Align phenylacetaldehyde dehydrogenase (EC 1.2.1.39) (characterized)
to candidate WP_011373513.1 SUDEN_RS09855 aldehyde dehydrogenase family protein
Query= BRENDA::V4GH04 (496 letters) >NCBI__GCF_000012965.1:WP_011373513.1 Length = 471 Score = 223 bits (569), Expect = 9e-63 Identities = 160/469 (34%), Positives = 248/469 (52%), Gaps = 19/469 (4%) Query: 29 GKTLNVYNPATGDILTEVPDGDVEDVNAAVESAAATLRSDTWRRMPPSARERILLRLADL 88 GK +N YN G++ +E + +D A+ A L S + + R LL +A Sbjct: 18 GKRVNPYN---GEVASEFVTCNADDAKKALN--IALLASKEASKTTIAQRCSWLLDVASK 72 Query: 89 LEVHGDELARLETLNNGKLLIYSKLMEVGASAQWLRYMAGWATKLTGSTLDLSLPLPPEV 148 L + +++A+ T GK + YS++ EV + + A + G T++ Sbjct: 73 LAQNKEDIAKTITDEVGKPITYSRI-EVERCIETVTLAAETMRTMHGETVNTDA-FASGK 130 Query: 149 RSRASTQRVPVGVVAAIIPWNFPLLMAVWKIAPALACGNTVVLKPAEETPLTALRLAELA 208 ++ + RVP GVV AI P+NFPL + KIAPAL GN V+LKP E PLTA + A+L Sbjct: 131 KTISFFSRVPCGVVVAITPFNFPLNLIAHKIAPALVAGNAVILKPTPEAPLTAYKFAKLF 190 Query: 209 MEAGLPA-GALNVVTGRGETAGDALVRH-PKVAKVAFTGSTEVGRIIGSACGRSLKAVSL 266 +E+ AL+VV G + G + P+V ++FTGS VG II + G +K VSL Sbjct: 191 IESEFAIKDALSVVYGDADVGGTLVTSEIPRV--ISFTGSVGVGEIITKSAG--IKKVSL 246 Query: 267 ELGGKSPVIVLADCDPQEAAEGAAAAIFFNHGQVCTAGSRLYVHESIYEDVIQRLAVIGE 326 ELGG + + + AA+ A F N GQVC + R+YVH+ IY + ++A + Sbjct: 247 ELGGNAATFIDKSANLDLAAQRCAIGAFVNSGQVCISLQRIYVHKDIYSEFALKIAEATK 306 Query: 327 SIVVGSGLEQGVHMGPMVSKKHHENVLRHIRNGIEDGADLICGGTEAPCAQGFFVKPTIF 386 +VVGS E+ MGP+V+ + + + +++ I++GA I P +G P + Sbjct: 307 KLVVGSPYEEDTFMGPLVNDEAAKRAMEWVQSAIKEGATPIL----EPRVEGRVFYPCVM 362 Query: 387 ANREKKDIRLLSQEVFGPVLVATPFSDIAEVVNEANRSVYGLGASIWTNDLSAALRINDE 446 A+ K+D+ ++ QEVF P++ D E + N S YGL SI+TNDL+ R +E Sbjct: 363 AD-VKEDMAIVCQEVFAPIVSLIEVKDFDEALPMMNNSPYGLQFSIFTNDLNLTKRAINE 421 Query: 447 LEAGTVWVNTHNMVDPNL-PFGGFKDSGVGREHGAAAIEHYTTTRSLVI 494 L+AG + +N + ++ P+GG K SGVGRE AIE + +S++I Sbjct: 422 LDAGGIVINDMPTLRFDIQPYGGVKLSGVGREGPRFAIEEMSEIKSVII 470 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: 518 Number of extensions: 23 Number of successful extensions: 4 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: 471 Length adjustment: 34 Effective length of query: 462 Effective length of database: 437 Effective search space: 201894 Effective search space used: 201894 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