Align aldehyde-alcohol dehydrogenase; EC 1.1.1.1; EC 1.2.1.10 (characterized)
to candidate WP_092346807.1 BLU87_RS08580 acetaldehyde dehydrogenase
Query= CharProtDB::CH_018413 (862 letters) >NCBI__GCF_900107645.1:WP_092346807.1 Length = 481 Score = 329 bits (843), Expect = 3e-94 Identities = 187/442 (42%), Positives = 266/442 (60%), Gaps = 6/442 (1%) Query: 3 VTTVKELDEKLKVIKEAQKKFSCYSQEMVDEIFRNAAMAAIDARIELAKAAVLETGMGLV 62 + +++E + ++ + AQ F+ SQE VD++ + A +LAK AV ETG G Sbjct: 6 LASIQEARDLVRKARVAQCDFAKLSQEKVDQVVQAIAKVMTAMAEDLAKLAVEETGYGNW 65 Query: 63 EDKVIKNHFAGEYIYNKYKDEKTCGIIERNEPYGITKIAEPIGVVAAIIPVTNPTSTTIF 122 EDK KN A E +Y + KT G+I + I KIA P GVVAA+IP TNPTSTTI+ Sbjct: 66 EDKKQKNLLASEKLYQRIHAVKTVGVIAEDREQKIDKIAVPAGVVAALIPSTNPTSTTIY 125 Query: 123 KSLISLKTRNGIFFSPHPRAKKSTILAAKTILDAAVKSGAPENIIGWIDEPSIELTQYLM 182 K++I+LK NG+ FSPHP A K I + E ++ P++E T LM Sbjct: 126 KAMIALKAGNGVVFSPHPTATKCIGKTVAIIHQILKEMHISEELVSMTTMPTLEGTGELM 185 Query: 183 QKADITLATGGPSLVKSAYSSGKPAIGVGPGNTPVIIDESAHIKMAVSSIILSKTYDNGV 242 ++AD+ LATGGP +VK+AYSSG PA+GVGPGN PV I++SA ++ AV I+ KT+D G Sbjct: 186 RQADLILATGGPGMVKAAYSSGTPALGVGPGNVPVFIEKSADVQAAVKRIMAGKTFDYGT 245 Query: 243 ICASEQSVIVLKSIYNKVKDEFQERGAYIIKKNELDKVREVIF-KDGSVNPKIVGQSAYT 301 +C+SEQ+++ +SI +VK G Y ++ DKV+ ++ GS+NP IVGQ A Sbjct: 246 VCSSEQALVTEESIVAEVKKSMLIEGCYFLEGAAADKVKGLMTGPRGSMNPAIVGQPASV 305 Query: 302 IAAMAGIKVPKTTRILIGEVTSLGEEEPFAHEKLSPVLAMYEADNFDDALKKAVTLINLG 361 +A MAGI++P TR+L+ E +G PF++EKL+ +L Y ++ A + L+ G Sbjct: 306 LAQMAGIEIPAGTRLLVYEEQGVGSGYPFSYEKLTCLLGFYTVPDWQSAGELCTRLLQNG 365 Query: 362 GLGHTSGIYADEIKARDKIDRFSSAMKTVRTFVNIPTSQGASGDLYNFRIPPSFTLGCGF 421 GLGH+ I+++ D I F+ + R VN P+S GA G N + PS TLGCGF Sbjct: 366 GLGHSMAIHSNN---EDIIRHFALSQPVSRLLVNTPSSLGAVGVTTN--LDPSLTLGCGF 420 Query: 422 WGGNSVSENVGPKHLLNIKTVA 443 GG+S S+NVG +HL NI+ VA Sbjct: 421 VGGSSTSDNVGGQHLFNIRYVA 442 Lambda K H 0.317 0.134 0.378 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: 924 Number of extensions: 41 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: 862 Length of database: 481 Length adjustment: 38 Effective length of query: 824 Effective length of database: 443 Effective search space: 365032 Effective search space used: 365032 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: 54 (25.4 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