Align 3,4-dehydroadipyl-CoA semialdehyde dehydrogenase; EC 1.2.1.77 (characterized)
to candidate GFF3676 PGA1_262p00800 phenylacetic acid degradation protein PaaZ
Query= SwissProt::Q84HH8 (515 letters) >FitnessBrowser__Phaeo:GFF3676 Length = 710 Score = 222 bits (566), Expect = 3e-62 Identities = 149/458 (32%), Positives = 232/458 (50%), Gaps = 17/458 (3%) Query: 3 LANYVYGQWIEGAGEGAALTDPVTGEALVRVSSDGIDVARALEFARTAGGAALKALTYEE 62 L + + +W + D T + ++ D +A++FAR GG AL+AL +++ Sbjct: 11 LQSLIAERWDHCGAQTQVFADAATNQPNAVLAYGSDDGIQAVDFARAVGGPALRALGFQD 70 Query: 63 RAAKLAAIAELLQAKRAEYFDISLRNSGATEGDASFDVDGAIFTVKSYARAGKALGA--- 119 RA +L A+A +L+ RA + SL GAT D + DVDG I + A AG+AL + Sbjct: 71 RAQQLRAVARILKDNRAALYRESL-TIGATRHDCALDVDGGIARLS--ALAGQALKSLPN 127 Query: 120 --GRHLKEGGRVALAKTDVFQGQHFLMPLTGVAVFINAFNFPAWGLWEKAAPALLAGVPV 177 HL++G + Q L PL+GVA+ + A + P GL E+ APAL+AGVP Sbjct: 128 APVLHLEDG----IGPGSTTGRQQILAPLSGVALHVTALDNPVSGLLEQIAPALIAGVPC 183 Query: 178 FAKPATPTAWLAQRMVADVVEAGILPPGAISIVCGGARDLLDHVTECDVVSFTGSADTAA 237 P TA +++R+V + + ILP GA+ ++ L+D+++ D +SF G TA Sbjct: 184 IVCPDPVTACVSERLVKMIHDGQILPTGALQLIYNPPLGLVDNLSAGDAISFAGFRSTAQ 243 Query: 238 RMRTHPNVVARSVRINIEADSVNSAILGPDAQPGTPEFDLAVKEIVREMTVKTGQKCTAI 297 ++R HP V VR+ +++AILG D PG+ E+ ++EI E+ ++ GQ+ A+ Sbjct: 244 KLRQHPAVATGLVRLQSCETGLSAAILGSDVAPGSQEYQFFLREIRSELILRAGQRRHAV 303 Query: 298 RRILAPAGVSRALADAVSGKLAGCKVGNPRSEGVRVGPLVSKAQQAAAFEGLAKLRQECE 357 RRIL P + +S LA VG P ++G LVS+ + L +LR E Sbjct: 304 RRILLPRHREAEVLADLSVTLADTIVGVPDDAATQMGALVSRGHLETVQKALDELRHGAE 363 Query: 358 VVFGGDPDFEPVDADAAVSAFVQPTLLYCDKGLAARHVHDVEVFGPVATMVPYADTRDAV 417 F DP PV+ AF+ P LL+C K VH V GPVAT + Y DA+ Sbjct: 364 --FVSDPIITPVETG---GAFLSPVLLHCAKPANTPDVHQTFVQGPVATAMAYDSLCDAI 418 Query: 418 AIARRGHGSLVASVYSGDAAFLGELVPGIADLHGRVMV 455 A+A S ++V++ D+ E + G++ + Sbjct: 419 ALANLAPCSRYSNVFTNDSPLAQEAAACLTSAEGQIRI 456 Lambda K H 0.319 0.135 0.399 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: 792 Number of extensions: 38 Number of successful extensions: 4 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: 515 Length of database: 710 Length adjustment: 37 Effective length of query: 478 Effective length of database: 673 Effective search space: 321694 Effective search space used: 321694 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