Align lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)
to candidate WP_085640679.1 MGEO_RS17260 betaine-aldehyde dehydrogenase
Query= BRENDA::P25553 (479 letters) >NCBI__GCF_002115805.1:WP_085640679.1 Length = 485 Score = 301 bits (772), Expect = 2e-86 Identities = 178/471 (37%), Positives = 270/471 (57%), Gaps = 7/471 (1%) Query: 10 YIDGQFVTWRGDAWIDVVNPATEAVISRIPDGQAEDARKAIDAAERAQPEWEALPAIERA 69 +IDG +V I V+ PAT I+ + KA+ AA RAQ W A+ ER Sbjct: 12 FIDGAYVEDTTGTPIPVIYPATGEQIATVYAATPAIVDKALAAAHRAQKAWAAMSGTERG 71 Query: 70 SWLRKISAGIRERASEISALIVEEGGK-IQQLAEVEVAFTADYIDYMAEWARRYEGEIIQ 128 LR+ + +RER ++S L + GK Q+ V+ AD ++Y A GE IQ Sbjct: 72 RILRRAADMMRERNHDLSVLETYDTGKPYQETIAVDATSGADALEYFGGLAGSLTGEHIQ 131 Query: 129 SDRPGENILLFKRA-LGVTTGILPWNFPFFLIARKMAPALLTGNTIVIKPSEFTPNNAIA 187 GE+ + +R LGV GI WN+P + K APAL GN +V KPSE TP A+ Sbjct: 132 L---GEDWVYTRREPLGVCVGIGAWNYPTQIACWKGAPALACGNAMVFKPSETTPLCALK 188 Query: 188 FAKIVDEIGLPRGVFNLVLGRGETVGQELAGNPKVAMVSMTGSVSAGEKIMATAAKNITK 247 A+I+ E GLP G++N+V G GE VG L +P+VA VS+TGSV G+K+ A AA+ + Sbjct: 189 VAEILHEAGLPAGIYNVVQGLGE-VGASLVTDPRVAKVSLTGSVPTGKKVYAAAAEQMKH 247 Query: 248 VCLELGGKAPAIVMDDADLELAVKAIVDSRVINSGQVCNCAERVYVQKGIYDQFVNRLGE 307 V +ELGGK+P ++ DDADLE AV + +SGQVC+ RV+VQKGI + F+ RL E Sbjct: 248 VTMELGGKSPLLIFDDADLENAVGGAILGNFYSSGQVCSNGTRVFVQKGIKEAFLKRLTE 307 Query: 308 AMQAVQFGNPAERNDIAMGPLINAAALERVEQKVARAVEEGARVAFGGKAVEGKGYYYPP 367 + G+P + GP+++ ++ V + + EGAR+ GG+ + G+Y P Sbjct: 308 RLSTAVVGDPLDEAT-NFGPMVSEKQMKIVLDYIEKGENEGARLVAGGRRLNRDGFYLQP 366 Query: 368 TLLLDVRQEMSIMHEETFGPVLPVVAFDTLEDAISMANDSDYGLTSSIYTQNLNVAMKAI 427 T+ DV+ +M I EE FGPV+ V+ F+T E+AI+ AN +++GL++ ++T++L+ A + I Sbjct: 367 TVFADVKDDMIIAREEIFGPVMAVLDFETEEEAITRANSTEFGLSAGVFTRDLSRAHRVI 426 Query: 428 KGLKFGETYINRENFEAMQGFHAGWRKSGIGGADGKHGLHEYLQTQVVYLQ 478 L+ G +IN N ++ G + SG+G + K ++ Y + + VY++ Sbjct: 427 AQLEAGSCFINSYNDAPVEAPFGGTKMSGVGRENSKAAINHYSEMKSVYVR 477 Lambda K H 0.318 0.135 0.392 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: 534 Number of extensions: 23 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: 479 Length of database: 485 Length adjustment: 34 Effective length of query: 445 Effective length of database: 451 Effective search space: 200695 Effective search space used: 200695 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 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