Align Phosphoglucosamine/phosphogalactosamine mutase; PGlcNM; EC 5.4.2.10; EC 5.4.2.13 (characterized)
to candidate WP_072906534.1 BUB13_RS05520 phosphoglucosamine mutase
Query= SwissProt::Q976E4 (455 letters) >NCBI__GCF_900142125.1:WP_072906534.1 Length = 452 Score = 169 bits (427), Expect = 2e-46 Identities = 135/453 (29%), Positives = 219/453 (48%), Gaps = 41/453 (9%) Query: 3 KLFGTDGVRGIVNKE-LTPELVLKLSKAIGTFFGKNS----KILVGRDVRAGGDMLVKIV 57 KLFGTDGVRG+ N E +T E+ ++L +A F K+ ++++G+D R G M+ + Sbjct: 4 KLFGTDGVRGVANIEPMTTEMAMQLGRAAAYVFKKDKNRRHRVVIGKDTRLSGYMIENAL 63 Query: 58 EGGLLSVGVEVYDGGMAPTPALQYAVKTLGYDGGVVITASHNPAPYNGIKVVDKDGIEIR 117 G+ S+GV+V G PTP + + ++ D GVVI+ASHN NGIK DG ++ Sbjct: 64 VAGICSMGVDVLLVGPLPTPGIAFITSSMRADAGVVISASHNAYQDNGIKFFSADGFKLP 123 Query: 118 REKENEIEDLFFTERFNTIE-WSSLTTEVKREDRVISTYV----NGILSHVDIEKIKKKN 172 E E EIEDL + + + + + R D I Y+ N +D++ + Sbjct: 124 DELELEIEDLILNHKLDDLRPVADEVGKAYRIDDAIGRYIVYLKNTFPGDLDLQGL---- 179 Query: 173 YKVLIDPANSVGALSTPLVARALGCKIYTI----NG-NLDPLFSARQPEPTFDSLKETAE 227 ++++D A+ G P V LG ++ TI NG N++ + PE AE Sbjct: 180 -RIVLDCAHGAGYKVAPAVLEELGAEVITIGVSPNGVNINEGCGSLHPE-------VMAE 231 Query: 228 VVKTLKVDLGVAHDGDADRAIFIDSEGRVQWGDRSGTLLSYWASVKNPKAIKKIVTAVSS 287 V+ + DLG+A DGDADR IF+D +G GD + + +V V S Sbjct: 232 KVREYRADLGIALDGDADRVIFVDEKGIEVDGDHIMAICGTEMIKQGDLKENTVVATVMS 291 Query: 288 SSLVEEYLSKYNIQVDWTKVGSVDIAHKVADENALAGFEENGGFMYPPHQYVRDGAMSFA 347 + ++ + K +V T VG + ++ G E++G ++ H DG +S Sbjct: 292 NMGLDIAMDKVGGKVVRTGVGDRYVVEEMRKSGYNLGGEQSGHMIFLDHITTGDGILSAL 351 Query: 348 LMLELLANENVSSAELFDRLPKYYLVKTKVDLKPGLMVEEIYKKILEVYSTSSVKAITID 407 +L ++ +E L K + L P ++V +K E+ + +K + ID Sbjct: 352 QVLAIIQRSGKRLSE---------LAKVMISL-PQILVNVRVRKKAELADIAPIKEV-ID 400 Query: 408 GV--KIIGKDFWFLVRKSGTEPIIRIMAEAKDE 438 V ++ GK LVR SGTEP++R+M E +D+ Sbjct: 401 EVEAELAGKG-RVLVRYSGTEPLLRVMIEGEDK 432 Lambda K H 0.316 0.136 0.384 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: 454 Number of extensions: 17 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: 455 Length of database: 452 Length adjustment: 33 Effective length of query: 422 Effective length of database: 419 Effective search space: 176818 Effective search space used: 176818 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 (21.6 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