Align Phosphoglucomutase/phosphomannomutase; PGM/PMM; EC 5.4.2.2; EC 5.4.2.8 (characterized)
to candidate WP_012971459.1 ALVIN_RS11305 phosphoglucosamine mutase
Query= SwissProt::Q68BJ6 (456 letters) >NCBI__GCF_000025485.1:WP_012971459.1 Length = 444 Score = 204 bits (520), Expect = 4e-57 Identities = 143/447 (31%), Positives = 221/447 (49%), Gaps = 18/447 (4%) Query: 1 MGKLFGTFGVRG-IANEEITPEFALKIGMAFGTLLKREGRERPLVVVGRDTRVSGEMLKD 59 M + FGT G+RG + + ITP+F LK+G A G +L G R +++G+DTR+SG M + Sbjct: 1 MRQYFGTDGIRGRVGSGNITPDFVLKLGWAAGRVL---GNGRGKILIGKDTRISGYMFES 57 Query: 60 ALISGLLSTGCDVIDVGIAPTPAIQWATNHFNADGGAVITASHNPPEYNGIKLLEPNGMG 119 AL +GL++ G D+ +G TP + + T F A G VITASHNP + NGIK NG Sbjct: 58 ALEAGLVAAGVDIRLLGPMTTPGVAYLTRTFRASAGIVITASHNPFDDNGIKFFSANGDK 117 Query: 120 LKKEREAIVEELFFSEDFHRAKWNEIGELRK-EDIIKPYIEAIKNRVDVEAIKKRRPFVV 178 L E E + E + + + +G++++ +D YIE K+ + ++ R +V Sbjct: 118 LPDEVELAI-EAELDQPLRTVESSALGKVKRIDDANGRYIEFCKSTIPA-SMNFRGLKLV 175 Query: 179 VDTSNGAGSLTLPYLLRELGCKVVSVNAHPDGHFPARNPEPNEENLKGFMEIVKALGADF 238 VD +NGA T P++ ELG VV + PDG N E V GAD Sbjct: 176 VDCANGATYNTAPFVFEELGANVVRLGNEPDGF--NINHGVGSTQPGALREAVVREGADL 233 Query: 239 GVAQDGDADRAVFIDENGRFIQGDKTFALVADAVLRENG-GGLLVTTIATSNLLDDIAKR 297 G+A DGD DR + +D G I GD+ L+A + L G +V T+ ++ + KR Sbjct: 234 GIAFDGDGDRVLMVDSRGHLIDGDQLLYLIAKSRLLTGAMRGEVVGTLMSNLGFEHALKR 293 Query: 298 NGAKVMRTKVGDLIVARALLENNGTIGGEENGGVIFPDFVLGRDGAMTTAKIVEIFAKSG 357 G RTKVGD + L ++G +GGE +G +I D DG ++ +++ + G Sbjct: 294 LGIGFARTKVGDRYIMERLKASDGILGGEPSGHIICRDRTTTGDGIVSALQVLAALDRLG 353 Query: 358 KKFSELIDELPKYYQFKTKRHVEGDRKAIVAKVAELAEKKGYKIDTTDGTKIIFDDGWVL 417 + ++ E+ Y Q +V D+ V + E+ + + G VL Sbjct: 354 TRLDDIGTEVELYPQVLV--NVRLDQPRDVLSLPEVQDA------VASAESELAGRGRVL 405 Query: 418 VRASGTEPIIRIFSEAKSEEKAREYLE 444 +R SGTEP++R+ E + E Sbjct: 406 LRPSGTEPLVRVMVEGSDRPQVERLAE 432 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: 542 Number of extensions: 28 Number of successful extensions: 6 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: 444 Length adjustment: 33 Effective length of query: 423 Effective length of database: 411 Effective search space: 173853 Effective search space used: 173853 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