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 17892 b3846 fused 3-hydroxybutyryl-CoA epimerase/delta(3)-cis-delta(2)-trans-enoyl-CoA isomerase/enoyl-CoA hydratase/3-hydroxyacyl-CoA dehydrogenase (NCBI)
Query= BRENDA::A4YDS4 (651 letters) >FitnessBrowser__Keio:17892 Length = 729 Score = 181 bits (458), Expect = 1e-49 Identities = 125/369 (33%), Positives = 186/369 (50%), Gaps = 31/369 (8%) Query: 2 KVTVIGSGVMGHGIAELAAIAGNEVWMNDISTEILQQAMERIKWSLSKLRESGSLKEGVE 61 + V+G+G+MG GIA +A G V M DI+ + L M L+K E G + +G++ Sbjct: 315 QAAVLGAGIMGGGIAYQSAWKGVPVVMKDINDKSLTLGMTEAAKLLNKQLERGKI-DGLK 373 Query: 62 Q--VLARIHPETDQAQALKGSDFVIEAVKEDLELKRTIFRNAEAHASPSAVLATNTSSLP 119 V++ IHP D A D V+EAV E+ ++K+ + E VLA+NTS++P Sbjct: 374 LAGVISTIHPTLDYA-GFDRVDIVVEAVVENPKVKKAVLAETEQKVRQDTVLASNTSTIP 432 Query: 120 ISEIASVLKSPQRVVGMHFFNPPVLMPLVEIVRGKDTSDEVVKTTAEMAKSMNKETIVVK 179 ISE+A+ L+ P+ GMHFFNP MPLVEI+RG+ +SDE + A M K IVV Sbjct: 433 ISELANALERPENFCGMHFFNPVHRMPLVEIIRGEKSSDETIAKVVAWASKMGKTPIVVN 492 Query: 180 DVPGFFVNRVLLRIMEAGCYLVEKGIASIQEVDSSAIEELGFPMGVFLLADYTGLDIGYS 239 D PGFFVNRVL L+ G A +++D ++ G+PMG L D G+D + Sbjct: 493 DCPGFFVNRVLFPYFAGFSQLLRDG-ADFRKIDKVMEKQFGWPMGPAYLLDVVGIDTAHH 551 Query: 240 VWKAVTARGF----KAFPCSSTEKLVSQGKLGVKSGSGYYQYPSPGK------------- 282 +AV A GF + + + L + G K+G G+++Y K Sbjct: 552 A-QAVMAAGFPQRMQKDYRDAIDALFDANRFGQKNGLGFWRYKEDSKGKPKKEEDAAVED 610 Query: 283 ----FVRPTLPSTSKKLGRYLISPAVNEVSYLLREGIVGKD-DAEKGCVLGLGLPK---G 334 +P + +++ ++ P VNEV L EGI+ +A+ V GLG P G Sbjct: 611 LLAEVSQPKRDFSEEEIIARMMIPMVNEVVRCLEEGIIATPAEADMALVYGLGFPPFHGG 670 Query: 335 ILSYADEIG 343 + D +G Sbjct: 671 AFRWLDTLG 679 Score = 111 bits (278), Expect = 1e-28 Identities = 61/181 (33%), Positives = 105/181 (58%), Gaps = 4/181 (2%) Query: 403 VEPPLAWIVLNRPTRYNAINGDMIREINQALDSLEEREDVRVIAITGQGRVFSAGADVTE 462 +E +A +V + P N ++ + + +A+ LE++ D++ + + F GAD+TE Sbjct: 13 LEDGIAELVFDAPGSVNKLDTATVASLGEAIGVLEQQSDLKGLLLRSNKAAFIVGADITE 72 Query: 463 FGSLTPVKAMIASRKFH---EVFMKIQFLTKPVIAVINGLALGGGMELALSADFRVASKT 519 F SL V S+ H VF +++ L P IA +NG ALGGG E L+ D+R+A+ Sbjct: 73 FLSLFLVPEEQLSQWLHFANSVFNRLEDLPVPTIAAVNGYALGGGCECVLATDYRLATPD 132 Query: 520 AEMGQPEINLGLIPGGGGTQRLSRLSGR-KGLELVLTGRRVKAEEAYRLGIVEFLAEPEE 578 +G PE LG++PG GG+ R+ R+ G LE++ G+ V A++A ++G+V+ + + E+ Sbjct: 133 LRIGLPETKLGIMPGFGGSVRMPRMLGADSALEIIAAGKDVGADQALKIGLVDGVVKAEK 192 Query: 579 L 579 L Sbjct: 193 L 193 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: 1038 Number of extensions: 62 Number of successful extensions: 8 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: 729 Length adjustment: 39 Effective length of query: 612 Effective length of database: 690 Effective search space: 422280 Effective search space used: 422280 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