Psyllid ID: psy16574

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150--
Protein Sequence
MSSTSTIQCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFARECATESVTCYNCSGQGHVAKDCTVKSSIICYNCNSSGHFARNCPNDSSKRCYACHQAGHMAKECPGQTAGKSPEPVVDMSLTCYVCGHQGHLSYDCKLVQKS
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccEEcccccccHHHHHHHHHHcccccHHHHHHHHccccccccHHHcHHHHHHHHHHccccccccccccHHHHHHHcccccccccccccccccccccccccccccccccccHHHHHHccccccccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
msststiqcyncfdfghyqyscpqkssadargdkVGIVCYkcnnyghfarecatesvtcyncsgqghvakdctvkssiicyncnssghfarncpndsskrcyachqaghmakecpgqtagkspepvvdmsltcyvcghqghlsydcklvqks
Flexible Loop (DISEMBL)
msststiqCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFARECATESVTCYNCSGQGHVAKDCTVKSSIICYNCNSSGHFARNCPNDSSKRCYACHQAGHMAKECPGQTAGKSPEPVVDMSLTCYVCGhqghlsydcklvqkS
Low Complexity Region (SEG)
MSSTSTIQCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFARECATESVTCYNCSGQGHVAKDCTVKSSIICYNCNSSGHFARNCPNDSSKRCYACHQAGHMAKECPGQTAGKSPEPVVDMSLTCYVCGHQGHLSYDCKLVQKS
Disordered region (IsUnstruct)
*****TIQCYNCFDFGHYQYSCPQK**ADARGDKVGIVCYKCNNYGHFARECATESVTCYNCSGQGHVAKDCTVKSSIICYNCNSSGHFARNC*********************************VDMSLTCYVCGHQGHLSYDCKLV***
Disordered Region (DISOPRED)
****STI*CYNCFDFGHYQYS******************YKCNNYGHFARECATESV*C*********************YNCNS*******C*NDSSKRCYACHQAGHMA*******************LTCYVCGHQGHLSY*CKL****
Disordered Region (DISEMBL)
MSSTSTIQCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFARECATESVTCYNCSGQGHVAKDCTVKSSIICYNCNSSGHFARNCPNDSSKRCYACHQAGHMAKECPGQTAGKSPEPVVDMSLTCYVCGHQGHLSYDCKLVQKS
Disordered Region (DISPRO)
******IQCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFARECATESVTCYNCSGQGHVAKDCTVKSSIICYNCNSSGHFARNCPNDSSKRCYACHQA*HMAKECPGQTAGKSPEPV**************************
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MSSTSTIQCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFARECATESVTCYNCSGQGHVAKDCTVKSSIICYNCNSSGHFARNCPNDSSKRCYACHQAGHMAKECPGQTAGKSPEPVVDMSLTCYVCGHQGHLSYDCKLVQKS
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	152	2.2.26 [Sep-21-2011]
Q8T8R1	165	CCHC-type zinc finger pro	yes	N/A	0.631	0.581	0.447	8e-22
Q04832	271	DNA-binding protein HEXBP	yes	N/A	0.927	0.520	0.311	2e-19
O65639	299	Cold shock protein 1 OS=A	yes	N/A	0.894	0.454	0.341	1e-17
Q3T0Q6	170	Cellular nucleic acid-bin	yes	N/A	0.947	0.847	0.303	2e-17
P62634	177	Cellular nucleic acid-bin	yes	N/A	0.947	0.813	0.302	6e-17
Q5R5R5	177	Cellular nucleic acid-bin	yes	N/A	0.947	0.813	0.302	6e-17
P62633	177	Cellular nucleic acid-bin	yes	N/A	0.947	0.813	0.302	6e-17
O42395	172	Cellular nucleic acid-bin	yes	N/A	0.947	0.837	0.305	2e-16
P53996	178	Cellular nucleic acid-bin	yes	N/A	0.947	0.808	0.306	4e-16
P53849	153	Zinc finger protein GIS2	yes	N/A	0.618	0.614	0.372	4e-14

>sp|Q8T8R1|Y3800_DROME CCHC-type zinc finger protein CG3800 OS=Drosophila melanogaster GN=CG3800 PE=1 SV=1

 Score =  102 bits (254), Expect = 8e-22,   Method: Compositional matrix adjust.
 Identities = 51/114 (44%), Positives = 67/114 (58%), Gaps = 18/114 (15%)

Query: 39  CYKCNNYGHFARECATESVTCYNCSGQGHVAKDCTVKSSIICYNCNSSGHFARNCPNDSS 98
           CYKCN +GHFAR C  E+  CY C+G GH++KDCT   +  CY CN +GH+ RNCP   +
Sbjct: 57  CYKCNQFGHFARACPEEAERCYRCNGIGHISKDCTQADNPTCYRCNKTGHWVRNCPEAVN 116

Query: 99  KR------CYACHQAGHMAKECPGQTAGKSPEPVVDMSLTCYVCGHQGHLSYDC 146
           +R      CY C++ GH++K CP            + S TCY CG  GHL  +C
Sbjct: 117 ERGPTNVSCYKCNRTGHISKNCP------------ETSKTCYGCGKSGHLRREC 158

Drosophila melanogaster (taxid: 7227)

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

 Score = 94.7 bits (234), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 57/183 (31%), Positives = 81/183 (44%), Gaps = 42/183 (22%)

Query: 3   STSTIQCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFARECATE------- 55
           + S+  C NC   GHY   CP+   AD++GD+    C++C   GH +REC  E       
Sbjct: 12  TESSTSCRNCGKEGHYARECPE---ADSKGDERSTTCFRCGEEGHMSRECPNEARSGAAG 68

Query: 56  SVTCYNCSGQGHVAKDCT------VKSSIICYNCNSSGHFARNCPN-------------- 95
           ++TC+ C   GH+++DC             CY C   GH +R+CP+              
Sbjct: 69  AMTCFRCGEAGHMSRDCPNSAKPGAAKGFECYKCGQEGHLSRDCPSSQGGSRGGYGQKRG 128

Query: 96  --------DSSKRCYACHQAGHMAKECPGQTAGKSPEPVVDMSLTCYVCGHQGHLSYDCK 147
                      + CY C  AGH++++CP    G S         TCY CG  GH+S DC 
Sbjct: 129 RSGAQGGYSGDRTCYKCGDAGHISRDCPNGQGGYS----GAGDRTCYKCGDAGHISRDCP 184

Query: 148 LVQ 150
             Q
Sbjct: 185 NGQ 187

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

Leishmania major (taxid: 5664)

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

 Score = 88.6 bits (218), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 58/170 (34%), Positives = 76/170 (44%), Gaps = 34/170 (20%)

Query: 9   CYNCFDFGHYQYSCPQKSSADARGDKVG--IVCYKCNNYGHFARECATESV--------- 57
           CYNC D GH+   C    + D RG   G    CY C + GH AR+C  +SV         
Sbjct: 134 CYNCGDTGHFARDCTSAGNGDQRGATKGGNDGCYTCGDVGHVARDCTQKSVGNGDQRGAV 193

Query: 58  -----TCYNCSGQGHVAKDCTVK-----------SSIICYNCNSSGHFARNCPNDS--SK 99
                 CY C   GH A+DCT K            S  CY+C   GH AR+C      S+
Sbjct: 194 KGGNDGCYTCGDVGHFARDCTQKVAAGNVRSGGGGSGTCYSCGGVGHIARDCATKRQPSR 253

Query: 100 RCYACHQAGHMAKECPGQTAGKSPEPVVDMSLTCYVCGHQGHLSYDCKLV 149
            CY C  +GH+A++C  + +G            CY CG +GH + +C  V
Sbjct: 254 GCYQCGGSGHLARDCDQRGSGGGGNDNA-----CYKCGKEGHFARECSSV 298

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

 Score = 88.2 bits (217), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 50/165 (30%), Positives = 76/165 (46%), Gaps = 21/165 (12%)

Query: 5   STIQCYNCFDFGHYQYSCPQKSSADAR-----------GDKVGIVCYKCNNYGHFARECA 53
           S+ +C+ C   GH+   CP                      +  +CY+C   GH A++C 
Sbjct: 2   SSNECFKCGRSGHWARECPTGGGRGRGMRSRGRGFQFVSSSLPDICYRCGESGHLAKDCD 61

Query: 54  TESVTCYNCSGQGHVAKDC---TVKSSIICYNCNSSGHFARNCPNDSSKRCYACHQAGHM 110
            +   CYNC   GH+AKDC     +    CYNC   GH AR+C +   ++CY+C + GH+
Sbjct: 62  LQEDACYNCGRGGHIAKDCKEPKREREQCCYNCGKPGHLARDCDHADEQKCYSCGEFGHI 121

Query: 111 AKECP-------GQTAGKSPEPVVDMSLTCYVCGHQGHLSYDCKL 148
            K+C        G+T   +        + CY CG  GHL+ +C +
Sbjct: 122 QKDCTKVKCYRCGETGHVAINCSKTSEVNCYRCGESGHLARECTI 166

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

Bos taurus (taxid: 9913)

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

 Score = 86.3 bits (212), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 52/172 (30%), Positives = 78/172 (45%), Gaps = 28/172 (16%)

Query: 5   STIQCYNCFDFGHYQYSCPQKSSADA-------------RG-----DKVGIVCYKCNNYG 46
           S+ +C+ C   GH+   CP                    RG       +  +CY+C   G
Sbjct: 2   SSNECFKCGRSGHWARECPTGGGRGRGMRSRGRGGFTSDRGFQFVSSSLPDICYRCGESG 61

Query: 47  HFARECATESVTCYNCSGQGHVAKDC---TVKSSIICYNCNSSGHFARNCPNDSSKRCYA 103
           H A++C  +   CYNC   GH+AKDC     +    CYNC   GH AR+C +   ++CY+
Sbjct: 62  HLAKDCDLQEDACYNCGRGGHIAKDCKEPKREREQCCYNCGKPGHLARDCDHADEQKCYS 121

Query: 104 CHQAGHMAKECP-------GQTAGKSPEPVVDMSLTCYVCGHQGHLSYDCKL 148
           C + GH+ K+C        G+T   +        + CY CG  GHL+ +C +
Sbjct: 122 CGEFGHIQKDCTKVKCYRCGETGHVAINCSKTSEVNCYRCGESGHLARECTI 173

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

Rattus norvegicus (taxid: 10116)

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

 Score = 86.3 bits (212), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 52/172 (30%), Positives = 78/172 (45%), Gaps = 28/172 (16%)

Query: 5   STIQCYNCFDFGHYQYSCPQKSSADA-------------RG-----DKVGIVCYKCNNYG 46
           S+ +C+ C   GH+   CP                    RG       +  +CY+C   G
Sbjct: 2   SSNECFKCGRSGHWARECPTGGGRGRGMRSRGRGGFTSDRGFQFVSSSLPDICYRCGESG 61

Query: 47  HFARECATESVTCYNCSGQGHVAKDC---TVKSSIICYNCNSSGHFARNCPNDSSKRCYA 103
           H A++C  +   CYNC   GH+AKDC     +    CYNC   GH AR+C +   ++CY+
Sbjct: 62  HLAKDCDLQEDACYNCGRGGHIAKDCKEPKREREQCCYNCGKPGHLARDCDHADEQKCYS 121

Query: 104 CHQAGHMAKECP-------GQTAGKSPEPVVDMSLTCYVCGHQGHLSYDCKL 148
           C + GH+ K+C        G+T   +        + CY CG  GHL+ +C +
Sbjct: 122 CGEFGHIQKDCTKVKCYRCGETGHVAINCSKTSEVNCYRCGESGHLARECTI 173

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

Pongo abelii (taxid: 9601)

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

 Score = 86.3 bits (212), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 52/172 (30%), Positives = 78/172 (45%), Gaps = 28/172 (16%)

Query: 5   STIQCYNCFDFGHYQYSCPQKSSADA-------------RG-----DKVGIVCYKCNNYG 46
           S+ +C+ C   GH+   CP                    RG       +  +CY+C   G
Sbjct: 2   SSNECFKCGRSGHWARECPTGGGRGRGMRSRGRGGFTSDRGFQFVSSSLPDICYRCGESG 61

Query: 47  HFARECATESVTCYNCSGQGHVAKDC---TVKSSIICYNCNSSGHFARNCPNDSSKRCYA 103
           H A++C  +   CYNC   GH+AKDC     +    CYNC   GH AR+C +   ++CY+
Sbjct: 62  HLAKDCDLQEDACYNCGRGGHIAKDCKEPKREREQCCYNCGKPGHLARDCDHADEQKCYS 121

Query: 104 CHQAGHMAKECP-------GQTAGKSPEPVVDMSLTCYVCGHQGHLSYDCKL 148
           C + GH+ K+C        G+T   +        + CY CG  GHL+ +C +
Sbjct: 122 CGEFGHIQKDCTKVKCYRCGETGHVAINCSKTSEVNCYRCGESGHLARECTI 173

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

Homo sapiens (taxid: 9606)

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

 Score = 85.1 bits (209), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 51/167 (30%), Positives = 76/167 (45%), Gaps = 23/167 (13%)

Query: 5   STIQCYNCFDFGHYQYSCPQKSSADAR------------GDKVGIVCYKCNNYGHFAREC 52
           S+ +C+ C   GH+   CP                       +  +CY+C   GH A++C
Sbjct: 2   SSNECFKCGRTGHWARECPTGIGRGRGMRSRGRAGFQFMSSSLPDICYRCGESGHLAKDC 61

Query: 53  -ATESVTCYNCSGQGHVAKDCT---VKSSIICYNCNSSGHFARNCPNDSSKRCYACHQAG 108
              E   CYNC   GH+AKDC     +    CYNC   GH AR+C +   ++CY+C + G
Sbjct: 62  DLQEDKACYNCGRGGHIAKDCKEPKREREQCCYNCGKPGHLARDCDHADEQKCYSCGEFG 121

Query: 109 HMAKECP-------GQTAGKSPEPVVDMSLTCYVCGHQGHLSYDCKL 148
           H+ K+C        G+T   +        + CY CG  GHL+ +C +
Sbjct: 122 HIQKDCTKVKCYRCGETGHVAINCSKTSEVNCYRCGESGHLARECTI 168

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

Gallus gallus (taxid: 9031)

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

 Score = 83.6 bits (205), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 53/173 (30%), Positives = 78/173 (45%), Gaps = 29/173 (16%)

Query: 5   STIQCYNCFDFGHYQYSCPQKSSADA-------------RG-----DKVGIVCYKCNNYG 46
           S+ +C+ C   GH+   CP                    RG       +  +CY+C   G
Sbjct: 2   SSNECFKCGRSGHWARECPTGGGRGRGMRSRGRGGFTSDRGFQFVSSSLPDICYRCGESG 61

Query: 47  HFAREC-ATESVTCYNCSGQGHVAKDCT---VKSSIICYNCNSSGHFARNCPNDSSKRCY 102
           H A++C   E   CYNC   GH+AKDC     +    CYNC   GH AR+C +   ++CY
Sbjct: 62  HLAKDCDLQEDEACYNCGRGGHIAKDCKEPKREREQCCYNCGKPGHLARDCDHADEQKCY 121

Query: 103 ACHQAGHMAKECP-------GQTAGKSPEPVVDMSLTCYVCGHQGHLSYDCKL 148
           +C + GH+ K+C        G+T   +        + CY CG  GHL+ +C +
Sbjct: 122 SCGEFGHIQKDCTKVKCYRCGETGHVAINCSKTSEVNCYRCGESGHLARECTI 174

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

Mus musculus (taxid: 10090)

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

 Score = 77.0 bits (188), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 44/118 (37%), Positives = 62/118 (52%), Gaps = 24/118 (20%)

Query: 8   QCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFARECAT-------ESVTCY 60
           QCYNC + GH +  C  +             C+ CN  GH +REC           V+CY
Sbjct: 48  QCYNCGETGHVRSECTVQR------------CFNCNQTGHISRECPEPKKTSRFSKVSCY 95

Query: 61  NCSGQGHVAKDCTVK---SSIICYNCNSSGHFARNCPNDSSKRCYACHQAGHMAKECP 115
            C G  H+AKDC  +   S + CY C  +GH +R+C ND  + CY C++ GH++K+CP
Sbjct: 96  KCGGPNHMAKDCMKEDGISGLKCYTCGQAGHMSRDCQND--RLCYNCNETGHISKDCP 151

May act in the sexual differentiation pathway.

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

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	152
389608533	144	similar to CG3800 [Papilio xuthus]	0.894	0.944	0.4	6e-23
389610781	145	simila to CG3800 [Papilio polytes]	0.894	0.937	0.397	8e-23
383858694	155	PREDICTED: CCHC-type zinc finger protein	0.868	0.851	0.456	1e-22
357619173	144	zinc finger protein [Danaus plexippus]	0.894	0.944	0.393	2e-22
289743447	150	E3 ubiquitin ligase interacting with arg	0.875	0.886	0.411	3e-22
121543757	142	zinc finger protein-like protein [Macone	0.815	0.873	0.435	6e-22
110759374	155	PREDICTED: CCHC-type zinc finger protein	0.835	0.819	0.423	2e-21
156536895	155	PREDICTED: CCHC-type zinc finger protein	0.861	0.845	0.408	2e-21
340719027	155	PREDICTED: CCHC-type zinc finger protein	0.842	0.825	0.420	2e-21
112982721	143	zinc finger protein [Bombyx mori] gi|598	0.881	0.937	0.385	2e-21

>gi|389608533|dbj|BAM17876.1| similar to CG3800 [Papilio xuthus]

 Score =  112 bits (279), Expect = 6e-23,   Method: Compositional matrix adjust.
 Identities = 62/155 (40%), Positives = 87/155 (56%), Gaps = 19/155 (12%)

Query: 5   STIQCYNCFDFGHYQYSCPQK--SSADARGDKVGIVCYKCNNYGHFARECATESVTCYNC 62
           S+  CY C   GH+   C Q   +S D   ++    C+KCN  GHFAR+C  E+  CY C
Sbjct: 2   SSSVCYKCNRTGHFARECTQGGVASRDTGFNRQREKCFKCNRTGHFARDCKEEADRCYRC 61

Query: 63  SGQGHVAKDCT-VKSSIICYNCNSSGHFARNCP----NDSSKRCYACHQAGHMAKECPGQ 117
           +G GH+A++C        CYNCN +GH ARNCP    + S + CY C++AGH+++ CP  
Sbjct: 62  NGTGHIARECAQSPDEPSCYNCNKTGHIARNCPEGGRDSSGQTCYTCNKAGHISRNCP-- 119

Query: 118 TAGKSPEPVVDMSLTCYVCGHQGHLSYDCKLVQKS 152
                     D + TCYVCG  GH+S DC   +++
Sbjct: 120 ----------DGTKTCYVCGKPGHISRDCDESERN 144

Source: Papilio xuthus

Species: Papilio xuthus

Genus: Papilio

Family: Papilionidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|389610781|dbj|BAM19001.1| simila to CG3800 [Papilio polytes]

 Score =  111 bits (278), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 62/156 (39%), Positives = 87/156 (55%), Gaps = 20/156 (12%)

Query: 5   STIQCYNCFDFGHYQYSCPQK---SSADARGDKVGIVCYKCNNYGHFARECATESVTCYN 61
           S+  CY C   GH+   C Q    +S D   ++    C+KCN  GHFAR+C  E+  CY 
Sbjct: 2   SSSVCYKCNRTGHFARECTQGGGVASRDTGFNRQREKCFKCNRTGHFARDCKEEADRCYR 61

Query: 62  CSGQGHVAKDCT-VKSSIICYNCNSSGHFARNCP----NDSSKRCYACHQAGHMAKECPG 116
           C+G GH+A++C        CYNCN +GH ARNCP    + S + CY C++AGH+++ CP 
Sbjct: 62  CNGTGHIARECAQSPDEPSCYNCNKTGHIARNCPEGGRDSSGQTCYTCNKAGHISRNCP- 120

Query: 117 QTAGKSPEPVVDMSLTCYVCGHQGHLSYDCKLVQKS 152
                      D + TCYVCG  GH+S DC   +++
Sbjct: 121 -----------DGTKTCYVCGKPGHISRDCDESERN 145

