Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate AO356_28685 AO356_28685 betaine-aldehyde dehydrogenase
Query= metacyc::MONOMER-16244 (495 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_28685 Length = 496 Score = 427 bits (1097), Expect = e-124 Identities = 215/482 (44%), Positives = 307/482 (63%), Gaps = 7/482 (1%) Query: 19 QPTGLFINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHSSWSTS 78 QP LFI + + + + F +P+TE + +V E D+D AV AA AAF +W+ Sbjct: 16 QPGRLFIGGTWQDAANGRRFAVENPATEHTLAEVAEGGERDVDAAVAAARAAFTGTWAQQ 75 Query: 79 DPQVRMKVLYKLADLIDEHADTLAHIEALDNGKSLMCSKGDVALTAAYFRSCAGWTDKIK 138 P R +L++LA+L+D+H + LA + L+NGK + ++G+ A A R AGW KI+ Sbjct: 76 SPAQRGLLLFRLAELLDQHREELAQLITLENGKPIGAARGEAASAANIIRYFAGWPTKIE 135 Query: 139 GSVI----ETGDTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAES 194 GS + +G NYT REP+GVC I+PWNFPL M WKLGPVL TGC VLK AE Sbjct: 136 GSTLPVSPSSGAPMLNYTLREPVGVCALIVPWNFPLTMCVWKLGPVLATGCVAVLKPAEQ 195 Query: 195 TPLSALYLASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKA 254 TPL A+ L LI+ AG P GVVN+++G G GAP++ HP + K+AFTGST GR I +A Sbjct: 196 TPLVAIRLVQLIEAAGFPAGVVNLLTGLGAQTGAPLAQHPDVDKIAFTGSTQVGRLIAQA 255 Query: 255 AAESNLKKVTLELGGKSPNIVFDDADVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIYD 314 A N+KKV+LELGGKSPNI+ DAD+ + GIFYN G+VC AGSR+YV + D Sbjct: 256 AT-GNMKKVSLELGGKSPNIILPDADIVRAAKGAADGIFYNQGQVCTAGSRLYVHASVLD 314 Query: 315 KIVSEFKNAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGGERFGN 374 +++ E + A + +G + MG S QL + Y+ G++EGA +I GG+R + Sbjct: 315 QVLEELQRHAAAHVLGPGLDPASSMGPLVSARQLGTVRGYLQRGQEEGAELICGGDRPAH 374 Query: 375 --KGYFIKPTIFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAGVHTT 432 +G+FI+P++F D E + R+EIFGPV+T+ + ++E++ ANDS YGLAAG+ T Sbjct: 375 LERGHFIRPSVFLDRAERACVAREEIFGPVLTVMSWTEIDELVLRANDSPYGLAAGLWTR 434 Query: 433 NLSTAISVSNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDNYTQVKAVRIG 492 +L +A V+ ++ +G++W+N +N P PFGGY QSG GREMG+ +D YT+ K+V + Sbjct: 435 DLRSAHRVAAQLKAGSVWINCWNVVDPASPFGGYKQSGWGREMGKNVIDAYTETKSVYVD 494 Query: 493 LS 494 L+ Sbjct: 495 LA 496 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: 632 Number of extensions: 25 Number of successful extensions: 4 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: 496 Length adjustment: 34 Effective length of query: 461 Effective length of database: 462 Effective search space: 212982 Effective search space used: 212982 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