Citrus Sinensis ID: 043522

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80----
Protein Sequence
NEALKKTYKHQYYPVPDESRWPPELHYNMLPPIIIRTTGRPQTKKRREADENRAFKRSSSVRCSNFEEWGHNVRTCKVDKGSKK
Secondary Structure (PSIPRED)
cHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccEEcccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cHHHHHHHHccEcccccccccccccccccccccEEcccccccccccccccccccccccEEEEEccccccccccccccccccccc
Coil and Loop (DISEMBL)
nealkktykhqyypvpdesrwppelhynmlppiiirttgrpqtkkrreadenrafkrsssvrcsnfeewghnvrtckvdkgskk
Flexible Loop (DISEMBL)
nealkktykhqyypvpdesrwppELHYNMlppiiirttgrpqtkkrreadenrafkrsssvrcsnfeewghnvrtckvdkgskk
Low Complexity Region (SEG)
NEALKKTYKHQYYPVPDESRWPPELHYNMLPPIIIRTTGRPQTKKRREADENRAFKRSSSVRCSNFEEWGHNVRTCKVDKGSKK
Disordered region (IsUnstruct)
***********YYPV****RWPPELHYNMLPPIIIR*****************************FEEWGHNVR**********
Disordered Region (DISOPRED)
NEALKKTYKHQYYPVPDESRWPPELHYNM**********************************SNFEEWGHNV***********
Disordered Region (DISEMBL)
NEALKKTYKHQYYPVPDESRWPPELHYNMLPPIIIRTT**********************VRCSNFEEWGHNVRTC********
Disordered Region (DISPRO)
NEALKKTYKHQYYPVPDESRWPPELHYNMLPPIIIRT*******************RSSSVRCSNFEE****************
Transmembrane Helix (TMHMM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
NEALKKTYKHQYYPVPDESRWPPELHYNMLPPIIIRTTGRPQTKKRREADENRAFKRSSSVRCSNFEEWGHNVRTCKVDKGSKK
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

No hits with e-value below 0.001 by BLAST

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	84
242093218	191	hypothetical protein SORBIDRAFT_10g02107	0.869	0.382	0.381	2e-07
222623571	894	hypothetical protein OsJ_08182 [Oryza sa	0.869	0.081	0.407	7e-07
222628642	1227	hypothetical protein OsJ_14341 [Oryza sa	0.869	0.059	0.407	9e-07
222623570	404	hypothetical protein OsJ_08180 [Oryza sa	0.869	0.180	0.407	1e-06
31432405	929	transposon protein, putative, Mutator su	0.892	0.080	0.379	5e-06
222612932	948	hypothetical protein OsJ_31731 [Oryza sa	0.892	0.079	0.379	6e-06
222640608	246	hypothetical protein OsJ_27422 [Oryza sa	0.916	0.313	0.365	1e-05
125553424	1005	hypothetical protein OsI_21092 [Oryza sa	0.916	0.076	0.365	6e-05
222622925	934	hypothetical protein OsJ_06863 [Oryza sa	0.880	0.079	0.358	0.0001
218194691	844	hypothetical protein OsI_15544 [Oryza sa	0.892	0.088	0.379	0.0001

>gi|242093218|ref|XP_002437099.1| hypothetical protein SORBIDRAFT_10g021075 [Sorghum bicolor] gi|241915322|gb|EER88466.1| hypothetical protein SORBIDRAFT_10g021075 [Sorghum bicolor]

 Score = 59.7 bits (143), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 29/76 (38%), Positives = 47/76 (61%), Gaps = 3/76 (3%)

Query: 4  LKKTYKHQYYPVPDESRWP-PELHYNMLPPIIIRTTGRPQTKKRREADENRAFKRSSSVR 62
           K TY+ +  P+PD S+WP  EL + + PP++ R  GRP+ +++R   E RA K+   V+
Sbjct: 25 FKATYEDRIEPIPDGSQWPIVELGFKVYPPLLGRGAGRPKVQRQRGYLEKRASKK--KVK 82

Query: 63 CSNFEEWGHNVRTCKV 78
          C    ++GH  +TCK+
Sbjct: 83 CKRCGDFGHFAKTCKL 98

Source: Sorghum bicolor

Species: Sorghum bicolor

Genus: Sorghum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|222623571|gb|EEE57703.1| hypothetical protein OsJ_08182 [Oryza sativa Japonica Group]

 Score = 58.2 bits (139), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 31/76 (40%), Positives = 46/76 (60%), Gaps = 3/76 (3%)

Query: 2   EALKKTYKHQYYPVPDESRWPPELHYNMLPPIIIRTTGRPQTKKRREADENRAFKRS--- 58
           +A  +TY    YPVPDE++W      ++ PP+     GRP+TK+ R +DE R   RS   
Sbjct: 740 DAYARTYCGMIYPVPDETQWEKTPFPDVDPPVARTQPGRPKTKRTRASDEPRVQGRSVAK 799

Query: 59  SSVRCSNFEEWGHNVR 74
           +++RCS  +E+GHN R
Sbjct: 800 TTIRCSVCKEFGHNSR 815

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|222628642|gb|EEE60774.1| hypothetical protein OsJ_14341 [Oryza sativa Japonica Group]

 Score = 57.8 bits (138), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 31/76 (40%), Positives = 46/76 (60%), Gaps = 3/76 (3%)

