Align Uronate isomerase; Glucuronate isomerase; Uronic isomerase; EC 5.3.1.12 (characterized)
to candidate BWI76_RS23645 BWI76_RS23645 uronate isomerase
Query= SwissProt::O34808 (473 letters) >FitnessBrowser__Koxy:BWI76_RS23645 Length = 471 Score = 445 bits (1145), Expect = e-129 Identities = 218/469 (46%), Positives = 309/469 (65%), Gaps = 3/469 (0%) Query: 3 PFMGKNFLLKNETAVSLYHNYAKDMPIIDYHCHLSPKEIYENKTFQNITEAWLYGDHYKW 62 P + +F++ N T LY A++ PIIDYHCHL K I+EN+ F +IT+ WL GDHYKW Sbjct: 2 PLINDSFMISNPTGKKLYLEIAREQPIIDYHCHLEAKAIWENEPFADITQLWLEGDHYKW 61 Query: 63 RIMRANGIEETYITGDAPDEEKFMAWAKTVPMAIGNPLYNWTHLELQRFFGIYEILNEKS 122 R MRANGI E ITG+A EEKF AWA+TV GNPLY+WTHLEL+ +F I + LN ++ Sbjct: 62 RAMRANGIPEEKITGNATAEEKFAAWAQTVEACFGNPLYHWTHLELKYYFNIDDTLNSRN 121 Query: 123 GSAIWKQTNKLLKGEGFGARDLIVKSNVKVVCTTDDPVDSLEYHLLLKEDKDFPVSVLPG 182 I + N+ L+ + F + LI +SNV+ +CTTD P+D+LEYH L + DF VLP Sbjct: 122 WHEIMTRCNEQLRRKEFLPQALIRRSNVEALCTTDGPLDNLEYHQRLAANSDFSPLVLPT 181 Query: 183 FRPDKGLEINREGFPEWVQALEDAAAISITTYDEFLKALEKRVRFFHSAGGRVSDHAIDT 242 FRPD+ + + E F ++ L + I I + +FL ALE R+ FFH+ G R+SDH Sbjct: 182 FRPDELFDTDPESFQTFISRLAEKTQIRIASLQDFLAALESRIDFFHTVGCRISDHGPLE 241 Query: 243 MVFAETTKEEAGRIFSDRLQGTEVSCEDEKKFKTYTLQFLCGLYAELDWAMQFHINALRN 302 +V+ + +F RL+ ++ ++++ + + L +Y + +WAMQ H A+RN Sbjct: 242 IVYNPLDEAALAALFQRRLKNEALTKDEQQAWDSAIFIALAKMYKQREWAMQIHFGAIRN 301 Query: 303 TNTKMMKRLGPDTGYDSMNDEE-IAKPLYKLLNSVEMKNQLPKTILYSLNPNDNYVIASM 361 N M K++G + G+DS+ D+ +A L LLN++ N LPKTILY+LN N V+AS Sbjct: 302 NNKPMFKKVGINCGFDSVGDQTLLAGSLNALLNAMGENNGLPKTILYNLNAGYNDVVASA 361 Query: 362 INSFQDGITPGK--IQFGTAWWFNDTKDGMLDQMKALSNVGLFSRFIGMLTDSRSFLSYT 419 I +FQ G K +QFG+ WWFNDT+ GM++Q+ L++ GL + F+GMLTDSRSF+SYT Sbjct: 362 IANFQSGEDGVKSPLQFGSGWWFNDTRRGMVNQLNTLADQGLLANFVGMLTDSRSFVSYT 421 Query: 420 RHEYFRRIVCNLIGEWVENGEVPRDMELLGSIVQGICYDNAKHYFQFQE 468 RH+YFRRI+C+LIG WVENGEVP D +L S+++ IC +NA+ YF+F + Sbjct: 422 RHDYFRRILCDLIGGWVENGEVPDDKNILTSMIRDICVENARRYFRFSQ 470 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: 636 Number of extensions: 25 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: 473 Length of database: 471 Length adjustment: 33 Effective length of query: 440 Effective length of database: 438 Effective search space: 192720 Effective search space used: 192720 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 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