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At2g13680.1/PDB C-terminus

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&&&&&&&&&&&&&&&&&&&& BEGIN  /usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues &&&&&&&&&&&&&&&&&&&&

Successfully read 2 file paths from WYRM_file_paths.txt

generic_input                                         /usr/local/www/html/proteins/workspace/
generic_output                                        /usr/local/www/html/proteins/htdocs/results/

======================================================

Sequence file type = 3

Sequence type = 3

Got here 1
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Sequence 1
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Sequence 2
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Read 2 amino_acid sequences from PIR Sequence file /usr/local/www/html/proteins/workspace/At2g13680-C-2ckj_A.pir.txt

======================================================

Assigned types to 943 residues in Sequence 2-13680-C, 47 remain unknown
Assigned types to 523 residues in Sequence 2ckj_A, 467 remain unknown

======================================================

Successfully read 576 entries for residue match scoring matrix /usr/local/www/html/proteins/workspace/BLOSUM62.dat

Read the residue match scoring matrix /usr/local/www/html/proteins/workspace/BLOSUM62.dat

======================================================

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 143  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 144  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 145  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 146  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 147  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 179  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 180  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 181  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 182  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 183  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 184  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 185  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 186  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 187  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 188  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 189  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 201  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 202  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 203  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 283  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 326  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 327  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 328  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 329  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 330  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 331  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 332  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 333  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 334  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 335  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 336  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 337  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 338  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 339  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 340  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 341  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 342  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 343  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 344  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 345  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 346  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 403  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 573  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 574  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 575  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 638  All residues are positively and negatively charged

Error in function WYRM_analyze_conservation_in_sequence_alignment()
Path index 639  All residues are positively and negatively charged

Translated sequence file At2g13680-C-2ckj_A.pir.txt into sequence alignment.

