Psyllid ID: psy12393

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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
DIVDSLCDLHLEKKSFKQPPSAYLCHLCFVGGHYITDCPLFNMSPFSKYRQLFLFQARPKGEGLTPYQGKKRCFGEYKCSKCKRKWMSGNSWANMGQECIKCNINVYPHKQRPLEKPDGLDVSDQSKVHPMYLCEKCKQLGYYCRKYCTPSSVRR
Secondary Structure (PSIPRED)
cHHHHHHHHHccccccccccccccEEEcccccEEEEcccccccccccHHHHHHHcccccccccccccccccccccEEEccccccccccccEEcccccccccccccccEEccEEccccccccccccccccHHHHHHHHHHcccccccccccccccc
Secondary Structure Prediction (SSPRO)
cHHHHHHHcccccccccccccccEEEEEEccccEccccccccccccccccccccHcccccccccccccccccEEEEEEccHccccccccccHHccccEHcccccccccccccccccccccccccccccccHHHHHHHHHHccccccccccccccc
Coil and Loop (DISEMBL)
DIVDSLCDLhlekksfkqppsaylchlcfvgghyitdcplfnmspfskYRQLFLFqarpkgegltpyqgkkrcfgeykcskckrkwmsgnswanMGQECIkcninvyphkqrplekpdgldvsdqskvhpmylcekckqlgyycrkyctpssvrr
Flexible Loop (DISEMBL)
DIVDSLCDLHLekksfkqppsAYLCHLCFVGGHYITDCPLFNMSPFSKYRQLFLFQArpkgegltpyqgkkrcfgeyKCSKCKRKWMSGNSWANMGQECIKCNINVYPHKQRPLEKPDGLDVSDQSKVHPMYLcekckqlgyycrkyctpssvrr
Low Complexity Region (SEG)
DIVDSLCDLHLEKKSFKQPPSAYLCHLCFVGGHYITDCPLFNMSPFSKYRQLFLFQARPKGEGLTPYQGKKRCFGEYKCSKCKRKWMSGNSWANMGQECIKCNINVYPHKQRPLEKPDGLDVSDQSKVHPMYLCEKCKQLGYYCRKYCTPSSVRR
Disordered region (IsUnstruct)
******CDLHL********PSAYLCHLCFVGGHYITDCPLFNMSPFSKYRQLFLFQARPKGEGLTPYQGKKRCFGEYKCSKCKRKWMSGNSWANMGQECIKCNINVYPH******************VHPMYLCEKCKQLGYYCRKYCT******
Disordered Region (DISOPRED)
***DSLC****************LCHLCFVGGHYIT***********************************RCFGEYKCSKCKRKWMSGNSWANMGQECIKCNINVYPHKQ********************YLCEKCKQLGYYCRKYCTPS*V**
Disordered Region (DISEMBL)
DIVDSLCDLHLEKKSFKQPPSAYLCHLCFVGGHYITDCPLFNMSPFSKYRQLFLFQARPKGEGLTPYQGKKRCFGEYKCSKCKRKWMSGNSWANMGQECIKCNINVYPHKQRPLEKPDGLDVSDQSKVHPMYLCEKCKQLGYYCRKYCTPSSVRR
Disordered Region (DISPRO)
D****LCDLHLEKKSFKQPPSAYLCHLCFVGGHYITDCPLFNMSPFSKYRQLFLFQARPKGEGLTPYQGKKRCFGEYKCSKCKRKWMSGNSWANMGQECIKCNINVYPHKQRPLEKPDGLDVSDQSKVHPMYLCEKCKQLGYYCRKYCT******
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
DIVDSLCDLHLEKKSFKQPPSAYLCHLCFVGGHYITDCPLFNMSPFSKYRQLFLFQARPKGEGLTPYQGKKRCFGEYKCSKCKRKWMSGNSWANMGQECIKCNINVYPHKQRPLEKPDGLDVSDQSKVHPMYLCEKCKQLGYYCRKYCTPSSVRR
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	155	2.2.26 [Sep-21-2011]
Q8N2G6	241	Zinc finger CCHC domain-c	yes	N/A	0.838	0.539	0.704	1e-54
B2RVL6	241	Zinc finger CCHC domain-c	yes	N/A	0.832	0.535	0.709	1e-54
Q8HXK7	241	Zinc finger CCHC domain-c	N/A	N/A	0.832	0.535	0.702	2e-54

>sp|Q8N2G6|ZCH24_HUMAN Zinc finger CCHC domain-containing protein 24 OS=Homo sapiens GN=ZCCHC24 PE=1 SV=1

 Score =  211 bits (538), Expect = 1e-54,   Method: Compositional matrix adjust.
 Identities = 105/149 (70%), Positives = 112/149 (75%), Gaps = 19/149 (12%)

Query: 1   DIVDSLCDLHL---EKKSFKQPPSAYLCHLCFVGGHYITDCPLFNMSPFSKYRQLFLFQA 57
            + +   DL L    +K  K+PP  YLCHLCF  GHYI DCP                QA
Sbjct: 107 SLTEHFSDLTLTSEARKPSKRPPPNYLCHLCFNKGHYIKDCP----------------QA 150

Query: 58  RPKGEGLTPYQGKKRCFGEYKCSKCKRKWMSGNSWANMGQECIKCNINVYPHKQRPLEKP 117
           RPKGEGLTPYQGKKRCFGEYKC KCKRKWMSGNSWANMGQECIKC+INVYPHKQRPLEKP
Sbjct: 151 RPKGEGLTPYQGKKRCFGEYKCPKCKRKWMSGNSWANMGQECIKCHINVYPHKQRPLEKP 210

Query: 118 DGLDVSDQSKVHPMYLCEKCKQLGYYCRK 146
           DGLDVSDQSK HP +LCEKCK LGYYCR+
Sbjct: 211 DGLDVSDQSKEHPQHLCEKCKVLGYYCRR 239

Homo sapiens (taxid: 9606)

>sp|B2RVL6|ZCH24_MOUSE Zinc finger CCHC domain-containing protein 24 OS=Mus musculus GN=Zcchc24 PE=2 SV=1

 Score =  211 bits (537), Expect = 1e-54,   Method: Compositional matrix adjust.
 Identities = 105/148 (70%), Positives = 112/148 (75%), Gaps = 19/148 (12%)

Query: 2   IVDSLCDLHL---EKKSFKQPPSAYLCHLCFVGGHYITDCPLFNMSPFSKYRQLFLFQAR 58
           + +   DL L    +K  K+PP  YLCHLCF  GHYI DCP                QAR
Sbjct: 108 LTEHFSDLTLTSEARKPSKRPPPNYLCHLCFNKGHYIKDCP----------------QAR 151

Query: 59  PKGEGLTPYQGKKRCFGEYKCSKCKRKWMSGNSWANMGQECIKCNINVYPHKQRPLEKPD 118
           PKGEGLTPYQGKKRCFGEYKC KCKRKWMSGNSWANMGQECIKC+INVYPHKQRPLEKPD
Sbjct: 152 PKGEGLTPYQGKKRCFGEYKCPKCKRKWMSGNSWANMGQECIKCHINVYPHKQRPLEKPD 211

Query: 119 GLDVSDQSKVHPMYLCEKCKQLGYYCRK 146
           GLDVSDQSK HP +LCEKCK LGYYCR+
Sbjct: 212 GLDVSDQSKEHPQHLCEKCKVLGYYCRR 239

Mus musculus (taxid: 10090)

>sp|Q8HXK7|ZCH24_MACFA Zinc finger CCHC domain-containing protein 24 OS=Macaca fascicularis GN=ZCCHC24 PE=2 SV=1

 Score =  210 bits (535), Expect = 2e-54,   Method: Compositional matrix adjust.
 Identities = 104/148 (70%), Positives = 112/148 (75%), Gaps = 19/148 (12%)

Query: 2   IVDSLCDLHL---EKKSFKQPPSAYLCHLCFVGGHYITDCPLFNMSPFSKYRQLFLFQAR 58
           + +   DL L    +K  K+PP  YLCHLCF  GHYI DCP                QAR
Sbjct: 108 LTEHFSDLTLTSEARKPSKRPPPNYLCHLCFNKGHYIKDCP----------------QAR 151

Query: 59  PKGEGLTPYQGKKRCFGEYKCSKCKRKWMSGNSWANMGQECIKCNINVYPHKQRPLEKPD 118
           PKGEGLTPYQGKKRCFGEYKC KCKRKWMSGNSWANMGQECIKC+INVYPHKQRPLEKPD
Sbjct: 152 PKGEGLTPYQGKKRCFGEYKCPKCKRKWMSGNSWANMGQECIKCHINVYPHKQRPLEKPD 211

Query: 119 GLDVSDQSKVHPMYLCEKCKQLGYYCRK 146
           GLDVSDQSK HP +LCE+CK LGYYCR+
Sbjct: 212 GLDVSDQSKEHPQHLCEECKVLGYYCRR 239

Macaca fascicularis (taxid: 9541)

