Align phenylacetaldehyde dehydrogenase (EC 1.2.1.39) (characterized)
to candidate AO353_04290 AO353_04290 1-pyrroline dehydrogenase
Query= BRENDA::V4GH04 (496 letters) >FitnessBrowser__pseudo3_N2E3:AO353_04290 Length = 474 Score = 358 bits (918), Expect = e-103 Identities = 202/481 (41%), Positives = 284/481 (59%), Gaps = 10/481 (2%) Query: 16 QMLIGGQWVSAQSGKTLNVYNPATGDILTEVPDGDVEDVNAAVESAAATLRSDTWRRMPP 75 ++LI GQ V+ + G V+NPA G +L E+ + V+AAV +A A W + PP Sbjct: 4 KLLINGQLVTGE-GPAQAVFNPALGRVLVEINEASEAQVDAAVRAADAAFEG--WSQTPP 60 Query: 76 SARERILLRLADLLEVHGDELARLETLNNGKLLIYSKLMEVGASAQWLRYMAGWATKLTG 135 R +LL+LAD+++ HG+ELA+LE+ N GK + E+ A A R+ AG + ++G Sbjct: 61 KDRSLLLLKLADVIQAHGEELAKLESDNCGKPYSAALNDEIPAIADVFRFFAGASRCMSG 120 Query: 136 STLDLSLPLPPEVRSRASTQRVPVGVVAAIIPWNFPLLMAVWKIAPALACGNTVVLKPAE 195 S LP + +R PVGV+A+I PWN+PL+M WKIAPALA GNTVVLKP+E Sbjct: 121 SAGGEYLP-----GHTSMIRRDPVGVIASIAPWNYPLMMVAWKIAPALAAGNTVVLKPSE 175 Query: 196 ETPLTALRLAELAMEAGLPAGALNVVTGRGETAGDALVRHPKVAKVAFTGSTEVGRIIGS 255 +TPLTALRLAELA E PAG LN+V GRG T G LV HPKV V+ TGS G I S Sbjct: 176 QTPLTALRLAELASEI-FPAGVLNLVFGRGPTVGSPLVTHPKVRMVSLTGSIATGSNIIS 234 Query: 256 ACGRSLKAVSLELGGKSPVIVLADCDPQEAAEGAAAAIFFNHGQVCTAGSRLYVHESIYE 315 + S+K + +ELGGK+PVI+ D D A EG F+N GQ CTA R+Y IYE Sbjct: 235 STADSVKRMHMELGGKAPVIIFDDADIDAAVEGIRTFGFYNAGQDCTAACRIYAQAGIYE 294 Query: 316 DVIQRLAVIGESIVVGSGLEQGVHMGPMVSKKHHENVLRHIRNGIEDGADLICGGTEAPC 375 +++L SI G + +GP+++ +H + V + I + G +A Sbjct: 295 KFVEKLGAAVSSIKYGLQDDPSTELGPLITAQHRDRVAGFVERAIAQPHIRLITGGKAVE 354 Query: 376 AQGFFVKPTIFANREKKDIRLLSQEVFGPVLVATPFSDIAEVVNEANRSVYGLGASIWTN 435 GFF +PT+ A+ ++D ++ +EVFGPV+ T F+D +V+ AN S YGL +S+WT+ Sbjct: 355 GNGFFFEPTVLAD-ARQDDEIVRREVFGPVVSVTSFADETQVLAWANDSDYGLASSVWTS 413 Query: 436 DLSAALRINDELEAGTVWVNTHNMVDPNLPFGGFKDSGVGREHGAAAIEHYTTTRSLVIA 495 D+ A R+ L+ G WVNTH M+ +P GG K SG G++ +E YTT R ++ Sbjct: 414 DVGRAHRLAARLQYGCTWVNTHFMLVSEMPHGGQKLSGYGKDMSMYGLEDYTTVRHVMFK 473 Query: 496 Y 496 + Sbjct: 474 H 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: 603 Number of extensions: 21 Number of successful extensions: 5 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