Align phosphopentomutase (EC 5.4.2.7) (characterized)
to candidate WP_011973151.1 MAEO_RS02160 phosphoglucosamine mutase
Query= BRENDA::Q6I7B6 (450 letters) >NCBI__GCF_000017185.1:WP_011973151.1 Length = 452 Score = 275 bits (702), Expect = 3e-78 Identities = 170/460 (36%), Positives = 260/460 (56%), Gaps = 36/460 (7%) Query: 1 MRLFGTAGIRGTLWEKVTPELAMKVGMAVGTYKSGKALVGRDGRTSSVMLKNAMISGLLS 60 M+LFGT+GIR + +TPE+A KVG AV +VGRD RT+ +++N++ +GLL+ Sbjct: 1 MKLFGTSGIR---MKNLTPEIAYKVGFAVSQIAKN-VVVGRDTRTTGDLIRNSLFAGLLN 56 Query: 61 TGMEVLDADLIPTPALAWGTRKLADAGVMITASHNPPTDNGVKVFNGDGTEFYVEQERGL 120 G E++D ++PTP L + R D G+MITASHNP NG+K+FN DGT F EQE+ + Sbjct: 57 GGAEIVDIGIVPTPTLGYSARNY-DMGIMITASHNPSEYNGIKLFNKDGTSFRPEQEQNI 115 Query: 121 EEIIFSG-NFRKARWDEIKPVRNVE-VIPDYINAVLDFVGHETNLKVLYDGANGAGSLVA 178 E+II++ N ++ W+ IK V E + Y + +LD V N V+ D AN AG + + Sbjct: 116 EDIIYNKKNQKRVSWNSIKKVWTDESALKKYSDFILDSVEINKNFSVVVDCANSAGCVAS 175 Query: 179 PYLLREMGAKVLSVNAHVDGHFPGRKPEPRYENIAYLGKLVRELGVD------LAIAQDG 232 PYL ++GA V+SVN H+DG F GR PEP +N+ +++ L + + IA DG Sbjct: 176 PYLFTDVGAHVISVNGHIDGRFIGRSPEPNEKNLQDTMHMIKGLNENNKGNKYIGIAHDG 235 Query: 233 DADRIAVFDEKGNYVDEDTVIALFAKLYVEEHGGGTVVVSIDTGSRIDAVVERAGGRVVR 292 DADR+ DEKG D D ++A+F++ E+ G T++ ++D I+ ++ V+R Sbjct: 236 DADRMIAIDEKGRLTDFDKLLAVFSRYMAEKTGTKTIITTVDASMAIEEYLKDLNVNVIR 295 Query: 293 IPLGQ--PHDGIKRY-KAIFAAEPWKLVHPKFGPWIDPFVTM---GLL--IKLID----E 340 +G D + ++ AIF EP G WI + + G+L ++L++ Sbjct: 296 TKVGDVAVSDELNKHDDAIFGGEP-------SGTWIHKDIHLTPDGILSGLRLLEMMEFY 348 Query: 341 NGPLSELVKEIPTYYLKKANVLCPDEYKAEVVRRAAEEVERKLSSEIKEVLTISGFRIAL 400 + L EL+ ++P Y + + CPD+ K V+ + E +E++ TI G R +L Sbjct: 349 DKKLYELIDDVPCYSNLREKLPCPDDKKIIVMDFVIKNGENIFDAEVE---TIDGARFSL 405 Query: 401 NDGSWILIRPSGTEPKIRVVAEAPTEKRRDELFEMAYSTV 440 +DG W+LIRPSGTEP +RV EA + EL E V Sbjct: 406 DDG-WVLIRPSGTEPFVRVRVEAKNDIIAKELLEKGIKLV 444 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: 572 Number of extensions: 34 Number of successful extensions: 8 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: 452 Length adjustment: 33 Effective length of query: 417 Effective length of database: 419 Effective search space: 174723 Effective search space used: 174723 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 Apr 09 2024. 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