Citrus Sinensis ID: 012461

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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-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460---
Protein Sequence
MEFKFRAIDERTTPCRSSPSPSSHSLSYFSEQALRVNYSMDPNFMHNPRDFYTIQREIEKERIRHEIITAENLRRRLLEEEVRRELMMEREMARASEMGLSMDERLSMQLHSRYPLMHQLNNRWLEDRFPFPGSRGMGFGHDVLPPTLPQFSDAMKDEIRNALEVNKKDKLIMLAKPDPNLCGSKRKASTPPAASVELPLMSSKKTKEWSCALCQVSATSERGLDEHLQGKKHKAKEAGLLRAQKMCNNSISSMSKKSGKKIKLRESKDSSGQEMKTDVEEESTEVNKAVVGSERKAEVVEDSEIKNEGLPKKDLTAKTRKKKNGIPTAEKTKRKPPLRKKFKFWCEDCQVGTHSAVVMEGHKRGKKHIARSNESKKNDDAVPATSSMTIVAPPDPTEKAEDEDVVAEEPNEKTTGCVTEKDEDEEVVAKKAKKEMAENVTGDSNGTRPSIVADVVDLMQKTH
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccHHHHHcccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHccccccHHHHHHHccccccccccccccccccccccccccccccccccEEccccEEEEccHHHHHHHHccccHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEcccccEEcccHHHHHHHHccHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHcccccccccccccccccccEEHHHHHHHcccc
Secondary Structure Prediction (SSPRO)
cccEEEEcccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccEccccccccccccccHHHcccccccccccccccccccccccccccccccccccccccccccEEEEEEcccccccccccccccccccccccccccccccccEEEEEEEEEcccHHHHHHHHcccccHHHHHHHHHHHHcccccccccccccccccEEEcccccccccccccccEEcccccccccccccccEEEEccccccccccccccccHccccccccccHHcccccccHHcccEEEEEEEEEEcccHHHHHHHHccHHHHHHHHHHccccccccccccccccccccccccHcccccccccccccccccEEccccccccEHHHcccccccccccccccccccHHHHHHHHHHHcc
Coil and Loop (DISEMBL)
mefkfraiderttpcrsspspsshslsyfseQALRVnysmdpnfmhnprdFYTIQREIEKERIRHEIITAENLRRRLLEEEVRRELMMEREMARASEMGLSMDERLSMqlhsryplmhqlnnrwledrfpfpgsrgmgfghdvlpptlpqfsDAMKDEIRNALEvnkkdklimlakpdpnlcgskrkastppaasvelplmsskktkeWSCALCQVsatsergldehlqgkkhKAKEAGLLRAQKMCNNSIssmskksgkkiklreskdssgqemktDVEEESTEVNKAVVgserkaevvedseikneglpkkdltaktrkkkngiptaektkrkpplrkkfkfwcedcqvgthsavvmeghkrgkkhiarsneskknddavpatssmtivappdptekaededvvaeepnekttgcvtekdeDEEVVAKKAKKEMaenvtgdsngtrpsIVADVVDLMQKTH
Flexible Loop (DISEMBL)
mefkfraiderttpcrsspspsshslSYFSEQALRVNYSMDPNFMHNPRDFYTIQREIEKErirheiitaenlrrrlleeEVRRELMMEREMARASEMGLSMDERLSMQLHSRYPLMHQLNNRWLEDRFPFPGSRGMGFGHDVLPPTLPQFSDAMKDEIRNALevnkkdklimlakpdpnlcgskrkastppaasveLPLMSSKKTKEWSCALCQVSATsergldehlqgKKHKAKEAGLLRAQKMCNnsissmskksgkkiklreskdssgqemktdveeestevnkavvgserkaevvedseikneglpkkdltaktrkkkngiptaektkrkpplrkkFKFWCEDCQVGthsavvmeghkrgkkhiarsneskknddavpatssmtivappdptekaededvvaeepnekttgcvtekdedEEVVAKKakkemaenvtgdsngtrpsiVADVVDLMQKTH
Low Complexity Region (SEG)
MEFKFRAIDERTTPCRsspspsshslsyfsEQALRVNYSMDPNFMHNPRDFYTIQreiekerirheiiTaenlrrrlleeevrrelmmeremarasemGLSMDERLSMQLHSRYPLMHQLNNRWLEDRFPFPGSRGMGFGHDVLPPTLPQFSDAMKDEIRNALEVNKKDKLIMLAKPDPNLCGSKRKASTPPAASVELPLMSSKKTKEWSCALCQVSATSERGLDEHLQGKKHKAKEAGLLRAQKMCNNsissmskksgkkiklreskDSSGQEMKTDVEEESTEVNKAVVGSERKAEVVEDSEIKNEGLPkkdltaktrkkkNGIPTAEktkrkpplrkkfkfWCEDCQVGTHSAVVMEGHKRGKKHIARSNESKKNDDAVPATSSMTIVAPPDPTEKaededvvaeePNEKTTGCVTekdedeevvakkakkeMAENVTGDSNGTRPSIVADVVDLMQKTH
Disordered region (IsUnstruct)
********************************ALRVNYSMDPNFMHNPRDFYTIQREIEKERIRHEIITAENLRRRL***********************************RYPLMHQLNNRWLEDRFPFPGSRGMGFGHDVL****************************************************************WSCALCQV****************************************************************************************************************************KFKFWCEDCQVGTHSAVVM********************************************************************************************************
Disordered Region (DISOPRED)
**FKFR**********************************************************************************************************************************************************************************************************WSCALCQVSATSERGLDEHLQG******************************************************************************************************************WCEDCQVGTHSAVVM********************************************************************************************VADVVDLMQ***
Disordered Region (DISEMBL)
MEFKFRAIDE***************LSYFSEQALRVNYSMDPNFMHNPRDFYTIQREIEKERIRHEIITAENLRRRLLEEEVRRELMMEREMARASEMGLSMDERLSMQLHSRYPLMHQLNNRWLEDRFPFPGSRGMGFGHDVLPPTLPQFSDAMKDEIRNALEVNKKDKLIMLAKPDPNLC************SVELPLMSSKKTKEWSCALCQVSATSERGLDEHLQGKKHKAKEAGLLRAQKMCNNSIS************************************AVVGSERKAEVVEDSEIKNEGLPKKDLTAKTRKKKNGIPTAEKTKRKPPLRKKFKFWCEDCQVGTHSAVVME***********************ATSSMTIVAP**********************GCVTEKDEDEEVVAKKAKKEMAENVTGDSNGTRPSIVADVVDLMQKTH
Disordered Region (DISPRO)
*EFKFR**DERTT**RSS**********FSEQALRVNYSMDPNFMHNPRDFYTIQREIEKERIRHEIITAENLRRRLLEEEVRRELMMEREMARA**MGLSMDERLSMQLHSRYPLMHQLNNRWLEDRFPFPGSRGMGFGHDVLPPTLPQF****K*EIRNALEVNKKDKLIMLAKPDP******************L******KTKEWSCALCQVSATSERGLDEHLQGKKHKAKEAGLLR********************************MKTDVEEESTEVNKA**********************************************PPLRKKFKFWCEDCQVGTHSAVVMEGHKRGKKHIARSNE****************************************************************************IVADVVD******
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
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TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MEFKFRAIDERTTPCRSSPSPSSHSLSYFSEQALRVNYSMDPNFMHNPRDFYTIQREIExxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxEMARASEMGLSMDERLSMQLHSRYPLMHQLNNRWLEDRFPFPGSRGMGFGHDVLPPTLPQFSDAMKDEIRNALEVNKKDKLIMLAKPDPNLCGSKRKASTPPAASVELPLMSSKKTKEWSCALCQVSATSERGLDEHLQGKKHKAKEAGLLRAQKMCNNSISSMSKKSGKKIKLRESKDSSGQEMKTDVEEESTEVNKAVVGSERKAEVVEDSEIKNEGLPKKDLTAKTRKKKNGIPTAEKTKRKPPLRKKFKFWCEDCQVGTHSAVVMEGHKRGKKHIARSNESKKNDDAVPATSSMTIVAPPDPTEKAEDEDVVAEEPNEKTTGCVTEKDEDEEVVAKKAKKEMAENVTGDSNGTRPSIVADVVDLMQKTH
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	463	2.2.26 [Sep-21-2011]
Q6AXX3	395	Zinc finger protein 385D	yes	no	0.328	0.384	0.260	5e-05

