Align Phosphoglucomutase; PGM; Alpha-phosphoglucomutase; Glucose phosphomutase; EC 5.4.2.2 (characterized)
to candidate WP_009142044.1 HMPREF9452_RS10150 phospho-sugar mutase
Query= SwissProt::P18159 (581 letters) >NCBI__GCF_000225705.1:WP_009142044.1 Length = 564 Score = 402 bits (1034), Expect = e-116 Identities = 230/561 (40%), Positives = 330/561 (58%), Gaps = 21/561 (3%) Query: 14 EHLDLELKERLIELEGDEQALEDCFYKDLEFGTGGMRGEIGAGTNRMNIYTVRKASAGFA 73 E L ELK ++ GDE A+ D F++DL FGT G+RG IGAGTNRMNIYTV +A+ GFA Sbjct: 18 EELLAELKA--MQEAGDEDAITDAFFQDLAFGTAGLRGTIGAGTNRMNIYTVGRATQGFA 75 Query: 74 AYISKQGEEAKKRGVVIAYDSRHKSPEFAMEAAKTLATQGIQTYVFDELRPTPELSFAVR 133 Y++K E V IA DSR+K F A LA G+ +YV+ ++ P P LS+A R Sbjct: 76 DYLNKAFENPT---VAIARDSRNKGELFVKTTAAILAANGVTSYVYPKISPVPTLSWATR 132 Query: 134 QLNAYGGIVVTASHNPPEYNGYKVYGDDGGQLPPKEADIVIEQVNAIENELTITVDEENK 193 L GGI +TASHNP YNGYK YG DG Q+ + AD + +NA + I + + Sbjct: 133 YLKCSGGICMTASHNPAPYNGYKAYGPDGCQITSEAADAISAAMNACDPFKDIKTMDFDV 192 Query: 194 LKEKGLIKIIGEDIDKVYTEKLTSISVHPELSEEV---DVKVVFTPLHGTANKPVRRGLE 250 E+GL+K I +++ Y + +T SV+ E++ +K+V+TPL+GT PV L Sbjct: 193 AVEQGLVKWIDDEVLDAYYDAVTDKSVNNLTDEQIANAPLKLVYTPLNGTGLIPVTTVLN 252 Query: 251 ALGYKNVTVVKEQELPDSNFSTVTSPNPEEHAAFEYAIKLGEEQNADILIATDPDADRLG 310 +G ++TVV EQ PD +F T PNPE A + I L +E D+L+ATDPDADR+G Sbjct: 253 KVGITDITVVPEQRDPDGDFPTCPYPNPEIREAMQKGIDLCQEVKPDLLLATDPDADRVG 312 Query: 311 IAVKNDQGKYTVLTGNQTGALLLHYLLSEKKKQGILPDNGVVLKTIVTSEIGRAVASSFG 370 +A D YT+LTGN+ G LLL Y+ + ++G + V + TIV+S + A+A+ +G Sbjct: 313 VACA-DGDDYTLLTGNEMGVLLLDYICKMRAERGEDLSSKVAVTTIVSSAMVDALAAEYG 371 Query: 371 LDTIDTLTGFKFIGEKIKEYEASGQY-TFQFGYEESYGYLIGDFARDKDAIQAALLAVEV 429 + LTGFK+IG+ I +G+ F FG+EESYGYL GD RDKDA+ A++L ++ Sbjct: 372 FELRRCLTGFKYIGDIITGLSDAGEVDRFIFGFEESYGYLSGDHVRDKDAVNASMLICQM 431 Query: 430 CAFYKKQGMSLYEALINLFNEYGFYREGLKSLTLKGKQGAEQIEAILASFRQNPPQKMAG 489 +YK QG +L EA+ +L+ ++G+Y SL+ G GA ++ I+ S R P ++AG Sbjct: 432 AQYYKLQGKNLVEAMRDLYEKHGYYHNKTVSLSYPGADGAAKMAGIMKSLRSEAPAEIAG 491 Query: 490 KQVVTAEDYAVSKRTLLTESKEEAIDLPKSNVLKYFLEDGSWFCLRPSGTEPKVKFYFAV 549 +V DYA LP ++V+++ LE G+ +RPSGTEPK+K Y Sbjct: 492 SKVEAVVDYATCVN-----------GLPAADVIEFDLEGGNKAIVRPSGTEPKIKLYIFA 540 Query: 550 KGSSLEDSEKRLAVLSEDVMK 570 KG ++ +A + ED K Sbjct: 541 KGEDAAAADALIAAIEEDGRK 561 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: 745 Number of extensions: 35 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: 581 Length of database: 564 Length adjustment: 36 Effective length of query: 545 Effective length of database: 528 Effective search space: 287760 Effective search space used: 287760 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