Align phenylacetaldehyde dehydrogenase (EC 1.2.1.39) (characterized)
to candidate WP_073948994.1 RH94_RS20650 aldehyde dehydrogenase family protein
Query= BRENDA::V4GH04 (496 letters) >NCBI__GCF_001906585.1:WP_073948994.1 Length = 462 Score = 333 bits (854), Expect = 8e-96 Identities = 197/477 (41%), Positives = 262/477 (54%), Gaps = 24/477 (5%) Query: 17 MLIGGQWVSAQSGKTLNVYNPATGDILTEVPDGDVEDVNAAVESAAATLRSDTWRRMPPS 76 M I G W A + V NPA ++ VP G EDV+AAV +A A L W PP+ Sbjct: 7 MYIDGAWRPAAGRDAIEVVNPADEQVIATVPAGTAEDVDAAVRAARAALPG--WAATPPA 64 Query: 77 ARERILLRLADLLEVHGDELARLETLNNGKLLIYSKLMEVGASAQWLRYMAGWATKLTGS 136 R L L D+L DE+A T G L +S+ + AG + GS Sbjct: 65 ERAARLTALRDVLVARKDEIAETVTAELGSPLAFSQAVH-----------AGVPIAVAGS 113 Query: 137 TLDLSLPLPPEVRSRAST-QRVPVGVVAAIIPWNFPLLMAVWKIAPALACGNTVVLKPAE 195 DL+ E + ST PVGVV AI PWN+PL V K APALA G T+VLKPAE Sbjct: 114 YADLAATYAFEEKVGNSTVHHEPVGVVGAITPWNYPLHQIVAKAAPALAAGCTIVLKPAE 173 Query: 196 ETPLTALRLAELAMEAGLPAGALNVVTGRGETAGDALVRHPKVAKVAFTGSTEVGRIIGS 255 +TPLTA AE A EAG+PAG LN+VTG G AG AL HP V V+FTGST VGR IG+ Sbjct: 174 DTPLTAQLFAEAAHEAGIPAGVLNLVTGLGPVAGQALAEHPDVDLVSFTGSTAVGRRIGA 233 Query: 256 ACGRSLKAVSLELGGKSPVIVLADCDPQEAAEGAAAAIFFNHGQVCTAGSRLYVHESIYE 315 G ++K V+LELGGKS ++L D A A + N GQ C+A +R+ VH Y+ Sbjct: 234 TAGAAVKRVALELGGKSANVILPSADLARAVNVGVANVMSNSGQTCSAWTRMLVHRDQYD 293 Query: 316 DVIQRLAVIGESIVVGSGLEQGVHMGPMVSKKHHENVLRHIRNGIEDGADLICGGTEAPC 375 + ++ A + + G +GP+V+ K V +I GI +GA L+ GG EAPC Sbjct: 294 EAVELAAT--------AAAKYGDRIGPVVNAKQRARVRGYIEKGIAEGARLVAGGPEAPC 345 Query: 376 AQGFFVKPTIFANREKKDIRLLSQEVFGPVLVATPFSDIAEVVNEANRSVYGLGASIWTN 435 +G+FV PT+FA+ D+ + +E+FGPVL + D + + AN +VYGL ++W Sbjct: 346 EKGYFVSPTVFAD-VTPDMTVAQEEIFGPVLSILRYDDEDDALRIANGTVYGLAGAVWAA 404 Query: 436 DLSAALRINDELEAGTVWVNTHNMVDPNLPFGGFKDSGVGREHGAAAIEHYTTTRSL 492 D + A+ ++ G V +N +P PFGG+K SGVGRE GA + Y T+SL Sbjct: 405 DETEAVAFARRMDTGQVDIN-GGRFNPLAPFGGYKQSGVGRELGAHGLTEYLQTKSL 460 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: 576 Number of extensions: 29 Number of successful extensions: 6 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: 496 Length of database: 462 Length adjustment: 34 Effective length of query: 462 Effective length of database: 428 Effective search space: 197736 Effective search space used: 197736 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: 51 (24.3 bits)
This GapMind analysis is from Sep 24 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