Align mannose-1-phosphate guanylyltransferase (EC 2.7.7.13) (characterized)
to candidate WP_029133029.1 A3GO_RS0108450 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase
Query= BRENDA::P07874 (481 letters) >NCBI__GCF_000428045.1:WP_029133029.1 Length = 469 Score = 558 bits (1439), Expect = e-163 Identities = 281/470 (59%), Positives = 344/470 (73%), Gaps = 4/470 (0%) Query: 1 MIPVILSGGSGSRLWPLSRKQYPKQFLALTGDDTLFQQTIKRL-AFDGMQAPLLVCNKEH 59 MIPVILSGGSG+RLWPLSR QYPKQFL L D+T+ Q+T+ RL G+ AP++VCN++H Sbjct: 1 MIPVILSGGSGTRLWPLSRSQYPKQFLPLVTDNTMLQETLIRLDGLQGIAAPIVVCNEDH 60 Query: 60 RFIVQEQLEAQNLASQAILLEPFGRNTAPAVAIAAMKLVAEGRDELLLILPADHVIEDQR 119 RF+V EQL + +QAILLEP GRNTAPAVA+AA L AE DELLL+L ADHVI D Sbjct: 61 RFMVAEQLREMGVTAQAILLEPVGRNTAPAVALAA--LAAESPDELLLVLAADHVIVDMP 118 Query: 120 AFQQALALATNAAEKGEMVLFGIPASRPETGYGYIRASADAQLPEGVSRVQSFVEKPDEA 179 AF A+A A AA +V FG+ + PETGYGYIR +A + + V SFVEKPD A Sbjct: 119 AFHAAIARAAEAATADRLVTFGVVPTGPETGYGYIRRG-EAGAWDDIYTVDSFVEKPDLA 177 Query: 180 RAREFVAAGGYYWNSGMFLFRASRYLEELKKHDADIYDTCLLALERSQHDGDLVNIDAAT 239 AR +V++ YYWNSGMF+F+AS+YL+ L++H ++ C A S+ D V +D Sbjct: 178 TARGYVSSSDYYWNSGMFVFKASQYLQALERHHPEMLAACKHAYASSRRSPDFVRLDKDA 237 Query: 240 FECCPDNSIDYAVMEKTSRACVVPLSAGWNDVGSWSSIWDVHAKDANGNVTKGDVLVHDS 299 F CP +SIDYAVMEKT RA VVPL AGWNDVGSWS++W+V KD GN KGDVL D+ Sbjct: 238 FTACPADSIDYAVMEKTDRAVVVPLDAGWNDVGSWSALWEVTTKDGQGNSLKGDVLSVDT 297 Query: 300 HNCLVHGNGKLVSVIGLEDIVVVETKDAMMIAHKDRVQDVKHVVKDLDAQGRSETQNHCE 359 HN + KLV+V+GL+D+VVVET DA+M++ K RVQ+VK +V L GRSE++ H + Sbjct: 298 HNSYIQSENKLVAVVGLDDMVVVETDDAVMVSPKSRVQEVKQIVDLLRVAGRSESELHRK 357 Query: 360 VYRPWGSYDSVDMGGRFQVKHITVKPGARLSLQMHHHRAEHWIVVSGTAQVTCDDKTFLL 419 VYRPWG YDS+D+G R Q K I V PGA+LSLQMHHHRAEHWIVV GTA VT ++ LL Sbjct: 358 VYRPWGYYDSIDLGERHQAKRIVVNPGAKLSLQMHHHRAEHWIVVKGTASVTRGEEVLLL 417 Query: 420 TENQSTYIPIASVHRLANPGKIPLEIIEVQSGSYLGEDDIERLEDVYGRT 469 TENQSTYIPI + H L N G IPLE++EVQ+GSYLGEDDI R ED+YGRT Sbjct: 418 TENQSTYIPIGTTHSLENRGVIPLEMVEVQTGSYLGEDDIVRFEDLYGRT 467 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: 660 Number of extensions: 24 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: 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 24 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