Align oxepin-CoA hydrolase (EC 3.3.2.12) (characterized)
to candidate SM_b21635 SM_b21635 bifunctional aldehyde dehydrogenase/enoyl-CoA hydratase
Query= BRENDA::P77455 (681 letters) >FitnessBrowser__Smeli:SM_b21635 Length = 688 Score = 709 bits (1829), Expect = 0.0 Identities = 372/680 (54%), Positives = 465/680 (68%), Gaps = 13/680 (1%) Query: 2 QQLASFLSGTWQSGRGRSRLIHHAISGEALWEVTSEGLDMAAARQFAIEKGAPALRAMTF 61 ++L S+++G W G + A +G + V S G+D AAA + EKG PALR M+F Sbjct: 9 RRLESYIAGAWMRGSKDGVTLCDAATGAPVALVDSSGIDFAAALAYGREKGGPALRRMSF 68 Query: 62 IERAAMLKAVAKHLLSEKERFYALSAQTGATRADSWVDIEGGIGTLFTYASLGSRELPDD 121 ERA MLKA+A+ L+ KE FYALS TGATRADSW+DIEGGIGTLF+YAS G RELP+ Sbjct: 69 HERAMMLKALAQALMERKEEFYALSTATGATRADSWIDIEGGIGTLFSYASKGRRELPNS 128 Query: 122 TLWPEDELIPLSKEGGFAARHLLTSKSGVAVHINAFNFPCWGMLEKLAPTWLGGMPAIIK 181 + + ++ LS++G F+A+H+LT G+AVHINAFNFPCWGMLEKLAPT L GMPAI+K Sbjct: 129 HVLLDGDVEALSRDGTFSAQHILTPLQGIAVHINAFNFPCWGMLEKLAPTLLAGMPAIVK 188 Query: 182 PATATAQLTQAMVKSIVDSGLVPEGAISLICGSAGDLLDHLDSQDVVTFTGSAATGQMLR 241 PA+ TA L + +V+ IVD+GL+PEGA+ L+CGS GDLLD + QDVVTFTGSA TG+ L+ Sbjct: 189 PASQTAYLAELVVRRIVDTGLLPEGALQLVCGSPGDLLDRVGDQDVVTFTGSATTGRKLK 248 Query: 242 VQPNIVAKSIPFTMEADSLNCCVLGEDVTPDQPEFALFIREVVREMTTKAGQKCTAIRRI 301 P IV S+ FTMEADSLN VLG D P EF LF+REV REMT+KAGQKCTAIRR+ Sbjct: 249 THPAIVGNSVRFTMEADSLNAAVLGLDAAPGAEEFGLFVREVAREMTSKAGQKCTAIRRV 308 Query: 302 IVPQALVNAVSDALVARLQKVVVGDPAQEGVKMGALVNAEQRADVQEKVNILLAAGCEIR 361 I P+A +A+ AL RL KV +GDPA E V+MG L + +QR +V+ ++ + L EI Sbjct: 309 IAPRAHCDALITALGERLAKVPLGDPADENVRMGPLASRDQREEVRARI-LDLTTDAEIV 367 Query: 362 LGGQA------DLSAAGAFFPPTLLYCPQPDETPAVHATEAFGPVATLMPAQNQRHALQL 415 G A + AGAF P LLYC PD +VH EAFGPV+T+MP A+ L Sbjct: 368 AGDPARPQLVSGDAEAGAFLNPVLLYCDSPDAARSVHDVEAFGPVSTVMPYDTAEEAVDL 427 Query: 416 ACAGGGSLAGTLVTADPQIARQFIADAARTHGRIQILNEESAKESTGHGSPLPQLVHGGP 475 G GSL ++ T DP IAR+ + A HGR+ I N SAK STGHGSPLP LVHGGP Sbjct: 428 VRRGRGSLVTSVFTNDPDIARELVIGMAPFHGRVMIGNRLSAKSSTGHGSPLPGLVHGGP 487 Query: 476 GRAGGGEELGGLRAVKHYMQRTAVQGSPTMLAAISKQWVRGAKVEEDRIHPFRKYFEELQ 535 GRAGGGEELGG+R V+HYMQRTAVQG+P ++AA++ +W+ GA HPFRK EL+ Sbjct: 488 GRAGGGEELGGMRGVRHYMQRTAVQGAPGLVAAVTGRWMEGAPARSGGEHPFRKSLAELR 547 Query: 536 PGDSLLTPRRTMTEADIVNFACLSGDHFYAHMDKIAA-AESIFGERVVHGYFVLSAAAGL 594 GD ++T RT+T DI +FA +GD FYAHMD+ AA A F RV HGY V+S AAGL Sbjct: 548 VGDQIVTETRTVTLEDIEHFAEFTGDTFYAHMDEEAARANPFFDGRVAHGYLVVSLAAGL 607 Query: 595 FVDAGVGPVIANYGLESLRFIEPVKPGDTIQVRLTCKRKTLKKQRSAEEKPTGVVEWAVE 654 FVD GPV+ANYG++ +RF+ PV PGDT+QVRLTCK + + G V W Sbjct: 608 FVDPAPGPVLANYGVDGMRFLTPVYPGDTLQVRLTCKEISPR-----INSDYGEVRWDCR 662 Query: 655 VFNQHQTPVALYSILTLVAR 674 V NQ VA Y +LT+VA+ Sbjct: 663 VTNQTGATVAQYDVLTMVAK 682 Lambda K H 0.319 0.134 0.395 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: 1194 Number of extensions: 56 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: 681 Length of database: 688 Length adjustment: 39 Effective length of query: 642 Effective length of database: 649 Effective search space: 416658 Effective search space used: 416658 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: 54 (25.4 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