Align UTP-glucose-1-phosphate uridylyltransferase (EC 2.7.7.9) (characterized)
to candidate Synpcc7942_1973 Synpcc7942_1973 mannose-1-phosphate guanyltransferase
Query= BRENDA::P74285 (388 letters) >FitnessBrowser__SynE:Synpcc7942_1973 Length = 389 Score = 619 bits (1595), Expect = 0.0 Identities = 290/367 (79%), Positives = 340/367 (92%) Query: 1 MKAMILAAGKGTRVRPITHTIPKPMIPILQKPVMEFLLELLRQHGFDQIMVNVSHLAEEI 60 MKAMILAAGKGTRVRPIT+TIPKPMIPILQKPVMEFLLELL++HGF ++MVNVSHLA+EI Sbjct: 1 MKAMILAAGKGTRVRPITYTIPKPMIPILQKPVMEFLLELLKEHGFKEVMVNVSHLAQEI 60 Query: 61 ESYFRDGQRFGVQIAYSFEGNIVDGDLVGKALGSAGGLKKIQEFNPFFDDTFVVLCGDAL 120 ESYFRDGQRFGV++AYSFEG I DG L+G+ALGSAGG+K+IQ+F+PFFDDTFVVLCGDAL Sbjct: 61 ESYFRDGQRFGVEVAYSFEGRIEDGQLIGEALGSAGGMKRIQDFSPFFDDTFVVLCGDAL 120 Query: 121 IDLDLTTAVKLHREKGAIATIITKTVPQELVSSYGVVVTDDNGKILTFQEKPAVEEALST 180 IDLDLT AV+ H+EKGA+ATI+ KTVP+E VSSYGVVVTD +G+I FQEKP+VEEALST Sbjct: 121 IDLDLTEAVRWHKEKGALATIVMKTVPREEVSSYGVVVTDSDGRIQAFQEKPSVEEALST 180 Query: 181 EINTGIYIFEPEVIDYIPSGQEYDLGGDLFPKLVDSGLPFYAVNMDFEWVDIGKVPDYWQ 240 INTGIYIFEPE+++YIPSGQEYD+GGDLFPKLV++G PFY ++MDF+W+DIGKVPDYWQ Sbjct: 181 TINTGIYIFEPEILNYIPSGQEYDIGGDLFPKLVETGAPFYGISMDFQWIDIGKVPDYWQ 240 Query: 241 AIRGVLSREIKNVQIPGIEVRPGVYTGINVAANWDNIEIEGPVYIGGMTRIEDGVKIIGP 300 AIR VL+ E++NV IPG +VRPGVYTG+NVA +WD++ IEGPVYIGGMTRI++GV+I+GP Sbjct: 241 AIRSVLNGEVRNVAIPGKQVRPGVYTGLNVAIDWDSVAIEGPVYIGGMTRIDEGVRIVGP 300 Query: 301 SMIGPSCLICQGAVVDNSVIFEYSRLGPGARLVDKLVFGRYCVDKTGAAIDVQAAALDWL 360 +MIGP+C IC+GA ++NSVIFEYSRLG G RLVDKLVFGRYCVD+ G AIDVQAAALDWL Sbjct: 301 AMIGPNCHICKGATIENSVIFEYSRLGSGVRLVDKLVFGRYCVDRNGNAIDVQAAALDWL 360 Query: 361 ITDARHA 367 ITDAR A Sbjct: 361 ITDARRA 367 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: 544 Number of extensions: 16 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: 388 Length of database: 389 Length adjustment: 30 Effective length of query: 358 Effective length of database: 359 Effective search space: 128522 Effective search space used: 128522 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: 50 (23.9 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