Source: Papilio polytes

Species: Papilio polytes

Genus: Papilio

Family: Papilionidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383858694|ref|XP_003704834.1| PREDICTED: CCHC-type zinc finger protein CG3800-like [Megachile rotundata]

 Score =  110 bits (276), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 73/160 (45%), Positives = 89/160 (55%), Gaps = 28/160 (17%)

Query: 4   TSTIQCYNCFDFGHYQYSCPQKSSADARGD-----KVGIV-----CYKCNNYGHFARECA 53
            S+  CY C   GHY   CPQ S   ARGD     + G V     CYKCN YGHFAREC 
Sbjct: 1   MSSSACYKCNRMGHYARECPQGSGGGARGDRGRDREGGFVRGRDKCYKCNQYGHFARECK 60

Query: 54  TESVTCYNCSGQGHVAKDCTVKSSIICYNCNSSGHFARNCP---NDSSK----RCYACHQ 106
            +   CY CSG GH+AKDC     + CYNCN +GH AR+CP   NDS +     CY C++
Sbjct: 61  EDQDLCYRCSGVGHIAKDCQQGPEMSCYNCNKTGHIARSCPEGGNDSGRFAMQSCYNCNK 120

Query: 107 AGHMAKECPGQTAGKSPEPVVDMSLTCYVCGHQGHLSYDC 146
            GH+A+ C  +  GK          TCY+CG  GH+S +C
Sbjct: 121 TGHIARNCT-EAGGK----------TCYMCGKPGHISREC 149

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|357619173|gb|EHJ71850.1| zinc finger protein [Danaus plexippus]

 Score =  110 bits (276), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 61/155 (39%), Positives = 87/155 (56%), Gaps = 19/155 (12%)

Query: 5   STIQCYNCFDFGHYQYSCPQKS--SADARGDKVGIVCYKCNNYGHFARECATESVTCYNC 62
           S+  CY C   GH+   C Q    + DA  ++    C+KCN  GHFAR+C  E+  CY C
Sbjct: 2   SSSVCYKCNRKGHFARECTQSGVGALDAGFNRQREKCFKCNRTGHFARDCKEEADRCYRC 61

Query: 63  SGQGHVAKDCT-VKSSIICYNCNSSGHFARNCP----NDSSKRCYACHQAGHMAKECPGQ 117
           +G GH+A++C        CYNCN +GH ARNCP    ++S++ CY C++ GH+++ CP  
Sbjct: 62  NGTGHIARECAQSPDEPSCYNCNKTGHIARNCPEGGRDNSNQTCYNCNKTGHISRNCP-- 119

Query: 118 TAGKSPEPVVDMSLTCYVCGHQGHLSYDCKLVQKS 152
                     D + TCYVCG  GH+S DC    ++
Sbjct: 120 ----------DGTKTCYVCGKPGHISRDCDEADRN 144

Source: Danaus plexippus

Species: Danaus plexippus

Genus: Danaus

Family: Nymphalidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|289743447|gb|ADD20471.1| E3 ubiquitin ligase interacting with arginine methyltransferase [Glossina morsitans morsitans]

 Score =  109 bits (273), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 65/158 (41%), Positives = 81/158 (51%), Gaps = 25/158 (15%)

Query: 1   MSSTSTIQCYNCFDFGHYQYSC-----PQKSSADARGDKVGIVCYKCNNYGHFARECATE 55
           MS  ST  CY C   GH+   C           D R       C+KCN YGHFAR C  E
Sbjct: 1   MSMAST--CYKCNRTGHFARDCNFGGGGGGGGRDMRRGNNREKCFKCNQYGHFARACPEE 58

Query: 56  SVTCYNCSGQGHVAKDCTVKSSIICYNCNSSGHFARNCPNDSSKR------CYACHQAGH 109
           S  CY C+G GH++KDCT   +  CY C+  GH+ARNCP  S+ R      CY C++ GH
Sbjct: 59  SERCYRCNGVGHISKDCTQPDNPTCYKCHKVGHWARNCPEASNDRSSSNISCYKCNRTGH 118

Query: 110 MAKECPGQTAGKSPEPVVDMSLTCYVCGHQGHLSYDCK 147
           ++K CP            D + TCY CG  GHL  +C+
Sbjct: 119 ISKNCP------------DTAKTCYGCGKSGHLRRECE 144

Source: Glossina morsitans morsitans

Species: Glossina morsitans

Genus: Glossina

Family: Glossinidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|121543757|gb|ABM55551.1| zinc finger protein-like protein [Maconellicoccus hirsutus]

 Score =  108 bits (271), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 64/147 (43%), Positives = 82/147 (55%), Gaps = 23/147 (15%)

Query: 9   CYNCFDFGHYQYSCPQ-KSSADARGDKVGIVCYKCNNYGHFARECATESVTCYNCSGQGH 67
           CY C + GH+   CP  +     R +K    CYKCN +GHFAR+C  +   CY C+  GH
Sbjct: 7   CYRCRETGHFARECPSFEPGKPIRREK----CYKCNAFGHFARDCKEDQDRCYRCNEIGH 62

Query: 68  VAKDCTV-KSSIICYNCNSSGHFARNCPNDSSK-------RCYACHQAGHMAKECPGQTA 119
           +A+DC    SS  CY+C   GH AR+CP+ SS         CY C++AGHMA++CP    
Sbjct: 63  IARDCVRSDSSPQCYSCKGIGHIARDCPDSSSNNSRHFSANCYNCNKAGHMARDCPNSGG 122

Query: 120 GKSPEPVVDMSLTCYVCGHQGHLSYDC 146
           GK          TCYVC  QGH+S DC
Sbjct: 123 GK----------TCYVCRKQGHISRDC 139

Source: Maconellicoccus hirsutus

Species: Maconellicoccus hirsutus

Genus: Maconellicoccus

Family: Pseudococcidae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|110759374|ref|XP_001119951.1| PREDICTED: CCHC-type zinc finger protein CG3800-like [Apis mellifera] gi|328780974|ref|XP_003249895.1| PREDICTED: CCHC-type zinc finger protein CG3800-like [Apis mellifera] gi|328780976|ref|XP_003249896.1| PREDICTED: CCHC-type zinc finger protein CG3800-like [Apis mellifera] gi|328780978|ref|XP_003249897.1| PREDICTED: CCHC-type zinc finger protein CG3800-like [Apis mellifera] gi|380028029|ref|XP_003697714.1| PREDICTED: CCHC-type zinc finger protein CG3800-like [Apis florea] gi|380028031|ref|XP_003697715.1| PREDICTED: CCHC-type zinc finger protein CG3800-like [Apis florea] gi|380028033|ref|XP_003697716.1| PREDICTED: CCHC-type zinc finger protein CG3800-like [Apis florea] gi|380028035|ref|XP_003697717.1| PREDICTED: CCHC-type zinc finger protein CG3800-like [Apis florea] gi|380028037|ref|XP_003697718.1| PREDICTED: CCHC-type zinc finger protein CG3800-like [Apis florea]

 Score =  107 bits (267), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 69/163 (42%), Positives = 83/163 (50%), Gaps = 36/163 (22%)

Query: 5   STIQCYNCFDFGHYQYSCPQKSSAD-------------ARG-DKVGIVCYKCNNYGHFAR 50
           S+  CY C   GHY   CPQ                  ARG DK    CYKCN +GHFAR
Sbjct: 2   SSSACYKCNRMGHYARECPQGGGGGGRGDRGRDREGGFARGRDK----CYKCNQFGHFAR 57

Query: 51  ECATESVTCYNCSGQGHVAKDCTVKSSIICYNCNSSGHFARNCP---NDSSK----RCYA 103
           EC  +   CY C G GH+AKDC     + CYNCN +GH AR+CP   NDS +     CY 
Sbjct: 58  ECKEDQDLCYRCQGVGHIAKDCQQGPEMSCYNCNKTGHMARSCPEGGNDSGRFGMQSCYN 117

Query: 104 CHQAGHMAKECPGQTAGKSPEPVVDMSLTCYVCGHQGHLSYDC 146
           C++ GH A+ C  +  GK+          CY CG  GHLS +C
Sbjct: 118 CNKTGHFARNCT-EVGGKA----------CYTCGKTGHLSREC 149

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|156536895|ref|XP_001607266.1| PREDICTED: CCHC-type zinc finger protein CG3800-like isoform 2 [Nasonia vitripennis] gi|156536897|ref|XP_001607260.1| PREDICTED: CCHC-type zinc finger protein CG3800-like isoform 1 [Nasonia vitripennis] gi|345479376|ref|XP_003423939.1| PREDICTED: CCHC-type zinc finger protein CG3800-like [Nasonia vitripennis]

 Score =  107 bits (266), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 65/159 (40%), Positives = 84/159 (52%), Gaps = 28/159 (17%)

Query: 5   STIQCYNCFDFGHYQYSCPQKSSADARGDKVGIV----------CYKCNNYGHFARECAT 54
           S+  CY C   GH+   CPQ  +   RG                C+KCN YGHFAREC  
Sbjct: 2   SSSACYKCNRMGHFARECPQGGATGGRGGDRRDRDGGFGRGREKCFKCNQYGHFARECKE 61

Query: 55  ESVTCYNCSGQGHVAKDCTVKSSIICYNCNSSGHFARNCP---NDSSK----RCYACHQA 107
           +   CY C+G GH+AKDC     + CYNCN +GH AR+CP   NDS +     CY C++ 
Sbjct: 62  DQDLCYRCNGVGHIAKDCQQGPEMSCYNCNKTGHMARSCPESGNDSGRFNMQSCYTCNKT 121

Query: 108 GHMAKECPGQTAGKSPEPVVDMSLTCYVCGHQGHLSYDC 146
           GH+A+ CP +  GK          TCY+C   GH+S +C
Sbjct: 122 GHIARNCP-EGGGK----------TCYICHKTGHISREC 149

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340719027|ref|XP_003397959.1| PREDICTED: CCHC-type zinc finger protein CG3800-like isoform 1 [Bombus terrestris] gi|340719029|ref|XP_003397960.1| PREDICTED: CCHC-type zinc finger protein CG3800-like isoform 2 [Bombus terrestris] gi|350399027|ref|XP_003485390.1| PREDICTED: CCHC-type zinc finger protein CG3800-like [Bombus impatiens]

 Score =  107 bits (266), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 69/164 (42%), Positives = 83/164 (50%), Gaps = 36/164 (21%)

Query: 4   TSTIQCYNCFDFGHYQYSCPQKSSAD-------------ARG-DKVGIVCYKCNNYGHFA 49
            S+  CY C   GHY   CPQ                  ARG DK    CYKCN +GHFA
Sbjct: 1   MSSSACYKCNRMGHYARECPQGGGGGGRGDRGRDREGGFARGRDK----CYKCNQFGHFA 56

Query: 50  RECATESVTCYNCSGQGHVAKDCTVKSSIICYNCNSSGHFARNCP---NDSSK----RCY 102
           REC  +   CY C G GH+AKDC     + CYNCN +GH AR+CP   NDS +     CY
Sbjct: 57  RECKEDQDLCYRCQGVGHIAKDCQQGPEMSCYNCNKTGHMARSCPEGGNDSGRFGMQSCY 116

Query: 103 ACHQAGHMAKECPGQTAGKSPEPVVDMSLTCYVCGHQGHLSYDC 146
            C++ GH A+ C  +  GK+          CY CG  GHLS +C
Sbjct: 117 NCNKTGHFARNCT-EVGGKA----------CYTCGKPGHLSREC 149

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|112982721|ref|NP_001037117.1| zinc finger protein [Bombyx mori] gi|59858992|gb|AAX09282.1| zinc finger protein [Bombyx mori]

 Score =  106 bits (265), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 59/153 (38%), Positives = 85/153 (55%), Gaps = 19/153 (12%)

Query: 5   STIQCYNCFDFGHYQYSCPQKS--SADARGDKVGIVCYKCNNYGHFARECATESVTCYNC 62
           S+  CY C   GH+   C Q    S D+  ++    C+KCN  GHFAR+C  E+  CY C
Sbjct: 2   SSSVCYKCNRTGHFARECTQGGVVSRDSGFNRQREKCFKCNRTGHFARDCKEEADRCYRC 61

Query: 63  SGQGHVAKDCT-VKSSIICYNCNSSGHFARNCP----NDSSKRCYACHQAGHMAKECPGQ 117
           +G GH+A++C        CYNCN +GH ARNCP      +++ CY C+++GH+++ CP  
Sbjct: 62  NGTGHIARECAQSPDEPSCYNCNKTGHIARNCPEGGRESATQTCYNCNKSGHISRNCP-- 119

Query: 118 TAGKSPEPVVDMSLTCYVCGHQGHLSYDCKLVQ 150
                     D + TCYVCG  GH+S +C   +
Sbjct: 120 ----------DGTKTCYVCGKPGHISRECDEAR 142

Source: Bombyx mori

Species: Bombyx mori

Genus: Bombyx

Family: Bombycidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

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	152
FB|FBgn0034802	165	CG3800 [Drosophila melanogaste	0.631	0.581	0.447	5.2e-26
ZFIN|ZDB-GENE-030131-5045	163	cnbpa "CCHC-type zinc finger,	0.947	0.883	0.352	1.4e-25
UNIPROTKB|B4DP17	160	CNBP "cDNA FLJ61146, highly si	0.940	0.893	0.339	2.2e-25
ZFIN|ZDB-GENE-030131-7782	243	cnbpb "CCHC-type zinc finger,	0.947	0.592	0.326	2e-24
UNIPROTKB|G3MZ41	175	ZCCHC13 "Uncharacterized prote	0.967	0.84	0.295	8.7e-24
UNIPROTKB|Q3T0Q6	170	CNBP "Cellular nucleic acid-bi	0.947	0.847	0.321	8.7e-24
UNIPROTKB|F1N8C2	171	CNBP "Cellular nucleic acid-bi	0.940	0.836	0.323	1.1e-23
UNIPROTKB|P62633	177	CNBP "Cellular nucleic acid-bi	0.730	0.627	0.363	2.6e-22
UNIPROTKB|Q4R501	177	Q4R501 "Brain cDNA, clone: Qnp	0.730	0.627	0.363	2.6e-22
UNIPROTKB|Q5R5R5	177	CNBP "Cellular nucleic acid-bi	0.730	0.627	0.363	2.6e-22

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

 Score = 294 (108.6 bits), Expect = 5.2e-26, P = 5.2e-26
 Identities = 51/114 (44%), Positives = 67/114 (58%)

Query:    39 CYKCNNYGHFARECATESVTCYNCSGQGHVAKDCTVKSSIICYNCNSSGHFARNCPNDSS 98
             CYKCN +GHFAR C  E+  CY C+G GH++KDCT   +  CY CN +GH+ RNCP   +
Sbjct:    57 CYKCNQFGHFARACPEEAERCYRCNGIGHISKDCTQADNPTCYRCNKTGHWVRNCPEAVN 116

Query:    99 KR------CYACHQAGHMAKECPGQTAGKSPEPVVDMSLTCYVCGHQGHLSYDC 146
             +R      CY C++ GH++K CP            + S TCY CG  GHL  +C
Sbjct:   117 ERGPTNVSCYKCNRTGHISKNCP------------ETSKTCYGCGKSGHLRREC 158

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 = 290 (107.1 bits), Expect = 1.4e-25, P = 1.4e-25
 Identities = 55/156 (35%), Positives = 77/156 (49%)

Query:     5 STIQCYNCFDFGHYQYSCPQKSSADARGDKVG--IVCYKCNNYGHFARECATESVTCYNC 62
             ST +C+ C   GH+  +CP       RG   G  + CY+C   GH AR+C      CYNC
Sbjct:     4 STSECFGCGRSGHWIKNCPNAGRGRGRGRGRGKDLFCYRCGEQGHIARDCEQTEDACYNC 63

Query:    63 SGQGHVAKDCTV---KSSIICYNCNSSGHFARNCPNDSSKRCYACHQAGHMAKECPG--- 116
                GH+++DC     +    CYNC  +GH AR+C + + ++CY+C   GH  K C     
Sbjct:    64 HRSGHISRDCKEPKKEREQCCYNCGKAGHVARDCDHANEQKCYSCGGFGHFQKLCDKVKC 123

Query:   117 QTAGKSPEPVVDMS----LTCYVCGHQGHLSYDCKL 148
                G+     V  S    + CY CG  GHL+ DC +
Sbjct:   124 YRCGEIGHVAVQCSKATEVNCYNCGKTGHLARDCSI 159

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

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

 Score = 288 (106.4 bits), Expect = 2.2e-25, P = 2.2e-25
 Identities = 53/156 (33%), Positives = 80/156 (51%)

Query:     5 STIQCYNCFDFGHYQYSCPQKSSADARG--DKVGIVCYKCNNYGHFARECATESVTCYNC 62
             S+ +C+ C   GH+   CP       RG   +   +CY+C   GH A++C  +   CYNC
Sbjct:     2 SSNECFKCGRSGHWARECPT-GGGRGRGMRSRGRDICYRCGESGHLAKDCDLQEDACYNC 60

Query:    63 SGQGHVAKDCTV---KSSIICYNCNSSGHFARNCPNDSSKRCYACHQAGHMAKECPG--- 116
                GH+AKDC     +    CYNC   GH AR+C +   ++CY+C + GH+ K+C     
Sbjct:    61 GRGGHIAKDCKEPKREREQCCYNCGKPGHLARDCDHADEQKCYSCGEFGHIQKDCTKVKC 120

Query:   117 QTAGKSPEPVVDMSLT----CYVCGHQGHLSYDCKL 148
                G++    ++ S T    CY CG  GHL+ +C +
Sbjct:   121 YRCGETGHVAINCSKTSEVNCYRCGESGHLARECTI 156

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

ZFIN|ZDB-GENE-030131-7782 cnbpb "CCHC-type zinc finger, nucleic acid binding protein b" [Danio rerio (taxid:7955)]

 Score = 279 (103.3 bits), Expect = 2.0e-24, P = 2.0e-24
 Identities = 51/156 (32%), Positives = 79/156 (50%)

Query:     5 STIQCYNCFDFGHYQYSCPQ--KSSADARGDKVGIVCYKCNNYGHFARECATESVTCYNC 62
             S+ +C+ C   GH+  +CP   +     RG    + CY+C   GH AR+C      CYNC
Sbjct:    84 SSNECFGCGRTGHWIKNCPNAGRGRGKGRGRGKDLFCYRCGEPGHVARDCERTEDACYNC 143

Query:    63 SGQGHVAKDCTV---KSSIICYNCNSSGHFARNCPNDSSKRCYACHQAGHMAKECPG--- 116
                GH+++DC     +   +CYNC  +GH AR+C + + ++CY+C   GH+ K C     
Sbjct:   144 GRGGHISRDCKEPKKEREQVCYNCGKAGHMARDCDHANEQKCYSCGGFGHIQKGCEKVKC 203

Query:   117 QTAGKSPEPVVDMS----LTCYVCGHQGHLSYDCKL 148
                G+     V  S    + CY CG  GH++ +C +
Sbjct:   204 YRCGEIGHVAVQCSKASEVNCYNCGKSGHVAKECTI 239

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

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

 Score = 273 (101.2 bits), Expect = 8.7e-24, P = 8.7e-24
 Identities = 50/169 (29%), Positives = 83/169 (49%)

Query:     2 SSTSTIQCYNCFDFGHYQYSCPQKSSADARGDK------------VGIVCYKCNNYGHFA 49
             ++ S+ +C+ C   GH+  +C +   A  RG +            + ++CY+C  +GH+A
Sbjct:     3 TAMSSKECFKCGRVGHWAPACSKGGGARGRGARGRGHGAQCSSTTLPVICYRCGKFGHYA 62

Query:    50 RECATESVTCYNCSGQGHVAKDCTV---KSSIICYNCNSSGHFARNCPNDSSKRCYACHQ 106
             ++C      CYNC   GH+AKDC     +    CY C   GH AR+C     ++CY+C +
Sbjct:    63 KDCDLLDDICYNCGKSGHIAKDCAEPKREGERCCYTCGRPGHLARDCDRQEERKCYSCGK 122

Query:   107 AGHMAKECPG---QTAGKSPEPVVDM----SLTCYVCGHQGHLSYDCKL 148
             +GH+ K C        G+     ++      + CY CG  GHL+ +C +
Sbjct:   123 SGHIQKYCTQVKCYRCGEIGHVAINCRKMNEVNCYRCGESGHLTRECPI 171

