Align Uronate isomerase; EC 5.3.1.12; Glucuronate isomerase; Uronic isomerase (uncharacterized)
to candidate CCNA_01557 CCNA_01557 uronate isomerase
Query= curated2:Q1GNM2 (470 letters) >FitnessBrowser__Caulo:CCNA_01557 Length = 487 Score = 627 bits (1618), Expect = 0.0 Identities = 313/474 (66%), Positives = 365/474 (77%), Gaps = 8/474 (1%) Query: 1 MPRPLYLSPDRLFPSDPAQRDIARRLYKAVAGLPIVSPHGHTDPAWFAGDAPFGNAAELL 60 M RPL DRLFPSDPA R AR LY V LPI+SPHGHTDP+WFA +APF +A +LL Sbjct: 1 MARPLSFHEDRLFPSDPATRSYARGLYALVKDLPIISPHGHTDPSWFATNAPFQDATDLL 60 Query: 61 LHPDHYVFRMLYSQGVSLDALGI----GNADADPRESWRLFAENYHLFRATPSRMWMDWV 116 L PDHY+FRMLYSQGVSLDAL + G D DPRE+WR+FA +++LFR TPS +W++ V Sbjct: 61 LAPDHYLFRMLYSQGVSLDALKVRSKAGVPDTDPREAWRVFASHFYLFRGTPSWVWLNHV 120 Query: 117 FAEVFGFDVQLSAETSDLYYDRITEALAIDAFRPRALFDRFGIEVIATTESPLDSLDHHA 176 F++VFGF L A +D Y+DRIT ALA DAFRPRALFDRF IE +ATTE P +SL HHA Sbjct: 121 FSQVFGFTEFLEASNADDYFDRITAALATDAFRPRALFDRFNIETLATTEGPHESLQHHA 180 Query: 177 VIRAANASGEWGGRVITAYRPDPVVDPEFEGFRDNLARFSNLSGEDAFSYSGYLAAHRKR 236 IR + WGG VITAYRPD V+D E E RF+ SG+D +S+ YL AHR R Sbjct: 181 AIRESG----WGGHVITAYRPDAVIDFEDERSPRAFERFAETSGQDVYSWKSYLEAHRLR 236 Query: 237 RAFFASMGATSTDHGHPSAATADLSETQAEALFARVTGEDMSAADAELFRAHMLTVMAGM 296 R F GATS+DHGHP+AATADLS+ +AEALF + D++ AELFRA MLT MA M Sbjct: 237 RQAFIDAGATSSDHGHPTAATADLSDVEAEALFNSLVKGDVTPEKAELFRAQMLTEMAKM 296 Query: 297 SLDDGLVMQIHPGAFRNHNPWLFANHGRDKGADIPTATDYVHALRPLLGRYGNEADLTII 356 SLDDGLVMQIHPG+ RNHN L +HGRDKGADIP T+YV AL+PLL R GN+ L+II Sbjct: 297 SLDDGLVMQIHPGSHRNHNVGLLNSHGRDKGADIPMRTEYVDALKPLLTRLGNDPRLSII 356 Query: 357 LFTLDETSYARELAPLAGHYPALKLGPAWWFHDSPEGMRRFRSQMTETAGFYNTVGFNDD 416 LFTLDET+Y+RELAPLAGHYP LKLGP+WWFHDSPEGM RFR Q+TETAGFYNTVGFNDD Sbjct: 357 LFTLDETTYSRELAPLAGHYPVLKLGPSWWFHDSPEGMMRFREQVTETAGFYNTVGFNDD 416 Query: 417 TRAFLSIPARHDVARRIDCGFLAQLVSEHRLEEWEAAELAADLSYNLAKASYKL 470 TRAFLSIPARHDVARR+D FLA++V+EHR++ EA EL DL+YNL K +YKL Sbjct: 417 TRAFLSIPARHDVARRVDSAFLARMVAEHRMDLVEAEELIVDLTYNLPKKAYKL 470 Lambda K H 0.322 0.136 0.423 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: 831 Number of extensions: 36 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: 470 Length of database: 487 Length adjustment: 34 Effective length of query: 436 Effective length of database: 453 Effective search space: 197508 Effective search space used: 197508 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 (21.9 bits) S2: 51 (24.3 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