Align phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) (EC 5.4.2.2) (characterized)
to candidate GFF2629 PS417_13395 phosphoglucomutase
Query= BRENDA::I6Y2G3 (547 letters) >FitnessBrowser__WCS417:GFF2629 Length = 547 Score = 639 bits (1648), Expect = 0.0 Identities = 337/549 (61%), Positives = 399/549 (72%), Gaps = 7/549 (1%) Query: 1 MVANPRAGQPAQPEDLVDLPHLVTAYYSIEPDPDDLAQQVAFGTSGHRGSALTGTFNELH 60 M +P AG+PA + LVD+P LVTAYY+ +PD Q+VAFGTSGHRG++ +FNE H Sbjct: 1 MTISPFAGKPAPAQLLVDIPRLVTAYYTGQPDAAISTQRVAFGTSGHRGNSFELSFNEWH 60 Query: 61 ILAITQAIVEYRAAQGTTGPLFIGRDTHGLSEPAWVSALEVLAANQVVAVVDSRDRYTPT 120 +LAI+QAI YR AQG GPLF+G DTH LS PA SALEVLAAN V ++ D YTPT Sbjct: 61 VLAISQAICLYREAQGINGPLFVGLDTHALSTPAGASALEVLAANGVHVMLAEGDEYTPT 120 Query: 121 PAISHAILTYNRGRTEALADGIVVTPSHNPPSDGGIKYNPPNGGPADTAATTAIAKRANE 180 PAISHAI+ YNRGRT LADGIV+TPSHNPP GG KYNPPNGGPADT T I +ANE Sbjct: 121 PAISHAIICYNRGRTSGLADGIVITPSHNPPQSGGYKYNPPNGGPADTHVTKWIEAKANE 180 Query: 181 ILLAR-SMVKRLPLARALR--TAQRHDYLGHYVDDLPNVVDIAAIREAGVRIGADPLGGA 237 +L + + VKR+ A+AL+ T RHDYL YV DL NV+D+ AIR A +R+G DPLGGA Sbjct: 181 LLAKKLAGVKRITHAQALKADTTHRHDYLNTYVADLVNVIDMDAIRSADLRLGVDPLGGA 240 Query: 238 SVDYWGEIAHRHGLDLTVVNPLVDATWRFMTLDTDGKIRMDCSSPDAMAGLIRTMFGNRE 297 V YW IA + L+L VVN VDAT+RFM +D DG+IRMD SS AM GLI G +E Sbjct: 241 GVRYWSAIAEHYRLNLEVVNTEVDATFRFMCVDWDGQIRMDPSSSYAMQGLI----GLKE 296 Query: 298 RYQIATGNDADADRHGIVTPDEGLLNPNHYLAVAIEYLYTHRPSWPAGIAVGKTVVSSSI 357 R+ +A D D DRHGIVTP GLL PN+YLAV+I+YL+ +RP W A AVGKTVVSS + Sbjct: 297 RFDVAFACDPDHDRHGIVTPSGGLLAPNNYLAVSIDYLFQNRPDWRADAAVGKTVVSSGL 356 Query: 358 IDRVVAGIGRQLVEVPVGFKWFVDGLIGATLGFGGEESAGASFLRRDGSVWTTDKDGIIM 417 IDRV A IGR+L EVPVGFKWF DGL +LGFGGEESAGASFLR+DG+VW+TDKDG+I Sbjct: 357 IDRVAARIGRRLYEVPVGFKWFADGLFDGSLGFGGEESAGASFLRKDGTVWSTDKDGLIP 416 Query: 418 ALLAAEILAVTGATPSQRYHALAGEYGGPCYARIDAPADREQKARLARLSADQVSATELA 477 ALLAAE+ + G PSQ Y L G P R+DA A QKA L +LS DQV++TELA Sbjct: 417 ALLAAEMTSRKGQDPSQIYRGLTDALGEPFAIRVDAKATPAQKALLGKLSPDQVTSTELA 476 Query: 478 GEPITAKLTTAPGNGAALGGLKVTTANAWFAARPSGTEDVYKIYAESFRGPQHLVEVQQT 537 GE I L+ APGN A+GGLKV T N WFAARPSGTED+YKIYAESF G HL ++ + Sbjct: 477 GESIQQILSHAPGNDQAIGGLKVMTENGWFAARPSGTEDIYKIYAESFIGEDHLKQLVEE 536 Query: 538 AREVVDRVI 546 A+ +VD I Sbjct: 537 AQVLVDGAI 545 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: 972 Number of extensions: 36 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: 547 Length of database: 547 Length adjustment: 36 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 (21.7 bits) S2: 52 (24.6 bits)
Align candidate GFF2629 PS417_13395 (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.13643.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.5e-267 872.4 0.0 6.2e-267 872.2 0.0 1.0 1 lcl|FitnessBrowser__WCS417:GFF2629 PS417_13395 phosphoglucomutase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__WCS417:GFF2629 PS417_13395 phosphoglucomutase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 872.2 0.0 6.2e-267 6.2e-267 1 545 [. 1 545 [. 1 546 [. 