Align lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)
to candidate Ga0059261_1680 Ga0059261_1680 NAD-dependent aldehyde dehydrogenases
Query= BRENDA::P25553 (479 letters) >FitnessBrowser__Korea:Ga0059261_1680 Length = 469 Score = 243 bits (619), Expect = 1e-68 Identities = 152/455 (33%), Positives = 230/455 (50%), Gaps = 16/455 (3%) Query: 26 VVNPATEAVISRIPDGQAEDARKAIDAAERAQPEWEALPAIERASWLRKISAGIRERASE 85 V++PAT + P D A+ AA RA P W A P +RA+ + I+ I E Sbjct: 21 VIDPATGRPFADAPLASTADLDAAVAAARRAFPGWAATPIEDRAAAILAIADSIEAAKDE 80 Query: 86 ISALIVEEGGKIQQLAEVEVAFTADYIDYMAEWARRYEG-----EIIQSDRPGENILLFK 140 ++ L+ E GK A E+ WAR G ++++ D + + + Sbjct: 81 LARLLSAEQGKPVPNAVGEIMGAL-------AWARATAGLRPAVDVLKDD-DSVRVEVHR 132 Query: 141 RALGVTTGILPWNFPFFLIARKMAPALLTGNTIVIKPSEFTPNNAIAFAKIVDEIGLPRG 200 + LGV I PWNFP + + P L+ GNT+V+KPS FTP A+ +I + LP G Sbjct: 133 KPLGVVASISPWNFPVMIAIWHIIPGLVAGNTVVMKPSSFTPLAALRMVEIANA-HLPPG 191 Query: 201 VFNLVLGRGETVGQELAGNPKVAMVSMTGSVSAGEKIMATAAKNITKVCLELGGKAPAIV 260 V N V G E +G+ +A +P + + TGS G IMA A N+ ++ LELGG AIV Sbjct: 192 VLNSVTGEVE-IGRAIASHPGIDKIVFTGSTPTGRSIMADGAANLKRLTLELGGNDAAIV 250 Query: 261 MDDADLELAVKAIVDSRVINSGQVCNCAERVYVQKGIYDQFVNRLGEAMQAVQFGNPAER 320 + DAD++ I NSGQ+C +RVYV + I+D +L E + G P Sbjct: 251 LPDADVDKVAAKIFAKAFGNSGQICAAVKRVYVHESIHDALAEKLAEMARTAVVG-PGSD 309 Query: 321 NDIAMGPLINAAALERVEQKVARAVEEGARVAFGGKAVEGKGYYYPPTLLLDVRQEMSIM 380 GP+ N + V A G R GG+A EG GY++P ++++DV M I+ Sbjct: 310 AASQFGPVQNRKQFDLVRALADDARAHGGRFLAGGEAREGDGYFFPLSVVVDVTDGMRIV 369 Query: 381 HEETFGPVLPVVAFDTLEDAISMANDSDYGLTSSIYTQNLNVAMKAIKGLKFGETYINRE 440 EE FGP+LPV+ + EDA++ AN ++ GL S+++ + A+ + L+ G ++N Sbjct: 370 DEEQFGPILPVIRYSDPEDALARANANENGLGGSVWSADPAAALAFAQRLEAGTVWVNDH 429 Query: 441 NFEAMQGFHAGWRKSGIGGADGKHGLHEYLQTQVV 475 + G ++SG+G G +GL EY+Q Q V Sbjct: 430 ASISPDVPFGGAKQSGVGTEFGLYGLEEYMQLQTV 464 Lambda K H 0.318 0.135 0.392 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: 583 Number of extensions: 27 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: 479 Length of database: 469 Length adjustment: 33 Effective length of query: 446 Effective length of database: 436 Effective search space: 194456 Effective search space used: 194456 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 (21.7 bits) S2: 51 (24.3 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