======================================================

>2CKJ.pdb  Made from 39530 ATOM records in 2CKJ.pdb
ADKLVFFVNGRKVVEKNADPETTLLAYLRRKLGLSGTKLGCGEGGCGACT
VMLSKYDRLQNKIVHFSANACLAPICSLHHVAVTTVEGIGSTKTRLHPVQ
ERIAKSHGSQCGFCTPGIVMSMYTLLRNQPEPTMEEIENAFQGNLCRCTG
YRPILQGFRTFARPSLFKPEEFTPLDPTQEPIFPPELLRLKDTPRKQLRF
EGERVTWIQASTLKELLDLKAQHPDAKLVVGNTEIGIEMKFKNMLFPMIV
CPAWIPELNSVEHGPDGISFGAACPLSIVEKTLVDAVAKLPAQKTEVFRG
VLEQLRWFAGKQVKSVASVGGNIITASPISDLNPVFMASGAKLTLVSRGT
RRTVQMDHTFFPGYRKTLLSPEEILLSIEIPYSREGEYFSAFKQASDIAK
VTSGMRVLFKPGTTEVQELALCYGGMANRTISALKTTQRQLSKLWKEELL
QDVCAGLAEELHLPPDAPGGMVDFRCTLTLSFFFKFYLTVLQKLGQENLE
VQLFQEVPKGQSEEDMVGRPLPHLAADMQASGEAVYCDDIPRYENELSLR
LVTSTRAHAKIKSIDTSEAKKVPGFVCFISADDVPGSNITGICNDETVFA
KDKVTCVGHIIGAVVADTPEHTQRAAQGVKITYEELPAIITIEDAIKNNS
FYGPELKIEKGDLKKGFSEADNVVSGEIYIGGQEHFYLETHCTIAVPKGE
AGEMELFVSTQNTMKTQSFVAKMLGVPANRIVVRVKRMGGGFGGKETRST
VVSTAVALAAYKTGRPVRCMLDRDEDMLITGGRHPFLARYKVGFMKTGTV
VALEVDHFSNVGNTQDLSQSIMERALFHMDNCYKIPNIRGTGRLCKTNLP
SNTAFRGFGGPQGMLIAECWMSEVAVTCGMPAEEVRRKNLYKEGDLTHFN
QKLEGFTLPRCWEECLASSQYHARKSEVDKFNKENCWKKRGLCIIPTKFG
ISFTVPFLNQAGALLHVYTDGSVLLTHGGTEMGQGLHTKMVQVASRALKI
PTSKIYISETSTNTVPNTSPTAASVSADLNGQAVYAACQTILKRLEPYKK
KNPSGSWEDWVTAAYMDTVSLSATGFYRTPNLGYSFETNSGNPFHYFSYG
VACSEVEIDCLTGDHKNLRTDIVMDVGSSLNPAIDIGQVEGAFVQGLGLF
TLEELHYSPEGSLHTRGPSTYKIPAFGSIPIEFRVSLLRDCPNKKAIYAS
KAVGEPPLFLAASIFFAIKDAIRAARAQHTGNNVKELFRLDSPATPEKIR
NACVDKFTTLCVTWTADKLVFFVNGRKVVEKNADPETTLLAYLRRKLGLS
GTKLGCGEGGCGACTVMLSKYDRLQNKIVHFSANACLAPICSLHHVAVTT
VEGIGSTKTRLHPVQERIAKSHGSQCGFCTPGIVMSMYTLLRNQPEPTME
EIENAFQGNLCRCTGYRPILQGFRTFARPSLFKPEEFTPLDPTQEPIFPP
ELLRLKDTPRKQLRFEGERVTWIQASTLKELLDLKAQHPDAKLVVGNTEI
GIEMKFKNMLFPMIVCPAWIPELNSVEHGPDGISFGAACPLSIVEKTLVD
AVAKLPAQKTEVFRGVLEQLRWFAGKQVKSVASVGGNIITASPISDLNPV
FMASGAKLTLVSRGTRRTVQMDHTFFPGYRKTLLSPEEILLSIEIPYSRE
GEYFSAFKQASRREDDIAKVTSGMRVLFKPGTTEVQELALCYGGMANRTI
SALKTTQRQLSKLWKEELLQDVCAGLAEELHLPPDAPGGMVDFRCTLTLS
FFFKFYLTVLQKLGQENLEDKCGKLDPTFASATDVQLFQEVPKGQSEEDM
VGRPLPHLAADMQASGEAVYCDDIPRYENELSLRLVTSTRAHAKIKSIDT
SEAKKVPGFVCFISADDVPGSNITGICNDETVFAKDKVTCVGHIIGAVVA
DTPEHTQRAAQGVKITYEELPAIITIEDAIKNNSFYGPELKIEKGDLKKG
FSEADNVVSGEIYIGGQEHFYLETHCTIAVPKGEAGEMELFVSTQNTMKT
QSFVAKMLGVPANRIVVRVKRMGGGFGGKETRSTVVSTAVALAAYKTGRP
VRCMLDRDEDMLITGGRHPFLARYKVGFMKTGTVVALEVDHFSNVGNTQD
LSQSIMERALFHMDNCYKIPNIRGTGRLCKTNLPSNTAFRGFGGPQGMLI
AECWMSEVAVTCGMPAEEVRRKNLYKEGDLTHFNQKLEGFTLPRCWEECL
ASSQYHARKSEVDKFNKENCWKKRGLCIIPTKFGISFTVPFLNQAGALLH
VYTDGSVLLTHGGTEMGQGLHTKMVQVASRALKIPTSKIYISETSTNTVP
NTSPTAASVSADLNGQAVYAACQTILKRLEPYKKKNPSGSWEDWVTAAYM
DTVSLSATGFYRTPNLGYSFETNSGNPFHYFSYGVACSEVEIDCLTGDHK
NLRTDIVMDVGSSLNPAIDIGQVEGAFVQGLGLFTLEELHYSPEGSLHTR
GPSTYKIPAFGSIPIEFRVSLLRDCPNKKAIYASKAVGEPPLFLAASIFF
