Align UTP-glucose-1-phosphate uridylyltransferase (EC 2.7.7.9) (characterized)
to candidate Synpcc7942_0498 Synpcc7942_0498 mannose-1-phosphate guanyltransferase
Query= BRENDA::P74285 (388 letters) >FitnessBrowser__SynE:Synpcc7942_0498 Length = 837 Score = 196 bits (498), Expect = 2e-54 Identities = 121/355 (34%), Positives = 189/355 (53%), Gaps = 20/355 (5%) Query: 1 MKAMILAAGKGTRVRPITHTIPKPMIPILQKPVMEFLLELLRQHGFDQIMVNVSHLAEEI 60 M+A++LA G GTR+RP+T PKPM+PIL +P+ +L+LL +HG+ +I+ + + E I Sbjct: 1 MRAVLLAGGLGTRLRPLTCDRPKPMVPILNRPIAAHILQLLHRHGYQEILATLYYRPETI 60 Query: 61 ESYFRDGQRFGVQIAYSFEGNIVDGDLVGKALGSAGGLKKIQEFNPFFDDTFVVLCGDAL 120 + YF++GQ +GV + Y E + + LG+AG +K + +TF+V GD L Sbjct: 61 QQYFQEGQDWGVDLRYILEAD--------RPLGTAGSVKNL---TSQLQETFLVASGDCL 109 Query: 121 IDLDLTTAVKLHREKGAIATIITKTVPQELVSSYGVVVTDDNGKILTFQEKPAVEEALST 180 D DLT A+ HR++ AIAT+I V Q L +G VV D +I+ EKP E +S Sbjct: 110 SDFDLTAALAWHRQQQAIATVILARVDQPL--EFGCVVCDRQQRIIRLIEKPDASELISD 167 Query: 181 EINTGIYIFEPEVIDYIPSGQEYDLGGDLFPKLVDSGLPFYAVNMDFEWVDIGKVPDYWQ 240 +N+G YI EPE +DY+P + D L P+L+ +G W DIG Y + Sbjct: 168 TVNSGFYILEPEALDYLPLDEPSDFATHLLPRLLAAGEVVTGYVDQGYWCDIGNRQAYQR 227 Query: 241 AIRGVLSREIKNVQIPGIEVRPGVYTGINVAANWDNIEIEGPVYIGGMTRIEDGVKIIGP 300 A L ++ +Q +E RPG+Y G + ++E P++IG I + V++ Sbjct: 228 AQLDALLGRVR-LQANQMEWRPGIYVGEGTTIA-SSAQLEPPLWIGQHCYIGEEVQLKAG 285 Query: 301 SMIGPSCLICQGAVVDNSVIFEYSRLG-----PGARLVDKLVFGRYCVDKTGAAI 350 ++IG I GA +D +V++ ++G G L D + R+ GA I Sbjct: 286 TVIGDESRIEAGACLDRAVVWNRVQIGQRSHLEGCVLADGVRLERHVQIHEGAVI 340 Lambda K H 0.321 0.141 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: 639 Number of extensions: 27 Number of successful extensions: 5 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: 388 Length of database: 837 Length adjustment: 36 Effective length of query: 352 Effective length of database: 801 Effective search space: 281952 Effective search space used: 281952 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: 53 (25.0 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