Psyllid ID: psy16623

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90---
Protein Sequence
MHQRLENSLWNNYVLGILLIIKQRNEGLLFVLRVEMSSTSTIQCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFARECATESPT
Secondary Structure (PSIPRED)
cHHHHHHHHHHHHHHHHHHHHHHcccccEEEEcEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cHHHHHHHHHHHHHHHHHHHHHcccccEEEEEEEEEccccccEEEcccccccEEcccccccccccccccccEEEEEccccccccccccccccc
Coil and Loop (DISEMBL)
mhqrlenslwnnYVLGILLIIKQRNEGLLFVLRVEmsststiqcyncfdfghyqyscpqkssadargdkVGIVCYkcnnyghfarecatespt
Flexible Loop (DISEMBL)
mhqrlensLWNNYVLGILLIIKQRNEGLLFVLRVEMSSTSTIQCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFarecatespt
Low Complexity Region (SEG)
MHQRLENSLWNNYVLGILLIIKQRNEGLLFVLRVEMSSTSTIQCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFARECATESPT
Disordered region (IsUnstruct)
*******SLWNNYVLGILLIIKQRNEGLLFVLRVEMSSTSTIQCYNCFDFGHYQYSCPQKS*ADARGDKVGIVCYKCNNYGHFAREC******
Disordered Region (DISOPRED)
*****ENSLWNNYVLGIL********************TSTIQCYNCFDFGHYQY*****************VCYKCNNYGHF***C******
Disordered Region (DISEMBL)
MHQRLENSLWNNYVLGILLIIKQRNEGLLFVLRVEMSSTSTIQCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFAR********
Disordered Region (DISPRO)
*H*RLENSLWNNYVLGILLIIKQRNEGLLFVLRVEMSSTSTIQCYNCFDFGHYQYSCPQKS*******KVGIVCYKCNNYGHF***C******
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MHQRLENSLWNNYVLGILLIIKQRNEGLLFVLRVEMSSTSTIQCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFARECATESPT
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	93	2.2.26 [Sep-21-2011]
Q04832	271	DNA-binding protein HEXBP	yes	N/A	0.526	0.180	0.403	7e-06
Q8NIW7	607	Branchpoint-bridging prot	N/A	N/A	0.419	0.064	0.431	3e-05
Q4WXV6	566	Branchpoint-bridging prot	yes	N/A	0.419	0.068	0.409	0.0001
O65639	299	Cold shock protein 1 OS=A	no	N/A	0.516	0.160	0.42	0.0002
P27973	1470	Gag-Pol polyprotein OS=Si	N/A	N/A	0.387	0.024	0.4	0.0002
P05892	519	Gag polyprotein OS=Simian	N/A	N/A	0.397	0.071	0.369	0.0002
P05895	1467	Gag-Pol polyprotein OS=Si	N/A	N/A	0.397	0.025	0.369	0.0003
P27980	1465	Gag-Pol polyprotein OS=Si	N/A	N/A	0.397	0.025	0.369	0.0003
P27978	521	Gag polyprotein OS=Simian	N/A	N/A	0.397	0.071	0.369	0.0003
P27972	520	Gag polyprotein OS=Simian	N/A	N/A	0.387	0.069	0.4	0.0004

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

 Score = 49.3 bits (116), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 21/52 (40%), Positives = 30/52 (57%), Gaps = 3/52 (5%)

Query: 40 STIQCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFARECATES 91
          S+  C NC   GHY   CP+   AD++GD+    C++C   GH +REC  E+
Sbjct: 14 SSTSCRNCGKEGHYARECPE---ADSKGDERSTTCFRCGEEGHMSRECPNEA 62

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

>sp|Q8NIW7|BBP_NEUCR Branchpoint-bridging protein OS=Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987) GN=bpb-1 PE=3 SV=1

 Score = 47.4 bits (111), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 19/44 (43%), Positives = 24/44 (54%), Gaps = 5/44 (11%)

Query: 44  CYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFAREC 87
           C NC   GH +Y CP+K +  A      I+C  C N GH AR+C
Sbjct: 321 CQNCGQIGHRKYDCPEKQNYTA-----NIICRVCGNAGHMARDC 359

Necessary for the splicing of pre-mRNA. Has a role in the recognition of the branch site (5'-UACUAAC-3'), the pyrimidine tract and the 3'-splice site at the 3'-end of introns.

Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987) (taxid: 367110)

>sp|Q4WXV6|BBP_ASPFU Branchpoint-bridging protein OS=Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100) GN=bbp PE=3 SV=1

 Score = 45.4 bits (106), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 18/44 (40%), Positives = 23/44 (52%), Gaps = 5/44 (11%)

Query: 44  CYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFAREC 87
           C NC   GH +Y CP++     R     I+C  C N GH AR+C
Sbjct: 306 CQNCGQIGHRKYDCPEQ-----RNFTANIICRVCGNAGHMARDC 344

Necessary for the splicing of pre-mRNA. Has a role in the recognition of the branch site (5'-UACUAAC-3'), the pyrimidine tract and the 3'-splice site at the 3'-end of introns.

Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100) (taxid: 330879)

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

 Score = 44.7 bits (104), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 21/50 (42%), Positives = 26/50 (52%), Gaps = 2/50 (4%)

Query: 44  CYNCFDFGHYQYSCPQKSSADARGDKVG--IVCYKCNNYGHFARECATES 91
           CYNC D GH+   C    + D RG   G    CY C + GH AR+C  +S
Sbjct: 134 CYNCGDTGHFARDCTSAGNGDQRGATKGGNDGCYTCGDVGHVARDCTQKS 183

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)

>sp|P27973|POL_SIVV1 Gag-Pol polyprotein OS=Simian immunodeficiency virus agm.vervet (isolate AGM155) GN=gag-pol PE=3 SV=2

 Score = 44.3 bits (103), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 18/45 (40%), Positives = 22/45 (48%), Gaps = 9/45 (20%)

Query: 43  QCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFAREC 87
           +CYNC  FGH Q  CP+            I C KC   GH A++C
Sbjct: 399 KCYNCGKFGHMQRQCPEPRK---------IKCLKCGKPGHLAKDC 434

Integrase catalyzes viral DNA integration into the host chromosome, by performing a series of DNA cutting and joining reactions. This enzyme activity takes place after virion entry into a cell and reverse transcription of the RNA genome in dsDNA. The first step in the integration process is 3' processing. This step requires a complex comprising the viral genome, matrix protein, Vpr and integrase. This complex is called the pre-integration complex (PIC). The integrase protein removes 2 nucleotides from each 3' end of the viral DNA, leaving recessed CA OH's at the 3' ends. In the second step, the PIC enters cell nucleus. This process is mediated through integrase and Vpr proteins, and allows the virus to infect a non dividing cell. This ability to enter the nucleus is specific of lentiviruses, other retroviruses cannot and rely on cell division to access cell chromosomes. In the third step, termed strand transfer, the integrase protein joins the previously processed 3' ends to the 5' ends of strands of target cellular DNA at the site of integration. The 5'-ends are produced by integrase-catalyzed staggered cuts, 5 bp apart. A Y-shaped, gapped, recombination intermediate results, with the 5'-ends of the viral DNA strands and the 3' ends of target DNA strands remaining unjoined, flanking a gap of 5 bp. The last step is viral DNA integration into host chromosome. This involves host DNA repair synthesis in which the 5 bp gaps between the unjoined strands are filled in and then ligated. Since this process occurs at both cuts flanking the SIV genome, a 5 bp duplication of host DNA is produced at the ends of SIV integration. Alternatively, Integrase may catalyze the excision of viral DNA just after strand transfer, this is termed disintegration.

Cercopithecidae (taxid: 9527)

EC: 3

EC: .

EC: 1

EC: .

EC: 1

EC: 3

EC: .

EC: 2

>sp|P05892|GAG_SIVVT Gag polyprotein OS=Simian immunodeficiency virus agm.vervet (isolate AGM TYO-1) GN=gag PE=3 SV=1

 Score = 44.3 bits (103), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 17/46 (36%), Positives = 22/46 (47%), Gaps = 9/46 (19%)

Query: 42  IQCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFAREC 87
           ++CYNC  FGH Q  CP+              C KC   GH A++C
Sbjct: 397 LRCYNCGKFGHMQRQCPEPRKTK---------CLKCGKLGHLAKDC 433

p6-gag plays a role in budding of the assembled particle by interacting with the host class E VPS proteins TSG101 and PDCD6IP/AIP1.

Cercopithecidae (taxid: 9527)

>sp|P05895|POL_SIVVT Gag-Pol polyprotein OS=Simian immunodeficiency virus agm.vervet (isolate AGM TYO-1) GN=gag-pol PE=3 SV=2

 Score = 43.9 bits (102), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 17/46 (36%), Positives = 23/46 (50%), Gaps = 9/46 (19%)

Query: 42  IQCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFAREC 87
           ++CYNC  FGH Q  CP+            + C KC   GH A++C
Sbjct: 402 VKCYNCGKFGHMQRQCPEPRK---------MRCLKCGKPGHLAKDC 438

Integrase catalyzes viral DNA integration into the host chromosome, by performing a series of DNA cutting and joining reactions. This enzyme activity takes place after virion entry into a cell and reverse transcription of the RNA genome in dsDNA. The first step in the integration process is 3' processing. This step requires a complex comprising the viral genome, matrix protein, Vpr and integrase. This complex is called the pre-integration complex (PIC). The integrase protein removes 2 nucleotides from each 3' end of the viral DNA, leaving recessed CA OH's at the 3' ends. In the second step, the PIC enters cell nucleus. This process is mediated through integrase and Vpr proteins, and allows the virus to infect a non dividing cell. This ability to enter the nucleus is specific of lentiviruses, other retroviruses cannot and rely on cell division to access cell chromosomes. In the third step, termed strand transfer, the integrase protein joins the previously processed 3' ends to the 5' ends of strands of target cellular DNA at the site of integration. The 5'-ends are produced by integrase-catalyzed staggered cuts, 5 bp apart. A Y-shaped, gapped, recombination intermediate results, with the 5'-ends of the viral DNA strands and the 3' ends of target DNA strands remaining unjoined, flanking a gap of 5 bp. The last step is viral DNA integration into host chromosome. This involves host DNA repair synthesis in which the 5 bp gaps between the unjoined strands are filled in and then ligated. Since this process occurs at both cuts flanking the SIV genome, a 5 bp duplication of host DNA is produced at the ends of SIV integration. Alternatively, Integrase may catalyze the excision of viral DNA just after strand transfer, this is termed disintegration.

Cercopithecidae (taxid: 9527)

EC: 3

EC: .

EC: 1

EC: .

EC: 1

EC: 3

EC: .

EC: 2

>sp|P27980|POL_SIVVG Gag-Pol polyprotein OS=Simian immunodeficiency virus agm.vervet (isolate AGM3) GN=gag-pol PE=3 SV=2

 Score = 43.9 bits (102), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 17/46 (36%), Positives = 23/46 (50%), Gaps = 9/46 (19%)

Query: 42  IQCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFAREC 87
           ++CYNC  FGH Q  CP+            + C KC   GH A++C
Sbjct: 402 VKCYNCGKFGHMQRQCPEPRK---------MRCLKCGKPGHLAKDC 438

Integrase catalyzes viral DNA integration into the host chromosome, by performing a series of DNA cutting and joining reactions. This enzyme activity takes place after virion entry into a cell and reverse transcription of the RNA genome in dsDNA. The first step in the integration process is 3' processing. This step requires a complex comprising the viral genome, matrix protein, Vpr and integrase. This complex is called the pre-integration complex (PIC). The integrase protein removes 2 nucleotides from each 3' end of the viral DNA, leaving recessed CA OH's at the 3' ends. In the second step, the PIC enters cell nucleus. This process is mediated through integrase and Vpr proteins, and allows the virus to infect a non dividing cell. This ability to enter the nucleus is specific of lentiviruses, other retroviruses cannot and rely on cell division to access cell chromosomes. In the third step, termed strand transfer, the integrase protein joins the previously processed 3' ends to the 5' ends of strands of target cellular DNA at the site of integration. The 5'-ends are produced by integrase-catalyzed staggered cuts, 5 bp apart. A Y-shaped, gapped, recombination intermediate results, with the 5'-ends of the viral DNA strands and the 3' ends of target DNA strands remaining unjoined, flanking a gap of 5 bp. The last step is viral DNA integration into host chromosome. This involves host DNA repair synthesis in which the 5 bp gaps between the unjoined strands are filled in and then ligated. Since this process occurs at both cuts flanking the SIV genome, a 5 bp duplication of host DNA is produced at the ends of SIV integration. Alternatively, Integrase may catalyze the excision of viral DNA just after strand transfer, this is termed disintegration.

Cercopithecidae (taxid: 9527)

EC: 3

EC: .

EC: 1

EC: .

EC: 1

EC: 3

EC: .

EC: 2

>sp|P27978|GAG_SIVVG Gag polyprotein OS=Simian immunodeficiency virus agm.vervet (isolate AGM3) GN=gag PE=3 SV=1

 Score = 43.5 bits (101), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 17/46 (36%), Positives = 23/46 (50%), Gaps = 9/46 (19%)

Query: 42  IQCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFAREC 87
           ++CYNC  FGH Q  CP+            + C KC   GH A++C
Sbjct: 402 VKCYNCGKFGHMQRQCPEPRK---------MRCLKCGKPGHLAKDC 438

p6-gag plays a role in budding of the assembled particle by interacting with the host class E VPS proteins TSG101 and PDCD6IP/AIP1.

