Align phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) (EC 5.4.2.2) (characterized)
to candidate WP_084572619.1 DL86_RS19035 alpha-D-glucose phosphate-specific phosphoglucomutase
Query= BRENDA::Q9SCY0 (623 letters) >NCBI__GCF_000746085.1:WP_084572619.1 Length = 1041 Score = 611 bits (1576), Expect = e-179 Identities = 309/571 (54%), Positives = 413/571 (72%), Gaps = 14/571 (2%) Query: 53 ASSSSSSVVAGTDSIEIKSLPTKPIEGQKTGTSGLRKKVKVFMEDNYLANWIQALFNSLP 112 A++ + + +S I++L T P EGQ+ GTSGLRKKVKVF + YL N++Q++F+ L Sbjct: 485 AANGNKREIPTLESPMIQTLATTPFEGQRPGTSGLRKKVKVFQQPRYLENFVQSIFDCL- 543 Query: 113 LEDYKNATLVLGGDGRYFNKEASQIIIKIAAGNGVGQILVGKEGILSTPAVSAVIRKRKA 172 E TLV+GGDGR+FN+EA QI++KIA NG G+IL+G+ GILSTPA S +IRK A Sbjct: 544 -EGAHGQTLVVGGDGRFFNREAIQIVVKIALANGFGRILIGRGGILSTPAASNLIRKYGA 602 Query: 173 NGGFIMSASHNPGGPEYDWGIKFNYSSGQPAPETITDKIYGNTLSISEIKVAEIPDIDLS 232 GG I+SASHNPGGP+ D+GIK+N S+G PAPE +T+ ++ T +I E ++ + PDIDL Sbjct: 603 FGGVILSASHNPGGPDGDFGIKYNASNGGPAPEKLTEAVFARTKAIKEYRILDAPDIDLD 662 Query: 233 QVGVTKYGNFSVEVIDPVSDYLELMEDVFDFDLIRGLLSRSDFGFMFDAMHAVTGAYAKP 292 ++G G +EVIDPV DY LM+ +FDFD IRGLL +S F FDAM AVTG YAK Sbjct: 663 RLGALGLGPGLIEVIDPVDDYALLMQSLFDFDKIRGLL-QSGFRLRFDAMSAVTGPYAKR 721 Query: 293 IFVDNLGAKPDSISNGVPLEDFGHGHPDPNLTYAKDLVDVMYRDNGPDFGAASDGDGDRN 352 IFVD LGA DS+ NG PL DFG HPDPNL AK L+D+ +GPD AASDGDGDRN Sbjct: 722 IFVDLLGASADSVLNGTPLPDFGGHHPDPNLVNAKHLLDLAMSKDGPDLCAASDGDGDRN 781 Query: 353 MVLGNKFFVTPSDSVAIIAANAQEAIPYFRAGPKGLARSMPTSGALDRVAEKLKLPFFEV 412 +++G +VTPSDS+AI+A NA A P + G G+ARSMPTS A D+VAE+L + +E Sbjct: 782 LIIGAGRYVTPSDSLAILAGNAHLA-PGYARGVAGVARSMPTSAAADKVAERLGVNLYET 840 Query: 413 PTGWKFFGNLMDAGKLSICGEESFGTGSDHIREKDGIWAVLAWLSILAHRNKDTKPGDKL 472 PTGWKFFGNL+DAG +ICGEES GTGSDH+REKDG+WA+L WL+ILA R + Sbjct: 841 PTGWKFFGNLLDAGLATICGEESAGTGSDHVREKDGLWAILLWLNILAVRGQ-------- 892 Query: 473 VSVADVVKEYWATYGRNFFSRYDYEECESEGANKMIEYLREILSKSKAGDVYGNYVLQFA 532 SVA +V ++WA YGRN++ R DYEE E+EGAN +++ LR+ L + G +G + A Sbjct: 893 -SVAAIVADHWAEYGRNYYCRRDYEEVEAEGANALVQALRDALPE-LPGKSFGGLKIAKA 950 Query: 533 DDFSYTDPVDGSVASKQGVRFVFTDGSRIIFRLSGTGSAGATVRIYIEQFEPDVSKHDVD 592 DDF+Y DPVDGS ++QG+R +F++G RI++RLSGTG++GAT+R+YIE++EPD +K ++D Sbjct: 951 DDFAYHDPVDGSDTTQQGIRLLFSEGGRIVYRLSGTGTSGATLRVYIERYEPDPAKQNLD 1010 Query: 593 AQIALKPLIDLALSVSKLKDFTGREKPTVIT 623 + AL LI L+ ++ + +TGR P+V+T Sbjct: 1011 TETALADLIALSQEIAGIAHYTGRLAPSVVT 1041 Lambda K H 0.317 0.136 0.399 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: 1730 Number of extensions: 93 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: 623 Length of database: 1041 Length adjustment: 41 Effective length of query: 582 Effective length of database: 1000 Effective search space: 582000 Effective search space used: 582000 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: 56 (26.2 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