Align mannose-1-phosphate guanylyltransferase (EC 2.7.7.13) (characterized)
to candidate 3608502 Dshi_1897 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase (RefSeq)
Query= BRENDA::P07874 (481 letters) >FitnessBrowser__Dino:3608502 Length = 476 Score = 408 bits (1049), Expect = e-118 Identities = 214/470 (45%), Positives = 290/470 (61%), Gaps = 4/470 (0%) Query: 1 MIPVILSGGSGSRLWPLSRKQYPKQFLALTGDDTLFQQTIKRLAFDGMQAPLLVCNKEHR 60 +IPVIL+GGSGSRLWP SRK YPKQF L G +LFQ T+ RL AP ++ + R Sbjct: 2 IIPVILAGGSGSRLWPASRKSYPKQFTELVGARSLFQDTLARLQGPHFAAPTIITGDDFR 61 Query: 61 FIVQEQLEAQNLASQAILLEPFGRNTAPAVAIAAMKLVAEGRDELLLILPADHVIEDQRA 120 FI EQL+ + ILLEP GRNTAPA+ AA++ A D +LL+ P+DH I D A Sbjct: 62 FITAEQLDDAGVTGADILLEPAGRNTAPAILAAALRHEATP-DAVLLVSPSDHRIADGAA 120 Query: 121 FQQALALATNAAEKGEMVLFGIPASRPETGYGYIRASADAQLPEGVSRVQSFVEKPDEAR 180 F A+A AAE+G +V FG+ ETGYGY+ S +P ++SFVEKPD A+ Sbjct: 121 FLDAVAAGKAAAEEGHLVTFGVTPIAAETGYGYLELSG-TPVPGQPQVLKSFVEKPDAAQ 179 Query: 181 AREFVAAGGYYWNSGMFLFRASRYLEELKKHDADIYDTCLLALERSQHDGDLVNIDAATF 240 A + +AAG + WN+G+F+F+ ++ ++ + A+ + D + A + Sbjct: 180 AAQLLAAGRHLWNAGIFMFKVGTIIDAFERLAPRLVMPVRAAMAAGEDDLCFYRLGAQAY 239 Query: 241 ECCPDNSIDYAVMEKTSRACVVPLSAGWNDVGSWSSIWDVHAKDANGNVTKGDVLVHDSH 300 C D SIDYA+ME V+P+S GW D+GSW S+ +D GN +G L D Sbjct: 240 ARCEDISIDYAIMEAAEALRVIPVSCGWTDLGSWRSVHGASDQDTEGNTVQGSALQIDCR 299 Query: 301 NCLVHGN--GKLVSVIGLEDIVVVETKDAMMIAHKDRVQDVKHVVKDLDAQGRSETQNHC 358 N L+ G + +GL++I + T DA+++A+ D + VK VV L QG S+ ++ Sbjct: 300 NSLLKSTAPGTRLVGLGLQNIAAIATDDAILVANLDDSERVKEVVAALKVQGASQAESFR 359 Query: 359 EVYRPWGSYDSVDMGGRFQVKHITVKPGARLSLQMHHHRAEHWIVVSGTAQVTCDDKTFL 418 +RPWG ++++ +G RFQVK I VKPGA LSLQ H HRAEHW+VV G+A VT D L Sbjct: 360 RCHRPWGYFETLSLGERFQVKRIMVKPGAALSLQSHFHRAEHWVVVEGSAHVTVDRDVSL 419 Query: 419 LTENQSTYIPIASVHRLANPGKIPLEIIEVQSGSYLGEDDIERLEDVYGR 468 ++ENQS YIP+ +VHRL N GK+PL +IEVQSG+YLGEDDI R EDVY R Sbjct: 420 ISENQSVYIPLGAVHRLENRGKVPLNLIEVQSGAYLGEDDIVRYEDVYAR 469 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: 573 Number of extensions: 22 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: 476 Length adjustment: 34 Effective length of query: 447 Effective length of database: 442 Effective search space: 197574 Effective search space used: 197574 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