Align mannose-1-phosphate guanylyltransferase (EC 2.7.7.13) (characterized)
to candidate 8501977 DvMF_2691 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase (RefSeq)
Query= BRENDA::P07874 (481 letters) >FitnessBrowser__Miya:8501977 Length = 501 Score = 369 bits (948), Expect = e-106 Identities = 213/486 (43%), Positives = 288/486 (59%), Gaps = 22/486 (4%) Query: 4 VILSGGSGSRLWPLSRKQYPKQFLALTGDDTLFQQTIKR-LAFDGMQAPLLVCNKEHRFI 62 VIL+GGSG+RLWPLSR +PKQ LAL GD +L QQT++R L+ + +V N+EH F Sbjct: 19 VILAGGSGTRLWPLSRALFPKQLLALNGDLSLLQQTVRRVLSLFPPERVHIVTNEEHVFE 78 Query: 63 VQEQLEA--QNLASQAILLEPFGRNTAPAVAI---AAMKLV---AEGRDE----LLLILP 110 V+ Q A + L +Q +L EP GRNT PA+ + AAM AE D LL + P Sbjct: 79 VRAQARALDERLDTQ-VLAEPVGRNTLPAILLGLDAAMNAATGTAEADDAAQPPLLAVFP 137 Query: 111 ADHVIEDQRAFQQALALATNAAEKGEMVLFGIPASRPETGYGYIR-----ASADAQLPEG 165 +DH + D+ + A+ A +G V FG+P + PETGYGYIR ++A+A Sbjct: 138 SDHQLHDEVRWGAAVTRGAGLAAEGWTVTFGVPPTTPETGYGYIRRGELLSNANAAAQGA 197 Query: 166 VSRVQSFVEKPDEARAREFVAAGGYYWNSGMFLFRASRYLEELKKHDADIYDTCLLALER 225 V FVEKPD AR F+ G ++WNSGMF+F L +++ + + Sbjct: 198 AFAVDGFVEKPDLETARGFLRQGMHFWNSGMFVFNGGVLLAAVERFQPTLATWWTTRTDA 257 Query: 226 SQHDGDLVNIDAATFECCPDNSIDYAVMEKTSRACVVPLSAGWNDVGSWSSIWDVHAKDA 285 S G + +T P SIDY +ME R VV + GW+D+GSW +++ + AKD Sbjct: 258 SLAPGIPLTHGYSTL---PSISIDYGIMEHVDRIAVVEAAFGWDDLGSWEALYRLGAKDE 314 Query: 286 NGNVTKGDVLVHDSHNCLVHGNGKLVSVIGLEDIVVVETKDAMMIAHKDRVQDVKHVVKD 345 G V +GD + D +CL+ G + IGL +++ V+T+DA +I KD+VQ VK VV+ Sbjct: 315 RGCVIQGDTMALDCDDCLLLSRGGKLVAIGLSNVIAVQTRDATLICAKDQVQRVKDVVEK 374 Query: 346 LDAQGRSETQNHCEVYRPWGSYDSVDMGGRFQVKHITVKPGARLSLQMHHHRAEHWIVVS 405 L A+ H V RPWG+Y +D G +VK I V PGARLSLQMHHHR+EHW+V Sbjct: 375 LKAEKSPLVDVHLTVRRPWGNYTVLDEGPGRKVKRIEVNPGARLSLQMHHHRSEHWVVAK 434 Query: 406 GTAQVTCDDKTFLLTENQSTYIPIASVHRLANPGKIPLEIIEVQSGSYLGEDDIERLEDV 465 G A V ++ LTEN+ IP A++HRL NPG+IPLE+IE+QSG YLGEDDI R +DV Sbjct: 435 GAALVQVGNEERTLTENEWVDIPKATLHRLTNPGRIPLELIEIQSGPYLGEDDIVRFDDV 494 Query: 466 YGRTAE 471 YGR E Sbjct: 495 YGRRKE 500 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: 625 Number of extensions: 26 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: 501 Length adjustment: 34 Effective length of query: 447 Effective length of database: 467 Effective search space: 208749 Effective search space used: 208749 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: 52 (24.6 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