Align mannose-1-phosphate guanylyltransferase (EC 2.7.7.13) (characterized)
to candidate Synpcc7942_1608 Synpcc7942_1608 mannose-1-phosphate guanylyltransferase (GDP)
Query= BRENDA::P07874 (481 letters) >FitnessBrowser__SynE:Synpcc7942_1608 Length = 469 Score = 544 bits (1401), Expect = e-159 Identities = 271/470 (57%), Positives = 337/470 (71%), Gaps = 3/470 (0%) Query: 1 MIPVILSGGSGSRLWPLSRKQYPKQFLALTGDDTLFQQTIKRL-AFDGMQAPLLVCNKEH 59 ++PVILSGGSGSRLWPLSR+ YPKQF AL D +L Q+T+ RL G+ +PLL+CN++H Sbjct: 2 LVPVILSGGSGSRLWPLSRESYPKQFHALLSDYSLLQETLLRLEGLPGLASPLLICNEQH 61 Query: 60 RFIVQEQLEAQNLASQAILLEPFGRNTAPAVAIAAMKLVAEGRDELLLILPADHVIEDQR 119 RF+V E L A + AI+LEP GRNTAPAVAIAA++ ++G D LLL+LP+DH I D Sbjct: 62 RFLVAEHLRAIGQTAAAIVLEPEGRNTAPAVAIAALQAQSQGEDPLLLVLPSDHSIADPA 121 Query: 120 AFQQALALATNAAEKGEMVLFGIPASRPETGYGYIRASADAQLPEGVSRVQSFVEKPDEA 179 AF+ + A A G +V FGI PETGYGYI+A +D L G + F+EKP+ A Sbjct: 122 AFRATVQTAIALATAGHLVTFGIVPEAPETGYGYIKAGSDLDL--GGFAIDRFIEKPNLA 179 Query: 180 RAREFVAAGGYYWNSGMFLFRASRYLEELKKHDADIYDTCLLALERSQHDGDLVNIDAAT 239 A +VA+G YYWNSGMFL RAS YL EL ++ +++ C A ++ Q D D V +D AT Sbjct: 180 TAENYVASGCYYWNSGMFLIRASVYLSELARYAPEMFTACEAAWQKRQADLDFVRLDPAT 239 Query: 240 FECCPDNSIDYAVMEKTSRACVVPLSAGWNDVGSWSSIWDVHAKDANGNVTKGDVLVHDS 299 F CP +SIDYAVME T + V+PL AGW DVGSWSS+W +D GNVT GD L D Sbjct: 240 FAQCPSDSIDYAVMEHTQQGAVLPLQAGWTDVGSWSSLWQALEQDGAGNVTVGDSLALDC 299 Query: 300 HNCLVHGNGKLVSVIGLEDIVVVETKDAMMIAHKDRVQDVKHVVKDLDAQGRSETQNHCE 359 N + G+LV +GLED+V VET DA++IAH+DR Q VK VV+ L + R E++ H + Sbjct: 300 RNVYLRSEGRLVVGVGLEDVVAVETDDALLIAHRDRTQTVKQVVEALQREARRESRAHRK 359 Query: 360 VYRPWGSYDSVDMGGRFQVKHITVKPGARLSLQMHHHRAEHWIVVSGTAQVTCDDKTFLL 419 +YRPWG YDS+D+G RFQVK ITV PGA LSLQMHHHRAEHWIVV GTA VT D++ LL Sbjct: 360 IYRPWGRYDSLDLGDRFQVKRITVNPGASLSLQMHHHRAEHWIVVKGTALVTRDNEEVLL 419 Query: 420 TENQSTYIPIASVHRLANPGKIPLEIIEVQSGSYLGEDDIERLEDVYGRT 469 TENQSTYIP+ HRL+NPG++PLE+IEVQSGSYL EDDI R ED YGR+ Sbjct: 420 TENQSTYIPVGCKHRLSNPGRVPLEMIEVQSGSYLEEDDIVRFEDHYGRS 469 Lambda K H 0.319 0.134 0.400 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: 627 Number of extensions: 26 Number of successful extensions: 3 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: 481 Length of database: 469 Length adjustment: 33 Effective length of query: 448 Effective length of database: 436 Effective search space: 195328 Effective search space used: 195328 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: 51 (24.3 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