Citrus Sinensis ID: 035848

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240----
Protein Sequence
MENAKAAPTGCFKCGRPGHWSRDCPSSSSSAPSNSNFPSNNTASGGGGGGSGVGDGGVSVSKSAIGVKEKPKKLPRSRPKLTPDLLLSDDGLGFVLRHFPRAFKYRGRGHEVSDLGHLIGLYSEWHSHLLPYYSFDHFVSKVEQVAASRRVKMCIRDLRDRVANGGDPTKLHEAAVEHDGPVDEQAPAEAMSSERQPHQQDPASNVHAADDFNDLFNKVYRTATEVSIFSNLILRLFLFIFCFL
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHccccccccccccHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHcHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHccccHHHHHHHHHHHHHHHcc
Secondary Structure Prediction (SSPRO)
cccccccccccEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHcccccHHHHHHHcHHHccEccccccHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHcccHHHHHHHHHHHHHHccccccccccccccccccccccccccHHcccccccccccccccccccccHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHc
Coil and Loop (DISEMBL)
menakaaptgcfkcgrpghwsrdcpsssssapsnsnfpsnntasggggggsgvgdggvsvsksaigvkekpkklprsrpkltpdlllsddglgfVLRHFPrafkyrgrghevsdlGHLIGLYSEwhshllpyysfdhfVSKVEQVAASRRVKMCIRDLRdrvanggdptklheaavehdgpvdeqapaeamsserqphqqdpasnvhaadDFNDLFNKVYRTATEVSIFSNLILRLFLFIFCFL
Flexible Loop (DISEMBL)
menakaaptgcfkcgrpgHWSRDCPSSSSSAPSNSNFPSNNTASGGGGGGSGVGDGGVSVSKsaigvkekpkklprsrpkltpdlllsddglGFVLRHFPRAFKYRGRGHEVSDLGHLIGLYSEWHSHLLPYYSFDHFVSKVEQVAASRRVKMCIRDLRDRVANGGDPTKLHEAAVEHDGPVDEQAPAEAMSSERQPHQQDPASNVHAADDFNDLFNKVYRTATEVSIFSNLILRLFLFIFCFL
Low Complexity Region (SEG)
MENAKAAPTGCFKCGRPGHWSRDCpsssssapsnsnfpsnntasggggggsgvgdggvsvsKSAIGVKEkpkklprsrpkltpDLLLSDDGLGFVLRHFPRAFKYRGRGHEVSDLGHLIGLYSEWHSHLLPYYSFDHFVSKVEQVAASRRVKMCIRDLRDRVANGGDPTKLHEAAVEHDGPVDEQAPAEAMSSERQPHQQDPASNVHAADDFNDLFNKVYRTATEVSifsnlilrlflfifcfl
Disordered region (IsUnstruct)
************************************************************************************LLLSDDGLGFVLRHFPRAFKYRGRGHEVSDLGHLIGLYSEWHSHLLPYYSFDHFVSKVEQVAASRRVKMCIRDLRD*************************************************DDFNDLFNKVYRTATEVSIFSNLILRLFLFIFCF*
Disordered Region (DISOPRED)
***********FKCGRPGHWSR*************************G********************************LTPDLLLSDDGLGFVLRHFPRAFKYRGRGHEVSDLGHLIGLYSEWHSHLLPYYSFDHFVSKVEQVAASRRVKMCIRDLRD*********************************************************************SNLILRLFLFIFCFL
Disordered Region (DISEMBL)
MENAKAAPTGCFKCGRPG*******************PSNNTASGGGGGGSGVGDGGVSVSKSAI************RPKLTPDLLLSDDGLGFVLRHFPRAFKYRGRGHEVSDLGHLIGLYSEWHSHLLPYYSFDHFVSKVEQVAASRRVKMCIRDLRDRVANGGDPTKLHEAAVEHDGPVD*********************NVHAADDFNDLFNKVYRTATEVSIFSNLILRLFLFIFCFL
Disordered Region (DISPRO)
********T*CFKC*RPGHWS*DCP****************************************************RPKLTPDLLLSDDGLGFVLRHFPRAFKYRGRGHEVSDLGHLIGLYSEWHSHLLPYYSFDHFVSKVEQVAASRRVKMCIRDLRDRVAN*********************************************DDFNDLFNKVYRTATEVSIFSNLILRLFLFIFCFL
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHi
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MENAKAAPTGCFKCGRPGHWSRDCPSSSSSAPSNSNFPSNNTASGGGGGGSGVGDGGVSVSKSAIGVKEKPKKLPRSRPKLTPDLLLSDDGLGFVLRHFPRAFKYRGRGHEVSDLGHLIGLYSEWHSHLLPYYSFDHFVSKVEQVAASRRVKMCIRDLRDRVANGGDPTKLHEAAVEHDGPVDEQAPAEAMSSERQPHQQDPASNVHAADDFNDLFNKVYRTATEVSIFSNLILRLFLFIFCFL
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	244	2.2.26 [Sep-21-2011]
Q9BVW5	301	TIMELESS-interacting prot	yes	no	0.561	0.455	0.319	2e-10
Q5F416	283	TIMELESS-interacting prot	yes	no	0.356	0.307	0.363	3e-10
Q3ZCC4	290	TIMELESS-interacting prot	yes	no	0.438	0.368	0.339	6e-10
Q6DBR4	294	TIMELESS-interacting prot	yes	no	0.553	0.459	0.305	1e-09
Q91WA1	278	TIMELESS-interacting prot	yes	no	0.393	0.345	0.357	2e-09
Q4QR88	276	TIMELESS-interacting prot	yes	no	0.360	0.318	0.355	3e-09
Q0UJ25	244	Chromosome segregation in	N/A	no	0.561	0.561	0.261	7e-09
O14350	181	Swi1-interacting protein	yes	no	0.418	0.563	0.351	1e-08
Q0CU66	302	Chromosome segregation in	N/A	no	0.680	0.549	0.288	2e-08
Q0IHI4	360	TIMELESS-interacting prot	N/A	no	0.475	0.322	0.276	6e-08

>sp|Q9BVW5|TIPIN_HUMAN TIMELESS-interacting protein OS=Homo sapiens GN=TIPIN PE=1 SV=2

 Score = 65.9 bits (159), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 47/147 (31%), Positives = 72/147 (48%), Gaps = 10/147 (6%)

Query: 54  GDGGVSVSKSAIG--VKEKPKK-LPRSRPKLTPDLLLSDDGLGFVLRHFPRAFKYRGRGH 110
           G+G     +S  G  V+  PK+ + R+ PKL    L+S+ GL   LRH     K++G+GH
Sbjct: 37  GEGTEPDEESGNGAPVRVPPKRTVKRNIPKLDAQRLISERGLP-ALRHVFDKAKFKGKGH 95

Query: 111 EVSDLGHLIGLYSEWHSHLLPYYSFDHFVSKVEQVAASRRVKMCIRDLRDRVANGGDPTK 170
           E  DL  LI     W   L P   F+ F+ +VE + + + V+ C++ +R       D   
Sbjct: 96  EAEDLKMLIRHMEHWAHRLFPKLQFEDFIDRVEYLGSKKEVQTCLKRIR------LDLPI 149

Query: 171 LHEAAVEHDGPVDEQAPAEAMSSERQP 197
           LHE  V ++  V E    +  S+E  P
Sbjct: 150 LHEDFVSNNDEVAENNEHDVTSTELDP 176

Required for normal progression of S-phase. Important for cell survival after DNA damage or replication stress. May be specifically required for the ATR-CHEK1 pathway in the replication checkpoint induced by hydroxyurea or ultraviolet light.
Homo sapiens (taxid: 9606)

>sp|Q5F416|TIPIN_CHICK TIMELESS-interacting protein OS=Gallus gallus GN=TIPIN PE=2 SV=1

 Score = 65.5 bits (158), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 32/88 (36%), Positives = 48/88 (54%), Gaps = 1/88 (1%)

Query: 72  KKLPRSRPKLTPDLLLSDDGLGFVLRHFPRAFKYRGRGHEVSDLGHLIGLYSEWHSHLLP 131
           K + RS PKL  + L+S+ GL   LRH     K++G+GHE  DL  L+     W   L P
Sbjct: 65  KAVKRSIPKLDANRLVSERGLP-ALRHMFDNVKFKGKGHEAEDLKTLLRHMEHWAHRLFP 123

Query: 132 YYSFDHFVSKVEQVAASRRVKMCIRDLR 159
              FD F+ +VE +   + V+ C++ +R
Sbjct: 124 KLQFDDFIDRVESLGNKKEVQTCLKRIR 151

Required for normal progression of S-phase. Important for cell survival after DNA damage or replication stress. May be required in the replication checkpoint induced by hydroxyurea or ultraviolet light.

Gallus gallus (taxid: 9031)

>sp|Q3ZCC4|TIPIN_BOVIN TIMELESS-interacting protein OS=Bos taurus GN=TIPIN PE=2 SV=1

 Score = 64.7 bits (156), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 39/115 (33%), Positives = 60/115 (52%), Gaps = 8/115 (6%)

Query: 71  PKK-LPRSRPKLTPDLLLSDDGLGFVLRHFPRAFKYRGRGHEVSDLGHLIGLYSEWHSHL 129
           PK+ + R+ PKL  + L+S+ GL   LRH     K++G+GHE  DL  LI     W   L
Sbjct: 56  PKRTVKRNIPKLNAERLISERGLP-ALRHVFEKAKFKGKGHEAEDLKTLIRHMEHWAHRL 114

Query: 130 LPYYSFDHFVSKVEQVAASRRVKMCIRDLRDRVANGGDPTKLHEAAVEHDGPVDE 184
            P   F+ F+ +VE +   + V+ C++ +R       D   LHE  V ++  V+E
Sbjct: 115 FPKLQFEDFIDRVECLGNKKEVQTCLKRIR------LDLPILHEDFVSNNDEVEE 163

Required for normal progression of S-phase. Important for cell survival after DNA damage or replication stress. May be specifically required for the ATR-CHEK1 pathway in the replication checkpoint induced by hydroxyurea or ultraviolet light.

Bos taurus (taxid: 9913)

>sp|Q6DBR4|TIPIN_DANRE TIMELESS-interacting protein OS=Danio rerio GN=tipin PE=2 SV=1

 Score = 63.5 bits (153), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 44/144 (30%), Positives = 68/144 (47%), Gaps = 9/144 (6%)

Query: 50  GSGVGDGGVSVSKSAIGVKEKPKKLPRSRPKLTPDLLLSDDGLGFVLRHFPRAFKYRGRG 109
           G+  G+    VSK A     K + + R RPKL  + L+S+ GL   LR      K++G+G
Sbjct: 43  GNAEGEEEGEVSKLAEVPVAKRRTVKRPRPKLDANRLISEKGLP-ALRTLFEDVKFKGKG 101

Query: 110 HEVSDLGHLIGLYSEWHSHLLPYYSFDHFVSKVEQVAASRRVKMCIRDLRDRVANGGDPT 169
           HE  +L  L+     W   L P   F+ F+ KVE +   + V+ C++ +R       D  
Sbjct: 102 HETENLKLLMLKMENWAHRLYPKMQFEEFIDKVENLGGKKEVQTCLKRIR------LDMP 155

Query: 170 KLHEAAVEHDGPVDEQAPAEAMSS 193
             HE  V  +  +  Q P E++ S
Sbjct: 156 ITHEDYVAEEAEI--QVPEESVPS 177

Required for normal progression of S-phase. Important for cell survival after DNA damage or replication stress. May be required in the replication checkpoint induced by hydroxyurea or ultraviolet light.

Danio rerio (taxid: 7955)

>sp|Q91WA1|TIPIN_MOUSE TIMELESS-interacting protein OS=Mus musculus GN=Tipin PE=1 SV=2

 Score = 63.2 bits (152), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 35/98 (35%), Positives = 51/98 (52%), Gaps = 2/98 (2%)

Query: 63  SAIGVKEKPKK-LPRSRPKLTPDLLLSDDGLGFVLRHFPRAFKYRGRGHEVSDLGHLIGL 121
           S  GV   PK+ + R+ PKL    L S+ GL   LRH     K++G+GHE  DL  LI  
Sbjct: 45  SGSGVPVPPKRTVKRNLPKLDATRLTSERGLP-ALRHVFDKTKFKGKGHEAEDLKTLIRH 103

Query: 122 YSEWHSHLLPYYSFDHFVSKVEQVAASRRVKMCIRDLR 159
              W   L P   F+ F+ +VE +   + V+ C++ +R
Sbjct: 104 MEHWAHRLFPKLQFEDFIDRVENLGNKKEVQTCLKRIR 141

Required for normal progression of S-phase. Important for cell survival after DNA damage or replication stress. May be specifically required for the ATR-CHEK1 pathway in the replication checkpoint induced by hydroxyurea or ultraviolet light.

Mus musculus (taxid: 10090)

>sp|Q4QR88|TIPIN_RAT TIMELESS-interacting protein OS=Rattus norvegicus GN=Tipin PE=2 SV=1

 Score = 62.0 bits (149), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 32/90 (35%), Positives = 48/90 (53%), Gaps = 2/90 (2%)

Query: 71  PKKL-PRSRPKLTPDLLLSDDGLGFVLRHFPRAFKYRGRGHEVSDLGHLIGLYSEWHSHL 129
           PK++  R+ PKL    L S+ GL   LRH     K++G+GHE  DL  LI     W   L
Sbjct: 53  PKRIVKRNIPKLDATRLTSERGLP-ALRHVFDKTKFKGKGHEAEDLKTLIRHMEHWAHRL 111

Query: 130 LPYYSFDHFVSKVEQVAASRRVKMCIRDLR 159
            P   F+ F+ +VE +   + V+ C++ +R
Sbjct: 112 FPKLQFEDFIDRVENLGNKKEVQTCLKRIR 141

Required for normal progression of S-phase. Important for cell survival after DNA damage or replication stress. May be specifically required for the ATR-CHEK1 pathway in the replication checkpoint induced by hydroxyurea or ultraviolet light.

Rattus norvegicus (taxid: 10116)

>sp|Q0UJ25|CSM3_PHANO Chromosome segregation in meiosis protein 3 OS=Phaeosphaeria nodorum (strain SN15 / ATCC MYA-4574 / FGSC 10173) GN=CSM3 PE=3 SV=1

 Score = 61.2 bits (147), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 40/153 (26%), Positives = 70/153 (45%), Gaps = 16/153 (10%)

Query: 43  ASGGGGGGSGVG-DGGVSVSKSAIGVKEKPKKLPRSRPKLTPDLLLSDDGLGFVLRHFPR 101
           + G G  G G+G D  + ++K  I +           PKL  + LLSD G+  + R    
Sbjct: 41  SKGSGNAGDGLGIDEEIIITKKRIPI-----------PKLDDNRLLSDPGIPRLRRISKD 89

Query: 102 AFKYRGRGHEVSDLGHLIGLYSEWHSHLLPYYSFDHFVSKVEQVAASRRVKMCIRDLRDR 161
             +++G+GHE  D+  ++ +Y  W   L P   F   ++ +E+V  ++R++M    +R  
Sbjct: 90  RLRFKGKGHEYGDIARMLNMYQLWLDDLYPRAKFADALTIIEKVGHTKRMQM----MRKE 145

Query: 162 VANGGDPTKLHEAAVEHDGPVDEQAPAEAMSSE 194
             + G P +      E    V  QAP    ++E
Sbjct: 146 WIDEGKPRRTSAYEEEDADEVVVQAPTTEQATE 178

Forms a fork protection complex (FPC) with TOF1 and which is required for chromosome segregation during meiosis and DNA damage repair. FPC coordinates leading and lagging strand synthesis and moves with the replication fork. FPC stabilizes replication forks in a configuration that is recognized by replication checkpoint sensors.

