Align mannose-1-phosphate guanylyltransferase (EC 2.7.7.13) (characterized)
to candidate GFF1782 Psest_1821 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase
Query= BRENDA::P07874 (481 letters) >FitnessBrowser__psRCH2:GFF1782 Length = 469 Score = 560 bits (1444), Expect = e-164 Identities = 275/471 (58%), Positives = 353/471 (74%), Gaps = 7/471 (1%) Query: 1 MIPVILSGGSGSRLWPLSRKQYPKQFLALTGDD-TLFQQTIKRLAFDGMQA--PLLVCNK 57 ++PVI++GGSGSRLWPLSR+ PKQFLALT ++ Q TI+RL DG++A PLL+CN+ Sbjct: 2 LLPVIIAGGSGSRLWPLSRQLNPKQFLALTDAQLSMLQSTIRRL--DGLEAGLPLLICNE 59 Query: 58 EHRFIVQEQLEAQNLASQAILLEPFGRNTAPAVAIAAMKLVAEGRDELLLILPADHVIED 117 +HRF+ EQL ++ +ILLEP GRNTAPA+A+AA++ EG D +LL+L ADH+I+D Sbjct: 60 QHRFLAAEQLRQLSMEQASILLEPVGRNTAPAIALAALQATQEGDDPILLVLAADHLIQD 119 Query: 118 QRAFQQALALATNAAEKGEMVLFGIPASRPETGYGYIRASADAQLPEGVSRVQSFVEKPD 177 AF ++ A A G++V FGI + PETGYGYI + L EG V FVEKP Sbjct: 120 VDAFHSSIQAAMPFATNGKLVTFGIVPTNPETGYGYIEKGKE--LGEGGFAVNRFVEKPS 177 Query: 178 EARAREFVAAGGYYWNSGMFLFRASRYLEELKKHDADIYDTCLLALERSQHDGDLVNIDA 237 A E++A+G Y+WNSGMF+FRASRYL+EL++H I C AL D V +DA Sbjct: 178 LDIAEEYLASGEYFWNSGMFMFRASRYLDELERHQPSILAACRQALAAGTQDMHFVRVDA 237 Query: 238 ATFECCPDNSIDYAVMEKTSRACVVPLSAGWNDVGSWSSIWDVHAKDANGNVTKGDVLVH 297 ATF CP++S+DYAVMEKT+ A +VPL AGW+DVGSW+++W+ KDA GNV KGDVL H Sbjct: 238 ATFAACPEDSVDYAVMEKTNDAVMVPLDAGWSDVGSWTALWEASNKDAEGNVFKGDVLGH 297 Query: 298 DSHNCLVHGNGKLVSVIGLEDIVVVETKDAMMIAHKDRVQDVKHVVKDLDAQGRSETQNH 357 + N VH + +LV+ +G+ED+V+VETKDA+++AHK++VQDVK +V+ + A R E NH Sbjct: 298 ATRNSFVHADSRLVATLGVEDLVIVETKDAVLVAHKNQVQDVKKLVERIKADNRHEHLNH 357 Query: 358 CEVYRPWGSYDSVDMGGRFQVKHITVKPGARLSLQMHHHRAEHWIVVSGTAQVTCDDKTF 417 EVYRPWG YD++D G R+QVK ITV+PGA+LS+QMHHHRAEHW+VVSGTA+VT DKT+ Sbjct: 358 REVYRPWGVYDAIDSGHRYQVKRITVQPGAKLSVQMHHHRAEHWVVVSGTAKVTNGDKTY 417 Query: 418 LLTENQSTYIPIASVHRLANPGKIPLEIIEVQSGSYLGEDDIERLEDVYGR 468 L+TENQSTYIP+ VH L NPG IPLE+IEVQSGSYLGEDDI R ED YGR Sbjct: 418 LVTENQSTYIPVGQVHALENPGVIPLELIEVQSGSYLGEDDIVRFEDQYGR 468 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: 674 Number of extensions: 29 Number of successful extensions: 3 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: 469 Length adjustment: 33 Effective length of query: 448 Effective length of database: 436 Effective search space: 195328 Effective search space used: 195328 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