Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate GFF1170 PS417_05945 gamma-aminobutyraldehyde dehydrogenase
Query= BRENDA::P77674 (474 letters) >FitnessBrowser__WCS417:GFF1170 Length = 485 Score = 611 bits (1576), Expect = e-179 Identities = 301/470 (64%), Positives = 363/470 (77%) Query: 5 LLINGELVSGEGEKQPVYNPATGDVLLEIAEASAEQVDAAVRAADAAFAEWGQTTPKVRA 64 LLI+GELV G+G +P+ NPATG+VL +IAEASAEQV+ A+ AA AFA W +TTP+ R+ Sbjct: 12 LLIDGELVHGQGFAEPILNPATGEVLTQIAEASAEQVETAILAAHRAFAGWSRTTPQQRS 71 Query: 65 ECLLKLADVIEENGQVFAELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNGLAAG 124 LL +AD IE+ A LES NCGKPLH A D++ A VDVFRFFAGA RC G +G Sbjct: 72 NILLGIADAIEKQADYLARLESLNCGKPLHLARQDDLSATVDVFRFFAGAVRCQTGQLSG 131 Query: 125 EYLEGHTSMIRRDPLGVVASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITPLTALKL 184 EYL G+TSM+RRDP+GVVASIAPWNYPLMMAAWK+APALAAGN +V KPSE TPL+ L L Sbjct: 132 EYLPGYTSMVRRDPIGVVASIAPWNYPLMMAAWKIAPALAAGNTLVFKPSEHTPLSILAL 191 Query: 185 AELAKDIFPAGVINILFGRGKTVGDPLTGHPKVRMVSLTGSIATGEHIISHTASSIKRTH 244 A + K++ P GVINIL G G+ VG L HPKVRMVSLTG I TG+ I+ + ++KRTH Sbjct: 192 APVLKELLPRGVINILCGGGEGVGSHLVSHPKVRMVSLTGDIVTGQKILQAASKTLKRTH 251 Query: 245 MELGGKAPVIVFDDADIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDTLVEKLGAAV 304 +ELGGKAPVIV +DAD+ AVV+GVR +GYYNAGQDCTAACRIYAQ GI+D LV +LGAAV Sbjct: 252 LELGGKAPVIVCNDADLHAVVDGVRAYGYYNAGQDCTAACRIYAQAGIHDKLVAELGAAV 311 Query: 305 ATLKSGAPDDESTELGPLSSLAHLERVGKAVEEAKATGHIKVITGGEKRKGNGYYYAPTL 364 ++L+ D ELGPL S +RV VE A HI+ ITG G G+YY PTL Sbjct: 312 SSLRFAGKRDADNELGPLISTRQRDRVASFVERALGQPHIERITGAAVHSGAGFYYQPTL 371 Query: 365 LAGALQDDAIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTKDVGRAHRVSAR 424 LAG Q+D IVQ+EVFGPVV+VT FD EQ V+WANDS+YGLASSVWT+++ +A +V+AR Sbjct: 372 LAGCKQNDEIVQREVFGPVVTVTRFDELEQAVDWANDSEYGLASSVWTQNLDKAMQVAAR 431 Query: 425 LQYGCTWVNTHFMLVSEMPHGGQKLSGYGKDMSLYGLEDYTVVRHVMVKH 474 LQYGCTW+N+HFMLVSEMPHGG K SGYGKD+S L+DY+VVRH+M +H Sbjct: 432 LQYGCTWINSHFMLVSEMPHGGLKRSGYGKDLSSDSLQDYSVVRHIMARH 481 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: 676 Number of extensions: 22 Number of successful extensions: 1 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: 485 Length adjustment: 34 Effective length of query: 440 Effective length of database: 451 Effective search space: 198440 Effective search space used: 198440 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: 51 (24.3 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