Align Phosphoglucomutase/phosphomannomutase; PGM/PMM; EC 5.4.2.2; EC 5.4.2.8 (characterized)
to candidate WP_010877198.1 MTH_RS07615 phosphoglucosamine mutase
Query= SwissProt::Q68BJ6 (456 letters) >NCBI__GCF_000008645.1:WP_010877198.1 Length = 449 Score = 333 bits (853), Expect = 9e-96 Identities = 184/443 (41%), Positives = 268/443 (60%), Gaps = 20/443 (4%) Query: 3 KLFGTFGVRGIANEEITPEFALKIGMAFGTLLKREGRERPLVVVGRDTRVSGEMLKDALI 62 +LFGT G+RG E++T E + A T L +G VVVG DTR S ++L++ALI Sbjct: 7 RLFGTSGIRGRFGEKVTLELTAEHRKALATHLGGDGE----VVVGYDTRTSSQLLENALI 62 Query: 63 SGLLSTGCDVIDVGIAPTPAIQWATNHFNADGGAVITASHNPPEYNGIKLLEPNGMGLKK 122 +G++ GCDV +G+ PTP + +A + A G +ITASHNP YNGIKL P+GM + Sbjct: 63 AGIVECGCDVTRLGMVPTPLVGYAASRLGAAAGVMITASHNPAPYNGIKLWNPDGMAYRP 122 Query: 123 EREAIVEELFFSEDFHRAKWNEIGELRKEDIIKPYIEAIKNRVDVEAIKKRRPFVVVDTS 182 +E ++E + S DF R W+E+G + D+ Y+ A+ V+++ K VV+D+ Sbjct: 123 SQERVIESIIHSRDFKRKAWDELGSITTVDMRDDYVRAVLETVEIKKPLK----VVIDSG 178 Query: 183 NGAGSLTLPYLLRELGCKVVSVNAHPDGHFPARNPEPNEENLKGFMEIVKALGADFGVAQ 242 GA S P + R+ GC+V+++N+ PDG FP R+PEP ENL ME V++ GAD G+A Sbjct: 179 CGAASHLSPLIFRKAGCRVITLNSQPDGFFPGRDPEPVPENLSELMETVRSTGADLGIAH 238 Query: 243 DGDADRAVFIDENGRFIQGDKTFALVADAVLRENGGGLLVTTIATSNLLDDIAKRNGAKV 302 DGDADR V ID+ GRF DK AL+A + GG ++TT+ S +D+ G +V Sbjct: 239 DGDADRMVAIDDQGRFASFDKLLALMAREI-----GGKIITTVDASLCVDECLGDRG-EV 292 Query: 303 MRTKVGDLIVARALLENNGTIGGEENGGVIFPDFVLGRDGAMTTAKIVEIFAKSGKKFSE 362 +RT+VGD+ VA + E GGE +G + PDF + DG ++ ++ E+ + G SE Sbjct: 293 IRTRVGDVHVANTIAEEGARFGGEPSGTWLHPDFCMCPDGILSALRVAELVSARG-PLSE 351 Query: 363 LIDELPKYYQFKTKRHVEGDRKAIVAK--VAELAEK--KGYKIDTTDGTKIIFDDG-WVL 417 L++E+P Y + K ++K I+ + AEL+++ + I+T DG +I DDG WVL Sbjct: 352 LLEEVPSYPNIRDKVPCPDEKKDIIMERVAAELSDQFSETSDINTIDGVRISLDDGSWVL 411 Query: 418 VRASGTEPIIRIFSEAKSEEKAR 440 VR SGTEP IRI E K+EEKAR Sbjct: 412 VRPSGTEPYIRITLEGKTEEKAR 434 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: 530 Number of extensions: 32 Number of successful extensions: 7 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: 449 Length adjustment: 33 Effective length of query: 423 Effective length of database: 416 Effective search space: 175968 Effective search space used: 175968 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