Cercopithecidae (taxid: 9527)

>sp|P27972|GAG_SIVV1 Gag polyprotein OS=Simian immunodeficiency virus agm.vervet (isolate AGM155) GN=gag PE=3 SV=1

 Score = 43.5 bits (101), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 18/45 (40%), Positives = 22/45 (48%), Gaps = 9/45 (20%)

Query: 43  QCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFAREC 87
           +CYNC  FGH Q  CP+            I C KC   GH A++C
Sbjct: 399 KCYNCGKFGHMQRQCPEPRK---------IKCLKCGKPGHLAKDC 434

p6-gag plays a role in budding of the assembled particle by interacting with the host class E VPS proteins TSG101 and PDCD6IP/AIP1.

Cercopithecidae (taxid: 9527)

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	93
134140561	516	gag protein [Simian immunodeficiency vir	0.827	0.149	0.296	1e-05
297815456	556	hypothetical protein ARALYDRAFT_323091 [	0.752	0.125	0.366	1e-05
307211630	271	Cellular nucleic acid-binding protein [H	0.516	0.177	0.436	2e-05
225710824	220	DNA-binding protein HEXBP [Caligus roger	0.483	0.204	0.489	6e-05
213401537	560	branchpoint-bridging protein [Schizosacc	0.419	0.069	0.454	9e-05
15229721	551	zinc knuckle (CCHC-type) family protein	0.602	0.101	0.403	0.0001
307183860	190	hypothetical protein EAG_06199 [Camponot	0.763	0.373	0.312	0.0001
307200429	205	Cellular nucleic acid-binding protein [H	0.537	0.243	0.385	0.0002
307180464	159	Gag-Pol polyprotein [Camponotus floridan	0.516	0.301	0.4	0.0002
157876792	271	putative universal minicircle sequence b	0.526	0.180	0.403	0.0003

>gi|134140561|gb|ABO61035.1| gag protein [Simian immunodeficiency virus]

 Score = 53.5 bits (127), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 27/91 (29%), Positives = 44/91 (48%), Gaps = 14/91 (15%)

Query: 1   MHQRLENSLWNNYVLGILLIIKQRNEGLLFVLRVEMSSTSTIQCYNCFDFGHYQYSCPQK 60
           M + + N+L  N +  I ++ +Q   G++   R      ++ +CYNC  FGH    CP+ 
Sbjct: 364 MAEAMTNALRQNTINTINMVQRQSPRGVMGKKR-----ENSTRCYNCGQFGHLARDCPKP 418

Query: 61  SSADARGDKVGIVCYKCNNYGHFARECATES 91
            S           C+KC   GH AR+C T++
Sbjct: 419 KSTR---------CFKCGKEGHLARQCRTDT 440

Source: Simian immunodeficiency virus

Species: Simian immunodeficiency virus

Genus: Lentivirus

Family: Retroviridae

Superkingdom: Viruses

>gi|297815456|ref|XP_002875611.1| hypothetical protein ARALYDRAFT_323091 [Arabidopsis lyrata subsp. lyrata] gi|297321449|gb|EFH51870.1| hypothetical protein ARALYDRAFT_323091 [Arabidopsis lyrata subsp. lyrata]

 Score = 53.5 bits (127), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 26/71 (36%), Positives = 39/71 (54%), Gaps = 1/71 (1%)

Query: 22  KQRNEGLLFVLRVEMSSTSTIQCYNCFDFGHYQYSCPQKSS-ADARGDKVGIVCYKCNNY 80
           ++RNE     L    ++    +CY C + GH+   CP  SS + ++G +   +CY+CN  
Sbjct: 305 EERNENDSSSLSFPENNREASECYRCGEEGHFARECPNSSSISTSQGRESQSLCYRCNGA 364

Query: 81  GHFARECATES 91
           GHFAREC   S
Sbjct: 365 GHFARECPNSS 375

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|307211630|gb|EFN87666.1| Cellular nucleic acid-binding protein [Harpegnathos saltator]

 Score = 53.1 bits (126), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 24/55 (43%), Positives = 31/55 (56%), Gaps = 7/55 (12%)

Query: 33  RVEMSSTSTIQCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFAREC 87
           + E+     +QCY C + GH Q +C  KSS D R +     CY+C  YGH AREC
Sbjct: 222 KAELLQARALQCYKCLEKGHVQVNC--KSSNDRREN-----CYRCGEYGHLAREC 269

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|225710824|gb|ACO11258.1| DNA-binding protein HEXBP [Caligus rogercresseyi]

 Score = 51.6 bits (122), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 23/47 (48%), Positives = 31/47 (65%), Gaps = 2/47 (4%)

Query: 42  IQCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFARECA 88
           IQC+ C +FGH  ++CPQKSS+ A   K  I C+KC +YGH +  C 
Sbjct: 86  IQCHVCQEFGHLSFACPQKSSSSAA--KADIQCFKCKDYGHISFACP 130

Source: Caligus rogercresseyi

Species: Caligus rogercresseyi

Genus: Caligus

Family: Caligidae

Order: Siphonostomatoida

Class: Maxillopoda

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|213401537|ref|XP_002171541.1| branchpoint-bridging protein [Schizosaccharomyces japonicus yFS275] gi|211999588|gb|EEB05248.1| branchpoint-bridging protein [Schizosaccharomyces japonicus yFS275]

 Score = 50.8 bits (120), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 20/44 (45%), Positives = 27/44 (61%), Gaps = 5/44 (11%)

Query: 44  CYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFAREC 87
           C NC + GH +Y CP++S+  A      I+C  CNN GH AR+C
Sbjct: 309 CQNCGNVGHRKYDCPERSNYTA-----NIICRYCNNAGHIARDC 347

Source: Schizosaccharomyces japonicus yFS275

Species: Schizosaccharomyces japonicus

Genus: Schizosaccharomyces

Family: Schizosaccharomycetaceae

Order: Schizosaccharomycetales

Class: Schizosaccharomycetes

Phylum: Ascomycota

Superkingdom: Eukaryota

>gi|15229721|ref|NP_189945.1| zinc knuckle (CCHC-type) family protein [Arabidopsis thaliana] gi|9967508|emb|CAC05633.1| putative protein [Arabidopsis thaliana] gi|20466716|gb|AAM20675.1| putative protein [Arabidopsis thaliana] gi|25084296|gb|AAN72214.1| putative protein [Arabidopsis thaliana] gi|332644290|gb|AEE77811.1| zinc knuckle (CCHC-type) family protein [Arabidopsis thaliana]

 Score = 50.4 bits (119), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 23/57 (40%), Positives = 32/57 (56%), Gaps = 1/57 (1%)

Query: 36  MSSTSTIQCYNCFDFGHYQYSCPQKSS-ADARGDKVGIVCYKCNNYGHFARECATES 91
            +S    +CY C + GH+   CP  SS + + G +   +CY+CN  GHFAREC   S
Sbjct: 319 FNSREASECYRCGEEGHFARECPNSSSISTSHGRESQTLCYRCNGSGHFARECPNSS 375

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|307183860|gb|EFN70483.1| hypothetical protein EAG_06199 [Camponotus floridanus]

 Score = 50.4 bits (119), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 25/80 (31%), Positives = 40/80 (50%), Gaps = 9/80 (11%)

Query: 10  WNNYVLGILLIIKQRNEGLL--FVLRVEMSSTSTIQCYNCFDFGHYQYSCPQKSSADARG 67
           W    L + + +  R + ++     RVE+     +QC+ C++FGH Q +C   S+AD RG
Sbjct: 117 WVRLPLAVAVRVAGRRKIMIGWATARVELLDAKPMQCWKCWEFGHVQANC--SSNADRRG 174

Query: 68  DKVGIVCYKCNNYGHFAREC 87
                 C++C   G  AR C
Sbjct: 175 S-----CFRCGQAGQVARNC 189

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307200429|gb|EFN80639.1| Cellular nucleic acid-binding protein [Harpegnathos saltator]

 Score = 50.1 bits (118), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 22/57 (38%), Positives = 33/57 (57%), Gaps = 7/57 (12%)

Query: 33  RVEMSSTSTIQCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFARECAT 89
           +VE+     +QC+ C + GH Q +C  KSS D R +     CY+C   GH AR+C++
Sbjct: 156 KVELLQARALQCFKCLERGHVQINC--KSSNDRRAN-----CYRCGEPGHLARDCSS 205

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307180464|gb|EFN68486.1| Gag-Pol polyprotein [Camponotus floridanus]

 Score = 49.7 bits (117), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 22/55 (40%), Positives = 32/55 (58%), Gaps = 7/55 (12%)

Query: 33  RVEMSSTSTIQCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFAREC 87
           RV++     IQC+ C+ FGH   +C  +S+AD RG     +C++C   GH  REC
Sbjct: 110 RVQLLEAKVIQCFRCWRFGHTMGAC--QSAADMRG-----LCFRCGQSGHQVREC 157

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|157876792|ref|XP_001686738.1| putative universal minicircle sequence binding protein [Leishmania major strain Friedlin] gi|68129813|emb|CAJ09119.1| putative universal minicircle sequence binding protein [Leishmania major strain Friedlin]

 Score = 49.3 bits (116), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 21/52 (40%), Positives = 30/52 (57%), Gaps = 3/52 (5%)

Query: 40 STIQCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFARECATES 91
          S+  C NC   GHY   CP+   AD++GD+    C++C   GH +REC  E+
Sbjct: 14 SSTSCRNCGKEGHYARECPE---ADSKGDERSTTCFRCGEEGHMSRECPNEA 62

Source: Leishmania major strain Friedlin

Species: Leishmania major

Genus: Leishmania

Family: Trypanosomatidae

Order: Kinetoplastida

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	93
TAIR|locus:2079859	551	AT3G43590 [Arabidopsis thalian	0.591	0.099	0.410	6.6e-08
TAIR|locus:2135139	299	CSDP1 "cold shock domain prote	0.505	0.157	0.448	1.6e-06
DICTYBASE|DDB_G0293328	131	DDB_G0293328 "Cellular nucleic	0.462	0.328	0.454	2.1e-06
WB|WBGene00019537	151	K08D12.3 [Caenorhabditis elega	0.473	0.291	0.422	2.1e-06
FB|FBgn0034802	165	CG3800 [Drosophila melanogaste	0.505	0.284	0.38	3.4e-06
ZFIN|ZDB-GENE-030131-5045	163	cnbpa "CCHC-type zinc finger,	0.516	0.294	0.38	3.4e-06
ASPGD|ASPL0000040986	233	AN9093 [Emericella nidulans (t	0.483	0.193	0.44	5.3e-06
CGD|CAL0002417	175	GIS2 [Candida albicans (taxid:	0.397	0.211	0.422	7.2e-06
UNIPROTKB|Q59YJ9	175	GIS2 "Putative uncharacterized	0.397	0.211	0.422	7.2e-06
SGD|S000005199	153	GIS2 "Translational activator	0.537	0.326	0.388	9e-06

TAIR|locus:2079859 AT3G43590 [Arabidopsis thaliana (taxid:3702)]

 Score = 133 (51.9 bits), Expect = 6.6e-08, P = 6.6e-08
 Identities = 23/56 (41%), Positives = 32/56 (57%)

Query:    37 SSTSTIQCYNCFDFGHYQYSCPQKSS-ADARGDKVGIVCYKCNNYGHFARECATES 91
             +S    +CY C + GH+   CP  SS + + G +   +CY+CN  GHFAREC   S
Sbjct:   320 NSREASECYRCGEEGHFARECPNSSSISTSHGRESQTLCYRCNGSGHFARECPNSS 375

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

GO:0005634 "nucleus" evidence=ISM

GO:0008270 "zinc ion binding" evidence=IEA

TAIR|locus:2135139 CSDP1 "cold shock domain protein 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 116 (45.9 bits), Expect = 1.6e-06, P = 1.6e-06
 Identities = 22/49 (44%), Positives = 27/49 (55%)

Query:    44 CYNCFDFGHYQYSCPQKSSA-DARGDKVGI-VCYKCNNYGHFARECATE 90
             CY C D GH+   C QK +A + R    G   CY C   GH AR+CAT+
Sbjct:   200 CYTCGDVGHFARDCTQKVAAGNVRSGGGGSGTCYSCGGVGHIARDCATK 248

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

GO:0003677 "DNA binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0009409 "response to cold" evidence=IGI;IEP

GO:0003690 "double-stranded DNA binding" evidence=IDA

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

GO:0003723 "RNA binding" evidence=IDA

GO:0009414 "response to water deprivation" evidence=IEP

GO:0009651 "response to salt stress" evidence=IEP

GO:0010501 "RNA secondary structure unwinding" evidence=IDA

GO:0032508 "DNA duplex unwinding" evidence=IDA

GO:0009631 "cold acclimation" evidence=IGI

GO:0009165 "nucleotide biosynthetic process" evidence=RCA

DICTYBASE|DDB_G0293328 DDB_G0293328 "Cellular nucleic acid-binding protein" [Dictyostelium discoideum (taxid:44689)]

 Score = 109 (43.4 bits), Expect = 2.1e-06, P = 2.1e-06
 Identities = 20/44 (45%), Positives = 23/44 (52%)

Query:    44 CYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFAREC 87
             CY C   GH    CPQ         K  I CY+CN +GHFAR+C
Sbjct:    33 CYVCNVVGHLSRECPQNPQPTFE-KKDPIKCYQCNGFGHFARDC 75

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

GO:0044351 "macropinocytosis" evidence=RCA

WB|WBGene00019537 K08D12.3 [Caenorhabditis elegans (taxid:6239)]

 Score = 109 (43.4 bits), Expect = 2.1e-06, P = 2.1e-06
 Identities = 19/45 (42%), Positives = 23/45 (51%)

Query:    44 CYNCFDFGHYQYSCPQ-KSSADARGDKVGIVCYKCNNYGHFAREC 87
             CY C   GH   +CP  +S    RG   G  CY C   GHF+R+C
Sbjct:     6 CYKCQQPGHISRNCPNGESDGGRRGGGGGSTCYNCQETGHFSRDC 50