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

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

 Score = 273 (101.2 bits), Expect = 8.7e-24, P = 8.7e-24
 Identities = 53/165 (32%), Positives = 81/165 (49%)

Query:     5 STIQCYNCFDFGHYQYSCPQKSSAD----ARG-------DKVGIVCYKCNNYGHFARECA 53
             S+ +C+ C   GH+   CP          +RG         +  +CY+C   GH A++C 
Sbjct:     2 SSNECFKCGRSGHWARECPTGGGRGRGMRSRGRGFQFVSSSLPDICYRCGESGHLAKDCD 61

Query:    54 TESVTCYNCSGQGHVAKDCTV---KSSIICYNCNSSGHFARNCPNDSSKRCYACHQAGHM 110
              +   CYNC   GH+AKDC     +    CYNC   GH AR+C +   ++CY+C + GH+
Sbjct:    62 LQEDACYNCGRGGHIAKDCKEPKREREQCCYNCGKPGHLARDCDHADEQKCYSCGEFGHI 121

Query:   111 AKECPG---QTAGKSPEPVVDMSLT----CYVCGHQGHLSYDCKL 148
              K+C        G++    ++ S T    CY CG  GHL+ +C +
Sbjct:   122 QKDCTKVKCYRCGETGHVAINCSKTSEVNCYRCGESGHLARECTI 166

GO:0005783 "endoplasmic reticulum" evidence=IEA

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

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

GO:0005829 "cytosol" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

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

GO:0003677 "DNA binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

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

 Score = 272 (100.8 bits), Expect = 1.1e-23, P = 1.1e-23
 Identities = 54/167 (32%), Positives = 83/167 (49%)

Query:     5 STIQCYNCFDFGHYQYSCP----QKSSADARGDKVGI---------VCYKCNNYGHFARE 51
             S+ +C+ C   GH+   CP    +     +RG + G          +CY+C   GH A++
Sbjct:     2 SSNECFKCGRTGHWARECPTGIGRGRGMRSRG-RAGFQFMSSSLPDICYRCGESGHLAKD 60

Query:    52 CATESVTCYNCSGQGHVAKDCTV---KSSIICYNCNSSGHFARNCPNDSSKRCYACHQAG 108
             C  +   CYNC   GH+AKDC     +    CYNC   GH AR+C +   ++CY+C + G
Sbjct:    61 CDLQEDACYNCGRGGHIAKDCKEPKREREQCCYNCGKPGHLARDCDHADEQKCYSCGEFG 120

Query:   109 HMAKECPG---QTAGKSPEPVVDMSLT----CYVCGHQGHLSYDCKL 148
             H+ K+C        G++    ++ S T    CY CG  GHL+ +C +
Sbjct:   121 HIQKDCTKVKCYRCGETGHVAINCSKTSEVNCYRCGESGHLARECTI 167

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005783 "endoplasmic reticulum" evidence=IEA

GO:0005829 "cytosol" evidence=IEA

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

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

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

 Score = 259 (96.2 bits), Expect = 2.6e-22, P = 2.6e-22
 Identities = 44/121 (36%), Positives = 66/121 (54%)

Query:    38 VCYKCNNYGHFARECATESVTCYNCSGQGHVAKDCTV---KSSIICYNCNSSGHFARNCP 94
             +CY+C   GH A++C  +   CYNC   GH+AKDC     +    CYNC   GH AR+C 
Sbjct:    53 ICYRCGESGHLAKDCDLQEDACYNCGRGGHIAKDCKEPKREREQCCYNCGKPGHLARDCD 112

Query:    95 NDSSKRCYACHQAGHMAKECPG---QTAGKSPEPVVDMSLT----CYVCGHQGHLSYDCK 147
             +   ++CY+C + GH+ K+C        G++    ++ S T    CY CG  GHL+ +C 
Sbjct:   113 HADEQKCYSCGEFGHIQKDCTKVKCYRCGETGHVAINCSKTSEVNCYRCGESGHLARECT 172

Query:   148 L 148
             +
Sbjct:   173 I 173

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

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

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

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

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

GO:0005634 "nucleus" evidence=ISS

GO:0005783 "endoplasmic reticulum" evidence=ISS

GO:0005829 "cytosol" evidence=ISS

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

GO:0006695 "cholesterol biosynthetic process" evidence=TAS

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

UNIPROTKB|Q4R501 Q4R501 "Brain cDNA, clone: QnpA-14556, similar to human zinc finger protein 9 (a cellular retroviral nucleicacid binding protein) (ZNF9)," [Macaca fascicularis (taxid:9541)]

 Score = 259 (96.2 bits), Expect = 2.6e-22, P = 2.6e-22
 Identities = 44/121 (36%), Positives = 66/121 (54%)

Query:    38 VCYKCNNYGHFARECATESVTCYNCSGQGHVAKDCTV---KSSIICYNCNSSGHFARNCP 94
             +CY+C   GH A++C  +   CYNC   GH+AKDC     +    CYNC   GH AR+C 
Sbjct:    53 ICYRCGESGHLAKDCDLQEDACYNCGRGGHIAKDCKEPKREREQCCYNCGKPGHLARDCD 112

Query:    95 NDSSKRCYACHQAGHMAKECPG---QTAGKSPEPVVDMSLT----CYVCGHQGHLSYDCK 147
             +   ++CY+C + GH+ K+C        G++    ++ S T    CY CG  GHL+ +C 
Sbjct:   113 HADEQKCYSCGEFGHIQKDCTKVKCYRCGETGHVAINCSKTSEVNCYRCGESGHLARECT 172

Query:   148 L 148
             +
Sbjct:   173 I 173

GO:0005634 "nucleus" evidence=ISS

GO:0005783 "endoplasmic reticulum" evidence=ISS

GO:0005829 "cytosol" evidence=ISS

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

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

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

UNIPROTKB|Q5R5R5 CNBP "Cellular nucleic acid-binding protein" [Pongo abelii (taxid:9601)]

 Score = 259 (96.2 bits), Expect = 2.6e-22, P = 2.6e-22
 Identities = 44/121 (36%), Positives = 66/121 (54%)

Query:    38 VCYKCNNYGHFARECATESVTCYNCSGQGHVAKDCTV---KSSIICYNCNSSGHFARNCP 94
             +CY+C   GH A++C  +   CYNC   GH+AKDC     +    CYNC   GH AR+C 
Sbjct:    53 ICYRCGESGHLAKDCDLQEDACYNCGRGGHIAKDCKEPKREREQCCYNCGKPGHLARDCD 112

Query:    95 NDSSKRCYACHQAGHMAKECPG---QTAGKSPEPVVDMSLT----CYVCGHQGHLSYDCK 147
             +   ++CY+C + GH+ K+C        G++    ++ S T    CY CG  GHL+ +C 
Sbjct:   113 HADEQKCYSCGEFGHIQKDCTKVKCYRCGETGHVAINCSKTSEVNCYRCGESGHLARECT 172

Query:   148 L 148
             +
Sbjct:   173 I 173

GO:0005634 "nucleus" evidence=ISS

GO:0005783 "endoplasmic reticulum" evidence=ISS

GO:0005829 "cytosol" evidence=ISS

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

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

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

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
P53849	GIS2_YEAST	No assigned EC number	0.3728	0.6184	0.6143	yes	N/A
Q5R5R5	CNBP_PONAB	No assigned EC number	0.3023	0.9473	0.8135	yes	N/A
P62634	CNBP_RAT	No assigned EC number	0.3023	0.9473	0.8135	yes	N/A
P62633	CNBP_HUMAN	No assigned EC number	0.3023	0.9473	0.8135	yes	N/A
P53996	CNBP_MOUSE	No assigned EC number	0.3063	0.9473	0.8089	yes	N/A
P36627	BYR3_SCHPO	No assigned EC number	0.3809	0.7565	0.6424	yes	N/A
O42395	CNBP_CHICK	No assigned EC number	0.3053	0.9473	0.8372	yes	N/A
Q3T0Q6	CNBP_BOVIN	No assigned EC number	0.3030	0.9473	0.8470	yes	N/A

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	152
PTZ00368	148	PTZ00368, PTZ00368, universal minicircle sequence	6e-22
PTZ00368	148	PTZ00368, PTZ00368, universal minicircle sequence	3e-20
PTZ00368	148	PTZ00368, PTZ00368, universal minicircle sequence	2e-18
COG5082	190	COG5082, AIR1, Arginine methyltransferase-interact	6e-17
COG5082	190	COG5082, AIR1, Arginine methyltransferase-interact	8e-12
COG5082	190	COG5082, AIR1, Arginine methyltransferase-interact	3e-11
PTZ00368	148	PTZ00368, PTZ00368, universal minicircle sequence	8e-08
COG5082	190	COG5082, AIR1, Arginine methyltransferase-interact	4e-05

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

 Score = 85.2 bits (211), Expect = 6e-22
 Identities = 57/153 (37%), Positives = 72/153 (47%), Gaps = 23/153 (15%)

Query: 9   CYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFAREC-----ATESVTCYNCS 63
           CY C   GH    CP  + A A        CYKC   GH +REC          +CYNC 
Sbjct: 3   CYRCGGVGHQSRECPNSAPAGAAK---ARPCYKCGEPGHLSRECPSAPGGRGERSCYNCG 59

Query: 64  GQGHVAKDC----TVKSSIICYNCNSSGHFARNCPNDSS-----KRCYACHQAGHMAKEC 114
             GH++++C           CYNC  +GH +R CPN +      + CY C   GH++++C
Sbjct: 60  KTGHLSRECPEAPPGSGPRSCYNCGQTGHISRECPNRAKGGAARRACYNCGGEGHISRDC 119

Query: 115 PGQTAGKSPEPVVDMSLTCYVCGHQGHLSYDCK 147
           P   AGK P        TCY CG  GHLS DC 
Sbjct: 120 P--NAGKRPGG----DKTCYNCGQTGHLSRDCP 146

Length = 148

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

 Score = 81.0 bits (200), Expect = 3e-20
 Identities = 44/130 (33%), Positives = 63/130 (48%), Gaps = 20/130 (15%)

Query: 1   MSSTSTIQCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFAREC-----ATE 55
             +     CY C + GH    CP  S+   RG++    CY C   GH +REC      + 
Sbjct: 22  AGAAKARPCYKCGEPGHLSRECP--SAPGGRGER---SCYNCGKTGHLSRECPEAPPGSG 76

Query: 56  SVTCYNCSGQGHVAKDCT-----VKSSIICYNCNSSGHFARNCPNDSS-----KRCYACH 105
             +CYNC   GH++++C        +   CYNC   GH +R+CPN        K CY C 
Sbjct: 77  PRSCYNCGQTGHISRECPNRAKGGAARRACYNCGGEGHISRDCPNAGKRPGGDKTCYNCG 136

Query: 106 QAGHMAKECP 115
           Q GH++++CP
Sbjct: 137 QTGHLSRDCP 146

Length = 148

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

 Score = 76.0 bits (187), Expect = 2e-18
 Identities = 44/124 (35%), Positives = 62/124 (50%), Gaps = 21/124 (16%)

Query: 38  VCYKCNNYGHFAREC-------ATESVTCYNCSGQGHVAKDCTVKSSII----CYNCNSS 86
           VCY+C   GH +REC       A ++  CY C   GH++++C           CYNC  +
Sbjct: 2   VCYRCGGVGHQSRECPNSAPAGAAKARPCYKCGEPGHLSRECPSAPGGRGERSCYNCGKT 61

Query: 87  GHFARNCPN----DSSKRCYACHQAGHMAKECPGQTAGKSPEPVVDMSLTCYVCGHQGHL 142
           GH +R CP        + CY C Q GH+++ECP +  G +          CY CG +GH+
Sbjct: 62  GHLSRECPEAPPGSGPRSCYNCGQTGHISRECPNRAKGGAARR------ACYNCGGEGHI 115

Query: 143 SYDC 146
           S DC
Sbjct: 116 SRDC 119

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 = 73.3 bits (180), Expect = 6e-17
 Identities = 39/117 (33%), Positives = 53/117 (45%), Gaps = 8/117 (6%)

Query: 36  GIVCYKCNNYGHFARECATESVTCYNCSGQGHVAKDCTVKSSIICYNCNSSGHFARNCP- 94
             VC+ C   GH  R+C      CYNCS  GH +  C       CYNC  +GH +R+C  
Sbjct: 60  NPVCFNCGQNGHLRRDC--PHSICYNCSWDGHRSNHCPKP--KKCYNCGETGHLSRDCNP 115

Query: 95  -NDSSKRCYACHQAGHMAKECP--GQTAGKSPEPVVDMSLTCYVCGHQGHLSYDCKL 148
             D  K C+ C+   H +++CP   +    +      +   CY CG  GH   DCK 
Sbjct: 116 SKDQQKSCFDCNSTRHSSEDCPSIWKHYVLNNGDGHPIKKFCYSCGSAGHFGDDCKE 172

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 = 59.9 bits (145), Expect = 8e-12
 Identities = 32/94 (34%), Positives = 47/94 (50%), Gaps = 14/94 (14%)

Query: 59  CYNCSGQGHVAKDCTVKSSIICYNCNSSGHFARNCPNDSSKRCYACHQAGHMAKECPGQT 118
           C+NC   GH+ +DC      ICYNC+  GH + +CP    K+CY C + GH++++C    
Sbjct: 63  CFNCGQNGHLRRDCP---HSICYNCSWDGHRSNHCP--KPKKCYNCGETGHLSRDCN--- 114

Query: 119 AGKSPEPVVDMSLTCYVCGHQGHLSYDCKLVQKS 152
                 P  D   +C+ C    H S DC  + K 
Sbjct: 115 ------PSKDQQKSCFDCNSTRHSSEDCPSIWKH 142

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 = 58.3 bits (141), Expect = 3e-11
 Identities = 33/119 (27%), Positives = 50/119 (42%), Gaps = 28/119 (23%)

Query: 9   CYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFARECA---TESVTCYNCSGQ 65
           CYNC   GH    CP+              CY C   GH +R+C     +  +C++C+  
Sbjct: 81  CYNCSWDGHRSNHCPKP-----------KKCYNCGETGHLSRDCNPSKDQQKSCFDCNST 129

Query: 66  GHVAKDC-------------TVKSSIICYNCNSSGHFARNC-PNDSSKRCYACHQAGHM 110
            H ++DC                    CY+C S+GHF  +C    SS+  Y C + G++
Sbjct: 130 RHSSEDCPSIWKHYVLNNGDGHPIKKFCYSCGSAGHFGDDCKEPRSSRVPYVCGKKGYV 188

Length = 190

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

 Score = 48.3 bits (115), Expect = 8e-08
 Identities = 26/78 (33%), Positives = 34/78 (43%), Gaps = 10/78 (12%)

Query: 4   TSTIQCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFARECATESV------ 57
           +    CYNC   GH    CP ++   A        CY C   GH +R+C           
Sbjct: 75  SGPRSCYNCGQTGHISRECPNRAKGGAARRA----CYNCGGEGHISRDCPNAGKRPGGDK 130

Query: 58  TCYNCSGQGHVAKDCTVK 75
           TCYNC   GH+++DC  K
Sbjct: 131 TCYNCGQTGHLSRDCPDK 148

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 = 41.4 bits (97), Expect = 4e-05
 Identities = 23/103 (22%), Positives = 33/103 (32%), Gaps = 22/103 (21%)

Query: 4   TSTIQCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFAREC----------- 52
               +CYNC + GH    C                C+ CN+  H + +C           
Sbjct: 95  PKPKKCYNCGETGHLSRDCNPSKD-------QQKSCFDCNSTRHSSEDCPSIWKHYVLNN 147

Query: 53  ---ATESVTCYNCSGQGHVAKDCTVKSSI-ICYNCNSSGHFAR 91
                    CY+C   GH   DC    S  + Y C   G+ + 
Sbjct: 148 GDGHPIKKFCYSCGSAGHFGDDCKEPRSSRVPYVCGKKGYVSF 190

Length = 190

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	152
PTZ00368	148	universal minicircle sequence binding protein (UMS	99.98
PTZ00368	148	universal minicircle sequence binding protein (UMS	99.91
COG5082	190	AIR1 Arginine methyltransferase-interacting protei	99.9
COG5082	190	AIR1 Arginine methyltransferase-interacting protei	99.88
KOG4400|consensus	261		99.67
KOG4400|consensus	261		99.62
PF00098	18	zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc fi	98.37
PF00098	18	zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc fi	98.34
PF13696	32	zf-CCHC_2: Zinc knuckle	96.78
PF13696	32	zf-CCHC_2: Zinc knuckle	96.71
PF13917	42	zf-CCHC_3: Zinc knuckle	96.19
PF13917	42	zf-CCHC_3: Zinc knuckle	95.76
KOG0119|consensus	554		95.69
smart00343	26	ZnF_C2HC zinc finger.	95.13
KOG0119|consensus	554		95.07
smart00343	26	ZnF_C2HC zinc finger.	94.8
PF15288	40	zf-CCHC_6: Zinc knuckle	91.99
PF14392	49	zf-CCHC_4: Zinc knuckle	91.16
PF15288	40	zf-CCHC_6: Zinc knuckle	90.99
PF14392	49	zf-CCHC_4: Zinc knuckle	90.88
PF14787	36	zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB:	89.22
KOG0109|consensus	346		87.21
KOG0109|consensus	346		86.76
PF14787	36	zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB:	84.68
COG5222	427	Uncharacterized conserved protein, contains RING Z	84.51
COG5222	427	Uncharacterized conserved protein, contains RING Z	84.16

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

Probab=99.98  E-value=1.6e-32  Score=200.83  Aligned_cols=134  Identities=39%  Similarity=0.987  Sum_probs=114.8

Q ss_pred             cccccccccCccCCCCCCCCCCCCCCCCCCccceecCCCCcCcccCCCC-----CCcccccCCCCcccccCCCC----CC
Q psy16574          7 IQCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFARECATE-----SVTCYNCSGQGHVAKDCTVK----SS   77 (152)
Q Consensus         7 ~~C~~C~~~GH~~~~Cp~~~~~~~~~~~~~~~C~~Cg~~GH~~~~Cp~~-----~~~C~~Cg~~GH~~~~Cp~~----~~   77 (152)
                      ++||+|++.||++++||....   .+..+.+.||+|++.||++++||..     ...||+|++.||++.+||..    ..
T Consensus         1 ~~C~~C~~~GH~~~~c~~~~~---~~~~~~~~C~~Cg~~GH~~~~Cp~~~~~~~~~~C~~Cg~~GH~~~~Cp~~~~~~~~   77 (148)
T PTZ00368          1 MVCYRCGGVGHQSRECPNSAP---AGAAKARPCYKCGEPGHLSRECPSAPGGRGERSCYNCGKTGHLSRECPEAPPGSGP   77 (148)
T ss_pred             CcCCCCCCCCcCcccCcCCCC---CCCCCCccCccCCCCCcCcccCcCCCCCCCCcccCCCCCcCcCcccCCCcccCCCC
Confidence            479999999999999998642   1234468999999999999999986     24799999999999999984    24


Q ss_pred             cccccCCCCCCCCCCCCCCC-----CcCCcccCCCCcCCCCCCCCCCCCCCCccccccccccccccccccCCCCCCC
Q psy16574         78 IICYNCNSSGHFARNCPNDS-----SKRCYACHQAGHMAKECPGQTAGKSPEPVVDMSLTCYVCGHQGHLSYDCKLV  149 (152)
Q Consensus        78 ~~C~~Cg~~GH~~~~Cp~~~-----~~~C~~C~~~GH~~~~Cp~~~~~~~~~~~~~~~~~C~~Cg~~GH~~~~C~~~  149 (152)
                      ..|++|++.||++++||+.+     ...||+|++.||++++||+.|...      ...++||+|++.|||++|||++
T Consensus        78 ~~C~~Cg~~GH~~~~C~~~~~~~~~~~~C~~Cg~~gH~~~~C~~~~~~~------~~~~~C~~Cg~~gH~~~dCp~~  148 (148)
T PTZ00368         78 RSCYNCGQTGHISRECPNRAKGGAARRACYNCGGEGHISRDCPNAGKRP------GGDKTCYNCGQTGHLSRDCPDK  148 (148)
T ss_pred             cccCcCCCCCcccccCCCcccccccchhhcccCcCCcchhcCCCccccC------CCCCccccCCCcCcccccCCCC
Confidence            58999999999999999965     358999999999999999986422      2357999999999999999974

