Citrus Sinensis ID: 041609

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70-
Protein Sequence
MFHGIYLTTKERTYGYYVRILVDVDLSGPLPNSVMVELPDDCILVKVMYENLPLKCIVCGNIGHDRTQCQR
Secondary Structure (PSIPRED)
ccccccccccccccccEEEEEEEEEccccccEEEEEEccccEEEEEEEEccccccccccccEEcccccccc
Secondary Structure Prediction (SSPRO)
ccccEEEccccccccEEEEEEEEccccHHHHcEEEEEEcccEEEEEEEEcccccHHHHHHHccccHHHccc
Coil and Loop (DISEMBL)
mfhgiylttkertYGYYVRILVDvdlsgplpnsvmvelpddCILVKVMYenlplkcivcgnighdrtqcqr
Flexible Loop (DISEMBL)
mfhgiylttkertygYYVRILVDVDLSGPLPNSVMVELPDDCILVKVMYENLPLKCIVCGNIGHDRTQCQR
Low Complexity Region (SEG)
MFHGIYLTTKERTYGYYVRILVDVDLSGPLPNSVMVELPDDCILVKVMYENLPLKCIVCGNIGHDRTQCQR
Disordered region (IsUnstruct)
**HGIYLTTKERTYGYYVRILVDVDLSGPLPNSVMVELPDDCILVKVMYENLPLKCIVCGNIGH*******
Disordered Region (DISOPRED)
*FHGIYLTTKERTYGYYVRILVDVDLSGPLPNSVMVELPDDCILVKVMYENLPLKCIVCGNIGHDR*QC**
Disordered Region (DISEMBL)
MFHGIYLTTKERTYGYYVRILVDVDLSGPLPNSVMVELPDDCILVKVMYENLPLKCIVCGNIGHDRTQCQR
Disordered Region (DISPRO)
*FHGIYLTTKERTYGYYVRILVDVDLSGPLPNSVMVELPDDCILVKVMYENLPLKCIVCGNIGHDR**C*R
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MFHGIYLTTKERTYGYYVRILVDVDLSGPLPNSVMVELPDDCILVKVMYENLPLKCIVCGNIGHDRTQCQR
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	71
357443871	651	hypothetical protein MTR_1g100160 [Medic	0.873	0.095	0.483	8e-09
357438831	509	hypothetical protein MTR_1g035150 [Medic	0.873	0.121	0.435	1e-08
357501405	351	Histone H4 [Medicago truncatula] gi|3554	0.901	0.182	0.421	5e-08
124365552	289	Histone H4; Histone-fold [Medicago trunc	0.901	0.221	0.421	5e-08
357515097	1731	NBS resistance protein [Medicago truncat	0.873	0.035	0.467	6e-08
357500595	679	hypothetical protein MTR_6g087240 [Medic	0.873	0.091	0.451	8e-08
357438275	612	hypothetical protein MTR_1g023970 [Medic	0.873	0.101	0.451	8e-08
357485709	288	hypothetical protein MTR_5g033250 [Medic	0.887	0.218	0.476	8e-08
357517505	340	hypothetical protein MTR_8g072470 [Medic	0.887	0.185	0.460	1e-07
357485473	664	hypothetical protein MTR_5g031820 [Medic	0.873	0.093	0.451	1e-07

>gi|357443871|ref|XP_003592213.1| hypothetical protein MTR_1g100160 [Medicago truncatula] gi|355481261|gb|AES62464.1| hypothetical protein MTR_1g100160 [Medicago truncatula]

 Score = 64.3 bits (155), Expect = 8e-09,   Method: Composition-based stats.
 Identities = 30/62 (48%), Positives = 38/62 (61%)

Query: 9  TKERTYGYYVRILVDVDLSGPLPNSVMVELPDDCILVKVMYENLPLKCIVCGNIGHDRTQ 68
          TK RT+G+Y RIL+D+DLS  + N +MVE       V+V YE LP  C  C  IGH   Q
Sbjct: 36 TKNRTFGHYARILIDLDLSKRIFNEIMVEREGFSFYVEVQYEQLPEYCNNCATIGHSIGQ 95

Query: 69 CQ 70
          C+
Sbjct: 96 CK 97

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357438831|ref|XP_003589692.1| hypothetical protein MTR_1g035150 [Medicago truncatula] gi|355478740|gb|AES59943.1| hypothetical protein MTR_1g035150 [Medicago truncatula]

 Score = 63.9 bits (154), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 27/62 (43%), Positives = 39/62 (62%)

Query: 9   TKERTYGYYVRILVDVDLSGPLPNSVMVELPDDCILVKVMYENLPLKCIVCGNIGHDRTQ 68
           T+ R +G+Y R+LVD+DLS  + N VM+E       + + YE LP+ C  CGNIGH  + 
Sbjct: 203 TQNRVFGHYARVLVDMDLSKHIFNEVMIERTGFSFAIGISYERLPVFCTHCGNIGHHTSS 262

Query: 69  CQ 70
           C+
Sbjct: 263 CR 264

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357501405|ref|XP_003620991.1| Histone H4 [Medicago truncatula] gi|355496006|gb|AES77209.1| Histone H4 [Medicago truncatula]

 Score = 62.0 bits (149), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 27/64 (42%), Positives = 41/64 (64%)

Query: 8   TTKERTYGYYVRILVDVDLSGPLPNSVMVELPDDCILVKVMYENLPLKCIVCGNIGHDRT 67
           +TK RT+G+Y RIL+D+DLS P+ N+++V   +    VK+ YE  PL C  C +I H   
Sbjct: 122 STKIRTFGHYARILIDLDLSQPILNNLLVGREESAFFVKIEYEKQPLFCNNCKHIRHSIQ 181

Query: 68  QCQR 71
            C++
Sbjct: 182 NCKK 185

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|124365552|gb|ABN09786.1| Histone H4; Histone-fold [Medicago truncatula]

