Align phosphopentomutase (EC 5.4.2.7) (characterized)
to candidate WP_011383016.1 AMB_RS02965 phosphomannomutase/phosphoglucomutase
Query= BRENDA::Q6I7B6 (450 letters) >NCBI__GCF_000009985.1:WP_011383016.1 Length = 460 Score = 124 bits (311), Expect = 6e-33 Identities = 119/441 (26%), Positives = 190/441 (43%), Gaps = 41/441 (9%) Query: 9 IRGTLWEKVTPELAMKVGMAVGTY--KSGKALV--GRDGRTSSVMLKNAMISGLLSTGME 64 IRG + E + A +G A GT ++G +V G DGR SS + A+ GL++ G Sbjct: 15 IRGIIGETLFAADAEAIGRAFGTRVRRNGGHVVCLGWDGRLSSPEMAEALTKGLMAAGCT 74 Query: 65 VLDADLIPTPALAWGTR-KLADAGVMITASHNPPTDNGVKVFNGDGTEFYVEQERGLEEI 123 V PTP L + + + AD G+M+T SHNPP NG K+ G F+ + L I Sbjct: 75 VRRVGRGPTPMLYFAAKVRDADGGIMVTGSHNPPNHNGFKMVLA-GRPFFGPDIQSLGTI 133 Query: 124 IFSGNFRKARWDEIKPVRNVEVIPDYINAVLDFVGHETNLKVLYDGANGAGSLVAPYLLR 183 +G+F ++ V +Y++ + +L+V++D NGA V L++ Sbjct: 134 AAAGDFASGEGKAVED----SVFEEYVSRLAQDYDGLRDLRVVWDCGNGATGEVLHALVK 189 Query: 184 EMGAKVLSVNAHVDGHFPGRKPEPRY-ENIAYLGKLVRELGVDLAIAQDGDADRIAVFDE 242 + + +DGHFP P+P N+ L V L IA DGD DRI V D Sbjct: 190 RLPGTHTVLFGEIDGHFPNHHPDPTEPHNLVALQDKVLTESAHLGIAFDGDGDRIGVVDA 249 Query: 243 KGNYVDEDTVIALFAKLYVEEHGGGTVVVSIDTGSRIDAVVERAGGRVVRIPLGQPHDGI 302 +G + D ++ + A+ ++ G T++ + V R GG V G H I Sbjct: 250 EGRILYGDQILVILAEDLLKSLPGATIIADVKASKVFFDEVRRMGGNAVMGRTG--HSLI 307 Query: 303 KRYKA-------------IFAAEPWKLVHPKFGPWIDPFVTMGLLIKLID--ENGPLSEL 347 K A IF A+ ++ + D L+ ++ ++ + + Sbjct: 308 KTQMAETGAPLAGEMSGHIFFAD-------RYYGFDDALYAAIRLLGIVARWDHTTIGQR 360 Query: 348 VKEIP-TYYLKKANVLCPDEYKAEVVRRAAEEVERKLSSEIKEVLTISGFRIALNDGSWI 406 +P + CP+E K VV EV+ +L +E I G R+ DG W Sbjct: 361 RDRLPHMVNTPELRFDCPEERKFAVV----AEVKARLEAEGASFSAIDGVRVDTPDG-WW 415 Query: 407 LIRPSGTEPKIRVVAEAPTEK 427 L+R S T+ + EA + + Sbjct: 416 LLRASNTQAVLVARCEAASSE 436 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: 497 Number of extensions: 31 Number of successful extensions: 4 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: 460 Length adjustment: 33 Effective length of query: 417 Effective length of database: 427 Effective search space: 178059 Effective search space used: 178059 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