Psyllid ID: psy16600

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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

---

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 psy16600         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 psy16600        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 psy16600          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 psy16600         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 psy16600         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 psy16600         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 psy16600         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 psy16600         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 psy16600          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 psy16600         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 psy16600        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 psy16600          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 psy16600          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 psy16600         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 psy16600        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 psy16600         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 psy16600          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 psy16600         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 psy16600        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 psy16600         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 psy16600          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 psy16600         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 psy16600         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 psy16600         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 psy16600        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 psy16600          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 psy16600          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 psy16600        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 psy16600          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 psy16600        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 psy16600          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 psy16600        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 psy16600        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 psy16600         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 psy16600         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 psy16600          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 psy16600          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 psy16600        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 psy16600          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 psy16600        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 psy16600         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 psy16600          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