Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate WP_085640679.1 MGEO_RS17260 betaine-aldehyde dehydrogenase
Query= BRENDA::P77674 (474 letters) >NCBI__GCF_002115805.1:WP_085640679.1 Length = 485 Score = 311 bits (798), Expect = 2e-89 Identities = 170/461 (36%), Positives = 266/461 (57%), Gaps = 9/461 (1%) Query: 16 GEKQPVYNPATGDVLLEIAEASAEQVDAAVRAADAAFAEWGQTTPKVRAECLLKLADVIE 75 G PV PATG+ + + A+ VD A+ AA A W + R L + AD++ Sbjct: 23 GTPIPVIYPATGEQIATVYAATPAIVDKALAAAHRAQKAWAAMSGTERGRILRRAADMMR 82 Query: 76 ENGQVFAELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNGLAAGEYLEGHTSMI- 134 E + LE+ + GKP + + D +F G A G GE+++ + Sbjct: 83 ERNHDLSVLETYDTGKPYQETIAVDATSGADALEYFGGLA----GSLTGEHIQLGEDWVY 138 Query: 135 -RRDPLGVVASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITPLTALKLAELAKDI-F 192 RR+PLGV I WNYP +A WK APALA GN +V KPSE TPL ALK+AE+ + Sbjct: 139 TRREPLGVCVGIGAWNYPTQIACWKGAPALACGNAMVFKPSETTPLCALKVAEILHEAGL 198 Query: 193 PAGVINILFGRGKTVGDPLTGHPKVRMVSLTGSIATGEHIISHTASSIKRTHMELGGKAP 252 PAG+ N++ G G+ VG L P+V VSLTGS+ TG+ + + A +K MELGGK+P Sbjct: 199 PAGIYNVVQGLGE-VGASLVTDPRVAKVSLTGSVPTGKKVYAAAAEQMKHVTMELGGKSP 257 Query: 253 VIVFDDADIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDTLVEKLGAAVATLKSGAP 312 +++FDDAD+E V G +Y++GQ C+ R++ QKGI + +++L ++T G P Sbjct: 258 LLIFDDADLENAVGGAILGNFYSSGQVCSNGTRVFVQKGIKEAFLKRLTERLSTAVVGDP 317 Query: 313 DDESTELGPLSSLAHLERVGKAVEEAKATGHIKVITGGEKRKGNGYYYAPTLLAGALQDD 372 DE+T GP+ S ++ V +E+ + G +++ GG + +G+Y PT+ A D Sbjct: 318 LDEATNFGPMVSEKQMKIVLDYIEKGENEG-ARLVAGGRRLNRDGFYLQPTVFADVKDDM 376 Query: 373 AIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTKDVGRAHRVSARLQYGCTWV 432 I ++E+FGPV++V F+ EE+ + AN +++GL++ V+T+D+ RAHRV A+L+ G ++ Sbjct: 377 IIAREEIFGPVMAVLDFETEEEAITRANSTEFGLSAGVFTRDLSRAHRVIAQLEAGSCFI 436 Query: 433 NTHFMLVSEMPHGGQKLSGYGKDMSLYGLEDYTVVRHVMVK 473 N++ E P GG K+SG G++ S + Y+ ++ V V+ Sbjct: 437 NSYNDAPVEAPFGGTKMSGVGRENSKAAINHYSEMKSVYVR 477 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: 30 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 Sep 24 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