Align Phosphoglucosamine/phosphogalactosamine mutase; PGlcNM; EC 5.4.2.10; EC 5.4.2.13 (characterized)
to candidate Echvi_1178 Echvi_1178 phosphoglucosamine mutase
Query= SwissProt::Q976E4 (455 letters) >FitnessBrowser__Cola:Echvi_1178 Length = 463 Score = 216 bits (549), Expect = 2e-60 Identities = 147/473 (31%), Positives = 245/473 (51%), Gaps = 35/473 (7%) Query: 1 MGKLFGTDGVRGIVNKE----LTPELVLKLSKAIGTFF---GKNSKILVGRDVRAGGDML 53 M + G+RG + + LTP ++K + A G + N +I++GRD R GDM+ Sbjct: 1 MALIKSISGIRGTIGGKSGEGLTPVDIVKFTSAYGAWILEKTNNPRIVIGRDARISGDMV 60 Query: 54 VKIVEGGLLSVGVEVYDGGMAPTPALQYAVKTLGYDGGVVITASHNPAPYNGIKVV---- 109 K+V L +G++V D G++ TP +++AV GG+++TASHNP +N +K++ Sbjct: 61 SKLVTATLQGLGIQVIDLGLSTTPTVEFAVPLEKAGGGIILTASHNPIQWNALKLLNDKG 120 Query: 110 ----DKDGIEIRREKENEIEDLFFTERFNTIEWSSLTTEVKRE-DRVISTYVNGILSHVD 164 D+DG E+ + E ED F N ++ + + R D V+S L VD Sbjct: 121 EFISDQDGKEVLEKAEK--EDFEFATVKNIGAYTLVEDYIDRHIDHVLS------LDLVD 172 Query: 165 IEKIKKKNYKVLIDPANSVGALSTPLVARALGCK-IYTINGNLDPLFSARQPEPTFDSLK 223 E I +N++V+ID NS G ++ P + +ALG + + + D F PEP ++L+ Sbjct: 173 KEAIAARNFRVVIDCVNSTGGIALPKLLKALGVEHVEEMYCEPDGHF-PHNPEPLPENLR 231 Query: 224 ETAEVVKTLKVDLGVAHDGDADRAIFIDSEGRVQWGDRSGTLLSYWASVKNPKAIKKIVT 283 + + +K K DLG+ D D DR F+ +G + + ++ + + P V+ Sbjct: 232 DISSKLKNGKFDLGIVVDPDVDRLAFLTEDGSAFGEEYTLVAIADYVLSQTP---GNTVS 288 Query: 284 AVSSSSLVEEYLSKYNIQVDWTKVGSVDIAHKVADENALAGFEENGGFMYPPHQYVRDGA 343 +SS+ + + K+ + VG V++ +K+ + NA+ G E NGG +YP Y RD Sbjct: 289 NLSSTRALRDVTEKHEGTYNAAAVGEVNVVNKMKETNAIIGGEGNGGVIYPSSHYGRDAL 348 Query: 344 MSFALMLELLANENVSSAELFDRLPKYYLVKTKVDLKPGLMVEEIYKKILEVYSTSSVKA 403 + L L LA ++ L P YY+ K K++L P + V+ I +I YS + Sbjct: 349 VGIGLFLTHLAKFGKTANRLRASYPNYYISKNKIELTPEIDVDAILDEISRKYSKQPIN- 407 Query: 404 ITIDGVKIIGKDFWFLVRKSGTEPIIRIMAE----AKDENVANNLVNELKKIV 452 IDG+KI + W +RKS TEPIIRI +E A E++AN L+ ++K+++ Sbjct: 408 -DIDGIKIEFEKEWVHLRKSNTEPIIRIYSESETKATAEHLANKLILDIKEVI 459 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: 471 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: 463 Length adjustment: 33 Effective length of query: 422 Effective length of database: 430 Effective search space: 181460 Effective search space used: 181460 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