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 5210423 Shew_2864 3-hydroxyacyl-CoA dehydrogenase, NAD-binding (RefSeq)
Query= BRENDA::A4YDS4 (651 letters) >FitnessBrowser__PV4:5210423 Length = 708 Score = 172 bits (436), Expect = 5e-47 Identities = 133/409 (32%), Positives = 202/409 (49%), Gaps = 41/409 (10%) Query: 2 KVTVIGSGVMGHGIAELAAIAGNEVWMNDISTEILQQAMERIKWSLSKLRESGSLKEG-V 60 KV VIGSG MG GIA G + D++ E L++ + I+ + + G L + + Sbjct: 301 KVAVIGSGTMGGGIAMNFINVGIPTQILDLNGEALERGLGVIRKNYEYTLKKGKLSQAQL 360 Query: 61 EQVLARIHPETDQAQALKGSDFVIEAVKEDLELKRTIFRNAEAHASPSAVLATNTSSLPI 120 ++ +A + TD A + D VIEAV E +E+K+ +F+ +A P A+LATNTS+L + Sbjct: 361 DERMALLSGTTDYAD-IADVDLVIEAVFEKMEIKKQVFKTLDATCKPGAILATNTSTLDV 419 Query: 121 SEIASVLKSPQRVVGMHFFNPPVLMPLVEIVRGKDTSDEVVKTTAEMAKSMNKETIVVKD 180 EIA+ PQ V+G+HFF+P +M L+EIVR T+ + + TT ++A+ + K +V Sbjct: 420 DEIAAETSRPQDVLGLHFFSPANVMRLLEIVRANKTAPDALLTTVQLAQRIKKVPVVSGV 479 Query: 181 VPGFFVNRVLLRIMEAGCYLVEKGIASIQEVDSSAIEELGFPMGVFLLADYTGLDIGYSV 240 GF NR + L+ +G AS ++D E G PMG+ + D G+D+G Sbjct: 480 CWGFIGNRATDSYLRESMSLILEG-ASPAQID-KVHTEFGMPMGLPSMVDLAGIDVG--- 534 Query: 241 WKAVTARGFKAFPC-------SSTEKLVSQGKLGVKSGSGYYQYPSPGKFVRPTL----P 289 +T KAF + KL ++ + G K+G G Y Y K P + Sbjct: 535 --ILTREDRKAFTTDLDPSHFAILHKLYAKQRYGQKTGRGLYIYEGRDKQEDPEVLELAA 592 Query: 290 STSKKLG---------------RYLISPAVNEVSYLLREGI-VGKDDAEKGCVLGLGLP- 332 +K+ G I P +NE + +L EGI + D + G G P Sbjct: 593 EAAKEFGVTRRSPEQISDQEILERTIYPIINEGARILEEGIALRASDIDIVLAYGFGFPI 652 Query: 333 --KGILSYADEIGIDVVVNTLEEMRQT--SGMDHYSPDPLLLSMVKEGK 377 G + YADEIG++ V+ L + R T G + P PLL +VKEGK Sbjct: 653 FRGGPMQYADEIGLERVLTALNKYRDTLDKGELWFKPAPLLERLVKEGK 701 Score = 107 bits (268), Expect = 1e-27 Identities = 62/167 (37%), Positives = 96/167 (57%), Gaps = 6/167 (3%) Query: 408 AWIVLNRPTRYNAINGDMIREINQALDSLEEREDVRVIAITGQGRVFSAGADVTEFGSLT 467 A I+LN+P N++ + + L E E V I + G++F GAD++EF S Sbjct: 14 AVIILNQPP-VNSLGLALRTHLLADLKRAEADESVDAIVLASSGKLFCGGADISEFSS-- 70 Query: 468 PVKAMIASRKFHEVFMKIQFLTKPVIAVINGLALGGGMELALSADFRVASKTAEMGQPEI 527 +A +V ++ K V+A +NGLALGGG EL L+ D+R+A A++G PE+ Sbjct: 71 --DDALAEPNLPQVCDALEASPKLVVAAVNGLALGGGCELTLACDYRIALPAAKLGLPEV 128 Query: 528 NLGLIPGGGGTQRLSRLSG-RKGLELVLTGRRVKAEEAYRLGIVEFL 573 NLG++PG GGTQRL R+ G + LE++ +GR + A G+++ L Sbjct: 129 NLGILPGAGGTQRLPRIGGVQLALEMITSGRPLGAAAMLDAGVIDNL 175 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: 928 Number of extensions: 56 Number of successful extensions: 9 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 651 Length of database: 708 Length adjustment: 39 Effective length of query: 612 Effective length of database: 669 Effective search space: 409428 Effective search space used: 409428 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