Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate WP_068168204.1 HTA01S_RS06375 betaine-aldehyde dehydrogenase
Query= BRENDA::P77674 (474 letters) >NCBI__GCF_001592305.1:WP_068168204.1 Length = 485 Score = 346 bits (887), Expect = 1e-99 Identities = 191/472 (40%), Positives = 275/472 (58%), Gaps = 10/472 (2%) Query: 7 INGELVSGEGEKQPVYNPATGDVLLEIAEASAEQVDAAVRAADAAFAEWGQTTPKVRAEC 66 ING+ V+G G+ NPATG + EA+ + V+ AV AA A FA W + R Sbjct: 10 INGQTVNGGGQVFESVNPATGRAYAVVHEATQDDVNRAVEAAGAGFALWSAMSATERGRI 69 Query: 67 LLKLADVIEENGQVFAELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNGLAAGEY 126 L + AD++ E A LE R+CGKP+ A ++ + D +FAGAA L G +Y Sbjct: 70 LRRAADILRERNHELAALEVRDCGKPIQEALVVDVMSGADCIEYFAGAAATLTGQ---QY 126 Query: 127 -LEGHTSMIRRDPLGVVASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITPLTALKLA 185 L+ + R++PLGV I WNYP+ +A WK APALAAGN ++ KPSE+TP TA+KLA Sbjct: 127 PLKNAFAYTRKEPLGVCVGIGAWNYPIQIACWKSAPALAAGNAMIFKPSELTPATAVKLA 186 Query: 186 ELAKDI-FPAGVINILFGRGKTVGDPLTGHPKVRMVSLTGSIATGEHIISHTASSIKRTH 244 E+ + P GV N++ GRG VG L HP V VS+TGS+ TG+ ++ A ++KR Sbjct: 187 EVYLEAGVPPGVFNVVQGRG-AVGAMLAAHPDVAKVSVTGSVPTGKRVMETAAGTLKRVT 245 Query: 245 MELGGKAPVIVFDDADIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDTLVEKLGAAV 304 MELGGK+P++VFDDAD+E V +Y G+ CT R++ Q+GI + +L Sbjct: 246 MELGGKSPLLVFDDADLEQAVAAAMMGNFYTQGEVCTNCTRVFVQRGIAPRFLARLKERT 305 Query: 305 ATLKSGAPDDESTELGPLSSLAHLERVGKAVEEAKATGHIKVITGGEKRKGNG---YYYA 361 L+ G P D TE+G L S AH RV + +A G ++ GGE+ G + A Sbjct: 306 LLLRVGDPTDPDTEIGALISEAHTARVMDYIASGQAEG-ATLVCGGERVAVEGLGDQFVA 364 Query: 362 PTLLAGALQDDAIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTKDVGRAHRV 421 PT+ A D IV++E+FGPV+S+ FD E + + AN S++ LA+ V+T D+ R HRV Sbjct: 365 PTIFADCRDDMRIVREEIFGPVLSMLTFDTEAEAIARANQSRFSLAAGVFTTDLQRGHRV 424 Query: 422 SARLQYGCTWVNTHFMLVSEMPHGGQKLSGYGKDMSLYGLEDYTVVRHVMVK 473 +A+++ G W+N + + EMP GG SG G + S+ L+ YT ++ V V+ Sbjct: 425 AAQIRAGICWINNYNITPIEMPFGGVGESGIGSENSMAALDHYTQLKTVYVE 476 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: 554 Number of extensions: 25 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: 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 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