Align phosphomannose mutase (EC 5.4.2.8) (characterized)
to candidate WP_041938852.1 FRAAL_RS04860 phosphoglucosamine mutase
Query= metacyc::MONOMER-13382 (455 letters) >NCBI__GCF_000058485.1:WP_041938852.1 Length = 455 Score = 221 bits (563), Expect = 4e-62 Identities = 154/452 (34%), Positives = 230/452 (50%), Gaps = 25/452 (5%) Query: 1 MGKLFGTFGVRGIANEKITPEFAMKIGMAFGTLLKREGRK-------KPLVVVGRDTRVS 53 M +LFGT GVRG+AN +T E A+ + A LL GR +PLVVVGRDTR S Sbjct: 1 MTRLFGTDGVRGVANVNLTAEQALSLASAAVELLGAPGRSAGPAQRPRPLVVVGRDTRPS 60 Query: 54 GEMLKEALISGLLSVGCDVIDVGIAPTPAVQWATKHFNADGGAVITASHNPPEYNGIKLL 113 GE L+ A+++GL + G DV +G+APTPAV A +A G +++ASHNP NGIK+ Sbjct: 61 GEFLEAAVVAGLAASGADVARIGVAPTPAVAHAVAASDATFGVMLSASHNPMPDNGIKVF 120 Query: 114 EPNGMGLKKEREAIVEELFFKEDFDRAKWYEIGEVRRE-DIIKPYIEAIKSKVDVEAIKK 172 G+ L E E +E + R ++G +R E ++ Y + + + + V Sbjct: 121 AAGGLKLPDEVEDAIERRMAQPPGPRPVGADVGRIRDEPGLLDRYADHLLAALPVRLDNL 180 Query: 173 RKPFVVVDTSNGAGSLTLPYLLRELGCKVITVNAQPDGYFPARNPEPNEENLKEFMEIVK 232 R VVVD + GA S P +LR G VI ++A DG A N +L V Sbjct: 181 R---VVVDCAQGAASALAPRVLRAAGADVIALHADGDG--AAINDGSGVTHLDSLRAAVV 235 Query: 233 ALGADFGVAQDGDADRAVFIDENGRFIQGDKTFALVADAVLK--EKGGGLLVTTVATSNL 290 AD G+A DGDADR + +D G + GD+ A+ A A+ + E +V TV ++ Sbjct: 236 DQAADVGIAHDGDADRCLAVDAAGEIVDGDQILAICALALAERGELADDTVVVTVMSNLG 295 Query: 291 LDDIAKKHGAKVMRTKVGDLIVARALYENNGTIGGEENGGVIFPEHVLGRDGAMTVAKVV 350 ++ G V+ T VGD V A+ +GGE++G V+F +H DG +T +++ Sbjct: 296 FHHAMREAGITVVTTPVGDRYVVEAMRAGGYVLGGEQSGHVVFLDHATTGDGLLTALRLL 355 Query: 351 EIFAKSGKKFSELIDELPKYYQIKTKRHVEG-DRHAIVNKVAEMARERGYTVDTTDGAKI 409 A++G+ EL + + Q+ +V G DR + A + DG Sbjct: 356 GRVAETGQPLGELAKAMTRLPQVLV--NVRGVDRTRVDTSPQLRAAVAAAEAELGDG--- 410 Query: 410 IFEDGWVLVRASGTEPIIRIFSEAKSKEKAQE 441 G VL+R SGTEP++R+ EA++ A++ Sbjct: 411 ----GRVLLRPSGTEPLVRVMVEAETDAVARD 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: 501 Number of extensions: 25 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: 455 Length adjustment: 33 Effective length of query: 422 Effective length of database: 422 Effective search space: 178084 Effective search space used: 178084 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