Citrus Sinensis ID: 034642

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------
Protein Sequence
MGQIQYSEKYFDDTYEYRHVVLPPDVAKLLPKNRLLSETEWRAIGVQQSRGWVHYAIHRPEPHIMLFRRPLNYQQQQENQAQQNILAK
Secondary Structure (PSIPRED)
cccEEEccccccccEEEEEEEEcHHHHHHccccccccHHHHHHHcccccccEEEEEEcccccEEEEEEcccccHHHHHHHHHHHHHHc
Secondary Structure Prediction (SSPRO)
ccccEEcccEEEcccEEccEEccHHHHccccccccccHHHHHHHccccccccccccccccccccccccccccHHHcccccHHHHHHcc
Coil and Loop (DISEMBL)
mgqiqysekyfddtyeyrhvvlppdvakllpknrllseTEWRAIGvqqsrgwvhyaihrpephimlfrrplnyQQQQENQAQQNILAK
Flexible Loop (DISEMBL)
MGQIQYSEKYFDDTYEYRHVVLPPDVAKLLPKNRLLSETEWRAIGVQQSRGWVHYAIHRPEPHIMLFRRPLNYQQQQENQAQQNILAK
Low Complexity Region (SEG)
MGQIQYSEKYFDDTYEYRHVVLPPDVAKLLPKNRLLSETEWRAIGVQQSRGWVHYAIHRPEPHIMLFRRPLnyqqqqenqaqqnILAK
Disordered region (IsUnstruct)
******SEKYFDDTYEYRHVVLPPDVAKLLPKNRLLSETEWRAIGVQQSRGWVHYAIHRPEPHIMLFRRPL*****************
Disordered Region (DISOPRED)
*GQIQYSEKYFDDTYEYRHVVLPPDVAKLLPKNRLLSETEWRAIGVQQSRGWVHYAIHRPEPHIMLFRR*******************
Disordered Region (DISEMBL)
MGQIQYSEKYFDDTYEYRHVVLPPDVAKLLPKNRLLSETEWRAIGVQQSRGWVHYAIHRPEPHIMLFRRPLNYQ**************
Disordered Region (DISPRO)
*GQIQYSEKYFDDTYEYRHVVLPPDVAKLLPKNRLLSETEWRAIGVQQSRGWVHYAIHRPEPHIMLFRRPLNYQ**************
Transmembrane Helix (TMHMM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MGQIQYSEKYFDDTYEYRHVVLPPDVAKLLPKNRLLSETEWRAIGVQQSRGWVHYAIHRPEPHIMLFRRPLNYQQQQENQAQQNILAK
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	88	2.2.26 [Sep-21-2011]
Q9SJJ5	83	Cyclin-dependent kinases	yes	no	0.909	0.963	0.902	3e-38
Q6PS57	90	Cyclin-dependent kinases	yes	no	0.829	0.811	0.958	9e-37
A2XCH8	90	Cyclin-dependent kinases	N/A	no	0.829	0.811	0.958	9e-37
O23249	87	Cyclin-dependent kinases	no	no	0.806	0.816	0.943	2e-35
P55933	84	Probable cyclin-dependent	N/A	no	0.75	0.785	0.818	3e-28
P41384	76	Cyclin-dependent kinases	N/A	no	0.818	0.947	0.666	5e-25
Q25330	99	Cyclin-dependent kinases	N/A	no	0.772	0.686	0.661	7e-25
P61025	79	Cyclin-dependent kinases	no	no	0.784	0.873	0.710	9e-25
P61024	79	Cyclin-dependent kinases	yes	no	0.784	0.873	0.710	9e-25
Q0P5A5	79	Cyclin-dependent kinases	yes	no	0.784	0.873	0.710	9e-25

>sp|Q9SJJ5|CKS2_ARATH Cyclin-dependent kinases regulatory subunit 2 OS=Arabidopsis thaliana GN=CKS2 PE=3 SV=1

 Score =  156 bits (395), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 74/82 (90%), Positives = 80/82 (97%), Gaps = 2/82 (2%)

Query: 1  MGQIQYSEKYFDDTYEYRHVVLPPDVAKLLPKNRLLSETEWRAIGVQQSRGWVHYAIHRP 60
          MGQIQYS+KYFDDT+EYRHVVLPP+VAKLLPKNR+LSE+EWRAIGVQQSRGWVHYAIHRP
Sbjct: 1  MGQIQYSDKYFDDTFEYRHVVLPPEVAKLLPKNRILSESEWRAIGVQQSRGWVHYAIHRP 60

Query: 61 EPHIMLFRRPLNYQQQQENQAQ 82
          EPHIMLFRRPLNY  QQE+QAQ
Sbjct: 61 EPHIMLFRRPLNY--QQEHQAQ 80

Binds to the catalytic subunit of the cyclin dependent kinases and is essential for their biological function.
Arabidopsis thaliana (taxid: 3702)

>sp|Q6PS57|CKS1_ORYSJ Cyclin-dependent kinases regulatory subunit 1 OS=Oryza sativa subsp. japonica GN=CKS1 PE=2 SV=1

 Score =  151 bits (382), Expect = 9e-37,   Method: Compositional matrix adjust.
 Identities = 70/73 (95%), Positives = 72/73 (98%)

Query: 1  MGQIQYSEKYFDDTYEYRHVVLPPDVAKLLPKNRLLSETEWRAIGVQQSRGWVHYAIHRP 60
          MGQIQYSEKYFDDTYEYRHVVLPP+VAKLLPKNRLLSE EWRAIGVQQSRGWVHYAIHRP
Sbjct: 1  MGQIQYSEKYFDDTYEYRHVVLPPEVAKLLPKNRLLSENEWRAIGVQQSRGWVHYAIHRP 60

Query: 61 EPHIMLFRRPLNY 73
          EPHIMLFRRPLN+
Sbjct: 61 EPHIMLFRRPLNF 73

Binds to the catalytic subunit of the cyclin dependent kinases and is essential for their biological function.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|A2XCH8|CKS1_ORYSI Cyclin-dependent kinases regulatory subunit 1 OS=Oryza sativa subsp. indica GN=CKS1 PE=2 SV=1

 Score =  151 bits (382), Expect = 9e-37,   Method: Compositional matrix adjust.
 Identities = 70/73 (95%), Positives = 72/73 (98%)

Query: 1  MGQIQYSEKYFDDTYEYRHVVLPPDVAKLLPKNRLLSETEWRAIGVQQSRGWVHYAIHRP 60
          MGQIQYSEKYFDDTYEYRHVVLPP+VAKLLPKNRLLSE EWRAIGVQQSRGWVHYAIHRP
Sbjct: 1  MGQIQYSEKYFDDTYEYRHVVLPPEVAKLLPKNRLLSENEWRAIGVQQSRGWVHYAIHRP 60

Query: 61 EPHIMLFRRPLNY 73
          EPHIMLFRRPLN+
Sbjct: 61 EPHIMLFRRPLNF 73

Binds to the catalytic subunit of the cyclin dependent kinases and is essential for their biological function.

Oryza sativa subsp. indica (taxid: 39946)

>sp|O23249|CKS1_ARATH Cyclin-dependent kinases regulatory subunit 1 OS=Arabidopsis thaliana GN=CKS1 PE=1 SV=1

 Score =  147 bits (370), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 67/71 (94%), Positives = 70/71 (98%)

Query: 1  MGQIQYSEKYFDDTYEYRHVVLPPDVAKLLPKNRLLSETEWRAIGVQQSRGWVHYAIHRP 60
          MGQIQYSEKYFDDT+EYRHVVLPP+VAKLLPKNRLLSE EWRAIGVQQSRGWVHYA+HRP
Sbjct: 1  MGQIQYSEKYFDDTFEYRHVVLPPEVAKLLPKNRLLSENEWRAIGVQQSRGWVHYAVHRP 60

Query: 61 EPHIMLFRRPL 71
          EPHIMLFRRPL
Sbjct: 61 EPHIMLFRRPL 71

Associates with cyclin-dependent kinases (CDKs) and plays an essential role in the regulation of the cell cycle that affects plant growth rate. May inhibits both the G1/S and G2/M phases.

Arabidopsis thaliana (taxid: 3702)

>sp|P55933|CKS1_PHYPO Probable cyclin-dependent kinases regulatory subunit OS=Physarum polycephalum PE=1 SV=1

 Score =  123 bits (309), Expect = 3e-28,   Method: Compositional matrix adjust.
 Identities = 54/66 (81%), Positives = 62/66 (93%)

Query: 4  IQYSEKYFDDTYEYRHVVLPPDVAKLLPKNRLLSETEWRAIGVQQSRGWVHYAIHRPEPH 63
          IQYSEKY+DD +EYRHV+LPPDVAK +PKNRLLSE EWR +GVQQS+GWVHYA+HRPEPH
Sbjct: 6  IQYSEKYYDDKFEYRHVILPPDVAKEIPKNRLLSEGEWRGLGVQQSQGWVHYALHRPEPH 65

Query: 64 IMLFRR 69
          I+LFRR
Sbjct: 66 ILLFRR 71

Binds to the catalytic subunit of the cyclin dependent kinases and is essential for their biological function.

Physarum polycephalum (taxid: 5791)

>sp|P41384|CKS1_PATVU Cyclin-dependent kinases regulatory subunit OS=Patella vulgata PE=3 SV=1

 Score =  112 bits (281), Expect = 5e-25,   Method: Compositional matrix adjust.
 Identities = 48/72 (66%), Positives = 60/72 (83%)

Query: 3  QIQYSEKYFDDTYEYRHVVLPPDVAKLLPKNRLLSETEWRAIGVQQSRGWVHYAIHRPEP 62
          QI YS+KYFD+ +EYRHV+LP D+AK++PKN L+SE EWR+IGVQQS GW+HY  H PEP
Sbjct: 5  QIYYSDKYFDEDFEYRHVMLPKDIAKMVPKNHLMSEAEWRSIGVQQSHGWIHYMKHEPEP 64

Query: 63 HIMLFRRPLNYQ 74
          HI+LFRR +  Q
Sbjct: 65 HILLFRRKVTGQ 76

Binds to the catalytic subunit of the cyclin dependent kinases and is essential for their biological function.

Patella vulgata (taxid: 6465)

>sp|Q25330|CKS1_LEIME Cyclin-dependent kinases regulatory subunit OS=Leishmania mexicana PE=3 SV=1

 Score =  112 bits (280), Expect = 7e-25,   Method: Compositional matrix adjust.
 Identities = 45/68 (66%), Positives = 61/68 (89%)

Query: 3  QIQYSEKYFDDTYEYRHVVLPPDVAKLLPKNRLLSETEWRAIGVQQSRGWVHYAIHRPEP 62
          +I YS+KY+DD +EYRHV+LP D+A+L+P +RL+SE EWR +GVQQS+GWVHY IH+PEP
Sbjct: 30 KILYSDKYYDDMFEYRHVILPKDLARLVPTSRLMSEMEWRQLGVQQSQGWVHYMIHKPEP 89

Query: 63 HIMLFRRP 70
          H++LF+RP
Sbjct: 90 HVLLFKRP 97

Binds to the catalytic subunit of the cyclin dependent kinases (Cdc2) and is essential for their biological function.

