Align Glucuronate isomerase (EC 5.3.1.12) (characterized)
to candidate Echvi_3102 Echvi_3102 Glucuronate isomerase
Query= reanno::Pedo557:CA265_RS19870 (466 letters) >FitnessBrowser__Cola:Echvi_3102 Length = 475 Score = 572 bits (1473), Expect = e-167 Identities = 270/463 (58%), Positives = 341/463 (73%) Query: 4 FLDENFLLQSKTAEKLYHNFAKSLPIIDYHNHLIPEQIANNTQFANISQVWLAGDHYKWR 63 F+ ENFLLQ++ A LYH++AK++PIIDYH HL P+ +A N +F NIS++WLAGDHYKWR Sbjct: 12 FIKENFLLQTEMANVLYHDYAKNMPIIDYHCHLSPKDLAENRKFDNISKIWLAGDHYKWR 71 Query: 64 AMRANGVDEKYITGVGSDYEKFEKWAETVPYTLRNPLYHWTHLELQRYFGITDLLSGKTA 123 AMR G+DE YITG SD EKF+KWA TVPYT+RNPLYHWTHLEL RYFGI +LLS A Sbjct: 72 AMRTLGIDETYITGTASDKEKFQKWAYTVPYTMRNPLYHWTHLELLRYFGIEELLSADNA 131 Query: 124 QKIFDECSAKLQTPEYSVRGLLAKMNVEAVCTTDDPLDSLNFHQQLAREGANLKMLPAFR 183 +I+ + + +L+ +S + LL MNVE VCTTDDP DSL FH++ A + + P FR Sbjct: 132 DEIYQQTNRQLEQDSHSTQSLLTGMNVETVCTTDDPTDSLEFHRKAAENDMPIGLFPTFR 191 Query: 184 PDKAMNSDDIEGLNEYIDKLESVADKTISNFQDYIDALKSRHDYFAANGCSVSDHGLEQI 243 PDK+ +++ Y+++L S ++ I++ + + AL++R D+F +G ++DHGLEQ+ Sbjct: 192 PDKSFAVENLGQYKAYLEQLGSASNMEINSHEQLMAALENRIDFFHQHGGRLADHGLEQL 251 Query: 244 YAEDYTEAEIASIFDKIRSKQHISYEENLKFKSAMLVYFAEWDHEKGWVQQYHLGALRNN 303 Y +I +F KI + + + EE FK L+ H KGW QQ+HLGALRN Sbjct: 252 YYFPLGTFDIEILFKKILADKPLDREETAYFKFVTLLELCRLYHAKGWTQQFHLGALRNT 311 Query: 304 NARMLRQLGPDTGWDSIGDFSQARMLSKFLNRLDNQDKLAKTIIYNLNPADNELIATMIG 363 N RML LGPDTG+DSIGDF QA+ LS+FLN LD D+L KTI+YNLNP DNE++ATM G Sbjct: 312 NERMLETLGPDTGFDSIGDFDQAKSLSQFLNELDKTDQLCKTILYNLNPRDNEVMATMTG 371 Query: 364 NFNDGSVAGKVQFGSAWWFLDQKDGMIKQLNALSNMGLVSRLVGMLTDSRSFLSFPRHEY 423 NFNDGS+ GKVQFGS WWFLDQKDGM KQ+N LSNMGL+S VGMLTDSRSFLSFPRHEY Sbjct: 372 NFNDGSIRGKVQFGSGWWFLDQKDGMEKQMNTLSNMGLLSCFVGMLTDSRSFLSFPRHEY 431 Query: 424 FRRIVCNLFGEDIENGELPNDLEWVGKIVQDISYFNAKNYFKF 466 FRR +CNL G D+ NGELP D +W+GK+VQDI Y NAK+YF F Sbjct: 432 FRRTLCNLLGNDVANGELPADEKWLGKLVQDICYNNAKSYFNF 474 Lambda K H 0.319 0.135 0.410 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: 758 Number of extensions: 25 Number of successful extensions: 1 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: 466 Length of database: 475 Length adjustment: 33 Effective length of query: 433 Effective length of database: 442 Effective search space: 191386 Effective search space used: 191386 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