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	155
307174140	237	Zinc finger CCHC domain-containing prote	0.838	0.548	0.734	7e-56
332031354	285	Zinc finger CCHC domain-containing prote	0.825	0.449	0.703	4e-55
322797537	240	hypothetical protein SINV_05085 [Solenop	0.838	0.541	0.694	6e-55
291230954	246	PREDICTED: Zinc finger, CCHC domain cont	0.838	0.528	0.721	2e-54
198433126	240	PREDICTED: similar to mCG17917 [Ciona in	0.838	0.541	0.709	5e-54
383852792	233	PREDICTED: zinc finger CCHC domain-conta	0.838	0.557	0.714	6e-54
443717834	190	hypothetical protein CAPTEDRAFT_136592 [	0.838	0.684	0.702	1e-53
91089623	225	PREDICTED: similar to mCG17917 [Triboliu	0.838	0.577	0.664	1e-53
348529009	239	PREDICTED: zinc finger CCHC domain-conta	0.832	0.539	0.716	1e-53
383852824	219	PREDICTED: zinc finger CCHC domain-conta	0.838	0.593	0.714	1e-53

>gi|307174140|gb|EFN64798.1| Zinc finger CCHC domain-containing protein 24 [Camponotus floridanus]

 Score =  221 bits (563), Expect = 7e-56,   Method: Compositional matrix adjust.
 Identities = 108/147 (73%), Positives = 116/147 (78%), Gaps = 17/147 (11%)

Query: 1   DIVDSLCDLHL-EKKSFKQPPSAYLCHLCFVGGHYITDCPLFNMSPFSKYRQLFLFQARP 59
           D+ +   DL L ++K  K+PPS YLCHLCF  GHYI DCP                QARP
Sbjct: 102 DLAEHFTDLSLNDRKPTKRPPSTYLCHLCFKKGHYIKDCP----------------QARP 145

Query: 60  KGEGLTPYQGKKRCFGEYKCSKCKRKWMSGNSWANMGQECIKCNINVYPHKQRPLEKPDG 119
           KGEGLTPYQGKKRCFGEYKC KCKRKWMSGNSWANMGQECIKC+INVYPHKQRPLEKPDG
Sbjct: 146 KGEGLTPYQGKKRCFGEYKCPKCKRKWMSGNSWANMGQECIKCHINVYPHKQRPLEKPDG 205

Query: 120 LDVSDQSKVHPMYLCEKCKQLGYYCRK 146
           LDVSDQSKVHP +LCEKCK LGYYCR+
Sbjct: 206 LDVSDQSKVHPQHLCEKCKTLGYYCRR 232

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332031354|gb|EGI70867.1| Zinc finger CCHC domain-containing protein 24 [Acromyrmex echinatior]

 Score =  219 bits (557), Expect = 4e-55,   Method: Compositional matrix adjust.
 Identities = 107/152 (70%), Positives = 116/152 (76%), Gaps = 24/152 (15%)

Query: 3   VDSLCDLHL--------EKKSFKQPPSAYLCHLCFVGGHYITDCPLFNMSPFSKYRQLFL 54
            +S+ DL +        ++K  K+PPS YLCHLCF  GHYI DCP               
Sbjct: 145 TESIADLAVHFNELTVGDRKPAKKPPSTYLCHLCFKKGHYIKDCP--------------- 189

Query: 55  FQARPKGEGLTPYQGKKRCFGEYKCSKCKRKWMSGNSWANMGQECIKCNINVYPHKQRPL 114
            QARPKGEGLTPYQGKKRCFGEYKC KCKRKWMSGNSWANMGQECIKC+INVYPHKQRPL
Sbjct: 190 -QARPKGEGLTPYQGKKRCFGEYKCPKCKRKWMSGNSWANMGQECIKCHINVYPHKQRPL 248

Query: 115 EKPDGLDVSDQSKVHPMYLCEKCKQLGYYCRK 146
           EKPDGLDVSDQSKVHP +LCEKCK LGYYCR+
Sbjct: 249 EKPDGLDVSDQSKVHPQHLCEKCKTLGYYCRR 280

Source: Acromyrmex echinatior

Species: Acromyrmex echinatior

Genus: Acromyrmex

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|322797537|gb|EFZ19581.1| hypothetical protein SINV_05085 [Solenopsis invicta]

 Score =  218 bits (555), Expect = 6e-55,   Method: Compositional matrix adjust.
 Identities = 107/154 (69%), Positives = 117/154 (75%), Gaps = 24/154 (15%)

Query: 1   DIVDSLCDLHL--------EKKSFKQPPSAYLCHLCFVGGHYITDCPLFNMSPFSKYRQL 52
           +  +S+ DL +        ++K  K+PPS YLCHLCF  GHYI DCP             
Sbjct: 98  NTTESIADLAVPFNELAVGDRKPAKKPPSTYLCHLCFKKGHYIKDCP------------- 144

Query: 53  FLFQARPKGEGLTPYQGKKRCFGEYKCSKCKRKWMSGNSWANMGQECIKCNINVYPHKQR 112
              QARPKGEGLTPYQGKKRCFGEYKC KCKRKWMSGNSWANMGQECIKC+INVYPHKQR
Sbjct: 145 ---QARPKGEGLTPYQGKKRCFGEYKCPKCKRKWMSGNSWANMGQECIKCHINVYPHKQR 201

Query: 113 PLEKPDGLDVSDQSKVHPMYLCEKCKQLGYYCRK 146
           PLEKPDGLDVSDQSKVHP +LCEKCK LGYYCR+
Sbjct: 202 PLEKPDGLDVSDQSKVHPQHLCEKCKTLGYYCRR 235

Source: Solenopsis invicta

Species: Solenopsis invicta

Genus: Solenopsis

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|291230954|ref|XP_002735427.1| PREDICTED: Zinc finger, CCHC domain containing 24-like isoform 1 [Saccoglossus kowalevskii]

 Score =  216 bits (551), Expect = 2e-54,   Method: Compositional matrix adjust.
 Identities = 109/151 (72%), Positives = 114/151 (75%), Gaps = 21/151 (13%)

Query: 1   DIVDSLCDLHL-----EKKSFKQPPSAYLCHLCFVGGHYITDCPLFNMSPFSKYRQLFLF 55
           DI D   DL L     E+K  K+PP  YLCHLCF  GHYI DCP                
Sbjct: 110 DIADQFSDLTLGNPLIERKREKRPPPTYLCHLCFQKGHYIKDCP---------------- 153

Query: 56  QARPKGEGLTPYQGKKRCFGEYKCSKCKRKWMSGNSWANMGQECIKCNINVYPHKQRPLE 115
           QARPKGEGLTPYQGKKRCFGEYKC KCKRKWMSGNSWANMGQECIKC+INVYPHKQRPLE
Sbjct: 154 QARPKGEGLTPYQGKKRCFGEYKCPKCKRKWMSGNSWANMGQECIKCHINVYPHKQRPLE 213

Query: 116 KPDGLDVSDQSKVHPMYLCEKCKQLGYYCRK 146
           KPDGLDVSDQSK HP +LCEKCK LGYYCR+
Sbjct: 214 KPDGLDVSDQSKEHPQHLCEKCKALGYYCRR 244

Source: Saccoglossus kowalevskii

Species: Saccoglossus kowalevskii

Genus: Saccoglossus

Family: Harrimaniidae

Class: Enteropneusta

Phylum: Hemichordata

Superkingdom: Eukaryota

>gi|198433126|ref|XP_002127125.1| PREDICTED: similar to mCG17917 [Ciona intestinalis]

 Score =  215 bits (547), Expect = 5e-54,   Method: Compositional matrix adjust.
 Identities = 105/148 (70%), Positives = 115/148 (77%), Gaps = 18/148 (12%)

Query: 1   DIVDSLCDLHL--EKKSFKQPPSAYLCHLCFVGGHYITDCPLFNMSPFSKYRQLFLFQAR 58
           D+V+   DL L  + ++ K PP+ YLCHLCF  GHYI DCP                 AR
Sbjct: 107 DLVEGFGDLTLGFQTQTTKLPPANYLCHLCFTKGHYIKDCP----------------HAR 150

Query: 59  PKGEGLTPYQGKKRCFGEYKCSKCKRKWMSGNSWANMGQECIKCNINVYPHKQRPLEKPD 118
           PKGEGLTPYQGKKRCFGEYKCSKCKRKWMSGNSWANMGQ+CIKC+INVYPHKQRPLEKPD
Sbjct: 151 PKGEGLTPYQGKKRCFGEYKCSKCKRKWMSGNSWANMGQDCIKCHINVYPHKQRPLEKPD 210

Query: 119 GLDVSDQSKVHPMYLCEKCKQLGYYCRK 146
           GLDVSDQSK HP +LCEKCK LGYYCR+
Sbjct: 211 GLDVSDQSKEHPQHLCEKCKALGYYCRR 238

Source: Ciona intestinalis

Species: Ciona intestinalis

Genus: Ciona

Family: Cionidae

Order: Enterogona

Class: Ascidiacea

Phylum: Chordata

Superkingdom: Eukaryota

>gi|383852792|ref|XP_003701909.1| PREDICTED: zinc finger CCHC domain-containing protein 24-like [Megachile rotundata]

 Score =  215 bits (547), Expect = 6e-54,   Method: Compositional matrix adjust.
 Identities = 105/147 (71%), Positives = 114/147 (77%), Gaps = 17/147 (11%)