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0000003 "reproduction" evidence=IMP

GO:0040011 "locomotion" evidence=IMP

GO:0009792 "embryo development ending in birth or egg hatching" evidence=IMP

GO:0040007 "growth" evidence=IMP

GO:0002119 "nematode larval development" evidence=IMP

FB|FBgn0034802 CG3800 [Drosophila melanogaster (taxid:7227)]

 Score = 107 (42.7 bits), Expect = 3.4e-06, P = 3.4e-06
 Identities = 19/50 (38%), Positives = 27/50 (54%)

Query:    44 CYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFARECATESPT 93
             CY C   GH+  +CP+  + + RG    + CYKCN  GH ++ C   S T
Sbjct:    98 CYRCNKTGHWVRNCPE--AVNERGP-TNVSCYKCNRTGHISKNCPETSKT 144

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

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

GO:0008270 "zinc ion binding" evidence=IEA

ZFIN|ZDB-GENE-030131-5045 cnbpa "CCHC-type zinc finger, nucleic acid binding protein a" [Danio rerio (taxid:7955)]

 Score = 107 (42.7 bits), Expect = 3.4e-06, P = 3.4e-06
 Identities = 19/50 (38%), Positives = 26/50 (52%)

Query:    40 STIQCYNCFDFGHYQYSCPQKSSADARGDKVG--IVCYKCNNYGHFAREC 87
             ST +C+ C   GH+  +CP       RG   G  + CY+C   GH AR+C
Sbjct:     4 STSECFGCGRSGHWIKNCPNAGRGRGRGRGRGKDLFCYRCGEQGHIARDC 53

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0060322 "head development" evidence=IMP

GO:0014029 "neural crest formation" evidence=IMP

GO:0014036 "neural crest cell fate specification" evidence=IMP

GO:0051216 "cartilage development" evidence=IMP

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

GO:0003723 "RNA binding" evidence=IDA

GO:0046872 "metal ion binding" evidence=IEA

ASPGD|ASPL0000040986 AN9093 [Emericella nidulans (taxid:162425)]

 Score = 109 (43.4 bits), Expect = 5.3e-06, P = 5.3e-06
 Identities = 22/50 (44%), Positives = 24/50 (48%)

Query:    38 STSTIQCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFAREC 87
             +T T QCYNC   GH Q  CP      A G      CY C+  GH AR C
Sbjct:    46 TTETKQCYNCQGLGHVQADCPTLRLNGANGR-----CYNCSQPGHLARNC 90

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

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

GO:0003729 "mRNA binding" evidence=IEA

GO:0045182 "translation regulator activity" evidence=IEA

GO:0010494 "cytoplasmic stress granule" evidence=IEA

GO:0042788 "polysomal ribosome" evidence=IEA

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

GO:0008270 "zinc ion binding" evidence=IEA

CGD|CAL0002417 GIS2 [Candida albicans (taxid:5476)]

 Score = 104 (41.7 bits), Expect = 7.2e-06, P = 7.2e-06
 Identities = 19/45 (42%), Positives = 25/45 (55%)

Query:    43 QCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFAREC 87
             QCY+C D GH Q  CP +    A+G K    CY C  +GH ++ C
Sbjct:    52 QCYSCGDVGHIQTECPNQ----AQGAK----CYNCGQFGHISKNC 88

GO:0070417 "cellular response to cold" evidence=IMP

GO:0003676 "nucleic acid binding" evidence=NAS

GO:0071470 "cellular response to osmotic stress" evidence=IMP

GO:0035690 "cellular response to drug" evidence=IMP

GO:0042788 "polysomal ribosome" 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

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

GO:0003729 "mRNA binding" evidence=IEA

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

GO:0045182 "translation regulator activity" evidence=IEA

UNIPROTKB|Q59YJ9 GIS2 "Putative uncharacterized protein GIS2" [Candida albicans SC5314 (taxid:237561)]

 Score = 104 (41.7 bits), Expect = 7.2e-06, P = 7.2e-06
 Identities = 19/45 (42%), Positives = 25/45 (55%)

Query:    43 QCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFAREC 87
             QCY+C D GH Q  CP +    A+G K    CY C  +GH ++ C
Sbjct:    52 QCYSCGDVGHIQTECPNQ----AQGAK----CYNCGQFGHISKNC 88

GO:0003676 "nucleic acid binding" evidence=NAS

GO:0035690 "cellular response to drug" evidence=IMP

GO:0070417 "cellular response to cold" evidence=IMP

GO:0071470 "cellular response to osmotic stress" evidence=IMP

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

 Score = 103 (41.3 bits), Expect = 9.0e-06, P = 9.0e-06
 Identities = 21/54 (38%), Positives = 27/54 (50%)

Query:    38 STSTIQ-CYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFARECATE 90
             S  T+Q C+NC   GH    CP+     +R  KV   CYKC    H A++C  E
Sbjct:    60 SECTVQRCFNCNQTGHISRECPEPKKT-SRFSKVS--CYKCGGPNHMAKDCMKE 110

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

---

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 EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	93
PTZ00368	148	PTZ00368, PTZ00368, universal minicircle sequence	1e-07
PTZ00368	148	PTZ00368, PTZ00368, universal minicircle sequence	5e-07
PTZ00368	148	PTZ00368, PTZ00368, universal minicircle sequence	1e-06
PTZ00368	148	PTZ00368, PTZ00368, universal minicircle sequence	2e-05
COG5082	190	COG5082, AIR1, Arginine methyltransferase-interact	6e-05
PTZ00368	148	PTZ00368, PTZ00368, universal minicircle sequence	3e-04
COG5082	190	COG5082, AIR1, Arginine methyltransferase-interact	3e-04
COG5082	190	COG5082, AIR1, Arginine methyltransferase-interact	0.002

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

 Score = 46.0 bits (109), Expect = 1e-07
 Identities = 17/44 (38%), Positives = 19/44 (43%), Gaps = 5/44 (11%)

Query: 44 CYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFAREC 87
          CYNC   GH    CP+     A        CY C   GH +REC
Sbjct: 55 CYNCGKTGHLSRECPE-----APPGSGPRSCYNCGQTGHISREC 93

Length = 148

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

 Score = 44.4 bits (105), Expect = 5e-07
 Identities = 19/57 (33%), Positives = 25/57 (43%), Gaps = 5/57 (8%)

Query: 36 MSSTSTIQCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFARECATESP 92
            +     CY C + GH    CP  S+   RG++    CY C   GH +REC    P
Sbjct: 22 AGAAKARPCYKCGEPGHLSRECP--SAPGGRGERS---CYNCGKTGHLSRECPEAPP 73

Length = 148

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

 Score = 43.3 bits (102), Expect = 1e-06
 Identities = 16/52 (30%), Positives = 21/52 (40%), Gaps = 4/52 (7%)

Query: 39  TSTIQCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFARECATE 90
           +    CYNC   GH    CP ++   A        CY C   GH +R+C   
Sbjct: 75  SGPRSCYNCGQTGHISRECPNRAKGGAARRA----CYNCGGEGHISRDCPNA 122

Length = 148

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

 Score = 40.2 bits (94), Expect = 2e-05
 Identities = 18/44 (40%), Positives = 20/44 (45%), Gaps = 4/44 (9%)

Query: 44  CYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFAREC 87
           CYNC   GH    CP        GDK    CY C   GH +R+C
Sbjct: 106 CYNCGGEGHISRDCPNAGKR-PGGDKT---CYNCGQTGHLSRDC 145

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 = 39.1 bits (91), Expect = 6e-05
 Identities = 15/44 (34%), Positives = 18/44 (40%), Gaps = 11/44 (25%)

Query: 44  CYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFAREC 87
           CYNC   GH    CP+              CY C   GH +R+C
Sbjct: 81  CYNCSWDGHRSNHCPKP-----------KKCYNCGETGHLSRDC 113

Length = 190

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

 Score = 37.1 bits (86), Expect = 3e-04
 Identities = 18/44 (40%), Positives = 20/44 (45%), Gaps = 3/44 (6%)

Query: 44 CYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFAREC 87
          CY C   GH    CP  + A A        CYKC   GH +REC
Sbjct: 3  CYRCGGVGHQSRECPNSAPAGAAK---ARPCYKCGEPGHLSREC 43

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 = 37.5 bits (87), Expect = 3e-04
 Identities = 16/54 (29%), Positives = 20/54 (37%), Gaps = 4/54 (7%)

Query: 43  QCYNCFDFGHYQYSCPQ--KSSADARGDKVGI--VCYKCNNYGHFARECATESP 92
            C++C    H    CP   K      GD   I   CY C + GHF  +C     
Sbjct: 122 SCFDCNSTRHSSEDCPSIWKHYVLNNGDGHPIKKFCYSCGSAGHFGDDCKEPRS 175

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 = 34.8 bits (80), Expect = 0.002
 Identities = 12/49 (24%), Positives = 18/49 (36%), Gaps = 7/49 (14%)

Query: 39  TSTIQCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFAREC 87
               +CYNC + GH    C                C+ CN+  H + +C
Sbjct: 95  PKPKKCYNCGETGHLSRDCNPSKD-------QQKSCFDCNSTRHSSEDC 136

Length = 190

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	93
PTZ00368	148	universal minicircle sequence binding protein (UMS	98.96
COG5082	190	AIR1 Arginine methyltransferase-interacting protei	98.9
PTZ00368	148	universal minicircle sequence binding protein (UMS	98.77
PF00098	18	zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc fi	98.63
COG5082	190	AIR1 Arginine methyltransferase-interacting protei	98.5
KOG4400|consensus	261		98.5
PF00098	18	zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc fi	98.44
KOG4400|consensus	261		98.24
PF13696	32	zf-CCHC_2: Zinc knuckle	97.84
KOG0119|consensus	554		97.28
PF13696	32	zf-CCHC_2: Zinc knuckle	97.09
PF13917	42	zf-CCHC_3: Zinc knuckle	96.76
smart00343	26	ZnF_C2HC zinc finger.	96.62
PF13917	42	zf-CCHC_3: Zinc knuckle	96.51
smart00343	26	ZnF_C2HC zinc finger.	96.08
PF14392	49	zf-CCHC_4: Zinc knuckle	95.55
KOG0109|consensus	346		95.54
PF14392	49	zf-CCHC_4: Zinc knuckle	94.82
PF14787	36	zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB:	94.81
COG5222	427	Uncharacterized conserved protein, contains RING Z	94.66
PF15288	40	zf-CCHC_6: Zinc knuckle	94.42
PF15288	40	zf-CCHC_6: Zinc knuckle	93.31
KOG0109|consensus	346		93.08
PF14787	36	zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB:	91.23
COG5222	427	Uncharacterized conserved protein, contains RING Z	89.96
KOG3116|consensus	177		89.34
KOG0107|consensus	195		89.24
KOG0314|consensus	448		85.98
KOG2044|consensus	931		85.39

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

Probab=98.96  E-value=3.8e-10  Score=76.12  Aligned_cols=43  Identities=35%  Similarity=0.914  Sum_probs=20.7

Q ss_pred             ceeecCCCCccccccCCCCCCCCCCCcccccceeccccccccccCCC
Q psy16623         43 QCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFARECAT   89 (93)
Q Consensus        43 ~C~~Cg~~GH~~~~C~~~~~~~~~~~~~~~~C~~Cg~~GH~ar~C~~   89 (93)
                      .||+|++.||++++||........    ...||+|++.|||++|||+
T Consensus       105 ~C~~Cg~~gH~~~~C~~~~~~~~~----~~~C~~Cg~~gH~~~dCp~  147 (148)
T PTZ00368        105 ACYNCGGEGHISRDCPNAGKRPGG----DKTCYNCGQTGHLSRDCPD  147 (148)
T ss_pred             hhcccCcCCcchhcCCCccccCCC----CCccccCCCcCcccccCCC
Confidence            355555555555555543100000    1456666666666666664

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

Probab=98.90  E-value=7.7e-10  Score=78.09  Aligned_cols=49  Identities=31%  Similarity=0.707  Sum_probs=34.7

Q ss_pred             CCcceeecCCCCccccccC-----CCCCC-CCCC-CcccccceeccccccccccCC
Q psy16623         40 STIQCYNCFDFGHYQYSCP-----QKSSA-DARG-DKVGIVCYKCNNYGHFARECA   88 (93)
Q Consensus        40 ~~~~C~~Cg~~GH~~~~C~-----~~~~~-~~~~-~~~~~~C~~Cg~~GH~ar~C~   88 (93)
                      ....||+|++.||.++|||     .-... -++. -...+.||+||+.||++++|+
T Consensus        59 ~~~~C~nCg~~GH~~~DCP~~iC~~C~~~~H~s~~C~~~~~C~~Cg~~GH~~~dC~  114 (190)
T COG5082          59 ENPVCFNCGQNGHLRRDCPHSICYNCSWDGHRSNHCPKPKKCYNCGETGHLSRDCN  114 (190)
T ss_pred             cccccchhcccCcccccCChhHhhhcCCCCcccccCCcccccccccccCccccccC
Confidence            3567999999999999999     11000 0110 011278999999999999994

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

Probab=98.77  E-value=6.3e-09  Score=70.17  Aligned_cols=44  Identities=36%  Similarity=0.915  Sum_probs=29.2

Q ss_pred             cceeecCCCCccccccCCCCCCCCCCCcccccceeccccccccccCCCC
Q psy16623         42 IQCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFARECATE   90 (93)
Q Consensus        42 ~~C~~Cg~~GH~~~~C~~~~~~~~~~~~~~~~C~~Cg~~GH~ar~C~~~   90 (93)
                      ..||+|++.||++++||+......     ...||+|++.||++++||+.
T Consensus        53 ~~C~~Cg~~GH~~~~Cp~~~~~~~-----~~~C~~Cg~~GH~~~~C~~~   96 (148)
T PTZ00368         53 RSCYNCGKTGHLSRECPEAPPGSG-----PRSCYNCGQTGHISRECPNR   96 (148)
T ss_pred             cccCCCCCcCcCcccCCCcccCCC-----CcccCcCCCCCcccccCCCc
Confidence            357777777777777766432111     15688888888888888774

>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=98.63  E-value=1.2e-08  Score=46.79  Aligned_cols=17  Identities=41%  Similarity=1.189  Sum_probs=11.3

Q ss_pred             cceeccccccccccCCC
Q psy16623         73 VCYKCNNYGHFARECAT   89 (93)
Q Consensus        73 ~C~~Cg~~GH~ar~C~~   89 (93)
                      .||+|++.||++++||+
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            46667777777776664

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 ....

