Align phosphopentomutase (EC 5.4.2.7) (characterized)
to candidate WP_022949929.1 H035_RS0115785 phosphoglucosamine mutase
Query= BRENDA::Q6I7B6 (450 letters) >NCBI__GCF_000421465.1:WP_022949929.1 Length = 446 Score = 131 bits (330), Expect = 4e-35 Identities = 134/463 (28%), Positives = 212/463 (45%), Gaps = 45/463 (9%) Query: 2 RLFGTAGIRGTLWEK-VTPELAMKVGMAVGTY----KSGKALVGRDGRTSSVMLKNAMIS 56 R FGT GIRG + E +TP+ +K+G A G S LVG+D R S M ++A+ + Sbjct: 4 RYFGTDGIRGKVGEAPITPDFVLKLGWAAGQVFRDNGSSHVLVGKDTRISGYMFESALEA 63 Query: 57 GLLSTGMEVLDADLIPTPALAWGTRKL-ADAGVMITASHNPPTDNGVKVFNGDGTEFYVE 115 GL + G++ +PTP +A+ TR L A AG++I+ASHNP TDNG+K F+G G + E Sbjct: 64 GLSAAGVDTQLLGPMPTPGIAYLTRTLRAKAGIVISASHNPYTDNGIKFFSGAGKKLPDE 123 Query: 116 QERGLE-------EIIFSGNFRKARWDEIKPVRNVEVIPDYINAVLDFVGHETNLKVLYD 168 E +E + S KA R +E + + +D G L ++ D Sbjct: 124 IEAAIETHLEQPMTTVASDRLGKALRIGDAAGRYIEFCKSTVPSCMDLSG----LHLVLD 179 Query: 169 GANGAGSLVAPYLLREMGAKVLSVNAHVDGHFPGRKPEPRYENIAYLGKLVRELGVDLAI 228 A+GA +AP++ E+GA+V + +G + + L + V G DL I Sbjct: 180 CAHGATYHIAPHVFTEVGARVDCIGTQPNG--LNINQDCGSIHAQALQREVVARGADLGI 237 Query: 229 AQDGDADRIAVFDEKGNYVDEDTVIALFAKLYVEEHG-GGTVVVSIDTGSRIDAVVERAG 287 A DGD DR+ + D G VD D ++ + A + G VV ++ T ++ + G Sbjct: 238 AFDGDGDRVLMVDHTGALVDGDELLYIIAASRLGAGKLEGPVVGTLMTNLGLEHALAELG 297 Query: 288 GRVVRIPLGQPH--DGIKRYKAIFAAE-PWKLVHPKFGPWIDPFVT-MGLLIKLIDENGP 343 ++R +G + + ++ + I E ++ D V+ + +L ++ Sbjct: 298 VDLLRAQVGDRYVMEMLETHGGILGGEGSGHIICLDRTTTGDGIVSALQVLAEMWRSGKS 357 Query: 344 LSELVKEIPTYYLKKANVLC----PDEYKAEVVRRAAEEVERKLSSEIKEVLTISGFRIA 399 L++L + + Y NV P V A E VERKL + Sbjct: 358 LAQLRQGMRKYPQVLHNVRVKAKPPRLDTVAPVWTAKEGVERKLQGSGR----------- 406 Query: 400 LNDGSWILIRPSGTEPKIRVVAEAPTEKRRDELFEMAYSTVSR 442 +L+RPSGTEP IRV+ E DEL + S V++ Sbjct: 407 ------VLLRPSGTEPVIRVMIEGRDADLIDELAQELASIVAQ 443 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: 28 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 450 Length of database: 446 Length adjustment: 33 Effective length of query: 417 Effective length of database: 413 Effective search space: 172221 Effective search space used: 172221 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