Align phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) (EC 5.4.2.2) (characterized)
to candidate WP_009546684.1 CCE_RS02910 alpha-D-glucose phosphate-specific phosphoglucomutase
Query= BRENDA::Q9SCY0 (623 letters) >NCBI__GCF_000017845.1:WP_009546684.1 Length = 544 Score = 661 bits (1705), Expect = 0.0 Identities = 323/555 (58%), Positives = 419/555 (75%), Gaps = 13/555 (2%) Query: 69 IKSLPTKPIEGQKTGTSGLRKKVKVFMEDNYLANWIQALFNSLPLEDYKNATLVLGGDGR 128 I+++ T P + QK GTSGLRK V F + +YL N+IQ++F+SL + + TLV+GGDGR Sbjct: 3 IRTVTTTPFDDQKPGTSGLRKAVPTFQKPHYLENFIQSIFDSL--DGCEGQTLVVGGDGR 60 Query: 129 YFNKEASQIIIKIAAGNGVGQILVGKEGILSTPAVSAVIRKRKANGGFIMSASHNPGGPE 188 Y+N++A Q+I+K+AA N +G+ILVG GI STPA SAVIRK A GG I+SASHNPGGP Sbjct: 61 YYNRQAIQVILKMAAANNIGRILVGCGGIFSTPAASAVIRKYNAFGGIILSASHNPGGPN 120 Query: 189 YDWGIKFNYSSGQPAPETITDKIYGNTLSISEIKVAEIPDIDLSQVGVTKYGNFSVEVID 248 D+G+K+N S+G PAPE +T+ IY T +I+E K+ + DI+L + G K G VEVID Sbjct: 121 GDFGVKYNVSNGGPAPEKVTNAIYECTKTINEYKILDAADINLDRPGSFKLGTMDVEVID 180 Query: 249 PVSDYLELMEDVFDFDLIRGLLSRSDFGFMFDAMHAVTGAYAKPIFVDNLGAKPDSISNG 308 V+ Y+ELM+ +FDFD I+ ++S +F D++HAVTG YA+ +F LGAK ++ NG Sbjct: 181 SVTPYVELMQQLFDFDKIKSMVSSDNFRMCMDSLHAVTGPYARALFEQYLGAKEGTVQNG 240 Query: 309 VPLEDFGHGHPDPNLTYAKDLVDVMYRDNGPDFGAASDGDGDRNMVLGNKFFVTPSDSVA 368 PLEDFG GHPDPNL YA DLVD+M+ DN PDFGAASDGDGDRNM+LG FFVTPSDS+A Sbjct: 241 TPLEDFGGGHPDPNLVYAHDLVDIMFGDNAPDFGAASDGDGDRNMILGKNFFVTPSDSLA 300 Query: 369 IIAANAQEAIPYFRAGPKGLARSMPTSGALDRVAEKLKLPFFEVPTGWKFFGNLMDAGKL 428 ++ ANA +P + G G+ARSMPTS A DRVA KL + +E PTGWKFFGNL+DAGK Sbjct: 301 VLTANA-TLVPGYEGGIAGVARSMPTSAAADRVAAKLGIDCYETPTGWKFFGNLLDAGKA 359 Query: 429 SICGEESFGTGSDHIREKDGIWAVLAWLSILAHRNKDTKPGDKLVSVADVVKEYWATYGR 488 ++CGEESFGTGS+HIREKDG+WAVL WL+ILA + + SV +V+++W YGR Sbjct: 360 TLCGEESFGTGSNHIREKDGLWAVLFWLNILAVKGE---------SVEKIVRDHWQEYGR 410 Query: 489 NFFSRYDYEECESEGANKMIEYLREILSKSKAGDVYGNYVLQFADDFSYTDPVDGSVASK 548 NF+SR+DYEE ES AN+++ LR ++ K G YGNY + ++DDF+YTDPVDGSV+ K Sbjct: 411 NFYSRHDYEEVESGPANELMNRLRSMVGDMK-GKTYGNYEVAYSDDFAYTDPVDGSVSEK 469 Query: 549 QGVRFVFTDGSRIIFRLSGTGSAGATVRIYIEQFEPDVSKHDVDAQIALKPLIDLALSVS 608 QG+R FTDGSRI+FRLSGTG+ GAT+R+Y+E +EPD SKHDVD Q AL LI+LA ++ Sbjct: 470 QGIRIGFTDGSRIVFRLSGTGTKGATLRVYLESYEPDGSKHDVDTQEALSSLIELAEEIA 529 Query: 609 KLKDFTGREKPTVIT 623 ++K FTGR+KPTVIT Sbjct: 530 QIKKFTGRDKPTVIT 544 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: 1023 Number of extensions: 35 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: 623 Length of database: 544 Length adjustment: 36 Effective length of query: 587 Effective length of database: 508 Effective search space: 298196 Effective search space used: 298196 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: 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