1.00 Alignments for each domain: == domain 1 score: 872.2 bits; conditional E-value: 6.2e-267 TIGR01132 1 mainpraGqkaqqedlldvaklvadyyllkpdaenaaqkvefGtsGhrGsalkgtfneahilaiaqavvevraaq 75 m+i p aG++a+++ l+d+++lv++yy+ +pda ++q+v+fGtsGhrG + + +fne h+lai+qa+ +r+aq lcl|FitnessBrowser__WCS417:GFF2629 1 MTISPFAGKPAPAQLLVDIPRLVTAYYTGQPDAAISTQRVAFGTSGHRGNSFELSFNEWHVLAISQAICLYREAQ 75 7899*********************************************************************** PP TIGR01132 76 GitGplyiGkdthalsepafvsvlevlaanqvevivqennrytptpavshailtynkgkkealadGivitpshnp 150 Gi Gpl++G dthals pa s+levlaan+v+v++ e + ytptpa+shai+ yn+g++++ladGivitpshnp lcl|FitnessBrowser__WCS417:GFF2629 76 GINGPLFVGLDTHALSTPAGASALEVLAANGVHVMLAEGDEYTPTPAISHAIICYNRGRTSGLADGIVITPSHNP 150 *************************************************************************** PP TIGR01132 151 pedGGikynppnGGpaetevtkaiedranellkdrlkgvkrldlekalksetvkekdlvkpyvddladvvdlaai 225 p+ GG kynppnGGpa+t+vtk+ie +anell+++l+gvkr++ ++alk++t++++d+++ yv+dl++v+d++ai lcl|FitnessBrowser__WCS417:GFF2629 151 PQSGGYKYNPPNGGPADTHVTKWIEAKANELLAKKLAGVKRITHAQALKADTTHRHDYLNTYVADLVNVIDMDAI 225 *************************************************************************** PP TIGR01132 226 rkaglrlGvdplGGagvdywkeiaekynldltlvneavdatfrfmtldkdGkirmdcsspyamagllklkdkydl 300 r+a+lrlGvdplGGagv yw iae+y l+l +vn +vdatfrfm +d+dG+irmd ss yam gl+ lk+++d+ lcl|FitnessBrowser__WCS417:GFF2629 226 RSADLRLGVDPLGGAGVRYWSAIAEHYRLNLEVVNTEVDATFRFMCVDWDGQIRMDPSSSYAMQGLIGLKERFDV 300 *************************************************************************** PP TIGR01132 301 afgndadadrhGivtpdkGllnpnhylavaieylykhrqqwaaevavGktlvssalidrvvadlgrklvevpvGf 375 af+ d+d drhGivtp+ Gll pn ylav+i+yl+++r++w a+ avGkt+vss lidrv+a +gr+l+evpvGf lcl|FitnessBrowser__WCS417:GFF2629 301 AFACDPDHDRHGIVTPSGGLLAPNNYLAVSIDYLFQNRPDWRADAAVGKTVVSSGLIDRVAARIGRRLYEVPVGF 375 *************************************************************************** PP TIGR01132 376 kwfvdGlldgslGfGGeesaGasflrkdGtvwstdkdGiilallaaeitavtGknpqqrydelaakyGdpiyari 450 kwf dGl+dgslGfGGeesaGasflrkdGtvwstdkdG+i allaae+t+ G++p+q y l+ +G+p+ r+ lcl|FitnessBrowser__WCS417:GFF2629 376 KWFADGLFDGSLGFGGEESAGASFLRKDGTVWSTDKDGLIPALLAAEMTSRKGQDPSQIYRGLTDALGEPFAIRV 450 *************************************************************************** PP TIGR01132 451 daaatsaqkarlkklspdevsattlaGdaitakltkapGngaaiGGlkvttdegwfaarpsGtedvykiyaesfk 525 da at+aqka l klspd+v++t+laG++i l++apGn+ aiGGlkv+t++gwfaarpsGted+ykiyaesf lcl|FitnessBrowser__WCS417:GFF2629 451 DAKATPAQKALLGKLSPDQVTSTELAGESIQQILSHAPGNDQAIGGLKVMTENGWFAARPSGTEDIYKIYAESFI 525 *************************************************************************** PP TIGR01132 526 geehlkeiekeaeeivdevl 545 ge+hlk++ +ea+ +vd ++ lcl|FitnessBrowser__WCS417:GFF2629 526 GEDHLKQLVEEAQVLVDGAI 545 ***************99765 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (546 nodes) Target sequences: 1 (547 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: 11.05 // [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