User:Eric Martz/Cavities tests: Difference between revisions

Eric Martz (talk | contribs)
x
Eric Martz (talk | contribs)
x
Line 33: Line 33:


''E. coli'' dnaC (245 residues, pI 9.4) has been crystallized by RIKEN Structural Genomics Initiative (Japan), but the crystals may not be of diffraction quality. It has been cloned, expressed as a soluble protein, and purified (but not yet crystallized) by 3 Structural Genomics Groups (RIKEN Structural Genomics Initiative (Japan), Montreal-Kingston Bacterial Structural Genomics Initiative, Midwest Center for Structural Genomics), as have several proteins with >40% sequence identity. So there is reason for optimism that either a crystal structure, or a more suitable template for homology modeling, will be forthcoming soon. One might consider contacting the groups who have reported purification of dnaC to inquire about progress, and possibly request priority for dnaC.
''E. coli'' dnaC (245 residues, pI 9.4) has been crystallized by RIKEN Structural Genomics Initiative (Japan), but the crystals may not be of diffraction quality. It has been cloned, expressed as a soluble protein, and purified (but not yet crystallized) by 3 Structural Genomics Groups (RIKEN Structural Genomics Initiative (Japan), Montreal-Kingston Bacterial Structural Genomics Initiative, Midwest Center for Structural Genomics), as have several proteins with >40% sequence identity. So there is reason for optimism that either a crystal structure, or a more suitable template for homology modeling, will be forthcoming soon. One might consider contacting the groups who have reported purification of dnaC to inquire about progress, and possibly request priority for dnaC.
 
{{Clear}}
==Gaps in the Template Model==
==Gaps in the Template Model==
<applet load='Dnac_from_2ggz_a.pdb' size='500' frame='true' align='right'
<applet load='Dnac_from_2ggz_a.pdb' size='500' frame='true' align='right'
Line 86: Line 86:
Below is the alignment of dnaC with 2QGZ according to TargetDB (see above).
Below is the alignment of dnaC with 2QGZ according to TargetDB (see above).
<pre>
<pre>
Target Query Results
ID:  DR58  Center: NESGC
There are 16 sequences that match your request.
 
 
 
ID:  DR58    Latest update:  2007-09-21    E Value:  0.00028:  view alignment
Lab:  Northeast Structural Genomics Consortium
Name:  Putative primosome component (Helicase loader).
Status:  Selected, Cloned, Expressed, Soluble, Purified, Crystallized, Diffraction, Crystal Structure, In PDB
URL:
http://spine.nesg.org/target.cgi?id=DR58
Database Reference:    PDB: 2QGZ  PFAM: PF07319  MEGA: 3.40.50.300 
Source Organism:    Streptococcus pyogenes
Sequence:
