Align Lactaldehyde dehydrogenase; EC 1.2.1.22 (uncharacterized)
to candidate WP_013459096.1 SULKU_RS01190 aldehyde dehydrogenase
Query= curated2:A6UVT6 (465 letters) >NCBI__GCF_000183725.1:WP_013459096.1 Length = 471 Score = 312 bits (799), Expect = 2e-89 Identities = 170/453 (37%), Positives = 272/453 (60%), Gaps = 11/453 (2%) Query: 17 NPYNNEIIGYIPSLSRNETKEAIKIAEEHKSTMKNLSPTIRYNILMKIASELSKNKRELA 76 +PY+ ++ S ++ ++A+ IA+ K ++ R L+ +AS+L + + E A Sbjct: 22 SPYDGRVVSRAAECSADDARQALIIAQNASKIAKKVALHQRCAWLLDVASKLKEQREEFA 81 Query: 77 KLITIDVGKPIKQSIIEVDRTITTFKFSAFYSRELRGETIPFDD------GMVITKREPV 130 +++ +VGKPI + IEVDR I T SA R + GE+I D +RE Sbjct: 82 RVLCDEVGKPITYARIEVDRCIETITLSAETMRTMHGESINTDAMPSGRAAHAYWRREAA 141 Query: 131 GLVGAITPFNFPLNLFAHKIAPAIAMGNSIVAHPSSKAPMITIELTKIIEKVLKSKKIPL 190 G+V AITPFNFPLNL AHK+APA+ GN++V P+ +AP+ +L ++ ++S Sbjct: 142 GVVVAITPFNFPLNLVAHKLAPALVAGNAVVLKPTPEAPLCAYKLAQLF---IESPYATP 198 Query: 191 GVFNLLTGEGHIVGDEIVKNNKINKLSFTGSVEVGESITKKAGFKKITLELGGNNPMIIL 250 +++ G+ VG +V ++ +SFTGSV VG IT+ AG KKI+LELGGN I Sbjct: 199 DALSVVYGDAE-VGSALVGSDIPRVISFTGSVGVGNIITRSAGIKKISLELGGNAATYID 257 Query: 251 KDANINKAVESCMSGKFLNSGQVCISVGRVLIEQEVADEFINKIVEKVKKLKIGNPLDED 310 A++ A C G F+NSGQVCIS+ R+ ++ V DEF K+ E KL +G+P ++D Sbjct: 258 TSADLEYAAARCAIGAFVNSGQVCISLQRIYVDSSVYDEFALKMAEATSKLVVGSPYNDD 317 Query: 311 TNISSLISLDSAERVEKLINKSIGQGGKLICGGKRENSIIYPTIL-EITADNILANIEIF 369 T + LI+ ++A R + +I +G + + + E I YP ++ ++T + E+F Sbjct: 318 TFLGPLINDEAASRAMSWVESAIEEGARALTPPRCEGRIFYPCVMADVTESMKIVCEEVF 377 Query: 370 APVLPIIRVNDMNEALNQANNSNYGLHSGVFTQDINKALYFADNLEYGGVLINNSPTFRI 429 AP++ ++RV+ +++A+ + NNS YGL VFT +++ A D L+ GGV+IN+ PT R Sbjct: 378 APIVSLVRVDGIDDAITRMNNSPYGLQFSVFTNNLSHATKAIDELDAGGVVINDMPTLRF 437 Query: 430 DNMPFGGIKHSGLGREGIKYAIDEMSEIKTIIV 462 D P+GG+K SG+GREG ++AI+E +EIK+I++ Sbjct: 438 DIQPYGGVKLSGVGREGPRFAIEEFTEIKSIVI 470 Lambda K H 0.316 0.136 0.377 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: 493 Number of extensions: 21 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: 465 Length of database: 471 Length adjustment: 33 Effective length of query: 432 Effective length of database: 438 Effective search space: 189216 Effective search space used: 189216 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: 51 (24.3 bits)
This GapMind analysis is from Sep 24 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