Align mannose-1-phosphate guanylyltransferase (EC 2.7.7.13) (characterized)
to candidate AZOBR_RS33830 AZOBR_RS33830 mannose-1-phosphate guanylyltransferase
Query= BRENDA::P07874 (481 letters) >FitnessBrowser__azobra:AZOBR_RS33830 Length = 481 Score = 526 bits (1354), Expect = e-154 Identities = 257/468 (54%), Positives = 327/468 (69%) Query: 3 PVILSGGSGSRLWPLSRKQYPKQFLALTGDDTLFQQTIKRLAFDGMQAPLLVCNKEHRFI 62 PVILSGG+GSRLWPLSR YPKQFL L + T+ Q+T R++ D APL++CN+EHRFI Sbjct: 12 PVILSGGAGSRLWPLSRASYPKQFLPLASEQTMIQETALRVSSDRFAAPLVICNEEHRFI 71 Query: 63 VQEQLEAQNLASQAILLEPFGRNTAPAVAIAAMKLVAEGRDELLLILPADHVIEDQRAFQ 122 V EQL A +++ I+LEP GRNTAPAV IAA+ L+ G D L+L++P+DHVI F Sbjct: 72 VAEQLRAASVSPAEIILEPVGRNTAPAVCIAALALLESGEDRLMLVMPSDHVIARSDRFL 131 Query: 123 QALALATNAAEKGEMVLFGIPASRPETGYGYIRASADAQLPEGVSRVQSFVEKPDEARAR 182 +A+ A AA G +V FGI PETGYGYI+A + + V+ FVEKPD A A+ Sbjct: 132 EAVEQAAVAAAAGSLVTFGITPVAPETGYGYIKAGGPLGTGDNIRVVERFVEKPDLATAQ 191 Query: 183 EFVAAGGYYWNSGMFLFRASRYLEELKKHDADIYDTCLLALERSQHDGDLVNIDAATFEC 242 ++A G Y WNSG+FLF A+ Y+ EL+K + I + C A + D ++ F Sbjct: 192 TYLADGRYLWNSGIFLFSAAAYVAELEKSNPAIVEACRQARSSAARDLTFCRLEKEAFAA 251 Query: 243 CPDNSIDYAVMEKTSRACVVPLSAGWNDVGSWSSIWDVHAKDANGNVTKGDVLVHDSHNC 302 P +S+DYAVMEKT +A VV + GWNDVG+WS++WD+ KD +GNV GDV++H++ N Sbjct: 252 SPSDSVDYAVMEKTDQAAVVAVDMGWNDVGAWSALWDIAEKDESGNVVHGDVVLHNARNS 311 Query: 303 LVHGNGKLVSVIGLEDIVVVETKDAMMIAHKDRVQDVKHVVKDLDAQGRSETQNHCEVYR 362 V +LV+V GL+D+VV+ T DA+++A + VQDVK +V+ L A+ R E H VYR Sbjct: 312 YVRSEEQLVAVAGLDDVVVIATDDAVLVADRKHVQDVKLIVERLKAEKRDEHALHTTVYR 371 Query: 363 PWGSYDSVDMGGRFQVKHITVKPGARLSLQMHHHRAEHWIVVSGTAQVTCDDKTFLLTEN 422 PWGSY +D+G RFQVK ITVKPG RLSLQMHHHRAEHWIVV GTA VTC +K LL EN Sbjct: 372 PWGSYRGIDIGDRFQVKRITVKPGERLSLQMHHHRAEHWIVVQGTALVTCGEKQELLFEN 431 Query: 423 QSTYIPIASVHRLANPGKIPLEIIEVQSGSYLGEDDIERLEDVYGRTA 470 QS YIP+ + HRL NPGK+PL +IEVQSGSYLGEDDI R ED YGR A Sbjct: 432 QSVYIPMGTTHRLENPGKVPLHLIEVQSGSYLGEDDIVRFEDGYGRVA 479 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: 638 Number of extensions: 22 Number of successful extensions: 1 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: 481 Length adjustment: 34 Effective length of query: 447 Effective length of database: 447 Effective search space: 199809 Effective search space used: 199809 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