MEKIGETMAKLGQNTRVNSDQLIQTILADPEVASFISQHHLSQEQINLSLSKFNQFLVERQ
KYQLKDPSYIAKGYQPILAMNEGYADVSYLETKELVEAQKQAAISERIQLVSLPKSYRHI
HLSDIDVNNASRMEAFSAILDFVEQYPSAEQKGLYLYGDMGIGKSYLLAAMAHELSEKKG
VSTTLLHFPSFAIDVKNAISNGSVKEEIDAVKNVPVLILDDIGAEQATSWVRDEVLQVIL
QYRMLEELPTFFTSNYSFADLERKWATIKGSDETWQAKRVMERVRYLAREFHLEGANRR
Domain Annotation:    Pfam
Other Sources:
Superfamily | TIGR Families | ProDom | iProClass | Prosite
Protein Properties:
Number of Residues Mol. Weight Avg. Hydropathy Score Charge pI Value
300 34146 -0.321 -4.5 5.4
ID:  hso002001071.2    Latest update:  2008-09-07    E Value:  0.14:  view alignment
Lab:  RSGI
Status:  Selected, Cloned, Expressed, Soluble, Purified, NMR Assigned, HSQC, NMR Structure, In PDB
Database Reference:    PDB: 2EAO 
Source Organism:    Homo sapiens
Sequence:
SQPLLDRSIPDFTAFTTVDDWLSAIKMVQYRDSFLTAGFTSLQLVTQMTSEDLLRIGITLA
GHQKKILNSIHSMRVQISQSPTAMA
Domain Annotation:    Pfam
Other Sources:
Superfamily | TIGR Families | ProDom | iProClass | Prosite
Protein Properties:
Number of Residues Mol. Weight Avg. Hydropathy Score Charge pI Value
86 9585 0.056 1.0 7.7
ID:  NYSGXRC-10353u    Latest update:  2007-03-09    E Value:  0.69:  view alignment
Lab:  SGX Pharmaceuticals
Name:  Q4QL22_HAEI8
Status:  Selected, Cloned, Expressed, Soluble, Purified, Crystallized, Diffraction, Native diffraction-data, Phasing diffraction-data, In PDB
Database Reference:    PDB: 3BGE  BIG: BIG_278  UNIPROT: Q4QL22_HAEI8 
Source Organism:    Haemophilus influenzae
Sequence:
MSNLNFDFAENDFRPLAAKMRPTNLEQYFGQSHLIGEGKPLRKAIQAGHIHSMILWGPPGT
GKTTLAEIIAQRINAEVERISAVTSGIKEIREAIDRAKQNRLADRKTILFVDEVHRFNKS
QQDAFLPHIEDGTVIFIGATTENPSFELNNALLSRARVYVLKSLTTAEIEQVLQQAVEDP
ERGLGKERLILEENLLQVLAEYVNGDARLALNCLELMVDMADEMENGKKIDRTLLKEVLG
ERQARFDKQGDRFYDLISALHKSVRGSAPDAALYWYARILTAGGDPLYVARRLLAIASED
VGNADPRAMQVALAAWDCFTRVGAYEGERAIAQAIIYLAVAPKSNAVYTAFNTAKQQAKD
LPDYDVPPHLRNAPTNLMKELGYGAEYRYAHDEPNAYAAGENYFPPELKDTQYYFPTNRG
MEIQIKEKLERLREQDKSTVKKRYK
Domain Annotation:    Pfam
Other Sources:
Superfamily | TIGR Families | ProDom | iProClass | Prosite
Protein Properties:
Number of Residues Mol. Weight Avg. Hydropathy Score Charge pI Value
446 50278 -0.436 -1.0 6.3
ID:  hsi002013839.1    Latest update:  2008-09-07    E Value:  0.9:  view alignment
Lab:  RSGI
Status:  Selected, Cloned, Expressed, Soluble, Purified, NMR Assigned, HSQC, NMR Structure, In PDB
Database Reference:    PDB: 2EEE 
Source Organism:    Homo sapiens
Sequence:
GSRITYVKGDLFACPKTDSLAHCISEDCRMGAGIAVLFKKKFGGVQELLNQQKKSGEVAVL
KRDGRYIYYLITKKRASHKPTYENLQKSLEAMKSHCLKNGVTDLSMPRIGCGLDRLQWEN
VSAMIEEVFEATDIKITVYTL
Other Sources:
Pfam |  Superfamily | TIGR Families | ProDom | iProClass | Prosite
Protein Properties:
Number of Residues Mol. Weight Avg. Hydropathy Score Charge pI Value
