Align phosphomannose mutase (EC 5.4.2.8) (characterized)
to candidate Dsui_3057 Dsui_3057 phosphoglucosamine mutase
Query= metacyc::MONOMER-13382 (455 letters) >FitnessBrowser__PS:Dsui_3057 Length = 451 Score = 177 bits (450), Expect = 5e-49 Identities = 146/446 (32%), Positives = 207/446 (46%), Gaps = 28/446 (6%) Query: 3 KLFGTFGVRGIANEK-ITPEFAMKIGMAFGTLLKRE----GRKKPLVVVGRDTRVSGEML 57 K FGT GVRG E ITP+FAM++G + G +L + ++P V++G+DTR+SG ML Sbjct: 4 KYFGTDGVRGRVGEAPITPDFAMRLGYSAGQVLVAQDGLPAGERPAVLIGKDTRISGYML 63 Query: 58 KEALISGLLSVGCDVIDVGIAPTPAVQWATKHFNADGGAVITASHNPPEYNGIKLLEPNG 117 + AL +G + G DV VG PTPAV + T+ G VI+ASHNP NGIK G Sbjct: 64 EAALEAGFSAAGVDVCLVGPMPTPAVAYLTRALRLQAGIVISASHNPFYDNGIKFFSAQG 123 Query: 118 MGLKKEREAIVEELFFKEDFDRAKWYEIGEVRR-EDIIKPYIEAIKS----KVDVEAIKK 172 L E + E + +G+ RR +D YIE KS +D+ +K Sbjct: 124 TKLPDAVEHAI-EAGVEAPMGCVPSDRLGKARRIDDARGRYIEFCKSTFPNDLDLRGLK- 181 Query: 173 RKPFVVVDTSNGAGSLTLPYLLRELGCKVITVNAQPDGYFPARNPEPNEENLKEFMEIVK 232 +VVD ++GA P + ELG V+ + +PDG N K E V Sbjct: 182 ----IVVDCAHGAAYHIAPDVFHELGADVVAIGNRPDGL--NINAAVGATAPKALKEAVL 235 Query: 233 ALGADFGVAQDGDADRAVFIDENGRFIQGDK-TFALVADAVLKEKGGGLLVTTVATSNLL 291 AD G+A DGD DR V +D G GD+ +A+V G + T+ T+ L Sbjct: 236 GQRADLGIALDGDGDRLVMVDGEGNVYDGDQLLYAIVRGRQALGPVAG-VAGTLMTNLAL 294 Query: 292 DDIAKKHGAKVMRTKVGDLIVARALYENNGTIGGEENGGVIFPEHVLGRDGAMTVAKVVE 351 +D K R VGD V L +N GGE +G ++ + DG + +V+ Sbjct: 295 EDALKALDIPFARAAVGDRYVLEKLVQNGWLYGGENSGHILCLDRHTTGDGIIAALQVLA 354 Query: 352 IFAKSGKKFSELIDELPKYYQIKTKRHVEGDRHAIVNKVAEMARERGYTVDTTDGAKIIF 411 + G L+ +L Y Q K + A A +R + DG Sbjct: 355 ALRQQGGSLKALLGDLVLYPQ-KLINVPMPKGFPWQDSPAIAAAQRAVEAE-LDGR---- 408 Query: 412 EDGWVLVRASGTEPIIRIFSEAKSKE 437 G VL+RASGTEP++R+ E + E Sbjct: 409 --GRVLLRASGTEPLLRVMVEGRDGE 432 Lambda K H 0.317 0.138 0.391 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: 501 Number of extensions: 36 Number of successful extensions: 7 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: 451 Length adjustment: 33 Effective length of query: 422 Effective length of database: 418 Effective search space: 176396 Effective search space used: 176396 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