V Sbjct: 332 KVGILGAGMMGAGIAYVSANAGIEVVLIDAA----QESADRGKAHAAGILDKGIARKKVT 387 Query: 61 ----EQVLARIHPETDQAQALKGSDFVIEAVKEDLELKRTIFRNAEAHASPSAVLATNTS 116 ++VLARI TD A AL+G D V+EAV ED +K + AEA A+ ATNTS Sbjct: 388 PEKKDEVLARITATTDYA-ALEGCDLVVEAVFEDPGVKAEVTAKAEAVIPGDAIFATNTS 446 Query: 117 SLPISEIASVLKSPQRVVGMHFFNPPVLMPLVEIVRGKDTSDEVVKTTAEMAKSMNKETI 176 +LPISE+A P++ +G+HFF+P M LVEI++G+ T D V + + + K I Sbjct: 447 TLPISELAKASARPEQFIGIHFFSPVDKMLLVEIIKGRQTGDVAVAKALDFVRQIRKTPI 506 Query: 177 VVKDVPGFFVNRVLLRIMEAGCYLVEKGIASIQEVDSSAIEELGFPMGVFLLADYTGLDI 236 VV D F+ NR ++ + G +V +G+ + +A + +G P+G L D T +D+ Sbjct: 507 VVNDARFFYANRCIIPYINEGIRMVAEGVT--PALVENAAKLVGMPLGPLQLVDETSIDL 564 Query: 237 GYSVWKAVTARGFKAFPCSSTEK----LVSQGKLGVKSGSGYYQYPSPGKF--------- 283 G + KA A A+P + ++ + +G+LG KS +G+Y Y GK Sbjct: 565 GVKIAKATKAAMGDAYPDGAVDEVLFWMADEGRLGRKSNAGFYTYDEAGKRGLLWEGLAD 624 Query: 284 ---VRPTLPSTSKKLGRYLISPAVNEVSYLLREGIVGKDDAEKGCVLGLGLPK---GILS 337 P + R L++ + V L ++ + + G +LG G G LS Sbjct: 625 RYPAAKEQPELTAVQHRLLMAQVLEAVRALEDGVLMDIREGDVGAILGWGFAPWSGGPLS 684 Query: 338 YADEIGIDVVVNTLEEMRQTSGMDHYSPDPLLLSMVKEGK 377 + D IG V + + T G +P LL M ++G+ Sbjct: 685 WLDMIGAARAVEICDALTDTHGARFTTP-ALLREMAEKGE 723 Score = 65.1 bits (157), Expect = 1e-14 Identities = 50/180 (27%), Positives = 83/180 (46%), Gaps = 19/180 (10%) Query: 419 NAINGDMIREINQALDSLEEREDVRVIAITGQGRVFSAGADVTEFGSLT------PVKAM 472 N +N +++ +D + V+ I IT F+ G D+ + P + + Sbjct: 29 NVMNQQGFEDLDALVDKALADDTVKGIIITSGKDSFAGGMDLNVIAKMRDDAGDDPARGL 88 Query: 473 IAS-RKFHEVFMKIQFLT---------KPVIAVINGLALGGGMELALSAD--FRVASKTA 520 H + KI+ KPV A + G ALG G+E+ L+ F + A Sbjct: 89 FEGVMAMHGILRKIERAGMDPKTNKGGKPVAAALPGTALGIGLEIPLACHRIFAADNPKA 148 Query: 521 EMGQPEINLGLIPGGGGTQRLSR-LSGRKGLELVLTGRRVKAEEAYRLGIVEFLAEPEEL 579 ++G PEI +G+ PG GGT R+SR L + ++L G+ + ++A GIV+ + EEL Sbjct: 149 KIGLPEIMVGIFPGAGGTMRVSRKLGAMQAAPILLEGKLFEPKKAKMAGIVDEVVPAEEL 208 Score = 46.2 bits (108), Expect = 5e-09 Identities = 34/93 (36%), Positives = 47/93 (50%), Gaps = 6/93 (6%) Query: 300 ISPAVNEVSYLLREGIVGKDDAEKGCVLGLGLPKGILSYADEIGIDVVVNTLEEMRQTSG 359 I P +NE ++ EG+ E L +G+P G L DE ID+ V + + G Sbjct: 520 IIPYINEGIRMVAEGVTPAL-VENAAKL-VGMPLGPLQLVDETSIDLGVKIAKATKAAMG 577 Query: 360 MDHY---SPDPLLLSMVKEGKLGRKSGQGFHTY 389 D Y + D +L M EG+LGRKS GF+TY Sbjct: 578 -DAYPDGAVDEVLFWMADEGRLGRKSNAGFYTY 609 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: 1001 Number of extensions: 47 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: 3 Length of query: 651 Length of database: 737 Length adjustment: 39 Effective length of query: 612 Effective length of database: 698 Effective search space: 427176 Effective search space used: 427176 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