Align NADH-dependent aldehyde reductase (EC 1.1.1.77; EC 1.1.1.244; EC 1.1.1.1) (characterized)
to candidate WP_012384476.1 BIND_RS07545 NAD-dependent dehydratase
Query= metacyc::G3O-32155-MONOMER (298 letters) >NCBI__GCF_000019845.1:WP_012384476.1 Length = 298 Score = 226 bits (575), Expect = 6e-64 Identities = 122/293 (41%), Positives = 176/293 (60%), Gaps = 5/293 (1%) Query: 1 MKVFITGASGFIGSAVLSELISSGHEVVGLARSDEAAAKIKSIDPAAKILRGDLKDLEIL 60 M+VF+TGA+G IGS V+ +LI++GH+V+GL RS+E AA + ++ A+ RG + D + L Sbjct: 1 MRVFVTGATGNIGSNVVKDLIAAGHQVIGLYRSEEKAAALAAV--GAQAYRGSIADPDSL 58 Query: 61 KKGATESDGVIHLGFVHDFKNFEQCCEIDRQATVAMLESLKGSNKPFLYTNGT--LSLRP 118 K+GA SDGVIHL F HDF F Q CE DR A+ L GSN+P + T+GT + P Sbjct: 59 KEGAARSDGVIHLAFNHDFSRFVQSCEDDRHIIAALGSVLAGSNRPLVITSGTPIANTIP 118 Query: 119 NKVANEQDGIDEDSKILRAVTEQVALSYKDKGVSARIVRLPFSVHGKGDKAFVPILMNIA 178 + A E + I + RA +E+ A + +GV+ +VRLP VH + + + + Sbjct: 119 GEPAREDNPIVGSNMHPRAASEEAAATLAAQGVNVSVVRLP-QVHDPVTQGLITPAIQMY 177 Query: 179 KAAGKSGYVGQGTNAWAAVHRLDTAPLFRLVLEKGKTGQVYHCVGEQGIPFKDIARVIGE 238 + G YVG G N W A H LD A L+RL +EK + YH V E+G+P +DIA IG Sbjct: 178 REKGVCTYVGDGLNRWPAAHVLDVARLYRLAIEKAEPNAKYHAVAEEGVPMRDIAEAIGR 237 Query: 239 ILNVPVASIPVDDAESHFGFLTCFVTRDGPVSSEGTRKELGWQPQQIGLLEDI 291 L++PV SI ++ ++FG+L F D P SS TR++LGW+P L+ D+ Sbjct: 238 RLSLPVKSITKEETPAYFGWLAMFAGLDMPASSAQTRQKLGWEPTGPSLIADL 290 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: 220 Number of extensions: 11 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: 298 Length of database: 298 Length adjustment: 27 Effective length of query: 271 Effective length of database: 271 Effective search space: 73441 Effective search space used: 73441 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 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