Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate WP_043765410.1 U743_RS02990 aldehyde dehydrogenase family protein
Query= metacyc::MONOMER-16244 (495 letters) >NCBI__GCF_000733765.1:WP_043765410.1 Length = 508 Score = 336 bits (862), Expect = 1e-96 Identities = 187/484 (38%), Positives = 285/484 (58%), Gaps = 9/484 (1%) Query: 17 YEQPTGLFINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHSSWS 76 +++ G FI+ ++VQ S + ++P+ + ++ + +ED AV+AA AF +WS Sbjct: 20 FQKEYGHFIDGKWVQGASGERIPMINPANGQVLSHIQSGNAEDARRAVDAAAQAF-PAWS 78 Query: 77 TSDPQVRMKVLYKLADLIDEHADTLAHIEALDNGKSLM-CSKGDVALTAAYFRSCAGWTD 135 + R +VLY++A + A ++ LDNGK M D+ + F +G Sbjct: 79 QTPRSERQRVLYEMARRLRARMADYAMMDCLDNGKPAMEAMHFDLPMAIEQFEIFSGAPW 138 Query: 136 KIKGSVIETGDTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAEST 195 + G I+ +T REP+GV QIIPWN PL+M + KL P L G T VLK +E Sbjct: 139 FLHGQSIDAPNT-LGIVLREPLGVVAQIIPWNVPLIMMAAKLAPALAAGNTVVLKPSEIV 197 Query: 196 PLSALYLASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKAA 255 LS L + + PPGVVNVV+G+GP+ G + +HPK++KVAFTGS T + +M+ A Sbjct: 198 CLSVLEFFREMADL-LPPGVVNVVTGYGPSVGEALVTHPKVRKVAFTGSRPTAQKLMQYA 256 Query: 256 AESNLKKVTLELGGKSPNIVFDDADVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIYDK 315 + N+ T+ELGGKS NIV +DAD+ + + N GEVC AGSR++V E + D Sbjct: 257 SV-NIIPQTMELGGKSANIVCEDADLDAAAEGAAMSTVLNKGEVCLAGSRVFVHEKVKDV 315 Query: 316 IVSEFKNAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGGERFGNK 375 + +F + + +K GDP + T +G Q S+ Q DKI+ Y+++G++EGA + GG + Sbjct: 316 FLDKFTSLLKRVKAGDPREPTTQIGPQVSKAQYDKIMGYLELGQQEGAKLAAGGRKAAPA 375 Query: 376 GY----FIKPTIFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAGVHT 431 G+ FI+PT+F DV +I ++EIFGPV + F+ +EV+ +ANDS YGL G+ T Sbjct: 376 GFEDGLFIEPTVFFDVDNSMRIAQEEIFGPVSCVIGFRDDDEVVRMANDSVYGLGGGLWT 435 Query: 432 TNLSTAISVSNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDNYTQVKAVRI 491 +LS A ++ + +GT+WVN Y +F +P GGY QSG GRE E +++YT K+V I Sbjct: 436 KDLSRAHRIARALETGTVWVNRYYNFLGGMPIGGYKQSGFGREFAAEVMNHYTLTKSVII 495 Query: 492 GLSQ 495 L++ Sbjct: 496 NLAE 499 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: 624 Number of extensions: 33 Number of successful extensions: 6 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: 508 Length adjustment: 34 Effective length of query: 461 Effective length of database: 474 Effective search space: 218514 Effective search space used: 218514 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