Align Phosphoglucomutase; PGM; Alpha-phosphoglucomutase; Glucose phosphomutase; EC 5.4.2.2 (characterized)
to candidate WP_010538804.1 KCY_RS0120345 phospho-sugar mutase
Query= SwissProt::P18159 (581 letters) >NCBI__GCF_000226135.1:WP_010538804.1 Length = 581 Score = 466 bits (1199), Expect = e-135 Identities = 248/550 (45%), Positives = 364/550 (66%), Gaps = 17/550 (3%) Query: 8 ERWKQTEHLDLELK---ERLIELEGDEQALEDCFYKDLEFGTGGMRGEIGAGTNRMNIYT 64 E+W T D E + +R++E E D+ L + FYKDLEFGTGG+RG +G G+NRMNIYT Sbjct: 15 EKWL-TPAYDAETQAEVKRMLENE-DKTELIEAFYKDLEFGTGGLRGIMGVGSNRMNIYT 72 Query: 65 VRKASAGFAAYISKQGEEAKKRGVVIAYDSRHKSPEFAMEAAKTLATQGIQTYVFDELRP 124 V A+ G + Y+ K ++ + VV+ +D R+ S FA +A + GI+ Y+FD++RP Sbjct: 73 VGAATQGLSNYLKKNFKDLPQISVVVGHDCRNNSRLFAETSANIFSANGIKVYLFDDMRP 132 Query: 125 TPELSFAVRQLNAYGGIVVTASHNPPEYNGYKVYGDDGGQ-LPPKEADIVIEQVNAIENE 183 TPE+SFA+R L GI++TASHNP EYNGYK Y DDG Q L P +A I I++VN I + Sbjct: 133 TPEMSFAIRHLGCQSGIILTASHNPKEYNGYKAYWDDGAQVLAPHDAGI-IDEVNNIASA 191 Query: 184 LTITVDEENKLKEKGLIKIIGEDIDKVYTEKLTSISVHPE-LSEEVDVKVVFTPLHGTAN 242 I LI+IIGEDIDK+Y + + ++S+ PE ++ D+K+V+TP+HGT Sbjct: 192 ADIKFQ-----GNPDLIQIIGEDIDKIYLDMVKTVSIDPEAIARHKDMKIVYTPIHGTGM 246 Query: 243 KPVRRGLEALGYKNVTVVKEQELPDSNFSTVTSPNPEEHAAFEYAIKLGEEQNADILIAT 302 + R L+ G++NV V EQ + D NF TV SPNPE A A+ L +E +A++++A+ Sbjct: 247 MLIPRALKMWGFENVFTVPEQMIKDGNFPTVVSPNPENAEALSMAVNLAKEIDAELVMAS 306 Query: 303 DPDADRLGIAVKNDQGKYTVLTGNQTGALLLHYLLSEKKKQGILPDNGVVLKTIVTSEIG 362 DPDADR+GIA K+D+G++ ++ GNQT + L+Y+L++ K+ G + N +KTIVT+E+ Sbjct: 307 DPDADRVGIACKDDKGEWVLINGNQTCMMYLYYILTQYKQLGKIQGNEFCVKTIVTTELI 366 Query: 363 RAVASSFGLDTIDTLTGFKFIGEKIKEYEASGQYTFQFGYEESYGYLIGDFARDKDAIQA 422 + +A ++ +D TGFK+I +I+ E +Y G EESYG+L DF RDKDA+ A Sbjct: 367 KKIADKNNIEMLDCYTGFKWIAREIRLREGKKKYI--GGGEESYGFLAEDFVRDKDAVSA 424 Query: 423 ALLAVEVCAFYKKQGMSLYEALINLFNEYGFYREGLKSLTLKGKQGAEQIEAILASFRQN 482 L EV A+ K G SLY+ L++++ EYGF +E ++ GK GAE+I+A++ +FR N Sbjct: 425 CCLIAEVAAWAKDNGKSLYQLLLDIYVEYGFSKEFTVNVVKPGKSGAEEIKAMMENFRAN 484 Query: 483 PPQKMAGKQVVTAEDYAVSKRTLLTESKEEAIDLPK-SNVLKYFLEDGSWFCLRPSGTEP 541 PP+++ G +V+ ++DY K+T E K A+D+P+ SNVL+YF EDGS +RPSGTEP Sbjct: 485 PPKELGGSKVILSKDYKTLKQT-DAEGKVTALDMPETSNVLQYFTEDGSKVSVRPSGTEP 543 Query: 542 KVKFYFAVKG 551 K+KFY V+G Sbjct: 544 KIKFYMEVQG 553 Lambda K H 0.313 0.133 0.371 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: 822 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: 581 Length of database: 581 Length adjustment: 36 Effective length of query: 545 Effective length of database: 545 Effective search space: 297025 Effective search space used: 297025 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 53 (25.0 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