Query: 2   EALKKTYKHQYYPVPDESRWPPELHYNMLPPIIIRTTGRPQTKKRREADENRAFKRS--- 58
           +A  +TY    YPVPDE++W      ++ PP+     GRP+TK+ R +DE R   RS   
Sbjct: 700 DAYARTYCGMIYPVPDETQWEKTPFPDVDPPVARTQPGRPKTKRTRASDEPRVQGRSVAK 759

Query: 59  SSVRCSNFEEWGHNVR 74
           +++RCS  +E+GHN R
Sbjct: 760 TTIRCSVCKEFGHNSR 775

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|222623570|gb|EEE57702.1| hypothetical protein OsJ_08180 [Oryza sativa Japonica Group]

 Score = 57.4 bits (137), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 31/76 (40%), Positives = 46/76 (60%), Gaps = 3/76 (3%)

Query: 2   EALKKTYKHQYYPVPDESRWPPELHYNMLPPIIIRTTGRPQTKKRREADENRAFKRS--- 58
           +A  +TY    YPVPDE++W      ++ PP+     GRP+TK+ R +DE R   RS   
Sbjct: 281 DAYARTYCGMIYPVPDETQWEKTPFPDVDPPVARTQPGRPKTKRTRASDEPRVQGRSVAK 340

Query: 59  SSVRCSNFEEWGHNVR 74
           +++RCS  +E+GHN R
Sbjct: 341 TTIRCSVCKEFGHNSR 356

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|31432405|gb|AAP54042.1| transposon protein, putative, Mutator sub-class [Oryza sativa Japonica Group]

 Score = 55.1 bits (131), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 30/79 (37%), Positives = 44/79 (55%), Gaps = 4/79 (5%)

Query: 2   EALKKTYKHQYYPVPDESRWPPELHYNMLPPIIIRTTGRPQTKKRREADE----NRAFKR 57
           +A K TYKH   PV   + WP +    +  P  I+  GRP+T++RREA E    ++A K 
Sbjct: 765 DAFKSTYKHCLLPVEGMNAWPEDDREPLTAPGYIKMPGRPRTERRREAHEPAKPSKASKF 824

Query: 58  SSSVRCSNFEEWGHNVRTC 76
            + VRC   ++ GHN  +C
Sbjct: 825 GTKVRCRTCKQVGHNKSSC 843

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|222612932|gb|EEE51064.1| hypothetical protein OsJ_31731 [Oryza sativa Japonica Group]

 Score = 55.1 bits (131), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 30/79 (37%), Positives = 44/79 (55%), Gaps = 4/79 (5%)

Query: 2   EALKKTYKHQYYPVPDESRWPPELHYNMLPPIIIRTTGRPQTKKRREADE----NRAFKR 57
           +A K TYKH   PV   + WP +    +  P  I+  GRP+T++RREA E    ++A K 
Sbjct: 784 DAFKSTYKHCLLPVEGMNAWPEDDREPLTAPGYIKMPGRPRTERRREAHEPAKPSKASKF 843

Query: 58  SSSVRCSNFEEWGHNVRTC 76
            + VRC   ++ GHN  +C
Sbjct: 844 GTKVRCRTCKQVGHNKSSC 862

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|222640608|gb|EEE68740.1| hypothetical protein OsJ_27422 [Oryza sativa Japonica Group]

 Score = 53.9 bits (128), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 30/82 (36%), Positives = 43/82 (52%), Gaps = 5/82 (6%)

Query: 2  EALKKTYKHQYYPVPDESRWPPELHYNMLPPIIIRTTGRPQTKKRREADE-----NRAFK 56
          E  KKTY+H   PV  ES WP   +   LPP + +  GRP+  +R++  E      ++ K
Sbjct: 16 ERYKKTYQHVLQPVEHESAWPVSPNPKPLPPRVKKMPGRPKKNRRKDPSEPVKSGTKSSK 75

Query: 57 RSSSVRCSNFEEWGHNVRTCKV 78
            + +RC     +GHN RTC V
Sbjct: 76 VGTKIRCRRCGNYGHNSRTCCV 97

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|125553424|gb|EAY99133.1| hypothetical protein OsI_21092 [Oryza sativa Indica Group]

 Score = 51.6 bits (122), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 30/82 (36%), Positives = 43/82 (52%), Gaps = 5/82 (6%)

Query: 2   EALKKTYKHQYYPVPDESRWPPELHYNMLPPIIIRTTGRPQTKKRREADE-----NRAFK 56
           E  KKTY+H   PV  ES WP   +   LPP + +  GRP+  +R++  E      ++ K
Sbjct: 775 ERYKKTYQHVLQPVEHESAWPVSPNPKPLPPRVKKMPGRPKKNRRKDPSEPVKSGTKSSK 834

Query: 57  RSSSVRCSNFEEWGHNVRTCKV 78
             + +RC     +GHN RTC V
Sbjct: 835 VGTKIRCRRCGNYGHNSRTCCV 856

Source: Oryza sativa Indica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|222622925|gb|EEE57057.1| hypothetical protein OsJ_06863 [Oryza sativa Japonica Group]

 Score = 50.8 bits (120), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 28/78 (35%), Positives = 41/78 (52%), Gaps = 4/78 (5%)

Query: 3   ALKKTYKHQYYPVPDESRWPPELHYNMLPPIIIRTTGRPQTKKRREADE----NRAFKRS 58
           A KKTY+H   PV   S WP +    +  P  I+  GRP+T++RRE  E     +  K  
Sbjct: 753 AFKKTYEHCLEPVEGMSSWPEDERVPLNAPGYIKMPGRPKTERRRERGEPPKPTKLSKMG 812