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

Probab=99.91  E-value=8.5e-25  Score=159.95  Aligned_cols=107  Identities=38%  Similarity=1.057  Sum_probs=93.5

Q ss_pred             CccccccccccCccCCCCCCCCCCCCCCCCCCccceecCCCCcCcccCCCC-----CCcccccCCCCcccccCCCCC---
Q psy16574          5 STIQCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFARECATE-----SVTCYNCSGQGHVAKDCTVKS---   76 (152)
Q Consensus         5 ~~~~C~~C~~~GH~~~~Cp~~~~~~~~~~~~~~~C~~Cg~~GH~~~~Cp~~-----~~~C~~Cg~~GH~~~~Cp~~~---   76 (152)
                      ....||+|+++||++++||.....     .....|++|++.||++++||..     ...||+|++.||++++||+..   
T Consensus        26 ~~~~C~~Cg~~GH~~~~Cp~~~~~-----~~~~~C~~Cg~~GH~~~~Cp~~~~~~~~~~C~~Cg~~GH~~~~C~~~~~~~  100 (148)
T PTZ00368         26 KARPCYKCGEPGHLSRECPSAPGG-----RGERSCYNCGKTGHLSRECPEAPPGSGPRSCYNCGQTGHISRECPNRAKGG  100 (148)
T ss_pred             CCccCccCCCCCcCcccCcCCCCC-----CCCcccCCCCCcCcCcccCCCcccCCCCcccCcCCCCCcccccCCCccccc
Confidence            456899999999999999987421     1346899999999999999986     347999999999999999842   


Q ss_pred             --CcccccCCCCCCCCCCCCCCC-----CcCCcccCCCCcCCCCCCC
Q psy16574         77 --SIICYNCNSSGHFARNCPNDS-----SKRCYACHQAGHMAKECPG  116 (152)
Q Consensus        77 --~~~C~~Cg~~GH~~~~Cp~~~-----~~~C~~C~~~GH~~~~Cp~  116 (152)
                        ...|++|++.||++++||+.+     .+.||+|++.|||++|||+
T Consensus       101 ~~~~~C~~Cg~~gH~~~~C~~~~~~~~~~~~C~~Cg~~gH~~~dCp~  147 (148)
T PTZ00368        101 AARRACYNCGGEGHISRDCPNAGKRPGGDKTCYNCGQTGHLSRDCPD  147 (148)
T ss_pred             ccchhhcccCcCCcchhcCCCccccCCCCCccccCCCcCcccccCCC
Confidence              458999999999999999963     5799999999999999997

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

Probab=99.90  E-value=4.6e-24  Score=159.65  Aligned_cols=112  Identities=35%  Similarity=0.891  Sum_probs=96.9

Q ss_pred             CccceecCCCCcCcccCCCCCCcccccCCCCcccccCCCCCCcccccCCCCCCCCCCC-CCCC-CcCCcccCCCCcCCCC
Q psy16574         36 GIVCYKCNNYGHFARECATESVTCYNCSGQGHVAKDCTVKSSIICYNCNSSGHFARNC-PNDS-SKRCYACHQAGHMAKE  113 (152)
Q Consensus        36 ~~~C~~Cg~~GH~~~~Cp~~~~~C~~Cg~~GH~~~~Cp~~~~~~C~~Cg~~GH~~~~C-p~~~-~~~C~~C~~~GH~~~~  113 (152)
                      ..+||+||+.||++++||.  .+||+|...||.+..||.  .+.|++||+.||++++| |.++ .+.|+.|...+|++++
T Consensus        60 ~~~C~nCg~~GH~~~DCP~--~iC~~C~~~~H~s~~C~~--~~~C~~Cg~~GH~~~dC~P~~~~~~~C~~C~s~~H~s~~  135 (190)
T COG5082          60 NPVCFNCGQNGHLRRDCPH--SICYNCSWDGHRSNHCPK--PKKCYNCGETGHLSRDCNPSKDQQKSCFDCNSTRHSSED  135 (190)
T ss_pred             ccccchhcccCcccccCCh--hHhhhcCCCCcccccCCc--ccccccccccCccccccCcccccCcceeccCCCcccccc
Confidence            5789999999999999994  599999889999999999  48999999999999999 6766 5689999999999999


Q ss_pred             CCCCCCCCCCC--ccccccccccccccccccCCCCCCCcC
Q psy16574        114 CPGQTAGKSPE--PVVDMSLTCYVCGHQGHLSYDCKLVQK  151 (152)
Q Consensus       114 Cp~~~~~~~~~--~~~~~~~~C~~Cg~~GH~~~~C~~~~~  151 (152)
                      ||+.|+.+...  ......++||+|+..+||+.||++...
T Consensus       136 Cp~~~k~y~~~~~~~~~~~~~cy~c~~~~H~~~dc~~~~~  175 (190)
T COG5082         136 CPSIWKHYVLNNGDGHPIKKFCYSCGSAGHFGDDCKEPRS  175 (190)
T ss_pred             CcccccccccccCCCcceeeeccccCCccccCCCCCCCcc
Confidence            99999765322  233446799999999999999997654

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

Probab=99.88  E-value=7.9e-23  Score=153.03  Aligned_cols=117  Identities=37%  Similarity=0.939  Sum_probs=102.3

Q ss_pred             CCccccccccccCccCCCCCCCCCCCCCCCCCCccceecCCCCcCcccCCCCCCcccccCCCCcccccC-CCC-CCcccc
Q psy16574          4 TSTIQCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFARECATESVTCYNCSGQGHVAKDC-TVK-SSIICY   81 (152)
Q Consensus         4 ~~~~~C~~C~~~GH~~~~Cp~~~~~~~~~~~~~~~C~~Cg~~GH~~~~Cp~~~~~C~~Cg~~GH~~~~C-p~~-~~~~C~   81 (152)
                      +.+.+||+|++.||+++||| .           .+|++|...||.+..||.. .+|++||+.||++++| |.+ ....|+
T Consensus        58 ~~~~~C~nCg~~GH~~~DCP-~-----------~iC~~C~~~~H~s~~C~~~-~~C~~Cg~~GH~~~dC~P~~~~~~~C~  124 (190)
T COG5082          58 EENPVCFNCGQNGHLRRDCP-H-----------SICYNCSWDGHRSNHCPKP-KKCYNCGETGHLSRDCNPSKDQQKSCF  124 (190)
T ss_pred             ccccccchhcccCcccccCC-h-----------hHhhhcCCCCcccccCCcc-cccccccccCccccccCcccccCccee
Confidence            56789999999999999999 3           4899998899999999998 8999999999999999 565 456999


Q ss_pred             cCCCCCCCCCCCCCCC-------------CcCCcccCCCCcCCCCCCCCCCCCCCCccccccccccccccccccC
Q psy16574         82 NCNSSGHFARNCPNDS-------------SKRCYACHQAGHMAKECPGQTAGKSPEPVVDMSLTCYVCGHQGHLS  143 (152)
Q Consensus        82 ~Cg~~GH~~~~Cp~~~-------------~~~C~~C~~~GH~~~~Cp~~~~~~~~~~~~~~~~~C~~Cg~~GH~~  143 (152)
                      .|...+|++++||..|             .+.||+|+..+|++.||+..|+...         . |.++..+|+.
T Consensus       125 ~C~s~~H~s~~Cp~~~k~y~~~~~~~~~~~~~cy~c~~~~H~~~dc~~~~~s~~---------~-~~~~~~~~~~  189 (190)
T COG5082         125 DCNSTRHSSEDCPSIWKHYVLNNGDGHPIKKFCYSCGSAGHFGDDCKEPRSSRV---------P-YVCGKKGYVS  189 (190)
T ss_pred             ccCCCccccccCcccccccccccCCCcceeeeccccCCccccCCCCCCCccccc---------c-ccccccccCC
Confidence            9999999999999988             4789999999999999999985432         1 6677776653

>KOG4400|consensus

Probab=99.67  E-value=1.8e-16  Score=125.65  Aligned_cols=137  Identities=33%  Similarity=0.804  Sum_probs=103.3

Q ss_pred             CCccccccccccCccCCCCCCCCCCC---C---CC------------CCCCccceecCCCCcCcccCCCCCCcccccCCC
Q psy16574          4 TSTIQCYNCFDFGHYQYSCPQKSSAD---A---RG------------DKVGIVCYKCNNYGHFARECATESVTCYNCSGQ   65 (152)
Q Consensus         4 ~~~~~C~~C~~~GH~~~~Cp~~~~~~---~---~~------------~~~~~~C~~Cg~~GH~~~~Cp~~~~~C~~Cg~~   65 (152)
                      ++...++++++.+|.+..++......   .   .+            ......|+.|++.||.+.+|+.....|++|++.
T Consensus        22 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~c~~~g~~~~~~~~~~~~~~~c~~C~~~  101 (261)
T KOG4400|consen   22 DSSPNELKCLKSGHKAVSCTDGDSRGDSSKSDGPGCVSTSPNGPLKSECPEVSCYICGEKGHLGRRCTRIAAACFNCGEG  101 (261)
T ss_pred             ccchhhhhhccccCcceecccCCcccccccCCCCcccccccCcccCCCCCCceeeecCCCCchhhcCcccchhhhhCCCC
Confidence            45567888899999998888764321   0   00            123677999999999999998755789999999


Q ss_pred             CcccccCCCCC-----CcccccCCCCCCCC-CCCCCCC---CcCCcccCCCCcCCCCCCCCCCCCCCCcccccccccccc
Q psy16574         66 GHVAKDCTVKS-----SIICYNCNSSGHFA-RNCPNDS---SKRCYACHQAGHMAKECPGQTAGKSPEPVVDMSLTCYVC  136 (152)
Q Consensus        66 GH~~~~Cp~~~-----~~~C~~Cg~~GH~~-~~Cp~~~---~~~C~~C~~~GH~~~~Cp~~~~~~~~~~~~~~~~~C~~C  136 (152)
                      ||++++||...     ...|+.|+..+|.. .++....   .+.||+|++.||+..+||+.           ....||.|
T Consensus       102 gH~~~~c~~~~~~~~~~~~~~~c~~~gh~~~~~~~~~~~~~~~~Cy~Cg~~GH~s~~C~~~-----------~~~~c~~c  170 (261)
T KOG4400|consen  102 GHIERDCPEAGKEGSSETSCYSCGKTGHRGCPDADPVDGPKPAKCYSCGEQGHISDDCPEN-----------KGGTCFRC  170 (261)
T ss_pred             ccchhhCCcccCcccccceeeccCCCccccCcccccccCCCCCccCCCCcCCcchhhCCCC-----------CCCccccC
Confidence            99999998862     23588999999988 3333222   25699999999999999876           13689999


Q ss_pred             ccccccCCCCCCCcC
Q psy16574        137 GHQGHLSYDCKLVQK  151 (152)
Q Consensus       137 g~~GH~~~~C~~~~~  151 (152)
                      ++.||.+.|||..+.
T Consensus       171 ~~~~h~~~~C~~~~~  185 (261)
T KOG4400|consen  171 GKVGHGSRDCPSKQK  185 (261)
T ss_pred             CCcceecccCCcccc
Confidence            999999999998764

>KOG4400|consensus

Probab=99.62  E-value=1.1e-15  Score=121.20  Aligned_cols=105  Identities=30%  Similarity=0.896  Sum_probs=84.2

Q ss_pred             CccccccccccCccCCCCCCCCCCCCCCCCCCccceecCCCCcCcccCCCC--C----CcccccCCCCccc-ccCCCC-C
Q psy16574          5 STIQCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFARECATE--S----VTCYNCSGQGHVA-KDCTVK-S   76 (152)
Q Consensus         5 ~~~~C~~C~~~GH~~~~Cp~~~~~~~~~~~~~~~C~~Cg~~GH~~~~Cp~~--~----~~C~~Cg~~GH~~-~~Cp~~-~   76 (152)
                      ..+.|+.|++.||.+++|+..          ...|++|++.||++++||..  .    ..||.|+..||.. .++... .
T Consensus        71 ~~~~c~~~g~~~~~~~~~~~~----------~~~c~~C~~~gH~~~~c~~~~~~~~~~~~~~~c~~~gh~~~~~~~~~~~  140 (261)
T KOG4400|consen   71 PEVSCYICGEKGHLGRRCTRI----------AAACFNCGEGGHIERDCPEAGKEGSSETSCYSCGKTGHRGCPDADPVDG  140 (261)
T ss_pred             CCceeeecCCCCchhhcCccc----------chhhhhCCCCccchhhCCcccCcccccceeeccCCCccccCcccccccC
Confidence            456799999999999999873          35899999999999999988  2    2578999999998 333221 1


Q ss_pred             --CcccccCCCCCCCCCCCCCCCCcCCcccCCCCcCCCCCCCCCC
Q psy16574         77 --SIICYNCNSSGHFARNCPNDSSKRCYACHQAGHMAKECPGQTA  119 (152)
Q Consensus        77 --~~~C~~Cg~~GH~~~~Cp~~~~~~C~~C~~~GH~~~~Cp~~~~  119 (152)
                        ...||+|++.||+..+||+.....|+.|++.+|++.+||..+.
T Consensus       141 ~~~~~Cy~Cg~~GH~s~~C~~~~~~~c~~c~~~~h~~~~C~~~~~  185 (261)
T KOG4400|consen  141 PKPAKCYSCGEQGHISDDCPENKGGTCFRCGKVGHGSRDCPSKQK  185 (261)
T ss_pred             CCCCccCCCCcCCcchhhCCCCCCCccccCCCcceecccCCcccc
Confidence              1569999999999999995434789999999999999999874

>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=98.37  E-value=1.8e-07  Score=44.67  Aligned_cols=17  Identities=41%  Similarity=1.194  Sum_probs=11.9

Q ss_pred             cccccccccccCCCCCC
Q psy16574        132 TCYVCGHQGHLSYDCKL  148 (152)
Q Consensus       132 ~C~~Cg~~GH~~~~C~~  148 (152)
                      .||+|++.||+++|||+
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            57777777777777764

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

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

Probab=98.34  E-value=2.4e-07  Score=44.22  Aligned_cols=16  Identities=44%  Similarity=1.177  Sum_probs=10.0

Q ss_pred             ccccccccCccCCCCC
Q psy16574          8 QCYNCFDFGHYQYSCP   23 (152)
Q Consensus         8 ~C~~C~~~GH~~~~Cp   23 (152)
                      +||+|++.||++++||
T Consensus         2 ~C~~C~~~GH~~~~Cp   17 (18)
T PF00098_consen    2 KCFNCGEPGHIARDCP   17 (18)
T ss_dssp             BCTTTSCSSSCGCTSS
T ss_pred             cCcCCCCcCcccccCc
Confidence            4666666666666665

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

>PF13696 zf-CCHC_2: Zinc knuckle

Probab=96.78  E-value=0.0005  Score=37.34  Aligned_cols=19  Identities=32%  Similarity=0.786  Sum_probs=11.6

Q ss_pred             cccccccccCccCCCCCCC
Q psy16574          7 IQCYNCFDFGHYQYSCPQK   25 (152)
Q Consensus         7 ~~C~~C~~~GH~~~~Cp~~   25 (152)
                      -+|+.|++.||+.++||..
T Consensus         9 Y~C~~C~~~GH~i~dCP~~   27 (32)
T PF13696_consen    9 YVCHRCGQKGHWIQDCPTN   27 (32)
T ss_pred             CEeecCCCCCccHhHCCCC
Confidence            3566666666666666653

>PF13696 zf-CCHC_2: Zinc knuckle

Probab=96.71  E-value=0.00065  Score=36.91  Aligned_cols=20  Identities=35%  Similarity=0.816  Sum_probs=17.1

Q ss_pred             cccccccccccccCCCCCCC
Q psy16574        130 SLTCYVCGHQGHLSYDCKLV  149 (152)
Q Consensus       130 ~~~C~~Cg~~GH~~~~C~~~  149 (152)
                      .-.|+.|++.||+..|||+.
T Consensus         8 ~Y~C~~C~~~GH~i~dCP~~   27 (32)
T PF13696_consen    8 GYVCHRCGQKGHWIQDCPTN   27 (32)
T ss_pred             CCEeecCCCCCccHhHCCCC
Confidence            45899999999999999984

>PF13917 zf-CCHC_3: Zinc knuckle

Probab=96.19  E-value=0.0025  Score=36.85  Aligned_cols=21  Identities=33%  Similarity=1.031  Sum_probs=13.9

Q ss_pred             CCccccccccccCccCCCCCC
Q psy16574          4 TSTIQCYNCFDFGHYQYSCPQ   24 (152)
Q Consensus         4 ~~~~~C~~C~~~GH~~~~Cp~   24 (152)
                      ++...|.+|++.||++.+||.
T Consensus         2 ~~~~~CqkC~~~GH~tyeC~~   22 (42)
T PF13917_consen    2 NARVRCQKCGQKGHWTYECPN   22 (42)
T ss_pred             CCCCcCcccCCCCcchhhCCC
Confidence            445667777777777777773

>PF13917 zf-CCHC_3: Zinc knuckle

Probab=95.76  E-value=0.005  Score=35.57  Aligned_cols=18  Identities=39%  Similarity=1.204  Sum_probs=12.6

Q ss_pred             cccccccccccccCCCCC
Q psy16574        130 SLTCYVCGHQGHLSYDCK  147 (152)
Q Consensus       130 ~~~C~~Cg~~GH~~~~C~  147 (152)
                      ...|.+|++.||+..+|+
T Consensus         4 ~~~CqkC~~~GH~tyeC~   21 (42)
T PF13917_consen    4 RVRCQKCGQKGHWTYECP   21 (42)
T ss_pred             CCcCcccCCCCcchhhCC
Confidence            356777777777777777

>KOG0119|consensus

Probab=95.69  E-value=0.0072  Score=51.76  Aligned_cols=39  Identities=31%  Similarity=0.766  Sum_probs=26.3

Q ss_pred             CccceecCCCCcCcccCCCC----CCcccccCCCCcccccCCC
Q psy16574         36 GIVCYKCNNYGHFARECATE----SVTCYNCSGQGHVAKDCTV   74 (152)
Q Consensus        36 ~~~C~~Cg~~GH~~~~Cp~~----~~~C~~Cg~~GH~~~~Cp~   74 (152)
                      ..+|.+|+..||...+||.+    ..+|+.|+..||++.+|+.
T Consensus       261 ~~~c~~cg~~~H~q~~cp~r~~~~~n~c~~cg~~gH~~~dc~~  303 (554)
T KOG0119|consen  261 NRACRNCGSTGHKQYDCPGRIPNTTNVCKICGPLGHISIDCKV  303 (554)
T ss_pred             cccccccCCCccccccCCcccccccccccccCCcccccccCCC
Confidence            35777777777777777766    2366666666666666655

>smart00343 ZnF_C2HC zinc finger

Probab=95.13  E-value=0.0097  Score=30.49  Aligned_cols=17  Identities=47%  Similarity=1.288  Sum_probs=12.6

Q ss_pred             cccccccccccCCCCCC
Q psy16574        132 TCYVCGHQGHLSYDCKL  148 (152)
Q Consensus       132 ~C~~Cg~~GH~~~~C~~  148 (152)
                      .|++|++.||++.+|++
T Consensus         1 ~C~~CG~~GH~~~~C~~   17 (26)
T smart00343        1 KCYNCGKEGHIARDCPK   17 (26)
T ss_pred             CCccCCCCCcchhhCCc
Confidence            37778888888888773

>KOG0119|consensus

Probab=95.07  E-value=0.019  Score=49.25  Aligned_cols=47  Identities=32%  Similarity=0.726  Sum_probs=38.8

