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 CA265_RS19200 CA265_RS19200 mannose-1-phosphate guanylyltransferase
Query= BRENDA::O58649 (464 letters) >FitnessBrowser__Pedo557:CA265_RS19200 Length = 349 Score = 199 bits (506), Expect = 1e-55 Identities = 121/350 (34%), Positives = 186/350 (53%), Gaps = 31/350 (8%) Query: 6 LAGGKGTRLWPLSREAMPKQFIKVFS-DRSLFQKTVERALIFSKPKEIFVVTNKEYRFRV 64 +AGG G+R WP SR PKQFI + +SL Q T ER L ++I+++TN+ Y V Sbjct: 1 MAGGVGSRFWPKSRNHFPKQFIDILGLGKSLLQLTYERFLNICPKEQIYILTNESYSGLV 60 Query: 65 LDDLNELGLKVPEENILLEPVGKNTLPAIYWGLKVINDNYGDSVVAVLPSDHAIEVNESY 124 D L L NILLEP NT P I + I D+ + V PSDH I + + Sbjct: 61 ADQLPNL----LANNILLEPSRNNTAPCIAYASYKIFQINPDANIVVAPSDHLILKEQEF 116 Query: 125 MEAFKKAEKLAEKY--LVTFGIKPTKPHTGYGYIKPGEKIEVEGKVLGYLVDEFKEKPDL 182 + +A A ++ L+T GI PT+P TGYGYI+ + + KV + F EKP L Sbjct: 117 LTKVDQALTFAAEHDALLTLGISPTRPDTGYGYIRYQDGLSEVKKV-----EAFMEKPSL 171 Query: 183 ETARKYVENG-YYWNSGMFMFKVSVFMEEARKHSPDVVKAF----------EEGKSIEEI 231 E A +Y+ NG Y WN+G+F++ V + K++ D+ K F EE I E Sbjct: 172 EKAEEYLANGDYVWNAGIFIWSVKAIKKAFNKYATDIDKIFTRGDNFYNTKEETNYIIEN 231 Query: 232 YELAPEISVDYGIMEKTNKAAVVPLNTYWNDLGSFDAVYEALEKDENGNAVHVTGFKAKY 291 Y AP IS+DY I+EK + +P + W+DLG++ +++ KD N NAV+ + Sbjct: 232 YPTAPNISIDYAILEKADNVYTIPADIGWSDLGTWASLHTVANKDVNANAVN-----CAF 286 Query: 292 INVDSRNNLVL---TERLTATVGVEDLVIIDTGDALLVAKRGETQKVKEV 338 +++D +N ++ + G+E+ +I+D G LL+ + + Q++K+V Sbjct: 287 LHLDKTSNCIIQLPDNKAAVIKGMENYIIVDDGKVLLIYPKSDEQEIKQV 336 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: 399 Number of extensions: 22 Number of successful extensions: 7 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: 349 Length adjustment: 31 Effective length of query: 433 Effective length of database: 318 Effective search space: 137694 Effective search space used: 137694 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