Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate 3609634 Dshi_3017 aldehyde dehydrogenase (RefSeq)
Query= metacyc::MONOMER-16244 (495 letters) >FitnessBrowser__Dino:3609634 Length = 780 Score = 330 bits (847), Expect = 8e-95 Identities = 191/468 (40%), Positives = 271/468 (57%), Gaps = 20/468 (4%) Query: 22 GLFINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHSSWSTSDPQ 81 G+FI F KTF T +P+ E+ QV + DI+ AV AA A +W+ Q Sbjct: 34 GVFIGGTF--QAPGKTFATRNPARGTELAQVTQGTEADIEAAVTAARRA-QPAWARLGGQ 90 Query: 82 VRMKVLYKLADLIDEHADTLAHIEALDNGKSLMCSKG-DVALTAAYFRSCAGWTDKIKGS 140 +VLY +A L+ +H+ A +E LDNGK + S+ D+ L +F AG ++ Sbjct: 91 GWARVLYAIARLLQKHSRLFAVLETLDNGKPIRESRDIDIPLAQRHFYYHAGMAALMEDE 150 Query: 141 VIETGDTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTPLSAL 200 + + R P+GVCGQI+PWNFPLLM +WK+ P L G T VLK AE TPL+AL Sbjct: 151 LPD----------RVPVGVCGQIVPWNFPLLMLAWKIAPALAMGNTVVLKPAEWTPLTAL 200 Query: 201 YLASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKAAAESNL 260 A + EAG PPGVVN+V+G G T GA + SHP + K+AFTGST GR I +A A + Sbjct: 201 LFAEICGEAGVPPGVVNIVTGDGAT-GAALVSHPGVDKIAFTGSTDVGREIRRATAGTG- 258 Query: 261 KKVTLELGGKSPNIVFDDADVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIYDKIVSEF 320 K +TLELGGKSP +VF+DAD+ S ++ LV I++N G+VCCAGSR+ VQEGI + ++ Sbjct: 259 KALTLELGGKSPYVVFEDADLDSAVEGLVDAIWFNQGQVCCAGSRLLVQEGIAEAFYAKL 318 Query: 321 KNAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGGERFGNKGYFIK 380 + +L+IGDP + +GA K+ + + E + +G F Sbjct: 319 RARMATLRIGDPLDKCIDVGAMVDPAHCAKVAEMVAGSNGE----VHQPGTVPAEGAFYP 374 Query: 381 PTIFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAGVHTTNLSTAISV 440 PT+ ++ ++RDEIFGPV+ T F+T E + +AN + YGLAA + + N++ A+ + Sbjct: 375 PTLITGLEPADPLMRDEIFGPVLVATTFRTPAEAVEVANATRYGLAATLWSENINRALDI 434 Query: 441 SNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDNYTQVKA 488 + K+ +G +WVN N F FGG +SG GRE G E L YT+ A Sbjct: 435 APKLAAGVVWVNATNLFDAAAGFGGVRESGFGREGGWEGLRAYTKQAA 482 Score = 88.6 bits (218), Expect = 7e-22 Identities = 66/216 (30%), Positives = 104/216 (48%), Gaps = 5/216 (2%) Query: 54 EAFSEDIDDAVEAATAAFHSSWSTSDPQVRMKVLYKLADLIDEHADTLAHIEALDNGKSL 113 E +DI +AVEAAT A +SW + +R ++LY +A+ + + A A G + Sbjct: 540 EGSRKDIRNAVEAATGA--ASWGRTTGHLRAQILYYVAENLSARTEEFATRIAEMTGSRV 597 Query: 114 MCSKGDVALTAAYFRSCAGWTDKIKGSVIETGDTHFNYTRREPIGVCGQIIPWNFPLLMA 173 ++ +V+ + A W DK G+V EP+GV G P + PLL A Sbjct: 598 PRAEAEVSAAIDRLFTYAAWADKYDGAVKPVPIRGVALAMPEPVGVIGAFAPDDAPLLGA 657 Query: 174 SWKLGPVLCTGCTTVLKTAESTPLSALYLASLIKEAGAPPGVVNVVSGFGPTAGAPISSH 233 LG L G VL +E PL+A L ++ + P GVVN+V+G P++SH Sbjct: 658 VSILGAALAMGNRLVLVPSEPFPLAATDLYQVLDTSDVPAGVVNIVTGAHEALAKPLASH 717 Query: 234 PKIKKV-AFTGSTATGRHIMKAAAESNLKKVTLELG 268 + V +F+G+ + ++A A NLK+ + G Sbjct: 718 LGVDAVWSFSGADIS--TTIEAEAAGNLKRTWVNHG 751 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: 885 Number of extensions: 43 Number of successful extensions: 9 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 495 Length of database: 780 Length adjustment: 37 Effective length of query: 458 Effective length of database: 743 Effective search space: 340294 Effective search space used: 340294 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: 53 (25.0 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