Align phenylacetaldehyde dehydrogenase (EC 1.2.1.39) (characterized)
to candidate AZOBR_RS22315 AZOBR_RS22315 aldehyde dehydrogenase
Query= BRENDA::V4GH04 (496 letters) >FitnessBrowser__azobra:AZOBR_RS22315 Length = 497 Score = 325 bits (832), Expect = 3e-93 Identities = 190/487 (39%), Positives = 278/487 (57%), Gaps = 15/487 (3%) Query: 13 LPHQMLIGGQWVSAQSGKTLNVYNPATGDILTEVPDGDVEDVNAAVESAAATLRSDTWRR 72 L + GG++ A SGK V NPATG+ + E G+ DV+AAV +A A + W + Sbjct: 18 LSSKHFFGGEFRPASSGKGFPVVNPATGETVAEAAFGEAADVDAAVAAAVAAQKE--WAK 75 Query: 73 MPPSARERILLRLADLLEVHGDELARLETLNNGKLLIYSKLMEVGASAQWLRYMAGWATK 132 P R +++ +L+ H +E+A+L L GK L +E G + + G A + Sbjct: 76 RPVRERGKLVAECGRVLDAHKEEIAKLIALETGKALRTESRVEAGVLSDAFVFFGGLAPE 135 Query: 133 LTGSTLDLSLPLPPEVRSRASTQRVPVGVVAAIIPWNFPLLMAVWKIAPALACGNTVVLK 192 L G T+ P P + + T R PVGVV AIIPWN PLL+ KIAPA+ GN VV+K Sbjct: 136 LKGETI----PFNPSMLTM--TVREPVGVVGAIIPWNVPLLLMALKIAPAMVAGNAVVVK 189 Query: 193 PAEETPLTALRLAELAMEAGLPAGALNVVTGRGETAGDALVRHPKVAKVAFTGSTEVGRI 252 AEE PL LR+ +L + +PAG +N+++G G G LV H V KV FTGS E G+I Sbjct: 190 SAEEAPLAVLRVVQL-INTVIPAGVVNILSGYGPECGAPLVAHKDVKKVTFTGSVETGKI 248 Query: 253 IGSACGRSLKAVSLELGGKSPVIVLADCDPQEAAEGAAAAI-FFNHGQVCTAGSRLYVHE 311 + L V+LELGGKSP+IV D D +A GA A + F GQ CTA SR++VH+ Sbjct: 249 VYKTAAEKLIPVTLELGGKSPMIVCGDADLDQAIAGAIAGMRFTRQGQSCTASSRIFVHD 308 Query: 312 SIYEDVIQRLAVIGESIVVGSGLEQGVHMGPMVSKKHHENVLRHIRNGIEDGADL-ICGG 370 SI++ +++L ++ +G L++ +G +VS + + V +I G E GA +C Sbjct: 309 SIHDAFVEKLKEKVNAMKMGDPLDESTDIGTIVSPQQLDRVQSYIAIGKEGGATPHVCSA 368 Query: 371 --TEAPCAQGFFVKPTIFANREKKDIRLLSQEVFGPVLVATPFSDIAEVVNEANRSVYGL 428 ++ +G +V+P IF + D R+ +E+FGPV ++D EV+ +AN + YGL Sbjct: 369 MPSDPKLTKGLYVQPHIFTGVKNSD-RIAQEEIFGPVCCVIRWTDYEEVIAQANDTEYGL 427 Query: 429 GASIWTNDLSAALRINDELEAGTVWVNTHNMVDPNLPFGGFKDSGVGREHG-AAAIEHYT 487 A+IWT DL A+ LEAG V VN + +V PNL +GG K SG+G+E A +EH+T Sbjct: 428 AATIWTRDLKVAMDAVHRLEAGFVQVNQNLVVQPNLSYGGVKSSGLGKEASLEAMLEHFT 487 Query: 488 TTRSLVI 494 ++++I Sbjct: 488 HKKTIII 494 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: 577 Number of extensions: 25 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: 497 Length adjustment: 34 Effective length of query: 462 Effective length of database: 463 Effective search space: 213906 Effective search space used: 213906 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