Align 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_068167433.1 HTA01S_RS04710 3-hydroxyacyl-CoA dehydrogenase/enoyl-CoA hydratase family protein
Query= BRENDA::Q0KEG0 (807 letters) >NCBI__GCF_001592305.1:WP_068167433.1 Length = 799 Score = 966 bits (2498), Expect = 0.0 Identities = 501/809 (61%), Positives = 600/809 (74%), Gaps = 12/809 (1%) Query: 1 MSNFIVKKVAVLGAGVMGAQIAAHLINARVPVVLFDLPAKEGPKNGIALRAIENLKKLSP 60 M+ F VKKVAVLGAGVMGAQIAAHL+N +VPVVLFDLPAKEG KNGI RA+ENLKKL P Sbjct: 1 MNRFQVKKVAVLGAGVMGAQIAAHLVNVKVPVVLFDLPAKEGHKNGIVTRAVENLKKLKP 60 Query: 61 APLGIKEEAGLIQAANYEDDIALLKECDLVIEAIAERMDWKHDLYKKVAPHLASHAIFAT 120 +PLG+ +A LI ANYE+ + LK+CDL+IEAIAERMDWK DLY K+AP +A HAI A+ Sbjct: 61 SPLGVAADADLIGQANYEEHMEQLKDCDLIIEAIAERMDWKLDLYTKIAPFIAPHAIVAS 120 Query: 121 NTSGLSITALSDGFDADLKSRFCGVHFFNPPRYMHLVELIPTATTQPQILDQLEAFLTTT 180 NTSGLSIT LS+ +K RFCG+HFFNPPRYM LVELI T TT+PQILD LE F+T+ Sbjct: 121 NTSGLSITKLSEVLPEAIKPRFCGIHFFNPPRYMTLVELIATPTTEPQILDDLETFVTSG 180 Query: 181 LGKGVVRAKDTPNFIANRVGIFSILAVFAEAEKFGIPFDVVDDLTGSKLGRAKSATFRTA 240 LGKGVVRAKDTPNF+ANR+GI +LA E E FG+ +DVVDDLTG +LGRA S TFRTA Sbjct: 181 LGKGVVRAKDTPNFVANRIGIAGMLATMKEVENFGLTYDVVDDLTGKRLGRASSGTFRTA 240 Query: 241 DVVGLDTMAHVIKTMQDTLHD--DPFAPVYKTPAVLKGLVDAGALGQKTGAGFYKKEGKA 298 DVVGLDTMAHV+KT+QD L D DPF + TP VLK L++ G LGQK AGF+KK G+ Sbjct: 241 DVVGLDTMAHVVKTLQDNLDDSTDPFYGSFGTPPVLKKLIEMGNLGQKAKAGFFKKVGRD 300 Query: 299 IKVLDAKTGQYVDAGKKADEIVVRMLKKDAAERIKLLRESTNPQAQFLWAVFRDVFHYIA 358 I+ D +G+YV AG+KADE+ RMLK+ AAER+KLLR + PQ QFLWA+ R+ FHY A Sbjct: 301 IQRFDLASGEYVPAGEKADEVYGRMLKRPAAERLKLLRNAEGPQGQFLWAILRNSFHYAA 360 Query: 359 VYLEQIAGSAADIDLAIRWGFGWNSGPFEDWQSAGWKQVAEWVKEDVEAGKALSAAPLPA 418 V+L IA +A D+D A+RWGFG GPFE WQ AGW +VA+ ++ED+ AGKALS APLP Sbjct: 361 VHLATIAETARDVDQAMRWGFGMKQGPFELWQEAGWLEVAKMIQEDIAAGKALSTAPLPE 420 Query: 419 WVFEGPVAENQGVHAAAGSWSPATQSFVARSKLPVYQRQAFRAAIKGTAAADPRKAGRTV 478 WVF+GPVAE GVH A GSW+P+ F R +LPVYQRQ F + G A AG T+ Sbjct: 421 WVFKGPVAEAGGVHTAQGSWNPSKGEFQGRLQLPVYQRQHFPELLLGEAGPKFETAGTTI 480 Query: 479 EENDAVRIWVSEGQDDVLVVSFKSKMNTIGPDVIDGLTRAIDLAEAGYKGLVVWQPTSLQ 538 EENDA+RIW +G DVL+ S K+KM+ I PDV +GL AIDLAE Y+GLVVW Sbjct: 481 EENDAIRIWSLDG--DVLIASIKTKMHAISPDVCEGLMAAIDLAEKEYQGLVVWSGDE-- 536 Query: 539 LGAPGGPFSAGANLEAAMPAFMMGGAKGIEPFVKRFQDGMMRVKYASVPVVSAASGIALG 598 PFSAGA+L+A +PAFM G IE Q M+R++YA+VPVVSA G+ALG Sbjct: 537 ------PFSAGADLQAMLPAFMAVGVSAIEDAEGFMQQTMLRLRYANVPVVSAVRGLALG 590 Query: 599 GGCELMLHSASRVAALETYIGLVEVGVGLVPAGGGLKEAALAAARAAQAAGSTNILQFLT 658 GGCEL ++SA RV +E+YIGLVEVGVGLVP GGL A AA A+ + ++L FLT Sbjct: 591 GGCELAVYSARRVVHMESYIGLVEVGVGLVPGAGGLTYIARRAAENAETSTGKDLLPFLT 650 Query: 659 SRFQSAAMAKVSASALEARQMGYLQPSDKIVFNVHELLYVAQNEVRALASAGYRAPLPTL 718 F +AAMAKV SALE+R++GY+ SD IV + ELL+VA +E ++L + GYRAP L Sbjct: 651 EGFTAAAMAKVGTSALESRKLGYVLHSDVIVPHKDELLFVAISEAKSLFNGGYRAPHKRL 710 Query: 719 VPVAGRSGIATIKASLVNMRDGGFISTHDFLIASRIAEAVCGGDVEAGSLVSEDWLLALE 778 PVAGR G ATI SLVNMRDGGFIS HDF IAS IA V GGDVE G+LV+ED+L+ LE Sbjct: 711 FPVAGRDGKATILGSLVNMRDGGFISQHDFHIASLIANVVTGGDVEPGTLVNEDYLMTLE 770 Query: 779 RKAFVDLLGTGKTQERIMGMLQTGKPVRN 807 R+AF L+ KTQERI+GML TGKPVRN Sbjct: 771 RRAFCSLIVHAKTQERILGMLNTGKPVRN 799 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: 1656 Number of extensions: 64 Number of successful extensions: 4 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: 799 Length adjustment: 41 Effective length of query: 766 Effective length of database: 758 Effective search space: 580628 Effective search space used: 580628 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 Apr 09 2024. 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