Phaeosphaeria nodorum (strain SN15 / ATCC MYA-4574 / FGSC 10173) (taxid: 321614)

>sp|O14350|SWI3_SCHPO Swi1-interacting protein swi3 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=swi3 PE=1 SV=2

 Score = 60.5 bits (145), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 38/108 (35%), Positives = 58/108 (53%), Gaps = 6/108 (5%)

Query: 65  IGVKEKPK--KLPRSR-PKLTPDLLLSDDGLGFVLRHFPRAFKYRGRGHEVSDLGHLIGL 121
           +G++E P   K PR R  K   + L+S++G+   LR   R  K +G+GHE  DL  L+G+
Sbjct: 33  LGLEENPDSVKKPRKRLAKFDEERLISENGIP-KLRKMMRKVKLKGKGHEAKDLKQLLGM 91

Query: 122 YSEWHSHLLPYYSFDHFVSKVEQVAASRRVKMCIRDLRDRVA--NGGD 167
           Y  W   L P  +FD  +S ++ +   R VK+  R   + +A  NG D
Sbjct: 92  YHIWTHELYPRATFDDSISYLKTLGKHRSVKVRRRGWINEIAVENGSD 139

Forms a fork protection complex (FPC) with swi1. FPC coordinates leading and lagging strand synthesis and moves with the replication fork. It is required for programmed fork-pausing which is necessary for mating-type switching. FPC stabilizes replication forks in a configuration that is recognized by replication checkpoint sensors. It is involved in termination at the mat1-proximal polar-terminator of replication (RTS1) and also required for activation of the Rad53-like checkpoint kinase cds1.

Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)

>sp|Q0CU66|CSM3_ASPTN Chromosome segregation in meiosis protein 3 OS=Aspergillus terreus (strain NIH 2624 / FGSC A1156) GN=csm3 PE=3 SV=2

 Score = 59.7 bits (143), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 56/194 (28%), Positives = 83/194 (42%), Gaps = 28/194 (14%)

Query: 28  SSSAPSNSNFPSNNTASGGGGGGSGVGDGGVSVSKSAIGVKEKPKKLPRSRPKLTPDLLL 87
            SS  SN N P  + + G G G     D  V V++         K+ P +  KL    LL
Sbjct: 33  ESSTRSNINAPQTSESRGLGLGL----DDEVKVTR---------KRQPIA--KLDEGRLL 77

Query: 88  SDDGLGFVLRHFPRAFKYRGRGHEVSDLGHLIGLYSEWHSHLLPYYSFDHFVSKVEQVAA 147
           S  G+  + R   +  K++G+GHE SD   L+  Y  W   L P   F   ++ +E++  
Sbjct: 78  SQAGIPKLRRSAKQKLKFKGKGHEFSDAARLLNFYQLWLDDLFPRAKFTDGLAMIEKLGH 137

Query: 148 SRRVKMCIRDLRDRV---ANGGDPTKLHEAAVEHDGPVDEQA--PAEAMSSERQPHQQDP 202
           S+R++   R+  D+        D   L EA   H       A  P++  S+ RQ      
Sbjct: 138 SKRIQTMRREWIDQEKPRQRDDDDEPLQEAEGSHHNETSNAADQPSDRQSNSRQ------ 191

Query: 203 ASNVHAADDFNDLF 216
             + H  DD NDLF
Sbjct: 192 --SPHPNDDSNDLF 203

Forms a fork protection complex (FPC) with tof1 and which is required for chromosome segregation during meiosis and DNA damage repair. FPC coordinates leading and lagging strand synthesis and moves with the replication fork. FPC stabilizes replication forks in a configuration that is recognized by replication checkpoint sensors.

Aspergillus terreus (strain NIH 2624 / FGSC A1156) (taxid: 341663)

>sp|Q0IHI4|TIPIN_XENLA TIMELESS-interacting protein OS=Xenopus laevis GN=tipin PE=2 SV=1

 Score = 58.2 bits (139), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 34/123 (27%), Positives = 58/123 (47%), Gaps = 7/123 (5%)

Query: 39  SNNTASGGGGGGSGVGDGGVSVSKSAIGVKEKPKK--LPRSRPKLTPDLLLSDDGLGFVL 96
           +++ A     G     + G +  + A     KP +  + R +PKL    L S  GL   L
Sbjct: 34  ADDEAEDVANGDDWTENAGQTQREEA----PKPARRVVKRPQPKLDGQRLASQRGLP-AL 88

Query: 97  RHFPRAFKYRGRGHEVSDLGHLIGLYSEWHSHLLPYYSFDHFVSKVEQVAASRRVKMCIR 156
           RH     K++G+GHE  DL  L+     W   L P   F+ F++++E +   + V+ C++
Sbjct: 89  RHMFDDVKFKGKGHETEDLKILLRQMENWAHRLFPKLQFEDFLNRLESMGNKKEVQTCLK 148

Query: 157 DLR 159
            +R
Sbjct: 149 KIR 151

Required for normal progression of S-phase. Important for cell survival after DNA damage or replication stress. May be required in the replication checkpoint induced by hydroxyurea or ultraviolet light.

Xenopus laevis (taxid: 8355)

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	244
224111344	283	predicted protein [Populus trichocarpa]	0.922	0.795	0.569	5e-64
225425110	291	PREDICTED: TIMELESS-interacting protein	0.889	0.745	0.589	5e-61
449528333	284	PREDICTED: TIMELESS-interacting protein-	0.852	0.732	0.564	3e-60
449443255	280	PREDICTED: TIMELESS-interacting protein-	0.852	0.742	0.564	4e-60
255555549	267	nucleic acid binding protein, putative [	0.815	0.745	0.537	4e-60
356540972	309	PREDICTED: LOW QUALITY PROTEIN: TIMELESS	0.852	0.673	0.543	1e-58
297828740	287	hypothetical protein ARALYDRAFT_896259 [	0.844	0.717	0.493	3e-57
30678682	282	CCHC-type zinc knuckle protein [Arabidop	0.844	0.730	0.495	3e-56
357473945	286	TIMELESS-interacting protein [Medicago t	0.852	0.727	0.559	4e-56
242097166	321	hypothetical protein SORBIDRAFT_10g03108	0.897	0.682	0.477	5e-49

>gi|224111344|ref|XP_002315820.1| predicted protein [Populus trichocarpa] gi|222864860|gb|EEF01991.1| predicted protein [Populus trichocarpa]

 Score =  249 bits (637), Expect = 5e-64,   Method: Compositional matrix adjust.
 Identities = 131/230 (56%), Positives = 159/230 (69%), Gaps = 5/230 (2%)

Query: 1   MENAKAAPTGCFKCGRPGHWSRDCPSSSSSAPSNSNFPSNNTASGGGGGGSGVGDGGVSV 60
           ME   AAPTGC+KCGRPGHWSRDCP S+ +   +SN  S  +        S   +     
Sbjct: 1   MEKTNAAPTGCYKCGRPGHWSRDCPDSNPNPNPSSNPNSPRSFPSNNNSSSNNSNYFSGS 60

Query: 61  SKSAIGVKEKPKKLPRSRPKLTPDLLL-SDDGLGFVLRHFPRAFKYRGRGHEVSDLGHLI 119
           +       EKPKK+PRSRPKLTP+LLL  D+GLGF+LRHFPR FKYRGRGHEVSDLG+LI
Sbjct: 61  NSKPAKAAEKPKKVPRSRPKLTPELLLGEDNGLGFILRHFPRNFKYRGRGHEVSDLGNLI 120

Query: 120 GLYSEWHSHLLPYYSFDHFVSKVEQVAASRRVKMCIRDLRDRVANGGDPTKLHEAAVEH- 178
           GLYSEWHSHLLPYYSFD FV KVEQVAA++R KMC+R+LR+RVA+GGDPTKL E+  EH 
Sbjct: 121 GLYSEWHSHLLPYYSFDQFVHKVEQVAATKRAKMCVRELRERVASGGDPTKLRESLTEHV 180

Query: 179 --DGPVDEQAPAEAMSSERQPHQQDPASNVHAADDF-NDLFNKVYRTATE 225
             +   D   P E ++SE   +++DP S     D    D+ ++VY  ATE
Sbjct: 181 SANVEHDLSTPDEGLNSEVTHNEEDPLSKNQDVDGLPEDMLHEVYDRATE 230

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225425110|ref|XP_002272919.1| PREDICTED: TIMELESS-interacting protein [Vitis vinifera] gi|297738277|emb|CBI27478.3| unnamed protein product [Vitis vinifera]

 Score =  239 bits (611), Expect = 5e-61,   Method: Compositional matrix adjust.
 Identities = 135/229 (58%), Positives = 160/229 (69%), Gaps = 12/229 (5%)

Query: 1   MENAKAAPTGCFKCGRPGHWSRDCPSSSSSAPSNSNFPSNNTASGGGGGGSGVGDGGVSV 60
           ME + AAPTGC+KCGRPGHWSRDCPSS+++   N N   N+         S    G  + 
Sbjct: 1   MEKSGAAPTGCYKCGRPGHWSRDCPSSNTNPNPNPNPNPNSQNQY-----SSFNKG--TA 53

Query: 61  SKSAIGVKEKPKKLPRSRPKLTPDLLLSDDGLGFVLRHFPRAFKYRGRGHEVSDLGHLIG 120
           SK      EKPKK PR+RP LTP+LLLSD+GLG+VLRHFP AFK+RGRGHEVSDLG+LIG
Sbjct: 54  SKPLAKSSEKPKKAPRTRPNLTPELLLSDNGLGYVLRHFPGAFKFRGRGHEVSDLGNLIG 113

Query: 121 LYSEWHSHLLPYYSFDHFVSKVEQVAASRRVKMCIRDLRDRVANGGDPTKLHEAAVEH-D 179
           LYSEWHSHLLPYYSFD FV KVE+V  ++RVK+CIR+LR+RV NGGD TK HE  VEH D
Sbjct: 114 LYSEWHSHLLPYYSFDQFVHKVEKVGTTKRVKICIRELRERVENGGDLTKFHEPPVEHED 173

Query: 180 GPVDEQ---APAEAMSSERQPHQQDPASNVHAADDFNDLFNKVYRTATE 225
            P  +Q   A  E M+S    H Q   S  H  D   D+ ++VYR+ATE
Sbjct: 174 CPNHDQGLPATEEVMNSVDPSHYQGDTSLNH-EDVQEDMLHEVYRSATE 221

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449528333|ref|XP_004171159.1| PREDICTED: TIMELESS-interacting protein-like [Cucumis sativus]

 Score =  237 bits (604), Expect = 3e-60,   Method: Compositional matrix adjust.
 Identities = 127/225 (56%), Positives = 152/225 (67%), Gaps = 17/225 (7%)

Query: 3   NAKAAPTGCFKCGRPGHWSRDCPSSSSSAPSNSNFPSNNTASGGGGGGSGVGDGGVSVSK 62
           NA  APTGCFKCG+PGHWSRDCPSS+ +    SN  + + +S        V         
Sbjct: 6   NAVPAPTGCFKCGKPGHWSRDCPSSAPNPNPTSNSSTPSFSSPPAAPSKAV--------- 56

Query: 63  SAIGVKEKPKKLPRSRPKLTPDLLLSDDGLGFVLRHFPRAFKYRGRGHEVSDLGHLIGLY 122
                 EKPKK PR+RPKLTP+LLLSDDGLG+VLRHFPRAFKYRGRGHE++DL +LIGLY
Sbjct: 57  ------EKPKKAPRTRPKLTPELLLSDDGLGYVLRHFPRAFKYRGRGHEINDLENLIGLY 110

Query: 123 SEWHSHLLPYYSFDHFVSKVEQVAASRRVKMCIRDLRDRVANGGDPTKLHEAAVEHDGPV 182
            EWHSH+LPYYSF+HFV KVEQVAA++RVKMC+ +LR+RVA GGDPTK  EA + +D   
Sbjct: 111 REWHSHILPYYSFEHFVHKVEQVAATKRVKMCLGELRERVARGGDPTKWREAPILNDDDD 170

Query: 183 DEQAPAEAMSSERQPHQQDPAS--NVHAADDFNDLFNKVYRTATE 225
           D     EA   +     Q+ AS  N  A D   D+  +VY  ATE
Sbjct: 171 DVNNEKEAKDPDDVFDNQEEASLRNNGADDIEEDMLQEVYEKATE 215

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449443255|ref|XP_004139395.1| PREDICTED: TIMELESS-interacting protein-like [Cucumis sativus]

 Score =  237 bits (604), Expect = 4e-60,   Method: Compositional matrix adjust.
 Identities = 127/225 (56%), Positives = 152/225 (67%), Gaps = 17/225 (7%)

Query: 3   NAKAAPTGCFKCGRPGHWSRDCPSSSSSAPSNSNFPSNNTASGGGGGGSGVGDGGVSVSK 62
           NA  APTGCFKCG+PGHWSRDCPSS+ +    SN  + + +S        V         
Sbjct: 6   NAVPAPTGCFKCGKPGHWSRDCPSSAPNPNPTSNSSTPSFSSPPAAPSKAV--------- 56

Query: 63  SAIGVKEKPKKLPRSRPKLTPDLLLSDDGLGFVLRHFPRAFKYRGRGHEVSDLGHLIGLY 122
                 EKPKK PR+RPKLTP+LLLSDDGLG+VLRHFPRAFKYRGRGHE++DL +LIGLY
Sbjct: 57  ------EKPKKAPRTRPKLTPELLLSDDGLGYVLRHFPRAFKYRGRGHEINDLENLIGLY 110

Query: 123 SEWHSHLLPYYSFDHFVSKVEQVAASRRVKMCIRDLRDRVANGGDPTKLHEAAVEHDGPV 182
            EWHSH+LPYYSF+HFV KVEQVAA++RVKMC+ +LR+RVA GGDPTK  EA + +D   
Sbjct: 111 REWHSHILPYYSFEHFVHKVEQVAATKRVKMCLGELRERVARGGDPTKWREAPILNDDDD 170

Query: 183 DEQAPAEAMSSERQPHQQDPAS--NVHAADDFNDLFNKVYRTATE 225
           D     EA   +     Q+ AS  N  A D   D+  +VY  ATE
Sbjct: 171 DVNNEKEAKDPDDVFDNQEEASLRNNGADDIEEDMLQEVYEKATE 215

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255555549|ref|XP_002518811.1| nucleic acid binding protein, putative [Ricinus communis] gi|223542192|gb|EEF43736.1| nucleic acid binding protein, putative [Ricinus communis]

 Score =  237 bits (604), Expect = 4e-60,   Method: Compositional matrix adjust.
 Identities = 129/240 (53%), Positives = 158/240 (65%), Gaps = 41/240 (17%)

Query: 1   MENAKAAPTGCFKCGRPGHWSRDCPSSSSSAPSN----------SNFPSNNTASGGGGGG 50
           ME  KAAPTGC+KCGRPGHWSRDCP S+S+   +          ++FP+ +T S      
Sbjct: 1   MEPGKAAPTGCYKCGRPGHWSRDCPDSNSNPNPSSSNPSNSKFPTSFPNTSTNSKP---- 56

Query: 51  SGVGDGGVSVSKSAIGVKEKPKKLPRSRPKLTPDLLLSDDGLGFVLRHFPRAFKYRGRGH 110
                           V EKPKK+PRSRPKLTPD+LL DDGLG+VLRHFPR FKYRGRGH
Sbjct: 57  ----------------VAEKPKKVPRSRPKLTPDILLGDDGLGYVLRHFPRNFKYRGRGH 100

Query: 111 EVSDLGHLIGLYSEWHSHLLPYYSFDHFVSKVEQVAASRRVKMCIRDLRDRVANGGDPTK 170
           EVSDLG+LI LYSEWHS LLPYYS+D FV KVEQVA+++RV++C+RDLR+RVA+GGDP K
Sbjct: 101 EVSDLGNLIRLYSEWHSRLLPYYSYDEFVHKVEQVASTKRVRVCLRDLRERVASGGDPMK 160

