Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate WP_043765072.1 U743_RS01785 aldehyde dehydrogenase family protein
Query= metacyc::MONOMER-16244 (495 letters) >NCBI__GCF_000733765.1:WP_043765072.1 Length = 506 Score = 361 bits (927), Expect = e-104 Identities = 209/500 (41%), Positives = 291/500 (58%), Gaps = 21/500 (4%) Query: 8 PIKLPNGTTYEQPTGLFINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAA 67 P K P + Y+ FI ++V +S K F VSP T +I ++ + + D++ A++AA Sbjct: 10 PAKTPFKSRYDN----FIGGDWVAPESGKYFDNVSPVTGGKICEIARSEAADVEKALDAA 65 Query: 68 TAAFHSSWSTSDPQVRMKVLYKLADLIDEHADTLAHIEALDNGKSLMCSK-GDVALTAAY 126 AA + W+ + R +L +A ++++ + LA E DNGK++ S DV L + Sbjct: 66 HAA-RARWANTSTTERSNILNAIAQRMEDNLEALAQAETWDNGKAVRESTVADVPLAIDH 124 Query: 127 FRSCAGWTDKIKGSVIETGDTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCT 186 FR AG +GS+ + Y EP+GV GQIIPWNFPLLMA WKL P L G Sbjct: 125 FRYFAGAIRAQEGSISMIDEQTVAYHFHEPLGVVGQIIPWNFPLLMAVWKLAPALAAGNC 184 Query: 187 TVLKTAESTPLSALYLASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTA 246 V+K AE TP S L+ +I + PPGV+N+V+GFG AG P++S P+I K AFTG T Sbjct: 185 VVIKPAEQTPASILHWMEMIADL-LPPGVINIVNGFGLEAGKPLASSPRIAKAAFTGETT 243 Query: 247 TGRHIMKAAAESNLKKVTLELGGKSPNIVF------DDADVKSTIQHLVTGIFYNTGEVC 300 TGR IM+ AA+ NL VTLELGGKSPN+ F DDA I+ V N GEVC Sbjct: 244 TGRMIMQYAAQ-NLIPVTLELGGKSPNVFFEDVMREDDAYFDKAIEGFVL-FALNQGEVC 301 Query: 301 CAGSRIYVQEGIYDKIVSEFKNAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKK 360 SR +QE I+D+ + E++++GDP DT MGAQ S Q++KIL Y DIGK+ Sbjct: 302 TCPSRALIQESIFDRFMERALKRVEAIQMGDPLSMDTMMGAQASSEQMEKILSYFDIGKQ 361 Query: 361 EGATVITGGERFG-----NKGYFIKPTIFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVI 415 EGA V+TGG R GY+IKPT+F + ++ ++EIFGPVV++T FK E + Sbjct: 362 EGAEVLTGGGRAQLDGELANGYYIKPTVFRGHNK-MRVFQEEIFGPVVSVTTFKDEAEAL 420 Query: 416 ALANDSEYGLAAGVHTTNLSTAISVSNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREM 475 +AND+ YGL AGV + + + + I +G +W N Y+ + FGGY QSGIGRE Sbjct: 421 EIANDTLYGLGAGVWSRDANICYRMGRGIQAGRVWTNCYHAYPAHAAFGGYKQSGIGREN 480 Query: 476 GEEALDNYTQVKAVRIGLSQ 495 + LD+Y Q K + + + Sbjct: 481 HKMMLDHYQQTKNMLVSYDE 500 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: 614 Number of extensions: 31 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 495 Length of database: 506 Length adjustment: 34 Effective length of query: 461 Effective length of database: 472 Effective search space: 217592 Effective search space used: 217592 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