Query: 1   DIVDSLCDLHL-EKKSFKQPPSAYLCHLCFVGGHYITDCPLFNMSPFSKYRQLFLFQARP 59
           +I D   DL+L + K  K+PP  YLCHLCF  GHYI +CP                QARP
Sbjct: 101 EITDRFADLNLLDAKPTKRPPPTYLCHLCFNKGHYIKNCP----------------QARP 144

Query: 60  KGEGLTPYQGKKRCFGEYKCSKCKRKWMSGNSWANMGQECIKCNINVYPHKQRPLEKPDG 119
           KGEGLTPYQGKKRCFGEYKC KCKRKWMSGNSWANMGQECIKC +NVYPHKQRPLEKPDG
Sbjct: 145 KGEGLTPYQGKKRCFGEYKCPKCKRKWMSGNSWANMGQECIKCRVNVYPHKQRPLEKPDG 204

Query: 120 LDVSDQSKVHPMYLCEKCKQLGYYCRK 146
           LDVSDQSKVHP +LC+KCK LGYYCR+
Sbjct: 205 LDVSDQSKVHPQHLCQKCKTLGYYCRR 231

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|443717834|gb|ELU08722.1| hypothetical protein CAPTEDRAFT_136592 [Capitella teleta]

 Score =  214 bits (545), Expect = 1e-53,   Method: Compositional matrix adjust.
 Identities = 104/148 (70%), Positives = 117/148 (79%), Gaps = 18/148 (12%)

Query: 1   DIVDSLCDLHL--EKKSFKQPPSAYLCHLCFVGGHYITDCPLFNMSPFSKYRQLFLFQAR 58
           D+ D   +L L  ++K  K+PP++YLCHLCF  GHYI DCP                QAR
Sbjct: 57  DLTDHFSELSLALDRKPSKKPPNSYLCHLCFQKGHYIKDCP----------------QAR 100

Query: 59  PKGEGLTPYQGKKRCFGEYKCSKCKRKWMSGNSWANMGQECIKCNINVYPHKQRPLEKPD 118
           PKGEGLTPYQGKKRCFGEYKC KCKRKWMSGNSWANMGQECIKC+INV+PHKQRPLEKPD
Sbjct: 101 PKGEGLTPYQGKKRCFGEYKCPKCKRKWMSGNSWANMGQECIKCHINVFPHKQRPLEKPD 160

Query: 119 GLDVSDQSKVHPMYLCEKCKQLGYYCRK 146
           GLDVSDQSK+HP +LC+KCK LGYYCR+
Sbjct: 161 GLDVSDQSKIHPQHLCQKCKMLGYYCRR 188

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

>gi|91089623|ref|XP_973411.1| PREDICTED: similar to mCG17917 [Tribolium castaneum] gi|270012610|gb|EFA09058.1| hypothetical protein TcasGA2_TC006773 [Tribolium castaneum]

 Score =  214 bits (544), Expect = 1e-53,   Method: Compositional matrix adjust.
 Identities = 97/146 (66%), Positives = 116/146 (79%), Gaps = 16/146 (10%)

Query: 1   DIVDSLCDLHLEKKSFKQPPSAYLCHLCFVGGHYITDCPLFNMSPFSKYRQLFLFQARPK 60
           D+ +   DL L+K++ K+PP +Y+CHLCF  GHYI DCP                +ARPK
Sbjct: 93  DLTEQFADLALDKRTLKRPPPSYMCHLCFQKGHYIKDCP----------------KARPK 136

Query: 61  GEGLTPYQGKKRCFGEYKCSKCKRKWMSGNSWANMGQECIKCNINVYPHKQRPLEKPDGL 120
           GEG TPYQG+KRCFGE+KC KCKRKWMSGNSWAN+GQ+CIKC INVYPHKQRPLEKPDGL
Sbjct: 137 GEGKTPYQGRKRCFGEFKCPKCKRKWMSGNSWANIGQDCIKCQINVYPHKQRPLEKPDGL 196

Query: 121 DVSDQSKVHPMYLCEKCKQLGYYCRK 146
           DVSDQSKVHP +LC+KC++LG+YCR+
Sbjct: 197 DVSDQSKVHPQHLCQKCRELGFYCRR 222

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|348529009|ref|XP_003452007.1| PREDICTED: zinc finger CCHC domain-containing protein 24-like [Oreochromis niloticus]

 Score =  214 bits (544), Expect = 1e-53,   Method: Compositional matrix adjust.
 Identities = 106/148 (71%), Positives = 112/148 (75%), Gaps = 19/148 (12%)

Query: 2   IVDSLCDLHLE---KKSFKQPPSAYLCHLCFVGGHYITDCPLFNMSPFSKYRQLFLFQAR 58
           + D   DL L    +K  K+PP  YLCHLCF  GHYI DCP                QAR
Sbjct: 106 LTDHFSDLSLSSETRKPNKRPPPNYLCHLCFNKGHYIKDCP----------------QAR 149

Query: 59  PKGEGLTPYQGKKRCFGEYKCSKCKRKWMSGNSWANMGQECIKCNINVYPHKQRPLEKPD 118
           PKGEGLTPYQGKKRCFGEYKC KCKRKWMSGNSWANMGQECIKC+INVYPHKQRPLEKPD
Sbjct: 150 PKGEGLTPYQGKKRCFGEYKCPKCKRKWMSGNSWANMGQECIKCHINVYPHKQRPLEKPD 209

Query: 119 GLDVSDQSKVHPMYLCEKCKQLGYYCRK 146
           GLDVSDQSK HP +LCEKCK LGYYCR+
Sbjct: 210 GLDVSDQSKEHPQHLCEKCKVLGYYCRR 237

Source: Oreochromis niloticus

Species: Oreochromis niloticus

Genus: Oreochromis

Family: Cichlidae

Order: Perciformes

Class: Actinopterygii

Phylum: Chordata

Superkingdom: Eukaryota

>gi|383852824|ref|XP_003701925.1| PREDICTED: zinc finger CCHC domain-containing protein 24-like [Megachile rotundata]

 Score =  214 bits (544), Expect = 1e-53,   Method: Compositional matrix adjust.
 Identities = 105/147 (71%), Positives = 114/147 (77%), Gaps = 17/147 (11%)

Query: 1   DIVDSLCDLHL-EKKSFKQPPSAYLCHLCFVGGHYITDCPLFNMSPFSKYRQLFLFQARP 59
           +I D   DL+L + K  K+PP  YLCHLCF  GHYI +CP                QARP
Sbjct: 87  EITDRFADLNLLDAKPTKRPPPTYLCHLCFNKGHYIKNCP----------------QARP 130

Query: 60  KGEGLTPYQGKKRCFGEYKCSKCKRKWMSGNSWANMGQECIKCNINVYPHKQRPLEKPDG 119
           KGEGLTPYQGKKRCFGEYKC KCKRKWMSGNSWANMGQECIKC +NVYPHKQRPLEKPDG
Sbjct: 131 KGEGLTPYQGKKRCFGEYKCPKCKRKWMSGNSWANMGQECIKCRVNVYPHKQRPLEKPDG 190

Query: 120 LDVSDQSKVHPMYLCEKCKQLGYYCRK 146
           LDVSDQSKVHP +LC+KCK LGYYCR+
Sbjct: 191 LDVSDQSKVHPQHLCQKCKTLGYYCRR 217

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

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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	155
ZFIN|ZDB-GENE-030131-3573	238	zcchc24 "zinc finger, CCHC dom	0.832	0.542	0.716	4.8e-55
UNIPROTKB|E1BQZ5	239	ZCCHC24 "Uncharacterized prote	0.832	0.539	0.709	1.3e-54
UNIPROTKB|E1BIP9	202	LOC616669 "Uncharacterized pro	0.761	0.584	0.761	2.1e-54
UNIPROTKB|F1P7U6	258	ZCCHC24 "Uncharacterized prote	0.761	0.457	0.761	2.1e-54
UNIPROTKB|Q8N2G6	241	ZCCHC24 "Zinc finger CCHC doma	0.761	0.489	0.761	2.1e-54
MGI|MGI:1919168	241	Zcchc24 "zinc finger, CCHC dom	0.761	0.489	0.761	2.1e-54
RGD|1306164	241	Zcchc24 "zinc finger, CCHC dom	0.761	0.489	0.761	2.1e-54
UNIPROTKB|I3LHN8	166	ZCCHC24 "Uncharacterized prote	0.535	0.5	0.727	4.4e-36
WB|WBGene00012794	267	Y43E12A.2 [Caenorhabditis eleg	0.541	0.314	0.5	1.6e-22

ZFIN|ZDB-GENE-030131-3573 zcchc24 "zinc finger, CCHC domain containing 24" [Danio rerio (taxid:7955)]

 Score = 568 (205.0 bits), Expect = 4.8e-55, P = 4.8e-55
 Identities = 106/148 (71%), Positives = 112/148 (75%)

Query:     2 IVDSLCDLHLE---KKSFKQPPSAYLCHLCFVGGHYITDCPLFNMSPFSKYRQLFLFQAR 58
             + D   DL L    +K  K+PP  YLCHLCF  GHYI DCP                QAR
Sbjct:   105 LTDHFSDLSLSSEPRKPSKRPPPNYLCHLCFNKGHYIKDCP----------------QAR 148

