Align Uronate isomerase; EC 5.3.1.12; Glucuronate isomerase; Uronic isomerase (uncharacterized)
to candidate AZOBR_RS31425 AZOBR_RS31425 glucuronate isomerase
Query= curated2:Q1GNM2 (470 letters) >FitnessBrowser__azobra:AZOBR_RS31425 Length = 467 Score = 639 bits (1649), Expect = 0.0 Identities = 314/470 (66%), Positives = 370/470 (78%), Gaps = 10/470 (2%) Query: 7 LSPDRLFPSDPAQRDIARRLYKAVAGLPIVSPHGHTDPAWFAGDAPFGNAAELLLHPDHY 66 L PDRLFPSDP QRDIARRLY V LPI+SPHGHTDP+WFA + F N A L + PDHY Sbjct: 2 LHPDRLFPSDPTQRDIARRLYAEVGHLPIISPHGHTDPSWFAKNEAFPNPAALFVVPDHY 61 Query: 67 VFRMLYSQGVSLDALGI-----GNADADPRESWRLFAENYHLFRATPSRMWMDWVFAEVF 121 FRMLYSQGV+L++LG+ G ++DPR+ WR A+N+HLFR TP+RMW+D F VF Sbjct: 62 AFRMLYSQGVALESLGVPRTDGGAVESDPRKIWRQLAQNWHLFRGTPTRMWLDHAFETVF 121 Query: 122 GFDVQLSAETSDLYYDRITEALAIDAFRPRALFDRFGIEVIATTESPLDSLDHHAVIRAA 181 G +LS ++D +D+I L F PRALF+RF IE++ATTESPLD+L+HH IR + Sbjct: 122 GVTERLSGASADRIFDQIDACLQKPEFLPRALFERFNIELLATTESPLDTLEHHRAIRES 181 Query: 182 NASGEWGGRVITAYRPDPVVDPEFEGFRDNLARFSNLSGEDAFSYSGYLAAHRKRRAFFA 241 W GRVITA+RPDPVVDPEFEGF+ N+ R LSGE+ +++GYLAA R RR +F Sbjct: 182 G----WKGRVITAFRPDPVVDPEFEGFQANVERLGALSGENTGTWAGYLAALRNRRQYFK 237 Query: 242 SMG-ATSTDHGHPSAATADLSETQAEALFARVTGEDMSAADAELFRAHMLTVMAGMSLDD 300 +G ATSTDHGH +A TADLS+ AE LF + ++AA+AE+FR MLT MA MSLDD Sbjct: 238 EVGGATSTDHGHATATTADLSDADAERLFEKALRGTITAAEAEIFRGQMLTEMAKMSLDD 297 Query: 301 GLVMQIHPGAFRNHNPWLFANHGRDKGADIPTATDYVHALRPLLGRYGNEADLTIILFTL 360 GLVMQIHPG+FRNHNP +F GRDKGADIPT T+YV AL+PLL R GNE DLTIILFTL Sbjct: 298 GLVMQIHPGSFRNHNPGVFERFGRDKGADIPTGTEYVRALKPLLDRVGNERDLTIILFTL 357 Query: 361 DETSYARELAPLAGHYPALKLGPAWWFHDSPEGMRRFRSQMTETAGFYNTVGFNDDTRAF 420 DETSYARELAPLAGHYPAL++GPAWWFHDSPEGMRR+R +TETAGFYNTVGFNDDTRAF Sbjct: 358 DETSYARELAPLAGHYPALRVGPAWWFHDSPEGMRRYREMITETAGFYNTVGFNDDTRAF 417 Query: 421 LSIPARHDVARRIDCGFLAQLVSEHRLEEWEAAELAADLSYNLAKASYKL 470 SIPARHDVARR+DC FLA+LV+EHRLEE EAAE+A DL+Y LAK +YKL Sbjct: 418 CSIPARHDVARRVDCAFLARLVAEHRLEEDEAAEVAVDLAYTLAKKAYKL 467 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: 806 Number of extensions: 31 Number of successful extensions: 6 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: 467 Length adjustment: 33 Effective length of query: 437 Effective length of database: 434 Effective search space: 189658 Effective search space used: 189658 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