Align oxepin-CoA hydrolase (EC 3.3.2.12) (characterized)
to candidate HSERO_RS20590 HSERO_RS20590 enoyl-CoA hydratase
Query= BRENDA::P77455 (681 letters) >FitnessBrowser__HerbieS:HSERO_RS20590 Length = 686 Score = 771 bits (1990), Expect = 0.0 Identities = 401/679 (59%), Positives = 486/679 (71%), Gaps = 10/679 (1%) Query: 4 LASFLSGTWQSGRGRSRLIHHAISGEALWEVTSEGLDMAAARQFAIEKGAPALRAMTFIE 63 L SF++G W G+ S+ +H A++G A+ E +D A + A + G PAL A+ F + Sbjct: 8 LQSFIAGRWL-GQRPSQALHSAVNGSAVASTHEESIDFGEALEHARKTGLPALMALDFQQ 66 Query: 64 RAAMLKAVAKHLLSEKERFYALSAQTGATRADSWVDIEGGIGTLFTYASLGSRELPDDTL 123 RAA+LKA+AK+L+ KE YA+SA TGATRADSW+DIEGG GTLFTYAS+G+ E P L Sbjct: 67 RAAILKALAKYLMEHKEVLYAVSAHTGATRADSWIDIEGGSGTLFTYASIGANEFPSSNL 126 Query: 124 WPEDELIPLSKEGGFAARHLLTSKSGVAVHINAFNFPCWGMLEKLAPTWLGGMPAIIKPA 183 E + L K+G FA H+L + GVAVHINAFNFP WGMLEK APT+L GMP I+KPA Sbjct: 127 VHEGPAMRLGKQGRFAGTHILVPRGGVAVHINAFNFPVWGMLEKFAPTFLAGMPCIVKPA 186 Query: 184 TATAQLTQAMVKSIVDSGLVPEGAISLICGSAGDLLDHLDSQDVVTFTGSAATGQMLRVQ 243 TAT+ L +A V+ I SGL+PEG++ L+ GS GDLL+ L +QDVVTFTGSA T LR Sbjct: 187 TATSYLAEAAVRLIQQSGLLPEGSLQLVIGSTGDLLERLQAQDVVTFTGSADTAAKLRAH 246 Query: 244 PNIVAKSIPFTMEADSLNCCVLGEDVTPDQPEFALFIREVVREMTTKAGQKCTAIRRIIV 303 PN++A SIPF EADSLNC +LG D+T D EF LF++EV REMTTKAGQKCTAIRR IV Sbjct: 247 PNLIANSIPFNAEADSLNCAILGPDITADDEEFDLFVKEVAREMTTKAGQKCTAIRRAIV 306 Query: 304 PQALVNAVSDALVARLQKVVVGDPAQEGVKMGALVNAEQRADVQEKV-------NILLAA 356 P+ V+AV++ L ARL K+VVGDPA E V+MG L + Q+ DV+E+V +++L A Sbjct: 307 PRRHVDAVAERLAARLSKIVVGDPALETVRMGPLASRAQQRDVEERVALLRHSADLILGA 366 Query: 357 GCEIRLGGQADLSAAGAFFPPTLLYCPQPDETPAVHATEAFGPVATLMPAQNQRHALQLA 416 G GQ GAFF PTLL VH EAFGPV+TLMP + AL LA Sbjct: 367 GSAFAPQGQG--VGEGAFFAPTLLLARDTAAGSPVHEVEAFGPVSTLMPYDDLDEALALA 424 Query: 417 CAGGGSLAGTLVTADPQIARQFIADAARTHGRIQILNEESAKESTGHGSPLPQLVHGGPG 476 G GSL +LVT P +A + I AA HGR+ +L+ E+A ESTGHGSPLPQL HGGPG Sbjct: 425 ARGRGSLVASLVTRTPAVAARAIPVAAAWHGRLLVLDREAAAESTGHGSPLPQLKHGGPG 484 Query: 477 RAGGGEELGGLRAVKHYMQRTAVQGSPTMLAAISKQWVRGAKVEEDRIHPFRKYFEELQP 536 RAGGGEELGG RAVKHY+QRTAVQGSPTMLAA+ + VRGA+V E IHPFR YFE+LQ Sbjct: 485 RAGGGEELGGSRAVKHYLQRTAVQGSPTMLAAVVGEHVRGARVRESGIHPFRHYFEDLQI 544 Query: 537 GDSLLTPRRTMTEADIVNFACLSGDHFYAHMDKIAAAESIFGERVVHGYFVLSAAAGLFV 596 GDSL T RRT+TEADIVNF CLSGDHFY H D+IAA +S FG+R+ HGYFVLSAAAGLFV Sbjct: 545 GDSLTTHRRTVTEADIVNFGCLSGDHFYMHFDEIAARQSPFGKRIAHGYFVLSAAAGLFV 604 Query: 597 DAGVGPVIANYGLESLRFIEPVKPGDTIQVRLTCKRKTLKKQRSAEEKPTGVVEWAVEVF 656 GPV+ANYGL++LRF++PV GDTI RLTCKRK + ++ A + GVV W VEV Sbjct: 605 SPAPGPVLANYGLDTLRFVKPVGIGDTISARLTCKRKIDRNKKDANGQGQGVVAWDVEVS 664 Query: 657 NQHQTPVALYSILTLVARQ 675 NQ VA Y ILTLVA++ Sbjct: 665 NQEGELVASYDILTLVAKK 683 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: 1203 Number of extensions: 42 Number of successful extensions: 2 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: 686 Length adjustment: 39 Effective length of query: 642 Effective length of database: 647 Effective search space: 415374 Effective search space used: 415374 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