Align Phenylacetaldehyde dehydrogenase; PAD; EC 1.2.1.39 (characterized)
to candidate CCNA_03242 CCNA_03242 succinic semialdehyde dehydrogenase
Query= SwissProt::O06837 (502 letters) >FitnessBrowser__Caulo:CCNA_03242 Length = 485 Score = 304 bits (778), Expect = 5e-87 Identities = 180/476 (37%), Positives = 267/476 (56%), Gaps = 13/476 (2%) Query: 24 LIGGQWVNAQSDKTLNVYNPATGDTLTDVPDGDVEDVNAAVESAAATLQSDAWRRMPPSA 83 LI GQWV ++ + +V NPA G + V D + A+++A L AW Sbjct: 15 LIDGQWVRGEA--SFDVLNPADGTLIAAVADLGAAETTLAIDAAHRALP--AWAARTAKE 70 Query: 84 RERILLRLADLLEAHGDELARLETLNNGKLLIYSKMMEVGASAQWLRYMAGWATKLTGST 143 R IL R +DL+ AH D+LARL T GK L +K EV A ++ + A A + G T Sbjct: 71 RGAILRRWSDLILAHADDLARLMTDEQGKPLAEAKG-EVVYGASFIDWFAEEAKRAYGHT 129 Query: 144 LDLSLPLPPDVRSRASTQRVPVGVVAAIIPWNFPLLMAVWKIAPALACGNTVVLKPAEET 203 + +P R ++ + PVGV AAI PWNFP+ M K+ PALA G TVV+KPA ET Sbjct: 130 IPTPMP-----GKRLASIKQPVGVCAAIAPWNFPIAMITRKVGPALAAGCTVVVKPAAET 184 Query: 204 PLTALRLAELAMEAGLPAGALNVVTG-RGETAGDALVRHPKVAKVAFTGSTEVGRIIGSA 262 PL+AL +A LA EAG+PAG LN+VT R G L +V K++FTGST +G+++ Sbjct: 185 PLSALAIARLATEAGVPAGVLNIVTTTRSSEVGKVLCDDSRVRKLSFTGSTPIGKVLYQQ 244 Query: 263 CGRSLKAVSLELGGKSPVIVLADCDPQEAAEGAAAAIFFNHGQVCTAGSRLYVHESIYED 322 C ++K +SLELGG +P IV D D + A +GA A+ + N GQ C +RL V I++ Sbjct: 245 CAGTMKKLSLELGGNAPFIVFDDADLEAAVDGAIASKYRNAGQTCVCANRLIVQSGIHDA 304 Query: 323 VIQRLAVIGESIVVGSGLEQGVHMGPMVSKKHHENVLRHIRNGIEDGADLICGGTEAPCA 382 RLA ++ VG G +GV +GP++++K V+ + ++ GA+++ GG + Sbjct: 305 FAARLAEKVAALKVGPGTGEGVQIGPLINEKALTKVVGLVSGAVQAGAEVLTGG-DVHGL 363 Query: 383 QGFFVKPTIFANREKKDIRLLSQEVFGPVLVATPFSDIAEVVNEANRSVYGLGASIWTND 442 G F +PT+ ++R+ +E+FGPV F AE V AN + +GL A ++ D Sbjct: 364 GGHFYQPTVLVG-ATPEMRIFQEEIFGPVAPIVKFETEAEAVELANATPFGLAAYFYSRD 422 Query: 443 LSAALRINDELEAGTVWVNTHNMVDPNLPFGGFKDSGVGREHGAAAIEHYTTTRSL 498 + R+ +++EAG V +N + PFGG K+SG+GRE + ++ Y T+ L Sbjct: 423 VGRCWRVAEQIEAGMVGINEGLISTEVAPFGGVKESGLGREGASEGLDEYLETKYL 478 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: 589 Number of extensions: 32 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: 502 Length of database: 485 Length adjustment: 34 Effective length of query: 468 Effective length of database: 451 Effective search space: 211068 Effective search space used: 211068 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