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

Probab=98.50  E-value=6.3e-08  Score=68.45  Aligned_cols=49  Identities=22%  Similarity=0.398  Sum_probs=28.7

Q ss_pred             CcceeeeechHHHHHHHHhcCceeeEEEeeeecCCCCcceeecCCCCcccccc-CCC
Q psy16623          5 LENSLWNNYVLGILLIIKQRNEGLLFVLRVEMSSTSTIQCYNCFDFGHYQYSC-PQK   60 (93)
Q Consensus         5 ~~~~~~~~~p~~~a~~i~~~g~~~~~~~~~~~~~~~~~~C~~Cg~~GH~~~~C-~~~   60 (93)
                      ..||+.-++|-.+...-...++..      . -=...+.||+||+.||++++| |..
T Consensus        68 ~~GH~~~DCP~~iC~~C~~~~H~s------~-~C~~~~~C~~Cg~~GH~~~dC~P~~  117 (190)
T COG5082          68 QNGHLRRDCPHSICYNCSWDGHRS------N-HCPKPKKCYNCGETGHLSRDCNPSK  117 (190)
T ss_pred             ccCcccccCChhHhhhcCCCCccc------c-cCCcccccccccccCccccccCccc
Confidence            346677777743333332233321      1 001126899999999999999 554

>KOG4400|consensus

Probab=98.50  E-value=6.5e-08  Score=70.59  Aligned_cols=42  Identities=31%  Similarity=0.906  Sum_probs=36.4

Q ss_pred             cceeecCCCCccccccCCCCCCCCCCCcccccceeccccccccccCCCCCC
Q psy16623         42 IQCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFARECATESP   92 (93)
Q Consensus        42 ~~C~~Cg~~GH~~~~C~~~~~~~~~~~~~~~~C~~Cg~~GH~ar~C~~~~~   92 (93)
                      +.||+|++.||++.+||.+.    .     ..||.|++.+|++++||...+
T Consensus       144 ~~Cy~Cg~~GH~s~~C~~~~----~-----~~c~~c~~~~h~~~~C~~~~~  185 (261)
T KOG4400|consen  144 AKCYSCGEQGHISDDCPENK----G-----GTCFRCGKVGHGSRDCPSKQK  185 (261)
T ss_pred             CccCCCCcCCcchhhCCCCC----C-----CccccCCCcceecccCCcccc
Confidence            56999999999999999761    1     689999999999999998754

>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=98.44  E-value=7.8e-08  Score=44.01  Aligned_cols=17  Identities=41%  Similarity=1.138  Sum_probs=16.0

Q ss_pred             ceeecCCCCccccccCC
Q psy16623         43 QCYNCFDFGHYQYSCPQ   59 (93)
Q Consensus        43 ~C~~Cg~~GH~~~~C~~   59 (93)
                      .||+|++.||++++||+
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            69999999999999985

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 ....

>KOG4400|consensus

Probab=98.24  E-value=6.7e-07  Score=65.28  Aligned_cols=50  Identities=28%  Similarity=0.773  Sum_probs=37.5

Q ss_pred             CcceeecCCCCccccccCCCCCCCC-------CC-----C--------cc-cccceeccccccccccCCCC
Q psy16623         41 TIQCYNCFDFGHYQYSCPQKSSADA-------RG-----D--------KV-GIVCYKCNNYGHFARECATE   90 (93)
Q Consensus        41 ~~~C~~Cg~~GH~~~~C~~~~~~~~-------~~-----~--------~~-~~~C~~Cg~~GH~ar~C~~~   90 (93)
                      ...||+|++.||+.++||.......       .+     .        .+ ...||+||+.||+.++||..
T Consensus        92 ~~~c~~C~~~gH~~~~c~~~~~~~~~~~~~~~c~~~gh~~~~~~~~~~~~~~~~Cy~Cg~~GH~s~~C~~~  162 (261)
T KOG4400|consen   92 AAACFNCGEGGHIERDCPEAGKEGSSETSCYSCGKTGHRGCPDADPVDGPKPAKCYSCGEQGHISDDCPEN  162 (261)
T ss_pred             chhhhhCCCCccchhhCCcccCcccccceeeccCCCccccCcccccccCCCCCccCCCCcCCcchhhCCCC
Confidence            5679999999999999997765430       00     0        00 14599999999999999964

>PF13696 zf-CCHC_2: Zinc knuckle

Probab=97.84  E-value=8.4e-06  Score=42.36  Aligned_cols=21  Identities=38%  Similarity=1.073  Sum_probs=16.0

Q ss_pred             ccceeccccccccccCCCCCC
Q psy16623         72 IVCYKCNNYGHFARECATESP   92 (93)
Q Consensus        72 ~~C~~Cg~~GH~ar~C~~~~~   92 (93)
                      ..|+.|++.||+.+|||...|
T Consensus         9 Y~C~~C~~~GH~i~dCP~~~P   29 (32)
T PF13696_consen    9 YVCHRCGQKGHWIQDCPTNKP   29 (32)
T ss_pred             CEeecCCCCCccHhHCCCCCC
Confidence            668888888888888887654

>KOG0119|consensus

Probab=97.28  E-value=0.00018  Score=57.32  Aligned_cols=49  Identities=31%  Similarity=0.741  Sum_probs=39.3

Q ss_pred             ecCCCCcceeecCCCCccccccCCCCCCCCCCCcccccceeccccccccccCCCC
Q psy16623         36 MSSTSTIQCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFARECATE   90 (93)
Q Consensus        36 ~~~~~~~~C~~Cg~~GH~~~~C~~~~~~~~~~~~~~~~C~~Cg~~GH~ar~C~~~   90 (93)
                      +.......|..|+..||...+||.... ...     ..|+.|+..||+++||+..
T Consensus       256 ~r~~d~~~c~~cg~~~H~q~~cp~r~~-~~~-----n~c~~cg~~gH~~~dc~~~  304 (554)
T KOG0119|consen  256 LRDDDNRACRNCGSTGHKQYDCPGRIP-NTT-----NVCKICGPLGHISIDCKVN  304 (554)
T ss_pred             CCccccccccccCCCccccccCCcccc-ccc-----ccccccCCcccccccCCCc
Confidence            444445689999999999999998731 122     4799999999999999875

>PF13696 zf-CCHC_2: Zinc knuckle

Probab=97.09  E-value=0.00035  Score=36.27  Aligned_cols=21  Identities=29%  Similarity=0.695  Sum_probs=18.7

Q ss_pred             CcceeecCCCCccccccCCCC
Q psy16623         41 TIQCYNCFDFGHYQYSCPQKS   61 (93)
Q Consensus        41 ~~~C~~Cg~~GH~~~~C~~~~   61 (93)
                      ...|+.|++.||+..|||...
T Consensus         8 ~Y~C~~C~~~GH~i~dCP~~~   28 (32)
T PF13696_consen    8 GYVCHRCGQKGHWIQDCPTNK   28 (32)
T ss_pred             CCEeecCCCCCccHhHCCCCC
Confidence            467999999999999999854

>PF13917 zf-CCHC_3: Zinc knuckle

Probab=96.76  E-value=0.00069  Score=37.20  Aligned_cols=17  Identities=41%  Similarity=1.077  Sum_probs=9.0

Q ss_pred             ccceeccccccccccCC
Q psy16623         72 IVCYKCNNYGHFARECA   88 (93)
Q Consensus        72 ~~C~~Cg~~GH~ar~C~   88 (93)
                      ..|.+|++.||++.+|+
T Consensus         5 ~~CqkC~~~GH~tyeC~   21 (42)
T PF13917_consen    5 VRCQKCGQKGHWTYECP   21 (42)
T ss_pred             CcCcccCCCCcchhhCC
Confidence            34555555555555555

>smart00343 ZnF_C2HC zinc finger

Probab=96.62  E-value=0.0008  Score=32.78  Aligned_cols=17  Identities=47%  Similarity=1.247  Sum_probs=14.4

Q ss_pred             cceeccccccccccCCC
Q psy16623         73 VCYKCNNYGHFARECAT   89 (93)
Q Consensus        73 ~C~~Cg~~GH~ar~C~~   89 (93)
                      .|++|++.||++++||+
T Consensus         1 ~C~~CG~~GH~~~~C~~   17 (26)
T smart00343        1 KCYNCGKEGHIARDCPK   17 (26)
T ss_pred             CCccCCCCCcchhhCCc
Confidence            38899999999999984

>PF13917 zf-CCHC_3: Zinc knuckle

Probab=96.51  E-value=0.0014  Score=36.00  Aligned_cols=19  Identities=37%  Similarity=1.111  Sum_probs=17.2

Q ss_pred             CcceeecCCCCccccccCC
Q psy16623         41 TIQCYNCFDFGHYQYSCPQ   59 (93)
Q Consensus        41 ~~~C~~Cg~~GH~~~~C~~   59 (93)
                      ...|.+|++.||+..+|++
T Consensus         4 ~~~CqkC~~~GH~tyeC~~   22 (42)
T PF13917_consen    4 RVRCQKCGQKGHWTYECPN   22 (42)
T ss_pred             CCcCcccCCCCcchhhCCC
Confidence            4579999999999999995

>smart00343 ZnF_C2HC zinc finger

Probab=96.08  E-value=0.0027  Score=30.85  Aligned_cols=18  Identities=44%  Similarity=1.069  Sum_probs=16.0

Q ss_pred             ceeecCCCCccccccCCC
Q psy16623         43 QCYNCFDFGHYQYSCPQK   60 (93)
Q Consensus        43 ~C~~Cg~~GH~~~~C~~~   60 (93)
                      .||+|++.||++++||..
T Consensus         1 ~C~~CG~~GH~~~~C~~~   18 (26)
T smart00343        1 KCYNCGKEGHIARDCPKX   18 (26)
T ss_pred             CCccCCCCCcchhhCCcc
Confidence            499999999999999844

>PF14392 zf-CCHC_4: Zinc knuckle

Probab=95.55  E-value=0.01  Score=33.07  Aligned_cols=31  Identities=26%  Similarity=0.603  Sum_probs=20.7

Q ss_pred             CceeeEEEeeeecCCCCcceeecCCCCccccccC
Q psy16623         25 NEGLLFVLRVEMSSTSTIQCYNCFDFGHYQYSCP   58 (93)
Q Consensus        25 g~~~~~~~~~~~~~~~~~~C~~Cg~~GH~~~~C~   58 (93)
                      |+..+.....+-.   +..|++|+..||...+||
T Consensus        18 g~~~~~~v~YE~l---p~~C~~C~~~gH~~~~C~   48 (49)
T PF14392_consen   18 GESFWVKVKYERL---PRFCFHCGRIGHSDKECP   48 (49)
T ss_pred             CcEEEEEEEECCc---ChhhcCCCCcCcCHhHcC
Confidence            4443444444433   347999999999999987

>KOG0109|consensus

Probab=95.54  E-value=0.0052  Score=46.53  Aligned_cols=19  Identities=37%  Similarity=1.139  Sum_probs=17.5

Q ss_pred             ccceeccccccccccCCCC
Q psy16623         72 IVCYKCNNYGHFARECATE   90 (93)
Q Consensus        72 ~~C~~Cg~~GH~ar~C~~~   90 (93)
                      ..||+||++|||+++||..
T Consensus       161 ~~cyrcGkeghwskEcP~~  179 (346)
T KOG0109|consen  161 SGCYRCGKEGHWSKECPVD  179 (346)
T ss_pred             HHheeccccccccccCCcc
Confidence            6799999999999999975

>PF14392 zf-CCHC_4: Zinc knuckle

Probab=94.82  E-value=0.0096  Score=33.22  Aligned_cols=18  Identities=33%  Similarity=1.001  Sum_probs=16.5

Q ss_pred             ccceeccccccccccCCC
Q psy16623         72 IVCYKCNNYGHFARECAT   89 (93)
Q Consensus        72 ~~C~~Cg~~GH~ar~C~~   89 (93)
                      ..|+.||..||..++||.
T Consensus        32 ~~C~~C~~~gH~~~~C~k   49 (49)
T PF14392_consen   32 RFCFHCGRIGHSDKECPK   49 (49)
T ss_pred             hhhcCCCCcCcCHhHcCC
Confidence            679999999999999984

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

Probab=94.81  E-value=0.011  Score=31.43  Aligned_cols=18  Identities=33%  Similarity=0.735  Sum_probs=11.4

Q ss_pred             ccceeccccccccccCCC
Q psy16623         72 IVCYKCNNYGHFARECAT   89 (93)
Q Consensus        72 ~~C~~Cg~~GH~ar~C~~   89 (93)
                      ..|++|++..|+|++|..
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            479999999999999954

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

Probab=94.66  E-value=0.017  Score=44.13  Aligned_cols=21  Identities=43%  Similarity=1.189  Sum_probs=18.5

