Align Phosphoglucosamine/phosphogalactosamine mutase; PGlcNM; EC 5.4.2.10; EC 5.4.2.13 (characterized)
to candidate CA265_RS13185 CA265_RS13185 phosphoglucosamine mutase
Query= SwissProt::Q976E4 (455 letters) >FitnessBrowser__Pedo557:CA265_RS13185 Length = 461 Score = 224 bits (572), Expect = 3e-63 Identities = 143/450 (31%), Positives = 241/450 (53%), Gaps = 17/450 (3%) Query: 9 GVRGIVNKE----LTPELVLKLSKAIGTFFGK---NSKILVGRDVRAGGDMLVKIVEGGL 61 G+RG + LTP ++K + A G++ + N +I++GRD R G+M+ +V G L Sbjct: 9 GIRGTIGGRAGDGLTPFDIVKFTAAFGSWVVQKTGNKRIVLGRDARISGEMVNNLVIGTL 68 Query: 62 LSVGVEVYDGGMAPTPALQYAVKTLGYDGGVVITASHNPAPYNGIKVVDKDGIEIRREKE 121 +G+EV D G++ TP ++ AV GG+++TASHNP +N +K+++ G I Sbjct: 69 QGLGIEVIDLGLSTTPTVEVAVPDEKAGGGIILTASHNPKQWNALKLLNASGEFISDADG 128 Query: 122 NEIEDLFFTERFNTIEWSSLTTEVKREDRVISTYVNGILS--HVDIEKIKKKNYKVLIDP 179 E+ DL + F+ + L +K D + +++ +L+ VD+E IKK ++KV+ID Sbjct: 129 KEVLDLAESADFDFADVDKLGKVIK-NDTYLQKHIDKVLALPLVDVEAIKKADFKVVIDC 187 Query: 180 ANSVGALSTPLVARALG-CKIYTINGNLDPLFSARQPEPTFDSLKETAEVVKTLKVDLGV 238 NS G + P + +ALG K+ + D F PEP ++L E ++ V+ DLG+ Sbjct: 188 VNSTGGIFIPALLKALGVSKVVELYCTPDGHF-PHNPEPLPENLTEISKEVQKQNADLGI 246 Query: 239 AHDGDADRAIFIDSEGRVQWGDRSGTLLSYWASVKNPKAIKKIVTAVSSSSLVEEYLSKY 298 D D DR F++ +G + + + ++ + P V+ +SS+ + + Sbjct: 247 VVDPDVDRLCFVNEDGSMFGEEYTLVAVADYVLKNTP---GNTVSNLSSTRALRDVTESA 303 Query: 299 NIQVDWTKVGSVDIAHKVADENALAGFEENGGFMYPPHQYVRDGAMSFALMLELLANENV 358 + + + VG V++ +K+ NA+ G E NGG +YP Y RD + AL L LA Sbjct: 304 GAEYNASAVGEVNVVNKMKATNAIIGGEGNGGIIYPESHYGRDALVGIALFLTHLAKFGK 363 Query: 359 SSAELFDRLPKYYLVKTKVDLKPGLMVEEIYKKILEVYSTSSVKAITIDGVKIIGKDFWF 418 S + L P+Y++ K K+ L P + ++ + K++ E Y TIDG+KI W Sbjct: 364 SISVLRSSYPQYHISKNKITLTPEMDIDNLLKQVEEKYKNQPYS--TIDGLKIEFDKTWV 421 Query: 419 LVRKSGTEPIIRIMAEAKDENVANNLVNEL 448 +R+S TEPIIRI +EA++E +A NL N++ Sbjct: 422 HLRRSNTEPIIRIYSEAENETIAENLANKI 451 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: 490 Number of extensions: 29 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 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