Align phenylacetaldehyde dehydrogenase (EC 1.2.1.39) (characterized)
to candidate WP_029133426.1 A3GO_RS0110905 aldehyde dehydrogenase
Query= BRENDA::Q5P171 (474 letters) >NCBI__GCF_000428045.1:WP_029133426.1 Length = 470 Score = 547 bits (1409), Expect = e-160 Identities = 275/471 (58%), Positives = 338/471 (71%), Gaps = 6/471 (1%) Query: 4 FDMIINGKPVRAGS-TFDVVNPATGEVFARVQAGDASHVDQAVAAARAAFPGWSRTPDAE 62 + ++I G V + +FDV+NPAT V A +D AVAAA AF W + + Sbjct: 5 YKLLIGGAWVAGDNGSFDVLNPATEAVVAACPTASVGQLDAAVAAAGEAFRQWQFSSNDT 64 Query: 63 RKRLMHALGAALEAHMPELMELVTKEAGKPLGGLNGVGSGMEVGGAIAWTHVTADLELPV 122 RK+L+H + +EAH EL E+V E GKP+ + EVGGA+AWT TA+L++PV Sbjct: 65 RKQLLHDIADKIEAHAAELAEIVVAEQGKPM-----FLAQAEVGGAVAWTRATAELDIPV 119 Query: 123 EVIQDNDDARIEVHRKPLGVVGSITPWNWPLMIAIWHVIPALRAGNTVVIKPSGMTPTAT 182 EVI+D+ RIE+HRKPLGVVGSITPWNWPLMIA+WH++PALR GNTVVIKPS TP T Sbjct: 120 EVIEDSPGKRIEMHRKPLGVVGSITPWNWPLMIAVWHIMPALRTGNTVVIKPSEFTPLNT 179 Query: 183 IRFVELANAILPPGVLNIVTGESGVGSAIAKHPDINKIVFTGSTPTGKNIMQNAAGNLKR 242 +R VEL N + P GV+N+VTG S +G A++ H INKIVFTGST TGK+IM +AA NLKR Sbjct: 180 LRLVELINEVAPKGVVNVVTGMSDIGRAMSVHTRINKIVFTGSTATGKDIMFHAANNLKR 239 Query: 243 LTLELGGNDAGIVLPDVDPKAIAPKLFGVGFHNNGQTCACLKRLYVHDSIYEKVCAELAR 302 LTLELGGNDAGIVLP D A+A +F F N GQTCA LKRLYVHDSIYE +C +L Sbjct: 240 LTLELGGNDAGIVLPGTDVDAVAMPIFQGAFLNMGQTCAALKRLYVHDSIYEAMCGKLTE 299 Query: 303 IAKETVVGDGLVEGTELGPVQNKAQLDFVQELVEDARAHGARILSGGKARSGGGFFFEPT 362 IA++ +G G+ EG GPVQNK QL V +LVEDAR +GARIL GG+ +G G+F+ PT Sbjct: 300 IAQQQQLGSGMDEGVTFGPVQNKKQLQIVSDLVEDARNNGARILCGGERLAGSGYFYPPT 359 Query: 363 VIADAKDGMRVVDEEQFGPVLPVIRYSDIEEVIARANNNENGLGGSIWSKDHAKAAELAL 422 ++A+A DGMR+VDEEQFGPVLPVIRYSD+++ + RAN+ + GLGGS+W D A ++A Sbjct: 360 IVAEASDGMRIVDEEQFGPVLPVIRYSDVDDAVRRANDCDAGLGGSVWGADVESATQVAT 419 Query: 423 RLECGTAWVNEHGAVQPDAPFGGVKQSGLGVEFGRYGLEEYTSIQTLKIMK 473 RLECGTAW+N H V P APFGG K SG GVEFG GL EYTS Q L I K Sbjct: 420 RLECGTAWINGHAEVLPHAPFGGCKMSGFGVEFGVEGLLEYTSPQLLNINK 470 Lambda K H 0.317 0.136 0.405 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: 720 Number of extensions: 26 Number of successful extensions: 2 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: 474 Length of database: 470 Length adjustment: 33 Effective length of query: 441 Effective length of database: 437 Effective search space: 192717 Effective search space used: 192717 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 (21.6 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Sep 24 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