Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate BWI76_RS12820 BWI76_RS12820 NAD-dependent phenylacetaldehyde dehydrogenase
Query= BRENDA::P77674 (474 letters) >FitnessBrowser__Koxy:BWI76_RS12820 Length = 499 Score = 331 bits (848), Expect = 4e-95 Identities = 191/486 (39%), Positives = 283/486 (58%), Gaps = 18/486 (3%) Query: 2 QHKLLINGELVSGEGEKQ-PVYNPATGDVLLEIAEASAEQVDAAVRAADAAFAE--WGQT 58 QH L ++G + E E++ V+NPATG + A+A+A VD AV +A AF W Sbjct: 19 QHGLYLDGTQQAAESEQRLTVWNPATGQAIASTADANAADVDRAVMSAWRAFVSRSWAGR 78 Query: 59 TPKVRAECLLKLADVIEENGQVFAELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCL 118 TP R LL+ AD++E++G+ A+LE+ GK ++ + E+ ++ R+ AG + Sbjct: 79 TPADRERILLRFADLVEQHGEELAQLETLEQGKSINISRAFEVGCTLNWMRYTAGLTTKI 138 Query: 119 NGL---------AAGEYLEGHTSMIRRDPLGVVASIAPWNYPLMMAAWKLAPALAAGNCV 169 +G A G Y + +++P+GVVA I PWN+PLM+ WK+ PALAAG + Sbjct: 139 SGRTLDVSIPFPAGGRY----QAWTKKEPVGVVAGIVPWNFPLMIGMWKVMPALAAGCSI 194 Query: 170 VLKPSEITPLTALKLAELAKDI-FPAGVINILFGRGKTVGDPLTGHPKVRMVSLTGSIAT 228 V+KPSE TPLT L++AELA + P GV N++ G G G LT HP V VS TGS AT Sbjct: 195 VIKPSETTPLTLLRVAELATEAGVPDGVFNVVTGSGAGCGAALTSHPLVAKVSFTGSTAT 254 Query: 229 GEHIISHTASSIKRTHMELGGKAPVIVFDDADIEAVVEGVRTFGYYNAGQDCTAACRIYA 288 G+ I A + R +ELGGK P IV DAD + V+EG+ T + N GQ C A+ RIY Sbjct: 255 GKQIARVAADRLTRVTLELGGKNPAIVLKDADPQWVIEGLMTGSFLNQGQVCAASSRIYI 314 Query: 289 QKGIYDTLVEKLGAAVATLKSGAPDDESTELGPLSSLAHLERVGKAVEEAKATGHIKVIT 348 + ++DTLV AV +L+ G ES+++ P+ S AH +V ++EA+ ++I+ Sbjct: 315 EAPLFDTLVSGFEQAVKSLQVGPGMLESSQINPVVSQAHCAKVAAYLDEARQQ-KAELIS 373 Query: 349 GGEKRKGNGYYYAPTLLAGALQDDAIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLAS 408 G GYY APTL+ + ++EVFGPVV++ + E+ + ANDS +GL + Sbjct: 374 GHAGPDAQGYYIAPTLVINPDAGLRLCREEVFGPVVNLVRVADGEEALLLANDSDFGLTA 433 Query: 409 SVWTKDVGRAHRVSARLQYGCTWVNTHFMLVSEMPHGGQKLSGYGKDMSLYGLEDYTVVR 468 SVWT+D+ +A + RLQ G WVN+H ++ + +P GG K SG G+D L+D+ + Sbjct: 434 SVWTRDLTQALSYTDRLQAGTVWVNSHTLIDANLPFGGMKQSGTGRDFGPDWLDDWCETK 493 Query: 469 HVMVKH 474 V V++ Sbjct: 494 SVCVRY 499 Lambda K H 0.317 0.134 0.397 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: 569 Number of extensions: 29 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: 474 Length of database: 499 Length adjustment: 34 Effective length of query: 440 Effective length of database: 465 Effective search space: 204600 Effective search space used: 204600 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