Query: 171 LHEAAVEHDGPVDEQAPAEAMSSERQPHQQD---PASNVHAAD-DFNDLFNKVYRTATEV 226
           LHE+  E+  P  EQ           P + D   P+S  H AD +  D+   ++  ATE 
Sbjct: 161 LHESPPEYVDPKLEQ-------DHSIPTENDMGGPSSTNHDADVEQEDMLCDIFDRATEA 213

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356540972|ref|XP_003538958.1| PREDICTED: LOW QUALITY PROTEIN: TIMELESS-interacting protein-like [Glycine max]

 Score =  232 bits (591), Expect = 1e-58,   Method: Compositional matrix adjust.
 Identities = 119/219 (54%), Positives = 147/219 (67%), Gaps = 11/219 (5%)

Query: 9   TGCFKCGRPGHWSRDCPSSSSSAPSNSNFPSNNTASGGGGGGSGVGDGGVSVSKSAIGVK 68
           TGC+KCG+PGHWSRDCP S+         P+ N  S      +       S S  +    
Sbjct: 21  TGCYKCGKPGHWSRDCPFSA---------PNPNPNSNTATTPNPNTPNPSSSSFKSRSAT 71

Query: 69  EKPKKLPRSRPKLTPDLLLSDDGLGFVLRHFPRAFKYRGRGHEVSDLGHLIGLYSEWHSH 128
           EKPKKLPR++PKLTP+LLLSDDGLG+VLR+FPR FKYRGRGHEV DLG+L+ LY+EWHS 
Sbjct: 72  EKPKKLPRTKPKLTPELLLSDDGLGYVLRYFPREFKYRGRGHEVRDLGNLLRLYTEWHSR 131

Query: 129 LLPYYSFDHFVSKVEQVAASRRVKMCIRDLRDRVANGGDPTKLHEAAVEHDGPVDEQAPA 188
           LLPYYSF+ FV KVE+VAA+RRVK C+R+LR+RVA+GGDPTKL E  V HD P DE   +
Sbjct: 132 LLPYYSFNQFVHKVEKVAATRRVKTCLRELRERVASGGDPTKLREPPVVHDIPSDEHGFS 191

Query: 189 EAMSSERQPHQQ-DPASNVHAADDFN-DLFNKVYRTATE 225
            +       HQ+ D  +     +D   D+ N +Y  ATE
Sbjct: 192 VSAEDGGATHQEADLFAEFENVNDIQEDMLNDIYDKATE 230

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297828740|ref|XP_002882252.1| hypothetical protein ARALYDRAFT_896259 [Arabidopsis lyrata subsp. lyrata] gi|297328092|gb|EFH58511.1| hypothetical protein ARALYDRAFT_896259 [Arabidopsis lyrata subsp. lyrata]

 Score =  227 bits (579), Expect = 3e-57,   Method: Compositional matrix adjust.
 Identities = 118/239 (49%), Positives = 158/239 (66%), Gaps = 33/239 (13%)

Query: 5   KAAPTGCFKCGRPGHWSRDCPSSSSSAPS-------------NSNFPSNNTASGGGGGGS 51
           ++APTGCFKCGRPGHWSRDCPSS+  A +             N+ F  ++  SG    G+
Sbjct: 2   ESAPTGCFKCGRPGHWSRDCPSSAPVAGNNSVSSSSGPSQIPNNEFQRSSNKSGNPAAGT 61

Query: 52  GVGDGGVSVSKSAIGVKEKPKKLPRSRPKLTPDLLLSDDGLGFVLRHFPRAFKYRGRGHE 111
            +      V+K+ +            RPKLTP+LLLS+DGLG+VLR+FP++FKYRGRG E
Sbjct: 62  SIA-PVPKVTKTRV-----------QRPKLTPELLLSEDGLGYVLRYFPKSFKYRGRGKE 109

Query: 112 VSDLGHLIGLYSEWHSHLLPYYSFDHFVSKVEQVAASRRVKMCIRDLRDRVANGGDPTKL 171
           VSDLG+LI LYSEWHSHLLPYYSFDHFV KV+QVA+++RVK CI +LR+RVA+G DP KL
Sbjct: 110 VSDLGNLIRLYSEWHSHLLPYYSFDHFVHKVQQVASTKRVKNCINELRERVASGVDPNKL 169

Query: 172 HEAAVEHDGPVDEQAPAEAMSSERQPHQQDPASNVHA---ADDFND-LFNKVYRTATEV 226
           +E   E+ GP D+Q     M    Q  +  P+ +  A   AD F D + N+++ +A+++
Sbjct: 170 YEKPEENTGPYDDQ----DMDQPGQEEENIPSKSADADTNADAFEDSMLNEIFDSASQL 224

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|30678682|ref|NP_186931.2| CCHC-type zinc knuckle protein [Arabidopsis thaliana] gi|26453004|dbj|BAC43578.1| putative CCHC-type zinc finger protein [Arabidopsis thaliana] gi|106879191|gb|ABF82625.1| At3g02820 [Arabidopsis thaliana] gi|332640342|gb|AEE73863.1| CCHC-type zinc knuckle protein [Arabidopsis thaliana]

 Score =  224 bits (570), Expect = 3e-56,   Method: Compositional matrix adjust.
 Identities = 116/234 (49%), Positives = 154/234 (65%), Gaps = 28/234 (11%)

Query: 5   KAAPTGCFKCGRPGHWSRDCPSSSSSAPSNS--------NFPSNNTASGGGGGGSGVGDG 56
           ++APTGCFKCGRPGHWSRDCPSS+  A +NS          P+N         G+ +   
Sbjct: 2   ESAPTGCFKCGRPGHWSRDCPSSAPVAGNNSVSSSSAPSQIPNNEFQRSSSKSGTSIA-P 60

Query: 57  GVSVSKSAIGVKEKPKKLPRSRPKLTPDLLLSDDGLGFVLRHFPRAFKYRGRGHEVSDLG 116
              V+K+ +            RPKLTP+LLLS+DGLG+VLR+FP++FKYRGRG EVSDLG
Sbjct: 61  APKVTKTRV-----------QRPKLTPELLLSEDGLGYVLRYFPKSFKYRGRGKEVSDLG 109

Query: 117 HLIGLYSEWHSHLLPYYSFDHFVSKVEQVAASRRVKMCIRDLRDRVANGGDPTKLHEAAV 176
           +LI LYSEWH+HLLPYYSFDHFV KV+QVA+++RVK CI +LR+RVA+G DP KL+E   
Sbjct: 110 NLIRLYSEWHTHLLPYYSFDHFVHKVQQVASTKRVKNCINELRERVASGVDPNKLYEKQE 169

Query: 177 EHDGPVDEQAPAEAMSSERQPHQQDPASNVHA---ADDFND-LFNKVYRTATEV 226
           E+  P D+Q     M       +  P+ +V A   AD F D + N+++  A+++
Sbjct: 170 ENTVPSDDQ----DMDQPSHDEENIPSKSVDADTNADAFEDSMLNEIFDNASKL 219

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357473945|ref|XP_003607257.1| TIMELESS-interacting protein [Medicago truncatula] gi|355508312|gb|AES89454.1| TIMELESS-interacting protein [Medicago truncatula]

 Score =  223 bits (569), Expect = 4e-56,   Method: Compositional matrix adjust.
 Identities = 122/218 (55%), Positives = 149/218 (68%), Gaps = 10/218 (4%)

Query: 9   TGCFKCGRPGHWSRDCPSSSSSAPSNSNFPSNNTASGGGGGGSGVGDGGVSVSKSAIGVK 68
           TGC+KCGRPGHWSRDCP +S ++ SN N   N T S              S  +SA+   
Sbjct: 8   TGCYKCGRPGHWSRDCPFTSPASNSNLNPNPNATTSTADPPPP-TSTFKPSGPRSAV--- 63

Query: 69  EKPKKLPRSRPKLTPDLLLSDDGLGFVLRHFPRAFKYRGRGHEVSDLGHLIGLYSEWHSH 128
           EKPKK PR+RPKLTP+LLLSDDGLG+VLR+FPR FKY GRGHEV DLG L+ LYS+WHS 
Sbjct: 64  EKPKKPPRTRPKLTPELLLSDDGLGYVLRYFPRNFKYHGRGHEVRDLGKLLHLYSDWHSR 123

Query: 129 LLPYYSFDHFVSKVEQVAASRRVKMCIRDLRDRVANGGDPTKLHEAAVEHDGPVDEQAPA 188
           LLPYYSF+ FV+KVE+VAA+RRVK  +R+LR+RVANGGDP+KL E  V  D P  EQ   
Sbjct: 124 LLPYYSFNQFVNKVEKVAATRRVKTSLRELRERVANGGDPSKLREPPVVDDVPDGEQENG 183

Query: 189 EAMSSERQPHQQ-DPASNVHAADDFNDLFNKVYRTATE 225
           EA   + +   + +  +N+       DLFN +Y  ATE
Sbjct: 184 EASHQDNEMFAEPETVNNIQ-----EDLFNDIYDKATE 216

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|242097166|ref|XP_002439073.1| hypothetical protein SORBIDRAFT_10g031080 [Sorghum bicolor] gi|241917296|gb|EER90440.1| hypothetical protein SORBIDRAFT_10g031080 [Sorghum bicolor]

 Score =  200 bits (508), Expect = 5e-49,   Method: Compositional matrix adjust.
 Identities = 118/247 (47%), Positives = 147/247 (59%), Gaps = 28/247 (11%)

Query: 4   AKAAPTGCFKCGRPGHWSRDCPSSSSSAPSNSNFPSNNTAS---------GGGGGGSGVG 54
           A AAPTGCFKCGRPGHWSRDCPS ++ AP+N   PS   AS              G G  
Sbjct: 2   AAAAPTGCFKCGRPGHWSRDCPSDAA-APTNPGHPSAAAASRFNAKPRPSAAAPEGDGTD 60

Query: 55  DGGVSVSKSAIGVKEKPKKLPRSRPKLTPDLLLSDDGLGFVLRHFPRAFKYRGR-GHEVS 113
            G     +   G K+K ++   +RPKLTPDLLLSD G+GFVLR+ P+AFK R R GHEV 
Sbjct: 61  GGAPPQPQDGKGKKKKKERA--TRPKLTPDLLLSDGGIGFVLRYLPKAFKPRARPGHEVE 118

Query: 114 DLGHLIGLYSEWHSHLLPYYSFDHFVSKVEQVAASRRVKMCIRDLRDRVANGGDPTKLHE 173
           DLG+LI LY++WHS L+PYYSF+ FV KVE++ A  RV+ C+ +LRDRVA GGDPT L+E
Sbjct: 119 DLGNLIKLYADWHSRLIPYYSFEQFVRKVEKLGAGNRVRRCVSELRDRVARGGDPTLLYE 178

Query: 174 AAVEHDGP---VDEQAPAEAMSSERQP----HQQDP----ASNVHAADDFN----DLFNK 218
             V  D P    D  AP + +     P    H  DP    A      +D +    DL N+
Sbjct: 179 PPVHEDMPEGEPDGTAPEDPIFGSEAPLSDNHVSDPVRGDADPPMETNDMDPMEEDLLNE 238

Query: 219 VYRTATE 225
           +Y  A +
Sbjct: 239 IYEKAAD 245

Source: Sorghum bicolor

Species: Sorghum bicolor

Genus: Sorghum

Family: Poaceae

Order: Poales

Class: Liliopsida

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	244
TAIR|locus:2075507	282	AT3G02820 [Arabidopsis thalian	0.569	0.492	0.551	6.8e-49
UNIPROTKB|Q5F416	283	TIPIN "TIMELESS-interacting pr	0.450	0.388	0.322	1.1e-10
UNIPROTKB|H3BU04	294	TIPIN "TIMELESS-interacting pr	0.426	0.353	0.336	1.6e-09
UNIPROTKB|Q9BVW5	301	TIPIN "TIMELESS-interacting pr	0.426	0.345	0.336	1.7e-09
UNIPROTKB|E2RR93	286	TIPIN "Uncharacterized protein	0.426	0.363	0.318	1.8e-09
POMBASE|SPBC30D10.04	181	swi3 "replication fork protect	0.487	0.657	0.320	4.7e-09
UNIPROTKB|F1NK30	283	TIPIN "TIMELESS-interacting pr	0.450	0.388	0.322	1.8e-08
UNIPROTKB|Q3ZCC4	290	TIPIN "TIMELESS-interacting pr	0.413	0.348	0.327	1.9e-08
UNIPROTKB|F1SJJ8	289	TIPIN "Uncharacterized protein	0.483	0.408	0.283	3.2e-08
UNIPROTKB|Q0IHI4	360	tipin "TIMELESS-interacting pr	0.483	0.327	0.286	6.8e-08

TAIR|locus:2075507 AT3G02820 [Arabidopsis thaliana (taxid:3702)]

 Score = 407 (148.3 bits), Expect = 6.8e-49, Sum P(2) = 6.8e-49
 Identities = 81/147 (55%), Positives = 109/147 (74%)

Query:    84 DLLLSDDGLGFVLRHFPRAFKYRGRGHEVSDLGHLIGLYSEWHSHLLPYYSFDHFVSKVE 143
             +LLLS+DGLG+VLR+FP++FKYRGRG EVSDLG+LI LYSEWH+HLLPYYSFDHFV KV+
Sbjct:    77 ELLLSEDGLGYVLRYFPKSFKYRGRGKEVSDLGNLIRLYSEWHTHLLPYYSFDHFVHKVQ 136

Query:   144 QVAASRRVKMCIRDLRDRVANGGDPTKLHEAAVEHDGPVDEQAPAEAMSSERQPHQQDPA 203
             QVA+++RVK CI +LR+RVA+G DP KL+E   E+  P D+Q     M       +  P+
Sbjct:   137 QVASTKRVKNCINELRERVASGVDPNKLYEKQEENTVPSDDQD----MDQPSHDEENIPS 192

Query:   204 SNVHA---ADDFND-LFNKVYRTATEV 226
              +V A   AD F D + N+++  A+++
Sbjct:   193 KSVDADTNADAFEDSMLNEIFDNASKL 219

GO:0003676 "nucleic acid binding" evidence=IEA;ISS

GO:0005634 "nucleus" evidence=ISM;IEA

GO:0006974 "response to DNA damage stimulus" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0048478 "replication fork protection" evidence=IEA

GO:0006261 "DNA-dependent DNA replication" evidence=RCA

GO:0006270 "DNA replication initiation" evidence=RCA

GO:0006275 "regulation of DNA replication" evidence=RCA

GO:0010228 "vegetative to reproductive phase transition of meristem" evidence=RCA

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

UNIPROTKB|Q5F416 TIPIN "TIMELESS-interacting protein" [Gallus gallus (taxid:9031)]

 Score = 133 (51.9 bits), Expect = 1.1e-10, Sum P(2) = 1.1e-10
 Identities = 41/127 (32%), Positives = 59/127 (46%)

Query:    86 LLSDDGLGFVLRHFPRAFKYRGRGHEVSDLGHLIGLYSEWHSHLLPYYSFDHFVSKVEQV 145
             L+S+ GL   LRH     K++G+GHE  DL  L+     W   L P   FD F+ +VE +
Sbjct:    79 LVSERGLP-ALRHMFDNVKFKGKGHEAEDLKTLLRHMEHWAHRLFPKLQFDDFIDRVESL 137

Query:   146 AASRRVKMCIRDLR--------DRVAN---GGDPTKLHEAAVE-HD--GPVDE--QAPAE 189
                + V+ C++ +R        D  AN   GG+   L  A  E H   G V E    P  
Sbjct:   138 GNKKEVQTCLKRIRLDLPILHEDFTANEGGGGESNGLDMATEEVHSFSGNVGELDSLPGT 197

