Align Phosphoglucomutase/phosphomannomutase; PGM/PMM; EC 5.4.2.2; EC 5.4.2.8 (characterized)
to candidate WP_028490374.1 Q394_RS0117455 phosphoglucosamine mutase
Query= SwissProt::Q68BJ6 (456 letters) >NCBI__GCF_000621325.1:WP_028490374.1 Length = 444 Score = 219 bits (558), Expect = 1e-61 Identities = 151/457 (33%), Positives = 236/457 (51%), Gaps = 41/457 (8%) Query: 3 KLFGTFGVRG-IANEEITPEFALKIGMAFGTLLKREGRERPLVVVGRDTRVSGEMLKDAL 61 K FGT G+RG I +TP+F LK+G A G +L G LV++G+DTR+SG ML+ AL Sbjct: 4 KYFGTDGIRGKIGQYPMTPDFVLKLGWAAGKVLASSGNS--LVLIGKDTRISGYMLESAL 61 Query: 62 ISGLLSTGCDVIDVGIAPTPAIQWATNHFNADGGAVITASHNPPEYNGIKLLEPNGMGLK 121 +GL++ G D+ +G PTPA+ + T F A G VI+ASHNP + NG+K +G L Sbjct: 62 QAGLVAAGVDIRLLGPMPTPAVAYLTRAFRASAGIVISASHNPYDDNGLKFFSGDGTKLP 121 Query: 122 KEREAIVEELFFSEDFHRAKWNEIGE-LRKEDIIKPYIE----AIKNRVDVEAIKKRRPF 176 E +E + +F +E+G+ +R +D YIE A+ NRV ++ ++ Sbjct: 122 DTVEEEIER-WLDMEFKTVSSDELGKVVRAKDAAGRYIEFCKRALPNRVSLKGVR----- 175 Query: 177 VVVDTSNGAGSLTLPYLLRELGCKVVSVNAHPDGHFPARNPEPNEENLKGFMEIVKALGA 236 +VVD +NGA P + ELG +V+++ HPDG N ++ G E V A Sbjct: 176 IVVDCANGATYHVAPEVFSELGAEVIAIGNHPDG--ININEACGATHVDGLCEAVLRYRA 233 Query: 237 DFGVAQDGDADRAVFIDENGRFIQGDKTFALVADAVLRENGGGLL----VTTIATSNLLD 292 D G+A DGD DR + +DE+G+ + GD+ A++A +G G L V T+ ++ L+ Sbjct: 234 DVGIALDGDGDRLIMVDEHGQTVDGDEILAIIAH---HSHGEGKLQGGVVGTLMSNLGLE 290 Query: 293 DIAKRNGAKVMRTKVGDLIVARALLENNGTIGGEENGGVIFPDFVLGRDGAMTTAKIVEI 352 +R G R VGD V + +++ +GGE +G +I +F+ DG + +++ Sbjct: 291 KSIQRLGVPFYRANVGDRYVIEQMNQHDCNLGGESSGHIIVSNFITTGDGIVAALQVLRA 350 Query: 353 FAKSGKKFSELIDELPKYYQ----FKTKRHVEGDRK-AIVAKVAELAEKKGYKIDTTDGT 407 + K EL + KY Q + + + D AI V ++ E+ G + Sbjct: 351 MRLTNKPLHELKKVMTKYPQTLINVRIREKINLDESVAIQDAVRQVEEQLGNR------- 403 Query: 408 KIIFDDGWVLVRASGTEPIIRIFSEAKSEEKAREYLE 444 G VL+RASGTEP+IR+ E + + E Sbjct: 404 ------GRVLLRASGTEPLIRVMVEGEDAHETAALAE 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: 495 Number of extensions: 32 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