Align UTP-glucose-1-phosphate uridylyltransferase (EC 2.7.7.9) (characterized)
to candidate GFF5033 PS417_25785 mannose-1-phosphate guanylyltransferase
Query= BRENDA::P74285 (388 letters) >FitnessBrowser__WCS417:GFF5033 Length = 224 Score = 88.2 bits (217), Expect = 2e-22 Identities = 52/126 (41%), Positives = 75/126 (59%), Gaps = 11/126 (8%) Query: 1 MKAMILAAGKGTRVRPITHTIPKPMIPILQKPVMEFLLELLRQHGFDQIMVNVSHLAEEI 60 MKAMILAAGKG R+RP+T PKP++ K ++E+ LE L + GF I++N + L ++I Sbjct: 1 MKAMILAAGKGERMRPLTLHTPKPLVQAGGKRLIEYHLEALAKAGFTDIVINHAWLGQQI 60 Query: 61 ESYFRDGQRFGVQIAYSFEGNIVDGDLVGKALGSAGGLKKIQEFNPFFDDTFVVLCGDAL 120 E+Y DG +FG++I YS E G+ L + GG+ Q D+ F+V+ GD Sbjct: 61 ENYLGDGAQFGLRIRYSPE---------GEPLETGGGI--FQALPLLGDEPFLVVNGDIW 109 Query: 121 IDLDLT 126 D D T Sbjct: 110 TDYDFT 115 Score = 25.8 bits (55), Expect = 0.001 Identities = 16/39 (41%), Positives = 19/39 (48%), Gaps = 2/39 (5%) Query: 194 IDYIPSGQEYDLGGDLFPKLVDSG-LPFYAVNMDFEWVD 231 I Y P G+ + GG +F L G PF VN D W D Sbjct: 74 IRYSPEGEPLETGGGIFQALPLLGDEPFLVVNGDI-WTD 111 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: 222 Number of extensions: 12 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 388 Length of database: 224 Length adjustment: 26 Effective length of query: 362 Effective length of database: 198 Effective search space: 71676 Effective search space used: 71676 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: 48 (23.1 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