Citrus Sinensis ID: 024209

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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-------250-------260-------270-
Protein Sequence
MSSRSRSISRSRSRSRSRSPRDRRFRSRHSSYCDPPLRRETRRSFSQGNLCNNCKRPGHFARECPNVAVCNNCGLPGHIASECTTQARCWNCREPGHMASNCHNEGICHSCGKTGHRARDCSTHVQSGGDLRLCNNCYKPGHIAADCTNDKACKNCRKTGHIARDCQNEPVCNLCNIAGHVARQCPKGDSLGERGGGGGGERGGGGGGDGGGGGGRYVGYHDVICRSCNQMGHMSRDCVGPLIICRNCGGRGHMAYECPSGRIADRGYRRY
Secondary Structure (PSIPRED)
ccccccccccccccccccccccHHccccccccccccccHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHccccHHHcccccccccccccccHHHHcccccccccccccccccccccccccccccccccccccccccccEccccccccccccccccccHHcccccccccccccccccHHccccccccccccccccccccccccccccccccccccccccccccccccccEEEEccccccccccccccccccccccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
mssrsrsisrsrsrsrsrsprdrrfrsrhssycdpplrretrrsfsqgnlcnnckrpghfarecpnvavcnncglpghiasecttqarcwncrepghmasnchnegichscgktghrardcsthvqsggdlrlcnncykpghiaadctndkackncrktghiardcqnepvcnlcniaghvarqcpkgdslgerggggggerggggggdggggggryvGYHDVICRscnqmghmsrdcvgpliicrncggrghmayecpsgriadrgyrry
Flexible Loop (DISEMBL)
mssrsrsisrsrsrsrsrsprdrrfrsrhssycdpplrretrrsfsqgnLCNNCKRPGHFARECPNVAVCNNCGLPGHIASECTTQARCWNCREPGHMASNCHNEGICHSCGKTGHRARDCSTHVQSGGDLRLCNNCYKPGHIAADCTNDKACKNCRKTGhiardcqnepVCNLCNIAGHVARQCPKGDSLGERGGGGGGERGGGGGGDGGGGGGRYVGYHDVICRSCNQMGHMSRDCVGPLIICRNCGGRghmayecpsgriadrgyrry
Low Complexity Region (SEG)
MssrsrsisrsrsrsrsrsprdrrfrsrhssYCDPPLRRETRRSFSQGNLCNNCKRPGHFARECPNVAVCNNCGLPGHIASECTTQARCWNCREPGHMASNCHNEGICHSCGKTGHRARDCSTHVQSGGDLRLCNNCYKPGHIAADCTNDKACKNCRKTGHIARDCQNEPVCNLCNIAGHVARQCPKGDSLgerggggggerggggggdggggggrYVGYHDVICRSCNQMGHMSRDCVGPLIICRNCGGRGHMAYECPSGRIADRGYRRY
Disordered region (IsUnstruct)
************************************************NLCNNCKRPGHFARECPNVAVCNNCGLPGHIASECTTQARCWNC**************ICHSCGKTGHRARDCSTHVQSGGDLRLCNNCYKPGHIAADCTNDKACKNCRKTGHIARDCQNEPVCNLCNIAGHVAR*********************************YVGYHDVICRSCNQMGHMSRDCVGPLIICRNC***********************
Disordered Region (DISOPRED)
**************************************************CNNCKRPGHFARECPNVAVCNNCGLPGHIASECTTQARC*************************************************K*GHIAADCTNDKACKNCRKTGHIARDCQNEPVCNLCNIAGHVARQCP*****************GGGGGDGGGGGGRYVGYHDVICRSCNQMGHMSRDCVGPLIICRNCGGRGHMAYECPS******GYRR*
Disordered Region (DISEMBL)
*****************************SSYCDPPLRRETRRSFSQGNLCNNCKRPGHFARECPNVAVCNNCGLPGHIASECTTQARCWNCREPGHMASNCHNEGICHSC*************VQSGGDLRLCNNCYKPGHIAADCTNDKACKNCRKTGHIARDCQNEPVCNLCNIAGHVARQCPKGDSLGERGGGGGGERGGGGGGDGGGGGGRYVGYHDVICRSCNQMGHMSRDCVGPLIICRNCGGRGHMAYECPSGRIADRGYRRY
Disordered Region (DISPRO)
************************************************NLCNNCKRPGHFARECPNVAVCNNCGLPGHIASECTTQARCWNCREPGHMASNCHNEGICHSCGKTGHRARDCSTHV**GGDLRLCNNCYKPGHIAADCTNDKACKNCRKTGHIARDCQNEPVCNLCNIAGHVARQC**********************************YHDVICRSCNQMGHMSRDCVGPLIICRNCGGRGHMAYECPSGRI**R*****
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MSSRSRSISRSRSRSRSRSPRDRRFRSRHSSYCDPPLRRETRRSFSQGNLCNNCKRPGHFARECPNVAVCNNCGLPGHIASECTTQARCWNCREPGHMASNCHNEGICHSCGKTGHRARDCSTHVQSGGDLRLCNNCYKPGHIAADCTNDKACKNCRKTGHIARDCQNEPVCNLCNIAGHVARQCPKGDSLGERGGGGGGERGGGGGGDGGGGGGRYVGYHDVICRSCNQMGHMSRDCVGPLIICRNCGGRGHMAYECPSGRIADRGYRRY
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	271	2.2.26 [Sep-21-2011]
Q04832	271	DNA-binding protein HEXBP	yes	no	0.671	0.671	0.295	2e-18
P53849	153	Zinc finger protein GIS2	yes	no	0.498	0.882	0.357	6e-18
Q3T0Q6	170	Cellular nucleic acid-bin	yes	no	0.483	0.770	0.371	2e-15
P36627	179	Cellular nucleic acid-bin	yes	no	0.542	0.821	0.388	2e-15
O42395	172	Cellular nucleic acid-bin	yes	no	0.483	0.761	0.366	3e-15
P62634	177	Cellular nucleic acid-bin	yes	no	0.483	0.740	0.356	1e-14
Q5R5R5	177	Cellular nucleic acid-bin	yes	no	0.483	0.740	0.356	1e-14
P62633	177	Cellular nucleic acid-bin	yes	no	0.483	0.740	0.356	1e-14
P53996	178	Cellular nucleic acid-bin	yes	no	0.483	0.735	0.354	1e-14
O65639	299	Cold shock protein 1 OS=A	no	no	0.424	0.384	0.329	3e-12

>sp|Q04832|HEXP_LEIMA DNA-binding protein HEXBP OS=Leishmania major GN=HEXBP PE=4 SV=1

 Score = 93.2 bits (230), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 83/281 (29%), Positives = 109/281 (38%), Gaps = 99/281 (35%)

Query: 51  CNNCKRPGHFARECPNV--------AVCNNCGLPGHIASECTTQAR--------CWNCRE 94
           C NC + GH+ARECP            C  CG  GH++ EC  +AR        C+ C E
Sbjct: 18  CRNCGKEGHYARECPEADSKGDERSTTCFRCGEEGHMSRECPNEARSGAAGAMTCFRCGE 77

Query: 95  PGHMASNCHNEGI--------CHSCGKTGHRARDCSTH----------------VQSG-- 128
            GHM+ +C N           C+ CG+ GH +RDC +                  Q G  
Sbjct: 78  AGHMSRDCPNSAKPGAAKGFECYKCGQEGHLSRDCPSSQGGSRGGYGQKRGRSGAQGGYS 137

Query: 129 GDLRLCNNCYKPGHIAADCTN---------DKACKNCRKTGHIARDCQN---------EP 170
           GD R C  C   GHI+ DC N         D+ C  C   GHI+RDC N         + 
Sbjct: 138 GD-RTCYKCGDAGHISRDCPNGQGGYSGAGDRTCYKCGDAGHISRDCPNGQGGYSGAGDR 196

Query: 171 VCNLCNIAGHVARQCPKGDSLGERGGGGGGERGGGGGGDGGGGGGRYVGYHDVICRSCNQ 230
            C  C  +GH++R+CP   S G                             D  C  C +
Sbjct: 197 KCYKCGESGHMSRECPSAGSTGS---------------------------GDRACYKCGK 229

Query: 231 MGHMSRDCVGPLI-----------ICRNCGGRGHMAYECPS 260
            GH+SR+C                 C  CG  GH++ +CPS
Sbjct: 230 PGHISRECPEAGGSYGGSRGGGDRTCYKCGEAGHISRDCPS 270

Binds to single-stranded DNA located in the 5' hexanucleotide repeat region of the L.major leishmanolysin (GP63) gene.
Leishmania major (taxid: 5664)

>sp|P53849|GIS2_YEAST Zinc finger protein GIS2 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=GIS2 PE=1 SV=1

 Score = 91.3 bits (225), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 54/151 (35%), Positives = 84/151 (55%), Gaps = 16/151 (10%)

Query: 51  CNNCKRPGHFARECPNVAVCNNCGLPGHIASECTTQ-----ARCWNCREPGHMASNCHNE 105
           C  C + GH A +C +  +C NC  PGH+ ++CT        +C+NC E GH+ S C  +
Sbjct: 6   CYVCGKIGHLAEDCDSERLCYNCNKPGHVQTDCTMPRTVEFKQCYNCGETGHVRSECTVQ 65

Query: 106 GICHSCGKTGHRARDCSTHVQSGGDLRLCNNCYK---PGHIAADCTNDK-----ACKNCR 157
             C +C +TGH +R+C    ++    ++  +CYK   P H+A DC  +       C  C 
Sbjct: 66  R-CFNCNQTGHISRECPEPKKTSRFSKV--SCYKCGGPNHMAKDCMKEDGISGLKCYTCG 122

Query: 158 KTGHIARDCQNEPVCNLCNIAGHVARQCPKG 188
           + GH++RDCQN+ +C  CN  GH+++ CPK 
Sbjct: 123 QAGHMSRDCQNDRLCYNCNETGHISKDCPKA 153

May act in the sexual differentiation pathway.

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (taxid: 559292)

>sp|Q3T0Q6|CNBP_BOVIN Cellular nucleic acid-binding protein OS=Bos taurus GN=CNBP PE=2 SV=1

 Score = 83.2 bits (204), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 62/167 (37%), Positives = 81/167 (48%), Gaps = 36/167 (21%)

Query: 49  NLCNNCKRPGHFARECPNVA----------------------VCNNCGLPGHIASECTTQ 86
           N C  C R GH+ARECP                         +C  CG  GH+A +C  Q
Sbjct: 4   NECFKCGRSGHWARECPTGGGRGRGMRSRGRGFQFVSSSLPDICYRCGESGHLAKDCDLQ 63

Query: 87  A-RCWNCREPGHMASNCHN-----EGICHSCGKTGHRARDCSTHVQSGGDLRLCNNCYKP 140
              C+NC   GH+A +C       E  C++CGK GH ARDC        D + C +C + 
Sbjct: 64  EDACYNCGRGGHIAKDCKEPKREREQCCYNCGKPGHLARDCDH-----ADEQKCYSCGEF 118

Query: 141 GHIAADCTNDKACKNCRKTGHIARDCQ--NEPVCNLCNIAGHVARQC 185
           GHI  DCT  K C  C +TGH+A +C   +E  C  C  +GH+AR+C
Sbjct: 119 GHIQKDCTKVK-CYRCGETGHVAINCSKTSEVNCYRCGESGHLAREC 164

Single stranded DNA-binding protein, with specificity to the sterol regulatory element (SRE). Involved in sterol-mediated repression.

Bos taurus (taxid: 9913)

>sp|P36627|BYR3_SCHPO Cellular nucleic acid-binding protein homolog OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=byr3 PE=4 SV=1

 Score = 82.8 bits (203), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 66/170 (38%), Positives = 83/170 (48%), Gaps = 23/170 (13%)

Query: 35  PPLRRETRRSFSQGNLCNNCKRPGHFARECPNVAVCNNCGLPGHIASECT---TQARCWN 91
           P + + TR     G  C NC   GH AREC   ++C NC   GH ASECT    +  C+ 
Sbjct: 7   PTVPQTTR----PGPRCYNCGENGHQARECTKGSICYNCNQTGHKASECTEPQQEKTCYA 62

Query: 92  CREPGHMASNCHNE------GICHSCGKTGHRARDCSTH-VQSGGDL---RLCNNCY--- 138
           C   GH+  +C +         C+ CG+ GH ARDC T+  QSGG     R   NCY   
Sbjct: 63  CGTAGHLVRDCPSSPNPRQGAECYKCGRVGHIARDCRTNGQQSGGRFGGHRSNMNCYACG 122

Query: 139 KPGHIAADCTNDKACKNCRKTGHIARDCQNEP---VCNLCNIAGHVARQC 185
             GH A DCT    C +C K GH + +CQ      +C  CN  GH+A  C
Sbjct: 123 SYGHQARDCTMGVKCYSCGKIGHRSFECQQASDGQLCYKCNQPGHIAVNC 172

Acts in the sexual differentiation pathway. Is required for efficient conjugation. Double stranded DNA-binding protein.

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

>sp|O42395|CNBP_CHICK Cellular nucleic acid-binding protein OS=Gallus gallus GN=CNBP PE=2 SV=1

 Score = 82.4 bits (202), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 62/169 (36%), Positives = 81/169 (47%), Gaps = 38/169 (22%)

Query: 49  NLCNNCKRPGHFARECPNVA-----------------------VCNNCGLPGHIASECTT 85
           N C  C R GH+ARECP                          +C  CG  GH+A +C  
Sbjct: 4   NECFKCGRTGHWARECPTGIGRGRGMRSRGRAGFQFMSSSLPDICYRCGESGHLAKDCDL 63

Query: 86  QA--RCWNCREPGHMASNCHN-----EGICHSCGKTGHRARDCSTHVQSGGDLRLCNNCY 138
           Q    C+NC   GH+A +C       E  C++CGK GH ARDC        D + C +C 
Sbjct: 64  QEDKACYNCGRGGHIAKDCKEPKREREQCCYNCGKPGHLARDCDH-----ADEQKCYSCG 118

Query: 139 KPGHIAADCTNDKACKNCRKTGHIARDCQ--NEPVCNLCNIAGHVARQC 185
           + GHI  DCT  K C  C +TGH+A +C   +E  C  C  +GH+AR+C
Sbjct: 119 EFGHIQKDCTKVK-CYRCGETGHVAINCSKTSEVNCYRCGESGHLAREC 166

Single stranded DNA-binding protein, with specificity to the sterol regulatory element (SRE). Involved in sterol-mediated repression.

Gallus gallus (taxid: 9031)

>sp|P62634|CNBP_RAT Cellular nucleic acid-binding protein OS=Rattus norvegicus GN=Cnbp PE=2 SV=1

 Score = 80.9 bits (198), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 62/174 (35%), Positives = 81/174 (46%), Gaps = 43/174 (24%)

Query: 49  NLCNNCKRPGHFARECPNVA-----------------------------VCNNCGLPGHI 79
           N C  C R GH+ARECP                                +C  CG  GH+
Sbjct: 4   NECFKCGRSGHWARECPTGGGRGRGMRSRGRGGFTSDRGFQFVSSSLPDICYRCGESGHL 63

Query: 80  ASECTTQA-RCWNCREPGHMASNCHN-----EGICHSCGKTGHRARDCSTHVQSGGDLRL 133
           A +C  Q   C+NC   GH+A +C       E  C++CGK GH ARDC        D + 
Sbjct: 64  AKDCDLQEDACYNCGRGGHIAKDCKEPKREREQCCYNCGKPGHLARDCDH-----ADEQK 118

Query: 134 CNNCYKPGHIAADCTNDKACKNCRKTGHIARDCQ--NEPVCNLCNIAGHVARQC 185
           C +C + GHI  DCT  K C  C +TGH+A +C   +E  C  C  +GH+AR+C
Sbjct: 119 CYSCGEFGHIQKDCTKVK-CYRCGETGHVAINCSKTSEVNCYRCGESGHLAREC 171

Single stranded DNA-binding protein, with specificity to the sterol regulatory element (SRE). Involved in sterol-mediated repression.

Rattus norvegicus (taxid: 10116)

>sp|Q5R5R5|CNBP_PONAB Cellular nucleic acid-binding protein OS=Pongo abelii GN=CNBP PE=2 SV=1

 Score = 80.9 bits (198), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 62/174 (35%), Positives = 81/174 (46%), Gaps = 43/174 (24%)

Query: 49  NLCNNCKRPGHFARECPNVA-----------------------------VCNNCGLPGHI 79
           N C  C R GH+ARECP                                +C  CG  GH+
Sbjct: 4   NECFKCGRSGHWARECPTGGGRGRGMRSRGRGGFTSDRGFQFVSSSLPDICYRCGESGHL 63

Query: 80  ASECTTQA-RCWNCREPGHMASNCHN-----EGICHSCGKTGHRARDCSTHVQSGGDLRL 133
           A +C  Q   C+NC   GH+A +C       E  C++CGK GH ARDC        D + 
Sbjct: 64  AKDCDLQEDACYNCGRGGHIAKDCKEPKREREQCCYNCGKPGHLARDCDH-----ADEQK 118

Query: 134 CNNCYKPGHIAADCTNDKACKNCRKTGHIARDCQ--NEPVCNLCNIAGHVARQC 185
           C +C + GHI  DCT  K C  C +TGH+A +C   +E  C  C  +GH+AR+C
Sbjct: 119 CYSCGEFGHIQKDCTKVK-CYRCGETGHVAINCSKTSEVNCYRCGESGHLAREC 171

Single stranded DNA-binding protein, with specificity to the sterol regulatory element (SRE). Involved in sterol-mediated repression.

Pongo abelii (taxid: 9601)

>sp|P62633|CNBP_HUMAN Cellular nucleic acid-binding protein OS=Homo sapiens GN=CNBP PE=1 SV=1

 Score = 80.9 bits (198), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 62/174 (35%), Positives = 81/174 (46%), Gaps = 43/174 (24%)

Query: 49  NLCNNCKRPGHFARECPNVA-----------------------------VCNNCGLPGHI 79
           N C  C R GH+ARECP                                +C  CG  GH+
Sbjct: 4   NECFKCGRSGHWARECPTGGGRGRGMRSRGRGGFTSDRGFQFVSSSLPDICYRCGESGHL 63

Query: 80  ASECTTQA-RCWNCREPGHMASNCHN-----EGICHSCGKTGHRARDCSTHVQSGGDLRL 133
           A +C  Q   C+NC   GH+A +C       E  C++CGK GH ARDC        D + 
Sbjct: 64  AKDCDLQEDACYNCGRGGHIAKDCKEPKREREQCCYNCGKPGHLARDCDH-----ADEQK 118

Query: 134 CNNCYKPGHIAADCTNDKACKNCRKTGHIARDCQ--NEPVCNLCNIAGHVARQC 185
           C +C + GHI  DCT  K C  C +TGH+A +C   +E  C  C  +GH+AR+C
Sbjct: 119 CYSCGEFGHIQKDCTKVK-CYRCGETGHVAINCSKTSEVNCYRCGESGHLAREC 171

Single stranded DNA-binding protein, with specificity to the sterol regulatory element (SRE). Involved in sterol-mediated repression.

Homo sapiens (taxid: 9606)

>sp|P53996|CNBP_MOUSE Cellular nucleic acid-binding protein OS=Mus musculus GN=Cnbp PE=2 SV=2

 Score = 80.5 bits (197), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 62/175 (35%), Positives = 81/175 (46%), Gaps = 44/175 (25%)

Query: 49  NLCNNCKRPGHFARECPNVA-----------------------------VCNNCGLPGHI 79
           N C  C R GH+ARECP                                +C  CG  GH+
Sbjct: 4   NECFKCGRSGHWARECPTGGGRGRGMRSRGRGGFTSDRGFQFVSSSLPDICYRCGESGHL 63

Query: 80  ASECTTQA--RCWNCREPGHMASNCHN-----EGICHSCGKTGHRARDCSTHVQSGGDLR 132
           A +C  Q    C+NC   GH+A +C       E  C++CGK GH ARDC        D +
Sbjct: 64  AKDCDLQEDEACYNCGRGGHIAKDCKEPKREREQCCYNCGKPGHLARDCDH-----ADEQ 118

Query: 133 LCNNCYKPGHIAADCTNDKACKNCRKTGHIARDCQ--NEPVCNLCNIAGHVARQC 185
            C +C + GHI  DCT  K C  C +TGH+A +C   +E  C  C  +GH+AR+C
Sbjct: 119 KCYSCGEFGHIQKDCTKVK-CYRCGETGHVAINCSKTSEVNCYRCGESGHLAREC 172

Single stranded DNA-binding protein, with specificity to the sterol regulatory element (SRE). Involved in sterol-mediated repression.

