Align mannose-1-phosphate guanylyltransferase (EC 2.7.7.13) (characterized)
to candidate WP_057508396.1 ABB28_RS09495 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase
Query= BRENDA::P07874 (481 letters) >NCBI__GCF_001431535.1:WP_057508396.1 Length = 467 Score = 541 bits (1395), Expect = e-158 Identities = 267/465 (57%), Positives = 341/465 (73%), Gaps = 5/465 (1%) Query: 4 VILSGGSGSRLWPLSRKQYPKQFLALTGDDTLFQQTIKRLAFDGMQAPLLVCNKEHRFIV 63 VILSGGSG+RLWPLSR+ YPKQFL LT D T+ Q T KR+ + PL++ N+EHRF+ Sbjct: 7 VILSGGSGTRLWPLSREAYPKQFLPLTSDLTMLQDTWKRVEAIAARGPLVIANEEHRFVA 66 Query: 64 QEQLEAQNLASQAILLEPFGRNTAPAVAIAAMKLVAEGRDELLLILPADHVIEDQRAFQQ 123 EQL+ + AI+LEP GRNTAPA+A+AA++ +G D LLL+LP+DHV+ D AF + Sbjct: 67 AEQLQQVGASPAAIILEPVGRNTAPAIAVAALEATRDGADALLLVLPSDHVVSDNAAFLR 126 Query: 124 ALALATNAAEKGEMVLFGIPASRPETGYGYIRASADAQLPEGVSRVQSFVEKPDEARARE 183 A+ A AAE G++V FGI + PETGYGYI+A+A EG V+ FVEKPD A A + Sbjct: 127 AVEQAAGAAEAGKLVTFGIVPAGPETGYGYIKAAAG----EGARAVERFVEKPDLATATD 182 Query: 184 FVAAGGYYWNSGMFLFRASRYLEELKKHDADIYDTCLLALERSQHDGDLVNIDAATFECC 243 +VA+G YYWNSGMFLF+ASRYL+EL++ + A +++ D D +D F Sbjct: 183 YVASGQYYWNSGMFLFKASRYLQELERFQPAMLAGSRDAWSKARRDADFTRLDKDAFTAV 242 Query: 244 PDNSIDYAVMEKTSRACVVPLSAGWNDVGSWSSIWDVHAKDANGNVTKGDVLVHDSHNCL 303 P +SIDYAVMEKT+ A VVPL AGWNDVGSW+++ DV +D +GN +GDV+ D N Sbjct: 243 PSDSIDYAVMEKTADAVVVPLDAGWNDVGSWTALRDVSQQDGDGNAHQGDVIAIDCRNTY 302 Query: 304 VHGNGKLVSVIGLEDIVVVETKDAMMIAHKDRVQDVKHVVKDLDAQGRSETQNHCEVYRP 363 +G +LV+++GL+D++VVET DA+++ DR+Q+VK VV L A+GRSE H +VYRP Sbjct: 303 AYGQ-RLVAMVGLDDVIVVETDDAVLVGKGDRMQEVKAVVAQLKAEGRSEATWHRKVYRP 361 Query: 364 WGSYDSVDMGGRFQVKHITVKPGARLSLQMHHHRAEHWIVVSGTAQVTCDDKTFLLTENQ 423 WG+YDS+D G RFQVK ITVKPG LSLQMHHHRAEHWIVVSGTA+VT ++ LL+ENQ Sbjct: 362 WGAYDSIDNGARFQVKRITVKPGGTLSLQMHHHRAEHWIVVSGTAEVTRGEEVLLLSENQ 421 Query: 424 STYIPIASVHRLANPGKIPLEIIEVQSGSYLGEDDIERLEDVYGR 468 STYIP+ HRL NPG++PLE+IEVQSGSYLGEDDI R ED YGR Sbjct: 422 STYIPLGVTHRLRNPGRLPLELIEVQSGSYLGEDDIVRFEDTYGR 466 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: 673 Number of extensions: 32 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: 467 Length adjustment: 33 Effective length of query: 448 Effective length of database: 434 Effective search space: 194432 Effective search space used: 194432 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