Align Phosphoglucomutase/phosphomannomutase; PGM/PMM; EC 5.4.2.2; EC 5.4.2.8 (characterized)
to candidate WP_093429069.1 BM272_RS12180 phosphoglucosamine mutase
Query= SwissProt::Q68BJ6 (456 letters) >NCBI__GCF_900112605.1:WP_093429069.1 Length = 451 Score = 197 bits (501), Expect = 6e-55 Identities = 150/463 (32%), Positives = 224/463 (48%), Gaps = 28/463 (6%) Query: 3 KLFGTFGVRG-IANEEITPEFALKIGMAFGTLLKREGRERPLVVVGRDTRVSGEMLKDAL 61 K FGT G+RG + + ITP+F L++G A G +L E R VV+G+DTR+SG M + AL Sbjct: 5 KYFGTDGIRGRVGHPPITPDFVLRLGWAAGRVLGGEHGGR--VVIGKDTRISGYMFESAL 62 Query: 62 ISGLLSTGCDVIDVGIAPTPAIQWATNHFNADGGAVITASHNPPEYNGIKLLEPNGMGLK 121 +GL + G D +G PTPAI + T A G VI+ASHNP + NGIK G+ L Sbjct: 63 EAGLSAAGLDTHLLGPIPTPAIAYLTRTLRARAGIVISASHNPFDDNGIKFFSAEGVKLP 122 Query: 122 KEREAIVEELFFSEDFHRAKWNEIGE-LRKEDIIKPYIEAIKNRVDVEAIKKRRPFVVVD 180 E +EEL E +G+ R D YIE K V + +VVD Sbjct: 123 DATEEAIEEL-LEEPLTTRNSASLGKAYRVPDAAGRYIEFCKGTVP-NGLTLEGLHIVVD 180 Query: 181 TSNGAGSLTLPYLLRELGCKVVSVNAHPDGHFPARNPEPNEENLKGFMEIVKALGADFGV 240 ++GA P + ELG +V ++ PDG N + + V+ AD GV Sbjct: 181 CAHGATYQVAPAVFSELGARVTAIGVDPDG--LNINEGVGSTRPEALQDAVRRERADLGV 238 Query: 241 AQDGDADRAVFIDENGRFIQGDKTFALVADAVLRENGG--GLLVTTIATSNLLDDIAKRN 298 A DGD DR + +D G + GD+ ++A A NGG G + T+ ++ L+ + Sbjct: 239 AFDGDGDRVIMVDAGGEVVDGDELLYIIA-AHRHGNGGFPGGVAGTLMSNLGLELALQGL 297 Query: 299 GAKVMRTKVGDLIVARALLENNGTIGGEENGGVIFPDFVLGRDGAMTTAKIVEIFAKSG- 357 G R KVGD V+ L + +GGE +G +I D DG + +++ + G Sbjct: 298 GIPFRRAKVGDRYVSELLAAEDWLLGGETSGHIICRDRNTSGDGIIAALQVLTALVERGE 357 Query: 358 --KKFSELIDELPK-YYQFKTKRHVEGDRKAIVAKVAELAEKKGYKIDTTDGTKIIFDDG 414 + F + + +LP+ + +R ++ + + E AE + D G Sbjct: 358 TLESFRQGMTKLPQTLVNVRVERMIDVHASPAITEAVESAEAD------------LADCG 405 Query: 415 WVLVRASGTEPIIRIFSEAKSEEKAREYLE-LGIKLLEEALKG 456 VL+R SGTEP++R+ E + E++ RE E L + EEA G Sbjct: 406 RVLLRPSGTEPVVRVMVEGEDEQQVRELAERLAHVVREEAAGG 448 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: 551 Number of extensions: 33 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: 456 Length of database: 451 Length adjustment: 33 Effective length of query: 423 Effective length of database: 418 Effective search space: 176814 Effective search space used: 176814 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