Align Phosphoglucomutase/phosphomannomutase; PGM/PMM; EC 5.4.2.2; EC 5.4.2.8 (characterized)
to candidate WP_048186807.1 METBO_RS12185 phosphoglucosamine mutase
Query= SwissProt::Q68BJ6 (456 letters) >NCBI__GCF_000191585.1:WP_048186807.1 Length = 448 Score = 467 bits (1202), Expect = e-136 Identities = 239/457 (52%), Positives = 321/457 (70%), Gaps = 11/457 (2%) Query: 1 MGKLFGTFGVRGIANEEITPEFALKIGMAFGTLLKREGRERPLVVVGRDTRVSGEMLKDA 60 M +LFGTFGVR IAN+E+TPEFA ++ A+G+++K V VG D R S EM+K A Sbjct: 1 MKRLFGTFGVRRIANQELTPEFASRLAAAYGSIVKGT------VAVGGDPRTSTEMIKHA 54 Query: 61 LISGLLSTGCDVIDVGIAPTPAIQWATNHFNADGGAVITASHNPPEYNGIKLLEPNGMGL 120 +I+GLLS GC VID+GI PTPA+Q+A ++ DGG +ITASHNPP+YNG+K ++ +G+G+ Sbjct: 55 VIAGLLSAGCKVIDLGILPTPAVQFAVRNYY-DGGVMITASHNPPKYNGLKFVDSDGIGI 113 Query: 121 KKEREAIVEELFFSEDFHRAKWNEIGELRKED-IIKPYIEAIKNRVDVEAIKKRRPFVVV 179 +++ E +E +FF E+ R WN I E K I++ YIE + RVD +AIK+ V+V Sbjct: 114 EEKWEQKIEAMFFDEEPVRVSWNAIEESTKNHGIVEEYIENVIERVDSQAIKEANLKVIV 173 Query: 180 DTSNGAGSLTLPYLLRELGCKVVSVNAHPDGHFPARNPEPNEENLKGFMEIVKALGADFG 239 D +GA T PYLLR LGC+V ++N PDG FP RNPEP ENL+ +VKA GAD G Sbjct: 174 DCGSGAACFTTPYLLRRLGCQVTTMNCQPDGFFPGRNPEPTSENLEELKNVVKATGADLG 233 Query: 240 VAQDGDADRAVFIDENGRFIQGDKTFALVADAVLRENGGGLLVTTIATSNLLDDIAKRNG 299 +A DGDADR + IDENG F+ GDKTFALV A+L+ENGGG +VTT+ATS + DIA+ Sbjct: 234 IAHDGDADRTICIDENGEFVFGDKTFALVEKAMLKENGGGTIVTTVATSAAIYDIAEEYN 293 Query: 300 AKVMRTKVGDLIVARALLENNGTIGGEENGGVIFPDFVLGRDGAMTTAKIVEIFAKSGKK 359 +V+ T+VGDL+VAR L + NG GGEENGG+IFP+FV GRD A++TAKIVEI AK K Sbjct: 294 GEVIATRVGDLLVARELKDQNGLFGGEENGGLIFPEFVYGRDAALSTAKIVEIMAKEAKP 353 Query: 360 FSELIDELPKYYQFKTKRHVEGDRKA-IVAKVAELAEKKGYKIDTTDGTKIIFDDGWVLV 418 SELI ELPKY K K +K+ ++ ++ E +++DT DG KI+ + GWV++ Sbjct: 354 LSELIQELPKYCSAKLKVECADHQKSTVMDRIVEAT--SDHEVDTKDGVKILTEKGWVII 411 Query: 419 RASGTEPIIRIFSEAKSEEKAREYLELGIKLLEEALK 455 R SGTEPI R F+EA++EE A + + GI L+EE ++ Sbjct: 412 RPSGTEPIFRCFAEAQTEEDALKMAKWGISLVEENME 448 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: 650 Number of extensions: 22 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: 448 Length adjustment: 33 Effective length of query: 423 Effective length of database: 415 Effective search space: 175545 Effective search space used: 175545 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