Align Phosphoglucomutase/phosphomannomutase; PGM/PMM; EC 5.4.2.2; EC 5.4.2.8 (characterized)
to candidate WP_010877192.1 MTH_RS07585 phosphoglucosamine mutase
Query= SwissProt::Q68BJ6 (456 letters) >NCBI__GCF_000008645.1:WP_010877192.1 Length = 455 Score = 476 bits (1224), Expect = e-139 Identities = 243/461 (52%), Positives = 329/461 (71%), Gaps = 15/461 (3%) Query: 1 MGKLFGTFGVRGIANEEITPEFALKIGMAFGTLLKREGRERPLVVVGRDTRVSGEMLKDA 60 M KLFGTFGVR +ANE +TPEFA K+ A+G+ + EG+ + VG DTR S M+K+A Sbjct: 1 MKKLFGTFGVRRLANEVLTPEFASKLAAAYGSTV--EGK----IAVGGDTRTSTVMIKNA 54 Query: 61 LISGLLSTGCDVIDVGIAPTPAIQWATNHFNADGGAVITASHNPPEYNGIKLLEPNGMGL 120 +ISGLLS+GCDV+D+GI PTPA+Q+A + DGG ++TASHNPP+YNGIK ++ +G+G+ Sbjct: 55 VISGLLSSGCDVVDLGILPTPAVQYAVRKYY-DGGVIVTASHNPPQYNGIKFVDSDGIGI 113 Query: 121 KKEREAIVEELFFSEDFHRAKWNEIGELRKE-DIIKPYIEAIKNRVDVEAIKKRRPFVVV 179 + E +E +FFSEDF RA W++IG L II+ Y + + RVD EAI++R+ VVV Sbjct: 114 PDDLEEEIERIFFSEDFRRASWDKIGNLTSNPSIIREYQDGVIARVDAEAIRRRKFRVVV 173 Query: 180 DTSNGAGSLTLPYLLRELGCKVVSVNAHPDGHFPARNPEPNEENLKGFMEIVKALGADFG 239 D GA S T+PY+LR LGC+V+++N+ PDG FP R+PEP ENL ME V++ GAD G Sbjct: 174 DCGCGAASYTMPYILRRLGCQVIALNSQPDGFFPGRDPEPVPENLSELMETVRSTGADLG 233 Query: 240 VAQDGDADRAVFIDENGRFIQGDKTFALVADAVLRENGGGLLVTTIATSNLLDDIAKRNG 299 +A DGDADR + IDE G F+ GDKTFALV +L+E GGG++VTT+ATS+ + DIA N Sbjct: 234 IAHDGDADRTICIDERGEFVLGDKTFALVEKRMLQEKGGGIIVTTVATSSAIYDIASENN 293 Query: 300 AKVMRTKVGDLIVARALLENNGTIGGEENGGVIFPDFVLGRDGAMTTAKIVEIFAKSGKK 359 +V+ T VGDL+VAR L E +G GGEENGG+IFPDFV GRD A+T A I+EI A + Sbjct: 294 GEVITTAVGDLLVARKLKETDGLFGGEENGGLIFPDFVYGRDAALTAATILEIMAHEDRP 353 Query: 360 FSELIDELPKYYQFKTK----RHVEGDRKAIVAKVAELAEKKGYK-IDTTDGTKIIFDDG 414 S L+ ELP YY K K ++GD +V+K+ LA+++G + IDTTDG KI + G Sbjct: 354 LSALVSELPAYYSSKRKIECPDEIKGDVMDLVSKM--LADEEGVRDIDTTDGVKIFSEAG 411 Query: 415 WVLVRASGTEPIIRIFSEAKSEEKAREYLELGIKLLEEALK 455 WV++R SGTEPI R F+E++++E+A E GI L+E A++ Sbjct: 412 WVIIRPSGTEPIFRCFAESETQEQADEMARWGISLVERAME 452 Lambda K H 0.317 0.139 0.396 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: 602 Number of extensions: 28 Number of successful extensions: 5 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: 456 Length of database: 455 Length adjustment: 33 Effective length of query: 423 Effective length of database: 422 Effective search space: 178506 Effective search space used: 178506 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Sep 24 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