142 15951 -0.273 7.5 9.2
ID:  GO.36728    Latest update:  2008-01-14    E Value:  0.95:  view alignment
Lab:  CESG
Name:  BC011709
Status:  Selected, Expressed, Purified, NMR Assigned, HSQC, NMR Structure, In PDB, Other
Database Reference:    PDB: 2JYC 
Source Organism:    Homo sapiens
Sequence:
MASSLNEDPEGSRITYVKGDLFACPKTDSLAHCISEDCRMGAGIAVLFKKKFGGVQELLNQ
QKKSGEVAVLKRDGRYIYYLITKKRASHKPTYENLQKSLEAMKSHCLKNGVTDLSMPRIG
CGLDRLQWENVSAMIEEVFEATDIKITVYTL
Other Sources:
Pfam |  Superfamily | TIGR Families | ProDom | iProClass | Prosite
Protein Properties:
Number of Residues Mol. Weight Avg. Hydropathy Score Charge pI Value
152 17025 -0.319 4.5 8.5
ID:  NYSGXRC-10354e    Latest update:  2008-03-19    E Value:  1.6:  view alignment
Lab:  SGX Pharmaceuticals
Name:  Q7V3J8_PROMP
Status:  Selected, Cloned, Expressed, Soluble, Purified, Crystallized, Diffraction, Native diffraction-data, Phasing diffraction-data, In PDB
Database Reference:    PDB: 3CTD  BIG: BIG_278  UNIPROT: Q7V3J8_PROMP 
Source Organism:    Prochlorococcus marinus
Sequence:
MESDNLFSNTYRIESNAPLADKLRPKNLDDFFGQESILGHDSLLRNAILNDKVGNIIFSGP
PGVGKTTLIEIISSNTRSSLIKLNAVLSSIKELRTEIANAKERLRSSNRKTILFIDEVHR
FTSVQQDALLPSIENGTITFIGATTENPFFAVNKALISRARIFSLLPLNKNDLKKIIDKV
IKYYSCLKDSKVVEIKEEAINHLIKFSGGDARNLINALELGISITKENKENLVVIDLAIA
EDSIQKKNIVYDKNGQNHFDVISAFIKSIRGSDPDATLYWLANMVEAGEDPNFIFRRLLI
SACEDIGLADPNAIVVVQSCCDAFDRVGFPEGLFFLSQASLYLAISPKSNSTKSIFKALE
AIKATNVSLVPNHLKNNASNYLNPHNYQGKWLQQEYLPTDLQGIKFWKPKDSGWEKNKYE
DLPKKQKS
Domain Annotation:    Pfam
Other Sources:
Superfamily | TIGR Families | ProDom | iProClass | Prosite
Protein Properties:
Number of Residues Mol. Weight Avg. Hydropathy Score Charge pI Value
429 48010 -0.245 6.0 8.5
ID:  SR1    Latest update:  2008-05-05    E Value:  1.9:  view alignment
Lab:  Northeast Structural Genomics Consortium
Name:  Putative sigma L-dependent transcriptional regulator yplP.
Status:  Selected, Cloned, Expressed, Soluble, Purified, HSQC, In PDB, Work Stopped
URL:
http://spine.nesg.org/target.cgi?id=SR1
Database Reference:    PDB: 1XYZ  MEGA: 1.10.8.60  MEGA: 3.40.50.300 
Source Organism:    Bacillus subtilis
Sequence:
MNSAPKLNTFQHLIGEHQTFLEAKRIAKQFSLSELPVLITGKIGTGKNHFAHAIHLESSRS
NEPFISVNCSTHSEETLIHELFGPNGNTGVFQKAVRGTLFLDDVWRMPASVQAQLLKALD
SDTEKPRMICASADRSVEHTFRQDLFYRLNILTLTLPELSERKSDIPLLTQHFLSNSGQQ
LLIDPSVFPVLEKHAFEGNVRELKNAADYMAAVSSGGTIQPYDLPPYIRGTIDGKTSKKK
AKLLTLMEKAEFLFILETIKVLNEKGEPASRRIISEHSKNTQTSLTPQQVRSRLDYLEKK
DYVTKSRGRAGTKITFEGLSFIETLKNQMI
Domain Annotation:    Pfam
Other Sources:
Superfamily | TIGR Families | ProDom | iProClass | Prosite
Protein Properties:
Number of Residues Mol. Weight Avg. Hydropathy Score Charge pI Value
