Align phosphopentomutase (EC 5.4.2.7) (characterized)
to candidate WP_085636384.1 MGEO_RS08970 phosphoglucosamine mutase
Query= BRENDA::Q6I7B6 (450 letters) >NCBI__GCF_002115805.1:WP_085636384.1 Length = 447 Score = 151 bits (382), Expect = 4e-41 Identities = 137/453 (30%), Positives = 206/453 (45%), Gaps = 55/453 (12%) Query: 2 RLFGTAGIRGTLWE-KVTPELAMKVGMAVGTY----KSG--KALVGRDGRTSSVMLKNAM 54 +LFGT G+RGT +T ++A+++G AVG + G + ++G+D R S M +NA+ Sbjct: 4 KLFGTDGVRGTANAYPMTADMALRIGAAVGRHFRQDSKGVHRVVIGKDTRQSGYMFENAL 63 Query: 55 ISGLLSTGMEVLDADLIPTPALAWGTRKL-ADAGVMITASHNPPTDNGVKVFNGDGTEFY 113 +GL STGM VL +PTPA+ T + AD G+MI+ASHNP DNG+K F DG + Sbjct: 64 TAGLTSTGMNVLLLGPVPTPAVGLLTPSMRADLGIMISASHNPARDNGIKFFGPDGFKLS 123 Query: 114 VEQERGLEEIIFSG-------NFRKARWDEIKPVRNVEVIPDYINAVLDFVGHETNLKVL 166 E +E +I +G N +A+ + R E + A L G LKV+ Sbjct: 124 DADEAEIEALIETGVEPAQAENIGRAKRIDDGRFRYQERVKSTFPADLRLDG----LKVV 179 Query: 167 YDGANGAGSLVAPYLLREMGAKVLSVNAHVDGHFPGRKPEPRYENIAYLGKLVRELGVDL 226 D ANGA AP +L E+GA V+ + +G + +A + G D+ Sbjct: 180 IDCANGAAYKAAPEVLWELGADVIPLGVTPNGSNINEGCGSTHPQLAAAAVVAH--GADI 237 Query: 227 AIAQDGDADRIAVFDEKGNYVDEDTVIALFAKLYVEEH--GGGTVVVSIDTGSRIDAVVE 284 I DGDADR+ + DE G D D ++AL A + EE G +V ++ + ++ ++ Sbjct: 238 GICLDGDADRVILIDETGQVADGDQIMALMAARWAEEQRLRDGVLVATVMSNLGLERFLD 297 Query: 285 RAGGRVVRIPLGQPH--DGIKRYKAIFAAEPWKLVHPKFGPWI-DPFVTMG--------L 333 G R+ R +G + + ++R W L + G + + T G Sbjct: 298 GRGLRLERTGVGDRYVVEAMRR-------GGWNLGGEQSGHIVMTDYATTGDGLMAGLQF 350 Query: 334 LIKLIDENGPLSELVKEIPTYYLKKANVLCPDEYKAEVVRRAAEEVERKLSSEIKEVLTI 393 L ++ P S L + NV Y V V+ I Sbjct: 351 LGEMCRTGKPASALARSFDPVPQLLKNV----RYDPSVAPLETASVK----------AAI 396 Query: 394 SGFRIALNDGSWILIRPSGTEPKIRVVAEAPTE 426 + LN +LIR SGTEP IRV+AE E Sbjct: 397 ADAEARLNGSGRLLIRKSGTEPLIRVMAECEDE 429 Lambda K H 0.318 0.138 0.402 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: 512 Number of extensions: 35 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 450 Length of database: 447 Length adjustment: 33 Effective length of query: 417 Effective length of database: 414 Effective search space: 172638 Effective search space used: 172638 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