Align phosphopentomutase (EC 5.4.2.7) (characterized)
to candidate Dsui_3057 Dsui_3057 phosphoglucosamine mutase
Query= BRENDA::Q6I7B6 (450 letters) >FitnessBrowser__PS:Dsui_3057 Length = 451 Score = 125 bits (315), Expect = 2e-33 Identities = 131/479 (27%), Positives = 206/479 (43%), Gaps = 65/479 (13%) Query: 2 RLFGTAGIRGTLWEK-VTPELAMKVGMAVGTYKSGK----------ALVGRDGRTSSVML 50 + FGT G+RG + E +TP+ AM++G + G + L+G+D R S ML Sbjct: 4 KYFGTDGVRGRVGEAPITPDFAMRLGYSAGQVLVAQDGLPAGERPAVLIGKDTRISGYML 63 Query: 51 KNAMISGLLSTGMEVLDADLIPTPALAWGTRKLA-DAGVMITASHNPPTDNGVKVFNGDG 109 + A+ +G + G++V +PTPA+A+ TR L AG++I+ASHNP DNG+K F+ G Sbjct: 64 EAALEAGFSAAGVDVCLVGPMPTPAVAYLTRALRLQAGIVISASHNPFYDNGIKFFSAQG 123 Query: 110 TEFYVEQERGLEE-------IIFSGNFRKARWDEIKPVRNVEVIPDYINAVLDFVGHETN 162 T+ E +E + S KAR + R +E LD G Sbjct: 124 TKLPDAVEHAIEAGVEAPMGCVPSDRLGKARRIDDARGRYIEFCKSTFPNDLDLRG---- 179 Query: 163 LKVLYDGANGAGSLVAPYLLREMGAKVLSVNAHVDG---HFPGRKPEPRYENIAYLGKLV 219 LK++ D A+GA +AP + E+GA V+++ DG + P+ A LG+ Sbjct: 180 LKIVVDCAHGAAYHIAPDVFHELGADVVAIGNRPDGLNINAAVGATAPKALKEAVLGQ-- 237 Query: 220 RELGVDLAIAQDGDADRIAVFDEKGNYVDEDTVIALFAKLYVEEHGGGTVVVSIDTGSRI 279 DL IA DGD DR+ + D +GN D D + L+A + + G V+ G+ + Sbjct: 238 ---RADLGIALDGDGDRLVMVDGEGNVYDGDQL--LYAIVRGRQALGPVAGVA---GTLM 289 Query: 280 DAVVERAGGRVVRIPLGQPHDGIKRYKAIFAAEPWKLVHPKFGP--WIDPFVT------- 330 + + + IP + G + W G +D T Sbjct: 290 TNLALEDALKALDIPFARAAVGDRYVLEKLVQNGWLYGGENSGHILCLDRHTTGDGIIAA 349 Query: 331 MGLLIKLIDENGPLSELVKEIPTYYLKKANVLCPDEY---KAEVVRRAAEEVERKLSSEI 387 + +L L + G L L+ ++ Y K NV P + + + A VE +L Sbjct: 350 LQVLAALRQQGGSLKALLGDLVLYPQKLINVPMPKGFPWQDSPAIAAAQRAVEAELDGRG 409 Query: 388 KEVLTISGFRIALNDGSWILIRPSGTEPKIRVVAEAPTEKRRDELFEMAYSTVSRIVKE 446 + +L+R SGTEP +RV+ E + L E V + V E Sbjct: 410 R-----------------VLLRASGTEPLLRVMVEGRDGELIARLAEKLAGAVRQAVGE 451 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: 486 Number of extensions: 29 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: 451 Length adjustment: 33 Effective length of query: 417 Effective length of database: 418 Effective search space: 174306 Effective search space used: 174306 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