Align enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_011385366.1 AMB_RS15050 multifunctional fatty acid oxidation complex subunit alpha
Query= BRENDA::P07896 (722 letters) >NCBI__GCF_000009985.1:WP_011385366.1 Length = 703 Score = 441 bits (1133), Expect = e-128 Identities = 262/707 (37%), Positives = 394/707 (55%), Gaps = 27/707 (3%) Query: 5 LRLPHSLAMIRLCNPPVNAVSPTVIREVRNGLQKAGSDHTVK----AIVICGANGNFCAG 60 L + +A + + +PPVNA VR GLQK +D + A+++ A F AG Sbjct: 7 LSVSDRIATVTIDSPPVNAAD----HPVRAGLQKVFTDLAARSDYDAVLVLCAGRTFMAG 62 Query: 61 ADIHGFSAFTPGLALGSLVDEIQRYQKPVLAAIQGVALGGGLELALGCHYRIANAKARVG 120 ADI F L + ++ KPV+AA+ G ALG G ELA+ CHYRIA+ AR+G Sbjct: 63 ADIGEFDTGIKAPHHQDLFNLVENCAKPVVAALHGTALGAGTELAMACHYRIADKGARIG 122 Query: 121 LPEVTLGILPGARGTQLLPRVVGVPVALDLITSGKYLSADEALRLGILDAVVKSDPVEEA 180 LPE++LGI+PGA GTQ PR++G+ A+DL+ SGK L A +A LG++D + D A Sbjct: 123 LPELSLGIIPGAGGTQRAPRLIGLDAAMDLVLSGKPLPAPKAAELGLVDEIASGDLNAAA 182 Query: 181 IKFAQKIIDKPIEPRRIFNKPVPSLPNMDSVFAEAIAKVRKQYPGVLAPETCVRSIQASV 240 + FA+K++ + RR + + A A+V K +P + ++ A+ Sbjct: 183 LAFAKKLVAEGKGVRRTCDMAPKDAAKDAEIIAARQAQVAKTMKNRTSPLKALEAMAATT 242 Query: 241 KHPYEVGIKEEEKLFMYLRASGQAKALQYAFFAEKSANKWSTPSGASWKTASAQPVSSVG 300 + G++ E + L + +A+A+++ FFA++ K + K A+P+ VG Sbjct: 243 TLSFAEGLRLEADISKQLEHAVEARAMRHLFFADREVRKIPGIT----KDIKARPIRKVG 298 Query: 301 VLGLGTMGRGIAISFARVGISVVAVESDPKQLDAAKKIITFTLEKEASRAH--QNGQASA 358 ++G GTMG GIA+ FA +GI V ++ + L +I E+ SR Q S Sbjct: 299 IIGAGTMGGGIAMCFANIGIPVTIIDVSDENLQRGLGVIRKNYERSVSRGSLTQEQLESR 358 Query: 359 KPKLRFSSSTKELSTVDLVVEAVFEDMNLKKKVFAELSALCKPGAFLCTNTSALNVDDIA 418 L S+ L DL +EAVFE M LKK +FA+L A+ GA L TNTS L++D+IA Sbjct: 359 MGLLSASTDYAALKDADLAIEAVFEKMELKKDIFAKLDAVLPAGAILGTNTSTLDIDEIA 418 Query: 419 SSTDRPQLVIGTHFFSPAHVMRLLEVIPSRYSSPTTIATVMSLSKKIGKIGVVVGNCYGF 478 ++T RP VIG HFFSPA+VM LLE++ + ++ + T + ++K I K GVV CYGF Sbjct: 419 NTTKRPADVIGLHFFSPANVMPLLEIVQGKQTAMDVLLTALDMAKLIKKTGVVSKVCYGF 478 Query: 479 VGNRMLAPYYNQGFFLLEEGSKPEDVDGVLEEFGFKMGPFRVSDLAGLDVGWKIRKGQGL 538 +GNRM+ PY + ++ EG+ P ++DG LE +G MG V D+AG++VG R + Sbjct: 479 IGNRMMDPYGREAERMVLEGATPAEIDGALEGWGMAMGILAVYDMAGVEVGDNTR----I 534 Query: 539 TGPSLPPGTPVRKRGNSRYSPLGDMLCEAGRFGQKTGKGWYQYDKPLGRIHKPDPWLSTF 598 P + P P R ++ +L GQK G+G+Y+YD P R DP + Sbjct: 535 ANPHMVPDDPSFYRCST-------LLVANKWLGQKVGRGYYRYDSP-DRKRASDPEVIEM 586 Query: 599 LSQYREVHHIEQRTISKEEILERCLYSLINEAFRILEEGMAARPEHIDVIYLHGYGWPRH 658 + + ++ R K+EILERCLYS+INE ++LEEG+A R IDV+Y GYG+PR+ Sbjct: 587 MHAEGKRLNVPARKPGKDEILERCLYSMINEGAKLLEEGIALRASDIDVVYTAGYGFPRY 646 Query: 659 KGGPMFYAASVGLPTVLEKLQKYYRQNPDIPQLEPSDYLRRLVAQGS 705 +GGPMFYA ++GL + +K+ + +++ D P+ L +L GS Sbjct: 647 RGGPMFYADTIGLKVIYDKIVE-FQKTLDPRYWTPAPLLEKLAKAGS 692 Lambda K H 0.319 0.136 0.405 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: 1195 Number of extensions: 69 Number of successful extensions: 5 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: 722 Length of database: 703 Length adjustment: 39 Effective length of query: 683 Effective length of database: 664 Effective search space: 453512 Effective search space used: 453512 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 (21.7 bits) S2: 55 (25.8 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