Align phosphoglucomutase; EC 5.4.2.2 (characterized)
to candidate WP_019614677.1 G327_RS0110225 alpha-D-glucose phosphate-specific phosphoglucomutase
Query= CharProtDB::CH_002452 (546 letters) >NCBI__GCF_000381745.1:WP_019614677.1 Length = 550 Score = 709 bits (1829), Expect = 0.0 Identities = 348/543 (64%), Positives = 427/543 (78%), Gaps = 2/543 (0%) Query: 1 MAIHNRAGQPAQQSDLINVAQLTAQYYVLKPEAGNAEHAVKFGTSGHRGSAARHSFNEPH 60 MAIH RAG+ AQ SDL+++ +L + YY+ P+ A V FGTSGHRG + +++F E H Sbjct: 1 MAIHPRAGKTAQASDLVDIPKLVSAYYINIPDVSIASEQVAFGTSGHRGCSFKNAFTELH 60 Query: 61 ILAIAQAIAEERAKNGITGPCYVGKDTHALSEPAFISVLEVLAANGVDVIVQENNGFTPT 120 ILAI+QA+AE R + G TGP ++GKDTHALSEPAF S ++VL ANG+ VIVQ G+TPT Sbjct: 61 ILAISQALAEYRIEQGYTGPMFIGKDTHALSEPAFASAVQVLVANGIKVIVQAGGGYTPT 120 Query: 121 PAVSNAILVHNKKGGP-LADGIVITPSHNPPEDGGIKYNPPNGGPADTNVTKVVEDRANA 179 P +S+AIL +N + LADGIVITPSHNPPEDGG KYNPPNGGPAD++VTK+++DRAN Sbjct: 121 PVISHAILQYNNENPDNLADGIVITPSHNPPEDGGFKYNPPNGGPADSDVTKIIQDRANQ 180 Query: 180 LLADGLKGVKRISLDEAMASGHVKEQDLVQPFVEGLADIVDMAAIQKAGLTLGVDPLGGS 239 +L D +K+ EAM S V+E D +QP+V+ L +++++ AI KAG+ +GVD LGGS Sbjct: 181 ILDDQFDDIKQWDFSEAMESEFVEEYDYIQPYVDDLKNVLNVEAIAKAGIKIGVDTLGGS 240 Query: 240 GIEYWKRIGEYYNLNLTIVNDQVDQTFRFMHLDKDGAIRMDCSSECAMAGLLALRDKFDL 299 G+ YW I + Y L++ +VND+VD TF FM LDKDG IRMDCSS AMAGL+ L+DKFD+ Sbjct: 241 GVAYWPVIAKTYGLDIEVVNDRVDPTFSFMTLDKDGKIRMDCSSPYAMAGLIELKDKFDV 300 Query: 300 AFANDPDYDRHGIVTPA-GLMNPNHYLAVAINYLFQHRPQWGKDVAVGKTLVSSAMIDRV 358 A ANDPDYDRHGIVT + GL+NPNHYLAVAINYLF+HR W +D VGKTLVSS+MIDRV Sbjct: 301 AIANDPDYDRHGIVTKSSGLLNPNHYLAVAINYLFKHRTDWPQDAIVGKTLVSSSMIDRV 360 Query: 359 VNDLGRKLVEVPVGFKWFVDGLFDGSFGFGGEESAGASFLRFDGTPWSTDKDGIIMCLLA 418 V +L R++ EVPVGFKWFVDGL++G GFGGEESAGASFLR DGT WSTDKDGII+ LLA Sbjct: 361 VVELEREMSEVPVGFKWFVDGLYEGKLGFGGEESAGASFLRKDGTVWSTDKDGIILALLA 420 Query: 419 AEITAVTGKNPQEHYNELAKRFGAPSYNRLQAAATSAQKAALSKLSPEMVSASTLAGDPI 478 AEI AVTGK+P EHY E ++FG+P Y R A AT QKA L+ LSPEMV A TLAG+ I Sbjct: 421 AEIIAVTGKDPGEHYAEFTEKFGSPIYQRFDAPATPEQKAVLANLSPEMVEAETLAGERI 480 Query: 479 TARLTAAPGNGASIGGLKVMTDNGWFAARPSGTEDAYKIYCESFLGEEHRKQIEKEAVEI 538 TA+LT A GNGA+IGGLKV T+NGWFAARPSGTE+ YKIY ESF+G EH +I+KEA EI Sbjct: 481 TAKLTHASGNGAAIGGLKVTTENGWFAARPSGTENIYKIYSESFIGAEHIAEIQKEAQEI 540 Query: 539 VSE 541 V++ Sbjct: 541 VAQ 543 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: 936 Number of extensions: 37 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: 546 Length of database: 550 Length adjustment: 36 Effective length of query: 510 Effective length of database: 514 Effective search space: 262140 Effective search space used: 262140 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: 53 (25.0 bits)
Align candidate WP_019614677.1 G327_RS0110225 (alpha-D-glucose phosphate-specific phosphoglucomutase)
