Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate WP_085640679.1 MGEO_RS17260 betaine-aldehyde dehydrogenase
Query= metacyc::MONOMER-16244 (495 letters) >NCBI__GCF_002115805.1:WP_085640679.1 Length = 485 Score = 343 bits (879), Expect = 1e-98 Identities = 184/472 (38%), Positives = 282/472 (59%), Gaps = 11/472 (2%) Query: 24 FINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHSSWSTSDPQVR 83 FI+ +V+ + + P+T E+I VY A +D A+ AA A +W+ R Sbjct: 12 FIDGAYVEDTTGTPIPVIYPATGEQIATVYAATPAIVDKALAAAHRA-QKAWAAMSGTER 70 Query: 84 MKVLYKLADLIDEHADTLAHIEALDNGKSLMCSKGDVALTAA----YFRSCAGWTDKIKG 139 ++L + AD++ E L+ +E D GK + A + A YF AG + G Sbjct: 71 GRILRRAADMMRERNHDLSVLETYDTGKPYQETIAVDATSGADALEYFGGLAG---SLTG 127 Query: 140 SVIETGDTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTPLSA 199 I+ G+ + YTRREP+GVC I WN+P +A WK P L G V K +E+TPL A Sbjct: 128 EHIQLGED-WVYTRREPLGVCVGIGAWNYPTQIACWKGAPALACGNAMVFKPSETTPLCA 186 Query: 200 LYLASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKAAAESN 259 L +A ++ EAG P G+ NVV G G GA + + P++ KV+ TGS TG+ + AAAE Sbjct: 187 LKVAEILHEAGLPAGIYNVVQGLGEV-GASLVTDPRVAKVSLTGSVPTGKKVYAAAAEQ- 244 Query: 260 LKKVTLELGGKSPNIVFDDADVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIYDKIVSE 319 +K VT+ELGGKSP ++FDDAD+++ + + G FY++G+VC G+R++VQ+GI + + Sbjct: 245 MKHVTMELGGKSPLLIFDDADLENAVGGAILGNFYSSGQVCSNGTRVFVQKGIKEAFLKR 304 Query: 320 FKNAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGGERFGNKGYFI 379 + +GDP E T G S+ Q+ +L YI+ G+ EGA ++ GG R G+++ Sbjct: 305 LTERLSTAVVGDPLDEATNFGPMVSEKQMKIVLDYIEKGENEGARLVAGGRRLNRDGFYL 364 Query: 380 KPTIFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAGVHTTNLSTAIS 439 +PT+F DVK+D I R+EIFGPV+ + F+T EE I AN +E+GL+AGV T +LS A Sbjct: 365 QPTVFADVKDDMIIAREEIFGPVMAVLDFETEEEAITRANSTEFGLSAGVFTRDLSRAHR 424 Query: 440 VSNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDNYTQVKAVRI 491 V ++ +G+ ++N+YND PFGG SG+GRE + A+++Y+++K+V + Sbjct: 425 VIAQLEAGSCFINSYNDAPVEAPFGGTKMSGVGRENSKAAINHYSEMKSVYV 476 Lambda K H 0.316 0.133 0.389 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: 648 Number of extensions: 37 Number of successful extensions: 5 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: 495 Length of database: 485 Length adjustment: 34 Effective length of query: 461 Effective length of database: 451 Effective search space: 207911 Effective search space used: 207911 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 (21.6 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