Mus musculus (taxid: 10090)

>sp|O65639|CSP1_ARATH Cold shock protein 1 OS=Arabidopsis thaliana GN=CSP1 PE=2 SV=1

 Score = 72.4 bits (176), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 55/167 (32%), Positives = 70/167 (41%), Gaps = 52/167 (31%)

Query: 51  CNNCKRPGHFARECPNVAV-------------CNNCGLPGHIASECTTQAR--------- 88
           C NC   GHFAR+C +                C  CG  GH+A +CT ++          
Sbjct: 134 CYNCGDTGHFARDCTSAGNGDQRGATKGGNDGCYTCGDVGHVARDCTQKSVGNGDQRGAV 193

Query: 89  ------CWNCREPGHMASNCHNE-------------GICHSCGKTGHRARDCSTHVQSGG 129
                 C+ C + GH A +C  +             G C+SCG  GH ARDC+T  Q   
Sbjct: 194 KGGNDGCYTCGDVGHFARDCTQKVAAGNVRSGGGGSGTCYSCGGVGHIARDCATKRQP-- 251

Query: 130 DLRLCNNCYKPGHIAADCT--------NDKACKNCRKTGHIARDCQN 168
             R C  C   GH+A DC         ND AC  C K GH AR+C +
Sbjct: 252 -SRGCYQCGGSGHLARDCDQRGSGGGGNDNACYKCGKEGHFARECSS 297

Chaperone that binds to RNA, single- (ssDNA) and double-stranded (dsDNA) DNA, and unwinds nucleic acid duplex. Exhibits a DNA melting activity. May be involved in cold resistance. Prevents seed germination under dehydration or salt stress conditions.

Arabidopsis thaliana (taxid: 3702)

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	271
255538826	256	cellular nucleic acid binding protein, p	0.822	0.871	0.770	1e-100
225458095	254	PREDICTED: zinc finger protein GIS2-like	0.826	0.881	0.775	1e-100
225427758	258	PREDICTED: zinc finger protein GIS2-like	0.933	0.980	0.674	2e-99
302142593	272	unnamed protein product [Vitis vinifera]	0.804	0.801	0.778	3e-98
224085782	239	predicted protein [Populus trichocarpa]	0.859	0.974	0.710	1e-95
359475089	246	PREDICTED: zinc finger protein GIS2-like	0.867	0.955	0.690	2e-95
297744732	259	unnamed protein product [Vitis vinifera]	0.867	0.907	0.686	8e-95
449461615	260	PREDICTED: DNA-binding protein HEXBP-lik	0.904	0.942	0.710	2e-93
224080454	242	predicted protein [Populus trichocarpa]	0.881	0.987	0.675	3e-93
356516892	259	PREDICTED: zinc finger protein GIS2-like	0.900	0.942	0.706	1e-91

>gi|255538826|ref|XP_002510478.1| cellular nucleic acid binding protein, putative [Ricinus communis] gi|223551179|gb|EEF52665.1| cellular nucleic acid binding protein, putative [Ricinus communis]

 Score =  370 bits (950), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 185/240 (77%), Positives = 200/240 (83%), Gaps = 17/240 (7%)

Query: 32  YCDPPLRRETRRSFSQGNLCNNCKRPGHFARECPNVAVCNNCGLPGHIASECTTQARCWN 91
           Y D P RRETRR FSQ +LCNNCKRPGHFARECPNVAVCNNCGLPGHIA+ECTTQ+RCWN
Sbjct: 34  YRDAPYRRETRRGFSQSSLCNNCKRPGHFARECPNVAVCNNCGLPGHIAAECTTQSRCWN 93

Query: 92  CREPGHMASNCHNEGICHSCGKTGHRARDCSTHVQSGGDLRLCNNCYKPGHIAADCTNDK 151
           CREPGH+ASNC NEGICHSCGK+GHRARDCST     GDLRLCNNCYKPGHIAA CTNDK
Sbjct: 94  CREPGHVASNCPNEGICHSCGKSGHRARDCSTPDMPPGDLRLCNNCYKPGHIAAQCTNDK 153

Query: 152 ACKNCRKTGHIARDCQNEPVCNLCNIAGHVARQCPKGDSLGERGGGGGGERGGGGGGDGG 211
           ACKNCRKTGH+ARDCQNEPVCN CNIAGHVARQCPK D   ER                 
Sbjct: 154 ACKNCRKTGHVARDCQNEPVCNFCNIAGHVARQCPKVDIHAER----------------- 196

Query: 212 GGGGRYVGYHDVICRSCNQMGHMSRDCVGPLIICRNCGGRGHMAYECPSGRIADRGYRRY 271
           GG GR+ GY D+ICR+CNQ+GHMSRDC+GP+IIC NCGGRGH A+ECPSGR +DRG+RRY
Sbjct: 197 GGWGRHNGYRDLICRTCNQVGHMSRDCIGPMIICHNCGGRGHRAFECPSGRFSDRGFRRY 256

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225458095|ref|XP_002279453.1| PREDICTED: zinc finger protein GIS2-like isoform 1 [Vitis vinifera]

 Score =  369 bits (947), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 187/241 (77%), Positives = 196/241 (81%), Gaps = 17/241 (7%)

Query: 31  SYCDPPLRRETRRSFSQGNLCNNCKRPGHFARECPNVAVCNNCGLPGHIASECTTQARCW 90
           SY D P RRE+RR FSQGNLCNNCKRPGHFARECPNVA+CNNC LPGHIASECTTQ+ CW
Sbjct: 31  SYRDAPYRRESRRGFSQGNLCNNCKRPGHFARECPNVAICNNCNLPGHIASECTTQSLCW 90

Query: 91  NCREPGHMASNCHNEGICHSCGKTGHRARDCSTHVQSGGDLRLCNNCYKPGHIAADCTND 150
           NCREPGHMASNC NEGICHSC KTGHRARDC T     GDLRLCNNCYK GHIAADCTND
Sbjct: 91  NCREPGHMASNCPNEGICHSCNKTGHRARDCPTPGLPSGDLRLCNNCYKQGHIAADCTND 150

Query: 151 KACKNCRKTGHIARDCQNEPVCNLCNIAGHVARQCPKGDSLGERGGGGGGERGGGGGGDG 210
           KACKNCRKTGHIARDCQNEPVCNLCNIAGHVARQCPK +  GER                
Sbjct: 151 KACKNCRKTGHIARDCQNEPVCNLCNIAGHVARQCPKAEIFGER---------------- 194

Query: 211 GGGGGRYVGYHDVICRSCNQMGHMSRDCVGPLIICRNCGGRGHMAYECPSGRIADRGYRR 270
            GGGGR  G+ DVICRSCNQ+GHMSRDC+  L+IC NCGGRGHMA+ECPSGR  DR  RR
Sbjct: 195 -GGGGRNTGFRDVICRSCNQVGHMSRDCMVSLVICNNCGGRGHMAFECPSGRFMDRMPRR 253

Query: 271 Y 271
           Y
Sbjct: 254 Y 254

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225427758|ref|XP_002267480.1| PREDICTED: zinc finger protein GIS2-like isoform 1 [Vitis vinifera]

 Score =  367 bits (943), Expect = 2e-99,   Method: Compositional matrix adjust.
 Identities = 182/270 (67%), Positives = 213/270 (78%), Gaps = 17/270 (6%)

Query: 2   SSRSRSISRSRSRSRSRSPRDRRFRSRHSSYCDPPLRRETRRSFSQGNLCNNCKRPGHFA 61
            +R RS + ++ +SRSRSP+DR+ R+   SY + P RR++RR FSQGNLC NCKRPGH+A
Sbjct: 6   QARLRSRNITQHKSRSRSPQDRKIRTDRLSYRNAPYRRDSRRGFSQGNLCKNCKRPGHYA 65

Query: 62  RECPNVAVCNNCGLPGHIASECTTQARCWNCREPGHMASNCHNEGICHSCGKTGHRARDC 121
           RECPNVAVC+NC LPGHIASECTT++ CWNC+EPGH ASNC NEGICH+CGKTGH ARDC
Sbjct: 66  RECPNVAVCHNCSLPGHIASECTTRSLCWNCQEPGHTASNCPNEGICHTCGKTGHLARDC 125

Query: 122 STHVQSGGDLRLCNNCYKPGHIAADCTNDKACKNCRKTGHIARDCQNEPVCNLCNIAGHV 181
           S      GDLRLCNNCYK GHIAADCTNDKAC NCRKTGH+ARDC+N+PVCNLCN++GHV
Sbjct: 126 SAPPVPPGDLRLCNNCYKQGHIAADCTNDKACNNCRKTGHLARDCRNDPVCNLCNVSGHV 185

Query: 182 ARQCPKGDSLGERGGGGGGERGGGGGGDGGGGGGRYVGYHDVICRSCNQMGHMSRDCVGP 241
           ARQCPK + LG+R                 GGG R  G+ D++CR+C Q+GHMSRDC  P
Sbjct: 186 ARQCPKANVLGDR-----------------GGGPRSSGFRDIVCRNCQQLGHMSRDCAAP 228

Query: 242 LIICRNCGGRGHMAYECPSGRIADRGYRRY 271
           L+ICRNCGGRGHMA+ECPSGR  DR  RRY
Sbjct: 229 LMICRNCGGRGHMAFECPSGRFMDRFPRRY 258

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|302142593|emb|CBI19796.3| unnamed protein product [Vitis vinifera]

 Score =  364 bits (934), Expect = 3e-98,   Method: Compositional matrix adjust.
 Identities = 183/235 (77%), Positives = 192/235 (81%), Gaps = 17/235 (7%)

Query: 31  SYCDPPLRRETRRSFSQGNLCNNCKRPGHFARECPNVAVCNNCGLPGHIASECTTQARCW 90
           SY D P RRE+RR FSQGNLCNNCKRPGHFARECPNVA+CNNC LPGHIASECTTQ+ CW
Sbjct: 31  SYRDAPYRRESRRGFSQGNLCNNCKRPGHFARECPNVAICNNCNLPGHIASECTTQSLCW 90

Query: 91  NCREPGHMASNCHNEGICHSCGKTGHRARDCSTHVQSGGDLRLCNNCYKPGHIAADCTND 150
           NCREPGHMASNC NEGICHSC KTGHRARDC T     GDLRLCNNCYK GHIAADCTND
Sbjct: 91  NCREPGHMASNCPNEGICHSCNKTGHRARDCPTPGLPSGDLRLCNNCYKQGHIAADCTND 150

Query: 151 KACKNCRKTGHIARDCQNEPVCNLCNIAGHVARQCPKGDSLGERGGGGGGERGGGGGGDG 210
           KACKNCRKTGHIARDCQNEPVCNLCNIAGHVARQCPK +  GER                
Sbjct: 151 KACKNCRKTGHIARDCQNEPVCNLCNIAGHVARQCPKAEIFGER---------------- 194

Query: 211 GGGGGRYVGYHDVICRSCNQMGHMSRDCVGPLIICRNCGGRGHMAYECPSGRIAD 265
            GGGGR  G+ DVICRSCNQ+GHMSRDC+  L+IC NCGGRGHMA+ECPSGR  D
Sbjct: 195 -GGGGRNTGFRDVICRSCNQVGHMSRDCMVSLVICNNCGGRGHMAFECPSGRFMD 248

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224085782|ref|XP_002307695.1| predicted protein [Populus trichocarpa] gi|222857144|gb|EEE94691.1| predicted protein [Populus trichocarpa]

 Score =  355 bits (911), Expect = 1e-95,   Method: Compositional matrix adjust.
 Identities = 182/256 (71%), Positives = 202/256 (78%), Gaps = 23/256 (8%)

Query: 19  SPRDRRFRSRHSSYCDPPLRRETRRS------FSQGNLCNNCKRPGHFARECPNVAVCNN 72
           SPRDRRFRS+ +SY D P RRET R       FSQ NLC+NCKR GHFARECPN AVCNN
Sbjct: 1   SPRDRRFRSQRNSYRDGPYRRETHRERDRDRGFSQTNLCHNCKRAGHFARECPNAAVCNN 60

Query: 73  CGLPGHIASECTTQARCWNCREPGHMASNCHNEGICHSCGKTGHRARDCSTHVQSGGDLR 132
           CGLPGH+ASECTTQ +CWNCREPGH+ASNC NEGICH+CG++GHRA+DC     S GD+R
Sbjct: 61  CGLPGHVASECTTQLQCWNCREPGHVASNCPNEGICHACGRSGHRAKDCPNPEPSPGDVR 120

Query: 133 LCNNCYKPGHIAADCTNDKACKNCRKTGHIARDCQNEPVCNLCNIAGHVARQCPKGDSLG 192
           LCNNCYKPGH AADCTNDKACKNCRKTGH+ARDCQNEPVCNLCNI+GHVARQC +G+S  
Sbjct: 121 LCNNCYKPGHFAADCTNDKACKNCRKTGHMARDCQNEPVCNLCNISGHVARQCTRGNSFP 180

Query: 193 ERGGGGGGERGGGGGGDGGGGGGRYVGYHDVICRSCNQMGHMSRDCVGPLIICRNCGGRG 252
           +R                 GG GR   Y DVICR+CNQ+GHMSRDC+GP+IIC NCGGRG
Sbjct: 181 DR-----------------GGWGRNSSYRDVICRTCNQVGHMSRDCIGPMIICHNCGGRG 223

Query: 253 HMAYECPSGRIADRGY 268
           H A ECPSGRIA R Y
Sbjct: 224 HRAIECPSGRIAFRRY 239

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359475089|ref|XP_003631583.1| PREDICTED: zinc finger protein GIS2-like isoform 2 [Vitis vinifera]

 Score =  354 bits (908), Expect = 2e-95,   Method: Compositional matrix adjust.
 Identities = 174/252 (69%), Positives = 200/252 (79%), Gaps = 17/252 (6%)

Query: 20  PRDRRFRSRHSSYCDPPLRRETRRSFSQGNLCNNCKRPGHFARECPNVAVCNNCGLPGHI 79
           P+DR+ R+   SY + P RR++RR FSQGNLC NCKRPGH+ARECPNVAVC+NC LPGHI
Sbjct: 12  PQDRKIRTDRLSYRNAPYRRDSRRGFSQGNLCKNCKRPGHYARECPNVAVCHNCSLPGHI 71

Query: 80  ASECTTQARCWNCREPGHMASNCHNEGICHSCGKTGHRARDCSTHVQSGGDLRLCNNCYK 139
           ASECTT++ CWNC+EPGH ASNC NEGICH+CGKTGH ARDCS      GDLRLCNNCYK
Sbjct: 72  ASECTTRSLCWNCQEPGHTASNCPNEGICHTCGKTGHLARDCSAPPVPPGDLRLCNNCYK 131

Query: 140 PGHIAADCTNDKACKNCRKTGHIARDCQNEPVCNLCNIAGHVARQCPKGDSLGERGGGGG 199
            GHIAADCTNDKAC NCRKTGH+ARDC+N+PVCNLCN++GHVARQCPK + LG+R     
Sbjct: 132 QGHIAADCTNDKACNNCRKTGHLARDCRNDPVCNLCNVSGHVARQCPKANVLGDR----- 186

Query: 200 GERGGGGGGDGGGGGGRYVGYHDVICRSCNQMGHMSRDCVGPLIICRNCGGRGHMAYECP 259
                       GGG R  G+ D++CR+C Q+GHMSRDC  PL+ICRNCGGRGHMA+ECP
Sbjct: 187 ------------GGGPRSSGFRDIVCRNCQQLGHMSRDCAAPLMICRNCGGRGHMAFECP 234

Query: 260 SGRIADRGYRRY 271
           SGR  DR  RRY
Sbjct: 235 SGRFMDRFPRRY 246

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297744732|emb|CBI37994.3| unnamed protein product [Vitis vinifera]

 Score =  352 bits (903), Expect = 8e-95,   Method: Compositional matrix adjust.
 Identities = 173/252 (68%), Positives = 199/252 (78%), Gaps = 17/252 (6%)

Query: 20  PRDRRFRSRHSSYCDPPLRRETRRSFSQGNLCNNCKRPGHFARECPNVAVCNNCGLPGHI 79
           P+DR+ R+   SY + P RR++RR FSQGNLC NCKRPGH+ARECPNVAVC+NC LPGHI
Sbjct: 12  PQDRKIRTDRLSYRNAPYRRDSRRGFSQGNLCKNCKRPGHYARECPNVAVCHNCSLPGHI 71

Query: 80  ASECTTQARCWNCREPGHMASNCHNEGICHSCGKTGHRARDCSTHVQSGGDLRLCNNCYK 139
           ASECTT++ CWNC+EPGH ASNC NEGICH+CGKTGH ARDCS      GDLRLCNNCYK
Sbjct: 72  ASECTTRSLCWNCQEPGHTASNCPNEGICHTCGKTGHLARDCSAPPVPPGDLRLCNNCYK 131

Query: 140 PGHIAADCTNDKACKNCRKTGHIARDCQNEPVCNLCNIAGHVARQCPKGDSLGERGGGGG 199
            GHIAADCTNDKAC NCRKTGH+ARDC+N+PVCNLCN++GHVARQCPK + LG+R     
Sbjct: 132 QGHIAADCTNDKACNNCRKTGHLARDCRNDPVCNLCNVSGHVARQCPKANVLGDR----- 186

Query: 200 GERGGGGGGDGGGGGGRYVGYHDVICRSCNQMGHMSRDCVGPLIICRNCGGRGHMAYECP 259
                       GGG R  G+ D++CR+C Q+GHMSRDC  PL+ICRNCGGRGHMA+ECP
Sbjct: 187 ------------GGGPRSSGFRDIVCRNCQQLGHMSRDCAAPLMICRNCGGRGHMAFECP 234

Query: 260 SGRIADRGYRRY 271
           SGR  DR  RR 
Sbjct: 235 SGRFMDRFPRRL 246

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449461615|ref|XP_004148537.1| PREDICTED: DNA-binding protein HEXBP-like [Cucumis sativus] gi|449519884|ref|XP_004166964.1| PREDICTED: DNA-binding protein HEXBP-like [Cucumis sativus]

 Score =  347 bits (891), Expect = 2e-93,   Method: Compositional matrix adjust.
 Identities = 179/252 (71%), Positives = 203/252 (80%), Gaps = 7/252 (2%)

Query: 20  PRDRRFRSRHSSYCDPPLRRETRRSFSQGNLCNNCKRPGHFARECPNVAVCNNCGLPGHI 79
           P DR+ RS   SY D P RRE+RR FS+ NLC NCKRPGHFARECPNVA+C+NCGLPGHI
Sbjct: 16  PLDRKIRSDRFSYRDAPYRRESRRGFSRDNLCKNCKRPGHFARECPNVAICHNCGLPGHI 75

Query: 80  ASECTTQARCWNCREPGHMASNCHNEGICHSCGKTGHRARDCSTHVQSGGDLRLCNNCYK 139
           ASECTT++ CWNCREPGHMAS+C NEGICH+CGK GHRARDC+      GDLRLCNNCYK
Sbjct: 76  ASECTTKSLCWNCREPGHMASSCPNEGICHTCGKAGHRARDCTAPPMPPGDLRLCNNCYK 135

