Align 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_036133695.1 N800_RS01000 3-hydroxyacyl-CoA dehydrogenase/enoyl-CoA hydratase family protein
Query= BRENDA::Q0KEG0 (807 letters) >NCBI__GCF_000768355.1:WP_036133695.1 Length = 791 Score = 886 bits (2289), Expect = 0.0 Identities = 465/810 (57%), Positives = 567/810 (70%), Gaps = 22/810 (2%) Query: 1 MSN-FIVKKVAVLGAGVMGAQIAAHLINARVPVVLFDLPAKEGPKNGIALRAIENLKKLS 59 MSN +V++ AVLGAGVMGAQIAAHL NA V VLFDLPAKEG NG+ +AI NL KLS Sbjct: 1 MSNKLLVRRAAVLGAGVMGAQIAAHLTNAGVDTVLFDLPAKEGDPNGVVTKAIANLVKLS 60 Query: 60 PAPLGIKEEAGLIQAANYEDDIALLKECDLVIEAIAERMDWKHDLYKKVAPHLASHAIFA 119 PAPL K A I ANYE + LLK CDL+IEAIAERMDWK DLYKK+AP + +H + A Sbjct: 61 PAPLADKALAERIVPANYETGLELLKGCDLIIEAIAERMDWKQDLYKKIAPFVPAHTVLA 120 Query: 120 TNTSGLSITALSDGFDADLKSRFCGVHFFNPPRYMHLVELIPTATTQPQILDQLEAFLTT 179 +NTSGL I L++ +++ RFCGVHFFNPPRYMHL ELIP TT +L+ LE FLTT Sbjct: 121 SNTSGLGINKLAEVLPEEMRHRFCGVHFFNPPRYMHLAELIPARTTDASVLEGLETFLTT 180 Query: 180 TLGKGVVRAKDTPNFIANRVGIFSILAVFAEAEKFGIPFDVVDDLTGSKLGRAKSATFRT 239 TLGKGVV AKDTPNFI NR+G+FS+LA E+ G+ FD VD LTG +GR KSAT+RT Sbjct: 181 TLGKGVVIAKDTPNFIGNRIGVFSMLAAMHHTEQLGLGFDTVDALTGPAIGRPKSATYRT 240 Query: 240 ADVVGLDTMAHVIKTMQDTLHDDPFAPVYKTPAVLKGLVDAGALGQKTGAGFYKKEGKAI 299 ADVVGLDTMAHVIKTM DTL +DP+ +K P L L++ GALGQKTGAG Y K GK I Sbjct: 241 ADVVGLDTMAHVIKTMADTLPEDPWHAYFKAPKWLLALIEKGALGQKTGAGVYTKRGKDI 300 Query: 300 KVLDAKTGQY-VDAGKKADEIVVRMLKKDAAERIKLLRESTNPQAQFLWAVFRDVFHYIA 358 VLD + Y AG+ E+ + ++D A++ LR S++PQA+FLWA FRD FHY A Sbjct: 301 LVLDLQAQDYRAQAGELDAEVAALLKERDPAKKFAALRASSHPQAKFLWACFRDTFHYSA 360 Query: 359 VYLEQIAGSAADIDLAIRWGFGWNSGPFEDWQSAGWKQVAEWVKEDVEAGKALSAAPLPA 418 +LE IA +A D+D A+RWG+GW+ GPFE WQ+AGWKQVAEW+ ED+ G A+S APLP Sbjct: 361 FHLESIADTARDVDFAMRWGYGWSMGPFESWQAAGWKQVAEWIAEDIVQGNAMSNAPLPN 420 Query: 419 WVFEGPVAENQGVHAAAGSWSPATQSFVARSKLPVYQRQAFRAAIKGTAAADPRKAGRTV 478 WVF+G +GVH AGS+SP + VARS PVYQRQ F + G + G TV Sbjct: 421 WVFDG----REGVHGTAGSYSPGRNTMVARSANPVYQRQRFPDPLLG----EKFSQGVTV 472 Query: 479 EENDAVRIWVSEGQDDVLVVSFKSKMNTIGPDVIDGLTRAIDLAEAGYKGLVVWQPTSLQ 538 END VR+W +G DD+ VVSFK+KM+T+ V+DGL +A+ +AE +KGLV+WQP Sbjct: 473 YENDGVRMWADDG-DDIAVVSFKTKMHTVSDAVLDGLQQAVAIAEQKFKGLVIWQPKE-- 529 Query: 539 LGAPGGPFSAGANLEAAMPAFMMGGAKGIEPFVKRFQDGMMRVKYASVPVVSAASGIALG 598 PFSAGA+L A+ A G E V FQ R+KYA VPVV+A G+ALG Sbjct: 530 ------PFSAGADLAGALGALQAGKIAEFEAMVANFQATSQRIKYAQVPVVAAVRGMALG 583 Query: 599 GGCELMLHSASRVAALETYIGLVEVGVGLVPAGGGLKEAALAAARAAQAAGSTNILQFLT 658 GGCE +HSA V ALE+YIGLVE GVGL+PAGGGLKE A+ A+ A G ++ L Sbjct: 584 GGCEFQMHSARTVLALESYIGLVEAGVGLLPAGGGLKEFAVRASEKAGPNG--DVFAELK 641 Query: 659 SRFQSAAMAKVSASALEARQMGYLQPSDKIVFNVHELLYVAQNEVRALASAGYRAPLPT- 717 + F+S AM KVSASA EAR + + SD +VFN HELLYVA+ + RALA +GYR PLP Sbjct: 642 TAFESVAMGKVSASAFEARNLKLARDSDVVVFNAHELLYVAKQQARALAESGYRPPLPAR 701 Query: 718 LVPVAGRSGIATIKASLVNMRDGGFISTHDFLIASRIAEAVCGGDVEAGSLVSEDWLLAL 777 + VAG GIAT K LVNM +G FIS HD+ IA+RIA VCGG+V+ G++V E+WLL L Sbjct: 702 AIRVAGDVGIATFKMLLVNMLEGRFISPHDYEIATRIATVVCGGEVDRGAVVDEEWLLKL 761 Query: 778 ERKAFVDLLGTGKTQERIMGMLQTGKPVRN 807 ER+ FV L KTQERI ML+TGKP+RN Sbjct: 762 EREHFVALAQMPKTQERIAHMLKTGKPLRN 791 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: 1554 Number of extensions: 51 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: 791 Length adjustment: 41 Effective length of query: 766 Effective length of database: 750 Effective search space: 574500 Effective search space used: 574500 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