Align phosphopentomutase (EC 5.4.2.7) (characterized)
to candidate 17247 b3176 phosphoglucosamine mutase (NCBI)
Query= BRENDA::Q6I7B6 (450 letters) >FitnessBrowser__Keio:17247 Length = 445 Score = 140 bits (354), Expect = 6e-38 Identities = 131/455 (28%), Positives = 210/455 (46%), Gaps = 51/455 (11%) Query: 2 RLFGTAGIRGTLWEK-VTPELAMKVGMAVGT----YKSGKALVGRDGRTSSVMLKNAMIS 56 + FGT GIRG + + +TP+ +K+G A G + S K ++G+D R S ML++A+ + Sbjct: 5 KYFGTDGIRGRVGDAPITPDFVLKLGWAAGKVLARHGSRKIIIGKDTRISGYMLESALEA 64 Query: 57 GLLSTGMEVLDADLIPTPALAWGTRKL-ADAGVMITASHNPPTDNGVKVFNGDGTEFYVE 115 GL + G+ L +PTPA+A+ TR A+AG++I+ASHNP DNG+K F+ DGT+ Sbjct: 65 GLAAAGLSALFTGPMPTPAVAYLTRTFRAEAGIVISASHNPFYDNGIKFFSIDGTKLPDA 124 Query: 116 QERGLEEIIFSGNFRKARWDEIKPVRNVEVIPDYINAVLDFVGHE---TNLKVLYDGANG 172 E +E + + K R V+ YI +E + LK++ D ANG Sbjct: 125 VEEAIEAEMEKEISCVDSAELGKASRIVDAAGRYIEFCKATFPNELSLSELKIVVDCANG 184 Query: 173 AGSLVAPYLLREMGAKVLSVNAHVDGHFPGRKPEPRYENIAYLGKLVRELGVDLAIAQDG 232 A +AP +LRE+GA V+++ +G E ++ L V DL IA DG Sbjct: 185 ATYHIAPNVLRELGANVIAIGCEPNG--VNINAEVGATDVRALQARVLAEKADLGIAFDG 242 Query: 233 DADRIAVFDEKGNYVDEDTVIALFAKLYVEE---HGGGTVVVSIDTGSRIDAVVERAGGR 289 D DR+ + D +GN VD D ++ + A+ + + GG + + G ++ +++ G Sbjct: 243 DGDRVIMVDHEGNKVDGDQIMYIIAREGLRQGQLRGGAVGTLMSNMG--LELALKQLG-- 298 Query: 290 VVRIPLGQPHDGIKRYKAIFAAEPWKLVHPKFGPWI--DPFVT-------MGLLIKLIDE 340 IP + G + + W++ G I D T + +L + Sbjct: 299 ---IPFARAKVGDRYVLEKMQEKGWRIGAENSGHVILLDKTTTGDGIVAGLQVLAAMARN 355 Query: 341 NGPLSELVKEIPTYYLKKANVL----CPDEYKAEVVRRAAEEVERKLSSEIKEVLTISGF 396 + L +L + + NV D + E V+ EVE Sbjct: 356 HMSLHDLCSGMKMFPQILVNVRYTAGSGDPLEHESVKAVTAEVE---------------- 399 Query: 397 RIALNDGSWILIRPSGTEPKIRVVAEAPTEKRRDE 431 AL + +L+R SGTEP IRV+ E E + E Sbjct: 400 -AALGNRGRVLLRKSGTEPLIRVMVEGEDEAQVTE 433 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: 456 Number of extensions: 27 Number of successful extensions: 5 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: 445 Length adjustment: 33 Effective length of query: 417 Effective length of database: 412 Effective search space: 171804 Effective search space used: 171804 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