Align phenylacetaldehyde dehydrogenase (EC 1.2.1.39) (characterized)
to candidate WP_057507564.1 ABB28_RS04920 CoA-acylating methylmalonate-semialdehyde dehydrogenase
Query= BRENDA::V4GH04 (496 letters) >NCBI__GCF_001431535.1:WP_057507564.1 Length = 501 Score = 220 bits (560), Expect = 1e-61 Identities = 156/490 (31%), Positives = 239/490 (48%), Gaps = 31/490 (6%) Query: 16 QMLIGGQWVSAQSGKTLNVYNPATGDILTEVPDGDVEDVNAAVESAAATLRSDTWRRMPP 75 ++LI GQ++ + + +V NPAT D+L +VP +V+ AV AAA TWR+ P Sbjct: 9 RLLIDGQFIESSTAHWQDVVNPATQDVLAQVPFATTSEVDDAV--AAAKEAFKTWRKTPI 66 Query: 76 SARERILLRLADLLEVHGDELARLETLNNGKLL------IYSKLMEVGASAQWLRYMAGW 129 R RI L+ L+ + ELA + GK + ++ L V +A G Sbjct: 67 GTRARIFLKYQQLIRENMSELAHTLSAEQGKTVPDAEGDVFRGLEVVEHAAAIGNLQLGE 126 Query: 130 ATKLTGSTLDLSLPLPPEVRSRASTQRVPVGVVAAIIPWNFPLLMAVWKIAPALACGNTV 189 + +D T P+GV A I P+NFP ++ +W A+A GNT Sbjct: 127 LANNVANGVD------------TYTLMQPLGVCAGITPFNFPAMIPLWMFPMAIATGNTF 174 Query: 190 VLKPAEETPLTALRLAELAMEAGLPAGALNVVTGRGETAGDALVRHPKVAKVAFTGSTEV 249 VLKP+E+ P+ +RL ELA+EAG+P G LNVV G GE +A+ HP + V+F GST V Sbjct: 175 VLKPSEQDPMVTMRLVELALEAGIPKGVLNVVHG-GEEVVNAICDHPDIKAVSFVGSTRV 233 Query: 250 GRIIGSACGRSLKAVSLELGGKSPVIVLADCDPQEAAEGAAAAIFFNHGQVCTAGSRLYV 309 G + + + K V +G K+ +VL D + ++ A F GQ C A S L V Sbjct: 234 GTHVYNRASLAGKRVQCMMGAKNHAVVLPDANKEQTLNAMVGAAFGAAGQRCMAASTL-V 292 Query: 310 HESIYEDVIQRLAVIGESIVVGSGLEQGVHMGPMVSKKHHENVLRHIRNGIEDGADLICG 369 + L +++ V +G G +GP++S E V I +G+E GA L Sbjct: 293 LVGEARSWVPDLVAKAKTLKVSAGSVAGTDVGPVISCSARERVEGLIASGLEQGATLDLD 352 Query: 370 GTEAPCAQGF----FVKPTIFANREKKDIRLLSQEVFGPVLVATPFSDIAEVVNEANRSV 425 G P GF FV PTIF+ D+R+ +E+FGPVLV + + + N + Sbjct: 353 GRN-PQVDGFEKGNFVGPTIFSG-VTTDMRIYQEEIFGPVLVILEAETLEDAIALVNSNP 410 Query: 426 YGLGASIWTNDLSAALRINDELEAGTVWVNTHNMVD-PNLPFGGFKDSGVG--REHGAAA 482 G G +++T +AA + ++++ G V +N V P F G + S +G +G Sbjct: 411 NGNGTAVFTQSGAAARKFQEDIDVGQVGINVPIPVPVPLFSFTGSRASKLGDLGPYGKQV 470 Query: 483 IEHYTTTRSL 492 + YT T+++ Sbjct: 471 VMFYTQTKTI 480 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: 628 Number of extensions: 37 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 496 Length of database: 501 Length adjustment: 34 Effective length of query: 462 Effective length of database: 467 Effective search space: 215754 Effective search space used: 215754 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 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