Align phosphomannose mutase (EC 5.4.2.8) (characterized)
to candidate GFF945 Psest_0974 phosphoglucosamine mutase
Query= metacyc::MONOMER-13382 (455 letters) >FitnessBrowser__psRCH2:GFF945 Length = 445 Score = 210 bits (535), Expect = 7e-59 Identities = 142/449 (31%), Positives = 226/449 (50%), Gaps = 33/449 (7%) Query: 3 KLFGTFGVRG-IANEKITPEFAMKIGMAFGTLLKREGRKKPLVVVGRDTRVSGEMLKEAL 61 K FGT G+RG + ITP+F +K+G A G +++G+ + +++G+DTR+SG M + AL Sbjct: 4 KYFGTDGIRGHVGQAPITPDFMLKLGWAAGMAFRKQGKCR--ILIGKDTRISGYMFESAL 61 Query: 62 ISGLLSVGCDVIDVGIAPTPAVQWATKHFNADGGAVITASHNPPEYNGIKLLEPNGMGLK 121 +GL + G DV+ +G PTPAV + T+ F+A+ G VI+ASHNP NGIK G L Sbjct: 62 QAGLSAAGADVLLLGPMPTPAVAYLTRTFHAEAGIVISASHNPHHDNGIKFFSGRGTKLP 121 Query: 122 KEREAIVEELFFKEDFDRAKWYEIGEVRR-EDIIKPYIEAIKSKV----DVEAIKKRKPF 176 E E ++EEL + ++G+ R D YIE KS V D +K Sbjct: 122 DEVELMIEEL-IDAPMTVVESAQLGKASRINDAAGRYIEFCKSSVPTSTDFSGLK----- 175 Query: 177 VVVDTSNGAGSLTLPYLLRELGCKVITVNAQPDGYFPARNPEPNEENLKEFMEIVKALGA 236 +V+D ++GA P + RELG +V+ + AQPDG N + ++ + + V GA Sbjct: 176 LVIDCAHGATYKVAPSVFRELGAEVVVIGAQPDGL--NINADVGSTHVGQLQKAVVDHGA 233 Query: 237 DFGVAQDGDADRAVFIDENGRFIQGDKTFALVA-DAVLKEKGGGLLVTTVATSNLLDDIA 295 D G+A DGD DR + +D G + GD+ ++A D +++ G +V T+ ++ L+ Sbjct: 234 DLGIAFDGDGDRVMMVDHTGAVVDGDELLYIIATDLQERDRLSGGVVGTLMSNLGLELAL 293 Query: 296 KKHGAKVMRTKVGDLIVARALYENNGTIGGEENGGVIFPEHVLGRDGAMTVAKVVEIFAK 355 K R KVGD V + + + +GGE +G ++ +H D + +VV + Sbjct: 294 KARDIPFTRAKVGDRYVIAEMLDRSWVLGGENSGHIVCAQHTTTGDAIIAALQVVLALRR 353 Query: 356 SGKKFSELIDELPKYYQIKTKRHVEGDR----HAIVNKVAEMARERGYTVDTTDGAKIIF 411 G+ ++ K Q+ GDR H V + ER + Sbjct: 354 RGQTLAQERLAWHKCPQVLINVRFSGDRDPISHPSVQAACDSVTER------------MA 401 Query: 412 EDGWVLVRASGTEPIIRIFSEAKSKEKAQ 440 G VL+R SGTEP++R+ E + + + Sbjct: 402 GRGRVLLRKSGTEPLVRVMVEGDDETQVR 430 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: 481 Number of extensions: 38 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: 445 Length adjustment: 33 Effective length of query: 422 Effective length of database: 412 Effective search space: 173864 Effective search space used: 173864 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