Query:   190 AMSSERQ 196
              ++ E+Q
Sbjct:   198 TLTEEQQ 204

GO:0048478 "replication fork protection" evidence=IEA

GO:0007067 "mitosis" evidence=IEA

GO:0051301 "cell division" evidence=IEA

GO:0000076 "DNA replication checkpoint" evidence=ISS

GO:0000790 "nuclear chromatin" evidence=ISS

GO:0005634 "nucleus" evidence=ISS

GO:0031573 "intra-S DNA damage checkpoint" evidence=ISS

GO:0005737 "cytoplasm" evidence=IEA

GO:0008284 "positive regulation of cell proliferation" evidence=ISS

GO:0033261 "regulation of S phase" evidence=ISS

UNIPROTKB|H3BU04 TIPIN "TIMELESS-interacting protein" [Homo sapiens (taxid:9606)]

 Score = 143 (55.4 bits), Expect = 1.6e-09, P = 1.6e-09
 Identities = 38/113 (33%), Positives = 58/113 (51%)

Query:    86 LLSDDGLGFVLRH-FPRAFKYRGRGHEVSDLGHLIGLYSEWHSHLLPYYSFDHFVSKVEQ 144
             L+S+ GL   LRH F +A K++G+GHE  DL  LI     W   L P   F+ F+ +VE 
Sbjct:    72 LISERGLP-ALRHVFDKA-KFKGKGHEAEDLKMLIRHMEHWAHRLFPKLQFEDFIDRVEY 129

Query:   145 VAASRRVKMCIRDLRDRVANGGDPTKLHEAAVEHDGPVDEQAPAEAMSSERQP 197
             + + + V+ C++ +R       D   LHE  V ++  V E    +  S+E  P
Sbjct:   130 LGSKKEVQTCLKRIRL------DLPILHEDFVSNNDEVAENNEHDVTSTELDP 176

GO:0005634 "nucleus" evidence=IEA

GO:0048478 "replication fork protection" evidence=IEA

GO:0000077 "DNA damage checkpoint" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0009411 "response to UV" evidence=IEA

UNIPROTKB|Q9BVW5 TIPIN "TIMELESS-interacting protein" [Homo sapiens (taxid:9606)]

 Score = 143 (55.4 bits), Expect = 1.7e-09, P = 1.7e-09
 Identities = 38/113 (33%), Positives = 58/113 (51%)

Query:    86 LLSDDGLGFVLRH-FPRAFKYRGRGHEVSDLGHLIGLYSEWHSHLLPYYSFDHFVSKVEQ 144
             L+S+ GL   LRH F +A K++G+GHE  DL  LI     W   L P   F+ F+ +VE 
Sbjct:    72 LISERGLP-ALRHVFDKA-KFKGKGHEAEDLKMLIRHMEHWAHRLFPKLQFEDFIDRVEY 129

Query:   145 VAASRRVKMCIRDLRDRVANGGDPTKLHEAAVEHDGPVDEQAPAEAMSSERQP 197
             + + + V+ C++ +R       D   LHE  V ++  V E    +  S+E  P
Sbjct:   130 LGSKKEVQTCLKRIRL------DLPILHEDFVSNNDEVAENNEHDVTSTELDP 176

GO:0048478 "replication fork protection" evidence=IEA

GO:0007067 "mitosis" evidence=IEA

GO:0051301 "cell division" evidence=IEA

GO:0009411 "response to UV" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0000076 "DNA replication checkpoint" evidence=IMP

GO:0000790 "nuclear chromatin" evidence=IDA

GO:0008284 "positive regulation of cell proliferation" evidence=IMP

GO:0031573 "intra-S DNA damage checkpoint" evidence=IMP

GO:0033261 "regulation of S phase" evidence=IMP

GO:0005634 "nucleus" evidence=IDA

GO:0033262 "regulation of DNA replication involved in S phase" evidence=TAS

GO:0005730 "nucleolus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

GO:0005794 "Golgi apparatus" evidence=IDA

GO:0043231 "intracellular membrane-bounded organelle" evidence=IDA

UNIPROTKB|E2RR93 TIPIN "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 142 (55.0 bits), Expect = 1.8e-09, P = 1.8e-09
 Identities = 36/113 (31%), Positives = 57/113 (50%)

Query:    86 LLSDDGLGFVLRH-FPRAFKYRGRGHEVSDLGHLIGLYSEWHSHLLPYYSFDHFVSKVEQ 144
             L+S+ GL   LRH F  A K++G+GHE  DL  LI     W   L P   F+ F+ +VE 
Sbjct:    72 LISERGLP-ALRHVFDNA-KFKGKGHEAEDLKTLIRHMEHWAHRLFPKLQFEDFIDRVEY 129

Query:   145 VAASRRVKMCIRDLRDRVANGGDPTKLHEAAVEHDGPVDEQAPAEAMSSERQP 197
             + + + V+ C++ +R       D   +HE  + +DG   E    +  ++E  P
Sbjct:   130 LGSKKEVQTCLKRIRL------DLPIIHEDFISNDGEAGENHGYDKTATELDP 176

GO:0033261 "regulation of S phase" evidence=IEA

GO:0031573 "intra-S DNA damage checkpoint" evidence=IEA

GO:0009411 "response to UV" evidence=IEA

GO:0008284 "positive regulation of cell proliferation" evidence=IEA

GO:0005794 "Golgi apparatus" evidence=IEA

GO:0000790 "nuclear chromatin" evidence=IEA

GO:0000076 "DNA replication checkpoint" evidence=IEA

GO:0048478 "replication fork protection" evidence=IEA

POMBASE|SPBC30D10.04 swi3 "replication fork protection complex subunit Swi3" [Schizosaccharomyces pombe (taxid:4896)]

 Score = 134 (52.2 bits), Expect = 4.7e-09, P = 4.7e-09
 Identities = 42/131 (32%), Positives = 64/131 (48%)

Query:    86 LLSDDGLGFVLRHFPRAFKYRGRGHEVSDLGHLIGLYSEWHSHLLPYYSFDHFVSKVEQV 145
             L+S++G+   LR   R  K +G+GHE  DL  L+G+Y  W   L P  +FD  +S ++ +
Sbjct:    57 LISENGIP-KLRKMMRKVKLKGKGHEAKDLKQLLGMYHIWTHELYPRATFDDSISYLKTL 115

Query:   146 AASRRVKMCIRDLRDRVA--NGGDPTKLHEAAVEHDGPVDEQAPAEAMSSERQPHQQDPA 203
                R VK+  R   + +A  NG D      A++   GP    +     S +  P+ QD A
Sbjct:   116 GKHRSVKVRRRGWINEIAVENGSDSN----ASL-FTGP-SSNSLVNLTSGD--PYVQDTA 167

Query:   204 SNVHAADDFND 214
              +   A D ND
Sbjct:   168 DDAFVAQD-ND 177

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IDA

GO:0005739 "mitochondrion" evidence=IDA

GO:0006974 "response to DNA damage stimulus" evidence=IEA

GO:0031298 "replication fork protection complex" evidence=TAS

GO:0043111 "replication fork arrest" evidence=IC

GO:0043596 "nuclear replication fork" evidence=IC

GO:0048478 "replication fork protection" evidence=IDA

GO:0071515 "genetic imprinting at mating-type locus" evidence=IMP

UNIPROTKB|F1NK30 TIPIN "TIMELESS-interacting protein" [Gallus gallus (taxid:9031)]

 Score = 133 (51.9 bits), Expect = 1.8e-08, P = 1.8e-08
 Identities = 41/127 (32%), Positives = 59/127 (46%)

Query:    86 LLSDDGLGFVLRHFPRAFKYRGRGHEVSDLGHLIGLYSEWHSHLLPYYSFDHFVSKVEQV 145
             L+S+ GL   LRH     K++G+GHE  DL  L+     W   L P   FD F+ +VE +
Sbjct:    79 LVSERGLP-ALRHMFDNVKFKGKGHEAEDLKTLLRHMEHWAHRLFPKLQFDDFIDRVESL 137

Query:   146 AASRRVKMCIRDLR--------DRVAN---GGDPTKLHEAAVE-HD--GPVDE--QAPAE 189
                + V+ C++ +R        D  AN   GG+   L  A  E H   G V E    P  
Sbjct:   138 GNKKEVQTCLKRIRLDLPILHEDFTANEGGGGESNGLDMATEEVHSFSGNVGELDSLPGT 197

Query:   190 AMSSERQ 196
              ++ E+Q
Sbjct:   198 TLTEEQQ 204

GO:0048478 "replication fork protection" evidence=IEA

GO:0000076 "DNA replication checkpoint" evidence=IEA

GO:0000790 "nuclear chromatin" evidence=IEA

GO:0005794 "Golgi apparatus" evidence=IEA

GO:0008284 "positive regulation of cell proliferation" evidence=IEA

GO:0009411 "response to UV" evidence=IEA

GO:0031573 "intra-S DNA damage checkpoint" evidence=IEA

GO:0033261 "regulation of S phase" evidence=IEA

UNIPROTKB|Q3ZCC4 TIPIN "TIMELESS-interacting protein" [Bos taurus (taxid:9913)]

 Score = 133 (51.9 bits), Expect = 1.9e-08, P = 1.9e-08
 Identities = 36/110 (32%), Positives = 57/110 (51%)

Query:    86 LLSDDGLGFVLRH-FPRAFKYRGRGHEVSDLGHLIGLYSEWHSHLLPYYSFDHFVSKVEQ 144
             L+S+ GL   LRH F +A K++G+GHE  DL  LI     W   L P   F+ F+ +VE 
Sbjct:    72 LISERGLP-ALRHVFEKA-KFKGKGHEAEDLKTLIRHMEHWAHRLFPKLQFEDFIDRVEC 129

Query:   145 VAASRRVKMCIRDLRDRVANGGDPTKLHEAAVEHDGPVDEQAPAEAMSSE 194
             +   + V+ C++ +R       D   LHE  V ++  V+E    +  ++E
Sbjct:   130 LGNKKEVQTCLKRIRL------DLPILHEDFVSNNDEVEENNGHDVTATE 173

GO:0008284 "positive regulation of cell proliferation" evidence=ISS

GO:0000790 "nuclear chromatin" evidence=ISS

GO:0000076 "DNA replication checkpoint" evidence=ISS

GO:0005634 "nucleus" evidence=ISS

GO:0033261 "regulation of S phase" evidence=ISS

GO:0031573 "intra-S DNA damage checkpoint" evidence=ISS

GO:0009411 "response to UV" evidence=IEA

GO:0005794 "Golgi apparatus" evidence=IEA

GO:0051301 "cell division" evidence=IEA

GO:0007067 "mitosis" evidence=IEA

GO:0048478 "replication fork protection" evidence=IEA

UNIPROTKB|F1SJJ8 TIPIN "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 131 (51.2 bits), Expect = 3.2e-08, P = 3.2e-08
 Identities = 36/127 (28%), Positives = 61/127 (48%)

Query:    86 LLSDDGLGFVLRH-FPRAFKYRGRGHEVSDLGHLIGLYSEWHSHLLPYYSFDHFVSKVEQ 144
             L+S+ GL   LRH F +A K++G+GHE  DL  LI     W   L P   F+ F+ +VE 
Sbjct:    71 LISERGLP-ALRHVFDKA-KFKGKGHEAEDLKMLIRHMEHWAHRLFPKLQFEDFIDRVEY 128

Query:   145 VAASRRVKMCIRDLRDRVANGGDPTKLHEAAVEHDGPVDEQAPAEAMSSERQPHQQDPAS 204
             +   + V+ C++ +R       D   LH+  + ++  V E    +   +E  P   + + 
Sbjct:   129 LGNKKEVQTCLKRIRL------DLPILHDDFISNNDDVGEDNGHDVTVTELDPFLTNSSE 182

Query:   205 NVHAADD 211
             +   A +
Sbjct:   183 SAKFASE 189

GO:0033261 "regulation of S phase" evidence=IEA

GO:0031573 "intra-S DNA damage checkpoint" evidence=IEA

GO:0009411 "response to UV" evidence=IEA

GO:0008284 "positive regulation of cell proliferation" evidence=IEA

GO:0005794 "Golgi apparatus" evidence=IEA

GO:0000790 "nuclear chromatin" evidence=IEA

GO:0000076 "DNA replication checkpoint" evidence=IEA

GO:0048478 "replication fork protection" evidence=IEA

UNIPROTKB|Q0IHI4 tipin "TIMELESS-interacting protein" [Xenopus laevis (taxid:8355)]

 Score = 130 (50.8 bits), Expect = 6.8e-08, P = 6.8e-08
 Identities = 35/122 (28%), Positives = 56/122 (45%)

Query:    86 LLSDDGLGFVLRHFPRAFKYRGRGHEVSDLGHLIGLYSEWHSHLLPYYSFDHFVSKVEQV 145
             L S  GL   LRH     K++G+GHE  DL  L+     W   L P   F+ F++++E +
Sbjct:    79 LASQRGLP-ALRHMFDDVKFKGKGHETEDLKILLRQMENWAHRLFPKLQFEDFLNRLESM 137

Query:   146 AASRRVKMCIRDLRDRVANGGDPTKLHEAAVE-HDGPVDEQAPAEAMSSERQPHQQDPAS 204
                + V+ C++ +R  +    D     E  V+  D  +D   P+E  S   + H   P+ 
Sbjct:   138 GNKKEVQTCLKKIRMDLPIVHDDFLSEEVVVQTEDHAID--MPSEDFSFPDELHVPSPSQ 195

Query:   205 NV 206
              V
Sbjct:   196 PV 197

GO:0000076 "DNA replication checkpoint" evidence=ISS

GO:0000790 "nuclear chromatin" evidence=ISS

GO:0005634 "nucleus" evidence=ISS

GO:0008284 "positive regulation of cell proliferation" evidence=ISS

GO:0031573 "intra-S DNA damage checkpoint" evidence=ISS

GO:0033261 "regulation of S phase" evidence=ISS

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

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!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

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	244
pfam07962	84	pfam07962, Swi3, Replication Fork Protection Compo	6e-28
pfam00098	18	pfam00098, zf-CCHC, Zinc knuckle	2e-06
smart00343	17	smart00343, ZnF_C2HC, zinc finger	7e-06
PTZ00368	148	PTZ00368, PTZ00368, universal minicircle sequence	0.001
PTZ00368	148	PTZ00368, PTZ00368, universal minicircle sequence	0.002
PTZ00368	148	PTZ00368, PTZ00368, universal minicircle sequence	0.003

>gnl|CDD|219667 pfam07962, Swi3, Replication Fork Protection Component Swi3

 Score =  101 bits (254), Expect = 6e-28
 Identities = 29/82 (35%), Positives = 46/82 (56%), Gaps = 1/82 (1%)

Query: 80  KLTPDLLLSDDGLGFVLRHFPRAFKYRGRGHEVSDLGHLIGLYSEWHSHLLPYYSFDHFV 139
           KL  + LLS  G+  + + F + FK++G+GHE SDL  L+  Y  W   L P   F  F+
Sbjct: 1   KLDEERLLSPKGIPALRKTF-KDFKFKGKGHEYSDLARLLQFYQLWAHDLFPKAKFKDFL 59

Query: 140 SKVEQVAASRRVKMCIRDLRDR 161
           + VE++   ++V+   R+LR  
Sbjct: 60  NLVEKLGHKKQVQTYRRELRLE 81

Replication fork pausing is required to initiate a recombination events. More specifically, Swi1 is required for recombination near the mat1 locus. Swi3 has been found to co-purify with Swi1 Swi3, together with Swi1, define a fork protection complex that coordinates leading- and lagging-strand synthesis and stabilises stalled replication forks. The Swi1-Swi3 complex is required for accurate replication, fork protection and replication checkpoint signalling. Length = 84

>gnl|CDD|189387 pfam00098, zf-CCHC, Zinc knuckle

 Score = 42.4 bits (101), Expect = 2e-06
 Identities = 9/17 (52%), Positives = 12/17 (70%)