Query: 140 PGHIAADCTNDKACKNCRKTGHIARDCQNEPVCNLCNIAGHVARQCPKGDSLGERGGGGG 199
            GHIAADCTN+KAC NCRKTGH+ARDC N+P+CNLCN++GHVARQCPK + LG+RG  G 
Sbjct: 136 QGHIAADCTNEKACNNCRKTGHLARDCPNDPICNLCNVSGHVARQCPKSNVLGDRGDRGI 195

Query: 200 GERGGGGGGDGGGGGGRYVGYHDVICRSCNQMGHMSRDCVGPLIICRNCGGRGHMAYECP 259
              GG G G G        GY DV+CR+C Q+GHMSRDC+GPL+IC NCGGRGH+AYECP
Sbjct: 196 SSGGGSGRGSGS-------GYRDVVCRNCQQLGHMSRDCMGPLMICHNCGGRGHLAYECP 248

Query: 260 SGRIADRGYRRY 271
           SGR  DR  RRY
Sbjct: 249 SGRFMDRFPRRY 260

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224080454|ref|XP_002306137.1| predicted protein [Populus trichocarpa] gi|222849101|gb|EEE86648.1| predicted protein [Populus trichocarpa]

 Score =  347 bits (890), Expect = 3e-93,   Method: Compositional matrix adjust.
 Identities = 175/259 (67%), Positives = 201/259 (77%), Gaps = 20/259 (7%)

Query: 15  SRSRSPRDRRFRSRHSSYCDPPLRRETRRS--FSQGNLCNNCKRPGHFARECPNVAVCNN 72
           SRSRSP DRR RS   SY   P RRE+RR   F Q NLC NCKRPGH+ARECPNVA+C+N
Sbjct: 1   SRSRSPMDRRIRSDRFSYRGAPYRRESRRGYRFLQSNLCKNCKRPGHYARECPNVAICHN 60

Query: 73  CGLPGHIASECTTQARCWNCREPGHMASNCHNEGICHSCGKTGHRARDCSTHVQSGGDLR 132
           CGLPGHIASECTT++ CWNCREPGHMASNC NEGICH+CGK GHRA++C+      GDLR
Sbjct: 61  CGLPGHIASECTTKSLCWNCREPGHMASNCPNEGICHTCGKAGHRAKECTAPPMPPGDLR 120

Query: 133 LCNNCYKPGHIAADCTNDKACKNCRKTGHIARDCQNEPVCNLCNIAGHVARQCPKGDSLG 192
           LCNNCYK GHIAADCTNDKAC NCRKTGH+AR+C NEP+CN+CN+AGHVARQCPK + LG
Sbjct: 121 LCNNCYKQGHIAADCTNDKACNNCRKTGHLARECPNEPICNMCNVAGHVARQCPKSNMLG 180

Query: 193 ERGGGGGGERGGGGGGDGGGGGGRYVGYHDVICRSCNQMGHMSRDCVGPLIICRNCGGRG 252
           +RGG   G                  GY D++CR+C+Q GHMSRDC+GPL+IC NCGGRG
Sbjct: 181 DRGGMRSG------------------GYQDIVCRNCHQYGHMSRDCMGPLMICHNCGGRG 222

Query: 253 HMAYECPSGRIADRGYRRY 271
           H A ECPSGR+ DR  +R+
Sbjct: 223 HRAIECPSGRMMDRYPQRF 241

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356516892|ref|XP_003527126.1| PREDICTED: zinc finger protein GIS2-like [Glycine max]

 Score =  342 bits (877), Expect = 1e-91,   Method: Compositional matrix adjust.
 Identities = 178/252 (70%), Positives = 206/252 (81%), Gaps = 8/252 (3%)

Query: 20  PRDRRFRSRHSSYCDPPLRRETRRSFSQGNLCNNCKRPGHFARECPNVAVCNNCGLPGHI 79
           P DR+ RS   SY D P RR++RR FS+ NLC NCKRPGH+ARECPNVA+C+NCGLPGHI
Sbjct: 16  PMDRKIRSDRFSYRDAPYRRDSRRGFSRDNLCKNCKRPGHYARECPNVAICHNCGLPGHI 75

Query: 80  ASECTTQARCWNCREPGHMASNCHNEGICHSCGKTGHRARDCSTHVQSGGDLRLCNNCYK 139
           ASECTT++ CWNC+EPGHMAS+C NEGICH+CGK GHRAR+CS      GDLRLCNNCYK
Sbjct: 76  ASECTTKSLCWNCKEPGHMASSCPNEGICHTCGKAGHRARECSAPPMPPGDLRLCNNCYK 135

Query: 140 PGHIAADCTNDKACKNCRKTGHIARDCQNEPVCNLCNIAGHVARQCPKGDSLGERGGGGG 199
            GHIAA+CTN+KAC NCRKTGH+ARDC N+P+CNLCN++GHVARQCPK + LG+R GGGG
Sbjct: 136 QGHIAAECTNEKACNNCRKTGHLARDCPNDPICNLCNVSGHVARQCPKANVLGDRSGGGG 195

Query: 200 GERGGGGGGDGGGGGGRYVGYHDVICRSCNQMGHMSRDCVGPLIICRNCGGRGHMAYECP 259
           G  G  GGG G        GY DV+CR+C Q+GHMSRDC+GPL+IC NCGGRGH+AYECP
Sbjct: 196 GGGGARGGGGG--------GYRDVVCRNCQQLGHMSRDCMGPLMICHNCGGRGHLAYECP 247

Query: 260 SGRIADRGYRRY 271
           SGR  DR  RRY
Sbjct: 248 SGRFMDRYPRRY 259

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	271
TAIR|locus:2005719	257	AT1G75560 [Arabidopsis thalian	0.586	0.618	0.788	2.4e-91
POMBASE|SPAC13D6.02c	179	byr3 "zinc finger protein Byr3	0.472	0.715	0.409	2.2e-27
SGD|S000005199	153	GIS2 "Translational activator	0.501	0.888	0.358	7.3e-27
UNIPROTKB|F1N8C2	171	CNBP "Cellular nucleic acid-bi	0.498	0.789	0.367	4e-26
ASPGD|ASPL0000028407	171	AN5111 [Emericella nidulans (t	0.464	0.736	0.370	8e-21
UNIPROTKB|O42395	172	CNBP "Cellular nucleic acid-bi	0.409	0.645	0.412	5.5e-22
UNIPROTKB|B4DP17	160	CNBP "cDNA FLJ61146, highly si	0.409	0.693	0.416	3.4e-22
UNIPROTKB|Q3T0Q6	170	CNBP "Cellular nucleic acid-bi	0.409	0.652	0.416	3.4e-22
UNIPROTKB|G3MZ41	175	ZCCHC13 "Uncharacterized prote	0.450	0.697	0.385	3.9e-21
UNIPROTKB|P62633	177	CNBP "Cellular nucleic acid-bi	0.409	0.627	0.416	3.4e-22

TAIR|locus:2005719 AT1G75560 [Arabidopsis thaliana (taxid:3702)]

 Score = 770 (276.1 bits), Expect = 2.4e-91, Sum P(2) = 2.4e-91
 Identities = 127/161 (78%), Positives = 143/161 (88%)

Query:    32 YCDPPLRRET--RRSFSQGNLCNNCKRPGHFARECPNVAVCNNCGLPGHIASECTTQARC 89
             Y D P RRE   RR+FSQGNLCNNCKRPGHFAR+C NV+VCNNCGLPGHIA+ECT ++RC
Sbjct:    36 YHDAPSRREREPRRAFSQGNLCNNCKRPGHFARDCSNVSVCNNCGLPGHIAAECTAESRC 95

Query:    90 WNCREPGHMASNCHNEGICHSCGKTGHRARDCSTHVQSGGDLRLCNNCYKPGHIAADCTN 149
             WNCREPGH+ASNC NEGICHSCGK+GHRARDCS      GDLRLCNNC+K GH+AADCTN
Sbjct:    96 WNCREPGHVASNCSNEGICHSCGKSGHRARDCSNSDSRAGDLRLCNNCFKQGHLAADCTN 155

Query:   150 DKACKNCRKTGHIARDCQNEPVCNLCNIAGHVARQCPKGDS 190
             DKACKNCR +GHIARDC+N+PVCN+C+I+GHVAR CPKGDS
Sbjct:   156 DKACKNCRTSGHIARDCRNDPVCNICSISGHVARHCPKGDS 196

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

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0008270 "zinc ion binding" evidence=IEA

GO:0006457 "protein folding" evidence=RCA

GO:0009408 "response to heat" evidence=RCA

GO:0009644 "response to high light intensity" evidence=RCA

GO:0034976 "response to endoplasmic reticulum stress" evidence=RCA

GO:0042542 "response to hydrogen peroxide" evidence=RCA

POMBASE|SPAC13D6.02c byr3 "zinc finger protein Byr3" [Schizosaccharomyces pombe (taxid:4896)]

 Score = 260 (96.6 bits), Expect = 2.2e-27, Sum P(2) = 2.2e-27
 Identities = 59/144 (40%), Positives = 73/144 (50%)

Query:    48 GNLCNNCKRPGHFARECPNVAVCNNCGLPGHIASECTT---QARCWNCREPGHMASNCHN 104
             G  C NC   GH AREC   ++C NC   GH ASECT    +  C+ C   GH+  +C +
Sbjct:    16 GPRCYNCGENGHQARECTKGSICYNCNQTGHKASECTEPQQEKTCYACGTAGHLVRDCPS 75

Query:   105 -----EGI-CHSCGKTGHRARDCSTH-VQSGGDL---RLCNNCY---KPGHIAADCTNDK 151
                  +G  C+ CG+ GH ARDC T+  QSGG     R   NCY     GH A DCT   
Sbjct:    76 SPNPRQGAECYKCGRVGHIARDCRTNGQQSGGRFGGHRSNMNCYACGSYGHQARDCTMGV 135

Query:   152 ACKNCRKTGHIARDCQNEPVCNLC 175
              C +C K GH + +CQ      LC
Sbjct:   136 KCYSCGKIGHRSFECQQASDGQLC 159

GO:0000747 "conjugation with cellular fusion" evidence=IMP

GO:0003677 "DNA binding" evidence=IEA

GO:0005730 "nucleolus" evidence=IDA

GO:0005829 "cytosol" evidence=IDA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0031137 "regulation of conjugation with cellular fusion" evidence=IGI

SGD|S000005199 GIS2 "Translational activator for mRNAs with internal ribosome entry sites" [Saccharomyces cerevisiae (taxid:4932)]

 Score = 302 (111.4 bits), Expect = 7.3e-27, P = 7.3e-27
 Identities = 53/148 (35%), Positives = 82/148 (55%)

Query:    51 CNNCKRPGHFARECPNVAVCNNCGLPGHIASECTTQA-----RCWNCREPGHMASNCHNE 105
             C  C + GH A +C +  +C NC  PGH+ ++CT        +C+NC E GH+ S C  +
Sbjct:     6 CYVCGKIGHLAEDCDSERLCYNCNKPGHVQTDCTMPRTVEFKQCYNCGETGHVRSECTVQ 65

Query:   106 GICHSCGKTGHRARDCSTHVQSGGDLRL-CNNCYKPGHIAADCTNDKA-----CKNCRKT 159
               C +C +TGH +R+C    ++    ++ C  C  P H+A DC  +       C  C + 
Sbjct:    66 R-CFNCNQTGHISRECPEPKKTSRFSKVSCYKCGGPNHMAKDCMKEDGISGLKCYTCGQA 124

Query:   160 GHIARDCQNEPVCNLCNIAGHVARQCPK 187
             GH++RDCQN+ +C  CN  GH+++ CPK
Sbjct:   125 GHMSRDCQNDRLCYNCNETGHISKDCPK 152

GO:0008270 "zinc ion binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA;IDA

GO:0000932 "cytoplasmic mRNA processing body" evidence=IDA

GO:0003729 "mRNA binding" evidence=IDA

GO:0010494 "cytoplasmic stress granule" evidence=IDA

GO:0046872 "metal ion binding" evidence=IEA

GO:0042788 "polysomal ribosome" evidence=IPI

GO:0045182 "translation regulator activity" evidence=IDA

GO:0045727 "positive regulation of translation" evidence=IDA

GO:0003697 "single-stranded DNA binding" evidence=IDA

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|F1N8C2 CNBP "Cellular nucleic acid-binding protein" [Gallus gallus (taxid:9031)]

 Score = 258 (95.9 bits), Expect = 4.0e-26, Sum P(2) = 4.0e-26
 Identities = 54/147 (36%), Positives = 77/147 (52%)

Query:    49 NLCNNCKRPGHFARECPNVAVCNNCGLP--GHIASECTTQAR---CWNCREPGHMASNCH 103
             N C  C R GH+ARECP   +    G+   G    +  + +    C+ C E GH+A +C 
Sbjct:     4 NECFKCGRTGHWARECPT-GIGRGRGMRSRGRAGFQFMSSSLPDICYRCGESGHLAKDCD 62

Query:   104 -NEGICHSCGKTGHRARDCSTHVQSGGDLRLCNNCYKPGHIAADC--TNDKACKNCRKTG 160
               E  C++CG+ GH A+DC    +     + C NC KPGH+A DC   +++ C +C + G
Sbjct:    63 LQEDACYNCGRGGHIAKDCKEPKRERE--QCCYNCGKPGHLARDCDHADEQKCYSCGEFG 120

Query:   161 HIARDCQNEPVCNLCNIAGHVARQCPK 187
             HI +DC  +  C  C   GHVA  C K
Sbjct:   121 HIQKDC-TKVKCYRCGETGHVAINCSK 146

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005783 "endoplasmic reticulum" evidence=IEA

GO:0005829 "cytosol" evidence=IEA

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

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=IEA

ASPGD|ASPL0000028407 AN5111 [Emericella nidulans (taxid:162425)]

 Score = 245 (91.3 bits), Expect = 8.0e-21, P = 8.0e-21
 Identities = 56/151 (37%), Positives = 70/151 (46%)

Query:    51 CNNCKRPGHFAREC---PNVAVCNNCGLPGHIASECTTQARCWNCREPGHMASNCHNEGI 107
             C NC   GH +REC   P    C  CG  GHI+ EC       N R  G           
Sbjct:    29 CYNCGGQGHVSRECTVAPKEKSCYRCGAVGHISRECPQAGE--NERPAGGQE-------- 78

Query:   108 CHSCGKTGHRARDCSTHVQSGGDL--------RLCNNCYKPGHIAADCTNDKACKNCRKT 159
             C+ CG+ GH AR+CS     GG          + C +C   GH+A DCT  + C NC +T
Sbjct:    79 CYKCGRVGHIARNCSQGGSYGGGFGGGYGGRQQTCYSCGGFGHMARDCTQGQKCYNCGET 138

Query:   160 GHIARDC----QNEPVCNLCNIAGHVARQCP 186
             GH++RDC    + E VC  C   GH+   CP
Sbjct:   139 GHVSRDCPTEAKGERVCYQCKQPGHIQSACP 169

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

GO:0005829 "cytosol" evidence=IEA

GO:0000747 "conjugation with cellular fusion" evidence=IEA

GO:0031137 "regulation of conjugation with cellular fusion" evidence=IEA

UNIPROTKB|O42395 CNBP "Cellular nucleic acid-binding protein" [Gallus gallus (taxid:9031)]

 Score = 256 (95.2 bits), Expect = 5.5e-22, P = 5.5e-22
 Identities = 52/126 (41%), Positives = 70/126 (55%)

Query:    69 VCNNCGLPGHIASECTTQA--RCWNCREPGHMASNC-----HNEGICHSCGKTGHRARDC 121
             +C  CG  GH+A +C  Q    C+NC   GH+A +C       E  C++CGK GH ARDC
Sbjct:    47 ICYRCGESGHLAKDCDLQEDKACYNCGRGGHIAKDCKEPKREREQCCYNCGKPGHLARDC 106

Query:   122 STHVQSGGDLRLCNNCYKPGHIAADCTNDKACKNCRKTGHIARDCQ--NEPVCNLCNIAG 179
               H     D + C +C + GHI  DCT  K C  C +TGH+A +C   +E  C  C  +G
Sbjct:   107 D-HA----DEQKCYSCGEFGHIQKDCTKVK-CYRCGETGHVAINCSKTSEVNCYRCGESG 160

Query:   180 HVARQC 185
             H+AR+C
Sbjct:   161 HLAREC 166

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0005783 "endoplasmic reticulum" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005829 "cytosol" evidence=IEA

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

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=IEA

UNIPROTKB|B4DP17 CNBP "cDNA FLJ61146, highly similar to Cellular nucleic acid-binding protein" [Homo sapiens (taxid:9606)]

 Score = 258 (95.9 bits), Expect = 3.4e-22, P = 3.4e-22
 Identities = 52/125 (41%), Positives = 70/125 (56%)

Query:    69 VCNNCGLPGHIASECTTQA-RCWNCREPGHMASNC-----HNEGICHSCGKTGHRARDCS 122
             +C  CG  GH+A +C  Q   C+NC   GH+A +C       E  C++CGK GH ARDC 
Sbjct:    36 ICYRCGESGHLAKDCDLQEDACYNCGRGGHIAKDCKEPKREREQCCYNCGKPGHLARDCD 95

Query:   123 THVQSGGDLRLCNNCYKPGHIAADCTNDKACKNCRKTGHIARDCQ--NEPVCNLCNIAGH 180
              H     D + C +C + GHI  DCT  K C  C +TGH+A +C   +E  C  C  +GH
Sbjct:    96 -HA----DEQKCYSCGEFGHIQKDCTKVK-CYRCGETGHVAINCSKTSEVNCYRCGESGH 149

Query:   181 VARQC 185
             +AR+C
Sbjct:   150 LAREC 154

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

UNIPROTKB|Q3T0Q6 CNBP "Cellular nucleic acid-binding protein" [Bos taurus (taxid:9913)]

 Score = 258 (95.9 bits), Expect = 3.4e-22, P = 3.4e-22
 Identities = 52/125 (41%), Positives = 70/125 (56%)

Query:    69 VCNNCGLPGHIASECTTQA-RCWNCREPGHMASNC-----HNEGICHSCGKTGHRARDCS 122
             +C  CG  GH+A +C  Q   C+NC   GH+A +C       E  C++CGK GH ARDC 
Sbjct:    46 ICYRCGESGHLAKDCDLQEDACYNCGRGGHIAKDCKEPKREREQCCYNCGKPGHLARDCD 105

Query:   123 THVQSGGDLRLCNNCYKPGHIAADCTNDKACKNCRKTGHIARDCQ--NEPVCNLCNIAGH 180
              H     D + C +C + GHI  DCT  K C  C +TGH+A +C   +E  C  C  +GH
Sbjct:   106 -HA----DEQKCYSCGEFGHIQKDCTKVK-CYRCGETGHVAINCSKTSEVNCYRCGESGH 159

Query:   181 VARQC 185
             +AR+C
Sbjct:   160 LAREC 164

GO:0005783 "endoplasmic reticulum" evidence=IEA

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=IEA

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

GO:0005829 "cytosol" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

UNIPROTKB|G3MZ41 ZCCHC13 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 248 (92.4 bits), Expect = 3.9e-21, P = 3.9e-21
 Identities = 54/140 (38%), Positives = 74/140 (52%)

Query:    58 GHFARECPNVA---VCNNCGLPGHIASECTT-QARCWNCREPGHMASNC---HNEG--IC 108
             GH A +C +     +C  CG  GH A +C      C+NC + GH+A +C     EG   C
Sbjct:    38 GHGA-QCSSTTLPVICYRCGKFGHYAKDCDLLDDICYNCGKSGHIAKDCAEPKREGERCC 96

Query:   109 HSCGKTGHRARDCSTHVQSGGDLRLCNNCYKPGHIAADCTNDKACKNCRKTGHIARDCQ- 167
             ++CG+ GH ARDC    +     R C +C K GHI   CT  K C  C + GH+A +C+ 
Sbjct:    97 YTCGRPGHLARDCDRQEE-----RKCYSCGKSGHIQKYCTQVK-CYRCGEIGHVAINCRK 150

Query:   168 -NEPVCNLCNIAGHVARQCP 186
              NE  C  C  +GH+ R+CP
Sbjct:   151 MNEVNCYRCGESGHLTRECP 170

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|P62633 CNBP "Cellular nucleic acid-binding protein" [Homo sapiens (taxid:9606)]

 Score = 258 (95.9 bits), Expect = 3.4e-22, P = 3.4e-22
 Identities = 52/125 (41%), Positives = 70/125 (56%)

Query:    69 VCNNCGLPGHIASECTTQA-RCWNCREPGHMASNC-----HNEGICHSCGKTGHRARDCS 122
             +C  CG  GH+A +C  Q   C+NC   GH+A +C       E  C++CGK GH ARDC 
Sbjct:    53 ICYRCGESGHLAKDCDLQEDACYNCGRGGHIAKDCKEPKREREQCCYNCGKPGHLARDCD 112

Query:   123 THVQSGGDLRLCNNCYKPGHIAADCTNDKACKNCRKTGHIARDCQ--NEPVCNLCNIAGH 180
              H     D + C +C + GHI  DCT  K C  C +TGH+A +C   +E  C  C  +GH
Sbjct:   113 -HA----DEQKCYSCGEFGHIQKDCTKVK-CYRCGETGHVAINCSKTSEVNCYRCGESGH 166

Query:   181 VARQC 185
             +AR+C
Sbjct:   167 LAREC 171

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=ISS

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

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=ISS

GO:0005634 "nucleus" evidence=ISS

GO:0005783 "endoplasmic reticulum" evidence=ISS

GO:0005829 "cytosol" evidence=ISS

GO:0006355 "regulation of transcription, DNA-dependent" evidence=TAS

GO:0006695 "cholesterol biosynthetic process" evidence=TAS

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=TAS

---

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

Your Input: gw1.V.1606.1 hypothetical protein (239 aa) (Populus trichocarpa)

Predicted Functional Partners:

Sorry, there are no predicted associations at the current settings.