Query:    59 PKGEGLTPYQGKKRCFGEYKCSKCKRKWMSGNSWANMGQECIKCNINVYPHKQRPLEKPD 118
             PKGEGLTPYQGKKRCFGEYKC KCKRKWMSGNSWANMGQECIKC+INVYPHKQRPLEKPD
Sbjct:   149 PKGEGLTPYQGKKRCFGEYKCPKCKRKWMSGNSWANMGQECIKCHINVYPHKQRPLEKPD 208

Query:   119 GLDVSDQSKVHPMYLCEKCKQLGYYCRK 146
             GLDVSDQSK HP +LCEKCK LGYYCR+
Sbjct:   209 GLDVSDQSKEHPQHLCEKCKVLGYYCRR 236

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|E1BQZ5 ZCCHC24 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 564 (203.6 bits), Expect = 1.3e-54, P = 1.3e-54
 Identities = 105/148 (70%), Positives = 112/148 (75%)

Query:     2 IVDSLCDLHLE---KKSFKQPPSAYLCHLCFVGGHYITDCPLFNMSPFSKYRQLFLFQAR 58
             + +   DL L    +K  K+PP  YLCHLCF  GHYI DCP                QAR
Sbjct:   106 LTEHFSDLSLSSEARKPSKRPPPNYLCHLCFNKGHYIKDCP----------------QAR 149

Query:    59 PKGEGLTPYQGKKRCFGEYKCSKCKRKWMSGNSWANMGQECIKCNINVYPHKQRPLEKPD 118
             PKGEGLTPYQGKKRCFGEYKC KCKRKWMSGNSWANMGQECIKC+INVYPHKQRPLEKPD
Sbjct:   150 PKGEGLTPYQGKKRCFGEYKCPKCKRKWMSGNSWANMGQECIKCHINVYPHKQRPLEKPD 209

Query:   119 GLDVSDQSKVHPMYLCEKCKQLGYYCRK 146
             GLDVSDQSK HP +LCEKCK LGYYCR+
Sbjct:   210 GLDVSDQSKEHPQHLCEKCKVLGYYCRR 237

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0014013 "regulation of gliogenesis" evidence=IDA

UNIPROTKB|E1BIP9 LOC616669 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 562 (202.9 bits), Expect = 2.1e-54, P = 2.1e-54
 Identities = 102/134 (76%), Positives = 107/134 (79%)

Query:    13 KKSFKQPPSAYLCHLCFVGGHYITDCPLFNMSPFSKYRQLFLFQARPKGEGLTPYQGKKR 72
             +K  K+PP  YLCHLCF  GHYI DCP                QARPKGEGLTPYQGKKR
Sbjct:    83 RKPSKRPPPNYLCHLCFNKGHYIKDCP----------------QARPKGEGLTPYQGKKR 126

Query:    73 CFGEYKCSKCKRKWMSGNSWANMGQECIKCNINVYPHKQRPLEKPDGLDVSDQSKVHPMY 132
             CFGEYKC KCKRKWMSGNSWANMGQECIKC+INVYPHKQRPLEKPDGLDVSDQSK HP +
Sbjct:   127 CFGEYKCPKCKRKWMSGNSWANMGQECIKCHINVYPHKQRPLEKPDGLDVSDQSKEHPQH 186

Query:   133 LCEKCKQLGYYCRK 146
             LCEKCK LGYYCR+
Sbjct:   187 LCEKCKVLGYYCRR 200

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|F1P7U6 ZCCHC24 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 562 (202.9 bits), Expect = 2.1e-54, P = 2.1e-54
 Identities = 102/134 (76%), Positives = 107/134 (79%)

Query:    13 KKSFKQPPSAYLCHLCFVGGHYITDCPLFNMSPFSKYRQLFLFQARPKGEGLTPYQGKKR 72
             +K  K+PP  YLCHLCF  GHYI DCP                QARPKGEGLTPYQGKKR
Sbjct:   139 RKPSKRPPPNYLCHLCFNKGHYIKDCP----------------QARPKGEGLTPYQGKKR 182

Query:    73 CFGEYKCSKCKRKWMSGNSWANMGQECIKCNINVYPHKQRPLEKPDGLDVSDQSKVHPMY 132
             CFGEYKC KCKRKWMSGNSWANMGQECIKC+INVYPHKQRPLEKPDGLDVSDQSK HP +
Sbjct:   183 CFGEYKCPKCKRKWMSGNSWANMGQECIKCHINVYPHKQRPLEKPDGLDVSDQSKEHPQH 242

Query:   133 LCEKCKQLGYYCRK 146
             LCEKCK LGYYCR+
Sbjct:   243 LCEKCKVLGYYCRR 256

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|Q8N2G6 ZCCHC24 "Zinc finger CCHC domain-containing protein 24" [Homo sapiens (taxid:9606)]

 Score = 562 (202.9 bits), Expect = 2.1e-54, P = 2.1e-54
 Identities = 102/134 (76%), Positives = 107/134 (79%)

Query:    13 KKSFKQPPSAYLCHLCFVGGHYITDCPLFNMSPFSKYRQLFLFQARPKGEGLTPYQGKKR 72
             +K  K+PP  YLCHLCF  GHYI DCP                QARPKGEGLTPYQGKKR
Sbjct:   122 RKPSKRPPPNYLCHLCFNKGHYIKDCP----------------QARPKGEGLTPYQGKKR 165

Query:    73 CFGEYKCSKCKRKWMSGNSWANMGQECIKCNINVYPHKQRPLEKPDGLDVSDQSKVHPMY 132
             CFGEYKC KCKRKWMSGNSWANMGQECIKC+INVYPHKQRPLEKPDGLDVSDQSK HP +
Sbjct:   166 CFGEYKCPKCKRKWMSGNSWANMGQECIKCHINVYPHKQRPLEKPDGLDVSDQSKEHPQH 225

Query:   133 LCEKCKQLGYYCRK 146
             LCEKCK LGYYCR+
Sbjct:   226 LCEKCKVLGYYCRR 239

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

MGI|MGI:1919168 Zcchc24 "zinc finger, CCHC domain containing 24" [Mus musculus (taxid:10090)]

 Score = 562 (202.9 bits), Expect = 2.1e-54, P = 2.1e-54
 Identities = 102/134 (76%), Positives = 107/134 (79%)

Query:    13 KKSFKQPPSAYLCHLCFVGGHYITDCPLFNMSPFSKYRQLFLFQARPKGEGLTPYQGKKR 72
             +K  K+PP  YLCHLCF  GHYI DCP                QARPKGEGLTPYQGKKR
Sbjct:   122 RKPSKRPPPNYLCHLCFNKGHYIKDCP----------------QARPKGEGLTPYQGKKR 165

Query:    73 CFGEYKCSKCKRKWMSGNSWANMGQECIKCNINVYPHKQRPLEKPDGLDVSDQSKVHPMY 132
             CFGEYKC KCKRKWMSGNSWANMGQECIKC+INVYPHKQRPLEKPDGLDVSDQSK HP +
Sbjct:   166 CFGEYKCPKCKRKWMSGNSWANMGQECIKCHINVYPHKQRPLEKPDGLDVSDQSKEHPQH 225

Query:   133 LCEKCKQLGYYCRK 146
             LCEKCK LGYYCR+
Sbjct:   226 LCEKCKVLGYYCRR 239

GO:0003674 "molecular_function" evidence=ND

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

GO:0008270 "zinc ion binding" evidence=IEA

GO:0014013 "regulation of gliogenesis" evidence=ISO

GO:0046872 "metal ion binding" evidence=IEA

RGD|1306164 Zcchc24 "zinc finger, CCHC domain containing 24" [Rattus norvegicus (taxid:10116)]

 Score = 562 (202.9 bits), Expect = 2.1e-54, P = 2.1e-54
 Identities = 102/134 (76%), Positives = 107/134 (79%)

Query:    13 KKSFKQPPSAYLCHLCFVGGHYITDCPLFNMSPFSKYRQLFLFQARPKGEGLTPYQGKKR 72
             +K  K+PP  YLCHLCF  GHYI DCP                QARPKGEGLTPYQGKKR
Sbjct:   122 RKPSKRPPPNYLCHLCFNKGHYIKDCP----------------QARPKGEGLTPYQGKKR 165

Query:    73 CFGEYKCSKCKRKWMSGNSWANMGQECIKCNINVYPHKQRPLEKPDGLDVSDQSKVHPMY 132
             CFGEYKC KCKRKWMSGNSWANMGQECIKC+INVYPHKQRPLEKPDGLDVSDQSK HP +
Sbjct:   166 CFGEYKCPKCKRKWMSGNSWANMGQECIKCHINVYPHKQRPLEKPDGLDVSDQSKEHPQH 225

Query:   133 LCEKCKQLGYYCRK 146
             LCEKCK LGYYCR+
Sbjct:   226 LCEKCKVLGYYCRR 239

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

UNIPROTKB|I3LHN8 ZCCHC24 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 389 (142.0 bits), Expect = 4.4e-36, P = 4.4e-36
 Identities = 72/99 (72%), Positives = 75/99 (75%)

