Align oxepin-CoA hydrolase (EC 3.3.2.12) (characterized)
to candidate PfGW456L13_2419 Aldehyde dehydrogenase (EC 1.2.1.3), PaaZ
Query= BRENDA::P77455 (681 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2419 Length = 689 Score = 748 bits (1931), Expect = 0.0 Identities = 394/677 (58%), Positives = 479/677 (70%), Gaps = 6/677 (0%) Query: 4 LASFLSGTWQSGRGRSRLIHHAISGEALWEVTSEGLDMAAARQFAIEKGAPALRAMTFIE 63 L SF++G W G ++++ AI G + E D A A + +G L A+ F + Sbjct: 12 LQSFIAGRWIGQHG-AQVLRSAIDGHEIARTHEERPDFAEAIEHGRRQGISGLMALDFQQ 70 Query: 64 RAAMLKAVAKHLLSEKERFYALSAQTGATRADSWVDIEGGIGTLFTYASLGSRELPDDTL 123 RA LKA+A +L KE+ YA+S +GATRADSW+DIEGG TLFTYASLGSRELP + Sbjct: 71 RAQRLKALALYLSERKEQLYAISHHSGATRADSWIDIEGGNSTLFTYASLGSRELPSGNI 130 Query: 124 WPEDELIPLSKEGGFAARHLLTSKSGVAVHINAFNFPCWGMLEKLAPTWLGGMPAIIKPA 183 E + LSK G FA H+L + G+AVHINAFNFP WGMLEK AP++L GMP I+KPA Sbjct: 131 VHEGPAMQLSKMGTFAGTHILVPRGGLAVHINAFNFPIWGMLEKFAPSFLAGMPCIVKPA 190 Query: 184 TATAQLTQAMVKSIVDSGLVPEGAISLICGSAGDLLDHLDSQDVVTFTGSAATGQMLRVQ 243 +AT+ LT+A+V+ + +SGL+P G++ LI GS GDLLD L QDVVTFTGSA T LRV Sbjct: 191 SATSYLTEAVVRLMDESGLLPAGSLQLIIGSTGDLLDRLQGQDVVTFTGSADTAAKLRVN 250 Query: 244 PNIVAKSIPFTMEADSLNCCVLGEDVTPDQPEFALFIREVVREMTTKAGQKCTAIRRIIV 303 PN++ S+PF EADSLNC +L DVTPD EF LFI+EV REMTTKAGQKCTAIRR IV Sbjct: 251 PNLIRNSVPFNAEADSLNCAILAPDVTPDDEEFELFIKEVAREMTTKAGQKCTAIRRAIV 310 Query: 304 PQALVNAVSDALVARLQKVVVGDPAQEGVKMGALVNAEQRADVQEKVNILLAA-----GC 358 P ++AV+ L RL KVVVGDP+ EGV+MGAL + +Q+ DV E++ LL + G Sbjct: 311 PAKHIDAVATRLRDRLAKVVVGDPSVEGVRMGALASHDQQKDVAERLESLLQSSDMLFGA 370 Query: 359 EIRLGGQADLSAAGAFFPPTLLYCPQPDETPAVHATEAFGPVATLMPAQNQRHALQLACA 418 + + GAFF PTLL P H EAFGPV+TLM + AL LA Sbjct: 371 RDGFEPRGENVDKGAFFAPTLLQARDPHAEGGAHDIEAFGPVSTLMAYDDLDEALALAAR 430 Query: 419 GGGSLAGTLVTADPQIARQFIADAARTHGRIQILNEESAKESTGHGSPLPQLVHGGPGRA 478 G GSL +LVT DPQIA + I AA HGR+ +L+ SA ESTGHGSPLPQL HGGPGRA Sbjct: 431 GKGSLVASLVTKDPQIAAKAIPVAAAWHGRLLVLDRHSAGESTGHGSPLPQLKHGGPGRA 490 Query: 479 GGGEELGGLRAVKHYMQRTAVQGSPTMLAAISKQWVRGAKVEEDRIHPFRKYFEELQPGD 538 GGGEELGGLRAVKHY+QR AVQGSPTMLAA++ ++VRGAKV E +HPFR++F++LQ G+ Sbjct: 491 GGGEELGGLRAVKHYLQRAAVQGSPTMLAAVTGEYVRGAKVIETDVHPFRRHFQDLQIGE 550 Query: 539 SLLTPRRTMTEADIVNFACLSGDHFYAHMDKIAAAESIFGERVVHGYFVLSAAAGLFVDA 598 SLLT RRT+TEAD+VNF CLSGDHFY H D+IAA ES FG+R+ HGYFVLSAAAGLFV Sbjct: 551 SLLTHRRTVTEADLVNFGCLSGDHFYMHFDEIAAKESQFGKRIAHGYFVLSAAAGLFVSP 610 Query: 599 GVGPVIANYGLESLRFIEPVKPGDTIQVRLTCKRKTLKKQRSAEEKPTGVVEWAVEVFNQ 658 GPV+ANYGL++LRFI PV GDTIQ RLTCKRK + ++S + P GVV W VEV NQ Sbjct: 611 APGPVLANYGLDTLRFINPVGIGDTIQARLTCKRKIDQGKKSPQGIPQGVVAWDVEVTNQ 670 Query: 659 HQTPVALYSILTLVARQ 675 VA Y ILTLV ++ Sbjct: 671 LGELVASYDILTLVVKR 687 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: 1188 Number of extensions: 36 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: 689 Length adjustment: 39 Effective length of query: 642 Effective length of database: 650 Effective search space: 417300 Effective search space used: 417300 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