---

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	271
PTZ00368	148	PTZ00368, PTZ00368, universal minicircle sequence	1e-18
PTZ00368	148	PTZ00368, PTZ00368, universal minicircle sequence	1e-15
COG5082	190	COG5082, AIR1, Arginine methyltransferase-interact	2e-13
COG5082	190	COG5082, AIR1, Arginine methyltransferase-interact	2e-12
COG5082	190	COG5082, AIR1, Arginine methyltransferase-interact	6e-10
COG5082	190	COG5082, AIR1, Arginine methyltransferase-interact	1e-06
COG4907	595	COG4907, COG4907, Predicted membrane protein [Func	2e-04
PTZ00146	293	PTZ00146, PTZ00146, fibrillarin; Provisional	6e-04
PTZ00146	293	PTZ00146, PTZ00146, fibrillarin; Provisional	7e-04
PLN03138	796	PLN03138, PLN03138, Protein TOC75; Provisional	0.001
PLN03138	796	PLN03138, PLN03138, Protein TOC75; Provisional	0.001
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	0.002
PTZ00146	293	PTZ00146, PTZ00146, fibrillarin; Provisional	0.003
PTZ00146	293	PTZ00146, PTZ00146, fibrillarin; Provisional	0.003
PLN03138	796	PLN03138, PLN03138, Protein TOC75; Provisional	0.003
PRK06958	182	PRK06958, PRK06958, single-stranded DNA-binding pr	0.004

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

 Score = 79.9 bits (197), Expect = 1e-18
 Identities = 54/145 (37%), Positives = 74/145 (51%), Gaps = 27/145 (18%)

Query: 49  NLCNNCKRPGHFARECPNVAV--------CNNCGLPGHIASECTT------QARCWNCRE 94
            +C  C   GH +RECPN A         C  CG PGH++ EC +      +  C+NC +
Sbjct: 1   MVCYRCGGVGHQSRECPNSAPAGAAKARPCYKCGEPGHLSRECPSAPGGRGERSCYNCGK 60

Query: 95  PGHMASNCHNEG------ICHSCGKTGHRARDCSTHVQSGGDLRLCNNCYKPGHIAADCT 148
            GH++  C           C++CG+TGH +R+C    + G   R C NC   GHI+ DC 
Sbjct: 61  TGHLSRECPEAPPGSGPRSCYNCGQTGHISRECPNRAKGGAARRACYNCGGEGHISRDCP 120

Query: 149 N-------DKACKNCRKTGHIARDC 166
           N       DK C NC +TGH++RDC
Sbjct: 121 NAGKRPGGDKTCYNCGQTGHLSRDC 145

Length = 148

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

 Score = 72.1 bits (177), Expect = 1e-15
 Identities = 51/172 (29%), Positives = 75/172 (43%), Gaps = 46/172 (26%)

Query: 108 CHSCGKTGHRARDCSTHVQSG-GDLRLCNNCYKPGHIAADCTN------DKACKNCRKTG 160
           C+ CG  GH++R+C     +G    R C  C +PGH++ +C +      +++C NC KTG
Sbjct: 3   CYRCGGVGHQSRECPNSAPAGAAKARPCYKCGEPGHLSRECPSAPGGRGERSCYNCGKTG 62

Query: 161 HIARDCQNEP------VCNLCNIAGHVARQCPKGDSLGERGGGGGGERGGGGGGDGGGGG 214
           H++R+C   P       C  C   GH++R+CP                         GG 
Sbjct: 63  HLSRECPEAPPGSGPRSCYNCGQTGHISRECPNRAK---------------------GGA 101

Query: 215 GRYVGYHDVICRSCNQMGHMSRDCVGPLI------ICRNCGGRGHMAYECPS 260
            R   Y+      C   GH+SRDC            C NCG  GH++ +CP 
Sbjct: 102 ARRACYN------CGGEGHISRDCPNAGKRPGGDKTCYNCGQTGHLSRDCPD 147

Length = 148

>gnl|CDD|227414 COG5082, AIR1, Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]

 Score = 67.2 bits (164), Expect = 2e-13
 Identities = 40/138 (28%), Positives = 49/138 (35%), Gaps = 31/138 (22%)

Query: 108 CHSCGKTGHRARDCSTHVQSGGDLRLCNNCYKPGHIAADCTNDKACKNCRKTGHIARDCQ 167
           C +CG+ GH  RDC           +C NC   GH +  C   K C NC +TGH++RDC 
Sbjct: 63  CFNCGQNGHLRRDC--------PHSICYNCSWDGHRSNHCPKPKKCYNCGETGHLSRDCN 114

Query: 168 N----EPVCNLCNIAGHVARQCPKGDSLGERGGGGGGERGGGGGGDGGGGGGRYVGYHDV 223
                +  C  CN   H +  CP                 G G                 
Sbjct: 115 PSKDQQKSCFDCNSTRHSSEDCP-------SIWKHYVLNNGDGHP------------IKK 155

Query: 224 ICRSCNQMGHMSRDCVGP 241
            C SC   GH   DC  P
Sbjct: 156 FCYSCGSAGHFGDDCKEP 173

Length = 190

>gnl|CDD|227414 COG5082, AIR1, Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]

 Score = 64.1 bits (156), Expect = 2e-12
 Identities = 36/118 (30%), Positives = 55/118 (46%), Gaps = 13/118 (11%)

Query: 43  RSFSQGNLCNNCKRPGHFARECPNVAVCNNCGLPGHIASECTTQARCWNCREPGHMASNC 102
               +  +C NC + GH  R+CP+  +C NC   GH ++ C    +C+NC E GH++ +C
Sbjct: 55  AIREENPVCFNCGQNGHLRRDCPHS-ICYNCSWDGHRSNHCPKPKKCYNCGETGHLSRDC 113

Query: 103 HNEG----ICHSCGKTGHRARDCST----HVQSGGDLR----LCNNCYKPGHIAADCT 148
           +        C  C  T H + DC +    +V + GD       C +C   GH   DC 
Sbjct: 114 NPSKDQQKSCFDCNSTRHSSEDCPSIWKHYVLNNGDGHPIKKFCYSCGSAGHFGDDCK 171

Length = 190

>gnl|CDD|227414 COG5082, AIR1, Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]

 Score = 56.8 bits (137), Expect = 6e-10
 Identities = 35/118 (29%), Positives = 52/118 (44%), Gaps = 19/118 (16%)

Query: 68  AVCNNCGLPGHIASECTTQARCWNCREPGHMASNCHNEGICHSCGKTGHRARDCSTHVQS 127
            VC NCG  GH+  +C   + C+NC   GH +++C     C++CG+TGH +RDC+     
Sbjct: 61  PVCFNCGQNGHLRRDC-PHSICYNCSWDGHRSNHCPKPKKCYNCGETGHLSRDCNPSKDQ 119

Query: 128 GGDLRLCNNCYKPGHIAADC---------------TNDKACKNCRKTGHIARDCQNEP 170
               + C +C    H + DC                  K C +C   GH   DC+   
Sbjct: 120 Q---KSCFDCNSTRHSSEDCPSIWKHYVLNNGDGHPIKKFCYSCGSAGHFGDDCKEPR 174

Length = 190

>gnl|CDD|227414 COG5082, AIR1, Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]

 Score = 47.5 bits (113), Expect = 1e-06
 Identities = 32/123 (26%), Positives = 40/123 (32%), Gaps = 26/123 (21%)

Query: 150 DKACKNCRKTGHIARDCQNEPVCNLCNIAGHVARQCPKGDSLGERGGGGGGERGGGGGGD 209
           +  C NC + GH+ RDC    +C  C+  GH +  CPK       G  G   R      D
Sbjct: 60  NPVCFNCGQNGHLRRDCP-HSICYNCSWDGHRSNHCPKPKKCYNCGETGHLSRDCNPSKD 118

Query: 210 GGGGGGRYVGYHDVICRSCNQMGHMSRDC--------------VGPLIICRNCGGRGHMA 255
                          C  CN   H S DC                    C +CG  GH  
Sbjct: 119 QQ-----------KSCFDCNSTRHSSEDCPSIWKHYVLNNGDGHPIKKFCYSCGSAGHFG 167

Query: 256 YEC 258
            +C
Sbjct: 168 DDC 170

Length = 190

>gnl|CDD|227244 COG4907, COG4907, Predicted membrane protein [Function unknown]

 Score = 41.8 bits (98), Expect = 2e-04
 Identities = 15/29 (51%), Positives = 15/29 (51%), Gaps = 2/29 (6%)

Query: 188 GDSLGERGGGGGGERGGGGGGDGGGGGGR 216
                   GGGGG  GGG GG  GGGG R
Sbjct: 569 SSRRSSSSGGGGGFSGGGSGG--GGGGAR 595

Length = 595

>gnl|CDD|240291 PTZ00146, PTZ00146, fibrillarin; Provisional

 Score = 40.1 bits (94), Expect = 6e-04
 Identities = 18/31 (58%), Positives = 18/31 (58%)

Query: 186 PKGDSLGERGGGGGGERGGGGGGDGGGGGGR 216
             G   G RGGG GG RG G GG GGG GG 
Sbjct: 19  GGGRGGGGRGGGRGGGRGRGRGGGGGGRGGG 49

Length = 293

>gnl|CDD|240291 PTZ00146, PTZ00146, fibrillarin; Provisional

 Score = 40.1 bits (94), Expect = 7e-04
 Identities = 20/29 (68%), Positives = 20/29 (68%)

Query: 187 KGDSLGERGGGGGGERGGGGGGDGGGGGG 215
            G   G RGGG G  RGGGGGG GGGGGG
Sbjct: 24  GGGRGGGRGGGRGRGRGGGGGGRGGGGGG 52

Length = 293

>gnl|CDD|215598 PLN03138, PLN03138, Protein TOC75; Provisional

 Score = 39.8 bits (93), Expect = 0.001
 Identities = 18/26 (69%), Positives = 19/26 (73%)

Query: 192 GERGGGGGGERGGGGGGDGGGGGGRY 217
           G  GGG GG  GGGGGG GGGGG R+
Sbjct: 81  GGGGGGFGGFGGGGGGGGGGGGGWRF 106

Length = 796

>gnl|CDD|215598 PLN03138, PLN03138, Protein TOC75; Provisional

 Score = 39.5 bits (92), Expect = 0.001
 Identities = 18/30 (60%), Positives = 18/30 (60%)

Query: 186 PKGDSLGERGGGGGGERGGGGGGDGGGGGG 215
                 G  GGGG G  GGGGGG GGGGGG
Sbjct: 74  SAISGGGGGGGGGFGGFGGGGGGGGGGGGG 103

Length = 796

>gnl|CDD|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family

 Score = 38.7 bits (90), Expect = 0.002
 Identities = 20/47 (42%), Positives = 20/47 (42%), Gaps = 4/47 (8%)

Query: 2  SSRSRSISRSRSRSRSRS----PRDRRFRSRHSSYCDPPLRRETRRS 44
            RSR  SRSR RSR R      R RR RSR  S       R  R  
Sbjct: 21 RERSRRRSRSRDRSRRRRDRDYYRGRRGRSRSRSPNRYYRPRGDRSY 67

This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed. Length = 457

>gnl|CDD|240291 PTZ00146, PTZ00146, fibrillarin; Provisional

 Score = 38.2 bits (89), Expect = 0.003
 Identities = 18/33 (54%), Positives = 18/33 (54%)

Query: 192 GERGGGGGGERGGGGGGDGGGGGGRYVGYHDVI 224
           G  GG GGG   G GGG GG GGG   G   VI
Sbjct: 26  GRGGGRGGGRGRGRGGGGGGRGGGGGGGPGKVI 58

Length = 293

>gnl|CDD|240291 PTZ00146, PTZ00146, fibrillarin; Provisional

 Score = 37.8 bits (88), Expect = 0.003
 Identities = 16/30 (53%), Positives = 17/30 (56%)

Query: 187 KGDSLGERGGGGGGERGGGGGGDGGGGGGR 216
           +G   G  GGGG G  G GGG  GG G GR
Sbjct: 10  RGGGRGGGGGGGRGGGGRGGGRGGGRGRGR 39

Length = 293

>gnl|CDD|215598 PLN03138, PLN03138, Protein TOC75; Provisional

 Score = 38.7 bits (90), Expect = 0.003
 Identities = 17/30 (56%), Positives = 19/30 (63%)

Query: 186 PKGDSLGERGGGGGGERGGGGGGDGGGGGG 215
               ++   GGGGGG  GG GGG GGGGGG
Sbjct: 71  LSASAISGGGGGGGGGFGGFGGGGGGGGGG 100

Length = 796

>gnl|CDD|180777 PRK06958, PRK06958, single-stranded DNA-binding protein; Provisional

 Score = 37.1 bits (86), Expect = 0.004
 Identities = 20/31 (64%), Positives = 20/31 (64%)

Query: 191 LGERGGGGGGERGGGGGGDGGGGGGRYVGYH 221
           LG RGG GGG  GG  GG GGGGGG   GY 
Sbjct: 108 LGGRGGSGGGGGGGDEGGYGGGGGGGGGGYG 138

Length = 182

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	271
PTZ00368	148	universal minicircle sequence binding protein (UMS	99.94
PTZ00368	148	universal minicircle sequence binding protein (UMS	99.93
COG5082	190	AIR1 Arginine methyltransferase-interacting protei	99.81
COG5082	190	AIR1 Arginine methyltransferase-interacting protei	99.79
KOG4400	261	consensus E3 ubiquitin ligase interacting with arg	99.72
KOG4400	261	consensus E3 ubiquitin ligase interacting with arg	99.58
PF00098	18	zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc fi	98.18
PF00098	18	zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc fi	97.95
PF13696	32	zf-CCHC_2: Zinc knuckle	96.23
PF13917	42	zf-CCHC_3: Zinc knuckle	95.74
PF13696	32	zf-CCHC_2: Zinc knuckle	95.65
smart00343	26	ZnF_C2HC zinc finger.	93.87
KOG0119	554	consensus Splicing factor 1/branch point binding p	92.64
PF13917	42	zf-CCHC_3: Zinc knuckle	92.06
smart00343	26	ZnF_C2HC zinc finger.	91.64
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	90.71
KOG0119	554	consensus Splicing factor 1/branch point binding p	90.49
PF14392	49	zf-CCHC_4: Zinc knuckle	90.05
KOG4368	757	consensus Predicted RNA binding protein, contains	88.45
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	85.66
PF15288	40	zf-CCHC_6: Zinc knuckle	85.23
PF14392	49	zf-CCHC_4: Zinc knuckle	83.85
PF15288	40	zf-CCHC_6: Zinc knuckle	82.63
PF14787	36	zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB:	80.71

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

Probab=99.94  E-value=1.8e-27  Score=198.92  Aligned_cols=133  Identities=34%  Similarity=0.819  Sum_probs=92.8

Q ss_pred             cCcCCCCCCCCCCCCCC--------CCccccCCCCCcCCCCCCCCcccCCCCcccccCCCCCCCCcCCCCCccccccCCC
Q 024209           88 RCWNCREPGHMASNCHN--------EGICHSCGKTGHRARDCSTHVQSGGDLRLCNNCYKPGHIAADCTNDKACKNCRKT  159 (271)
Q Consensus        88 ~C~~Cg~~GH~~~~Cp~--------~~~C~~Cg~~GH~~~~Cp~~~~~~~~~~~C~~Cg~~GH~a~dC~~~~~C~~Cg~~  159 (271)
                      +||+|++.||++++||+        ...||+|++.||++++||..... .....|++|++.||++.+||+...     . 
T Consensus         2 ~C~~C~~~GH~~~~c~~~~~~~~~~~~~C~~Cg~~GH~~~~Cp~~~~~-~~~~~C~~Cg~~GH~~~~Cp~~~~-----~-   74 (148)
T PTZ00368          2 VCYRCGGVGHQSRECPNSAPAGAAKARPCYKCGEPGHLSRECPSAPGG-RGERSCYNCGKTGHLSRECPEAPP-----G-   74 (148)
T ss_pred             cCCCCCCCCcCcccCcCCCCCCCCCCccCccCCCCCcCcccCcCCCCC-CCCcccCCCCCcCcCcccCCCccc-----C-
Confidence            46666666666666665        24677777777777777765321 123456666666666666654210     0 


Q ss_pred             CcccccCCCCCCCCccccCCcCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccCccccccCCCCCcCCCCC
Q 024209          160 GHIARDCQNEPVCNLCNIAGHVARQCPKGDSLGERGGGGGGERGGGGGGDGGGGGGRYVGYHDVICRSCNQMGHMSRDCV  239 (271)
Q Consensus       160 GH~~~~Cp~~~~C~~C~~~GH~a~~Cp~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~C~~C~~~gH~~~dCp  239 (271)
                             .....|++|++.||++++||+....    +                       ....+||+|++.||+++|||
T Consensus        75 -------~~~~~C~~Cg~~GH~~~~C~~~~~~----~-----------------------~~~~~C~~Cg~~gH~~~~C~  120 (148)
T PTZ00368         75 -------SGPRSCYNCGQTGHISRECPNRAKG----G-----------------------AARRACYNCGGEGHISRDCP  120 (148)
T ss_pred             -------CCCcccCcCCCCCcccccCCCcccc----c-----------------------ccchhhcccCcCCcchhcCC
Confidence                   0235799999999999999985421    0                       12478999999999999999


Q ss_pred             CC------CcceEcCCCCCcCCCCCCCC
Q 024209          240 GP------LIICRNCGGRGHMAYECPSG  261 (271)
Q Consensus       240 ~~------~~~C~~Cg~~GH~~~~Cp~~  261 (271)
                      ++      .++||+|+++|||++|||+.
T Consensus       121 ~~~~~~~~~~~C~~Cg~~gH~~~dCp~~  148 (148)
T PTZ00368        121 NAGKRPGGDKTCYNCGQTGHLSRDCPDK  148 (148)
T ss_pred             CccccCCCCCccccCCCcCcccccCCCC
Confidence            84      58999999999999999974

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

Probab=99.93  E-value=5.9e-26  Score=189.83  Aligned_cols=126  Identities=43%  Similarity=0.976  Sum_probs=77.7

