Align alcohol dehydrogenase (EC 1.1.1.1); all-trans-retinol dehydrogenase (NAD+) (EC 1.1.1.105) (characterized)
to candidate GFF2761 Psest_2816 S-(hydroxymethyl)glutathione dehydrogenase/class III alcohol dehydrogenase
Query= BRENDA::C7R702 (374 letters) >FitnessBrowser__psRCH2:GFF2761 Length = 371 Score = 612 bits (1578), Expect = e-180 Identities = 293/369 (79%), Positives = 332/369 (89%) Query: 6 IKCKAAVAWEAGKPLSIEEVEVQPPQKGEVRVKIVATGVCHTDAFTLSGDDPEGVFPSIL 65 IK +AAVA+ +PL I EV+V PP+ GEV ++IVATGVCHTDA+TLSG+D EGVFP IL Sbjct: 3 IKSRAAVAFGPNQPLQIVEVDVAPPKAGEVLIRIVATGVCHTDAYTLSGEDSEGVFPCIL 62 Query: 66 GHEGGGIVESVGEGVTSVKPGDHVIPLYTPECGDCKFCLSGKTNLCQKIRETQGKGLMPD 125 GHEGGGIVE+VGEGVTSV GDHVIPLYT EC +CKFC SGKTNLC +R TQGKGLMPD Sbjct: 63 GHEGGGIVEAVGEGVTSVAVGDHVIPLYTAECRECKFCKSGKTNLCSSVRATQGKGLMPD 122 Query: 126 GTTRFSINGKPIYHYMGTSTFSEYTVLPEISLAKVNPKAPLEEVCLLGCGVTTGMGAVMN 185 GTTRFS NG+PIYHYMG STFSEYTVLPE+S+AK+ +APLE+VCLLGCGVTTG+GAV+N Sbjct: 123 GTTRFSYNGEPIYHYMGCSTFSEYTVLPEVSVAKIPKEAPLEKVCLLGCGVTTGIGAVLN 182 Query: 186 TAKVEEGATVAIFGLGGIGLSAVIGAVMAKASRIIAIDINESKFELAKKLGATDCVNPKD 245 TAKVEEGATVAIFGLGGIGL+A+IGA MAKASRIIAIDIN KF +A++LGATD VNPKD Sbjct: 183 TAKVEEGATVAIFGLGGIGLAAIIGAKMAKASRIIAIDINPGKFAIAEELGATDFVNPKD 242 Query: 246 YDKPIQEVIVEMTDGGVDYSFECIGNVNVMRSALECCHKGWGESVIIGVAGAGQEISTRP 305 +DKPIQEVIVEMTDGGVDYSFEC+GNV +MR+ALECCHKGWGES IIGVAGAGQEISTRP Sbjct: 243 HDKPIQEVIVEMTDGGVDYSFECVGNVQLMRAALECCHKGWGESTIIGVAGAGQEISTRP 302 Query: 306 FQLVTGRVWKGTAFGGVKGRSELPDYVERYLAGEFKLDDFITHTMPLEKINDAFDLMHEG 365 FQLVTGRVW+G+AFGGVKGR+ELP YVE+ +GE LD FITH +PL+KIN+AFDLMHEG Sbjct: 303 FQLVTGRVWRGSAFGGVKGRTELPSYVEKAQSGEIPLDTFITHNLPLDKINEAFDLMHEG 362 Query: 366 KSIRSVIHY 374 KSIR+VIH+ Sbjct: 363 KSIRTVIHF 371 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: 608 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: 371 Length adjustment: 30 Effective length of query: 344 Effective length of database: 341 Effective search space: 117304 Effective search space used: 117304 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: 50 (23.9 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