Align mannose-1-phosphate guanylyltransferase (EC 2.7.7.13); glucose-1-phosphate guanylyltransferase (EC 2.7.7.34); aldose-1-phosphate nucleotidyltransferase (EC 2.7.7.37); mannose-6-phosphate isomerase (EC 5.3.1.8) (characterized)
to candidate 350086 BT0558 mannose-1-phosphate guanylyltransferase (NCBI ptt file)
Query= BRENDA::O58649 (464 letters) >FitnessBrowser__Btheta:350086 Length = 350 Score = 199 bits (506), Expect = 1e-55 Identities = 120/353 (33%), Positives = 196/353 (55%), Gaps = 26/353 (7%) Query: 4 LILAGGKGTRLWPLSREAMPKQFIKVFS-DRSLFQKTVERALIFSKPKEIFVVTNKEYRF 62 +I+AGG G+R WP+S PKQFI V R+L Q T +R + ++VVT+++Y Sbjct: 8 VIMAGGIGSRFWPMSTPECPKQFIDVMGCGRTLIQLTADRFDGVCPRENVWVVTSEKY-- 65 Query: 63 RVLDDLNELGLKVPEENILLEPVGKNTLPAIYWGLKVINDNYGDSVVAVLPSDHAIEVNE 122 +D + E ++PE NIL EP +NT P I + I + ++ V V PSD + Sbjct: 66 --IDIVREQLPEIPESNILAEPCARNTAPCIAYACWKIKKKHPNANVVVTPSDALVINTG 123 Query: 123 SYMEAFKKAEKLAEKY--LVTFGIKPTKPHTGYGYIKPGEKIEVEGKVLGYLVDEFKEKP 180 + +KA + + +VT GIKPT+P TGYGYI G++I + ++ + VD FKEKP Sbjct: 124 EFRRVVEKALRFTDNSSAIVTLGIKPTRPETGYGYIAAGDQIMTDKEI--FTVDAFKEKP 181 Query: 181 DLETARKYVENG-YYWNSGMFMFKVSVFMEEARKHSPDVVKAFE----------EGKSIE 229 D ETA +Y+ G Y+WN+G+F++ V R ++P + + F+ E ++I+ Sbjct: 182 DRETADRYLAEGNYFWNAGIFVWNVRTITSVMRVYAPGIAQIFDRIFPDFYTEKENETIK 241 Query: 230 EIYELAPEISVDYGIMEKTNKAAVVPLNTYWNDLGSFDAVYEALEKDENGNAVHVTGFKA 289 +++ IS+DY +MEK + V+P + W+DLG++ A+ L +D++GNA A Sbjct: 242 KLFPTCEAISIDYAVMEKAQEIYVLPASFGWSDLGTWGALRGLLPQDKSGNAT----VGA 297 Query: 290 KYINVDSRNNLVLT--ERLTATVGVEDLVIIDTGDALLVAKRGETQKVKEVYK 340 +S+N +V T E+ G++ +I + + LL+ K E Q++KE K Sbjct: 298 DVRLYESKNCIVHTSEEKRVVIQGLDGYIIAEKDNTLLICKLDEEQRIKEFSK 350 Lambda K H 0.316 0.137 0.395 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: 388 Number of extensions: 19 Number of successful extensions: 6 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: 464 Length of database: 350 Length adjustment: 31 Effective length of query: 433 Effective length of database: 319 Effective search space: 138127 Effective search space used: 138127 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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