>sp|Q6AXX3|Z385D_RAT Zinc finger protein 385D OS=Rattus norvegicus GN=Znf385d PE=2 SV=1

 Score = 49.7 bits (117), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 45/173 (26%), Positives = 77/173 (44%), Gaps = 21/173 (12%)

Query: 201 MSSKKTKEWSCALCQVSATSERGLDEHLQGKKHKAKEAGLLRAQKMCNNSISSMSKKSGK 260
           +  +K +  SC +CQ+   S+     H +G KH  K    L+A       + SM  K  K
Sbjct: 72  LPHRKKQIISCNICQLRFNSDSQAAAHYKGTKHAKK----LKA-------LESMKNKQ-K 119

Query: 261 KIKLRESKDSSGQEMKTDVEEESTEVNKAVVGSE---RKAEVVEDSEIKNE--GLPKKDL 315
            +  ++S  ++   + T+    S++  ++  G++   R A++ + SE+  E     +K L
Sbjct: 120 SVTAKDSAKTTFTSITTNPITTSSDKTESTAGTQVIARSADMRKSSEVTTELTSNAEKSL 179

Query: 316 TAKTRKKKNGIPTAEKTKRKPPLRKKFKFWCEDCQVGTHSAVVMEGHKRGKKH 368
           TA      N  P  E  + K     K   +C  C+V  +SA  +E H  G KH
Sbjct: 180 TAAVAAGNNSSPPTETEEEK----AKRLLYCSLCKVAVNSASQLEAHNSGTKH 228

Rattus norvegicus (taxid: 10116)

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	463
255577041	423	hypothetical protein RCOM_0623850 [Ricin	0.803	0.879	0.425	1e-59
224091795	291	predicted protein [Populus trichocarpa]	0.557	0.886	0.435	4e-44
356500669	332	PREDICTED: uncharacterized protein LOC10	0.591	0.825	0.328	4e-27
357480033	556	hypothetical protein MTR_4g130690 [Medic	0.548	0.456	0.338	8e-25
224091801	187	predicted protein [Populus trichocarpa]	0.347	0.860	0.455	6e-22
449454103	418	PREDICTED: uncharacterized protein LOC10	0.753	0.834	0.290	7e-19
359484879	186	PREDICTED: uncharacterized protein LOC10	0.263	0.655	0.496	8e-19
297743659	220	unnamed protein product [Vitis vinifera]	0.263	0.554	0.496	2e-18
147784015	203	hypothetical protein VITISV_012828 [Viti	0.263	0.600	0.488	2e-18
297825315	456	predicted protein [Arabidopsis lyrata su	0.801	0.813	0.275	2e-16

>gi|255577041|ref|XP_002529405.1| hypothetical protein RCOM_0623850 [Ricinus communis] gi|223531153|gb|EEF33001.1| hypothetical protein RCOM_0623850 [Ricinus communis]

 Score =  237 bits (604), Expect = 1e-59,   Method: Compositional matrix adjust.
 Identities = 171/402 (42%), Positives = 232/402 (57%), Gaps = 30/402 (7%)

Query: 1   MEFKFRAIDERTTPCRSSPSPSSHSLSYFSEQALRVNY-----SMDPNFMHNPRDFYTIQ 55
           MEF+FRA D R  P      PSS   +YFSE A R NY     + D + M N      + 
Sbjct: 1   MEFRFRAADSR--PPEYFFHPSSSGTAYFSEHAFRANYHVIDSTQDSDLMRNE----MLH 54

Query: 56  REIEKERIRHEIITAE-NLRRRLLEEEVRRELMMEREMARASEMGL---SMDERLS-MQL 110
           RE+EK+RIR +II  E  +RRR+LE EVRRE+M+ERE+A  +  G    S +E L    L
Sbjct: 55  REMEKDRIREQIIMEEMTMRRRILEAEVRREMMIEREIAMRAVGGYNDDSYEETLEPTIL 114

Query: 111 HSRYPLMHQLNNRWLEDRFPFPGSRGMGFGHDVLPPTLPQFSDAMKDEIRNALEVNKKDK 170
             ++  M+QLNNR +EDR  FPG    GF    L  +  + S+A      NA + N K K
Sbjct: 115 APQFHFMNQLNNRRVEDRPAFPGR---GF----LDHSPRRLSEAWAGPDVNAAKENSKGK 167

Query: 171 LIMLAKPDPNLCGSKRKASTPPAASV-ELP--LMSSKKTKEWSCALCQVSATSERGLDEH 227
           +++LAKPDPNL G KRKA+TPP     ELP  ++  K  +EWSCALC+VSATSE+GL+ H
Sbjct: 168 VVVLAKPDPNLFGVKRKAATPPVGGTHELPCTVLKKKPKEEWSCALCRVSATSEQGLNNH 227

Query: 228 LQGKKHKAKEAGLLRAQKMCNNSISS-MSKKSGKKIKLRESKDSSGQEMKTDVEEESTEV 286
           L+GKKHKAKEA  LRA KM     S  + KKS ++ KL  S      E + + E    + 
Sbjct: 228 LRGKKHKAKEA-RLRANKMAKTPCSRPLPKKSLRQTKLTVSTADLELEPEAEAESVQVDK 286

Query: 287 NKAVVGSERKAEVVEDSEIKNEGLPKKDLTAKTRKKKNGIPTAEKTKRKPPLRKKFKFWC 346
           N      +   +V E++  K + + K       +K        E+   +  ++KKFKFWC
Sbjct: 287 NDDDTDKKMGNKVAENNNDKLQ-VQKNGSVKSKKKNVVKKVLKEERTAEFRMKKKFKFWC 345

Query: 347 EDCQVGTHSAVVMEGHKRGKKHIARSNESKKNDD-AVPATSS 387
           E C++G +SAVVME H++GKKH+A+  E  +N + AV A+SS
Sbjct: 346 EMCRIGAYSAVVMEAHEKGKKHLAQLQELGENGEVAVVASSS 387

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224091795|ref|XP_002309354.1| predicted protein [Populus trichocarpa] gi|222855330|gb|EEE92877.1| predicted protein [Populus trichocarpa]

 Score =  185 bits (469), Expect = 4e-44,   Method: Compositional matrix adjust.
 Identities = 124/285 (43%), Positives = 176/285 (61%), Gaps = 27/285 (9%)

Query: 173 MLAKPDPNLCGSKRKASTPPAASV-ELPLMSSKKT--KEWSCALCQVSATSERGLDEHLQ 229
           M  KPDPNLCG+KRKA TP A SV ELP    KK   +EWSCALCQVSATSERGL+EHLQ
Sbjct: 1   MKKKPDPNLCGAKRKAVTPAAESVGELPFAGIKKKPKEEWSCALCQVSATSERGLNEHLQ 60

Query: 230 GKKHKAKEAGLLRAQKMCNN-SISSMSKKSGKKIKLRESKDSSGQEMKTDVEEESTEVNK 288
           G++HKAKEAG LRAQKM  N + +S+ K++ K  K+  +  ++G EM+  +E+ES ++NK
Sbjct: 61  GRRHKAKEAG-LRAQKMARNPNKASLPKETTKTAKV--TIPTAGLEMEAKIEDESLQLNK 117

