Align Phosphoglucosamine/phosphogalactosamine mutase; PGlcNM; EC 5.4.2.10; EC 5.4.2.13 (characterized)
to candidate WP_068216838.1 AWW68_RS04035 phosphoglucosamine mutase
Query= SwissProt::Q976E4 (455 letters) >NCBI__GCF_001592965.1:WP_068216838.1 Length = 461 Score = 219 bits (559), Expect = 1e-61 Identities = 144/459 (31%), Positives = 246/459 (53%), Gaps = 29/459 (6%) Query: 10 VRGIVNKELTPELVLKLSKAIGTFF----GKNSKILVGRDVRAGGDMLVKIVEGGLLSVG 65 + G V + LTP +K + A G++ GK KI++GRD R G M+ +V L+ +G Sbjct: 14 IGGAVGESLTPVDAVKFAAAFGSWVVAKTGKK-KIIIGRDARPSGQMISDLVSSTLIGLG 72 Query: 66 VEVYDGGMAPTPALQYAVKTLGYDGGVVITASHNPAPYNGIKVVDKDGIEIRREKENEIE 125 ++V D G++ TP ++ AV GG+++TASHNP +N +K+++ G I + E+ Sbjct: 73 IDVVDLGLSTTPTVEIAVPLEEAGGGIILTASHNPVQWNALKLLNDKGEFISGDDGKEVL 132 Query: 126 DLFFTERFNTIEWSSLTTEVKREDRVISTYVNGILS--HVDIEKIKKKNYKVLIDPANSV 183 ++ + F + L +V D I ++ +L+ VD+E IKK +K+++D NS Sbjct: 133 EIAEKDNFKFADVKKL-GKVTTNDSYIQKHIEMVLALPLVDVEAIKKAKFKIVVDAVNST 191 Query: 184 GALSTPLVARALGCKIYTINGNLDPLFS------ARQPEPTFDSLKETAEVVKTLKVDLG 237 G +S + +ALG + ++PL+ PEP + L + + ++++ K DLG Sbjct: 192 GGISVLPLLKALGVE------TVEPLYCEPNGQFPHNPEPLPEHLGQISSMLESGKYDLG 245 Query: 238 VAHDGDADRAIFIDSEGRVQWGDRSGTLLSYWASVKNPKAIKKIVTAVSSSSLVEEYLSK 297 + D D DR F+D G V +G+ TL++ A + V+ +SS+ + + K Sbjct: 246 IVVDPDVDRLAFVDESGSV-FGEEY-TLVAV-ADYVLSQTKGNTVSNLSSTRALRDVTEK 302 Query: 298 YNIQVDWTKVGSVDIAHKVADENALAGFEENGGFMYPPHQYVRDGAMSFALMLELLANEN 357 Y Q + + VG V++ K+ + A+ G E NGG +YP Y RD + AL L LA Sbjct: 303 YGCQYEPSAVGEVNVVVKMKEIGAVIGGEGNGGIIYPELHYGRDALVGIALFLTHLAKFG 362 Query: 358 VSSAELFDRLPKYYLVKTKVDLKPGLMVEEIYKKILEVYSTSSVKAITIDGVKIIGKDFW 417 + L + P Y++ K K++L P + V+++ K+ E Y + T+DGVKI W Sbjct: 363 KRVSMLRAKYPSYHISKNKIELSPEIDVDKVLTKMKEQYKKQPIN--TVDGVKIEFDKEW 420 Query: 418 FLVRKSGTEPIIRIMAEAKD----ENVANNLVNELKKIV 452 +RKS TEPIIRI AE++ E++A +++++++IV Sbjct: 421 VHLRKSNTEPIIRIYAESESAATAEHLAQKIMSDIREIV 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: 472 Number of extensions: 17 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: 461 Length adjustment: 33 Effective length of query: 422 Effective length of database: 428 Effective search space: 180616 Effective search space used: 180616 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