Query:    13 KKSFKQPPSAYLCHLCFVGGHYITDCPLFNMSPFSKYRQLFLFQARPKGEGLTPYQGKKR 72
             +K  K+PP  YLCHLCF  GHYI DCP                QARPKGEGLTPYQGKKR
Sbjct:    68 RKPSKRPPPNYLCHLCFNKGHYIKDCP----------------QARPKGEGLTPYQGKKR 111

Query:    73 CFGEYKCSKCKRKWMSGNSWANMGQECIKCNINVYPHKQ 111
             CFGEYKC KCKRKWMSGNSWANMGQECIKC+INVYPHKQ
Sbjct:   112 CFGEYKCPKCKRKWMSGNSWANMGQECIKCHINVYPHKQ 150

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

WB|WBGene00012794 Y43E12A.2 [Caenorhabditis elegans (taxid:6239)]

 Score = 261 (96.9 bits), Expect = 1.6e-22, P = 1.6e-22
 Identities = 51/102 (50%), Positives = 65/102 (63%)

Query:    17 KQPPSAYLCHLCFVGGH-YITDCPL-FNMSPFSKYRQLFLFQARPKGEGLTPYQGKKRCF 74
             K PP  Y CH+C+  GH YI+DCP  FN +P+ +               LTPYQG+K+C+
Sbjct:   147 KTPPPRYQCHICYATGHHYISDCPQRFN-TPYDE---------------LTPYQGRKKCY 190

Query:    75 GEYKCSKCKRKWMSGNSWANMGQECIKCNINVYPHKQRPLEK 116
             GE+ C  CKRKW S NS AN  Q CIKC++ V+PHKQ P+EK
Sbjct:   191 GEFTCQLCKRKWNSQNSVANEPQSCIKCHVPVFPHKQLPVEK 232


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.324   0.140   0.479    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0      155       155   0.00096  105 3  11 22  0.46    31
                                                     30  0.41    34


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  9
  No. of states in DFA:  609 (65 KB)
  Total size of DFA:  191 KB (2108 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:02
  No. of threads or processors used:  24
  Search cpu time:  17.14u 0.07s 17.21t   Elapsed:  00:00:16
  Total cpu time:  17.14u 0.07s 17.21t   Elapsed:  00:00:18
  Start:  Thu Aug 15 14:01:40 2013   End:  Thu Aug 15 14:01:58 2013

GO:0005739 "mitochondrion" evidence=IDA

---

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)
B2RVL6	ZCH24_MOUSE	No assigned EC number	0.7094	0.8322	0.5352	yes	N/A
Q8N2G6	ZCH24_HUMAN	No assigned EC number	0.7046	0.8387	0.5394	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	155
pfam13695	96	pfam13695, zf-3CxxC, Zinc-binding domain	7e-14
pfam13696	32	pfam13696, zf-CCHC_2, Zinc knuckle	1e-05

>gnl|CDD|222324 pfam13695, zf-3CxxC, Zinc-binding domain

 Score = 62.8 bits (153), Expect = 7e-14
 Identities = 21/96 (21%), Positives = 24/96 (25%), Gaps = 27/96 (28%)

Query: 72  RCFGEYKCSKCKRKWMSGNSWAN-------------MGQECIKCNINVYPHKQRPL---- 114
             FG + CS C R W SGN W                 Q C KC     P+         
Sbjct: 1   NIFGRFTCSNCSRGWSSGNVWITFRMYPGGKYNARVYKQRCKKCQRLERPYLDENYVERI 60

Query: 115 ----------EKPDGLDVSDQSKVHPMYLCEKCKQL 140
                                   H   LCE C+  
Sbjct: 61  AYRCYKWAGISVEKPPHSGKSKGPHNRELCEACRAG 96

This is a family with several pairs of CxxC motifs possibly representing a multiple zinc-binding region. Only one pair of cysteines is associated with a highly conserved histidine residue. Length = 96

>gnl|CDD|205872 pfam13696, zf-CCHC_2, Zinc knuckle

 Score = 39.8 bits (93), Expect = 1e-05
 Identities = 17/23 (73%), Positives = 18/23 (78%)

Query: 17 KQPPSAYLCHLCFVGGHYITDCP 39
          K PP  YLCHLCF  GHYI+DCP
Sbjct: 3  KAPPPNYLCHLCFQKGHYISDCP 25

This is a zinc-binding domain of the form CxxCxxxGHxxxxC from a variety of different species. Length = 32

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	155
PF13695	98	zf-3CxxC: Zinc-binding domain	99.58
PF13696	32	zf-CCHC_2: Zinc knuckle	99.5
COG5222	427	Uncharacterized conserved protein, contains RING Z	98.48
PF00098	18	zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc fi	96.52
KOG0314|consensus	448		96.06
PF13917	42	zf-CCHC_3: Zinc knuckle	95.68
PF15135	278	UPF0515: Uncharacterised protein UPF0515	95.26
smart00343	26	ZnF_C2HC zinc finger.	85.76
smart00834	41	CxxC_CXXC_SSSS Putative regulatory protein. CxxC_C	83.23

>PF13695 zf-3CxxC: Zinc-binding domain

Probab=99.58  E-value=1.2e-15  Score=111.60  Aligned_cols=68  Identities=37%  Similarity=0.719  Sum_probs=55.0

Q ss_pred             cceeeeecccCcCccccceEEec-------------ccccccccCccccceeeec---cc-------------CCCCCCC
Q psy12393         72 RCFGEYKCSKCKRKWMSGNSWAN-------------MGQECIKCNINVYPHKQRP---LE-------------KPDGLDV  122 (155)
Q Consensus        72 R~fG~F~Ck~C~~~WsSaNsWan-------------~gQ~C~kC~~~vyPyrq~~---l~-------------~~~k~~~  122 (155)
                      +.||.|+|+.|++.|+|++||.+             .+|.|++|+...+|+..++   ++             .+.....
T Consensus         1 ~~~grF~C~~C~~~W~S~~v~i~f~~~~~g~v~~rv~~Q~C~~C~~~~~P~~~e~~~lv~ri~~~~y~~~~~~~~~~~~~   80 (98)
T PF13695_consen    1 NAFGRFQCSKCSRGWTSAKVWILFHMYRGGQVNMRVFGQRCKKCNPLERPYFSEEQNLVERIRYRCYGWAGIQVEEPRIS   80 (98)
T ss_pred             CcEEEEECCCCCCCCccCEEEEEEEEcCCCeEEEEEECCCCCCCCCCCCccCcccccHHHHHHHHHhcccCCccCcCccc
Confidence            47999999999999999999999             7999999999999999543   21             1111223


Q ss_pred             CCCCCCChhhhhHHHhh
Q psy12393        123 SDQSKVHPMYLCEKCKQ  139 (155)
Q Consensus       123 ~d~krPHpQ~LCgkCK~  139 (155)
                      .+..+||.++|||.|++
T Consensus        81 ~~~~~pH~~~lCE~C~~   97 (98)
T PF13695_consen   81 GKSTGPHESELCEACKQ   97 (98)
T ss_pred             CCCCCCCChhhChhhcC
Confidence            34479999999999986

>PF13696 zf-CCHC_2: Zinc knuckle

Probab=99.50  E-value=8.2e-15  Score=90.75  Aligned_cols=26  Identities=50%  Similarity=1.150  Sum_probs=24.8

Q ss_pred             cCCCCCCceeeeeccCCCcccccCCC
Q psy12393         15 SFKQPPSAYLCHLCFVGGHYITDCPL   40 (155)
Q Consensus        15 ~~~~pp~~y~ch~c~~~ghyi~dcp~   40 (155)
                      |+++||++|+||+|+++||||+|||+
T Consensus         1 ~~k~pP~~Y~C~~C~~~GH~i~dCP~   26 (32)
T PF13696_consen    1 PRKKPPPGYVCHRCGQKGHWIQDCPT   26 (32)
T ss_pred             CCCCCCCCCEeecCCCCCccHhHCCC
Confidence            57899999999999999999999997

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

Probab=98.48  E-value=5.7e-08  Score=86.57  Aligned_cols=40  Identities=35%  Similarity=0.672  Sum_probs=36.2

Q ss_pred             cccCCCCCCceeeeeccCCCcccccCCCCCCCchhhHhhh
Q psy12393         13 KKSFKQPPSAYLCHLCFVGGHYITDCPLFNMSPFSKYRQL   52 (155)
Q Consensus        13 ~~~~~~pp~~y~ch~c~~~ghyi~dcp~~~~~~~~~~r~~   52 (155)
                      .+.-++|||+|+|-+|+++||||+.||||.++-||-+|-+
T Consensus       167 q~~~kppPpgY~CyRCGqkgHwIqnCpTN~DpnfdgkRir  206 (427)
T COG5222         167 QKHNKPPPPGYVCYRCGQKGHWIQNCPTNQDPNFDGKRIR  206 (427)
T ss_pred             ccCCCCCCCceeEEecCCCCchhhcCCCCCCCCccceeee
Confidence            4567899999999999999999999999999999988743

