Align NADP-retinol dehydrogenase (EC 1.1.1.300); alcohol dehydrogenase [NAD(P)+] (EC 1.1.1.71) (characterized)
to candidate WP_089217430.1 CHB69_RS18510 SDR family NAD(P)-dependent oxidoreductase
Query= BRENDA::Q9HBH5 (336 letters) >NCBI__GCF_900188185.1:WP_089217430.1 Length = 306 Score = 176 bits (445), Expect = 9e-49 Identities = 119/303 (39%), Positives = 159/303 (52%), Gaps = 32/303 (10%) Query: 43 GKTVLITGANSGLGRATAAELLRLGARVIMGCRDRARAEEAAGQLRRELRQAAECGPEPG 102 GK +++TGANSG+G A+ L ARV++ CRD ++A A ++R+ Sbjct: 17 GKCLIVTGANSGVGFEVASALAARRARVLLACRDESKARAAMDKIRQR------------ 64 Query: 103 VSGVGELIVRELDLASLRSVRAFCQEMLQEEPRLDVLINNAGIFQCPYMKTEDGFEMQFG 162 S +L LDLA L SVR E+ +EPR+DVLINNAG+ T GFE+ FG Sbjct: 65 -SSGADLAFLPLDLADLASVRK-AAEVAAKEPRIDVLINNAGVTVPTRQTTRQGFELLFG 122 Query: 163 VNHLGHFLLTNLLLGLLKSSAPSRIVVVSSKLYKYGDINFDDLNSEQSYNKSFCYSRSKL 222 VNHLG F LT L+L L+ + SRIV+ SS +K I +DDLN+E++YN Y SKL Sbjct: 123 VNHLGSFALTALMLPKLRETPGSRIVITSSGQHKGAKIEWDDLNAEKNYNWLSRYGASKL 182 Query: 223 ANILFTRELARRLEGTNVTVNVL--HPGIVRTNLGRHIHIPLLVKPLFNLVSWAFFKTPV 280 AN+LF EL RRL+ + V + HPG RTN GR L L V F TP Sbjct: 183 ANLLFMLELNRRLQAAEMPVTTVGCHPGFARTNFGR----ASLAGRLAVGVGGLLFNTPA 238 Query: 281 EGAQTSIYLASSPEVEGVSGRYFGDCKEEEL---------LPKAMDESVARKLWDISEVM 331 GA ++ A+ G Y+G EL A + +AR+LWD+S M Sbjct: 239 MGAWPTLQAATG---NVKPGGYYGPTAFAELRGPSFECTPSDDARNPQLARRLWDVSIEM 295 Query: 332 VGL 334 G+ Sbjct: 296 TGI 298 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: 248 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: 336 Length of database: 306 Length adjustment: 28 Effective length of query: 308 Effective length of database: 278 Effective search space: 85624 Effective search space used: 85624 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