Align phosphopentomutase (EC 5.4.2.7) (characterized)
to candidate WP_013010594.1 DACET_RS06525 phosphoglucosamine mutase
Query= BRENDA::Q6I7B6 (450 letters) >NCBI__GCF_000025725.1:WP_013010594.1 Length = 454 Score = 160 bits (406), Expect = 6e-44 Identities = 143/475 (30%), Positives = 231/475 (48%), Gaps = 52/475 (10%) Query: 2 RLFGTAGIRGTLWE-KVTPELAMKVGMAV------GTYKSGKALVGRDGRTSSVMLKNAM 54 + FGT G+RG E +T A+++G AV G K K ++G+D R S M ++A+ Sbjct: 3 KYFGTDGVRGKANEFPMTATFALRLGQAVAKQFSNGGKKIHKVVIGKDTRVSGYMFESAL 62 Query: 55 ISGLLSTGMEVLDADLIPTPALAWGTRKL-ADAGVMITASHNPPTDNGVKVFNGDGTEFY 113 +SG+ S G++ + ++PTPA+++ TR L ADAGV+I+ASHNP DNG+K F+GDG + Sbjct: 63 VSGITSMGLDAVLVGVLPTPAISFITRSLRADAGVVISASHNPYYDNGIKFFSGDGYKLP 122 Query: 114 VEQERGLEEI-----------IFSGNFRKARWDEIKPVRNVEVIPDYINAVLDFVGHETN 162 E E +E+ I + KA + R VE + +D G Sbjct: 123 DETEISIEQTTDEMIQNGEIPISTDRIGKAYRVDTAIGRYVEFSKSTFDKDIDLSG---- 178 Query: 163 LKVLYDGANGAGSLVAPYLLREMGAKVLSVNAHVDGHFPGRKPEPRYENIAYLGKLVREL 222 ++++ D +NGA VAP E+ AK+ + DG Y A K V+E Sbjct: 179 MRLVVDCSNGANYKVAPMAFEELAAKINVMGNEPDGMNINSGCGSVYPE-AMCAK-VKEK 236 Query: 223 GVDLAIAQDGDADRIAVFDEKGNYVDEDTVIALFAKLYVEEHG---GGTVVVSIDTGSRI 279 G DL I+ DGD DR+ DE G VD D ++ + AK Y+ G T+V ++ + Sbjct: 237 GADLGISFDGDGDRVIFSDENGEMVDGDIIMGICAK-YMNSLGYLNKNTMVCTVMSNFGF 295 Query: 280 DAVVERAGGRVVRIPLGQPH---DGIKRYKAIFAAEPWKLVHPKFGPWIDPFVTMGLLIK 336 + + AG ++VR +G + + +K + + ++ + D V+ L+K Sbjct: 296 EKSMLEAGVKLVRTDVGDRYVMAEMLKNGYNLGGEQSGHIIFSDYNTTGDGLVSAMQLLK 355 Query: 337 LIDENG-PLSELVKEIPTYYLKKANVLCPDEYKAEVVRRAAEEVERKLSSEIKEVLTISG 395 +I +G PLSEL K I Y N + + + R ++E++ ++ E+ Sbjct: 356 VIVRSGKPLSELKKFITLYPQVLKNFKVQKKIPVDYLERTSKEIQ-AVNKEL-------- 406 Query: 396 FRIALNDGSW-ILIRPSGTEPKIRVVAEAPTEKRRDELFEMAYSTVSRIVKEAEK 449 DG+ +L+R SGTE K+RV+ E R + E A + + VKE E+ Sbjct: 407 ------DGTGRVLVRYSGTENKLRVMLEGEDLSR---ITEYAENIGANAVKEIEE 452 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: 516 Number of extensions: 29 Number of successful extensions: 5 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: 454 Length adjustment: 33 Effective length of query: 417 Effective length of database: 421 Effective search space: 175557 Effective search space used: 175557 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