AIKDAIRAARAQHTGNNVKELFRLDSPATPEKIRNACVDKFTTLCVCKPW
SVRADKLVFFVNGRKVVEKNADPETTLLAYLRRKLGLSGTKLGCGEGGCG
ACTVMLSKYDRLQNKIVHFSANACLAPICSLHHVAVTTVEGIGSTKTRLH
PVQERIAKSHGSQCGFCTPGIVMSMYTLLRNQPEPTMEEIENAFQGNLCR
CTGYRPILQGFRTFARPSLFKPEEFTPLDPTQEPIFPPELLRLKDTPRKQ
LRFEGERVTWIQASTLKELLDLKAQHPDAKLVVGNTEIGIEMKFKNMLFP
MIVCPAWIPELNSVEHGPDGISFGAACPLSIVEKTLVDAVAKLPAQKTEV
FRGVLEQLRWFAGKQVKSVASVGGNIITASPISDLNPVFMASGAKLTLVS
RGTRRTVQMDHTFFPGYRKTLLSPEEILLSIEIPYSREGEYFSAFKQASR
REAKVTSGMRVLFKPGTTEVQELALCYGGMANRTISALKTTQRQLSKLWK
EELLQDVCAGLAEELHLPPDAPGGMVDFRCTLTLSFFFKFYLTVLQKLGQ
ENLEDKCGKLDPTFASATDVQLFQEVPKGQSEEDMVGRPLPHLAADMQAS
GEAVYCDDIPRYENELSLRLVTSTRAHAKIKSIDTSEAKKVPGFVCFISA
DDVPGSNITGICNDETVFAKDKVTCVGHIIGAVVADTPEHTQRAAQGVKI
TYEELPAIITIEDAIKNNSFYGPELKIEKGDLKKGFSEADNVVSGEIYIG
GQEHFYLETHCTIAVPKGEAGEMELFVSTQNTMKTQSFVAKMLGVPANRI
VVRVKRMGGGFGGKETRSTVVSTAVALAAYKTGRPVRCMLDRDEDMLITG
GRHPFLARYKVGFMKTGTVVALEVDHFSNVGNTQDLSQSIMERALFHMDN
CYKIPNIRGTGRLCKTNLPSNTAFRGFGGPQGMLIAECWMSEVAVTCGMP
AEEVRRKNLYKEGDLTHFNQKLEGFTLPRCWEECLASSQYHARKSEVDKF
NKENCWKKRGLCIIPTKFGISFTVPFLNQAGALLHVYTDGSVLLTHGGTE
MGQGLHTKMVQVASRALKIPTSKIYISETSTNTVPNTSPTAASVSADLNG
QAVYAACQTILKRLEPYKKKNPSGSWEDWVTAAYMDTVSLSATGFYRTPN
LGYSFETNSGNPFHYFSYGVACSEVEIDCLTGDHKNLRTDIVMDVGSSLN
PAIDIGQVEGAFVQGLGLFTLEELHYSPEGSLHTRGPSTYKIPAFGSIPI
EFRVSLLRDCPNKKAIYASKAVGEPPLFLAASIFFAIKDAIRAARAQHTG
NNVKELFRLDSPATPEKIRNACVDKFTTLCVPWSVRADKLVFFVNGRKVV
EKNADPETTLLAYLRRKLGLSGTKLGCGEGGCGACTVMLSKYDRLQNKIV
HFSANACLAPICSLHHVAVTTVEGIGSTKTRLHPVQERIAKSHGSQCGFC
TPGIVMSMYTLLRNQPEPTMEEIENAFQGNLCRCTGYRPILQGFRTFARP
SLFKPEEFTPLDPTQEPIFPPELLRLKDTPRKQLRFEGERVTWIQASTLK
ELLDLKAQHPDAKLVVGNTEIGIEMKFKNMLFPMIVCPAWIPELNSVEHG
PDGISFGAACPLSIVEKTLVDAVAKLPAQKTEVFRGVLEQLRWFAGKQVK
SVASVGGNIITASPISDLNPVFMASGAKLTLVSRGTRRTVQMDHTFFPGY
RKTLLSPEEILLSIEIPYSREGEYFSAFKQASRREDDIAKVTSGMRVLFK
PGTTEVQELALCYGGMANRTISALKTTQRQLSKLWKEELLQDVCAGLAEE
LHLPPDAPGGMVDFRCTLTLSFFFKFYLTVLQKLGQENLEDKCGKLDPDV
QLFQEVPKGQSEEDMVGRPLPHLAADMQASGEAVYCDDIPRYENELSLRL
VTSTRAHAKIKSIDTSEAKKVPGFVCFISADDVPGSNITGICNDETVFAK
DKVTCVGHIIGAVVADTPEHTQRAAQGVKITYEELPAIITIEDAIKNNSF
YGPELKIEKGDLKKGFSEADNVVSGEIYIGGQEHFYLETHCTIAVPKGEA
GEMELFVSTQNTMKTQSFVAKMLGVPANRIVVRVKRMGGGFGGKETRSTV
VSTAVALAAYKTGRPVRCMLDRDEDMLITGGRHPFLARYKVGFMKTGTVV
ALEVDHFSNVGNTQDLSQSIMERALFHMDNCYKIPNIRGTGRLCKTNLPS
NTAFRGFGGPQGMLIAECWMSEVAVTCGMPAEEVRRKNLYKEGDLTHFNQ
KLEGFTLPRCWEECLASSQYHARKSEVDKFNKENCWKKRGLCIIPTKFGI
SFTVPFLNQAGALLHVYTDGSVLLTHGGTEMGQGLHTKMVQVASRALKIP
TSKIYISETSTNTVPNTSPTAASVSADLNGQAVYAACQTILKRLEPYKKK
NPSGSWEDWVTAAYMDTVSLSATGFYRTPNLGYSFETNSGNPFHYFSYGV
ACSEVEIDCLTGDHKNLRTDIVMDVGSSLNPAIDIGQVEGAFVQGLGLFT
LEELHYSPEGSLHTRGPSTYKIPAFGSIPIEFRVSLLRDCPNKKAIYASK
AVGEPPLFLAASIFFAIKDAIRAARAQHTGNNVKELFRLDSPATPEKIRN
ACVDKFTTLCVTCKPWSVR