Leishmania mexicana (taxid: 5665)

>sp|P61025|CKS1_MOUSE Cyclin-dependent kinases regulatory subunit 1 OS=Mus musculus GN=Cks1b PE=2 SV=1

 Score =  112 bits (279), Expect = 9e-25,   Method: Compositional matrix adjust.
 Identities = 49/69 (71%), Positives = 60/69 (86%)

Query: 3  QIQYSEKYFDDTYEYRHVVLPPDVAKLLPKNRLLSETEWRAIGVQQSRGWVHYAIHRPEP 62
          QI YS+KY D+ +EYRHV+LP D+AKL+PK  L+SE+EWR +GVQQS+GWVHY IH PEP
Sbjct: 5  QIYYSDKYDDEEFEYRHVMLPKDIAKLVPKTHLMSESEWRNLGVQQSQGWVHYMIHEPEP 64

Query: 63 HIMLFRRPL 71
          HI+LFRRPL
Sbjct: 65 HILLFRRPL 73

Binds to the catalytic subunit of the cyclin dependent kinases and is essential for their biological function.

Mus musculus (taxid: 10090)

>sp|P61024|CKS1_HUMAN Cyclin-dependent kinases regulatory subunit 1 OS=Homo sapiens GN=CKS1B PE=1 SV=1

 Score =  112 bits (279), Expect = 9e-25,   Method: Compositional matrix adjust.
 Identities = 49/69 (71%), Positives = 60/69 (86%)

Query: 3  QIQYSEKYFDDTYEYRHVVLPPDVAKLLPKNRLLSETEWRAIGVQQSRGWVHYAIHRPEP 62
          QI YS+KY D+ +EYRHV+LP D+AKL+PK  L+SE+EWR +GVQQS+GWVHY IH PEP
Sbjct: 5  QIYYSDKYDDEEFEYRHVMLPKDIAKLVPKTHLMSESEWRNLGVQQSQGWVHYMIHEPEP 64

Query: 63 HIMLFRRPL 71
          HI+LFRRPL
Sbjct: 65 HILLFRRPL 73

Binds to the catalytic subunit of the cyclin dependent kinases and is essential for their biological function.

Homo sapiens (taxid: 9606)

>sp|Q0P5A5|CKS1_BOVIN Cyclin-dependent kinases regulatory subunit 1 OS=Bos taurus GN=CKS1B PE=3 SV=1

 Score =  112 bits (279), Expect = 9e-25,   Method: Compositional matrix adjust.
 Identities = 49/69 (71%), Positives = 60/69 (86%)

Query: 3  QIQYSEKYFDDTYEYRHVVLPPDVAKLLPKNRLLSETEWRAIGVQQSRGWVHYAIHRPEP 62
          QI YS+KY D+ +EYRHV+LP D+AKL+PK  L+SE+EWR +GVQQS+GWVHY IH PEP
Sbjct: 5  QIYYSDKYDDEEFEYRHVMLPKDIAKLVPKTHLMSESEWRNLGVQQSQGWVHYMIHEPEP 64

Query: 63 HIMLFRRPL 71
          HI+LFRRPL
Sbjct: 65 HILLFRRPL 73

Binds to the catalytic subunit of the cyclin dependent kinases and is essential for their biological function.

Bos taurus (taxid: 9913)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	88
224106860	84	regulatory subunit of cyclin-dependent k	0.954	1.0	0.886	1e-38
117165994	1291	hypothetical protein [Ipomoea trifida]	1.0	0.068	0.920	7e-38
15226297	83	cyclin-dependent kinases regulatory subu	0.909	0.963	0.902	1e-36
45935118	88	putative CDK regulatory subunit [Ipomoea	1.0	1.0	0.920	1e-36
351725771	88	cyclin-dependent kinases regulatory subu	1.0	1.0	0.943	3e-36
357472055	88	Cyclin-dependent kinases regulatory subu	1.0	1.0	0.931	4e-36
224118450	83	regulatory subunit of cyclin-dependent k	0.886	0.939	0.923	6e-36
225436438	88	PREDICTED: cyclin-dependent kinases regu	1.0	1.0	0.943	1e-35
90856236	88	cyclin-dependent kinases regulatory subu	1.0	1.0	0.920	1e-35
388515343	88	unknown [Lotus japonicus]	1.0	1.0	0.931	2e-35

>gi|224106860|ref|XP_002314309.1| regulatory subunit of cyclin-dependent kinase [Populus trichocarpa] gi|118485577|gb|ABK94640.1| unknown [Populus trichocarpa] gi|222850717|gb|EEE88264.1| regulatory subunit of cyclin-dependent kinase [Populus trichocarpa]

 Score =  163 bits (412), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 78/88 (88%), Positives = 83/88 (94%), Gaps = 4/88 (4%)

Query: 1  MGQIQYSEKYFDDTYEYRHVVLPPDVAKLLPKNRLLSETEWRAIGVQQSRGWVHYAIHRP 60
          MGQIQYS+KYFDDT+EYRHVVLPP+VAKLLPKNRLLSE EWRAIGVQQSRGWVHYAIHRP
Sbjct: 1  MGQIQYSDKYFDDTFEYRHVVLPPEVAKLLPKNRLLSENEWRAIGVQQSRGWVHYAIHRP 60

Query: 61 EPHIMLFRRPLNYQQQQENQAQQNILAK 88
          EPHIMLFRRPLN+QQQQENQ    +LAK
Sbjct: 61 EPHIMLFRRPLNFQQQQENQ----VLAK 84

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|117165994|dbj|BAF36296.1| hypothetical protein [Ipomoea trifida]

 Score =  160 bits (406), Expect = 7e-38,   Method: Compositional matrix adjust.
 Identities = 81/88 (92%), Positives = 86/88 (97%)

Query: 1    MGQIQYSEKYFDDTYEYRHVVLPPDVAKLLPKNRLLSETEWRAIGVQQSRGWVHYAIHRP 60
            MGQIQYSEKYFDDT+EYRHVVLPP+VAKLLPKNRLLSE EWRAIGVQQSRGWVHYAIHRP
Sbjct: 1204 MGQIQYSEKYFDDTFEYRHVVLPPEVAKLLPKNRLLSENEWRAIGVQQSRGWVHYAIHRP 1263

Query: 61   EPHIMLFRRPLNYQQQQENQAQQNILAK 88
            EPHIMLFRRPLNYQQQQE+QAQ N++AK
Sbjct: 1264 EPHIMLFRRPLNYQQQQESQAQLNLIAK 1291

Source: Ipomoea trifida

Species: Ipomoea trifida

Genus: Ipomoea

Family: Convolvulaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15226297|ref|NP_180364.1| cyclin-dependent kinases regulatory subunit 2 [Arabidopsis thaliana] gi|297822483|ref|XP_002879124.1| cdk-subunit 2 [Arabidopsis lyrata subsp. lyrata] gi|75206284|sp|Q9SJJ5.1|CKS2_ARATH RecName: Full=Cyclin-dependent kinases regulatory subunit 2 gi|4510419|gb|AAD21505.1| putative cyclin-dependent kinase regulatory subunit [Arabidopsis thaliana] gi|38566522|gb|AAR24151.1| At2g27970 [Arabidopsis thaliana] gi|40823612|gb|AAR92293.1| At2g27970 [Arabidopsis thaliana] gi|297324963|gb|EFH55383.1| cdk-subunit 2 [Arabidopsis lyrata subsp. lyrata] gi|330252971|gb|AEC08065.1| cyclin-dependent kinases regulatory subunit 2 [Arabidopsis thaliana]

 Score =  156 bits (395), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 74/82 (90%), Positives = 80/82 (97%), Gaps = 2/82 (2%)

Query: 1  MGQIQYSEKYFDDTYEYRHVVLPPDVAKLLPKNRLLSETEWRAIGVQQSRGWVHYAIHRP 60
          MGQIQYS+KYFDDT+EYRHVVLPP+VAKLLPKNR+LSE+EWRAIGVQQSRGWVHYAIHRP
Sbjct: 1  MGQIQYSDKYFDDTFEYRHVVLPPEVAKLLPKNRILSESEWRAIGVQQSRGWVHYAIHRP 60

Query: 61 EPHIMLFRRPLNYQQQQENQAQ 82
          EPHIMLFRRPLNY  QQE+QAQ
Sbjct: 61 EPHIMLFRRPLNY--QQEHQAQ 80

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|45935118|gb|AAS79576.1| putative CDK regulatory subunit [Ipomoea trifida]

 Score =  156 bits (395), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 81/88 (92%), Positives = 86/88 (97%)

Query: 1  MGQIQYSEKYFDDTYEYRHVVLPPDVAKLLPKNRLLSETEWRAIGVQQSRGWVHYAIHRP 60
          MGQIQYSEKYFDDT+EYRHVVLPP+VAKLLPKNRLLSE EWRAIGVQQSRGWVHYAIHRP
Sbjct: 1  MGQIQYSEKYFDDTFEYRHVVLPPEVAKLLPKNRLLSENEWRAIGVQQSRGWVHYAIHRP 60

Query: 61 EPHIMLFRRPLNYQQQQENQAQQNILAK 88
          EPHIMLFRRPLNYQQQQE+QAQ N++AK
Sbjct: 61 EPHIMLFRRPLNYQQQQESQAQLNLIAK 88

Source: Ipomoea trifida

Species: Ipomoea trifida

Genus: Ipomoea

Family: Convolvulaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|351725771|ref|NP_001237104.1| cyclin-dependent kinases regulatory subunit [Glycine max] gi|356542684|ref|XP_003539796.1| PREDICTED: cyclin-dependent kinases regulatory subunit 2-like [Glycine max] gi|42362268|gb|AAS13367.1| cyclin-dependent kinases regulatory subunit [Glycine max] gi|255628843|gb|ACU14766.1| unknown [Glycine max] gi|388501782|gb|AFK38957.1| unknown [Lotus japonicus]

 Score =  155 bits (392), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 83/88 (94%), Positives = 86/88 (97%)

Query: 1  MGQIQYSEKYFDDTYEYRHVVLPPDVAKLLPKNRLLSETEWRAIGVQQSRGWVHYAIHRP 60
          MGQIQYSEKYFDDTYEYRHVVLPP+VAKLLPKNRLLSE EWRAIGVQQSRGWVHYAIHRP
Sbjct: 1  MGQIQYSEKYFDDTYEYRHVVLPPEVAKLLPKNRLLSENEWRAIGVQQSRGWVHYAIHRP 60

Query: 61 EPHIMLFRRPLNYQQQQENQAQQNILAK 88
          EPHIMLFRRPLNYQQQQENQAQQ++L K
Sbjct: 61 EPHIMLFRRPLNYQQQQENQAQQSMLVK 88

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357472055|ref|XP_003606312.1| Cyclin-dependent kinases regulatory subunit [Medicago truncatula] gi|355507367|gb|AES88509.1| Cyclin-dependent kinases regulatory subunit [Medicago truncatula] gi|388496380|gb|AFK36256.1| unknown [Medicago truncatula]

