Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate Ac3H11_1486 5-carboxymethyl-2-hydroxymuconate semialdehyde dehydrogenase (EC 1.2.1.60)
Query= metacyc::MONOMER-16244 (495 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1486 Length = 485 Score = 325 bits (834), Expect = 2e-93 Identities = 188/468 (40%), Positives = 264/468 (56%), Gaps = 12/468 (2%) Query: 33 KSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHSSWSTSDPQVRMKVLYKLAD 92 +S++ F TV+P+T+E + +V + ++ AV AA AF +W+ R K++ KL D Sbjct: 13 ESREYFETVNPATQEVLAEVASGGAAEVHAAVAAAKDAF-PAWAGLPAPERAKLVRKLGD 71 Query: 93 LIDEHADTLAHIEALDNGKSL-MCSKGDVALTAAYFRSCAGWTDKIKGSVIETGDTHFNY 151 LI TLA E D G+ + K + A F A ++ G T TH NY Sbjct: 72 LIAAEVPTLALTETKDTGQVIGQTGKALIPRAADNFYYFAEMCTRVDGHTYPT-PTHLNY 130 Query: 152 TRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTPLSALYLASLIKEAGA 211 T P+GVC I PWN P + ++WK+ P L G T VLK +E +PL+A L L EAG Sbjct: 131 TLFHPVGVCALISPWNVPFMTSTWKVAPALAFGNTAVLKMSELSPLTAARLGELALEAGI 190 Query: 212 PPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKAAAESNLKKVTLELGGKS 271 P GV+NVV G+G AG P+ +HP ++ ++FTGSTATG I++AA LKK ++ELGGKS Sbjct: 191 PAGVLNVVHGYGKDAGEPLCTHPDVRAISFTGSTATGNRIVQAA---GLKKFSMELGGKS 247 Query: 272 PNIVFDDADVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIYDKIVSEFKNAAESLKIGD 331 P +VF DAD+ + + IF N GE C AGSRI VQ+ IY +F A + +GD Sbjct: 248 PFVVFADADLDRALDAALFMIFSNNGERCTAGSRILVQKSIYADFAEKFAARARRIVVGD 307 Query: 332 PFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGG------ERFGNKGYFIKPTIFG 385 P E T +G SQ L K+ YI++G KEGAT++ GG KG F+ PT+F Sbjct: 308 PLDEKTIVGPMISQAHLAKVRSYIELGPKEGATLLCGGLGTPDLPAHLQKGNFVLPTVFA 367 Query: 386 DVKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAGVHTTNLSTAISVSNKIN 445 DV +I ++EIFGPV + F+ E I LAND +YGL++ V T N+ A V+ I Sbjct: 368 DVDNRMKIAQEEIFGPVACLIPFEDEAEAIRLANDIQYGLSSYVWTENIGRAHRVAAGIE 427 Query: 446 SGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDNYTQVKAVRIGL 493 +G +VN+ N PFGG SG GRE G + + + + K + + + Sbjct: 428 AGMCFVNSQNVRDLRQPFGGTKGSGTGREGGTWSYEVFLEPKNIAVSM 475 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: 618 Number of extensions: 30 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: 485 Length adjustment: 34 Effective length of query: 461 Effective length of database: 451 Effective search space: 207911 Effective search space used: 207911 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