Align Phosphoglucosamine/phosphogalactosamine mutase; PGlcNM; EC 5.4.2.10; EC 5.4.2.13 (characterized)
to candidate GFF3130 HP15_3072 phosphoglucosamine mutase
Query= SwissProt::Q976E4 (455 letters) >FitnessBrowser__Marino:GFF3130 Length = 447 Score = 160 bits (406), Expect = 6e-44 Identities = 138/457 (30%), Positives = 209/457 (45%), Gaps = 24/457 (5%) Query: 3 KLFGTDGVRGIVNK-ELTPELVLKLSKAIGTFF---GKNSKILVGRDVRAGGDMLVKIVE 58 K FGTDG+RG V + +TPE +LKL A G F G+ + +L+G+D R G M +E Sbjct: 5 KYFGTDGIRGHVGEFPITPEFMLKLGWAAGQAFKRDGQRNSVLIGKDTRLSGYMFESALE 64 Query: 59 GGLLSVGVEVYDGGMAPTPALQYAVKTLGYDGGVVITASHNPAPYNGIKVVDKDGIEIRR 118 GL + GV+V G PTPA+ Y +T G+VI+ASHNP NGIK G ++ Sbjct: 65 AGLAAAGVDVKLLGPMPTPAIAYLTRTFRASAGIVISASHNPHHDNGIKFFSAAGTKLDD 124 Query: 119 EKENEIEDLFFTERFNTIEWSSLTTEVKREDRVISTYVNGILSHVDIEKIKKKNYKVLID 178 E EIE + ++ + + + R D YV S V E +++D Sbjct: 125 ALEAEIER--WLDKPIEVCGPTELGKASRVDDAPGRYVEFCKSTVPNE-FTLDGMNIVLD 181 Query: 179 PANSVGALSTPLVARALGCKIYTINGNLDPLFSARQPEPTFDSLKETAEVVKTLKVDLGV 238 A+ P V R LG K+ I G+ D L T + A + K DLG+ Sbjct: 182 CAHGATYHVAPKVFRELGAKVSVIGGDPDGLNINLNVGSTHLQALKAAVIEK--NADLGI 239 Query: 239 AHDGDADRAIFIDSEGRVQWGDRSGTLLSYWASVKNPKAIKK--IVTAVSSSSLVEEYLS 296 A DGD DR + +D +G GD LL AS + + K +V + ++ VE L+ Sbjct: 240 AFDGDGDRVLMVDRDGSEVDGDE---LLYVIASQRFAEDRLKGGVVGTLMTNLGVELALN 296 Query: 297 KYNIQVDWTKVGSVDIAHKVADENALAGFEENGGFMYPPHQYVRDGAMSFALMLELLANE 356 + I+ + KVG + ++ N + G E +G + DG +S +L + Sbjct: 297 EIGIEFERAKVGDRYVMERLLANNWVLGGEGSGHMVIRDCTSTGDGIVSALQVLLSVWKS 356 Query: 357 NVSSAELFDRLPKYYLVKTKVDLKPGLMVEEIYKKILEVYSTSSVKAITIDGVKIIGKDF 416 + A+L + K P M+ + + +S + A +G Sbjct: 357 GKTLADLRKGMSKL----------PQKMINVRVAQRFDPFSRDDIVAAVRKAETELGSSG 406 Query: 417 WFLVRKSGTEPIIRIMAEAKDENVANNLVNELKKIVE 453 L+R SGTEP+IR+MAE +D + +V EL K+VE Sbjct: 407 RILLRASGTEPLIRVMAEGQDASEILRVVEELAKVVE 443 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: 451 Number of extensions: 19 Number of successful extensions: 6 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: 447 Length adjustment: 33 Effective length of query: 422 Effective length of database: 414 Effective search space: 174708 Effective search space used: 174708 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