Align phenylacetaldehyde dehydrogenase (EC 1.2.1.39) (characterized)
to candidate WP_005460069.1 SACCYDRAFT_RS23635 NAD-dependent succinate-semialdehyde dehydrogenase
Query= BRENDA::V4GH04 (496 letters) >NCBI__GCF_000244975.1:WP_005460069.1 Length = 486 Score = 308 bits (788), Expect = 4e-88 Identities = 186/485 (38%), Positives = 261/485 (53%), Gaps = 11/485 (2%) Query: 12 RLPHQMLIGGQWVSAQSGKTLNVYNPATGDILTEVPDGDVEDVNAAVESAAATLRSDTWR 71 R+P Q+ + G W ++ G V +P T L EV DG +D AAVE+A + W Sbjct: 9 RVPKQVFVDGAWRASSDGSVFGVDDPGTESTLCEVADGQADDAKAAVEAAVEA--QEEWA 66 Query: 72 RMPPSARERILLRLADLLEVHGDELARLETLNNGKLLIYSKLMEVGASAQWLRYMAGWAT 131 PP R IL R L+ DELA L TL GK L S+ EV +A + R+ + A Sbjct: 67 ATPPRQRGEILRRAWQLMTDRTDELATLMTLEMGKSLTESRA-EVAYAADYFRWFSEEAV 125 Query: 132 KLTGSTLDLSLPLPPEVRSRASTQRVPVGVVAAIIPWNFPLLMAVWKIAPALACGNTVVL 191 ++ G P+ ++R R PVG I PWNFPL M KI PA+A G T+++ Sbjct: 126 RIDGD-----YSRTPDGKARMIVTRQPVGPCLLITPWNFPLAMGTRKIGPAVAAGCTMIV 180 Query: 192 KPAEETPLTALRLAELAMEAGLPAGALNVVTGRGET-AGDALVRHPKVAKVAFTGSTEVG 250 KPA+ TPL+ L LA+L EAGLP G LNVV + + ++ P++ K++FTGSTEVG Sbjct: 181 KPAQLTPLSMLALADLLTEAGLPGGVLNVVPSTSASRVVNPVLADPRIRKMSFTGSTEVG 240 Query: 251 RIIGSACGRSLKAVSLELGGKSPVIVLADCDPQEAAEGAAAAIFFNHGQVCTAGSRLYVH 310 R + C +L+ +S+ELGG + +V D D A EGA A N+G+ C A +R VH Sbjct: 241 RKLVEQCAPNLQRMSMELGGNAAFLVFEDADLDAAVEGAVTAKMRNNGESCVAANRFLVH 300 Query: 311 ESIYEDVIQRLAVIGESIVVGSGLEQGVHMGPMVSKKHHENVLRHIRNGIEDGADLICGG 370 SI E+ +RL + +G G E V +GP+V+ V + + + GA GG Sbjct: 301 TSIAEEFTRRLTDRMAGLRMGHGTEPDVVVGPLVNDGQRAKVSELVEDAVSRGARATTGG 360 Query: 371 TEAPCAQGFFVKPTIFANREKKDIRLLSQEVFGPVLVATPFSDIAEVVNEANRSVYGLGA 430 E G+F +PT+ A+ D R+L +EVFGPV T F+D E + AN + YGL Sbjct: 361 -EPGDGAGYFYRPTVLAD-VGDDARILREEVFGPVAPVTTFADEDEALAGANDTEYGLVG 418 Query: 431 SIWTNDLSAALRINDELEAGTVWVNTHNMVDPNLPFGGFKDSGVGREHGAAAIEHYTTTR 490 ++T DL A+R+ + L G V +NT + + + PFGG K SG GRE G I Y T+ Sbjct: 419 YVFTRDLERAVRVGEGLATGMVGINTGLVSNTSAPFGGVKASGFGREGGHEGITEYLDTK 478 Query: 491 SLVIA 495 L +A Sbjct: 479 YLSLA 483 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: 565 Number of extensions: 25 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: 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