Align Phosphoglucosamine/phosphogalactosamine mutase; PGlcNM; EC 5.4.2.10; EC 5.4.2.13 (characterized)
to candidate PfGW456L13_5092 Phosphoglucosamine mutase (EC 5.4.2.10)
Query= SwissProt::Q976E4 (455 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5092 Length = 445 Score = 159 bits (401), Expect = 2e-43 Identities = 138/453 (30%), Positives = 202/453 (44%), Gaps = 19/453 (4%) Query: 3 KLFGTDGVRGIVNK-ELTPELVLKLSKAIGTFFGKNS--KILVGRDVRAGGDMLVKIVEG 59 K FGTDG+RG V + +TP+ +LKL A G F K K+LVG+D R G M +E Sbjct: 4 KYFGTDGIRGRVGEYPITPDFMLKLGWAAGMAFRKMGACKVLVGKDTRISGYMFESALEA 63 Query: 60 GLLSVGVEVYDGGMAPTPALQYAVKTLGYDGGVVITASHNPAPYNGIKVVDKDGIEIRRE 119 GL S G +V G PTPA+ Y +T + G+VI+ASHNP NGIK G ++ E Sbjct: 64 GLTSAGADVMLLGPMPTPAIAYLTRTFHAEAGIVISASHNPHDDNGIKFFSGQGTKLPDE 123 Query: 120 KENEIEDLFFTERFNTIEWSSLTTEVKREDRVISTYVNGILSHVDIEKIKKKNYKVLIDP 179 E+ IE+L T T+ SS +V R + Y+ S V K++ID Sbjct: 124 VEHMIEELLDTPM--TVVESSKIGKVSRINDASGRYIEFCKSSVP-TGTSFTGLKIVIDC 180 Query: 180 ANSVGALSTPLVARALGCKIYTINGNLDPLFSARQPEPTFDSLKETAEVVKTLKVDLGVA 239 A+ P V R LG ++ ++ + L T + A V + K DLG+A Sbjct: 181 AHGATYKVAPSVFRELGAEVVVLSAQPNGLNINDNCGSTHMGSLQAAVVAE--KADLGIA 238 Query: 240 HDGDADRAIFIDSEGRVQWGDRSGTLLSYWASVKNPKAIKKIVTAVSSSSLVEEYLSKYN 299 DGD DR +D G V GD +++ + K +V + S+ +E L+ Sbjct: 239 FDGDGDRVQMVDHTGAVVDGDELLFIIARDLHERG-KLQGGVVGTLMSNLGLELALADLG 297 Query: 300 IQVDWTKVGSVDIAHKVADENALAGFEENGGFMYPPHQYVRDGAMSFALMLELLANENVS 359 I + VG + ++ + N + G E +G + H D ++ +L L + Sbjct: 298 IPLVRANVGDRYVIAELLERNWIVGGENSGHIVCFSHTTTGDAIIAALQVLMALGRRDEG 357 Query: 360 SAELFDRLPKYYLVKTKVDLKPGLMVEEIYKKILEVYSTSSVKAITIDGVKIIGKDFWFL 419 A+ L K V V G E SVK + K + L Sbjct: 358 LAQSRQALRKCPQVLINVRFGGGASPLE----------HPSVKEASERVTKAMAGRGRVL 407 Query: 420 VRKSGTEPIIRIMAEAKDENVANNLVNELKKIV 452 +RKSGTEP++R+M E +DE EL K+V Sbjct: 408 LRKSGTEPLVRVMVEGEDETQVRGYAEELAKLV 440 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: 426 Number of extensions: 19 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: 455 Length of database: 445 Length adjustment: 33 Effective length of query: 422 Effective length of database: 412 Effective search space: 173864 Effective search space used: 173864 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