Align phenylacetaldehyde dehydrogenase (EC 1.2.1.39) (characterized)
to candidate WP_019744147.1 BA79_RS03900 CoA-acylating methylmalonate-semialdehyde dehydrogenase
Query= BRENDA::V4GH04 (496 letters) >NCBI__GCF_000691145.1:WP_019744147.1 Length = 486 Score = 291 bits (745), Expect = 4e-83 Identities = 178/489 (36%), Positives = 272/489 (55%), Gaps = 27/489 (5%) Query: 19 IGGQWVSAQSGKTLNVYNPATGDILTEVPDGDVEDVNAAVESAAATLRSDTWRRMPPSAR 78 IGGQWV A++ +T VYNPATG+++ EVP DV AV++A TW + R Sbjct: 13 IGGQWVDAETNQTEAVYNPATGEVIAEVPLSTKTDVEHAVQAAQEAFT--TWSKTAVPRR 70 Query: 79 ERILLRLADLLEVHGDELARLETLNNGKLLIYSKLMEVGASAQWLRYMAGWATKLTGSTL 138 RIL + LL DELA L TL NGK + +K EV + + + AG T + G L Sbjct: 71 ARILFKYQQLLVEKWDELAELVTLENGKSVTEAK-GEVQRGIECVEFAAGAPTLMMGKQL 129 Query: 139 DLSLPLPPEVRS--RASTQRVPVGVVAAIIPWNFPLLMAVWKIAPALACGNTVVLKPAEE 196 P++ + + R P+GV+ I P+NFP+++ W A+ACGNT VLKP+E Sbjct: 130 -------PDIATGLESGMYRYPIGVIGGITPFNFPMMVPCWMFPLAIACGNTFVLKPSER 182 Query: 197 TPLTALRLAELAMEAGLPAGALNVVTGRGETAGDALVRHPKVAKVAFTGSTEVGRII--- 253 TP+ A RLAEL EAGLP G LN+V G + + L+ H KV ++F GS V + Sbjct: 183 TPILAARLAELFEEAGLPKGVLNIVNGAHDVV-NGLLEHEKVKAISFVGSQPVAEYVYKK 241 Query: 254 GSACGRSLKAVSLELGGKSPVIVLADCDPQEAAEGAAAAIFFNHGQVCTAGSRLYVHESI 313 G+A G+ ++A++ G K+ IVL D D + A + A F + G+ C A + + V E + Sbjct: 242 GTAHGKRVQALA---GAKNHSIVLKDADLESATKQIIGAAFGSAGERCMAAAVVAVEEDV 298 Query: 314 YEDVIQRLAVIGESIVVGSGLEQGVHMGPMVSKKHHENVLRHIRNGIEDGADLICGGTE- 372 +D+IQ+L +V+G+G+ + V +GP++ K+H E L++I++GIE+GA LI G + Sbjct: 299 ADDLIQQLVDESNQLVIGNGINKDVFLGPVIRKEHKERTLQYIQSGIEEGASLIRDGRQD 358 Query: 373 -APCAQGFFVKPTIFANREKKDIRLLSQEVFGPVLVATPFSDIAEVVNEANRSVYGLGAS 431 +G+FV PTIF + +++ E+F PVL S +AE ++ +N+S + GA Sbjct: 359 NETNGEGYFVGPTIF-DHVTNQMKIWQDEIFAPVLSIVRVSSLAEAIDLSNQSKFANGAC 417 Query: 432 IWTNDLSAALRINDELEAGTVWVNTHNMVDPN--LPFGGFKDSGVGREH--GAAAIEHYT 487 ++T+ S+ + +EAG + +N + P PF G+KDS G H G +E YT Sbjct: 418 LYTDSASSIREFRENIEAGMLGINI-GVPAPMAFFPFSGWKDSFYGDLHANGTDGVEFYT 476 Query: 488 TTRSLVIAY 496 + + Y Sbjct: 477 RKKMVTARY 485 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: 583 Number of extensions: 33 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: 486 Length adjustment: 34 Effective length of query: 462 Effective length of database: 452 Effective search space: 208824 Effective search space used: 208824 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 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