Align phosphopentomutase (EC 5.4.2.7) (characterized)
to candidate Pf1N1B4_1165 Phosphoglucosamine mutase (EC 5.4.2.10)
Query= BRENDA::Q6I7B6 (450 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1165 Length = 445 Score = 138 bits (347), Expect = 4e-37 Identities = 103/289 (35%), Positives = 154/289 (53%), Gaps = 33/289 (11%) Query: 2 RLFGTAGIRGTLWE-KVTPELAMKVGMAVG----TYKSGKALVGRDGRTSSVMLKNAMIS 56 + FGT GIRG + + +TP+ +K+G A G + + K LVG+D R S M ++A+ + Sbjct: 4 KYFGTDGIRGRVGQYPITPDFMLKLGWAAGMAFRSMGACKVLVGKDTRISGYMFESALEA 63 Query: 57 GLLSTGMEVLDADLIPTPALAWGTRKL-ADAGVMITASHNPPTDNGVKVFNGDGTEFYVE 115 GL S G +V+ +PTPA+A+ TR A+AG++I+ASHNP DNG+K F+G GT+ E Sbjct: 64 GLTSAGADVMLLGPMPTPAIAYLTRTFHAEAGIVISASHNPHDDNGIKFFSGKGTKLPDE 123 Query: 116 QERGLEEIIFSGNFRKARWDEIKPVRNVEVIPDYINAVLDFVGHE-------TNLKVLYD 168 E +EE++ + E + V I D ++F T LK++ D Sbjct: 124 VELMIEELLDT----PMTVVESSKIGKVSRINDASGRYIEFCKSSVPTGTSFTGLKIVID 179 Query: 169 GANGAGSLVAPYLLREMGAKVLSVNAHVDG-----HFPGRKPEPRYENIAYLGKLVRELG 223 A+GA VAP + RE+GA+V+ ++AH DG + EP L V Sbjct: 180 CAHGATYKVAPSVFRELGAEVVVLSAHPDGLNINENCGSTHMEP-------LQAAVLAEH 232 Query: 224 VDLAIAQDGDADRIAVFDEKGNYVDEDTVIALFAKLYVEEHG---GGTV 269 DL IA DGD DR+ + D G VD D ++ + A+ ++E G GG V Sbjct: 233 ADLGIAFDGDGDRVQMVDHTGAVVDGDELLFIIAR-DLQERGKLQGGVV 280 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: 468 Number of extensions: 26 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