Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate SMa1731 SMa1731 betaine aldehyde dehydrogenase
Query= BRENDA::P77674 (474 letters) >FitnessBrowser__Smeli:SMa1731 Length = 489 Score = 316 bits (809), Expect = 1e-90 Identities = 173/453 (38%), Positives = 262/453 (57%), Gaps = 9/453 (1%) Query: 23 NPATGDVLLEIAEASAEQVDAAVRAADAAFAEWGQTTPKVRAECLLKLADVIEENGQVFA 82 NP G+++ ++ A++ ++ A+ +A A EW + P R L + AD++ + + Sbjct: 39 NPVDGEIIAKLHGATSCIIEKAIASAKRAQKEWARKEPAERGRVLSRAADIMRARNRELS 98 Query: 83 ELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNG--LAAGEYLEGHTSMIRRDPLG 140 LE+R+ GKP+ + + D +F A L+G + GE RR+PLG Sbjct: 99 VLETRDTGKPISETLVADAASGADCLEYFGAIAATLSGDSIQFGE----DWVYTRREPLG 154 Query: 141 VVASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITPLTALKLAELAKDI-FPAGVINI 199 V I WNYP+ +AAWK APALA GN ++ KPSE+TPL+ALKLAE+ + P GV NI Sbjct: 155 VCLGIGAWNYPIQIAAWKAAPALACGNAMIFKPSEVTPLSALKLAEILTEAGLPPGVFNI 214 Query: 200 LFGRGKTVGDPLTGHPKVRMVSLTGSIATGEHIISHTASSIKRTHMELGGKAPVIVFDDA 259 + G G VG L HP + VSLTGS+ TG + S + I+ MELGGK+ +IVFDDA Sbjct: 215 VQGAGD-VGAELATHPAIAKVSLTGSVKTGARVASAAMAGIRPVTMELGGKSALIVFDDA 273 Query: 260 DIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDTLVEKLGAAVATLKSGAPDDESTEL 319 D+EA V G +Y+AGQ C+ R++ Q+GI + + +L A VA LK G P DE T++ Sbjct: 274 DVEAAVSGAILGNFYSAGQICSNGTRVFLQRGIREAFLARLLARVAALKIGDPMDEETDI 333 Query: 320 GPLSSLAHLERVGKAVEEAKATGHIKVITGGEKRKGNGYYYAPTLLAGALQDDAIVQKEV 379 GPL S AH RV V A+ G ++ + G+ ++ P + + ++EV Sbjct: 334 GPLVSAAHRNRVATYVARAEVEGAYQMAPPRKLPPGDA-WHEPVVFTNVTDWMTLAREEV 392 Query: 380 FGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTKDVGRAHRVSARLQYGCTWVNTHFMLV 439 FGPV++V FD+E+ VV AN + +GLA+ ++T+D+ RAHR++A L+ G W+N + + Sbjct: 393 FGPVMAVLDFDDEQDVVARANATDFGLAAGIFTRDLVRAHRLAAELEAGTVWINAYNLTP 452 Query: 440 SEMPHGGQKLSGYGKDMSLYGLEDYTVVRHVMV 472 + M GG K SG G++ ++ YT ++ V V Sbjct: 453 AGMAFGGIKRSGIGRENGRVAIDHYTQLKSVFV 485 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: 513 Number of extensions: 20 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