Q ss_pred             CCCccccccccccCccCCCCCCCCCCCCCCCCCCccceecCCCCcCcccCCCC
Q psy16574          3 STSTIQCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFARECATE   55 (152)
Q Consensus         3 ~~~~~~C~~C~~~GH~~~~Cp~~~~~~~~~~~~~~~C~~Cg~~GH~~~~Cp~~   55 (152)
                      ...+.+|.+|+..||-.-+||.....      ...+|++|+..||++.+|+..
T Consensus       258 ~~d~~~c~~cg~~~H~q~~cp~r~~~------~~n~c~~cg~~gH~~~dc~~~  304 (554)
T KOG0119|consen  258 DDDNRACRNCGSTGHKQYDCPGRIPN------TTNVCKICGPLGHISIDCKVN  304 (554)
T ss_pred             ccccccccccCCCccccccCCccccc------ccccccccCCcccccccCCCc
Confidence            34457999999999999999997321      123899999999999999976

>smart00343 ZnF_C2HC zinc finger

Probab=94.80  E-value=0.013  Score=29.98  Aligned_cols=17  Identities=47%  Similarity=1.145  Sum_probs=11.5

Q ss_pred             ccccccccCccCCCCCC
Q psy16574          8 QCYNCFDFGHYQYSCPQ   24 (152)
Q Consensus         8 ~C~~C~~~GH~~~~Cp~   24 (152)
                      .|++|++.||++++||.
T Consensus         1 ~C~~CG~~GH~~~~C~~   17 (26)
T smart00343        1 KCYNCGKEGHIARDCPK   17 (26)
T ss_pred             CCccCCCCCcchhhCCc
Confidence            36677777777777763

>PF15288 zf-CCHC_6: Zinc knuckle

Probab=91.99  E-value=0.094  Score=29.89  Aligned_cols=20  Identities=40%  Similarity=0.974  Sum_probs=14.3

Q ss_pred             cccccccccCccC--CCCCCCC
Q psy16574          7 IQCYNCFDFGHYQ--YSCPQKS   26 (152)
Q Consensus         7 ~~C~~C~~~GH~~--~~Cp~~~   26 (152)
                      +.|.+||+.||++  +.||...
T Consensus         2 ~kC~~CG~~GH~~t~k~CP~~~   23 (40)
T PF15288_consen    2 VKCKNCGAFGHMRTNKRCPMYC   23 (40)
T ss_pred             ccccccccccccccCccCCCCC
Confidence            4677888888877  4577764

>PF14392 zf-CCHC_4: Zinc knuckle

Probab=91.16  E-value=0.073  Score=31.52  Aligned_cols=19  Identities=32%  Similarity=0.838  Sum_probs=15.6

Q ss_pred             cccccccccccccCCCCCC
Q psy16574        130 SLTCYVCGHQGHLSYDCKL  148 (152)
Q Consensus       130 ~~~C~~Cg~~GH~~~~C~~  148 (152)
                      ..+|++|+..||...+||+
T Consensus        31 p~~C~~C~~~gH~~~~C~k   49 (49)
T PF14392_consen   31 PRFCFHCGRIGHSDKECPK   49 (49)
T ss_pred             ChhhcCCCCcCcCHhHcCC
Confidence            4578889999998888874

>PF15288 zf-CCHC_6: Zinc knuckle

Probab=90.99  E-value=0.16  Score=28.93  Aligned_cols=18  Identities=44%  Similarity=0.984  Sum_probs=10.2

Q ss_pred             cCCcccCCCCcCC--CCCCC
Q psy16574         99 KRCYACHQAGHMA--KECPG  116 (152)
Q Consensus        99 ~~C~~C~~~GH~~--~~Cp~  116 (152)
                      +.|.+||..||+.  +.||.
T Consensus         2 ~kC~~CG~~GH~~t~k~CP~   21 (40)
T PF15288_consen    2 VKCKNCGAFGHMRTNKRCPM   21 (40)
T ss_pred             ccccccccccccccCccCCC
Confidence            4566666666654  34553

>PF14392 zf-CCHC_4: Zinc knuckle

Probab=90.88  E-value=0.08  Score=31.34  Aligned_cols=16  Identities=38%  Similarity=1.061  Sum_probs=9.9

Q ss_pred             ccccccccCccCCCCC
Q psy16574          8 QCYNCFDFGHYQYSCP   23 (152)
Q Consensus         8 ~C~~C~~~GH~~~~Cp   23 (152)
                      .|++|+..||..++||
T Consensus        33 ~C~~C~~~gH~~~~C~   48 (49)
T PF14392_consen   33 FCFHCGRIGHSDKECP   48 (49)
T ss_pred             hhcCCCCcCcCHhHcC
Confidence            4666666666666665

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

Probab=89.22  E-value=0.34  Score=26.90  Aligned_cols=21  Identities=24%  Similarity=0.369  Sum_probs=13.0

Q ss_pred             cccccccccCccCCCCCCCCC
Q psy16574          7 IQCYNCFDFGHYQYSCPQKSS   27 (152)
Q Consensus         7 ~~C~~C~~~GH~~~~Cp~~~~   27 (152)
                      ..|++|++..|++++|.....
T Consensus         3 ~~CprC~kg~Hwa~~C~sk~d   23 (36)
T PF14787_consen    3 GLCPRCGKGFHWASECRSKTD   23 (36)
T ss_dssp             -C-TTTSSSCS-TTT---TCC
T ss_pred             ccCcccCCCcchhhhhhhhhc
Confidence            469999999999999988754

>KOG0109|consensus

Probab=87.21  E-value=0.34  Score=39.33  Aligned_cols=22  Identities=32%  Similarity=0.827  Sum_probs=19.1

Q ss_pred             cccccccccCccCCCCCCCCCC
Q psy16574          7 IQCYNCFDFGHYQYSCPQKSSA   28 (152)
Q Consensus         7 ~~C~~C~~~GH~~~~Cp~~~~~   28 (152)
                      ..|+.||++|||+.+||.....
T Consensus       161 ~~cyrcGkeghwskEcP~~~~~  182 (346)
T KOG0109|consen  161 SGCYRCGKEGHWSKECPVDRTG  182 (346)
T ss_pred             HHheeccccccccccCCccCCC
Confidence            3699999999999999998643

>KOG0109|consensus

Probab=86.76  E-value=0.35  Score=39.24  Aligned_cols=22  Identities=41%  Similarity=1.002  Sum_probs=18.3

Q ss_pred             CcCCcccCCCCcCCCCCCCCCC
Q psy16574         98 SKRCYACHQAGHMAKECPGQTA  119 (152)
Q Consensus        98 ~~~C~~C~~~GH~~~~Cp~~~~  119 (152)
                      ...||.|+++||++++||..+.
T Consensus       160 q~~cyrcGkeghwskEcP~~~~  181 (346)
T KOG0109|consen  160 QSGCYRCGKEGHWSKECPVDRT  181 (346)
T ss_pred             HHHheeccccccccccCCccCC
Confidence            4579999999999999998873

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

Probab=84.68  E-value=0.55  Score=26.06  Aligned_cols=18  Identities=28%  Similarity=0.652  Sum_probs=8.7

Q ss_pred             cccccccccccCCCCCCC
Q psy16574        132 TCYVCGHQGHLSYDCKLV  149 (152)
Q Consensus       132 ~C~~Cg~~GH~~~~C~~~  149 (152)
                      .|++|++-.|.++||..+
T Consensus         4 ~CprC~kg~Hwa~~C~sk   21 (36)
T PF14787_consen    4 LCPRCGKGFHWASECRSK   21 (36)
T ss_dssp             C-TTTSSSCS-TTT---T
T ss_pred             cCcccCCCcchhhhhhhh
Confidence            566677777777776554

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

Probab=84.51  E-value=0.57  Score=38.24  Aligned_cols=20  Identities=40%  Similarity=1.283  Sum_probs=11.7

Q ss_pred             CcccccCCCCCCCCCCCCCC
Q psy16574         77 SIICYNCNSSGHFARNCPND   96 (152)
Q Consensus        77 ~~~C~~Cg~~GH~~~~Cp~~   96 (152)
                      ...||+||+.||+..+||..
T Consensus       176 gY~CyRCGqkgHwIqnCpTN  195 (427)
T COG5222         176 GYVCYRCGQKGHWIQNCPTN  195 (427)
T ss_pred             ceeEEecCCCCchhhcCCCC
Confidence            45566666666666666543

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

Probab=84.16  E-value=0.41  Score=39.06  Aligned_cols=21  Identities=33%  Similarity=0.861  Sum_probs=18.4

Q ss_pred             ccccccccccCccCCCCCCCC
Q psy16574          6 TIQCYNCFDFGHYQYSCPQKS   26 (152)
Q Consensus         6 ~~~C~~C~~~GH~~~~Cp~~~   26 (152)
                      +-+||.||+.|||..+||...
T Consensus       176 gY~CyRCGqkgHwIqnCpTN~  196 (427)
T COG5222         176 GYVCYRCGQKGHWIQNCPTNQ  196 (427)
T ss_pred             ceeEEecCCCCchhhcCCCCC
Confidence            347999999999999999864

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	152
2lli_A	124	Low Resolution Structure Of Rna-Binding Subunit Of		3e-05
2ec7_A	49	Solution Structure Of Human Immunodificiency Virus		2e-04
2m3z_A	55	Nmr Solution Structure Of Hiv-1 Nucleocapsid Protei		3e-04
1f6u_A	56	Nmr Structure Of The Hiv-1 Nucleocapsid Protein Bou		3e-04
1a1t_A	55	Structure Of The Hiv-1 Nucleocapsid Protein Bound T		3e-04
2l4l_A	45	Structural Insights Into The Ctar Dna Recognition B		5e-04
2exf_A	44	Solution Structure Of The Hiv-1 Nucleocapsid (Ncp7(		6e-04
1bj6_A	42	1h Nmr Of (12-53) Ncp7D(ACGCC) COMPLEX, 10 STRUCTUR		9e-04

>pdb|2LLI|A Chain A, Low Resolution Structure Of Rna-Binding Subunit Of The Tramp Complex Length = 124

Iteration: 1
 Score = 43.9 bits (102), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 32/116 (27%), Positives = 45/116 (38%), Gaps = 27/116 (23%)
Query: 59  CYNCSGQGHVAKDCT-----------------VKSSIICYNCNSSGHFARNCPNDSSK-R 100
           C NCS +GH+ KDC                     +I C  C+  GH+   CP+   K +
Sbjct: 7   CNNCSQRGHLKKDCPHIICSYCGATDDHYSRHCPKAIQCSKCDEVGHYRSQCPHKWKKVQ 66
Query: 101 CYACHQAGHMAKECPG---------QTAGKSPEPVVDMSLTCYVCGHQGHLSYDCK 147
           C  C    H  + CP                P+ +   ++ CY CG +GH   DCK
Sbjct: 67  CTLCKSKKHSKERCPSIWRAYILVDDNEKAKPKVLPFHTIYCYNCGGKGHFGDDCK 122

>pdb|2EC7|A Chain A, Solution Structure Of Human Immunodificiency Virus Type-2 Nucleocapsid Protein Length = 49

Iteration: 1
 Score = 41.2 bits (95), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 17/46 (36%), Positives = 25/46 (54%)
Query: 75  KSSIICYNCNSSGHFARNCPNDSSKRCYACHQAGHMAKECPGQTAG 120
           +  I C+NC   GH AR C     + C+ C + GH+  +CP + AG
Sbjct: 4   RKVIRCWNCGKEGHSARQCRAPRRQGCWKCGKTGHVMAKCPERQAG 49

>pdb|2M3Z|A Chain A, Nmr Solution Structure Of Hiv-1 Nucleocapsid Protein In Complex With An Inhibitor Displaying A 2 Inhibitors:1 Nc Stoichiometry Length = 55

Iteration: 1
 Score = 40.8 bits (94), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 16/45 (35%), Positives = 25/45 (55%)
Query: 75  KSSIICYNCNSSGHFARNCPNDSSKRCYACHQAGHMAKECPGQTA 119
           + ++ C+NC   GH A+NC     K C+ C + GH  K+C  + A
Sbjct: 10  RKTVKCFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKDCTERQA 54

>pdb|1F6U|A Chain A, Nmr Structure Of The Hiv-1 Nucleocapsid Protein Bound To Stem-Loop Sl2 Of The Psi-Rna Packaging Signal. Implications For Genome Recognition Length = 56

Iteration: 1
 Score = 40.8 bits (94), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 16/45 (35%), Positives = 25/45 (55%)
Query: 75  KSSIICYNCNSSGHFARNCPNDSSKRCYACHQAGHMAKECPGQTA 119
           + ++ C+NC   GH A+NC     K C+ C + GH  K+C  + A
Sbjct: 10  RKTVKCFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKDCTERQA 54

>pdb|1A1T|A Chain A, Structure Of The Hiv-1 Nucleocapsid Protein Bound To The Sl3 Psi-Rna Recognition Element, Nmr, 25 Structures Length = 55

Iteration: 1
 Score = 40.8 bits (94), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 16/45 (35%), Positives = 25/45 (55%)
Query: 75  KSSIICYNCNSSGHFARNCPNDSSKRCYACHQAGHMAKECPGQTA 119
           + ++ C+NC   GH A+NC     K C+ C + GH  K+C  + A
Sbjct: 10  RKTVKCFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKDCTERQA 54

>pdb|2L4L|A Chain A, Structural Insights Into The Ctar Dna Recognition By The Hiv-1 Nucleocapsid Protein: Role Of Sugar Deoxyriboses In The Binding Polarity Of Nc Length = 45

Iteration: 1
 Score = 40.0 bits (92), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 17/44 (38%), Positives = 24/44 (54%)
Query: 76  SSIICYNCNSSGHFARNCPNDSSKRCYACHQAGHMAKECPGQTA 119
            ++ C+NC   GH ARNC     K C+ C + GH  K+C  + A
Sbjct: 1   KNVKCFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDCTERQA 44

>pdb|2EXF|A Chain A, Solution Structure Of The Hiv-1 Nucleocapsid (Ncp7(12-55)) Complexed With The Dna (-) Primer Binding Site Length = 44

Iteration: 1
 Score = 39.7 bits (91), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 17/43 (39%), Positives = 24/43 (55%)
Query: 77  SIICYNCNSSGHFARNCPNDSSKRCYACHQAGHMAKECPGQTA 119
           ++ C+NC   GH ARNC     K C+ C + GH  K+C  + A
Sbjct: 1   NVKCFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDCTERQA 43

>pdb|1BJ6|A Chain A, 1h Nmr Of (12-53) Ncp7D(ACGCC) COMPLEX, 10 STRUCTURES Length = 42

Iteration: 1
 Score = 39.3 bits (90), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 16/37 (43%), Positives = 21/37 (56%)
Query: 78  IICYNCNSSGHFARNCPNDSSKRCYACHQAGHMAKEC 114
           + C+NC   GH ARNC     K C+ C + GH  K+C
Sbjct: 2   VKCFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDC 38

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	152
2lli_A	124	Protein AIR2; RNA surveillance, RNA degradation, R	1e-13
2lli_A	124	Protein AIR2; RNA surveillance, RNA degradation, R	3e-08
2lli_A	124	Protein AIR2; RNA surveillance, RNA degradation, R	2e-05
2ihx_A	61	Nucleocapsid (NC) protein; protein-RNA complex, vi	3e-09
2ihx_A	61	Nucleocapsid (NC) protein; protein-RNA complex, vi	2e-06
2ihx_A	61	Nucleocapsid (NC) protein; protein-RNA complex, vi	8e-06
2ihx_A	61	Nucleocapsid (NC) protein; protein-RNA complex, vi	2e-05
2ihx_A	61	Nucleocapsid (NC) protein; protein-RNA complex, vi	3e-05
3ts2_A	148	Protein LIN-28 homolog A; microrna biogenesis, pro	2e-08
3ts2_A	148	Protein LIN-28 homolog A; microrna biogenesis, pro	3e-07
3ts2_A	148	Protein LIN-28 homolog A; microrna biogenesis, pro	2e-04
1cl4_A	60	Protein (GAG polyprotein); nucleocapsid protein, R	8e-08
1cl4_A	60	Protein (GAG polyprotein); nucleocapsid protein, R	1e-05
1cl4_A	60	Protein (GAG polyprotein); nucleocapsid protein, R	1e-05
1cl4_A	60	Protein (GAG polyprotein); nucleocapsid protein, R	4e-05
2li8_A	74	Protein LIN-28 homolog A; zinc finger, micro RNA,	4e-07
2li8_A	74	Protein LIN-28 homolog A; zinc finger, micro RNA,	3e-06
2li8_A	74	Protein LIN-28 homolog A; zinc finger, micro RNA,	5e-05
2cqf_A	63	RNA-binding protein LIN-28; CCHC zinc-finger, stru	5e-07
2cqf_A	63	RNA-binding protein LIN-28; CCHC zinc-finger, stru	6e-06
2cqf_A	63	RNA-binding protein LIN-28; CCHC zinc-finger, stru	4e-04
2ec7_A	49	GAG polyprotein (PR55GAG); nucleocapsid protein, H	8e-06
3nyb_B	83	Protein AIR2; polya RNA polymerase, zinc knuckle p	2e-05
3nyb_B	83	Protein AIR2; polya RNA polymerase, zinc knuckle p	4e-05
3nyb_B	83	Protein AIR2; polya RNA polymerase, zinc knuckle p	1e-04
1a1t_A	55	Nucleocapsid protein; stem-loop RNA, viral protein	3e-05
2a51_A	39	Nucleocapsid protein; sivlhoest, structure, NCP8,	3e-04

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

 Score = 62.5 bits (151), Expect = 1e-13
 Identities = 38/145 (26%), Positives = 49/145 (33%), Gaps = 27/145 (18%)

Query: 5   STIQCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNY-GHFARECATESVTCYNCS 63
           +  +C NC   GH +  CP              +C  C     H++R C  +++ C  C 
Sbjct: 3   AAPKCNNCSQRGHLKKDCPHI------------ICSYCGATDDHYSRHC-PKAIQCSKCD 49

Query: 64  GQGHVAKDCTVKSSII-CYNCNSSGHFARNCPNDSSKRCYACHQAGHMAKECPGQTAGKS 122
             GH    C  K   + C  C S  H    CP  S  R Y        AK          
Sbjct: 50  EVGHYRSQCPHKWKKVQCTLCKSKKHSKERCP--SIWRAYILVDDNEKAKPKVLPFHTI- 106

Query: 123 PEPVVDMSLTCYVCGHQGHLSYDCK 147
                     CY CG +GH   DCK
Sbjct: 107 ---------YCYNCGGKGHFGDDCK 122

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

 Score = 48.6 bits (115), Expect = 3e-08
 Identities = 26/98 (26%), Positives = 44/98 (44%), Gaps = 16/98 (16%)

Query: 56  SVTCYNCSGQGHVAKDCTVKSSIICYNCNSS-GHFARNCPNDSSKRCYACHQAGHMAKEC 114
           +  C NCS +GH+ KDC      IC  C ++  H++R+CP   + +C  C + GH   +C
Sbjct: 4   APKCNNCSQRGHLKKDCPHI---ICSYCGATDDHYSRHCPK--AIQCSKCDEVGHYRSQC 58

Query: 115 PGQTAGKSPEPVVDMSLTCYVCGHQGHLSYDCKLVQKS 152
           P +               C +C  + H    C  + ++
Sbjct: 59  PHKWKKV----------QCTLCKSKKHSKERCPSIWRA 86

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

 Score = 41.3 bits (96), Expect = 2e-05
 Identities = 17/77 (22%), Positives = 28/77 (36%), Gaps = 15/77 (19%)

Query: 75  KSSIICYNCNSSGHFARNCPNDSSKRCYACHQAGHMAKECPGQTAGKSPEPVVDMSLTCY 134
           +++  C NC+  GH  ++CP+     C       H ++ CP              ++ C 
Sbjct: 2   EAAPKCNNCSQRGHLKKDCPHIICSYC--GATDDHYSRHCP-------------KAIQCS 46

Query: 135 VCGHQGHLSYDCKLVQK 151
            C   GH    C    K
Sbjct: 47  KCDEVGHYRSQCPHKWK 63

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

 Score = 49.5 bits (118), Expect = 3e-09
 Identities = 18/56 (32%), Positives = 28/56 (50%), Gaps = 5/56 (8%)

Query: 75  KSSIICYNCNSSGHFARNCPN-----DSSKRCYACHQAGHMAKECPGQTAGKSPEP 125
           ++  +CY C S GH+   CP      +S +RC  C+  GH AK+C  +   +   P
Sbjct: 2   RARGLCYTCGSPGHYQAQCPKKRKSGNSRERCQLCNGMGHNAKQCRKRDGNQGQRP 57

