Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate GFF3174 PGA1_c32250 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase PuuC
Query= metacyc::MONOMER-16244 (495 letters) >FitnessBrowser__Phaeo:GFF3174 Length = 494 Score = 330 bits (846), Expect = 7e-95 Identities = 189/481 (39%), Positives = 269/481 (55%), Gaps = 8/481 (1%) Query: 15 TTYEQPTGLF---INNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAF 71 T QP F I+ + V + T +SP +TQ+ D++ A+ +A AAF Sbjct: 8 TLRAQPVPCFSHLIDGQQVAASDGATMDVLSPIDGRLLTQIARGTVRDMERAIASARAAF 67 Query: 72 HSS-WSTSDPQVRMKVLYKLADLIDEHADTLAHIEALDNGKSL-MCSKGDVALTAAYFRS 129 W+ P R KVL K A+LI+ A LA + DNG + M K + AA R Sbjct: 68 EDRRWAGQPPAARKKVLMKWAELIEADALNLAVLGVRDNGTEITMALKAEPGSAAATIRY 127 Query: 130 CAGWTDKIKGSVIETGDTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVL 189 A DKI G + T +EP+GV G IIPWNFP+++ +WKL P L G + VL Sbjct: 128 YAEALDKIYGEIAPTSSDVLGMVHKEPVGVVGAIIPWNFPMMIGAWKLAPALAMGNSVVL 187 Query: 190 KTAESTPLSALYLASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGR 249 K +E+ LS + + L EAG PPGV+N V+G G G + + + FTGS TGR Sbjct: 188 KPSETASLSLMRMVELALEAGLPPGVLNAVTGEGAVVGEALGLSMDVDVLVFTGSGQTGR 247 Query: 250 HIMKAAAESNLKKVTLELGGKSPNIVFDDA-DVKSTIQHLVTGIFYNTGEVCCAGSRIYV 308 +M+ AA SNLK+V LELGGKSPNIVF DA D+ + GIF N+G+VC AGSR+ V Sbjct: 248 RLMEYAARSNLKRVYLELGGKSPNIVFADAPDLADAAKVTAAGIFRNSGQVCVAGSRLLV 307 Query: 309 QEGIYDKIVSEFKNAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITG 368 + I+D V E AA+ +++GDP + DT +GA S+ QL + L+++ + EG +ITG Sbjct: 308 EASIHDAFVEEVAKAAQMMRVGDPLRLDTQIGAINSEAQLARNLQFVARAEVEGGQIITG 367 Query: 369 GERFGNK--GYFIKPTIFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLA 426 G+R ++ G ++ PTI V D + ++E+FGPV+ +T F+T E + +AN + YGLA Sbjct: 368 GQRLLSETGGSYMAPTIVTGVTPDATLAQEEVFGPVLAVTPFETDAEALRIANATVYGLA 427 Query: 427 AGVHTTNLSTAISVSNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDNYTQV 486 V T+ L+ A + + +G + VNTY VP GG QSG G + A+D Y + Sbjct: 428 GAVWTSGLTRAHRMVQGVRTGVMHVNTYGGADGTVPLGGVGQSGNGADKSLHAIDKYINL 487 Query: 487 K 487 K Sbjct: 488 K 488 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: 511 Number of extensions: 26 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: 494 Length adjustment: 34 Effective length of query: 461 Effective length of database: 460 Effective search space: 212060 Effective search space used: 212060 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 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