Align phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) (EC 5.4.2.2) (characterized)
to candidate SMc03925 SMc03925 phosphoglucomutase
Query= BRENDA::Q9SCY0 (623 letters) >FitnessBrowser__Smeli:SMc03925 Length = 542 Score = 607 bits (1566), Expect = e-178 Identities = 305/555 (54%), Positives = 405/555 (72%), Gaps = 14/555 (2%) Query: 69 IKSLPTKPIEGQKTGTSGLRKKVKVFMEDNYLANWIQALFNSLPLEDYKNATLVLGGDGR 128 I+++ T P QK GTSGLRKKV VF + NY N+IQ++F+SL E ++ TLV+GGDGR Sbjct: 2 IRTVSTNPYGDQKPGTSGLRKKVPVFQQKNYAENFIQSIFDSL--EGFEGQTLVIGGDGR 59 Query: 129 YFNKEASQIIIKIAAGNGVGQILVGKEGILSTPAVSAVIRKRKANGGFIMSASHNPGGPE 188 Y+N+E Q +K+AA NG G++LVG+ GILSTPA S VIRK KA GG ++SASHNPGGP Sbjct: 60 YYNREVIQKAVKMAAANGFGRVLVGRGGILSTPAASNVIRKYKAFGGIVLSASHNPGGPT 119 Query: 189 YDWGIKFNYSSGQPAPETITDKIYGNTLSISEIKVAEIPDIDLSQVGVTKYGNFSVEVID 248 D+GIK+N +G PAPE +TD IY + +I K+A+ PD++L G + + +V VID Sbjct: 120 EDFGIKYNVGNGGPAPEKVTDAIYSRSKAIDSYKIADAPDVNLDVEGSQQVEDMTVTVID 179 Query: 249 PVSDYLELMEDVFDFDLIRGLLSRSDFGFMFDAMHAVTGAYAKPIFVDNLGAKPDSISNG 308 PV+DY ELME +FDFD IR L++ F +FDAM AVTG YAK I LGA S+ N Sbjct: 180 PVADYAELMESLFDFDAIRKLIA-GGFRVVFDAMSAVTGPYAKEIIEKRLGAPKGSVMNF 238 Query: 309 VPLEDFGHGHPDPNLTYAKDLVDVMYRDNGPDFGAASDGDGDRNMVLGNKFFVTPSDSVA 368 +PL DFG HPDPNL +A+ L + M + PDFGAASDGDGDRN+++G FVTPSDS+A Sbjct: 239 IPLPDFGGHHPDPNLVHARALYETMMAPDAPDFGAASDGDGDRNLIIGKGIFVTPSDSLA 298 Query: 369 IIAANAQEAIPYFRAGPKGLARSMPTSGALDRVAEKLKLPFFEVPTGWKFFGNLMDAGKL 428 ++AANA A P + G G+ARSMPTSGA DRVAEKL + +E PTGWKFFGNL+D G Sbjct: 299 MLAANAHLA-PGYAKGLAGIARSMPTSGAADRVAEKLGVGIYETPTGWKFFGNLLDEGLA 357 Query: 429 SICGEESFGTGSDHIREKDGIWAVLAWLSILAHRNKDTKPGDKLVSVADVVKEYWATYGR 488 +ICGEES GTGS+H+REKDG+WAVL WL+ILA R + S ++ +++WATYGR Sbjct: 358 TICGEESAGTGSNHVREKDGLWAVLLWLNILAARKE---------SALEIARKHWATYGR 408 Query: 489 NFFSRYDYEECESEGANKMIEYLREILSKSKAGDVYGNYVLQFADDFSYTDPVDGSVASK 548 N++SR+DYEE +++ AN +I LR+ L+ + G +G ++ ADDFSY DPVD SV+ Sbjct: 409 NYYSRHDYEEVDTDAANGLIAALRDKLA-ALPGKSFGALTVETADDFSYHDPVDKSVSKN 467 Query: 549 QGVRFVFTDGSRIIFRLSGTGSAGATVRIYIEQFEPDVSKHDVDAQIALKPLIDLALSVS 608 QGVR +F GSR++FRLSGTG++GAT+R+YIE++EPD ++HD+D Q AL LI +A ++ Sbjct: 468 QGVRILFKGGSRVVFRLSGTGTSGATLRVYIERYEPDPTRHDLDTQEALADLIAVADEIA 527 Query: 609 KLKDFTGREKPTVIT 623 ++K TGR++P+VIT Sbjct: 528 EIKANTGRDEPSVIT 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: 1019 Number of extensions: 59 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