Align phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) (EC 5.4.2.2) (characterized)
to candidate AZOBR_RS02670 AZOBR_RS02670 phosphoglucomutase
Query= BRENDA::Q9SCY0 (623 letters) >FitnessBrowser__azobra:AZOBR_RS02670 Length = 543 Score = 608 bits (1568), Expect = e-178 Identities = 305/551 (55%), Positives = 401/551 (72%), Gaps = 14/551 (2%) Query: 73 PTKPIEGQKTGTSGLRKKVKVFMEDNYLANWIQALFNSLPLEDYKNATLVLGGDGRYFNK 132 PT P +GQK GTSGLRK VKVF + YL N++Q++F+ + + ATLV+GGDGRY N+ Sbjct: 7 PTTPFDGQKPGTSGLRKAVKVFEQPRYLENFVQSIFDCV--DGLSGATLVIGGDGRYHNR 64 Query: 133 EASQIIIKIAAGNGVGQILVGKEGILSTPAVSAVIRKRKANGGFIMSASHNPGGPEYDWG 192 A Q I+++AA NGV + +VG+ GILSTPA S VIRKR A GG I+SASHNPGGP+ D+G Sbjct: 65 TAVQTILRMAAANGVARAVVGRGGILSTPAASCVIRKRGAIGGVILSASHNPGGPDGDFG 124 Query: 193 IKFNYSSGQPAPETITDKIYGNTLSISEIKVAEIPDIDLSQVGVTKYGNFSVEVIDPVSD 252 IKFN ++G PAPE++TD + + +I+E K E PD+DL ++G T G +VEVIDPV+D Sbjct: 125 IKFNAANGGPAPESMTDAFFARSKAITEYKTLESPDLDLDRLGETALGGIAVEVIDPVAD 184 Query: 253 YLELMEDVFDFDLIRGLLSRSDFGFMFDAMHAVTGAYAKPIFVDNLGAKPDSISNGVPLE 312 Y ELME +FD IR L + S F +FDAMHAVTG YA I LGA ++ NG PLE Sbjct: 185 YAELMESLFDMAAIRKLFA-SGFRMVFDAMHAVTGPYATEILERRLGAPAGTVINGTPLE 243 Query: 313 DFGHGHPDPNLTYAKDLVDVMYRDNGPDFGAASDGDGDRNMVLGNKFFVTPSDSVAIIAA 372 DFG HPDPNL +A++LV ++ + PDFGAASDGDGDRNM+LG FV+PSDS+A++AA Sbjct: 244 DFGGHHPDPNLAHAEELVGRLFGPDAPDFGAASDGDGDRNMILGRNVFVSPSDSLAVLAA 303 Query: 373 NAQEAIPYFRAGPKGLARSMPTSGALDRVAEKLKLPFFEVPTGWKFFGNLMDAGKLSICG 432 NA +P F+ G G+ARSMPTS A+DRVA KL + +E PTGWKFFG L+DAG++++CG Sbjct: 304 NATH-VPAFKGGLAGVARSMPTSRAVDRVAAKLGISCYETPTGWKFFGTLLDAGRINLCG 362 Query: 433 EESFGTGSDHIREKDGIWAVLAWLSILAHRNKDTKPGDKLVSVADVVKEYWATYGRNFFS 492 EESFGTG+DH+REKDG+WAVL WL++LA R +SVA+++ E+W TYGR ++ Sbjct: 363 EESFGTGADHVREKDGLWAVLMWLNVLAARG---------LSVAELMAEHWGTYGRTYYG 413 Query: 493 RYDYEECESEGANKMIEYLREILSKSKAGDVYGNYVLQFADDFSYTDPVDGSVASKQGVR 552 R+DYE E A+ +I LR LS S AG G + AD+F+YTDPVDGS + +QG+R Sbjct: 414 RHDYEAIPQEAADALIAELRGTLS-SLAGTDLGGRTVAAADEFAYTDPVDGSRSERQGLR 472 Query: 553 FVFTDGSRIIFRLSGTGSAGATVRIYIEQFEPDVSKHDVDAQIALKPLIDLALSVSKLKD 612 F DGSRI++RLSGTG++GAT+R+Y E++EP +H +DA +ALKPL DLA ++ ++ Sbjct: 473 VGFEDGSRIVYRLSGTGTSGATLRVYFERYEPVGGEHGLDAPVALKPLADLAAELAGIER 532 Query: 613 FTGREKPTVIT 623 TGR KP V T Sbjct: 533 HTGRTKPDVAT 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: 1013 Number of extensions: 48 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