YRC Public Data Repository - Protein Structure Prediction

Protein:	SMC1
Organism:	Saccharomyces cerevisiae
Length:	1225 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 SMC1.

Description	E-value	Query Range	Subject Range
SMC1_YEAST - Structural maintenance of chromosomes protein 1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S2... SMC1 - Subunit of the multiprotein cohesin complex, essential protein involved in chromosome segregation an...	0.0	[1..1225]	[1..1225]
MYH2_PIG - Myosin-2 OS=Sus scrofa GN=MYH2 PE=2 SV=1 gi\|55741490 - ref\|NP_999301.1\| myosin heavy chain 2a [Sus scrofa]	0.0	[66..1096]	[840..1915]
MYH2_BOVIN - Myosin-2 OS=Bos taurus GN=MYH2 PE=2 SV=1	0.0	[66..1096]	[841..1916]
MYSS_CYPCA - Myosin heavy chain, fast skeletal muscle OS=Cyprinus carpio PE=2 SV=2	0.0	[66..1096]	[837..1912]
MYH1 - myosin, heavy chain 1, skeletal muscle, adult	0.0	[66..1096]	[840..1915]
gi\|6469332 - gi\|6469332\|gb\|AAF13306.1\|AF185287_1 XCAP-C/SMC4 homolog Gluon [Drosophila melanogaster]	0.0	[4..1215]	[89..1291]
MYH4_RABIT - Myosin-4 OS=Oryctolagus cuniculus GN=MYH4 PE=1 SV=1	0.0	[66..1096]	[839..1914]

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Predicted Domain #1

Region A:
Residues: [1-49]

      1          11         21         31         41         51         
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    1 MGRLVGLELS NFKSYRGVTK VGFGESNFTS IIGPNGSGKS NMMDAISFV

[Run NCBI BLAST on this sequence.]

Detection Method:	ORFEUS
Confidence:	10.32
Match:	1ii8A
Description:	Rad50
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
motor activity	2.79327761685782	bayes_pls_golite062009
microtubule motor activity	2.74365461017633	bayes_pls_golite062009
DNA-dependent ATPase activity	2.72462789867829	bayes_pls_golite062009
binding	2.64537357529343	bayes_pls_golite062009
DNA helicase activity	2.2817164193758	bayes_pls_golite062009
nucleoside-triphosphatase activity	2.16381244011837	bayes_pls_golite062009
pyrophosphatase activity	2.13284212711072	bayes_pls_golite062009
bubble DNA binding	2.11656807287934	bayes_pls_golite062009
hydrolase activity, acting on acid anhydrides	2.11265775498161	bayes_pls_golite062009
hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides	2.11046854230259	bayes_pls_golite062009
ATP-dependent DNA helicase activity	1.88455339138556	bayes_pls_golite062009
	1.75135117904448	bayes_pls_golite062009
helicase activity	1.70242731830224	bayes_pls_golite062009
hydrolase activity	1.66122526893602	bayes_pls_golite062009
ATPase activity	1.53315090215319	bayes_pls_golite062009
RNA helicase activity	1.42791449104435	bayes_pls_golite062009
nucleic acid binding	1.41477043612798	bayes_pls_golite062009
cytoskeletal protein binding	1.40488517180956	bayes_pls_golite062009
RNA-dependent ATPase activity	1.39335733374328	bayes_pls_golite062009
ATP-dependent RNA helicase activity	1.36724390116598	bayes_pls_golite062009
protein-DNA loading ATPase activity	1.29640539057136	bayes_pls_golite062009
structure-specific DNA binding	1.2539059700735	bayes_pls_golite062009
purine ribonucleotide binding	1.21658213854831	bayes_pls_golite062009
ribonucleotide binding	1.21652144153182	bayes_pls_golite062009
purine nucleotide binding	1.21571071905795	bayes_pls_golite062009
nucleotide binding	1.20347573865566	bayes_pls_golite062009
purine NTP-dependent helicase activity	1.19311444180077	bayes_pls_golite062009
ATP-dependent helicase activity	1.19311444180077	bayes_pls_golite062009
DNA clamp loader activity	1.12431517057397	bayes_pls_golite062009
double-stranded DNA binding	1.117585097627	bayes_pls_golite062009
DNA binding	1.11699929651302	bayes_pls_golite062009
catalytic activity	1.00104173493322	bayes_pls_golite062009
transcription regulator activity	0.989226939888218	bayes_pls_golite062009
tubulin binding	0.979946830272106	bayes_pls_golite062009
microtubule binding	0.907162506177187	bayes_pls_golite062009
actin binding	0.883285269827407	bayes_pls_golite062009
RNA binding	0.715902454627085	bayes_pls_golite062009
single-stranded DNA binding	0.568457189190858	bayes_pls_golite062009
kinetochore binding	0.534490088080411	bayes_pls_golite062009
recombinase activity	0.45851158693664	bayes_pls_golite062009
guanyl nucleotide binding	0.388587892299301	bayes_pls_golite062009
guanyl ribonucleotide binding	0.372638007722845	bayes_pls_golite062009
GTP binding	0.364508542344128	bayes_pls_golite062009
centromeric DNA binding	0.322818640526369	bayes_pls_golite062009
mismatched DNA binding	0.31144582840038	bayes_pls_golite062009
four-way junction helicase activity	0.26252931460003	bayes_pls_golite062009
GTPase activity	0.234351968078991	bayes_pls_golite062009
exodeoxyribonuclease V activity	0.185603938981231	bayes_pls_golite062009
protein binding	0.170837278876362	bayes_pls_golite062009
dynein binding	0.150959629961177	bayes_pls_golite062009
3'-5' DNA helicase activity	0.0769112340058804	bayes_pls_golite062009
transcription factor activity	0.0434163635422169	bayes_pls_golite062009
microfilament motor activity	0.0313060889304495	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [50-366]

