Align Phosphoglucomutase/phosphomannomutase; PGM/PMM; EC 5.4.2.2; EC 5.4.2.8 (characterized)
to candidate WP_012566976.1 RC1_RS08600 phosphoglucosamine mutase
Query= SwissProt::Q68BJ6 (456 letters) >NCBI__GCF_000016185.1:WP_012566976.1 Length = 473 Score = 208 bits (530), Expect = 3e-58 Identities = 158/457 (34%), Positives = 227/457 (49%), Gaps = 46/457 (10%) Query: 3 KLFGTFGVRGIANEE-ITPEFALKIGMAFGTLLKREGRERPLVVVGRDTRVSGEMLKDAL 61 +LFGT G+RG AN + +T E ALK+ MA +R G R +VV+ +DTR+SG ML+ AL Sbjct: 4 RLFGTDGIRGTANTDPMTAEMALKVAMATAAQFRR-GSHRHVVVIAKDTRLSGYMLEPAL 62 Query: 62 ISGLLSTGCDVIDVGIAPTPAIQWATNHFNADGGAVITASHNPPEYNGIKLLEPNGMGLK 121 +G +S G DV+ VG PTPA+ T AD G +++ASHNP NGIKL P+G L Sbjct: 63 TAGFVSMGMDVVLVGPLPTPAVAMLTRSLRADLGVMVSASHNPFHDNGIKLFGPDGYKLS 122 Query: 122 KEREAIVE--------------ELFFSEDFHRAKWNEIGELRKEDIIKPYIEAIK----N 163 E EA +E +L D RA R ED YIE +K Sbjct: 123 DEMEAAIEARIAADGAAGGPAADLAGPRDLGRAS-------RLEDAPGRYIEQVKASFPR 175 Query: 164 RVDVEAIKKRRPFVVVDTSNGAGSLTLPYLLRELGCKVVSVNAHPDGHFPARNPEPNEEN 223 + ++ +K +VVD +NGA P +L ELG +VV + PDG N + Sbjct: 176 GLRLDGLK-----IVVDCANGAAYRVAPKVLWELGAEVVPLAVGPDGF--NINRDCGATA 228 Query: 224 LKGFMEIVKALGADFGVAQDGDADRAVFIDENGRFIQGDKTFALVADAVL---RENGGGL 280 V A G+A DGDADR + DE+G I GD+ AL+ + R GGG+ Sbjct: 229 PAAMRAAVLEHKAHLGLALDGDADRLILADESGTQIDGDQIMALIGRSWAEDGRLKGGGV 288 Query: 281 LVTTIATSNL-LDDIAKRNGAKVMRTKVGDLIVARALLENNGTIGGEENGGVIFPDFVLG 339 + T + SNL L+ + G ++RT VGD V + E +GGE++G ++ DF Sbjct: 289 VATVM--SNLGLELFLRDRGLTLVRTPVGDRYVVEHMREYGFNVGGEQSGHIVLSDFATT 346 Query: 340 RDGAMTTAKIVEIFAKSGKKFSELIDELPKYYQFKTKRHVEGDRKAIVAKVAELAEKKGY 399 DG + +++ ++G+ SE++ Q R+V D V + E G Sbjct: 347 GDGLLAALQVLAEIQRTGRPASEVLRVFQPLPQL--LRNVRFDPAGGVRPL----EAAGV 400 Query: 400 KIDTTDGTKIIFDDGWVLVRASGTEPIIRIFSEAKSE 436 + G + G VL+R SGTEP+IR+ +E + E Sbjct: 401 QAAIRAGEARLGGRGRVLIRKSGTEPLIRVMAEGEDE 437 Lambda K H 0.317 0.139 0.396 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: 527 Number of extensions: 24 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: 456 Length of database: 473 Length adjustment: 33 Effective length of query: 423 Effective length of database: 440 Effective search space: 186120 Effective search space used: 186120 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 24 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