Align phenylacetaldehyde dehydrogenase (EC 1.2.1.39) (characterized)
to candidate 15565 b1444 medium chain aldehyde dehydrogenase (NCBI)
Query= BRENDA::V4GH04 (496 letters) >FitnessBrowser__Keio:15565 Length = 474 Score = 348 bits (893), Expect = e-100 Identities = 196/484 (40%), Positives = 279/484 (57%), Gaps = 10/484 (2%) Query: 13 LPHQMLIGGQWVSAQSGKTLNVYNPATGDILTEVPDGDVEDVNAAVESAAATLRSDTWRR 72 + H++LI G+ VS + G+ VYNPATGD+L E+ + E V+AAV +A A W + Sbjct: 1 MQHKLLINGELVSGE-GEKQPVYNPATGDVLLEIAEASAEQVDAAVRAADAAFAE--WGQ 57 Query: 73 MPPSARERILLRLADLLEVHGDELARLETLNNGKLLIYSKLMEVGASAQWLRYMAGWATK 132 P R LL+LAD++E +G A LE+ N GK L + E+ A R+ AG A Sbjct: 58 TTPKVRAECLLKLADVIEENGQVFAELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARC 117 Query: 133 LTGSTLDLSLPLPPEVRSRASTQRVPVGVVAAIIPWNFPLLMAVWKIAPALACGNTVVLK 192 L G L + +R P+GVVA+I PWN+PL+MA WK+APALA GN VVLK Sbjct: 118 LNGLAAGEYLE-----GHTSMIRRDPLGVVASIAPWNYPLMMAAWKLAPALAAGNCVVLK 172 Query: 193 PAEETPLTALRLAELAMEAGLPAGALNVVTGRGETAGDALVRHPKVAKVAFTGSTEVGRI 252 P+E TPLTAL+LAELA + PAG +N++ GRG+T GD L HPKV V+ TGS G Sbjct: 173 PSEITPLTALKLAELAKDI-FPAGVINILFGRGKTVGDPLTGHPKVRMVSLTGSIATGEH 231 Query: 253 IGSACGRSLKAVSLELGGKSPVIVLADCDPQEAAEGAAAAIFFNHGQVCTAGSRLYVHES 312 I S S+K +ELGGK+PVIV D D + EG ++N GQ CTA R+Y + Sbjct: 232 IISHTASSIKRTHMELGGKAPVIVFDDADIEAVVEGVRTFGYYNAGQDCTAACRIYAQKG 291 Query: 313 IYEDVIQRLAVIGESIVVGSGLEQGVHMGPMVSKKHHENVLRHIRNGIEDGADLICGGTE 372 IY+ ++++L ++ G+ ++ +GP+ S H E V + + G + G E Sbjct: 292 IYDTLVEKLGAAVATLKSGAPDDESTELGPLSSLAHLERVGKAVEEAKATGHIKVITGGE 351 Query: 373 APCAQGFFVKPTIFANREKKDIRLLSQEVFGPVLVATPFSDIAEVVNEANRSVYGLGASI 432 G++ PT+ A + D ++ +EVFGPV+ TPF + +VVN AN S YGL +S+ Sbjct: 352 KRKGNGYYYAPTLLAGALQDD-AIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSV 410 Query: 433 WTNDLSAALRINDELEAGTVWVNTHNMVDPNLPFGGFKDSGVGREHGAAAIEHYTTTRSL 492 WT D+ A R++ L+ G WVNTH M+ +P GG K SG G++ +E YT R + Sbjct: 411 WTKDVGRAHRVSARLQYGCTWVNTHFMLVSEMPHGGQKLSGYGKDMSLYGLEDYTVVRHV 470 Query: 493 VIAY 496 ++ + Sbjct: 471 MVKH 474 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: 574 Number of extensions: 24 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: 496 Length of database: 474 Length adjustment: 34 Effective length of query: 462 Effective length of database: 440 Effective search space: 203280 Effective search space used: 203280 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