Align mannose-1-phosphate guanylyltransferase (EC 2.7.7.13) (characterized)
to candidate WP_011382484.1 AMB_RS00190 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase
Query= BRENDA::P07874 (481 letters) >NCBI__GCF_000009985.1:WP_011382484.1 Length = 464 Score = 484 bits (1247), Expect = e-141 Identities = 241/468 (51%), Positives = 317/468 (67%), Gaps = 7/468 (1%) Query: 1 MIPVILSGGSGSRLWPLSRKQYPKQFLALTGDDTLFQQTIKRLAFDGMQAPLLVCNKEHR 60 +IPVILSGG+G+RLWPLSR+ PKQ L LTG+ TL Q T RL P++VCN EHR Sbjct: 4 LIPVILSGGAGTRLWPLSRELMPKQLLKLTGERTLLQDTAGRLGVP----PVVVCNVEHR 59 Query: 61 FIVQEQLEAQNLASQAILLEPFGRNTAPAVAIAAMKLVAEGRDELLLILPADHVIEDQRA 120 FIV EQL L +A+++EP GRNTAPA A+AA+ L D L+L++P+DH+I D A Sbjct: 60 FIVAEQLREVGLEPRAVVIEPVGRNTAPAAAVAALMLADSDPDALMLLMPSDHLIADVPA 119 Query: 121 FQQALALATNAAEKGEMVLFGIPASRPETGYGYIRASADAQLPEGVSRVQSFVEKPDEAR 180 F +AL A AE G +V FGIP + P TGYGYI+ + +G V+ FVEKPD A Sbjct: 120 FHRALEAAVPLAEAGRLVTFGIPPTNPNTGYGYIKRG---KALDGGFEVERFVEKPDLAT 176 Query: 181 AREFVAAGGYYWNSGMFLFRASRYLEELKKHDADIYDTCLLALERSQHDGDLVNIDAATF 240 A +VA+G Y WNSG+FL +L+EL +H + ++C AL++ + D +D F Sbjct: 177 AETYVASGDYTWNSGIFLLPVRLFLDELSRHAPGMAESCKAALDQGRSDLFFFRLDDKAF 236 Query: 241 ECCPDNSIDYAVMEKTSRACVVPLSAGWNDVGSWSSIWDVHAKDANGNVTKGDVLVHDSH 300 SIDYAVMEK+ + VVP+ GW+D+GSWS++W + DA+GN +GDVL +S Sbjct: 237 AAIAGQSIDYAVMEKSDKVAVVPVDMGWSDIGSWSALWQETSHDADGNAIQGDVLALESS 296 Query: 301 NCLVHGNGKLVSVIGLEDIVVVETKDAMMIAHKDRVQDVKHVVKDLDAQGRSETQNHCEV 360 C + G+LV+ +GL+D+VV+ T DA+++A K R Q+VK VV+ L +GR E Sbjct: 297 GCYLRSQGRLVAAVGLKDMVVIATDDAVLVADKARDQEVKAVVEALKREGRPEATQGTRG 356 Query: 361 YRPWGSYDSVDMGGRFQVKHITVKPGARLSLQMHHHRAEHWIVVSGTAQVTCDDKTFLLT 420 +RPWG Y +V+ G RF+VKHI V PGA+LSLQ H HR+EHW+VV GTA VTC D TF+L Sbjct: 357 WRPWGWYQTVEQGERFKVKHIHVDPGAKLSLQKHWHRSEHWVVVRGTALVTCGDNTFVLR 416 Query: 421 ENQSTYIPIASVHRLANPGKIPLEIIEVQSGSYLGEDDIERLEDVYGR 468 EN+ST+IP S HRL NPGK+PL +IEVQSG Y+GEDDI R+ED YGR Sbjct: 417 ENESTFIPAGSNHRLENPGKVPLRLIEVQSGEYVGEDDIVRIEDDYGR 464 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: 630 Number of extensions: 29 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: 464 Length adjustment: 33 Effective length of query: 448 Effective length of database: 431 Effective search space: 193088 Effective search space used: 193088 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