Align mannose-1-phosphate guanylyltransferase (EC 2.7.7.13) (characterized)
to candidate GFF456 HP15_444 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase
Query= BRENDA::P07874 (481 letters) >FitnessBrowser__Marino:GFF456 Length = 473 Score = 523 bits (1348), Expect = e-153 Identities = 263/473 (55%), Positives = 338/473 (71%), Gaps = 11/473 (2%) Query: 3 PVILSGGSGSRLWPLSRKQYPKQFLALT-GDDTLFQQTIKRLAFDGMQA--PLLVCNKEH 59 PVI++GG+GSRLWP+SR+ PKQFL LT G ++ Q T+ RL +GM A PLL+CN+EH Sbjct: 4 PVIMAGGTGSRLWPMSRQLNPKQFLKLTNGPLSMLQATVARL--EGMDAANPLLICNEEH 61 Query: 60 RFIVQEQLEAQNLASQAILLEPFGRNTAPAVAIAAMKLVAEGR----DELLLILPADHVI 115 RF+ EQ+ I+LEP GRNTAPA+A+AA++L D L+L+L ADH+I Sbjct: 62 RFLAAEQMRQSGHEDTRIILEPCGRNTAPAIALAALQLTEAAENGADDPLMLVLAADHLI 121 Query: 116 EDQRAFQQALALATNAAEKGEMVLFGIPASRPETGYGYIRASADAQLPEGVSRVQSFVEK 175 +D AFQ+ + A A +G++V FGI + PETGYGYI + L V FVEK Sbjct: 122 KDVTAFQEGVKKAIPLAREGKLVTFGIVPNHPETGYGYIHRGTE--LGPDSYLVDKFVEK 179 Query: 176 PDEARAREFVAAGGYYWNSGMFLFRASRYLEELKKHDADIYDTCLLALERSQHDGDLVNI 235 PD+A A ++ +G Y WNSGMFLF A +YLEEL+ H DI C A+ + D I Sbjct: 180 PDQATANGYLDSGEYLWNSGMFLFGARQYLEELEAHRPDILAACRAAIADTADDLHFTRI 239 Query: 236 DAATFECCPDNSIDYAVMEKTSRACVVPLSAGWNDVGSWSSIWDVHAKDANGNVTKGDVL 295 +A F CP +S+DYAVMEKT +A VV L AGW+D+GSWS++W+V KDA+GN GDV+ Sbjct: 240 NAERFAECPSDSVDYAVMEKTDKAAVVSLDAGWSDIGSWSALWEVSDKDADGNSLTGDVI 299 Query: 296 VHDSHNCLVHGNGKLVSVIGLEDIVVVETKDAMMIAHKDRVQDVKHVVKDLDAQGRSETQ 355 H++ N L+ + +LV+ +G++++VV+ETKDA+++AHKD VQDVK VV+ + GR E Sbjct: 300 THNTANTLIRADSRLVATVGVDNLVVIETKDALLVAHKDSVQDVKTVVERIKTDGRHEHM 359 Query: 356 NHCEVYRPWGSYDSVDMGGRFQVKHITVKPGARLSLQMHHHRAEHWIVVSGTAQVTCDDK 415 NH EVYRPWG YDS+D G R+QVK ITVKPGA+LS+QMHHHRAEHWIVVSGTA+VT +K Sbjct: 360 NHREVYRPWGVYDSIDNGARYQVKRITVKPGAKLSVQMHHHRAEHWIVVSGTARVTNGEK 419 Query: 416 TFLLTENQSTYIPIASVHRLANPGKIPLEIIEVQSGSYLGEDDIERLEDVYGR 468 T+L+TENQSTYIP+ VH L NPG I LE+IEVQSGSYLGEDDI R ED YGR Sbjct: 420 TYLVTENQSTYIPVGQVHSLENPGVIDLELIEVQSGSYLGEDDIVRYEDRYGR 472 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: 644 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: 473 Length adjustment: 33 Effective length of query: 448 Effective length of database: 440 Effective search space: 197120 Effective search space used: 197120 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