Align enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_066599254.1 V473_RS00615 hypothetical protein
Query= BRENDA::P07896 (722 letters) >NCBI__GCF_001046645.1:WP_066599254.1 Length = 689 Score = 478 bits (1231), Expect = e-139 Identities = 277/680 (40%), Positives = 399/680 (58%), Gaps = 34/680 (5%) Query: 10 SLAMIRLCNPPVNA--VSPTVIREVRNGLQKAGSDHTVKAIVICGANGNFCAGADIHGFS 67 S+ ++R N PVNA V +++ + + +A +D V AI++ G F AGADI F Sbjct: 10 SVLVVRFDNSPVNALTVGGGLVQAIERRVAQAQTDERVDAIILTGGGTVFSAGADIADFE 69 Query: 68 AFTPGL-ALGSLVDEIQRYQKPVLAAIQGVALGGGLELALGCHYRIANAKARVGLPEVTL 126 + A+ SL+ I+ +KPV+AAI+G+ LGGGLELAL H+R+A++ A+ G PE++L Sbjct: 70 GAPERIDAIRSLMQSIENCRKPVVAAIEGLCLGGGLELALAAHFRVASSTAKFGFPEISL 129 Query: 127 GILPGARGTQLLPRVVGVPVALDLITSGKYLSADEALRLGILDAVVKSDPVEEAIKF-AQ 185 G+LPG GTQ PR+ G A+DL+ SGK +SA +AL +G++D + + D VE A+ A Sbjct: 130 GLLPGGGGTQRSPRLAGAGNAIDLMLSGKSVSAAKALEIGLIDRIAEGDVVEAALAMLAA 189 Query: 186 KIIDKPIEPRRIFNKPVPSLPNMDSVFAEAIAKVRKQYPGVLAPETCVRSIQASVKHPYE 245 ++ RR + PVP ++D+ A + G A CVR+I + + Sbjct: 190 GLVGST---RRSGSLPVPQ--DLDAAIDSAERRTGLTDAG-RAIIACVRAIAQT---DLQ 240 Query: 246 VGIKEEEKLFMYLRASGQAKALQYAFFAEKSANKWSTPSGASWKTASAQPVSSVGVLGLG 305 G+K E + F L S Q++AL++AFF + K P G ++ V V V+G G Sbjct: 241 AGLKLEAEQFGALMTSEQSRALRHAFFGRRIVGK--IPGGVR---VESKGVRHVTVVGGG 295 Query: 306 TMGRGIAISFARVGISVVAVESDPKQLDAAKKIITFTLEKEASRAHQNGQASAKP--KLR 363 MG GIAIS + V VE+ P+ D + I +L ++A +A + + L Sbjct: 296 LMGTGIAISLLNADLGVTVVEAKPEGFDKCRASIEASLRRDADKARITAATADRRIGALN 355 Query: 364 FSSSTKELSTVDLVVEAVFEDMNLKKKVFAELSALCKPGAFLCTNTSALNVDDIASSTDR 423 S E DL +EAVFEDM+ K++VF L + GA L +NTS L++D IA T R Sbjct: 356 MGRSIDEAMPSDLYIEAVFEDMDAKREVFQALDRIAPLGAILASNTSTLDLDAIAQFTSR 415 Query: 424 PQLVIGTHFFSPAHVMRLLEVIPSRYSSPTTIATVMSLSKKIGKIGVVVGNCYGFVGNRM 483 P+ V+G HFFSPA++MRLLEV+ +SP T+A+ M+ +K IGK GVV G C GF+GNR+ Sbjct: 416 PEAVVGLHFFSPANIMRLLEVVRGARTSPETLASAMAFAKSIGKTGVVAGVCDGFIGNRI 475 Query: 484 LAPYYNQGFFLLEEGSKPEDVDGVLEEFGFKMGPFRVSDLAGLDVGWKIRKGQGLTGPSL 543 Y Q +FLLEEG+ P +D LE FG MGP RV DLAG D+GW IRK + + P Sbjct: 476 FEEYLRQAWFLLEEGALPHQIDAALEAFGMAMGPCRVMDLAGQDIGWNIRKRRAVEQPDR 535 Query: 544 PPGTPVRKRGNSRYSPLGDMLCEAGRFGQKTGKGWYQYDKPLGRIHKPDPWLSTFLSQYR 603 P YS + D++CE GRFGQKTG G+Y Y P GR + DP + + + Sbjct: 536 P------------YSKIPDLVCELGRFGQKTGTGFYLY--PDGRTPQRDPLIEALIVSHS 581 Query: 604 EVHHIEQRTISKEEILERCLYSLINEAFRILEEGMAARPEHIDVIYLHGYGWPRHKGGPM 663 ++R I EI+ERC++++INE +++ EG+A RP +D+IYL GYG+P +GGPM Sbjct: 582 RQIDFDRRVIDDSEIVERCIFAMINEGAKLVGEGIAYRPVDVDIIYLDGYGFPASRGGPM 641 Query: 664 FYAASVGLPTVLEKLQKYYR 683 F+A VGLP +LEK+ +Y R Sbjct: 642 FHADQVGLPHLLEKMAQYAR 661 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: 1084 Number of extensions: 43 Number of successful extensions: 7 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: 689 Length adjustment: 39 Effective length of query: 683 Effective length of database: 650 Effective search space: 443950 Effective search space used: 443950 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: 54 (25.4 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