Align phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) (EC 5.4.2.2) (characterized)
to candidate WP_089299712.1 CHB84_RS01840 phosphomannomutase/phosphoglucomutase
Query= BRENDA::Q8PGN7 (450 letters) >NCBI__GCF_900188115.1:WP_089299712.1 Length = 452 Score = 303 bits (777), Expect = 6e-87 Identities = 186/451 (41%), Positives = 258/451 (57%), Gaps = 16/451 (3%) Query: 9 KAYDIRGRVPDELNEDLARRIGVALAAQL---DQGPVVLGHDVRLASPALQEALSAGLRA 65 KAYDIRG V ++L+ DL + G A A + V +GHD+R +SP L A + G+ + Sbjct: 9 KAYDIRGVVGEQLDADLVAQFGGAFARLVLAEGASAVAVGHDMRDSSPGLAGAFARGVTS 68 Query: 66 SGRDVIDIGLCGTEEVYFQTDYLKAAGGVMVTASHNPMDYNGMKLVREQARPISSDTGLF 125 G DV+ IGL T+++YF + L G M TASHNP +YNG+KL R A P+ ++GL Sbjct: 69 QGVDVVSIGLASTDQLYFASGSLNLPGA-MFTASHNPAEYNGIKLCRAGAAPVGQESGLA 127 Query: 126 AIRDTV---AADTAAPGEPTASEQSRTDKTAYLEHLLSYVDRSTLKPLKLVVNAGNGGAG 182 IR+ V + G D A+L HL VD S +PL++VV+AGNG AG Sbjct: 128 EIREVVEQGVPEFVGAGGTVGERDVLGDYAAHLRHL---VDLSGSRPLRIVVDAGNGMAG 184 Query: 183 LIVDLLAPHLPFEFVRVFHEPDGNFPNGIPNPLLPENRDATAKAVKDNGADFGIAWDGDF 242 V + LP E V ++ E DG+FPN NPL P N AV++ GAD G+A+DGD Sbjct: 185 HTVPTVFDGLPIEIVPMYFELDGSFPNHEANPLDPANLVDLQHAVREAGADAGLAFDGDA 244 Query: 243 DRCFFFDHTGRFIEGYYLVGLLAQAILAKQPGGKVVHDPRLTWNTVEQVEEAGGIPVLCK 302 DRC+ D G + + L+A LAK+PG ++H+ + E V E GGIPV + Sbjct: 245 DRCYVIDERGEPVPPSAITALVAVRALAKEPGAAIIHNLITSRAVPEIVAEHGGIPVRTR 304 Query: 303 SGHAFIKEKMRSENAVYGGEMSAHHYFREFAYADSGMIPWLLIAELVSQSGRSLADLVEA 362 GH+FIK+KM +A++GGE SAH+YFR+F AD+GM+ L + + L+ L Sbjct: 305 VGHSFIKQKMAETDAIFGGEHSAHYYFRDFWRADTGMLAALHVLAALGAHDGPLSTLT-G 363 Query: 363 RMQKFPCSGEINFKVADAKASVARVMEHYASL-SPELDYTDGISADF--GQWRFNLRSSN 419 R Q++ SGEIN V D A V E +A+ +D DG++ + G W FNLR+SN Sbjct: 364 RYQRYVASGEINSTVDDQHARQRAVREAFAARDGVGIDDLDGLTVELAGGAW-FNLRASN 422 Query: 420 TEPLLRLNVETRGDAALLETRTQEISNLLRG 450 TEPLLRLNVE + A+ E T E+ ++RG Sbjct: 423 TEPLLRLNVEAENEVAMREL-TDEVLAIIRG 452 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: 532 Number of extensions: 28 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: 452 Length adjustment: 33 Effective length of query: 417 Effective length of database: 419 Effective search space: 174723 Effective search space used: 174723 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