Align phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) (EC 5.4.2.2); phosphomannomutase (EC 5.4.2.8) (characterized)
to candidate WP_011383016.1 AMB_RS02965 phosphomannomutase/phosphoglucomutase
Query= BRENDA::M1T754 (460 letters) >NCBI__GCF_000009985.1:WP_011383016.1 Length = 460 Score = 523 bits (1347), Expect = e-153 Identities = 262/457 (57%), Positives = 324/457 (70%), Gaps = 2/457 (0%) Query: 1 MSHKFDPTTLREYDIRGIVGKTLNPADATAIGRGFGTLLRRAGGTRAAVGYDGRHSSPLL 60 M+H F PT LREYDIRGI+G+TL ADA AIGR FGT +RR GG +G+DGR SSP + Sbjct: 1 MTHIFHPTILREYDIRGIIGETLFAADAEAIGRAFGTRVRRNGGHVVCLGWDGRLSSPEM 60 Query: 61 EAALVQGLIASGIDVVRVGLGPTPMLYYAEAVLEVDGGIMITGSHNPPDYNGFKMVFQHR 120 AL +GL+A+G V RVG GPTPMLY+A V + DGGIM+TGSHNPP++NGFKMV R Sbjct: 61 AEALTKGLMAAGCTVRRVGRGPTPMLYFAAKVRDADGGIMVTGSHNPPNHNGFKMVLAGR 120 Query: 121 PFFGEDILKIGTMAAEGDWEEGEGTVTNADIMDMYVDRLIAGYQG-GAFKVAWDAGNGAA 179 PFFG DI +GT+AA GD+ GEG + + YV RL Y G +V WD GNGA Sbjct: 121 PFFGPDIQSLGTIAAAGDFASGEGKAVEDSVFEEYVSRLAQDYDGLRDLRVVWDCGNGAT 180 Query: 180 GPVIEKLVKFLPGEHHLLYTDVDGDFPNHHPDPTEEKNLVDLKALVAEKGLDFGIGFDGD 239 G V+ LVK LPG H +L+ ++DG FPNHHPDPTE NLV L+ V + GI FDGD Sbjct: 181 GEVLHALVKRLPGTHTVLFGEIDGHFPNHHPDPTEPHNLVALQDKVLTESAHLGIAFDGD 240 Query: 240 GDRIGAIDGKGRVVWGDQLLGILAEPVLKAVPGGTIIADVKTSQALYDRVAELGGKPLMW 299 GDRIG +D +GR+++GDQ+L ILAE +LK++PG TIIADVK S+ +D V +GG +M Sbjct: 241 GDRIGVVDAEGRILYGDQILVILAEDLLKSLPGATIIADVKASKVFFDEVRRMGGNAVMG 300 Query: 300 KTGHSLIKAKMKEVDSPLGGEMSGHIFFAWDYYGFDDAIYAAVRLMGAV-RHSGKSLTEL 358 +TGHSLIK +M E +PL GEMSGHIFFA YYGFDDA+YAA+RL+G V R ++ + Sbjct: 301 RTGHSLIKTQMAETGAPLAGEMSGHIFFADRYYGFDDALYAAIRLLGIVARWDHTTIGQR 360 Query: 359 KDAMPAMVNTPEMRFQVDESRKFAVIEEVLQRLEADGADINRTDGARVNTPDGWWLLRAS 418 +D +P MVNTPE+RF E RKFAV+ EV RLEA+GA + DG RV+TPDGWWLLRAS Sbjct: 361 RDRLPHMVNTPELRFDCPEERKFAVVAEVKARLEAEGASFSAIDGVRVDTPDGWWLLRAS 420 Query: 419 NTQDVLVARAEAKDEAGLERLLKQIDTQLELSHIARG 455 NTQ VLVAR EA GL+ L + + QL S ++ G Sbjct: 421 NTQAVLVARCEAASSEGLKHLRQTLADQLAASGVSLG 457 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: 676 Number of extensions: 34 Number of successful extensions: 3 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