Align mannose-1-phosphate guanylyltransferase (EC 2.7.7.13) (characterized)
to candidate HSERO_RS10000 HSERO_RS10000 mannose-1-phosphate guanylyltransferase
Query= BRENDA::P07874 (481 letters) >FitnessBrowser__HerbieS:HSERO_RS10000 Length = 471 Score = 508 bits (1308), Expect = e-148 Identities = 260/467 (55%), Positives = 329/467 (70%), Gaps = 2/467 (0%) Query: 3 PVILSGGSGSRLWPLSRKQYPKQFLALTGDDTLFQQTIKRL-AFDGMQAPLLVCNKEHRF 61 PVILSGG+G+RLWPLSR YPKQ L L + T+ Q+T+ R+ A+ APL+VC EHRF Sbjct: 5 PVILSGGAGTRLWPLSRAAYPKQLLPLVSEQTMLQETVARVCAWPEALAPLVVCGNEHRF 64 Query: 62 IVQEQLEAQNLASQAILLEPFGRNTAPAVAIAAMKLVAEGRDELLLILPADHVIEDQRAF 121 ++ EQL ++ AI+LEP G+NTAPAVA AA++L+ + D ++L+LPADHVI ++ AF Sbjct: 65 MIAEQLREMDVRPHAIVLEPQGKNTAPAVAAAALQLMRQDPDAVMLVLPADHVITNREAF 124 Query: 122 QQALALATNAAEKGEMVLFGIPASRPETGYGYIRASADAQLPEGVSRVQSFVEKPDEARA 181 +A+ A + E+G +V FGI S+PETGYGYI A A G V+ FVEKPD RA Sbjct: 125 HEAVRAAMRSVEQGALVTFGITPSKPETGYGYILRGA-AHGDTGNFAVERFVEKPDLERA 183 Query: 182 REFVAAGGYYWNSGMFLFRASRYLEELKKHDADIYDTCLLALERSQHDGDLVNIDAATFE 241 + FVA G YYWNSGMFL RA YLEEL+ H I A+ ++ D D + A F Sbjct: 184 QGFVADGRYYWNSGMFLLRARDYLEELELHRPLIAAAVKDAVAKAYTDLDFCRLGEAAFG 243 Query: 242 CCPDNSIDYAVMEKTSRACVVPLSAGWNDVGSWSSIWDVHAKDANGNVTKGDVLVHDSHN 301 P SIDYAVME T RA VVP GW+DVGSWS++ +V DA GNVT+GDV + N Sbjct: 244 ASPAESIDYAVMENTRRAVVVPADIGWSDVGSWSALQEVMPADAQGNVTRGDVYLDGVSN 303 Query: 302 CLVHGNGKLVSVIGLEDIVVVETKDAMMIAHKDRVQDVKHVVKDLDAQGRSETQNHCEVY 361 LV ++V+V+GL+D++VVET DA+++AHKD+ QDVK VV L + RSE +H VY Sbjct: 304 SLVRAESRMVAVLGLQDLIVVETDDAVLVAHKDKAQDVKGVVDQLKDKKRSEHIHHKRVY 363 Query: 362 RPWGSYDSVDMGGRFQVKHITVKPGARLSLQMHHHRAEHWIVVSGTAQVTCDDKTFLLTE 421 RPWGSY+SVD G RFQVK I VKPG +LSLQMH+HRAEHW+VVSG+A VT ++ LL+E Sbjct: 364 RPWGSYESVDAGDRFQVKRIIVKPGEKLSLQMHYHRAEHWVVVSGSALVTRGEEVTLLSE 423 Query: 422 NQSTYIPIASVHRLANPGKIPLEIIEVQSGSYLGEDDIERLEDVYGR 468 N+S Y+PI HRL NPGK+PL +IEVQSGSYLGEDDI R +DVY R Sbjct: 424 NESIYLPIGVTHRLENPGKLPLHLIEVQSGSYLGEDDIVRFDDVYKR 470 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: 629 Number of extensions: 26 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: 471 Length adjustment: 33 Effective length of query: 448 Effective length of database: 438 Effective search space: 196224 Effective search space used: 196224 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