Align phosphomannomutase (EC 5.4.2.8) (characterized)
to candidate HSERO_RS02355 HSERO_RS02355 phosphoglucomutase
Query= BRENDA::P26276 (463 letters) >FitnessBrowser__HerbieS:HSERO_RS02355 Length = 458 Score = 523 bits (1346), Expect = e-153 Identities = 250/457 (54%), Positives = 332/457 (72%), Gaps = 2/457 (0%) Query: 8 TLPASIFRAYDIRGVVGDTLTAETAYWIGRAIGSESLARGEPCVAVGRDGRLSGPELVKQ 67 +L SIF+AYDIRG++G TL AY IG+A G+ +LA+G+ V +GRDGRLSGPEL + Sbjct: 3 SLSPSIFKAYDIRGIIGKTLDGTVAYRIGQAFGAAALAKGQKKVVIGRDGRLSGPELAAE 62 Query: 68 LIQGLVDCGCQVSDVGMVPTPVLYYAANVLEGKSGVMLTGSHNPPDYNGFKIVVAGETLA 127 L +GL G V D+GMV TP++Y+ +VL+ +SG+M+TGSHNPPDYNGFK+V+AGE + Sbjct: 63 LARGLQAVGVDVIDLGMVATPMVYFGTHVLDTQSGIMVTGSHNPPDYNGFKMVLAGEAIH 122 Query: 128 NEQIQALRERIEKNDLASGVGSVEQVDILPRYFKQIRDDIAMAKPMKVVVDCGNGVAGVI 187 E IQAL I K D G G DI Y +++ D+ +A+P+K+ VDCGNGVAG Sbjct: 123 GETIQALYHAIVKGDFPQGAGGYATHDIKAAYIERMLADVKLARPLKIAVDCGNGVAGAF 182 Query: 188 APQLIEALGCSVIPLYCEVDGNFPNHHPDPGKPENLKDLIAKVKAENADLGLAFDGDGDR 247 A ++ LGC V L+CEVDG FPNHHPDP PENL+DLI ++ + +LGLAFDGDGDR Sbjct: 183 AGEIYRTLGCEVTELFCEVDGTFPNHHPDPAHPENLQDLIRCLRETDCELGLAFDGDGDR 242 Query: 248 VGVVTNTGTIIYPDRLLMLFAKDVVSRNPGADIIFDVKCTRRLIALISGYGGRPVMWKTG 307 +G+VT G IIYPDR LMLFA+DV++R+PG +I++DVKCTR L I+ GGRP+MWKTG Sbjct: 243 LGLVTKDGQIIYPDRQLMLFAEDVLTRHPGKEILYDVKCTRHLAPWITARGGRPLMWKTG 302 Query: 308 HSLIKKKMKETGALLAGEMSGHVFFKERWFGFDDGIYSAARLLEILSQDQRDSEHVFSAF 367 HSL+K K++ETGA L GEMSGH+FFK+RWFGFDDG+Y+ R+LE++++ Q D V +A Sbjct: 303 HSLVKAKLRETGAPLGGEMSGHIFFKDRWFGFDDGLYAGVRMLELMAR-QADPSAVLNAL 361 Query: 368 PSDISTPEINITVTEDSKFAIIEALQRDAQW-GEGNITTLDGVRVDYPKGWGLVRASNTT 426 P +STPE+ + + E A+I LQ +A + G I +DG+RV+YP G+GL R+SNTT Sbjct: 362 PQSVSTPELQLKLQEGENVALIGKLQGEASFEGAQEIIAIDGLRVEYPDGFGLARSSNTT 421 Query: 427 PVLVLRFEADTEEELERIKTVFRNQLKAVDSSLPVPF 463 PV+VLRFEA+T E L RI+ FR + AV + +PF Sbjct: 422 PVVVLRFEAETPEALARIQAQFRQAILAVRPEVALPF 458 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: 605 Number of extensions: 19 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: 458 Length adjustment: 33 Effective length of query: 430 Effective length of database: 425 Effective search space: 182750 Effective search space used: 182750 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