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

Probab=96.52  E-value=0.001  Score=36.11  Aligned_cols=16  Identities=44%  Similarity=0.912  Sum_probs=15.2

Q ss_pred             eeeeccCCCcccccCC
Q psy12393         24 LCHLCFVGGHYITDCP   39 (155)
Q Consensus        24 ~ch~c~~~ghyi~dcp   39 (155)
                      .|..|.+.||+..|||
T Consensus         2 ~C~~C~~~GH~~~~Cp   17 (18)
T PF00098_consen    2 KCFNCGEPGHIARDCP   17 (18)
T ss_dssp             BCTTTSCSSSCGCTSS
T ss_pred             cCcCCCCcCcccccCc
Confidence            5899999999999999

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

>KOG0314|consensus

Probab=96.06  E-value=0.0027  Score=58.47  Aligned_cols=34  Identities=29%  Similarity=0.545  Sum_probs=30.1

Q ss_pred             CCCCceeeeeccCCCcccccCCCCCCCchhhHhh
Q psy12393         18 QPPSAYLCHLCFVGGHYITDCPLFNMSPFSKYRQ   51 (155)
Q Consensus        18 ~pp~~y~ch~c~~~ghyi~dcp~~~~~~~~~~r~   51 (155)
                      .|||.|.|-+|-++||+|+-|||+....++..+-
T Consensus       154 ~Pppsy~c~rc~~~g~wikacptv~~~~~~~~~~  187 (448)
T KOG0314|consen  154 SPPPSYKCVKCPTPGPWIKACPTVSGSYSLPSGT  187 (448)
T ss_pred             CCCCCcceecCCCCCccceeccccCCcccccCCc
Confidence            4999999999999999999999988888865553

>PF13917 zf-CCHC_3: Zinc knuckle

Probab=95.68  E-value=0.0058  Score=39.83  Aligned_cols=32  Identities=28%  Similarity=0.611  Sum_probs=26.0

Q ss_pred             ceeeeeccCCCcccccCCCCCCCchhhHhhhhhhhcCCCCC
Q psy12393         22 AYLCHLCFVGGHYITDCPLFNMSPFSKYRQLFLFQARPKGE   62 (155)
Q Consensus        22 ~y~ch~c~~~ghyi~dcp~~~~~~~~~~r~~~~~~~rp~~~   62 (155)
                      .-+|..|++.||+..+||..+.-+|         .+||.+.
T Consensus         4 ~~~CqkC~~~GH~tyeC~~~~~r~y---------~~RpSrt   35 (42)
T PF13917_consen    4 RVRCQKCGQKGHWTYECPNKNERKY---------TSRPSRT   35 (42)
T ss_pred             CCcCcccCCCCcchhhCCCCCCccc---------ccCCCHH
Confidence            4579999999999999997556666         7787654

>PF15135 UPF0515: Uncharacterised protein UPF0515

Probab=95.26  E-value=0.0092  Score=52.14  Aligned_cols=40  Identities=30%  Similarity=0.764  Sum_probs=34.0

Q ss_pred             ceeeeecccCcCccccceEEecc--cccccccCccccceeeeccc
Q psy12393         73 CFGEYKCSKCKRKWMSGNSWANM--GQECIKCNINVYPHKQRPLE  115 (155)
Q Consensus        73 ~fG~F~Ck~C~~~WsSaNsWan~--gQ~C~kC~~~vyPyrq~~l~  115 (155)
                      -+|+|+|.+|++.|.   .|+-+  .+-|..|+..|||+++.|-.
T Consensus       152 G~aef~C~~C~h~F~---G~~qm~v~sPCy~C~~~v~P~~IlPPr  193 (278)
T PF15135_consen  152 GIAEFHCPKCRHNFR---GFAQMGVPSPCYGCGNPVYPSRILPPR  193 (278)
T ss_pred             ceeeeecccccccch---hhhhcCCCCCccCCCCccCcccccCCC
Confidence            467999999999998   45555  58999999999999998743

>smart00343 ZnF_C2HC zinc finger

Probab=85.76  E-value=0.35  Score=27.34  Aligned_cols=17  Identities=41%  Similarity=0.796  Sum_probs=15.1

Q ss_pred             eeeeccCCCcccccCCC
Q psy12393         24 LCHLCFVGGHYITDCPL   40 (155)
Q Consensus        24 ~ch~c~~~ghyi~dcp~   40 (155)
                      .|-.|.+.||+..+||.
T Consensus         1 ~C~~CG~~GH~~~~C~~   17 (26)
T smart00343        1 KCYNCGKEGHIARDCPK   17 (26)
T ss_pred             CCccCCCCCcchhhCCc
Confidence            47889999999999993

>smart00834 CxxC_CXXC_SSSS Putative regulatory protein

Probab=83.23  E-value=1  Score=27.06  Aligned_cols=30  Identities=20%  Similarity=0.540  Sum_probs=22.3

Q ss_pred             eeecccCcCccccceEEe-cccccccccCcc
Q psy12393         76 EYKCSKCKRKWMSGNSWA-NMGQECIKCNIN  105 (155)
Q Consensus        76 ~F~Ck~C~~~WsSaNsWa-n~gQ~C~kC~~~  105 (155)
                      +|+|..|+..|+-.-+.. ...-.|-.|+..
T Consensus         5 ~y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~   35 (41)
T smart00834        5 EYRCEDCGHTFEVLQKISDDPLATCPECGGD   35 (41)
T ss_pred             EEEcCCCCCEEEEEEecCCCCCCCCCCCCCc
Confidence            589999999998544443 445679999873

CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	155
2ysa_A	55	Retinoblastoma-binding protein 6; zinc finger, CCH	8e-05

>2ysa_A Retinoblastoma-binding protein 6; zinc finger, CCHC, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 55

 Score = 37.5 bits (87), Expect = 8e-05
 Identities = 11/36 (30%), Positives = 14/36 (38%)

Query: 17 KQPPSAYLCHLCFVGGHYITDCPLFNMSPFSKYRQL 52
              S Y C  C   GHYI +CP      F    ++
Sbjct: 2  SSGSSGYTCFRCGKPGHYIKNCPTNGDKNFESGPRI 37

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	155
2ysa_A	55	Retinoblastoma-binding protein 6; zinc finger, CCH	98.63
1u6p_A	56	GAG polyprotein; MLV, A-minor K-turn, stem loop, b	96.92
1a6b_B	40	Momulv, zinc finger protein NCP10; nucleocapsid pr	96.79
1dsq_A	26	Nucleic acid binding protein P14; CCHC type zinc f	96.25
1nc8_A	29	Nucleocapsid protein; HIV-2, RNA recognition, zinc	94.99
2ec7_A	49	GAG polyprotein (PR55GAG); nucleocapsid protein, H	92.6
2bl6_A	37	Nucleocapsid protein P11; lentivirus, polyprotein,	92.09
1cl4_A	60	Protein (GAG polyprotein); nucleocapsid protein, R	92.06
2ihx_A	61	Nucleocapsid (NC) protein; protein-RNA complex, vi	91.46
2a51_A	39	Nucleocapsid protein; sivlhoest, structure, NCP8,	90.91
1a1t_A	55	Nucleocapsid protein; stem-loop RNA, viral protein	90.85
3ts2_A	148	Protein LIN-28 homolog A; microrna biogenesis, pro	90.67
3alr_A	106	Nanos protein; zinc-finger, translational repressi	90.27
2ec7_A	49	GAG polyprotein (PR55GAG); nucleocapsid protein, H	90.0
1a1t_A	55	Nucleocapsid protein; stem-loop RNA, viral protein	89.94
2bl6_A	37	Nucleocapsid protein P11; lentivirus, polyprotein,	88.73
2a51_A	39	Nucleocapsid protein; sivlhoest, structure, NCP8,	88.39
2cqf_A	63	RNA-binding protein LIN-28; CCHC zinc-finger, stru	87.58
2li8_A	74	Protein LIN-28 homolog A; zinc finger, micro RNA,	87.57
2ihx_A	61	Nucleocapsid (NC) protein; protein-RNA complex, vi	84.74
1cl4_A	60	Protein (GAG polyprotein); nucleocapsid protein, R	84.65
2cqf_A	63	RNA-binding protein LIN-28; CCHC zinc-finger, stru	81.14

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

Probab=98.63  E-value=6.2e-09  Score=69.75  Aligned_cols=29  Identities=38%  Similarity=0.752  Sum_probs=26.0

Q ss_pred             CCCCceeeeeccCCCcccccCCCCCCCch
Q psy12393         18 QPPSAYLCHLCFVGGHYITDCPLFNMSPF   46 (155)
Q Consensus        18 ~pp~~y~ch~c~~~ghyi~dcp~~~~~~~   46 (155)
                      .+|++|.|++|.++||+|+|||++.+..|
T Consensus         3 ~~p~~~~C~kCGk~GH~~k~Cp~~~~~~f   31 (55)
T 2ysa_A            3 SGSSGYTCFRCGKPGHYIKNCPTNGDKNF   31 (55)
T ss_dssp             CSSSSCCCTTTCCTTSCGGGCSGGGCSSC
T ss_pred             CCCCCCccccCCCcCcccccCCCCCCCCc
Confidence            46889999999999999999998777766

