Align phosphopentomutase (EC 5.4.2.7) (characterized)
to candidate WP_109968442.1 DK846_RS08105 phosphopentomutase/phosphoglucosamine mutase
Query= BRENDA::Q6I7B6 (450 letters) >NCBI__GCF_003173355.1:WP_109968442.1 Length = 418 Score = 201 bits (512), Expect = 3e-56 Identities = 147/452 (32%), Positives = 224/452 (49%), Gaps = 47/452 (10%) Query: 3 LFGTAGIRGTLWEKVTPELAMKVGMAVGTYKSGKALVGRDGRTSSVMLKNAMISGLLSTG 62 LFG++GIR L+++ LAM+VGMAVG ++ + LVG D RT+ L ++ I+G+ TG Sbjct: 2 LFGSSGIR-RLYDQDLLSLAMQVGMAVGN-RADQVLVGMDSRTTGPALSSSFIAGICYTG 59 Query: 63 MEVLDADLIPTPALAWGTRKLADAGVMITASHNPPTDNGVKVFNGDGTEFYVEQERGLEE 122 + L + PTP++A+ R A M+TASHNP NG+K+FN DG+ F Q+ +E+ Sbjct: 60 AKALQGGIAPTPSIAYCCRSFK-AACMVTASHNPEPYNGLKLFNPDGSSFQALQQDEIED 118 Query: 123 IIFSGNFRKARWDEIKPVRNVEVIPDYINAVLDFVGHETNLKVLYDGANGAGSLVAPYLL 182 I R A W + + + +A+L + + +L V+ D NGAGS++ P+LL Sbjct: 119 AISDN--RTADWLSQGETMKYDPLTPHHDAILSEIDVKKDLPVILDCGNGAGSVLTPHLL 176 Query: 183 REMGAKVLSVNAHVDGHFPGRKPEPRYENIAYLGKLVRELGVDLAIAQDGDADRIAVFDE 242 + GA V++VNA+ G F R EP EN+ YL L++++ A+ DGDADR+ FD Sbjct: 177 SDAGASVVAVNANPSGIF-SRPSEPLVENLPYLPALMKKVNARCAVVHDGDADRMMAFDN 235 Query: 243 KGNYVDEDTVIALFAKLYVEEHGGGTVVVSIDTGSRIDAVVERAGGRVVRIPLGQPHDGI 302 G Y+ D ++ LFAK G VV + D ++ + E V R P+G Sbjct: 236 TGTYIPGDLLLILFAKYL----GAKRVVTTYDASMAVEEIAE-----VRRTPVGDAFVSE 286 Query: 303 KRYK-AIFAAEPWKLVHPKFGPWIDPFVT--------MGLLIKLIDENGPLSELVKEIPT 353 + + F EP G WI P ++ GL ++ E ++E + IP Sbjct: 287 QLVQWGDFGGEP-------SGAWIFPQISYCPDGPFAAGLFCEMAGE-WNIAEELASIPK 338 Query: 354 YYLKKANVLCPDEYKAEVVRRAAEEVERKLSSEIKEVLTISGFRIALNDGSWILIRPSGT 413 Y + + + P ++ AA + G R+ +DG W L+R SGT Sbjct: 339 YPILRRSQQFPQSHEILYALGAANPTD--------------GLRLEEDDG-WCLVRASGT 383 Query: 414 EPKIRVVAEAPTEKRRDELFEMAYSTVSRIVK 445 EPKIR AE T + E V +K Sbjct: 384 EPKIRFTAEGRTLDDAKRMLERGEEMVRLALK 415 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: 461 Number of extensions: 26 Number of successful extensions: 6 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: 418 Length adjustment: 32 Effective length of query: 418 Effective length of database: 386 Effective search space: 161348 Effective search space used: 161348 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