 Score =  155 bits (391), Expect = 4e-36,   Method: Compositional matrix adjust.
 Identities = 82/88 (93%), Positives = 85/88 (96%)

Query: 1  MGQIQYSEKYFDDTYEYRHVVLPPDVAKLLPKNRLLSETEWRAIGVQQSRGWVHYAIHRP 60
          MGQIQYSEKYFDDTYEYRHVVLPP+VAKLLPKNRLLSE EWRAIGVQQSRGWVHYAIHRP
Sbjct: 1  MGQIQYSEKYFDDTYEYRHVVLPPEVAKLLPKNRLLSENEWRAIGVQQSRGWVHYAIHRP 60

Query: 61 EPHIMLFRRPLNYQQQQENQAQQNILAK 88
          EPHIMLFRRPLNYQQQQ+NQAQQ +L K
Sbjct: 61 EPHIMLFRRPLNYQQQQDNQAQQGMLVK 88

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224118450|ref|XP_002331485.1| regulatory subunit of cyclin-dependent kinase [Populus trichocarpa] gi|27435806|gb|AAO13226.1|AF149014_1 CKS1 protein [Populus tremula x Populus tremuloides] gi|118488360|gb|ABK95998.1| unknown [Populus trichocarpa] gi|118489795|gb|ABK96697.1| unknown [Populus trichocarpa x Populus deltoides] gi|222873563|gb|EEF10694.1| regulatory subunit of cyclin-dependent kinase [Populus trichocarpa]

 Score =  154 bits (389), Expect = 6e-36,   Method: Compositional matrix adjust.
 Identities = 72/78 (92%), Positives = 75/78 (96%)

Query: 1  MGQIQYSEKYFDDTYEYRHVVLPPDVAKLLPKNRLLSETEWRAIGVQQSRGWVHYAIHRP 60
          MGQIQYSEKY DDT+EYRHVVLPP+VAKLL KNRLLSE EWRAIGVQQSRGWVHYAIHRP
Sbjct: 1  MGQIQYSEKYLDDTFEYRHVVLPPEVAKLLIKNRLLSENEWRAIGVQQSRGWVHYAIHRP 60

Query: 61 EPHIMLFRRPLNYQQQQE 78
          EPHIMLFRRPLNYQQQQ+
Sbjct: 61 EPHIMLFRRPLNYQQQQD 78

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225436438|ref|XP_002274037.1| PREDICTED: cyclin-dependent kinases regulatory subunit 2 isoform 1 [Vitis vinifera] gi|147800865|emb|CAN60128.1| hypothetical protein VITISV_018192 [Vitis vinifera] gi|297734891|emb|CBI17125.3| unnamed protein product [Vitis vinifera]

 Score =  153 bits (387), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 83/88 (94%), Positives = 85/88 (96%)

Query: 1  MGQIQYSEKYFDDTYEYRHVVLPPDVAKLLPKNRLLSETEWRAIGVQQSRGWVHYAIHRP 60
          MGQIQYSEKYFDDTYEYRHVVLPP+VAKLL KNRLLSE EWRAIGVQQSRGWVHYAIHRP
Sbjct: 1  MGQIQYSEKYFDDTYEYRHVVLPPEVAKLLQKNRLLSENEWRAIGVQQSRGWVHYAIHRP 60

Query: 61 EPHIMLFRRPLNYQQQQENQAQQNILAK 88
          EPHIMLFRRPLNYQQQQENQAQQ +LAK
Sbjct: 61 EPHIMLFRRPLNYQQQQENQAQQGLLAK 88

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|90856236|gb|ABE01245.1| cyclin-dependent kinases regulatory subunit [Camellia sinensis]

 Score =  153 bits (386), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 81/88 (92%), Positives = 85/88 (96%)

Query: 1  MGQIQYSEKYFDDTYEYRHVVLPPDVAKLLPKNRLLSETEWRAIGVQQSRGWVHYAIHRP 60
          MGQIQYSEKYFDDTYEYRHVVLPP+VAKLLPKNRLLSE EWRAIGVQQSRGWVHYAIHRP
Sbjct: 1  MGQIQYSEKYFDDTYEYRHVVLPPEVAKLLPKNRLLSENEWRAIGVQQSRGWVHYAIHRP 60

Query: 61 EPHIMLFRRPLNYQQQQENQAQQNILAK 88
          EPHIMLFRRPLNYQQQQE QAQQ +++K
Sbjct: 61 EPHIMLFRRPLNYQQQQETQAQQIMVSK 88

Source: Camellia sinensis

Species: Camellia sinensis

Genus: Camellia

Family: Theaceae

Order: Ericales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388515343|gb|AFK45733.1| unknown [Lotus japonicus]

 Score =  153 bits (386), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 82/88 (93%), Positives = 85/88 (96%)

Query: 1  MGQIQYSEKYFDDTYEYRHVVLPPDVAKLLPKNRLLSETEWRAIGVQQSRGWVHYAIHRP 60
          MGQIQYSEKYFDDTY YRHVVLPP+VAKLLPKNRLLSE EWRAIGVQQSRGWVHYAIHRP
Sbjct: 1  MGQIQYSEKYFDDTYGYRHVVLPPEVAKLLPKNRLLSENEWRAIGVQQSRGWVHYAIHRP 60

Query: 61 EPHIMLFRRPLNYQQQQENQAQQNILAK 88
          EPHIMLFRRPLNYQQQQENQAQQ++L K
Sbjct: 61 EPHIMLFRRPLNYQQQQENQAQQSMLVK 88

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	88
TAIR|locus:2057836	87	CKS1 "AT2G27960" [Arabidopsis	0.806	0.816	0.943	1.7e-34
TAIR|locus:2057825	83	CKS2 "AT2G27970" [Arabidopsis	0.806	0.855	0.929	3.6e-34
FB|FBgn0037613	96	Cks85A "Cyclin-dependent kinas	0.761	0.697	0.731	6.6e-26
ZFIN|ZDB-GENE-040801-112	79	cks1b "CDC28 protein kinase re	0.784	0.873	0.724	1.1e-25
UNIPROTKB|Q0P5A5	79	CKS1B "Cyclin-dependent kinase	0.784	0.873	0.710	2.2e-25
UNIPROTKB|P61024	79	CKS1B "Cyclin-dependent kinase	0.784	0.873	0.710	2.2e-25
UNIPROTKB|I3L6M9	79	CKS1B "Uncharacterized protein	0.784	0.873	0.710	2.2e-25
MGI|MGI:1889208	79	Cks1b "CDC28 protein kinase 1b	0.784	0.873	0.710	2.2e-25
FB|FBgn0010314	74	Cks30A "Cyclin-dependent kinas	0.761	0.905	0.671	9.7e-25
RGD|2321453	92	LOC100364205 "CDC28 protein ki	0.784	0.75	0.695	9.7e-25

TAIR|locus:2057836 CKS1 "AT2G27960" [Arabidopsis thaliana (taxid:3702)]

 Score = 374 (136.7 bits), Expect = 1.7e-34, P = 1.7e-34
 Identities = 67/71 (94%), Positives = 70/71 (98%)

Query:     1 MGQIQYSEKYFDDTYEYRHVVLPPDVAKLLPKNRLLSETEWRAIGVQQSRGWVHYAIHRP 60
             MGQIQYSEKYFDDT+EYRHVVLPP+VAKLLPKNRLLSE EWRAIGVQQSRGWVHYA+HRP
Sbjct:     1 MGQIQYSEKYFDDTFEYRHVVLPPEVAKLLPKNRLLSENEWRAIGVQQSRGWVHYAVHRP 60

Query:    61 EPHIMLFRRPL 71
             EPHIMLFRRPL
Sbjct:    61 EPHIMLFRRPL 71

GO:0004693 "cyclin-dependent protein serine/threonine kinase activity" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

GO:0016538 "cyclin-dependent protein serine/threonine kinase regulator activity" evidence=IEA

GO:0000278 "mitotic cell cycle" evidence=RCA;IDA

GO:0042023 "DNA endoreduplication" evidence=RCA;IMP;IDA

GO:0051726 "regulation of cell cycle" evidence=IMP

GO:0005515 "protein binding" evidence=IPI

GO:0005737 "cytoplasm" evidence=IDA

GO:0006661 "phosphatidylinositol biosynthetic process" evidence=RCA

GO:0010440 "stomatal lineage progression" evidence=RCA

GO:0045736 "negative regulation of cyclin-dependent protein serine/threonine kinase activity" evidence=RCA

TAIR|locus:2057825 CKS2 "AT2G27970" [Arabidopsis thaliana (taxid:3702)]

 Score = 371 (135.7 bits), Expect = 3.6e-34, P = 3.6e-34
 Identities = 66/71 (92%), Positives = 71/71 (100%)

Query:     1 MGQIQYSEKYFDDTYEYRHVVLPPDVAKLLPKNRLLSETEWRAIGVQQSRGWVHYAIHRP 60
             MGQIQYS+KYFDDT+EYRHVVLPP+VAKLLPKNR+LSE+EWRAIGVQQSRGWVHYAIHRP
Sbjct:     1 MGQIQYSDKYFDDTFEYRHVVLPPEVAKLLPKNRILSESEWRAIGVQQSRGWVHYAIHRP 60

Query:    61 EPHIMLFRRPL 71
             EPHIMLFRRPL
Sbjct:    61 EPHIMLFRRPL 71

GO:0004693 "cyclin-dependent protein serine/threonine kinase activity" evidence=ISS

GO:0005634 "nucleus" evidence=ISM;IDA

GO:0016538 "cyclin-dependent protein serine/threonine kinase regulator activity" evidence=IEA

GO:0005737 "cytoplasm" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

GO:0000278 "mitotic cell cycle" evidence=RCA

GO:0001708 "cell fate specification" evidence=RCA

GO:0010440 "stomatal lineage progression" evidence=RCA

GO:0042023 "DNA endoreduplication" evidence=RCA

GO:0045736 "negative regulation of cyclin-dependent protein serine/threonine kinase activity" evidence=RCA

FB|FBgn0037613 Cks85A "Cyclin-dependent kinase subunit 85A" [Drosophila melanogaster (taxid:7227)]

 Score = 293 (108.2 bits), Expect = 6.6e-26, P = 6.6e-26
 Identities = 49/67 (73%), Positives = 59/67 (88%)

Query:     3 QIQYSEKYFDDTYEYRHVVLPPDVAKLLPKNRLLSETEWRAIGVQQSRGWVHYAIHRPEP 62
             QIQYSEKYFDD +EYRHV+LPPD+AK +PK  L++ETEWR +GVQQS GWVHY +H PEP
Sbjct:     5 QIQYSEKYFDDNFEYRHVILPPDLAKHVPKAHLMTETEWRNLGVQQSPGWVHYMVHAPEP 64

Query:    63 HIMLFRR 69
             H++LFRR
Sbjct:    65 HVILFRR 71

GO:0016538 "cyclin-dependent protein serine/threonine kinase regulator activity" evidence=ISS

