Align mannose-1-phosphate guanylyltransferase (EC 2.7.7.13) (characterized)
to candidate WP_004310859.1 C665_RS11925 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase
Query= BRENDA::P07874 (481 letters) >NCBI__GCF_000310185.1:WP_004310859.1 Length = 482 Score = 541 bits (1395), Expect = e-158 Identities = 272/476 (57%), Positives = 340/476 (71%), Gaps = 11/476 (2%) Query: 4 VILSGGSGSRLWPLSRKQYPKQFLALTGDDTLFQQTIKRLA-FDGMQA---PLLVCNKEH 59 VILSGGSG+RLWP SR+ YPKQ L LTG+ +L Q+T RL F G + PL+V N+E+ Sbjct: 6 VILSGGSGTRLWPASRESYPKQLLPLTGERSLLQETALRLKDFPGGEVDPRPLVVTNEEY 65 Query: 60 RFIVQEQLEAQNLASQAILLEPFGRNTAPAVAIAAMKLVAEGRDELLLILPADHVIEDQR 119 RFI+ EQL + S I+LEP GRNTAPA+ +AA+ V EG D +LL++PADHVI +Q Sbjct: 66 RFIIAEQLRQIGVRSPQIVLEPVGRNTAPALTLAALVAVEEG-DPILLVMPADHVITEQV 124 Query: 120 AFQQALALATNAAEKGEMVLFGIPASRPETGYGYIRASADAQLPEGVSRVQSFVEKPDEA 179 AFQ A+A+ AA KG +V FGI RPETGYGY+R+ EG + FVEKPD A Sbjct: 125 AFQHAIAIGAKAAAKGALVTFGIVPDRPETGYGYLRSGEALAEGEGARALLEFVEKPDRA 184 Query: 180 RAREFVAAGGYYWNSGMFLFRASRYLEELKKHDADIYDTCLLALERSQHDGDLVNIDAAT 239 A +VA+G YYWNSG+F+ +AS +L +++ ++ C A+ HD D + +D A Sbjct: 185 TAEAYVASGAYYWNSGIFMMKASVWLAAIRRFAPEMAAACTTAVTGCTHDADFIRLDTAA 244 Query: 240 FECCPDNSIDYAVMEKTSRA------CVVPLSAGWNDVGSWSSIWDVHAKDANGNVTKGD 293 FE P +SIDYAVMEK + A VVPLSAGW+DVG+W ++W V AKD GN +G+ Sbjct: 245 FERSPSDSIDYAVMEKLAEAPELGQGVVVPLSAGWSDVGAWDALWAVSAKDGEGNAARGE 304 Query: 294 VLVHDSHNCLVHGNGKLVSVIGLEDIVVVETKDAMMIAHKDRVQDVKHVVKDLDAQGRSE 353 VL N LVH +LV+ +G ED+VVVET DA+M+AHKDR QDVK VV L A+GR+ Sbjct: 305 VLFEACRNTLVHAGSRLVAAVGCEDMVVVETPDAVMVAHKDRTQDVKKVVARLKAEGRTL 364 Query: 354 TQNHCEVYRPWGSYDSVDMGGRFQVKHITVKPGARLSLQMHHHRAEHWIVVSGTAQVTCD 413 TQ+H +VYRPWG YDS+D G RFQVK I V PGA+LSLQMHHHRAEHWIVV GTA+VT Sbjct: 365 TQSHRKVYRPWGWYDSIDAGERFQVKRIVVNPGAKLSLQMHHHRAEHWIVVKGTAEVTNG 424 Query: 414 DKTFLLTENQSTYIPIASVHRLANPGKIPLEIIEVQSGSYLGEDDIERLEDVYGRT 469 +++FLL EN+STYIP+ HRL+NPGK+PLEIIEVQSGSYLGEDDI R ED YGR+ Sbjct: 425 ERSFLLAENESTYIPLGHTHRLSNPGKVPLEIIEVQSGSYLGEDDIVRFEDTYGRS 480 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: 643 Number of extensions: 28 Number of successful extensions: 4 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: 482 Length adjustment: 34 Effective length of query: 447 Effective length of database: 448 Effective search space: 200256 Effective search space used: 200256 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: 52 (24.6 bits)
This GapMind analysis is from Sep 24 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