Query: 10 GCFKCGRPGHWSRDCPS 26
           C+ CG+ GH +RDCP 
Sbjct: 2  KCYNCGKEGHLARDCPE 18

The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. The motifs are mostly from retroviral gag proteins (nucleocapsid). Prototype structure is from HIV. Also contains members involved in eukaryotic gene regulation, such as C. elegans GLH-1. Structure is an 18-residue zinc finger. Length = 18

>gnl|CDD|197667 smart00343, ZnF_C2HC, zinc finger

 Score = 41.3 bits (98), Expect = 7e-06
 Identities = 10/17 (58%), Positives = 13/17 (76%)

Query: 10 GCFKCGRPGHWSRDCPS 26
           C+ CG+ GH +RDCPS
Sbjct: 1  KCYNCGKEGHIARDCPS 17

Length = 17

>gnl|CDD|173561 PTZ00368, PTZ00368, universal minicircle sequence binding protein (UMSBP); Provisional

 Score = 37.9 bits (88), Expect = 0.001
 Identities = 16/27 (59%), Positives = 19/27 (70%), Gaps = 2/27 (7%)

Query: 1  MENAKAAPTGCFKCGRPGHWSRDCPSS 27
             AKA P  C+KCG PGH SR+CPS+
Sbjct: 22 AGAAKARP--CYKCGEPGHLSRECPSA 46

Length = 148

>gnl|CDD|173561 PTZ00368, PTZ00368, universal minicircle sequence binding protein (UMSBP); Provisional

 Score = 37.1 bits (86), Expect = 0.002
 Identities = 10/22 (45%), Positives = 12/22 (54%)

Query: 6   AAPTGCFKCGRPGHWSRDCPSS 27
                C+ CG+ GH SRDCP  
Sbjct: 127 GGDKTCYNCGQTGHLSRDCPDK 148

Length = 148

>gnl|CDD|173561 PTZ00368, PTZ00368, universal minicircle sequence binding protein (UMSBP); Provisional

 Score = 36.7 bits (85), Expect = 0.003
 Identities = 9/17 (52%), Positives = 13/17 (76%)

Query: 11 CFKCGRPGHWSRDCPSS 27
          C+ CG+ GH SR+CP +
Sbjct: 55 CYNCGKTGHLSRECPEA 71

Length = 148

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	244
PF07962	83	Swi3: Replication Fork Protection Component Swi3;	100.0
KOG3004	305	consensus Meiotic chromosome segregation protein [	99.96
PF00098	18	zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc fi	98.49
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	98.08
PF13696	32	zf-CCHC_2: Zinc knuckle	97.49
PF13917	42	zf-CCHC_3: Zinc knuckle	97.43
smart00343	26	ZnF_C2HC zinc finger.	97.12
PF14787	36	zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB:	97.09
COG5082	190	AIR1 Arginine methyltransferase-interacting protei	95.69
COG5082	190	AIR1 Arginine methyltransferase-interacting protei	95.59
PTZ00368	148	universal minicircle sequence binding protein (UMS	95.15
KOG4400	261	consensus E3 ubiquitin ligase interacting with arg	95.12
PF14392	49	zf-CCHC_4: Zinc knuckle	94.97
COG5222	427	Uncharacterized conserved protein, contains RING Z	94.93
PTZ00368	148	universal minicircle sequence binding protein (UMS	94.54
KOG4400	261	consensus E3 ubiquitin ligase interacting with arg	92.16
PF15288	40	zf-CCHC_6: Zinc knuckle	89.0
KOG0314	448	consensus Predicted E3 ubiquitin ligase [Posttrans	81.59

>PF07962 Swi3: Replication Fork Protection Component Swi3; InterPro: IPR012923 Replication fork pausing is required to initiate recombination events

Probab=100.00  E-value=1.8e-35  Score=226.73  Aligned_cols=81  Identities=38%  Similarity=0.800  Sum_probs=79.7

Q ss_pred             CcCcccccCCCChHHHHHhccccccccCCCchHHHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHhhcchHHHHHHHHHH
Q 035848           80 KLTPDLLLSDDGLGFVLRHFPRAFKYRGRGHEVSDLGHLIGLYSEWHSHLLPYYSFDHFVSKVEQVAASRRVKMCIRDLR  159 (244)
Q Consensus        80 KLd~eRLls~kGLp~Llr~fpk~~KfKGKGHE~~DL~~LL~~YQ~WaH~LfPK~~F~Dfi~rVEkLG~kk~Vk~~lrelR  159 (244)
                      |||++||+|++|||+|+++| ++++|+|||||++||.+||++||+|||+||||++|+|||++||+||++++||+||++||
T Consensus         1 KLd~~rL~~~~Glp~l~~~~-k~~k~kgkghE~~dL~~ll~~Yq~W~h~LfPk~~F~d~i~~vE~LG~~k~v~~~~~~lr   79 (83)
T PF07962_consen    1 KLDEERLLSPKGLPYLRKNF-KKFKFKGKGHEYEDLRRLLQFYQLWAHRLFPKASFEDFIERVEKLGKKKRVRNYRRELR   79 (83)
T ss_pred             CCCHHHccCCCCHHHHHHHH-HHcCcCCCCCHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            89999999999999999999 99999999999999999999999999999999999999999999999999999999999


Q ss_pred             HH
Q 035848          160 DR  161 (244)
Q Consensus       160 ~~  161 (244)
                      ++
T Consensus        80 ~~   81 (83)
T PF07962_consen   80 EE   81 (83)
T ss_pred             hh
Confidence            85

More specifically, Swi1 is required for recombination near the mat1 locus. Swi3 has been found to co-purify with Swi1. Together they define a fork protection complex that coordinates leading- and lagging-strand synthesis and stabilises stalled replication forks []. This complex is required for accurate replication, fork protection and replication checkpoint signalling [, ].; GO: 0006974 response to DNA damage stimulus, 0007049 cell cycle, 0048478 replication fork protection, 0005634 nucleus

>KOG3004 consensus Meiotic chromosome segregation protein [Cell cycle control, cell division, chromosome partitioning]

Probab=99.96  E-value=5.4e-30  Score=235.05  Aligned_cols=99  Identities=29%  Similarity=0.549  Sum_probs=93.6

Q ss_pred             ccCcCCCCccCCCCCCCcCcccccCCCChHHHHHhccccccccCCCchHHHHHHHHHHHHHHHhccCCCCCHHHHHHHHH
Q 035848           64 AIGVKEKPKKLPRSRPKLTPDLLLSDDGLGFVLRHFPRAFKYRGRGHEVSDLGHLIGLYSEWHSHLLPYYSFDHFVSKVE  143 (244)
Q Consensus        64 ~~~~~~kkkk~Rr~rpKLd~eRLls~kGLp~Llr~fpk~~KfKGKGHE~~DL~~LL~~YQ~WaH~LfPK~~F~Dfi~rVE  143 (244)
                      +...+++|+.+|++++||++++|+|++|||+ +|++++++||+|||||+.||..||++||+|+|+||||++|+|||.+||
T Consensus        48 ~k~l~~rKR~~~~~~~~lsa~~L~s~~Gip~-lR~~~k~~k~kgKg~e~~dL~~llr~y~~WgH~lfPk~kf~D~i~~~e  126 (305)
T KOG3004|consen   48 PKDLRGRKRAVRVKSPKLSAETLISEKGIPA-LRDCFKKAKFKGKGHEYIDLKELLRSYQHWGHELFPKAKFDDFINRVE  126 (305)
T ss_pred             ccccccccccccccccccchhhhcCccCchH-HHHHHhhcCcCCCCCcccCHHHHHHHHHHHHHhhcccchhHHHHHHHH
Confidence            6667888999999999999999999999999 666679999999999999999999999999999999999999999999


Q ss_pred             HhhcchHHHHHHHHHHHHhh
Q 035848          144 QVAASRRVKMCIRDLRDRVA  163 (244)
Q Consensus       144 kLG~kk~Vk~~lrelR~~~~  163 (244)
                      +||+++.||++|..||++++
T Consensus       127 tLGk~r~vkv~~~r~rLg~~  146 (305)
T KOG3004|consen  127 TLGKKREVKVDLLRYRLGYF  146 (305)
T ss_pred             hhccccchhhhhhHHHhccC
Confidence            99999999999999999774

>PF00098 zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=98.49  E-value=5.3e-08  Score=56.06  Aligned_cols=17  Identities=65%  Similarity=1.660  Sum_probs=16.0

Q ss_pred             cccccCCCCccCCCCCC
Q 035848           10 GCFKCGRPGHWSRDCPS   26 (244)
Q Consensus        10 ~Cy~CG~~GHwardCp~   26 (244)
                      .||+||+.||+|+|||.
T Consensus         2 ~C~~C~~~GH~~~~Cp~   18 (18)
T PF00098_consen    2 KCFNCGEPGHIARDCPK   18 (18)
T ss_dssp             BCTTTSCSSSCGCTSSS
T ss_pred             cCcCCCCcCcccccCcc
Confidence            69999999999999984

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the CysCysHisCys (CCHC) type zinc finger domains, and have the sequence: C-X2-C-X4-H-X4-C where X can be any amino acid, and number indicates the number of residues. These 18 residues CCHC zinc finger domains are mainly found in the nucleocapsid protein of retroviruses. It is required for viral genome packaging and for early infection process [, , ]. It is also found in eukaryotic proteins involved in RNA binding or single-stranded DNA binding []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding; PDB: 2L44_A 1A1T_A 1WWG_A 1U6P_A 1WWD_A 1WWE_A 1A6B_B 1F6U_A 1MFS_A 1NCP_C ....

>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]

Probab=98.08  E-value=1.3e-06  Score=81.87  Aligned_cols=28  Identities=36%  Similarity=1.196  Sum_probs=25.9

Q ss_pred             CCCCCCCcccccCCCCccCCCCCCCCCC
Q 035848            3 NAKAAPTGCFKCGRPGHWSRDCPSSSSS   30 (244)
Q Consensus         3 p~~~~~~~Cy~CG~~GHwardCp~~~~~   30 (244)
                      |+|+.+.+||+|||.||||.+||.+..+
T Consensus       155 pgmgDq~~cyrcGkeghwskEcP~~~~~  182 (346)
T KOG0109|consen  155 PGMGDQSGCYRCGKEGHWSKECPVDRTG  182 (346)
T ss_pred             CCCCCHHHheeccccccccccCCccCCC
Confidence            8999999999999999999999997653

>PF13696 zf-CCHC_2: Zinc knuckle

Probab=97.49  E-value=3.6e-05  Score=50.58  Aligned_cols=21  Identities=43%  Similarity=1.257  Sum_probs=18.4

Q ss_pred             CCCcccccCCCCccCCCCCCC
Q 035848            7 APTGCFKCGRPGHWSRDCPSS   27 (244)
Q Consensus         7 ~~~~Cy~CG~~GHwardCp~~   27 (244)
                      ..-.|+.|++.|||.+|||..
T Consensus         7 ~~Y~C~~C~~~GH~i~dCP~~   27 (32)
T PF13696_consen    7 PGYVCHRCGQKGHWIQDCPTN   27 (32)
T ss_pred             CCCEeecCCCCCccHhHCCCC
Confidence            445799999999999999974

>PF13917 zf-CCHC_3: Zinc knuckle

Probab=97.43  E-value=9.4e-05  Score=51.13  Aligned_cols=20  Identities=50%  Similarity=1.345  Sum_probs=18.0

Q ss_pred             CCCcccccCCCCccCCCCCC
Q 035848            7 APTGCFKCGRPGHWSRDCPS   26 (244)
Q Consensus         7 ~~~~Cy~CG~~GHwardCp~   26 (244)
                      ....|.+||+.|||+.+|+.
T Consensus         3 ~~~~CqkC~~~GH~tyeC~~   22 (42)
T PF13917_consen    3 ARVRCQKCGQKGHWTYECPN   22 (42)
T ss_pred             CCCcCcccCCCCcchhhCCC
Confidence            45789999999999999995

>smart00343 ZnF_C2HC zinc finger

Probab=97.12  E-value=0.00018  Score=43.78  Aligned_cols=18  Identities=50%  Similarity=1.437  Sum_probs=16.1

Q ss_pred             cccccCCCCccCCCCCCC
Q 035848           10 GCFKCGRPGHWSRDCPSS   27 (244)
Q Consensus        10 ~Cy~CG~~GHwardCp~~   27 (244)
                      .||+||+.||++++||..
T Consensus         1 ~C~~CG~~GH~~~~C~~~   18 (26)
T smart00343        1 KCYNCGKEGHIARDCPKX   18 (26)
T ss_pred             CCccCCCCCcchhhCCcc
Confidence            499999999999999843

>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A

Probab=97.09  E-value=0.00023  Score=48.02  Aligned_cols=22  Identities=36%  Similarity=0.987  Sum_probs=13.2

Q ss_pred             CCcccccCCCCccCCCCCCCCC
Q 035848            8 PTGCFKCGRPGHWSRDCPSSSS   29 (244)
Q Consensus         8 ~~~Cy~CG~~GHwardCp~~~~   29 (244)
                      +..|.+|||-.|||+||-.-..
T Consensus         2 ~~~CprC~kg~Hwa~~C~sk~d   23 (36)
T PF14787_consen    2 PGLCPRCGKGFHWASECRSKTD   23 (36)
T ss_dssp             --C-TTTSSSCS-TTT---TCC
T ss_pred             CccCcccCCCcchhhhhhhhhc
Confidence            5789999999999999976543

>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]

Probab=95.69  E-value=0.0043  Score=55.09  Aligned_cols=19  Identities=58%  Similarity=1.400  Sum_probs=16.5

Q ss_pred             CcccccCCCCccCCCC-CCC
Q 035848            9 TGCFKCGRPGHWSRDC-PSS   27 (244)
Q Consensus         9 ~~Cy~CG~~GHwardC-p~~   27 (244)
                      ..||+||+.||++||| |+.
T Consensus        98 ~~C~~Cg~~GH~~~dC~P~~  117 (190)
T COG5082          98 KKCYNCGETGHLSRDCNPSK  117 (190)
T ss_pred             cccccccccCccccccCccc
Confidence            6799999999999999 553

>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]

Probab=95.59  E-value=0.0055  Score=54.40  Aligned_cols=21  Identities=48%  Similarity=1.217  Sum_probs=19.0

Q ss_pred             CCCCCcccccCCCCccCCCCC
Q 035848            5 KAAPTGCFKCGRPGHWSRDCP   25 (244)
Q Consensus         5 ~~~~~~Cy~CG~~GHwardCp   25 (244)
                      +.+...||+||+-||.+||||
T Consensus        57 ~~~~~~C~nCg~~GH~~~DCP   77 (190)
T COG5082          57 REENPVCFNCGQNGHLRRDCP   77 (190)
T ss_pred             cccccccchhcccCcccccCC
Confidence            456778999999999999999

>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional

Probab=95.15  E-value=0.014  Score=48.06  Aligned_cols=20  Identities=60%  Similarity=1.469  Sum_probs=13.7

Q ss_pred             CCcccccCCCCccCCCCCCC
Q 035848            8 PTGCFKCGRPGHWSRDCPSS   27 (244)
Q Consensus         8 ~~~Cy~CG~~GHwardCp~~   27 (244)
                      ...||+||+.||+|++||..
T Consensus        27 ~~~C~~Cg~~GH~~~~Cp~~   46 (148)
T PTZ00368         27 ARPCYKCGEPGHLSRECPSA   46 (148)
T ss_pred             CccCccCCCCCcCcccCcCC
Confidence            45677777777777777654

>KOG4400 consensus E3 ubiquitin ligase interacting with arginine methyltransferase [Posttranslational modification, protein turnover, chaperones]

Probab=95.12  E-value=0.0087  Score=53.68  Aligned_cols=19  Identities=47%  Similarity=1.263  Sum_probs=17.2

