Align oxepin-CoA hydrolase (EC 3.3.2.12) (characterized)
to candidate BPHYT_RS13360 BPHYT_RS13360 aldehyde dehydrogenase
Query= BRENDA::P77455 (681 letters) >FitnessBrowser__BFirm:BPHYT_RS13360 Length = 531 Score = 409 bits (1052), Expect = e-118 Identities = 229/521 (43%), Positives = 317/521 (60%), Gaps = 14/521 (2%) Query: 4 LASFLSGTWQSGRGRSRLIHHAISGEALWEVTSEGLDMAAARQFAIEKGAPALRAMTFIE 63 L + ++G W +G G + ++G AL V+SEGLD+A A FA + G ALRA+T+ + Sbjct: 5 LKNHVAGQWIAGSGTGVTLTDPVTGVALVRVSSEGLDLAHAFGFARDTGGAALRALTYAQ 64 Query: 64 RAAMLKAVAKHLLSEKERFYALS-AQTGATRADSWVDIEGGIGTLFTYASLGSRELPDDT 122 RAA L + K L ++++ +YA++ A +G TR DS VDI+GGI TL YA LG+ L D Sbjct: 65 RAARLADIVKLLQAKRDDYYAIATANSGTTRNDSAVDIDGGIFTLSYYAKLGA-SLGDVH 123 Query: 123 LWPEDELIPLSKEGGFAARHLLTSKSGVAVHINAFNFPCWGMLEKLAPTWLGGMPAIIKP 182 + E + LSK+ F+ +H+LT GVA+ INAFNFP WG+ EK AP L G+P I+KP Sbjct: 124 ALRDGESVSLSKDQSFSVQHVLTPTRGVALFINAFNFPSWGLWEKAAPALLSGVPVIVKP 183 Query: 183 ATATAQLTQAMVKSIVDSGLVPEGAISLICGSAGDLLDHLDSQDVVTFTGSAATGQMLRV 242 ATATA LTQ MV +VD+G++P GA+S+ICGS+ LLD + S DVV+FTGSA T LR Sbjct: 184 ATATAWLTQRMVADVVDAGILPPGALSVICGSSAGLLDQIQSFDVVSFTGSAQTAATLRA 243 Query: 243 QPNIVAKSIPFTMEADSLNCCVLGEDVTPDQPEFALFIREVVREMTTKAGQKCTAIRRII 302 P V + +EADSLN +L D P P F LFI+EVVREMT K+GQKCTAIRR Sbjct: 244 HPAFVQRGARLNVEADSLNSAILCADAAPGTPAFDLFIKEVVREMTVKSGQKCTAIRRAF 303 Query: 303 VPQALVNAVSDALVARLQKVVVGDPAQEGVKMGALVNAEQRADVQEKVNILLAAGCEIRL 362 VP+ + AV +AL A+L K+ VGDP + V+MG+LV+ EQ +V + L Sbjct: 304 VPEGALEAVLEALNAKLAKITVGDPRNDTVRMGSLVSREQYENVLAGIAALREEAVLAFD 363 Query: 363 GGQADL----SAAGAFFPPTLLYCPQPDETPAVHATEAFGPVATLMPAQ--------NQR 410 G L S A P L PD +H E FGPVA++ P + + Sbjct: 364 GSAVPLIDADSNIAACIAPHLFVVNDPDNATLLHDVEVFGPVASVAPYRVATDAATLPEA 423 Query: 411 HALQLACAGGGSLAGTLVTADPQIARQFIADAARTHGRIQILNEESAKESTGHGSPLPQL 470 HA+ LA G GSL ++ + D + + A +HGR+ ++ + TGHG+ +P Sbjct: 424 HAVALARRGQGSLVASIYSNDEAHLGRLALELADSHGRVHAISPSVQQSQTGHGNVMPMS 483 Query: 471 VHGGPGRAGGGEELGGLRAVKHYMQRTAVQGSPTMLAAISK 511 +HGGPGRAGGGEELGGLRA+ Y +R+A+Q + + ++++ Sbjct: 484 LHGGPGRAGGGEELGGLRALGFYHRRSAIQAASAAIGSLTQ 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: 803 Number of extensions: 36 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)
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