Align Phenylacetaldehyde dehydrogenase; PAD; EC 1.2.1.39 (characterized)
to candidate Pf1N1B4_3024 4-aminobutyraldehyde dehydrogenase (EC 1.2.1.19)
Query= SwissProt::O06837 (502 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3024 Length = 474 Score = 349 bits (896), Expect = e-100 Identities = 198/481 (41%), Positives = 280/481 (58%), Gaps = 10/481 (2%) Query: 22 QMLIGGQWVNAQSDKTLNVYNPATGDTLTDVPDGDVEDVNAAVESAAATLQSDAWRRMPP 81 ++LI GQ VN V+NPA G L ++ + V+AAV +A Q AW + P Sbjct: 4 KLLINGQLVNGDGPAQA-VFNPALGRVLVEINEASEAQVDAAVRAADNAFQ--AWSQTTP 60 Query: 82 SARERILLRLADLLEAHGDELARLETLNNGKLLIYSKMMEVGASAQWLRYMAGWATKLTG 141 R +LL+LAD++EAHG+ELA+LE+ N GK + E+ A A R+ AG ++G Sbjct: 61 KERSLLLLKLADIIEAHGEELAKLESDNCGKPYSAALNDEIPAIADVFRFFAGANRCMSG 120 Query: 142 STLDLSLPLPPDVRSRASTQRVPVGVVAAIIPWNFPLLMAVWKIAPALACGNTVVLKPAE 201 + LP + +R PVGV+A+I PWN+PL+M WKIAPALA GNTVVLKP+E Sbjct: 121 ALGGEYLP-----GHTSMIRRDPVGVIASIAPWNYPLMMVAWKIAPALAAGNTVVLKPSE 175 Query: 202 ETPLTALRLAELAMEAGLPAGALNVVTGRGETAGDALVRHPKVAKVAFTGSTEVGRIIGS 261 +TPLTALRLAELA + PAG LN+V GRG G ALV HPKV V+ TGS G I S Sbjct: 176 QTPLTALRLAELASDI-FPAGVLNLVYGRGSAVGTALVNHPKVRMVSLTGSIATGSNIIS 234 Query: 262 ACGRSLKAVSLELGGKSPVIVLADCDPQEAAEGAAAAIFFNHGQVCTAGSRLYVHESIYE 321 + ++K + +ELGGK+PVI+ D D A EG F+N GQ CTA R+Y IY+ Sbjct: 235 STAGNVKRLHMELGGKAPVIIFDDADIDAAVEGIRTFGFYNAGQDCTAACRIYAQAGIYD 294 Query: 322 DVIQRLAVIGESIVVGSGLEQGVHMGPMVSKKHHENVLRHIRNGIEDGADLICGGTEAPC 381 +++L SI G + +GP++S +H + V + + + G +A Sbjct: 295 QFVEKLGAAVSSIKYGLQDDPSTELGPLISAQHRDRVTALVERAMAQPHIRLITGGKAVE 354 Query: 382 AQGFFVKPTIFANREKKDIRLLSQEVFGPVLVATPFSDIAEVVNEANRSVYGLGASIWTN 441 GFF +PT+ A+ ++ D ++ +EVFGPV+ T F+D A+ + AN S YGL +S+WT Sbjct: 355 GNGFFFEPTVLADVQQDD-EIVRREVFGPVVSVTRFTDEAQALAWANDSDYGLASSVWTT 413 Query: 442 DLSAALRINDELEAGTVWVNTHNMVDPNLPFGGFKDSGVGREHGAAAIEHYTTTRSLVIA 501 D+ A R++ L+ G WVNTH M+ +P GG K SG G++ +E YT R ++ Sbjct: 414 DVGRAHRLSARLQYGCTWVNTHFMLVSEMPHGGQKLSGYGKDMSMYGLEDYTVVRHVMFK 473 Query: 502 Y 502 + 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: 599 Number of extensions: 24 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: 502 Length of database: 474 Length adjustment: 34 Effective length of query: 468 Effective length of database: 440 Effective search space: 205920 Effective search space used: 205920 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