Query: 59  SSVRCSNFEEWGHNVRTC 76
           + +RC   ++ GHN  +C
Sbjct: 813 TVIRCRKCKQVGHNRTSC 830

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|218194691|gb|EEC77118.1| hypothetical protein OsI_15544 [Oryza sativa Indica Group]

 Score = 50.4 bits (119), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 30/79 (37%), Positives = 39/79 (49%), Gaps = 4/79 (5%)

Query: 2   EALKKTYKHQYYPVPDESRWPPELHYNMLPPIIIRTTGRPQTKKRREADEN----RAFKR 57
           EA  +TY H  YPVP E  W      ++ PP   +  GRP+  +RR A E      A  R
Sbjct: 689 EAYLRTYSHMVYPVPKEDGWTRTDSPDIDPPRFRKQAGRPKKSRRRSAGEEPTRASARAR 748

Query: 58  SSSVRCSNFEEWGHNVRTC 76
            ++V CSN +   H  RTC
Sbjct: 749 MNTVTCSNCKLHNHTYRTC 767

Source: Oryza sativa Indica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

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)

No hits with e-value below 0.001 by BLAST

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Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

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Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: Sb10g021075.1 hypothetical protein (191 aa) (Sorghum bicolor)

Predicted Functional Partners:

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

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Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	84
PF15288	40	zf-CCHC_6: Zinc knuckle	96.92
PF00098	18	zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc fi	96.66
PF13696	32	zf-CCHC_2: Zinc knuckle	94.87
PF14392	49	zf-CCHC_4: Zinc knuckle	92.66
COG5179	968	TAF1 Transcription initiation factor TFIID, subuni	90.93
smart00343	26	ZnF_C2HC zinc finger.	90.28
PF13917	42	zf-CCHC_3: Zinc knuckle	86.23

>PF15288 zf-CCHC_6: Zinc knuckle

Probab=96.92  E-value=0.00051  Score=37.44  Aligned_cols=20  Identities=30%  Similarity=0.689  Sum_probs=17.8

Q ss_pred             eeCCccCcCCCCc--CCCCCCC
Q 043522           61 VRCSNFEEWGHNV--RTCKVDK   80 (84)
Q Consensus        61 ~~Cs~C~~~GHn~--~tC~~~~   80 (84)
                      ++|..|+++||.+  ++||+..
T Consensus         2 ~kC~~CG~~GH~~t~k~CP~~~   23 (40)
T PF15288_consen    2 VKCKNCGAFGHMRTNKRCPMYC   23 (40)
T ss_pred             ccccccccccccccCccCCCCC
Confidence            6999999999997  7999865

>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=96.66  E-value=0.0013  Score=29.96  Aligned_cols=17  Identities=41%  Similarity=0.706  Sum_probs=15.7

Q ss_pred             eCCccCcCCCCcCCCCC
Q 043522           62 RCSNFEEWGHNVRTCKV   78 (84)
Q Consensus        62 ~Cs~C~~~GHn~~tC~~   78 (84)
                      +|-+|++.||..+.|++
T Consensus         2 ~C~~C~~~GH~~~~Cp~   18 (18)
T PF00098_consen    2 KCFNCGEPGHIARDCPK   18 (18)
T ss_dssp             BCTTTSCSSSCGCTSSS
T ss_pred             cCcCCCCcCcccccCcc
Confidence            69999999999999984

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

>PF13696 zf-CCHC_2: Zinc knuckle

Probab=94.87  E-value=0.013  Score=30.49  Aligned_cols=21  Identities=24%  Similarity=0.563  Sum_probs=18.9

Q ss_pred             eeeCCccCcCCCCcCCCCCCC
Q 043522           60 SVRCSNFEEWGHNVRTCKVDK   80 (84)
Q Consensus        60 ~~~Cs~C~~~GHn~~tC~~~~   80 (84)
                      ...|-+|++.||....|+.+.
T Consensus         8 ~Y~C~~C~~~GH~i~dCP~~~   28 (32)
T PF13696_consen    8 GYVCHRCGQKGHWIQDCPTNK   28 (32)
T ss_pred             CCEeecCCCCCccHhHCCCCC
Confidence            479999999999999999853

>PF14392 zf-CCHC_4: Zinc knuckle

Probab=92.66  E-value=0.047  Score=30.28  Aligned_cols=19  Identities=21%  Similarity=0.431  Sum_probs=17.2

Q ss_pred             eeeCCccCcCCCCcCCCCC
Q 043522           60 SVRCSNFEEWGHNVRTCKV   78 (84)
Q Consensus        60 ~~~Cs~C~~~GHn~~tC~~   78 (84)
                      ...|..|+..||....|+.
T Consensus        31 p~~C~~C~~~gH~~~~C~k   49 (49)
T PF14392_consen   31 PRFCFHCGRIGHSDKECPK   49 (49)
T ss_pred             ChhhcCCCCcCcCHhHcCC
Confidence            5689999999999999974

>COG5179 TAF1 Transcription initiation factor TFIID, subunit TAF1 [Transcription]

Probab=90.93  E-value=0.16  Score=42.28  Aligned_cols=26  Identities=19%  Similarity=0.410  Sum_probs=20.7

