Align phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) (EC 5.4.2.2) (characterized)
to candidate WP_092056345.1 BQ4888_RS08380 phosphomannomutase
Query= BRENDA::Q8PGN7 (450 letters) >NCBI__GCF_900111775.1:WP_092056345.1 Length = 450 Score = 583 bits (1502), Expect = e-171 Identities = 282/446 (63%), Positives = 342/446 (76%) Query: 3 MTLPAFKAYDIRGRVPDELNEDLARRIGVALAAQLDQGPVVLGHDVRLASPALQEALSAG 62 M L FKAYDIRGR+PDELN+++A RIG A A L G V++G DVRL+S L AL+ G Sbjct: 1 MQLNCFKAYDIRGRIPDELNDEVAYRIGRAYAQFLQPGKVIVGRDVRLSSAGLCAALARG 60 Query: 63 LRASGRDVIDIGLCGTEEVYFQTDYLKAAGGVMVTASHNPMDYNGMKLVREQARPISSDT 122 L A G DVIDIGLCGTEEVYF T Y +A GG+MVTASHNPMDYNGMKLVRE +RPIS D+ Sbjct: 61 LTAGGADVIDIGLCGTEEVYFATFYSRADGGIMVTASHNPMDYNGMKLVREGSRPISGDS 120 Query: 123 GLFAIRDTVAADTAAPGEPTASEQSRTDKTAYLEHLLSYVDRSTLKPLKLVVNAGNGGAG 182 GL IR P E T + ++ K Y+ HLL Y+D + L+PLK+VVNAGNG AG Sbjct: 121 GLHEIRRLAEKGDFLPAERTGTIETTDMKVPYIRHLLGYIDATRLRPLKIVVNAGNGCAG 180 Query: 183 LIVDLLAPHLPFEFVRVFHEPDGNFPNGIPNPLLPENRDATAKAVKDNGADFGIAWDGDF 242 ++D L LPFE ++ HEPDG FPNGIPNPLLPENRD T++AV ++GA GIAWDGDF Sbjct: 181 PVLDFLERQLPFEVFKICHEPDGTFPNGIPNPLLPENRDITSQAVLEHGAALGIAWDGDF 240 Query: 243 DRCFFFDHTGRFIEGYYLVGLLAQAILAKQPGGKVVHDPRLTWNTVEQVEEAGGIPVLCK 302 DRCF FD GRFIEGYY+VGLLA+A LA++PG K++HDPRLTWNT++ V AGG+PV+ K Sbjct: 241 DRCFLFDEQGRFIEGYYIVGLLAEAFLAREPGAKIIHDPRLTWNTIDMVHAAGGVPVMSK 300 Query: 303 SGHAFIKEKMRSENAVYGGEMSAHHYFREFAYADSGMIPWLLIAELVSQSGRSLADLVEA 362 +GHAFIKE+MR E+A YGGEMSAHHYFR+FAY DSGMIPWLL+ EL+ + + L++LV Sbjct: 301 TGHAFIKERMRLEDAAYGGEMSAHHYFRDFAYCDSGMIPWLLVLELMCRKRKLLSELVGE 360 Query: 363 RMQKFPCSGEINFKVADAKASVARVMEHYASLSPELDYTDGISADFGQWRFNLRSSNTEP 422 RM KFP SGEIN + D + ++ARV YA L P +D TDG+S +F WRFNLRSSNTEP Sbjct: 361 RMAKFPASGEINRVLDDPQGALARVEAAYAPLGPAIDRTDGLSMEFADWRFNLRSSNTEP 420 Query: 423 LLRLNVETRGDAALLETRTQEISNLL 448 +LRLNVE+RGDAAL+E +T E+ LL Sbjct: 421 VLRLNVESRGDAALMEAKTAELLALL 446 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: 627 Number of extensions: 20 Number of successful extensions: 1 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: 450 Length adjustment: 33 Effective length of query: 417 Effective length of database: 417 Effective search space: 173889 Effective search space used: 173889 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