Align Phenylacetaldehyde dehydrogenase; PAD; EC 1.2.1.39 (characterized)
to candidate WP_011318370.1 AVA_RS07875 aldehyde dehydrogenase family protein
Query= SwissProt::O06837 (502 letters) >NCBI__GCF_000204075.1:WP_011318370.1 Length = 498 Score = 313 bits (802), Expect = 9e-90 Identities = 181/487 (37%), Positives = 269/487 (55%), Gaps = 15/487 (3%) Query: 22 QMLIGGQWVNAQSDKTLNVYNPAT-GDTLTDVPDGDVEDVNAAVESAAATLQSDAWRRMP 80 Q I GQW+NA ++ TLN +NPA + + P +D + AV +A S WR++P Sbjct: 8 QNYINGQWLNAATETTLNSHNPANKSEIVATFPRSQADDTDRAVTAARQAYGS--WRKVP 65 Query: 81 PSARERILLRLADLLEAHGDELARLETLNNGKLLIYSKMMEVGASAQWLRYMAGWATKLT 140 AR + R+ +LL H +ELA+L + GK + ++ +V Y AG +L Sbjct: 66 APARAEYIFRVGELLLQHKEELAQLISREMGKPITEARG-DVQEGVDCAFYSAGEGRRLF 124 Query: 141 GSTLDLSLPLPPDVRSRASTQRVPVGVVAAIIPWNFPLLMAVWKIAPALACGNTVVLKPA 200 G T +P A T R+P+GV A I PWNFP+ + WK PAL CGNTV+LKPA Sbjct: 125 GQTTPSEMP-----NKFAMTVRMPIGVCALITPWNFPVAIPCWKAMPALVCGNTVILKPA 179 Query: 201 EETPLTALRLAELAMEAGLPAGALNVVTGRGETAGDALVRHPKVAKVAFTGSTEVGRIIG 260 E+TP A +L E+ AGLP G +N+V G GE AG ALV HP + V+FTGS+ G +G Sbjct: 180 EDTPACATKLIEIFAAAGLPPGVINLVHGVGEEAGKALVEHPNIDLVSFTGSSATGAYVG 239 Query: 261 SACGRSLKAVSLELGGKSPVIVLADCDPQEAAEGAAAAIFFNHGQVCTAGSRLYVHESIY 320 CGR+ K V LE+GGK+ +V+ D D + A +GA F GQ CTA SRL +H I Sbjct: 240 ETCGRTHKRVCLEMGGKNAQVVMEDADLELALDGALWGAFGTTGQRCTATSRLILHRDIK 299 Query: 321 EDVIQRLAVIGESIVVGSGLEQGVHMGPMVSKKHHENVLRHIRNGIEDGADLICGG---T 377 E L + +G+G E +GP+++ + + V ++ E+GA ++ GG T Sbjct: 300 EKFTTMLRERTSQLRLGAGTEPETDIGPIINNRQLQRVHEYMNIAREEGAKILIGGEIVT 359 Query: 378 EAPCAQGFFVKPTIFANREKKDIRLLSQEVFGPVLVATPFSDIAEVVNEANRSVYGLGAS 437 E QG+F +PTI N +R+ +E+FGPV+ S E + N + YGL +S Sbjct: 360 EGQLKQGYFFQPTILDN-VTPQMRVAREEIFGPVVALIEVSTFEEAIAILNDTKYGLSSS 418 Query: 438 IWTNDLSAALRINDELEAGTVWVNTHNM-VDPNLPFGGFKDSGVG-REHGAAAIEHYTTT 495 ++T D++ A ++E G ++N + + +LPFGG K +G G RE G A++ +T Sbjct: 419 VYTRDINRAFVAMRDIEVGITYINGPTIGAEVHLPFGGVKQTGNGHREAGTTALDVFTEW 478 Query: 496 RSLVIAY 502 +S+ + + Sbjct: 479 KSVYVDF 485 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: 594 Number of extensions: 28 Number of successful extensions: 7 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: 498 Length adjustment: 34 Effective length of query: 468 Effective length of database: 464 Effective search space: 217152 Effective search space used: 217152 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 Apr 09 2024. 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