Q ss_pred             cccCCeeeCCccCcCCCCc--CCCCCCC
Q 043522           55 FKRSSSVRCSNFEEWGHNV--RTCKVDK   80 (84)
Q Consensus        55 sk~~~~~~Cs~C~~~GHn~--~tC~~~~   80 (84)
                      .|+-++.+|+.|+|.||-+  +.||+-.
T Consensus       932 GRK~Ttr~C~nCGQvGHmkTNK~CP~f~  959 (968)
T COG5179         932 GRKNTTRTCGNCGQVGHMKTNKACPKFS  959 (968)
T ss_pred             CCCCcceecccccccccccccccCcccc
Confidence            4455689999999999987  5888753

>smart00343 ZnF_C2HC zinc finger

Probab=90.28  E-value=0.15  Score=24.51  Aligned_cols=18  Identities=33%  Similarity=0.661  Sum_probs=15.5

Q ss_pred             eCCccCcCCCCcCCCCCC
Q 043522           62 RCSNFEEWGHNVRTCKVD   79 (84)
Q Consensus        62 ~Cs~C~~~GHn~~tC~~~   79 (84)
                      .|.+|++.||..+.|+..
T Consensus         1 ~C~~CG~~GH~~~~C~~~   18 (26)
T smart00343        1 KCYNCGKEGHIARDCPKX   18 (26)
T ss_pred             CCccCCCCCcchhhCCcc
Confidence            488999999999999843

>PF13917 zf-CCHC_3: Zinc knuckle

Probab=86.23  E-value=0.41  Score=26.17  Aligned_cols=19  Identities=32%  Similarity=0.576  Sum_probs=17.4

Q ss_pred             eeeCCccCcCCCCcCCCCC
Q 043522           60 SVRCSNFEEWGHNVRTCKV   78 (84)
Q Consensus        60 ~~~Cs~C~~~GHn~~tC~~   78 (84)
                      ...|-+|.+.||-..-|++
T Consensus         4 ~~~CqkC~~~GH~tyeC~~   22 (42)
T PF13917_consen    4 RVRCQKCGQKGHWTYECPN   22 (42)
T ss_pred             CCcCcccCCCCcchhhCCC
Confidence            5799999999999999994

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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

No hit with e-value below 0.005

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	84
1dsq_A	26	Nucleic acid binding protein P14; CCHC type zinc f	96.24
1a6b_B	40	Momulv, zinc finger protein NCP10; nucleocapsid pr	95.25
1nc8_A	29	Nucleocapsid protein; HIV-2, RNA recognition, zinc	95.19
1u6p_A	56	GAG polyprotein; MLV, A-minor K-turn, stem loop, b	94.54
2a51_A	39	Nucleocapsid protein; sivlhoest, structure, NCP8,	94.38
2bl6_A	37	Nucleocapsid protein P11; lentivirus, polyprotein,	93.68
2a51_A	39	Nucleocapsid protein; sivlhoest, structure, NCP8,	93.01
2ec7_A	49	GAG polyprotein (PR55GAG); nucleocapsid protein, H	92.98
2ec7_A	49	GAG polyprotein (PR55GAG); nucleocapsid protein, H	92.88
2ihx_A	61	Nucleocapsid (NC) protein; protein-RNA complex, vi	92.52
2bl6_A	37	Nucleocapsid protein P11; lentivirus, polyprotein,	92.23
1a1t_A	55	Nucleocapsid protein; stem-loop RNA, viral protein	91.78
1a1t_A	55	Nucleocapsid protein; stem-loop RNA, viral protein	90.82
1cl4_A	60	Protein (GAG polyprotein); nucleocapsid protein, R	90.62
2ihx_A	61	Nucleocapsid (NC) protein; protein-RNA complex, vi	90.14
2li8_A	74	Protein LIN-28 homolog A; zinc finger, micro RNA,	89.6
3nyb_B	83	Protein AIR2; polya RNA polymerase, zinc knuckle p	89.36
2cqf_A	63	RNA-binding protein LIN-28; CCHC zinc-finger, stru	89.23
3nyb_B	83	Protein AIR2; polya RNA polymerase, zinc knuckle p	88.68
3ts2_A	148	Protein LIN-28 homolog A; microrna biogenesis, pro	87.63
2cqf_A	63	RNA-binding protein LIN-28; CCHC zinc-finger, stru	86.99
2lli_A	124	Protein AIR2; RNA surveillance, RNA degradation, R	86.59
2ysa_A	55	Retinoblastoma-binding protein 6; zinc finger, CCH	86.44
2li8_A	74	Protein LIN-28 homolog A; zinc finger, micro RNA,	85.15
3ts2_A	148	Protein LIN-28 homolog A; microrna biogenesis, pro	83.47
1cl4_A	60	Protein (GAG polyprotein); nucleocapsid protein, R	83.34
2lli_A	124	Protein AIR2; RNA surveillance, RNA degradation, R	80.17

>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=95.25  E-value=0.0083  Score=31.74  Aligned_cols=21  Identities=24%  Similarity=0.493  Sum_probs=19.4

Q ss_pred             eeeCCccCcCCCCcCCCCCCC
Q 043522           60 SVRCSNFEEWGHNVRTCKVDK   80 (84)
Q Consensus        60 ~~~Cs~C~~~GHn~~tC~~~~   80 (84)
                      ...|-.|++.||-.+.|+...
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            579999999999999999975

>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=95.19  E-value=0.0088  Score=29.16  Aligned_cols=21  Identities=33%  Similarity=0.773  Sum_probs=18.8

Q ss_pred             eeeCCccCcCCCCcCCCCCCC
Q 043522           60 SVRCSNFEEWGHNVRTCKVDK   80 (84)
Q Consensus        60 ~~~Cs~C~~~GHn~~tC~~~~   80 (84)
                      .+.|-.|++.||..+.|+.+.
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            578999999999999998764

