Align phosphomannomutase (EC 5.4.2.8) (characterized)
to candidate BPHYT_RS04470 BPHYT_RS04470 phosphoglucomutase
Query= BRENDA::P26276 (463 letters) >FitnessBrowser__BFirm:BPHYT_RS04470 Length = 464 Score = 508 bits (1307), Expect = e-148 Identities = 253/461 (54%), Positives = 337/461 (73%), Gaps = 10/461 (2%) Query: 12 SIFRAYDIRGVVGDTLTAETAYWIGRAIGSESLARGEPCVAVGRDGRLSGPELVKQLIQG 71 SIF+AYDIRGV+G TL A+ A IGRA GSE A+G V V RDGRLSGPELV+ L G Sbjct: 5 SIFKAYDIRGVIGKTLDADAARSIGRAFGSEVRAQGGDAVVVARDGRLSGPELVQALSDG 64 Query: 72 LVDCGCQVSDVGMVPTPVLYYAANV---LEG-----KSGVMLTGSHNPPDYNGFKIVVAG 123 L + G V +VGMVPTPV Y+AA+V L+G S +++TGSHNPPDYNGFK+V+ G Sbjct: 65 LREAGVDVVNVGMVPTPVGYFAASVPLQLDGGERRVDSCIVVTGSHNPPDYNGFKMVLRG 124 Query: 124 ETLANEQIQALRERIEKNDLASGVGSVEQVDILPRYFKQIRDDIAMAKPMKVVVDCGNGV 183 + EQI AL +RI + ++G G+ + DI Y ++I DI +A+P+K+VVD GNGV Sbjct: 125 AAIYGEQILALHQRIVDENFSTGSGTYTEYDIADAYLERITSDIKLARPIKIVVDTGNGV 184 Query: 184 AGVIAPQLIEALGCSVIPLYCEVDGNFPNHHPDPGKPENLKDLIAKVKAENADLGLAFDG 243 AG +AP+L + LGC ++ L+ E+DGNFPNHHPDP PENL+D+I +K +A++G AFDG Sbjct: 185 AGGLAPKLFKKLGCELVELFTEIDGNFPNHHPDPAHPENLQDVIRALKETDAEIGFAFDG 244 Query: 244 DGDRVGVVTNTGTIIYPDRLLMLFAKDVVSRNPGADIIFDVKCTRRLIALISGYGGRPVM 303 DGDR+GVVT G IIYPDR LMLFA++V+SRN GA II+DVKCTR L + GG P+M Sbjct: 245 DGDRLGVVTKDGEIIYPDRQLMLFAEEVLSRNKGAQIIYDVKCTRNLAKWVKDKGGEPLM 304 Query: 304 WKTGHSLIKKKMKETGALLAGEMSGHVFFKERWFGFDDGIYSAARLLEILSQDQRDSEHV 363 WKTGHSL+K K++ETGA LAGEMSGHVFFK+RW+GFDDG+Y+ ARLLEIL++ + D + Sbjct: 305 WKTGHSLVKAKLRETGAPLAGEMSGHVFFKDRWYGFDDGLYTGARLLEILTRVE-DPSKL 363 Query: 364 FSAFPSDISTPEINITVTEDSKFAIIEALQRDAQW-GEGNITTLDGVRVDYPKGWGLVRA 422 ++ P+ STPE+ + + E F +I LQ++A++ G ++ +DG+RV+YP G+GL R+ Sbjct: 364 LNSLPNSNSTPELQLKLEEGENFELIARLQQNAKFTGADDVVKIDGLRVEYPDGFGLARS 423 Query: 423 SNTTPVLVLRFEADTEEELERIKTVFRNQLKAVDSSLPVPF 463 SNTTPV+V+RFEAD + L+RI+ FR + A +PF Sbjct: 424 SNTTPVVVMRFEADNDAALKRIQEDFRRVIMAEKPDAKLPF 464 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: 627 Number of extensions: 21 Number of successful extensions: 3 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: 464 Length adjustment: 33 Effective length of query: 430 Effective length of database: 431 Effective search space: 185330 Effective search space used: 185330 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