GO:0007067 "mitosis" evidence=IMP;NAS

GO:0019005 "SCF ubiquitin ligase complex" evidence=IDA

GO:0007113 "endomitotic cell cycle" evidence=IMP

GO:0000278 "mitotic cell cycle" evidence=IMP

ZFIN|ZDB-GENE-040801-112 cks1b "CDC28 protein kinase regulatory subunit 1B" [Danio rerio (taxid:7955)]

 Score = 291 (107.5 bits), Expect = 1.1e-25, P = 1.1e-25
 Identities = 50/69 (72%), Positives = 60/69 (86%)

Query:     3 QIQYSEKYFDDTYEYRHVVLPPDVAKLLPKNRLLSETEWRAIGVQQSRGWVHYAIHRPEP 62
             QI YS+KY DD +EYRHV+LP D+AK +PK  L+SETEWR +GVQQS+GWVHY IH+PEP
Sbjct:     5 QIYYSDKYDDDKFEYRHVMLPKDIAKRVPKTHLMSETEWRNLGVQQSQGWVHYMIHQPEP 64

Query:    63 HIMLFRRPL 71
             HI+LFRRPL
Sbjct:    65 HILLFRRPL 73

GO:0016538 "cyclin-dependent protein serine/threonine kinase regulator activity" evidence=IEA

GO:0007049 "cell cycle" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

UNIPROTKB|Q0P5A5 CKS1B "Cyclin-dependent kinases regulatory subunit 1" [Bos taurus (taxid:9913)]

 Score = 288 (106.4 bits), Expect = 2.2e-25, P = 2.2e-25
 Identities = 49/69 (71%), Positives = 60/69 (86%)

Query:     3 QIQYSEKYFDDTYEYRHVVLPPDVAKLLPKNRLLSETEWRAIGVQQSRGWVHYAIHRPEP 62
             QI YS+KY D+ +EYRHV+LP D+AKL+PK  L+SE+EWR +GVQQS+GWVHY IH PEP
Sbjct:     5 QIYYSDKYDDEEFEYRHVMLPKDIAKLVPKTHLMSESEWRNLGVQQSQGWVHYMIHEPEP 64

Query:    63 HIMLFRRPL 71
             HI+LFRRPL
Sbjct:    65 HILLFRRPL 73

GO:0051301 "cell division" evidence=IEA

GO:0007049 "cell cycle" evidence=IEA

GO:0016538 "cyclin-dependent protein serine/threonine kinase regulator activity" evidence=IEA

UNIPROTKB|P61024 CKS1B "Cyclin-dependent kinases regulatory subunit 1" [Homo sapiens (taxid:9606)]

 Score = 288 (106.4 bits), Expect = 2.2e-25, P = 2.2e-25
 Identities = 49/69 (71%), Positives = 60/69 (86%)

Query:     3 QIQYSEKYFDDTYEYRHVVLPPDVAKLLPKNRLLSETEWRAIGVQQSRGWVHYAIHRPEP 62
             QI YS+KY D+ +EYRHV+LP D+AKL+PK  L+SE+EWR +GVQQS+GWVHY IH PEP
Sbjct:     5 QIYYSDKYDDEEFEYRHVMLPKDIAKLVPKTHLMSESEWRNLGVQQSQGWVHYMIHEPEP 64

Query:    63 HIMLFRRPL 71
             HI+LFRRPL
Sbjct:    65 HILLFRRPL 73

GO:0016538 "cyclin-dependent protein serine/threonine kinase regulator activity" evidence=IEA

GO:0051301 "cell division" evidence=IEA

GO:0000079 "regulation of cyclin-dependent protein serine/threonine kinase activity" evidence=TAS

GO:0008283 "cell proliferation" evidence=TAS

GO:0000080 "G1 phase of mitotic cell cycle" evidence=TAS

GO:0000082 "G1/S transition of mitotic cell cycle" evidence=TAS

GO:0000084 "S phase of mitotic cell cycle" evidence=TAS

GO:0000278 "mitotic cell cycle" evidence=TAS

GO:0005654 "nucleoplasm" evidence=TAS

GO:0005515 "protein binding" evidence=IPI

UNIPROTKB|I3L6M9 CKS1B "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 288 (106.4 bits), Expect = 2.2e-25, P = 2.2e-25
 Identities = 49/69 (71%), Positives = 60/69 (86%)

Query:     3 QIQYSEKYFDDTYEYRHVVLPPDVAKLLPKNRLLSETEWRAIGVQQSRGWVHYAIHRPEP 62
             QI YS+KY D+ +EYRHV+LP D+AKL+PK  L+SE+EWR +GVQQS+GWVHY IH PEP
Sbjct:     5 QIYYSDKYDDEEFEYRHVMLPKDIAKLVPKTHLMSESEWRNLGVQQSQGWVHYMIHEPEP 64

Query:    63 HIMLFRRPL 71
             HI+LFRRPL
Sbjct:    65 HILLFRRPL 73

GO:0016538 "cyclin-dependent protein serine/threonine kinase regulator activity" evidence=IEA

GO:0007049 "cell cycle" evidence=IEA

MGI|MGI:1889208 Cks1b "CDC28 protein kinase 1b" [Mus musculus (taxid:10090)]

 Score = 288 (106.4 bits), Expect = 2.2e-25, P = 2.2e-25
 Identities = 49/69 (71%), Positives = 60/69 (86%)

Query:     3 QIQYSEKYFDDTYEYRHVVLPPDVAKLLPKNRLLSETEWRAIGVQQSRGWVHYAIHRPEP 62
             QI YS+KY D+ +EYRHV+LP D+AKL+PK  L+SE+EWR +GVQQS+GWVHY IH PEP
Sbjct:     5 QIYYSDKYDDEEFEYRHVMLPKDIAKLVPKTHLMSESEWRNLGVQQSQGWVHYMIHEPEP 64

Query:    63 HIMLFRRPL 71
             HI+LFRRPL
Sbjct:    65 HILLFRRPL 73

GO:0007049 "cell cycle" evidence=IEA

GO:0016538 "cyclin-dependent protein serine/threonine kinase regulator activity" evidence=IEA

GO:0051301 "cell division" evidence=IEA

FB|FBgn0010314 Cks30A "Cyclin-dependent kinase subunit 30A" [Drosophila melanogaster (taxid:7227)]

 Score = 282 (104.3 bits), Expect = 9.7e-25, P = 9.7e-25
 Identities = 45/67 (67%), Positives = 59/67 (88%)

Query:     4 IQYSEKYFDDTYEYRHVVLPPDVAKLLPKNRLLSETEWRAIGVQQSRGWVHYAIHRPEPH 63
             I YS+KY+D+ +EYRHVVLP ++ K++PK  L++E EWR+IGVQQSRGW+HY IH+PEPH
Sbjct:     5 IYYSDKYYDEQFEYRHVVLPKELVKMVPKTHLMTEAEWRSIGVQQSRGWIHYMIHKPEPH 64

Query:    64 IMLFRRP 70
             I+LFRRP
Sbjct:    65 ILLFRRP 71

GO:0006468 "protein phosphorylation" evidence=ISS;NAS

GO:0004693 "cyclin-dependent protein serine/threonine kinase activity" evidence=ISS

GO:0005515 "protein binding" evidence=IPI

GO:0016538 "cyclin-dependent protein serine/threonine kinase regulator activity" evidence=ISS;NAS

GO:0004674 "protein serine/threonine kinase activity" evidence=NAS

GO:0045842 "positive regulation of mitotic metaphase/anaphase transition" evidence=NAS

GO:0051225 "spindle assembly" evidence=IMP

GO:0007488 "histoblast morphogenesis" evidence=IMP

GO:0007049 "cell cycle" evidence=IMP

GO:0035186 "syncytial blastoderm mitotic cell cycle" evidence=IMP

GO:0007057 "spindle assembly involved in female meiosis I" evidence=IMP

GO:0007144 "female meiosis I" evidence=IMP

GO:0007143 "female meiosis" evidence=IMP

GO:0008054 "cyclin catabolic process" evidence=IMP

RGD|2321453 LOC100364205 "CDC28 protein kinase 1B-like" [Rattus norvegicus (taxid:10116)]

 Score = 282 (104.3 bits), Expect = 9.7e-25, P = 9.7e-25
 Identities = 48/69 (69%), Positives = 59/69 (85%)

Query:     3 QIQYSEKYFDDTYEYRHVVLPPDVAKLLPKNRLLSETEWRAIGVQQSRGWVHYAIHRPEP 62
             QI YS+KY D+ +EYRHV+LP D+AKL+PK  L+ E+EWR +GVQQS+GWVHY IH PEP
Sbjct:    18 QIYYSDKYDDEEFEYRHVMLPKDIAKLVPKTHLMFESEWRNLGVQQSQGWVHYMIHEPEP 77

Query:    63 HIMLFRRPL 71
             HI+LFRRPL
Sbjct:    78 HILLFRRPL 86

GO:0007049 "cell cycle" evidence=IEA

GO:0016538 "cyclin-dependent protein serine/threonine kinase regulator activity" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q0P5A5	CKS1_BOVIN	No assigned EC number	0.7101	0.7840	0.8734	yes	no
P56390	CKS2_MOUSE	No assigned EC number	0.6666	0.8522	0.9493	yes	no
Q91879	CKS2_XENLA	No assigned EC number	0.6486	0.8409	0.9367	N/A	no
P61024	CKS1_HUMAN	No assigned EC number	0.7101	0.7840	0.8734	yes	no
O23249	CKS1_ARATH	No assigned EC number	0.9436	0.8068	0.8160	no	no
Q6PS57	CKS1_ORYSJ	No assigned EC number	0.9589	0.8295	0.8111	yes	no
P41384	CKS1_PATVU	No assigned EC number	0.6666	0.8181	0.9473	N/A	no
Q9SJJ5	CKS2_ARATH	No assigned EC number	0.9024	0.9090	0.9638	yes	no
P55933	CKS1_PHYPO	No assigned EC number	0.8181	0.75	0.7857	N/A	no
A2XCH8	CKS1_ORYSI	No assigned EC number	0.9589	0.8295	0.8111	N/A	no
Q17868	CKS1_CAEEL	No assigned EC number	0.5822	0.8977	0.8404	yes	no
B0G102	CKS1_DICDI	No assigned EC number	0.6060	0.75	0.8048	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

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Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	CKS1	SubName- Full=Putative uncharacterized protein; (84 aa)
		(Populus trichocarpa)
Predicted Functional Partners:
	gw1.I.2892.1	thymidylate kinase (EC-2.7.4.9) (210 aa)				•					0.428

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Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	88
PLN00010	86	PLN00010, PLN00010, cyclin-dependent kinases regul	2e-52
pfam01111	70	pfam01111, CKS, Cyclin-dependent kinase regulatory	2e-42
smart01084	70	smart01084, CKS, Cyclin-dependent kinase regulator	9e-38
PTZ00453	96	PTZ00453, PTZ00453, cyclin-dependent kinase; Provi	4e-35

>gnl|CDD|215027 PLN00010, PLN00010, cyclin-dependent kinases regulatory subunit; Provisional

