Align mannose-1-phosphate guanylyltransferase (EC 2.7.7.13) (characterized)
to candidate H281DRAFT_04847 H281DRAFT_04847 mannose-1-phosphate guanylyltransferase (GDP) (EC 2.7.7.22)/mannose-6-phosphate isomerase, type 2 (EC 5.3.1.8)
Query= BRENDA::P07874 (481 letters) >FitnessBrowser__Burk376:H281DRAFT_04847 Length = 477 Score = 547 bits (1410), Expect = e-160 Identities = 268/470 (57%), Positives = 348/470 (74%), Gaps = 4/470 (0%) Query: 1 MIPVILSGGSGSRLWPLSRKQYPKQFLALTGDDTLFQQTIKRLA-FDGMQAPLLVCNKEH 59 ++PVIL+GGSG+RLWPLSR +PKQFLALTG+ T+ Q+T+ RLA G+ +P+++C +H Sbjct: 6 IVPVILAGGSGTRLWPLSRALFPKQFLALTGERTMLQETLARLAGISGLGSPMVICQDDH 65 Query: 60 RFIVQEQLEAQNLASQAILLEPFGRNTAPAVAIAAMKLVAEGRDELLLILPADHVIEDQR 119 RFIV EQL I+LEP GRNTAPA+AIAA++ + + D LLL+L ADHVI D Sbjct: 66 RFIVAEQLREHTSRDATIILEPVGRNTAPAIAIAALQALKDHPDPLLLVLAADHVIADVD 125 Query: 120 AFQQALALATNAAEKGEMVLFGIPASRPETGYGYIRASADAQLPEGVSRVQSFVEKPDEA 179 AF +A+ A ++AE G + FGI PETGYGY+RA Q V R+ +FVEKPD A Sbjct: 126 AFHRAVDTAAHSAETGALTTFGIEPVAPETGYGYLRAQPGEQ--GQVKRLATFVEKPDLA 183 Query: 180 RAREFVAAGGYYWNSGMFLFRASRYLEELKKHDADIYDTCLLALERSQHDGDLVNIDAAT 239 A+ ++ +G Y+WNSGMFLFRAS YL EL+++D D+ C+ +L+R+ D D V +D Sbjct: 184 TAQAYLESGEYFWNSGMFLFRASVYLNELERYDPDMLKACVESLDRATKDLDFVRLDKEA 243 Query: 240 FECCPDNSIDYAVMEKTSRACVVPLSAGWNDVGSWSSIWDVHAKDANGNVTKGDVLVHDS 299 F CP+NSIDYAVMEKT +A +V L+AGWNDVGSWS++WDV KD +GNVTKGDV+ Sbjct: 244 FTQCPENSIDYAVMEKTDKAVIVALNAGWNDVGSWSALWDVADKDDDGNVTKGDVIELGC 303 Query: 300 HNCLVHGNG-KLVSVIGLEDIVVVETKDAMMIAHKDRVQDVKHVVKDLDAQGRSETQNHC 358 NC + +G +LV+ +GL++++VV+T DA++IA+KD VQ VK +V+ L GRSE H Sbjct: 304 ENCFLQSSGGRLVAAVGLDNLIVVDTDDAVLIANKDDVQHVKQIVEKLRQDGRSEAVQHR 363 Query: 359 EVYRPWGSYDSVDMGGRFQVKHITVKPGARLSLQMHHHRAEHWIVVSGTAQVTCDDKTFL 418 VYRPWGSYD +D G R+QVK ITV PGARLS+QMHHHRAEHW+VVSGTA+V + L Sbjct: 364 LVYRPWGSYDCIDRGSRYQVKRITVNPGARLSVQMHHHRAEHWVVVSGTARVKNGENETL 423 Query: 419 LTENQSTYIPIASVHRLANPGKIPLEIIEVQSGSYLGEDDIERLEDVYGR 468 LTEN+S YIP+ ++H L NPGKIPLE+IEVQSG+YLGEDDI R +D YGR Sbjct: 424 LTENESIYIPVGNIHALENPGKIPLELIEVQSGAYLGEDDIIRFDDRYGR 473 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: 700 Number of extensions: 27 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: 477 Length adjustment: 34 Effective length of query: 447 Effective length of database: 443 Effective search space: 198021 Effective search space used: 198021 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