Align phenylacetaldehyde dehydrogenase (EC 1.2.1.39) (characterized)
to candidate AZOBR_RS26825 AZOBR_RS26825 aldehyde dehydrogenase
Query= BRENDA::V4GH04 (496 letters) >FitnessBrowser__azobra:AZOBR_RS26825 Length = 494 Score = 333 bits (855), Expect = 6e-96 Identities = 199/485 (41%), Positives = 278/485 (57%), Gaps = 18/485 (3%) Query: 17 MLIGGQWVSAQSGKTLNVYNPATGDILTEVPDGDVEDVNAAVESAAATLRSDTWRRMPPS 76 +LIGG+ A +GKT +V NPATGD++ DG DV+AAV +A A W R+ Sbjct: 18 LLIGGELRPAATGKTFDVVNPATGDVIATAADGGERDVDAAVRAAVAA--QGAWARLSAR 75 Query: 77 ARERILLRLADLLEVHGDELARLETLNNGKLLIYSKLMEVGASAQWLRYMAGWATKLTGS 136 R R+L+ L H +E+ RL L GK + +E A L + G A++L G Sbjct: 76 ERGRLLVECGRRLVGHAEEIGRLLALETGKAIRTESRVEASLVADTLTFYGGLASELKGE 135 Query: 137 TLDLSLPLPPEVRSRASTQRVPVGVVAAIIPWNFPLLMAVWKIAPALACGNTVVLKPAEE 196 T+ P P++ + TQR P+GVV AIIPWN PL + KIAPAL GN V++K AEE Sbjct: 136 TV----PFHPKMLT--FTQREPIGVVGAIIPWNVPLYLMALKIAPALVAGNAVIVKSAEE 189 Query: 197 TPLTALRLAELAMEAGLPAGALNVVTGRGETAGDALVRHPKVAKVAFTGSTEVGRIIGSA 256 PL ALR+ ++ M LP G LN+++G G G LV HP V KV FTGS E G+II Sbjct: 190 APLAALRVIQV-MNQLLPPGVLNILSGDGPGCGAPLVTHPGVGKVTFTGSVETGKIISHL 248 Query: 257 CGRSLKAVSLELGGKSPVIVLADCDPQEAAEGAAAAI-FFNHGQVCTAGSRLYVHESIYE 315 L V+LELGGKSP+IV+ D D +A +GA A + F GQ CTA SR++VHES+++ Sbjct: 249 AADKLIPVTLELGGKSPMIVMGDADLDKAIDGAVAGMRFTRQGQSCTASSRIFVHESLHD 308 Query: 316 DVIQRLAVIGESIVVGSGLEQGVHMGPMVSKKHHENVLRHIRNGIEDGADLI---CGG-- 370 I +L +++ +G L++ +G ++S + E V +I G E A I C Sbjct: 309 AFIDKLKAKVDAMTMGDPLDEATDIGTIISPQQFERVQSYIALG-ETTAGAIAHRCSALP 367 Query: 371 TEAPCAQGFFVKPTIFANREKKDIRLLSQEVFGPVLVATPFSDIAEVVNEANRSVYGLGA 430 T+ A+G FV+P +F D RL +E+FGPV F D + + AN S +GL A Sbjct: 368 TDERLARGLFVQPVLFTGLAN-DHRLAREEIFGPVTCVIAFRDYEDALAMANDSDFGLAA 426 Query: 431 SIWTNDLSAALRINDELEAGTVWVNTHNMVDPNLPFGGFKDSGVGREHG-AAAIEHYTTT 489 +IWT DL AL L+AG V VN + +V P L +GGFK SG+G+E A ++H+T Sbjct: 427 TIWTRDLRTALDATRRLQAGFVQVNQNLVVQPGLSYGGFKQSGLGKEASLEAMLDHFTHK 486 Query: 490 RSLVI 494 ++++I Sbjct: 487 KTVII 491 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: 581 Number of extensions: 30 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: 494 Length adjustment: 34 Effective length of query: 462 Effective length of database: 460 Effective search space: 212520 Effective search space used: 212520 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