Align phosphopentomutase (EC 5.4.2.7) (characterized)
to candidate Pf6N2E2_3357 Phosphoglucosamine mutase (EC 5.4.2.10)
Query= BRENDA::Q6I7B6 (450 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3357 Length = 445 Score = 135 bits (339), Expect = 3e-36 Identities = 128/449 (28%), Positives = 210/449 (46%), Gaps = 50/449 (11%) Query: 2 RLFGTAGIRGTLWE-KVTPELAMKVGMAVGTY--KSG--KALVGRDGRTSSVMLKNAMIS 56 + FGT GIRG + E +TP+ +K+G A G K G K LVG+D R S M ++A+ + Sbjct: 4 KYFGTDGIRGRVGEYPITPDFMLKLGWAAGMAFRKMGACKVLVGKDTRISGYMFESALEA 63 Query: 57 GLLSTGMEVLDADLIPTPALAWGTRKL-ADAGVMITASHNPPTDNGVKVFNGDGTEFYVE 115 GL S G +V+ +PTPA+A+ TR A AG++I+ASHNP DNG+K F+G GT+ + Sbjct: 64 GLTSAGADVMLLGPMPTPAIAYLTRTFQAQAGIVISASHNPHDDNGIKFFSGQGTKLPDD 123 Query: 116 QERGLEE-------IIFSGNFRKARWDEIKPVRNVEVIPDYINAVLDFVGHETNLKVLYD 168 E +EE ++ S K R +E + F G LK++ D Sbjct: 124 IELMIEELLDTPMTVVESSKIGKVSRINDASGRYIEFCKGSVPTGTSFSG----LKIVVD 179 Query: 169 GANGAGSLVAPYLLREMGAKVLSVNAHVDGHFPGRKPEPRYENIAYLGKLVRELGVDLAI 228 A+GA VAP + RE+GA+V+ ++A +G + L + DL I Sbjct: 180 CAHGATYKVAPSVFRELGAEVVVLSAQPNGLNINHNCGSTHTEALQAAVLAEQ--ADLGI 237 Query: 229 AQDGDADRIAVFDEKGNYVDEDTVIALFAKLYVEEHGGGT----VVVSIDTGSRIDAVVE 284 A DGD DR+ + D G VD D ++ + A+ + HG G VV ++ + ++ + Sbjct: 238 AFDGDGDRVLMVDHTGTVVDGDELLFIIAR---DLHGRGKLQGGVVGTLMSNLGLELALA 294 Query: 285 RAGGRVVRIPLGQPH---DGIKRYKAIFAAEPWKLV---HPKFGPWIDPFVTMGLLIKLI 338 VR +G + + ++R I +V H G I + + + +K Sbjct: 295 DLDIPFVRANVGDRYVISELLERNWVIGGENSGHIVCFDHTTTGDAIIAALQVLMALKAR 354 Query: 339 DENGPLS-ELVKEIPTYYLKKANVLCPDEYKAEVVRRAAEEVERKLSSEIKEVLTISGFR 397 +E S + +++ P + + + V++A+E V + ++ + Sbjct: 355 NEGLAQSRQALRKCPQVLINVRFGGGVNPLEHAKVKQASEHVTQAMAGRGR--------- 405 Query: 398 IALNDGSWILIRPSGTEPKIRVVAEAPTE 426 +L+R SGTEP +RV+ E E Sbjct: 406 --------VLLRKSGTEPLVRVMVEGEDE 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: 466 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