Align phosphopentomutase (EC 5.4.2.7) (characterized)
to candidate WP_011320468.1 AVA_RS19095 phosphoglucosamine mutase
Query= BRENDA::Q6I7B6 (450 letters) >NCBI__GCF_000204075.1:WP_011320468.1 Length = 490 Score = 145 bits (367), Expect = 2e-39 Identities = 133/448 (29%), Positives = 218/448 (48%), Gaps = 49/448 (10%) Query: 3 LFGTAGIRGTLWEKVTPELAMKVGMAVGTYKSGKA------LVGRDGRTSSVMLKNAMIS 56 LFGT GIRG + E ++ LA+++G G A ++G+D R SS ML A+ + Sbjct: 42 LFGTDGIRGKVGELLSAPLALQIGFWAGVVLRSHAGQLRPVILGQDSRNSSDMLAMALSA 101 Query: 57 GLLSTGMEVLDADLIPTPALAWGTR-KLADAGVMITASHNPPTDNGVKVFNGDGTE---- 111 GL + G+EV L PTP +A+ T A GVMI+ASHNPP DNG+K+F +G + Sbjct: 102 GLTAAGLEVWYLGLCPTPCVAYLTSVSEAIGGVMISASHNPPEDNGIKIFGANGGKLSQA 161 Query: 112 FYVEQERGLE-EIIFSGNFRKARWDEIKPVRNVEVIPDYINAVLDFVGHETNL---KVLY 167 E E+GL + + N + E++ DY A+ ++ NL KV+ Sbjct: 162 LQAEIEKGLRGNLPITSNVSNCG----RHYSRRELVKDYGEALKRPWQNKVNLQGMKVVL 217 Query: 168 DGANGAGSLVAPYLLREMGAKVLSVNAHVDGHFPGRKPEPRYENIAYLGKLVRELGVDLA 227 D A GA +AP + EMGA+V+S++ DG ++ L V+E DL Sbjct: 218 DLAWGAAVGLAPSVFAEMGAEVISLHNAADG--DRINVNCGSTHLEMLQAAVQEHNADLG 275 Query: 228 IAQDGDADRIAVFDEKGNYVDEDTVIALFAKLYVEEHG---GGTVVVSIDTGSRIDAVVE 284 A DGDADR+ D G V+ D ++ L+ L++++ +V ++ + + Sbjct: 276 FAFDGDADRVLAVDPTGRPVNGDYILYLWG-LHLKQQNQLPDNLIVSTVMANLGFEKAWQ 334 Query: 285 RAGGRVVRIPLGQPH---DGIKRYKAIFAAEPWKLVHPKFGPWIDPFVTMGLLIKLIDEN 341 + GG+++R +G + + IK + + ++ +G D +T L L+ ++ Sbjct: 335 QQGGKLIRTAVGDQYVQAEMIKTGAMLGGEQSGHILCSHYGMTGDGLLTALHLASLVKQS 394 Query: 342 G-PLSELV-KEIPTYYLKKANVLCPDEYKAEVVRRAAEEVERKLS----SEIKEVLTISG 395 G L+EL+ + TY NV D +R+L+ + +++ + ++ Sbjct: 395 GVSLAELIDQSFQTYPQLLRNVRVVDR-------------DRRLNWQNCTPVQQAIALA- 440 Query: 396 FRIALNDGSWILIRPSGTEPKIRVVAEA 423 A+ D IL+R SGTEP IRV+ EA Sbjct: 441 -EKAMGDTGRILVRASGTEPVIRVMVEA 467 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: 502 Number of extensions: 27 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: 490 Length adjustment: 33 Effective length of query: 417 Effective length of database: 457 Effective search space: 190569 Effective search space used: 190569 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