Align NADH-dependent aldehyde reductase (EC 1.1.1.77; EC 1.1.1.244; EC 1.1.1.1) (characterized)
to candidate GFF4616 PS417_23620 epimerase
Query= metacyc::G3O-32155-MONOMER (298 letters) >FitnessBrowser__WCS417:GFF4616 Length = 297 Score = 126 bits (316), Expect = 7e-34 Identities = 95/307 (30%), Positives = 153/307 (49%), Gaps = 29/307 (9%) Query: 1 MKVFITGASGFIGSAVLSELISSGHEVVGLARSDEAAAKIKSIDPAAKILRGDLKDLEIL 60 MKVF+TGA+GFIG ++ + L+ +GH V GL RS E AA++ ++ I G L D +L Sbjct: 1 MKVFVTGAAGFIGGSIATGLVKAGHSVTGLVRSVEQAAEMTALGITPVI--GSLDDTAVL 58 Query: 61 KKGATESDGVIHLGFVHDFKNFEQCCEIDRQATVAMLESLKGSNKPFLYTNGTLSL---- 116 + A ++D VI+ R A +L +LKGSNKPFL+T+G+ + Sbjct: 59 TEQAQKADAVIN-----------AASSDHRAAVETLLVALKGSNKPFLHTSGSSIVGDAS 107 Query: 117 --RPNKVANEQDGIDEDS--KILRAVTEQVALSYKDKGVSARIV----RLPFSVHGKGDK 168 + ++V +D + E + K R + + L+ +GV++ ++ S+ K D Sbjct: 108 GGKSSEVIYFEDNLPEPTVDKAARVAIDNLILAAAKEGVNSAVICNTLIYGHSLGVKRDS 167 Query: 169 AFVPILMNIAKAAGKSGYVGQGTNAWAAVHRLDTAPLFRLVLEKGKTGQVYHCVGEQGIP 228 +P L+ A+ +G +VG G N W+ VH D L+ L L K G Y V Sbjct: 168 VQLPRLLKQARKSGVVRHVGSGQNIWSNVHIEDVVALYLLALTKNVPGTFYF-VESSEAA 226 Query: 229 FKDIARVIGEILNV-PVASIPVDDAESHFGF--LTCFVTRDGPVSSEGTRKELGWQPQQI 285 F D+ I E LN+ P+ DAE+ +G+ + + V + R+ LGW P++ Sbjct: 227 FIDMTTAIAEALNLGKPQDWPLADAEAEWGYEMANYGLGSNSRVRGKHARERLGWAPKRT 286 Query: 286 GLLEDIR 292 ++E IR Sbjct: 287 SVVEWIR 293 Lambda K H 0.318 0.136 0.393 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: 190 Number of extensions: 11 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: 298 Length of database: 297 Length adjustment: 26 Effective length of query: 272 Effective length of database: 271 Effective search space: 73712 Effective search space used: 73712 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: 48 (23.1 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