 Score = 62.0 bits (149), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 27/64 (42%), Positives = 41/64 (64%)

Query: 8   TTKERTYGYYVRILVDVDLSGPLPNSVMVELPDDCILVKVMYENLPLKCIVCGNIGHDRT 67
           +TK RT+G+Y RIL+D+DLS P+ N+++V   +    VK+ YE  PL C  C +I H   
Sbjct: 79  STKIRTFGHYARILIDLDLSQPILNNLLVGREESAFFVKIEYEKQPLFCNNCKHIRHSIQ 138

Query: 68  QCQR 71
            C++
Sbjct: 139 NCKK 142

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357515097|ref|XP_003627837.1| NBS resistance protein [Medicago truncatula] gi|355521859|gb|AET02313.1| NBS resistance protein [Medicago truncatula]

 Score = 61.6 bits (148), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 29/62 (46%), Positives = 39/62 (62%)

Query: 9    TKERTYGYYVRILVDVDLSGPLPNSVMVELPDDCILVKVMYENLPLKCIVCGNIGHDRTQ 68
            T+ RT+G+Y RILVD+DLS    + ++VE  D    V+V YE  PL C  C  IGHD + 
Sbjct: 1252 TRNRTFGHYARILVDIDLSKRTFDEILVERDDFAFKVEVQYERRPLFCHHCFAIGHDVST 1311

Query: 69   CQ 70
            C+
Sbjct: 1312 CR 1313

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357500595|ref|XP_003620586.1| hypothetical protein MTR_6g087240 [Medicago truncatula] gi|357500705|ref|XP_003620641.1| hypothetical protein MTR_6g088090 [Medicago truncatula] gi|355495601|gb|AES76804.1| hypothetical protein MTR_6g087240 [Medicago truncatula] gi|355495656|gb|AES76859.1| hypothetical protein MTR_6g088090 [Medicago truncatula]

 Score = 61.2 bits (147), Expect = 8e-08,   Method: Composition-based stats.
 Identities = 28/62 (45%), Positives = 40/62 (64%)

Query: 9   TKERTYGYYVRILVDVDLSGPLPNSVMVELPDDCILVKVMYENLPLKCIVCGNIGHDRTQ 68
           T+ RT+G+Y RILVD+DLS    + V+VE      +V++ YE  PL C  C +IGH+ T 
Sbjct: 201 TRNRTFGHYARILVDIDLSKKAYDEVLVERDGFAFMVEIQYERRPLFCHHCYSIGHNITT 260

Query: 69  CQ 70
           C+
Sbjct: 261 CR 262

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357438275|ref|XP_003589413.1| hypothetical protein MTR_1g023970 [Medicago truncatula] gi|355478461|gb|AES59664.1| hypothetical protein MTR_1g023970 [Medicago truncatula]

 Score = 61.2 bits (147), Expect = 8e-08,   Method: Composition-based stats.
 Identities = 28/62 (45%), Positives = 40/62 (64%)

Query: 9   TKERTYGYYVRILVDVDLSGPLPNSVMVELPDDCILVKVMYENLPLKCIVCGNIGHDRTQ 68
           T+ RT+G+Y RILVD+DLS    + V+VE      +V++ YE  PL C  C +IGH+ T 
Sbjct: 201 TRNRTFGHYARILVDIDLSKKAYDEVLVERDGFAFMVEIQYERRPLFCHHCYSIGHNITT 260

Query: 69  CQ 70
           C+
Sbjct: 261 CR 262

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357485709|ref|XP_003613142.1| hypothetical protein MTR_5g033250 [Medicago truncatula] gi|355514477|gb|AES96100.1| hypothetical protein MTR_5g033250 [Medicago truncatula]

 Score = 60.8 bits (146), Expect = 8e-08,   Method: Composition-based stats.
 Identities = 30/63 (47%), Positives = 39/63 (61%)

Query: 9   TKERTYGYYVRILVDVDLSGPLPNSVMVELPDDCILVKVMYENLPLKCIVCGNIGHDRTQ 68
           T +R +G+Y RILVD+D S  L + ++VE  D    V+V YE L   C  C NIGHD T 
Sbjct: 200 TSKRIFGHYARILVDMDFSRKLFHEIVVEREDYTFTVEVAYEWLSDFCTHCHNIGHDVTA 259

Query: 69  CQR 71
           C+R
Sbjct: 260 CRR 262

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357517505|ref|XP_003629041.1| hypothetical protein MTR_8g072470 [Medicago truncatula] gi|355523063|gb|AET03517.1| hypothetical protein MTR_8g072470 [Medicago truncatula]

 Score = 60.5 bits (145), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 29/63 (46%), Positives = 38/63 (60%)

Query: 9   TKERTYGYYVRILVDVDLSGPLPNSVMVELPDDCILVKVMYENLPLKCIVCGNIGHDRTQ 68
           T+ R +G Y R+LVDVDLS  L NSV+VE   +   ++V YE  PL C  C +IGH    
Sbjct: 151 TQSRVFGLYARVLVDVDLSKKLFNSVLVEREGNAFPMEVQYERQPLFCSHCKHIGHAILN 210

Query: 69  CQR 71
           C +
Sbjct: 211 CNK 213

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357485473|ref|XP_003613024.1| hypothetical protein MTR_5g031820 [Medicago truncatula] gi|355514359|gb|AES95982.1| hypothetical protein MTR_5g031820 [Medicago truncatula]

 Score = 60.5 bits (145), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 28/62 (45%), Positives = 40/62 (64%)

Query: 9   TKERTYGYYVRILVDVDLSGPLPNSVMVELPDDCILVKVMYENLPLKCIVCGNIGHDRTQ 68
           T+ R++G+Y RILVD+DLS    + V+VE      +V+V YE  PL C  C +IGH+ T 
Sbjct: 213 TRNRSFGHYARILVDIDLSKKAYDEVLVERDGFAFMVEVQYERRPLFCHHCYSIGHNITT 272

