Align S-(hydroxymethyl)glutathione dehydrogenase; EC 1.1.1.-; EC 1.1.1.1; EC 1.1.1.284 (characterized)
to candidate N515DRAFT_3331 N515DRAFT_3331 S-(hydroxymethyl)glutathione dehydrogenase / alcohol dehydrogenase
Query= CharProtDB::CH_002286 (369 letters) >FitnessBrowser__Dyella79:N515DRAFT_3331 Length = 369 Score = 615 bits (1585), Expect = 0.0 Identities = 289/369 (78%), Positives = 332/369 (89%) Query: 1 MKSRAAVAFAPGKPLEIVEIDVAPPKKGEVLIKVTHTGVCHTDAFTLSGDDPEGVFPVVL 60 MKSRAAVAF PGKPLEIVEIDVAPP+KGEVL+++THTGVCHTDAFTLSGDDPEG+FP VL Sbjct: 1 MKSRAAVAFGPGKPLEIVEIDVAPPRKGEVLVRITHTGVCHTDAFTLSGDDPEGIFPAVL 60 Query: 61 GHEGAGVVVEVGEGVTSVKPGDHVIPLYTAECGECEFCRSGKTNLCVAVRETQGKGLMPD 120 GHEG G+VVEVGEGV+SVKPGDHVIPLYTAEC +C+FC SGKTNLC AVR TQGKGLMPD Sbjct: 61 GHEGGGIVVEVGEGVSSVKPGDHVIPLYTAECRQCKFCLSGKTNLCQAVRATQGKGLMPD 120 Query: 121 GTTRFSYNGQPLYHYMGCSTFSEYTVVAEVSLAKINPEANHEHVCLLGCGVTTGIGAVHN 180 G+TRFSYNG+P+YHYMG STFSEYTVV E+SLA +NP+A E VCLLGCGVTTGIGAVHN Sbjct: 121 GSTRFSYNGEPVYHYMGTSTFSEYTVVPEISLAVVNPQAPLEKVCLLGCGVTTGIGAVHN 180 Query: 181 TAKVQPGDSVAVFGLGAIGLAVVQGARQAKAGRIIAIDTNPKKFDLARRFGATDCINPND 240 TAKV+PGD+VAVFGLG IGLAV+QGA QAKAGRII +DTNP KF LAR GATDC+NP D Sbjct: 181 TAKVKPGDTVAVFGLGGIGLAVIQGAVQAKAGRIIGVDTNPGKFALAREMGATDCVNPRD 240 Query: 241 YDKPIKDVLLDINKWGIDHTFECIGNVNVMRAALESAHRGWGQSVIIGVAVAGQEISTRP 300 + +PI++V++++ G+D +FECIGNV VMRAALE H+GWG+SVIIGVA AGQEI TRP Sbjct: 241 HARPIQEVIVEMTDGGVDFSFECIGNVEVMRAALECCHKGWGESVIIGVAGAGQEIRTRP 300 Query: 301 FQLVTGRVWKGSAFGGVKGRSQLPGMVEDAMKGDIDLEPFVTHTMSLDEINDAFDLMHEG 360 FQLVTGRVW+GSAFGGVKGR+QLPGMVE AM+G+I L+PF+TH + L+ IN+AF+LMHEG Sbjct: 301 FQLVTGRVWRGSAFGGVKGRTQLPGMVEQAMQGEIRLDPFITHNLPLERINEAFELMHEG 360 Query: 361 KSIRTVIRY 369 KSIRTVI + Sbjct: 361 KSIRTVIHF 369 Lambda K H 0.319 0.138 0.420 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: 581 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: 369 Length of database: 369 Length adjustment: 30 Effective length of query: 339 Effective length of database: 339 Effective search space: 114921 Effective search space used: 114921 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 (21.7 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