Align oxepin-CoA hydrolase (EC 3.3.2.12) (characterized)
to candidate GFF3676 PGA1_262p00800 phenylacetic acid degradation protein PaaZ
Query= BRENDA::P77455 (681 letters) >FitnessBrowser__Phaeo:GFF3676 Length = 710 Score = 352 bits (903), Expect = e-101 Identities = 237/684 (34%), Positives = 347/684 (50%), Gaps = 32/684 (4%) Query: 4 LASFLSGTWQSGRGRSRLIHHAISGEALWEVTSEGLDMAAARQFAIEKGAPALRAMTFIE 63 L S ++ W ++++ A + + + D A FA G PALRA+ F + Sbjct: 11 LQSLIAERWDHCGAQTQVFADAATNQPNAVLAYGSDDGIQAVDFARAVGGPALRALGFQD 70 Query: 64 RAAMLKAVAKHLLSEKERFYALSAQTGATRADSWVDIEGGIGTLFTYASLGSRELPD-DT 122 RA L+AVA+ L + Y S GATR D +D++GGI L A + LP+ Sbjct: 71 RAQQLRAVARILKDNRAALYRESLTIGATRHDCALDVDGGIARLSALAGQALKSLPNAPV 130 Query: 123 LWPEDELIPLSKEGGFAARHLLTSKSGVAVHINAFNFPCWGMLEKLAPTWLGGMPAIIKP 182 L ED + P S G + +L SGVA+H+ A + P G+LE++AP + G+P I+ P Sbjct: 131 LHLEDGIGPGSTTG---RQQILAPLSGVALHVTALDNPVSGLLEQIAPALIAGVPCIVCP 187 Query: 183 ATATAQLTQAMVKSIVDSGLVPEGAISLICGSAGDLLDHLDSQDVVTFTGSAATGQMLRV 242 TA +++ +VK I D ++P GA+ LI L+D+L + D ++F G +T Q LR Sbjct: 188 DPVTACVSERLVKMIHDGQILPTGALQLIYNPPLGLVDNLSAGDAISFAGFRSTAQKLRQ 247 Query: 243 QPNIVAKSIPFTMEADSLNCCVLGEDVTPDQPEFALFIREVVREMTTKAGQKCTAIRRII 302 P + + L+ +LG DV P E+ F+RE+ E+ +AGQ+ A+RRI+ Sbjct: 248 HPAVATGLVRLQSCETGLSAAILGSDVAPGSQEYQFFLREIRSELILRAGQRRHAVRRIL 307 Query: 303 VPQALVNAVSDALVARLQKVVVGDPAQEGVKMGALVNAEQRADVQEKVNILLAAGCEIRL 362 +P+ V L L +VG P +MGALV+ VQ+ ++ E+R Sbjct: 308 LPRHREAEVLADLSVTLADTIVGVPDDAATQMGALVSRGHLETVQKALD-------ELRH 360 Query: 363 GGQ-------ADLSAAGAFFPPTLLYCPQPDETPAVHATEAFGPVATLMPAQNQRHALQL 415 G + + GAF P LL+C +P TP VH T GPVAT M + A+ L Sbjct: 361 GAEFVSDPIITPVETGGAFLSPVLLHCAKPANTPDVHQTFVQGPVATAMAYDSLCDAIAL 420 Query: 416 ACAGGGSLAGTLVTADPQIARQFIADAARTHGRIQILNEESAKESTGHGSPLPQL----V 471 A S + T D +A++ A G+I+I E A++++ SP P + Sbjct: 421 ANLAPCSRYSNVFTNDSPLAQEAAACLTSAEGQIRICGSEMARQAS-ELSPDPSVPRLFA 479 Query: 472 HGGPGRAGGGEELGGLRAVKHYMQRTAVQGSPTMLAAISKQWVRGAKVEEDRIHPFRKYF 531 + G E++ AV YM RT + P +L A++ +WV GA+ + HPFRK Sbjct: 480 ATHHAQVCGAEDI--RHAVAAYMMRTEIHAPPQLLTALTGRWVEGAETRHNG-HPFRKSL 536 Query: 532 EELQPGDSLLTPRRTMTEADIVNFACLSGDHFYAHMDKIAA-AESIFGERVVHGYFVLSA 590 E L+ GD L+T R +TE D+ FA +GD FYAHMD+ AA + F +RV HG V+S Sbjct: 537 ETLRIGDQLITETRQITEQDVEQFAHFTGDVFYAHMDREAARSHPFFDDRVAHGQLVVSF 596 Query: 591 AAGLFVDAGVGPVIANYGLESLRFIEPVKPGDTIQVRLTCKRKTLKKQRSAEEKPTGVVE 650 A GL VD GPV+AN G ++LRF PV GD + VR+TCK T + P G V Sbjct: 597 ANGLLVDPAPGPVLANIGSDNLRFHAPVYFGDCLHVRVTCKEITPR-----ASAPFGDVR 651 Query: 651 WAVEVFNQHQTPVALYSILTLVAR 674 W V N VA + +LTLV + Sbjct: 652 WDCCVLNACGVVVARFDLLTLVMK 675 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: 1072 Number of extensions: 50 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: 681 Length of database: 710 Length adjustment: 39 Effective length of query: 642 Effective length of database: 671 Effective search space: 430782 Effective search space used: 430782 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