Query: 289 AVVGSERKAEVVEDSEIKNE-GLPKKDLTAKTRKKKNGIPTAEKTKRKPP---LRKKFKF 344
           +   S +K E  E+   +N+  L +K+   +   K   +  A +TK + P   ++KKFKF
Sbjct: 118 SDNFSNKKIENKEERGNRNDVQLEQKNQQLEDLNK--SMAEAVQTKERTPEIKMKKKFKF 175

Query: 345 WCEDCQVGTHSAVVMEGHKRGKKHIARSNESKKNDDAVPATSSMTIVAPPDPTEKAEDED 404
           WCE CQ+G +S +VME HK+GKKH+AR  +S +N +AV A             +KA+D +
Sbjct: 176 WCEMCQIGAYSEMVMEAHKKGKKHLARLQKSSQNGEAVQA------------DKKAKDSE 223

Query: 405 VVAEEPNEKTTGCVTEKDEDEEVVAKKAKKEMAENVTGDSNGTRP 449
           V  +E  +  +  V E+  D  + A+    E  E    +++  RP
Sbjct: 224 VAVKETED--SEFVAERATDSGLAARGTDTERTETTVANADEPRP 266

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356500669|ref|XP_003519154.1| PREDICTED: uncharacterized protein LOC100786802 [Glycine max]

 Score =  129 bits (323), Expect = 4e-27,   Method: Compositional matrix adjust.
 Identities = 125/380 (32%), Positives = 179/380 (47%), Gaps = 106/380 (27%)

Query: 1   MEFKFRAIDERTTPCRSSPSPSSHSLSYFSEQALRVNYSMD----PNFMHNPRDFYT--- 53
           MEFK+RA+ +R TP    P     + +Y  +  LR  Y       P+ +  PR F T   
Sbjct: 1   MEFKYRAVQDRRTPPPPPPPHPLSTGTYVFDSPLR-GYEFSSGGYPSNVSAPRVFLTPVP 59

Query: 54  ---------------IQREIEKERIRHEIITAENLRRRLLEEEVRRELMMEREMARASEM 98
                          I RE+EKE IR EI+  E  +RR LEEEV RE+ +ER +      
Sbjct: 60  VNVGEAFRRELEKKQILRELEKEEIRREILAREMAQRRELEEEVMREITVERVL------ 113

Query: 99  GLSMDERLSMQLHSRYPLMHQLNNRWLEDRFPFPGSRGMGFGHDVLPPTLPQFSDAMKDE 158
           G+S  E++SM L+  + +   +NN        F GS+          P LP   D     
Sbjct: 114 GISFREQVSMSLNQNHRMNKPINNNI------FGGSQ----------PRLPPQID----- 152

Query: 159 IRNALEVNKKDKLIMLA--KPDPNLCGSKRKASTPP--------AASVELPLMSSKKTKE 208
               ++ + KDK+I+LA  KPD +  G+KRKA  PP          SVE      K  +E
Sbjct: 153 ----IKQSNKDKVIILAGAKPDVDPYGAKRKAGKPPTIDDNHHSGFSVE-----KKPKRE 203

Query: 209 WSCALCQVSATSERGLDEHLQGKKHKAKEAGLLRAQKMCNNSISSMSKKSGKKIKLRESK 268
           WSC LCQ++ T+E+GL+ HL+GKKHKAK +  LR                 KKI L    
Sbjct: 204 WSCGLCQITTTNEKGLNNHLEGKKHKAKAS--LRT----------------KKIGLDARL 245

Query: 269 DSSGQEMKTDVEEESTEVNKAVVGSERKAEVVEDSEIKNEGLPKKDLTAKTRKKKNGIPT 328
           D  GQ+++  +    T  N  ++   ++ +VV++S    +GL   D        +N I T
Sbjct: 246 D--GQKLQRGI----TSTNIGILEPRKEDQVVQNS----QGLGGLD-------NENEIAT 288

Query: 329 AEKTKRKPPL--RKKFKFWC 346
           +++T     L  RKKFKF+C
Sbjct: 289 SKETGETNALTKRKKFKFYC 308

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357480033|ref|XP_003610302.1| hypothetical protein MTR_4g130690 [Medicago truncatula] gi|355511357|gb|AES92499.1| hypothetical protein MTR_4g130690 [Medicago truncatula]

 Score =  121 bits (303), Expect = 8e-25,   Method: Compositional matrix adjust.
 Identities = 104/307 (33%), Positives = 157/307 (51%), Gaps = 53/307 (17%)

Query: 1   MEFKFRAIDERTTPCRSSPSPSSHSLSYFSEQALRVNYSMDPNFMHNPRDFYT----IQR 56
           MEFKFRAID    P  S+  PS  +++Y  +++L     MD  F        T    ++R
Sbjct: 88  MEFKFRAID-NINP--STMQPSHPTVTYLPDRSL----PMDGGFAGFRAPLATNEAALRR 140

Query: 57  EIEKERIRHEIITAENLRRRLLEEEVRRELMMEREMARASEMGLSMDERLSMQLHSRYPL 116
           E+EKE+IR ++     LRR  LE+EVRREL ME           +M + L+    +  P+
Sbjct: 141 EMEKEQIRRDM-----LRRIELEDEVRRELAMEGAFG-------TMQKPLNSVWSNSTPM 188

Query: 117 MHQLNNRWLEDRFPFPGSRGMGFGHDVLPPTLPQFSDAMKDEIRNALEVNKKDKLIMLAK 176
           M       + +      S+         PP           EI++  + + KDK+I+LAK
Sbjct: 189 M-------MMNPVAVDASQ---------PP-----------EIKHFPQTSDKDKVILLAK 221

Query: 177 PDPNLCGSKRKASTPPAASVELPLMSSKKT--KEWSCALCQVSATSERGLDEHLQGKKHK 234
           PDP+L G+KRKA T  A + +   +  KK   +EWSC LCQ+ ATSE GL+ HL GKKHK
Sbjct: 222 PDPDLYGAKRKALTLDAPNDDPYAIGMKKKPKEEWSCELCQIKATSESGLNAHLNGKKHK 281

Query: 235 AKEAGLLRAQKMCNNSISSMSKKSGKKIKLRESKDSSGQEMKTDVEEESTEVNKAVVGSE 294
           AKEAG  R    C+      ++K    + +   + +    +  +V +E T V+K +  S+
Sbjct: 282 AKEAGQKRKIDKCSRKSQKTAEKITDTVVVETDQQAPQPCLALEVMDE-TMVDKGLTESK 340

Query: 295 RKAEVVE 301
           ++ ++VE
Sbjct: 341 KEEQLVE 347

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224091801|ref|XP_002309355.1| predicted protein [Populus trichocarpa] gi|222855331|gb|EEE92878.1| predicted protein [Populus trichocarpa]

 Score =  112 bits (279), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 82/180 (45%), Positives = 104/180 (57%), Gaps = 19/180 (10%)

Query: 1   MEFKFRAIDERTTPCRSSPSPSSHSLSYFSEQALRVNY-SMDPNFMHNPRDFYTIQREIE 59
           MEFKFRA D R   C S   PSS S+ YF EQALR +Y + DP  +  P       R IE
Sbjct: 1   MEFKFRAGDNRPPVCFS---PSS-SIGYFYEQALRASYPNADPRQIPEPMRNELFLRRIE 56

Query: 60  KERIRHEIITAENLRRRLLEEEVRRELMMEREMARASEMGLSMDERLSMQLHSRYPLM-- 117
           KERIR EII  E   R+ LE EVRRELM+EREMA     G+S +ERL+MQ  SR PL+  
Sbjct: 57  KERIREEIIAQEMAWRQELEAEVRRELMVEREMAMRGGRGMSFEERLTMQFDSRKPLLPG 116

