Align Phosphoglucosamine/phosphogalactosamine mutase; PGlcNM; EC 5.4.2.10; EC 5.4.2.13 (characterized)
to candidate WP_085636384.1 MGEO_RS08970 phosphoglucosamine mutase
Query= SwissProt::Q976E4 (455 letters) >NCBI__GCF_002115805.1:WP_085636384.1 Length = 447 Score = 159 bits (401), Expect = 2e-43 Identities = 139/458 (30%), Positives = 211/458 (46%), Gaps = 38/458 (8%) Query: 3 KLFGTDGVRGIVNK-ELTPELVLKLSKAIGTFFGKNSK----ILVGRDVRAGGDMLVKIV 57 KLFGTDGVRG N +T ++ L++ A+G F ++SK +++G+D R G M + Sbjct: 4 KLFGTDGVRGTANAYPMTADMALRIGAAVGRHFRQDSKGVHRVVIGKDTRQSGYMFENAL 63 Query: 58 EGGLLSVGVEVYDGGMAPTPALQYAVKTLGYDGGVVITASHNPAPYNGIKVVDKDGIEIR 117 GL S G+ V G PTPA+ ++ D G++I+ASHNPA NGIK DG ++ Sbjct: 64 TAGLTSTGMNVLLLGPVPTPAVGLLTPSMRADLGIMISASHNPARDNGIKFFGPDGFKLS 123 Query: 118 REKENEIEDLFFTERFNTIEWSSLTT--EVKREDRVISTYVNGILSHVDIEKIKKKNYKV 175 E EIE L T +E + KR D Y + S + ++ KV Sbjct: 124 DADEAEIEALIET----GVEPAQAENIGRAKRIDDGRFRYQERVKSTFPAD-LRLDGLKV 178 Query: 176 LIDPANSVGALSTPLVARALGCKI----YTING-NLDPLFSARQPEPTFDSLKETAEVVK 230 +ID AN + P V LG + T NG N++ + P+ A V Sbjct: 179 VIDCANGAAYKAAPEVLWELGADVIPLGVTPNGSNINEGCGSTHPQ-------LAAAAVV 231 Query: 231 TLKVDLGVAHDGDADRAIFIDSEGRVQWGDRSGTLL-SYWASVKNPKAIKKIVTAVSSSS 289 D+G+ DGDADR I ID G+V GD+ L+ + WA + + + T +S+ Sbjct: 232 AHGADIGICLDGDADRVILIDETGQVADGDQIMALMAARWAEEQRLRDGVLVATVMSNLG 291 Query: 290 LVEEYLSKYNIQVDWTKVGSVDIAHKVADENALAGFEENGGFMYPPHQYVRDGAMSFALM 349 L E +L ++++ T VG + + G E++G + + DG M+ Sbjct: 292 L-ERFLDGRGLRLERTGVGDRYVVEAMRRGGWNLGGEQSGHIVMTDYATTGDGLMAGLQF 350 Query: 350 L-ELLANENVSSAELFDRLPKYYLVKTKVDLKPGLMVEEIYKKILEVYSTSSVKAITIDG 408 L E+ +SA + D P L+ Y + T+SVKA D Sbjct: 351 LGEMCRTGKPASA-----------LARSFDPVPQLLKNVRYDPSVAPLETASVKAAIADA 399 Query: 409 VKIIGKDFWFLVRKSGTEPIIRIMAEAKDENVANNLVN 446 + L+RKSGTEP+IR+MAE +DE + +V+ Sbjct: 400 EARLNGSGRLLIRKSGTEPLIRVMAECEDEALLVEVVD 437 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: 467 Number of extensions: 27 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: 447 Length adjustment: 33 Effective length of query: 422 Effective length of database: 414 Effective search space: 174708 Effective search space used: 174708 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