 Score =  157 bits (399), Expect = 2e-52
 Identities = 79/83 (95%), Positives = 80/83 (96%)

Query: 1  MGQIQYSEKYFDDTYEYRHVVLPPDVAKLLPKNRLLSETEWRAIGVQQSRGWVHYAIHRP 60
          MGQIQYSEKYFDDTYEYRHVVLPP+VAKLLPKNRLLSE EWRAIGVQQSRGWVHYAIHRP
Sbjct: 1  MGQIQYSEKYFDDTYEYRHVVLPPEVAKLLPKNRLLSENEWRAIGVQQSRGWVHYAIHRP 60

Query: 61 EPHIMLFRRPLNYQQQQENQAQQ 83
          EPHIMLFRRPLNYQQQQE QA Q
Sbjct: 61 EPHIMLFRRPLNYQQQQEAQAAQ 83

Length = 86

>gnl|CDD|144631 pfam01111, CKS, Cyclin-dependent kinase regulatory subunit

 Score =  131 bits (333), Expect = 2e-42
 Identities = 49/70 (70%), Positives = 61/70 (87%)

Query: 3  QIQYSEKYFDDTYEYRHVVLPPDVAKLLPKNRLLSETEWRAIGVQQSRGWVHYAIHRPEP 62
          +I YS+KYFDD YEYRHV+LP ++AK +PK++LLSE EWR +G+QQS GWVHY +H PEP
Sbjct: 1  EIYYSDKYFDDYYEYRHVILPKEIAKKIPKDKLLSEMEWRGLGIQQSPGWVHYMVHEPEP 60

Query: 63 HIMLFRRPLN 72
          HI+LFRRPLN
Sbjct: 61 HILLFRRPLN 70

Length = 70

>gnl|CDD|198152 smart01084, CKS, Cyclin-dependent kinase regulatory subunit

 Score =  120 bits (303), Expect = 9e-38
 Identities = 50/70 (71%), Positives = 60/70 (85%)

Query: 3  QIQYSEKYFDDTYEYRHVVLPPDVAKLLPKNRLLSETEWRAIGVQQSRGWVHYAIHRPEP 62
           I YS+KY DD YEYRHV+LP ++AKL+PK RLLSE EWR +G+QQS+GW HY IH+PEP
Sbjct: 1  PIYYSDKYEDDEYEYRHVILPKEIAKLVPKIRLLSENEWRKLGIQQSKGWEHYMIHKPEP 60

Query: 63 HIMLFRRPLN 72
          HI+LFRRPLN
Sbjct: 61 HILLFRRPLN 70

Cyclin-dependent kinase regulatory subunit. Length = 70

>gnl|CDD|185632 PTZ00453, PTZ00453, cyclin-dependent kinase; Provisional

 Score =  114 bits (287), Expect = 4e-35
 Identities = 45/68 (66%), Positives = 60/68 (88%)

Query: 3  QIQYSEKYFDDTYEYRHVVLPPDVAKLLPKNRLLSETEWRAIGVQQSRGWVHYAIHRPEP 62
          +I YS+KY+DD YEYRHV+LP D A+L+P++RL+SE+EWR +GVQQS GW HY IH+PEP
Sbjct: 27 KILYSDKYYDDEYEYRHVILPKDFARLVPRSRLMSESEWRQLGVQQSVGWRHYMIHKPEP 86

Query: 63 HIMLFRRP 70
          H++LF+RP
Sbjct: 87 HVLLFKRP 94

Length = 96

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	88
KOG3484	91	consensus Cyclin-dependent protein kinase CDC28, r	100.0
PLN00010	86	cyclin-dependent kinases regulatory subunit; Provi	100.0
PF01111	70	CKS: Cyclin-dependent kinase regulatory subunit; I	100.0
PTZ00453	96	cyclin-dependent kinase; Provisional	100.0

>KOG3484 consensus Cyclin-dependent protein kinase CDC28, regulatory subunit CKS1, and related proteins [Cell cycle control, cell division, chromosome partitioning]

Probab=100.00  E-value=6.8e-54  Score=290.22  Aligned_cols=81  Identities=74%  Similarity=1.296  Sum_probs=76.8

Q ss_pred             CCCccccCCcCCCceeEEEEEcCHHHHhhCCCCCCcCHHHHHHhcccccCceeeeeeeCCCceeEEeeccCCchhhhHHH
Q 034642            1 MGQIQYSEKYFDDTYEYRHVVLPPDVAKLLPKNRLLSETEWRAIGVQQSRGWVHYAIHRPEPHIMLFRRPLNYQQQQENQ   80 (88)
Q Consensus         1 ~~~I~YS~kY~Dd~yeYRhViLpke~~k~vpk~~LlsE~EWR~LGIqqS~GW~Hy~~h~pEphiLlFRRpl~~~~~~~~~   80 (88)
                      |++|+||+||+||+||||||+||++++|.|||+|||||+|||+||||||+||+|||||.|||||||||||++++++..++
T Consensus         3 ~~qi~YS~kY~Dd~fEYRHV~Lpk~~~K~vPk~rllsE~EWR~lGvqQS~GW~hYmiH~PEpHIlLFrRp~~~~~q~~~~   82 (91)
T KOG3484|consen    3 MDQIYYSDKYFDDEFEYRHVMLPKEVAKLVPKNRLLSETEWRGLGVQQSLGWVHYMIHAPEPHILLFRRPLNYAQQKTAA   82 (91)
T ss_pred             ccceecccccccccceeEEeecCHHHHhhCCccccccHHHHhhhCccccCCeeEEEecCCCceEEEEecccchHHHHHHH
Confidence            68999999999999999999999999999999999999999999999999999999999999999999999998765443


Q ss_pred             H
Q 034642           81 A   81 (88)
Q Consensus        81 ~   81 (88)
                      .
T Consensus        83 ~   83 (91)
T KOG3484|consen   83 T   83 (91)
T ss_pred             H
Confidence            3

>PLN00010 cyclin-dependent kinases regulatory subunit; Provisional

Probab=100.00  E-value=8.1e-53  Score=283.44  Aligned_cols=83  Identities=95%  Similarity=1.514  Sum_probs=80.1

Q ss_pred             CCCccccCCcCCCceeEEEEEcCHHHHhhCCCCCCcCHHHHHHhcccccCceeeeeeeCCCceeEEeeccCCchhhhHHH
Q 034642            1 MGQIQYSEKYFDDTYEYRHVVLPPDVAKLLPKNRLLSETEWRAIGVQQSRGWVHYAIHRPEPHIMLFRRPLNYQQQQENQ   80 (88)
Q Consensus         1 ~~~I~YS~kY~Dd~yeYRhViLpke~~k~vpk~~LlsE~EWR~LGIqqS~GW~Hy~~h~pEphiLlFRRpl~~~~~~~~~   80 (88)
                      |++|+||+||+||+|||||||||++++|.+|+++||||+|||+||||||+||+|||+|+|||||||||||++.+++.+++
T Consensus         1 ~~~I~YS~kY~Dd~yeYRhViLPk~~~k~ipk~~LL~E~EWR~LGIqqS~GW~Hy~~h~pEphILlFrRp~~~~~~~~~~   80 (86)
T PLN00010          1 MGQIQYSEKYFDDTYEYRHVVLPPEVAKLLPKNRLLSENEWRAIGVQQSRGWVHYAIHRPEPHIMLFRRPLNYQQQQEAQ   80 (86)
T ss_pred             CCccEeCCceeCCCcEEEEEEeCHHHHHhCCcCcccCHHHHHHhccccCCCcEEeeecCCCceEEEEEccCCCCCcccch
Confidence            78999999999999999999999999999999999999999999999999999999999999999999999999888777


Q ss_pred             HHH
Q 034642           81 AQQ   83 (88)
Q Consensus        81 ~~~   83 (88)
                      +++
T Consensus        81 ~~~   83 (86)
T PLN00010         81 AAQ   83 (86)
T ss_pred             hhh
Confidence            765

>PF01111 CKS: Cyclin-dependent kinase regulatory subunit; InterPro: IPR000789 Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases

Probab=100.00  E-value=3.1e-51  Score=266.81  Aligned_cols=70  Identities=73%  Similarity=1.395  Sum_probs=56.0

Q ss_pred             CccccCCcCCCceeEEEEEcCHHHHhhCCCCCCcCHHHHHHhcccccCceeeeeeeCCCceeEEeeccCC
Q 034642            3 QIQYSEKYFDDTYEYRHVVLPPDVAKLLPKNRLLSETEWRAIGVQQSRGWVHYAIHRPEPHIMLFRRPLN   72 (88)
Q Consensus         3 ~I~YS~kY~Dd~yeYRhViLpke~~k~vpk~~LlsE~EWR~LGIqqS~GW~Hy~~h~pEphiLlFRRpl~   72 (88)
                      +|+||+||+||+|||||||||+++++++|+++||||+|||+||||||+||+|||+|+|||||||||||+|
T Consensus         1 ~I~YS~kY~Dd~yeYRhViLpk~~~k~vp~~~llsE~EWR~LGIqqS~GW~Hy~~h~pephiLlFrRp~n   70 (70)
T PF01111_consen    1 QIYYSDKYYDDEYEYRHVILPKEIAKLVPKDRLLSEEEWRGLGIQQSPGWEHYMIHKPEPHILLFRRPLN   70 (70)
T ss_dssp             G-EEE--EEBSSEEEEEEE--HHHHGTS-CCS---HHHHHHTT--S-TT-EEECETTSSTTEEEEEEECT
T ss_pred             CccccccccCCceEEEEEECCHHHHhhCccCcccCHHHHHhhCCccCCCcEEEEEeCCCCcEEEEecCCC
Confidence            5999999999999999999999999999999999999999999999999999999999999999999986

Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity []: Serine/threonine-protein kinases Tyrosine-protein kinases Dual specific protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins) Protein kinase function has been evolutionarily conserved from Escherichia coli to human []. Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation []. Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved [], leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases []. In eukaryotes, cyclin-dependent protein kinases interact with cyclins to regulate cell cycle progression, and are required for the G1 and G2 stages of cell division []. The proteins bind to a regulatory subunit, cyclin-dependent kinase regulatory subunit (CKS), which is essential for their function. This regulatory subunit is a small protein of 79 to 150 residues. In yeast (gene CKS1) and in fission yeast (gene suc1) a single isoform is known, while mammals have two highly related isoforms. The regulatory subunits exist as hexamers, formed by the symmetrical assembly of 3 interlocked homodimers, creating an unusual 12-stranded beta-barrel structure []. Through the barrel centre runs a 12A diameter tunnel, lined by 6 exposed helix pairs []. Six kinase units can be modelled to bind the hexameric structure, which may thus act as a hub for cyclin-dependent protein kinase multimerisation [, ].; GO: 0016538 cyclin-dependent protein kinase regulator activity, 0007049 cell cycle; PDB: 1CKS_C 3QY2_B 1QB3_C 1SCE_B 1PUC_A 1DKS_B 2AST_C 1BUH_B 1DKT_B 2ASS_C.