Q ss_pred             cccccCCCCCCCCCCCCCC--------cccccCCCCCCccCCCCCcccCcCCCCCCCCCCCCCCCCccccCCCCCcCCCC
Q 024209           49 NLCNNCKRPGHFARECPNV--------AVCNNCGLPGHIASECTTQARCWNCREPGHMASNCHNEGICHSCGKTGHRARD  120 (271)
Q Consensus        49 ~~C~nCg~~GH~~~~Cp~~--------~~C~~Cg~~GH~~~~Cp~~~~C~~Cg~~GH~~~~Cp~~~~C~~Cg~~GH~~~~  120 (271)
                      ++||||++.||++++||..        ..||+|+..||++.+||....             -.....|++|++.||++++
T Consensus         1 ~~C~~C~~~GH~~~~c~~~~~~~~~~~~~C~~Cg~~GH~~~~Cp~~~~-------------~~~~~~C~~Cg~~GH~~~~   67 (148)
T PTZ00368          1 MVCYRCGGVGHQSRECPNSAPAGAAKARPCYKCGEPGHLSRECPSAPG-------------GRGERSCYNCGKTGHLSRE   67 (148)
T ss_pred             CcCCCCCCCCcCcccCcCCCCCCCCCCccCccCCCCCcCcccCcCCCC-------------CCCCcccCCCCCcCcCccc
Confidence            5899999999999999972        245555555555555554210             0001235555555555555


Q ss_pred             CCCCcccCCCCcccccCCCCCCCCcCCCCCc-------cccccCCCCcccccCCC-------CCCCCccccCCcCCCCCC
Q 024209          121 CSTHVQSGGDLRLCNNCYKPGHIAADCTNDK-------ACKNCRKTGHIARDCQN-------EPVCNLCNIAGHVARQCP  186 (271)
Q Consensus       121 Cp~~~~~~~~~~~C~~Cg~~GH~a~dC~~~~-------~C~~Cg~~GH~~~~Cp~-------~~~C~~C~~~GH~a~~Cp  186 (271)
                      ||...... ..+.|++|++.||++.+|++..       +||+|++.||++++||+       .++||+|++.|||++|||
T Consensus        68 Cp~~~~~~-~~~~C~~Cg~~GH~~~~C~~~~~~~~~~~~C~~Cg~~gH~~~~C~~~~~~~~~~~~C~~Cg~~gH~~~dCp  146 (148)
T PTZ00368         68 CPEAPPGS-GPRSCYNCGQTGHISRECPNRAKGGAARRACYNCGGEGHISRDCPNAGKRPGGDKTCYNCGQTGHLSRDCP  146 (148)
T ss_pred             CCCcccCC-CCcccCcCCCCCcccccCCCcccccccchhhcccCcCCcchhcCCCccccCCCCCccccCCCcCcccccCC
Confidence            55543211 2345666666666666665422       46666666666666665       368999999999999999


Q ss_pred             CC
Q 024209          187 KG  188 (271)
Q Consensus       187 ~~  188 (271)
                      +.
T Consensus       147 ~~  148 (148)
T PTZ00368        147 DK  148 (148)
T ss_pred             CC
Confidence            73

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

Probab=99.81  E-value=3.1e-20  Score=159.46  Aligned_cols=101  Identities=35%  Similarity=0.807  Sum_probs=54.0

Q ss_pred             CcccccCCCCCCCCcCCCCCccccccCCCCcccccCCCCCCCCccccCCcCCCCC-CCCCCCCCCCCCCCCCCCCCCCCC
Q 024209          131 LRLCNNCYKPGHIAADCTNDKACKNCRKTGHIARDCQNEPVCNLCNIAGHVARQC-PKGDSLGERGGGGGGERGGGGGGD  209 (271)
Q Consensus       131 ~~~C~~Cg~~GH~a~dC~~~~~C~~Cg~~GH~~~~Cp~~~~C~~C~~~GH~a~~C-p~~~~~~~~~~~~~~~~~~~~g~~  209 (271)
                      .+.|++|++.||++.||| ..+|++|...+|.+..||..++|++|++.||++++| |..+                    
T Consensus        60 ~~~C~nCg~~GH~~~DCP-~~iC~~C~~~~H~s~~C~~~~~C~~Cg~~GH~~~dC~P~~~--------------------  118 (190)
T COG5082          60 NPVCFNCGQNGHLRRDCP-HSICYNCSWDGHRSNHCPKPKKCYNCGETGHLSRDCNPSKD--------------------  118 (190)
T ss_pred             ccccchhcccCcccccCC-hhHhhhcCCCCcccccCCcccccccccccCccccccCcccc--------------------
Confidence            345555555555555555 345555544555555555555555555555555555 3322                    


Q ss_pred             CCCCCCCCCcccCccccccCCCCCcCCCCCC--------------CCcceEcCCCCCcCCCCCCCCCc
Q 024209          210 GGGGGGRYVGYHDVICRSCNQMGHMSRDCVG--------------PLIICRNCGGRGHMAYECPSGRI  263 (271)
Q Consensus       210 ~~~~~~~~~~~~~~~C~~C~~~gH~~~dCp~--------------~~~~C~~Cg~~GH~~~~Cp~~~~  263 (271)
                                 ..+.|+.|...+|.+++||.              ..+.||+|+..+||+.||+.++.
T Consensus       119 -----------~~~~C~~C~s~~H~s~~Cp~~~k~y~~~~~~~~~~~~~cy~c~~~~H~~~dc~~~~~  175 (190)
T COG5082         119 -----------QQKSCFDCNSTRHSSEDCPSIWKHYVLNNGDGHPIKKFCYSCGSAGHFGDDCKEPRS  175 (190)
T ss_pred             -----------cCcceeccCCCccccccCcccccccccccCCCcceeeeccccCCccccCCCCCCCcc
Confidence                       12445555555555555554              24556666666666666665443

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

Probab=99.79  E-value=2.1e-19  Score=154.32  Aligned_cols=83  Identities=33%  Similarity=0.897  Sum_probs=74.6

Q ss_pred             ccCCCCcccccCCCCCCCCCCCCCCcccccCCCCCCccCCCCCcccCcCCCCCCCCCCCC-CCC---CccccCCCCCcCC
Q 024209           43 RSFSQGNLCNNCKRPGHFARECPNVAVCNNCGLPGHIASECTTQARCWNCREPGHMASNC-HNE---GICHSCGKTGHRA  118 (271)
Q Consensus        43 ~~~~~~~~C~nCg~~GH~~~~Cp~~~~C~~Cg~~GH~~~~Cp~~~~C~~Cg~~GH~~~~C-p~~---~~C~~Cg~~GH~~  118 (271)
                      .......+||||++.||+++||| ..+|++|...||.+..||..++|++|++.||++++| |..   ..|+.|....|++
T Consensus        55 ~~~~~~~~C~nCg~~GH~~~DCP-~~iC~~C~~~~H~s~~C~~~~~C~~Cg~~GH~~~dC~P~~~~~~~C~~C~s~~H~s  133 (190)
T COG5082          55 AIREENPVCFNCGQNGHLRRDCP-HSICYNCSWDGHRSNHCPKPKKCYNCGETGHLSRDCNPSKDQQKSCFDCNSTRHSS  133 (190)
T ss_pred             cccccccccchhcccCcccccCC-hhHhhhcCCCCcccccCCcccccccccccCccccccCcccccCcceeccCCCcccc
Confidence            33445789999999999999999 679999988999999999988999999999999999 553   4799999999999


Q ss_pred             CCCCCCcc
Q 024209          119 RDCSTHVQ  126 (271)
Q Consensus       119 ~~Cp~~~~  126 (271)
                      .+||.+|+
T Consensus       134 ~~Cp~~~k  141 (190)
T COG5082         134 EDCPSIWK  141 (190)
T ss_pred             ccCccccc
Confidence            99999997

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

Probab=99.72  E-value=2.6e-17  Score=149.56  Aligned_cols=191  Identities=30%  Similarity=0.625  Sum_probs=144.8

Q ss_pred             CcccccCCCCCCCCCCCCCCc-----------ccccCCCCCCccCCCCCcccCcCCCCCCCCCCCCCC-CCccccCCCCC
Q 024209           48 GNLCNNCKRPGHFARECPNVA-----------VCNNCGLPGHIASECTTQARCWNCREPGHMASNCHN-EGICHSCGKTG  115 (271)
Q Consensus        48 ~~~C~nCg~~GH~~~~Cp~~~-----------~C~~Cg~~GH~~~~Cp~~~~C~~Cg~~GH~~~~Cp~-~~~C~~Cg~~G  115 (271)
                      ...++.+.+.+|.+..|+...           .+..+...+|....++. ..|+.|++.||+..+|+. ...|++|++.|
T Consensus        24 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~c~~~g~~~~~~~~~~~~~~~c~~C~~~g  102 (261)
T KOG4400|consen   24 SPNELKCLKSGHKAVSCTDGDSRGDSSKSDGPGCVSTSPNGPLKSECPE-VSCYICGEKGHLGRRCTRIAAACFNCGEGG  102 (261)
T ss_pred             chhhhhhccccCcceecccCCcccccccCCCCcccccccCcccCCCCCC-ceeeecCCCCchhhcCcccchhhhhCCCCc
Confidence            578899999999999998642           34445566777777776 799999999999999996 67899999999


Q ss_pred             cCCCCCCCCcccCCCCcccccCCCCCCCC-cCCC-----CCccccccCCCCcccccCCC--CCCCCccccCCcCCCCCCC
Q 024209          116 HRARDCSTHVQSGGDLRLCNNCYKPGHIA-ADCT-----NDKACKNCRKTGHIARDCQN--EPVCNLCNIAGHVARQCPK  187 (271)
Q Consensus       116 H~~~~Cp~~~~~~~~~~~C~~Cg~~GH~a-~dC~-----~~~~C~~Cg~~GH~~~~Cp~--~~~C~~C~~~GH~a~~Cp~  187 (271)
                      |++++||.++........|+.|++.||.. .++.     ....||+|++.||++.+||.  ...||.|++.+|++++||.
T Consensus       103 H~~~~c~~~~~~~~~~~~~~~c~~~gh~~~~~~~~~~~~~~~~Cy~Cg~~GH~s~~C~~~~~~~c~~c~~~~h~~~~C~~  182 (261)
T KOG4400|consen  103 HIERDCPEAGKEGSSETSCYSCGKTGHRGCPDADPVDGPKPAKCYSCGEQGHISDDCPENKGGTCFRCGKVGHGSRDCPS  182 (261)
T ss_pred             cchhhCCcccCcccccceeeccCCCccccCcccccccCCCCCccCCCCcCCcchhhCCCCCCCccccCCCcceecccCCc
Confidence            99999999987433455789999999999 3332     22459999999999999994  7899999999999999999


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccCccccccCCCCCcCCCCCC------CCcceEcCCCCCcCCCCCCC
Q 024209          188 GDSLGERGGGGGGERGGGGGGDGGGGGGRYVGYHDVICRSCNQMGHMSRDCVG------PLIICRNCGGRGHMAYECPS  260 (271)
Q Consensus       188 ~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~C~~C~~~gH~~~dCp~------~~~~C~~Cg~~GH~~~~Cp~  260 (271)
                      ...........                  .  ..--.++ +...+|+.++++.      ....+|++...+|.+.+|-+
T Consensus       183 ~~~~~~~~~~~------------------~--~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  240 (261)
T KOG4400|consen  183 KQKSKSKQGGQ------------------R--KGFGACY-DYPQGHKQRACGGSGPDDNFNDSCYNKLSSGKLDQDCKQ  240 (261)
T ss_pred             cccccccCccc------------------c--cccccCc-cccccccccccCCCCcccccccccccccccccccchhhh
Confidence            87532111100                  0  0111233 5678888888875      35667777766666665543

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

Probab=99.58  E-value=1.4e-14  Score=131.68  Aligned_cols=179  Identities=33%  Similarity=0.694  Sum_probs=131.8

Q ss_pred             CcccccCCCCCCCCCCCCCCcccccCCCCCCccCCCCC-cccCcCCCCCCCCCCCCCCCC-------ccccCCCCCcCC-
Q 024209           48 GNLCNNCKRPGHFARECPNVAVCNNCGLPGHIASECTT-QARCWNCREPGHMASNCHNEG-------ICHSCGKTGHRA-  118 (271)
Q Consensus        48 ~~~C~nCg~~GH~~~~Cp~~~~C~~Cg~~GH~~~~Cp~-~~~C~~Cg~~GH~~~~Cp~~~-------~C~~Cg~~GH~~-  118 (271)
                      ...+..+...+|+...++.. .|+.|++.+|....|+. ...|++|++.||++++|++..       .||.|+..+|.. 
T Consensus        54 ~~~~~~~~~~~~~~~~~~~~-~c~~~g~~~~~~~~~~~~~~~c~~C~~~gH~~~~c~~~~~~~~~~~~~~~c~~~gh~~~  132 (261)
T KOG4400|consen   54 GPGCVSTSPNGPLKSECPEV-SCYICGEKGHLGRRCTRIAAACFNCGEGGHIERDCPEAGKEGSSETSCYSCGKTGHRGC  132 (261)
T ss_pred             CCcccccccCcccCCCCCCc-eeeecCCCCchhhcCcccchhhhhCCCCccchhhCCcccCcccccceeeccCCCccccC
Confidence            34556678888888888875 89999999999999985 578999999999999999852       578999999999 


Q ss_pred             CCCCCCcccCCCCcccccCCCCCCCCcCCCC--CccccccCCCCcccccCCCCC--------------CCCccccCCcCC
Q 024209          119 RDCSTHVQSGGDLRLCNNCYKPGHIAADCTN--DKACKNCRKTGHIARDCQNEP--------------VCNLCNIAGHVA  182 (271)
Q Consensus       119 ~~Cp~~~~~~~~~~~C~~Cg~~GH~a~dC~~--~~~C~~Cg~~GH~~~~Cp~~~--------------~C~~C~~~GH~a  182 (271)
                      .++..... +.. +.||+|++.||+..+||+  ...|+.|+..+|++++||...              .++ +...+|+.
T Consensus       133 ~~~~~~~~-~~~-~~Cy~Cg~~GH~s~~C~~~~~~~c~~c~~~~h~~~~C~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~  209 (261)
T KOG4400|consen  133 PDADPVDG-PKP-AKCYSCGEQGHISDDCPENKGGTCFRCGKVGHGSRDCPSKQKSKSKQGGQRKGFGACY-DYPQGHKQ  209 (261)
T ss_pred             cccccccC-CCC-CccCCCCcCCcchhhCCCCCCCccccCCCcceecccCCccccccccCcccccccccCc-cccccccc
Confidence            33322211 112 679999999999999994  578999999999999999521              233 34566777


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccCccccccCCCCCcCCCCCCCCcceEcCCCCCcCCCCCCCCC
Q 024209          183 RQCPKGDSLGERGGGGGGERGGGGGGDGGGGGGRYVGYHDVICRSCNQMGHMSRDCVGPLIICRNCGGRGHMAYECPSGR  262 (271)
Q Consensus       183 ~~Cp~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~C~~C~~~gH~~~dCp~~~~~C~~Cg~~GH~~~~Cp~~~  262 (271)
                      ++++......                           .....+|++...+|.+.+|          .+.++++++|...+
T Consensus       210 ~~~~~~~~~~---------------------------~~~~~~~~~~~~~~~~~~~----------~~~~~~~~~~~~~~  252 (261)
T KOG4400|consen  210 RACGGSGPDD---------------------------NFNDSCYNKLSSGKLDQDC----------KQSSMKSNSCGTKR  252 (261)
T ss_pred             cccCCCCccc---------------------------ccccccccccccccccchh----------hhhccccccccchh
Confidence            6665544311                           1247789999888888777          45556666666555


Q ss_pred             cCCCC
Q 024209          263 IADRG  267 (271)
Q Consensus       263 ~~~~~  267 (271)
                      +....
T Consensus       253 ~~~~~  257 (261)
T KOG4400|consen  253 LFYNT  257 (261)
T ss_pred             hcccc
Confidence            55544

>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=98.18  E-value=6.9e-07  Score=48.87  Aligned_cols=17  Identities=53%  Similarity=1.253  Sum_probs=10.0

Q ss_pred             ceEcCCCCCcCCCCCCC
Q 024209          244 ICRNCGGRGHMAYECPS  260 (271)
Q Consensus       244 ~C~~Cg~~GH~~~~Cp~  260 (271)
                      .||+|++.||+++|||+
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            45666666666666653

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 ....

>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=97.95  E-value=4.8e-06  Score=45.50  Aligned_cols=17  Identities=41%  Similarity=1.028  Sum_probs=16.0

Q ss_pred             cccccCCCCCcCCCCCC
Q 024209          224 ICRSCNQMGHMSRDCVG  240 (271)
Q Consensus       224 ~C~~C~~~gH~~~dCp~  240 (271)
                      +||+|+++||+++|||+
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 ....

>PF13696 zf-CCHC_2: Zinc knuckle

Probab=96.23  E-value=0.0036  Score=39.10  Aligned_cols=19  Identities=37%  Similarity=1.097  Sum_probs=12.1

Q ss_pred             CcceEcCCCCCcCCCCCCC
Q 024209          242 LIICRNCGGRGHMAYECPS  260 (271)
Q Consensus       242 ~~~C~~Cg~~GH~~~~Cp~  260 (271)
                      .-+|+.|++.|||..|||+
T Consensus         8 ~Y~C~~C~~~GH~i~dCP~   26 (32)
T PF13696_consen    8 GYVCHRCGQKGHWIQDCPT   26 (32)
T ss_pred             CCEeecCCCCCccHhHCCC
Confidence            4556666666666666665

>PF13917 zf-CCHC_3: Zinc knuckle

Probab=95.74  E-value=0.0055  Score=40.71  Aligned_cols=18  Identities=50%  Similarity=1.383  Sum_probs=13.5

Q ss_pred             CcceEcCCCCCcCCCCCC
Q 024209          242 LIICRNCGGRGHMAYECP  259 (271)
Q Consensus       242 ~~~C~~Cg~~GH~~~~Cp  259 (271)
                      .+.|.+|++.|||..|||
T Consensus         4 ~~~CqkC~~~GH~tyeC~   21 (42)
T PF13917_consen    4 RVRCQKCGQKGHWTYECP   21 (42)
T ss_pred             CCcCcccCCCCcchhhCC
Confidence            466777777777777777

>PF13696 zf-CCHC_2: Zinc knuckle

Probab=95.65  E-value=0.0066  Score=37.95  Aligned_cols=20  Identities=35%  Similarity=0.846  Sum_probs=14.4

Q ss_pred             CCCCCccccCCcCCCCCCCC
Q 024209          169 EPVCNLCNIAGHVARQCPKG  188 (271)
Q Consensus       169 ~~~C~~C~~~GH~a~~Cp~~  188 (271)
                      .-+|+.|+++||+..|||++
T Consensus         8 ~Y~C~~C~~~GH~i~dCP~~   27 (32)
T PF13696_consen    8 GYVCHRCGQKGHWIQDCPTN   27 (32)
T ss_pred             CCEeecCCCCCccHhHCCCC
Confidence            45677777777777777773

>smart00343 ZnF_C2HC zinc finger

Probab=93.87  E-value=0.031  Score=32.82  Aligned_cols=16  Identities=56%  Similarity=1.425  Sum_probs=11.3

Q ss_pred             eEcCCCCCcCCCCCCC
Q 024209          245 CRNCGGRGHMAYECPS  260 (271)
Q Consensus       245 C~~Cg~~GH~~~~Cp~  260 (271)
                      |++|++.||++.+||+
T Consensus         2 C~~CG~~GH~~~~C~~   17 (26)
T smart00343        2 CYNCGKEGHIARDCPK   17 (26)
T ss_pred             CccCCCCCcchhhCCc
Confidence            6777777777777763

>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]

Probab=92.64  E-value=0.082  Score=52.07  Aligned_cols=41  Identities=34%  Similarity=0.865  Sum_probs=36.1