Query: 69  CQ 70
           C+
Sbjct: 273 CR 274

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

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

No confident hit detected by STRING

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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

ID	Length	Definition	E-value
Query	71
pfam14392	49	pfam14392, zf-CCHC_4, Zinc knuckle	4e-08

>gnl|CDD|222730 pfam14392, zf-CCHC_4, Zinc knuckle

 Score = 44.2 bits (105), Expect = 4e-08
 Identities = 20/47 (42%), Positives = 26/47 (55%), Gaps = 1/47 (2%)

Query: 24 VDLSGPLPNSVMVELPDD-CILVKVMYENLPLKCIVCGNIGHDRTQC 69
          +D+S PL   V V+ P     +VKV YE LP  C  CG +GH   +C
Sbjct: 1  LDVSKPLRFEVNVKFPSGEEAVVKVRYERLPNFCFHCGRLGHSDKEC 47

The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. This particular family is found in plant proteins. Length = 49

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	71
PF14392	49	zf-CCHC_4: Zinc knuckle	99.83
PF00098	18	zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc fi	97.15
PF13696	32	zf-CCHC_2: Zinc knuckle	94.81
smart00343	26	ZnF_C2HC zinc finger.	94.05
PF15288	40	zf-CCHC_6: Zinc knuckle	91.83
COG5082	190	AIR1 Arginine methyltransferase-interacting protei	90.77
COG5082	190	AIR1 Arginine methyltransferase-interacting protei	86.97
PF13917	42	zf-CCHC_3: Zinc knuckle	85.49
KOG4400	261	consensus E3 ubiquitin ligase interacting with arg	84.0
PTZ00368	148	universal minicircle sequence binding protein (UMS	81.68

>PF14392 zf-CCHC_4: Zinc knuckle

Probab=99.83  E-value=1.8e-21  Score=108.00  Aligned_cols=47  Identities=40%  Similarity=0.837  Sum_probs=45.0

Q ss_pred             eeCCCCCccceeccc-CcceEEEEEEeCCCccccccccceecCCCcCC
Q 041609           24 VDLSGPLPNSVMVEL-PDDCILVKVMYENLPLKCIVCGNIGHDRTQCQ   70 (71)
Q Consensus        24 iDl~kpL~~~i~ve~-~g~~~~v~v~YE~LP~fC~~Cg~iGH~~~~C~   70 (71)
                      ||+++||++++.|+. +|+.++++|+|||||.||++||.+||+.++|+
T Consensus         1 id~~kPL~~~i~v~~~~g~~~~~~v~YE~lp~~C~~C~~~gH~~~~C~   48 (49)
T PF14392_consen    1 IDVSKPLRREIKVKFPEGESFWVKVKYERLPRFCFHCGRIGHSDKECP   48 (49)
T ss_pred             CCCCCcccceEEEEeCCCcEEEEEEEECCcChhhcCCCCcCcCHhHcC
Confidence            699999999999997 58899999999999999999999999999997

>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=97.15  E-value=0.0002  Score=32.27  Aligned_cols=16  Identities=44%  Similarity=1.043  Sum_probs=15.0

Q ss_pred             ccccccceecCCCcCC
Q 041609           55 KCIVCGNIGHDRTQCQ   70 (71)
Q Consensus        55 fC~~Cg~iGH~~~~C~   70 (71)
                      -|+.||..||...+|+
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            4999999999999997

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=94.81  E-value=0.0093  Score=30.60  Aligned_cols=18  Identities=33%  Similarity=0.728  Sum_probs=16.2

Q ss_pred             cccccccceecCCCcCCC
Q 041609           54 LKCIVCGNIGHDRTQCQR   71 (71)
Q Consensus        54 ~fC~~Cg~iGH~~~~C~~   71 (71)
                      +.|..|+.-||.+++|+.
T Consensus         9 Y~C~~C~~~GH~i~dCP~   26 (32)
T PF13696_consen    9 YVCHRCGQKGHWIQDCPT   26 (32)
T ss_pred             CEeecCCCCCccHhHCCC
Confidence            479999999999999973

>smart00343 ZnF_C2HC zinc finger

Probab=94.05  E-value=0.022  Score=27.06  Aligned_cols=16  Identities=44%  Similarity=1.003  Sum_probs=14.6

Q ss_pred             ccccccceecCCCcCC
Q 041609           55 KCIVCGNIGHDRTQCQ   70 (71)
Q Consensus        55 fC~~Cg~iGH~~~~C~   70 (71)
                      .|+.||..||...+|+
T Consensus         1 ~C~~CG~~GH~~~~C~   16 (26)
T smart00343        1 KCYNCGKEGHIARDCP   16 (26)
T ss_pred             CCccCCCCCcchhhCC
Confidence            4899999999999996

>PF15288 zf-CCHC_6: Zinc knuckle

Probab=91.83  E-value=0.078  Score=28.44  Aligned_cols=16  Identities=50%  Similarity=1.173  Sum_probs=13.1

Q ss_pred             ccccccceecCC--CcCC
Q 041609           55 KCIVCGNIGHDR--TQCQ   70 (71)
Q Consensus        55 fC~~Cg~iGH~~--~~C~   70 (71)
                      -|..||.+||..  ..|+
T Consensus         3 kC~~CG~~GH~~t~k~CP   20 (40)
T PF15288_consen    3 KCKNCGAFGHMRTNKRCP   20 (40)
T ss_pred             cccccccccccccCccCC
Confidence            599999999985  5565

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

Probab=90.77  E-value=0.1  Score=36.30  Aligned_cols=18  Identities=39%  Similarity=0.864  Sum_probs=16.4

