Align phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) (EC 5.4.2.2); phosphomannomutase (EC 5.4.2.8) (characterized)
to candidate WP_011372256.1 SUDEN_RS03250 phosphomannomutase/phosphoglucomutase
Query= BRENDA::M1T754 (460 letters) >NCBI__GCF_000012965.1:WP_011372256.1 Length = 452 Score = 298 bits (763), Expect = 2e-85 Identities = 177/439 (40%), Positives = 250/439 (56%), Gaps = 26/439 (5%) Query: 11 REYDIRGIVGKTLNPADATAIGRGFGTLLRRAGGTRAAVGYDGRHSSPLLEAALVQGLIA 70 REYDIRGI + LN T IG + ++ G AVGYD R SP+L LV GL A Sbjct: 5 REYDIRGIYEQELNEQSVTRIGYALASKIK---GEYVAVGYDARDHSPILFEYLVHGLNA 61 Query: 71 SGIDVVRVGLGPTPMLYYAEAVLEVDG-----GIMITGSHNPPDYNGFKMVFQHRPFFGE 125 G V+ +G+ PTP+ Y+ E DG +MITGSHNP +YNGFK+ PFFGE Sbjct: 62 GGKKVLDIGMVPTPVNYFCN-YNEFDGILASASVMITGSHNPSEYNGFKITIDKAPFFGE 120 Query: 126 DILKIGTMAAE-GDWEEGEGTVTNADIMDMYVDRLIAGYQ---GGAFKVAWDAGNGAAGP 181 DI +G + + VT D + YVD L++ +Q G ++ +D GNG AG Sbjct: 121 DIYALGRECETIKSIPKVKREVTKIDALSRYVDFLVSEFQHLKGMPTRIVYDCGNGVAGI 180 Query: 182 VIEKLVKFLPGEHHLLYTDVDGDFPNHHPDPTEEKNLVDLKALVAEKGLDFGIGFDGDGD 241 V E++ L LY + DG FPNHHPDP++E NL D+K L+A +G D +DGD D Sbjct: 181 VTERIFSALELHVKGLYVNPDGTFPNHHPDPSDEHNLEDIKKLLATEG-DIAFAYDGDAD 239 Query: 242 RIGAIDGKGRVVWGDQLLGILAEPVLKAVPGGTIIADVKTSQALYDRVAELGGKPLMWKT 301 RI + K + GD + + + + K T++ +VK SQ +YD + + G K +M+KT Sbjct: 240 RIAVLTHKNNIK-GDMMALLYSLKMDKP----TVVGEVKCSQVMYDELEKRGAKAIMYKT 294 Query: 302 GHSLIKAKMKEVDSPLGGEMSGHIFFAWDYYGFDDAIYAAVRLMGAVRHSGKSLTELKDA 361 GHS +K KM+E+++ L E+SGH+FF Y+G+DDAIYA +R++ V H G L Sbjct: 295 GHSNLKVKMQEINADLACEVSGHVFFKNRYFGYDDAIYATLRMLELV-HDGIDLDAELAK 353 Query: 362 MPAMVNTPEMRFQVDESRKFAVIEEVLQRLEADGA------DINRTDGARVNTPDGWWLL 415 +P + +T E++ + ES KF +I+ V + L+ A +I DG R+N GW L+ Sbjct: 354 LPQVFSTEEIKVKTTESEKFKIIDRVKELLKTPPAHFPKIKNIIDVDGVRINFEHGWGLV 413 Query: 416 RASNTQDVLVARAEAKDEA 434 RASNT VLV R E+ +A Sbjct: 414 RASNTTPVLVTRFESTSQA 432 Lambda K H 0.318 0.139 0.417 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: 492 Number of extensions: 18 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: 460 Length of database: 452 Length adjustment: 33 Effective length of query: 427 Effective length of database: 419 Effective search space: 178913 Effective search space used: 178913 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 (21.7 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