Query: 118 ---HQLNNRWLEDRFPFPGSRGMGFGHDVLPPTLPQFSDAMKDEIRNALEVNKKDKLIML 174
              +Q +  W EDR  F G      G   + P +P+  ++   E++ + E N KDK+I+L
Sbjct: 117 PFVNQFDCSWPEDRLAFHGH-----GVSYMLPPVPRLPES---EMKPSTE-NNKDKVIVL 167

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449454103|ref|XP_004144795.1| PREDICTED: uncharacterized protein LOC101215299 [Cucumis sativus]

 Score =  101 bits (252), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 129/444 (29%), Positives = 186/444 (41%), Gaps = 95/444 (21%)

Query: 1   MEFKFRAIDERTT-----------------PCRSSP--SPSSHSLS------YFSEQALR 35
           MEFKFR  D R                   P    P  SP+ + LS      +F + A  
Sbjct: 1   MEFKFRVDDLRKPPPPPPPPQMHFLPPMPPPMHFLPPASPAVYCLSEQGFPDFFMDSADA 60

Query: 36  VNYSMDPNFMHNPRDFYT-IQREIEKERIRHEIITAENLRRRLLEEEVRREL-MMEREMA 93
              + +   +  P +    +  E+E  R+R E +  E  R R L+EE RREL + ERE+A
Sbjct: 61  FRQTTNIGTLRQPFNLNEEMHLEMEFMRLREEKLIGEIERERFLKEEARRELRLFEREIA 120

Query: 94  RASEMGLSMDERLSMQLHSRYPLMHQLNNRWLEDRF-------------PFPG------- 133
                GL+       Q    YP   Q   RW+   F             P P        
Sbjct: 121 IR---GLT-------QSAVGYPF--QQPQRWVAPPFCPVTGPPSSAVAVPCPSPSQALVV 168

Query: 134 --------------SRGMGFGHDVLPPTLPQFSDAMKDEIRNALEVNKKDKLIMLAKPDP 179
                         S  +GFG   L P +       K E  N      + KLI   KP P
Sbjct: 169 QSYHEWQNMEQVKTSDRLGFGAVALRPRIQPLMVEDKKEAAN------ERKLI--EKPVP 220

Query: 180 NLCGSKRKASTPPAASVE--LPLMSSKKTK-EWSCALCQVSATSERGLDEHLQGKKHKAK 236
           N    +RKA T  + S++  LP +  K +K EWSCALCQV+   E+  ++HL+GKKH+ K
Sbjct: 221 NAFREERKAETTTSPSIKHILPSLVKKTSKDEWSCALCQVTTAEEKSFNDHLRGKKHRRK 280

Query: 237 EAGLLRAQKMCNNSISSMSKKSGKKIKLRESKDSSGQEMKTDVEEESTEVNKAVVGSERK 296
           EA  LRA+K    S  +    S K+ KL+++  ++        E   T+  +A VG    
Sbjct: 281 EAN-LRAEKESKVSRVAHEPLSKKRRKLQKAMAAAAGGGAEGKE---TKDGEADVG---- 332

Query: 297 AEVVEDSEIKNEGLPKKDLTAKTRKKKNGIPTAEKTKRKPPLRKKFKFWCEDCQVGTHSA 356
            E  E S   N  +P        ++++N   T      K  +  KF FWCE C+VG +  
Sbjct: 333 -EKSEGSVDMNALIPYFLKKENKQQQENNPTTNNDVMAKSSV--KFSFWCEKCKVGAYVT 389

Query: 357 VVMEGHKRGKKHIARSNESKKNDD 380
            VM  H  GK+H A+  ++ + ++
Sbjct: 390 KVMLAHVNGKQHQAKLKKANQTEE 413

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359484879|ref|XP_002275550.2| PREDICTED: uncharacterized protein LOC100241709 [Vitis vinifera]

 Score =  101 bits (251), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 67/135 (49%), Positives = 85/135 (62%), Gaps = 13/135 (9%)

Query: 1   MEFKFRAIDERTTPCRSSPSPSSHSLSYFSEQALRVNYS----MDPNFMHNPRDFY-TIQ 55
           MEFKFRA+D+R     SSPS     ++YF+EQALR  YS    +    + NP D    IQ
Sbjct: 1   MEFKFRAVDDRPPYLSSSPS----MINYFTEQALRAGYSNNGILLNELLSNPSDMREAIQ 56

Query: 56  REIEKERIRHEIITAENLRRRLLEEEVRRELMMERE-MARASEMGLSMDERLSMQLHSRY 114
           RE+EKERIR EII  E  RRRLLE EVRREL+ME+E M   +E    +    +M+L  R+
Sbjct: 57  RELEKERIREEIIAREIARRRLLEAEVRRELLMEQELMLTKTEFKSPVSS--AMRL-DRF 113

Query: 115 PLMHQLNNRWLEDRF 129
           PL HQ ++R LE+R 
Sbjct: 114 PLFHQSDSRALEERL 128

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297743659|emb|CBI36542.3| unnamed protein product [Vitis vinifera]

 Score =  100 bits (249), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 67/135 (49%), Positives = 85/135 (62%), Gaps = 13/135 (9%)

Query: 1   MEFKFRAIDERTTPCRSSPSPSSHSLSYFSEQALRVNYS----MDPNFMHNPRDFY-TIQ 55
           MEFKFRA+D+R     SSPS     ++YF+EQALR  YS    +    + NP D    IQ
Sbjct: 1   MEFKFRAVDDRPPYLSSSPS----MINYFTEQALRAGYSNNGILLNELLSNPSDMREAIQ 56

Query: 56  REIEKERIRHEIITAENLRRRLLEEEVRRELMMERE-MARASEMGLSMDERLSMQLHSRY 114
           RE+EKERIR EII  E  RRRLLE EVRREL+ME+E M   +E    +    +M+L  R+
Sbjct: 57  RELEKERIREEIIAREIARRRLLEAEVRRELLMEQELMLTKTEFKSPVSS--AMRL-DRF 113

Query: 115 PLMHQLNNRWLEDRF 129
           PL HQ ++R LE+R 
Sbjct: 114 PLFHQSDSRALEERL 128

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147784015|emb|CAN76834.1| hypothetical protein VITISV_012828 [Vitis vinifera]

 Score = 99.8 bits (247), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 66/135 (48%), Positives = 85/135 (62%), Gaps = 13/135 (9%)

Query: 1   MEFKFRAIDERTTPCRSSPSPSSHSLSYFSEQALRVNYS----MDPNFMHNPRDFY-TIQ 55
           MEFKFRA+D+R     SSPS     ++YF+EQALR  YS    +    + NP D    IQ
Sbjct: 1   MEFKFRAVDDRPPYLSSSPS----MINYFTEQALRAGYSNNGILLNELLSNPSDMREAIQ 56

Query: 56  REIEKERIRHEIITAENLRRRLLEEEVRRELMMERE-MARASEMGLSMDERLSMQLHSRY 114
           RE+EKERIR EII  E  RRRLLE EVRREL+ME+E M   +E    +    +M+L  R+
Sbjct: 57  RELEKERIREEIIAREIARRRLLEAEVRRELLMEQELMLTKTEFKSPVSS--AMRL-DRF 113

Query: 115 PLMHQLNNRWLEDRF 129
           PL HQ ++R LZ+R 
Sbjct: 114 PLFHQSDSRALZERL 128

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297825315|ref|XP_002880540.1| predicted protein [Arabidopsis lyrata subsp. lyrata] gi|297326379|gb|EFH56799.1| predicted protein [Arabidopsis lyrata subsp. lyrata]

 Score = 93.6 bits (231), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 122/443 (27%), Positives = 202/443 (45%), Gaps = 72/443 (16%)

Query: 1   MEFKFRAIDERTTPCRSSPSPSSH---SLSYFSEQALRVNYSMDPNFMHNPRDFYTIQRE 57
           MEF++RAID    P  +  +PS     S  +FS +      SM        R+   IQRE
Sbjct: 1   MEFRYRAIDSNRPPPATETTPSQSPNPSFPFFSAR------SMSGKSEEQVREAM-IQRE 53