Q ss_pred             ccccccccceecCCCcCC
Q 041609           53 PLKCIVCGNIGHDRTQCQ   70 (71)
Q Consensus        53 P~fC~~Cg~iGH~~~~C~   70 (71)
                      -.+|++||..||...+|+
T Consensus        60 ~~~C~nCg~~GH~~~DCP   77 (190)
T COG5082          60 NPVCFNCGQNGHLRRDCP   77 (190)
T ss_pred             ccccchhcccCcccccCC
Confidence            358999999999999997

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

Probab=86.97  E-value=0.28  Score=34.10  Aligned_cols=16  Identities=44%  Similarity=1.014  Sum_probs=15.0

Q ss_pred             cccccccceecCCCcC
Q 041609           54 LKCIVCGNIGHDRTQC   69 (71)
Q Consensus        54 ~fC~~Cg~iGH~~~~C   69 (71)
                      ..|++||..||...+|
T Consensus        98 ~~C~~Cg~~GH~~~dC  113 (190)
T COG5082          98 KKCYNCGETGHLSRDC  113 (190)
T ss_pred             cccccccccCcccccc
Confidence            6899999999999999

>PF13917 zf-CCHC_3: Zinc knuckle

Probab=85.49  E-value=0.45  Score=25.60  Aligned_cols=18  Identities=33%  Similarity=0.861  Sum_probs=16.1

Q ss_pred             ccccccccceecCCCcCC
Q 041609           53 PLKCIVCGNIGHDRTQCQ   70 (71)
Q Consensus        53 P~fC~~Cg~iGH~~~~C~   70 (71)
                      -..|..|+..||...+|+
T Consensus         4 ~~~CqkC~~~GH~tyeC~   21 (42)
T PF13917_consen    4 RVRCQKCGQKGHWTYECP   21 (42)
T ss_pred             CCcCcccCCCCcchhhCC
Confidence            357999999999999997

>KOG4400 consensus E3 ubiquitin ligase interacting with arginine methyltransferase [Posttranslational modification, protein turnover, chaperones]

Probab=84.00  E-value=0.48  Score=33.26  Aligned_cols=25  Identities=32%  Similarity=0.542  Sum_probs=20.0

Q ss_pred             EEEEeCCCccccccccceecCCCcCC
Q 041609           45 VKVMYENLPLKCIVCGNIGHDRTQCQ   70 (71)
Q Consensus        45 v~v~YE~LP~fC~~Cg~iGH~~~~C~   70 (71)
                      ..+.+.+- .+|+.||..||...+|+
T Consensus       136 ~~~~~~~~-~~Cy~Cg~~GH~s~~C~  160 (261)
T KOG4400|consen  136 DPVDGPKP-AKCYSCGEQGHISDDCP  160 (261)
T ss_pred             ccccCCCC-CccCCCCcCCcchhhCC
Confidence            34555555 78999999999999997

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

Probab=81.68  E-value=0.74  Score=29.64  Aligned_cols=18  Identities=33%  Similarity=0.824  Sum_probs=12.1

Q ss_pred             ccccccccceecCCCcCC
Q 041609           53 PLKCIVCGNIGHDRTQCQ   70 (71)
Q Consensus        53 P~fC~~Cg~iGH~~~~C~   70 (71)
                      +..|+.|+..||...+|+
T Consensus       129 ~~~C~~Cg~~gH~~~dCp  146 (148)
T PTZ00368        129 DKTCYNCGQTGHLSRDCP  146 (148)
T ss_pred             CCccccCCCcCcccccCC
Confidence            346777777777777665

---

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	71
1dsq_A	26	Nucleic acid binding protein P14; CCHC type zinc f	96.28
1nc8_A	29	Nucleocapsid protein; HIV-2, RNA recognition, zinc	96.27
1a6b_B	40	Momulv, zinc finger protein NCP10; nucleocapsid pr	95.67
2hqh_E	26	Restin; beta/BETA structure, zinc finger motif, st	95.36
2ysa_A	55	Retinoblastoma-binding protein 6; zinc finger, CCH	95.25
1u6p_A	56	GAG polyprotein; MLV, A-minor K-turn, stem loop, b	95.08
2ec7_A	49	GAG polyprotein (PR55GAG); nucleocapsid protein, H	94.55
1a1t_A	55	Nucleocapsid protein; stem-loop RNA, viral protein	94.3
2ihx_A	61	Nucleocapsid (NC) protein; protein-RNA complex, vi	94.27
2bl6_A	37	Nucleocapsid protein P11; lentivirus, polyprotein,	94.13
2a51_A	39	Nucleocapsid protein; sivlhoest, structure, NCP8,	94.13
2bl6_A	37	Nucleocapsid protein P11; lentivirus, polyprotein,	94.06
2a51_A	39	Nucleocapsid protein; sivlhoest, structure, NCP8,	94.04
3nyb_B	83	Protein AIR2; polya RNA polymerase, zinc knuckle p	93.69
2cqf_A	63	RNA-binding protein LIN-28; CCHC zinc-finger, stru	93.38
2ec7_A	49	GAG polyprotein (PR55GAG); nucleocapsid protein, H	93.07
2li8_A	74	Protein LIN-28 homolog A; zinc finger, micro RNA,	92.92
1a1t_A	55	Nucleocapsid protein; stem-loop RNA, viral protein	92.24
2ihx_A	61	Nucleocapsid (NC) protein; protein-RNA complex, vi	91.79
1cl4_A	60	Protein (GAG polyprotein); nucleocapsid protein, R	91.67
2cqf_A	63	RNA-binding protein LIN-28; CCHC zinc-finger, stru	90.79
3ts2_A	148	Protein LIN-28 homolog A; microrna biogenesis, pro	88.93
2pzo_E	42	CAP-Gly domain-containing linker protein 1; struct	88.21
3ts2_A	148	Protein LIN-28 homolog A; microrna biogenesis, pro	88.11
2li8_A	74	Protein LIN-28 homolog A; zinc finger, micro RNA,	88.04
2lli_A	124	Protein AIR2; RNA surveillance, RNA degradation, R	86.95
3e2u_E	42	CAP-Gly domain-containing linker protein 1; struct	85.53
2lli_A	124	Protein AIR2; RNA surveillance, RNA degradation, R	83.78

