Align phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) (EC 5.4.2.2); phosphomannomutase (EC 5.4.2.8) (characterized)
to candidate WP_047006996.1 AAW01_RS08900 phosphomannomutase/phosphoglucomutase
Query= BRENDA::M1T754 (460 letters) >NCBI__GCF_001010925.1:WP_047006996.1 Length = 472 Score = 632 bits (1630), Expect = 0.0 Identities = 316/472 (66%), Positives = 362/472 (76%), Gaps = 12/472 (2%) Query: 1 MSHKFDPTTLREYDIRGIVGKTLNPADATAIGRGFGTLLRRAGGTRA-----AVGYDGRH 55 MSH FDPTTLREYDIRGI+G+TL P DA AIGRGF TLL R G AVGYDGR Sbjct: 1 MSHIFDPTTLREYDIRGIIGETLGPDDARAIGRGFATLLLREGSVEGRRPCVAVGYDGRV 60 Query: 56 SSPLLEAALVQGLIASGIDVVRVGLGPTPMLYYAEAVLE-VDGGIMITGSHNPPDYNGFK 114 SSP+LE AL++GL + G V R+G+ TPMLYYAEA E VDGGI ITGSHNP +YNGFK Sbjct: 61 SSPMLEHALIEGLTSGGCAVRRIGMSATPMLYYAEASAEEVDGGIQITGSHNPANYNGFK 120 Query: 115 MVFQHRPFFGEDILKIGTMAAEGDWEEGEGTVTNADIMDMYVDRLIAGYQG------GAF 168 MVF+ RPFFG DI ++G +AA GDW G G V + DI++ YV+RL+ G Sbjct: 121 MVFEGRPFFGGDIQRLGELAAAGDWTSGMGEVDSVDIIEQYVERLLTALSGIDEGVLSGL 180 Query: 169 KVAWDAGNGAAGPVIEKLVKFLPGEHHLLYTDVDGDFPNHHPDPTEEKNLVDLKALVAEK 228 ++ WDAGNGAAGP +E L + LPGEHHLLYT+VDG+FPNHHPDPT E NLVDL+ALVA K Sbjct: 181 RIGWDAGNGAAGPALELLTQRLPGEHHLLYTEVDGNFPNHHPDPTVEANLVDLRALVAAK 240 Query: 229 GLDFGIGFDGDGDRIGAIDGKGRVVWGDQLLGILAEPVLKAVPGGTIIADVKTSQALYDR 288 LDFG+ FDGDGDRIGAIDG+GRVVWGDQLL I AE +L +P T+IADVK S+AL+D Sbjct: 241 NLDFGVAFDGDGDRIGAIDGEGRVVWGDQLLMIYAEDLLGRLPNATVIADVKASRALFDH 300 Query: 289 VAELGGKPLMWKTGHSLIKAKMKEVDSPLGGEMSGHIFFAWDYYGFDDAIYAAVRLMGAV 348 VA GGKP+MWKTGHSLIK+KMKEV SPL GEMSGH+FFA DYYGFDDA+YAAVRLM A Sbjct: 301 VAAHGGKPVMWKTGHSLIKSKMKEVSSPLAGEMSGHVFFADDYYGFDDALYAAVRLMAAS 360 Query: 349 RHSGKSLTELKDAMPAMVNTPEMRFQVDESRKFAVIEEVLQRLEADGADINRTDGARVNT 408 G+S+TEL+ AMP M+NTPEMRFQVDESRKFA IEE+ R+ A A + TDG RV T Sbjct: 361 ARLGRSVTELRGAMPEMINTPEMRFQVDESRKFAAIEEIAARIAASDAVADTTDGVRVTT 420 Query: 409 PDGWWLLRASNTQDVLVARAEAKDEAGLERLLKQIDTQLELSHIARGEQAGH 460 DGWWLLRASNTQDVLVARAE+ + GLERLL ID QL LS + RG GH Sbjct: 421 DDGWWLLRASNTQDVLVARAESDTQEGLERLLASIDEQLALSGLERGSNVGH 472 Lambda K H 0.318 0.139 0.417 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: 730 Number of extensions: 36 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: 460 Length of database: 472 Length adjustment: 33 Effective length of query: 427 Effective length of database: 439 Effective search space: 187453 Effective search space used: 187453 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 (21.7 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