YRC Public Data Repository - Protein Structure Prediction

Protein:	SMC2
Organism:	Saccharomyces cerevisiae
Length:	1170 amino acids
Reference:	Malmström L, et al. (2007) Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology. PLoS Biol 5(4): e76. doi:10.1371/journal.pbio.0050076

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Top Sequence Alignment Hits

Listed below are up to the top 10 sequence alignment matches, by species, for the PSI-BLAST search against the protein sequence for SMC2.

Description	E-value	Query Range	Subject Range
SMC2_YEAST - Structural maintenance of chromosomes protein 2 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S2... SMC2 - Subunit of the condensin complex; essential SMC chromosomal ATPase family member that forms a comple...	0.0	[1..1168]	[1..1168]
gi\|6177744 - gi\|6177744\|dbj\|BAA06453.2\| cut14 protein [Schizosaccharomyces pombe]	0.0	[1..1169]	[1..1171]
SMC2_SCHPO - Structural maintenance of chromosomes protein 2 OS=Schizosaccharomyces pombe (strain 972 / ATCC 2484... cut14 - condensin subunit Cut14	0.0	[1..1169]	[1..1171]
SMC22_ARATH - Structural maintenance of chromosomes protein 2-2 OS=Arabidopsis thaliana GN=SMC2-2 PE=2 SV=1	0.0	[1..1167]	[1..1163]
gi\|7507776 - gi\|7507776\|pir\|\|T16867 probable cytochrome P450 T13C5.1 [similarity] - Caenorhabditis elegans	0.0	[1..1169]	[1..1171]
SMC2 - structural maintenance of chromosomes 2	0.0	[1..1167]	[1..1168]
gi\|221230335, gi... - gi\|221230335\|ref\|YP_002503751.1\| putative cell division protein [Mycobacterium leprae Br4923], gi\|21... SMC_MYCLE - Chromosome partition protein Smc OS=Mycobacterium leprae GN=smc PE=3 SV=1 SMC_MYCLE - Chromosome partition protein Smc OS=Mycobacterium leprae (strain TN) GN=smc PE=3 SV=1	0.0	[1..1169]	[1..1187]

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Predicted Domain #1

Region A:
Residues: [1-213]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MKVEELIIDG FKSYATRTVI TDWDPQFNAI TGLNGSGKSN ILDAICFVLG IASMSTVRAS  60
   61 SLQDLIYKRG QAGVTKASVT IVFDNTDKSN SPIGFTNSPQ ISVTRQVVLG GTSKYLINGH 120
  121 RAPQQSVLQL FQSVQLNINN PNFLIMQGKI TKVLNMKPSE ILSLIEEAAG TKMFEDRREK 180
  181 AERTMSKKET KLQENRTLLT EEIEPKLEKL RNE

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	9.69897
Match:	1ii8A_
Description:	Rad50
Matching Structure (courtesy of the PDB):

Predicted Domain #2

Region A:
Residues: [214-282]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 KRMFLEFQST QTDLEKTERI VVSYEYYNIK HKHTSIRETL ENGETRMKML NEFVKKTSEE  60
   61 IDSLNEDVE

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	9.69897
Match:	2tmaA_
Description:	Tropomyosin
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
binding	2.87991790206998	bayes_pls_golite062009
sequence-specific DNA binding	2.16596178759795	bayes_pls_golite062009
transcription regulator activity	2.122580758085	bayes_pls_golite062009
DNA binding	1.98453325263719	bayes_pls_golite062009
nucleic acid binding	1.93681952439958	bayes_pls_golite062009
chromatin binding	1.68308196781423	bayes_pls_golite062009
transcription factor activity	1.36872096268289	bayes_pls_golite062009
transcription factor binding	1.23930219500076	bayes_pls_golite062009
cytoskeletal protein binding	1.14048290764066	bayes_pls_golite062009
centromeric DNA binding	1.13545283098583	bayes_pls_golite062009
RNA polymerase II transcription factor activity	1.09150919349912	bayes_pls_golite062009
protein binding	1.03780839342631	bayes_pls_golite062009
transcription cofactor activity	0.69917765277148	bayes_pls_golite062009
actin binding	0.618026108235131	bayes_pls_golite062009
DNA-dependent ATPase activity	0.526073636025138	bayes_pls_golite062009
telomeric DNA binding	0.284650049512347	bayes_pls_golite062009
transcription activator activity	0.174325083775401	bayes_pls_golite062009
histone binding	0.0391625783266718	bayes_pls_golite062009

Predicted Domain #3

Region A:
Residues: [283-364]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 EIKLQKEKEL HKEGTISKLE NKENGLLNEI SRLKTSLSIK VENLNDTTEK SKALESEIAS  60
   61 SSAKLIEKKS AYANTEKDYK MV

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	9.69897
Match:	2tmaA_
Description:	Tropomyosin
Matching Structure (courtesy of the PDB):

Predicted Domain #4

Region A:
Residues: [365-426]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 QEQLSKQRDL YKRKEELVST LTTGISSTGA ADGGYNAQLA KAKTELNEVS LAIKKSSMKM  60
   61 EL