Q ss_pred             ccccccCCCCCcCCCCCCC----CcceEcCCCCCcCCCCCCCCCc
Q 024209          223 VICRSCNQMGHMSRDCVGP----LIICRNCGGRGHMAYECPSGRI  263 (271)
Q Consensus       223 ~~C~~C~~~gH~~~dCp~~----~~~C~~Cg~~GH~~~~Cp~~~~  263 (271)
                      ..|.+|+..||..-|||..    ..+|..|+..|||+.||+...+
T Consensus       262 ~~c~~cg~~~H~q~~cp~r~~~~~n~c~~cg~~gH~~~dc~~~~q  306 (554)
T KOG0119|consen  262 RACRNCGSTGHKQYDCPGRIPNTTNVCKICGPLGHISIDCKVNDQ  306 (554)
T ss_pred             ccccccCCCccccccCCcccccccccccccCCcccccccCCCccc
Confidence            5799999999999999972    3499999999999999998733

>PF13917 zf-CCHC_3: Zinc knuckle

Probab=92.06  E-value=0.074  Score=35.33  Aligned_cols=19  Identities=37%  Similarity=0.896  Sum_probs=17.3

Q ss_pred             CccccccCCCCCcCCCCCC
Q 024209          222 DVICRSCNQMGHMSRDCVG  240 (271)
Q Consensus       222 ~~~C~~C~~~gH~~~dCp~  240 (271)
                      ...|.+|++.|||..+||+
T Consensus         4 ~~~CqkC~~~GH~tyeC~~   22 (42)
T PF13917_consen    4 RVRCQKCGQKGHWTYECPN   22 (42)
T ss_pred             CCcCcccCCCCcchhhCCC
Confidence            4789999999999999993

>smart00343 ZnF_C2HC zinc finger

Probab=91.64  E-value=0.087  Score=30.90  Aligned_cols=17  Identities=41%  Similarity=1.060  Sum_probs=15.5

Q ss_pred             cccccCCCCCcCCCCCC
Q 024209          224 ICRSCNQMGHMSRDCVG  240 (271)
Q Consensus       224 ~C~~C~~~gH~~~dCp~  240 (271)
                      .|++|++.||++++||+
T Consensus         1 ~C~~CG~~GH~~~~C~~   17 (26)
T smart00343        1 KCYNCGKEGHIARDCPK   17 (26)
T ss_pred             CCccCCCCCcchhhCCc
Confidence            48999999999999984

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

Probab=90.71  E-value=0.13  Score=47.76  Aligned_cols=19  Identities=32%  Similarity=0.735  Sum_probs=11.8

Q ss_pred             CccccccCCCCCcCCCCCC
Q 024209          222 DVICRSCNQMGHMSRDCVG  240 (271)
Q Consensus       222 ~~~C~~C~~~gH~~~dCp~  240 (271)
                      ...||.|+++|||+.+||.
T Consensus       160 q~~cyrcGkeghwskEcP~  178 (346)
T KOG0109|consen  160 QSGCYRCGKEGHWSKECPV  178 (346)
T ss_pred             HHHheeccccccccccCCc
Confidence            3556666666666666663

>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]

Probab=90.49  E-value=0.19  Score=49.60  Aligned_cols=39  Identities=41%  Similarity=0.997  Sum_probs=27.2

Q ss_pred             ccccccCCCCcccccCCCC-----CCCCccccCCcCCCCCCCCC
Q 024209          151 KACKNCRKTGHIARDCQNE-----PVCNLCNIAGHVARQCPKGD  189 (271)
Q Consensus       151 ~~C~~Cg~~GH~~~~Cp~~-----~~C~~C~~~GH~a~~Cp~~~  189 (271)
                      ..|.+|+..||...+||..     .+|..|+..||++.||+...
T Consensus       262 ~~c~~cg~~~H~q~~cp~r~~~~~n~c~~cg~~gH~~~dc~~~~  305 (554)
T KOG0119|consen  262 RACRNCGSTGHKQYDCPGRIPNTTNVCKICGPLGHISIDCKVND  305 (554)
T ss_pred             ccccccCCCccccccCCcccccccccccccCCcccccccCCCcc
Confidence            3566666666666666642     27888888888888887763

>PF14392 zf-CCHC_4: Zinc knuckle

Probab=90.05  E-value=0.12  Score=35.10  Aligned_cols=25  Identities=32%  Similarity=0.679  Sum_probs=20.6

Q ss_pred             ccccCCCCcccccCCCCCCCCCCCC
Q 024209           41 TRRSFSQGNLCNNCKRPGHFARECP   65 (271)
Q Consensus        41 ~~~~~~~~~~C~nCg~~GH~~~~Cp   65 (271)
                      ...++..+..|++|+..||...+||
T Consensus        24 ~v~YE~lp~~C~~C~~~gH~~~~C~   48 (49)
T PF14392_consen   24 KVKYERLPRFCFHCGRIGHSDKECP   48 (49)
T ss_pred             EEEECCcChhhcCCCCcCcCHhHcC
Confidence            3455666889999999999999997

>KOG4368 consensus Predicted RNA binding protein, contains SWAP, RPR and G-patch domains [General function prediction only]

Probab=88.45  E-value=0.3  Score=49.15  Aligned_cols=17  Identities=82%  Similarity=0.837  Sum_probs=8.1

Q ss_pred             CccccccccccCCCCCC
Q 024209            3 SRSRSISRSRSRSRSRS   19 (271)
Q Consensus         3 ~~~~~~~~~~~~~~~~~   19 (271)
                      +|+|++|++|||||++.
T Consensus       601 ~RdrsrskSRSRSpS~~  617 (757)
T KOG4368|consen  601 SRSRSRSKSRSRSPSRS  617 (757)
T ss_pred             ccccccccccCCCcccc
Confidence            44444444444444443

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

Probab=85.66  E-value=0.4  Score=44.55  Aligned_cols=24  Identities=38%  Similarity=0.780  Sum_probs=20.6

Q ss_pred             CcceEcCCCCCcCCCCCCCCCcCC
Q 024209          242 LIICRNCGGRGHMAYECPSGRIAD  265 (271)
Q Consensus       242 ~~~C~~Cg~~GH~~~~Cp~~~~~~  265 (271)
                      .-.||.||.+|||+.|||..+..+
T Consensus       160 q~~cyrcGkeghwskEcP~~~~~r  183 (346)
T KOG0109|consen  160 QSGCYRCGKEGHWSKECPVDRTGR  183 (346)
T ss_pred             HHHheeccccccccccCCccCCCc
Confidence            468999999999999999876543

>PF15288 zf-CCHC_6: Zinc knuckle

Probab=85.23  E-value=0.69  Score=30.40  Aligned_cols=19  Identities=47%  Similarity=1.006  Sum_probs=8.9

Q ss_pred             ceEcCCCCCcCC--CCCCCCC
Q 024209          244 ICRNCGGRGHMA--YECPSGR  262 (271)
Q Consensus       244 ~C~~Cg~~GH~~--~~Cp~~~  262 (271)
                      .|.+||..||+.  +.||...
T Consensus         3 kC~~CG~~GH~~t~k~CP~~~   23 (40)
T PF15288_consen    3 KCKNCGAFGHMRTNKRCPMYC   23 (40)
T ss_pred             cccccccccccccCccCCCCC
Confidence            444555555544  3355443

>PF14392 zf-CCHC_4: Zinc knuckle

Probab=83.85  E-value=0.4  Score=32.52  Aligned_cols=18  Identities=28%  Similarity=0.909  Sum_probs=10.7

Q ss_pred             CccccccCCCCCcCCCCC
Q 024209          222 DVICRSCNQMGHMSRDCV  239 (271)
Q Consensus       222 ~~~C~~C~~~gH~~~dCp  239 (271)
                      +..|++|+..||...+||
T Consensus        31 p~~C~~C~~~gH~~~~C~   48 (49)
T PF14392_consen   31 PRFCFHCGRIGHSDKECP   48 (49)
T ss_pred             ChhhcCCCCcCcCHhHcC
Confidence            345666666666666665

>PF15288 zf-CCHC_6: Zinc knuckle

Probab=82.63  E-value=0.7  Score=30.37  Aligned_cols=18  Identities=39%  Similarity=1.017  Sum_probs=15.7

Q ss_pred             ccccccCCCCCcC--CCCCC
Q 024209          223 VICRSCNQMGHMS--RDCVG  240 (271)
Q Consensus       223 ~~C~~C~~~gH~~--~dCp~  240 (271)
                      ++|.+||..||++  +.||.
T Consensus         2 ~kC~~CG~~GH~~t~k~CP~   21 (40)
T PF15288_consen    2 VKCKNCGAFGHMRTNKRCPM   21 (40)
T ss_pred             ccccccccccccccCccCCC
Confidence            6899999999998  56984

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

Probab=80.71  E-value=1.1  Score=28.80  Aligned_cols=18  Identities=39%  Similarity=0.898  Sum_probs=9.3

Q ss_pred             cccccCCCCCCCCCCCCC
Q 024209           49 NLCNNCKRPGHFARECPN   66 (271)
Q Consensus        49 ~~C~nCg~~GH~~~~Cp~   66 (271)
                      ..|+.|++..||+.+|-.
T Consensus         3 ~~CprC~kg~Hwa~~C~s   20 (36)
T PF14787_consen    3 GLCPRCGKGFHWASECRS   20 (36)
T ss_dssp             -C-TTTSSSCS-TTT---
T ss_pred             ccCcccCCCcchhhhhhh
Confidence            467777777777777743

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	271
2bl6_A	37	Solution Structure Of The Zn Complex Of Eiav Ncp11(		5e-04

>pdb|2BL6|A Chain A, Solution Structure Of The Zn Complex Of Eiav Ncp11(22-58) Peptide, Including Two Cchc Zn-Binding Motifs Length = 37

Iteration: 1
 Score = 41.6 bits (96), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 15/36 (41%), Positives = 23/36 (63%)
Query: 69  VCNNCGLPGHIASECTTQARCWNCREPGHMASNCHN 104
            C NCG PGH++S+C     C+ C++PGH +  C +
Sbjct: 2   TCYNCGKPGHLSSQCRAPKVCFKCKQPGHFSKQCRS 37

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	271
2lli_A	124	Protein AIR2; RNA surveillance, RNA degradation, R	99.94
2lli_A	124	Protein AIR2; RNA surveillance, RNA degradation, R	99.91
3nyb_B	83	Protein AIR2; polya RNA polymerase, zinc knuckle p	99.65
2li8_A	74	Protein LIN-28 homolog A; zinc finger, micro RNA,	99.52
3nyb_B	83	Protein AIR2; polya RNA polymerase, zinc knuckle p	99.47
2a51_A	39	Nucleocapsid protein; sivlhoest, structure, NCP8,	99.33
2bl6_A	37	Nucleocapsid protein P11; lentivirus, polyprotein,	99.27
2ec7_A	49	GAG polyprotein (PR55GAG); nucleocapsid protein, H	99.27
1a1t_A	55	Nucleocapsid protein; stem-loop RNA, viral protein	99.25
2ihx_A	61	Nucleocapsid (NC) protein; protein-RNA complex, vi	99.24
2cqf_A	63	RNA-binding protein LIN-28; CCHC zinc-finger, stru	99.22
1cl4_A	60	Protein (GAG polyprotein); nucleocapsid protein, R	99.2
2li8_A	74	Protein LIN-28 homolog A; zinc finger, micro RNA,	99.19
1a1t_A	55	Nucleocapsid protein; stem-loop RNA, viral protein	99.09
2bl6_A	37	Nucleocapsid protein P11; lentivirus, polyprotein,	99.08
2a51_A	39	Nucleocapsid protein; sivlhoest, structure, NCP8,	99.05
2cqf_A	63	RNA-binding protein LIN-28; CCHC zinc-finger, stru	98.99
2ihx_A	61	Nucleocapsid (NC) protein; protein-RNA complex, vi	98.94
2ec7_A	49	GAG polyprotein (PR55GAG); nucleocapsid protein, H	98.9
3ts2_A	148	Protein LIN-28 homolog A; microrna biogenesis, pro	98.86
1cl4_A	60	Protein (GAG polyprotein); nucleocapsid protein, R	98.83
3ts2_A	148	Protein LIN-28 homolog A; microrna biogenesis, pro	98.57
1dsq_A	26	Nucleic acid binding protein P14; CCHC type zinc f	98.04
1a6b_B	40	Momulv, zinc finger protein NCP10; nucleocapsid pr	97.96
1nc8_A	29	Nucleocapsid protein; HIV-2, RNA recognition, zinc	97.82
1dsq_A	26	Nucleic acid binding protein P14; CCHC type zinc f	97.74
1a6b_B	40	Momulv, zinc finger protein NCP10; nucleocapsid pr	97.65
1nc8_A	29	Nucleocapsid protein; HIV-2, RNA recognition, zinc	97.55
1u6p_A	56	GAG polyprotein; MLV, A-minor K-turn, stem loop, b	97.51
1u6p_A	56	GAG polyprotein; MLV, A-minor K-turn, stem loop, b	97.15
2ysa_A	55	Retinoblastoma-binding protein 6; zinc finger, CCH	96.89
2ysa_A	55	Retinoblastoma-binding protein 6; zinc finger, CCH	96.17

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

Probab=99.94  E-value=6.2e-27  Score=189.19  Aligned_cols=77  Identities=27%  Similarity=0.758  Sum_probs=69.3

Q ss_pred             CccccCCCCCcCCCCCCCCcccCCCCcccccCCCC-CCCCcCCCCCccccccCCCCcccccCCCC---CCCCccccCCcC
Q 024209          106 GICHSCGKTGHRARDCSTHVQSGGDLRLCNNCYKP-GHIAADCTNDKACKNCRKTGHIARDCQNE---PVCNLCNIAGHV  181 (271)
Q Consensus       106 ~~C~~Cg~~GH~~~~Cp~~~~~~~~~~~C~~Cg~~-GH~a~dC~~~~~C~~Cg~~GH~~~~Cp~~---~~C~~C~~~GH~  181 (271)
                      ..||+|++.||++++||.+        .|++|++. ||++.+||+...|++|++.||++++||+.   +.||+|++.||+
T Consensus         5 ~~C~~C~~~GH~~~~Cp~~--------~C~~Cg~~~gH~~~~C~~~~~C~~Cg~~GH~~~~C~~~~~~~~C~~Cg~~GH~   76 (124)
T 2lli_A            5 PKCNNCSQRGHLKKDCPHI--------ICSYCGATDDHYSRHCPKAIQCSKCDEVGHYRSQCPHKWKKVQCTLCKSKKHS   76 (124)
T ss_dssp             SCCSSCSSSSCCTTTTTSC--------CCTTTCCTTTCCTTTGGGSSCSSSSSCSSSSTTTSCCCCCCCSSSSSCSSCCC
T ss_pred             CcccCCCCCCcCcccCcCC--------cCcCCCCcCCccCcccCCcccccccCCCCCccccCcCcccCccCCCCCcCCcc
Confidence            5699999999999999863        79999998 99999999888899999999999999974   689999999999


Q ss_pred             CCCCCCCCC
Q 024209          182 ARQCPKGDS  190 (271)
Q Consensus       182 a~~Cp~~~~  190 (271)
                      +++||+.+.
T Consensus        77 ~~~Cp~~~~   85 (124)
T 2lli_A           77 KERCPSIWR   85 (124)
T ss_dssp             TTTCCCSTT
T ss_pred             hhhCCCccc
Confidence            999998765

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

Probab=99.91  E-value=1.5e-24  Score=175.23  Aligned_cols=78  Identities=31%  Similarity=0.856  Sum_probs=68.6

Q ss_pred             CcccccCCCCCCCCCCCCCCcccccCCCC-CCccCCCCCcccCcCCCCCCCCCCCCCCC---CccccCCCCCcCCCCCCC
Q 024209           48 GNLCNNCKRPGHFARECPNVAVCNNCGLP-GHIASECTTQARCWNCREPGHMASNCHNE---GICHSCGKTGHRARDCST  123 (271)
Q Consensus        48 ~~~C~nCg~~GH~~~~Cp~~~~C~~Cg~~-GH~~~~Cp~~~~C~~Cg~~GH~~~~Cp~~---~~C~~Cg~~GH~~~~Cp~  123 (271)
                      ++.||+|+++||++++||.. +||+|++. ||++.+||....||+|++.||++++||+.   ..|++|++.||++++||.
T Consensus         4 ~~~C~~C~~~GH~~~~Cp~~-~C~~Cg~~~gH~~~~C~~~~~C~~Cg~~GH~~~~C~~~~~~~~C~~Cg~~GH~~~~Cp~   82 (124)
T 2lli_A            4 APKCNNCSQRGHLKKDCPHI-ICSYCGATDDHYSRHCPKAIQCSKCDEVGHYRSQCPHKWKKVQCTLCKSKKHSKERCPS   82 (124)
T ss_dssp             SSCCSSCSSSSCCTTTTTSC-CCTTTCCTTTCCTTTGGGSSCSSSSSCSSSSTTTSCCCCCCCSSSSSCSSCCCTTTCCC
T ss_pred             CCcccCCCCCCcCcccCcCC-cCcCCCCcCCccCcccCCcccccccCCCCCccccCcCcccCccCCCCCcCCcchhhCCC
Confidence            57899999999999999985 89999998 99999999877899999999999999975   578888888888888888


Q ss_pred             Ccc
Q 024209          124 HVQ  126 (271)
Q Consensus       124 ~~~  126 (271)
                      .|.
T Consensus        83 ~~~   85 (124)
T 2lli_A           83 IWR   85 (124)
T ss_dssp             STT
T ss_pred             ccc
Confidence            775

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

Probab=99.65  E-value=3.6e-17  Score=123.32  Aligned_cols=62  Identities=29%  Similarity=0.581  Sum_probs=38.4

Q ss_pred             CCCCCccccCCcCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccCccccccCCCCCcCCCCCCC--CcceE
Q 024209          169 EPVCNLCNIAGHVARQCPKGDSLGERGGGGGGERGGGGGGDGGGGGGRYVGYHDVICRSCNQMGHMSRDCVGP--LIICR  246 (271)
Q Consensus       169 ~~~C~~C~~~GH~a~~Cp~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~C~~C~~~gH~~~dCp~~--~~~C~  246 (271)
                      .+.||+|++.||++++||+.                                  ..||+|++.+|++++|+.+  .++||
T Consensus         5 ~~~C~~Cg~~GH~~~~Cp~~----------------------------------~rcY~c~~~gh~~~~c~~p~~~~~CY   50 (83)
T 3nyb_B            5 KVQCTLCKSKKHSKERCPSI----------------------------------WRAYILVDDNEKAKPKVLPFHTIYCY   50 (83)
T ss_dssp             --CCSSSCCSSSCGGGCGGG----------------------------------TCCCCBC-------------CCCBCS
T ss_pred             cCCCCCCCCCCCccccCCCc----------------------------------ccccccccCCcccccccCCCCCCeec
Confidence            46788888888888888763                                  2488888888888888653  58899


Q ss_pred             cCCCCCcCCCCCCCCCcC
Q 024209          247 NCGGRGHMAYECPSGRIA  264 (271)
Q Consensus       247 ~Cg~~GH~~~~Cp~~~~~  264 (271)
                      |||+.|||++|||+.+.+
T Consensus        51 nCG~~GH~~rdC~~~r~s   68 (83)
T 3nyb_B           51 NCGGKGHFGDDCKEKRSS   68 (83)
T ss_dssp             SSSCBSSCGGGCSSCCSC
T ss_pred             ccCCCCcCcccCCccccC
Confidence            999999999999888754

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

Probab=99.52  E-value=5.9e-15  Score=108.88  Aligned_cols=66  Identities=21%  Similarity=0.395  Sum_probs=42.2

