Align mannose-1-phosphate guanylyltransferase (EC 2.7.7.13) (characterized)
to candidate BPHYT_RS09705 BPHYT_RS09705 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase
Query= BRENDA::P07874 (481 letters) >FitnessBrowser__BFirm:BPHYT_RS09705 Length = 517 Score = 466 bits (1200), Expect = e-136 Identities = 239/492 (48%), Positives = 323/492 (65%), Gaps = 29/492 (5%) Query: 3 PVILSGGSGSRLWPLSRKQYPKQFLALTGDDTLFQQTIKRLAFDGMQA--PL-----LVC 55 PVIL+GGSG+RLWP+SR+Q+PKQ + L GDD+L Q T +RL +G++A PL +V Sbjct: 28 PVILAGGSGTRLWPMSREQHPKQLIGLLGDDSLLQSTTRRL--EGLEAGYPLTEQLVVVA 85 Query: 56 NKEHRFIVQEQLEAQNLASQAILLEPFGRNTAPAVAIAAMKLVAEGRDELLLILPADHVI 115 N+E RF EQL ++ ++LEP GR+TAPA+ +AA+ + A+ D +++++PADH + Sbjct: 86 NEEQRFTTAEQLRTSGKPTR-LILEPAGRDTAPALTVAALSVAAQDEDGIMVVMPADHAV 144 Query: 116 EDQRAFQQALALATNAAEKGEMVLFGIPASRPETGYGYIRASA-----------DAQLPE 164 D F A+A A G +V GI +R ETGYGYIR A DA++ Sbjct: 145 TDIDGFHAAVAAGVQHAAAGHIVTMGIVPTRAETGYGYIRIGAALGTTNHTQEADAEVTG 204 Query: 165 --GVSRVQSFVEKPDEARAREFVAAGGYYWNSGMFLFRASRYLEELKKHDADIYDTCLLA 222 G ++ FVEKP A+ ++ + Y+WNSG+F+ RAS +L+ ++ IY+ C A Sbjct: 205 KVGAHKLDRFVEKPHLELAQRYIDSKEYWWNSGIFIMRASTWLKAIRHFQPAIYEACDAA 264 Query: 223 LERSQHDGDLVNIDAATFECCPDNSIDYAVMEK------TSRACVVPLSAGWNDVGSWSS 276 + DGD + F P NSIDYAVME+ + VVPL AGW+DVGSW + Sbjct: 265 FAGGKADGDFFRLQRDAFSASPSNSIDYAVMEQLGNDQSAASGVVVPLQAGWSDVGSWDA 324 Query: 277 IWDVHAKDANGNVTKGDVLVHDSHNCLVHGNGKLVSVIGLEDIVVVETKDAMMIAHKDRV 336 IWD+ KDA+ NV +G V+ + + H G+L++ +G +D+VVVET DA+++A K RV Sbjct: 325 IWDISDKDADQNVGRGRVMFEGAASTFAHSEGRLIACVGTQDLVVVETADAILVADKSRV 384 Query: 337 QDVKHVVKDLDAQGRSETQNHCEVYRPWGSYDSVDMGGRFQVKHITVKPGARLSLQMHHH 396 QDVK +V + G E NH +V+RPWG+YDSVD G RFQVK I VKPGARLSLQMHHH Sbjct: 385 QDVKKIVGRIRNDGGLEAANHRKVHRPWGNYDSVDTGERFQVKRIVVKPGARLSLQMHHH 444 Query: 397 RAEHWIVVSGTAQVTCDDKTFLLTENQSTYIPIASVHRLANPGKIPLEIIEVQSGSYLGE 456 RAEHWIVV GTA VT ++ F+++EN+S YIP+ HRL NPGK+PLE+IEVQSGSYLGE Sbjct: 445 RAEHWIVVRGTALVTRGEERFIVSENESAYIPLGVTHRLENPGKMPLEMIEVQSGSYLGE 504 Query: 457 DDIERLEDVYGR 468 DDI R +D YGR Sbjct: 505 DDIVRFDDTYGR 516 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: 661 Number of extensions: 32 Number of successful extensions: 5 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: 517 Length adjustment: 34 Effective length of query: 447 Effective length of database: 483 Effective search space: 215901 Effective search space used: 215901 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 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