>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=94.54  E-value=0.017  Score=32.56  Aligned_cols=21  Identities=24%  Similarity=0.493  Sum_probs=19.4

Q ss_pred             eeeCCccCcCCCCcCCCCCCC
Q 043522           60 SVRCSNFEEWGHNVRTCKVDK   80 (84)
Q Consensus        60 ~~~Cs~C~~~GHn~~tC~~~~   80 (84)
                      ..+|-.|++.||-.+.|+...
T Consensus        23 ~~~C~~Cge~GH~ardCp~~~   43 (56)
T 1u6p_A           23 RDQCAYCKEKGHWAKDCPKKP   43 (56)
T ss_dssp             TTBCSSSCCBSSCGGGCTTCC
T ss_pred             CCcceeCCCCCcccccCcCCc
Confidence            579999999999999999875

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

Probab=94.38  E-value=0.021  Score=29.36  Aligned_cols=19  Identities=32%  Similarity=0.667  Sum_probs=13.8

Q ss_pred             eeCCccCcCCCCcCCCCCC
Q 043522           61 VRCSNFEEWGHNVRTCKVD   79 (84)
Q Consensus        61 ~~Cs~C~~~GHn~~tC~~~   79 (84)
                      ++|-+|++.||..+.|+.+
T Consensus         1 i~C~~Cg~~GH~a~~C~~~   19 (39)
T 2a51_A            1 LTCFNCGKPGHTARMCRQP   19 (39)
T ss_dssp             CBCTTTCCBSSCTTTCCSC
T ss_pred             CeeeccCCCCcccccCCCC
Confidence            3577777788877777764

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

Probab=93.68  E-value=0.028  Score=28.52  Aligned_cols=17  Identities=24%  Similarity=0.556  Sum_probs=10.4

Q ss_pred             eeCCccCcCCCCcCCCC
Q 043522           61 VRCSNFEEWGHNVRTCK   77 (84)
Q Consensus        61 ~~Cs~C~~~GHn~~tC~   77 (84)
                      ..|-+|++.||..+.|+
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            55666666666666665

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

Probab=93.01  E-value=0.05  Score=27.88  Aligned_cols=18  Identities=22%  Similarity=0.342  Sum_probs=16.6

Q ss_pred             eeCCccCcCCCCcCCCCC
Q 043522           61 VRCSNFEEWGHNVRTCKV   78 (84)
Q Consensus        61 ~~Cs~C~~~GHn~~tC~~   78 (84)
                      ..|-+|++.||..+.|++
T Consensus        22 ~~C~~Cg~~GH~~~~C~~   39 (39)
T 2a51_A           22 EGCWNCGSKEHRFAQCPK   39 (39)
T ss_dssp             SSCTTTCCSSSCTTTSCC
T ss_pred             CccccCCCCCCccCcCcC
Confidence            589999999999999985

>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=92.98  E-value=0.054  Score=29.13  Aligned_cols=19  Identities=21%  Similarity=0.401  Sum_probs=9.7

Q ss_pred             eeCCccCcCCCCcCCCCCC
Q 043522           61 VRCSNFEEWGHNVRTCKVD   79 (84)
Q Consensus        61 ~~Cs~C~~~GHn~~tC~~~   79 (84)
                      ..|-+|++.||..+.|+..
T Consensus        28 ~~C~~Cg~~GH~~~~C~~~   46 (49)
T 2ec7_A           28 QGCWKCGKTGHVMAKCPER   46 (49)
T ss_dssp             CSCSSSCCSSCCGGGCCSS
T ss_pred             CeeCcCCCcCCccCCCcCC
Confidence            3455555555555555543

>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=92.88  E-value=0.054  Score=29.16  Aligned_cols=20  Identities=35%  Similarity=0.767  Sum_probs=18.3

Q ss_pred             eeeCCccCcCCCCcCCCCCC
Q 043522           60 SVRCSNFEEWGHNVRTCKVD   79 (84)
Q Consensus        60 ~~~Cs~C~~~GHn~~tC~~~   79 (84)
                      ...|-+|++.||..+.|+.+
T Consensus         6 ~~~C~~Cg~~GH~a~~C~~~   25 (49)
T 2ec7_A            6 VIRCWNCGKEGHSARQCRAP   25 (49)
T ss_dssp             CCBCTTTCCBTCCTTTCCCS
T ss_pred             cCeeeecCCCCcChhhCcCC
Confidence            57899999999999999975

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

Probab=92.52  E-value=0.054  Score=30.40  Aligned_cols=21  Identities=29%  Similarity=0.659  Sum_probs=18.6

Q ss_pred             eeeCCccCcCCCCcCCCCCCC
Q 043522           60 SVRCSNFEEWGHNVRTCKVDK   80 (84)
Q Consensus        60 ~~~Cs~C~~~GHn~~tC~~~~   80 (84)
                      ...|-+|++.||..+.|+...
T Consensus        30 ~~~C~~Cg~~GH~ar~C~~~~   50 (61)
T 2ihx_A           30 RERCQLCNGMGHNAKQCRKRD   50 (61)
T ss_dssp             CSBCTTTCCBSSCGGGCCCCC
T ss_pred             CCeeCCCCCCCCCcCCCcCCC
Confidence            368999999999999999876

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

Probab=92.23  E-value=0.06  Score=27.25  Aligned_cols=17  Identities=29%  Similarity=0.598  Sum_probs=15.5

