Align Phosphoglucosamine/phosphogalactosamine mutase; PGlcNM; EC 5.4.2.10; EC 5.4.2.13 (characterized)
to candidate WP_051302736.1 A3GO_RS24860 phosphoglucosamine mutase
Query= SwissProt::Q976E4 (455 letters) >NCBI__GCF_000428045.1:WP_051302736.1 Length = 459 Score = 154 bits (388), Expect = 8e-42 Identities = 139/455 (30%), Positives = 216/455 (47%), Gaps = 29/455 (6%) Query: 3 KLFGTDGVRGIVNK-ELTPELVLKLSKAIGTFFG--KNSKILVGRDVRAGGDMLVKIVEG 59 K FGTDG+RG V + ++TPE V++L A G G + SK+L+G+D R G +L +E Sbjct: 4 KYFGTDGIRGRVGEGKITPEFVMRLGWAAGRVLGNGRGSKVLIGKDTRISGYLLESALEA 63 Query: 60 GLLSVGVEVYDGGMAPTPALQYAVKTLGYDGGVVITASHNPAPYNGIKVVDKDGIEIRRE 119 GL++ GV+++ G PTP + Y +TL G+VI+ASHNP NGIK +G ++ E Sbjct: 64 GLVAAGVDIHLLGPMPTPGIAYLTRTLHAQAGIVISASHNPHCDNGIKFFSSEGKKLPDE 123 Query: 120 KENEIEDLFFTERFNTIEWSSLTTEVKREDRVISTYVNGILSHVDIEKIKKKNYKVLIDP 179 E IE + T+E L + D Y+ S + + K K+++D Sbjct: 124 VELAIE-RELDKPMTTVESEQLGKAYRVGD-AAGRYIEFCKSTIP-WTMSFKGMKIVVDC 180 Query: 180 ANSVGALSTPLVARALGCKIYTINGNLDPL-FSARQPEPTFDSLKETAEVVKTLKVDLGV 238 A+ P V R +G ++ I D L +A ++L++ EV+K + DLG+ Sbjct: 181 AHGATYHIAPHVFREVGAEVVAIGAEPDGLNINAGVGSTHIETLQK--EVLKQ-QADLGI 237 Query: 239 AHDGDADRAIFIDSEGRVQWGDRSGTLLSYWASVKNPKAIKK--IVTAVSSSSLVEEYLS 296 A DGD DR I +D+ G V GD +L A + + I +V ++ +E L+ Sbjct: 238 ALDGDGDRLIMVDANGSVLDGD---DILYIIACSRLRRGILNGGVVGTKMTNFGLEHALN 294 Query: 297 KYNIQVDWTKVGSVDIAHKVADENALAGFEENGGFMYPPHQYVRDGAMSFALMLELLANE 356 ++ I++ T VG I ++ E G E +G + DG +S L++LA Sbjct: 295 EHGIELVRTDVGDRYILERLQLERWSLGGEPSGHIICLDRTTTGDGIIS---ALQVLAEI 351 Query: 357 NVSSA---ELFDRLPKYYLVKTKVDLKPGLMVEEIYKKILEVYSTSSVKAITIDGVKIIG 413 N S EL D K+ V V L E ++ S A D + G Sbjct: 352 NKSGRKLHELRDGYQKFPQVTRNVKLGNVPATE-----LMAAESVQQAVAAAEDALAGSG 406 Query: 414 KDFWFLVRKSGTEPIIRIMAEAKDENVANNLVNEL 448 + L+R SGTEP+IR+ E D+ NL ++ Sbjct: 407 R---VLLRPSGTEPLIRVTVEGPDDGQVQNLSQQI 438 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: 438 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: 459 Length adjustment: 33 Effective length of query: 422 Effective length of database: 426 Effective search space: 179772 Effective search space used: 179772 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