>1dsq_A Nucleic acid binding protein P14; CCHC type zinc finger, virus/viral protein; NMR {Mouse mammary tumor virus} SCOP: g.40.1.1

Probab=96.28  E-value=0.0016  Score=30.68  Aligned_cols=18  Identities=33%  Similarity=0.914  Sum_probs=16.0

Q ss_pred             ccccccccceecCCCcCC
Q 041609           53 PLKCIVCGNIGHDRTQCQ   70 (71)
Q Consensus        53 P~fC~~Cg~iGH~~~~C~   70 (71)
                      +.-|+.||..||..++|+
T Consensus         2 ~~~Cf~CG~~GH~ardC~   19 (26)
T 1dsq_A            2 GPVCFSCGKTGHIKRDCK   19 (26)
T ss_dssp             CCBCTTTCCBSSCTTTTT
T ss_pred             CCeeEeCCCCCcccccCC
Confidence            346999999999999996

>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=96.27  E-value=0.0013  Score=31.66  Aligned_cols=18  Identities=39%  Similarity=1.025  Sum_probs=15.9

Q ss_pred             ccccccccceecCCCcCC
Q 041609           53 PLKCIVCGNIGHDRTQCQ   70 (71)
Q Consensus        53 P~fC~~Cg~iGH~~~~C~   70 (71)
                      +.-|++||..||...+|+
T Consensus         6 ~~~C~nCgk~GH~ar~C~   23 (29)
T 1nc8_A            6 VIRCWNCGKEGHSARQCR   23 (29)
T ss_dssp             CCBCTTTSCBSSCGGGCC
T ss_pred             CCEEEECCccccCHhHCc
Confidence            356999999999999996

>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=95.67  E-value=0.0031  Score=32.87  Aligned_cols=17  Identities=29%  Similarity=0.694  Sum_probs=15.8

Q ss_pred             cccccccceecCCCcCC
Q 041609           54 LKCIVCGNIGHDRTQCQ   70 (71)
Q Consensus        54 ~fC~~Cg~iGH~~~~C~   70 (71)
                      .-|+.||..||...+|+
T Consensus        11 ~~C~~Cgk~GH~ardCP   27 (40)
T 1a6b_B           11 DQCAYCKEKGHWAKDCP   27 (40)
T ss_dssp             SSCSSSCCTTCCTTSCS
T ss_pred             CeeeECCCCCcchhhCc
Confidence            47999999999999997

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

Probab=95.36  E-value=0.0046  Score=29.67  Aligned_cols=17  Identities=35%  Similarity=0.769  Sum_probs=15.8

Q ss_pred             cccccccceecCCCcCC
Q 041609           54 LKCIVCGNIGHDRTQCQ   70 (71)
Q Consensus        54 ~fC~~Cg~iGH~~~~C~   70 (71)
                      +||.+|.+.||...+|.
T Consensus         4 pYCe~CE~FGH~t~~C~   20 (26)
T 2hqh_E            4 PYCEICEMFGHWATNCN   20 (26)
T ss_dssp             CEETTTTEESSCGGGCC
T ss_pred             ccchHHHHhCcccccCC
Confidence            68999999999999995

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

Probab=95.25  E-value=0.0042  Score=34.41  Aligned_cols=17  Identities=35%  Similarity=0.909  Sum_probs=15.7

Q ss_pred             cccccccceecCCCcCC
Q 041609           54 LKCIVCGNIGHDRTQCQ   70 (71)
Q Consensus        54 ~fC~~Cg~iGH~~~~C~   70 (71)
                      .-|+.||..||-+++|+
T Consensus         8 ~~C~kCGk~GH~~k~Cp   24 (55)
T 2ysa_A            8 YTCFRCGKPGHYIKNCP   24 (55)
T ss_dssp             CCCTTTCCTTSCGGGCS
T ss_pred             CccccCCCcCcccccCC
Confidence            46999999999999997

>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=95.08  E-value=0.006  Score=33.87  Aligned_cols=17  Identities=29%  Similarity=0.694  Sum_probs=15.8

Q ss_pred             cccccccceecCCCcCC
Q 041609           54 LKCIVCGNIGHDRTQCQ   70 (71)
Q Consensus        54 ~fC~~Cg~iGH~~~~C~   70 (71)
                      .-|+.||..||...+|+
T Consensus        24 ~~C~~Cge~GH~ardCp   40 (56)
T 1u6p_A           24 DQCAYCKEKGHWAKDCP   40 (56)
T ss_dssp             TBCSSSCCBSSCGGGCT
T ss_pred             CcceeCCCCCcccccCc
Confidence            56999999999999997

>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=94.55  E-value=0.016  Score=30.67  Aligned_cols=17  Identities=41%  Similarity=1.120  Sum_probs=9.3

Q ss_pred             cccccccceecCCCcCC
Q 041609           54 LKCIVCGNIGHDRTQCQ   70 (71)
Q Consensus        54 ~fC~~Cg~iGH~~~~C~   70 (71)
                      ..|+.||..||...+|+
T Consensus         7 ~~C~~Cg~~GH~a~~C~   23 (49)
T 2ec7_A            7 IRCWNCGKEGHSARQCR   23 (49)
T ss_dssp             CBCTTTCCBTCCTTTCC
T ss_pred             CeeeecCCCCcChhhCc
Confidence            44555555555555553

>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=94.30  E-value=0.014  Score=31.36  Aligned_cols=18  Identities=39%  Similarity=0.992  Sum_probs=13.4

