Align phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) (EC 5.4.2.2) (characterized)
to candidate GFF39 Psest_0039 phosphoglucomutase, alpha-D-glucose phosphate-specific
Query= BRENDA::I6Y2G3 (547 letters) >FitnessBrowser__psRCH2:GFF39 Length = 554 Score = 686 bits (1771), Expect = 0.0 Identities = 353/550 (64%), Positives = 410/550 (74%), Gaps = 14/550 (2%) Query: 7 AGQPAQPEDLVDLPHLVTAYYSIEPDPDDLAQQVAFGTSGHRGSALTGTFNELHILAITQ 66 AG+ P L LP LV YYS PDP D AQQVAFGTSGHRGS+L G+FNE HILA TQ Sbjct: 7 AGRLPDPHTLTHLPRLVARYYSDRPDPSDPAQQVAFGTSGHRGSSLKGSFNEWHILATTQ 66 Query: 67 AIVEYRAAQGTTGPLFIGRDTHGLSEPAWVSALEVLAANQVVAVVDS-------RDRYTP 119 AI +YR +G GPLF+G DTH LSEPA++SALEVLAAN + +D+ YTP Sbjct: 67 AICDYRRQEGIDGPLFMGMDTHALSEPAFISALEVLAANGIETRIDAGCAETGGEPGYTP 126 Query: 120 TPAISHAILTYNRGRTEALADGIVVTPSHNPPSDGGIKYNPPNGGPADTAATTAIAKRAN 179 TPAIS+AIL+YNRGRT LADGIV+TPSHNPP DGG KYNP NGGPADT T I +RAN Sbjct: 127 TPAISNAILSYNRGRTSGLADGIVITPSHNPPGDGGFKYNPTNGGPADTGVTKWIQERAN 186 Query: 180 EILLAR-SMVKRLPLARALR--TAQRHDYLGHYVDDLPNVVDIAAIREAGVRIGADPLGG 236 +L+A VKR+ +AL+ T QR D++ YV L V+D+ AIR +G++ DPLGG Sbjct: 187 ALLVAGLEGVKRMDYRQALKATTTQRFDFIDAYVGGLERVIDLDAIRGSGLKFAVDPLGG 246 Query: 237 ASVDYWGEIAHRHGLDLTVVNPLVDATWRFMTLDTDGKIRMDCSSPDAMAGLIRTMFGNR 296 A V YW IA R GL L V++ +VD T+RFM LD DGKIRMDCSSP AMAGLI N+ Sbjct: 247 AGVHYWPRIAERFGLPLEVLSTVVDPTFRFMRLDWDGKIRMDCSSPHAMAGLIE----NK 302 Query: 297 ERYQIATGNDADADRHGIVTPDEGLLNPNHYLAVAIEYLYTHRPSWPAGIAVGKTVVSSS 356 +R+ +A D D DRHGIVT GL+NPNHYLAVAIEYL+THRP W A +GKT+VSSS Sbjct: 303 DRFDVAFACDTDHDRHGIVTRSGGLMNPNHYLAVAIEYLFTHRPGWSAEAGIGKTLVSSS 362 Query: 357 IIDRVVAGIGRQLVEVPVGFKWFVDGLIGATLGFGGEESAGASFLRRDGSVWTTDKDGII 416 +IDRV AGI R+LVEVPVGFKWFVDGL+ +LGFGGEESAGASFL + G W+TDKDG+I Sbjct: 363 MIDRVAAGIERRLVEVPVGFKWFVDGLMDGSLGFGGEESAGASFLDKQGGAWSTDKDGLI 422 Query: 417 MALLAAEILAVTGATPSQRYHALAGEYGGPCYARIDAPADREQKARLARLSADQVSATEL 476 + LLAAEI AVTG PS+RY AL +G P Y RIDA A+REQKARL +LSA QVSA EL Sbjct: 423 LGLLAAEITAVTGKDPSERYQALTDRFGAPVYQRIDAAANREQKARLGKLSASQVSAKEL 482 Query: 477 AGEPITAKLTTAPGNGAALGGLKVTTANAWFAARPSGTEDVYKIYAESFRGPQHLVEVQQ 536 AG+PIT LT APGNGAA+GGLKV TAN WFAARPSGTEDVYKIYAESF G HL +Q Sbjct: 483 AGQPITRILTEAPGNGAAIGGLKVETANGWFAARPSGTEDVYKIYAESFEGEAHLKRIQA 542 Query: 537 TAREVVDRVI 546 A+ +VD V+ Sbjct: 543 EAKALVDSVL 552 Lambda K H 0.318 0.135 0.401 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: 1048 Number of extensions: 44 Number of successful extensions: 4 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: 547 Length of database: 554 Length adjustment: 36 Effective length of query: 511 Effective length of database: 518 Effective search space: 264698 Effective search space used: 264698 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: 53 (25.0 bits)
