Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate Ac3H11_4393 Aldehyde dehydrogenase (EC 1.2.1.3)
Query= metacyc::MONOMER-16244 (495 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4393 Length = 507 Score = 365 bits (936), Expect = e-105 Identities = 209/492 (42%), Positives = 297/492 (60%), Gaps = 17/492 (3%) Query: 16 TYEQPTGLFINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHSSW 75 TY+ FI +FV + F ++P + + T+ + +EDI+ A++AA AA SW Sbjct: 15 TYKPQYDNFIGGKFVPPVKGQYFDVITPVSGKVYTRAARSTAEDIELALDAAHAAA-DSW 73 Query: 76 STSDPQVRMKVLYKLADLIDEHADTLAHIEALDNGKSLMCS-KGDVALTAAYFRSCAGWT 134 +D R +L K+A+ I+E+ + LA+ E +DNGK++ + D+ LT +FR AG Sbjct: 74 GKTDAATRANILLKIANRIEENLERLAYAETVDNGKAIRETLNADIPLTVDHFRYFAGCV 133 Query: 135 DKIKGSVIETGDTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAES 194 +G++ + Y +EP+GV GQIIPWNFP+LMA+WKL P L G VLK AES Sbjct: 134 RAQEGALSNIDENTVAYHIQEPLGVVGQIIPWNFPILMAAWKLAPALGAGNCVVLKPAES 193 Query: 195 TPLSALYLASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKA 254 TP+S L L LI + PPGV+N+V+GFG AG P++ +I K+AFTGST+TGR I +A Sbjct: 194 TPISILILVELIADL-LPPGVLNIVNGFGREAGMPLAQSKRIAKIAFTGSTSTGRVIAQA 252 Query: 255 AAESNLKKVTLELGGKSPNIVF------DDADVKSTIQHLVTGIFYNTGEVCCAGSRIYV 308 AA +NL TLELGGKSPNI F DDA + I+ LV F N GEVC SR + Sbjct: 253 AA-NNLIPATLELGGKSPNIFFADIMDKDDAFLDKAIEGLVLFAF-NQGEVCTCPSRAII 310 Query: 309 QEGIYDKIVSEFKNAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITG 368 QE IYD+ + ++K +P D+ MGAQ S+ QL KIL Y+D+GK+EGA V+ G Sbjct: 311 QESIYDQFMERVLKRVAAIKHQNPLDTDSMMGAQASKEQLTKILSYLDLGKQEGAEVLAG 370 Query: 369 GERFG-----NKGYFIKPTIFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSEY 423 G + GY+++PT+F + +I ++EIFGPV+ +T FK E +A+AND+ Y Sbjct: 371 GGQAHLGGDLEGGYYVQPTLFKGHNK-MRIFQEEIFGPVLAVTTFKDEAEALAIANDTLY 429 Query: 424 GLAAGVHTTNLSTAISVSNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDNY 483 GL AGV + N + A + I +G +W N Y+ + FGGY +SGIGRE + LD+Y Sbjct: 430 GLGAGVWSRNGNVAYRMGRAIKAGRVWTNCYHAYPAHAAFGGYKESGIGRETHKMMLDHY 489 Query: 484 TQVKAVRIGLSQ 495 Q K + + S+ Sbjct: 490 QQTKNLLVSYSE 501 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: 592 Number of extensions: 27 Number of successful extensions: 7 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: 507 Length adjustment: 34 Effective length of query: 461 Effective length of database: 473 Effective search space: 218053 Effective search space used: 218053 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