Query: 58  IEKERIRHEIITAENLRRRLLEEEVRRELMMEREMA--RASEMGLSMDERLSMQLHSR-- 113
           IEKE+IR EII AE  R+R L  EV +E+ +EREM+  R S+ G+S++E+L M ++ R  
Sbjct: 54  IEKEKIRQEIIIAEAARKRELIAEVLQEMAIEREMSIRRVSDTGMSLEEKLIMWINQRKL 113

Query: 114 -YPLMHQLNNRWLEDRFPFPGSRGMGFGHDVLPPT----LPQFSDAMKDEIRNALEVNKK 168
                +Q NN   + ++ +  S      ++ L  +    LPQ     +    + LE N K
Sbjct: 114 PNQNQNQNNNNLFKAKYSYIDSLINTGSYNSLVTSPMMQLPQLQQISEATGTSMLESN-K 172

Query: 169 DKLIMLAKPDPNLCGSKRKASTPPAASVELPLMSS-----------KKTKEWSCALCQVS 217
           +KLI+L++ D    G+K KA +    +++LP +             +  KE    L +  
Sbjct: 173 EKLIVLSRADH--IGAKPKADS--VGTMQLPQLQQMPETTTGTSVLESNKEKLIVLARAD 228

Query: 218 ATSER--------GLDEHLQGKKHKAKEAGL----LRAQKMCNNSISSMSK-KSGKKIKL 264
              E+        GL+E LQ K+ K+KE+      L + ++ ++ +  + K   GKK+++
Sbjct: 229 PVGEKRKAEDTQTGLNEDLQMKRQKSKESEAKTMSLESGEIVSSKLPCLGKLGCGKKVEI 288

Query: 265 RESKDSSGQEMKTDVEEESTEVNKAV----VGSERKAEVVEDS---EIKNEGLPKKDLTA 317
              K  S  +   ++ +  T     +    +G + KA V + +   E  +  L    +TA
Sbjct: 289 ---KVRSNYKFWCEICKVGTYCQTVMRDHELGKKHKAAVTQQNEAPEAASTSLSPASVTA 345

Query: 318 ----KTRKKKNGIPTAE----------KTKRKPPLRKKFKFWCEDCQVGTHSAVVMEGHK 363
                T  +++  P  +              +   +KK  FWC+ C + T+S   M  H 
Sbjct: 346 PQSEATTVREDANPQGKVDEMSAKETTGKTTEGEKKKKGTFWCKTCNIQTNSEQTMRNHT 405

Query: 364 RGKKHIARSNESKKNDDAVPATS 386
            GKKH+A   + +K    VP  S
Sbjct: 406 LGKKHMALIGKQQKKLITVPVRS 428

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	463
TAIR|locus:2061486	455	AT2G24030 [Arabidopsis thalian	0.112	0.114	0.384	2.7e-06

TAIR|locus:2061486 AT2G24030 [Arabidopsis thaliana (taxid:3702)]

 Score = 110 (43.8 bits), Expect = 2.7e-06, Sum P(3) = 2.7e-06
 Identities = 20/52 (38%), Positives = 28/52 (53%)

Query:   345 WCEDCQVGTHSAVVMEGHKRGKKHIARSNESKKNDDAVPATSSMTIVAPPDP 396
             WCE C+VGT+  +VM  H+ GKKH A   +  +  +A   + S   V  P P
Sbjct:   295 WCEICKVGTYCQIVMRDHELGKKHKAAVTQQNETPEAASTSLSPASVTAPQP 346

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005622 "intracellular" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0008270 "zinc ion binding" evidence=IEA

---

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!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

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	463
pfam12874	25	pfam12874, zf-met, Zinc-finger of C2H2 type	2e-06
pfam12874	25	pfam12874, zf-met, Zinc-finger of C2H2 type	4e-04
smart00451	35	smart00451, ZnF_U1, U1-like zinc finger	0.003

>gnl|CDD|205121 pfam12874, zf-met, Zinc-finger of C2H2 type

 Score = 43.6 bits (104), Expect = 2e-06
 Identities = 14/25 (56%), Positives = 17/25 (68%)

Query: 209 WSCALCQVSATSERGLDEHLQGKKH 233
           + C LC V+ TSE  L  HL+GKKH
Sbjct: 1   FYCELCNVTFTSESQLKSHLRGKKH 25

This is a zinc-finger domain with the CxxCx(12)Hx(6)H motif, found in multiple copies in a wide range of proteins from plants to metazoans. Some member proteins, particularly those from plants, are annotated as being RNA-binding. Length = 25

>gnl|CDD|205121 pfam12874, zf-met, Zinc-finger of C2H2 type

 Score = 37.1 bits (87), Expect = 4e-04
 Identities = 12/25 (48%), Positives = 15/25 (60%)

Query: 344 FWCEDCQVGTHSAVVMEGHKRGKKH 368
           F+CE C V   S   ++ H RGKKH
Sbjct: 1   FYCELCNVTFTSESQLKSHLRGKKH 25

This is a zinc-finger domain with the CxxCx(12)Hx(6)H motif, found in multiple copies in a wide range of proteins from plants to metazoans. Some member proteins, particularly those from plants, are annotated as being RNA-binding. Length = 25

>gnl|CDD|197732 smart00451, ZnF_U1, U1-like zinc finger

 Score = 34.9 bits (81), Expect = 0.003
 Identities = 13/30 (43%), Positives = 18/30 (60%)

Query: 209 WSCALCQVSATSERGLDEHLQGKKHKAKEA 238
           + C LC V+ T E  ++ HL+GKKHK    
Sbjct: 4   FYCKLCNVTFTDEISVEAHLKGKKHKKNVK 33

Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins. Length = 35

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	463
PF12874	25	zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG	98.29
smart00451	35	ZnF_U1 U1-like zinc finger. Family of C2H2-type zi	98.26
PF12874	25	zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG	98.22
smart00451	35	ZnF_U1 U1-like zinc finger. Family of C2H2-type zi	98.03
KOG3792	816	consensus Transcription factor NFAT, subunit NF90	97.87
PF12171	27	zf-C2H2_jaz: Zinc-finger double-stranded RNA-bindi	97.7
PF12171	27	zf-C2H2_jaz: Zinc-finger double-stranded RNA-bindi	97.58
PF06220	38	zf-U1: U1 zinc finger; InterPro: IPR013085 Zinc fi	96.78
KOG4727	193	consensus U1-like Zn-finger protein [General funct	96.69
PF06220	38	zf-U1: U1 zinc finger; InterPro: IPR013085 Zinc fi	96.04
KOG2785	390	consensus C2H2-type Zn-finger protein [General fun	95.27
KOG3032	264	consensus Uncharacterized conserved protein [Funct	94.46
KOG4727	193	consensus U1-like Zn-finger protein [General funct	94.27
PF14968	336	CCDC84: Coiled coil protein 84	93.34
KOG0227	222	consensus Splicing factor 3a, subunit 2 [RNA proce	93.11
KOG3408	129	consensus U1-like Zn-finger-containing protein, pr	92.55
PLN02748	468	tRNA dimethylallyltransferase	92.39
smart00586	49	ZnF_DBF Zinc finger in DBF-like proteins.	92.34
KOG0717	508	consensus Molecular chaperone (DnaJ superfamily) [	92.27
KOG0717	508	consensus Molecular chaperone (DnaJ superfamily) [	92.05
KOG0227	222	consensus Splicing factor 3a, subunit 2 [RNA proce	92.02
PLN02748	468	tRNA dimethylallyltransferase	91.94
KOG4722	672	consensus Zn-finger protein [General function pred	91.8
COG5246	222	PRP11 Splicing factor 3a, subunit 2 [RNA processin	91.65
KOG3032	264	consensus Uncharacterized conserved protein [Funct	91.53
PF07535	49	zf-DBF: DBF zinc finger; InterPro: IPR006572 Zinc	91.05
KOG3792	816	consensus Transcription factor NFAT, subunit NF90	91.02
PF13894	24	zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP	90.57
PF12756	100	zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB:	90.28
PF07535	49	zf-DBF: DBF zinc finger; InterPro: IPR006572 Zinc	89.91
smart00586	49	ZnF_DBF Zinc finger in DBF-like proteins.	89.47
PF13894	24	zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP	89.35
KOG0150	336	consensus Spliceosomal protein FBP21 [RNA processi	89.05
COG5246	222	PRP11 Splicing factor 3a, subunit 2 [RNA processin	88.3
KOG3408	129	consensus U1-like Zn-finger-containing protein, pr	88.25
KOG3454	165	consensus U1 snRNP-specific protein C [RNA process	87.53
PF00096	23	zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR0070	86.96
PF13912	27	zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9	85.25
PF12756	100	zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB:	84.58
KOG0150	336	consensus Spliceosomal protein FBP21 [RNA processi	82.96
PF00096	23	zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR0070	82.61
KOG3454	165	consensus U1 snRNP-specific protein C [RNA process	82.59
KOG2785	390	consensus C2H2-type Zn-finger protein [General fun	81.58
smart00355	26	ZnF_C2H2 zinc finger.	81.23