Align candidate GFF39 Psest_0039 (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.2802.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.2e-280 914.6 0.0 1e-279 914.4 0.0 1.0 1 lcl|FitnessBrowser__psRCH2:GFF39 Psest_0039 phosphoglucomutase, a Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__psRCH2:GFF39 Psest_0039 phosphoglucomutase, alpha-D-glucose phosphate-specific # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 914.4 0.0 1e-279 1e-279 1 545 [. 1 552 [. 1 553 [. 0.99 Alignments for each domain: == domain 1 score: 914.4 bits; conditional E-value: 1e-279 TIGR01132 1 mainpraGqkaqqedlldvaklvadyyllkpdaenaaqkvefGtsGhrGsalkgtfneahilaiaqavvevraaqGi 77 m+i + aG+ + ++ l+++++lva yy+ +pd+ ++aq+v+fGtsGhrGs+lkg+fne hila +qa+ ++r+++Gi lcl|FitnessBrowser__psRCH2:GFF39 1 MSIAANAGRLPDPHTLTHLPRLVARYYSDRPDPSDPAQQVAFGTSGHRGSSLKGSFNEWHILATTQAICDYRRQEGI 77 678899*********************************************************************** PP TIGR01132 78 tGplyiGkdthalsepafvsvlevlaanqvevivq.......ennrytptpavshailtynkgkkealadGivitps 147 Gpl++G+dthalsepaf+s+levlaan++e+ ++ + +ytptpa+s+ail yn+g++++ladGivitps lcl|FitnessBrowser__psRCH2:GFF39 78 DGPLFMGMDTHALSEPAFISALEVLAANGIETRIDagcaetgGEPGYTPTPAISNAILSYNRGRTSGLADGIVITPS 154 **********************************988886666789******************************* PP TIGR01132 148 hnppedGGikynppnGGpaetevtkaiedranellkdrlkgvkrldlekalksetvkekdlvkpyvddladvvdlaa 224 hnpp dGG+kynp nGGpa+t vtk+i++ran+ll ++l+gvkr+d+ +alk++t+++ d+++ yv +l v+dl+a lcl|FitnessBrowser__psRCH2:GFF39 155 HNPPGDGGFKYNPTNGGPADTGVTKWIQERANALLVAGLEGVKRMDYRQALKATTTQRFDFIDAYVGGLERVIDLDA 231 ***************************************************************************** PP TIGR01132 225 irkaglrlGvdplGGagvdywkeiaekynldltlvneavdatfrfmtldkdGkirmdcsspyamagllklkdkydla 301 ir +gl++ vdplGGagv+yw +iae+++l l +++ vd+tfrfm ld+dGkirmdcssp+amagl+++kd++d+a lcl|FitnessBrowser__psRCH2:GFF39 232 IRGSGLKFAVDPLGGAGVHYWPRIAERFGLPLEVLSTVVDPTFRFMRLDWDGKIRMDCSSPHAMAGLIENKDRFDVA 308 ***************************************************************************** PP TIGR01132 302 fgndadadrhGivtpdkGllnpnhylavaieylykhrqqwaaevavGktlvssalidrvvadlgrklvevpvGfkwf 378 f+ d+d drhGivt + Gl+npnhylavaieyl++hr++w+ae +Gktlvss++idrv+a ++r+lvevpvGfkwf lcl|FitnessBrowser__psRCH2:GFF39 309 FACDTDHDRHGIVTRSGGLMNPNHYLAVAIEYLFTHRPGWSAEAGIGKTLVSSSMIDRVAAGIERRLVEVPVGFKWF 385 ***************************************************************************** PP TIGR01132 379 vdGlldgslGfGGeesaGasflrkdGtvwstdkdGiilallaaeitavtGknpqqrydelaakyGdpiyaridaaat 455 vdGl+dgslGfGGeesaGasfl k+G +wstdkdG+il llaaeitavtGk+p++ry++l+ ++G+p+y+ridaaa+ lcl|FitnessBrowser__psRCH2:GFF39 386 VDGLMDGSLGFGGEESAGASFLDKQGGAWSTDKDGLILGLLAAEITAVTGKDPSERYQALTDRFGAPVYQRIDAAAN 462 ***************************************************************************** PP TIGR01132 456 saqkarlkklspdevsattlaGdaitakltkapGngaaiGGlkvttdegwfaarpsGtedvykiyaesfkgeehlke 532 ++qkarl kls+ +vsa++laG++it lt+apGngaaiGGlkv t++gwfaarpsGtedvykiyaesf+ge+hlk+ lcl|FitnessBrowser__psRCH2:GFF39 463 REQKARLGKLSASQVSAKELAGQPITRILTEAPGNGAAIGGLKVETANGWFAARPSGTEDVYKIYAESFEGEAHLKR 539 ***************************************************************************** PP TIGR01132 533 iekeaeeivdevl 545 i+ ea+++vd+vl lcl|FitnessBrowser__psRCH2:GFF39 540 IQAEAKALVDSVL 552 ***********98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (546 nodes) Target sequences: 1 (554 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: 10.74 // [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