Align phenylacetaldehyde dehydrogenase (EC 1.2.1.39) (characterized)
to candidate GFF3174 PGA1_c32250 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase PuuC
Query= BRENDA::V4GH04 (496 letters) >FitnessBrowser__Phaeo:GFF3174 Length = 494 Score = 317 bits (811), Expect = 8e-91 Identities = 190/477 (39%), Positives = 263/477 (55%), Gaps = 10/477 (2%) Query: 18 LIGGQWVSAQSGKTLNVYNPATGDILTEVPDGDVEDVNAAVESAAATLRSDTWRRMPPSA 77 LI GQ V+A G T++V +P G +LT++ G V D+ A+ SA A W PP+A Sbjct: 20 LIDGQQVAASDGATMDVLSPIDGRLLTQIARGTVRDMERAIASARAAFEDRRWAGQPPAA 79 Query: 78 RERILLRLADLLEVHGDELARLETLNNGKLLIYSKLMEVGASAQWLRYMAGWATKLTGST 137 R+++L++ A+L+E LA L +NG + + E G++A +RY A K+ G Sbjct: 80 RKKVLMKWAELIEADALNLAVLGVRDNGTEITMALKAEPGSAAATIRYYAEALDKIYGEI 139 Query: 138 LDLSLPLPPEVRSRASTQRVPVGVVAAIIPWNFPLLMAVWKIAPALACGNTVVLKPAEET 197 S + V PVGVV AIIPWNFP+++ WK+APALA GN+VVLKP+E Sbjct: 140 APTSSDVLGMVHKE------PVGVVGAIIPWNFPMMIGAWKLAPALAMGNSVVLKPSETA 193 Query: 198 PLTALRLAELAMEAGLPAGALNVVTGRGETAGDALVRHPKVAKVAFTGSTEVGRIIGSAC 257 L+ +R+ ELA+EAGLP G LN VTG G G+AL V + FTGS + GR + Sbjct: 194 SLSLMRMVELALEAGLPPGVLNAVTGEGAVVGEALGLSMDVDVLVFTGSGQTGRRLMEYA 253 Query: 258 GRS-LKAVSLELGGKSPVIVLADC-DPQEAAEGAAAAIFFNHGQVCTAGSRLYVHESIYE 315 RS LK V LELGGKSP IV AD D +AA+ AA IF N GQVC AGSRL V SI++ Sbjct: 254 ARSNLKRVYLELGGKSPNIVFADAPDLADAAKVTAAGIFRNSGQVCVAGSRLLVEASIHD 313 Query: 316 DVIQRLAVIGESIVVGSGLEQGVHMGPMVSKKHHENVLRHIRNGIEDGADLICGGTEAPC 375 ++ +A + + VG L +G + S+ L+ + +G +I GG Sbjct: 314 AFVEEVAKAAQMMRVGDPLRLDTQIGAINSEAQLARNLQFVARAEVEGGQIITGGQRLLS 373 Query: 376 -AQGFFVKPTIFANREKKDIRLLSQEVFGPVLVATPFSDIAEVVNEANRSVYGLGASIWT 434 G ++ PTI D L +EVFGPVL TPF AE + AN +VYGL ++WT Sbjct: 374 ETGGSYMAPTIVTG-VTPDATLAQEEVFGPVLAVTPFETDAEALRIANATVYGLAGAVWT 432 Query: 435 NDLSAALRINDELEAGTVWVNTHNMVDPNLPFGGFKDSGVGREHGAAAIEHYTTTRS 491 + L+ A R+ + G + VNT+ D +P GG SG G + AI+ Y ++ Sbjct: 433 SGLTRAHRMVQGVRTGVMHVNTYGGADGTVPLGGVGQSGNGADKSLHAIDKYINLKT 489 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: 595 Number of extensions: 27 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: 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