Align phosphomannomutase (EC 5.4.2.8) (characterized)
to candidate GFF5428 PS417_27785 phosphoglucomutase
Query= BRENDA::P26276 (463 letters) >FitnessBrowser__WCS417:GFF5428 Length = 465 Score = 728 bits (1879), Expect = 0.0 Identities = 365/466 (78%), Positives = 404/466 (86%), Gaps = 4/466 (0%) Query: 1 MSTAK--APTLPASIFRAYDIRGVVGDTLTAETAYWIGRAIGSESLARGEPCVAVGRDGR 58 MSTA PT P SIFRAYDIRGVV TLTAETAYWIGRAIGS+SLA+ EP V+VGRDGR Sbjct: 1 MSTAARVVPTFPDSIFRAYDIRGVVPKTLTAETAYWIGRAIGSQSLAQDEPNVSVGRDGR 60 Query: 59 LSGPELVKQLIQGLVDCGCQVSDVGMVPTPVLYYAANVLEGKSGVMLTGSHNPPDYNGFK 118 LSGPELV+QLIQGL D GC VSDVG+VPTP LYYAANVL GKSGVMLTGSHNP DYNGFK Sbjct: 61 LSGPELVEQLIQGLADSGCHVSDVGLVPTPALYYAANVLAGKSGVMLTGSHNPSDYNGFK 120 Query: 119 IVVAGETLANEQIQALRERIEKNDLASGVGSVEQVDILPRYFKQIRDDIAMAKPMKVVVD 178 IV+AG+TLANEQIQAL +R++ NDL SG G+V +VDIL RY +I D+ +A+ +KVVVD Sbjct: 121 IVIAGDTLANEQIQALHDRLKNNDLTSGKGTVTKVDILQRYSDEITRDVKLARRLKVVVD 180 Query: 179 CGNGVAGVIAPQLIEALGCSVIPLYCEVDGNFPNHHPDPGKPENLKDLIAKVKAENADLG 238 CGNG AGVIAPQL+EAL C VIPL+CEVDGNFPNHHPDPGKPENL DLIAKVK AD+G Sbjct: 181 CGNGAAGVIAPQLLEALNCEVIPLFCEVDGNFPNHHPDPGKPENLVDLIAKVKETGADVG 240 Query: 239 LAFDGDGDRVGVVTNTGTIIYPDRLLMLFAKDVVSRNPGADIIFDVKCTRRLIALISGYG 298 LAFDGDGDRVGVVT TG I++PDRLLMLFA+DVV+RN A+IIFDVKCTRRL LI YG Sbjct: 241 LAFDGDGDRVGVVTETGEIVFPDRLLMLFARDVVARNANAEIIFDVKCTRRLTPLIKEYG 300 Query: 299 GRPVMWKTGHSLIKKKMKETGALLAGEMSGHVFFKERWFGFDDGIYSAARLLEILSQDQR 358 GRP+MWKTGHSLIKKKMKETGALLAGEMSGHVFFKERWFGFDDGIYSAARLLEILS+++ Sbjct: 301 GRPLMWKTGHSLIKKKMKETGALLAGEMSGHVFFKERWFGFDDGIYSAARLLEILSKEKS 360 Query: 359 DSEHVFSAFPSDISTPEINITVTEDSKFAIIEALQRDAQWGEG-NITTLDGVRVDYPKGW 417 +E +F FP+DISTPEINI VTE+SKF+II+AL DAQWGEG N+TT+DGVRVDY KGW Sbjct: 361 TAEELFQTFPNDISTPEINIHVTEESKFSIIDAL-HDAQWGEGANLTTIDGVRVDYAKGW 419 Query: 418 GLVRASNTTPVLVLRFEADTEEELERIKTVFRNQLKAVDSSLPVPF 463 GLVRASNTTPVLVLRFEADTE EL+RIK VF QLK V L +PF Sbjct: 420 GLVRASNTTPVLVLRFEADTEAELQRIKDVFHAQLKRVAPDLQLPF 465 Lambda K H 0.319 0.138 0.410 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: 716 Number of extensions: 18 Number of successful extensions: 2 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: 463 Length of database: 465 Length adjustment: 33 Effective length of query: 430 Effective length of database: 432 Effective search space: 185760 Effective search space used: 185760 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 51 (24.3 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