Align phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) (EC 5.4.2.2) (characterized)
to candidate WP_011383017.1 AMB_RS02970 alpha-D-glucose phosphate-specific phosphoglucomutase
Query= BRENDA::Q9SCY0 (623 letters) >NCBI__GCF_000009985.1:WP_011383017.1 Length = 542 Score = 640 bits (1652), Expect = 0.0 Identities = 319/555 (57%), Positives = 405/555 (72%), Gaps = 16/555 (2%) Query: 69 IKSLPTKPIEGQKTGTSGLRKKVKVFMEDNYLANWIQALFNSLPLEDYKNATLVLGGDGR 128 +K++PT P GQK GTSGLRKKVKVF + +YL N++QA+F+S+ D TLV+GGDGR Sbjct: 4 VKTIPTTPFSGQKPGTSGLRKKVKVFAQPHYLENFVQAVFDSIG--DLGGKTLVVGGDGR 61 Query: 129 YFNKEASQIIIKIAAGNGVGQILVGKEGILSTPAVSAVIRKRKANGGFIMSASHNPGGPE 188 Y N+ A Q I+K+AA +G +++VG+ GILSTPA S VIRK K GG I+SASHNPGGP+ Sbjct: 62 YHNRTAIQTILKMAAASGFAKVMVGRGGILSTPAASCVIRKYKTFGGIILSASHNPGGPD 121 Query: 189 YDWGIKFNYSSGQPAPETITDKIYGNTLSISEIKVAEIPDIDLSQVGVTKYGNFSVEVID 248 D+GIK+N +G PAPE IT+ IY T IS K+ E D+DL +G G +V+V D Sbjct: 122 EDFGIKYNIPAGGPAPEAITEAIYARTQEISSYKIIEAADVDLDTIGERGLGGMTVQVFD 181 Query: 249 PVSDYLELMEDVFDFDLIRGLLSRSDFGFMFDAMHAVTGAYAKPIFVDNLGAKPDSISNG 308 PV+DY ELME +FDF IR + + F FDAMHAVTG YA I + LGA ++ NG Sbjct: 182 PVADYAELMESLFDFGAIRAAFA-AGFRMKFDAMHAVTGPYATEILENRLGAPKGTVMNG 240 Query: 309 VPLEDFGHGHPDPNLTYAKDLVDVMYRDNGPDFGAASDGDGDRNMVLGNKFFVTPSDSVA 368 VPLEDFGHGHPDPNL +A DLV+ + PDFGAASDGDGDRNM+LG F+VTPSDS+A Sbjct: 241 VPLEDFGHGHPDPNLVHAHDLVEALTGAGAPDFGAASDGDGDRNMILGRDFYVTPSDSLA 300 Query: 369 IIAANAQEAIPYFRAGPKGLARSMPTSGALDRVAEKLKLPFFEVPTGWKFFGNLMDAGKL 428 ++AANA P + G KG+ARSMPTS A DRVA KL +P +E PTGWKFFG L+DAGK Sbjct: 301 VLAANA-TLCPGYARGLKGIARSMPTSAAPDRVAAKLGIPAWETPTGWKFFGTLLDAGKA 359 Query: 429 SICGEESFGTGSDHIREKDGIWAVLAWLSILAHRNKDTKPGDKLVSVADVVKEYWATYGR 488 + CGEESFGTGSDH+REKDG+WAVLAWL++LA R + SVAD+V +W YGR Sbjct: 360 TFCGEESFGTGSDHVREKDGLWAVLAWLNVLAVRKQ---------SVADIVTAHWREYGR 410 Query: 489 NFFSRYDYEECESEGANKMIEYLREILSKSKAGDVYGNYVLQFADDFSYTDPVDGSVASK 548 N +SR+DYE +S A ++E+LR + S G+ G Y + F DDF+YTDPVDGSV+ K Sbjct: 411 NVYSRHDYEGIDSAAAEGLMEHLRGL---SLKGERLGTYTVAFNDDFAYTDPVDGSVSKK 467 Query: 549 QGVRFVFTDGSRIIFRLSGTGSAGATVRIYIEQFEPDVSKHDVDAQIALKPLIDLALSVS 608 QG+R VF DGSR++FRLSGTG+ GAT+R+YIE+FEPD +KH +D Q+AL LI +A ++ Sbjct: 468 QGIRVVFEDGSRVVFRLSGTGTEGATLRVYIERFEPDATKHHLDPQVALADLITIARDLA 527 Query: 609 KLKDFTGREKPTVIT 623 +++ TGR +PTVIT Sbjct: 528 QIEARTGRTEPTVIT 542 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: 1002 Number of extensions: 44 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: 542 Length adjustment: 36 Effective length of query: 587 Effective length of database: 506 Effective search space: 297022 Effective search space used: 297022 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 17 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