Align scyllo-inosose 3-dehydrogenase; 2-keto-myo-inositol dehydrogenase; EC 1.1.1.- (characterized)
to candidate WP_076949143.1 C1M55_RS05845 glutathione-dependent formaldehyde dehydrogenase
Query= SwissProt::Q9WYP3 (395 letters) >NCBI__GCF_002893965.1:WP_076949143.1 Length = 395 Score = 101 bits (251), Expect = 4e-26 Identities = 88/278 (31%), Positives = 124/278 (44%), Gaps = 38/278 (13%) Query: 27 LTWLGSKVWRYPEVRVEEVPEPRIEKPTEIIIKVKACGICGSDVHMAQTDEEGYILYPGL 86 +TW G + +V V+ VP+P+I +PT+ IIKV ICGSD+H+ +T G + G Sbjct: 4 VTWQGKR-----KVSVDTVPDPKIVEPTDAIIKVTTTNICGSDLHLYET--LGAFMNAG- 55 Query: 87 TGFPVTLGHEFSGVVVEAGPEAINRRTNKRFEIGEPVCAEEMLWCGHCRPCAEGFPNHCE 146 LGHE G+V E G E N IG+ V + CG+C C CE Sbjct: 56 ----DILGHEPMGIVEEVGSEVTN------LGIGDRVVIPFQISCGNCFMCDSSLYTQCE 105 Query: 147 --------------NLNELGFNVDGAFAEYVKVDAKYAWSLRELEGVYEGDRLFLAGSLV 192 +EL +V G AEY++V + ++ EG D F+ S V Sbjct: 106 TTQVRDQGTGAALFGFSELYGSVPGGQAEYLRVPQAHFTHIKVPEG--PADSRFVYLSDV 163 Query: 193 EPTSVAYNAVIVRGGGIRPGDNVVILGGGPIGLAAVAILKHAGASKVILSEPSEVRRNLA 252 PT A+ + V I PG +V ILG GPIG A I H G + + E LA Sbjct: 164 LPT--AWQS--VEYADIPPGGSVTILGLGPIGDMAARIAHHKGFRVIGVDRVPERLARLA 219 Query: 253 KELGADHVIDPTKENFVEAVLDYTNGLGAKLFLEATGV 290 + +D +A+ D TNG G ++A G+ Sbjct: 220 ERGIETLNLDDYGSKIGDAIRDATNGRGTDSVIDAVGM 257 Lambda K H 0.319 0.138 0.418 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: 360 Number of extensions: 25 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: 395 Length of database: 395 Length adjustment: 31 Effective length of query: 364 Effective length of database: 364 Effective search space: 132496 Effective search space used: 132496 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: 50 (23.9 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