Q ss_pred             eCCccCcCCCCcCCCCC
Q 043522           62 RCSNFEEWGHNVRTCKV   78 (84)
Q Consensus        62 ~Cs~C~~~GHn~~tC~~   78 (84)
                      .|-+|++.||..+.|+.
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            69999999999999975

>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=91.78  E-value=0.091  Score=28.65  Aligned_cols=20  Identities=20%  Similarity=0.503  Sum_probs=14.1

Q ss_pred             eeCCccCcCCCCcCCCCCCC
Q 043522           61 VRCSNFEEWGHNVRTCKVDK   80 (84)
Q Consensus        61 ~~Cs~C~~~GHn~~tC~~~~   80 (84)
                      ..|-+|++.||..+.|+...
T Consensus        34 ~~C~~Cg~~GH~~~~C~~~~   53 (55)
T 1a1t_A           34 KGCWKCGKEGHQMKDCTERQ   53 (55)
T ss_dssp             CBCTTTCCBSSCGGGCSSSC
T ss_pred             CEeCCCCCcCCccCCCcCcC
Confidence            46777777777777777643

>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=90.82  E-value=0.1  Score=28.45  Aligned_cols=20  Identities=30%  Similarity=0.702  Sum_probs=18.2

Q ss_pred             eeeCCccCcCCCCcCCCCCC
Q 043522           60 SVRCSNFEEWGHNVRTCKVD   79 (84)
Q Consensus        60 ~~~Cs~C~~~GHn~~tC~~~   79 (84)
                      ...|-+|++.||..+.|+.+
T Consensus        12 ~~~C~~Cg~~GH~a~~C~~~   31 (55)
T 1a1t_A           12 TVKCFNCGKEGHIAKNCRAP   31 (55)
T ss_dssp             TCBCTTTCCBSSCGGGCSSC
T ss_pred             CcceeeeCCCCcChhhcCCC
Confidence            47899999999999999876

>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=90.62  E-value=0.15  Score=28.25  Aligned_cols=21  Identities=19%  Similarity=0.316  Sum_probs=19.0

Q ss_pred             eeeCCccCcCCCCcCCCCCCC
Q 043522           60 SVRCSNFEEWGHNVRTCKVDK   80 (84)
Q Consensus        60 ~~~Cs~C~~~GHn~~tC~~~~   80 (84)
                      ...|-+|++.||..+.|+...
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            468999999999999999875

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

Probab=90.14  E-value=0.12  Score=28.97  Aligned_cols=21  Identities=19%  Similarity=0.311  Sum_probs=18.7

Q ss_pred             eeeCCccCcCCCCcCCCCCCC
Q 043522           60 SVRCSNFEEWGHNVRTCKVDK   80 (84)
Q Consensus        60 ~~~Cs~C~~~GHn~~tC~~~~   80 (84)
                      ...|-+|++.||..+.|+...
T Consensus         4 ~~~C~~Cg~~GH~a~~C~~~~   24 (61)
T 2ihx_A            4 RGLCYTCGSPGHYQAQCPKKR   24 (61)
T ss_dssp             TTBCSSSCCBTCCGGGCTTTT
T ss_pred             CCcccccCCCCeehhhCcCCc
Confidence            468999999999999999864

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

Probab=89.60  E-value=0.27  Score=28.75  Aligned_cols=19  Identities=21%  Similarity=0.531  Sum_probs=11.7

Q ss_pred             eeCCccCcCCCCcCCCCCC
Q 043522           61 VRCSNFEEWGHNVRTCKVD   79 (84)
Q Consensus        61 ~~Cs~C~~~GHn~~tC~~~   79 (84)
                      ..|-+|++.||..+.|+..
T Consensus        47 ~~C~~Cg~~GH~ar~Cp~~   65 (74)
T 2li8_A           47 KKCHFCQSISHMVASCPLK   65 (74)
T ss_dssp             CCCTTTCCTTSCGGGCTTG
T ss_pred             CccCCcCCcCCccCcCcCC
Confidence            4566666666666666554

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

Probab=89.36  E-value=0.11  Score=31.25  Aligned_cols=21  Identities=19%  Similarity=0.303  Sum_probs=17.2

Q ss_pred             eeeCCccCcCCCCcCCCCCCC
Q 043522           60 SVRCSNFEEWGHNVRTCKVDK   80 (84)
Q Consensus        60 ~~~Cs~C~~~GHn~~tC~~~~   80 (84)
                      .+.|-+|++.||..+.||..+
T Consensus         5 ~~~C~~Cg~~GH~~~~Cp~~~   25 (83)
T 3nyb_B            5 KVQCTLCKSKKHSKERCPSIW   25 (83)
T ss_dssp             --CCSSSCCSSSCGGGCGGGT
T ss_pred             cCCCCCCCCCCCccccCCCcc
Confidence            478999999999999998753

>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=89.23  E-value=0.26  Score=27.74  Aligned_cols=20  Identities=20%  Similarity=0.511  Sum_probs=14.9

Q ss_pred             eeeCCccCcCCCCcCCCCCC
Q 043522           60 SVRCSNFEEWGHNVRTCKVD   79 (84)
Q Consensus        60 ~~~Cs~C~~~GHn~~tC~~~   79 (84)
                      ...|-+|++.||..+.|+..
T Consensus        29 ~~~C~~Cg~~GH~ar~Cp~~   48 (63)
T 2cqf_A           29 PKKCHFCQSISHMVASCPLK   48 (63)
T ss_dssp             SSCCTTTCCSSSCTTTCTGG
T ss_pred             CCccCCcCCcCCccCcCCCc
Confidence            46777788888888877764

