Align Phosphoglucosamine/phosphogalactosamine mutase; PGlcNM; EC 5.4.2.10; EC 5.4.2.13 (characterized)
to candidate GFF641 PGA1_c06550 phosphoglucosamine mutase GlmM
Query= SwissProt::Q976E4 (455 letters) >FitnessBrowser__Phaeo:GFF641 Length = 448 Score = 158 bits (399), Expect = 4e-43 Identities = 131/458 (28%), Positives = 208/458 (45%), Gaps = 20/458 (4%) Query: 1 MGKLFGTDGVRGIVN-KELTPELVLKLSKAIGTFFGKNS----KILVGRDVRAGGDMLVK 55 M K FGTDGVRG N +T ++ L++ A+G +F +++ ++++G+D R G M Sbjct: 1 MRKFFGTDGVRGTANIHPMTADMALRIGAAVGRYFRRDASGVHRVVIGKDTRLSGYMFES 60 Query: 56 IVEGGLLSVGVEVYDGGMAPTPALQYAVKTLGYDGGVVITASHNPAPYNGIKVVDKDGIE 115 + GL S G+ V G PTPA+ +++ D GV+I+ASHNPA NGIK DG + Sbjct: 61 ALTAGLTSTGMNVLLLGPVPTPAVGLMTRSMRADLGVMISASHNPAADNGIKFFGPDGFK 120 Query: 116 IRREKENEIEDLFFTERFNTIEWSSLTTEVKREDRVISTYVNGILSHVDIEKIKKKNYKV 175 + E E+E L E + KR D Y + S + I+ KV Sbjct: 121 LSDTVEMELEALI--EAGVEPAQAQNIGRAKRIDDARFRYGERVKSSLP-RDIRLDGLKV 177 Query: 176 LIDPANSVGALSTPLVARALGCKIYTINGNLDPLFSARQPEPTFDSLKETAEVVKTLKVD 235 +ID AN + P + LG ++ + + D R T AE V Sbjct: 178 VIDCANGAAHRAAPEILWELGAEVIPVGVSPDGTNINRDCGSTHPG--TAAETVVAHGAH 235 Query: 236 LGVAHDGDADRAIFIDSEGRVQWGDRSGTLLSYWASVKNPKAIKKIVTAVSSSSLVEEYL 295 +G+ DGDADR I ID G+V GD+ LL+ + A +V+ V S+ +E +L Sbjct: 236 VGICLDGDADRVIIIDDTGKVADGDQLMALLATRWAEDGVLAGNALVSTVMSNLGLERHL 295 Query: 296 SKYNIQVDWTKVGSVDIAHKVADENALAGFEENGGFMYPPHQYVRDGAMSFALMLELLAN 355 + I ++ T VG + ++ + G E++G + + DG M+ L + Sbjct: 296 AARGIALERTAVGDRYVVERMREGGFNLGGEQSGHIVMTDYATTGDGLMAGLHFLAEMVR 355 Query: 356 ENVSSAELFDRLPKYYLVKTKVDLKPGLMVEEIYKKILEVYSTSSVKAITIDGVKIIGKD 415 + +++L + + V G E S AI + + G+ Sbjct: 356 ADKPASQLAQQFAPVPQLLKNVRFAAGQTPLE---------SDQVQTAIRVAEETLAGQG 406 Query: 416 FWFLVRKSGTEPIIRIMAEAKDENVANNLVNELKKIVE 453 L+RKSGTEP++R+MAE +D V V+ + VE Sbjct: 407 -RLLIRKSGTEPLVRVMAECEDAKVLTAAVDSVVAAVE 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: 412 Number of extensions: 24 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: 448 Length adjustment: 33 Effective length of query: 422 Effective length of database: 415 Effective search space: 175130 Effective search space used: 175130 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