Align NADP-retinol dehydrogenase (EC 1.1.1.300); alcohol dehydrogenase [NAD(P)+] (EC 1.1.1.71) (characterized)
to candidate WP_057507613.1 ABB28_RS05165 oxidoreductase
Query= BRENDA::Q9HBH5 (336 letters) >NCBI__GCF_001431535.1:WP_057507613.1 Length = 305 Score = 181 bits (460), Expect = 2e-50 Identities = 122/303 (40%), Positives = 165/303 (54%), Gaps = 32/303 (10%) Query: 43 GKTVLITGANSGLGRATAAELLRLGARVIMGCRDRARAEEAAGQLRRELRQAAECGPEPG 102 GKT ++TGAN+G+G T+ L GARV++GCR+ A E AA LR +A Sbjct: 17 GKTFIVTGANAGIGLETSRVLALRGARVLLGCRNAATFEAAAVDLRHSAPRA-------- 68 Query: 103 VSGVGELIVRELDLASLRSVRAFCQEMLQEEPRLDVLINNAGIFQCPYMKTEDGFEMQFG 162 +L LDLA L SVRA + Q+E R+D LINNAG+ P +T GFE+QFG Sbjct: 69 -----DLAWMPLDLADLDSVRA-AVAVAQQEARIDGLINNAGVMIPPLTRTRQGFELQFG 122 Query: 163 VNHLGHFLLTNLLLGLLKSSAPSRIVVVSSKLYKYGDINFDDLNSEQSYNKSFCYSRSKL 222 VNHLG F LT+LLL L + +R+V+ SS + G + +DDLN+E Y ++ Y SKL Sbjct: 123 VNHLGPFALTSLLLPKLAETQGARVVITSSIAHFKGRMEWDDLNAEAGYRRAARYRSSKL 182 Query: 223 ANILFTRELARRLEGTNVTVNVL--HPGIVRTNLGRHIHIPLLVKPLFNLVSWAFFKTPV 280 AN L EL RRL N + + HPG+ T LGRH+ I V PL F T V Sbjct: 183 ANALHLFELDRRLRAANSHIVAVGCHPGVAYTRLGRHVGIAQWVGPLVG----RFLNTAV 238 Query: 281 EGAQTSIYLASSPEVEGVSGRYFGDCKEEELL---------PKAMDESVARKLWDISEVM 331 +GA ++ A++ +VE G Y+G + A+D AR+LWDIS + Sbjct: 239 QGAWPTLQ-AATGDVE--PGGYYGPTGLAQARGVSGPARRGESALDPVAARRLWDISVQL 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: 238 Number of extensions: 10 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: 305 Length adjustment: 28 Effective length of query: 308 Effective length of database: 277 Effective search space: 85316 Effective search space used: 85316 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 Apr 09 2024. 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