>PTZ00453 cyclin-dependent kinase; Provisional

Probab=100.00  E-value=3.9e-49  Score=269.84  Aligned_cols=72  Identities=63%  Similarity=1.271  Sum_probs=69.8

Q ss_pred             CCCccccCCcCCCceeEEEEEcCHHHHhhCCCCCCcCHHHHHHhcccccCceeeeeeeCCCceeEEeeccCC
Q 034642            1 MGQIQYSEKYFDDTYEYRHVVLPPDVAKLLPKNRLLSETEWRAIGVQQSRGWVHYAIHRPEPHIMLFRRPLN   72 (88)
Q Consensus         1 ~~~I~YS~kY~Dd~yeYRhViLpke~~k~vpk~~LlsE~EWR~LGIqqS~GW~Hy~~h~pEphiLlFRRpl~   72 (88)
                      .++|+||+||+||+|||||||||++++|.+|+++||||+|||+||||||+||+|||+|+|||||||||||++
T Consensus        25 ~~~I~YS~kY~DD~yEYRHViLPk~~~k~ipk~~LL~E~EWR~LGIqqS~GW~HY~~h~pEphILLFRRp~t   96 (96)
T PTZ00453         25 QSKILYSDKYYDDEYEYRHVILPKDFARLVPRSRLMSESEWRQLGVQQSVGWRHYMIHKPEPHVLLFKRPKT   96 (96)
T ss_pred             cccceeCCceeCCCcEEEEEEeCHHHHHhCCCCccccHHHHHHhhhccCCCcEEeeecCCCCcEEEEecCCC
Confidence            368999999999999999999999999999999999999999999999999999999999999999999974

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	88
1dks_A	79	Ckshs1: Human Cyclin Dependent Kinase Subunit, Type		1e-25
2ass_C	69	Crystal Structure Of The Skp1-Skp2-Cks1 Complex Len		1e-25
1cks_A	79	Human Ckshs2 Atomic Structure: A Role For Its Hexam		3e-24
1qb3_A	150	Crystal Structure Of The Cell Cycle Regulatory Prot		2e-18
3qy2_A	117	Crystal Structure Of The P93a Monomer Mutant Of S.		1e-17
1puc_A	105	P13suc1 In A Strand-Exchanged Dimer Length = 105		2e-16
1sce_A	112	Crystal Structure Of The Cell Cycle Regulatory Prot		2e-16

>pdb|1DKS|A Chain A, Ckshs1: Human Cyclin Dependent Kinase Subunit, Type 1 In Complex With Phosphate Length = 79

Iteration: 1
 Score =  111 bits (277), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 49/69 (71%), Positives = 60/69 (86%)
Query: 3  QIQYSEKYFDDTYEYRHVVLPPDVAKLLPKNRLLSETEWRAIGVQQSRGWVHYAIHRPEP 62
          QI YS+KY D+ +EYRHV+LP D+AKL+PK  L+SE+EWR +GVQQS+GWVHY IH PEP
Sbjct: 5  QIYYSDKYDDEEFEYRHVMLPKDIAKLVPKTHLMSESEWRNLGVQQSQGWVHYMIHEPEP 64
Query: 63 HIMLFRRPL 71
          HI+LFRRPL
Sbjct: 65 HILLFRRPL 73

>pdb|2ASS|C Chain C, Crystal Structure Of The Skp1-Skp2-Cks1 Complex Length = 69

Iteration: 1
 Score =  110 bits (276), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 49/69 (71%), Positives = 60/69 (86%)
Query: 3  QIQYSEKYFDDTYEYRHVVLPPDVAKLLPKNRLLSETEWRAIGVQQSRGWVHYAIHRPEP 62
          QI YS+KY D+ +EYRHV+LP D+AKL+PK  L+SE+EWR +GVQQS+GWVHY IH PEP
Sbjct: 1  QIYYSDKYDDEEFEYRHVMLPKDIAKLVPKTHLMSESEWRNLGVQQSQGWVHYMIHEPEP 60
Query: 63 HIMLFRRPL 71
          HI+LFRRPL
Sbjct: 61 HILLFRRPL 69

>pdb|1CKS|A Chain A, Human Ckshs2 Atomic Structure: A Role For Its Hexameric Assembly In Cell Cycle Control Length = 79

Iteration: 1
 Score =  106 bits (265), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 48/69 (69%), Positives = 58/69 (84%)
Query: 3  QIQYSEKYFDDTYEYRHVVLPPDVAKLLPKNRLLSETEWRAIGVQQSRGWVHYAIHRPEP 62
          QI YS+KYFD+ YEYRHV+LP +++K +PK  L+SE EWR +GVQQS GWVHY IH PEP
Sbjct: 5  QIYYSDKYFDEHYEYRHVMLPRELSKQVPKTHLMSEEEWRRLGVQQSLGWVHYMIHEPEP 64
Query: 63 HIMLFRRPL 71
          HI+LFRRPL
Sbjct: 65 HILLFRRPL 73

>pdb|1QB3|A Chain A, Crystal Structure Of The Cell Cycle Regulatory Protein Cks1 Length = 150

Iteration: 1
 Score = 87.8 bits (216), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 40/77 (51%), Positives = 52/77 (67%), Gaps = 9/77 (11%)
Query: 4   IQYSEKYFDDTYEYRHVVLPPDVAKLLPKN---------RLLSETEWRAIGVQQSRGWVH 54
           I YS +Y DD YEYRHV+LP  + K++P +         R+L+E EWR +G+ QS GW H
Sbjct: 28  IHYSPRYSDDNYEYRHVMLPKAMLKVIPSDYFNSEVGTLRILTEDEWRGLGITQSLGWEH 87
Query: 55  YAIHRPEPHIMLFRRPL 71
           Y  H PEPHI+LF+RPL
Sbjct: 88  YECHAPEPHILLFKRPL 104

>pdb|3QY2|A Chain A, Crystal Structure Of The P93a Monomer Mutant Of S. Cerevisiae Cks1 Length = 117

Iteration: 1
 Score = 85.1 bits (209), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 39/77 (50%), Positives = 51/77 (66%), Gaps = 9/77 (11%)
Query: 4   IQYSEKYFDDTYEYRHVVLPPDVAKLLPKN---------RLLSETEWRAIGVQQSRGWVH 54
           I YS +Y DD YEYRHV+LP  + K++P +         R+L+E EWR +G+ QS GW H
Sbjct: 28  IHYSPRYSDDNYEYRHVMLPKAMLKVIPSDYFNSEVGTLRILTEDEWRGLGITQSLGWEH 87
Query: 55  YAIHRPEPHIMLFRRPL 71
           Y  H  EPHI+LF+RPL
Sbjct: 88  YECHAAEPHILLFKRPL 104

>pdb|1PUC|A Chain A, P13suc1 In A Strand-Exchanged Dimer Length = 105

Iteration: 1
 Score = 80.5 bits (197), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 38/78 (48%), Positives = 50/78 (64%), Gaps = 9/78 (11%)
Query: 1  MGQIQYSEKYFDDTYEYRHVVLPPDVAKLLPKN---------RLLSETEWRAIGVQQSRG 51
          + QI YS +Y DD YEYRHV+LP  + K +P +         R+L E EWR +G+ QS G
Sbjct: 21 IDQIHYSPRYADDEYEYRHVMLPKAMLKAIPTDYFNPETGTLRILQEEEWRGLGITQSLG 80
Query: 52 WVHYAIHRPEPHIMLFRR 69
          W  Y +H PEPHI+LF+R
Sbjct: 81 WEMYEVHVPEPHILLFKR 98

>pdb|1SCE|A Chain A, Crystal Structure Of The Cell Cycle Regulatory Protein Suc1 Reveals A Novel Beta-Hinge Conformational Switch Length = 112

Iteration: 1
 Score = 80.5 bits (197), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 38/78 (48%), Positives = 50/78 (64%), Gaps = 9/78 (11%)
Query: 1  MGQIQYSEKYFDDTYEYRHVVLPPDVAKLLPKN---------RLLSETEWRAIGVQQSRG 51
          + QI YS +Y DD YEYRHV+LP  + K +P +         R+L E EWR +G+ QS G
Sbjct: 22 IDQIHYSPRYADDEYEYRHVMLPKAMLKAIPTDYFNPETGTLRILQEEEWRGLGITQSLG 81
Query: 52 WVHYAIHRPEPHIMLFRR 69
          W  Y +H PEPHI+LF+R
Sbjct: 82 WEMYEVHVPEPHILLFKR 99

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	88
1cks_A	79	Cyclin-dependent kinase subunit, type 2; cell divi	4e-43
1puc_A	105	P13SUC1, P13; cell cycle, domain swapping, strand-	9e-40
3qy2_A	117	Cyclin-dependent kinases regulatory subunit; prote	2e-39
1qb3_A	150	Cyclin-dependent kinases regulatory subunit; cell	1e-35

>1cks_A Cyclin-dependent kinase subunit, type 2; cell division; 2.10A {Homo sapiens} SCOP: d.97.1.1 PDB: 1buh_B 1dks_A 1dkt_A* 2ast_C* 2ass_C* Length = 79

 Score =  133 bits (337), Expect = 4e-43
 Identities = 50/75 (66%), Positives = 61/75 (81%)

Query: 3  QIQYSEKYFDDTYEYRHVVLPPDVAKLLPKNRLLSETEWRAIGVQQSRGWVHYAIHRPEP 62
          QI YS+KYFD+ YEYRHV+LP +++K +PK  L+SE EWR +GVQQS GWVHY IH PEP
Sbjct: 5  QIYYSDKYFDEHYEYRHVMLPRELSKQVPKTHLMSEEEWRRLGVQQSLGWVHYMIHEPEP 64

Query: 63 HIMLFRRPLNYQQQQ 77
          HI+LFRRPL   QQ+
Sbjct: 65 HILLFRRPLPKDQQK 79

>1puc_A P13SUC1, P13; cell cycle, domain swapping, strand-exchanged dimer, binding protein; HET: CPS; 1.95A {Schizosaccharomyces pombe} SCOP: d.97.1.1 PDB: 1sce_A Length = 105

 Score =  126 bits (317), Expect = 9e-40
 Identities = 40/85 (47%), Positives = 54/85 (63%), Gaps = 9/85 (10%)

Query: 1   MGQIQYSEKYFDDTYEYRHVVLPPDVAKLLPKN---------RLLSETEWRAIGVQQSRG 51
           + QI YS +Y DD YEYRHV+LP  + K +P +         R+L E EWR +G+ QS G
Sbjct: 21  IDQIHYSPRYADDEYEYRHVMLPKAMLKAIPTDYFNPETGTLRILQEEEWRGLGITQSLG 80

Query: 52  WVHYAIHRPEPHIMLFRRPLNYQQQ 76
           W  Y +H PEPHI+LF+R  +YQ +
Sbjct: 81  WEMYEVHVPEPHILLFKREKDYQMK 105

>3qy2_A Cyclin-dependent kinases regulatory subunit; protein kinase activator, ubiquitin binding, transcription, cell cycle, transferase RE; HET: FLC; 2.59A {Saccharomyces cerevisiae} Length = 117

