Align phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) (EC 5.4.2.2); phosphomannomutase (EC 5.4.2.8) (characterized)
to candidate Ga0059261_2456 Ga0059261_2456 Phosphomannomutase
Query= BRENDA::M1T754 (460 letters) >FitnessBrowser__Korea:Ga0059261_2456 Length = 460 Score = 741 bits (1912), Expect = 0.0 Identities = 360/460 (78%), Positives = 397/460 (86%) Query: 1 MSHKFDPTTLREYDIRGIVGKTLNPADATAIGRGFGTLLRRAGGTRAAVGYDGRHSSPLL 60 ++H+FDPT+LREYDIRGIVGKTL P DA AIGRGF TLLRRAGG R AVG DGR SSP L Sbjct: 1 VTHRFDPTSLREYDIRGIVGKTLGPDDARAIGRGFATLLRRAGGHRVAVGRDGRVSSPEL 60 Query: 61 EAALVQGLIASGIDVVRVGLGPTPMLYYAEAVLEVDGGIMITGSHNPPDYNGFKMVFQHR 120 EAALV+GL ASG DVVRVG+GPTPMLYYAEA+LEVDGGI ITGSHNP DYNGFKMVFQHR Sbjct: 61 EAALVEGLTASGCDVVRVGMGPTPMLYYAEAILEVDGGIQITGSHNPGDYNGFKMVFQHR 120 Query: 121 PFFGEDILKIGTMAAEGDWEEGEGTVTNADIMDMYVDRLIAGYQGGAFKVAWDAGNGAAG 180 PFFG+DI +IG +A GDW+EGEGTV++ADI+D YV RL AGY GG F++ WD GNGAAG Sbjct: 121 PFFGQDIQEIGKLAEAGDWDEGEGTVSDADILDDYVGRLFAGYAGGTFRIGWDTGNGAAG 180 Query: 181 PVIEKLVKFLPGEHHLLYTDVDGDFPNHHPDPTEEKNLVDLKALVAEKGLDFGIGFDGDG 240 PVIEKLV+ LPGEHH L+TDVDG+FPNHHPDPTEEKNL DL+ LVAEK LDFG+ FDGDG Sbjct: 181 PVIEKLVQLLPGEHHTLFTDVDGNFPNHHPDPTEEKNLADLRRLVAEKNLDFGLAFDGDG 240 Query: 241 DRIGAIDGKGRVVWGDQLLGILAEPVLKAVPGGTIIADVKTSQALYDRVAELGGKPLMWK 300 DRIGAIDG+GRV+WGDQLL ILAEPVLK PG TIIADVK SQ L+DRVAELGG+PLMWK Sbjct: 241 DRIGAIDGEGRVIWGDQLLSILAEPVLKKAPGATIIADVKASQMLFDRVAELGGQPLMWK 300 Query: 301 TGHSLIKAKMKEVDSPLGGEMSGHIFFAWDYYGFDDAIYAAVRLMGAVRHSGKSLTELKD 360 TGHSL+K KMKE SPL GEMSGHIFFA DYYGFDDA YAAV+L+ AV G SLTE++ Sbjct: 301 TGHSLVKTKMKETHSPLAGEMSGHIFFAQDYYGFDDAQYAAVQLINAVHLIGTSLTEIRG 360 Query: 361 AMPAMVNTPEMRFQVDESRKFAVIEEVLQRLEADGADINRTDGARVNTPDGWWLLRASNT 420 MPA VNTPEMRFQVDESRKFAVI+EVL RL+A GAD+N TDGARVNTPDGWWLLRASNT Sbjct: 361 NMPAFVNTPEMRFQVDESRKFAVIDEVLDRLKATGADVNDTDGARVNTPDGWWLLRASNT 420 Query: 421 QDVLVARAEAKDEAGLERLLKQIDTQLELSHIARGEQAGH 460 QDVLVARAEA+ + L+RLL QID QLE S + RG QA H Sbjct: 421 QDVLVARAEARSQEALDRLLAQIDAQLEASGLKRGPQAAH 460 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: 803 Number of extensions: 37 Number of successful extensions: 1 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: 460 Length adjustment: 33 Effective length of query: 427 Effective length of database: 427 Effective search space: 182329 Effective search space used: 182329 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 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