======================================================

Best alignment:
2CKJ.pdb    294  KTEVFRGVLEQLRWFAGKQVKSVASVGGNIITASPI   329
                 +  +F G +  L WF   Q  S  ++G  ++ ASP+
2-13680-C   368  REHIFTGSVSSLAWFMSNQETSFVTIGQRVL-ASPL   402

======================================================

Highlighted IDENTICAL residue VAL  326  index1  297  path  413  %Seq 100.00
Highlighted IDENTICAL residue VAL  330  index1  301  path  417  %Seq 100.00
Highlighted IDENTICAL residue GLU  332  index1  303  path  419  %Seq  50.00
Highlighted IDENTICAL residue GLN  333  index1  304  path  420  %Seq  50.00
Highlighted IDENTICAL residue LEU  334  index1  305  path  421  %Seq  50.00
Highlighted IDENTICAL residue ARG  335  index1  306  path  422  %Seq  50.00
Highlighted IDENTICAL residue TRP  336  index1  307  path  423  %Seq  50.00
Highlighted 7 residues for visualization

Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g13680-C-2ckj_A.pir.txt.2CKJ.pdb.conservation.pml

===============================================================================

The program

/usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g13680-C-2ckj_A.pir.txt PIR amino_acid 2CKJ.pdb _ 100.0 BLOSUM62.dat 

completed successfully.

@@@@@@@@@@@@@@@@@@@@ END  /usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues @@@@@@@@@@@@@@@@@@@@


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