Align phosphoglucomutase; EC 5.4.2.2 (characterized)
to candidate 14818 b0688 phosphoglucomutase (NCBI)
Query= CharProtDB::CH_002452 (546 letters) >FitnessBrowser__Keio:14818 Length = 546 Score = 1096 bits (2835), Expect = 0.0 Identities = 546/546 (100%), Positives = 546/546 (100%) Query: 1 MAIHNRAGQPAQQSDLINVAQLTAQYYVLKPEAGNAEHAVKFGTSGHRGSAARHSFNEPH 60 MAIHNRAGQPAQQSDLINVAQLTAQYYVLKPEAGNAEHAVKFGTSGHRGSAARHSFNEPH Sbjct: 1 MAIHNRAGQPAQQSDLINVAQLTAQYYVLKPEAGNAEHAVKFGTSGHRGSAARHSFNEPH 60 Query: 61 ILAIAQAIAEERAKNGITGPCYVGKDTHALSEPAFISVLEVLAANGVDVIVQENNGFTPT 120 ILAIAQAIAEERAKNGITGPCYVGKDTHALSEPAFISVLEVLAANGVDVIVQENNGFTPT Sbjct: 61 ILAIAQAIAEERAKNGITGPCYVGKDTHALSEPAFISVLEVLAANGVDVIVQENNGFTPT 120 Query: 121 PAVSNAILVHNKKGGPLADGIVITPSHNPPEDGGIKYNPPNGGPADTNVTKVVEDRANAL 180 PAVSNAILVHNKKGGPLADGIVITPSHNPPEDGGIKYNPPNGGPADTNVTKVVEDRANAL Sbjct: 121 PAVSNAILVHNKKGGPLADGIVITPSHNPPEDGGIKYNPPNGGPADTNVTKVVEDRANAL 180 Query: 181 LADGLKGVKRISLDEAMASGHVKEQDLVQPFVEGLADIVDMAAIQKAGLTLGVDPLGGSG 240 LADGLKGVKRISLDEAMASGHVKEQDLVQPFVEGLADIVDMAAIQKAGLTLGVDPLGGSG Sbjct: 181 LADGLKGVKRISLDEAMASGHVKEQDLVQPFVEGLADIVDMAAIQKAGLTLGVDPLGGSG 240 Query: 241 IEYWKRIGEYYNLNLTIVNDQVDQTFRFMHLDKDGAIRMDCSSECAMAGLLALRDKFDLA 300 IEYWKRIGEYYNLNLTIVNDQVDQTFRFMHLDKDGAIRMDCSSECAMAGLLALRDKFDLA Sbjct: 241 IEYWKRIGEYYNLNLTIVNDQVDQTFRFMHLDKDGAIRMDCSSECAMAGLLALRDKFDLA 300 Query: 301 FANDPDYDRHGIVTPAGLMNPNHYLAVAINYLFQHRPQWGKDVAVGKTLVSSAMIDRVVN 360 FANDPDYDRHGIVTPAGLMNPNHYLAVAINYLFQHRPQWGKDVAVGKTLVSSAMIDRVVN Sbjct: 301 FANDPDYDRHGIVTPAGLMNPNHYLAVAINYLFQHRPQWGKDVAVGKTLVSSAMIDRVVN 360 Query: 361 DLGRKLVEVPVGFKWFVDGLFDGSFGFGGEESAGASFLRFDGTPWSTDKDGIIMCLLAAE 420 DLGRKLVEVPVGFKWFVDGLFDGSFGFGGEESAGASFLRFDGTPWSTDKDGIIMCLLAAE Sbjct: 361 DLGRKLVEVPVGFKWFVDGLFDGSFGFGGEESAGASFLRFDGTPWSTDKDGIIMCLLAAE 420 Query: 421 ITAVTGKNPQEHYNELAKRFGAPSYNRLQAAATSAQKAALSKLSPEMVSASTLAGDPITA 480 ITAVTGKNPQEHYNELAKRFGAPSYNRLQAAATSAQKAALSKLSPEMVSASTLAGDPITA Sbjct: 421 ITAVTGKNPQEHYNELAKRFGAPSYNRLQAAATSAQKAALSKLSPEMVSASTLAGDPITA 480 Query: 481 RLTAAPGNGASIGGLKVMTDNGWFAARPSGTEDAYKIYCESFLGEEHRKQIEKEAVEIVS 540 RLTAAPGNGASIGGLKVMTDNGWFAARPSGTEDAYKIYCESFLGEEHRKQIEKEAVEIVS Sbjct: 481 RLTAAPGNGASIGGLKVMTDNGWFAARPSGTEDAYKIYCESFLGEEHRKQIEKEAVEIVS 540 Query: 541 EVLKNA 546 EVLKNA Sbjct: 541 EVLKNA 546 Lambda K H 0.316 0.134 0.395 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: 1211 Number of extensions: 50 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: 546 Length of database: 546 Length adjustment: 35 Effective length of query: 511 Effective length of database: 511 Effective search space: 261121 Effective search space used: 261121 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: 52 (24.6 bits)
Align candidate 14818 b0688 (phosphoglucomutase (NCBI))