Q ss_pred             ccccccccceecCCCcCC
Q 041609           53 PLKCIVCGNIGHDRTQCQ   70 (71)
Q Consensus        53 P~fC~~Cg~iGH~~~~C~   70 (71)
                      +..|+.|+..||...+|+
T Consensus        12 ~~~C~~Cg~~GH~a~~C~   29 (55)
T 1a1t_A           12 TVKCFNCGKEGHIAKNCR   29 (55)
T ss_dssp             TCBCTTTCCBSSCGGGCS
T ss_pred             CcceeeeCCCCcChhhcC
Confidence            456888888888777775

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

Probab=94.27  E-value=0.015  Score=32.05  Aligned_cols=16  Identities=44%  Similarity=0.974  Sum_probs=7.9

Q ss_pred             cccccccceecCCCcC
Q 041609           54 LKCIVCGNIGHDRTQC   69 (71)
Q Consensus        54 ~fC~~Cg~iGH~~~~C   69 (71)
                      ..|+.|+..||...+|
T Consensus         5 ~~C~~Cg~~GH~a~~C   20 (61)
T 2ihx_A            5 GLCYTCGSPGHYQAQC   20 (61)
T ss_dssp             TBCSSSCCBTCCGGGC
T ss_pred             CcccccCCCCeehhhC
Confidence            3455555555554444

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

Probab=94.13  E-value=0.018  Score=28.76  Aligned_cols=16  Identities=44%  Similarity=1.053  Sum_probs=12.5

Q ss_pred             ccccccceecCCCcCC
Q 041609           55 KCIVCGNIGHDRTQCQ   70 (71)
Q Consensus        55 fC~~Cg~iGH~~~~C~   70 (71)
                      .|+.|+..||...+|+
T Consensus         2 ~C~~Cg~~GH~~~~C~   17 (37)
T 2bl6_A            2 TCYNCGKPGHLSSQCR   17 (37)
T ss_dssp             CBSSSCCSSCCTTTSS
T ss_pred             cccccCCCCcchhhCc
Confidence            4788888888888775

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

Probab=94.13  E-value=0.016  Score=29.20  Aligned_cols=17  Identities=35%  Similarity=0.722  Sum_probs=15.1

Q ss_pred             cccccccceecCCCcCC
Q 041609           54 LKCIVCGNIGHDRTQCQ   70 (71)
Q Consensus        54 ~fC~~Cg~iGH~~~~C~   70 (71)
                      ..|+.||..||...+|+
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            57999999999999986

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

Probab=94.06  E-value=0.014  Score=29.20  Aligned_cols=18  Identities=39%  Similarity=0.866  Sum_probs=16.2

Q ss_pred             ccccccccceecCCCcCC
Q 041609           53 PLKCIVCGNIGHDRTQCQ   70 (71)
Q Consensus        53 P~fC~~Cg~iGH~~~~C~   70 (71)
                      |..|+.||..||..++|+
T Consensus        19 ~~~C~~Cg~~GH~a~~C~   36 (37)
T 2bl6_A           19 PKVCFKCKQPGHFSKQCR   36 (37)
T ss_dssp             BTTCSSCCCTTGGGGTTC
T ss_pred             cCeEccCCCcCCccCcCc
Confidence            357999999999999996

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

Probab=94.04  E-value=0.019  Score=28.99  Aligned_cols=16  Identities=38%  Similarity=1.051  Sum_probs=14.8

Q ss_pred             ccccccceecCCCcCC
Q 041609           55 KCIVCGNIGHDRTQCQ   70 (71)
Q Consensus        55 fC~~Cg~iGH~~~~C~   70 (71)
                      .|+.||..||...+|+
T Consensus         2 ~C~~Cg~~GH~a~~C~   17 (39)
T 2a51_A            2 TCFNCGKPGHTARMCR   17 (39)
T ss_dssp             BCTTTCCBSSCTTTCC
T ss_pred             eeeccCCCCcccccCC
Confidence            5999999999999996

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

Probab=93.69  E-value=0.02  Score=33.76  Aligned_cols=17  Identities=35%  Similarity=0.915  Sum_probs=16.2

Q ss_pred             cccccccceecCCCcCC
Q 041609           54 LKCIVCGNIGHDRTQCQ   70 (71)
Q Consensus        54 ~fC~~Cg~iGH~~~~C~   70 (71)
                      .+|++||.-||..++|+
T Consensus        47 ~~CYnCG~~GH~~rdC~   63 (83)
T 3nyb_B           47 IYCYNCGGKGHFGDDCK   63 (83)
T ss_dssp             CBCSSSSCBSSCGGGCS
T ss_pred             CeecccCCCCcCcccCC
Confidence            79999999999999997

>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=93.38  E-value=0.031  Score=31.05  Aligned_cols=18  Identities=28%  Similarity=0.883  Sum_probs=12.0

Q ss_pred             ccccccccceecCCCcCC
Q 041609           53 PLKCIVCGNIGHDRTQCQ   70 (71)
Q Consensus        53 P~fC~~Cg~iGH~~~~C~   70 (71)
                      +..|+.|+..||...+|+
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            445777777777776665

>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=93.07  E-value=0.026  Score=29.86  Aligned_cols=17  Identities=35%  Similarity=0.882  Sum_probs=15.6

Q ss_pred             cccccccceecCCCcCC
Q 041609           54 LKCIVCGNIGHDRTQCQ   70 (71)
Q Consensus        54 ~fC~~Cg~iGH~~~~C~   70 (71)
                      ..|+.||..||...+|+
T Consensus        28 ~~C~~Cg~~GH~~~~C~   44 (49)
T 2ec7_A           28 QGCWKCGKTGHVMAKCP   44 (49)
T ss_dssp             CSCSSSCCSSCCGGGCC
T ss_pred             CeeCcCCCcCCccCCCc
Confidence            47999999999999996

