Align Phenylacetaldehyde dehydrogenase; PAD; EC 1.2.1.39 (characterized)
to candidate N515DRAFT_3729 N515DRAFT_3729 aminomuconate-semialdehyde/2-hydroxymuconate-6-semialdehyde dehydrogenase
Query= SwissProt::O06837 (502 letters) >FitnessBrowser__Dyella79:N515DRAFT_3729 Length = 483 Score = 338 bits (866), Expect = 3e-97 Identities = 197/484 (40%), Positives = 267/484 (55%), Gaps = 14/484 (2%) Query: 24 LIGGQWVNAQSDKTLNVYNPATGDTLTDVPDGDVEDVNAAVESAAATLQSDAWRRMPPSA 83 LI G+ + ++ L V+ PATG+ P+ DV+AAV AAA + W P Sbjct: 9 LIDGRLQAPRQERWLEVFEPATGEVFAHCPESSFADVDAAV--AAAVAAAPGWAATPSEQ 66 Query: 84 RERILLRLADLLEAHGDELARLETLNNGKLLIYSKMMEVGASAQWLRYMAGWATKLTGST 143 R R+L RLADL+EA DE A LE+ ++GK L ++ +++ + LRY A + + Sbjct: 67 RARLLQRLADLIEARLDEFAALESRDSGKPLSLARSLDIPRAVSNLRYFAAAIVPWSSES 126 Query: 144 LDLSLPLPPDVRSRASTQRVPVGVVAAIIPWNFPLLMAVWKIAPALACGNTVVLKPAEET 203 + L + T R P+GVVA I PWN PL + WKIAPALA GN VV KP+E T Sbjct: 127 HAMELG------AINYTLRQPLGVVACISPWNLPLYLFTWKIAPALAAGNAVVAKPSEIT 180 Query: 204 PLTALRLAELAMEAGLPAGALNVVTGRGETAGDALVRHPKVAKVAFTGSTEVGRIIGSAC 263 P TA L EL++EAG P G LN+V GRG G ALV H V V+FTGST G I +A Sbjct: 181 PCTAALLGELSIEAGFPPGVLNIVQGRGPEVGQALVEHRDVKAVSFTGSTRTGAQIAAAA 240 Query: 264 GRSLKAVSLELGGKSPVIVLADCDPQEA-AEGAAAAIFFNHGQVCTAGSRLYVHESIYED 322 K +SLELGGK+P IV AD D +A + + F N G++C GSRL V SIY+ Sbjct: 241 APRFKKLSLELGGKNPAIVFADADLSDANLDTIVRSGFANQGEICLCGSRLLVQRSIYDA 300 Query: 323 VIQRLAVIGESIVVGSGLEQGVHMGPMVSKKHHENVLRHIRNGIEDGADLICGG----TE 378 +R ++ VG E +G +VS++H + V I +G ++CGG Sbjct: 301 FRERYLAKVRALRVGDPREAATDLGALVSREHFDKVTGCIAQARAEGGRVLCGGDALALP 360 Query: 379 APCAQGFFVKPTIFANREKKDIRLLSQEVFGPVLVATPFSDIAEVVNEANRSVYGLGASI 438 P A G++V PT+ + QE+FGPV+ PF D A+ + AN + YGL AS+ Sbjct: 361 GPLAGGWYVAPTVIEGL-GPETATNQQEIFGPVVTLIPFDDEAQALAIANGTGYGLAASL 419 Query: 439 WTNDLSAALRINDELEAGTVWVNTHNMVDPNLPFGGFKDSGVGREHGAAAIEHYTTTRSL 498 WT DLS A R +L+ G VW+N + D PFGG K SGVGRE G A+ +T +++ Sbjct: 420 WTTDLSRAHRFGAQLDFGIVWINCWLLRDLRTPFGGAKQSGVGREGGVEALRFFTEPKNI 479 Query: 499 VIAY 502 I Y Sbjct: 480 CIRY 483 Lambda K H 0.317 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: 611 Number of extensions: 31 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: 502 Length of database: 483 Length adjustment: 34 Effective length of query: 468 Effective length of database: 449 Effective search space: 210132 Effective search space used: 210132 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: 52 (24.6 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