Align Enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_086510728.1 BZY95_RS15080 fatty acid oxidation complex subunit alpha FadB
Query= reanno::Marino:GFF1550 (715 letters) >NCBI__GCF_002151265.1:WP_086510728.1 Length = 725 Score = 970 bits (2507), Expect = 0.0 Identities = 490/719 (68%), Positives = 586/719 (81%), Gaps = 5/719 (0%) Query: 1 MIYEGKAITVKE--IEGG--IAQLNFDLQGESVNKFNRLTIEELRAATDALKAQKNLKGL 56 MIY+G AITV GG +A L FDL+ ES+NK + I EL A A++A+ LKGL Sbjct: 1 MIYQGNAITVARGTKNGGDDVAMLTFDLKDESINKLSSAVIAELDEAVQAIRAESGLKGL 60 Query: 57 VVTSSKDSFIVGADITEFTELFAGSEEDLVANNLKANEVFNAVEDLPFPTVTAINGMALG 116 V+ S+K+SFIVGADITEF +F E L + +K +++FNA+EDLPFPTVTAING+ALG Sbjct: 61 VIGSAKESFIVGADITEFQTMFGKGAEFLESMLMKVHDIFNAIEDLPFPTVTAINGLALG 120 Query: 117 GGFEMCLATDYRVMDKKAKVGLPEVKLGIFPGFGGTVRLSRLVGVDNAVEWISGGTENRA 176 GG E+ L TD+RVM KAK+GLPE KLGI PG+GG VRL R++G DNAVEWI+GGTENRA Sbjct: 121 GGCEVTLTTDFRVMGDKAKIGLPETKLGILPGWGGCVRLPRMIGSDNAVEWIAGGTENRA 180 Query: 177 DVALKVGAVDAVLDSDKLVDAAVAIINQCNEGKLDHEARREEKKGKIKLNAMESMMAFEI 236 D ALKVGAVDAV+ +D+L AA+ I+ + N G+LD++ARR EK G +KLNA+E MMAFE Sbjct: 181 DAALKVGAVDAVVPNDQLEAAALDILARANAGELDYQARRAEKTGPLKLNAIEQMMAFET 240 Query: 237 SKAFVAGKAGKNYPAPVEAIKVMQKHAGMTRDKAIEVEAKGFAKMAKTNVAACLVGLFLN 296 +K +VAGKAG +YPAP+EAIK +QK AG R +A +EAK FAK+A T+VA LVGLF+N Sbjct: 241 AKGYVAGKAGPHYPAPIEAIKAIQKGAGEERARAQAIEAKAFAKLAMTDVAFNLVGLFMN 300 Query: 297 DQELKKKAKAWEKEANDVNLAAVLGAGIMGGGVAFQSALKGTPIIMKDINQDGIALGLKE 356 DQ +KKKA +EK+A VN AVLGAGIMGGG+A+QSA KGTPI+MKDI ++ + LGLKE Sbjct: 301 DQVVKKKAGKFEKQAKAVNQTAVLGAGIMGGGIAYQSASKGTPILMKDIKEEAVELGLKE 360 Query: 357 AKKLLSKRVEKGKMKPDQMADVLNSITPTLNYGDFKNVDLVVEAVVENPKVKDAVLRETE 416 ++KL +K+VE+GK+ +QMA+ L I PTL+YGDF +VDLVVEAVVENPKVKDAVL E E Sbjct: 361 SRKLFAKQVERGKLTTEQMAEKLTLIRPTLSYGDFGHVDLVVEAVVENPKVKDAVLTEVE 420 Query: 417 DAVREDTILTSNTSTISIDLLAKNLKRPENFCGMHFFNPVHMMPLVEVIRGEKTSDRAIA 476 V EDTILTSNTSTISI LA+NLKRPENFCGMHFFNPVH MPLVEVIRGEKT D A+A Sbjct: 421 GLVSEDTILTSNTSTISITRLAQNLKRPENFCGMHFFNPVHRMPLVEVIRGEKTGDAAVA 480 Query: 477 TTVAYAKAMGKTPIVVNDCPGFLVNRVLFPYFGGFIGLVRDGADFQHVDKVMEKFGWPMG 536 TVAYA+AMGKTPIVVNDCPGFLVNRVLFPYFGGF LV GADFQ VDKVMEKFGWPMG Sbjct: 481 ATVAYARAMGKTPIVVNDCPGFLVNRVLFPYFGGFSLLVEQGADFQRVDKVMEKFGWPMG 540 Query: 537 PAYLLDVVGMDTGKHAGEVMADGFPDRMKHEGTTAIDVMFDNNRYGQKNDKGFYKYELDR 596 PAYLLDVVGMDT HA EVMA+GFP+RM +G TAI VM++N R GQKNDKGFY YE D+ Sbjct: 541 PAYLLDVVGMDTAVHANEVMAEGFPERMARDGKTAIQVMYENERLGQKNDKGFYAYEEDK 600 Query: 597 KGKQKKVVDEETYKLLEPVVQGKNEFSEEDIIARMMIPLCLETVRCLEDGIVEDPADADM 656 KGK KKV D++ Y+L++ VV + EFS+E+IIARMM+PLCLETVRCLED IVE PA+ADM Sbjct: 601 KGKPKKVSDDKAYELVKQVVVSEKEFSDEEIIARMMVPLCLETVRCLEDDIVETPAEADM 660 Query: 657 GLIFGIGFPPFRGGALRYIDDMGVDKFVELADKFA-DLGPLYHPTEKLREMAKTGKKFF 714 LI+GIGFPPFRGGALRYID MGV +FV+LAD A +LGPLY PT+KLR+MA++G++F+ Sbjct: 661 ALIYGIGFPPFRGGALRYIDAMGVAEFVKLADGLAEELGPLYAPTDKLRKMAESGERFY 719 Lambda K H 0.318 0.137 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: 1408 Number of extensions: 61 Number of successful extensions: 3 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: 715 Length of database: 725 Length adjustment: 40 Effective length of query: 675 Effective length of database: 685 Effective search space: 462375 Effective search space used: 462375 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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 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