Align oxepin-CoA hydrolase (EC 3.3.2.12) (characterized)
to candidate H281DRAFT_00370 H281DRAFT_00370 3,4-dehydroadipyl-CoA semialdehyde dehydrogenase (EC 1.2.1.77)
Query= BRENDA::P77455 (681 letters) >FitnessBrowser__Burk376:H281DRAFT_00370 Length = 531 Score = 415 bits (1067), Expect = e-120 Identities = 229/524 (43%), Positives = 320/524 (61%), Gaps = 14/524 (2%) Query: 1 MQQLASFLSGTWQSGRGRSRLIHHAISGEALWEVTSEGLDMAAARQFAIEKGAPALRAMT 60 ++ L + ++G W +G G + ++GEAL V+SEGLD++ A +FA ++ P+LRA+T Sbjct: 2 IELLKNHVAGEWVAGTGDGHTLTDPVTGEALVRVSSEGLDLSHAFRFARDEAGPSLRALT 61 Query: 61 FIERAAMLKAVAKHLLSEKERFYALS-AQTGATRADSWVDIEGGIGTLFTYASLGSRELP 119 + ERAA L V K L S+++ +YA++ A +G TR DS VDI+GGI TL YA LG+ L Sbjct: 62 YAERAARLADVVKLLQSKRDDYYAIALANSGTTRNDSAVDIDGGIFTLSYYARLGA-SLG 120 Query: 120 DDTLWPEDELIPLSKEGGFAARHLLTSKSGVAVHINAFNFPCWGMLEKLAPTWLGGMPAI 179 + + LSK+ F+ +H+LT GVA+ INAFNFP WG+ EK AP L G+P I Sbjct: 121 NVHALRDGNASALSKDQSFSVQHVLTPTRGVALFINAFNFPSWGLWEKAAPALLSGLPVI 180 Query: 180 IKPATATAQLTQAMVKSIVDSGLVPEGAISLICGSAGDLLDHLDSQDVVTFTGSAATGQM 239 +KPATATA LTQ M+ +VD+G++P GA+S+ICG + LLD + + DVV+FTGSA T Sbjct: 181 VKPATATAWLTQRMIADVVDAGILPRGALSVICGGSAGLLDQVQAFDVVSFTGSAETAAS 240 Query: 240 LRVQPNIVAKSIPFTMEADSLNCCVLGEDVTPDQPEFALFIREVVREMTTKAGQKCTAIR 299 LR P V + +EADSLN +L D TPD P F LFI+EVVREMT K+GQKCTAIR Sbjct: 241 LRAHPAFVVRGARLNVEADSLNSAILCADATPDTPAFDLFIKEVVREMTVKSGQKCTAIR 300 Query: 300 RIIVPQALVNAVSDALVARLQKVVVGDPAQEGVKMGALVNAEQRADVQEKVNILLAAGCE 359 R VP ++AV DAL +L K+ VG+P + V+MG+LV+ Q +V + L Sbjct: 301 RAFVPDTALDAVVDALKTKLAKITVGNPRNDAVRMGSLVSRAQYENVLAGIAALRQEAVL 360 Query: 360 IRLGGQADL----SAAGAFFPPTLLYCPQPDETPAVHATEAFGPVATLMP--------AQ 407 G A L +A A P L PD +H E FGPVA++ P Sbjct: 361 AYDGSAAPLIDADAAVAACIAPHLFVVNDPDNATLLHDVEVFGPVASVAPYCVANGAGEL 420 Query: 408 NQRHALQLACAGGGSLAGTLVTADPQIARQFIADAARTHGRIQILNEESAKESTGHGSPL 467 + HA+ LA G GSL ++ + D + + A +HGR+ ++ + TGHG+ + Sbjct: 421 REAHAVDLARRGQGSLVASIYSNDDAHLGRLALELADSHGRVHAVSPSVEQSQTGHGNVM 480 Query: 468 PQLVHGGPGRAGGGEELGGLRAVKHYMQRTAVQGSPTMLAAISK 511 P +HGGPGRAGGGEELGGLRA+ Y +R+A+Q S + A+++ Sbjct: 481 PMSLHGGPGRAGGGEELGGLRALGFYHRRSAIQASAAAIDAVAQ 524 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: 794 Number of extensions: 30 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: 681 Length of database: 531 Length adjustment: 37 Effective length of query: 644 Effective length of database: 494 Effective search space: 318136 Effective search space used: 318136 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: 53 (25.0 bits)
Align oxepin-CoA hydrolase (EC 3.3.2.12) (characterized)
to candidate H281DRAFT_02531 H281DRAFT_02531 Acyl dehydratase
Query= BRENDA::P77455 (681 letters) >FitnessBrowser__Burk376:H281DRAFT_02531 Length = 161 Score = 60.8 bits (146), Expect = 4e-14 Identities = 47/132 (35%), Positives = 67/132 (50%), Gaps = 17/132 (12%) Query: 533 ELQPGDSLLTPRRTMTEADIVNFACLSGDHFYAHMDKIAAAESIFGERVVHGYFVLSAAA 592 +++ GD LT T+TE +VNFA +SGD++ H+D +AA E+ F R+ HG LS A Sbjct: 22 DIEAGDYYLTAGVTVTETHVVNFAGVSGDYYDIHVDDVAAQEAGFPGRIAHGLLGLSLAD 81 Query: 593 GLFVDAGVGPVIANYGLESL----RFIEPVKPGDTIQVRLTC--KRKTLKKQRSAEEKPT 646 GL PV+ GL +L F P+ GD I V + KR T + R Sbjct: 82 GLKTRC---PVLLK-GLATLGWNWSFRAPLMIGDRIHVDIEVIGKRPTKRPDR------- 130 Query: 647 GVVEWAVEVFNQ 658 G+ ++V NQ Sbjct: 131 GIATLRLKVLNQ 142 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: 223 Number of extensions: 9 Number of successful extensions: 1 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: 161 Length adjustment: 28 Effective length of query: 653 Effective length of database: 133 Effective search space: 86849 Effective search space used: 86849 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: 48 (23.1 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