Align phosphopentomutase (EC 5.4.2.7) (characterized)
to candidate WP_051939761.1 BS73_RS09785 phosphomannomutase/phosphoglucomutase
Query= BRENDA::Q6I7B6 (450 letters) >NCBI__GCF_000744815.1:WP_051939761.1 Length = 465 Score = 135 bits (339), Expect = 4e-36 Identities = 136/439 (30%), Positives = 193/439 (43%), Gaps = 40/439 (9%) Query: 9 IRGTL---WEKVTPELAMKVGMA-VGTYKSGKALVGRDGRTSSVMLKNAMISGLLSTGME 64 IRG + W++ T EL G A V +G + G D R SS L A G + G + Sbjct: 24 IRGVVPDDWDEATAEL---FGAAFVRVTGAGAIVTGHDMRPSSPGLAAAFARGATAQGAD 80 Query: 65 VLDADLIPTPALAWGTRKLADAGVMITASHNPPTDNGVKVFNGDGTEFYVEQERGL---- 120 V + L T L + + L AG M TASHNP NG+K+ V Q+ GL Sbjct: 81 VTEIGLCSTDQLYFASGSLGLAGAMFTASHNPARYNGIKLCRAGAEP--VGQDTGLAAIR 138 Query: 121 ---EEIIFSGNFRKARWDEIKPVRNVEVIPDY---INAVLDFVGHETNLKVLYDGANGAG 174 EE + +G + + E + DY + +++D +G LKV+ D NG G Sbjct: 139 ALVEEWLDAGRGPEPAAGPRGRTTSRETLADYAAHLRSLVD-LGAIRPLKVVVDAGNGMG 197 Query: 175 SLVAPYLLREMGAKVLSVNAHVDGHFPGRKPEPRYE-NIAYLGKLVRELGVDLAIAQDGD 233 P +L + V+ + +DG FP + P NI L VR G DL +A DGD Sbjct: 198 GHTVPTVLAGLPLTVVPMYFELDGTFPHHEANPLDPANIVDLRARVRAEGADLGLAFDGD 257 Query: 234 ADRIAVFDEKGNYVDEDTVIALFAKLYVEEHGGGTVVVSIDTGSRIDAVVERAGGRVVRI 293 ADR V DE+G V V AL A + EH G V+ ++ T + VV AGG VR Sbjct: 258 ADRCFVVDERGEPVSPSAVTALVAARELAEHPGAAVIHNLITSRTVPEVVREAGGIPVRT 317 Query: 294 PLGQPHDGIK----RYKAIFAAEPWKLVHPKFGPWIDP----FVTMGLLIKLIDENGPLS 345 +G H IK R A+F E H F + + + +L L ++ PLS Sbjct: 318 RVG--HSFIKAEMARAGAVFGGE--HSAHYYFRDFWNADTGMLAALHVLAALGEQPRPLS 373 Query: 346 ELVKEIPTYYLK-KANVLCPDEYKAEVVRRAAEEVERKLSSEIKEVLTISGFRIALNDGS 404 EL Y + N D+ + RAA ++ + + LT++G Sbjct: 374 ELTARYERYAASGEINSTVADQAERIAAVRAAWSGRPGVTLDELDGLTVAG------RDW 427 Query: 405 WILIRPSGTEPKIRVVAEA 423 W +RPS TEP +R+ EA Sbjct: 428 WFNLRPSNTEPLLRLNVEA 446 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: 492 Number of extensions: 29 Number of successful extensions: 4 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: 450 Length of database: 465 Length adjustment: 33 Effective length of query: 417 Effective length of database: 432 Effective search space: 180144 Effective search space used: 180144 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