331 37210 -0.358 10.5 9.5
ID:  APC90123.1    Latest update:  2007-03-01    E Value:  2.4:  view alignment
Lab:  Midwest Center for Structural Genomics
Name:  PG0945
Status:  Selected, Cloned, Expressed, Soluble, Purified, Crystallized, Diffraction-quality Crystals, Diffraction, Crystal Structure, In PDB
Remark:
ABC transporter, permease protein, putative (gi 34397011) ; targeted domain 44...183
Database Reference:    PDB: 2P0S  NCBI: AAQ66075.1  NCBI TAXONOMY DB: 242619 
Source Organism:    Porphyromonas gingivalis W83
Sequence:
QLGGDMKTIAIADRTGEYEQLFKENDEFRFVHAEKTAEEYRKMGADKSGIDAVLEIRQDLL
EDPNAVAIYGYKQLPASVSNHISRILSDYLSDKKIASYNIPDIKQILADSKIELSVHTYK
WSEDGTNERTSGELASGIS
Other Sources:
Pfam |  Superfamily | TIGR Families | ProDom | iProClass | Prosite
Protein Properties:
Number of Residues Mol. Weight Avg. Hydropathy Score Charge pI Value
140 15687 -0.571 -6.5 4.6
ID:  NYSGXRC-10108a    Latest update:  2006-10-13    E Value:  2.9:  view alignment
Lab:  SGX Pharmaceuticals
Name:  PRPR_ECOLI
Status:  Selected, Cloned, Expressed, Soluble, Purified, Crystallized, Diffraction, Native diffraction-data, Phasing diffraction-data, In PDB
Database Reference:    PDB: 2PJU  PFAM: PF06506  UNIPROT: P77743 
Source Organism:    Escherichia coli
Sequence:
MAHPPRLNDDKPVIWTVSVTRLFELFRDISLEFDHLANITPIQLGFEKAVTYIRKKLANER
CDAIIAAGSNGAYLKSRLSVPVILIKPSGYDVLQALAKAGKLTSSIGVVTYQETIPALVA
FQKTFNLRLDQRSYITEEDARGQINELKANGTEAVVGAGLITDLAEEAGMTGIFIYSAAT
VRQAFSDALDMTRMSLRHNTHDATRNALRTRYVLGDMLGQSPQMEQVRQTILLYARSSAA
VLIEGETGTGKELAAQAIHREYFARHDARQGKKSHPFVAVNCGAIAESLLEAELFGYEEG
AFTGSRRGGRAGLFEIAHGGTLFLDEIGEMPLPLQTRLLRVLEEKEVTRVGGHQPVPVDV
RVISATHCNLEEDMQQGRFRRDLFYRLSILRLQLPPLRERVADILPLAESFLKVSLAALS
APFSAALRQGLQASETVLLHYDWPGNIRELRNMMERLALFLSVEPTPDLTPQFMQLLLPE
LARESAKTPAPRLLTPQQALEKFNGDKTAAANYLGISRTTFWRRLKS
Domain Annotation:    Pfam
Other Sources:
Superfamily | TIGR Families | ProDom | iProClass | Prosite
Protein Properties:
Number of Residues Mol. Weight Avg. Hydropathy Score Charge pI Value
528 58649 -0.135 7.5 8.4
ID:  sto001002459.2    Latest update:  2008-09-07    E Value:  3.4:  view alignment
Lab:  RSGI
Status:  Selected, Cloned, Expressed, Soluble, Purified, Crystallized, Diffraction-quality Crystals, Native diffraction-data, Phasing diffraction-data, Crystal Structure, In PDB
Database Reference:    PDB: 2Z0M 
Source Organism:    Sulfolobus tokodaii
Sequence:
MNEKIEQAIREMGFKNFTEVQSKTIPLMLQGKNVVVRAKTGSGKTAAYAIPILELGMKSLV
VTPTRELTRQVASHIRDIGRYMDTKVAEVYGGMPYKAQINRVRNADIVVATPGRLLDLWS
KGVIDLSSFEIVIIDEADLMFEMGFIDDIKIILAQTSNRKITGLFSATIPEEIRKVVKDF
ITNYEEIEACIGLANVEHKFVHVKDDWRSKVQALRENKDKGVIVFVRTRNRVAKLVRLFD
NAIELRGDLPQSVRNRNIDAFREGEYDMLITTDVASRGLDIPLVEKVINFDAPQDLRTYI
