Align phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) (EC 5.4.2.2) (characterized)
to candidate WP_051939761.1 BS73_RS09785 phosphomannomutase/phosphoglucomutase
Query= BRENDA::Q8PGN7 (450 letters) >NCBI__GCF_000744815.1:WP_051939761.1 Length = 465 Score = 326 bits (836), Expect = 8e-94 Identities = 196/449 (43%), Positives = 252/449 (56%), Gaps = 10/449 (2%) Query: 9 KAYDIRGRVPDELNEDLARRIGVALAAQLDQGPVVLGHDVRLASPALQEALSAGLRASGR 68 KAYDIRG VPD+ +E A G A G +V GHD+R +SP L A + G A G Sbjct: 20 KAYDIRGVVPDDWDEATAELFGAAFVRVTGAGAIVTGHDMRPSSPGLAAAFARGATAQGA 79 Query: 69 DVIDIGLCGTEEVYFQTDYLKAAGGVMVTASHNPMDYNGMKLVREQARPISSDTGLFAIR 128 DV +IGLC T+++YF + L AG M TASHNP YNG+KL R A P+ DTGL AIR Sbjct: 80 DVTEIGLCSTDQLYFASGSLGLAGA-MFTASHNPARYNGIKLCRAGAEPVGQDTGLAAIR 138 Query: 129 DTVAA--DTAAPGEPTASEQSRTDKTA----YLEHLLSYVDRSTLKPLKLVVNAGNGGAG 182 V D EP A + RT Y HL S VD ++PLK+VV+AGNG G Sbjct: 139 ALVEEWLDAGRGPEPAAGPRGRTTSRETLADYAAHLRSLVDLGAIRPLKVVVDAGNGMGG 198 Query: 183 LIVDLLAPHLPFEFVRVFHEPDGNFPNGIPNPLLPENRDATAKAVKDNGADFGIAWDGDF 242 V + LP V ++ E DG FP+ NPL P N V+ GAD G+A+DGD Sbjct: 199 HTVPTVLAGLPLTVVPMYFELDGTFPHHEANPLDPANIVDLRARVRAEGADLGLAFDGDA 258 Query: 243 DRCFFFDHTGRFIEGYYLVGLLAQAILAKQPGGKVVHDPRLTWNTVEQVEEAGGIPVLCK 302 DRCF D G + + L+A LA+ PG V+H+ + E V EAGGIPV + Sbjct: 259 DRCFVVDERGEPVSPSAVTALVAARELAEHPGAAVIHNLITSRTVPEVVREAGGIPVRTR 318 Query: 303 SGHAFIKEKMRSENAVYGGEMSAHHYFREFAYADSGMIPWLLIAELVSQSGRSLADLVEA 362 GH+FIK +M AV+GGE SAH+YFR+F AD+GM+ L + + + R L++L A Sbjct: 319 VGHSFIKAEMARAGAVFGGEHSAHYYFRDFWNADTGMLAALHVLAALGEQPRPLSELT-A 377 Query: 363 RMQKFPCSGEINFKVADAKASVARVMEHYASL-SPELDYTDGISADFGQWRFNLRSSNTE 421 R +++ SGEIN VAD +A V ++ LD DG++ W FNLR SNTE Sbjct: 378 RYERYAASGEINSTVADQAERIAAVRAAWSGRPGVTLDELDGLTVAGRDWWFNLRPSNTE 437 Query: 422 PLLRLNVETRGDAALLETRTQEISNLLRG 450 PLLRLNVE R A+ R E+ L+RG Sbjct: 438 PLLRLNVEARDRPAMAALR-DEVLALVRG 465 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: 585 Number of extensions: 32 Number of successful extensions: 5 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: 465 Length adjustment: 33 Effective length of query: 417 Effective length of database: 432 Effective search space: 180144 Effective search space used: 180144 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