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	9.69897
Match:	2tmaA_
Description:	Tropomyosin
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
binding	2.87197012801422	bayes_pls_golite062009
protein binding	1.29499816770808	bayes_pls_golite062009
protein heterodimerization activity	0.82893422872344	bayes_pls_golite062009
structure-specific DNA binding	0.655291890141256	bayes_pls_golite062009
DNA secondary structure binding	0.597643104953011	bayes_pls_golite062009
protein dimerization activity	0.442459446636259	bayes_pls_golite062009
nucleoside-triphosphatase activity	0.340360347691162	bayes_pls_golite062009
pyrophosphatase activity	0.287295057420232	bayes_pls_golite062009
hydrolase activity, acting on acid anhydrides	0.273916899375488	bayes_pls_golite062009
hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides	0.271570433187831	bayes_pls_golite062009
double-stranded DNA binding	0.22807834114034	bayes_pls_golite062009
sequence-specific DNA binding	0.220174647358614	bayes_pls_golite062009
ATPase activity	0.142237490738159	bayes_pls_golite062009

Predicted Domain #5

Region A:
Residues: [427-487]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 LKKELLTIEP KLKEATKDNE LNVKHVKQCQ ETCDKLRARL VEYGFDPSRI KDLKQREDKL  60
   61 K

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	9.69897
Match:	2tmaA_
Description:	Tropomyosin
Matching Structure (courtesy of the PDB):

Predicted Domain #6

Region A:
Residues: [488-529]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 SHYYQTCKNS EYLKRRVTNL EFNYTKPYPN FEASFVHGVV GQ

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [553-583]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 FNVVVQDSQT ATQLLERGRL RKRVTIIPLD K

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	83.06601
Match:	1gxlA_
Description:	Smc hinge domain
Matching Structure (courtesy of the PDB):

Predicted Domain #7

Region A: Residues: [530-552]	1 11 21 31 41 51 \| \| \| \| \| \| 1 LFQIDNDNIR YATALQTCAG GRL [Run NCBI BLAST on this sequence.]
Region B: Residues: [584-587]	1 11 21 31 41 51 \| \| \| \| \| \| 1 IYTR [Run NCBI BLAST on this sequence.]
Region C: Residues: [609-627]	1 11 21 31 41 51 \| \| \| \| \| \| 1 INLIRFDESI TKAMEFIFG [Run NCBI BLAST on this sequence.]
Region D: Residues: [670-687]	1 11 21 31 41 51 \| \| \| \| \| \| 1 RNTSESLLVD IQKYNQIQ [Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	83.06601
Match:	1gxlA_
Description:	Smc hinge domain
Matching Structure (courtesy of the PDB):

Predicted Domain #8

Region A:
Residues: [588-608]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 PISSQVLDLA KKIAPGKVEL A

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [628-669]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 NSLICEDPET AKKITFHPKI RARSITLQGD VYDPEGTLSG GS

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	83.06601
Match:	1gxlA_
Description:	Smc hinge domain
Matching Structure (courtesy of the PDB):

Predicted Domain #9

Region A:
Residues: [688-981]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 KQIETIQADL NHVTEELQTQ YATSQKTKTI QSDLNLSLHK LDLAKRNLDA NPSSQIIARN  60
   61 EEILRDIGEC ENEIKTKQMS LKKCQEEVST IEKDMKEYDS DKGSKLNELK KELKLLAKEL 120
  121 EEQESESERK YDLFQNLELE TEQLSSELDS NKTLLHNHLK SIESLKLENS DLEGKIRGVE 180
  181 DDLVTVQTEL NEEKKRLMDI DDELNELETL IKKKQDEKKS SELELQKLVH DLNKYKSNTN 240
  241 NMEKIIEDLR QKHEFLEDFD LVRNIVKQNE GIDLDTYRER SKQLNEKFQE LRKK

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	50.9691
Match:	1i84S_
Description:	Heavy meromyosin subfragment
Matching Structure (courtesy of the PDB):

Predicted Domain #10

Region A:
Residues: [982-1170]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 VNPNIMNMIE NVEKKEAALK TMIKTIEKDK MKIQETISKL NEYKRETLVK TWEKVTLDFG  60
   61 NIFADLLPNS FAKLVPCEGK DVTQGLEVKV KLGNIWKESL IELSGGQRSL IALSLIMALL 120
  121 QFRPAPMYIL DEVDAALDLS HTQNIGHLIK TRFKGSQFIV VSLKEGMFAN ANRVFRTRFQ 180
  181 DGTSVVSIM

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	157.68867
Match:	1e69A_
Description:	Smc head domain
Matching Structure (courtesy of the PDB):

TMHMM	2.0c	PSIPRED	v2.61
SignalP	3.0	COILS	1999
DISOPRED	v0.1	NCBI nr	06/2007
PSI-BLAST	2.2.18	FFAS	ffas03
PDB	06/2007	Pfam	22
HMMER	2.3.2

View Structure Prediction Details

Top Sequence Alignment Hits

Predicted functions:

Predicted functions: