Align phosphopentomutase (EC 5.4.2.7) (characterized)
to candidate WP_086510461.1 BZY95_RS13600 phosphoglucosamine mutase
Query= BRENDA::Q6I7B6 (450 letters) >NCBI__GCF_002151265.1:WP_086510461.1 Length = 449 Score = 148 bits (374), Expect = 3e-40 Identities = 137/442 (30%), Positives = 213/442 (48%), Gaps = 40/442 (9%) Query: 2 RLFGTAGIRGTLWE-KVTPELAMKVGMAVGTY---KSGKA--LVGRDGRTSSVMLKNAMI 55 + FGT GIRGT+ E +TP+ +K+G AVG +SG+A L+G+D R S M ++A+ Sbjct: 4 KYFGTDGIRGTVGEYPITPDFMLKLGWAVGRVLARESGRARVLIGKDTRISGYMFESALE 63 Query: 56 SGLLSTGMEVLDADLIPTPALAWGTRKL-ADAGVMITASHNPPTDNGVKVFNGDGTEFYV 114 +GL + G++V +PTP +A+ TR ADAG++I+ASHNP DNG+K F+ GT+ Sbjct: 64 AGLSAAGVDVALLGPMPTPGIAYLTRTFRADAGIVISASHNPFADNGIKFFSTAGTKLAD 123 Query: 115 EQERGLEEIIFSGNFRKARWDEIKPVRNVEVIPDYINAVLDFVGHETN---LKVLYDGAN 171 E E +E ++ A K +R + YI + + + L+++ D A+ Sbjct: 124 ELEERIEAMLDEPLTTVAADRLGKAMRIDDAAGRYIEFCKSTIPNRVSLHGLRMVLDCAH 183 Query: 172 GAGSLVAPYLLREMGAKVLSVNAHVDGHFPGRKPEPRYENIAYLGKLVRELGVDLAIAQD 231 GA +AP + RE+GA+V V A DG R + + A L V + DL IA D Sbjct: 184 GATYHIAPSVFRELGAEVSLVGASPDGLNINR--DVGSTSPATLRAAVIQQSADLGIAFD 241 Query: 232 GDADRIAVFDEKGNYVDEDTVIALFAKLYVEEHGGGTVVVSIDTGSRIDAVVERAGGRVV 291 GD DR+ + D G +D D ++ L A+ + H G +V + G+ + + Sbjct: 242 GDGDRVLMVDADGREIDGDDILYLIAR---DRHQRGQLVGGV-VGTLMTNFGLAMALENM 297 Query: 292 RIPLGQPHDGIKRYKAIFAAEPWKLVHPKFGPWI--------DPFVT-MGLLIKLIDENG 342 IP + G + A W+L G + D V+ + +L +I E Sbjct: 298 DIPFERAKVGDRYVVERLLANDWQLGGESSGHIVCADVQSTGDGIVSALQVLAIMISEGK 357 Query: 343 PLSELVKEIPTYYLKKANV-LCP-DEYKAEVVRRAAEEVERKLSSEIKEVLTISGFRIAL 400 PL L+ + NV L P + KA + A ++ + +E L Sbjct: 358 PLHTLLAGLEKVPQVLVNVRLTPGSDAKALMASPAVKDAVAEAEAE-------------L 404 Query: 401 NDGSWILIRPSGTEPKIRVVAE 422 D +L+RPSGTEP IRV+ E Sbjct: 405 GDEGRVLLRPSGTEPLIRVMVE 426 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: 453 Number of extensions: 32 Number of successful extensions: 7 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: 449 Length adjustment: 33 Effective length of query: 417 Effective length of database: 416 Effective search space: 173472 Effective search space used: 173472 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