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

Probab=92.92  E-value=0.036  Score=31.93  Aligned_cols=19  Identities=26%  Similarity=0.800  Sum_probs=16.5

Q ss_pred             CccccccccceecCCCcCC
Q 041609           52 LPLKCIVCGNIGHDRTQCQ   70 (71)
Q Consensus        52 LP~fC~~Cg~iGH~~~~C~   70 (71)
                      .+..|+.||..||...+|+
T Consensus        23 r~~~C~~Cg~~GH~a~~C~   41 (74)
T 2li8_A           23 KGDRCYNCGGLDHHAKECK   41 (74)
T ss_dssp             TTSCCTTTCCSSSCTTTCS
T ss_pred             CCCcccccCCcCcCcccCC
Confidence            4568999999999999996

>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=92.24  E-value=0.041  Score=29.45  Aligned_cols=17  Identities=35%  Similarity=0.888  Sum_probs=15.7

Q ss_pred             cccccccceecCCCcCC
Q 041609           54 LKCIVCGNIGHDRTQCQ   70 (71)
Q Consensus        54 ~fC~~Cg~iGH~~~~C~   70 (71)
                      ..|+.||..||...+|+
T Consensus        34 ~~C~~Cg~~GH~~~~C~   50 (55)
T 1a1t_A           34 KGCWKCGKEGHQMKDCT   50 (55)
T ss_dssp             CBCTTTCCBSSCGGGCS
T ss_pred             CEeCCCCCcCCccCCCc
Confidence            57999999999999997

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

Probab=91.79  E-value=0.056  Score=29.69  Aligned_cols=18  Identities=33%  Similarity=1.021  Sum_probs=16.2

Q ss_pred             ccccccccceecCCCcCC
Q 041609           53 PLKCIVCGNIGHDRTQCQ   70 (71)
Q Consensus        53 P~fC~~Cg~iGH~~~~C~   70 (71)
                      +..|+.|+..||...+|+
T Consensus        30 ~~~C~~Cg~~GH~ar~C~   47 (61)
T 2ihx_A           30 RERCQLCNGMGHNAKQCR   47 (61)
T ss_dssp             CSBCTTTCCBSSCGGGCC
T ss_pred             CCeeCCCCCCCCCcCCCc
Confidence            357999999999999996

>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=91.67  E-value=0.062  Score=29.21  Aligned_cols=19  Identities=26%  Similarity=0.532  Sum_probs=16.7

Q ss_pred             CccccccccceecCCCcCC
Q 041609           52 LPLKCIVCGNIGHDRTQCQ   70 (71)
Q Consensus        52 LP~fC~~Cg~iGH~~~~C~   70 (71)
                      ...-|+.||..||...+|+
T Consensus        29 ~~~~C~~Cg~~GH~ar~C~   47 (60)
T 1cl4_A           29 VPGLCPRCKRGKHWANECK   47 (60)
T ss_dssp             CCCSCSSCSSCSSCSTTCC
T ss_pred             CCcceeECCCCCCccCcCC
Confidence            3467999999999999996

>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=90.79  E-value=0.088  Score=29.12  Aligned_cols=18  Identities=39%  Similarity=0.870  Sum_probs=16.4

Q ss_pred             ccccccccceecCCCcCC
Q 041609           53 PLKCIVCGNIGHDRTQCQ   70 (71)
Q Consensus        53 P~fC~~Cg~iGH~~~~C~   70 (71)
                      +..|+.|+..||...+|+
T Consensus        29 ~~~C~~Cg~~GH~ar~Cp   46 (63)
T 2cqf_A           29 PKKCHFCQSISHMVASCP   46 (63)
T ss_dssp             SSCCTTTCCSSSCTTTCT
T ss_pred             CCccCCcCCcCCccCcCC
Confidence            468999999999999996

>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=88.93  E-value=0.11  Score=33.26  Aligned_cols=16  Identities=31%  Similarity=1.109  Sum_probs=14.9

Q ss_pred             ccccccceecCCCcCC
Q 041609           55 KCIVCGNIGHDRTQCQ   70 (71)
Q Consensus        55 fC~~Cg~iGH~~~~C~   70 (71)
                      -|++||..||...+|+
T Consensus        99 ~C~~Cg~~GH~a~~C~  114 (148)
T 3ts2_A           99 RCYNCGGLDHHAKECK  114 (148)
T ss_dssp             CCTTTCCSSCCGGGCC
T ss_pred             cccEeCCccchhhhCC
Confidence            5999999999999996

>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=88.11  E-value=0.15  Score=32.65  Aligned_cols=18  Identities=39%  Similarity=0.870  Sum_probs=16.5

Q ss_pred             ccccccccceecCCCcCC
Q 041609           53 PLKCIVCGNIGHDRTQCQ   70 (71)
Q Consensus        53 P~fC~~Cg~iGH~~~~C~   70 (71)
                      +.-|+.||..||...+|+
T Consensus       119 ~~~C~~Cg~~GH~~r~Cp  136 (148)
T 3ts2_A          119 PKKCHFCQSINHMVASCP  136 (148)
T ss_dssp             CCCCTTTCCSSCCGGGCT
T ss_pred             CCcccccCCcCCEeccCc
Confidence            568999999999999997

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

Probab=88.04  E-value=0.12  Score=29.62  Aligned_cols=18  Identities=39%  Similarity=0.870  Sum_probs=16.4

Q ss_pred             ccccccccceecCCCcCC
Q 041609           53 PLKCIVCGNIGHDRTQCQ   70 (71)
Q Consensus        53 P~fC~~Cg~iGH~~~~C~   70 (71)
                      +.-|+.||..||...+|+
T Consensus        46 ~~~C~~Cg~~GH~ar~Cp   63 (74)
T 2li8_A           46 PKKCHFCQSISHMVASCP   63 (74)
T ss_dssp             CCCCTTTCCTTSCGGGCT
T ss_pred             CCccCCcCCcCCccCcCc
Confidence            468999999999999996