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

 Score = 42.2 bits (99), Expect = 2e-06
 Identities = 14/49 (28%), Positives = 16/49 (32%), Gaps = 5/49 (10%)

Query: 58  TCYNCSGQGHVAKDCT-----VKSSIICYNCNSSGHFARNCPNDSSKRC 101
            CY C   GH    C        S   C  CN  GH A+ C      + 
Sbjct: 6   LCYTCGSPGHYQAQCPKKRKSGNSRERCQLCNGMGHNAKQCRKRDGNQG 54

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

 Score = 40.2 bits (94), Expect = 8e-06
 Identities = 12/51 (23%), Positives = 18/51 (35%), Gaps = 6/51 (11%)

Query: 97  SSKRCYACHQAGHMAKECPGQTAGKSPEPVVDMSLTCYVCGHQGHLSYDCK 147
           +   CY C   GH   +CP            +    C +C   GH +  C+
Sbjct: 3   ARGLCYTCGSPGHYQAQCP------KKRKSGNSRERCQLCNGMGHNAKQCR 47

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

 Score = 39.5 bits (92), Expect = 2e-05
 Identities = 19/58 (32%), Positives = 26/58 (44%), Gaps = 4/58 (6%)

Query: 9  CYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFARECATESVTCYNCSGQG 66
          CY C   GHYQ  CP+K  +    ++    C  CN  GH A++C           G+G
Sbjct: 7  CYTCGSPGHYQAQCPKKRKSGNSRER----CQLCNGMGHNAKQCRKRDGNQGQRPGKG 60

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

 Score = 38.7 bits (90), Expect = 3e-05
 Identities = 14/44 (31%), Positives = 19/44 (43%), Gaps = 6/44 (13%)

Query: 36 GIVCYKCNNYGHFAREC------ATESVTCYNCSGQGHVAKDCT 73
            +CY C + GH+  +C            C  C+G GH AK C 
Sbjct: 4  RGLCYTCGSPGHYQAQCPKKRKSGNSRERCQLCNGMGHNAKQCR 47

>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 = 49.2 bits (117), Expect = 2e-08
 Identities = 15/42 (35%), Positives = 21/42 (50%), Gaps = 1/42 (2%)

Query: 59  CYNCSGQGHVAKDCTVKSSI-ICYNCNSSGHFARNCPNDSSK 99
           CYNC G  H AK+C +      C+ C S  H   +CP  + +
Sbjct: 100 CYNCGGLDHHAKECKLPPQPKKCHFCQSINHMVASCPLKAQQ 141

>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 = 46.2 bits (109), Expect = 3e-07
 Identities = 14/40 (35%), Positives = 18/40 (45%), Gaps = 1/40 (2%)

Query: 80  CYNCNSSGHFARNCPNDS-SKRCYACHQAGHMAKECPGQT 118
           CYNC    H A+ C      K+C+ C    HM   CP + 
Sbjct: 100 CYNCGGLDHHAKECKLPPQPKKCHFCQSINHMVASCPLKA 139

>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 = 38.5 bits (89), Expect = 2e-04
 Identities = 14/51 (27%), Positives = 16/51 (31%), Gaps = 10/51 (19%)

Query: 96  DSSKRCYACHQAGHMAKECPGQTAGKSPEPVVDMSLTCYVCGHQGHLSYDC 146
               RCY C    H AKEC      K           C+ C    H+   C
Sbjct: 95  KGGDRCYNCGGLDHHAKECKLPPQPKK----------CHFCQSINHMVASC 135

>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 = 45.7 bits (108), Expect = 8e-08
 Identities = 15/47 (31%), Positives = 20/47 (42%), Gaps = 8/47 (17%)

Query: 80  CYNCNSSGHFARNCPNDSSKR--------CYACHQAGHMAKECPGQT 118
           C+ C   GHFA+NC   +           C  C +  H A EC  +T
Sbjct: 4   CFKCGKKGHFAKNCHEHAHNNAEPKVPGLCPRCKRGKHWANECKSKT 50

>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 = 39.9 bits (93), Expect = 1e-05
 Identities = 13/46 (28%), Positives = 20/46 (43%), Gaps = 8/46 (17%)

Query: 58 TCYNCSGQGHVAKDC--------TVKSSIICYNCNSSGHFARNCPN 95
          +C+ C  +GH AK+C          K   +C  C    H+A  C +
Sbjct: 3  SCFKCGKKGHFAKNCHEHAHNNAEPKVPGLCPRCKRGKHWANECKS 48

>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 = 39.9 bits (93), Expect = 1e-05
 Identities = 13/47 (27%), Positives = 18/47 (38%), Gaps = 3/47 (6%)

Query: 101 CYACHQAGHMAKECPGQTAGKSPEPVVDMSLTCYVCGHQGHLSYDCK 147
           C+ C + GH AK C       +   V      C  C    H + +CK
Sbjct: 4   CFKCGKKGHFAKNCHEHAHNNAEPKVPG---LCPRCKRGKHWANECK 47

>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 = 38.4 bits (89), Expect = 4e-05
 Identities = 13/44 (29%), Positives = 22/44 (50%), Gaps = 1/44 (2%)

Query: 9  CYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFAREC 52
          C+ C   GH+  +C + +  +A     G+ C +C    H+A EC
Sbjct: 4  CFKCGKKGHFAKNCHEHAHNNAEPKVPGL-CPRCKRGKHWANEC 46

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

 Score = 44.2 bits (104), Expect = 4e-07
 Identities = 14/37 (37%), Positives = 17/37 (45%), Gaps = 1/37 (2%)

Query: 80  CYNCNSSGHFARNCPNDS-SKRCYACHQAGHMAKECP 115
           CYNC    H A+ C      K+C+ C    HM   CP
Sbjct: 27  CYNCGGLDHHAKECKLPPQPKKCHFCQSISHMVASCP 63

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

 Score = 41.9 bits (98), Expect = 3e-06
 Identities = 15/47 (31%), Positives = 22/47 (46%), Gaps = 1/47 (2%)

Query: 55  ESVTCYNCSGQGHVAKDCTV-KSSIICYNCNSSGHFARNCPNDSSKR 100
           +   CYNC G  H AK+C +      C+ C S  H   +CP  + + 
Sbjct: 23  KGDRCYNCGGLDHHAKECKLPPQPKKCHFCQSISHMVASCPLKAQQG 69

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

 Score = 38.4 bits (89), Expect = 5e-05
 Identities = 13/49 (26%), Positives = 19/49 (38%), Gaps = 2/49 (4%)

Query: 31 RGDKVGIVCYKCNNYGHFARECATE--SVTCYNCSGQGHVAKDCTVKSS 77
          +    G  CY C    H A+EC        C+ C    H+   C +K+ 
Sbjct: 19 KRRSKGDRCYNCGGLDHHAKECKLPPQPKKCHFCQSISHMVASCPLKAQ 67

>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 = 43.8 bits (103), Expect = 5e-07
 Identities = 15/42 (35%), Positives = 18/42 (42%), Gaps = 1/42 (2%)

Query: 75  KSSIICYNCNSSGHFARNCPNDSS-KRCYACHQAGHMAKECP 115
            S   CYNC    H A+ C      K+C+ C    HM   CP
Sbjct: 5   SSGDRCYNCGGLDHHAKECKLPPQPKKCHFCQSISHMVASCP 46

>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 = 40.7 bits (95), Expect = 6e-06
 Identities = 15/49 (30%), Positives = 22/49 (44%), Gaps = 1/49 (2%)

Query: 53  ATESVTCYNCSGQGHVAKDCTV-KSSIICYNCNSSGHFARNCPNDSSKR 100
            +    CYNC G  H AK+C +      C+ C S  H   +CP  + + 
Sbjct: 4   GSSGDRCYNCGGLDHHAKECKLPPQPKKCHFCQSISHMVASCPLKAQQG 52

>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 = 35.7 bits (82), Expect = 4e-04
 Identities = 13/44 (29%), Positives = 18/44 (40%), Gaps = 2/44 (4%)

Query: 36 GIVCYKCNNYGHFARECATESV--TCYNCSGQGHVAKDCTVKSS 77
          G  CY C    H A+EC        C+ C    H+   C +K+ 
Sbjct: 7  GDRCYNCGGLDHHAKECKLPPQPKKCHFCQSISHMVASCPLKAQ 50

>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 Length = 49

 Score = 40.3 bits (94), Expect = 8e-06
 Identities = 17/46 (36%), Positives = 25/46 (54%)

Query: 75  KSSIICYNCNSSGHFARNCPNDSSKRCYACHQAGHMAKECPGQTAG 120
           +  I C+NC   GH AR C     + C+ C + GH+  +CP + AG
Sbjct: 4   RKVIRCWNCGKEGHSARQCRAPRRQGCWKCGKTGHVMAKCPERQAG 49

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

 Score = 39.6 bits (92), Expect = 2e-05
 Identities = 15/64 (23%), Positives = 20/64 (31%)

Query: 37  IVCYKCNNYGHFARECATESVTCYNCSGQGHVAKDCTVKSSIICYNCNSSGHFARNCPND 96
           + C  C +  H    C +                      +I CYNC   GHF  +C   
Sbjct: 6   VQCTLCKSKKHSKERCPSIWRAYILVDDNEKAKPKVLPFHTIYCYNCGGKGHFGDDCKEK 65

Query: 97  SSKR 100
            S R
Sbjct: 66  RSSR 69

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

 Score = 38.9 bits (90), Expect = 4e-05
 Identities = 19/70 (27%), Positives = 25/70 (35%), Gaps = 12/70 (17%)

Query: 78  IICYNCNSSGHFARNCPNDSSKRCYACHQAGHMAKECPGQTAGKSPEPVVDMSLTCYVCG 137
           + C  C S  H    CP  S  R Y                    P+ +   ++ CY CG
Sbjct: 6   VQCTLCKSKKHSKERCP--SIWRAY----------ILVDDNEKAKPKVLPFHTIYCYNCG 53

Query: 138 HQGHLSYDCK 147
            +GH   DCK
Sbjct: 54  GKGHFGDDCK 63

>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 = 1e-04
 Identities = 18/71 (25%), Positives = 25/71 (35%), Gaps = 9/71 (12%)

Query: 7  IQCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFARECATESVTCYNCSGQG 66
          +QC  C    H +  CP                   +N     +     ++ CYNC G+G
Sbjct: 6  VQCTLCKSKKHSKERCP---------SIWRAYILVDDNEKAKPKVLPFHTIYCYNCGGKG 56

Query: 67 HVAKDCTVKSS 77
          H   DC  K S
Sbjct: 57 HFGDDCKEKRS 67

>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 Length = 55

 Score = 38.8 bits (90), Expect = 3e-05
 Identities = 16/45 (35%), Positives = 25/45 (55%)

Query: 75  KSSIICYNCNSSGHFARNCPNDSSKRCYACHQAGHMAKECPGQTA 119
           + ++ C+NC   GH A+NC     K C+ C + GH  K+C  + A
Sbjct: 10  RKTVKCFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKDCTERQA 54

>2a51_A Nucleocapsid protein; sivlhoest, structure, NCP8, viral protein, metal binding protein; NMR {Synthetic} Length = 39

 Score = 36.0 bits (83), Expect = 3e-04
 Identities = 13/38 (34%), Positives = 18/38 (47%)

Query: 78  IICYNCNSSGHFARNCPNDSSKRCYACHQAGHMAKECP 115
           + C+NC   GH AR C     + C+ C    H   +CP
Sbjct: 1   LTCFNCGKPGHTARMCRQPRQEGCWNCGSKEHRFAQCP 38

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	152
2lli_A	124	Protein AIR2; RNA surveillance, RNA degradation, R	99.97
2lli_A	124	Protein AIR2; RNA surveillance, RNA degradation, R	99.95
3nyb_B	83	Protein AIR2; polya RNA polymerase, zinc knuckle p	99.72
3nyb_B	83	Protein AIR2; polya RNA polymerase, zinc knuckle p	99.59
2li8_A	74	Protein LIN-28 homolog A; zinc finger, micro RNA,	99.53
2li8_A	74	Protein LIN-28 homolog A; zinc finger, micro RNA,	99.5
2a51_A	39	Nucleocapsid protein; sivlhoest, structure, NCP8,	99.36
2ec7_A	49	GAG polyprotein (PR55GAG); nucleocapsid protein, H	99.35
2a51_A	39	Nucleocapsid protein; sivlhoest, structure, NCP8,	99.32
2bl6_A	37	Nucleocapsid protein P11; lentivirus, polyprotein,	99.29
2ec7_A	49	GAG polyprotein (PR55GAG); nucleocapsid protein, H	99.28
1a1t_A	55	Nucleocapsid protein; stem-loop RNA, viral protein	99.27
2bl6_A	37	Nucleocapsid protein P11; lentivirus, polyprotein,	99.26
2ihx_A	61	Nucleocapsid (NC) protein; protein-RNA complex, vi	99.24
2cqf_A	63	RNA-binding protein LIN-28; CCHC zinc-finger, stru	99.23
2cqf_A	63	RNA-binding protein LIN-28; CCHC zinc-finger, stru	99.23
1cl4_A	60	Protein (GAG polyprotein); nucleocapsid protein, R	99.17
1a1t_A	55	Nucleocapsid protein; stem-loop RNA, viral protein	99.15
2ihx_A	61	Nucleocapsid (NC) protein; protein-RNA complex, vi	99.11
1cl4_A	60	Protein (GAG polyprotein); nucleocapsid protein, R	99.09
3ts2_A	148	Protein LIN-28 homolog A; microrna biogenesis, pro	98.9
3ts2_A	148	Protein LIN-28 homolog A; microrna biogenesis, pro	98.89
1dsq_A	26	Nucleic acid binding protein P14; CCHC type zinc f	98.34
1dsq_A	26	Nucleic acid binding protein P14; CCHC type zinc f	98.23
1nc8_A	29	Nucleocapsid protein; HIV-2, RNA recognition, zinc	98.11
1a6b_B	40	Momulv, zinc finger protein NCP10; nucleocapsid pr	98.01
1nc8_A	29	Nucleocapsid protein; HIV-2, RNA recognition, zinc	97.95
1a6b_B	40	Momulv, zinc finger protein NCP10; nucleocapsid pr	97.92
1u6p_A	56	GAG polyprotein; MLV, A-minor K-turn, stem loop, b	97.71
1u6p_A	56	GAG polyprotein; MLV, A-minor K-turn, stem loop, b	97.59
2ysa_A	55	Retinoblastoma-binding protein 6; zinc finger, CCH	97.15
2ysa_A	55	Retinoblastoma-binding protein 6; zinc finger, CCH	96.97
2hqh_E	26	Restin; beta/BETA structure, zinc finger motif, st	84.55
2yuc_A	76	TNF receptor-associated factor 4; ZF-TRAF, cystein	81.36

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

Probab=99.97  E-value=1.8e-30  Score=183.93  Aligned_cols=109  Identities=28%  Similarity=0.719  Sum_probs=82.7

Q ss_pred             ccceecCCCCcCcccCCCCCCcccccCCC-CcccccCCCCCCcccccCCCCCCCCCCCCCCC-CcCCcccCCCCcCCCCC
Q psy16574         37 IVCYKCNNYGHFARECATESVTCYNCSGQ-GHVAKDCTVKSSIICYNCNSSGHFARNCPNDS-SKRCYACHQAGHMAKEC  114 (152)
Q Consensus        37 ~~C~~Cg~~GH~~~~Cp~~~~~C~~Cg~~-GH~~~~Cp~~~~~~C~~Cg~~GH~~~~Cp~~~-~~~C~~C~~~GH~~~~C  114 (152)
                      +.||+|+++||++++||+.  .||+|++. ||++++||.  ...|++|++.||++++||..+ .+.|++|++.||+++||
T Consensus         5 ~~C~~C~~~GH~~~~Cp~~--~C~~Cg~~~gH~~~~C~~--~~~C~~Cg~~GH~~~~C~~~~~~~~C~~Cg~~GH~~~~C   80 (124)
T 2lli_A            5 PKCNNCSQRGHLKKDCPHI--ICSYCGATDDHYSRHCPK--AIQCSKCDEVGHYRSQCPHKWKKVQCTLCKSKKHSKERC   80 (124)
T ss_dssp             SCCSSCSSSSCCTTTTTSC--CCTTTCCTTTCCTTTGGG--SSCSSSSSCSSSSTTTSCCCCCCCSSSSSCSSCCCTTTC
T ss_pred             CcccCCCCCCcCcccCcCC--cCcCCCCcCCccCcccCC--cccccccCCCCCccccCcCcccCccCCCCCcCCcchhhC
Confidence            4677777777777777776  77777777 777777776  467888888888888887754 46799999999999999


Q ss_pred             CCCCCCCCCC---------ccccccccccccccccccCCCCCCC
Q psy16574        115 PGQTAGKSPE---------PVVDMSLTCYVCGHQGHLSYDCKLV  149 (152)
Q Consensus       115 p~~~~~~~~~---------~~~~~~~~C~~Cg~~GH~~~~C~~~  149 (152)
                      |+.|..+...         ......++||+|++.|||++|||+.
T Consensus        81 p~~~~~y~~~~~~~~~~~~~~~~~~~~Cy~Cg~~GH~a~dCp~~  124 (124)
T 2lli_A           81 PSIWRAYILVDDNEKAKPKVLPFHTIYCYNCGGKGHFGDDCKEK  124 (124)
T ss_dssp             CCSTTSCCSSSCCCCCCCSCCCCCCCCTTTTSSSCTTTTTSCCC
T ss_pred             CCccccccccCccccccccccCCCCCCcCCCCCCCcCcccCcCC
Confidence            9888643211         1223468999999999999999973

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

Probab=99.95  E-value=1.8e-28  Score=173.60  Aligned_cols=99  Identities=30%  Similarity=0.810  Sum_probs=90.4

Q ss_pred             ccccccccccCccCCCCCCCCCCCCCCCCCCccceecCCC-CcCcccCCCCCCcccccCCCCcccccCCCC-CCcccccC
Q psy16574          6 TIQCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNY-GHFARECATESVTCYNCSGQGHVAKDCTVK-SSIICYNC   83 (152)
Q Consensus         6 ~~~C~~C~~~GH~~~~Cp~~~~~~~~~~~~~~~C~~Cg~~-GH~~~~Cp~~~~~C~~Cg~~GH~~~~Cp~~-~~~~C~~C   83 (152)
                      .+.||+|+++||++++||..            +||+|+++ ||++++||.. ..||+|++.||++++||.. ....|++|
T Consensus         4 ~~~C~~C~~~GH~~~~Cp~~------------~C~~Cg~~~gH~~~~C~~~-~~C~~Cg~~GH~~~~C~~~~~~~~C~~C   70 (124)
T 2lli_A            4 APKCNNCSQRGHLKKDCPHI------------ICSYCGATDDHYSRHCPKA-IQCSKCDEVGHYRSQCPHKWKKVQCTLC   70 (124)
T ss_dssp             SSCCSSCSSSSCCTTTTTSC------------CCTTTCCTTTCCTTTGGGS-SCSSSSSCSSSSTTTSCCCCCCCSSSSS
T ss_pred             CCcccCCCCCCcCcccCcCC------------cCcCCCCcCCccCcccCCc-ccccccCCCCCccccCcCcccCccCCCC
Confidence            46799999999999999985            69999999 9999999986 6899999999999999985 35789999


Q ss_pred             CCCCCCCCCCCCCC--------------------CcCCcccCCCCcCCCCCCCC
Q psy16574         84 NSSGHFARNCPNDS--------------------SKRCYACHQAGHMAKECPGQ  117 (152)
Q Consensus        84 g~~GH~~~~Cp~~~--------------------~~~C~~C~~~GH~~~~Cp~~  117 (152)
                      ++.||++++||..|                    .+.||+|++.|||++|||+.
T Consensus        71 g~~GH~~~~Cp~~~~~y~~~~~~~~~~~~~~~~~~~~Cy~Cg~~GH~a~dCp~~  124 (124)
T 2lli_A           71 KSKKHSKERCPSIWRAYILVDDNEKAKPKVLPFHTIYCYNCGGKGHFGDDCKEK  124 (124)
T ss_dssp             CSSCCCTTTCCCSTTSCCSSSCCCCCCCSCCCCCCCCTTTTSSSCTTTTTSCCC
T ss_pred             CcCCcchhhCCCccccccccCccccccccccCCCCCCcCCCCCCCcCcccCcCC
Confidence            99999999999864                    36899999999999999973