 Score =  125 bits (316), Expect = 2e-39
 Identities = 41/91 (45%), Positives = 55/91 (60%), Gaps = 9/91 (9%)

Query: 1   MGQIQYSEKYFDDTYEYRHVVLPPDVAKLLPKN---------RLLSETEWRAIGVQQSRG 51
              I YS +Y DD YEYRHV+LP  + K++P +         R+L+E EWR +G+ QS G
Sbjct: 25  QDSIHYSPRYSDDNYEYRHVMLPKAMLKVIPSDYFNSEVGTLRILTEDEWRGLGITQSLG 84

Query: 52  WVHYAIHRPEPHIMLFRRPLNYQQQQENQAQ 82
           W HY  H  EPHI+LF+RPLNY+ +      
Sbjct: 85  WEHYECHAAEPHILLFKRPLNYEAELRAATA 115

>1qb3_A Cyclin-dependent kinases regulatory subunit; cell cycle mutagenesis domain swapping, cyclin-dependent KIN cycle; 3.00A {Saccharomyces cerevisiae} SCOP: d.97.1.1 Length = 150

 Score =  117 bits (294), Expect = 1e-35
 Identities = 42/90 (46%), Positives = 56/90 (62%), Gaps = 9/90 (10%)

Query: 3   QIQYSEKYFDDTYEYRHVVLPPDVAKLLPKN---------RLLSETEWRAIGVQQSRGWV 53
            I YS +Y DD YEYRHV+LP  + K++P +         R+L+E EWR +G+ QS GW 
Sbjct: 27  SIHYSPRYSDDNYEYRHVMLPKAMLKVIPSDYFNSEVGTLRILTEDEWRGLGITQSLGWE 86

Query: 54  HYAIHRPEPHIMLFRRPLNYQQQQENQAQQ 83
           HY  H PEPHI+LF+RPLNY+ +       
Sbjct: 87  HYECHAPEPHILLFKRPLNYEAELRAATAA 116

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	88
1cks_A	79	Cyclin-dependent kinase subunit, type 2; cell divi	100.0
3qy2_A	117	Cyclin-dependent kinases regulatory subunit; prote	100.0
1puc_A	105	P13SUC1, P13; cell cycle, domain swapping, strand-	100.0
1qb3_A	150	Cyclin-dependent kinases regulatory subunit; cell	100.0

>1cks_A Cyclin-dependent kinase subunit, type 2; cell division; 2.10A {Homo sapiens} SCOP: d.97.1.1 PDB: 1buh_B 1dks_A 1dkt_A* 2ast_C* 2ass_C*

Probab=100.00  E-value=9.7e-53  Score=278.36  Aligned_cols=75  Identities=67%  Similarity=1.222  Sum_probs=71.0

Q ss_pred             CCccccCCcCCCceeEEEEEcCHHHHhhCCCCCCcCHHHHHHhcccccCceeeeeeeCCCceeEEeeccCCchhh
Q 034642            2 GQIQYSEKYFDDTYEYRHVVLPPDVAKLLPKNRLLSETEWRAIGVQQSRGWVHYAIHRPEPHIMLFRRPLNYQQQ   76 (88)
Q Consensus         2 ~~I~YS~kY~Dd~yeYRhViLpke~~k~vpk~~LlsE~EWR~LGIqqS~GW~Hy~~h~pEphiLlFRRpl~~~~~   76 (88)
                      ++|+||+||+||+|||||||||++++|++|+++||||+|||+||||||+||+|||+|+|||||||||||++.+++
T Consensus         4 ~~I~YS~kY~Dd~yeYRhViLpke~~k~vpk~~LlsE~EWR~LGIqqS~GW~Hy~ih~pEphiLlFRRp~~~~~~   78 (79)
T 1cks_A            4 KQIYYSDKYFDEHYEYRHVMLPRELSKQVPKTHLMSEEEWRRLGVQQSLGWVHYMIHEPEPHILLFRRPLPKDQQ   78 (79)
T ss_dssp             CCCEECCCEECSSCEECCEECCHHHHHTSCSSSCCCHHHHHHHTCCCCTTCCCCBCCCCCCCCCCCCCCCCC---
T ss_pred             CCcEECCCccCCCeEEEEEEcCHHHHHhCCcccccCHHHHHHhCcccCCCeEEEEecCCCCeEEEEeccCCCCCC
Confidence            589999999999999999999999999999999999999999999999999999999999999999999988653

>3qy2_A Cyclin-dependent kinases regulatory subunit; protein kinase activator, ubiquitin binding, transcription, cell cycle, transferase RE; HET: FLC; 2.59A {Saccharomyces cerevisiae}

Probab=100.00  E-value=2.8e-50  Score=282.23  Aligned_cols=80  Identities=51%  Similarity=1.066  Sum_probs=69.7

Q ss_pred             CCccccCCcCCCceeEEEEEcCHHHHhhCCCC---------CCcCHHHHHHhcccccCceeeeeeeCCCceeEEeeccCC
Q 034642            2 GQIQYSEKYFDDTYEYRHVVLPPDVAKLLPKN---------RLLSETEWRAIGVQQSRGWVHYAIHRPEPHIMLFRRPLN   72 (88)
Q Consensus         2 ~~I~YS~kY~Dd~yeYRhViLpke~~k~vpk~---------~LlsE~EWR~LGIqqS~GW~Hy~~h~pEphiLlFRRpl~   72 (88)
                      ++|+||+||+||+|||||||||++++|.+|++         +||||+|||+||||||+||+|||+|+|||||||||||++
T Consensus        26 ~~I~YS~KY~Dd~yEYRHViLPke~~k~iPk~~~~~~~g~~rLLsE~EWR~LGIqqS~GW~HY~ih~pEPhILLFRRp~~  105 (117)
T 3qy2_A           26 DSIHYSPRYSDDNYEYRHVMLPKAMLKVIPSDYFNSEVGTLRILTEDEWRGLGITQSLGWEHYECHAAEPHILLFKRPLN  105 (117)
T ss_dssp             GGCEECCCEECSSEEEEEEECCGGGGGGSCGGGBCTTTSSBCCCCHHHHHHTTCCCCSSCEEECCTTSCTTEEEEEEECC
T ss_pred             ccceecCCccCCCeEEEEEEcCHHHHHhCchhhcccccccceecCHHHHHHhccccCCCcEEeeecCCCCeEEEEecCCC
Confidence            68999999999999999999999999999987         899999999999999999999999999999999999999


Q ss_pred             chhhhHHHH
Q 034642           73 YQQQQENQA   81 (88)
Q Consensus        73 ~~~~~~~~~   81 (88)
                      ++++.+.++
T Consensus       106 ~~~~~~~~~  114 (117)
T 3qy2_A          106 YEAELRAAT  114 (117)
T ss_dssp             ---------
T ss_pred             CCcchhhhh
Confidence            987665443

>1puc_A P13SUC1, P13; cell cycle, domain swapping, strand-exchanged dimer, binding protein; HET: CPS; 1.95A {Schizosaccharomyces pombe} SCOP: d.97.1.1 PDB: 1sce_A

Probab=100.00  E-value=7.3e-50  Score=275.92  Aligned_cols=74  Identities=54%  Similarity=1.083  Sum_probs=69.9

Q ss_pred             CCccccCCcCCCceeEEEEEcCHHHHhhCCCC---------CCcCHHHHHHhcccccCceeeeeeeCCCceeEEeeccCC
Q 034642            2 GQIQYSEKYFDDTYEYRHVVLPPDVAKLLPKN---------RLLSETEWRAIGVQQSRGWVHYAIHRPEPHIMLFRRPLN   72 (88)
Q Consensus         2 ~~I~YS~kY~Dd~yeYRhViLpke~~k~vpk~---------~LlsE~EWR~LGIqqS~GW~Hy~~h~pEphiLlFRRpl~   72 (88)
                      ++|+||+||+||+|||||||||++++|.+|++         +||||+|||+||||||+||+|||+|+|||||||||||++
T Consensus        22 ~~I~YS~kY~Dd~yEYRHViLPke~~k~ipk~~~~~~~gt~rLLtE~EWR~LGIqqS~GW~Hy~ih~pEPhiLLFRRp~~  101 (105)
T 1puc_A           22 DQIHYSPRYADDEYEYRHVMLPKAMLKAIPTDYFNPETGTLRILQEEEWRGLGITQSLGWEMYEVHVPEPHILLFKREKD  101 (105)
T ss_dssp             TTCEECCCEECSSCEECCEECCHHHHTTSCGGGBCTTTSSBCCCCHHHHHHTTCCCCSSCCCCCCCCCCTTCCCCCCCCC
T ss_pred             cCceeCCcccCCCeEEEEEEcCHHHHHhCcccccccccccccccCHHHHHHhCcccCCCcEEEeecCCCCeEEEEeccCC
Confidence            68999999999999999999999999999998         999999999999999999999999999999999999998


Q ss_pred             chh
Q 034642           73 YQQ   75 (88)
Q Consensus        73 ~~~   75 (88)
                      .++
T Consensus       102 ~~~  104 (105)
T 1puc_A          102 YQM  104 (105)
T ss_dssp             ---
T ss_pred             CCC
Confidence            864

>1qb3_A Cyclin-dependent kinases regulatory subunit; cell cycle mutagenesis domain swapping, cyclin-dependent KIN cycle; 3.00A {Saccharomyces cerevisiae} SCOP: d.97.1.1

Probab=100.00  E-value=4.1e-48  Score=280.21  Aligned_cols=81  Identities=52%  Similarity=1.082  Sum_probs=76.0

Q ss_pred             CCccccCCcCCCceeEEEEEcCHHHHhhCCCC---------CCcCHHHHHHhcccccCceeeeeeeCCCceeEEeeccCC
Q 034642            2 GQIQYSEKYFDDTYEYRHVVLPPDVAKLLPKN---------RLLSETEWRAIGVQQSRGWVHYAIHRPEPHIMLFRRPLN   72 (88)
Q Consensus         2 ~~I~YS~kY~Dd~yeYRhViLpke~~k~vpk~---------~LlsE~EWR~LGIqqS~GW~Hy~~h~pEphiLlFRRpl~   72 (88)
                      ++|+||+||+||+|||||||||++++|.+|++         +||||+|||+||||||+||+|||+|+|||||||||||++
T Consensus        26 ~~I~YS~KY~Dd~YEYRHViLPke~~k~iPk~y~~~~~gt~rLLtE~EWR~LGIqQS~GW~HYmih~PEPhILLFRRpl~  105 (150)
T 1qb3_A           26 DSIHYSPRYSDDNYEYRHVMLPKAMLKVIPSDYFNSEVGTLRILTEDEWRGLGITQSLGWEHYECHAPEPHILLFKRPLN  105 (150)
T ss_dssp             GGCEECCCEECSSEEEEEEECCHHHHHTSCGGGBCTTTSSBCCCCHHHHHHTTCCCCTTCEEESCCCCCTTEEEEEEETT
T ss_pred             hcceeccceecCceeEEEEecCHHHHhhccccccccccccccCCCHHHHHHHccccCcCcEEeeecCCCCcEEEecCCCC
Confidence            57999999999999999999999999999998         999999999999999999999999999999999999999