>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=96.92  E-value=0.00043  Score=46.26  Aligned_cols=26  Identities=27%  Similarity=0.591  Sum_probs=22.8

Q ss_pred             cCCCCCCceeeeeccCCCcccccCCC
Q psy12393         15 SFKQPPSAYLCHLCFVGGHYITDCPL   40 (155)
Q Consensus        15 ~~~~pp~~y~ch~c~~~ghyi~dcp~   40 (155)
                      ..+.+.+.-.|..|.+.|||.+|||.
T Consensus        16 ~~~~~~~~~~C~~Cge~GH~ardCp~   41 (56)
T 1u6p_A           16 RRRSQLDRDQCAYCKEKGHWAKDCPK   41 (56)
T ss_dssp             CCSTTCCTTBCSSSCCBSSCGGGCTT
T ss_pred             cCCCCCCCCcceeCCCCCcccccCcC
Confidence            44667788999999999999999995

>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=96.79  E-value=0.00052  Score=43.13  Aligned_cols=24  Identities=29%  Similarity=0.688  Sum_probs=21.7

Q ss_pred             CCCCCceeeeeccCCCcccccCCC
Q psy12393         17 KQPPSAYLCHLCFVGGHYITDCPL   40 (155)
Q Consensus        17 ~~pp~~y~ch~c~~~ghyi~dcp~   40 (155)
                      ..+.....|..|.+.|||+.|||.
T Consensus         5 ~~~~~~~~C~~Cgk~GH~ardCP~   28 (40)
T 1a6b_B            5 RSQLDRDQCAYCKEKGHWAKDCPK   28 (40)
T ss_dssp             CCSCCSSSCSSSCCTTCCTTSCSS
T ss_pred             cCCCCCCeeeECCCCCcchhhCcC
Confidence            567778999999999999999995

>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=94.99  E-value=0.01  Score=34.06  Aligned_cols=20  Identities=25%  Similarity=0.481  Sum_probs=17.4

Q ss_pred             CceeeeeccCCCcccccCCC
Q psy12393         21 SAYLCHLCFVGGHYITDCPL   40 (155)
Q Consensus        21 ~~y~ch~c~~~ghyi~dcp~   40 (155)
                      ....|..|.+.||+..|||.
T Consensus         5 ~~~~C~nCgk~GH~ar~C~~   24 (29)
T 1nc8_A            5 KVIRCWNCGKEGHSARQCRA   24 (29)
T ss_dssp             CCCBCTTTSCBSSCGGGCCS
T ss_pred             CCCEEEECCccccCHhHCcc
Confidence            34679999999999999993

>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=92.60  E-value=0.064  Score=33.73  Aligned_cols=18  Identities=33%  Similarity=0.693  Sum_probs=12.2

Q ss_pred             eeeeeccCCCcccccCCC
Q psy12393         23 YLCHLCFVGGHYITDCPL   40 (155)
Q Consensus        23 y~ch~c~~~ghyi~dcp~   40 (155)
                      -.|.+|.+.||+..|||.
T Consensus        28 ~~C~~Cg~~GH~~~~C~~   45 (49)
T 2ec7_A           28 QGCWKCGKTGHVMAKCPE   45 (49)
T ss_dssp             CSCSSSCCSSCCGGGCCS
T ss_pred             CeeCcCCCcCCccCCCcC
Confidence            457777777777777764

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

Probab=92.09  E-value=0.054  Score=32.17  Aligned_cols=17  Identities=29%  Similarity=0.815  Sum_probs=15.9

Q ss_pred             eeeeeccCCCcccccCC
Q psy12393         23 YLCHLCFVGGHYITDCP   39 (155)
Q Consensus        23 y~ch~c~~~ghyi~dcp   39 (155)
                      -.|.+|.++||+.+|||
T Consensus        20 ~~C~~Cg~~GH~a~~C~   36 (37)
T 2bl6_A           20 KVCFKCKQPGHFSKQCR   36 (37)
T ss_dssp             TTCSSCCCTTGGGGTTC
T ss_pred             CeEccCCCcCCccCcCc
Confidence            57999999999999998

>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=92.06  E-value=0.061  Score=34.75  Aligned_cols=21  Identities=29%  Similarity=0.591  Sum_probs=18.5

Q ss_pred             CceeeeeccCCCcccccCCCC
Q psy12393         21 SAYLCHLCFVGGHYITDCPLF   41 (155)
Q Consensus        21 ~~y~ch~c~~~ghyi~dcp~~   41 (155)
                      +.-.|.+|.+.||+.+|||..
T Consensus        29 ~~~~C~~Cg~~GH~ar~C~~~   49 (60)
T 1cl4_A           29 VPGLCPRCKRGKHWANECKSK   49 (60)
T ss_dssp             CCCSCSSCSSCSSCSTTCCCT
T ss_pred             CCcceeECCCCCCccCcCCCc
Confidence            457899999999999999963

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

Probab=91.46  E-value=0.079  Score=34.65  Aligned_cols=21  Identities=33%  Similarity=0.504  Sum_probs=18.0

Q ss_pred             CceeeeeccCCCcccccCCCC
Q psy12393         21 SAYLCHLCFVGGHYITDCPLF   41 (155)
Q Consensus        21 ~~y~ch~c~~~ghyi~dcp~~   41 (155)
                      +.-.|.+|.+.||+..|||..
T Consensus        29 ~~~~C~~Cg~~GH~ar~C~~~   49 (61)
T 2ihx_A           29 SRERCQLCNGMGHNAKQCRKR   49 (61)
T ss_dssp             CCSBCTTTCCBSSCGGGCCCC
T ss_pred             CCCeeCCCCCCCCCcCCCcCC
Confidence            356899999999999999953

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

Probab=90.91  E-value=0.084  Score=31.65  Aligned_cols=17  Identities=29%  Similarity=0.585  Sum_probs=12.8

Q ss_pred             eeeeeccCCCcccccCC
Q psy12393         23 YLCHLCFVGGHYITDCP   39 (155)
Q Consensus        23 y~ch~c~~~ghyi~dcp   39 (155)
                      -.|.+|.+.||+..|||
T Consensus        22 ~~C~~Cg~~GH~~~~C~   38 (39)
T 2a51_A           22 EGCWNCGSKEHRFAQCP   38 (39)
T ss_dssp             SSCTTTCCSSSCTTTSC
T ss_pred             CccccCCCCCCccCcCc
Confidence            46777777777777777

>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=90.85  E-value=0.11  Score=32.92  Aligned_cols=16  Identities=38%  Similarity=0.787  Sum_probs=8.4

Q ss_pred             eeeeccCCCcccccCC
Q psy12393         24 LCHLCFVGGHYITDCP   39 (155)
Q Consensus        24 ~ch~c~~~ghyi~dcp   39 (155)
                      .|.+|.+.||+..|||
T Consensus        35 ~C~~Cg~~GH~~~~C~   50 (55)
T 1a1t_A           35 GCWKCGKEGHQMKDCT   50 (55)
T ss_dssp             BCTTTCCBSSCGGGCS
T ss_pred             EeCCCCCcCCccCCCc
Confidence            4555555555555555

>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=90.67  E-value=0.12  Score=39.44  Aligned_cols=21  Identities=38%  Similarity=0.956  Sum_probs=14.3

Q ss_pred             CCceeeeeccCCCcccccCCC
Q psy12393         20 PSAYLCHLCFVGGHYITDCPL   40 (155)
Q Consensus        20 p~~y~ch~c~~~ghyi~dcp~   40 (155)
                      |..-.|++|.+.||+..|||.
T Consensus       117 ~~~~~C~~Cg~~GH~~r~Cp~  137 (148)
T 3ts2_A          117 PQPKKCHFCQSINHMVASCPL  137 (148)
T ss_dssp             CCCCCCTTTCCSSCCGGGCTT
T ss_pred             CCCCcccccCCcCCEeccCcC
Confidence            334567777777777777774

>3alr_A Nanos protein; zinc-finger, translational repression, RNA, 3'-UTR, metal BI protein; 2.10A {Danio rerio}

Probab=90.27  E-value=0.059  Score=40.47  Aligned_cols=24  Identities=33%  Similarity=0.690  Sum_probs=21.3

Q ss_pred             ceeeeeccCCC---cccccCCCCCCCc
Q psy12393         22 AYLCHLCFVGG---HYITDCPLFNMSP   45 (155)
Q Consensus        22 ~y~ch~c~~~g---hyi~dcp~~~~~~   45 (155)
                      .|.|.+|...|   |-|+-||++++..
T Consensus        71 ~Y~CpiCGATGd~AHT~kYCP~~~~~~   97 (106)
T 3alr_A           71 QYKCPLCGATGAKAHTKRFCPMVDKNY   97 (106)
T ss_dssp             GCCCTTTCCCGGGCCCGGGCTTCGGGG
T ss_pred             cccCCCCCCcCCcccceecCCCCCCcc
Confidence            69999999999   9999999977553

>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=90.00  E-value=0.13  Score=32.24  Aligned_cols=21  Identities=24%  Similarity=0.444  Sum_probs=17.9

