Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate GFF3684 HP15_3626 betaine aldehyde dehydrogenase
Query= BRENDA::P77674 (474 letters) >FitnessBrowser__Marino:GFF3684 Length = 489 Score = 322 bits (825), Expect = 2e-92 Identities = 180/468 (38%), Positives = 261/468 (55%), Gaps = 10/468 (2%) Query: 11 LVSGEGEKQPVYNPATGDVLLEIAEASAEQVDAAVRAADAAFAEWGQTTPKVRAECLLKL 70 L + GE PV NPATG V+ E+ A AA+ +A A FAEW T R+ LL+ Sbjct: 17 LANSTGETFPVVNPATGQVIYEVEVADESVQQAAIESARAGFAEWSAMTAIERSRILLRA 76 Query: 71 ADVIEENGQVFAELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNGLAAGEYLEGH 130 ++ E A E R+ GKP A ++ D FFAG A + G + L G Sbjct: 77 VAILRERNDELAAAEVRDTGKPWQEAEAVDVVTGADAVEFFAGLAPSIEGNQ--QDLGGD 134 Query: 131 TSMIRRDPLGVVASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITPLTALKLAELAKD 190 RR+PLG+ A I WNYP+ +A WK APALA GN ++ KPSE TP+ A+KLAE+ + Sbjct: 135 FYYTRREPLGICAGIGAWNYPIQIACWKSAPALACGNAMIFKPSEETPMGAVKLAEIFTE 194 Query: 191 I-FPAGVINILFGRGKTVGDPLTGHPKVRMVSLTGSIATGEHIISHTASSIKRTHMELGG 249 PAGV N++ G + VG LT HP++ VS TG +ATG+ +++ +S++K MELGG Sbjct: 195 AGVPAGVFNVVQGAAE-VGQWLTHHPEIAKVSFTGEVATGKKVMAAASSTLKDVTMELGG 253 Query: 250 KAPVIVFDDADIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDTLVEKLGAAVAT-LK 308 K+P+I+FDDAD+E + +Y G+ CT R++ + +Y +E+L +K Sbjct: 254 KSPLIIFDDADLENAISAAMVGNFYTQGEICTNGTRVFVHEDLYPRFIERLLERTRNNIK 313 Query: 309 SGAPDDESTELGPLSSLAH----LERVGKAVEEAKATGHIKVITGGEKRKGNGYYYAPTL 364 G P + T G L S H L+ + K + E H E KG GY+ PT+ Sbjct: 314 PGDPMNPDTNFGALISAKHRDLVLDYIAKGLSEGATLSHGGRAFEPEDSKG-GYFVEPTI 372 Query: 365 LAGALQDDAIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTKDVGRAHRVSAR 424 D IV++E+FGPV+SV F +E++V+ AN++ GLA+ V+T D+ RAHRV + Sbjct: 373 FTDCTDDMTIVKEEIFGPVMSVLTFRDEDEVIARANNTDTGLAAGVFTNDIRRAHRVIHQ 432 Query: 425 LQYGCTWVNTHFMLVSEMPHGGQKLSGYGKDMSLYGLEDYTVVRHVMV 472 +Q G W+N++ +EMP GG KLSG G++ + YT ++ V V Sbjct: 433 IQAGICWINSYGASPAEMPVGGYKLSGIGRENGRETIAHYTQIKSVYV 480 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: 557 Number of extensions: 21 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: 474 Length of database: 489 Length adjustment: 34 Effective length of query: 440 Effective length of database: 455 Effective search space: 200200 Effective search space used: 200200 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