Align 3-dehydro-scyllo-inosose hydrolase; Diketo-inositol hydrolase; EC 3.7.1.- (characterized)
to candidate WP_073037914.1 BUB04_RS05965 creatininase
Query= SwissProt::Q9WYP4 (311 letters) >NCBI__GCF_900129305.1:WP_073037914.1 Length = 321 Score = 349 bits (895), Expect = e-101 Identities = 165/307 (53%), Positives = 220/307 (71%), Gaps = 1/307 (0%) Query: 1 MERPTGVYFQTMTMKQIRERLKQCDLIIIPVGSTENHGPNAPTGEDTFLVTRMAEQVALK 60 M++PTG+YFQTMT +++ ERL++ D++I+PVGSTENHG P GEDTF+VTR+AE+VA Sbjct: 13 MDKPTGIYFQTMTKREVEERLQKNDILIVPVGSTENHGSAGPFGEDTFVVTRLAEEVAKA 72 Query: 61 TGCTVAEPIWYGYHPYHHIGMPGTVPVKDEAFIDYLVSVIAGFWNTGFRKQILLNGHGQE 120 TGCTVAEP+ YG HP+HH+G PGTV + D+ F DY+ ++IAGFWNTGFRKQI ++ HGQE Sbjct: 73 TGCTVAEPLHYGSHPFHHLGQPGTVVIPDDVFSDYIRAMIAGFWNTGFRKQIWISLHGQE 132 Query: 121 FVIPIAIHKFAKIFQVPAIIINLNWYHAIQDKFKTKEEGGPYETPFIHADEVETSWSLAL 180 ++IP A+ +F K +QVP ++ ++ + K GGPYE PF HA E E S S+AL Sbjct: 133 YIIPSALQEFGKRYQVPCMLFFVDVPRVMGQTLMDKAHGGPYEEPFQHACEAEQSISMAL 192 Query: 181 FPEFMHQEWAVDTEPKGFLPEGHIDKAGNLLHRPIAWYGHVGGGPIEVVAYPEGVVGKAT 240 FPE EWA DT+ +G+LP GHID+ G++ PI + HVG G IE V +PEGV+GK + Sbjct: 193 FPELCRPEWAEDTQIRGYLPPGHIDRGGDIYGYPIPGHCHVGAGGIECVMFPEGVLGKPS 252 Query: 241 LASAEKAKEGVEALLDYLEKLVRDIMERFPAGKLPPAEMLSQRPKEELEALTKEPLTEGW 300 A KA +E LDY+ +L DI+ERFPAGKLPP E +SQR + LE + K P T+G Sbjct: 253 KADPAKAVPSIEKFLDYMVQLHNDILERFPAGKLPPVEQMSQRDPKLLEDILKGP-TKGG 311 Query: 301 RNLYTAG 307 ++LY G Sbjct: 312 KHLYVLG 318 Lambda K H 0.319 0.139 0.437 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: 424 Number of extensions: 25 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: 311 Length of database: 321 Length adjustment: 27 Effective length of query: 284 Effective length of database: 294 Effective search space: 83496 Effective search space used: 83496 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: 48 (23.1 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