Align phosphomannose mutase (EC 5.4.2.8) (characterized)
to candidate WP_092056175.1 BQ4888_RS08015 phosphoglucosamine mutase
Query= metacyc::MONOMER-13382 (455 letters) >NCBI__GCF_900111775.1:WP_092056175.1 Length = 458 Score = 231 bits (588), Expect = 5e-65 Identities = 153/450 (34%), Positives = 246/450 (54%), Gaps = 26/450 (5%) Query: 3 KLFGTFGVRGIAN-EKITPEFAMKIGMAFGTLLK-REGRKKPLVVVGRDTRVSGEMLKEA 60 KLFGT GVRG+AN +T E M++G A + K ++ +++ +V+G+DTR+SG M++ A Sbjct: 4 KLFGTDGVRGVANIHPMTTEIVMQLGRAAAYIFKDKDEKRRHRIVIGKDTRLSGYMIENA 63 Query: 61 LISGLLSVGCDVIDVGIAPTPAVQWATKHFNADGGAVITASHNPPEYNGIKLLEPNGMGL 120 L++G+ S+G DV+ VG PTP + + T AD G VI+ASHNP + NGIK + G L Sbjct: 64 LVAGICSMGVDVLLVGPLPTPGIAFITSSMRADAGVVISASHNPYQDNGIKFFDGTGFKL 123 Query: 121 KKEREAIVEELFFKEDFD--RAKWYEIGEVRREDIIK-PYIEAIKS----KVDVEAIKKR 173 E E +E+L + + D R E+G+ R D K Y+ +K+ +D++ ++ Sbjct: 124 PDETELKIEDLIYSKKIDSLRPVASEVGKAFRIDDAKGRYVVFLKAAFPKDLDLKGLR-- 181 Query: 174 KPFVVVDTSNGAGSLTLPYLLRELGCKVITVNAQPDGYFPARNPEPNEENLKEFMEIVKA 233 +V+D +NGA P +L ELG +VI + P+G N + + + V Sbjct: 182 ---IVLDCANGAAYKVAPAVLEELGAEVIPLGISPNG--TNINAGCGSLHPQVIADAVVE 236 Query: 234 LGADFGVAQDGDADRAVFIDENGRFIQGDKTFALVADAVL--KEKGGGLLVTTVATSNLL 291 A G+A DGDADR +F+DE G + GD A+ A +L + LV TV ++ L Sbjct: 237 NRAHLGIALDGDADRVIFVDEFGNEVDGDHIMAICATDLLAKNQLAKKTLVATVMSNMGL 296 Query: 292 DDIAKKHGAKVMRTKVGDLIVARALYENNGTIGGEENGGVIFPEHVLGRDGAMTVAKVVE 351 D KK G +V++T VGD V + + +GGE++G +IF +H DG ++ +V+ Sbjct: 297 DIALKKAGGQVVKTAVGDRYVVEEMLRHGYNLGGEQSGHMIFLDHNTTGDGMISALQVLA 356 Query: 352 IFAKSGKKFSELIDELPKYYQIKTKRHVEGDRHAIVNKVAEMARERGYTVDTTDGAKIIF 411 I +SGK+ SEL + + Q+ V+ R + ++ E+ + +D + + + Sbjct: 357 IMQRSGKRLSELAEVMISLPQVLLNVRVKERRD--IGQIPEVQK----VIDAVE--EKLA 408 Query: 412 EDGWVLVRASGTEPIIRIFSEAKSKEKAQE 441 G VL+R SGTEP++RI E + K + E Sbjct: 409 GKGRVLIRYSGTEPLLRIMLEGQDKYQITE 438 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: 531 Number of extensions: 27 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: 458 Length adjustment: 33 Effective length of query: 422 Effective length of database: 425 Effective search space: 179350 Effective search space used: 179350 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 24 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