Q ss_pred             CCcCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccCccccccCCCCCcCCCCCC--CCcceEcCCCCCcCC
Q 024209          178 AGHVARQCPKGDSLGERGGGGGGERGGGGGGDGGGGGGRYVGYHDVICRSCNQMGHMSRDCVG--PLIICRNCGGRGHMA  255 (271)
Q Consensus       178 ~GH~a~~Cp~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~C~~C~~~gH~~~dCp~--~~~~C~~Cg~~GH~~  255 (271)
                      .|||++||+++.......                    +  ....+.||+|+++||++++||.  ..+.||+|++.||++
T Consensus         2 ~gh~~rdc~~~~~~~~~~--------------------~--~~r~~~C~~Cg~~GH~a~~C~~~~~~~~C~~Cg~~GH~a   59 (74)
T 2li8_A            2 SGLVPRGSHMPKGKSMQK--------------------R--RSKGDRCYNCGGLDHHAKECKLPPQPKKCHFCQSISHMV   59 (74)
T ss_dssp             ----------CCCCCCCS--------------------C--CSTTSCCTTTCCSSSCTTTCSSCCCCCCCTTTCCTTSCG
T ss_pred             CccccCcCCCCCcCcccc--------------------c--cCCCCcccccCCcCcCcccCCCCCCCCccCCcCCcCCcc
Confidence            589999999875321000                    0  0135789999999999999997  368999999999999


Q ss_pred             CCCCCCCcCC
Q 024209          256 YECPSGRIAD  265 (271)
Q Consensus       256 ~~Cp~~~~~~  265 (271)
                      +|||+..+..
T Consensus        60 r~Cp~~~~~~   69 (74)
T 2li8_A           60 ASCPLKAQQG   69 (74)
T ss_dssp             GGCTTGGGTC
T ss_pred             CcCcCCcCCC
Confidence            9999876543

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

Probab=99.47  E-value=1.3e-14  Score=109.24  Aligned_cols=60  Identities=18%  Similarity=0.250  Sum_probs=39.0

Q ss_pred             CcccccCCCCCCCCcCCCCCccccccCCCCcccccCCC---CCCCCccccCCcCCCCCCCCCC
Q 024209          131 LRLCNNCYKPGHIAADCTNDKACKNCRKTGHIARDCQN---EPVCNLCNIAGHVARQCPKGDS  190 (271)
Q Consensus       131 ~~~C~~Cg~~GH~a~dC~~~~~C~~Cg~~GH~~~~Cp~---~~~C~~C~~~GH~a~~Cp~~~~  190 (271)
                      .+.|++|++.||++.+||+.+.||+|+..+|++++|+.   .+.||+|++.|||++|||+...
T Consensus         5 ~~~C~~Cg~~GH~~~~Cp~~~rcY~c~~~gh~~~~c~~p~~~~~CYnCG~~GH~~rdC~~~r~   67 (83)
T 3nyb_B            5 KVQCTLCKSKKHSKERCPSIWRAYILVDDNEKAKPKVLPFHTIYCYNCGGKGHFGDDCKEKRS   67 (83)
T ss_dssp             --CCSSSCCSSSCGGGCGGGTCCCCBC-------------CCCBCSSSSCBSSCGGGCSSCCS
T ss_pred             cCCCCCCCCCCCccccCCCcccccccccCCcccccccCCCCCCeecccCCCCcCcccCCcccc
Confidence            45788888888888888776678888888888888864   4789999999999999998753

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

Probab=99.33  E-value=5.8e-13  Score=86.26  Aligned_cols=38  Identities=37%  Similarity=0.862  Sum_probs=35.3

Q ss_pred             ccccccCCCCCcCCCCCCC-CcceEcCCCCCcCCCCCCC
Q 024209          223 VICRSCNQMGHMSRDCVGP-LIICRNCGGRGHMAYECPS  260 (271)
Q Consensus       223 ~~C~~C~~~gH~~~dCp~~-~~~C~~Cg~~GH~~~~Cp~  260 (271)
                      ++||+|+++||++++||++ .+.||+|++.||+++|||+
T Consensus         1 i~C~~Cg~~GH~a~~C~~~~~~~C~~Cg~~GH~~~~C~~   39 (39)
T 2a51_A            1 LTCFNCGKPGHTARMCRQPRQEGCWNCGSKEHRFAQCPK   39 (39)
T ss_dssp             CBCTTTCCBSSCTTTCCSCCCSSCTTTCCSSSCTTTSCC
T ss_pred             CeeeccCCCCcccccCCCCCCCccccCCCCCCccCcCcC
Confidence            4799999999999999975 6899999999999999996

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

Probab=99.27  E-value=1.3e-12  Score=83.59  Aligned_cols=37  Identities=35%  Similarity=0.916  Sum_probs=34.3

Q ss_pred             ccccccCCCCCcCCCCCCCCcceEcCCCCCcCCCCCCC
Q 024209          223 VICRSCNQMGHMSRDCVGPLIICRNCGGRGHMAYECPS  260 (271)
Q Consensus       223 ~~C~~C~~~gH~~~dCp~~~~~C~~Cg~~GH~~~~Cp~  260 (271)
                      +.||+|+++||++++||.+ +.||+|++.||++++||+
T Consensus         1 ~~C~~Cg~~GH~~~~C~~~-~~C~~Cg~~GH~a~~C~~   37 (37)
T 2bl6_A            1 QTCYNCGKPGHLSSQCRAP-KVCFKCKQPGHFSKQCRS   37 (37)
T ss_dssp             CCBSSSCCSSCCTTTSSCB-TTCSSCCCTTGGGGTTCC
T ss_pred             CcccccCCCCcchhhCcCc-CeEccCCCcCCccCcCcC
Confidence            4699999999999999965 899999999999999995

>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=99.27  E-value=2.1e-12  Score=87.76  Aligned_cols=42  Identities=33%  Similarity=0.840  Sum_probs=38.2

Q ss_pred             CccccccCCCCCcCCCCCCC-CcceEcCCCCCcCCCCCCCCCc
Q 024209          222 DVICRSCNQMGHMSRDCVGP-LIICRNCGGRGHMAYECPSGRI  263 (271)
Q Consensus       222 ~~~C~~C~~~gH~~~dCp~~-~~~C~~Cg~~GH~~~~Cp~~~~  263 (271)
                      .+.||+|+++||+++|||.+ .+.||+|++.||+++|||+...
T Consensus         6 ~~~C~~Cg~~GH~a~~C~~~~~~~C~~Cg~~GH~~~~C~~~~~   48 (49)
T 2ec7_A            6 VIRCWNCGKEGHSARQCRAPRRQGCWKCGKTGHVMAKCPERQA   48 (49)
T ss_dssp             CCBCTTTCCBTCCTTTCCCSSCCSCSSSCCSSCCGGGCCSSCC
T ss_pred             cCeeeecCCCCcChhhCcCCCCCeeCcCCCcCCccCCCcCCCC
Confidence            57899999999999999975 4789999999999999998754

>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=99.25  E-value=1.9e-12  Score=89.80  Aligned_cols=44  Identities=30%  Similarity=0.782  Sum_probs=39.4

Q ss_pred             cCccccccCCCCCcCCCCCCC-CcceEcCCCCCcCCCCCCCCCcC
Q 024209          221 HDVICRSCNQMGHMSRDCVGP-LIICRNCGGRGHMAYECPSGRIA  264 (271)
Q Consensus       221 ~~~~C~~C~~~gH~~~dCp~~-~~~C~~Cg~~GH~~~~Cp~~~~~  264 (271)
                      ..+.||+|+++||++++||.+ ...||+|++.||+++|||+..++
T Consensus        11 ~~~~C~~Cg~~GH~a~~C~~~~~~~C~~Cg~~GH~~~~C~~~~~n   55 (55)
T 1a1t_A           11 KTVKCFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKDCTERQAN   55 (55)
T ss_dssp             GTCBCTTTCCBSSCGGGCSSCSCCBCTTTCCBSSCGGGCSSSCCC
T ss_pred             CCcceeeeCCCCcChhhcCCCCCCEeCCCCCcCCccCCCcCcCCC
Confidence            458899999999999999975 57899999999999999987653

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

Probab=99.24  E-value=2.4e-12  Score=91.31  Aligned_cols=43  Identities=28%  Similarity=0.601  Sum_probs=37.7

Q ss_pred             CccccccCCCCCcCCCCCCC------CcceEcCCCCCcCCCCCCCCCcC
Q 024209          222 DVICRSCNQMGHMSRDCVGP------LIICRNCGGRGHMAYECPSGRIA  264 (271)
Q Consensus       222 ~~~C~~C~~~gH~~~dCp~~------~~~C~~Cg~~GH~~~~Cp~~~~~  264 (271)
                      .+.||+|+++||+++|||.+      .+.||+|++.||+++|||+.+.+
T Consensus         4 ~~~C~~Cg~~GH~a~~C~~~~~~~~~~~~C~~Cg~~GH~ar~C~~~~~~   52 (61)
T 2ihx_A            4 RGLCYTCGSPGHYQAQCPKKRKSGNSRERCQLCNGMGHNAKQCRKRDGN   52 (61)
T ss_dssp             TTBCSSSCCBTCCGGGCTTTTSSSCCCSBCTTTCCBSSCGGGCCCCC--
T ss_pred             CCcccccCCCCeehhhCcCCcCCCCCCCeeCCCCCCCCCcCCCcCCCcC
Confidence            57899999999999999985      37899999999999999988764

>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=99.22  E-value=7.3e-12  Score=89.42  Aligned_cols=44  Identities=25%  Similarity=0.578  Sum_probs=38.9

Q ss_pred             cCccccccCCCCCcCCCCCCC--CcceEcCCCCCcCCCCCCCCCcC
Q 024209          221 HDVICRSCNQMGHMSRDCVGP--LIICRNCGGRGHMAYECPSGRIA  264 (271)
Q Consensus       221 ~~~~C~~C~~~gH~~~dCp~~--~~~C~~Cg~~GH~~~~Cp~~~~~  264 (271)
                      ....||+|+++||+++|||.+  .+.||+|+++||+++|||+....
T Consensus         6 r~~~C~~Cg~~GH~a~~C~~~~~~~~C~~Cg~~GH~ar~Cp~~~~~   51 (63)
T 2cqf_A            6 SGDRCYNCGGLDHHAKECKLPPQPKKCHFCQSISHMVASCPLKAQQ   51 (63)
T ss_dssp             SCCCCSSSCCSSSCTTTCCSCCCSSCCTTTCCSSSCTTTCTGGGCS
T ss_pred             CCCcccccCCCCcChhhCCCCCCCCccCCcCCcCCccCcCCCcccc
Confidence            357899999999999999973  78999999999999999986543

>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=99.20  E-value=4.1e-12  Score=89.69  Aligned_cols=42  Identities=29%  Similarity=0.593  Sum_probs=20.4

Q ss_pred             ccccccCCCCCcCCCCCCC---------CcceEcCCCCCcCCCCCCCCCcC
Q 024209          223 VICRSCNQMGHMSRDCVGP---------LIICRNCGGRGHMAYECPSGRIA  264 (271)
Q Consensus       223 ~~C~~C~~~gH~~~dCp~~---------~~~C~~Cg~~GH~~~~Cp~~~~~  264 (271)
                      ..||+|+++||+++|||+.         .+.||+|++.|||++|||+....
T Consensus         2 ~~Cf~Cg~~GH~a~~C~~~~~~~~~~~~~~~C~~Cg~~GH~ar~C~~~~~~   52 (60)
T 1cl4_A            2 GSCFKCGKKGHFAKNCHEHAHNNAEPKVPGLCPRCKRGKHWANECKSKTDN   52 (60)
T ss_dssp             ---------------------------CCCSCSSCSSCSSCSTTCCCTTSS
T ss_pred             CccccCCCCCcCHhhCcCCCCCccccCCCcceeECCCCCCccCcCCCcccc
Confidence            4699999999999999974         58899999999999999988643

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

Probab=99.19  E-value=1.3e-11  Score=90.98  Aligned_cols=38  Identities=29%  Similarity=0.797  Sum_probs=25.9

Q ss_pred             cccccCCCCcccccCC---CCCCCCccccCCcCCCCCCCCC
Q 024209          152 ACKNCRKTGHIARDCQ---NEPVCNLCNIAGHVARQCPKGD  189 (271)
Q Consensus       152 ~C~~Cg~~GH~~~~Cp---~~~~C~~C~~~GH~a~~Cp~~~  189 (271)
                      .||+|++.||++++|+   ....||+|+++||++++||+..
T Consensus        26 ~C~~Cg~~GH~a~~C~~~~~~~~C~~Cg~~GH~ar~Cp~~~   66 (74)
T 2li8_A           26 RCYNCGGLDHHAKECKLPPQPKKCHFCQSISHMVASCPLKA   66 (74)
T ss_dssp             CCTTTCCSSSCTTTCSSCCCCCCCTTTCCTTSCGGGCTTGG
T ss_pred             cccccCCcCcCcccCCCCCCCCccCCcCCcCCccCcCcCCc
Confidence            4555555555555555   2567888888999999998764

>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=99.09  E-value=3.7e-11  Score=83.27  Aligned_cols=48  Identities=31%  Similarity=0.713  Sum_probs=33.7

Q ss_pred             cchhccccCCCCcccccCCCCCCCCCCCCCC--cccccCCCCCCccCCCC
Q 024209           37 LRRETRRSFSQGNLCNNCKRPGHFARECPNV--AVCNNCGLPGHIASECT   84 (271)
Q Consensus        37 ~~r~~~~~~~~~~~C~nCg~~GH~~~~Cp~~--~~C~~Cg~~GH~~~~Cp   84 (271)
                      ||+.+++....++.||+|+++||++++||..  ..|++|++.||++.+||
T Consensus         1 ~q~~~f~g~~~~~~C~~Cg~~GH~a~~C~~~~~~~C~~Cg~~GH~~~~C~   50 (55)
T 1a1t_A            1 MQKGNFRNQRKTVKCFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKDCT   50 (55)
T ss_dssp             CCCGGGGGGGGTCBCTTTCCBSSCGGGCSSCSCCBCTTTCCBSSCGGGCS
T ss_pred             CCccccCCCCCCcceeeeCCCCcChhhcCCCCCCEeCCCCCcCCccCCCc
Confidence            5677777777788999999999999999864  34444444444444444

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

Probab=99.08  E-value=4.8e-11  Score=76.23  Aligned_cols=36  Identities=39%  Similarity=0.987  Sum_probs=24.5

Q ss_pred             cccccCCCCcccccCCCCCCCCccccCCcCCCCCCC
Q 024209          152 ACKNCRKTGHIARDCQNEPVCNLCNIAGHVARQCPK  187 (271)
Q Consensus       152 ~C~~Cg~~GH~~~~Cp~~~~C~~C~~~GH~a~~Cp~  187 (271)
                      .||+|++.||++++||....||+|+++||++++||+
T Consensus         2 ~C~~Cg~~GH~~~~C~~~~~C~~Cg~~GH~a~~C~~   37 (37)
T 2bl6_A            2 TCYNCGKPGHLSSQCRAPKVCFKCKQPGHFSKQCRS   37 (37)
T ss_dssp             CBSSSCCSSCCTTTSSCBTTCSSCCCTTGGGGTTCC
T ss_pred             cccccCCCCcchhhCcCcCeEccCCCcCCccCcCcC
Confidence            466666666666666666677777777777777764

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

Probab=99.05  E-value=1.1e-10  Score=75.32  Aligned_cols=36  Identities=44%  Similarity=0.870  Sum_probs=25.7

Q ss_pred             cccccCCCCcccccCCC--CCCCCccccCCcCCCCCCC
Q 024209          152 ACKNCRKTGHIARDCQN--EPVCNLCNIAGHVARQCPK  187 (271)
Q Consensus       152 ~C~~Cg~~GH~~~~Cp~--~~~C~~C~~~GH~a~~Cp~  187 (271)
                      .||+|++.||++++||+  ...||+|+++||++++||+
T Consensus         2 ~C~~Cg~~GH~a~~C~~~~~~~C~~Cg~~GH~~~~C~~   39 (39)
T 2a51_A            2 TCFNCGKPGHTARMCRQPRQEGCWNCGSKEHRFAQCPK   39 (39)
T ss_dssp             BCTTTCCBSSCTTTCCSCCCSSCTTTCCSSSCTTTSCC
T ss_pred             eeeccCCCCcccccCCCCCCCccccCCCCCCccCcCcC
Confidence            46666666666666664  3678888888888888874

>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=98.99  E-value=4e-10  Score=80.33  Aligned_cols=36  Identities=31%  Similarity=0.815  Sum_probs=17.8

Q ss_pred             ccccCCCCcccccCCC---CCCCCccccCCcCCCCCCCC
Q 024209          153 CKNCRKTGHIARDCQN---EPVCNLCNIAGHVARQCPKG  188 (271)
Q Consensus       153 C~~Cg~~GH~~~~Cp~---~~~C~~C~~~GH~a~~Cp~~  188 (271)
                      ||+|++.||++++||.   .+.||+|+++||++++||+.
T Consensus        10 C~~Cg~~GH~a~~C~~~~~~~~C~~Cg~~GH~ar~Cp~~   48 (63)
T 2cqf_A           10 CYNCGGLDHHAKECKLPPQPKKCHFCQSISHMVASCPLK   48 (63)
T ss_dssp             CSSSCCSSSCTTTCCSCCCSSCCTTTCCSSSCTTTCTGG
T ss_pred             ccccCCCCcChhhCCCCCCCCccCCcCCcCCccCcCCCc
Confidence            4444444444444442   34555555555555555553

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

Probab=98.94  E-value=4.3e-10  Score=79.62  Aligned_cols=22  Identities=50%  Similarity=0.913  Sum_probs=18.7

Q ss_pred             CCCCCccccCCcCCCCCCCCCC
Q 024209          169 EPVCNLCNIAGHVARQCPKGDS  190 (271)
Q Consensus       169 ~~~C~~C~~~GH~a~~Cp~~~~  190 (271)
                      ..+||+|+++||++++||+...
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            3679999999999999998754

>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=98.90  E-value=1.2e-09  Score=73.95  Aligned_cols=38  Identities=37%  Similarity=0.831  Sum_probs=22.9

Q ss_pred             CCcccccCCCCCCCCCCCCCC--cccccCCCCCCccCCCC
Q 024209           47 QGNLCNNCKRPGHFARECPNV--AVCNNCGLPGHIASECT   84 (271)
Q Consensus        47 ~~~~C~nCg~~GH~~~~Cp~~--~~C~~Cg~~GH~~~~Cp   84 (271)
                      .++.||+|+++||++++||..  ..||+|++.||++.+||
T Consensus         5 r~~~C~~Cg~~GH~a~~C~~~~~~~C~~Cg~~GH~~~~C~   44 (49)
T 2ec7_A            5 KVIRCWNCGKEGHSARQCRAPRRQGCWKCGKTGHVMAKCP   44 (49)
T ss_dssp             CCCBCTTTCCBTCCTTTCCCSSCCSCSSSCCSSCCGGGCC
T ss_pred             CcCeeeecCCCCcChhhCcCCCCCeeCcCCCcCCccCCCc
Confidence            357788888888888888764  23444444444444443

>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=98.86  E-value=1e-09  Score=90.88  Aligned_cols=43  Identities=26%  Similarity=0.593  Sum_probs=38.0

Q ss_pred             CccccccCCCCCcCCCCCCC--CcceEcCCCCCcCCCCCCCCCcC
Q 024209          222 DVICRSCNQMGHMSRDCVGP--LIICRNCGGRGHMAYECPSGRIA  264 (271)
Q Consensus       222 ~~~C~~C~~~gH~~~dCp~~--~~~C~~Cg~~GH~~~~Cp~~~~~  264 (271)
                      .+.||+|++.||++++||.+  ...||+|++.||+++|||+..+.
T Consensus        97 ~~~C~~Cg~~GH~a~~C~~~~~~~~C~~Cg~~GH~~r~Cp~~~~~  141 (148)
T 3ts2_A           97 GDRCYNCGGLDHHAKECKLPPQPKKCHFCQSINHMVASCPLKAQQ  141 (148)
T ss_dssp             SCCCTTTCCSSCCGGGCCSCCCCCCCTTTCCSSCCGGGCTTTTC-
T ss_pred             CCcccEeCCccchhhhCCCCCCCCcccccCCcCCEeccCcCCCCC
Confidence            47899999999999999973  48999999999999999987665