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

Probab=88.68  E-value=0.24  Score=29.67  Aligned_cols=23  Identities=30%  Similarity=0.505  Sum_probs=20.1

Q ss_pred             eeeCCccCcCCCCcCCCCCCCCC
Q 043522           60 SVRCSNFEEWGHNVRTCKVDKGS   82 (84)
Q Consensus        60 ~~~Cs~C~~~GHn~~tC~~~~~~   82 (84)
                      .+.|-+|++.||..+-|+....|
T Consensus        46 ~~~CYnCG~~GH~~rdC~~~r~s   68 (83)
T 3nyb_B           46 TIYCYNCGGKGHFGDDCKEKRSS   68 (83)
T ss_dssp             CCBCSSSSCBSSCGGGCSSCCSC
T ss_pred             CCeecccCCCCcCcccCCccccC
Confidence            47899999999999999987643

>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=87.63  E-value=0.3  Score=31.91  Aligned_cols=19  Identities=21%  Similarity=0.531  Sum_probs=11.5

Q ss_pred             eeCCccCcCCCCcCCCCCC
Q 043522           61 VRCSNFEEWGHNVRTCKVD   79 (84)
Q Consensus        61 ~~Cs~C~~~GHn~~tC~~~   79 (84)
                      ..|-+|++.||..+.|+..
T Consensus       120 ~~C~~Cg~~GH~~r~Cp~~  138 (148)
T 3ts2_A          120 KKCHFCQSINHMVASCPLK  138 (148)
T ss_dssp             CCCTTTCCSSCCGGGCTTT
T ss_pred             CcccccCCcCCEeccCcCC
Confidence            4566666666666666654

>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=86.99  E-value=0.23  Score=27.96  Aligned_cols=18  Identities=33%  Similarity=0.689  Sum_probs=16.5

Q ss_pred             eeeCCccCcCCCCcCCCC
Q 043522           60 SVRCSNFEEWGHNVRTCK   77 (84)
Q Consensus        60 ~~~Cs~C~~~GHn~~tC~   77 (84)
                      ...|-+|++.||..+.|+
T Consensus         7 ~~~C~~Cg~~GH~a~~C~   24 (63)
T 2cqf_A            7 GDRCYNCGGLDHHAKECK   24 (63)
T ss_dssp             CCCCSSSCCSSSCTTTCC
T ss_pred             CCcccccCCCCcChhhCC
Confidence            468999999999999998

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

Probab=86.59  E-value=0.38  Score=30.04  Aligned_cols=21  Identities=19%  Similarity=0.303  Sum_probs=18.1

Q ss_pred             eeeCCccCcCCCCcCCCCCCC
Q 043522           60 SVRCSNFEEWGHNVRTCKVDK   80 (84)
Q Consensus        60 ~~~Cs~C~~~GHn~~tC~~~~   80 (84)
                      .+.|-+|++.||..+.|+..+
T Consensus        64 ~~~C~~Cg~~GH~~~~Cp~~~   84 (124)
T 2lli_A           64 KVQCTLCKSKKHSKERCPSIW   84 (124)
T ss_dssp             CCSSSSSCSSCCCTTTCCCST
T ss_pred             CccCCCCCcCCcchhhCCCcc
Confidence            368999999999999999865

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

Probab=86.44  E-value=0.28  Score=27.34  Aligned_cols=20  Identities=20%  Similarity=0.556  Sum_probs=17.6

Q ss_pred             eeeCCccCcCCCCcCCCCCC
Q 043522           60 SVRCSNFEEWGHNVRTCKVD   79 (84)
Q Consensus        60 ~~~Cs~C~~~GHn~~tC~~~   79 (84)
                      ...|=+|++.||-.+-|+..
T Consensus         7 ~~~C~kCGk~GH~~k~Cp~~   26 (55)
T 2ysa_A            7 GYTCFRCGKPGHYIKNCPTN   26 (55)
T ss_dssp             SCCCTTTCCTTSCGGGCSGG
T ss_pred             CCccccCCCcCcccccCCCC
Confidence            46899999999999999943

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

Probab=85.15  E-value=0.35  Score=28.26  Aligned_cols=18  Identities=33%  Similarity=0.689  Sum_probs=16.7

Q ss_pred             eeeCCccCcCCCCcCCCC
Q 043522           60 SVRCSNFEEWGHNVRTCK   77 (84)
Q Consensus        60 ~~~Cs~C~~~GHn~~tC~   77 (84)
                      ...|-+|++.||..+.|+
T Consensus        24 ~~~C~~Cg~~GH~a~~C~   41 (74)
T 2li8_A           24 GDRCYNCGGLDHHAKECK   41 (74)
T ss_dssp             TSCCTTTCCSSSCTTTCS
T ss_pred             CCcccccCCcCcCcccCC
Confidence            578999999999999998

>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=83.47  E-value=0.46  Score=30.99  Aligned_cols=19  Identities=32%  Similarity=0.684  Sum_probs=17.4

Q ss_pred             eeeCCccCcCCCCcCCCCC
Q 043522           60 SVRCSNFEEWGHNVRTCKV   78 (84)
Q Consensus        60 ~~~Cs~C~~~GHn~~tC~~   78 (84)
                      ..+|-+|++.||-.+.|+.
T Consensus        97 ~~~C~~Cg~~GH~a~~C~~  115 (148)
T 3ts2_A           97 GDRCYNCGGLDHHAKECKL  115 (148)
T ss_dssp             SCCCTTTCCSSCCGGGCCS
T ss_pred             CCcccEeCCccchhhhCCC
Confidence            4789999999999999986