HRIGRTGRMGRKGEAITFILNEYWLEKEVKKVSQKA
Domain Annotation:    Pfam
Other Sources:
Superfamily | TIGR Families | ProDom | iProClass | Prosite
Protein Properties:
Number of Residues Mol. Weight Avg. Hydropathy Score Charge pI Value
337 38342 -0.210 9.0 9.8
ID:  ttk003000125.1    Latest update:  2008-09-07    E Value:  3.5:  view alignment
Lab:  RSGI
Status:  Selected, Cloned, Expressed, Soluble, Purified, Crystallized, Diffraction-quality Crystals, Native diffraction-data, Phasing diffraction-data, Crystal Structure, In PDB
Database Reference:    PDB: 2YWS 
Source Organism:    Thermus thermophilus
Sequence:
MKGMFTPGNGPVQISAEAIKKRVEELGGEIARDYQGKTPHLICVLNGAFIFMADLVRAIPL
PLTMDFIAISSYGNAFKSSGEVELLKDLRLPIHGRDVIVVEDIVDTGLTLSYLLDYLEAR
KPASVRVAALLSKPSRRQVEVPIHYLGFEIEDAYVYGYGLDRAQFDRNLPFITSIRPEEE
Domain Annotation:    Pfam
Other Sources:
Superfamily | TIGR Families | ProDom | iProClass | Prosite
Protein Properties:
Number of Residues Mol. Weight Avg. Hydropathy Score Charge pI Value
181 20170 0.022 -3.5 5.1
ID:  ttk003000125.3    Latest update:  2008-09-07    E Value:  3.5:  view alignment
Lab:  RSGI
Status:  Selected, Cloned, Expressed, Soluble, Purified, Crystallized, Diffraction-quality Crystals, Native diffraction-data, Phasing diffraction-data, Crystal Structure, In PDB
Database Reference:    PDB: 2YWU 
Source Organism:    Thermus thermophilus
Sequence:
MKGMFTPGNGPVQISAEAIKKRVEELGGEIARDYQGKTPHLICVLNGAFIFMADLVRAIPL
PLTMDFIAISSYGNAFKSSGEVELLKDLRLPIHGRDVIVVEDIVDTGLTLSYLLDYLEAR
KPASVRVAALLSKPSRRQVEVPIHYLGFEIEDAYVYGYGLDRAQFDRNLPFITSIRPEEE
Domain Annotation:    Pfam
Other Sources:
Superfamily | TIGR Families | ProDom | iProClass | Prosite
Protein Properties:
Number of Residues Mol. Weight Avg. Hydropathy Score Charge pI Value
181 20170 0.022 -3.5 5.1
ID:  ttk003000125.2    Latest update:  2008-09-07    E Value:  3.5:  view alignment
Lab:  RSGI
Status:  Selected, Cloned, Expressed, Soluble, Purified, Crystallized, Diffraction-quality Crystals, Native diffraction-data, Phasing diffraction-data, Crystal Structure, In PDB
Database Reference:    PDB: 2YWT 
Source Organism:    Thermus thermophilus
Sequence:
MKGMFTPGNGPVQISAEAIKKRVEELGGEIARDYQGKTPHLICVLNGAFIFMADLVRAIPL
PLTMDFIAISSYGNAFKSSGEVELLKDLRLPIHGRDVIVVEDIVDTGLTLSYLLDYLEAR
KPASVRVAALLSKPSRRQVEVPIHYLGFEIEDAYVYGYGLDRAQFDRNLPFITSIRPEEE
Domain Annotation:    Pfam
Other Sources:
Superfamily | TIGR Families | ProDom | iProClass | Prosite
Protein Properties:
Number of Residues Mol. Weight Avg. Hydropathy Score Charge pI Value
181 20170 0.022 -3.5 5.1
ID:  AtR62    Latest update:  2005-05-16    E Value:  4.7:  view alignment
Lab:  Northeast Structural Genomics Consortium
Name:  Hypothetical protein Atu3015 (AGR_L_3574p).
