Align 4-hydroxy-4-methyl-2-oxoglutarate aldolase; HMG aldolase; Oxaloacetate decarboxylase; OAA decarboxylase; Regulator of ribonuclease activity homolog; EC 4.1.3.17; EC 4.1.1.112 (characterized)
to candidate RR42_RS12215 RR42_RS12215 ribonuclease
Query= SwissProt::Q5SIP7 (164 letters) >FitnessBrowser__Cup4G11:RR42_RS12215 Length = 165 Score = 138 bits (348), Expect = 4e-38 Identities = 78/158 (49%), Positives = 102/158 (64%), Gaps = 6/158 (3%) Query: 1 MEARTTDLSDLYPEGEA------LPMVFKSFGGRARFAGRVRTLRVFEDNALVRKVLEEE 54 M TTDL D A L VF+ FG RA F+G TL+VFEDN+LVR+ +E Sbjct: 1 MSFATTDLCDANEARLADGSLRVLSPVFQHFGKRAAFSGPAATLKVFEDNSLVRETVESP 60 Query: 55 GAGQVLFVDGGGSLRTALLGGNLARLAWEKGWAGVVVHGAVRDTEELREVPIGLLALAAT 114 G G+VL VDGGGSLR AL+GGNL LA + GW G++V+G VRD+ EL IG+ ALA Sbjct: 61 GNGRVLVVDGGGSLRCALVGGNLGVLAEKNGWVGILVNGCVRDSGELAVCDIGVRALALH 120 Query: 115 PKKSAKEGKGEVDVPLKVLGVEVLPGSFLLADEDGLLL 152 P+KS K GE +V +++ G V PG+++ AD DG+L+ Sbjct: 121 PQKSQKRNVGEREVTVQMPGAVVRPGNWIYADADGVLV 158 Lambda K H 0.317 0.140 0.403 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: 93 Number of extensions: 4 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: 164 Length of database: 165 Length adjustment: 18 Effective length of query: 146 Effective length of database: 147 Effective search space: 21462 Effective search space used: 21462 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: 43 (21.2 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