Align aldehyde-alcohol dehydrogenase; EC 1.1.1.1; EC 1.2.1.10 (characterized)
to candidate GFF1905 PGA1_c19350 putative aldehyde dehydrogenase
Query= CharProtDB::CH_018413 (862 letters) >FitnessBrowser__Phaeo:GFF1905 Length = 469 Score = 246 bits (628), Expect = 2e-69 Identities = 141/397 (35%), Positives = 222/397 (55%), Gaps = 7/397 (1%) Query: 49 LAKAAVLETGMGLVEDKVIKNHFAGEYIYNKYKDEKTCGIIERNEPYGITKIAEPIGVVA 108 LA+ V E+G+G + K F + + + G++E +E G+ K A+P GV+A Sbjct: 55 LAEKGVDESGIGDRAGRPAKR-FKIQMVLRDVLRTPSTGVVEVDEEKGLVKYAKPAGVIA 113 Query: 109 AIIPVTNPTSTTIFKSLISLKTRNGIFFSPHPRAKKSTILAAKTILDAAVKSGAPENIIG 168 ++IP+TNP T + S RN + FSPHPR +T + + A V GAP ++ Sbjct: 114 SLIPMTNPAMTPPVTGVSSANARNAVIFSPHPRTAGTTFDMTEMMRKACVAVGAPADLFQ 173 Query: 169 WIDEPSIELTQYLMQKADITLATGGPSLVKSAYSSGKPAIGVGPGNTPVIIDESAHIKMA 228 + PSI LTQ+LM++ D+TLATGG +VK+AYSSG+PA GVG GN+ ++IDE+A I +A Sbjct: 174 AVRHPSIPLTQHLMEECDLTLATGGKPMVKAAYSSGRPAYGVGAGNSSIVIDETADIDIA 233 Query: 229 VSSIILSKTYDNGVICASEQSVIVLKSIYNKVKDEFQERGAYIIKKNELDKVREVIFKD- 287 + +SKT D G C+++ ++I+ +S+Y+ + + G Y+ E + + ++ + Sbjct: 234 AQNTRISKTSDFGSGCSADGNIIIQRSVYDDMVKALEAEGGYLCSPAEKTLLEKAMWDEK 293 Query: 288 GSVNPKIVGQSAYTIAAMAGIKVPKTTRILIGEVTS-LGEEEPFAHEKLSPVLAMYEADN 346 G+ + A +AG +P + L+ E S +G E F+ EKL+ V+A+Y + Sbjct: 294 GNRTFTTIACKPQQTADVAGFSIPDDRKFLMVENQSQIGPEHKFSKEKLTTVMALYHFET 353 Query: 347 FDDALKKAVTLINLGGLGHTSGIYADEIKARDKIDRFSSAMKTVRTFVNIPTSQGASGDL 406 FDDAL+ + GG+GH+ GIY+ D ID + R V P S+ +G Sbjct: 354 FDDALETVRQIYATGGVGHSCGIYSHN---DDNIDALARVAPVSRMMVRQPQSKANAGSW 410 Query: 407 YNFRIPPSFTLGCGFWGGNSVSENVGPKHLLNIKTVA 443 N +P + +LGCG WGGN +ENV KH++N VA Sbjct: 411 TN-GMPMTSSLGCGIWGGNITNENVTMKHMMNYTWVA 446 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: 847 Number of extensions: 29 Number of successful extensions: 3 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: 469 Length adjustment: 38 Effective length of query: 824 Effective length of database: 431 Effective search space: 355144 Effective search space used: 355144 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 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