Align mannose-1-phosphate guanylyltransferase (EC 2.7.7.13) (characterized)
to candidate CCNA_03733 CCNA_03733 mannose-1-phosphate guanylyltransferase
Query= BRENDA::P07874 (481 letters) >FitnessBrowser__Caulo:CCNA_03733 Length = 436 Score = 254 bits (650), Expect = 3e-72 Identities = 146/351 (41%), Positives = 203/351 (57%), Gaps = 4/351 (1%) Query: 3 PVILSGGSGSRLWPLSRKQYPKQFLALTGDDTLFQQTIKRLA-FDGMQAPLLVCNKEHRF 61 PVIL GGSG+RLWP SR +PKQFL L D + FQ+T+ R+ G+ ++V + Sbjct: 6 PVILCGGSGTRLWPASRSDHPKQFLKLVSDRSSFQETVLRVKDIPGVAEVVVVTGEAMVG 65 Query: 62 IVQEQLEAQNLASQAILLEPFGRNTAPAVAIAAMKLVAEGRDELLLILPADHVIEDQRAF 121 V EQ A+ A IL+EP R++APAVA AA + A+ ++L+L ADH I F Sbjct: 66 FVSEQT-AEIGAWATILVEPEARDSAPAVAAAAAYVEAQDPAGVVLMLAADHHIAQPEIF 124 Query: 122 QQALALATNAAEKGEMVLFGIPASRPETGYGYIRASADAQLPEGVSRVQSFVEKPDEARA 181 QQA AT AAE+G +V FG+ + P TG+GYIR A L V V +FVEKPD+A A Sbjct: 125 QQAALTATKAAEQGYIVTFGVQPTVPATGFGYIRPGAPL-LDGSVREVAAFVEKPDQATA 183 Query: 182 REFVAAGGYYWNSGMFLFRASRYLEELKKHDADIYDTCLLALERSQHDGDLVNIDAATFE 241 ++ G Y WNSG F F+A+ L E + + + + Q + + +D F Sbjct: 184 ERYLLEG-YLWNSGNFAFQAATLLGEFETFEPSVAAAAKACVAGLQLEAGIGRLDREAFA 242 Query: 242 CCPDNSIDYAVMEKTSRACVVPLSAGWNDVGSWSSIWDVHAKDANGNVTKGDVLVHDSHN 301 S+DYA+ME+T +A V P + W+D+G+W +IW+ +D +GN GDV +H S N Sbjct: 243 QAKKISLDYAIMERTQKAAVAPAAFAWSDLGAWDAIWEASTRDGDGNAQTGDVDLHGSSN 302 Query: 302 CLVHGNGKLVSVIGLEDIVVVETKDAMMIAHKDRVQDVKHVVKDLDAQGRS 352 LV G V VIG+ DIVVV DA+++ H+ Q VK +V L A+GRS Sbjct: 303 VLVRSTGPYVGVIGVNDIVVVAEPDAVLVCHRKDSQAVKTLVDGLKAKGRS 353 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: 493 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: 436 Length adjustment: 33 Effective length of query: 448 Effective length of database: 403 Effective search space: 180544 Effective search space used: 180544 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