Align Glucuronate isomerase (EC 5.3.1.12) (characterized)
to candidate 350351 BT_0823 glucuronate isomerase (RefSeq)
Query= reanno::Pedo557:CA265_RS19870 (466 letters) >FitnessBrowser__Btheta:350351 Length = 468 Score = 634 bits (1635), Expect = 0.0 Identities = 294/468 (62%), Positives = 374/468 (79%), Gaps = 2/468 (0%) Query: 1 MKPFLDENFLLQSKTAEKLYHNFAKSLPIIDYHNHLIPEQIANNTQFANISQVWLAGDHY 60 MK F+DENFLLQ++TA+KLYH A +PIIDYH HLIP+ +A++ +F +++++WL GDHY Sbjct: 1 MKNFMDENFLLQTETAQKLYHEHAAKMPIIDYHCHLIPQMVADDYKFKSLTEIWLGGDHY 60 Query: 61 KWRAMRANGVDEKYITGVGS-DYEKFEKWAETVPYTLRNPLYHWTHLELQRYFGITDLLS 119 KWRAMR NGVDE+Y TG + D+EKFEKWAETVPYT RNPLYHWTHLEL+ FGI +LS Sbjct: 61 KWRAMRTNGVDERYCTGKDTTDWEKFEKWAETVPYTFRNPLYHWTHLELKTAFGIDKILS 120 Query: 120 GKTAQKIFDECSAKLQTPEYSVRGLLAKMNVEAVCTTDDPLDSLNFHQQLAREGANLKML 179 KTA++I+DEC+ KL PEYS RG++ + +VE VCTTDDP+DSL +H Q G +KML Sbjct: 121 PKTAREIYDECNEKLAQPEYSARGMMRRYHVEVVCTTDDPIDSLEYHIQTRESGFEIKML 180 Query: 180 PAFRPDKAMNSDDIEGLNEYIDKLESVADKTISNFQDYIDALKSRHDYFAANGCSVSDHG 239 P +RPDKAM + Y++KL +V+ TISNF D I AL+ RHD+FA GC +SDHG Sbjct: 181 PTWRPDKAMAVEVPADFRAYVEKLSAVSGVTISNFDDMIAALRKRHDFFAEQGCRLSDHG 240 Query: 240 LEQIYAEDYTEAEIASIFDKIRSKQHISYEENLKFKSAMLVYFAEWDHEKGWVQQYHLGA 299 +E+ YAEDYT+AEI +IF+K+ ++ EE LKFKSAMLV F E D EKGW QQ+H GA Sbjct: 241 IEEFYAEDYTDAEIKAIFNKVYGGAELTKEEILKFKSAMLVIFGEMDWEKGWTQQFHYGA 300 Query: 300 LRNNNARMLRQLGPDTGWDSIGDFSQARMLSKFLNRLDNQDKLAKTIIYNLNPADNELIA 359 +RNNN +M + LGPDTG+DSIG+F+ A+ +SKFL+RL+ KL KTI+YNLNP NE+IA Sbjct: 301 IRNNNTKMFKLLGPDTGFDSIGEFTTAKAMSKFLDRLNVNGKLTKTILYNLNPCANEVIA 360 Query: 360 TMIGNFNDGSVAGKVQFGSAWWFLDQKDGMIKQLNALSNMGLVSRLVGMLTDSRSFLSFP 419 TM+GNF DGS+AGK+QFGS WWFLDQKDGM KQ+NALS +GL+SR VGMLTDSRSFLS+P Sbjct: 361 TMLGNFQDGSIAGKIQFGSGWWFLDQKDGMEKQMNALSVLGLLSRFVGMLTDSRSFLSYP 420 Query: 420 RHEYFRRIVCNLFGEDIENGELP-NDLEWVGKIVQDISYFNAKNYFKF 466 RHEYFRR +CNL G D+ENGE+P ++++ V ++++DISY NAKN+FKF Sbjct: 421 RHEYFRRTLCNLVGRDVENGEIPVSEMDRVNQMIEDISYNNAKNFFKF 468 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: 770 Number of extensions: 29 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: 466 Length of database: 468 Length adjustment: 33 Effective length of query: 433 Effective length of database: 435 Effective search space: 188355 Effective search space used: 188355 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