Q ss_pred             CCceeeeeccCCCcccccCCC
Q psy12393         20 PSAYLCHLCFVGGHYITDCPL   40 (155)
Q Consensus        20 p~~y~ch~c~~~ghyi~dcp~   40 (155)
                      ...-.|..|.+.||+..|||.
T Consensus         4 ~r~~~C~~Cg~~GH~a~~C~~   24 (49)
T 2ec7_A            4 RKVIRCWNCGKEGHSARQCRA   24 (49)
T ss_dssp             CCCCBCTTTCCBTCCTTTCCC
T ss_pred             CCcCeeeecCCCCcChhhCcC
Confidence            344579999999999999994

>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=89.94  E-value=0.076  Score=33.73  Aligned_cols=25  Identities=24%  Similarity=0.558  Sum_probs=20.2

Q ss_pred             CCCCCCceeeeeccCCCcccccCCC
Q psy12393         16 FKQPPSAYLCHLCFVGGHYITDCPL   40 (155)
Q Consensus        16 ~~~pp~~y~ch~c~~~ghyi~dcp~   40 (155)
                      .+.|.....|..|.+.||+..|||.
T Consensus         6 f~g~~~~~~C~~Cg~~GH~a~~C~~   30 (55)
T 1a1t_A            6 FRNQRKTVKCFNCGKEGHIAKNCRA   30 (55)
T ss_dssp             GGGGGGTCBCTTTCCBSSCGGGCSS
T ss_pred             cCCCCCCcceeeeCCCCcChhhcCC
Confidence            3444555789999999999999994

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

Probab=88.73  E-value=0.15  Score=30.24  Aligned_cols=17  Identities=29%  Similarity=0.600  Sum_probs=15.4

Q ss_pred             eeeeccCCCcccccCCC
Q psy12393         24 LCHLCFVGGHYITDCPL   40 (155)
Q Consensus        24 ~ch~c~~~ghyi~dcp~   40 (155)
                      .|-.|.+.||+..|||.
T Consensus         2 ~C~~Cg~~GH~~~~C~~   18 (37)
T 2bl6_A            2 TCYNCGKPGHLSSQCRA   18 (37)
T ss_dssp             CBSSSCCSSCCTTTSSC
T ss_pred             cccccCCCCcchhhCcC
Confidence            48899999999999994

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

Probab=88.39  E-value=0.13  Score=30.76  Aligned_cols=17  Identities=29%  Similarity=0.507  Sum_probs=15.5

Q ss_pred             eeeeccCCCcccccCCC
Q psy12393         24 LCHLCFVGGHYITDCPL   40 (155)
Q Consensus        24 ~ch~c~~~ghyi~dcp~   40 (155)
                      .|..|.+.||+..|||.
T Consensus         2 ~C~~Cg~~GH~a~~C~~   18 (39)
T 2a51_A            2 TCFNCGKPGHTARMCRQ   18 (39)
T ss_dssp             BCTTTCCBSSCTTTCCS
T ss_pred             eeeccCCCCcccccCCC
Confidence            58899999999999994

>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=87.58  E-value=0.22  Score=32.85  Aligned_cols=20  Identities=35%  Similarity=0.878  Sum_probs=15.0

Q ss_pred             CceeeeeccCCCcccccCCC
Q psy12393         21 SAYLCHLCFVGGHYITDCPL   40 (155)
Q Consensus        21 ~~y~ch~c~~~ghyi~dcp~   40 (155)
                      ..-.|.+|.+.||+..|||.
T Consensus        28 ~~~~C~~Cg~~GH~ar~Cp~   47 (63)
T 2cqf_A           28 QPKKCHFCQSISHMVASCPL   47 (63)
T ss_dssp             CSSCCTTTCCSSSCTTTCTG
T ss_pred             CCCccCCcCCcCCccCcCCC
Confidence            34578888888888888884

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

Probab=87.57  E-value=0.2  Score=34.38  Aligned_cols=17  Identities=35%  Similarity=0.944  Sum_probs=8.3

Q ss_pred             eeeeeccCCCcccccCC
Q psy12393         23 YLCHLCFVGGHYITDCP   39 (155)
Q Consensus        23 y~ch~c~~~ghyi~dcp   39 (155)
                      -.|.+|.+.||+..|||
T Consensus        47 ~~C~~Cg~~GH~ar~Cp   63 (74)
T 2li8_A           47 KKCHFCQSISHMVASCP   63 (74)
T ss_dssp             CCCTTTCCTTSCGGGCT
T ss_pred             CccCCcCCcCCccCcCc
Confidence            34444445555445554

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

Probab=84.74  E-value=0.31  Score=31.71  Aligned_cols=18  Identities=44%  Similarity=0.901  Sum_probs=16.3

Q ss_pred             eeeeeccCCCcccccCCC
Q psy12393         23 YLCHLCFVGGHYITDCPL   40 (155)
Q Consensus        23 y~ch~c~~~ghyi~dcp~   40 (155)
                      -.|..|.+.||+..|||.
T Consensus         5 ~~C~~Cg~~GH~a~~C~~   22 (61)
T 2ihx_A            5 GLCYTCGSPGHYQAQCPK   22 (61)
T ss_dssp             TBCSSSCCBTCCGGGCTT
T ss_pred             CcccccCCCCeehhhCcC
Confidence            369999999999999994

>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=84.65  E-value=0.18  Score=32.44  Aligned_cols=18  Identities=28%  Similarity=0.693  Sum_probs=0.0

Q ss_pred             eeeeccCCCcccccCCCC
Q psy12393         24 LCHLCFVGGHYITDCPLF   41 (155)
Q Consensus        24 ~ch~c~~~ghyi~dcp~~   41 (155)
                      .|..|.+.||+..|||..
T Consensus         3 ~Cf~Cg~~GH~a~~C~~~   20 (60)
T 1cl4_A            3 SCFKCGKKGHFAKNCHEH   20 (60)
T ss_dssp             ------------------
T ss_pred             ccccCCCCCcCHhhCcCC
Confidence            589999999999999953

>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=81.14  E-value=0.59  Score=30.69  Aligned_cols=18  Identities=28%  Similarity=0.384  Sum_probs=16.4

Q ss_pred             eeeeeccCCCcccccCCC
Q psy12393         23 YLCHLCFVGGHYITDCPL   40 (155)
Q Consensus        23 y~ch~c~~~ghyi~dcp~   40 (155)
                      -.|..|.+.||+..|||.
T Consensus         8 ~~C~~Cg~~GH~a~~C~~   25 (63)
T 2cqf_A            8 DRCYNCGGLDHHAKECKL   25 (63)
T ss_dssp             CCCSSSCCSSSCTTTCCS
T ss_pred             CcccccCCCCcChhhCCC
Confidence            469999999999999994

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	155
d2exfa1	42	HIV nucleocapsid {Human immunodeficiency virus typ	95.27
d1a6bb_	40	Zinc finger protein ncp10 {Moloney murine leukemia	90.05
d2exfa1	42	HIV nucleocapsid {Human immunodeficiency virus typ	87.43

>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=95.27  E-value=0.003  Score=38.04  Aligned_cols=19  Identities=32%  Similarity=0.571  Sum_probs=16.9

Q ss_pred             ceeeeeccCCCcccccCCC
Q psy12393         22 AYLCHLCFVGGHYITDCPL   40 (155)
Q Consensus        22 ~y~ch~c~~~ghyi~dcp~   40 (155)
                      ...|.+|.+.||.+.|||.
T Consensus        22 ~~~C~~Cg~~GH~~~~Cp~   40 (42)
T d2exfa1          22 KKGCWKCGKEGHQMKDCTE   40 (42)
T ss_dssp             CSSCSSSCCSSSCTTTCCS
T ss_pred             cCccccCCCCCeecccCCC
Confidence            4579999999999999995

>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=90.05  E-value=0.041  Score=33.46  Aligned_cols=22  Identities=32%  Similarity=0.706  Sum_probs=18.7

Q ss_pred             CCCceeeeeccCCCcccccCCC
Q psy12393         19 PPSAYLCHLCFVGGHYITDCPL   40 (155)
Q Consensus        19 pp~~y~ch~c~~~ghyi~dcp~   40 (155)
                      +=..=+|--|-+.||.++|||.
T Consensus         7 ~L~kDQCAyCke~GHW~~dCPk   28 (40)
T d1a6bb_           7 QLDRDQCAYCKEKGHWAKDCPK   28 (40)
T ss_dssp             SCCSSSCSSSCCTTCCTTSCSS
T ss_pred             cccchhhHHHhhcCchhhhCcc
Confidence            3345689999999999999994

>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=87.43  E-value=0.075  Score=31.56  Aligned_cols=17  Identities=29%  Similarity=0.618  Sum_probs=15.7

Q ss_pred             eeeeeccCCCcccccCC
Q psy12393         23 YLCHLCFVGGHYITDCP   39 (155)
Q Consensus        23 y~ch~c~~~ghyi~dcp   39 (155)
                      -.|.+|.+.||...|||
T Consensus         2 i~C~~Cg~~GH~~~~Cp   18 (42)
T d2exfa1           2 VKCFNCGKEGHTARNCR   18 (42)
T ss_dssp             CCCTTTCCSSSCTTTCS
T ss_pred             CccccCCCcCcCcccCc
Confidence            36999999999999999