Q ss_pred             CcccccCCCCccCCCCCCC
Q 035848            9 TGCFKCGRPGHWSRDCPSS   27 (244)
Q Consensus         9 ~~Cy~CG~~GHwardCp~~   27 (244)
                      ..||+||+.|||+++||.+
T Consensus       144 ~~Cy~Cg~~GH~s~~C~~~  162 (261)
T KOG4400|consen  144 AKCYSCGEQGHISDDCPEN  162 (261)
T ss_pred             CccCCCCcCCcchhhCCCC
Confidence            5699999999999999965

>PF14392 zf-CCHC_4: Zinc knuckle

Probab=94.97  E-value=0.0079  Score=41.83  Aligned_cols=20  Identities=50%  Similarity=1.243  Sum_probs=17.5

Q ss_pred             CCCcccccCCCCccCCCCCC
Q 035848            7 APTGCFKCGRPGHWSRDCPS   26 (244)
Q Consensus         7 ~~~~Cy~CG~~GHwardCp~   26 (244)
                      -+.-|++||.-||..++||.
T Consensus        30 lp~~C~~C~~~gH~~~~C~k   49 (49)
T PF14392_consen   30 LPRFCFHCGRIGHSDKECPK   49 (49)
T ss_pred             cChhhcCCCCcCcCHhHcCC
Confidence            35679999999999999983

>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]

Probab=94.93  E-value=0.012  Score=56.34  Aligned_cols=23  Identities=35%  Similarity=1.198  Sum_probs=19.6

Q ss_pred             CCcccccCCCCccCCCCCCCCCC
Q 035848            8 PTGCFKCGRPGHWSRDCPSSSSS   30 (244)
Q Consensus         8 ~~~Cy~CG~~GHwardCp~~~~~   30 (244)
                      .-.||+||+.|||-..||-++..
T Consensus       176 gY~CyRCGqkgHwIqnCpTN~Dp  198 (427)
T COG5222         176 GYVCYRCGQKGHWIQNCPTNQDP  198 (427)
T ss_pred             ceeEEecCCCCchhhcCCCCCCC
Confidence            35799999999999999987643

>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional

Probab=94.54  E-value=0.018  Score=47.49  Aligned_cols=19  Identities=53%  Similarity=1.268  Sum_probs=17.3

Q ss_pred             CcccccCCCCccCCCCCCC
Q 035848            9 TGCFKCGRPGHWSRDCPSS   27 (244)
Q Consensus         9 ~~Cy~CG~~GHwardCp~~   27 (244)
                      +.||+||+.||+|++||..
T Consensus         1 ~~C~~C~~~GH~~~~c~~~   19 (148)
T PTZ00368          1 MVCYRCGGVGHQSRECPNS   19 (148)
T ss_pred             CcCCCCCCCCcCcccCcCC
Confidence            4799999999999999974

>KOG4400 consensus E3 ubiquitin ligase interacting with arginine methyltransferase [Posttranslational modification, protein turnover, chaperones]

Probab=92.16  E-value=0.08  Score=47.54  Aligned_cols=24  Identities=54%  Similarity=1.111  Sum_probs=21.4

Q ss_pred             CCCcccccCCCCccCCCCCCCCCC
Q 035848            7 APTGCFKCGRPGHWSRDCPSSSSS   30 (244)
Q Consensus         7 ~~~~Cy~CG~~GHwardCp~~~~~   30 (244)
                      ....||.||+.||+++|||..+..
T Consensus       163 ~~~~c~~c~~~~h~~~~C~~~~~~  186 (261)
T KOG4400|consen  163 KGGTCFRCGKVGHGSRDCPSKQKS  186 (261)
T ss_pred             CCCccccCCCcceecccCCccccc
Confidence            478999999999999999998754

>PF15288 zf-CCHC_6: Zinc knuckle

Probab=89.00  E-value=0.35  Score=33.42  Aligned_cols=21  Identities=33%  Similarity=0.762  Sum_probs=17.6

Q ss_pred             CcccccCCCCccC--CCCCCCCC
Q 035848            9 TGCFKCGRPGHWS--RDCPSSSS   29 (244)
Q Consensus         9 ~~Cy~CG~~GHwa--rdCp~~~~   29 (244)
                      ..|.+||.-||.+  +.||.-..
T Consensus         2 ~kC~~CG~~GH~~t~k~CP~~~~   24 (40)
T PF15288_consen    2 VKCKNCGAFGHMRTNKRCPMYCW   24 (40)
T ss_pred             ccccccccccccccCccCCCCCC
Confidence            3699999999998  78998753

>KOG0314 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=81.59  E-value=0.87  Score=45.28  Aligned_cols=25  Identities=40%  Similarity=0.997  Sum_probs=21.1

Q ss_pred             CCCCcccccCCCCccCCCCCCCCCC
Q 035848            6 AAPTGCFKCGRPGHWSRDCPSSSSS   30 (244)
Q Consensus         6 ~~~~~Cy~CG~~GHwardCp~~~~~   30 (244)
                      ...-.||+|+.+|||...||.....
T Consensus       156 ppsy~c~rc~~~g~wikacptv~~~  180 (448)
T KOG0314|consen  156 PPSYKCVKCPTPGPWIKACPTVSGS  180 (448)
T ss_pred             CCCcceecCCCCCccceeccccCCc
Confidence            3456799999999999999987654

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	244
1cl4_A	60	Protein (GAG polyprotein); nucleocapsid protein, R	4e-06
1cl4_A	60	Protein (GAG polyprotein); nucleocapsid protein, R	5e-06
2ihx_A	61	Nucleocapsid (NC) protein; protein-RNA complex, vi	4e-06
2ihx_A	61	Nucleocapsid (NC) protein; protein-RNA complex, vi	1e-05
2lli_A	124	Protein AIR2; RNA surveillance, RNA degradation, R	4e-05
2lli_A	124	Protein AIR2; RNA surveillance, RNA degradation, R	4e-04
2bl6_A	37	Nucleocapsid protein P11; lentivirus, polyprotein,	1e-04
2cqf_A	63	RNA-binding protein LIN-28; CCHC zinc-finger, stru	1e-04
2li8_A	74	Protein LIN-28 homolog A; zinc finger, micro RNA,	2e-04

>1cl4_A Protein (GAG polyprotein); nucleocapsid protein, RNA binding protein, retrovirus, viral protein; NMR {Mason-pfizer monkey virus} SCOP: g.40.1.1 PDB: 1dsv_A Length = 60

 Score = 42.2 bits (99), Expect = 4e-06
 Identities = 8/25 (32%), Positives = 11/25 (44%)

Query: 3  NAKAAPTGCFKCGRPGHWSRDCPSS 27
               P  C +C R  HW+ +C S 
Sbjct: 25 AEPKVPGLCPRCKRGKHWANECKSK 49

>1cl4_A Protein (GAG polyprotein); nucleocapsid protein, RNA binding protein, retrovirus, viral protein; NMR {Mason-pfizer monkey virus} SCOP: g.40.1.1 PDB: 1dsv_A Length = 60

 Score = 41.9 bits (98), Expect = 5e-06
 Identities = 8/25 (32%), Positives = 15/25 (60%)

Query: 10 GCFKCGRPGHWSRDCPSSSSSAPSN 34
           CFKCG+ GH++++C   + +    
Sbjct: 3  SCFKCGKKGHFAKNCHEHAHNNAEP 27

>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA complex; NMR {Rous sarcoma virus} Length = 61

 Score = 42.2 bits (99), Expect = 4e-06
 Identities = 5/35 (14%), Positives = 10/35 (28%)

Query: 2  ENAKAAPTGCFKCGRPGHWSRDCPSSSSSAPSNSN 36
            +  +   C  C   GH ++ C     +      
Sbjct: 24 RKSGNSRERCQLCNGMGHNAKQCRKRDGNQGQRPG 58

>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA complex; NMR {Rous sarcoma virus} Length = 61

 Score = 40.6 bits (95), Expect = 1e-05
 Identities = 11/29 (37%), Positives = 13/29 (44%)

Query: 7  APTGCFKCGRPGHWSRDCPSSSSSAPSNS 35
          A   C+ CG PGH+   CP    S  S  
Sbjct: 3  ARGLCYTCGSPGHYQAQCPKKRKSGNSRE 31

>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae} Length = 124

 Score = 41.3 bits (96), Expect = 4e-05
 Identities = 9/22 (40%), Positives = 11/22 (50%)

Query: 5  KAAPTGCFKCGRPGHWSRDCPS 26
          K A   C  C + GH  +DCP 
Sbjct: 1  KEAAPKCNNCSQRGHLKKDCPH 22

>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae} Length = 124

 Score = 38.2 bits (88), Expect = 4e-04
 Identities = 7/15 (46%), Positives = 9/15 (60%)

Query: 11  CFKCGRPGHWSRDCP 25
           C+ CG  GH+  DC 
Sbjct: 108 CYNCGGKGHFGDDCK 122

>2bl6_A Nucleocapsid protein P11; lentivirus, polyprotein, core protein, retrovirus zinc finger-like domains; NMR {Equine infectious anemia virus} Length = 37

 Score = 37.6 bits (87), Expect = 1e-04
 Identities = 12/20 (60%), Positives = 15/20 (75%)

Query: 7  APTGCFKCGRPGHWSRDCPS 26
          AP  CFKC +PGH+S+ C S
Sbjct: 18 APKVCFKCKQPGHFSKQCRS 37

>2cqf_A RNA-binding protein LIN-28; CCHC zinc-finger, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 63

 Score = 38.0 bits (88), Expect = 1e-04
 Identities = 8/34 (23%), Positives = 11/34 (32%)

Query: 8  PTGCFKCGRPGHWSRDCPSSSSSAPSNSNFPSNN 41
          P  C  C    H    CP  +   PS      ++
Sbjct: 29 PKKCHFCQSISHMVASCPLKAQQGPSAQGSGPSS 62

>2li8_A Protein LIN-28 homolog A; zinc finger, micro RNA, transcription-RNA complex; NMR {Homo sapiens} Length = 74

 Score = 38.0 bits (88), Expect = 2e-04
 Identities = 8/27 (29%), Positives = 9/27 (33%)

Query: 8  PTGCFKCGRPGHWSRDCPSSSSSAPSN 34
          P  C  C    H    CP  +   PS 
Sbjct: 46 PKKCHFCQSISHMVASCPLKAQQGPSA 72

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	244
1dsq_A	26	Nucleic acid binding protein P14; CCHC type zinc f	98.75
1a6b_B	40	Momulv, zinc finger protein NCP10; nucleocapsid pr	98.61
1u6p_A	56	GAG polyprotein; MLV, A-minor K-turn, stem loop, b	98.5
1nc8_A	29	Nucleocapsid protein; HIV-2, RNA recognition, zinc	98.37
2ysa_A	55	Retinoblastoma-binding protein 6; zinc finger, CCH	98.28
3nyb_B	83	Protein AIR2; polya RNA polymerase, zinc knuckle p	98.15
1cl4_A	60	Protein (GAG polyprotein); nucleocapsid protein, R	98.0
2ec7_A	49	GAG polyprotein (PR55GAG); nucleocapsid protein, H	97.92
2bl6_A	37	Nucleocapsid protein P11; lentivirus, polyprotein,	97.89
2a51_A	39	Nucleocapsid protein; sivlhoest, structure, NCP8,	97.85
2cqf_A	63	RNA-binding protein LIN-28; CCHC zinc-finger, stru	97.83
2li8_A	74	Protein LIN-28 homolog A; zinc finger, micro RNA,	97.83
2a51_A	39	Nucleocapsid protein; sivlhoest, structure, NCP8,	97.81
2li8_A	74	Protein LIN-28 homolog A; zinc finger, micro RNA,	97.79
2ihx_A	61	Nucleocapsid (NC) protein; protein-RNA complex, vi	97.78
2bl6_A	37	Nucleocapsid protein P11; lentivirus, polyprotein,	97.77
2ec7_A	49	GAG polyprotein (PR55GAG); nucleocapsid protein, H	97.76
1a1t_A	55	Nucleocapsid protein; stem-loop RNA, viral protein	97.75
2cqf_A	63	RNA-binding protein LIN-28; CCHC zinc-finger, stru	97.75
2ihx_A	61	Nucleocapsid (NC) protein; protein-RNA complex, vi	97.74
1a1t_A	55	Nucleocapsid protein; stem-loop RNA, viral protein	97.72
1cl4_A	60	Protein (GAG polyprotein); nucleocapsid protein, R	97.71
3ts2_A	148	Protein LIN-28 homolog A; microrna biogenesis, pro	97.32
2lli_A	124	Protein AIR2; RNA surveillance, RNA degradation, R	97.16
3nyb_B	83	Protein AIR2; polya RNA polymerase, zinc knuckle p	96.66
2lli_A	124	Protein AIR2; RNA surveillance, RNA degradation, R	96.56

>1a6b_B Momulv, zinc finger protein NCP10; nucleocapsid protein, intercalation, nucleic acid, retrovirus, viral protein/DNA complex; HET: DNA; NMR {Synthetic} SCOP: g.40.1.1

Probab=98.61  E-value=3e-08  Score=66.60  Aligned_cols=24  Identities=33%  Similarity=0.977  Sum_probs=20.8

Q ss_pred             CCCCCcccccCCCCccCCCCCCCC
Q 035848            5 KAAPTGCFKCGRPGHWSRDCPSSS   28 (244)
Q Consensus         5 ~~~~~~Cy~CG~~GHwardCp~~~   28 (244)
                      ......||+||+.||||||||...
T Consensus         7 ~~~~~~C~~Cgk~GH~ardCP~~~   30 (40)
T 1a6b_B            7 QLDRDQCAYCKEKGHWAKDCPKKP   30 (40)
T ss_dssp             SCCSSSCSSSCCTTCCTTSCSSSC
T ss_pred             CCCCCeeeECCCCCcchhhCcCCc
Confidence            345689999999999999999865

>1u6p_A GAG polyprotein; MLV, A-minor K-turn, stem loop, bulge, G-U mismatch, G-A MIS U mismatch, A-C mismatch, zinc finger, NC, viral protein-RN; HET: AP7; NMR {Moloney murine leukemia virus} SCOP: g.40.1.1 PDB: 1wwd_A 1wwe_A 1wwf_A 1wwg_A

Probab=98.50  E-value=6.8e-08  Score=69.01  Aligned_cols=24  Identities=33%  Similarity=0.953  Sum_probs=20.4

Q ss_pred             CCCCcccccCCCCccCCCCCCCCC
Q 035848            6 AAPTGCFKCGRPGHWSRDCPSSSS   29 (244)
Q Consensus         6 ~~~~~Cy~CG~~GHwardCp~~~~   29 (244)
                      .....||+||+.||||||||....
T Consensus        21 ~~~~~C~~Cge~GH~ardCp~~~~   44 (56)
T 1u6p_A           21 LDRDQCAYCKEKGHWAKDCPKKPR   44 (56)
T ss_dssp             CCTTBCSSSCCBSSCGGGCTTCCC
T ss_pred             CCCCcceeCCCCCcccccCcCCcc
Confidence            345789999999999999998653

>1nc8_A Nucleocapsid protein; HIV-2, RNA recognition, zinc finger, viral protein; NMR {Human immunodeficiency virus 2} SCOP: g.40.1.1 PDB: 2di2_A

Probab=98.37  E-value=1.3e-07  Score=58.66  Aligned_cols=22  Identities=32%  Similarity=0.913  Sum_probs=19.0

Q ss_pred             CCCcccccCCCCccCCCCCCCC
Q 035848            7 APTGCFKCGRPGHWSRDCPSSS   28 (244)
Q Consensus         7 ~~~~Cy~CG~~GHwardCp~~~   28 (244)
                      +...||+||+.|||||+|+.+.
T Consensus         5 ~~~~C~nCgk~GH~ar~C~~pr   26 (29)
T 1nc8_A            5 KVIRCWNCGKEGHSARQCRAPR   26 (29)
T ss_dssp             CCCBCTTTSCBSSCGGGCCSSS
T ss_pred             CCCEEEECCccccCHhHCcccc
Confidence            4567999999999999998654

