Align NADP-retinol dehydrogenase (EC 1.1.1.300); alcohol dehydrogenase [NAD(P)+] (EC 1.1.1.71) (characterized)
to candidate WP_008628641.1 C943_RS13225 SDR family NAD(P)-dependent oxidoreductase
Query= BRENDA::Q9HBH5 (336 letters) >NCBI__GCF_000330725.2:WP_008628641.1 Length = 277 Score = 130 bits (326), Expect = 5e-35 Identities = 90/291 (30%), Positives = 143/291 (49%), Gaps = 24/291 (8%) Query: 46 VLITGANSGLGRATAAELLRLGARVIMGCRDRARAEEAAGQLRRELRQAAECGPEPGVSG 105 + ITGA SG+G T ++ +V + R++ +A+ L + Q Sbjct: 3 IAITGATSGIGWVTLKRIIPDAEQVFLLARNKDKADVLLKSLPSDQSQKVR--------- 53 Query: 106 VGELIVRELDLASLRSVRAFCQEMLQEEPRLDVLINNAGIFQCPYMKTEDGFEMQFGVNH 165 DLA SV A + + + LD L+NNAG T+DG EM NH Sbjct: 54 -----FVACDLADFDSVSAAAKTIQSQTTHLDCLVNNAGGIFDKKEFTKDGVEMSLAANH 108 Query: 166 LGHFLLTNLLLGLLKSSAPSRIVVVSSKLYKYGDINFDDLN-SEQSYNKSFCYSRSKLAN 224 LGHFLLTN L+ LL ++ +++ VSS+ ++ +FDDLN ++SY+ Y+ KL N Sbjct: 109 LGHFLLTNRLIPLLLAAKNPKVINVSSEAHRMAKPDFDDLNFVKKSYSSFLAYANVKLFN 168 Query: 225 ILFTRELARRLEGTNVTVNVLHPGIVRTNLGRHIHIPLLVKPLFNL---VSWAFFKTPVE 281 ILF++ L R + LHPG+V+TN G+ K +F+L ++ F + + Sbjct: 169 ILFSKSLVDRYGKKGLRSYSLHPGVVKTNFGKE------TKGIFSLFWKMAAPFMISADD 222 Query: 282 GAQTSIYLASSPEVEGVSGRYFGDCKEEELLPKAMDESVARKLWDISEVMV 332 GA+ S++L S +G YF + K ++ A +LW++SE M+ Sbjct: 223 GAKNSLFLIKSDFSAEQNGNYFKNQKPKKPSSLARSVKTREQLWEVSEKML 273 Lambda K H 0.322 0.138 0.403 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: 149 Number of extensions: 6 Number of successful extensions: 5 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: 336 Length of database: 277 Length adjustment: 27 Effective length of query: 309 Effective length of database: 250 Effective search space: 77250 Effective search space used: 77250 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 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