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

Probab=99.72  E-value=1.4e-18  Score=114.50  Aligned_cols=62  Identities=31%  Similarity=0.566  Sum_probs=29.0

Q ss_pred             cccccCCCCCCCCCCCCCCCCcCCcccCCCCcCCCCCCCCCCCCCCCccccccccccccccccccCCCCCCCcC
Q psy16574         78 IICYNCNSSGHFARNCPNDSSKRCYACHQAGHMAKECPGQTAGKSPEPVVDMSLTCYVCGHQGHLSYDCKLVQK  151 (152)
Q Consensus        78 ~~C~~Cg~~GH~~~~Cp~~~~~~C~~C~~~GH~~~~Cp~~~~~~~~~~~~~~~~~C~~Cg~~GH~~~~C~~~~~  151 (152)
                      +.|++|++.||++++||+.|  .||+|++.||++++|+.+.          ..++||+||+.|||++|||+.+.
T Consensus         6 ~~C~~Cg~~GH~~~~Cp~~~--rcY~c~~~gh~~~~c~~p~----------~~~~CYnCG~~GH~~rdC~~~r~   67 (83)
T 3nyb_B            6 VQCTLCKSKKHSKERCPSIW--RAYILVDDNEKAKPKVLPF----------HTIYCYNCGGKGHFGDDCKEKRS   67 (83)
T ss_dssp             -CCSSSCCSSSCGGGCGGGT--CCCCBC-----------------------CCCBCSSSSCBSSCGGGCSSCCS
T ss_pred             CCCCCCCCCCCccccCCCcc--cccccccCCcccccccCCC----------CCCeecccCCCCcCcccCCcccc
Confidence            45666666666666666542  4666666666666665431          23566666666666666666554

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

Probab=99.59  E-value=3.5e-16  Score=103.00  Aligned_cols=59  Identities=20%  Similarity=0.451  Sum_probs=29.8

Q ss_pred             cccccCCCCcccccCCCCCCcccccCCCCCCCCCCCCCC-CCcCCcccCCCCcCCCCCCCCC
Q psy16574         58 TCYNCSGQGHVAKDCTVKSSIICYNCNSSGHFARNCPND-SSKRCYACHQAGHMAKECPGQT  118 (152)
Q Consensus        58 ~C~~Cg~~GH~~~~Cp~~~~~~C~~Cg~~GH~~~~Cp~~-~~~~C~~C~~~GH~~~~Cp~~~  118 (152)
                      .||+|++.||++++||+  ...||+|+..||++++|+.+ ..+.||+|++.|||++|||+.+
T Consensus         7 ~C~~Cg~~GH~~~~Cp~--~~rcY~c~~~gh~~~~c~~p~~~~~CYnCG~~GH~~rdC~~~r   66 (83)
T 3nyb_B            7 QCTLCKSKKHSKERCPS--IWRAYILVDDNEKAKPKVLPFHTIYCYNCGGKGHFGDDCKEKR   66 (83)
T ss_dssp             CCSSSCCSSSCGGGCGG--GTCCCCBC-------------CCCBCSSSSCBSSCGGGCSSCC
T ss_pred             CCCCCCCCCCccccCCC--cccccccccCCcccccccCCCCCCeecccCCCCcCcccCCccc
Confidence            45555555555555554  23456666666666666443 2467888888888888888775

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

Probab=99.53  E-value=4.7e-15  Score=95.63  Aligned_cols=44  Identities=32%  Similarity=0.675  Sum_probs=32.9

Q ss_pred             CcCCcccCCCCcCCCCCCCCCCCCCCCccccccccccccccccccCCCCCCCcC
Q psy16574         98 SKRCYACHQAGHMAKECPGQTAGKSPEPVVDMSLTCYVCGHQGHLSYDCKLVQK  151 (152)
Q Consensus        98 ~~~C~~C~~~GH~~~~Cp~~~~~~~~~~~~~~~~~C~~Cg~~GH~~~~C~~~~~  151 (152)
                      ...||+|++.||++++||...          ..+.||+|++.||+++|||+..+
T Consensus        24 ~~~C~~Cg~~GH~a~~C~~~~----------~~~~C~~Cg~~GH~ar~Cp~~~~   67 (74)
T 2li8_A           24 GDRCYNCGGLDHHAKECKLPP----------QPKKCHFCQSISHMVASCPLKAQ   67 (74)
T ss_dssp             TSCCTTTCCSSSCTTTCSSCC----------CCCCCTTTCCTTSCGGGCTTGGG
T ss_pred             CCcccccCCcCcCcccCCCCC----------CCCccCCcCCcCCccCcCcCCcC
Confidence            357888888888888887642          13578888888888888887653

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

Probab=99.50  E-value=1.5e-14  Score=93.32  Aligned_cols=60  Identities=22%  Similarity=0.496  Sum_probs=31.8

Q ss_pred             cCccCCCCCCCCCCCCC-CCCCCccceecCCCCcCcccCCCC--CCcccccCCCCcccccCCC
Q psy16574         15 FGHYQYSCPQKSSADAR-GDKVGIVCYKCNNYGHFARECATE--SVTCYNCSGQGHVAKDCTV   74 (152)
Q Consensus        15 ~GH~~~~Cp~~~~~~~~-~~~~~~~C~~Cg~~GH~~~~Cp~~--~~~C~~Cg~~GH~~~~Cp~   74 (152)
                      .|||++||+.++..... .....+.||+|++.||++++||..  ...||+|++.||++++||.
T Consensus         2 ~gh~~rdc~~~~~~~~~~~~~r~~~C~~Cg~~GH~a~~C~~~~~~~~C~~Cg~~GH~ar~Cp~   64 (74)
T 2li8_A            2 SGLVPRGSHMPKGKSMQKRRSKGDRCYNCGGLDHHAKECKLPPQPKKCHFCQSISHMVASCPL   64 (74)
T ss_dssp             ----------CCCCCCCSCCSTTSCCTTTCCSSSCTTTCSSCCCCCCCTTTCCTTSCGGGCTT
T ss_pred             CccccCcCCCCCcCccccccCCCCcccccCCcCcCcccCCCCCCCCccCCcCCcCCccCcCcC
Confidence            59999999998643211 112356788888888888888853  3567777777777777765

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

Probab=99.36  E-value=3.3e-13  Score=76.56  Aligned_cols=39  Identities=28%  Similarity=0.674  Sum_probs=31.0

Q ss_pred             cccccccccCccCCCCCCCCCCCCCCCCCCccceecCCCCcCcccCCC
Q psy16574          7 IQCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFARECAT   54 (152)
Q Consensus         7 ~~C~~C~~~GH~~~~Cp~~~~~~~~~~~~~~~C~~Cg~~GH~~~~Cp~   54 (152)
                      +.||+|++.||++++||.+.         ...||+|++.||++++||+
T Consensus         1 i~C~~Cg~~GH~a~~C~~~~---------~~~C~~Cg~~GH~~~~C~~   39 (39)
T 2a51_A            1 LTCFNCGKPGHTARMCRQPR---------QEGCWNCGSKEHRFAQCPK   39 (39)
T ss_dssp             CBCTTTCCBSSCTTTCCSCC---------CSSCTTTCCSSSCTTTSCC
T ss_pred             CeeeccCCCCcccccCCCCC---------CCccccCCCCCCccCcCcC
Confidence            46889999999999998763         2578888888888888874

>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=99.35  E-value=5.6e-13  Score=79.30  Aligned_cols=42  Identities=33%  Similarity=0.854  Sum_probs=29.9

Q ss_pred             cCCcccCCCCcCCCCCCCCCCCCCCCccccccccccccccccccCCCCCCCcC
Q psy16574         99 KRCYACHQAGHMAKECPGQTAGKSPEPVVDMSLTCYVCGHQGHLSYDCKLVQK  151 (152)
Q Consensus        99 ~~C~~C~~~GH~~~~Cp~~~~~~~~~~~~~~~~~C~~Cg~~GH~~~~C~~~~~  151 (152)
                      ..||+|++.||++++||...           ...||+|++.||+++|||+.+.
T Consensus         7 ~~C~~Cg~~GH~a~~C~~~~-----------~~~C~~Cg~~GH~~~~C~~~~~   48 (49)
T 2ec7_A            7 IRCWNCGKEGHSARQCRAPR-----------RQGCWKCGKTGHVMAKCPERQA   48 (49)
T ss_dssp             CBCTTTCCBTCCTTTCCCSS-----------CCSCSSSCCSSCCGGGCCSSCC
T ss_pred             CeeeecCCCCcChhhCcCCC-----------CCeeCcCCCcCCccCCCcCCCC
Confidence            56777777777777777652           2467888888888888877664

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

Probab=99.32  E-value=1.6e-12  Score=73.65  Aligned_cols=38  Identities=29%  Similarity=0.781  Sum_probs=21.6

Q ss_pred             CCcccCCCCcCCCCCCCCCCCCCCCccccccccccccccccccCCCCCC
Q psy16574        100 RCYACHQAGHMAKECPGQTAGKSPEPVVDMSLTCYVCGHQGHLSYDCKL  148 (152)
Q Consensus       100 ~C~~C~~~GH~~~~Cp~~~~~~~~~~~~~~~~~C~~Cg~~GH~~~~C~~  148 (152)
                      .||+|++.||++++||...           ...||+|++.||+++|||+
T Consensus         2 ~C~~Cg~~GH~a~~C~~~~-----------~~~C~~Cg~~GH~~~~C~~   39 (39)
T 2a51_A            2 TCFNCGKPGHTARMCRQPR-----------QEGCWNCGSKEHRFAQCPK   39 (39)
T ss_dssp             BCTTTCCBSSCTTTCCSCC-----------CSSCTTTCCSSSCTTTSCC
T ss_pred             eeeccCCCCcccccCCCCC-----------CCccccCCCCCCccCcCcC
Confidence            4556666666666665432           2356666666666666653

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

Probab=99.29  E-value=1.3e-12  Score=73.29  Aligned_cols=36  Identities=42%  Similarity=1.068  Sum_probs=26.7

Q ss_pred             ccccccccCccCCCCCCCCCCCCCCCCCCccceecCCCCcCcccCCC
Q psy16574          8 QCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFARECAT   54 (152)
Q Consensus         8 ~C~~C~~~GH~~~~Cp~~~~~~~~~~~~~~~C~~Cg~~GH~~~~Cp~   54 (152)
                      .||+|+++||++++||.+           ..||+|+++||++++||+
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            577888888888888764           367777777777777764

>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=99.28  E-value=2.2e-12  Score=76.70  Aligned_cols=41  Identities=32%  Similarity=0.767  Sum_probs=27.3

Q ss_pred             ccccccccccCccCCCCCCCCCCCCCCCCCCccceecCCCCcCcccCCCC
Q psy16574          6 TIQCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFARECATE   55 (152)
Q Consensus         6 ~~~C~~C~~~GH~~~~Cp~~~~~~~~~~~~~~~C~~Cg~~GH~~~~Cp~~   55 (152)
                      .+.||+|++.||++++||.+.         ...||+|++.||++++||..
T Consensus         6 ~~~C~~Cg~~GH~a~~C~~~~---------~~~C~~Cg~~GH~~~~C~~~   46 (49)
T 2ec7_A            6 VIRCWNCGKEGHSARQCRAPR---------RQGCWKCGKTGHVMAKCPER   46 (49)
T ss_dssp             CCBCTTTCCBTCCTTTCCCSS---------CCSCSSSCCSSCCGGGCCSS
T ss_pred             cCeeeecCCCCcChhhCcCCC---------CCeeCcCCCcCCccCCCcCC
Confidence            346777777777777777653         23577777777777777654

>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=99.27  E-value=1.5e-12  Score=79.11  Aligned_cols=42  Identities=36%  Similarity=0.902  Sum_probs=29.8

Q ss_pred             cCCcccCCCCcCCCCCCCCCCCCCCCccccccccccccccccccCCCCCCCcC
Q psy16574         99 KRCYACHQAGHMAKECPGQTAGKSPEPVVDMSLTCYVCGHQGHLSYDCKLVQK  151 (152)
Q Consensus        99 ~~C~~C~~~GH~~~~Cp~~~~~~~~~~~~~~~~~C~~Cg~~GH~~~~C~~~~~  151 (152)
                      ..||+|++.||++++||...           ...||+|++.||+++|||+.++
T Consensus        13 ~~C~~Cg~~GH~a~~C~~~~-----------~~~C~~Cg~~GH~~~~C~~~~~   54 (55)
T 1a1t_A           13 VKCFNCGKEGHIAKNCRAPR-----------KKGCWKCGKEGHQMKDCTERQA   54 (55)
T ss_dssp             CBCTTTCCBSSCGGGCSSCS-----------CCBCTTTCCBSSCGGGCSSSCC
T ss_pred             cceeeeCCCCcChhhcCCCC-----------CCEeCCCCCcCCccCCCcCcCC
Confidence            46777777777777776642           3468888888888888877665

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

Probab=99.26  E-value=2.3e-12  Score=72.17  Aligned_cols=36  Identities=33%  Similarity=1.034  Sum_probs=24.1

Q ss_pred             CCcccCCCCcCCCCCCCCCCCCCCCccccccccccccccccccCCCCCC
Q psy16574        100 RCYACHQAGHMAKECPGQTAGKSPEPVVDMSLTCYVCGHQGHLSYDCKL  148 (152)
Q Consensus       100 ~C~~C~~~GH~~~~Cp~~~~~~~~~~~~~~~~~C~~Cg~~GH~~~~C~~  148 (152)
                      .||+|++.||++++||..             ..||+|++.||++++||+
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            466677777777777653             367777777777777764

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

Probab=99.24  E-value=3.4e-12  Score=79.20  Aligned_cols=47  Identities=26%  Similarity=0.688  Sum_probs=28.6

Q ss_pred             cCCcccCCCCcCCCCCCCCCCCCCCCccccccccccccccccccCCCCCCCcC
Q psy16574         99 KRCYACHQAGHMAKECPGQTAGKSPEPVVDMSLTCYVCGHQGHLSYDCKLVQK  151 (152)
Q Consensus        99 ~~C~~C~~~GH~~~~Cp~~~~~~~~~~~~~~~~~C~~Cg~~GH~~~~C~~~~~  151 (152)
                      ..||+|++.||++++||......      ...+.||+|++.||+++|||+.+.
T Consensus         5 ~~C~~Cg~~GH~a~~C~~~~~~~------~~~~~C~~Cg~~GH~ar~C~~~~~   51 (61)
T 2ihx_A            5 GLCYTCGSPGHYQAQCPKKRKSG------NSRERCQLCNGMGHNAKQCRKRDG   51 (61)
T ss_dssp             TBCSSSCCBTCCGGGCTTTTSSS------CCCSBCTTTCCBSSCGGGCCCCC-
T ss_pred             CcccccCCCCeehhhCcCCcCCC------CCCCeeCCCCCCCCCcCCCcCCCc
Confidence            45666666666666666653111      113567777777777777777654

>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=99.23  E-value=7.9e-12  Score=78.05  Aligned_cols=41  Identities=24%  Similarity=0.591  Sum_probs=20.9

Q ss_pred             cccccccccCccCCCCCCCCCCCCCCCCCCccceecCCCCcCcccCCCC
Q psy16574          7 IQCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFARECATE   55 (152)
Q Consensus         7 ~~C~~C~~~GH~~~~Cp~~~~~~~~~~~~~~~C~~Cg~~GH~~~~Cp~~   55 (152)
                      ..||+|+++||++++||....        .+.||+|+++||++++||..
T Consensus         8 ~~C~~Cg~~GH~a~~C~~~~~--------~~~C~~Cg~~GH~ar~Cp~~   48 (63)
T 2cqf_A            8 DRCYNCGGLDHHAKECKLPPQ--------PKKCHFCQSISHMVASCPLK   48 (63)
T ss_dssp             CCCSSSCCSSSCTTTCCSCCC--------SSCCTTTCCSSSCTTTCTGG
T ss_pred             CcccccCCCCcChhhCCCCCC--------CCccCCcCCcCCccCcCCCc
Confidence            445566666666655554321        13455555555555555543

>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=99.23  E-value=1.1e-11  Score=77.35  Aligned_cols=49  Identities=27%  Similarity=0.577  Sum_probs=32.0

Q ss_pred             CccceecCCCCcCcccCCCC--CCcccccCCCCcccccCCCCCCcccccCC
Q psy16574         36 GIVCYKCNNYGHFARECATE--SVTCYNCSGQGHVAKDCTVKSSIICYNCN   84 (152)
Q Consensus        36 ~~~C~~Cg~~GH~~~~Cp~~--~~~C~~Cg~~GH~~~~Cp~~~~~~C~~Cg   84 (152)
                      .+.||+|+++||++++||..  ...||+|++.||++++||.......+.++
T Consensus         7 ~~~C~~Cg~~GH~a~~C~~~~~~~~C~~Cg~~GH~ar~Cp~~~~~~~~~~g   57 (63)
T 2cqf_A            7 GDRCYNCGGLDHHAKECKLPPQPKKCHFCQSISHMVASCPLKAQQGPSAQG   57 (63)
T ss_dssp             CCCCSSSCCSSSCTTTCCSCCCSSCCTTTCCSSSCTTTCTGGGCSCCCCSC
T ss_pred             CCcccccCCCCcChhhCCCCCCCCccCCcCCcCCccCcCCCccccCCccCC
Confidence            35788888888888888863  35677777777777777664333444443

>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=99.17  E-value=8.3e-12  Score=77.11  Aligned_cols=20  Identities=25%  Similarity=0.471  Sum_probs=11.5

Q ss_pred             ccccccccccccCCCCCCCc
Q psy16574        131 LTCYVCGHQGHLSYDCKLVQ  150 (152)
Q Consensus       131 ~~C~~Cg~~GH~~~~C~~~~  150 (152)
                      ..||+|++.||+++|||+..
T Consensus        31 ~~C~~Cg~~GH~ar~C~~~~   50 (60)
T 1cl4_A           31 GLCPRCKRGKHWANECKSKT   50 (60)
T ss_dssp             CSCSSCSSCSSCSTTCCCTT
T ss_pred             cceeECCCCCCccCcCCCcc
Confidence            45666666666666665543

>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=99.15  E-value=2.4e-11  Score=73.74  Aligned_cols=16  Identities=38%  Similarity=1.169  Sum_probs=6.9

Q ss_pred             cceecCCCCcCcccCC
Q psy16574         38 VCYKCNNYGHFARECA   53 (152)
Q Consensus        38 ~C~~Cg~~GH~~~~Cp   53 (152)
                      .||+|++.||++++||
T Consensus        14 ~C~~Cg~~GH~a~~C~   29 (55)
T 1a1t_A           14 KCFNCGKEGHIAKNCR   29 (55)
T ss_dssp             BCTTTCCBSSCGGGCS
T ss_pred             ceeeeCCCCcChhhcC
Confidence            3444444444444444

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

Probab=99.11  E-value=4.3e-11  Score=74.17  Aligned_cols=45  Identities=38%  Similarity=0.798  Sum_probs=24.1

Q ss_pred             cccccccccCccCCCCCCCCCCCCCCCCCCccceecCCCCcCcccCCCC
Q psy16574          7 IQCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFARECATE   55 (152)
Q Consensus         7 ~~C~~C~~~GH~~~~Cp~~~~~~~~~~~~~~~C~~Cg~~GH~~~~Cp~~   55 (152)
                      ..||+|++.||++++||.....    +...+.||+|+++||++++||+.
T Consensus         5 ~~C~~Cg~~GH~a~~C~~~~~~----~~~~~~C~~Cg~~GH~ar~C~~~   49 (61)
T 2ihx_A            5 GLCYTCGSPGHYQAQCPKKRKS----GNSRERCQLCNGMGHNAKQCRKR   49 (61)
T ss_dssp             TBCSSSCCBTCCGGGCTTTTSS----SCCCSBCTTTCCBSSCGGGCCCC
T ss_pred             CcccccCCCCeehhhCcCCcCC----CCCCCeeCCCCCCCCCcCCCcCC
Confidence            4566666666666666665311    00123455555555555555544

