Align Phosphoglucomutase/phosphomannomutase; PGM/PMM; EC 5.4.2.2; EC 5.4.2.8 (characterized)
to candidate WP_009122713.1 BUB52_RS04025 phosphoglucosamine mutase
Query= SwissProt::Q68BJ6 (456 letters) >NCBI__GCF_900129655.1:WP_009122713.1 Length = 462 Score = 254 bits (648), Expect = 5e-72 Identities = 167/457 (36%), Positives = 248/457 (54%), Gaps = 13/457 (2%) Query: 6 GTFGVRGIANEEITPEFALKIGMAFGTLLKREGRERP-LVVVGRDTRVSGEMLKDALISG 64 GT G G E + P +K A+ TL+++ + +VVGRD R+SGEM+K+ ++ Sbjct: 12 GTIG--GGVGEGLNPLDIVKFTSAYATLIRKTCTVKSNKIVVGRDARISGEMVKNVVVGT 69 Query: 65 LLSTGCDVIDVGIAPTPAIQWATNHFNADGGAVITASHNPPEYNGIKLLEPNGMGLKKER 124 L+ G DV+D+ +A TP + A A GG ++TASHNP ++N +KLL G L KE Sbjct: 70 LMGMGWDVVDIDLASTPTTELAVTMEGASGGIILTASHNPKQWNALKLLNEKGEFLNKEE 129 Query: 125 EAIVEELFFSEDFHRAKWNEIGELRKE-DIIKPYIEAI--KNRVDVEAIKKRRPFVVVDT 181 V + +E F A+ +++G RK+ + +I+++ + VDVEAIKK V +D Sbjct: 130 GNEVLRIAEAEAFDFAEVDKLGSYRKDLTYNQKHIDSVLALDLVDVEAIKKAGFRVAIDC 189 Query: 182 SNGAGSLTLPYLLRELGCK-VVSVNAHPDGHFPARNPEPNEENLKGFMEIVKALGADFGV 240 N G + LP LL +LG + V + P G+F NPEP E+NL M ++K AD Sbjct: 190 VNSVGGIILPQLLEQLGVQHVEKLYCEPTGNF-QHNPEPLEKNLGDIMNLMKGGKADVAF 248 Query: 241 AQDGDADRAVFIDENGRFIQGDKTFALVADAVLRENGGGLLVTTIATSNLLDDIAKRNGA 300 D D DR I E+G+ + T VAD VL+ G V+ ++++ L D+ ++ Sbjct: 249 VVDPDVDRLAMICEDGKMYGEEYTLVTVADYVLKHTPGN-TVSNLSSTRALRDVTRKYDQ 307 Query: 301 KVMRTKVGDLIVARALLENNGTIGGEENGGVIFPDFVLGRDGAMTTAKIVEIFAKSGKKF 360 + + VG++ V + E IGGE NGGVI+P GRD + A + A GKK Sbjct: 308 QYYASAVGEVNVTTKMKEVGAVIGGEGNGGVIYPASHYGRDALVGIALFLSHLAHEGKKV 367 Query: 361 SELIDELPKYYQFKTKRHV--EGDRKAIVAKVAELAEKKGYKIDTTDGTKIIFDDGWVLV 418 SEL P Y+ K + + + D AI+AKV E+ K +I+ DG KI F D WV + Sbjct: 368 SELRATYPAYFMAKNRVDLTPDTDVDAILAKVKEI--YKNEEINDIDGVKIDFPDKWVHL 425 Query: 419 RASGTEPIIRIFSEAKSEEKAREYLELGIKLLEEALK 455 R S TEPIIR++SEA + E A E +K++E+ K Sbjct: 426 RKSNTEPIIRVYSEAATPEAAEEIGRQIMKVIEDLAK 462 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: 517 Number of extensions: 32 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: 462 Length adjustment: 33 Effective length of query: 423 Effective length of database: 429 Effective search space: 181467 Effective search space used: 181467 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