Align mannose-1-phosphate guanylyltransferase (EC 2.7.7.13) (characterized)
to candidate 206121 DVU0697 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase
Query= BRENDA::P07874 (481 letters) >MicrobesOnline__882:206121 Length = 472 Score = 384 bits (986), Expect = e-111 Identities = 210/470 (44%), Positives = 286/470 (60%), Gaps = 16/470 (3%) Query: 4 VILSGGSGSRLWPLSRKQYPKQFLALTGDDTLFQQTIKRLAFDGMQAPL-LVCNKEHRFI 62 +IL+GGSG+RLWP+SR +PKQ +AL GD TL Q+T+KR + +V N+EH F Sbjct: 11 IILAGGSGTRLWPISRSLFPKQLIALNGDLTLLQETLKRALTHFRPDHIHVVTNEEHVFE 70 Query: 63 VQEQLEAQNLASQA-ILLEPFGRNTAPAVAI---AAMKLVAEGRDELLLILPADHVIEDQ 118 V+ Q + +A ++ EP GRNT PA+ + AA + + + P+DH++ D Sbjct: 71 VRAQARTLDPRLEAGVIAEPRGRNTLPAILLGLDAAWRATGGETPPTIAVFPSDHMLGDI 130 Query: 119 RAFQQALALATNAAEKGEMVLFGIPASRPETGYGYIRASADAQLPEGVSRVQSFVEKPDE 178 +Q AL AT A+ G V FG+P + PETGYGYIR + + V+ FVEKPD Sbjct: 131 PRWQAALDEATRLADDGWFVTFGVPPTHPETGYGYIRRGDS--IADRSFEVEGFVEKPDH 188 Query: 179 ARAREFVAAGGYYWNSGMFLFRASRYLEELKKHDADIYDTCLLALERSQHDGDLVNIDAA 238 A A ++ G Y+WNSGMF+F +E + H +D+ + GD I+ Sbjct: 189 ATATAYLKDGRYFWNSGMFVFNGQSLIEAVHAHQSDLGHWW-------ESRGDRPLIEGY 241 Query: 239 TFECCPDNSIDYAVMEKTSRACVVPLSAGWNDVGSWSSIWDVHAKDANGNVTKGDVLVHD 298 T P S+DY +ME SR VV GW+D+GSW +++ + KD +G V +GD + D Sbjct: 242 T--SIPSISVDYGIMEHASRIAVVEADFGWDDLGSWEALYRLGKKDESGCVRRGDTMALD 299 Query: 299 SHNCLVHGNGKLVSVIGLEDIVVVETKDAMMIAHKDRVQDVKHVVKDLDAQGRSETQNHC 358 N ++ G + IGL+DIV V+T+DA ++ D+ Q VK VV+ L A+ S + H Sbjct: 300 CENSMLFSRGGKLVGIGLKDIVAVQTRDATLVCALDKTQRVKDVVELLKAESSSLAEVHL 359 Query: 359 EVYRPWGSYDSVDMGGRFQVKHITVKPGARLSLQMHHHRAEHWIVVSGTAQVTCDDKTFL 418 V+RPWGSY ++ G F++K ITV PGARLSLQMHHHR+EHW+VVSG A V + L Sbjct: 360 TVHRPWGSYTVLEEGKLFKIKRITVLPGARLSLQMHHHRSEHWVVVSGAALVQVGETETL 419 Query: 419 LTENQSTYIPIASVHRLANPGKIPLEIIEVQSGSYLGEDDIERLEDVYGR 468 LTENQ IP ++HRL+NPGKIPLE+IEVQSG YL EDDI R EDVYGR Sbjct: 420 LTENQWAVIPRGAMHRLSNPGKIPLELIEVQSGPYLEEDDIVRFEDVYGR 469 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: 628 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: 472 Length adjustment: 33 Effective length of query: 448 Effective length of database: 439 Effective search space: 196672 Effective search space used: 196672 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