Align phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) (EC 5.4.2.2) (characterized)
to candidate Synpcc7942_0156 Synpcc7942_0156 phosphoglucomutase
Query= BRENDA::Q9SCY0 (623 letters) >FitnessBrowser__SynE:Synpcc7942_0156 Length = 543 Score = 629 bits (1621), Expect = 0.0 Identities = 315/557 (56%), Positives = 412/557 (73%), Gaps = 14/557 (2%) Query: 67 IEIKSLPTKPIEGQKTGTSGLRKKVKVFMEDNYLANWIQALFNSLPLEDYKNATLVLGGD 126 + I ++ T+ QK GTSGLRK+V VF + +YL N++Q++F+SL E Y+ TLVLGGD Sbjct: 1 MNIHTVATQAFSDQKPGTSGLRKQVPVFQKRHYLENFVQSIFDSL--EGYQGQTLVLGGD 58 Query: 127 GRYFNKEASQIIIKIAAGNGVGQILVGKEGILSTPAVSAVIRKRKANGGFIMSASHNPGG 186 GRY+N+ A Q I+K+AA NG G++LVG+ GILSTPAVS +IR+ A GG I+SASHNPGG Sbjct: 59 GRYYNRTAIQTILKMAAANGWGRVLVGQGGILSTPAVSNLIRQNGAFGGIILSASHNPGG 118 Query: 187 PEYDWGIKFNYSSGQPAPETITDKIYGNTLSISEIKVAEIPDIDLSQVGVTKYGNFSVEV 246 PE D+GIK+N S+G PAPE +TD IY +L I ++ E D+DL ++G + G +VEV Sbjct: 119 PEGDFGIKYNISNGGPAPEKVTDAIYACSLKIEAYRILEAGDVDLDRLGSQQLGEMTVEV 178 Query: 247 IDPVSDYLELMEDVFDFDLIRGLLSRSDFGFMFDAMHAVTGAYAKPIFVDNLGAKPDSIS 306 ID V+DY LM+ +FDFD IR L R D+MHAVTG YA IF LGA ++ Sbjct: 179 IDSVADYSRLMQSLFDFDRIRDRL-RGGLRIAIDSMHAVTGPYATTIFEKELGAAAGTVF 237 Query: 307 NGVPLEDFGHGHPDPNLTYAKDLVDVMYRDNGPDFGAASDGDGDRNMVLGNKFFVTPSDS 366 NG PLEDFG GHPDPNL YA DLV++++ D PDFGAASDGDGDRNM+LGN FFVTPSDS Sbjct: 238 NGKPLEDFGGGHPDPNLVYAHDLVELLFGDRAPDFGAASDGDGDRNMILGNHFFVTPSDS 297 Query: 367 VAIIAANAQEAIPYFRAGPKGLARSMPTSGALDRVAEKLKLPFFEVPTGWKFFGNLMDAG 426 +AI+AANA +P +R G G+ARSMPTS A DRVA+ L LP +E PTGWKFFGNL+DA Sbjct: 298 LAILAANA-SLVPAYRNGLSGIARSMPTSAAADRVAQALNLPCYETPTGWKFFGNLLDAD 356 Query: 427 KLSICGEESFGTGSDHIREKDGIWAVLAWLSILAHRNKDTKPGDKLVSVADVVKEYWATY 486 ++++CGEESFGTGS+H+REKDG+WAVL WL+ILA R + SVA++V+E+W TY Sbjct: 357 RVTLCGEESFGTGSNHVREKDGLWAVLFWLNILAVREQ---------SVAEIVQEHWRTY 407 Query: 487 GRNFFSRYDYEECESEGANKMIEYLREILSKSKAGDVYGNYVLQFADDFSYTDPVDGSVA 546 GRN++SR+DYE ES+ A+ +++ LR L S G G Y + +ADDF Y DPVDGS++ Sbjct: 408 GRNYYSRHDYEGVESDRASTLVDKLRSQL-PSLTGQKLGAYTVAYADDFRYEDPVDGSIS 466 Query: 547 SKQGVRFVFTDGSRIIFRLSGTGSAGATVRIYIEQFEPDVSKHDVDAQIALKPLIDLALS 606 +QG+R F DGSR++FRLSGTG+AGAT+R+Y+E+FE D +K +D Q+AL LI +A Sbjct: 467 EQQGIRIGFEDGSRMVFRLSGTGTAGATLRLYLERFEGDTTKQGLDPQVALADLIAIADE 526 Query: 607 VSKLKDFTGREKPTVIT 623 V+++ TG ++PTVIT Sbjct: 527 VAQITTLTGFDQPTVIT 543 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: 41 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: 543 Length adjustment: 36 Effective length of query: 587 Effective length of database: 507 Effective search space: 297609 Effective search space used: 297609 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