Q ss_pred             cccceeccccccccccCCCCC
Q psy16623         71 GIVCYKCNNYGHFARECATES   91 (93)
Q Consensus        71 ~~~C~~Cg~~GH~ar~C~~~~   91 (93)
                      +..||+||+.|||..+||.+.
T Consensus       176 gY~CyRCGqkgHwIqnCpTN~  196 (427)
T COG5222         176 GYVCYRCGQKGHWIQNCPTNQ  196 (427)
T ss_pred             ceeEEecCCCCchhhcCCCCC
Confidence            478999999999999998764

>PF15288 zf-CCHC_6: Zinc knuckle

Probab=94.42  E-value=0.027  Score=30.60  Aligned_cols=12  Identities=33%  Similarity=1.077  Sum_probs=6.0

Q ss_pred             cceecccccccc
Q psy16623         73 VCYKCNNYGHFA   84 (93)
Q Consensus        73 ~C~~Cg~~GH~a   84 (93)
                      .|.+||..||.+
T Consensus         3 kC~~CG~~GH~~   14 (40)
T PF15288_consen    3 KCKNCGAFGHMR   14 (40)
T ss_pred             cccccccccccc
Confidence            355555555554

>PF15288 zf-CCHC_6: Zinc knuckle

Probab=93.31  E-value=0.045  Score=29.72  Aligned_cols=20  Identities=40%  Similarity=0.974  Sum_probs=16.8

Q ss_pred             cceeecCCCCccc--cccCCCC
Q psy16623         42 IQCYNCFDFGHYQ--YSCPQKS   61 (93)
Q Consensus        42 ~~C~~Cg~~GH~~--~~C~~~~   61 (93)
                      +.|.+||.+||++  +.||-..
T Consensus         2 ~kC~~CG~~GH~~t~k~CP~~~   23 (40)
T PF15288_consen    2 VKCKNCGAFGHMRTNKRCPMYC   23 (40)
T ss_pred             ccccccccccccccCccCCCCC
Confidence            4799999999998  5788664

>KOG0109|consensus

Probab=93.08  E-value=0.1  Score=39.76  Aligned_cols=22  Identities=32%  Similarity=0.819  Sum_probs=19.2

Q ss_pred             CcceeecCCCCccccccCCCCC
Q psy16623         41 TIQCYNCFDFGHYQYSCPQKSS   62 (93)
Q Consensus        41 ~~~C~~Cg~~GH~~~~C~~~~~   62 (93)
                      ...||+||+.||++.+||....
T Consensus       160 q~~cyrcGkeghwskEcP~~~~  181 (346)
T KOG0109|consen  160 QSGCYRCGKEGHWSKECPVDRT  181 (346)
T ss_pred             HHHheeccccccccccCCccCC
Confidence            4569999999999999998753

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

Probab=91.23  E-value=0.13  Score=27.29  Aligned_cols=20  Identities=25%  Similarity=0.379  Sum_probs=13.0

Q ss_pred             cceeecCCCCccccccCCCC
Q psy16623         42 IQCYNCFDFGHYQYSCPQKS   61 (93)
Q Consensus        42 ~~C~~Cg~~GH~~~~C~~~~   61 (93)
                      ..|++|++-.|++++|....
T Consensus         3 ~~CprC~kg~Hwa~~C~sk~   22 (36)
T PF14787_consen    3 GLCPRCGKGFHWASECRSKT   22 (36)
T ss_dssp             -C-TTTSSSCS-TTT---TC
T ss_pred             ccCcccCCCcchhhhhhhhh
Confidence            46999999999999999876

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

Probab=89.96  E-value=0.17  Score=38.84  Aligned_cols=21  Identities=33%  Similarity=0.861  Sum_probs=18.6

Q ss_pred             CcceeecCCCCccccccCCCC
Q psy16623         41 TIQCYNCFDFGHYQYSCPQKS   61 (93)
Q Consensus        41 ~~~C~~Cg~~GH~~~~C~~~~   61 (93)
                      +..||+||+.||+..+||.+.
T Consensus       176 gY~CyRCGqkgHwIqnCpTN~  196 (427)
T COG5222         176 GYVCYRCGQKGHWIQNCPTNQ  196 (427)
T ss_pred             ceeEEecCCCCchhhcCCCCC
Confidence            456999999999999999875

>KOG3116|consensus

Probab=89.34  E-value=0.084  Score=36.54  Aligned_cols=41  Identities=24%  Similarity=0.578  Sum_probs=27.3

Q ss_pred             HHHHHHhcCceeeEEEeeeecCCCCcceeecCCCCccccccCCCC
Q psy16623         17 ILLIIKQRNEGLLFVLRVEMSSTSTIQCYNCFDFGHYQYSCPQKS   61 (93)
Q Consensus        17 ~a~~i~~~g~~~~~~~~~~~~~~~~~~C~~Cg~~GH~~~~C~~~~   61 (93)
                      +|.+|.++..-......+    ...++|.+|.++||+.++|.+..
T Consensus         7 ~a~rL~~rk~~~~qA~a~----~~~~rCQKClq~GHWtYECk~kR   47 (177)
T KOG3116|consen    7 EAVRLGERKDKTMQASAV----GSSARCQKCLQAGHWTYECKNKR   47 (177)
T ss_pred             HHHHHHHhhhhhhhhhhc----ccchhHHHHHhhccceeeecCce
Confidence            367777766532111111    12358999999999999998764

>KOG0107|consensus

Probab=89.24  E-value=0.59  Score=33.26  Aligned_cols=45  Identities=22%  Similarity=0.296  Sum_probs=32.0

Q ss_pred             HHHHHHHHhcCceeeEEEeeeecCCCCc--------------ceeecCCCCccccccCC
Q psy16623         15 LGILLIIKQRNEGLLFVLRVEMSSTSTI--------------QCYNCFDFGHYQYSCPQ   59 (93)
Q Consensus        15 ~~~a~~i~~~g~~~~~~~~~~~~~~~~~--------------~C~~Cg~~GH~~~~C~~   59 (93)
                      .++|...++-..|.-+.++||++...+.              -|+.|++.||+.++|.+
T Consensus        60 A~DAvr~LDG~~~cG~r~rVE~S~G~~r~~r~gg~~~~~g~~~~~r~G~rg~~~r~~~~  118 (195)
T KOG0107|consen   60 AEDAVRYLDGKDICGSRIRVELSTGRPRGSRRGGSRPPRGRGFCYRCGERGHIGRNCKD  118 (195)
T ss_pred             HHHHHhhcCCccccCceEEEEeecCCccccccCCCCCcccccccccCCCcccccccccc
Confidence            3567777877777777788888764322              27778888888877766

>KOG0314|consensus

Probab=85.98  E-value=1  Score=35.95  Aligned_cols=49  Identities=18%  Similarity=0.170  Sum_probs=32.5

Q ss_pred             ceeecCCCCccccccCCCCCCCC-----C----------C-CcccccceeccccccccccCCCCC
Q psy16623         43 QCYNCFDFGHYQYSCPQKSSADA-----R----------G-DKVGIVCYKCNNYGHFARECATES   91 (93)
Q Consensus        43 ~C~~Cg~~GH~~~~C~~~~~~~~-----~----------~-~~~~~~C~~Cg~~GH~ar~C~~~~   91 (93)
                      .++.++..||..+.+........     .          + -..+..|++|+..||+.+.||...
T Consensus       114 ~~~~~~~~~~~~~~~t~~~~~~~~~~~~~~~~iq~~~~~g~Pppsy~c~rc~~~g~wikacptv~  178 (448)
T KOG0314|consen  114 MNGRMGGRGFGMRRQTPPPGYVCHRCNSPGHFIQHCSTNGSPPPSYKCVKCPTPGPWIKACPTVS  178 (448)
T ss_pred             hccccccCCcccccCCCcccceeeecccCccccccccccCCCCCCcceecCCCCCccceeccccC
Confidence            47777777777777643321100     0          0 012478999999999999999765

>KOG2044|consensus

Probab=85.39  E-value=0.65  Score=39.54  Aligned_cols=34  Identities=26%  Similarity=0.492  Sum_probs=28.2

Q ss_pred             eeEEEeeeecCCCCcceeecCCCCccccccCCCC
Q psy16623         28 LLFVLRVEMSSTSTIQCYNCFDFGHYQYSCPQKS   61 (93)
Q Consensus        28 ~~~~~~~~~~~~~~~~C~~Cg~~GH~~~~C~~~~   61 (93)
                      .++..|-++.+..+..||.|+++||.+.+|....
T Consensus       247 hF~IlRE~~~P~~~~~C~~cgq~gh~~~dc~g~~  280 (931)
T KOG2044|consen  247 HFSILREEFFPNKPRRCFLCGQTGHEAKDCEGKP  280 (931)
T ss_pred             ceEEeeeeecCCCcccchhhcccCCcHhhcCCcC
Confidence            3677777777777788999999999999998763

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	93
2ihx_A	61	Nucleocapsid (NC) protein; protein-RNA complex, vi	6e-09
1cl4_A	60	Protein (GAG polyprotein); nucleocapsid protein, R	7e-09
3ts2_A	148	Protein LIN-28 homolog A; microrna biogenesis, pro	4e-06
2lli_A	124	Protein AIR2; RNA surveillance, RNA degradation, R	5e-06
2lli_A	124	Protein AIR2; RNA surveillance, RNA degradation, R	4e-05
2cqf_A	63	RNA-binding protein LIN-28; CCHC zinc-finger, stru	3e-05
3nyb_B	83	Protein AIR2; polya RNA polymerase, zinc knuckle p	3e-05
2li8_A	74	Protein LIN-28 homolog A; zinc finger, micro RNA,	8e-05

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

 Score = 46.8 bits (111), Expect = 6e-09
 Identities = 17/44 (38%), Positives = 23/44 (52%), Gaps = 4/44 (9%)

Query: 44 CYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFAREC 87
          CY C   GHYQ  CP+K  +    ++    C  CN  GH A++C
Sbjct: 7  CYTCGSPGHYQAQCPKKRKSGNSRER----CQLCNGMGHNAKQC 46

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

 Score = 46.9 bits (111), Expect = 7e-09
 Identities = 13/44 (29%), Positives = 22/44 (50%), Gaps = 1/44 (2%)

Query: 44 CYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFAREC 87
          C+ C   GH+  +C + +  +A     G+ C +C    H+A EC
Sbjct: 4  CFKCGKKGHFAKNCHEHAHNNAEPKVPGL-CPRCKRGKHWANEC 46

>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* Length = 148

 Score = 41.5 bits (97), Expect = 4e-06
 Identities = 12/63 (19%), Positives = 19/63 (30%), Gaps = 8/63 (12%)

Query: 30  FVLRVEMSSTSTIQCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFARECAT 89
           F +  E       +CYNC    H+   C                C+ C +  H    C  
Sbjct: 86  FCIGSERRPKGGDRCYNCGGLDHHAKECKLPPQ--------PKKCHFCQSINHMVASCPL 137

Query: 90  ESP 92
           ++ 
Sbjct: 138 KAQ 140

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

 Score = 40.9 bits (95), Expect = 5e-06
 Identities = 14/57 (24%), Positives = 19/57 (33%), Gaps = 11/57 (19%)

Query: 42  IQCYNCFDFGHYQYSCPQ-----------KSSADARGDKVGIVCYKCNNYGHFAREC 87
           +QC  C    H +  CP            + +         I CY C   GHF  +C
Sbjct: 65  VQCTLCKSKKHSKERCPSIWRAYILVDDNEKAKPKVLPFHTIYCYNCGGKGHFGDDC 121

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

 Score = 38.6 bits (89), Expect = 4e-05
 Identities = 15/56 (26%), Positives = 23/56 (41%), Gaps = 8/56 (14%)

Query: 40 STIQCYNCFDFGHYQYSCPQKSSA--------DARGDKVGIVCYKCNNYGHFAREC 87
          +  +C NC   GH +  CP    +         +R     I C KC+  GH+  +C
Sbjct: 3  AAPKCNNCSQRGHLKKDCPHIICSYCGATDDHYSRHCPKAIQCSKCDEVGHYRSQC 58

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

 Score = 37.6 bits (87), Expect = 3e-05
 Identities = 12/51 (23%), Positives = 17/51 (33%), Gaps = 8/51 (15%)

Query: 37 SSTSTIQCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFAREC 87
          S +S  +CYNC    H+   C                C+ C +  H    C
Sbjct: 3  SGSSGDRCYNCGGLDHHAKECKL--------PPQPKKCHFCQSISHMVASC 45

>3nyb_B Protein AIR2; polya RNA polymerase, zinc knuckle protein, RNA surveillance binds to TRF4P/AIR2P heterodimer; 2.70A {Saccharomyces cerevisiae} Length = 83

 Score = 38.1 bits (88), Expect = 3e-05
 Identities = 14/57 (24%), Positives = 19/57 (33%), Gaps = 11/57 (19%)

Query: 42 IQCYNCFDFGHYQYSCPQ-----------KSSADARGDKVGIVCYKCNNYGHFAREC 87
          +QC  C    H +  CP            + +         I CY C   GHF  +C
Sbjct: 6  VQCTLCKSKKHSKERCPSIWRAYILVDDNEKAKPKVLPFHTIYCYNCGGKGHFGDDC 62

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

 Score = 36.5 bits (84), Expect = 8e-05
 Identities = 10/51 (19%), Positives = 16/51 (31%), Gaps = 8/51 (15%)

Query: 42 IQCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFARECATESP 92
           +CYNC    H+   C                C+ C +  H    C  ++ 
Sbjct: 25 DRCYNCGGLDHHAKECKLPPQPKK--------CHFCQSISHMVASCPLKAQ 67