      1          11         21         31         41         51         
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    1 LGVRSNHLRS NILKDLIYRG VLNDENSDDY DNEGAASSNP QSAYVKAFYQ KGNKLVELMR  60
   61 IISRNGDTSY KIDGKTVSYK DYSIFLENEN ILIKAKNFLV FQGDVEQIAA QSPVELSRMF 120
  121 EEVSGSIQYK KEYEELKEKI EKLSKSATES IKNRRRIHGE LKTYKEGINK NEEYRKQLDK 180
  181 KNELQKFQAL WQLYHLEQQK EELTDKLSAL NSEISSLKGK INNEMKSLQR SKSSFVKESA 240
  241 VISKQKSKLD YIFKDKEKLV SDLRLIKVPQ QAAGKRISHI EKRIESLQKD LQRQKTYVER 300
  301 FETQLKVVTR SKEAFEE

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	27.0
Match:	1i84S_
Description:	Heavy meromyosin subfragment
Matching Structure (courtesy of the PDB):

Predicted Domain #3

Region A:
Residues: [367-445]

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    1 EIKQSARNYD KFKLNENDLK TYNCLHEKYL TEGGSILEEK IAVLNNDKRE IQEELERFNK  60
   61 RADISKRRIT EELSITGEK

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	9.221849
Match:	2tmaA_
Description:	Tropomyosin
Matching Structure (courtesy of the PDB):

Predicted Domain #4

Region A:
Residues: [446-499]

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    1 LDTQLNDLRV SLNEKNALHT ERLHELKKLQ SDIESANNQE YDLNFKLRET LVKI

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	9.221849
Match:	2tmaA_
Description:	Tropomyosin
Matching Structure (courtesy of the PDB):

Predicted Domain #5

Region A:
Residues: [500-576]

      1          11         21         31         41         51         
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    1 DDLSANQRET MKERKLRENI AMLKRFFPGV KGLVHDLCHP KKEKYGLAVS TILGKNFDSV  60
   61 IVENLTVAQE CIAFLKK

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	134.0
Match:	1gxlA_
Description:	Smc hinge domain
Matching Structure (courtesy of the PDB):

Predicted Domain #6

Region A:
Residues: [577-726]

      1          11         21         31         41         51         
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    1 QRAGTASFIP LDTIETELPT LSLPDSQDYI LSINAIDYEP EYEKAMQYVC GDSIICNTLN  60
   61 IAKDLKWKKG IRGKLVTIEG ALIHKAGLMT GGISGDANNR WDKEEYQSLM SLKDKLLIQI 120
  121 DELSNGQRSN SIRAREVENS VSLLNSDIAN

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	5.30103
Match:	1cii__
Description:	Colicin Ia; Colicin Ia, N-terminal domain
Matching Structure (courtesy of the PDB):

Predicted Domain #7

Region A:
Residues: [727-1016]

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    1 LRTQVTQQKR SLDENRLEIK YHNDLIEKEI QPKITELKKK LDDLENTKDN LVKEKEALQN  60
   61 NIFKEFTSKI GFTIKEYENH SGELMRQQSK ELQQLQKQIL TVENKLQFET DRLSTTQRRY 120
  121 EKAQKDLENA QVEMKSLEEQ EYAIEMKIGS IESKLEEHKN HLDELQKKFV TKQSELNSSE 180
  181 DILEDMNSNL QVLKRERDGI KEDIEKFDLE RVTALKNCKI SNINIPISSE TTIDDLPISS 240
  241 TDNEAITISN SIDINYKGLP KKYKENNTDS ARKELEQKIH EVEEILNELQ

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	5.30103
Match:	1cii__
Description:	Colicin Ia; Colicin Ia, N-terminal domain
Matching Structure (courtesy of the PDB):

Predicted Domain #8

Region A:
Residues: [1017-1225]

      1          11         21         31         41         51         
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    1 PNARALERYD EAEGRFEVIN NETEQLKAEE KKILNQFLKI KKKRKELFEK TFDYVSDHLD  60
   61 AIYRELTKNP NSNVELAGGN ASLTIEDEDE PFNAGIKYHA TPPLKRFKDM EYLSGGEKTV 120
  121 AALALLFAIN SYQPSPFFVL DEVDAALDIT NVQRIAAYIR RHRNPDLQFI VISLKNTMFE 180
  181 KSDALVGVYR QQQENSSKII TLDLSNYAE

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	167.519517
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: