Align alcohol dehydrogenase (EC 1.1.1.1); all-trans-retinol dehydrogenase (NAD+) (EC 1.1.1.105) (characterized)
to candidate Pf1N1B4_3108 S-(hydroxymethyl)glutathione dehydrogenase (EC 1.1.1.284)
Query= BRENDA::C7R702 (374 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3108 Length = 370 Score = 611 bits (1576), Expect = e-180 Identities = 295/370 (79%), Positives = 333/370 (90%) Query: 5 VIKCKAAVAWEAGKPLSIEEVEVQPPQKGEVRVKIVATGVCHTDAFTLSGDDPEGVFPSI 64 +IK +AAVA+EA KPL I EV+V P+ GEV +++VA+GVCHTDA+TLSG DPEG+FPSI Sbjct: 1 MIKSRAAVAFEAKKPLEIVEVDVAMPKAGEVLLRVVASGVCHTDAYTLSGADPEGIFPSI 60 Query: 65 LGHEGGGIVESVGEGVTSVKPGDHVIPLYTPECGDCKFCLSGKTNLCQKIRETQGKGLMP 124 LGHEGG +VE++GEGVTSV GDHVIPLYTPECG CKFCLSGKTNLCQ IR TQGKGLMP Sbjct: 61 LGHEGGAVVEAIGEGVTSVAVGDHVIPLYTPECGKCKFCLSGKTNLCQAIRATQGKGLMP 120 Query: 125 DGTTRFSINGKPIYHYMGTSTFSEYTVLPEISLAKVNPKAPLEEVCLLGCGVTTGMGAVM 184 DGT+RFS G+ I+HYMGTSTFSEYTVLPEIS+AK+ +APLE+VCLLGCGVTTG+GAV+ Sbjct: 121 DGTSRFSYKGETIFHYMGTSTFSEYTVLPEISVAKIPKEAPLEKVCLLGCGVTTGIGAVI 180 Query: 185 NTAKVEEGATVAIFGLGGIGLSAVIGAVMAKASRIIAIDINESKFELAKKLGATDCVNPK 244 NTAKV+ G TVAIFGLGGIGLSAVIGAV AKA RIIAIDIN +KFE+AK+LGATDCVNPK Sbjct: 181 NTAKVKPGDTVAIFGLGGIGLSAVIGAVKAKAGRIIAIDINPAKFEIAKQLGATDCVNPK 240 Query: 245 DYDKPIQEVIVEMTDGGVDYSFECIGNVNVMRSALECCHKGWGESVIIGVAGAGQEISTR 304 D+D+PIQEVIV+MTDGGVD+SFECIGNV +MR+ALECCHKGWGESVIIGVAGAGQEISTR Sbjct: 241 DFDRPIQEVIVDMTDGGVDFSFECIGNVQLMRAALECCHKGWGESVIIGVAGAGQEISTR 300 Query: 305 PFQLVTGRVWKGTAFGGVKGRSELPDYVERYLAGEFKLDDFITHTMPLEKINDAFDLMHE 364 PFQLVTGRVW+G+AFGGV+GR+ELP YVE GE LD FITHTM LE IN AFDLMHE Sbjct: 301 PFQLVTGRVWRGSAFGGVRGRTELPSYVEMAQTGEIPLDTFITHTMGLEDINKAFDLMHE 360 Query: 365 GKSIRSVIHY 374 GKSIRSVIH+ Sbjct: 361 GKSIRSVIHF 370 Lambda K H 0.317 0.137 0.413 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: 598 Number of extensions: 18 Number of successful extensions: 1 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: 374 Length of database: 370 Length adjustment: 30 Effective length of query: 344 Effective length of database: 340 Effective search space: 116960 Effective search space used: 116960 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 (21.6 bits) S2: 49 (23.5 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