Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate YP_004139911.1 Mesci_0690 aldehyde dehydrogenase
Query= metacyc::MONOMER-16244 (495 letters) >NCBI__GCF_000185905.1:YP_004139911.1 Length = 495 Score = 370 bits (949), Expect = e-107 Identities = 203/477 (42%), Positives = 281/477 (58%), Gaps = 5/477 (1%) Query: 22 GLFINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHS-SWSTSDP 80 GLFI+ V++ S + SP + + + DID AV++A AF SWS + P Sbjct: 19 GLFIDGVQVEATSGASLPVTSPIDGRPFASIADGNAADIDRAVKSARKAFEKGSWSRATP 78 Query: 81 QVRMKVLYKLADLIDEHADTLAHIEALDNGKSL-MCSKGDVALTAAYFRSCAGWTDKIKG 139 R KVL K ADL+++HAD LA + DNG + M K + A R A DK+ G Sbjct: 79 AFRKKVLTKFADLVEKHADELAVLGVRDNGTEIGMAYKAEPLSAAGTIRYYAEAIDKVYG 138 Query: 140 SVIETGDTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTPLSA 199 + T + +EP+GV G I+PWNFPL++ +WK+ P L G V+K E L+ Sbjct: 139 EIAPTAENVLGLIHKEPLGVVGVIVPWNFPLMIGAWKIAPALAAGNCVVVKPPEIASLTL 198 Query: 200 LYLASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKAAAESN 259 L LA L EAG P GV+NVV+G G G + H + +AFTGS GR +++ +A SN Sbjct: 199 LRLAELASEAGLPAGVLNVVTGLGAVTGEALGLHMDVDAIAFTGSGPVGRRLLEYSARSN 258 Query: 260 LKKVTLELGGKSPNIVFDDA-DVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIYDKIVS 318 LK+V LELGGKSPNIVF DA D+K GIF N+G+VC AGSR+ VQ +YD+ + Sbjct: 259 LKRVFLELGGKSPNIVFADAPDLKQAAVVSANGIFRNSGQVCVAGSRLLVQSAVYDRFMD 318 Query: 319 EFKNAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGGERFGNK--G 376 E +A LK+GDP + +GA +S QLDK L ++ +EGA ++TGG+R + G Sbjct: 319 ELLSATMRLKVGDPLDLTSDVGAVSSAEQLDKNLGFVARATEEGARLVTGGQRMLTETGG 378 Query: 377 YFIKPTIFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAGVHTTNLST 436 ++ PTIF +V +D Q+ R+E+FGPV+ + +F+T EE + LAN + YGLA+ V T NLST Sbjct: 379 SYMAPTIFENVMQDMQLAREEVFGPVLGVMRFETEEEAVRLANSTVYGLASAVWTANLST 438 Query: 437 AISVSNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDNYTQVKAVRIGL 493 A + IN+G + VNTY VP GG QSG GR+ AL+ Y ++K I L Sbjct: 439 AHRMVRAINAGVVHVNTYGGADITVPLGGVKQSGFGRDKSLHALEKYLELKTAWIAL 495 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: 549 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: 495 Length adjustment: 34 Effective length of query: 461 Effective length of database: 461 Effective search space: 212521 Effective search space used: 212521 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