>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=83.34  E-value=0.23  Score=27.47  Aligned_cols=19  Identities=21%  Similarity=0.499  Sum_probs=0.0

Q ss_pred             eCCccCcCCCCcCCCCCCC
Q 043522           62 RCSNFEEWGHNVRTCKVDK   80 (84)
Q Consensus        62 ~Cs~C~~~GHn~~tC~~~~   80 (84)
                      .|-+|++.||..+.|+...
T Consensus         3 ~Cf~Cg~~GH~a~~C~~~~   21 (60)
T 1cl4_A            3 SCFKCGKKGHFAKNCHEHA   21 (60)
T ss_dssp             -------------------
T ss_pred             ccccCCCCCcCHhhCcCCC
Confidence            6899999999999999864

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

Probab=80.17  E-value=0.95  Score=28.15  Aligned_cols=19  Identities=32%  Similarity=0.510  Sum_probs=17.7

Q ss_pred             eeeCCccCcCCCCcCCCCC
Q 043522           60 SVRCSNFEEWGHNVRTCKV   78 (84)
Q Consensus        60 ~~~Cs~C~~~GHn~~tC~~   78 (84)
                      .+.|-+|++.||..+.|++
T Consensus       105 ~~~Cy~Cg~~GH~a~dCp~  123 (124)
T 2lli_A          105 TIYCYNCGGKGHFGDDCKE  123 (124)
T ss_dssp             CCCTTTTSSSCTTTTTSCC
T ss_pred             CCCcCCCCCCCcCcccCcC
Confidence            5899999999999999986

---

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	84
d2exfa1	42	HIV nucleocapsid {Human immunodeficiency virus typ	95.78
d1nc8a_	29	HIV nucleocapsid {Human immunodeficiency virus typ	95.05
d1a6bb_	40	Zinc finger protein ncp10 {Moloney murine leukemia	94.91
d2exfa1	42	HIV nucleocapsid {Human immunodeficiency virus typ	92.86
d1dsqa_	26	Nucleic acid binding protein p14 {Mouse mammary tu	88.1

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

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

Probab=95.78  E-value=0.002  Score=33.00  Aligned_cols=19  Identities=37%  Similarity=0.805  Sum_probs=15.0

Q ss_pred             eeCCccCcCCCCcCCCCCC
Q 043522           61 VRCSNFEEWGHNVRTCKVD   79 (84)
Q Consensus        61 ~~Cs~C~~~GHn~~tC~~~   79 (84)
                      ++|-+|++.||..+.|+.+
T Consensus         2 i~C~~Cg~~GH~~~~Cp~~   20 (42)
T d2exfa1           2 VKCFNCGKEGHTARNCRAP   20 (42)
T ss_dssp             CCCTTTCCSSSCTTTCSSC
T ss_pred             CccccCCCcCcCcccCcCC
Confidence            5788888888888888765

>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=95.05  E-value=0.0056  Score=29.04  Aligned_cols=21  Identities=33%  Similarity=0.773  Sum_probs=19.3

Q ss_pred             eeeCCccCcCCCCcCCCCCCC
Q 043522           60 SVRCSNFEEWGHNVRTCKVDK   80 (84)
Q Consensus        60 ~~~Cs~C~~~GHn~~tC~~~~   80 (84)
                      .++|=+|+..||..+.|..+-
T Consensus         6 ~ikCfNCGkeGH~ar~CrAPR   26 (29)
T d1nc8a_           6 VIRCWNCGKEGHSARQCRAPR   26 (29)
T ss_dssp             CCBCTTTSCBSSCGGGCCSSS
T ss_pred             eeEeecCCccchhhhhccCcc
Confidence            789999999999999998874

>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=94.91  E-value=0.011  Score=29.94  Aligned_cols=24  Identities=25%  Similarity=0.566  Sum_probs=20.8

Q ss_pred             eeeCCccCcCCCCcCCCCCCC-CCC
Q 043522           60 SVRCSNFEEWGHNVRTCKVDK-GSK   83 (84)
Q Consensus        60 ~~~Cs~C~~~GHn~~tC~~~~-~~~   83 (84)
                      .-+|.-|++.||=.+-||+.. |.|
T Consensus        10 kDQCAyCke~GHW~~dCPkkprg~k   34 (40)
T d1a6bb_          10 RDQCAYCKEKGHWAKDCPKKPRGPR   34 (40)
T ss_dssp             SSSCSSSCCTTCCTTSCSSSCCCTT
T ss_pred             chhhHHHhhcCchhhhCccCCCCCC
Confidence            468999999999999999886 554

>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=92.86  E-value=0.027  Score=28.48  Aligned_cols=19  Identities=21%  Similarity=0.503  Sum_probs=17.3

Q ss_pred             eeCCccCcCCCCcCCCCCC
Q 043522           61 VRCSNFEEWGHNVRTCKVD   79 (84)
Q Consensus        61 ~~Cs~C~~~GHn~~tC~~~   79 (84)
                      ..|-+|++.||..+.|+..
T Consensus        23 ~~C~~Cg~~GH~~~~Cp~r   41 (42)
T d2exfa1          23 KGCWKCGKEGHQMKDCTER   41 (42)
T ss_dssp             SSCSSSCCSSSCTTTCCSS
T ss_pred             CccccCCCCCeecccCCCC
Confidence            5799999999999999975