Align phosphoglucomutase; EC 5.4.2.2 (characterized)
to candidate BWI76_RS08290 BWI76_RS08290 phosphoglucomutase, alpha-D-glucose phosphate-specific
Query= CharProtDB::CH_002452 (546 letters) >FitnessBrowser__Koxy:BWI76_RS08290 Length = 546 Score = 1049 bits (2713), Expect = 0.0 Identities = 520/546 (95%), Positives = 534/546 (97%) Query: 1 MAIHNRAGQPAQQSDLINVAQLTAQYYVLKPEAGNAEHAVKFGTSGHRGSAARHSFNEPH 60 MAI RAGQPAQQSDLINVAQLTAQYYVLKPE GNAEHAVKFGTSGHRGSAARH+FNE H Sbjct: 1 MAIDKRAGQPAQQSDLINVAQLTAQYYVLKPEVGNAEHAVKFGTSGHRGSAARHNFNEQH 60 Query: 61 ILAIAQAIAEERAKNGITGPCYVGKDTHALSEPAFISVLEVLAANGVDVIVQENNGFTPT 120 ILAIAQAIAE+RAKNGI GPCYVGKDTHALSEPAFISVLEVLAANGVDVIVQENNGFTPT Sbjct: 61 ILAIAQAIAEDRAKNGIAGPCYVGKDTHALSEPAFISVLEVLAANGVDVIVQENNGFTPT 120 Query: 121 PAVSNAILVHNKKGGPLADGIVITPSHNPPEDGGIKYNPPNGGPADTNVTKVVEDRANAL 180 PA+SNAILVHNKK GPLADGIVITPSHNPPEDGGIKYNPPNGGPADTNVTKVVE+RAN L Sbjct: 121 PAISNAILVHNKKDGPLADGIVITPSHNPPEDGGIKYNPPNGGPADTNVTKVVENRANEL 180 Query: 181 LADGLKGVKRISLDEAMASGHVKEQDLVQPFVEGLADIVDMAAIQKAGLTLGVDPLGGSG 240 LA GL+GVKRISLD A+ASGHVKEQDLVQPF+EGLADIVDMAAIQKAGLTLGVDPLGGSG Sbjct: 181 LAAGLQGVKRISLDAALASGHVKEQDLVQPFIEGLADIVDMAAIQKAGLTLGVDPLGGSG 240 Query: 241 IEYWKRIGEYYNLNLTIVNDQVDQTFRFMHLDKDGAIRMDCSSECAMAGLLALRDKFDLA 300 IEYWKRI E+YNLNLTIVND VDQTFRFMHLDKDGAIRMDCSSECAMAGLLALRDKFDLA Sbjct: 241 IEYWKRIAEHYNLNLTIVNDHVDQTFRFMHLDKDGAIRMDCSSECAMAGLLALRDKFDLA 300 Query: 301 FANDPDYDRHGIVTPAGLMNPNHYLAVAINYLFQHRPQWGKDVAVGKTLVSSAMIDRVVN 360 FANDPDYDRHGIVTPAGLMNPNHYLAVAINYLFQHRPQWGKDVAVGKTLVSSAMIDRVVN Sbjct: 301 FANDPDYDRHGIVTPAGLMNPNHYLAVAINYLFQHRPQWGKDVAVGKTLVSSAMIDRVVN 360 Query: 361 DLGRKLVEVPVGFKWFVDGLFDGSFGFGGEESAGASFLRFDGTPWSTDKDGIIMCLLAAE 420 DLGRKLVEVPVGFKWFVDGLFDGSFGFGGEESAGASFLRFDGTPWSTDKDGIIMCLLAAE Sbjct: 361 DLGRKLVEVPVGFKWFVDGLFDGSFGFGGEESAGASFLRFDGTPWSTDKDGIIMCLLAAE 420 Query: 421 ITAVTGKNPQEHYNELAKRFGAPSYNRLQAAATSAQKAALSKLSPEMVSASTLAGDPITA 480 ITAVTGKNPQ+HY+ELA+RFGAPSYNRLQA+ATSAQKAALSKLSPEMVSASTLAGDPITA Sbjct: 421 ITAVTGKNPQQHYDELAERFGAPSYNRLQASATSAQKAALSKLSPEMVSASTLAGDPITA 480 Query: 481 RLTAAPGNGASIGGLKVMTDNGWFAARPSGTEDAYKIYCESFLGEEHRKQIEKEAVEIVS 540 RLTAAPGNGA+IGGLKVMTDNGWFAARPSGTEDAYKIYCESFLG EHR+QIEKEAVEIVS Sbjct: 481 RLTAAPGNGAAIGGLKVMTDNGWFAARPSGTEDAYKIYCESFLGAEHRQQIEKEAVEIVS 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: 1167 Number of extensions: 43 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 BWI76_RS08290 BWI76_RS08290 (phosphoglucomutase, alpha-D-glucose phosphate-specific)
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.10292.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 1059.5 0.7 0 1059.3 0.7 1.0 1 lcl|FitnessBrowser__Koxy:BWI76_RS08290 BWI76_RS08290 phosphoglucomutase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Koxy:BWI76_RS08290 BWI76_RS08290 phosphoglucomutase, alpha-D-glucose phosphate-specific # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1059.3 0.7 0 0 1 546 [] 1 544 [. 1 544 [. 