Align Phosphoglucosamine/phosphogalactosamine mutase; PGlcNM; EC 5.4.2.10; EC 5.4.2.13 (characterized)
to candidate 6938122 Sama_2243 phosphoglucosamine mutase (RefSeq)
Query= SwissProt::Q976E4 (455 letters) >FitnessBrowser__SB2B:6938122 Length = 452 Score = 167 bits (423), Expect = 6e-46 Identities = 133/450 (29%), Positives = 204/450 (45%), Gaps = 27/450 (6%) Query: 3 KLFGTDGVRGIVNK-ELTPELVLKLSKAIGTFFGKNS--KILVGRDVRAGGDMLVKIVEG 59 K FGTDGVRG V + +TP+ +KL A GT + ++++G+D R G ML +E Sbjct: 4 KYFGTDGVRGKVGEFPITPDFAMKLGWAAGTVMAASGTKEVIIGKDTRLSGYMLESAMEA 63 Query: 60 GLLSVGVEVYDGGMAPTPALQYAVKTLGYDGGVVITASHNPAPYNGIKVVDKDGIEIRRE 119 G + GV V G PTPA+ Y T D GVVI+ASHNP NGIK G ++ E Sbjct: 64 GFCAAGVNVALTGPLPTPAIAYLTSTFRADAGVVISASHNPYYDNGIKFFSNTGTKLTDE 123 Query: 120 KENEIEDLFFTERFNTIEWSSLTT-------EVKREDRVISTYVNGILSHVDIEKIKKKN 172 +E EIE L + IE ++T +V+R + Y+ + Sbjct: 124 QELEIERLL----VSAIEGGAMTCVASDKLGKVRRINDAAGRYIE-FCKGTFPNSLSLTG 178 Query: 173 YKVLIDPANSVGALSTPLVARALGCKIYTINGNLDPLFSARQPEPTFDSLKETAEVVKTL 232 K+++D A+ V R LG ++ +IN D + T +TA ++ Sbjct: 179 LKIVVDSAHGAAYHIAKNVYRELGAEVISINDKPDGININEHCGATHMDSLQTAVMIH-- 236 Query: 233 KVDLGVAHDGDADRAIFIDSEGRVQWGDRSGTLLSYWASVKNPKAIKKIVTAVSSSSLVE 292 + DLG+A DGDADR + +DS+G+V GD LL+ A + + + ++ + S+ E Sbjct: 237 EADLGIALDGDADRLMMVDSKGQVIDGDALLYLLAKSAQQRG-EQVSGVIGTLMSNLGFE 295 Query: 293 EYLSKYNIQVDWTKVGSVDIAHKVADENALAGFEENGGFMYPPHQYVRDGAMSFALMLEL 352 + L+ I KVG + + + G E +G + D ++ +L Sbjct: 296 QALANLGIPFKRAKVGDRYVVELLKETGWRLGGENSGHLLMLDFTTTGDAIVASLQVLRA 355 Query: 353 LANENVSSAELFDRLPKYYLVKTKVDLKPGLMVEEIYKKILEVYSTSSVKAITIDGVKII 412 L A+ L + V V L V + + + +T+ + Sbjct: 356 LLESGAGLADAITELNMFPQVLINVRLNGNAAVGLSHPSVSDAVATAE---------SAL 406 Query: 413 GKDFWFLVRKSGTEPIIRIMAEAKDENVAN 442 G D L+RKSGTEP+IR+M EAKD AN Sbjct: 407 GNDGRVLLRKSGTEPLIRVMVEAKDAVKAN 436 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: 415 Number of extensions: 19 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 17 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