Align mannose-1-phosphate guanylyltransferase (EC 2.7.7.13) (characterized)
to candidate SM_b21082 SM_b21082 mannose-6-phosphate isomerase, GDP-mannose pyrophosphorylase
Query= BRENDA::P07874 (481 letters) >FitnessBrowser__Smeli:SM_b21082 Length = 767 Score = 258 bits (660), Expect = 4e-73 Identities = 144/366 (39%), Positives = 209/366 (57%), Gaps = 13/366 (3%) Query: 5 ILSGGSGSRLWPLSRKQYPKQFLALTGDDTLFQQTIKRL-AFDGMQAPL-LVCNKEHRFI 62 ++SGG GSRLWPLSR+ PKQF L G ++ T++RL A P+ ++ ++ H Sbjct: 9 VMSGGVGSRLWPLSREDNPKQFHDLAGHGSMLVNTVRRLKARPAGDTPVHVIASERHSER 68 Query: 63 VQEQLEAQNLASQAILLEPFGRNTAPAVAIAAMKLVAEGRDELLLILPADHVIEDQRAFQ 122 V+ L +LA + EP GRNTA AVA+AA++ +A D L+L++P+DH I + F Sbjct: 69 VRADLAGIDLAGGHAIFEPVGRNTAAAVAVAALETIATHGDGLVLVVPSDHEISTEEQFW 128 Query: 123 QALALATNAAEKGEMVLFGIPASRPETGYGYIRASADAQLPEGVSRVQSFVEKPDEARAR 182 + AAE G +V+FGIP PETGYGYI + + + V FVEKP A+ Sbjct: 129 NTVEKGVPAAEAGRLVVFGIPPDSPETGYGYIESVGKGNVRD----VARFVEKPGLEMAK 184 Query: 183 EFVAAGGYYWNSGMFLFRASRYLEELKKHDADIYD--TCLLALERSQHDGDLVNIDAATF 240 +VA+G ++WN+G+FLFRA ++H A I+ C A ++ G + I+ + Sbjct: 185 AYVASGTFFWNAGIFLFRAGAMRAAFREHQAAIWQKTECAFAAAATEVSGTYLPIE--QY 242 Query: 241 ECCPDNSIDYAVMEKTSRACVVPLSAGWNDVGSWSSIWDVHAKDANGNVTKGDVLVHDSH 300 P SIDYA+ME S +VP S W+D+GSW S+ D+ D NGNV GDV+ D Sbjct: 243 STIPSASIDYAIMEHASGIAMVPASFYWSDLGSWQSLLDISPTDGNGNVVIGDVVAIDCE 302 Query: 301 NCLVHGNGKLVSVIGLEDIVVVETKDAMMIAHKDRVQDVKHVVKDLDAQGRSETQ---NH 357 + G+L+SVIGL D+ +V T DA +A + Q+VK +V+ L+ GR ET+ H Sbjct: 303 RSYLRSQGRLLSVIGLRDVAIVSTADATFVAPVAKSQEVKRIVEQLEKSGRLETKFTPAH 362 Query: 358 CEVYRP 363 V +P Sbjct: 363 ARVLQP 368 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: 886 Number of extensions: 42 Number of successful extensions: 3 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: 767 Length adjustment: 37 Effective length of query: 444 Effective length of database: 730 Effective search space: 324120 Effective search space used: 324120 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: 53 (25.0 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