>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=98.83  E-value=1.5e-09  Score=76.40  Aligned_cols=49  Identities=24%  Similarity=0.557  Sum_probs=19.5

Q ss_pred             ccccCCCCCCCCcCCCCCccccccCCCCcccccCCCCCCCCccccCCcCCCCCCCCCC
Q 024209          133 LCNNCYKPGHIAADCTNDKACKNCRKTGHIARDCQNEPVCNLCNIAGHVARQCPKGDS  190 (271)
Q Consensus       133 ~C~~Cg~~GH~a~dC~~~~~C~~Cg~~GH~~~~Cp~~~~C~~C~~~GH~a~~Cp~~~~  190 (271)
                      .||+|++.||++++||....       +-  .......+||+|++.||+|++||+...
T Consensus         3 ~Cf~Cg~~GH~a~~C~~~~~-------~~--~~~~~~~~C~~Cg~~GH~ar~C~~~~~   51 (60)
T 1cl4_A            3 SCFKCGKKGHFAKNCHEHAH-------NN--AEPKVPGLCPRCKRGKHWANECKSKTD   51 (60)
T ss_dssp             -----------------------------------CCCSCSSCSSCSSCSTTCCCTTS
T ss_pred             ccccCCCCCcCHhhCcCCCC-------Cc--cccCCCcceeECCCCCCccCcCCCccc
Confidence            46666666666666654310       00  000124689999999999999998753

>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=98.57  E-value=2.5e-08  Score=82.57  Aligned_cols=40  Identities=28%  Similarity=0.733  Sum_probs=31.9

Q ss_pred             ccccccCCCCcccccCCC---CCCCCccccCCcCCCCCCCCCC
Q 024209          151 KACKNCRKTGHIARDCQN---EPVCNLCNIAGHVARQCPKGDS  190 (271)
Q Consensus       151 ~~C~~Cg~~GH~~~~Cp~---~~~C~~C~~~GH~a~~Cp~~~~  190 (271)
                      ..||+|++.||++++||+   ...||+|++.||++++||+...
T Consensus        98 ~~C~~Cg~~GH~a~~C~~~~~~~~C~~Cg~~GH~~r~Cp~~~~  140 (148)
T 3ts2_A           98 DRCYNCGGLDHHAKECKLPPQPKKCHFCQSINHMVASCPLKAQ  140 (148)
T ss_dssp             CCCTTTCCSSCCGGGCCSCCCCCCCTTTCCSSCCGGGCTTTTC
T ss_pred             CcccEeCCccchhhhCCCCCCCCcccccCCcCCEeccCcCCCC
Confidence            357777777777777775   5789999999999999998654

>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=97.96  E-value=4e-06  Score=54.21  Aligned_cols=19  Identities=32%  Similarity=0.793  Sum_probs=9.9

Q ss_pred             CccccccCCCCCcCCCCCC
Q 024209          222 DVICRSCNQMGHMSRDCVG  240 (271)
Q Consensus       222 ~~~C~~C~~~gH~~~dCp~  240 (271)
                      ..+||+|++.||||+|||.
T Consensus        10 ~~~C~~Cgk~GH~ardCP~   28 (40)
T 1a6b_B           10 RDQCAYCKEKGHWAKDCPK   28 (40)
T ss_dssp             SSSCSSSCCTTCCTTSCSS
T ss_pred             CCeeeECCCCCcchhhCcC
Confidence            3455555555555555554

>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=97.82  E-value=5.4e-06  Score=49.80  Aligned_cols=18  Identities=33%  Similarity=0.940  Sum_probs=9.0

Q ss_pred             ccccccCCCCCcCCCCCC
Q 024209          223 VICRSCNQMGHMSRDCVG  240 (271)
Q Consensus       223 ~~C~~C~~~gH~~~dCp~  240 (271)
                      ++||+|+++||+++||+.
T Consensus         7 ~~C~nCgk~GH~ar~C~~   24 (29)
T 1nc8_A            7 IRCWNCGKEGHSARQCRA   24 (29)
T ss_dssp             CBCTTTSCBSSCGGGCCS
T ss_pred             CEEEECCccccCHhHCcc
Confidence            445555555555555543

>1dsq_A Nucleic acid binding protein P14; CCHC type zinc finger, virus/viral protein; NMR {Mouse mammary tumor virus} SCOP: g.40.1.1

Probab=97.74  E-value=1.1e-05  Score=47.18  Aligned_cols=19  Identities=42%  Similarity=1.011  Sum_probs=17.6

Q ss_pred             ccccccCCCCCcCCCCCCC
Q 024209          223 VICRSCNQMGHMSRDCVGP  241 (271)
Q Consensus       223 ~~C~~C~~~gH~~~dCp~~  241 (271)
                      .+||+|+++||+++|||.+
T Consensus         3 ~~Cf~CG~~GH~ardC~~~   21 (26)
T 1dsq_A            3 PVCFSCGKTGHIKRDCKEE   21 (26)
T ss_dssp             CBCTTTCCBSSCTTTTTCC
T ss_pred             CeeEeCCCCCcccccCCCc
Confidence            6899999999999999965

>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=97.65  E-value=2.6e-05  Score=50.38  Aligned_cols=24  Identities=38%  Similarity=0.895  Sum_probs=19.9

Q ss_pred             cCCCCcccccCCCCCCCCCCCCCC
Q 024209           44 SFSQGNLCNNCKRPGHFARECPNV   67 (271)
Q Consensus        44 ~~~~~~~C~nCg~~GH~~~~Cp~~   67 (271)
                      .......||+|++.|||+.+||..
T Consensus         6 ~~~~~~~C~~Cgk~GH~ardCP~~   29 (40)
T 1a6b_B            6 SQLDRDQCAYCKEKGHWAKDCPKK   29 (40)
T ss_dssp             CSCCSSSCSSSCCTTCCTTSCSSS
T ss_pred             CCCCCCeeeECCCCCcchhhCcCC
Confidence            345578999999999999999875

>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=97.55  E-value=2.8e-05  Score=46.59  Aligned_cols=21  Identities=38%  Similarity=0.708  Sum_probs=17.8

Q ss_pred             CCcccccCCCCCCCCCCCCCC
Q 024209           47 QGNLCNNCKRPGHFARECPNV   67 (271)
Q Consensus        47 ~~~~C~nCg~~GH~~~~Cp~~   67 (271)
                      .++.||||+++||++++|+.+
T Consensus         5 ~~~~C~nCgk~GH~ar~C~~p   25 (29)
T 1nc8_A            5 KVIRCWNCGKEGHSARQCRAP   25 (29)
T ss_dssp             CCCBCTTTSCBSSCGGGCCSS
T ss_pred             CCCEEEECCccccCHhHCccc
Confidence            367899999999999999764

>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=97.51  E-value=3.5e-05  Score=53.35  Aligned_cols=20  Identities=30%  Similarity=0.760  Sum_probs=13.9

Q ss_pred             cCccccccCCCCCcCCCCCC
Q 024209          221 HDVICRSCNQMGHMSRDCVG  240 (271)
Q Consensus       221 ~~~~C~~C~~~gH~~~dCp~  240 (271)
                      ...+||+|++.|||++|||.
T Consensus        22 ~~~~C~~Cge~GH~ardCp~   41 (56)
T 1u6p_A           22 DRDQCAYCKEKGHWAKDCPK   41 (56)
T ss_dssp             CTTBCSSSCCBSSCGGGCTT
T ss_pred             CCCcceeCCCCCcccccCcC
Confidence            34667777777777777775

>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=97.15  E-value=0.00021  Score=49.46  Aligned_cols=26  Identities=31%  Similarity=0.604  Sum_probs=22.2

Q ss_pred             CCcceEcCCCCCcCCCCCCCCCcCCC
Q 024209          241 PLIICRNCGGRGHMAYECPSGRIADR  266 (271)
Q Consensus       241 ~~~~C~~Cg~~GH~~~~Cp~~~~~~~  266 (271)
                      ....||+|++.|||++|||+....++
T Consensus        22 ~~~~C~~Cge~GH~ardCp~~~~~~~   47 (56)
T 1u6p_A           22 DRDQCAYCKEKGHWAKDCPKKPRGPR   47 (56)
T ss_dssp             CTTBCSSSCCBSSCGGGCTTCCCSSC
T ss_pred             CCCcceeCCCCCcccccCcCCccccC
Confidence            57899999999999999998765443

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

Probab=96.89  E-value=0.0002  Score=49.38  Aligned_cols=18  Identities=28%  Similarity=0.768  Sum_probs=13.0

Q ss_pred             ccccccCCCCCcCCCCCC
Q 024209          223 VICRSCNQMGHMSRDCVG  240 (271)
Q Consensus       223 ~~C~~C~~~gH~~~dCp~  240 (271)
                      ..||+|+++|||++|||.
T Consensus         8 ~~C~kCGk~GH~~k~Cp~   25 (55)
T 2ysa_A            8 YTCFRCGKPGHYIKNCPT   25 (55)
T ss_dssp             CCCTTTCCTTSCGGGCSG
T ss_pred             CccccCCCcCcccccCCC
Confidence            467777777777777773

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

Probab=96.17  E-value=0.0021  Score=44.21  Aligned_cols=22  Identities=32%  Similarity=0.754  Sum_probs=19.0

Q ss_pred             CCcceEcCCCCCcCCCCCCCCC
Q 024209          241 PLIICRNCGGRGHMAYECPSGR  262 (271)
Q Consensus       241 ~~~~C~~Cg~~GH~~~~Cp~~~  262 (271)
                      ....||+||+.|||+++||+..
T Consensus         6 ~~~~C~kCGk~GH~~k~Cp~~~   27 (55)
T 2ysa_A            6 SGYTCFRCGKPGHYIKNCPTNG   27 (55)
T ss_dssp             SSCCCTTTCCTTSCGGGCSGGG
T ss_pred             CCCccccCCCcCcccccCCCCC
Confidence            4678999999999999999544

---

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	271
d2exfa1	42	g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunod	2e-04
d2exfa1	42	g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunod	4e-04
d2exfa1	42	g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunod	0.001
d2exfa1	42	g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunod	0.002
d2exfa1	42	g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunod	0.002
d2exfa1	42	g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunod	0.003

>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 = 35.6 bits (82), Expect = 2e-04
 Identities = 16/36 (44%), Positives = 22/36 (61%), Gaps = 2/36 (5%)

Query: 88  RCWNCREPGHMASNCHN--EGICHSCGKTGHRARDC 121
           +C+NC + GH A NC    +  C  CGK GH+ +DC
Sbjct: 3   KCFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDC 38

>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 = 35.2 bits (81), Expect = 4e-04
 Identities = 14/39 (35%), Positives = 20/39 (51%), Gaps = 1/39 (2%)

Query: 222 DVICRSCNQMGHMSRDCVGP-LIICRNCGGRGHMAYECP 259
           +V C +C + GH +R+C  P    C  CG  GH   +C 
Sbjct: 1   NVKCFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDCT 39

>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 = 34.1 bits (78), Expect = 0.001
 Identities = 16/35 (45%), Positives = 18/35 (51%), Gaps = 2/35 (5%)

Query: 134 CNNCYKPGHIAADCTN--DKACKNCRKTGHIARDC 166
           C NC K GH A +C     K C  C K GH  +DC
Sbjct: 4   CFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDC 38

>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 = 33.3 bits (76), Expect = 0.002
 Identities = 17/42 (40%), Positives = 20/42 (47%), Gaps = 5/42 (11%)

Query: 108 CHSCGKTGHRARDCSTHVQSGGDLRLCNNCYKPGHIAADCTN 149
           C +CGK GH AR+C          + C  C K GH   DCT 
Sbjct: 4   CFNCGKEGHTARNCR-----APRKKGCWKCGKEGHQMKDCTE 40

>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 = 33.3 bits (76), Expect = 0.002
 Identities = 16/36 (44%), Positives = 18/36 (50%), Gaps = 2/36 (5%)

Query: 51 CNNCKRPGHFAREC--PNVAVCNNCGLPGHIASECT 84
          C NC + GH AR C  P    C  CG  GH   +CT
Sbjct: 4  CFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDCT 39

>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 = 32.5 bits (74), Expect = 0.003
 Identities = 14/37 (37%), Positives = 19/37 (51%), Gaps = 2/37 (5%)

Query: 153 CKNCRKTGHIARDCQN--EPVCNLCNIAGHVARQCPK 187
           C NC K GH AR+C+   +  C  C   GH  + C +
Sbjct: 4   CFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDCTE 40

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	271
d2exfa1	42	HIV nucleocapsid {Human immunodeficiency virus typ	99.35
d2exfa1	42	HIV nucleocapsid {Human immunodeficiency virus typ	99.16
d1nc8a_	29	HIV nucleocapsid {Human immunodeficiency virus typ	97.79
d1nc8a_	29	HIV nucleocapsid {Human immunodeficiency virus typ	97.49
d1dsqa_	26	Nucleic acid binding protein p14 {Mouse mammary tu	95.94
d1dsqa_	26	Nucleic acid binding protein p14 {Mouse mammary tu	95.55
d1a6bb_	40	Zinc finger protein ncp10 {Moloney murine leukemia	93.61
d1a6bb_	40	Zinc finger protein ncp10 {Moloney murine leukemia	93.1

>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=99.35  E-value=2.5e-13  Score=87.89  Aligned_cols=39  Identities=36%  Similarity=0.865  Sum_probs=36.3

Q ss_pred             ccccccCCCCCcCCCCCCC-CcceEcCCCCCcCCCCCCCC
Q 024209          223 VICRSCNQMGHMSRDCVGP-LIICRNCGGRGHMAYECPSG  261 (271)
Q Consensus       223 ~~C~~C~~~gH~~~dCp~~-~~~C~~Cg~~GH~~~~Cp~~  261 (271)
                      ++||+|++.||+++|||.+ ...||+|++.||+++|||+.
T Consensus         2 i~C~~Cg~~GH~~~~Cp~~~~~~C~~Cg~~GH~~~~Cp~r   41 (42)
T d2exfa1           2 VKCFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDCTER   41 (42)
T ss_dssp             CCCTTTCCSSSCTTTCSSCCCSSCSSSCCSSSCTTTCCSS
T ss_pred             CccccCCCcCcCcccCcCCCcCccccCCCCCeecccCCCC
Confidence            7899999999999999986 46899999999999999975

>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=99.16  E-value=1e-11  Score=80.09  Aligned_cols=39  Identities=33%  Similarity=0.722  Sum_probs=25.3

Q ss_pred             CCCCccccCCcCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccCccccccCCCCCcCCCCCC
Q 024209          170 PVCNLCNIAGHVARQCPKGDSLGERGGGGGGERGGGGGGDGGGGGGRYVGYHDVICRSCNQMGHMSRDCVG  240 (271)
Q Consensus       170 ~~C~~C~~~GH~a~~Cp~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~C~~C~~~gH~~~dCp~  240 (271)
                      ++||+|++.||++++||++.                                ...||+|++.||+++|||.
T Consensus         2 i~C~~Cg~~GH~~~~Cp~~~--------------------------------~~~C~~Cg~~GH~~~~Cp~   40 (42)
T d2exfa1           2 VKCFNCGKEGHTARNCRAPR--------------------------------KKGCWKCGKEGHQMKDCTE   40 (42)
T ss_dssp             CCCTTTCCSSSCTTTCSSCC--------------------------------CSSCSSSCCSSSCTTTCCS
T ss_pred             CccccCCCcCcCcccCcCCC--------------------------------cCccccCCCCCeecccCCC
Confidence            46677777777777776532                                2457777777777777763

>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=97.79  E-value=3.8e-06  Score=47.98  Aligned_cols=22  Identities=36%  Similarity=0.673  Sum_probs=18.7

Q ss_pred             CCCcccccCCCCCCCCCCCCCC
Q 024209           46 SQGNLCNNCKRPGHFARECPNV   67 (271)
Q Consensus        46 ~~~~~C~nCg~~GH~~~~Cp~~   67 (271)
                      ..++.|||||++||++++|..+
T Consensus         4 r~~ikCfNCGkeGH~ar~CrAP   25 (29)
T d1nc8a_           4 RKVIRCWNCGKEGHSARQCRAP   25 (29)
T ss_dssp             CCCCBCTTTSCBSSCGGGCCSS
T ss_pred             cceeEeecCCccchhhhhccCc
Confidence            4578999999999999999543

>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=97.49  E-value=1.2e-05  Score=45.83  Aligned_cols=21  Identities=33%  Similarity=0.846  Sum_probs=15.0

Q ss_pred             CccccccCCCCCcCCCCCCCC
Q 024209          222 DVICRSCNQMGHMSRDCVGPL  242 (271)
Q Consensus       222 ~~~C~~C~~~gH~~~dCp~~~  242 (271)
                      .++|||||++||++++|-+|.
T Consensus         6 ~ikCfNCGkeGH~ar~CrAPR   26 (29)
T d1nc8a_           6 VIRCWNCGKEGHSARQCRAPR   26 (29)
T ss_dssp             CCBCTTTSCBSSCGGGCCSSS
T ss_pred             eeEeecCCccchhhhhccCcc
Confidence            577777777777777776553

>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=95.94  E-value=0.0018  Score=35.19  Aligned_cols=17  Identities=35%  Similarity=1.075  Sum_probs=9.4

Q ss_pred             cccccCCCCCCCCCCCC
Q 024209           49 NLCNNCKRPGHFARECP   65 (271)
Q Consensus        49 ~~C~nCg~~GH~~~~Cp   65 (271)
                      .+||.||++||+.++|.
T Consensus         3 pvcfscgktghikkdck   19 (26)
T d1dsqa_           3 PVCFSCGKTGHIKRDCK   19 (26)
T ss_dssp             CBCTTTCCBSSCTTTTT
T ss_pred             CEEEecCCcccchhhhh
Confidence            45555555555555553

>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=95.55  E-value=0.0036  Score=33.92  Aligned_cols=18  Identities=28%  Similarity=1.032  Sum_probs=10.2

Q ss_pred             ccCcCCCCCCCCCCCCCC
Q 024209           87 ARCWNCREPGHMASNCHN  104 (271)
Q Consensus        87 ~~C~~Cg~~GH~~~~Cp~  104 (271)
                      .+||.|++.||+.++|.+
T Consensus         3 pvcfscgktghikkdck~   20 (26)
T d1dsqa_           3 PVCFSCGKTGHIKRDCKE   20 (26)
T ss_dssp             CBCTTTCCBSSCTTTTTC
T ss_pred             CEEEecCCcccchhhhhh
Confidence            355555555555555554

>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=93.61  E-value=0.02  Score=34.57  Aligned_cols=18  Identities=33%  Similarity=0.842  Sum_probs=11.5

Q ss_pred             ccccccCCCCCcCCCCCC
Q 024209          223 VICRSCNQMGHMSRDCVG  240 (271)
Q Consensus       223 ~~C~~C~~~gH~~~dCp~  240 (271)
                      ..|.-|.+.|||++|||.
T Consensus        11 DQCAyCke~GHW~~dCPk   28 (40)
T d1a6bb_          11 DQCAYCKEKGHWAKDCPK   28 (40)
T ss_dssp             SSCSSSCCTTCCTTSCSS
T ss_pred             hhhHHHhhcCchhhhCcc
Confidence            456666666666666664

>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=93.10  E-value=0.029  Score=33.81  Aligned_cols=21  Identities=38%  Similarity=1.062  Sum_probs=14.6

Q ss_pred             CCcccccCCCCCCCCCCCCCC
Q 024209           47 QGNLCNNCKRPGHFARECPNV   67 (271)
Q Consensus        47 ~~~~C~nCg~~GH~~~~Cp~~   67 (271)
                      ...-|.-|.+.|||+++||..
T Consensus         9 ~kDQCAyCke~GHW~~dCPkk   29 (40)
T d1a6bb_           9 DRDQCAYCKEKGHWAKDCPKK   29 (40)
T ss_dssp             CSSSCSSSCCTTCCTTSCSSS
T ss_pred             cchhhHHHhhcCchhhhCccC
Confidence            345677777777777777753