Align Phenylacetaldehyde dehydrogenase; PAD; EC 1.2.1.39 (characterized)
to candidate N515DRAFT_2488 N515DRAFT_2488 succinate-semialdehyde dehydrogenase / glutarate-semialdehyde dehydrogenase
Query= SwissProt::O06837 (502 letters) >FitnessBrowser__Dyella79:N515DRAFT_2488 Length = 463 Score = 218 bits (555), Expect = 4e-61 Identities = 144/460 (31%), Positives = 230/460 (50%), Gaps = 11/460 (2%) Query: 42 NPATGDTLTDVPDGDVEDVNAAVESAAATLQSDAWRRMPPSARERILLRLADLLEAHGDE 101 NP TG+T+ P +V A++ A A + AW+ + +AR ++L + ADLL + Sbjct: 7 NPYTGETVKTFPSATDAEVTQALDQAQAMFE--AWKDVGVAARVKVLQKAADLLRESHTQ 64 Query: 102 LARLETLNNGKLLIYSKMMEVGASAQWLRYMAGWATKLTGSTLDLSLPLPPDVRSRASTQ 161 A++ TL GK++ ++ EV AQ L Y A A +L LS P +S + Sbjct: 65 YAKVLTLEMGKVIGEAEG-EVELCAQILEYYADHAEQLLAPE-KLSSRHPSYTQSWV--E 120 Query: 162 RVPVGVVAAIIPWNFPLLMAVWKIAPALACGNTVVLKPAEETPLTALRLAELAMEAGLPA 221 VP G++ A+ PWNFP V AP LA GN ++LK A P A L EAGLP Sbjct: 121 HVPQGILLAVEPWNFPYYQIVRIAAPQLAAGNVLILKHASNVPQCAAAFERLFREAGLPQ 180 Query: 222 GAL-NVVTGRGETAGDALVRHPKVAKVAFTGSTEVGRIIGSACGRSLKAVSLELGGKSPV 280 G N+ R + A++ P+V VA TGS G ++ + G++LK ++ELGG Sbjct: 181 GGFTNLYATRDQLK--AIIEDPRVQGVALTGSEGAGAVVAAQAGQALKKSTMELGGADAF 238 Query: 281 IVLADCDPQEAAEGAAAAIFFNHGQVCTAGSRLYVHESIYEDVIQRLAVIGESIVVGSGL 340 +VLAD D +A + A +N GQVC + R+ V + IY+ +++ + G + Sbjct: 239 VVLADADLDKAVQWAVTGRHWNAGQVCCSSKRIIVVDEIYDAFLEKYKAGVARLRAGDPM 298 Query: 341 EQGVHMGPMVSKKHHENVLRHIRNGIEDGADLICGGTEAPCAQGFFVKPTIFANREKKDI 400 E + PM S+ +++ + + + GA + G E P ++G F +P + ++ D Sbjct: 299 EPSTTLAPMSSRGAVDDLKKQLEQAVAHGAKVEVIGAEVP-SRGAFFRPVLLSH-VSDDN 356 Query: 401 RLLSQEVFGPVLVATPFSDIAEVVNEANRSVYGLGASIWTNDLSAALRINDELEAGTVWV 460 E FGPV D A+ + AN S +GLG S++T D+ + + ++ G V++ Sbjct: 357 PARYWEFFGPVSQVIRARDEADAIRIANDSPFGLGGSVFTTDIKHGIEVAKKISTGMVYI 416 Query: 461 NTHNMVDPNLPFGGFKDSGVGREHGAAAIEHYTTTRSLVI 500 N V +LPFGG + SG GRE I+ + + + + Sbjct: 417 NHPTGVAADLPFGGVRRSGYGRELTGLGIKEFVNHKLIAV 456 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: 515 Number of extensions: 17 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: 463 Length adjustment: 34 Effective length of query: 468 Effective length of database: 429 Effective search space: 200772 Effective search space used: 200772 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