>2ysa_A Retinoblastoma-binding protein 6; zinc finger, CCHC, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.28  E-value=1.9e-07  Score=66.43  Aligned_cols=21  Identities=43%  Similarity=1.385  Sum_probs=18.4

Q ss_pred             CCCcccccCCCCccCCCCCCC
Q 035848            7 APTGCFKCGRPGHWSRDCPSS   27 (244)
Q Consensus         7 ~~~~Cy~CG~~GHwardCp~~   27 (244)
                      +...||+||++|||+++||..
T Consensus         6 ~~~~C~kCGk~GH~~k~Cp~~   26 (55)
T 2ysa_A            6 SGYTCFRCGKPGHYIKNCPTN   26 (55)
T ss_dssp             SSCCCTTTCCTTSCGGGCSGG
T ss_pred             CCCccccCCCcCcccccCCCC
Confidence            456899999999999999944

>3nyb_B Protein AIR2; polya RNA polymerase, zinc knuckle protein, RNA surveillance binds to TRF4P/AIR2P heterodimer; 2.70A {Saccharomyces cerevisiae}

Probab=98.15  E-value=9.1e-07  Score=67.23  Aligned_cols=23  Identities=35%  Similarity=0.910  Sum_probs=20.2

Q ss_pred             CCCcccccCCCCccCCCCCCCCC
Q 035848            7 APTGCFKCGRPGHWSRDCPSSSS   29 (244)
Q Consensus         7 ~~~~Cy~CG~~GHwardCp~~~~   29 (244)
                      ....||+||+.||++||||....
T Consensus        45 ~~~~CYnCG~~GH~~rdC~~~r~   67 (83)
T 3nyb_B           45 HTIYCYNCGGKGHFGDDCKEKRS   67 (83)
T ss_dssp             CCCBCSSSSCBSSCGGGCSSCCS
T ss_pred             CCCeecccCCCCcCcccCCcccc
Confidence            45789999999999999998763

>1cl4_A Protein (GAG polyprotein); nucleocapsid protein, RNA binding protein, retrovirus, viral protein; NMR {Mason-pfizer monkey virus} SCOP: g.40.1.1 PDB: 1dsv_A

Probab=98.00  E-value=3.5e-06  Score=59.26  Aligned_cols=23  Identities=35%  Similarity=0.934  Sum_probs=19.1

Q ss_pred             CCCcccccCCCCccCCCCCCCCC
Q 035848            7 APTGCFKCGRPGHWSRDCPSSSS   29 (244)
Q Consensus         7 ~~~~Cy~CG~~GHwardCp~~~~   29 (244)
                      ....||+||+.||||||||....
T Consensus        29 ~~~~C~~Cg~~GH~ar~C~~~~~   51 (60)
T 1cl4_A           29 VPGLCPRCKRGKHWANECKSKTD   51 (60)
T ss_dssp             CCCSCSSCSSCSSCSTTCCCTTS
T ss_pred             CCcceeECCCCCCccCcCCCccc
Confidence            35789999999999999987653

>2ec7_A GAG polyprotein (PR55GAG); nucleocapsid protein, HIV-2, RNA recognition, zinc finger, viral protein; NMR {Human immunodeficiency virus type 2} SCOP: g.40.1.1

Probab=97.92  E-value=4.5e-06  Score=56.96  Aligned_cols=22  Identities=32%  Similarity=0.907  Sum_probs=18.4

Q ss_pred             CCCCcccccCCCCccCCCCCCC
Q 035848            6 AAPTGCFKCGRPGHWSRDCPSS   27 (244)
Q Consensus         6 ~~~~~Cy~CG~~GHwardCp~~   27 (244)
                      .++..||+||+.||||++||.+
T Consensus         4 ~r~~~C~~Cg~~GH~a~~C~~~   25 (49)
T 2ec7_A            4 RKVIRCWNCGKEGHSARQCRAP   25 (49)
T ss_dssp             CCCCBCTTTCCBTCCTTTCCCS
T ss_pred             CCcCeeeecCCCCcChhhCcCC
Confidence            4567899999999999999865

>2bl6_A Nucleocapsid protein P11; lentivirus, polyprotein, core protein, retrovirus zinc finger-like domains; NMR {Equine infectious anemia virus}

Probab=97.89  E-value=4e-06  Score=54.07  Aligned_cols=17  Identities=47%  Similarity=1.394  Sum_probs=13.1

Q ss_pred             cccccCCCCccCCCCCC
Q 035848           10 GCFKCGRPGHWSRDCPS   26 (244)
Q Consensus        10 ~Cy~CG~~GHwardCp~   26 (244)
                      .||+||++||+|++||.
T Consensus         2 ~C~~Cg~~GH~~~~C~~   18 (37)
T 2bl6_A            2 TCYNCGKPGHLSSQCRA   18 (37)
T ss_dssp             CBSSSCCSSCCTTTSSC
T ss_pred             cccccCCCCcchhhCcC
Confidence            57888888888888875

>2a51_A Nucleocapsid protein; sivlhoest, structure, NCP8, viral protein, metal binding protein; NMR {Synthetic}

Probab=97.85  E-value=5.9e-06  Score=53.84  Aligned_cols=17  Identities=41%  Similarity=1.173  Sum_probs=11.2

Q ss_pred             CcccccCCCCccCCCCC
Q 035848            9 TGCFKCGRPGHWSRDCP   25 (244)
Q Consensus         9 ~~Cy~CG~~GHwardCp   25 (244)
                      ..||+||+.||+|||||
T Consensus        22 ~~C~~Cg~~GH~~~~C~   38 (39)
T 2a51_A           22 EGCWNCGSKEHRFAQCP   38 (39)
T ss_dssp             SSCTTTCCSSSCTTTSC
T ss_pred             CccccCCCCCCccCcCc
Confidence            45666666666666665

>2cqf_A RNA-binding protein LIN-28; CCHC zinc-finger, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=97.83  E-value=1.4e-05  Score=57.22  Aligned_cols=22  Identities=23%  Similarity=0.800  Sum_probs=14.8

Q ss_pred             CCCCcccccCCCCccCCCCCCC
Q 035848            6 AAPTGCFKCGRPGHWSRDCPSS   27 (244)
Q Consensus         6 ~~~~~Cy~CG~~GHwardCp~~   27 (244)
                      .+...||+||+.||||++||..
T Consensus         5 ~r~~~C~~Cg~~GH~a~~C~~~   26 (63)
T 2cqf_A            5 SSGDRCYNCGGLDHHAKECKLP   26 (63)
T ss_dssp             CSCCCCSSSCCSSSCTTTCCSC
T ss_pred             CCCCcccccCCCCcChhhCCCC
Confidence            4456677777777777777643

>2li8_A Protein LIN-28 homolog A; zinc finger, micro RNA, transcription-RNA complex; NMR {Homo sapiens}

Probab=97.83  E-value=9.4e-06  Score=60.27  Aligned_cols=23  Identities=22%  Similarity=0.783  Sum_probs=19.0

Q ss_pred             CCCCCcccccCCCCccCCCCCCC
Q 035848            5 KAAPTGCFKCGRPGHWSRDCPSS   27 (244)
Q Consensus         5 ~~~~~~Cy~CG~~GHwardCp~~   27 (244)
                      ..+...||+||+.||||++||..
T Consensus        21 ~~r~~~C~~Cg~~GH~a~~C~~~   43 (74)
T 2li8_A           21 RSKGDRCYNCGGLDHHAKECKLP   43 (74)
T ss_dssp             CSTTSCCTTTCCSSSCTTTCSSC
T ss_pred             cCCCCcccccCCcCcCcccCCCC
Confidence            34677899999999999999854

>2a51_A Nucleocapsid protein; sivlhoest, structure, NCP8, viral protein, metal binding protein; NMR {Synthetic}

Probab=97.81  E-value=6.1e-06  Score=53.75  Aligned_cols=18  Identities=50%  Similarity=1.289  Sum_probs=16.6

Q ss_pred             cccccCCCCccCCCCCCC
Q 035848           10 GCFKCGRPGHWSRDCPSS   27 (244)
Q Consensus        10 ~Cy~CG~~GHwardCp~~   27 (244)
                      .||+||+.||+|++||.+
T Consensus         2 ~C~~Cg~~GH~a~~C~~~   19 (39)
T 2a51_A            2 TCFNCGKPGHTARMCRQP   19 (39)
T ss_dssp             BCTTTCCBSSCTTTCCSC
T ss_pred             eeeccCCCCcccccCCCC
Confidence            599999999999999965

>2li8_A Protein LIN-28 homolog A; zinc finger, micro RNA, transcription-RNA complex; NMR {Homo sapiens}

Probab=97.79  E-value=8e-06  Score=60.65  Aligned_cols=22  Identities=27%  Similarity=0.677  Sum_probs=19.6

Q ss_pred             CCCcccccCCCCccCCCCCCCC
Q 035848            7 APTGCFKCGRPGHWSRDCPSSS   28 (244)
Q Consensus         7 ~~~~Cy~CG~~GHwardCp~~~   28 (244)
                      ....||+||+.||+|||||...
T Consensus        45 ~~~~C~~Cg~~GH~ar~Cp~~~   66 (74)
T 2li8_A           45 QPKKCHFCQSISHMVASCPLKA   66 (74)
T ss_dssp             CCCCCTTTCCTTSCGGGCTTGG
T ss_pred             CCCccCCcCCcCCccCcCcCCc
Confidence            4678999999999999999765

>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA complex; NMR {Rous sarcoma virus}

Probab=97.78  E-value=7.7e-06  Score=58.04  Aligned_cols=22  Identities=41%  Similarity=1.127  Sum_probs=15.3

Q ss_pred             CCCcccccCCCCccCCCCCCCC
Q 035848            7 APTGCFKCGRPGHWSRDCPSSS   28 (244)
Q Consensus         7 ~~~~Cy~CG~~GHwardCp~~~   28 (244)
                      ++..||+||+.||||++||...
T Consensus         3 ~~~~C~~Cg~~GH~a~~C~~~~   24 (61)
T 2ihx_A            3 ARGLCYTCGSPGHYQAQCPKKR   24 (61)
T ss_dssp             CTTBCSSSCCBTCCGGGCTTTT
T ss_pred             CCCcccccCCCCeehhhCcCCc
Confidence            3456777777777777777653

>2bl6_A Nucleocapsid protein P11; lentivirus, polyprotein, core protein, retrovirus zinc finger-like domains; NMR {Equine infectious anemia virus}

Probab=97.77  E-value=6.9e-06  Score=52.95  Aligned_cols=19  Identities=58%  Similarity=1.408  Sum_probs=17.2

Q ss_pred             CCcccccCCCCccCCCCCC
Q 035848            8 PTGCFKCGRPGHWSRDCPS   26 (244)
Q Consensus         8 ~~~Cy~CG~~GHwardCp~   26 (244)
                      +..||+||++||+||+||.
T Consensus        19 ~~~C~~Cg~~GH~a~~C~~   37 (37)
T 2bl6_A           19 PKVCFKCKQPGHFSKQCRS   37 (37)
T ss_dssp             BTTCSSCCCTTGGGGTTCC
T ss_pred             cCeEccCCCcCCccCcCcC
Confidence            4689999999999999984

>2ec7_A GAG polyprotein (PR55GAG); nucleocapsid protein, HIV-2, RNA recognition, zinc finger, viral protein; NMR {Human immunodeficiency virus type 2} SCOP: g.40.1.1

Probab=97.76  E-value=8.9e-06  Score=55.48  Aligned_cols=21  Identities=43%  Similarity=1.153  Sum_probs=18.7

Q ss_pred             CCcccccCCCCccCCCCCCCC
Q 035848            8 PTGCFKCGRPGHWSRDCPSSS   28 (244)
Q Consensus         8 ~~~Cy~CG~~GHwardCp~~~   28 (244)
                      ...||+||+.||+|||||..+
T Consensus        27 ~~~C~~Cg~~GH~~~~C~~~~   47 (49)
T 2ec7_A           27 RQGCWKCGKTGHVMAKCPERQ   47 (49)
T ss_dssp             CCSCSSSCCSSCCGGGCCSSC
T ss_pred             CCeeCcCCCcCCccCCCcCCC
Confidence            467999999999999999765

>1a1t_A Nucleocapsid protein; stem-loop RNA, viral protein/RNA complex; NMR {Human immunodeficiency virus 1} SCOP: g.40.1.1 PDB: 1mfs_A 1f6u_A* 1aaf_A 2l4l_A 2exf_A 2jzw_A* 1bj6_A* 1esk_A 1q3y_A 1q3z_A 2e1x_A 2iwj_A

Probab=97.75  E-value=8.5e-06  Score=56.33  Aligned_cols=21  Identities=33%  Similarity=1.064  Sum_probs=15.0

Q ss_pred             CCCcccccCCCCccCCCCCCC
Q 035848            7 APTGCFKCGRPGHWSRDCPSS   27 (244)
Q Consensus         7 ~~~~Cy~CG~~GHwardCp~~   27 (244)
                      +...||+||+.||||++||.+
T Consensus        11 ~~~~C~~Cg~~GH~a~~C~~~   31 (55)
T 1a1t_A           11 KTVKCFNCGKEGHIAKNCRAP   31 (55)
T ss_dssp             GTCBCTTTCCBSSCGGGCSSC
T ss_pred             CCcceeeeCCCCcChhhcCCC
Confidence            345677777777777777765

>2cqf_A RNA-binding protein LIN-28; CCHC zinc-finger, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=97.75  E-value=1.3e-05  Score=57.29  Aligned_cols=22  Identities=27%  Similarity=0.677  Sum_probs=19.6

Q ss_pred             CCCcccccCCCCccCCCCCCCC
Q 035848            7 APTGCFKCGRPGHWSRDCPSSS   28 (244)
Q Consensus         7 ~~~~Cy~CG~~GHwardCp~~~   28 (244)
                      ....||+||+.||+|||||...
T Consensus        28 ~~~~C~~Cg~~GH~ar~Cp~~~   49 (63)
T 2cqf_A           28 QPKKCHFCQSISHMVASCPLKA   49 (63)
T ss_dssp             CSSCCTTTCCSSSCTTTCTGGG
T ss_pred             CCCccCCcCCcCCccCcCCCcc
Confidence            5678999999999999999764

>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA complex; NMR {Rous sarcoma virus}

Probab=97.74  E-value=1e-05  Score=57.46  Aligned_cols=22  Identities=23%  Similarity=0.583  Sum_probs=18.9

Q ss_pred             CCcccccCCCCccCCCCCCCCC
Q 035848            8 PTGCFKCGRPGHWSRDCPSSSS   29 (244)
Q Consensus         8 ~~~Cy~CG~~GHwardCp~~~~   29 (244)
                      ...||+||+.||+|||||..+.
T Consensus        30 ~~~C~~Cg~~GH~ar~C~~~~~   51 (61)
T 2ihx_A           30 RERCQLCNGMGHNAKQCRKRDG   51 (61)
T ss_dssp             CSBCTTTCCBSSCGGGCCCCC-
T ss_pred             CCeeCCCCCCCCCcCCCcCCCc
Confidence            4679999999999999998764

>1a1t_A Nucleocapsid protein; stem-loop RNA, viral protein/RNA complex; NMR {Human immunodeficiency virus 1} SCOP: g.40.1.1 PDB: 1mfs_A 1f6u_A* 1aaf_A 2l4l_A 2exf_A 2jzw_A* 1bj6_A* 1esk_A 1q3y_A 1q3z_A 2e1x_A 2iwj_A