>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A

Probab=98.29  E-value=4.2e-07  Score=58.97  Aligned_cols=25  Identities=36%  Similarity=0.701  Sum_probs=24.4

Q ss_pred             eeccccccccCCHHHHHHhhhhhhH
Q 012461          344 FWCEDCQVGTHSAVVMEGHKRGKKH  368 (463)
Q Consensus       344 ~~C~lCnV~ctS~~~~~sHL~GkKH  368 (463)
                      |+|.+|++.|+++..|.+|++|++|
T Consensus         1 ~~C~~C~~~f~s~~~~~~H~~s~~H   25 (25)
T PF12874_consen    1 FYCDICNKSFSSENSLRQHLRSKKH   25 (25)
T ss_dssp             EEETTTTEEESSHHHHHHHHTTHHH
T ss_pred             CCCCCCCCCcCCHHHHHHHHCcCCC
Confidence            7899999999999999999999999

>smart00451 ZnF_U1 U1-like zinc finger

Probab=98.26  E-value=8.2e-07  Score=61.52  Aligned_cols=33  Identities=30%  Similarity=0.639  Sum_probs=30.7

Q ss_pred             ceeccccccccCCHHHHHHhhhhhhHHHHHHhh
Q 012461          343 KFWCEDCQVGTHSAVVMEGHKRGKKHIARSNES  375 (463)
Q Consensus       343 ~~~C~lCnV~ctS~~~~~sHL~GkKH~aklk~~  375 (463)
                      .|+|++|++.|++...+..|++|++|..+++++
T Consensus         3 ~~~C~~C~~~~~~~~~~~~H~~gk~H~~~~~~~   35 (35)
T smart00451        3 GFYCKLCNVTFTDEISVEAHLKGKKHKKNVKKR   35 (35)
T ss_pred             CeEccccCCccCCHHHHHHHHChHHHHHHHHcC
Confidence            588999999999999999999999999999763

Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.

>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A

Probab=98.22  E-value=5.4e-07  Score=58.44  Aligned_cols=25  Identities=44%  Similarity=0.850  Sum_probs=24.5

Q ss_pred             eeccccccccCCHHHHHHhhcccch
Q 012461          209 WSCALCQVSATSERGLDEHLQGKKH  233 (463)
Q Consensus       209 w~C~LC~Vt~tSe~~L~~HLqGKrH  233 (463)
                      |+|.||+++|+++..|+.|++|++|
T Consensus         1 ~~C~~C~~~f~s~~~~~~H~~s~~H   25 (25)
T PF12874_consen    1 FYCDICNKSFSSENSLRQHLRSKKH   25 (25)
T ss_dssp             EEETTTTEEESSHHHHHHHHTTHHH
T ss_pred             CCCCCCCCCcCCHHHHHHHHCcCCC
Confidence            8999999999999999999999998

>smart00451 ZnF_U1 U1-like zinc finger

Probab=98.03  E-value=2.9e-06  Score=58.73  Aligned_cols=32  Identities=41%  Similarity=0.735  Sum_probs=30.1

Q ss_pred             ceeccccccccCCHHHHHHhhcccchHHHHHH
Q 012461          208 EWSCALCQVSATSERGLDEHLQGKKHKAKEAG  239 (463)
Q Consensus       208 ~w~C~LC~Vt~tSe~~L~~HLqGKrHKkk~e~  239 (463)
                      .++|++|++.|++...+..|+.|++|+.+++.
T Consensus         3 ~~~C~~C~~~~~~~~~~~~H~~gk~H~~~~~~   34 (35)
T smart00451        3 GFYCKLCNVTFTDEISVEAHLKGKKHKKNVKK   34 (35)
T ss_pred             CeEccccCCccCCHHHHHHHHChHHHHHHHHc
Confidence            58999999999999999999999999999864

Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.

>KOG3792 consensus Transcription factor NFAT, subunit NF90 [General function prediction only]

Probab=97.87  E-value=3.7e-06  Score=92.58  Aligned_cols=90  Identities=24%  Similarity=0.356  Sum_probs=73.1

Q ss_pred             cCCCceeccccccccCCHHHHHHhhcccchHHHHHHHHHHhhhhcCCCcccccccccchhhccccCCCCccccccccccc
Q 012461          204 KKTKEWSCALCQVSATSERGLDEHLQGKKHKAKEAGLLRAQKMCNNSISSMSKKSGKKIKLRESKDSSGQEMKTDVEEES  283 (463)
Q Consensus       204 k~~k~w~C~LC~Vt~tSe~~L~~HLqGKrHKkk~e~L~~a~~~~k~~~as~s~ks~~~tk~~~s~~ts~~e~~~~~~~es  283 (463)
                      ...+..+|.+|++.|++.+++.+||+|.||+++...   +                                        
T Consensus       189 ~laqL~~~kw~k~~a~G~qs~re~lr~~r~l~krvp---t----------------------------------------  225 (816)
T KOG3792|consen  189 RLAQLHYCKWCKISAAGPQTYREHLRGQKHLKKEVP---T----------------------------------------  225 (816)
T ss_pred             HHHHhhhhHHHHHhccccHHHHHHHHHHHHHHhccC---C----------------------------------------
Confidence            445688999999999999999999999999998521   0                                        


Q ss_pred             ccccccccCcccchhhhhhhhhhccCCCcchhhhhhhcccCCCcccccccCCCccccCCceeccccccccCCHHHHHHhh
Q 012461          284 TEVNKAVVGSERKAEVVEDSEIKNEGLPKKDLTAKTRKKKNGIPTAEKTKRKPPLRKKFKFWCEDCQVGTHSAVVMEGHK  363 (463)
Q Consensus       284 l~~~~~~~~s~kK~~~~e~~~~kn~~~~~q~~~~~E~~~k~v~~~~~kg~r~~~~k~~~~~~C~lCnV~ctS~~~~~sHL  363 (463)
                             .+..+.                                           -...+.|++|.++|++.+-|..||
T Consensus       226 -------~~~~kg-------------------------------------------w~~el~cEksi~tcs~pd~~g~al  255 (816)
T KOG3792|consen  226 -------NGPLKG-------------------------------------------WPLELHCEKSIVTCSGPDAYGAAL  255 (816)
T ss_pred             -------CCCccc-------------------------------------------chHHHHHHHhhccccCccchHHHH
Confidence                   000000                                           114567999999999999999999


