Align 3,4-dehydroadipyl-CoA semialdehyde dehydrogenase (NADP+) (EC 1.2.1.77) (characterized)
to candidate 15509 b1387 fused aldehyde dehydrogenase/enoyl-CoA hydratase (NCBI)
Query= BRENDA::Q13WK4 (531 letters) >FitnessBrowser__Keio:15509 Length = 681 Score = 408 bits (1048), Expect = e-118 Identities = 229/524 (43%), Positives = 321/524 (61%), Gaps = 20/524 (3%) Query: 5 LKNHVAGQWIAGTGAGITLTDPVTGVALVRVSSEGLDLARAFSFAREDGGAALRALTYAQ 64 L + ++G W +G G + ++G AL V+SEGLD+A A FA E G ALRA+T+ + Sbjct: 4 LASFLSGTWQSGRGRSRLIHHAISGEALWEVTSEGLDMAAARQFAIEKGAPALRAMTFIE 63 Query: 65 RAARLADIVKLLQAKRGDYYAIATANSGTTRNDSAVDIDGGIFTLSYYAKLGA-SLGEVH 123 RAA L + K L +++ +YA++ A +G TR DS VDI+GGI TL YA LG+ L + Sbjct: 64 RAAMLKAVAKHLLSEKERFYALS-AQTGATRADSWVDIEGGIGTLFTYASLGSRELPDDT 122 Query: 124 ALRDGSAESLSKDRSFSAQHVLSPTRGVALFINAFNFPSWGLWEKAAPALLSGVPVIVKP 183 + LSK+ F+A+H+L+ GVA+ INAFNFP WG+ EK AP L G+P I+KP Sbjct: 123 LWPEDELIPLSKEGGFAARHLLTSKSGVAVHINAFNFPCWGMLEKLAPTWLGGMPAIIKP 182 Query: 184 ATATAWLTQRMVADVVDAGILPPGALSIICGSSAGLLDQIRSFDVVSFTGSADTAATLRA 243 ATATA LTQ MV +VD+G++P GA+S+ICGS+ LLD + S DVV+FTGSA T LR Sbjct: 183 ATATAQLTQAMVKSIVDSGLVPEGAISLICGSAGDLLDHLDSQDVVTFTGSAATGQMLRV 242 Query: 244 HPAFVQRGARLNVEADSLNSAILCADATPDTPAFDLFIKEVVREMTVKSGQKCTAIRRAF 303 P V + +EADSLN +L D TPD P F LFI+EVVREMT K+GQKCTAIRR Sbjct: 243 QPNIVAKSIPFTMEADSLNCCVLGEDVTPDQPEFALFIREVVREMTTKAGQKCTAIRRII 302 Query: 304 VPEAALEPVLEALKAKLAKITVGNPRNDAVRMGSLVSREQYENVLAGIAALREEAVLAYD 363 VP+A + V +AL A+L K+ VG+P + V+MG+LV+ EQ +V +E+ + Sbjct: 303 VPQALVNAVSDALVARLQKVVVGDPAQEGVKMGALVNAEQRADV-------QEKVNILLA 355 Query: 364 SSAVPLIDADANIAACVA---PHLFVVNDPDNATLLHDVEVFGPVASVAPYRVTTDTNAL 420 + + A+++A A P L PD +H E FGPVA++ P A Sbjct: 356 AGCEIRLGGQADLSAAGAFFPPTLLYCPQPDETPAVHATEAFGPVATLMP--------AQ 407 Query: 421 PEAHAVALARRGQGSLVASIYSNDDAHLGRLALELADSHGRVHAISPSVQHSQTGHGNVM 480 + HA+ LA G GSL ++ + D + + A +HGR+ ++ TGHG+ + Sbjct: 408 NQRHALQLACAGGGSLAGTLVTADPQIARQFIADAARTHGRIQILNEESAKESTGHGSPL 467 Query: 481 PMSLHGGPGRAGGGEELGGLRALAFYHRRSAIQAASAAIGTLTQ 524 P +HGGPGRAGGGEELGGLRA+ Y +R+A+Q + + +++ Sbjct: 468 PQLVHGGPGRAGGGEELGGLRAVKHYMQRTAVQGSPTMLAAISK 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: 759 Number of extensions: 28 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