Align phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) (EC 5.4.2.2) (characterized)
to candidate WP_010959952.1 MCA_RS03015 alpha-D-glucose phosphate-specific phosphoglucomutase
Query= BRENDA::Q9SCY0 (623 letters) >NCBI__GCF_000008325.1:WP_010959952.1 Length = 544 Score = 597 bits (1538), Expect = e-175 Identities = 295/558 (52%), Positives = 404/558 (72%), Gaps = 15/558 (2%) Query: 66 SIEIKSLPTKPIEGQKTGTSGLRKKVKVFMEDNYLANWIQALFNSLPLEDYKNATLVLGG 125 ++EI+ T P QK GTSGLRKKVKVF++ NYL N++Q++F+++ D ATLV+GG Sbjct: 2 AVEIRK--TTPYPDQKPGTSGLRKKVKVFLQGNYLENFVQSVFDTVETAD--GATLVVGG 57 Query: 126 DGRYFNKEASQIIIKIAAGNGVGQILVGKEGILSTPAVSAVIRKRKANGGFIMSASHNPG 185 DGRYFN++A QII+++AA NGVG++LVG+ G+LSTPA S VIRK +A GGF++SASHNPG Sbjct: 58 DGRYFNRQAIQIILRMAAANGVGRVLVGRGGLLSTPAASCVIRKHRALGGFVLSASHNPG 117 Query: 186 GPEYDWGIKFNYSSGQPAPETITDKIYGNTLSISEIKVAEIPDIDLSQVGVTKYGNFSVE 245 GPE D+GIKFN ++G PAPE+ TD++Y + I ++ PD+D+ G ++ G+ +E Sbjct: 118 GPEEDFGIKFNVANGGPAPESFTDRVYQRSRVIDAYRIVSAPDLDIDTPGRSRIGDMEIE 177 Query: 246 VIDPVSDYLELMEDVFDFDLIRGLLSRSDFGFMFDAMHAVTGAYAKPIFVDNLGAKPDSI 305 VIDPV+DY ELME +FDF LIR FDAMHAVTG YAK I + L A P S+ Sbjct: 178 VIDPVADYAELMEHLFDFGLIRSGFRSGALTLRFDAMHAVTGPYAKRILEETLSAAPGSV 237 Query: 306 SNGVPLEDFGHGHPDPNLTYAKDLVDVMYRDNGPDFGAASDGDGDRNMVLGNKFFVTPSD 365 N VPLEDFG GHPDPNL +A++L VMY P GAASDGDGDRNM++G FVTPSD Sbjct: 238 VNAVPLEDFGGGHPDPNLVHARELAAVMYSGRPPTLGAASDGDGDRNMIMGANCFVTPSD 297 Query: 366 SVAIIAANAQEAIPYFRAGPKGLARSMPTSGALDRVAEKLKLPFFEVPTGWKFFGNLMDA 425 S+AI+AANA +P ++ G +G+ARSMPT A+DRVA + + +E PTGWKFFGNL+DA Sbjct: 298 SLAILAANA-HLVPGYKDGLRGVARSMPTGRAVDRVAAAMGIECYETPTGWKFFGNLLDA 356 Query: 426 GKLSICGEESFGTGSDHIREKDGIWAVLAWLSILAHRNKDTKPGDKLVSVADVVKEYWAT 485 ++++CGEESFGTGSDH+REKDG+WAVL WL+++A R + SVA +V ++W Sbjct: 357 RRITLCGEESFGTGSDHVREKDGLWAVLFWLNLIALRKQ---------SVAAIVADHWRR 407 Query: 486 YGRNFFSRYDYEECESEGANKMIEYLREILSKSKAGDVYGNYVLQFADDFSYTDPVDGSV 545 +GR+++SR+DYE E A ++ L+++L++ G +G+Y + ADDF Y DPVDGSV Sbjct: 408 FGRDYYSRHDYEGIEVPVAEGIMGRLQDLLAE-LPGRAFGDYRVTLADDFRYVDPVDGSV 466 Query: 546 ASKQGVRFVFTDGSRIIFRLSGTGSAGATVRIYIEQFEPDVSKHDVDAQIALKPLIDLAL 605 + QG+R F + SRI+FRLSGTG+ GAT+R+Y+E++E D + H++ Q AL LI +A Sbjct: 467 SEHQGIRIAFDNSSRIVFRLSGTGTEGATLRVYMERYERDPNLHNLPTQEALADLIAIAE 526 Query: 606 SVSKLKDFTGREKPTVIT 623 + ++K TG +P+V+T Sbjct: 527 DLCQVKKRTGMAQPSVMT 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: 990 Number of extensions: 47 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