>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=99.09  E-value=3.8e-11  Score=74.09  Aligned_cols=21  Identities=33%  Similarity=0.714  Sum_probs=17.1

Q ss_pred             CcCCcccCCCCcCCCCCCCCC
Q psy16574         98 SKRCYACHQAGHMAKECPGQT  118 (152)
Q Consensus        98 ~~~C~~C~~~GH~~~~Cp~~~  118 (152)
                      ...||+|++.||+++|||+..
T Consensus        30 ~~~C~~Cg~~GH~ar~C~~~~   50 (60)
T 1cl4_A           30 PGLCPRCKRGKHWANECKSKT   50 (60)
T ss_dssp             CCSCSSCSSCSSCSTTCCCTT
T ss_pred             CcceeECCCCCCccCcCCCcc
Confidence            367888888888888888775

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

Probab=98.90  E-value=5.2e-10  Score=80.91  Aligned_cols=40  Identities=33%  Similarity=0.810  Sum_probs=29.2

Q ss_pred             CccceecCCCCcCcccCCCC--CCcccccCCCCcccccCCCC
Q psy16574         36 GIVCYKCNNYGHFARECATE--SVTCYNCSGQGHVAKDCTVK   75 (152)
Q Consensus        36 ~~~C~~Cg~~GH~~~~Cp~~--~~~C~~Cg~~GH~~~~Cp~~   75 (152)
                      ...||+|++.||++++||..  ...||+|++.||++++||..
T Consensus        97 ~~~C~~Cg~~GH~a~~C~~~~~~~~C~~Cg~~GH~~r~Cp~~  138 (148)
T 3ts2_A           97 GDRCYNCGGLDHHAKECKLPPQPKKCHFCQSINHMVASCPLK  138 (148)
T ss_dssp             SCCCTTTCCSSCCGGGCCSCCCCCCCTTTCCSSCCGGGCTTT
T ss_pred             CCcccEeCCccchhhhCCCCCCCCcccccCCcCCEeccCcCC
Confidence            35678887778888888763  35788888888888888763

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

Probab=98.89  E-value=5.9e-10  Score=80.61  Aligned_cols=39  Identities=36%  Similarity=0.877  Sum_probs=19.3

Q ss_pred             ccccCCCCCCCCCCCCCCC-CcCCcccCCCCcCCCCCCCC
Q psy16574         79 ICYNCNSSGHFARNCPNDS-SKRCYACHQAGHMAKECPGQ  117 (152)
Q Consensus        79 ~C~~Cg~~GH~~~~Cp~~~-~~~C~~C~~~GH~~~~Cp~~  117 (152)
                      .||+|++.||++++||... ...||+|++.||++++||+.
T Consensus        99 ~C~~Cg~~GH~a~~C~~~~~~~~C~~Cg~~GH~~r~Cp~~  138 (148)
T 3ts2_A           99 RCYNCGGLDHHAKECKLPPQPKKCHFCQSINHMVASCPLK  138 (148)
T ss_dssp             CCTTTCCSSCCGGGCCSCCCCCCCTTTCCSSCCGGGCTTT
T ss_pred             cccEeCCccchhhhCCCCCCCCcccccCCcCCEeccCcCC
Confidence            4555555555555555421 23455555555555555544

>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=98.11  E-value=9.1e-07  Score=46.47  Aligned_cols=22  Identities=27%  Similarity=0.931  Sum_probs=18.1

Q ss_pred             cccccccccccccCCCCCCCcC
Q psy16574        130 SLTCYVCGHQGHLSYDCKLVQK  151 (152)
Q Consensus       130 ~~~C~~Cg~~GH~~~~C~~~~~  151 (152)
                      .+.||||++.||+++||+.+++
T Consensus         6 ~~~C~nCgk~GH~ar~C~~prk   27 (29)
T 1nc8_A            6 VIRCWNCGKEGHSARQCRAPRR   27 (29)
T ss_dssp             CCBCTTTSCBSSCGGGCCSSSS
T ss_pred             CCEEEECCccccCHhHCccccc
Confidence            4679999999999999987754

>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=98.01  E-value=2.8e-06  Score=47.92  Aligned_cols=24  Identities=33%  Similarity=0.726  Sum_probs=18.1

Q ss_pred             CCccccccccccCccCCCCCCCCC
Q psy16574          4 TSTIQCYNCFDFGHYQYSCPQKSS   27 (152)
Q Consensus         4 ~~~~~C~~C~~~GH~~~~Cp~~~~   27 (152)
                      ...+.||+|++.|||+++||....
T Consensus         8 ~~~~~C~~Cgk~GH~ardCP~~~~   31 (40)
T 1a6b_B            8 LDRDQCAYCKEKGHWAKDCPKKPR   31 (40)
T ss_dssp             CCSSSCSSSCCTTCCTTSCSSSCC
T ss_pred             CCCCeeeECCCCCcchhhCcCCcc
Confidence            345678888888888888888653

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

Probab=97.95  E-value=2.4e-06  Score=44.85  Aligned_cols=21  Identities=33%  Similarity=0.735  Sum_probs=14.5

Q ss_pred             ccccccccccCccCCCCCCCC
Q psy16574          6 TIQCYNCFDFGHYQYSCPQKS   26 (152)
Q Consensus         6 ~~~C~~C~~~GH~~~~Cp~~~   26 (152)
                      .+.||||+++||++++||.+.
T Consensus         6 ~~~C~nCgk~GH~ar~C~~pr   26 (29)
T 1nc8_A            6 VIRCWNCGKEGHSARQCRAPR   26 (29)
T ss_dssp             CCBCTTTSCBSSCGGGCCSSS
T ss_pred             CCEEEECCccccCHhHCcccc
Confidence            456777777777777777653

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

Probab=97.92  E-value=4.4e-06  Score=47.09  Aligned_cols=21  Identities=29%  Similarity=0.616  Sum_probs=14.9

Q ss_pred             cccccccccccccCCCCCCCc
Q psy16574        130 SLTCYVCGHQGHLSYDCKLVQ  150 (152)
Q Consensus       130 ~~~C~~Cg~~GH~~~~C~~~~  150 (152)
                      ...||+|++.||+++|||+..
T Consensus        10 ~~~C~~Cgk~GH~ardCP~~~   30 (40)
T 1a6b_B           10 RDQCAYCKEKGHWAKDCPKKP   30 (40)
T ss_dssp             SSSCSSSCCTTCCTTSCSSSC
T ss_pred             CCeeeECCCCCcchhhCcCCc
Confidence            456777777777777777654

>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=97.71  E-value=1.1e-05  Score=48.71  Aligned_cols=20  Identities=40%  Similarity=0.881  Sum_probs=10.9

Q ss_pred             ccccccccccCccCCCCCCC
Q psy16574          6 TIQCYNCFDFGHYQYSCPQK   25 (152)
Q Consensus         6 ~~~C~~C~~~GH~~~~Cp~~   25 (152)
                      .+.||+|++.|||+++||..
T Consensus        23 ~~~C~~Cge~GH~ardCp~~   42 (56)
T 1u6p_A           23 RDQCAYCKEKGHWAKDCPKK   42 (56)
T ss_dssp             TTBCSSSCCBSSCGGGCTTC
T ss_pred             CCcceeCCCCCcccccCcCC
Confidence            34555555555555555554

>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=97.59  E-value=2.2e-05  Score=47.44  Aligned_cols=22  Identities=27%  Similarity=0.543  Sum_probs=17.3

Q ss_pred             ccccccccccccccCCCCCCCc
Q psy16574        129 MSLTCYVCGHQGHLSYDCKLVQ  150 (152)
Q Consensus       129 ~~~~C~~Cg~~GH~~~~C~~~~  150 (152)
                      ....||+|++.|||++|||+..
T Consensus        22 ~~~~C~~Cge~GH~ardCp~~~   43 (56)
T 1u6p_A           22 DRDQCAYCKEKGHWAKDCPKKP   43 (56)
T ss_dssp             CTTBCSSSCCBSSCGGGCTTCC
T ss_pred             CCCcceeCCCCCcccccCcCCc
Confidence            3467888888888888888754

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

Probab=97.15  E-value=0.00012  Score=44.00  Aligned_cols=18  Identities=39%  Similarity=1.028  Sum_probs=10.0

Q ss_pred             cccccccccCccCCCCCC
Q psy16574          7 IQCYNCFDFGHYQYSCPQ   24 (152)
Q Consensus         7 ~~C~~C~~~GH~~~~Cp~   24 (152)
                      ..||+|+++||++++||.
T Consensus         8 ~~C~kCGk~GH~~k~Cp~   25 (55)
T 2ysa_A            8 YTCFRCGKPGHYIKNCPT   25 (55)
T ss_dssp             CCCTTTCCTTSCGGGCSG
T ss_pred             CccccCCCcCcccccCCC
Confidence            345555555555555553

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

Probab=96.97  E-value=0.00018  Score=43.13  Aligned_cols=16  Identities=44%  Similarity=1.194  Sum_probs=9.9

Q ss_pred             cccccccccccCCCCC
Q psy16574        132 TCYVCGHQGHLSYDCK  147 (152)
Q Consensus       132 ~C~~Cg~~GH~~~~C~  147 (152)
                      .||+|++.||++.+||
T Consensus         9 ~C~kCGk~GH~~k~Cp   24 (55)
T 2ysa_A            9 TCFRCGKPGHYIKNCP   24 (55)
T ss_dssp             CCTTTCCTTSCGGGCS
T ss_pred             ccccCCCcCcccccCC
Confidence            5666666666666666

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

Probab=84.55  E-value=0.32  Score=24.26  Aligned_cols=19  Identities=26%  Similarity=0.583  Sum_probs=12.9

Q ss_pred             ccccccccccccCCCCCCC
Q psy16574        131 LTCYVCGHQGHLSYDCKLV  149 (152)
Q Consensus       131 ~~C~~Cg~~GH~~~~C~~~  149 (152)
                      .+|-+|...||-..||+..
T Consensus         4 pYCe~CE~FGH~t~~C~d~   22 (26)
T 2hqh_E            4 PYCEICEMFGHWATNCNDD   22 (26)
T ss_dssp             CEETTTTEESSCGGGCCTT
T ss_pred             ccchHHHHhCcccccCCcc
Confidence            4677777777777777654

>2yuc_A TNF receptor-associated factor 4; ZF-TRAF, cysteine-rich domain associated with ring and TRAF domains protein 1, malignant 62; NMR {Homo sapiens}

Probab=81.36  E-value=4.1  Score=24.63  Aligned_cols=10  Identities=20%  Similarity=0.840  Sum_probs=4.3

Q ss_pred             ccCCCCCCcc
Q psy16574         50 RECATESVTC   59 (152)
Q Consensus        50 ~~Cp~~~~~C   59 (152)
                      ..||.....|
T Consensus        10 ~~C~~~~v~C   19 (76)
T 2yuc_A           10 NTCSFNVIPC   19 (76)
T ss_dssp             CCCCCSCCBC
T ss_pred             HHCCCcccCC
Confidence            4444443444

---

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	152
d2exfa1	42	g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunod	5e-09
d2exfa1	42	g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunod	4e-07
d2exfa1	42	g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunod	3e-05

>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 = 47.2 bits (112), Expect = 5e-09
 Identities = 16/39 (41%), Positives = 22/39 (56%)

Query: 77  SIICYNCNSSGHFARNCPNDSSKRCYACHQAGHMAKECP 115
           ++ C+NC   GH ARNC     K C+ C + GH  K+C 
Sbjct: 1   NVKCFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDCT 39

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

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

 Score = 42.2 bits (99), Expect = 4e-07
 Identities = 13/40 (32%), Positives = 21/40 (52%)

Query: 56 SVTCYNCSGQGHVAKDCTVKSSIICYNCNSSGHFARNCPN 95
          +V C+NC  +GH A++C       C+ C   GH  ++C  
Sbjct: 1  NVKCFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDCTE 40

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

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

 Score = 37.1 bits (86), Expect = 3e-05
 Identities = 16/38 (42%), Positives = 20/38 (52%), Gaps = 1/38 (2%)

Query: 37 IVCYKCNNYGHFAREC-ATESVTCYNCSGQGHVAKDCT 73
          + C+ C   GH AR C A     C+ C  +GH  KDCT
Sbjct: 2  VKCFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDCT 39

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	152
d2exfa1	42	HIV nucleocapsid {Human immunodeficiency virus typ	99.46
d2exfa1	42	HIV nucleocapsid {Human immunodeficiency virus typ	99.43
d1nc8a_	29	HIV nucleocapsid {Human immunodeficiency virus typ	97.99
d1nc8a_	29	HIV nucleocapsid {Human immunodeficiency virus typ	97.98
d1dsqa_	26	Nucleic acid binding protein p14 {Mouse mammary tu	97.09
d1dsqa_	26	Nucleic acid binding protein p14 {Mouse mammary tu	97.04
d1a6bb_	40	Zinc finger protein ncp10 {Moloney murine leukemia	96.05
d1a6bb_	40	Zinc finger protein ncp10 {Moloney murine leukemia	95.68

>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=99.46  E-value=2.5e-14  Score=81.06  Aligned_cols=41  Identities=34%  Similarity=0.898  Sum_probs=29.7

Q ss_pred             cCCcccCCCCcCCCCCCCCCCCCCCCccccccccccccccccccCCCCCCCc
Q psy16574         99 KRCYACHQAGHMAKECPGQTAGKSPEPVVDMSLTCYVCGHQGHLSYDCKLVQ  150 (152)
Q Consensus        99 ~~C~~C~~~GH~~~~Cp~~~~~~~~~~~~~~~~~C~~Cg~~GH~~~~C~~~~  150 (152)
                      +.||+|++.||+++|||...           ...||+|++.||++.|||+++
T Consensus         2 i~C~~Cg~~GH~~~~Cp~~~-----------~~~C~~Cg~~GH~~~~Cp~rq   42 (42)
T d2exfa1           2 VKCFNCGKEGHTARNCRAPR-----------KKGCWKCGKEGHQMKDCTERQ   42 (42)
T ss_dssp             CCCTTTCCSSSCTTTCSSCC-----------CSSCSSSCCSSSCTTTCCSSC
T ss_pred             CccccCCCcCcCcccCcCCC-----------cCccccCCCCCeecccCCCCC
Confidence            56777777777777777642           246888888888888887764

>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=99.43  E-value=4.2e-14  Score=80.10  Aligned_cols=41  Identities=29%  Similarity=0.788  Sum_probs=31.6

Q ss_pred             ccccccccccCccCCCCCCCCCCCCCCCCCCccceecCCCCcCcccCCCC
Q psy16574          6 TIQCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFARECATE   55 (152)
Q Consensus         6 ~~~C~~C~~~GH~~~~Cp~~~~~~~~~~~~~~~C~~Cg~~GH~~~~Cp~~   55 (152)
                      ++.||+|++.||++++||.+.         ...|++|++.||++++||..
T Consensus         1 ni~C~~Cg~~GH~~~~Cp~~~---------~~~C~~Cg~~GH~~~~Cp~r   41 (42)
T d2exfa1           1 NVKCFNCGKEGHTARNCRAPR---------KKGCWKCGKEGHQMKDCTER   41 (42)
T ss_dssp             CCCCTTTCCSSSCTTTCSSCC---------CSSCSSSCCSSSCTTTCCSS
T ss_pred             CCccccCCCcCcCcccCcCCC---------cCccccCCCCCeecccCCCC
Confidence            467888888888888888763         24688888888888888864

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

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

Probab=97.99  E-value=8.3e-07  Score=44.21  Aligned_cols=22  Identities=32%  Similarity=0.703  Sum_probs=14.4

Q ss_pred             CccccccccccCccCCCCCCCC
Q psy16574          5 STIQCYNCFDFGHYQYSCPQKS   26 (152)
Q Consensus         5 ~~~~C~~C~~~GH~~~~Cp~~~   26 (152)
                      ..+.|||||++||++++|..+.
T Consensus         5 ~~ikCfNCGkeGH~ar~CrAPR   26 (29)
T d1nc8a_           5 KVIRCWNCGKEGHSARQCRAPR   26 (29)
T ss_dssp             CCCBCTTTSCBSSCGGGCCSSS
T ss_pred             ceeEeecCCccchhhhhccCcc
Confidence            3456777777777777776553

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

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

Probab=97.98  E-value=1.2e-06  Score=43.67  Aligned_cols=22  Identities=27%  Similarity=0.931  Sum_probs=17.8

Q ss_pred             cccccccccccccCCCCCCCcC
Q psy16574        130 SLTCYVCGHQGHLSYDCKLVQK  151 (152)
Q Consensus       130 ~~~C~~Cg~~GH~~~~C~~~~~  151 (152)
                      .+.|||||++||++++|.-+++
T Consensus         6 ~ikCfNCGkeGH~ar~CrAPRk   27 (29)
T d1nc8a_           6 VIRCWNCGKEGHSARQCRAPRR   27 (29)
T ss_dssp             CCBCTTTSCBSSCGGGCCSSSS
T ss_pred             eeEeecCCccchhhhhccCccc
Confidence            5688888888888888887764

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

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

Probab=97.09  E-value=0.00013  Score=34.60  Aligned_cols=20  Identities=25%  Similarity=0.713  Sum_probs=14.3

Q ss_pred             ccccccccccCccCCCCCCC
Q psy16574          6 TIQCYNCFDFGHYQYSCPQK   25 (152)
Q Consensus         6 ~~~C~~C~~~GH~~~~Cp~~   25 (152)
                      +.+||.||+.||+.++|...
T Consensus         2 gpvcfscgktghikkdck~e   21 (26)
T d1dsqa_           2 GPVCFSCGKTGHIKRDCKEE   21 (26)
T ss_dssp             CCBCTTTCCBSSCTTTTTCC
T ss_pred             CCEEEecCCcccchhhhhhh
Confidence            45777777777777777654

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

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

Probab=97.04  E-value=0.00014  Score=34.50  Aligned_cols=19  Identities=42%  Similarity=1.059  Sum_probs=15.3

Q ss_pred             ccccccccccccCCCCCCC
Q psy16574        131 LTCYVCGHQGHLSYDCKLV  149 (152)
Q Consensus       131 ~~C~~Cg~~GH~~~~C~~~  149 (152)
                      ..||.||+.||+.+||.+.
T Consensus         3 pvcfscgktghikkdck~e   21 (26)
T d1dsqa_           3 PVCFSCGKTGHIKRDCKEE   21 (26)
T ss_dssp             CBCTTTCCBSSCTTTTTCC
T ss_pred             CEEEecCCcccchhhhhhh
Confidence            4788888888888888764

>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=96.05  E-value=0.003  Score=33.27  Aligned_cols=23  Identities=39%  Similarity=0.982  Sum_probs=17.6

Q ss_pred             CcCCcccCCCCcCCCCCCCCCCC
Q psy16574         98 SKRCYACHQAGHMAKECPGQTAG  120 (152)
Q Consensus        98 ~~~C~~C~~~GH~~~~Cp~~~~~  120 (152)
                      ..+|..|.+.||+++|||...++
T Consensus        10 kDQCAyCke~GHW~~dCPkkprg   32 (40)
T d1a6bb_          10 RDQCAYCKEKGHWAKDCPKKPRG   32 (40)
T ss_dssp             SSSCSSSCCTTCCTTSCSSSCCC
T ss_pred             chhhHHHhhcCchhhhCccCCCC
Confidence            35788888888888888877644

>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=95.68  E-value=0.0033  Score=33.11  Aligned_cols=23  Identities=35%  Similarity=0.761  Sum_probs=14.8

Q ss_pred             CCccccccccccCccCCCCCCCC
Q psy16574          4 TSTIQCYNCFDFGHYQYSCPQKS   26 (152)
Q Consensus         4 ~~~~~C~~C~~~GH~~~~Cp~~~   26 (152)
                      +....|--|.+.|||+++||...
T Consensus         8 L~kDQCAyCke~GHW~~dCPkkp   30 (40)
T d1a6bb_           8 LDRDQCAYCKEKGHWAKDCPKKP   30 (40)
T ss_dssp             CCSSSCSSSCCTTCCTTSCSSSC
T ss_pred             ccchhhHHHhhcCchhhhCccCC
Confidence            34456677777777777777653