1.00 Alignments for each domain: == domain 1 score: 1059.3 bits; conditional E-value: 0 TIGR01132 1 mainpraGqkaqqedlldvaklvadyyllkpdaenaaqkvefGtsGhrGsalkgtfneahilaiaqavvev 71 mai++raGq+aqq+dl++va+l+a+yy+lkp+ +na+++v+fGtsGhrGsa+++ fne+hilaiaqa++e lcl|FitnessBrowser__Koxy:BWI76_RS08290 1 MAIDKRAGQPAQQSDLINVAQLTAQYYVLKPEVGNAEHAVKFGTSGHRGSAARHNFNEQHILAIAQAIAED 71 799******************************************************************** PP TIGR01132 72 raaqGitGplyiGkdthalsepafvsvlevlaanqvevivqennrytptpavshailtynkgkkealadGi 142 ra++Gi+Gp+y+Gkdthalsepaf+svlevlaan+v+vivqenn++tptpa+s+ail++nk k+++ladGi lcl|FitnessBrowser__Koxy:BWI76_RS08290 72 RAKNGIAGPCYVGKDTHALSEPAFISVLEVLAANGVDVIVQENNGFTPTPAISNAILVHNK-KDGPLADGI 141 *************************************************************.********* PP TIGR01132 143 vitpshnppedGGikynppnGGpaetevtkaiedranellkdrlkgvkrldlekalksetvkekdlvkpyv 213 vitpshnppedGGikynppnGGpa+t+vtk++e+ranell+++l+gvkr++l+ al+s++vke+dlv+p++ lcl|FitnessBrowser__Koxy:BWI76_RS08290 142 VITPSHNPPEDGGIKYNPPNGGPADTNVTKVVENRANELLAAGLQGVKRISLDAALASGHVKEQDLVQPFI 212 *********************************************************************** PP TIGR01132 214 ddladvvdlaairkaglrlGvdplGGagvdywkeiaekynldltlvneavdatfrfmtldkdGkirmdcss 284 ++lad+vd+aai+kagl+lGvdplGG+g++ywk+iae+ynl+lt+vn++vd+tfrfm+ldkdG+irmdcss lcl|FitnessBrowser__Koxy:BWI76_RS08290 213 EGLADIVDMAAIQKAGLTLGVDPLGGSGIEYWKRIAEHYNLNLTIVNDHVDQTFRFMHLDKDGAIRMDCSS 283 *********************************************************************** PP TIGR01132 285 pyamagllklkdkydlafgndadadrhGivtpdkGllnpnhylavaieylykhrqqwaaevavGktlvssa 355 ++amagll+l+dk+dlaf+nd+d+drhGivtp +Gl+npnhylavai+yl++hr+qw+++vavGktlvssa lcl|FitnessBrowser__Koxy:BWI76_RS08290 284 ECAMAGLLALRDKFDLAFANDPDYDRHGIVTP-AGLMNPNHYLAVAINYLFQHRPQWGKDVAVGKTLVSSA 353 ********************************.************************************** PP TIGR01132 356 lidrvvadlgrklvevpvGfkwfvdGlldgslGfGGeesaGasflrkdGtvwstdkdGiilallaaeitav 426 +idrvv+dlgrklvevpvGfkwfvdGl+dgs+GfGGeesaGasflr+dGt+wstdkdGii++llaaeitav lcl|FitnessBrowser__Koxy:BWI76_RS08290 354 MIDRVVNDLGRKLVEVPVGFKWFVDGLFDGSFGFGGEESAGASFLRFDGTPWSTDKDGIIMCLLAAEITAV 424 *********************************************************************** PP TIGR01132 427 tGknpqqrydelaakyGdpiyaridaaatsaqkarlkklspdevsattlaGdaitakltkapGngaaiGGl 497 tGknpqq+ydela+++G+p+y+r++a+atsaqka+l+klsp++vsa+tlaGd+ita+lt+apGngaaiGGl lcl|FitnessBrowser__Koxy:BWI76_RS08290 425 TGKNPQQHYDELAERFGAPSYNRLQASATSAQKAALSKLSPEMVSASTLAGDPITARLTAAPGNGAAIGGL 495 *********************************************************************** PP TIGR01132 498 kvttdegwfaarpsGtedvykiyaesfkgeehlkeiekeaeeivdevlk 546 kv+td+gwfaarpsGted+ykiy+esf g+eh+++iekea eiv+evlk lcl|FitnessBrowser__Koxy:BWI76_RS08290 496 KVMTDNGWFAARPSGTEDAYKIYCESFLGAEHRQQIEKEAVEIVSEVLK 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 0.02s 00:00:00.04 Elapsed: 00:00:00.03 # Mc/sec: 8.32 // [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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.
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