Align mannose-1-phosphate guanylyltransferase (EC 2.7.7.13) (characterized)
to candidate 3610760 Dshi_4146 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase (RefSeq)
Query= BRENDA::P07874 (481 letters) >FitnessBrowser__Dino:3610760 Length = 474 Score = 407 bits (1045), Expect = e-118 Identities = 212/473 (44%), Positives = 291/473 (61%), Gaps = 7/473 (1%) Query: 3 PVILSGGSGSRLWPLSRKQYPKQFLALTG-DDTLFQQTIKRLAFDGMQAPLLVCNKEHRF 61 PVIL GGSG+RLWPLSRK YPKQF+ L G +TLFQ + RL G+ PL+V + RF Sbjct: 4 PVILCGGSGTRLWPLSRKSYPKQFVPLAGVQETLFQASATRLKGPGIGLPLVVTGPDFRF 63 Query: 62 IVQEQLEAQNLASQAILLEPFGRNTAPAVAIAAMKLVAEGRDELLLILPADHVIEDQRAF 121 I +QL + +L+EP RNTAPA+ AA+ + A D L+L++P+DHVI D AF Sbjct: 64 IATDQLAEMGVEQATVLIEPAARNTAPAILAAALWVEARDPDALMLVMPSDHVIPDAAAF 123 Query: 122 QQALALATNAAEKGEMVLFGIPASRPETGYGYIRAS-ADAQLPEGVSRVQSFVEKPDEAR 180 +A A A G +V FGI R ETGYG++ S + P+ + R FVEKPD A Sbjct: 124 AATVARAEPEARAGRLVTFGIVPERAETGYGWLELSETPTEAPQPLKR---FVEKPDAAT 180 Query: 181 AREFVAAGGYYWNSGMFLFRASRYLEELKKHDADIYDTCLLALERSQHDGDLVNIDAATF 240 A + AG Y WN+G+FLF + + H D+ ++ ++ D +D A + Sbjct: 181 AEAMLEAGTYLWNAGIFLFSVAALRAAFEAHQPDMLAAVSASVAGARQDLSFHRLDPAPW 240 Query: 241 ECCPDNSIDYAVMEKTSRACVVPLSAGWNDVGSWSSIWDVHAKDANGNVTKGDVLVHDSH 300 D SIDYA+ME+ VVP W+D+G W ++W D +G VT G D Sbjct: 241 AEAADISIDYAIMERADNLSVVPYHGHWSDLGGWDAVWREAGPDEDGVVTTGPASALDCE 300 Query: 301 NCLVHGN--GKLVSVIGLEDIVVVETKDAMMIAHKDRVQDVKHVVKDLDAQGRSETQNHC 358 N L+H G+ V +GL D +VV DA+++A R Q+V+ V+ L +G ++ + Sbjct: 301 NTLLHATAEGQEVVGLGLRDTLVVAMPDAVLVADASRAQEVRAAVETLKIKGAAQAETFP 360 Query: 359 EVYRPWGSYDSVDMGGRFQVKHITVKPGARLSLQMHHHRAEHWIVVSGTAQVTCDDKTFL 418 +RPWG ++++ +G RFQVK I VKPGA LSLQ H HR+EHWIVV+GTA+VT DD T L Sbjct: 361 RDHRPWGWFETLALGDRFQVKRIVVKPGAALSLQSHVHRSEHWIVVAGTAKVTVDDTTRL 420 Query: 419 LTENQSTYIPIASVHRLANPGKIPLEIIEVQSGSYLGEDDIERLEDVYGRTAE 471 ++ENQS YIP+ +VHR+ NPGK+P+ +IEVQ+G+YLGEDDI R EDVY R ++ Sbjct: 421 ISENQSVYIPLGAVHRMDNPGKVPMVLIEVQTGAYLGEDDIIRYEDVYARDSD 473 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: 592 Number of extensions: 25 Number of successful extensions: 5 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: 474 Length adjustment: 34 Effective length of query: 447 Effective length of database: 440 Effective search space: 196680 Effective search space used: 196680 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