Align mannose-1-phosphate guanylyltransferase (EC 2.7.7.13) (characterized)
to candidate Ga0059261_1360 Ga0059261_1360 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase
Query= BRENDA::P07874 (481 letters) >FitnessBrowser__Korea:Ga0059261_1360 Length = 352 Score = 291 bits (745), Expect = 2e-83 Identities = 159/349 (45%), Positives = 220/349 (63%), Gaps = 6/349 (1%) Query: 1 MIPVILSGGSGSRLWPLSRKQYPKQFLALTGDDTLFQQTIKRL-AFDGMQAPLLVCNKEH 59 ++PVILSGGSG RLWP+SR + PKQ LALT ++T+ Q T +R A D AP++V N H Sbjct: 7 IVPVILSGGSGIRLWPMSRPEMPKQMLALTAEETMLQLTARRTPAGDRFAAPVIVANALH 66 Query: 60 RFIVQEQLEAQNLASQAILLEPFGRNTAPAVAIAAMKLVAEGRDELLLILPADHVIEDQR 119 +V+EQL A +QA++LEP GRNTAPA+A+AA L A G E LL++P+DHVI D Sbjct: 67 ADMVEEQLGAVEARAQALILEPMGRNTAPAIALAA--LAAGGGSEPLLVMPSDHVIGDVA 124 Query: 120 AFQQALALATNAAEKGEMVLFGIPASRPETGYGYIRASADAQLPEGVSRVQSFVEKPDEA 179 AF A+ A E G +V FGI PETGYGYI+ DA + GV +V+ FVEKP Sbjct: 125 AFHAAIDAALPLVEDGWLVTFGITPDAPETGYGYIKVG-DA-IRTGVHKVERFVEKPKRD 182 Query: 180 RAREFVAAGGYYWNSGMFLFRASRYLEELKKHDADIYDTCLLALERSQHDGDLVNIDAAT 239 A +AAGG+ WN G+FLFRA YL+ L + D+ A+ R+ +G + D Sbjct: 183 VAEAMIAAGGHAWNGGIFLFRADAYLDALGRFAPDMLVAVRAAMARAIREGTRILPDQIE 242 Query: 240 FECCPDNSIDYAVMEKTSRACVVPLSAGWNDVGSWSSIWDVHAKDANGNVTKGDVLVHDS 299 F P SIDYAVMEK R VVP++ GW+DVGSW ++ + D GN G+V+ D+ Sbjct: 243 FAKSPAESIDYAVMEKAERVAVVPVAMGWSDVGSWDALHAISDCDGAGNAFGGEVIAVDT 302 Query: 300 HNCLVH-GNGKLVSVIGLEDIVVVETKDAMMIAHKDRVQDVKHVVKDLD 347 +CLV G GK V+++G+ D++VV D +++ + R QDVK +++ ++ Sbjct: 303 TDCLVRAGPGKRVALVGISDLIVVADGDDVLVLPRGRSQDVKRIIEAMN 351 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: 436 Number of extensions: 17 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: 352 Length adjustment: 31 Effective length of query: 450 Effective length of database: 321 Effective search space: 144450 Effective search space used: 144450 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: 50 (23.9 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