Probab=97.72  E-value=6.6e-06  Score=56.88  Aligned_cols=22  Identities=41%  Similarity=1.087  Sum_probs=19.2

Q ss_pred             CCCcccccCCCCccCCCCCCCC
Q 035848            7 APTGCFKCGRPGHWSRDCPSSS   28 (244)
Q Consensus         7 ~~~~Cy~CG~~GHwardCp~~~   28 (244)
                      +...||+||+.||+|+|||..+
T Consensus        32 ~~~~C~~Cg~~GH~~~~C~~~~   53 (55)
T 1a1t_A           32 RKKGCWKCGKEGHQMKDCTERQ   53 (55)
T ss_dssp             SCCBCTTTCCBSSCGGGCSSSC
T ss_pred             CCCEeCCCCCcCCccCCCcCcC
Confidence            3468999999999999999765

>1cl4_A Protein (GAG polyprotein); nucleocapsid protein, RNA binding protein, retrovirus, viral protein; NMR {Mason-pfizer monkey virus} SCOP: g.40.1.1 PDB: 1dsv_A

Probab=97.71  E-value=4.8e-06  Score=58.52  Aligned_cols=20  Identities=40%  Similarity=1.247  Sum_probs=0.0

Q ss_pred             CcccccCCCCccCCCCCCCC
Q 035848            9 TGCFKCGRPGHWSRDCPSSS   28 (244)
Q Consensus         9 ~~Cy~CG~~GHwardCp~~~   28 (244)
                      ..||+||+.|||||+||...
T Consensus         2 ~~Cf~Cg~~GH~a~~C~~~~   21 (60)
T 1cl4_A            2 GSCFKCGKKGHFAKNCHEHA   21 (60)
T ss_dssp             --------------------
T ss_pred             CccccCCCCCcCHhhCcCCC
Confidence            36999999999999999764

>3ts2_A Protein LIN-28 homolog A; microrna biogenesis, protein-RNA complex, PRE-element, CCHC knuckle; HET: GMP; 2.01A {Mus musculus} PDB: 3trz_A* 3ts0_A*

Probab=97.32  E-value=8.4e-05  Score=61.20  Aligned_cols=20  Identities=25%  Similarity=0.843  Sum_probs=17.5

Q ss_pred             CCcccccCCCCccCCCCCCC
Q 035848            8 PTGCFKCGRPGHWSRDCPSS   27 (244)
Q Consensus         8 ~~~Cy~CG~~GHwardCp~~   27 (244)
                      ...||+||+.|||||+||.+
T Consensus        97 ~~~C~~Cg~~GH~a~~C~~~  116 (148)
T 3ts2_A           97 GDRCYNCGGLDHHAKECKLP  116 (148)
T ss_dssp             SCCCTTTCCSSCCGGGCCSC
T ss_pred             CCcccEeCCccchhhhCCCC
Confidence            35699999999999999864

>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae}

Probab=97.16  E-value=0.00016  Score=56.93  Aligned_cols=22  Identities=36%  Similarity=0.907  Sum_probs=17.9

Q ss_pred             CCCCcccccCCCCccCCCCCCC
Q 035848            6 AAPTGCFKCGRPGHWSRDCPSS   27 (244)
Q Consensus         6 ~~~~~Cy~CG~~GHwardCp~~   27 (244)
                      +++..||+||+.||||++||..
T Consensus         2 e~~~~C~~C~~~GH~~~~Cp~~   23 (124)
T 2lli_A            2 EAAPKCNNCSQRGHLKKDCPHI   23 (124)
T ss_dssp             CCSSCCSSCSSSSCCTTTTTSC
T ss_pred             CCCCcccCCCCCCcCcccCcCC
Confidence            4567799999999999999864

>3nyb_B Protein AIR2; polya RNA polymerase, zinc knuckle protein, RNA surveillance binds to TRF4P/AIR2P heterodimer; 2.70A {Saccharomyces cerevisiae}

Probab=96.66  E-value=0.0004  Score=52.58  Aligned_cols=22  Identities=27%  Similarity=0.498  Sum_probs=17.5

Q ss_pred             CCCcccccCCCCccCCCCCCCC
Q 035848            7 APTGCFKCGRPGHWSRDCPSSS   28 (244)
Q Consensus         7 ~~~~Cy~CG~~GHwardCp~~~   28 (244)
                      ....||+||+.||++++||...
T Consensus         4 k~~~C~~Cg~~GH~~~~Cp~~~   25 (83)
T 3nyb_B            4 KKVQCTLCKSKKHSKERCPSIW   25 (83)
T ss_dssp             ---CCSSSCCSSSCGGGCGGGT
T ss_pred             ccCCCCCCCCCCCccccCCCcc
Confidence            5678999999999999999754

>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding, exosome, RNA protein; NMR {Saccharomyces cerevisiae}

Probab=96.56  E-value=0.0013  Score=51.63  Aligned_cols=19  Identities=32%  Similarity=0.651  Sum_probs=9.7

Q ss_pred             CcccccCCCCccCCCCCCC
Q 035848            9 TGCFKCGRPGHWSRDCPSS   27 (244)
Q Consensus         9 ~~Cy~CG~~GHwardCp~~   27 (244)
                      ..||+||+.||+|||||..
T Consensus        65 ~~C~~Cg~~GH~~~~Cp~~   83 (124)
T 2lli_A           65 VQCTLCKSKKHSKERCPSI   83 (124)
T ss_dssp             CSSSSSCSSCCCTTTCCCS
T ss_pred             ccCCCCCcCCcchhhCCCc
Confidence            3455555555555555543

---

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	244
d2exfa1	42	g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunod	6e-05
d2exfa1	42	g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunod	4e-04

>d2exfa1 g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunodeficiency virus type 1, different isolates [TaxId: 11676]} Length = 42

class: Small proteins
fold: Retrovirus zinc finger-like domains
superfamily: Retrovirus zinc finger-like domains
family: Retrovirus zinc finger-like domains
domain: HIV nucleocapsid
species: Human immunodeficiency virus type 1, different isolates [TaxId: 11676]

 Score = 37.1 bits (86), Expect = 6e-05
 Identities = 8/16 (50%), Positives = 12/16 (75%)

Query: 11 CFKCGRPGHWSRDCPS 26
          CF CG+ GH +R+C +
Sbjct: 4  CFNCGKEGHTARNCRA 19

>d2exfa1 g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunodeficiency virus type 1, different isolates [TaxId: 11676]} Length = 42

class: Small proteins
fold: Retrovirus zinc finger-like domains
superfamily: Retrovirus zinc finger-like domains
family: Retrovirus zinc finger-like domains
domain: HIV nucleocapsid
species: Human immunodeficiency virus type 1, different isolates [TaxId: 11676]

 Score = 34.8 bits (80), Expect = 4e-04
 Identities = 9/18 (50%), Positives = 12/18 (66%)

Query: 8  PTGCFKCGRPGHWSRDCP 25
            GC+KCG+ GH  +DC 
Sbjct: 22 KKGCWKCGKEGHQMKDCT 39

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	244
d1nc8a_	29	HIV nucleocapsid {Human immunodeficiency virus typ	98.0
d2exfa1	42	HIV nucleocapsid {Human immunodeficiency virus typ	97.97
d2exfa1	42	HIV nucleocapsid {Human immunodeficiency virus typ	97.81
d1a6bb_	40	Zinc finger protein ncp10 {Moloney murine leukemia	97.3
d1dsqa_	26	Nucleic acid binding protein p14 {Mouse mammary tu	97.08
d1cl4a_	32	Nucleocapsid protein from mason-pfizer monkey viru	96.0
d1dsva_	31	Nucleic acid binding protein p14 {Mouse mammary tu	95.83

>d1nc8a_ g.40.1.1 (A:) HIV nucleocapsid {Human immunodeficiency virus type 2 [TaxId: 11709]}

class: Small proteins
fold: Retrovirus zinc finger-like domains
superfamily: Retrovirus zinc finger-like domains
family: Retrovirus zinc finger-like domains
domain: HIV nucleocapsid
species: Human immunodeficiency virus type 2 [TaxId: 11709]

Probab=98.00  E-value=7.2e-07  Score=54.69  Aligned_cols=23  Identities=30%  Similarity=0.865  Sum_probs=19.1

Q ss_pred             CCCCcccccCCCCccCCCCCCCC
Q 035848            6 AAPTGCFKCGRPGHWSRDCPSSS   28 (244)
Q Consensus         6 ~~~~~Cy~CG~~GHwardCp~~~   28 (244)
                      ...--||+|||.||.||+|-.+.
T Consensus         4 r~~ikCfNCGkeGH~ar~CrAPR   26 (29)
T d1nc8a_           4 RKVIRCWNCGKEGHSARQCRAPR   26 (29)
T ss_dssp             CCCCBCTTTSCBSSCGGGCCSSS
T ss_pred             cceeEeecCCccchhhhhccCcc
Confidence            34567999999999999997553

>d2exfa1 g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunodeficiency virus type 1, different isolates [TaxId: 11676]}

class: Small proteins
fold: Retrovirus zinc finger-like domains
superfamily: Retrovirus zinc finger-like domains
family: Retrovirus zinc finger-like domains
domain: HIV nucleocapsid
species: Human immunodeficiency virus type 1, different isolates [TaxId: 11676]

Probab=97.97  E-value=1.4e-06  Score=56.91  Aligned_cols=17  Identities=53%  Similarity=1.427  Sum_probs=9.0

Q ss_pred             cccccCCCCccCCCCCC
Q 035848           10 GCFKCGRPGHWSRDCPS   26 (244)
Q Consensus        10 ~Cy~CG~~GHwardCp~   26 (244)
                      .||+||+.|||++|||.
T Consensus        24 ~C~~Cg~~GH~~~~Cp~   40 (42)
T d2exfa1          24 GCWKCGKEGHQMKDCTE   40 (42)
T ss_dssp             SCSSSCCSSSCTTTCCS
T ss_pred             ccccCCCCCeecccCCC
Confidence            45555555555555553

>d2exfa1 g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunodeficiency virus type 1, different isolates [TaxId: 11676]}

class: Small proteins
fold: Retrovirus zinc finger-like domains
superfamily: Retrovirus zinc finger-like domains
family: Retrovirus zinc finger-like domains
domain: HIV nucleocapsid
species: Human immunodeficiency virus type 1, different isolates [TaxId: 11676]

Probab=97.81  E-value=3.4e-06  Score=55.07  Aligned_cols=19  Identities=42%  Similarity=1.186  Sum_probs=17.2

Q ss_pred             CcccccCCCCccCCCCCCC
Q 035848            9 TGCFKCGRPGHWSRDCPSS   27 (244)
Q Consensus         9 ~~Cy~CG~~GHwardCp~~   27 (244)
                      ..||+||+.||||+|||.+
T Consensus         2 i~C~~Cg~~GH~~~~Cp~~   20 (42)
T d2exfa1           2 VKCFNCGKEGHTARNCRAP   20 (42)
T ss_dssp             CCCTTTCCSSSCTTTCSSC
T ss_pred             CccccCCCcCcCcccCcCC
Confidence            4699999999999999965

>d1a6bb_ g.40.1.1 (B:) Zinc finger protein ncp10 {Moloney murine leukemia virus, MoMLV [TaxId: 11801]}

class: Small proteins
fold: Retrovirus zinc finger-like domains
superfamily: Retrovirus zinc finger-like domains
family: Retrovirus zinc finger-like domains
domain: Zinc finger protein ncp10
species: Moloney murine leukemia virus, MoMLV [TaxId: 11801]

Probab=97.30  E-value=7.7e-05  Score=48.48  Aligned_cols=22  Identities=36%  Similarity=1.061  Sum_probs=18.8

Q ss_pred             CCCcccccCCCCccCCCCCCCC
Q 035848            7 APTGCFKCGRPGHWSRDCPSSS   28 (244)
Q Consensus         7 ~~~~Cy~CG~~GHwardCp~~~   28 (244)
                      .-..|--|-+.|||+||||...
T Consensus         9 ~kDQCAyCke~GHW~~dCPkkp   30 (40)
T d1a6bb_           9 DRDQCAYCKEKGHWAKDCPKKP   30 (40)
T ss_dssp             CSSSCSSSCCTTCCTTSCSSSC
T ss_pred             cchhhHHHhhcCchhhhCccCC
Confidence            3467889999999999999764

>d1dsqa_ g.40.1.1 (A:) Nucleic acid binding protein p14 {Mouse mammary tumor virus [TaxId: 11757]}

class: Small proteins
fold: Retrovirus zinc finger-like domains
superfamily: Retrovirus zinc finger-like domains
family: Retrovirus zinc finger-like domains
domain: Nucleic acid binding protein p14
species: Mouse mammary tumor virus [TaxId: 11757]

Probab=97.08  E-value=8.1e-05  Score=43.95  Aligned_cols=19  Identities=47%  Similarity=1.190  Sum_probs=17.0

Q ss_pred             CcccccCCCCccCCCCCCC
Q 035848            9 TGCFKCGRPGHWSRDCPSS   27 (244)
Q Consensus         9 ~~Cy~CG~~GHwardCp~~   27 (244)
                      -.||.||+.||.-+||...
T Consensus         3 pvcfscgktghikkdck~e   21 (26)
T d1dsqa_           3 PVCFSCGKTGHIKRDCKEE   21 (26)
T ss_dssp             CBCTTTCCBSSCTTTTTCC
T ss_pred             CEEEecCCcccchhhhhhh
Confidence            4799999999999999764

>d1cl4a_ g.40.1.1 (A:) Nucleocapsid protein from mason-pfizer monkey virus (MPMV) {Mason-pfizer monkey virus [TaxId: 11855]}

class: Small proteins
fold: Retrovirus zinc finger-like domains
superfamily: Retrovirus zinc finger-like domains
family: Retrovirus zinc finger-like domains
domain: Nucleocapsid protein from mason-pfizer monkey virus (MPMV)
species: Mason-pfizer monkey virus [TaxId: 11855]

Probab=96.00  E-value=0.0024  Score=39.59  Aligned_cols=22  Identities=36%  Similarity=0.975  Sum_probs=18.9

Q ss_pred             CCcccccCCCCccCCCCCCCCC
Q 035848            8 PTGCFKCGRPGHWSRDCPSSSS   29 (244)
Q Consensus         8 ~~~Cy~CG~~GHwardCp~~~~   29 (244)
                      +..|-+|.|--|||+||-+.-.
T Consensus         2 P~lCPrC~kG~HWa~~Crsk~~   23 (32)
T d1cl4a_           2 PGLCPRCKRGKHWANECKSKTD   23 (32)
T ss_dssp             CCSCSSCSSCSSCSTTCCCTTS
T ss_pred             CccCccccCcchHHHHhhhhhc
Confidence            5789999999999999976543

>d1dsva_ g.40.1.1 (A:) Nucleic acid binding protein p14 {Mouse mammary tumor virus [TaxId: 11757]}

class: Small proteins
fold: Retrovirus zinc finger-like domains
superfamily: Retrovirus zinc finger-like domains
family: Retrovirus zinc finger-like domains
domain: Nucleic acid binding protein p14
species: Mouse mammary tumor virus [TaxId: 11757]

Probab=95.83  E-value=0.0017  Score=40.13  Aligned_cols=20  Identities=35%  Similarity=0.933  Sum_probs=17.7

Q ss_pred             CCcccccCCCCccCCCCCCC
Q 035848            8 PTGCFKCGRPGHWSRDCPSS   27 (244)
Q Consensus         8 ~~~Cy~CG~~GHwardCp~~   27 (244)
                      +..|-+|.|--|||+||-+.
T Consensus         2 p~lCPrC~kG~HWa~~Crsk   21 (31)
T d1dsva_           2 PGLCPRCKKGYHWKSECKSK   21 (31)
T ss_dssp             CCBCTTTCSSBSCTTTCCCS
T ss_pred             CccCccccCcchHHHHhhhh
Confidence            57899999999999999654