Align 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_053936559.1 WG78_RS04405 3-hydroxyacyl-CoA dehydrogenase/enoyl-CoA hydratase family protein
Query= BRENDA::Q0KEG0 (807 letters) >NCBI__GCF_001294205.1:WP_053936559.1 Length = 790 Score = 913 bits (2360), Expect = 0.0 Identities = 472/804 (58%), Positives = 586/804 (72%), Gaps = 22/804 (2%) Query: 6 VKKVAVLGAGVMGAQIAAHLINARVPVVLFDLPAKEGPKNGIALRAIENLKKLSPAPLGI 65 +++VAVLGAGVMGAQIAAHL+NA + VLFDLPAKEG NGI +A++NLKK+ PAP Sbjct: 7 IRRVAVLGAGVMGAQIAAHLVNAGIDTVLFDLPAKEGDANGIVKKAVDNLKKMKPAPFSS 66 Query: 66 KEEAGLIQAANYEDDIALLKECDLVIEAIAERMDWKHDLYKKVAPHLASHAIFATNTSGL 125 A I ANY D+ L +CDL+IEAIAER+DWK DLY K+APH+A HAI ATNTSGL Sbjct: 67 AARADYIAMANYGSDLEKLADCDLIIEAIAERLDWKLDLYAKIAPHVAEHAILATNTSGL 126 Query: 126 SITALSDGFDADLKSRFCGVHFFNPPRYMHLVELIPTATTQPQILDQLEAFLTTTLGKGV 185 SI L+DG L+ RFCG+HFFNPPRYM+LVELIPT T+ LD LE FLTT LGKGV Sbjct: 127 SIGKLADGVPEALRGRFCGIHFFNPPRYMYLVELIPTRYTEGAELDALETFLTTRLGKGV 186 Query: 186 VRAKDTPNFIANRVGIFSILAVFAEAEKFGIPFDVVDDLTGSKLGRAKSATFRTADVVGL 245 VRAKDTPNFIANR+G+FS+LA AE+ GI FDVVDDLTG +LGR KSATFRTADVVGL Sbjct: 187 VRAKDTPNFIANRIGVFSMLATIHHAERLGIRFDVVDDLTGPRLGRPKSATFRTADVVGL 246 Query: 246 DTMAHVIKTMQDTLHDDPFAPVYKTPAVLKGLVDAGALGQKTGAGFYKKEGKAIKVLDAK 305 DT AHV+KTM D L DDP+ Y PA ++ L++ GALGQKT G Y+KEG+ I VLD K Sbjct: 247 DTFAHVVKTMTDNLPDDPWHAFYTVPAWMQALIEKGALGQKTKGGIYRKEGRDIFVLDPK 306 Query: 306 TGQYVDAGKKADEIVVRMLK-KDAAERIKLLRESTNPQAQFLWAVFRDVFHYIAVYLEQI 364 TG+YV +G+K D+ V +LK ++ AE+ K LRES NPQAQFLWA RDV+ YIA +L I Sbjct: 307 TGEYVQSGQKGDDEVKAILKIENPAEKFKALRESQNPQAQFLWACMRDVWQYIAYWLGDI 366 Query: 365 AGSAADIDLAIRWGFGWNSGPFEDWQSAGWKQVAEWVKEDVEAGKALSAAPLPAWVFEGP 424 AG+A D+D AIRWGFGW GPFE WQ+AGWK +AE + ++ AG+ +S+A LPAW Sbjct: 367 AGNARDVDFAIRWGFGWKQGPFEMWQAAGWKAIAEAISGEIAAGQTMSSAALPAW----- 421 Query: 425 VAENQGVHAAAGSWSPATQSFVARSKLPVYQRQAFRAAIKGTAAADPRKAGRTVEENDAV 484 V GVH GS+S A S+ ARS LPVY+RQ + + G A + G T+ END V Sbjct: 422 VNSVDGVHTPQGSYSAADNSYKARSTLPVYERQIYPPTVFGEAEP---QYGETIYENDGV 478 Query: 485 RIWVSEGQDDVLVVSFKSKMNTIGPDVIDGLTRAIDLAEAGYKGLVVWQPTSLQLGAPGG 544 R+W+ G DDV VV+FKSK +++G V++GL ++ +AEA Y GLV+W P + Sbjct: 479 RMWLRAG-DDVPVVTFKSKAHSVGAPVLEGLQASVRIAEARYPGLVIWHPEA-------- 529 Query: 545 PFSAGANLEAAMPAFMMGGAKGIEPFVKRFQDGMMRVKYASVPVVSAASGIALGGGCELM 604 PFS GA+L + PAFM G IE V FQ M +KYA VPVV+AA G A GGGCE + Sbjct: 530 PFSVGADLASMGPAFMTGDFDAIEKMVAEFQKTSMTIKYAQVPVVAAAQGYAFGGGCEFL 589 Query: 605 LHSASRVAALETYIGLVEVGVGLVPAGGGLKEAALAAARAAQAAGSTNILQFLTSRFQSA 664 +HSA VAALE+YIGLVEVGVGL+PAGGG KE AL AAR A+ +IL L + + Sbjct: 590 MHSARVVAALESYIGLVEVGVGLLPAGGGCKEFALRAAREAKGG---DILAVLKDYYMAM 646 Query: 665 AMAKVSASALEARQMGYLQPSDKIVFNVHELLYVAQNEVRALASAGYRAPL-PTLVPVAG 723 AMAKV+ SA E +++GYL+ SD +VFN +E+L+VAQ++VRALA AGY+AP+ P PVAG Sbjct: 647 AMAKVATSAEEGKEIGYLRESDIVVFNANEILHVAQSQVRALADAGYKAPIKPKGFPVAG 706 Query: 724 RSGIATIKASLVNMRDGGFISTHDFLIASRIAEAVCGGDVEAGSLVSEDWLLALERKAFV 783 R+G ATI+ L+NM +GGFIS +D+ I +IAE VCGGDV+AG+LV+E+W+L LER+ F+ Sbjct: 707 RTGAATIRGQLINMLEGGFISKYDYHIGVQIAEVVCGGDVDAGTLVNEEWILTLERQRFM 766 Query: 784 DLLGTGKTQERIMGMLQTGKPVRN 807 LL GKTQERIM ML+ KP+RN Sbjct: 767 GLLKKGKTQERIMYMLENNKPLRN 790 Lambda K H 0.319 0.134 0.391 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: 1596 Number of extensions: 69 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 807 Length of database: 790 Length adjustment: 41 Effective length of query: 766 Effective length of database: 749 Effective search space: 573734 Effective search space used: 573734 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 55 (25.8 bits)
This GapMind analysis is from Sep 24 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