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

Probab=86.95  E-value=0.23  Score=30.27  Aligned_cols=18  Identities=33%  Similarity=0.866  Sum_probs=16.7

Q ss_pred             ccccccccceecCCCcCC
Q 041609           53 PLKCIVCGNIGHDRTQCQ   70 (71)
Q Consensus        53 P~fC~~Cg~iGH~~~~C~   70 (71)
                      ...|++||..||...+|+
T Consensus       105 ~~~Cy~Cg~~GH~a~dCp  122 (124)
T 2lli_A          105 TIYCYNCGGKGHFGDDCK  122 (124)
T ss_dssp             CCCTTTTSSSCTTTTTSC
T ss_pred             CCCcCCCCCCCcCcccCc
Confidence            469999999999999997

>3e2u_E CAP-Gly domain-containing linker protein 1; structural protein microtubule binding, dynactin, cytoskelet associated protein, P150glued; 2.60A {Homo sapiens}

Probab=85.53  E-value=0.25  Score=25.95  Aligned_cols=18  Identities=33%  Similarity=0.709  Sum_probs=16.4

Q ss_pred             ccccccccceecCCCcCC
Q 041609           53 PLKCIVCGNIGHDRTQCQ   70 (71)
Q Consensus        53 P~fC~~Cg~iGH~~~~C~   70 (71)
                      ..+|-.|-+.||...+|.
T Consensus        20 RpYCe~CEVFGH~t~eC~   37 (42)
T 3e2u_E           20 RPYCEICEMFGHWATNCN   37 (42)
T ss_dssp             CCEETTTTEESSCGGGCC
T ss_pred             CcccccceecccccccCC
Confidence            568999999999999996

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

Probab=83.78  E-value=0.37  Score=29.35  Aligned_cols=17  Identities=24%  Similarity=0.901  Sum_probs=14.1

Q ss_pred             cccccccceecCCCcCC
Q 041609           54 LKCIVCGNIGHDRTQCQ   70 (71)
Q Consensus        54 ~fC~~Cg~iGH~~~~C~   70 (71)
                      ..|+.|+..||...+|+
T Consensus        65 ~~C~~Cg~~GH~~~~Cp   81 (124)
T 2lli_A           65 VQCTLCKSKKHSKERCP   81 (124)
T ss_dssp             CSSSSSCSSCCCTTTCC
T ss_pred             ccCCCCCcCCcchhhCC
Confidence            56888888888888886

---

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	71
d1nc8a_	29	HIV nucleocapsid {Human immunodeficiency virus typ	96.78
d1dsqa_	26	Nucleic acid binding protein p14 {Mouse mammary tu	96.64
d2exfa1	42	HIV nucleocapsid {Human immunodeficiency virus typ	95.09
d2exfa1	42	HIV nucleocapsid {Human immunodeficiency virus typ	94.77

>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=96.78  E-value=0.00022  Score=33.83  Aligned_cols=19  Identities=37%  Similarity=0.934  Sum_probs=16.7

Q ss_pred             CccccccccceecCCCcCC
Q 041609           52 LPLKCIVCGNIGHDRTQCQ   70 (71)
Q Consensus        52 LP~fC~~Cg~iGH~~~~C~   70 (71)
                      -+.-|++||..||...+|+
T Consensus         5 ~~ikCfNCGkeGH~ar~Cr   23 (29)
T d1nc8a_           5 KVIRCWNCGKEGHSARQCR   23 (29)
T ss_dssp             CCCBCTTTSCBSSCGGGCC
T ss_pred             ceeEeecCCccchhhhhcc
Confidence            4567999999999999996

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

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

Probab=96.64  E-value=0.00033  Score=32.09  Aligned_cols=17  Identities=35%  Similarity=0.999  Sum_probs=15.7

Q ss_pred             cccccccceecCCCcCC
Q 041609           54 LKCIVCGNIGHDRTQCQ   70 (71)
Q Consensus        54 ~fC~~Cg~iGH~~~~C~   70 (71)
                      +.||+||.-||..++|+
T Consensus         3 pvcfscgktghikkdck   19 (26)
T d1dsqa_           3 PVCFSCGKTGHIKRDCK   19 (26)
T ss_dssp             CBCTTTCCBSSCTTTTT
T ss_pred             CEEEecCCcccchhhhh
Confidence            47999999999999996

>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=95.09  E-value=0.0037  Score=31.39  Aligned_cols=17  Identities=35%  Similarity=0.888  Sum_probs=15.0

Q ss_pred             cccccccceecCCCcCC
Q 041609           54 LKCIVCGNIGHDRTQCQ   70 (71)
Q Consensus        54 ~fC~~Cg~iGH~~~~C~   70 (71)
                      ..|+.||..||...+|+
T Consensus        23 ~~C~~Cg~~GH~~~~Cp   39 (42)
T d2exfa1          23 KGCWKCGKEGHQMKDCT   39 (42)
T ss_dssp             SSCSSSCCSSSCTTTCC
T ss_pred             CccccCCCCCeecccCC
Confidence            46999999999999997

>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=94.77  E-value=0.0045  Score=31.05  Aligned_cols=16  Identities=44%  Similarity=1.149  Sum_probs=15.0

Q ss_pred             ccccccceecCCCcCC
Q 041609           55 KCIVCGNIGHDRTQCQ   70 (71)
Q Consensus        55 fC~~Cg~iGH~~~~C~   70 (71)
                      -|+.||..||...+|+
T Consensus         3 ~C~~Cg~~GH~~~~Cp   18 (42)
T d2exfa1           3 KCFNCGKEGHTARNCR   18 (42)
T ss_dssp             CCTTTCCSSSCTTTCS
T ss_pred             ccccCCCcCcCcccCc
Confidence            5999999999999997