Align phosphomannose mutase (EC 5.4.2.8) (characterized)
to candidate Echvi_1178 Echvi_1178 phosphoglucosamine mutase
Query= metacyc::MONOMER-13382 (455 letters) >FitnessBrowser__Cola:Echvi_1178 Length = 463 Score = 250 bits (639), Expect = 6e-71 Identities = 165/456 (36%), Positives = 246/456 (53%), Gaps = 13/456 (2%) Query: 6 GTFGVRGIANEKITPEFAMKIGMAFGTLLKREGRKKPLVVVGRDTRVSGEMLKEALISGL 65 GT G G + E +TP +K A+G + E P +V+GRD R+SG+M+ + + + L Sbjct: 12 GTIG--GKSGEGLTPVDIVKFTSAYGAWIL-EKTNNPRIVIGRDARISGDMVSKLVTATL 68 Query: 66 LSVGCDVIDVGIAPTPAVQWATKHFNADGGAVITASHNPPEYNGIKLLEPNGMGLKKERE 125 +G VID+G++ TP V++A A GG ++TASHNP ++N +KLL G + + Sbjct: 69 QGLGIQVIDLGLSTTPTVEFAVPLEKAGGGIILTASHNPIQWNALKLLNDKGEFISDQDG 128 Query: 126 AIVEELFFKEDFDRAKWYEIGEVRR-EDIIKPYIEAIKS--KVDVEAIKKRKPFVVVDTS 182 V E KEDF+ A IG ED I +I+ + S VD EAI R VV+D Sbjct: 129 KEVLEKAEKEDFEFATVKNIGAYTLVEDYIDRHIDHVLSLDLVDKEAIAARNFRVVIDCV 188 Query: 183 NGAGSLTLPYLLRELGCK-VITVNAQPDGYFPARNPEPNEENLKEFMEIVKALGADFGVA 241 N G + LP LL+ LG + V + +PDG+FP NPEP ENL++ +K D G+ Sbjct: 189 NSTGGIALPKLLKALGVEHVEEMYCEPDGHFP-HNPEPLPENLRDISSKLKNGKFDLGIV 247 Query: 242 QDGDADRAVFIDENGRFIQGDKTFALVADAVLKEKGGGLLVTTVATSNLLDDIAKKHGAK 301 D D DR F+ E+G + T +AD VL + G V+ ++++ L D+ +KH Sbjct: 248 VDPDVDRLAFLTEDGSAFGEEYTLVAIADYVLSQTPGN-TVSNLSSTRALRDVTEKHEGT 306 Query: 302 VMRTKVGDLIVARALYENNGTIGGEENGGVIFPEHVLGRDGAMTVAKVVEIFAKSGKKFS 361 VG++ V + E N IGGE NGGVI+P GRD + + + AK GK + Sbjct: 307 YNAAAVGEVNVVNKMKETNAIIGGEGNGGVIYPSSHYGRDALVGIGLFLTHLAKFGKTAN 366 Query: 362 ELIDELPKYYQIKTKRHV--EGDRHAIVNKVAEMARERGYTVDTTDGAKIIFEDGWVLVR 419 L P YY K K + E D AI+++++ ++ ++ DG KI FE WV +R Sbjct: 367 RLRASYPNYYISKNKIELTPEIDVDAILDEISRKYSKQ--PINDIDGIKIEFEKEWVHLR 424 Query: 420 ASGTEPIIRIFSEAKSKEKAQEYLNLGIELLEKALS 455 S TEPIIRI+SE+++K A+ N I +++ +S Sbjct: 425 KSNTEPIIRIYSESETKATAEHLANKLILDIKEVIS 460 Lambda K H 0.317 0.138 0.391 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: 522 Number of extensions: 24 Number of successful extensions: 5 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: 455 Length of database: 463 Length adjustment: 33 Effective length of query: 422 Effective length of database: 430 Effective search space: 181460 Effective search space used: 181460 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: 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