Align mannose-1-phosphate guanylyltransferase (EC 2.7.7.13) (characterized)
to candidate Pf6N2E2_4241 Mannose-1-phosphate guanylyltransferase (GDP) (EC 2.7.7.22)
Query= BRENDA::P07874 (481 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4241 Length = 483 Score = 404 bits (1039), Expect = e-117 Identities = 214/478 (44%), Positives = 305/478 (63%), Gaps = 11/478 (2%) Query: 1 MIPVILSGGSGSRLWPLSRKQYPKQFLALTGDDTLFQQTIKRLA--FDGMQAPLLVCNKE 58 +IPVILSGG+G+RLWP+SR+ +PK F+ L +L +T +R A FDG + V N+E Sbjct: 2 LIPVILSGGAGTRLWPVSREGHPKPFMLLPDGQSLLGKTYRRAAGLFDGRGDIVTVTNRE 61 Query: 59 HRFIVQEQLEAQNLASQA--ILLEPFGRNTAPAVAIAAMKLVA-EGRDELLLILPADHVI 115 + F ++ ++ +L +LEP GRNTAPA+A AA+ + A G D +L+++PADH+I Sbjct: 62 YYFQSRDHYQSAHLERHRGHFVLEPTGRNTAPAIATAALAVQALHGDDPILVVMPADHLI 121 Query: 116 EDQRAFQQALALATNAAEKGEMVLFGIPASRPETGYGYIRASADAQLPEGVSRVQSFVEK 175 +D+ AFQ A+A A A+ G +V FG+ S PETG+GYI +G ++V FVEK Sbjct: 122 QDEAAFQTAVAHAVELAKNGHLVTFGVLPSTPETGFGYIERGKPLDT-KGAAKVVRFVEK 180 Query: 176 PDEARAREFVAAGGYYWNSGMFLFRASRYLEELKKHDADIYD---TCLLALERSQHDGDL 232 PD A +++ +G + WNSGMF F L EL+ H ++ + TC+ A + G + Sbjct: 181 PDLQTATQYLESGRFLWNSGMFCFSVKTLLAELQAHAPELLEQARTCVTASTAVETSGCV 240 Query: 233 VN-IDAATFECCPDNSIDYAVMEKTSRACVVPLSAGWNDVGSWSSIWDVHAKDANGNVTK 291 + AA F PD SIDYA+ME+++ V+P + W+D+GSWS++ + DA N Sbjct: 241 QQELSAAHFAEMPDISIDYALMERSANVVVIPAAFDWSDIGSWSAVAGLVPADAQNNRAT 300 Query: 292 GDVLVHDSHNCLVHGNGKLVSVIGLEDIVVVETKDAMMIAHKDRVQDVKHVVKDLDAQGR 351 G+ L DS N V +G+LV+ +G+E +++++T DA+++AH DR QDV+ V + L + Sbjct: 301 GEALFIDSQNNFVQSDGRLVAALGVEHLIIIDTADAVLVAHADRAQDVRRVARQLKDKDH 360 Query: 352 SETQNHCEVYRPWGSYDSVDMGGRFQVKHITVKPGARLSLQMHHHRAEHWIVVSGTAQVT 411 + H V RPWGSY ++ G RF++K I VKPGA LSLQMHHHR EHW+VV G A+VT Sbjct: 361 EAYRLHRTVSRPWGSYTVLEEGPRFKIKRIVVKPGASLSLQMHHHRNEHWVVVEGMAKVT 420 Query: 412 CDDK-TFLLTENQSTYIPIASVHRLANPGKIPLEIIEVQSGSYLGEDDIERLEDVYGR 468 + + L+ +N+ST+IP HRL NPG I L IIEVQSG YLGEDDI R ED YGR Sbjct: 421 NNGSGSHLVAKNESTFIPAGHKHRLENPGVIDLVIIEVQSGEYLGEDDIVRFEDHYGR 478 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: 637 Number of extensions: 39 Number of successful extensions: 6 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: 483 Length adjustment: 34 Effective length of query: 447 Effective length of database: 449 Effective search space: 200703 Effective search space used: 200703 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: 52 (24.6 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