Align 3,4-dehydroadipyl-CoA semialdehyde dehydrogenase (NADP+) (EC 1.2.1.77) (characterized)
to candidate BWI76_RS13085 BWI76_RS13085 bifunctional oxepin-CoA hydrolase/3-oxo-5,6-dehydrosuberyl-CoA semialdehyde dehydrogenase
Query= BRENDA::Q13WK4 (531 letters) >FitnessBrowser__Koxy:BWI76_RS13085 Length = 681 Score = 410 bits (1055), Expect = e-119 Identities = 232/524 (44%), Positives = 323/524 (61%), Gaps = 20/524 (3%) Query: 5 LKNHVAGQWIAGTGAGITLTDPVTGVALVRVSSEGLDLARAFSFAREDGGAALRALTYAQ 64 L ++++G W G G T+ ++G AL V+S GLD+A+A FA E GG AL+A+T+ + Sbjct: 4 LASYLSGTWQTGRGHARTIHHAISGDALWEVTSAGLDMAQARRFAIERGGKALQAMTFIE 63 Query: 65 RAARLADIVKLLQAKRGDYYAIATANSGTTRNDSAVDIDGGIFTLSYYAKLGA-SLGEVH 123 R+A L + + L ++ YAI+ A +G TR+DS VDI+GGI TL YA LG+ L + Sbjct: 64 RSAMLKAVARHLLEQKAALYAIS-AETGATRSDSWVDIEGGIGTLFTYAGLGSRELPDDT 122 Query: 124 ALRDGSAESLSKDRSFSAQHVLSPTRGVALFINAFNFPSWGLWEKAAPALLSGVPVIVKP 183 + LSK F+A+HVL+ GVA+ INAFNFP WG+ EK AP L+G+P I+KP Sbjct: 123 LWPEDELIPLSKQGGFAARHVLTSKSGVAVHINAFNFPCWGMLEKLAPTWLAGMPAIIKP 182 Query: 184 ATATAWLTQRMVADVVDAGILPPGALSIICGSSAGLLDQIRSFDVVSFTGSADTAATLRA 243 ATATA LTQ MV +VD+G++P GA+S+ICG + LLD + S DVV+FTGSA T LR Sbjct: 183 ATATAQLTQAMVKMIVDSGLVPEGAISLICGGAGDLLDHLDSQDVVTFTGSARTGQQLRV 242 Query: 244 HPAFVQRGARLNVEADSLNSAILCADATPDTPAFDLFIKEVVREMTVKSGQKCTAIRRAF 303 HP V + +EADSLN +L D TP+ P F LFI+EVVREMT K+GQKCTAIRR Sbjct: 243 HPNLVAKSIPFTMEADSLNCCVLGDDVTPEQPEFALFIREVVREMTAKAGQKCTAIRRII 302 Query: 304 VPEAALEPVLEALKAKLAKITVGNPRNDAVRMGSLVSREQYENVLAGIAALREEAVLAYD 363 VP+A ++ V +AL A+L + VG+P + V+MG+LV+ EQ ++V + L Sbjct: 303 VPQAQVKAVSDALIARLQNVVVGDPAQEGVKMGALVNYEQRQDVQDNVNRL-------VA 355 Query: 364 SSAVPLIDADANIAACVA---PHLFVVNDPDNATLLHDVEVFGPVASVAPYRVTTDTNAL 420 + L+ A++ A A P L PD +H +E FGPVA++ PY+ Sbjct: 356 AGCDVLLGGQADLRAAGAFFPPTLLFCPQPDETPAVHAIEAFGPVATLMPYQNI------ 409 Query: 421 PEAHAVALARRGQGSLVASIYSNDDAHLGRLALELADSHGRVHAISPSVQHSQTGHGNVM 480 HA++LAR G+GSL ++ + L A +HGR+ ++ S TGHG+ + Sbjct: 410 --EHAMSLARAGEGSLAGTLVTASGELARAFILGAARTHGRIQILNESSSAESTGHGSPL 467 Query: 481 PMSLHGGPGRAGGGEELGGLRALAFYHRRSAIQAASAAIGTLTQ 524 P +HGGPGRAGGGEELGGLRA+ Y +R+AIQ + + + Q Sbjct: 468 PQLVHGGPGRAGGGEELGGLRAVKHYMQRTAIQGSPTMLAAIGQ 511 Lambda K H 0.318 0.132 0.379 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: 784 Number of extensions: 29 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: 531 Length of database: 681 Length adjustment: 37 Effective length of query: 494 Effective length of database: 644 Effective search space: 318136 Effective search space used: 318136 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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