Q ss_pred             chhhhHHHHH
Q 034642           73 YQQQQENQAQ   82 (88)
Q Consensus        73 ~~~~~~~~~~   82 (88)
                      .++.....++
T Consensus       106 ~~~~~~~a~~  115 (150)
T 1qb3_A          106 YEAELRAATA  115 (150)
T ss_dssp             HHHHHHHHHH
T ss_pred             CCCCcchhhH
Confidence            9876654443

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Length	Definition	E-value
Query	88
d1cksa_	74	d.97.1.1 (A:) CksHs2 {Human (Homo sapiens) [TaxId:	4e-41
d1qb3a_	113	d.97.1.1 (A:) cks1 {Baker's yeast (Saccharomyces c	3e-39
d1puca_	101	d.97.1.1 (A:) suc1 {Fission yeast (Schizosaccharom	2e-38

>d1cksa_ d.97.1.1 (A:) CksHs2 {Human (Homo sapiens) [TaxId: 9606]} Length = 74

class: Alpha and beta proteins (a+b)
fold: Cell cycle regulatory proteins
superfamily: Cell cycle regulatory proteins
family: Cell cycle regulatory proteins
domain: CksHs2
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  127 bits (321), Expect = 4e-41
 Identities = 48/69 (69%), Positives = 58/69 (84%)

Query: 3  QIQYSEKYFDDTYEYRHVVLPPDVAKLLPKNRLLSETEWRAIGVQQSRGWVHYAIHRPEP 62
          QI YS+KYFD+ YEYRHV+LP +++K +PK  L+SE EWR +GVQQS GWVHY IH PEP
Sbjct: 4  QIYYSDKYFDEHYEYRHVMLPRELSKQVPKTHLMSEEEWRRLGVQQSLGWVHYMIHEPEP 63

Query: 63 HIMLFRRPL 71
          HI+LFRRPL
Sbjct: 64 HILLFRRPL 72

>d1qb3a_ d.97.1.1 (A:) cks1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 113

class: Alpha and beta proteins (a+b)
fold: Cell cycle regulatory proteins
superfamily: Cell cycle regulatory proteins
family: Cell cycle regulatory proteins
domain: cks1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score =  123 bits (311), Expect = 3e-39
 Identities = 42/91 (46%), Positives = 55/91 (60%), Gaps = 9/91 (9%)

Query: 3   QIQYSEKYFDDTYEYRHVVLPPDVAKLLPK---------NRLLSETEWRAIGVQQSRGWV 53
            I YS +Y DD YEYRHV+LP  + K++P           R+L+E EWR +G+ QS GW 
Sbjct: 22  SIHYSPRYSDDNYEYRHVMLPKAMLKVIPSDYFNSEVGTLRILTEDEWRGLGITQSLGWE 81

Query: 54  HYAIHRPEPHIMLFRRPLNYQQQQENQAQQN 84
           HY  H PEPHI+LF+RPLNY+ +        
Sbjct: 82  HYECHAPEPHILLFKRPLNYEAELRAATAAA 112

>d1puca_ d.97.1.1 (A:) suc1 {Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Cell cycle regulatory proteins
superfamily: Cell cycle regulatory proteins
family: Cell cycle regulatory proteins
domain: suc1
species: Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896]

 Score =  121 bits (305), Expect = 2e-38
 Identities = 38/81 (46%), Positives = 51/81 (62%), Gaps = 9/81 (11%)

Query: 1   MGQIQYSEKYFDDTYEYRHVVLPPDVAKLLPKN---------RLLSETEWRAIGVQQSRG 51
           + QI YS +Y DD YEYRHV+LP  + K +P +         R+L E EWR +G+ QS G
Sbjct: 21  IDQIHYSPRYADDEYEYRHVMLPKAMLKAIPTDYFNPETGTLRILQEEEWRGLGITQSLG 80

Query: 52  WVHYAIHRPEPHIMLFRRPLN 72
           W  Y +H PEPHI+LF+R  +
Sbjct: 81  WEMYEVHVPEPHILLFKREKD 101

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	88
d1cksa_	74	CksHs2 {Human (Homo sapiens) [TaxId: 9606]}	100.0
d1qb3a_	113	cks1 {Baker's yeast (Saccharomyces cerevisiae) [Ta	100.0
d1puca_	101	suc1 {Fission yeast (Schizosaccharomyces pombe) [T	100.0

>d1cksa_ d.97.1.1 (A:) CksHs2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Cell cycle regulatory proteins
superfamily: Cell cycle regulatory proteins
family: Cell cycle regulatory proteins
domain: CksHs2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=3.4e-52  Score=271.60  Aligned_cols=71  Identities=68%  Similarity=1.271  Sum_probs=69.8

Q ss_pred             CCccccCCcCCCceeEEEEEcCHHHHhhCCCCCCcCHHHHHHhcccccCceeeeeeeCCCceeEEeeccCC
Q 034642            2 GQIQYSEKYFDDTYEYRHVVLPPDVAKLLPKNRLLSETEWRAIGVQQSRGWVHYAIHRPEPHIMLFRRPLN   72 (88)
Q Consensus         2 ~~I~YS~kY~Dd~yeYRhViLpke~~k~vpk~~LlsE~EWR~LGIqqS~GW~Hy~~h~pEphiLlFRRpl~   72 (88)
                      ++|+||+||+||+|||||||||++++|.+|+++||||+|||+||||||+||+|||+|+|||||||||||++
T Consensus         3 ~~I~YS~kY~Dd~yeYRhViLpk~~~k~~pk~~LlsE~EWR~LGIqqS~GW~Hym~h~pEphiLlfRRpl~   73 (74)
T d1cksa_           3 KQIYYSDKYFDEHYEYRHVMLPRELSKQVPKTHLMSEEEWRRLGVQQSLGWVHYMIHEPEPHILLFRRPLP   73 (74)
T ss_dssp             CCCEECCCEECSSCEECCEECCHHHHHTSCSSSCCCHHHHHHHTCCCCTTCCCCBCCCCCCCCCCCCCCCC
T ss_pred             cceEeCCcccCCccEEEEEEeCHHHHhhCCCccccCHHHHHHhCcccCCCcEEeeeeCCCceEEEEeccCC
Confidence            68999999999999999999999999999999999999999999999999999999999999999999986

>d1qb3a_ d.97.1.1 (A:) cks1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Cell cycle regulatory proteins
superfamily: Cell cycle regulatory proteins
family: Cell cycle regulatory proteins
domain: cks1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=100.00  E-value=1.2e-49  Score=276.03  Aligned_cols=80  Identities=53%  Similarity=1.096  Sum_probs=74.7

Q ss_pred             CCccccCCcCCCceeEEEEEcCHHHHhhCCCC---------CCcCHHHHHHhcccccCceeeeeeeCCCceeEEeeccCC
Q 034642            2 GQIQYSEKYFDDTYEYRHVVLPPDVAKLLPKN---------RLLSETEWRAIGVQQSRGWVHYAIHRPEPHIMLFRRPLN   72 (88)
Q Consensus         2 ~~I~YS~kY~Dd~yeYRhViLpke~~k~vpk~---------~LlsE~EWR~LGIqqS~GW~Hy~~h~pEphiLlFRRpl~   72 (88)
                      ++|+||+||+||+|||||||||++++|.+|++         +||||+|||+||||||+||+|||+|+|||||||||||++
T Consensus        21 ~~I~YS~kY~DD~yeYRhViLpk~~~k~ipk~~~~~~~g~~rLLtE~EWR~LGIqqS~GW~Hymih~pEphiLLFRRpl~  100 (113)
T d1qb3a_          21 DSIHYSPRYSDDNYEYRHVMLPKAMLKVIPSDYFNSEVGTLRILTEDEWRGLGITQSLGWEHYECHAPEPHILLFKRPLN  100 (113)
T ss_dssp             GGCEECCCEECSSEEEEEEECCHHHHHTSCGGGBCTTTSSBCCCCHHHHHHTTCCCCTTCEEESCCCCCTTEEEEEEETT
T ss_pred             hhceecccccCCCeeEEEEEeCHHHHHhcchhhccccccccccCCHHHHHHhCcccCCCcEeeeecCCCCeEEEEecCCC
Confidence            57999999999999999999999999999985         599999999999999999999999999999999999999


Q ss_pred             chhhhHHHH
Q 034642           73 YQQQQENQA   81 (88)
Q Consensus        73 ~~~~~~~~~   81 (88)
                      +++++....
T Consensus       101 ~~~~~~~a~  109 (113)
T d1qb3a_         101 YEAELRAAT  109 (113)
T ss_dssp             HHHHHHHHH
T ss_pred             CCcCchhhh
Confidence            987665443

>d1puca_ d.97.1.1 (A:) suc1 {Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896]}

class: Alpha and beta proteins (a+b)
fold: Cell cycle regulatory proteins
superfamily: Cell cycle regulatory proteins
family: Cell cycle regulatory proteins
domain: suc1
species: Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896]

Probab=100.00  E-value=5.4e-49  Score=268.50  Aligned_cols=72  Identities=53%  Similarity=1.081  Sum_probs=69.1

Q ss_pred             CCCccccCCcCCCceeEEEEEcCHHHHhhCCCC---------CCcCHHHHHHhcccccCceeeeeeeCCCceeEEeeccC
Q 034642            1 MGQIQYSEKYFDDTYEYRHVVLPPDVAKLLPKN---------RLLSETEWRAIGVQQSRGWVHYAIHRPEPHIMLFRRPL   71 (88)
Q Consensus         1 ~~~I~YS~kY~Dd~yeYRhViLpke~~k~vpk~---------~LlsE~EWR~LGIqqS~GW~Hy~~h~pEphiLlFRRpl   71 (88)
                      +++|+||+||+||+|||||||||++++|.+|++         +||||+|||+||||||+||+|||+|+|||||||||||.
T Consensus        21 ~~~I~YS~kY~DD~yeYRhViLpk~~~k~ipk~~~~~~~g~~rLLtE~EWR~LGIqqS~GW~Hymih~pEPhiLLFRRp~  100 (101)
T d1puca_          21 IDQIHYSPRYADDEYEYRHVMLPKAMLKAIPTDYFNPETGTLRILQEEEWRGLGITQSLGWEMYEVHVPEPHILLFKREK  100 (101)
T ss_dssp             HTTCEECCCEECSSCEECCEECCHHHHTTSCGGGBCTTTSSBCCCCHHHHHHTTCCCCSSCCCCCCCCCCTTCCCCCCCC
T ss_pred             HhhccccccccCCCeEEEEEEeCHHHHHhcchhhccccccccccCCHHHHHHhccccCCCcEeeeeeCCCceEEEEecCC
Confidence            378999999999999999999999999999986         59999999999999999999999999999999999997


Q ss_pred             C
Q 034642           72 N   72 (88)
Q Consensus        72 ~   72 (88)
                      +
T Consensus       101 ~  101 (101)
T d1puca_         101 D  101 (101)
T ss_dssp             C
T ss_pred             C
Confidence            5