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	93
2a51_A	39	Nucleocapsid protein; sivlhoest, structure, NCP8,	99.55
2bl6_A	37	Nucleocapsid protein P11; lentivirus, polyprotein,	99.55
2ec7_A	49	GAG polyprotein (PR55GAG); nucleocapsid protein, H	99.53
1cl4_A	60	Protein (GAG polyprotein); nucleocapsid protein, R	99.48
2ihx_A	61	Nucleocapsid (NC) protein; protein-RNA complex, vi	99.48
1a1t_A	55	Nucleocapsid protein; stem-loop RNA, viral protein	99.48
2cqf_A	63	RNA-binding protein LIN-28; CCHC zinc-finger, stru	99.48
2li8_A	74	Protein LIN-28 homolog A; zinc finger, micro RNA,	99.42
3ts2_A	148	Protein LIN-28 homolog A; microrna biogenesis, pro	99.35
3nyb_B	83	Protein AIR2; polya RNA polymerase, zinc knuckle p	99.28
2lli_A	124	Protein AIR2; RNA surveillance, RNA degradation, R	99.15
2lli_A	124	Protein AIR2; RNA surveillance, RNA degradation, R	99.04
2li8_A	74	Protein LIN-28 homolog A; zinc finger, micro RNA,	98.84
1dsq_A	26	Nucleic acid binding protein P14; CCHC type zinc f	98.57
1dsq_A	26	Nucleic acid binding protein P14; CCHC type zinc f	98.3
1a6b_B	40	Momulv, zinc finger protein NCP10; nucleocapsid pr	98.3
1nc8_A	29	Nucleocapsid protein; HIV-2, RNA recognition, zinc	98.21
1nc8_A	29	Nucleocapsid protein; HIV-2, RNA recognition, zinc	98.2
1a6b_B	40	Momulv, zinc finger protein NCP10; nucleocapsid pr	98.19
1u6p_A	56	GAG polyprotein; MLV, A-minor K-turn, stem loop, b	98.15
2ysa_A	55	Retinoblastoma-binding protein 6; zinc finger, CCH	98.04
1u6p_A	56	GAG polyprotein; MLV, A-minor K-turn, stem loop, b	97.92
2a51_A	39	Nucleocapsid protein; sivlhoest, structure, NCP8,	97.82
2bl6_A	37	Nucleocapsid protein P11; lentivirus, polyprotein,	97.77
2ysa_A	55	Retinoblastoma-binding protein 6; zinc finger, CCH	97.69
1cl4_A	60	Protein (GAG polyprotein); nucleocapsid protein, R	97.68
2ec7_A	49	GAG polyprotein (PR55GAG); nucleocapsid protein, H	97.67
2cqf_A	63	RNA-binding protein LIN-28; CCHC zinc-finger, stru	97.61
2ihx_A	61	Nucleocapsid (NC) protein; protein-RNA complex, vi	97.58
1a1t_A	55	Nucleocapsid protein; stem-loop RNA, viral protein	97.54
3nyb_B	83	Protein AIR2; polya RNA polymerase, zinc knuckle p	97.48
3ts2_A	148	Protein LIN-28 homolog A; microrna biogenesis, pro	96.77
2hqh_E	26	Restin; beta/BETA structure, zinc finger motif, st	88.8

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

Probab=99.55  E-value=1.6e-15  Score=81.38  Aligned_cols=39  Identities=28%  Similarity=0.695  Sum_probs=34.9

Q ss_pred             cceeecCCCCccccccCCCCCCCCCCCcccccceeccccccccccCCC
Q psy16623         42 IQCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFARECAT   89 (93)
Q Consensus        42 ~~C~~Cg~~GH~~~~C~~~~~~~~~~~~~~~~C~~Cg~~GH~ar~C~~   89 (93)
                      +.||+|++.||++++||.+.    .     ..||+|++.||++++||+
T Consensus         1 i~C~~Cg~~GH~a~~C~~~~----~-----~~C~~Cg~~GH~~~~C~~   39 (39)
T 2a51_A            1 LTCFNCGKPGHTARMCRQPR----Q-----EGCWNCGSKEHRFAQCPK   39 (39)
T ss_dssp             CBCTTTCCBSSCTTTCCSCC----C-----SSCTTTCCSSSCTTTSCC
T ss_pred             CeeeccCCCCcccccCCCCC----C-----CccccCCCCCCccCcCcC
Confidence            36999999999999999863    2     689999999999999985

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

Probab=99.55  E-value=1.7e-15  Score=80.39  Aligned_cols=36  Identities=42%  Similarity=1.068  Sum_probs=33.7

Q ss_pred             ceeecCCCCccccccCCCCCCCCCCCcccccceeccccccccccCCC
Q psy16623         43 QCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFARECAT   89 (93)
Q Consensus        43 ~C~~Cg~~GH~~~~C~~~~~~~~~~~~~~~~C~~Cg~~GH~ar~C~~   89 (93)
                      .||+|++.||++++||.+           ..||+|++.||++++||+
T Consensus         2 ~C~~Cg~~GH~~~~C~~~-----------~~C~~Cg~~GH~a~~C~~   37 (37)
T 2bl6_A            2 TCYNCGKPGHLSSQCRAP-----------KVCFKCKQPGHFSKQCRS   37 (37)
T ss_dssp             CBSSSCCSSCCTTTSSCB-----------TTCSSCCCTTGGGGTTCC
T ss_pred             cccccCCCCcchhhCcCc-----------CeEccCCCcCCccCcCcC
Confidence            699999999999999986           579999999999999986

>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=99.53  E-value=4.3e-15  Score=83.26  Aligned_cols=44  Identities=32%  Similarity=0.759  Sum_probs=38.3

Q ss_pred             CCCcceeecCCCCccccccCCCCCCCCCCCcccccceeccccccccccCCCCC
Q psy16623         39 TSTIQCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFARECATES   91 (93)
Q Consensus        39 ~~~~~C~~Cg~~GH~~~~C~~~~~~~~~~~~~~~~C~~Cg~~GH~ar~C~~~~   91 (93)
                      .+...||+|++.||++++||.+.    .     ..||+||+.||++++||+..
T Consensus         4 ~r~~~C~~Cg~~GH~a~~C~~~~----~-----~~C~~Cg~~GH~~~~C~~~~   47 (49)
T 2ec7_A            4 RKVIRCWNCGKEGHSARQCRAPR----R-----QGCWKCGKTGHVMAKCPERQ   47 (49)
T ss_dssp             CCCCBCTTTCCBTCCTTTCCCSS----C-----CSCSSSCCSSCCGGGCCSSC
T ss_pred             CCcCeeeecCCCCcChhhCcCCC----C-----CeeCcCCCcCCccCCCcCCC
Confidence            34568999999999999999863    2     67999999999999999864

>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=99.48  E-value=6.9e-15  Score=85.31  Aligned_cols=49  Identities=29%  Similarity=0.698  Sum_probs=18.6

Q ss_pred             cceeecCCCCccccccCCCCCCCCCCCcccccceeccccccccccCCCCC
Q psy16623         42 IQCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFARECATES   91 (93)
Q Consensus        42 ~~C~~Cg~~GH~~~~C~~~~~~~~~~~~~~~~C~~Cg~~GH~ar~C~~~~   91 (93)
                      ..||+|++.||++++||........ ......||+|++.||+|++||+..
T Consensus         2 ~~Cf~Cg~~GH~a~~C~~~~~~~~~-~~~~~~C~~Cg~~GH~ar~C~~~~   50 (60)
T 1cl4_A            2 GSCFKCGKKGHFAKNCHEHAHNNAE-PKVPGLCPRCKRGKHWANECKSKT   50 (60)
T ss_dssp             ----------------------------CCCSCSSCSSCSSCSTTCCCTT
T ss_pred             CccccCCCCCcCHhhCcCCCCCccc-cCCCcceeECCCCCCccCcCCCcc
Confidence            4699999999999999987421110 001268999999999999999754

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

Probab=99.48  E-value=2.1e-14  Score=83.76  Aligned_cols=47  Identities=36%  Similarity=0.758  Sum_probs=38.2

Q ss_pred             CcceeecCCCCccccccCCCCCCCCCCCcccccceeccccccccccCCCCC
Q psy16623         41 TIQCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFARECATES   91 (93)
Q Consensus        41 ~~~C~~Cg~~GH~~~~C~~~~~~~~~~~~~~~~C~~Cg~~GH~ar~C~~~~   91 (93)
                      ...||+|++.||++++||....  ..  .....||+|++.||+|++||+..
T Consensus         4 ~~~C~~Cg~~GH~a~~C~~~~~--~~--~~~~~C~~Cg~~GH~ar~C~~~~   50 (61)
T 2ihx_A            4 RGLCYTCGSPGHYQAQCPKKRK--SG--NSRERCQLCNGMGHNAKQCRKRD   50 (61)
T ss_dssp             TTBCSSSCCBTCCGGGCTTTTS--SS--CCCSBCTTTCCBSSCGGGCCCCC
T ss_pred             CCcccccCCCCeehhhCcCCcC--CC--CCCCeeCCCCCCCCCcCCCcCCC
Confidence            4679999999999999998752  11  11267999999999999999864

>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=99.48  E-value=1.2e-14  Score=82.96  Aligned_cols=43  Identities=30%  Similarity=0.806  Sum_probs=37.8

Q ss_pred             CCcceeecCCCCccccccCCCCCCCCCCCcccccceeccccccccccCCCCC
Q psy16623         40 STIQCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFARECATES   91 (93)
Q Consensus        40 ~~~~C~~Cg~~GH~~~~C~~~~~~~~~~~~~~~~C~~Cg~~GH~ar~C~~~~   91 (93)
                      +...||+|++.||++++||.+.    .     ..||+|++.||++++||+..
T Consensus        11 ~~~~C~~Cg~~GH~a~~C~~~~----~-----~~C~~Cg~~GH~~~~C~~~~   53 (55)
T 1a1t_A           11 KTVKCFNCGKEGHIAKNCRAPR----K-----KGCWKCGKEGHQMKDCTERQ   53 (55)
T ss_dssp             GTCBCTTTCCBSSCGGGCSSCS----C-----CBCTTTCCBSSCGGGCSSSC
T ss_pred             CCcceeeeCCCCcChhhcCCCC----C-----CEeCCCCCcCCccCCCcCcC
Confidence            4568999999999999999863    2     68999999999999999864

>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=99.48  E-value=1.9e-14  Score=84.52  Aligned_cols=44  Identities=25%  Similarity=0.573  Sum_probs=37.7

Q ss_pred             CCCcceeecCCCCccccccCCCCCCCCCCCcccccceeccccccccccCCCC
Q psy16623         39 TSTIQCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFARECATE   90 (93)
Q Consensus        39 ~~~~~C~~Cg~~GH~~~~C~~~~~~~~~~~~~~~~C~~Cg~~GH~ar~C~~~   90 (93)
                      .+...||+|++.||++++||.+.   +.     ..||+|++.||+|++||+.
T Consensus         5 ~r~~~C~~Cg~~GH~a~~C~~~~---~~-----~~C~~Cg~~GH~ar~Cp~~   48 (63)
T 2cqf_A            5 SSGDRCYNCGGLDHHAKECKLPP---QP-----KKCHFCQSISHMVASCPLK   48 (63)
T ss_dssp             CSCCCCSSSCCSSSCTTTCCSCC---CS-----SCCTTTCCSSSCTTTCTGG
T ss_pred             CCCCcccccCCCCcChhhCCCCC---CC-----CccCCcCCcCCccCcCCCc
Confidence            34568999999999999999763   22     6899999999999999874

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

Probab=99.42  E-value=6.2e-14  Score=84.84  Aligned_cols=45  Identities=22%  Similarity=0.553  Sum_probs=38.1

Q ss_pred             CCCcceeecCCCCccccccCCCCCCCCCCCcccccceeccccccccccCCCCC
Q psy16623         39 TSTIQCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFARECATES   91 (93)
Q Consensus        39 ~~~~~C~~Cg~~GH~~~~C~~~~~~~~~~~~~~~~C~~Cg~~GH~ar~C~~~~   91 (93)
                      .+...||+|++.||++++|+...   ..     ..||+|++.||++++||+..
T Consensus        22 ~r~~~C~~Cg~~GH~a~~C~~~~---~~-----~~C~~Cg~~GH~ar~Cp~~~   66 (74)
T 2li8_A           22 SKGDRCYNCGGLDHHAKECKLPP---QP-----KKCHFCQSISHMVASCPLKA   66 (74)
T ss_dssp             STTSCCTTTCCSSSCTTTCSSCC---CC-----CCCTTTCCTTSCGGGCTTGG
T ss_pred             CCCCcccccCCcCcCcccCCCCC---CC-----CccCCcCCcCCccCcCcCCc
Confidence            35578999999999999999753   22     68999999999999999753

>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=99.35  E-value=4e-13  Score=90.46  Aligned_cols=42  Identities=24%  Similarity=0.589  Sum_probs=36.9

Q ss_pred             cceeecCCCCccccccCCCCCCCCCCCcccccceeccccccccccCCCCC
Q psy16623         42 IQCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFARECATES   91 (93)
Q Consensus        42 ~~C~~Cg~~GH~~~~C~~~~~~~~~~~~~~~~C~~Cg~~GH~ar~C~~~~   91 (93)
                      ..||+|++.||++++||.+.   ..     ..||+|++.||++++||+..
T Consensus        98 ~~C~~Cg~~GH~a~~C~~~~---~~-----~~C~~Cg~~GH~~r~Cp~~~  139 (148)
T 3ts2_A           98 DRCYNCGGLDHHAKECKLPP---QP-----KKCHFCQSINHMVASCPLKA  139 (148)
T ss_dssp             CCCTTTCCSSCCGGGCCSCC---CC-----CCCTTTCCSSCCGGGCTTTT
T ss_pred             CcccEeCCccchhhhCCCCC---CC-----CcccccCCcCCEeccCcCCC
Confidence            46999999999999999863   22     68999999999999999865

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

Probab=99.28  E-value=1.8e-12  Score=79.99  Aligned_cols=52  Identities=29%  Similarity=0.595  Sum_probs=36.4