to HMM TIGR01132 (pgm: phosphoglucomutase, alpha-D-glucose phosphate-specific (EC 5.4.2.2))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.carbon/TIGR01132.hmm # target sequence database: /tmp/gapView.29383.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01132 [M=546] Accession: TIGR01132 Description: pgm: phosphoglucomutase, alpha-D-glucose phosphate-specific Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 0 1074.3 0.3 0 1074.2 0.3 1.0 1 lcl|FitnessBrowser__Keio:14818 b0688 phosphoglucomutase (NCBI) Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Keio:14818 b0688 phosphoglucomutase (NCBI) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1074.2 0.3 0 0 1 546 [] 1 544 [. 1 544 [. 1.00 Alignments for each domain: == domain 1 score: 1074.2 bits; conditional E-value: 0 TIGR01132 1 mainpraGqkaqqedlldvaklvadyyllkpdaenaaqkvefGtsGhrGsalkgtfneahilaiaqavvevraaqGitG 79 mai++raGq+aqq+dl++va+l+a+yy+lkp+a+na+++v+fGtsGhrGsa++++fne hilaiaqa++e+ra++GitG lcl|FitnessBrowser__Keio:14818 1 MAIHNRAGQPAQQSDLINVAQLTAQYYVLKPEAGNAEHAVKFGTSGHRGSAARHSFNEPHILAIAQAIAEERAKNGITG 79 89***************************************************************************** PP TIGR01132 80 plyiGkdthalsepafvsvlevlaanqvevivqennrytptpavshailtynkgkkealadGivitpshnppedGGiky 158 p+y+Gkdthalsepaf+svlevlaan+v+vivqenn++tptpavs+ail++nk k ++ladGivitpshnppedGGiky lcl|FitnessBrowser__Keio:14818 80 PCYVGKDTHALSEPAFISVLEVLAANGVDVIVQENNGFTPTPAVSNAILVHNK-KGGPLADGIVITPSHNPPEDGGIKY 157 *****************************************************.************************* PP TIGR01132 159 nppnGGpaetevtkaiedranellkdrlkgvkrldlekalksetvkekdlvkpyvddladvvdlaairkaglrlGvdpl 237 nppnGGpa+t+vtk++edran+ll+d+lkgvkr++l++a++s++vke+dlv+p+v++lad+vd+aai+kagl+lGvdpl lcl|FitnessBrowser__Keio:14818 158 NPPNGGPADTNVTKVVEDRANALLADGLKGVKRISLDEAMASGHVKEQDLVQPFVEGLADIVDMAAIQKAGLTLGVDPL 236 ******************************************************************************* PP TIGR01132 238 GGagvdywkeiaekynldltlvneavdatfrfmtldkdGkirmdcsspyamagllklkdkydlafgndadadrhGivtp 316 GG+g++ywk+i+e+ynl+lt+vn++vd+tfrfm+ldkdG+irmdcss++amagll+l+dk+dlaf+nd+d+drhGivtp lcl|FitnessBrowser__Keio:14818 237 GGSGIEYWKRIGEYYNLNLTIVNDQVDQTFRFMHLDKDGAIRMDCSSECAMAGLLALRDKFDLAFANDPDYDRHGIVTP 315 ******************************************************************************* PP TIGR01132 317 dkGllnpnhylavaieylykhrqqwaaevavGktlvssalidrvvadlgrklvevpvGfkwfvdGlldgslGfGGeesa 395 +Gl+npnhylavai+yl++hr+qw+++vavGktlvssa+idrvv+dlgrklvevpvGfkwfvdGl+dgs+GfGGeesa lcl|FitnessBrowser__Keio:14818 316 -AGLMNPNHYLAVAINYLFQHRPQWGKDVAVGKTLVSSAMIDRVVNDLGRKLVEVPVGFKWFVDGLFDGSFGFGGEESA 393 .****************************************************************************** PP TIGR01132 396 GasflrkdGtvwstdkdGiilallaaeitavtGknpqqrydelaakyGdpiyaridaaatsaqkarlkklspdevsatt 474 Gasflr+dGt+wstdkdGii++llaaeitavtGknpq++y+ela+++G+p+y+r++aaatsaqka+l+klsp++vsa+t lcl|FitnessBrowser__Keio:14818 394 GASFLRFDGTPWSTDKDGIIMCLLAAEITAVTGKNPQEHYNELAKRFGAPSYNRLQAAATSAQKAALSKLSPEMVSAST 472 ******************************************************************************* PP TIGR01132 475 laGdaitakltkapGngaaiGGlkvttdegwfaarpsGtedvykiyaesfkgeehlkeiekeaeeivdevlk 546 laGd+ita+lt+apGnga+iGGlkv+td+gwfaarpsGted+ykiy+esf geeh+k+iekea eiv+evlk lcl|FitnessBrowser__Keio:14818 473 LAGDPITARLTAAPGNGASIGGLKVMTDNGWFAARPSGTEDAYKIYCESFLGEEHRKQIEKEAVEIVSEVLK 544 **********************************************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (546 nodes) Target sequences: 1 (546 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 12.64 // [ok]
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