Align Uronate isomerase; EC 5.3.1.12; Glucuronate isomerase; Uronic isomerase (uncharacterized)
to candidate WP_011649923.1 RL_RS00530 glucuronate isomerase
Query= curated2:Q1GNM2 (470 letters) >NCBI__GCF_000009265.1:WP_011649923.1 Length = 471 Score = 526 bits (1356), Expect = e-154 Identities = 262/469 (55%), Positives = 325/469 (69%), Gaps = 8/469 (1%) Query: 6 YLSPDRLFPSDPAQRDIARRLYKAVAGLPIVSPHGHTDPAWFAGDAPFGNAAELLLHPDH 65 +L PDRLFP+DPA R +AR LY+ V LPIVSPHGHT+P+WFA D PF +AA LL+ PDH Sbjct: 7 FLHPDRLFPADPATRTVARDLYETVRNLPIVSPHGHTEPSWFADDKPFEDAASLLVIPDH 66 Query: 66 YVFRMLYSQGVSLDALGIGNADADP----RESWRLFAENYHLFRATPSRMWMDWVFAEVF 121 Y+FRML+S GV+LD LG+ D P R WR FA +YHLFR TPS +W+D + V Sbjct: 67 YLFRMLHSVGVTLDELGVPRLDGKPVASGRAIWRTFAAHYHLFRGTPSSLWVDHAMSAVL 126 Query: 122 GFDVQLSAETSDLYYDRITEALAIDAFRPRALFDRFGIEVIATTESPLDSLDHHAVIRAA 181 G L+ + +D YD I LA+ FRPRAL RFGIE IATT+ LD L HH + Sbjct: 127 GCTEPLTPDNADALYDHINAQLALPEFRPRALHQRFGIETIATTDGALDPLAHHQKM--- 183 Query: 182 NASGEWGGRVITAYRPDPVVDPEFEGFRDNLARFSNLSGEDAFSYSGYLAAHRKRRAFFA 241 A+ W G+V T YRPD V DP+ GFRDNL +F ++G + + G + AHR+RRA+F Sbjct: 184 -AADGWIGKVRTTYRPDSVTDPDAVGFRDNLVKFGEITGTEVTRWDGLIEAHRRRRAYFR 242 Query: 242 SMGATSTDHGHPSAATADLSETQAEALFARVTGEDMSAADAELFRAHMLTVMAGMSLDDG 301 GAT+TDHG P+A TADL T+ +AL + +SA DAELFR M+T MAG+S +DG Sbjct: 243 QFGATATDHGVPTAFTADLPLTEKQALLDKALKGPLSAEDAELFRGQMMTEMAGLSAEDG 302 Query: 302 LVMQIHPGAFRNHNPWLFANHGRDKGADIPTATDYVHALRPLLGRYGNEADLTIILFTLD 361 +VMQIH G+ RN + LFA G + GADIPT+TD+V L LL +YG+ L ++LFTLD Sbjct: 303 MVMQIHAGSRRNTDSGLFATRGPNMGADIPTSTDWVGGLNALLSKYGHAPGLRVLLFTLD 362 Query: 362 ETSYARELAPLAGHYPALKLGPAWWFHDSPEGMRRFRSQMTETAGFYNTVGFNDDTRAFL 421 ET+YARELAP+ GH+P L +GP WWFHDSP G+RR+ Q+ ETAGF N GFNDDTRA L Sbjct: 363 ETTYARELAPMVGHWPCLMIGPPWWFHDSPLGIRRYLDQVVETAGFANMAGFNDDTRALL 422 Query: 422 SIPARHDVARRIDCGFLAQLVSEHRLEEWEAAELAADLSYNLAKASYKL 470 SIPARHDV RR C FLAQL EHRL + EA +A +LSY AK +YKL Sbjct: 423 SIPARHDVWRREVCRFLAQLAGEHRLSKREAEIVAGELSYGNAKKAYKL 471 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: 776 Number of extensions: 26 Number of successful extensions: 3 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: 471 Length adjustment: 33 Effective length of query: 437 Effective length of database: 438 Effective search space: 191406 Effective search space used: 191406 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 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