Q ss_pred             CCcceeecCCCCccccccCCCCCCCC---CC--------CcccccceeccccccccccCCCCC
Q psy16623         40 STIQCYNCFDFGHYQYSCPQKSSADA---RG--------DKVGIVCYKCNNYGHFARECATES   91 (93)
Q Consensus        40 ~~~~C~~Cg~~GH~~~~C~~~~~~~~---~~--------~~~~~~C~~Cg~~GH~ar~C~~~~   91 (93)
                      +.+.||+|++.||++++||+...-..   .+        ......||+||+.|||++|||+..
T Consensus         4 k~~~C~~Cg~~GH~~~~Cp~~~rcY~c~~~gh~~~~c~~p~~~~~CYnCG~~GH~~rdC~~~r   66 (83)
T 3nyb_B            4 KKVQCTLCKSKKHSKERCPSIWRAYILVDDNEKAKPKVLPFHTIYCYNCGGKGHFGDDCKEKR   66 (83)
T ss_dssp             ---CCSSSCCSSSCGGGCGGGTCCCCBC-------------CCCBCSSSSCBSSCGGGCSSCC
T ss_pred             ccCCCCCCCCCCCccccCCCcccccccccCCcccccccCCCCCCeecccCCCCcCcccCCccc
Confidence            34689999999999999997531100   00        011367999999999999999864

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

Probab=99.15  E-value=2.1e-11  Score=79.27  Aligned_cols=50  Identities=30%  Similarity=0.635  Sum_probs=36.9

Q ss_pred             CcceeecCCCCccccccCCCCCCC------CC---C--CcccccceeccccccccccCCCC
Q psy16623         41 TIQCYNCFDFGHYQYSCPQKSSAD------AR---G--DKVGIVCYKCNNYGHFARECATE   90 (93)
Q Consensus        41 ~~~C~~Cg~~GH~~~~C~~~~~~~------~~---~--~~~~~~C~~Cg~~GH~ar~C~~~   90 (93)
                      ...||+|++.||++++||......      ..   +  ......||+|++.||||+|||+.
T Consensus        64 ~~~C~~Cg~~GH~~~~Cp~~~~~y~~~~~~~~~~~~~~~~~~~~Cy~Cg~~GH~a~dCp~~  124 (124)
T 2lli_A           64 KVQCTLCKSKKHSKERCPSIWRAYILVDDNEKAKPKVLPFHTIYCYNCGGKGHFGDDCKEK  124 (124)
T ss_dssp             CCSSSSSCSSCCCTTTCCCSTTSCCSSSCCCCCCCSCCCCCCCCTTTTSSSCTTTTTSCCC
T ss_pred             CccCCCCCcCCcchhhCCCccccccccCccccccccccCCCCCCcCCCCCCCcCcccCcCC
Confidence            467999999999999999764210      00   0  01237899999999999999974

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

Probab=99.04  E-value=1e-10  Score=75.90  Aligned_cols=41  Identities=34%  Similarity=0.836  Sum_probs=33.0

Q ss_pred             cceeecCCCCccccccCCCCCCCCCCCcccccceeccccccccccCCCC
Q psy16623         42 IQCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFARECATE   90 (93)
Q Consensus        42 ~~C~~Cg~~GH~~~~C~~~~~~~~~~~~~~~~C~~Cg~~GH~ar~C~~~   90 (93)
                      ..||+|++.||++++||...   +.     ..||+|++.||++++||+.
T Consensus        43 ~~C~~Cg~~GH~~~~C~~~~---~~-----~~C~~Cg~~GH~~~~Cp~~   83 (124)
T 2lli_A           43 IQCSKCDEVGHYRSQCPHKW---KK-----VQCTLCKSKKHSKERCPSI   83 (124)
T ss_dssp             SCSSSSSCSSSSTTTSCCCC---CC-----CSSSSSCSSCCCTTTCCCS
T ss_pred             ccccccCCCCCccccCcCcc---cC-----ccCCCCCcCCcchhhCCCc
Confidence            46888888888888888753   22     6799999999999999975

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

Probab=98.84  E-value=1e-09  Score=66.20  Aligned_cols=42  Identities=21%  Similarity=0.420  Sum_probs=21.0

Q ss_pred             CCCccccccCCCCCCCCC-CCcccccceeccccccccccCCCC
Q psy16623         49 DFGHYQYSCPQKSSADAR-GDKVGIVCYKCNNYGHFARECATE   90 (93)
Q Consensus        49 ~~GH~~~~C~~~~~~~~~-~~~~~~~C~~Cg~~GH~ar~C~~~   90 (93)
                      ..||+++||+.+...... +......||+|++.||++++|+..
T Consensus         1 ~~gh~~rdc~~~~~~~~~~~~~r~~~C~~Cg~~GH~a~~C~~~   43 (74)
T 2li8_A            1 SSGLVPRGSHMPKGKSMQKRRSKGDRCYNCGGLDHHAKECKLP   43 (74)
T ss_dssp             -----------CCCCCCCSCCSTTSCCTTTCCSSSCTTTCSSC
T ss_pred             CCccccCcCCCCCcCccccccCCCCcccccCCcCcCcccCCCC
Confidence            369999999987643211 111236799999999999999963

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

Probab=98.30  E-value=2e-07  Score=50.02  Aligned_cols=20  Identities=30%  Similarity=0.841  Sum_probs=16.1

Q ss_pred             ccceeccccccccccCCCCC
Q psy16623         72 IVCYKCNNYGHFARECATES   91 (93)
Q Consensus        72 ~~C~~Cg~~GH~ar~C~~~~   91 (93)
                      ..||+||+.||||++||+..
T Consensus        11 ~~C~~Cgk~GH~ardCP~~~   30 (40)
T 1a6b_B           11 DQCAYCKEKGHWAKDCPKKP   30 (40)
T ss_dssp             SSCSSSCCTTCCTTSCSSSC
T ss_pred             CeeeECCCCCcchhhCcCCc
Confidence            57888888888888888753

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

Probab=98.21  E-value=3.6e-07  Score=45.55  Aligned_cols=19  Identities=42%  Similarity=1.017  Sum_probs=14.3

Q ss_pred             ccceeccccccccccCCCC
Q psy16623         72 IVCYKCNNYGHFARECATE   90 (93)
Q Consensus        72 ~~C~~Cg~~GH~ar~C~~~   90 (93)
                      ..||+||++||++++|+.+
T Consensus         7 ~~C~nCgk~GH~ar~C~~p   25 (29)
T 1nc8_A            7 IRCWNCGKEGHSARQCRAP   25 (29)
T ss_dssp             CBCTTTSCBSSCGGGCCSS
T ss_pred             CEEEECCccccCHhHCccc
Confidence            5688888888888888764

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

Probab=98.20  E-value=5.7e-07  Score=44.83  Aligned_cols=22  Identities=32%  Similarity=0.703  Sum_probs=19.3

Q ss_pred             CCcceeecCCCCccccccCCCC
Q psy16623         40 STIQCYNCFDFGHYQYSCPQKS   61 (93)
Q Consensus        40 ~~~~C~~Cg~~GH~~~~C~~~~   61 (93)
                      +...||+|++.||++++|+.+.
T Consensus         5 ~~~~C~nCgk~GH~ar~C~~pr   26 (29)
T 1nc8_A            5 KVIRCWNCGKEGHSARQCRAPR   26 (29)
T ss_dssp             CCCBCTTTSCBSSCGGGCCSSS
T ss_pred             CCCEEEECCccccCHhHCcccc
Confidence            4568999999999999999874

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

Probab=98.19  E-value=9e-07  Score=47.42  Aligned_cols=23  Identities=35%  Similarity=0.777  Sum_probs=20.2

Q ss_pred             CcceeecCCCCccccccCCCCCC
Q psy16623         41 TIQCYNCFDFGHYQYSCPQKSSA   63 (93)
Q Consensus        41 ~~~C~~Cg~~GH~~~~C~~~~~~   63 (93)
                      ...||+|++.||++++||.....
T Consensus        10 ~~~C~~Cgk~GH~ardCP~~~~~   32 (40)
T 1a6b_B           10 RDQCAYCKEKGHWAKDCPKKPRG   32 (40)
T ss_dssp             SSSCSSSCCTTCCTTSCSSSCCC
T ss_pred             CCeeeECCCCCcchhhCcCCccc
Confidence            46899999999999999998643

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

Probab=98.15  E-value=6.2e-07  Score=51.32  Aligned_cols=20  Identities=30%  Similarity=0.841  Sum_probs=17.2

Q ss_pred             ccceeccccccccccCCCCC
Q psy16623         72 IVCYKCNNYGHFARECATES   91 (93)
Q Consensus        72 ~~C~~Cg~~GH~ar~C~~~~   91 (93)
                      ..||+||+.||||+|||+..
T Consensus        24 ~~C~~Cge~GH~ardCp~~~   43 (56)
T 1u6p_A           24 DQCAYCKEKGHWAKDCPKKP   43 (56)
T ss_dssp             TBCSSSCCBSSCGGGCTTCC
T ss_pred             CcceeCCCCCcccccCcCCc
Confidence            67999999999999998754

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

Probab=98.04  E-value=7.3e-07  Score=50.84  Aligned_cols=17  Identities=29%  Similarity=1.185  Sum_probs=12.5

Q ss_pred             ccceeccccccccccCC
Q psy16623         72 IVCYKCNNYGHFARECA   88 (93)
Q Consensus        72 ~~C~~Cg~~GH~ar~C~   88 (93)
                      ..||+||+.||++++||
T Consensus         8 ~~C~kCGk~GH~~k~Cp   24 (55)
T 2ysa_A            8 YTCFRCGKPGHYIKNCP   24 (55)
T ss_dssp             CCCTTTCCTTSCGGGCS
T ss_pred             CccccCCCcCcccccCC
Confidence            56777777777777777

>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=97.92  E-value=5.9e-06  Score=47.20  Aligned_cols=22  Identities=36%  Similarity=0.804  Sum_probs=19.5

Q ss_pred             CcceeecCCCCccccccCCCCC
Q psy16623         41 TIQCYNCFDFGHYQYSCPQKSS   62 (93)
Q Consensus        41 ~~~C~~Cg~~GH~~~~C~~~~~   62 (93)
                      ...||+|++.||+++|||....
T Consensus        23 ~~~C~~Cge~GH~ardCp~~~~   44 (56)
T 1u6p_A           23 RDQCAYCKEKGHWAKDCPKKPR   44 (56)
T ss_dssp             TTBCSSSCCBSSCGGGCTTCCC
T ss_pred             CCcceeCCCCCcccccCcCCcc
Confidence            4679999999999999998763

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

Probab=97.82  E-value=5.5e-06  Score=43.60  Aligned_cols=18  Identities=39%  Similarity=0.979  Sum_probs=16.7

Q ss_pred             cceeccccccccccCCCC
Q psy16623         73 VCYKCNNYGHFARECATE   90 (93)
Q Consensus        73 ~C~~Cg~~GH~ar~C~~~   90 (93)
                      .||+|++.||++++||++
T Consensus         2 ~C~~Cg~~GH~a~~C~~~   19 (39)
T 2a51_A            2 TCFNCGKPGHTARMCRQP   19 (39)
T ss_dssp             BCTTTCCBSSCTTTCCSC
T ss_pred             eeeccCCCCcccccCCCC
Confidence            599999999999999975

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

Probab=97.77  E-value=7.2e-06  Score=42.67  Aligned_cols=18  Identities=33%  Similarity=1.071  Sum_probs=16.6

Q ss_pred             cceeccccccccccCCCC
Q psy16623         73 VCYKCNNYGHFARECATE   90 (93)
Q Consensus        73 ~C~~Cg~~GH~ar~C~~~   90 (93)
                      .||+|++.||++++||.+
T Consensus         2 ~C~~Cg~~GH~~~~C~~~   19 (37)
T 2bl6_A            2 TCYNCGKPGHLSSQCRAP   19 (37)
T ss_dssp             CBSSSCCSSCCTTTSSCB
T ss_pred             cccccCCCCcchhhCcCc
Confidence            599999999999999974

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

Probab=97.69  E-value=1.2e-05  Score=45.80  Aligned_cols=22  Identities=36%  Similarity=0.877  Sum_probs=18.7

Q ss_pred             CCcceeecCCCCccccccCCCC
Q psy16623         40 STIQCYNCFDFGHYQYSCPQKS   61 (93)
Q Consensus        40 ~~~~C~~Cg~~GH~~~~C~~~~   61 (93)
                      ....||+|++.||++++||+..
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            3557999999999999999553

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

Probab=97.68  E-value=5.7e-06  Score=47.25  Aligned_cols=19  Identities=42%  Similarity=1.078  Sum_probs=0.0

Q ss_pred             ccceeccccccccccCCCC
Q psy16623         72 IVCYKCNNYGHFARECATE   90 (93)
Q Consensus        72 ~~C~~Cg~~GH~ar~C~~~   90 (93)
                      ..||+|++.||+|++||+.
T Consensus         2 ~~Cf~Cg~~GH~a~~C~~~   20 (60)
T 1cl4_A            2 GSCFKCGKKGHFAKNCHEH   20 (60)
T ss_dssp             -------------------
T ss_pred             CccccCCCCCcCHhhCcCC
Confidence            5799999999999999985

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

Probab=97.67  E-value=1.3e-05  Score=44.19  Aligned_cols=19  Identities=42%  Similarity=1.017  Sum_probs=17.7

Q ss_pred             ccceeccccccccccCCCC
Q psy16623         72 IVCYKCNNYGHFARECATE   90 (93)
Q Consensus        72 ~~C~~Cg~~GH~ar~C~~~   90 (93)
                      ..||+|++.||++++||..
T Consensus         7 ~~C~~Cg~~GH~a~~C~~~   25 (49)
T 2ec7_A            7 IRCWNCGKEGHSARQCRAP   25 (49)
T ss_dssp             CBCTTTCCBTCCTTTCCCS
T ss_pred             CeeeecCCCCcChhhCcCC
Confidence            6899999999999999975

