Align mannose-1-phosphate guanylyltransferase (EC 2.7.7.13) (characterized)
to candidate RR42_RS21015 RR42_RS21015 mannose-1-phosphate guanyltransferase
Query= BRENDA::P07874 (481 letters) >FitnessBrowser__Cup4G11:RR42_RS21015 Length = 474 Score = 491 bits (1264), Expect = e-143 Identities = 248/473 (52%), Positives = 321/473 (67%), Gaps = 9/473 (1%) Query: 1 MIPVILSGGSGSRLWPLSRKQYPKQFLALTGDDTLFQQTIKRLA-FDGMQAPLLVCNKEH 59 ++PVIL GG+GSRLWPLSR YPKQFL L G D+L Q T+ R+ G QAP+LV N+ H Sbjct: 7 IVPVILCGGAGSRLWPLSRDGYPKQFLRLLGQDSLLQDTLLRVREIPGAQAPILVSNEAH 66 Query: 60 RFIVQEQLEAQNLASQAILLEPFGRNTAPAVAIAAMKLVAEGRDELLLILPADHVIEDQR 119 RF+V EQ A AI+LEP RNTAPA A+AA++ + G D +LL+LP+DH+I D+ Sbjct: 67 RFVVAEQAREAGCALCAIVLEPHPRNTAPAAAVAALQARSGGSDPVLLVLPSDHLIRDRA 126 Query: 120 AFQQALALATNAAEKGEMVLFGIPASRPETGYGYIRASADAQLPEGVSRVQS---FVEKP 176 AF + + A+ A G +V G+ + TGYGYI+A +P + + S FVEKP Sbjct: 127 AFARTVCQASAVAATGVVVTLGVVPTFAATGYGYIKA-----VPSNTADLLSVTRFVEKP 181 Query: 177 DEARAREFVAAGGYYWNSGMFLFRASRYLEELKKHDADIYDTCLLALERSQHDGDLVNID 236 A ++ G +WNSG+FLFRAS YL L++ DI A+ R D D +D Sbjct: 182 SLEMATGYLQEGNCFWNSGIFLFRASVYLAALERFAPDILLAAQEAMVRGHRDLDFFRLD 241 Query: 237 AATFECCPDNSIDYAVMEKTSRACVVPLSAGWNDVGSWSSIWDVHAKDANGNVTKGDVLV 296 F C +SIDYAVME A + PLSA W+DVGSW ++W K +GNV GDV+ Sbjct: 242 TDAFAACRSDSIDYAVMEHLRDAQMAPLSADWSDVGSWDAVWKAAEKTTDGNVAIGDVVT 301 Query: 297 HDSHNCLVHGNGKLVSVIGLEDIVVVETKDAMMIAHKDRVQDVKHVVKDLDAQGRSETQN 356 H + CLVH + ++V+V GL+D++VVET D +++ HKD QDVK +V+ + AQGR E Sbjct: 302 HHAQGCLVHASHRMVAVAGLDDVMVVETPDVVLVVHKDHCQDVKQLVEAVRAQGRPEATQ 361 Query: 357 HCEVYRPWGSYDSVDMGGRFQVKHITVKPGARLSLQMHHHRAEHWIVVSGTAQVTCDDKT 416 H +VYRPWG+YD+VD G R+QVK ITVKPGA+LSLQ+HHHRAEHW+VVSGTA+V D Sbjct: 362 HRKVYRPWGAYDAVDHGTRYQVKRITVKPGAKLSLQLHHHRAEHWVVVSGTARVRRGDVE 421 Query: 417 FLLTENQSTYIPIASVHRLANPGKIPLEIIEVQSGSYLGEDDIERLEDVYGRT 469 +LLTE+QSTYIPI H L NPG+IPLE+IE+QSGSYLGEDDI R+ D+YGRT Sbjct: 422 YLLTEDQSTYIPIGEAHSLENPGRIPLELIEIQSGSYLGEDDIIRMADIYGRT 474 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: 649 Number of extensions: 26 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: 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