Q ss_pred             hhhhHHHHHHhhhcCCCCcCCCC
Q 012461          364 RGKKHIARSNESKKNDDAVPATS  386 (463)
Q Consensus       364 ~GkKH~aklk~~~~~gk~Vp~~s  386 (463)
                      +|.+|....+.+...|++|+.-.
T Consensus       256 Rrv~ec~~skL~~k~G~gi~d~c  278 (816)
T KOG3792|consen  256 RRVKECKVSKLHKKLGKGIPDPC  278 (816)
T ss_pred             HHHHHhhhhcccccCCCCCCCcc
Confidence            99999999999999998876543

>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length

Probab=97.70  E-value=2.1e-05  Score=52.47  Aligned_cols=27  Identities=30%  Similarity=0.621  Sum_probs=25.1

Q ss_pred             ceeccccccccCCHHHHHHhhhhhhHH
Q 012461          343 KFWCEDCQVGTHSAVVMEGHKRGKKHI  369 (463)
Q Consensus       343 ~~~C~lCnV~ctS~~~~~sHL~GkKH~  369 (463)
                      .|+|.+|++.|+++..|..|++|++|+
T Consensus         1 q~~C~~C~k~f~~~~~~~~H~~sk~Hk   27 (27)
T PF12171_consen    1 QFYCDACDKYFSSENQLKQHMKSKKHK   27 (27)
T ss_dssp             -CBBTTTTBBBSSHHHHHCCTTSHHHH
T ss_pred             CCCcccCCCCcCCHHHHHHHHccCCCC
Confidence            378999999999999999999999996

The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.

>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length

Probab=97.58  E-value=3e-05  Score=51.71  Aligned_cols=27  Identities=37%  Similarity=0.728  Sum_probs=25.4

Q ss_pred             ceeccccccccCCHHHHHHhhcccchH
Q 012461          208 EWSCALCQVSATSERGLDEHLQGKKHK  234 (463)
Q Consensus       208 ~w~C~LC~Vt~tSe~~L~~HLqGKrHK  234 (463)
                      .|+|.+|+..|.++..|.+|+.||+||
T Consensus         1 q~~C~~C~k~f~~~~~~~~H~~sk~Hk   27 (27)
T PF12171_consen    1 QFYCDACDKYFSSENQLKQHMKSKKHK   27 (27)
T ss_dssp             -CBBTTTTBBBSSHHHHHCCTTSHHHH
T ss_pred             CCCcccCCCCcCCHHHHHHHHccCCCC
Confidence            379999999999999999999999997

The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.

>PF06220 zf-U1: U1 zinc finger; InterPro: IPR013085 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=96.78  E-value=0.0012  Score=48.20  Aligned_cols=33  Identities=24%  Similarity=0.541  Sum_probs=21.4

Q ss_pred             ceecccccccc--CCHHHHHHhhhhhhHHHHHHhh
Q 012461          343 KFWCEDCQVGT--HSAVVMEGHKRGKKHIARSNES  375 (463)
Q Consensus       343 ~~~C~lCnV~c--tS~~~~~sHL~GkKH~aklk~~  375 (463)
                      .+||+.|++.+  ++...-..|.+|+||+.++++.
T Consensus         3 ryyCdyC~~~~~~d~~~~Rk~H~~G~kH~~nv~~~   37 (38)
T PF06220_consen    3 RYYCDYCKKYLTHDSPSIRKQHERGWKHKENVKRY   37 (38)
T ss_dssp             S-B-TTT--B-S--SHHHHHHHT--THHHHHHHHH
T ss_pred             CeecccccceecCCChHHHHHhhccHHHHHHHHHh
Confidence            48999999999  5667779999999999999763

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. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a C2H2-type zinc finger motif found in several U1 small nuclear ribonucleoprotein C (U1-C) proteins. Some proteins contain multiple copies of this motif. The U1 small nuclear ribonucleoprotein (U1 snRNP) binds to the pre-mRNA 5' splice site at early stages of spliceosome assembly. Recruitment of U1 to a class of weak 5' splice site is promoted by binding of the protein TIA-1 to uridine-rich sequences immediately downstream from the 5' splice site. Binding of TIA-1 in the vicinity of a 5' splice site helps to stabilise U1 snRNP recruitment, at least in part, via a direct interaction with U1-C, thus providing one molecular mechanism for the function of this splicing regulator []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2VRD_A.

>KOG4727 consensus U1-like Zn-finger protein [General function prediction only]

Probab=96.69  E-value=0.0011  Score=62.88  Aligned_cols=36  Identities=25%  Similarity=0.459  Sum_probs=32.3

Q ss_pred             cCCceeccccccccCCHHHHHHhhhhhhHHHHHHhh
Q 012461          340 KKFKFWCEDCQVGTHSAVVMEGHKRGKKHIARSNES  375 (463)
Q Consensus       340 ~~~~~~C~lCnV~ctS~~~~~sHL~GkKH~aklk~~  375 (463)
                      +..-|+|.+|+-.+-.-.+|..|||||+|+.++.-.
T Consensus        72 q~~GyyCdVCdcvvKDSinflDHiNgKkHqrnlgms  107 (193)
T KOG4727|consen   72 QKGGYYCDVCDCVVKDSINFLDHINGKKHQRNLGMS  107 (193)
T ss_pred             ccCceeeeecceeehhhHHHHHHhccHHHHHHHhhh
Confidence            457799999999999999999999999999998544

>PF06220 zf-U1: U1 zinc finger; InterPro: IPR013085 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=96.04  E-value=0.005  Score=44.96  Aligned_cols=33  Identities=24%  Similarity=0.366  Sum_probs=20.9

Q ss_pred             Cceecccccccc--CCHHHHHHhhcccchHHHHHH
Q 012461          207 KEWSCALCQVSA--TSERGLDEHLQGKKHKAKEAG  239 (463)
Q Consensus       207 k~w~C~LC~Vt~--tSe~~L~~HLqGKrHKkk~e~  239 (463)
                      +.++|+.|++.+  ++...=..|++|.+|+.+++.
T Consensus         2 ~ryyCdyC~~~~~~d~~~~Rk~H~~G~kH~~nv~~   36 (38)
T PF06220_consen    2 PRYYCDYCKKYLTHDSPSIRKQHERGWKHKENVKR   36 (38)
T ss_dssp             -S-B-TTT--B-S--SHHHHHHHT--THHHHHHHH
T ss_pred             cCeecccccceecCCChHHHHHhhccHHHHHHHHH
Confidence            468999999999  566777999999999999865

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. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a C2H2-type zinc finger motif found in several U1 small nuclear ribonucleoprotein C (U1-C) proteins. Some proteins contain multiple copies of this motif. The U1 small nuclear ribonucleoprotein (U1 snRNP) binds to the pre-mRNA 5' splice site at early stages of spliceosome assembly. Recruitment of U1 to a class of weak 5' splice site is promoted by binding of the protein TIA-1 to uridine-rich sequences immediately downstream from the 5' splice site. Binding of TIA-1 in the vicinity of a 5' splice site helps to stabilise U1 snRNP recruitment, at least in part, via a direct interaction with U1-C, thus providing one molecular mechanism for the function of this splicing regulator []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2VRD_A.

