Align phenylacetaldehyde dehydrogenase (EC 1.2.1.39) (characterized)
to candidate WP_058929155.1 AU252_RS01160 aldehyde dehydrogenase family protein
Query= BRENDA::Q5P171 (474 letters) >NCBI__GCF_001484605.1:WP_058929155.1 Length = 486 Score = 423 bits (1087), Expect = e-123 Identities = 210/469 (44%), Positives = 290/469 (61%), Gaps = 6/469 (1%) Query: 6 MIINGKPVRAGSTFDVVNPATGEVFARVQAGDASHVDQAVAAARAAFPGWSRTPDAERKR 65 ++I+G+ V A STFDV NPATG+V A+ +D+AVAAA AFP W+ TP ER Sbjct: 19 LVIDGQAVSAMSTFDVFNPATGQVIAKAPDASVEQLDEAVAAAARAFPAWAATPIEERAA 78 Query: 66 LMHALGAALEAHMPELMELVTKEAGKPLGGLNGVGSGMEVGGAIAWTHVTADLELPVEVI 125 ++ A+G +E H + M L+T+E GKP G E+ G+ W A L EV+ Sbjct: 79 VLAAIGDRIEEHSEQFMALLTREQGKPRAGAE-----WEIMGSAIWCREIAKQRLTPEVL 133 Query: 126 QDNDDARIEVHRKPLGVVGSITPWNWPLMIAIWHVIPALRAGNTVVIKPSGMTPTATIRF 185 D+D+ R+ PLGV+G+I PWN+P+++AIW + PA+ AGNT+V+KPS TP T++ Sbjct: 134 VDDDNRRVTTRYTPLGVIGAIAPWNFPILLAIWKIAPAILAGNTIVVKPSPFTPLTTLKL 193 Query: 186 VELANAILPPGVLNIVTGESGVGSAIAKHPDINKIVFTGSTPTGKNIMQNAAGNLKRLTL 245 EL +LP GV N+VTG +G + HP I KI FTGST TG+++M +AA ++KR+TL Sbjct: 194 AELVQDLLPAGVFNVVTGGDDLGKRMTSHPGIAKIAFTGSTETGRHVMASAAKSIKRVTL 253 Query: 246 ELGGNDAGIVLPDVDPKAIAPKLFGVGFHNNGQTCACLKRLYVHDSIYEKVCAELARIAK 305 ELGGND IVLPDVDP +AP+LF F NN Q C KRLY+H+ +Y+ V L AK Sbjct: 254 ELGGNDPAIVLPDVDPATVAPQLFWAAFQNNAQFCNATKRLYIHEDVYDVVRDALVEYAK 313 Query: 306 ETVVGDGLVEGTELGPVQNKAQLDFVQELVEDARAHGARILSGGKA-RSGGGFFFEPTVI 364 VG+G T+LGP+QN Q + V+E D G GG+ S G+F + + Sbjct: 314 TVKVGNGAEPHTDLGPIQNAPQFEKVKEFFADCNDRGYAFALGGQIDESQPGWFIPVSFV 373 Query: 365 ADAKDGMRVVDEEQFGPVLPVIRYSDIEEVIARANNNENGLGGSIWSKDHAKAAELALRL 424 + + R+V EE FGP+LP++++ D E+VI+RAN+ + GLG S+W KD +A R+ Sbjct: 374 DNPPEDSRIVQEEPFGPILPLLKWRDEEDVISRANDTQWGLGASVWGKDEQALERIAARI 433 Query: 425 ECGTAWVNEHGAVQPDAPFGGVKQSGLGVEFGRYGLEEYTSIQTLKIMK 473 E GT W+NE P+ FGG KQSGLG E +GL EYT+ QT + K Sbjct: 434 EAGTVWINEVHQYAPNQAFGGHKQSGLGCENSLHGLAEYTNWQTTTLNK 482 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: 681 Number of extensions: 32 Number of successful extensions: 3 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: 486 Length adjustment: 34 Effective length of query: 440 Effective length of database: 452 Effective search space: 198880 Effective search space used: 198880 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 Apr 09 2024. 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