Align phosphomannose mutase (EC 5.4.2.8) (characterized)
to candidate CA265_RS13185 CA265_RS13185 phosphoglucosamine mutase
Query= metacyc::MONOMER-13382 (455 letters) >FitnessBrowser__Pedo557:CA265_RS13185 Length = 461 Score = 265 bits (678), Expect = 2e-75 Identities = 171/456 (37%), Positives = 259/456 (56%), Gaps = 15/456 (3%) Query: 6 GTFGVRGIANEKITPEFAMKIGMAFGT-LLKREGRKKPLVVVGRDTRVSGEMLKEALISG 64 GT G G A + +TP +K AFG+ ++++ G K+ +V+GRD R+SGEM+ +I Sbjct: 12 GTIG--GRAGDGLTPFDIVKFTAAFGSWVVQKTGNKR--IVLGRDARISGEMVNNLVIGT 67 Query: 65 LLSVGCDVIDVGIAPTPAVQWATKHFNADGGAVITASHNPPEYNGIKLLEPNGMGLKKER 124 L +G +VID+G++ TP V+ A A GG ++TASHNP ++N +KLL +G + Sbjct: 68 LQGLGIEVIDLGLSTTPTVEVAVPDEKAGGGIILTASHNPKQWNALKLLNASGEFISDAD 127 Query: 125 EAIVEELFFKEDFDRAKWYEIGEVRRED-IIKPYIEAIKS--KVDVEAIKKRKPFVVVDT 181 V +L DFD A ++G+V + D ++ +I+ + + VDVEAIKK VV+D Sbjct: 128 GKEVLDLAESADFDFADVDKLGKVIKNDTYLQKHIDKVLALPLVDVEAIKKADFKVVIDC 187 Query: 182 SNGAGSLTLPYLLRELG-CKVITVNAQPDGYFPARNPEPNEENLKEFMEIVKALGADFGV 240 N G + +P LL+ LG KV+ + PDG+FP NPEP ENL E + V+ AD G+ Sbjct: 188 VNSTGGIFIPALLKALGVSKVVELYCTPDGHFP-HNPEPLPENLTEISKEVQKQNADLGI 246 Query: 241 AQDGDADRAVFIDENGRFIQGDKTFALVADAVLKEKGGGLLVTTVATSNLLDDIAKKHGA 300 D D DR F++E+G + T VAD VLK G V+ ++++ L D+ + GA Sbjct: 247 VVDPDVDRLCFVNEDGSMFGEEYTLVAVADYVLKNTPGN-TVSNLSSTRALRDVTESAGA 305 Query: 301 KVMRTKVGDLIVARALYENNGTIGGEENGGVIFPEHVLGRDGAMTVAKVVEIFAKSGKKF 360 + + VG++ V + N IGGE NGG+I+PE GRD + +A + AK GK Sbjct: 306 EYNASAVGEVNVVNKMKATNAIIGGEGNGGIIYPESHYGRDALVGIALFLTHLAKFGKSI 365 Query: 361 SELIDELPKYYQIKTKRHV--EGDRHAIVNKVAEMARERGYTVDTTDGAKIIFEDGWVLV 418 S L P+Y+ K K + E D ++ +V E + + Y+ T DG KI F+ WV + Sbjct: 366 SVLRSSYPQYHISKNKITLTPEMDIDNLLKQVEEKYKNQPYS--TIDGLKIEFDKTWVHL 423 Query: 419 RASGTEPIIRIFSEAKSKEKAQEYLNLGIELLEKAL 454 R S TEPIIRI+SEA+++ A+ N I +++ L Sbjct: 424 RRSNTEPIIRIYSEAENETIAENLANKIISDIKEIL 459 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: 547 Number of extensions: 33 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: 455 Length of database: 461 Length adjustment: 33 Effective length of query: 422 Effective length of database: 428 Effective search space: 180616 Effective search space used: 180616 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