Align Phosphoglucomutase; PGM; Alpha-phosphoglucomutase; Glucose phosphomutase; EC 5.4.2.2 (characterized)
to candidate WP_011602402.1 FRAAL_RS05230 phospho-sugar mutase
Query= SwissProt::P18159 (581 letters) >NCBI__GCF_000058485.1:WP_011602402.1 Length = 650 Score = 253 bits (645), Expect = 2e-71 Identities = 195/580 (33%), Positives = 274/580 (47%), Gaps = 75/580 (12%) Query: 19 ELKERLIELEGDEQALE---DCFYKDLEFGTGGMRGEIGAGTNRMNIYTVRKASAGFAAY 75 EL E D AL+ D F L FGT G+RG + AG MN VR+ +AG AA+ Sbjct: 35 ELTRLCAEAVRDPAALDELADRFRAPLRFGTAGLRGPLRAGPGGMNTAVVRRTAAGLAAW 94 Query: 76 I-------------------SKQGEEAKKRG--------VVIAYDSRHKSPEFAMEAAKT 108 + ++ G +A G VVI YD+RH+S FA+++A+ Sbjct: 95 LRATVPAEAVAPAGAQADTTARAGAQAGAGGGTPAAPALVVIGYDARHRSEAFALDSARV 154 Query: 109 LATQGIQTYVFDELRPTPELSFAVRQLNAYGGIVVTASHNPPEYNGYKVY--------GD 160 LA G++ V E PTP L+FAVR L A G++VTASHNP NGYKVY G Sbjct: 155 LAGAGLRALVLPEPLPTPVLAFAVRHLRADAGVMVTASHNPATDNGYKVYLGGAEPDPGR 214 Query: 161 DGGQLPPKEADIVIEQVNAIENELTITVDE-----ENKLKEKGLIKIIGEDIDKVYTEKL 215 + P +ADI ++ A I + E + +L E + + +D T Sbjct: 215 GAQLVAPADADIE-RRIAAAGPAAAIPMAETWRQLDGRLVEDYIHAAVAAVLDLAPTADP 273 Query: 216 TSISVHPELSEE-----VDVKVVFTPLHGTANKPVRRGLEALGYKNVTVVKEQELPDSNF 270 + E E V V +TPLHG + + A G +V EQ PD +F Sbjct: 274 APTAGPDEPEPEPVPVPVPAIVAYTPLHGVGARTLAAVFAAAGLAAPALVDEQAEPDPDF 333 Query: 271 STVTSPNPEEHAAFEYAIKLGEEQNADILIATDPDADRLGIAVKNDQGKYTVLTGNQTGA 330 TV+ PNPEE + A+ LG+ AD+++ATDPDADR +AV +LTG++ G Sbjct: 334 PTVSRPNPEEAGTMDRALALGDRIGADLVLATDPDADRCAVAVGG-----RLLTGDEIGL 388 Query: 331 LLLHYLLSEKKKQGILPDNGVVLKTIVTSEIGRAVASSFGLDTIDTLTGFKFIGEKIKEY 390 LL +L + G V T+V+S RA+A S+G++ +TLTGFK+I Sbjct: 389 LLADQVLRHRP--------GPVATTLVSSSGLRALARSWGVEYRETLTGFKWI------- 433 Query: 391 EASGQYTFQFGYEESYGY-LIGDFARDKDAIQAALLAVEVCAFYKKQGMSLYEALINLFN 449 FGYEE+ GY L+ D RDKD I AAL + A K++G +L + L L Sbjct: 434 -MRADPGLVFGYEEALGYALVPDLVRDKDGITAALAVTLIAAAAKRRGRTLLDLLDELAA 492 Query: 450 EYGFYREGLKSLTLKGKQGAEQIEAILASFRQNPPQKMAGKQVVTAEDYAVSKRTLLTES 509 G + G +S+ A +I + R PP ++A + V D ++ Sbjct: 493 RIGVHETGQRSVRF---ADAARIATAMRRLRAQPPPRLADRAVTGRRDLLDDGVPPTADA 549 Query: 510 KEEAIDLPKSNVLKYFLEDGSWFCLRPSGTEPKVKFYFAV 549 A LP +++L FL D RPSGTEPK+K Y V Sbjct: 550 LPTADALPSADILVLFLGDDR-VTFRPSGTEPKLKVYLEV 588 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: 786 Number of extensions: 43 Number of successful extensions: 7 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: 650 Length adjustment: 37 Effective length of query: 544 Effective length of database: 613 Effective search space: 333472 Effective search space used: 333472 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