Status:  Selected, Cloned, Expressed, Soluble, Purified, Crystallized, Diffraction, HSQC, Crystal Structure, In PDB
URL:
http://spine.nesg.org/target.cgi?id=AtR62
Database Reference:    PDB: 1ZP6  MEGA: 3.40.50.300 
Source Organism:    Agrobacterium tumefaciens
Sequence:
MNMTDDLGGNILLLSGHPGSGKSTIAEALANLPGVPKVHFHSDDLWGYIKHGRIDPWLPQS
HQQNRMIMQIAADVAGRYAKEGYFVILDGVVRPDWLPAFTALARPLHYIVLRTTAAEAIE
RCLDRGGDSLSDPLVVADLHSQFADLGAFEHHVLPVSGKDTDQALQSAINALQSGRFRID
AS
Other Sources:
Pfam |  Superfamily | TIGR Families | ProDom | iProClass | Prosite
Protein Properties:
Number of Residues Mol. Weight Avg. Hydropathy Score Charge pI Value
183 19929 -0.098 -1.5 6.2
ID:  BSGCAIR31267    Latest update:  2006-08-16    E Value:  7.1:  view alignment
Lab:  Berkeley Structural Genomics Center
Status:  Selected, Cloned, Expressed, Soluble, Purified, Crystallized, Diffraction-quality Crystals, Diffraction, Crystal Structure, In PDB
Database Reference:    PDB: 2HQB 
Source Organism:    Bacillus halodurans
Sequence:
MVGLLVEDTIDDQGWNRKAYEGLLNIHSNLDVDVVLEEGVNSEQKAHRRIKELVDGGVNLI
FGHGHAFAEYFSTIHNQYPDVHFVSFNGEVKGENITSLHFEGYAMGYFGGMVAASMSETH
KVGVIAAFPWQPEVEGFVDGAKYMNESEAFVRYVGEWTDADKALELFQELQKEQVDVFYP
AGDGYHVPVVEAIKDQGDFAIGYVGDQADLGGSTILTSTVQHVDDLYVLVAKRFQEGKLE
SGNLYYDFQDGVVSLGEFSSVVPDEVREQITDAISTYIQTGQFPHEEER
Domain Annotation:    Pfam
Other Sources:
Superfamily | TIGR Families | ProDom | iProClass | Prosite
Protein Properties:
Number of Residues Mol. Weight Avg. Hydropathy Score Charge pI Value
290 32294 -0.260 -26.5 4.2
ID:  356698    Latest update:  2004-11-04    E Value:  8.3:  view alignment
Lab:  JCSG
Status:  Selected, Cloned, Expressed, Purified, Crystallized, Diffraction-quality Crystals, Diffraction, Crystal Structure, In PDB
Remark:
Accession:2649494 lacc:TB0541B Start:1 End:180;status_date::2008-10-01:3
Database Reference:    PDB: 2ISB 
Protein Name:
gi|11498698|ref|NP_069927.1| fumarase (fum-1) [Archaeoglobus fulgidus DSM 4304]
Source Organism:    ARCHAEOGLOBUS FULGIDUS
Sequence:
MVMEYELRTPLVKDQILKLKVGDVVYITGEIFTARDEAHARALEWMEEGKELPFSFDKGVV
YHCGPLVKKNDEWRVVSAGPTTSARMNPFTPKILEKVECMGIIGKGGMSEEVVEAMRGKA
AYFAFTGGAGALAAMSIKKVKGVVWEDLGMPEAVWLLEVERFGPCIVAIDAHGNSLYRR
Database Reference:    NCBI REFSEQ: NP_069927.1 
Domain Annotation:    Pfam
Other Sources:
Superfamily | TIGR Families | ProDom | iProClass | Prosite
Protein Properties:
Number of Residues Mol. Weight Avg. Hydropathy Score Charge pI Value
180 19926 -0.008 -0.5 6.3
 
 
ID:  DR58  Center: NESGC
E-value: 0.00028  Identity: 19.737%
E-value: 0.00028  Identity: 19.737%