Align phenylacetaldehyde dehydrogenase (EC 1.2.1.39) (characterized)
to candidate WP_011383730.1 AMB_RS06710 NAD-dependent succinate-semialdehyde dehydrogenase
Query= BRENDA::V4GH04 (496 letters) >NCBI__GCF_000009985.1:WP_011383730.1 Length = 485 Score = 299 bits (766), Expect = 1e-85 Identities = 187/489 (38%), Positives = 261/489 (53%), Gaps = 11/489 (2%) Query: 5 LSAIDGLRLPHQMLIGGQWVSAQSGKTLNVYNPATGDILTEVPDGDVEDVNAAVESAAAT 64 L D L I G WV+AQSG+ L V NPA G ++ VP + A+E AA Sbjct: 2 LDLSDSALLRDHAYINGSWVAAQSGERLAVTNPADGSLIIRVPAMGAAETRQAIE--AAD 59 Query: 65 LRSDTWRRMPPSARERILLRLADLLEVHGDELARLETLNNGKLLIYSKLMEVGASAQWLR 124 W+ R +L R +L+ ++LA+L T GK L +K EV A ++ Sbjct: 60 RAWGPWKAKTAKERSAVLRRWFELIMAAQNDLAKLMTAEQGKPLAEAK-GEVAYGASFVE 118 Query: 125 YMAGWATKLTGSTLDLSLPLPPEVRSRASTQRVPVGVVAAIIPWNFPLLMAVWKIAPALA 184 + A A ++ G T+ +P R + P+GVVAAI PWNFPL M K APALA Sbjct: 119 WFAEEAKRVYGDTIPEHMP-----GRRIVVVKEPIGVVAAITPWNFPLAMITRKCAPALA 173 Query: 185 CGNTVVLKPAEETPLTALRLAELAMEAGLPAGALNVVT-GRGETAGDALVRHPKVAKVAF 243 G VV+KPAE+TPL+AL LAELA AG P G NV+T G + G L +PKV K++F Sbjct: 174 AGCPVVVKPAEDTPLSALALAELAERAGFPPGVFNVITAGDPKAVGFELTANPKVRKLSF 233 Query: 244 TGSTEVGRIIGSACGRSLKAVSLELGGKSPVIVLADCDPQEAAEGAAAAIFFNHGQVCTA 303 TGSTEVG+++ + C ++K +SLELGG +P +V D D A GA A+ + N GQ C Sbjct: 234 TGSTEVGKLLMAQCAATVKKLSLELGGNAPFMVFDDADLDAAVAGAMASKYRNTGQTCVC 293 Query: 304 GSRLYVHESIYEDVIQRLAVIGESIVVGSGLEQGVHMGPMVSKKHHENVLRHIRNGIEDG 363 +RL V + IY+ RLA ++ VG GLE GP+++++ V RHI + + G Sbjct: 294 ANRLLVQDGIYDAFTARLAEAVAALKVGPGLEGDFQQGPLINEEAVRKVERHIADAVAKG 353 Query: 364 ADLICGGTEAPCAQGFFVKPTIFANREKKDIRLLSQEVFGPVLVATPFSDIAEVVNEANR 423 A ++ GG + G F +PTI A+ D+ +E FGPV F E V AN Sbjct: 354 ARVVMGG-KRHARGGTFFEPTILAD-VTPDMAPAREETFGPVAPLFRFKTEEEAVRMAND 411 Query: 424 SVYGLGASIWTNDLSAALRINDELEAGTVWVNTHNMVDPNLPFGGFKDSGVGREHGAAAI 483 + +GL A ++ D+ R++ LE G V +N + PFGG K+SG+GRE I Sbjct: 412 TEFGLAAYFYSRDVGRVWRVSRALEYGIVGINEGLISTEVAPFGGVKESGLGREGSKYGI 471 Query: 484 EHYTTTRSL 492 E + + L Sbjct: 472 EDFLEVKYL 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: 595 Number of extensions: 34 Number of successful extensions: 5 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: 485 Length adjustment: 34 Effective length of query: 462 Effective length of database: 451 Effective search space: 208362 Effective search space used: 208362 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 17 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