Align Phosphoglucomutase; PGM; Alpha-phosphoglucomutase; Glucose phosphomutase; EC 5.4.2.2 (characterized)
to candidate WP_015944244.1 DHAF_RS14085 phospho-sugar mutase
Query= SwissProt::P18159 (581 letters) >NCBI__GCF_000021925.1:WP_015944244.1 Length = 575 Score = 519 bits (1336), Expect = e-151 Identities = 268/575 (46%), Positives = 376/575 (65%), Gaps = 6/575 (1%) Query: 4 RKSYERWKQTEHLDLELKERLIELEGDEQALEDCFYKDLEFGTGGMRGEIGAGTNRMNIY 63 ++ Y W + + D + + + + DE+ +ED FY DLEFGTGG+RG +GAGTNRMNIY Sbjct: 3 QERYRFWLTSPYFDEDTRSEVAAIN-DEKEIEDRFYTDLEFGTGGLRGVLGAGTNRMNIY 61 Query: 64 TVRKASAGFAAYISKQGEEAKKRGVVIAYDSRHKSPEFAMEAAKTLATQGIQTYVFDELR 123 +RKA+ G A I + GE K RGVVIAYDSR S FA EAA LA GI+ Y+FD+LR Sbjct: 62 VIRKATQGLADLILEGGEAGKNRGVVIAYDSRRFSDRFAKEAALVLAGNGIKAYLFDDLR 121 Query: 124 PTPELSFAVRQLNAYGGIVVTASHNPPEYNGYKVYGDDGGQLPPKEADIVIEQVNAIENE 183 PTPELSFAVR L A G+V+TASHNP EYNGYKVY +DGGQ+PP D ++ + A + Sbjct: 122 PTPELSFAVRHLKAQAGLVITASHNPKEYNGYKVYWEDGGQVPPDRGDRILAHIKAHQAW 181 Query: 184 LTITVDEENKLKEKGLIKIIGEDIDKVYTEKLTSISVHPELSEE--VDVKVVFTPLHGTA 241 I EE + ++KGL+ IGE+ID VY K+ ++++PELS+ ++ +V+TPLHG Sbjct: 182 DDILPLEEAEARDKGLLVEIGEEIDAVYLSKVKELALYPELSQAKGSNLSIVYTPLHGAG 241 Query: 242 NKPVRRGLEALGYKNVTVVKEQELPDSNFSTVTSPNPEEHAAFEYAIKLGEEQNADILIA 301 N V R L +GY +V V EQE PD F+TV PNPE + F+ A G+ +NA +LIA Sbjct: 242 NVLVNRILTEMGY-SVFTVPEQEKPDPEFTTVPYPNPEIPSTFDLARSYGKARNAQMLIA 300 Query: 302 TDPDADRLGIAVKNDQGKYTVLTGNQTGALLLHYLLSEKKKQGILPDNGVVLKTIVTSEI 361 TDPDADRLG+A++ QG Y LTGNQ G LL +YLL++KK+ GILP+ VV+KTI ++++ Sbjct: 301 TDPDADRLGMALRTPQGDYRQLTGNQVGTLLSYYLLTQKKRLGILPEQAVVIKTIASTDL 360 Query: 362 GRAVASSFGLDTIDTLTGFKFIGEKIKEYEASGQYTFQFGYEESYGYLIGDFARDKDAIQ 421 + G + LTGFKFI EK +E E G FQFG+EESYGYL G F RDKDA+ Sbjct: 361 ADLLVKDLGARVENVLTGFKFIAEKEQEMEVQGSGDFQFGFEESYGYLAGHFVRDKDAVI 420 Query: 422 AALLAVEVCAFY-KKQGMSLYEALINLFNEYGFYREGLKSLTLKGKQGAEQIEAILASFR 480 A+LL E +Y +K+G SL E L +++ +YG++ + S+TL+GK G EQ+E ++ R Sbjct: 421 ASLLLAEAALYYQEKEGRSLLEVLEDIYGKYGYFIDDQISITLEGKAGKEQMEKMMVKLR 480 Query: 481 QNPPQKMAGKQVVTAEDYAVSK-RTLLTESKEEAIDLPKSNVLKYFLEDGSWFCLRPSGT 539 + + G V +DY + K R ++ + LP+SNV++Y + G + RPSGT Sbjct: 481 ETDVKSFGGIAVACIDDYELRKGRRMIAPFHSYELALPQSNVIRYSFQGGGFVMARPSGT 540 Query: 540 EPKVKFYFAVKGSSLEDSEKRLAVLSEDVMKTVDE 574 EPK+KFYF ++G + ++ L + +D+++ + + Sbjct: 541 EPKIKFYFNIRGVNPQELPTTLEAVKKDLLELIKD 575 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: 892 Number of extensions: 40 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: 575 Length adjustment: 36 Effective length of query: 545 Effective length of database: 539 Effective search space: 293755 Effective search space used: 293755 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