Align mannose-1-phosphate guanylyltransferase (EC 2.7.7.13) (characterized)
to candidate 16157 b2049 mannose-1-phosphate guanyltransferase (NCBI)
Query= BRENDA::P07874 (481 letters) >FitnessBrowser__Keio:16157 Length = 478 Score = 520 bits (1338), Expect = e-152 Identities = 262/472 (55%), Positives = 337/472 (71%), Gaps = 4/472 (0%) Query: 1 MIPVILSGGSGSRLWPLSRKQYPKQFLALTGDDTLFQQTIKRLAFDGMQAPLLVCNKEHR 60 + PV+++GGSGSRLWPLSR YPKQFL L GD T+ Q TI RL ++P+++CN++HR Sbjct: 6 LYPVVMAGGSGSRLWPLSRVLYPKQFLCLKGDLTMLQTTICRLNGVECESPVVICNEQHR 65 Query: 61 FIVQEQLEAQNLASQAILLEPFGRNTAPAVAIAAM--KLVAEGRDELLLILPADHVIEDQ 118 FIV EQL N ++ I+LEP GRNTAPA+A+AA+ K + D L+L+L ADHVI D+ Sbjct: 66 FIVAEQLRQLNKLTENIILEPAGRNTAPAIALAALAAKRHSPESDPLMLVLAADHVIADE 125 Query: 119 RAFQQALALATNAAEKGEMVLFGIPASRPETGYGYIR-ASADAQLPEGVS-RVQSFVEKP 176 AF+ A+ A AE G++V FGI PETGYGYIR A + V+ V FVEKP Sbjct: 126 DAFRAAVRNAMPYAEAGKLVTFGIVPDLPETGYGYIRRGEVSAGEQDMVAFEVAQFVEKP 185 Query: 177 DEARAREFVAAGGYYWNSGMFLFRASRYLEELKKHDADIYDTCLLALERSQHDGDLVNID 236 + A+ +VA+G YYWNSGMFLFRA RYLEELKK+ DI D C A+ D + + +D Sbjct: 186 NLETAQAYVASGEYYWNSGMFLFRAGRYLEELKKYRPDILDACEKAMSAVDPDLNFIRVD 245 Query: 237 AATFECCPDNSIDYAVMEKTSRACVVPLSAGWNDVGSWSSIWDVHAKDANGNVTKGDVLV 296 F CP+ S+DYAVME+T+ A VVP+ AGW+DVGSWSS+W++ A A GNV GDV+ Sbjct: 246 EEAFLACPEESVDYAVMERTADAVVVPMDAGWSDVGSWSSLWEISAHTAEGNVCHGDVIN 305 Query: 297 HDSHNCLVHGNGKLVSVIGLEDIVVVETKDAMMIAHKDRVQDVKHVVKDLDAQGRSETQN 356 H + N V+ LV+ +G++D+VVV+TKDA++IA ++ VQDVK VV+ + A GR E + Sbjct: 306 HKTENSYVYAESGLVTTVGVKDLVVVQTKDAVLIADRNAVQDVKKVVEQIKADGRHEHRV 365 Query: 357 HCEVYRPWGSYDSVDMGGRFQVKHITVKPGARLSLQMHHHRAEHWIVVSGTAQVTCDDKT 416 H EVYRPWG YDS+D G R+QVK ITVKPG LS+QMHHHRAEHW+VV+GTA+VT D Sbjct: 366 HREVYRPWGKYDSIDAGDRYQVKRITVKPGEGLSVQMHHHRAEHWVVVAGTAKVTIDGDI 425 Query: 417 FLLTENQSTYIPIASVHRLANPGKIPLEIIEVQSGSYLGEDDIERLEDVYGR 468 LL EN+S YIP+ + H L NPGKIPL++IEV+SGSYL EDD+ R D YGR Sbjct: 426 KLLGENESIYIPLGATHCLENPGKIPLDLIEVRSGSYLEEDDVVRFADRYGR 477 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: 645 Number of extensions: 33 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: 478 Length adjustment: 34 Effective length of query: 447 Effective length of database: 444 Effective search space: 198468 Effective search space used: 198468 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