Align Uronate isomerase; Glucuronate isomerase; Uronic isomerase; EC 5.3.1.12 (characterized)
to candidate WP_053935920.1 WG78_RS01015 glucuronate isomerase
Query= SwissProt::O34808 (473 letters) >NCBI__GCF_001294205.1:WP_053935920.1 Length = 464 Score = 450 bits (1158), Expect = e-131 Identities = 216/465 (46%), Positives = 305/465 (65%), Gaps = 4/465 (0%) Query: 1 MEPFMGKNFLLKNETAVSLYHNYAKDMPIIDYHCHLSPKEIYENKTFQNITEAWLYGDHY 60 M FM ++FLL + A LYH A D+PIIDYH HL EI K F+NI E WL GDHY Sbjct: 1 MTAFMDEDFLLDSHVAKRLYHEVAADLPIIDYHSHLQQGEIASRKQFRNIAELWLGGDHY 60 Query: 61 KWRIMRANGIEETYITGDAPDEEKFMAWAKTVPMAIGNPLYNWTHLELQRFFGIYEILNE 120 KWR+MR+ G+ E +ITG+ DEEKF A+ K +P+AIGNP+Y+W+HLEL+R FGI ++NE Sbjct: 61 KWRLMRSAGVSEDFITGNRTDEEKFRAFCKVLPLAIGNPIYHWSHLELRRIFGIDLLINE 120 Query: 121 KSGSAIWKQTNKLLKGEGFGARDLIVKSNVKVVCTTDDPVDSLEYHLLLKEDKDFPVSVL 180 K+ + IW++ N L G A + ++ V+V CTTDDP D L H +K+ D VL Sbjct: 121 KNAAQIWERANARLAGMDTWA--FLEQAGVEVACTTDDPADDLAQHAAIKQ-MDLKTRVL 177 Query: 181 PGFRPDKGLEINREGFPEWVQALEDAAAISITTYDEFLKALEKRVRFFHSAGGRVSDHAI 240 P +RPDK + IN++ F E++Q L A + I ++ + ++AL +RV FF G R+SDHA+ Sbjct: 178 PAYRPDKAMRINQQDFVEYLQRLGAVADVQIASFADMMQALAQRVTFFDEQGARISDHAV 237 Query: 241 DTMV-FAETTKEEAGRIFSDRLQGTEVSCEDEKKFKTYTLQFLCGLYAELDWAMQFHINA 299 D + E+ ++F RL GT + + ++ L L +YA DW M HI A Sbjct: 238 DVALPVTPLPPEQIEQLFQKRLGGTLLEAAEVAQYVLAVLTGLGRVYAAHDWTMCLHIGA 297 Query: 300 LRNTNTKMMKRLGPDTGYDSMNDEEIAKPLYKLLNSVEMKNQLPKTILYSLNPNDNYVIA 359 RN N +M+ RLG DTGYDS++D + L LL++++ + +LPKT+L+ LNP N +++ Sbjct: 298 QRNNNRRMLARLGADTGYDSISDMSCSAGLAGLLDTLDSEARLPKTMLFCLNPGMNEILS 357 Query: 360 SMINSFQDGITPGKIQFGTAWWFNDTKDGMLDQMKALSNVGLFSRFIGMLTDSRSFLSYT 419 ++I +FQDG GK+Q+G AWWFND K+G L Q+ L+N G+ +GM+TDSRSF SY Sbjct: 358 TLIGNFQDGSVAGKVQYGPAWWFNDHKEGNLQQLITLANHGVLGTSVGMVTDSRSFASYP 417 Query: 420 RHEYFRRIVCNLIGEWVENGEVPRDMELLGSIVQGICYDNAKHYF 464 RH+YFRR++C +G+WV GE P D E L ++V+GICY+NAK YF Sbjct: 418 RHDYFRRLLCRQLGQWVAGGEFPDDFEALSTVVRGICYENAKRYF 462 Lambda K H 0.320 0.137 0.418 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: 540 Number of extensions: 22 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: 473 Length of database: 464 Length adjustment: 33 Effective length of query: 440 Effective length of database: 431 Effective search space: 189640 Effective search space used: 189640 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: 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