Align Uronate isomerase; EC 5.3.1.12; Glucuronate isomerase; Uronic isomerase (uncharacterized)
to candidate Ga0059261_2969 Ga0059261_2969 Glucuronate isomerase
Query= curated2:Q1GNM2 (470 letters) >FitnessBrowser__Korea:Ga0059261_2969 Length = 479 Score = 640 bits (1652), Expect = 0.0 Identities = 315/472 (66%), Positives = 365/472 (77%), Gaps = 8/472 (1%) Query: 3 RPLYLSPDRLFPSDPAQRDIARRLYKAVAGLPIVSPHGHTDPAWFAGDAPFGNAAELLLH 62 RPL L PDRLFP++P R IA LYK +AGLPIVSPHGHTDP+WFA D + NA EL L Sbjct: 2 RPLALDPDRLFPAEPTTRAIACDLYKEIAGLPIVSPHGHTDPSWFATDDAWENATELFLA 61 Query: 63 PDHYVFRMLYSQGVSLDALGIGNADA----DPRESWRLFAENYHLFRATPSRMWMDWVFA 118 PDHYVFRMLYSQGV LDAL + D DPR +WRLFA NYHLFR TPSRMW+D VFA Sbjct: 62 PDHYVFRMLYSQGVDLDALRVPRIDGVPATDPRAAWRLFASNYHLFRGTPSRMWLDHVFA 121 Query: 119 EVFGFDVQLSAETSDLYYDRITEALAIDAFRPRALFDRFGIEVIATTESPLDSLDHHAVI 178 EVFG + L + T+D YYD I EALA A+RPRALF+RF I+ +ATTE D L+HHA I Sbjct: 122 EVFGIERLLDSGTADHYYDTINEALATPAYRPRALFERFKIDFLATTEGADDPLEHHAAI 181 Query: 179 RAANASGEWGGRVITAYRPDPVVDPEFEGFRDNLARFSNLSGEDAFSYSGYLAAHRKRRA 238 R + WGGRV+T YRPD V+D E E F+ L F+ L+GED S+ GYLAAHRKRRA Sbjct: 182 RRSG----WGGRVVTTYRPDSVIDVEHEAFKGALEAFAGLTGEDVHSWKGYLAAHRKRRA 237 Query: 239 FFASMGATSTDHGHPSAATADLSETQAEALFARVTGEDMSAADAELFRAHMLTVMAGMSL 298 F GAT+TDHG +A TA+LS ++EALF R+ AADAELFRA MLT MA MS+ Sbjct: 238 DFRIAGATATDHGFATAQTANLSTAESEALFGRIMSGKWDAADAELFRAQMLTEMAKMSV 297 Query: 299 DDGLVMQIHPGAFRNHNPWLFANHGRDKGADIPTATDYVHALRPLLGRYGNEADLTIILF 358 +DG+ MQIHPGA RNHN LF +HGRDKGADIPT TDYVHAL+P+L GNE LT+ILF Sbjct: 298 EDGMTMQIHPGACRNHNAKLFHSHGRDKGADIPTRTDYVHALKPMLDVVGNEPGLTVILF 357 Query: 359 TLDETSYARELAPLAGHYPALKLGPAWWFHDSPEGMRRFRSQMTETAGFYNTVGFNDDTR 418 TLDE++YARELAPLAGHYP L+LGP+WWFHDSPEGMRRFR TETAGFYNTVGFNDDTR Sbjct: 358 TLDESTYARELAPLAGHYPCLRLGPSWWFHDSPEGMRRFREMTTETAGFYNTVGFNDDTR 417 Query: 419 AFLSIPARHDVARRIDCGFLAQLVSEHRLEEWEAAELAADLSYNLAKASYKL 470 AF SIPARHDVARR+DC FLA+LV+E R+++WEAAELA +L+ L + +YKL Sbjct: 418 AFFSIPARHDVARRVDCAFLARLVAEGRMQDWEAAELAYELTNGLVRKAYKL 469 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: 817 Number of extensions: 27 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: 479 Length adjustment: 33 Effective length of query: 437 Effective length of database: 446 Effective search space: 194902 Effective search space used: 194902 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