Align Metapyrocatechase 2; MPC; EC 1.13.11.2; CatO2ase; Catechol 2,3-dioxygenase II (uncharacterized)
to candidate RR42_RS34600 RR42_RS34600 metapyrocatechase
Query= curated2:P17296 (320 letters) >FitnessBrowser__Cup4G11:RR42_RS34600 Length = 312 Score = 439 bits (1129), Expect = e-128 Identities = 211/305 (69%), Positives = 234/305 (76%), Gaps = 1/305 (0%) Query: 17 ARPRH-AVHSIDHYALEVPDLAVAERFLDAFGLTVARTPECLEVYAADQRCWARFYEGER 75 AR R AVHS+DHYAL VPDL+ AE FL AFGLTV R + LEV A D WAR++ GER Sbjct: 7 AREREPAVHSLDHYALTVPDLSAAEHFLGAFGLTVVRQDDTLEVLAQDGWVWARYFPGER 66 Query: 76 KRLAYLSFSCFEGDFAGIRQQLAASGATLVEDPRYGDESGVWFFDPDGNLVQVKIGPKTS 135 K LAYLSF+CF GDF GIR++L A+ T + G+WF D DGNL+QVKIGPKTS Sbjct: 67 KALAYLSFNCFAGDFEGIRRKLLAANVTFASGAAHATAEGLWFLDADGNLIQVKIGPKTS 126 Query: 136 PSSKSPARLEGAPGGQRGAVVRSQVQRVLPRRLSHVLLFTPSVQRALDFYRDALGLRLSD 195 PS+K+P + P RGA R QV +V PRRLSHVLLFTP V RA+ FY D LGLRLSD Sbjct: 127 PSAKNPLKDIHGPADMRGAAFRDQVGKVRPRRLSHVLLFTPDVSRAVSFYNDTLGLRLSD 186 Query: 196 RSDDVIAFTHAPYGSDHHLLALVKSSARGWHHAAWDVADVNEVGQGASQMAKAGYTQGWG 255 RS D IAF HAP+G DHHLLA KSSARGWHHAAWDVA V+EVGQGA QMA AGY +GWG Sbjct: 187 RSGDGIAFLHAPHGCDHHLLAFAKSSARGWHHAAWDVASVDEVGQGAGQMAVAGYKEGWG 246 Query: 256 TGRHVLGSNYFFYVLDPWGSFCEYSADIDYIPAGQAWPAGDFAAEDSLYQWGPDVPEYFV 315 TGRHVLGSN+F YV DPWGSFCEYSADIDYI AG AWPAGD+ EDSLYQWGPDVP YF+ Sbjct: 247 TGRHVLGSNFFHYVRDPWGSFCEYSADIDYISAGHAWPAGDYPPEDSLYQWGPDVPPYFI 306 Query: 316 RNTEA 320 NTEA Sbjct: 307 HNTEA 311 Lambda K H 0.320 0.136 0.430 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: 434 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: 320 Length of database: 312 Length adjustment: 27 Effective length of query: 293 Effective length of database: 285 Effective search space: 83505 Effective search space used: 83505 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 (21.8 bits) S2: 48 (23.1 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