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

Probab=97.61  E-value=2.6e-05  Score=45.11  Aligned_cols=19  Identities=37%  Similarity=0.887  Sum_probs=17.4

Q ss_pred             ccceeccccccccccCCCC
Q psy16623         72 IVCYKCNNYGHFARECATE   90 (93)
Q Consensus        72 ~~C~~Cg~~GH~ar~C~~~   90 (93)
                      ..||+|++.||++++||..
T Consensus         8 ~~C~~Cg~~GH~a~~C~~~   26 (63)
T 2cqf_A            8 DRCYNCGGLDHHAKECKLP   26 (63)
T ss_dssp             CCCSSSCCSSSCTTTCCSC
T ss_pred             CcccccCCCCcChhhCCCC
Confidence            6799999999999999964

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

Probab=97.58  E-value=2.5e-05  Score=44.83  Aligned_cols=19  Identities=32%  Similarity=1.018  Sum_probs=17.8

Q ss_pred             ccceeccccccccccCCCC
Q psy16623         72 IVCYKCNNYGHFARECATE   90 (93)
Q Consensus        72 ~~C~~Cg~~GH~ar~C~~~   90 (93)
                      ..||+|++.||++++||..
T Consensus         5 ~~C~~Cg~~GH~a~~C~~~   23 (61)
T 2ihx_A            5 GLCYTCGSPGHYQAQCPKK   23 (61)
T ss_dssp             TBCSSSCCBTCCGGGCTTT
T ss_pred             CcccccCCCCeehhhCcCC
Confidence            6799999999999999985

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

Probab=97.54  E-value=2.4e-05  Score=43.83  Aligned_cols=19  Identities=32%  Similarity=1.041  Sum_probs=17.6

Q ss_pred             ccceeccccccccccCCCC
Q psy16623         72 IVCYKCNNYGHFARECATE   90 (93)
Q Consensus        72 ~~C~~Cg~~GH~ar~C~~~   90 (93)
                      ..||+|++.||++++||..
T Consensus        13 ~~C~~Cg~~GH~a~~C~~~   31 (55)
T 1a1t_A           13 VKCFNCGKEGHIAKNCRAP   31 (55)
T ss_dssp             CBCTTTCCBSSCGGGCSSC
T ss_pred             cceeeeCCCCcChhhcCCC
Confidence            6799999999999999975

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

Probab=97.48  E-value=4.1e-05  Score=46.73  Aligned_cols=23  Identities=48%  Similarity=0.912  Sum_probs=20.0

Q ss_pred             CCcceeecCCCCccccccCCCCC
Q psy16623         40 STIQCYNCFDFGHYQYSCPQKSS   62 (93)
Q Consensus        40 ~~~~C~~Cg~~GH~~~~C~~~~~   62 (93)
                      ..+.||+|++.||+++|||...+
T Consensus        45 ~~~~CYnCG~~GH~~rdC~~~r~   67 (83)
T 3nyb_B           45 HTIYCYNCGGKGHFGDDCKEKRS   67 (83)
T ss_dssp             CCCBCSSSSCBSSCGGGCSSCCS
T ss_pred             CCCeecccCCCCcCcccCCcccc
Confidence            35789999999999999998753

>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=96.77  E-value=0.00047  Score=45.88  Aligned_cols=21  Identities=33%  Similarity=0.676  Sum_probs=19.1

Q ss_pred             CcceeecCCCCccccccCCCC
Q psy16623         41 TIQCYNCFDFGHYQYSCPQKS   61 (93)
Q Consensus        41 ~~~C~~Cg~~GH~~~~C~~~~   61 (93)
                      ...||+|++.||++++||+..
T Consensus       119 ~~~C~~Cg~~GH~~r~Cp~~~  139 (148)
T 3ts2_A          119 PKKCHFCQSINHMVASCPLKA  139 (148)
T ss_dssp             CCCCTTTCCSSCCGGGCTTTT
T ss_pred             CCcccccCCcCCEeccCcCCC
Confidence            568999999999999999875

>2hqh_E Restin; beta/BETA structure, zinc finger motif, structural protein, binding; 1.80A {Homo sapiens}

Probab=88.80  E-value=0.13  Score=24.63  Aligned_cols=18  Identities=33%  Similarity=1.001  Sum_probs=11.1

Q ss_pred             cceeccccccccccCCCC
Q psy16623         73 VCYKCNNYGHFARECATE   90 (93)
Q Consensus        73 ~C~~Cg~~GH~ar~C~~~   90 (93)
                      -|-.|...||.+.+|++.
T Consensus         5 YCe~CE~FGH~t~~C~d~   22 (26)
T 2hqh_E            5 YCEICEMFGHWATNCNDD   22 (26)
T ss_dssp             EETTTTEESSCGGGCCTT
T ss_pred             cchHHHHhCcccccCCcc
Confidence            466666666666666543

---

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	93
d2exfa1	42	g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunod	4e-06

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

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

 Score = 37.9 bits (88), Expect = 4e-06
 Identities = 12/46 (26%), Positives = 19/46 (41%), Gaps = 9/46 (19%)

Query: 42 IQCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFAREC 87
          ++C+NC   GH   +C                C+KC   GH  ++C
Sbjct: 2  VKCFNCGKEGHTARNCRAPRK---------KGCWKCGKEGHQMKDC 38

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	93
d2exfa1	42	HIV nucleocapsid {Human immunodeficiency virus typ	99.57
d1nc8a_	29	HIV nucleocapsid {Human immunodeficiency virus typ	98.27
d1nc8a_	29	HIV nucleocapsid {Human immunodeficiency virus typ	98.25
d2exfa1	42	HIV nucleocapsid {Human immunodeficiency virus typ	97.9
d1dsqa_	26	Nucleic acid binding protein p14 {Mouse mammary tu	97.55
d1dsqa_	26	Nucleic acid binding protein p14 {Mouse mammary tu	97.24
d1a6bb_	40	Zinc finger protein ncp10 {Moloney murine leukemia	96.78
d1a6bb_	40	Zinc finger protein ncp10 {Moloney murine leukemia	95.09
d1cl4a_	32	Nucleocapsid protein from mason-pfizer monkey viru	92.58
d1dsva_	31	Nucleic acid binding protein p14 {Mouse mammary tu	92.3
d1cl4a_	32	Nucleocapsid protein from mason-pfizer monkey viru	84.25

>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=99.57  E-value=5.4e-16  Score=83.43  Aligned_cols=40  Identities=30%  Similarity=0.835  Sum_probs=36.0

Q ss_pred             cceeecCCCCccccccCCCCCCCCCCCcccccceeccccccccccCCCC
Q psy16623         42 IQCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFARECATE   90 (93)
Q Consensus        42 ~~C~~Cg~~GH~~~~C~~~~~~~~~~~~~~~~C~~Cg~~GH~ar~C~~~   90 (93)
                      +.||+|++.||++++||.+.    .     ..||+||+.||++++||+.
T Consensus         2 i~C~~Cg~~GH~~~~Cp~~~----~-----~~C~~Cg~~GH~~~~Cp~r   41 (42)
T d2exfa1           2 VKCFNCGKEGHTARNCRAPR----K-----KGCWKCGKEGHQMKDCTER   41 (42)
T ss_dssp             CCCTTTCCSSSCTTTCSSCC----C-----SSCSSSCCSSSCTTTCCSS
T ss_pred             CccccCCCcCcCcccCcCCC----c-----CccccCCCCCeecccCCCC
Confidence            58999999999999999863    2     5799999999999999975

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

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

Probab=98.27  E-value=1.5e-07  Score=45.32  Aligned_cols=20  Identities=35%  Similarity=0.775  Sum_probs=11.9

Q ss_pred             CcceeecCCCCccccccCCC
Q psy16623         41 TIQCYNCFDFGHYQYSCPQK   60 (93)
Q Consensus        41 ~~~C~~Cg~~GH~~~~C~~~   60 (93)
                      .+.||+||+.||++++|..+
T Consensus         6 ~ikCfNCGkeGH~ar~CrAP   25 (29)
T d1nc8a_           6 VIRCWNCGKEGHSARQCRAP   25 (29)
T ss_dssp             CCBCTTTSCBSSCGGGCCSS
T ss_pred             eeEeecCCccchhhhhccCc
Confidence            34566666666666666554

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

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

Probab=98.25  E-value=1.7e-07  Score=45.18  Aligned_cols=19  Identities=42%  Similarity=1.017  Sum_probs=17.4

Q ss_pred             ccceeccccccccccCCCC
Q psy16623         72 IVCYKCNNYGHFARECATE   90 (93)
Q Consensus        72 ~~C~~Cg~~GH~ar~C~~~   90 (93)
                      ..||+||++||+|++|..+
T Consensus         7 ikCfNCGkeGH~ar~CrAP   25 (29)
T d1nc8a_           7 IRCWNCGKEGHSARQCRAP   25 (29)
T ss_dssp             CBCTTTSCBSSCGGGCCSS
T ss_pred             eEeecCCccchhhhhccCc
Confidence            7899999999999999765

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

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

Probab=97.90  E-value=1.6e-06  Score=45.44  Aligned_cols=19  Identities=37%  Similarity=1.020  Sum_probs=17.7

Q ss_pred             ccceeccccccccccCCCC
Q psy16623         72 IVCYKCNNYGHFARECATE   90 (93)
Q Consensus        72 ~~C~~Cg~~GH~ar~C~~~   90 (93)
                      ..||+|++.||+++|||.+
T Consensus         2 i~C~~Cg~~GH~~~~Cp~~   20 (42)
T d2exfa1           2 VKCFNCGKEGHTARNCRAP   20 (42)
T ss_dssp             CCCTTTCCSSSCTTTCSSC
T ss_pred             CccccCCCcCcCcccCcCC
Confidence            6799999999999999985

>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=96.78  E-value=0.00026  Score=36.03  Aligned_cols=19  Identities=32%  Similarity=0.879  Sum_probs=15.9

Q ss_pred             ccceeccccccccccCCCC
Q psy16623         72 IVCYKCNNYGHFARECATE   90 (93)
Q Consensus        72 ~~C~~Cg~~GH~ar~C~~~   90 (93)
                      ..|-.|.+.|||++|||+.
T Consensus        11 DQCAyCke~GHW~~dCPkk   29 (40)
T d1a6bb_          11 DQCAYCKEKGHWAKDCPKK   29 (40)
T ss_dssp             SSCSSSCCTTCCTTSCSSS
T ss_pred             hhhHHHhhcCchhhhCccC
Confidence            4688899999999999875

>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=95.09  E-value=0.0059  Score=30.79  Aligned_cols=20  Identities=40%  Similarity=0.891  Sum_probs=18.3

Q ss_pred             cceeecCCCCccccccCCCC
Q psy16623         42 IQCYNCFDFGHYQYSCPQKS   61 (93)
Q Consensus        42 ~~C~~Cg~~GH~~~~C~~~~   61 (93)
                      .+|--|.+.||++++||...
T Consensus        11 DQCAyCke~GHW~~dCPkkp   30 (40)
T d1a6bb_          11 DQCAYCKEKGHWAKDCPKKP   30 (40)
T ss_dssp             SSCSSSCCTTCCTTSCSSSC
T ss_pred             hhhHHHhhcCchhhhCccCC
Confidence            48999999999999999875

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

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

Probab=92.58  E-value=0.025  Score=27.22  Aligned_cols=18  Identities=33%  Similarity=0.822  Sum_probs=15.8

Q ss_pred             ccceeccccccccccCCC
Q psy16623         72 IVCYKCNNYGHFARECAT   89 (93)
Q Consensus        72 ~~C~~Cg~~GH~ar~C~~   89 (93)
                      ..|.+|.+.-|+|+||.+
T Consensus         3 ~lCPrC~kG~HWa~~Crs   20 (32)
T d1cl4a_           3 GLCPRCKRGKHWANECKS   20 (32)
T ss_dssp             CSCSSCSSCSSCSTTCCC
T ss_pred             ccCccccCcchHHHHhhh
Confidence            479999999999999965

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

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

Probab=92.30  E-value=0.026  Score=26.96  Aligned_cols=18  Identities=28%  Similarity=0.717  Sum_probs=15.8

Q ss_pred             ccceeccccccccccCCC
Q psy16623         72 IVCYKCNNYGHFARECAT   89 (93)
Q Consensus        72 ~~C~~Cg~~GH~ar~C~~   89 (93)
                      ..|-+|.+.-|+|+||.+
T Consensus         3 ~lCPrC~kG~HWa~~Crs   20 (31)
T d1dsva_           3 GLCPRCKKGYHWKSECKS   20 (31)
T ss_dssp             CBCTTTCSSBSCTTTCCC
T ss_pred             ccCccccCcchHHHHhhh
Confidence            579999999999999975

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

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

Probab=84.25  E-value=0.36  Score=22.90  Aligned_cols=21  Identities=24%  Similarity=0.458  Sum_probs=18.6

Q ss_pred             CcceeecCCCCccccccCCCC
Q psy16623         41 TIQCYNCFDFGHYQYSCPQKS   61 (93)
Q Consensus        41 ~~~C~~Cg~~GH~~~~C~~~~   61 (93)
                      +..|-+|.+--|++++|....
T Consensus         2 P~lCPrC~kG~HWa~~Crsk~   22 (32)
T d1cl4a_           2 PGLCPRCKRGKHWANECKSKT   22 (32)
T ss_dssp             CCSCSSCSSCSSCSTTCCCTT
T ss_pred             CccCccccCcchHHHHhhhhh
Confidence            347999999999999999876