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.945789.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-284 930.4 0.7 1.7e-284 930.2 0.7 1.0 1 NCBI__GCF_000381745.1:WP_019614677.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000381745.1:WP_019614677.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 930.2 0.7 1.7e-284 1.7e-284 1 545 [. 1 545 [. 1 546 [. 1.00 Alignments for each domain: == domain 1 score: 930.2 bits; conditional E-value: 1.7e-284 TIGR01132 1 mainpraGqkaqqedlldvaklvadyyllkpdaenaaqkvefGtsGhrGsalkgtfneahilaiaqavvevra 73 mai+praG+ aq++dl+d++klv++yy pd a+++v+fGtsGhrG++ k++f e hilai+qa++e+r NCBI__GCF_000381745.1:WP_019614677.1 1 MAIHPRAGKTAQASDLVDIPKLVSAYYINIPDVSIASEQVAFGTSGHRGCSFKNAFTELHILAISQALAEYRI 73 89*********************************************************************** PP TIGR01132 74 aqGitGplyiGkdthalsepafvsvlevlaanqvevivqennrytptpavshailtynkgkkealadGivitp 146 +qG tGp++iGkdthalsepaf s+++vl+an+++vivq +ytptp +shail yn+ + ++ladGivitp NCBI__GCF_000381745.1:WP_019614677.1 74 EQGYTGPMFIGKDTHALSEPAFASAVQVLVANGIKVIVQAGGGYTPTPVISHAILQYNNENPDNLADGIVITP 146 ************************************************************************* PP TIGR01132 147 shnppedGGikynppnGGpaetevtkaiedranellkdrlkgvkrldlekalksetvkekdlvkpyvddladv 219 shnppedGG+kynppnGGpa+++vtk+i+dran++l d+ +k+ d+++a++se v+e d+++pyvddl +v NCBI__GCF_000381745.1:WP_019614677.1 147 SHNPPEDGGFKYNPPNGGPADSDVTKIIQDRANQILDDQFDDIKQWDFSEAMESEFVEEYDYIQPYVDDLKNV 219 ************************************************************************* PP TIGR01132 220 vdlaairkaglrlGvdplGGagvdywkeiaekynldltlvneavdatfrfmtldkdGkirmdcsspyamagll 292 ++++ai kag+++Gvd lGG+gv yw ia++y+ld+ +vn+ vd+tf fmtldkdGkirmdcsspyamagl+ NCBI__GCF_000381745.1:WP_019614677.1 220 LNVEAIAKAGIKIGVDTLGGSGVAYWPVIAKTYGLDIEVVNDRVDPTFSFMTLDKDGKIRMDCSSPYAMAGLI 292 ************************************************************************* PP TIGR01132 293 klkdkydlafgndadadrhGivtpdkGllnpnhylavaieylykhrqqwaaevavGktlvssalidrvvadlg 365 +lkdk+d+a++nd+d+drhGivt ++Gllnpnhylavai+yl+khr +w+++ vGktlvss++idrvv +l+ NCBI__GCF_000381745.1:WP_019614677.1 293 ELKDKFDVAIANDPDYDRHGIVTKSSGLLNPNHYLAVAINYLFKHRTDWPQDAIVGKTLVSSSMIDRVVVELE 365 ************************************************************************* PP TIGR01132 366 rklvevpvGfkwfvdGlldgslGfGGeesaGasflrkdGtvwstdkdGiilallaaeitavtGknpqqrydel 438 r++ evpvGfkwfvdGl++g+lGfGGeesaGasflrkdGtvwstdkdGiilallaaei+avtGk+p+++y e+ NCBI__GCF_000381745.1:WP_019614677.1 366 REMSEVPVGFKWFVDGLYEGKLGFGGEESAGASFLRKDGTVWSTDKDGIILALLAAEIIAVTGKDPGEHYAEF 438 ************************************************************************* PP TIGR01132 439 aakyGdpiyaridaaatsaqkarlkklspdevsattlaGdaitakltkapGngaaiGGlkvttdegwfaarps 511 ++k+G+piy+r da+at++qka+l++lsp++v a+tlaG+ itaklt+a GngaaiGGlkvtt++gwfaarps NCBI__GCF_000381745.1:WP_019614677.1 439 TEKFGSPIYQRFDAPATPEQKAVLANLSPEMVEAETLAGERITAKLTHASGNGAAIGGLKVTTENGWFAARPS 511 ************************************************************************* PP TIGR01132 512 Gtedvykiyaesfkgeehlkeiekeaeeivdevl 545 Gte++ykiy+esf g+eh+ ei+kea+eiv +++ NCBI__GCF_000381745.1:WP_019614677.1 512 GTENIYKIYSESFIGAEHIAEIQKEAQEIVAQAF 545 ******************************9986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (546 nodes) Target sequences: 1 (550 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 34.97 // [ok]
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