Align phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) (EC 5.4.2.2) (characterized)
to candidate WP_012967600.1 KVAR_RS07890 phosphomannomutase
Query= BRENDA::Q8PGN7 (450 letters) >NCBI__GCF_000025465.1:WP_012967600.1 Length = 460 Score = 512 bits (1318), Expect = e-149 Identities = 258/453 (56%), Positives = 323/453 (71%), Gaps = 8/453 (1%) Query: 5 LPAFKAYDIRGRVPDELNEDLARRIGVALAAQLDQGPVVLGHDVRLASPALQEALSAGLR 64 L FKAYDIRG + +ELNED+A RIG A L G +V+G DVRL S +L+ AL+ GL Sbjct: 4 LTCFKAYDIRGELGEELNEDIAYRIGRAYGEFLKPGKIVVGGDVRLTSESLKLALARGLM 63 Query: 65 ASGRDVIDIGLCGTEEVYFQTDYLKAAGGVMVTASHNPMDYNGMKLVREQARPISSDTGL 124 +G DV+DIGL GTEE+YF T +L GG+ VTASHNPM+YNGMKLVRE A+PIS DTGL Sbjct: 64 DAGTDVLDIGLSGTEEIYFATFHLGVDGGIEVTASHNPMNYNGMKLVRENAKPISGDTGL 123 Query: 125 FAIRDTVAADTAAPGEPTASEQSRTDKTA--YLEHLLSYVDRSTL-KPLKLVVNAGNGGA 181 I+ + P +P R Y++HL+ YVD + +PLKLVVN+GNG A Sbjct: 124 RDIQRLAEENQFPPVDPARRGTLRQISVLKEYVDHLMGYVDLANFTRPLKLVVNSGNGAA 183 Query: 182 GLIVD-----LLAPHLPFEFVRVFHEPDGNFPNGIPNPLLPENRDATAKAVKDNGADFGI 236 G ++D A P F++V H+PDG+FPNGIPNPLLPE R TA AV+ + AD GI Sbjct: 184 GHVIDEVEKRFAAAGAPVTFIKVHHQPDGHFPNGIPNPLLPECRQDTADAVRAHQADMGI 243 Query: 237 AWDGDFDRCFFFDHTGRFIEGYYLVGLLAQAILAKQPGGKVVHDPRLTWNTVEQVEEAGG 296 A+DGDFDRCF FD FIEGYY+VGLLA+A L KQPG K++HDPRLTWNTV+ V +GG Sbjct: 244 AFDGDFDRCFLFDDEASFIEGYYIVGLLAEAFLQKQPGAKIIHDPRLTWNTVDIVTRSGG 303 Query: 297 IPVLCKSGHAFIKEKMRSENAVYGGEMSAHHYFREFAYADSGMIPWLLIAELVSQSGRSL 356 PV+ K+GHAFIKE+MR E+A+YGGEMSAHHYFR+FAY DSGMIPWLL+AEL+ SL Sbjct: 304 QPVMSKTGHAFIKERMRQEDAIYGGEMSAHHYFRDFAYCDSGMIPWLLVAELLCLKNSSL 363 Query: 357 ADLVEARMQKFPCSGEINFKVADAKASVARVMEHYASLSPELDYTDGISADFGQWRFNLR 416 LV R FP SGEIN K+ +A ++AR+ Y + +D TDGIS ++ +WRFNLR Sbjct: 364 KSLVADRQAAFPASGEINRKLGNAAEAIARIRAQYEPAAAHIDTTDGISIEYPEWRFNLR 423 Query: 417 SSNTEPLLRLNVETRGDAALLETRTQEISNLLR 449 +SNTEP++RLNVE+R D AL+ +T E+ NLL+ Sbjct: 424 TSNTEPVVRLNVESRADTALMNEKTAELLNLLK 456 Lambda K H 0.319 0.136 0.404 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: 634 Number of extensions: 18 Number of successful extensions: 4 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: 450 Length of database: 460 Length adjustment: 33 Effective length of query: 417 Effective length of database: 427 Effective search space: 178059 Effective search space used: 178059 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 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