>KOG2785 consensus C2H2-type Zn-finger protein [General function prediction only]

Probab=95.27  E-value=0.019  Score=60.37  Aligned_cols=100  Identities=18%  Similarity=0.303  Sum_probs=69.0

Q ss_pred             ceeccccccccCCHHHHHHhhcccchHHHHHHHHHHhhhhcCCCcccccccccchhhccccCCCCccccccccccccccc
Q 012461          208 EWSCALCQVSATSERGLDEHLQGKKHKAKEAGLLRAQKMCNNSISSMSKKSGKKIKLRESKDSSGQEMKTDVEEESTEVN  287 (463)
Q Consensus       208 ~w~C~LC~Vt~tSe~~L~~HLqGKrHKkk~e~L~~a~~~~k~~~as~s~ks~~~tk~~~s~~ts~~e~~~~~~~esl~~~  287 (463)
                      -++|.-|+|.|.+...-+-|+.--=|+=|+.. +.|         ++|.-+-                      +-  + 
T Consensus         3 ~ftC~tC~v~F~~ad~Qr~HyKSdWHRYNLKR-kVA---------~lPPIta----------------------E~--F-   47 (390)
T KOG2785|consen    3 GFTCNTCNVEFDDADEQRAHYKSDWHRYNLKR-KVA---------SLPPITA----------------------EE--F-   47 (390)
T ss_pred             cceeeceeeeeccHHHHHHHhhhhHHHhhHHh-Hhh---------cCCCcCH----------------------HH--H-
Confidence            46899999999999999999999999999877 333         2222110                      00  0 


Q ss_pred             ccccCcccchhhhhhhhhhccCCCcchhhhhhhcccCCCcccccccCCCccccCCceeccccccccCCHHHHHHhhhhhh
Q 012461          288 KAVVGSERKAEVVEDSEIKNEGLPKKDLTAKTRKKKNGIPTAEKTKRKPPLRKKFKFWCEDCQVGTHSAVVMEGHKRGKK  367 (463)
Q Consensus       288 ~~~~~s~kK~~~~e~~~~kn~~~~~q~~~~~E~~~k~v~~~~~kg~r~~~~k~~~~~~C~lCnV~ctS~~~~~sHL~GkK  367 (463)
                           ..+.++.+..           +.+.++                   .....+.|.+|+..+.|...+..||..++
T Consensus        48 -----~~k~~s~~~~-----------~~~~~e-------------------~~~~~~~c~~c~k~~~s~~a~~~hl~Sk~   92 (390)
T KOG2785|consen   48 -----NEKVLSDDSE-----------KEENLE-------------------EAESVVYCEACNKSFASPKAHENHLKSKK   92 (390)
T ss_pred             -----hHHHhhhhhh-----------hhhhhh-------------------hcccceehHHhhccccChhhHHHHHHHhh
Confidence                 0000100000           000011                   13478899999999999999999999999


Q ss_pred             HHHHHHhhhc
Q 012461          368 HIARSNESKK  377 (463)
Q Consensus       368 H~aklk~~~~  377 (463)
                      |..++..+..
T Consensus        93 h~~~~~~~~r  102 (390)
T KOG2785|consen   93 HVENLSNHQR  102 (390)
T ss_pred             cchhhhhhhc
Confidence            9999999875

>KOG3032 consensus Uncharacterized conserved protein [Function unknown]

Probab=94.46  E-value=0.048  Score=54.29  Aligned_cols=50  Identities=22%  Similarity=0.286  Sum_probs=38.4

Q ss_pred             CCceeccccccccCCHHHHHHhhhhhhHHHHHHhhhcCCCCcCCCCCcccC
Q 012461          341 KFKFWCEDCQVGTHSAVVMEGHKRGKKHIARSNESKKNDDAVPATSSMTIV  391 (463)
Q Consensus       341 ~~~~~C~lCnV~ctS~~~~~sHL~GkKH~aklk~~~~~gk~Vp~~s~~~~~  391 (463)
                      +..+.|-+|||-.- +.....|++|++|.-++..++-.|.-|.-..+|+|.
T Consensus        33 sgql~C~vCn~piK-p~lW~vHvnsKkHre~id~lKs~~~Kv~k~~~T~~p   82 (264)
T KOG3032|consen   33 SGQLVCRVCNVPIK-PSLWDVHVNSKKHREAIDSLKSRGSKVAKTRPTKIP   82 (264)
T ss_pred             CCCeeEEEecCccc-HHHHHHHhccHHHHHHHHHHHhhhcccccCcCccCc
Confidence            46789999999999 999999999999999998887443333333444433

>KOG4727 consensus U1-like Zn-finger protein [General function prediction only]

Probab=94.27  E-value=0.03  Score=53.47  Aligned_cols=37  Identities=22%  Similarity=0.489  Sum_probs=33.4

Q ss_pred             CceeccccccccCCHHHHHHhhcccchHHHHHHHHHH
Q 012461          207 KEWSCALCQVSATSERGLDEHLQGKKHKAKEAGLLRA  243 (463)
Q Consensus       207 k~w~C~LC~Vt~tSe~~L~~HLqGKrHKkk~e~L~~a  243 (463)
                      .-+||.||.-.+-.-..|.+|++||+|+-|+..+.+.
T Consensus        74 ~GyyCdVCdcvvKDSinflDHiNgKkHqrnlgmsm~v  110 (193)
T KOG4727|consen   74 GGYYCDVCDCVVKDSINFLDHINGKKHQRNLGMSMRV  110 (193)
T ss_pred             CceeeeecceeehhhHHHHHHhccHHHHHHHhhhhcc
Confidence            3689999999999999999999999999999986554

>PF14968 CCDC84: Coiled coil protein 84

Probab=93.34  E-value=0.071  Score=55.53  Aligned_cols=39  Identities=15%  Similarity=0.257  Sum_probs=30.7

Q ss_pred             cCCceeccccccccCCH------HHHHHhhhhhhHHHHHHhhhcC
Q 012461          340 KKFKFWCEDCQVGTHSA------VVMEGHKRGKKHIARSNESKKN  378 (463)
Q Consensus       340 ~~~~~~C~lCnV~ctS~------~~~~sHL~GkKH~aklk~~~~~  378 (463)
                      ....|||-.|+....--      ..+..||.+.-|+++++...-.
T Consensus        55 ~~~~fWC~fC~~ev~~~~s~~~~~~ai~HLaS~eH~k~vk~F~w~   99 (336)
T PF14968_consen   55 HRNRFWCVFCDCEVREHDSSFACGGAIEHLASPEHRKNVKKFWWK   99 (336)
T ss_pred             ccceeEeeCccchhhhccchhhhccHHhhcCCHHHHHHHHHHHHH
Confidence            45789999997665533      4678899999999999998443

>KOG0227 consensus Splicing factor 3a, subunit 2 [RNA processing and modification]

Probab=93.11  E-value=0.048  Score=52.97  Aligned_cols=36  Identities=22%  Similarity=0.269  Sum_probs=32.4

Q ss_pred             CCceeccccccccCCHHHHHHhhhhhhHHHHHHhhh
Q 012461          341 KFKFWCEDCQVGTHSAVVMEGHKRGKKHIARSNESK  376 (463)
Q Consensus       341 ~~~~~C~lCnV~ctS~~~~~sHL~GkKH~aklk~~~  376 (463)
                      ...+-|.||.-.-+++..|..|++||||+.+|-+-.
T Consensus        51 ~G~yeCkLClT~H~ne~Syl~HtqGKKHq~Nlarra   86 (222)
T KOG0227|consen   51 LGKYECKLCLTLHNNEGSYLAHTQGKKHQTNLARRA   86 (222)
T ss_pred             CcceeehhhhhhhcchhhhhhhhccchhhHHHHHHH
Confidence            378999999999999999999999999999886553

>KOG3408 consensus U1-like Zn-finger-containing protein, probabl erole in RNA processing/splicing [RNA processing and modification]

Probab=92.55  E-value=0.091  Score=47.77  Aligned_cols=36  Identities=25%  Similarity=0.378  Sum_probs=34.0

Q ss_pred             CCceeccccccccCCHHHHHHhhhhhhHHHHHHhhh
Q 012461          341 KFKFWCEDCQVGTHSAVVMEGHKRGKKHIARSNESK  376 (463)
Q Consensus       341 ~~~~~C~lCnV~ctS~~~~~sHL~GkKH~aklk~~~  376 (463)
                      ...|+|-.|.-.|-+..+|..|+.||.|.++||.+.
T Consensus        55 ~GqfyCi~CaRyFi~~~~l~~H~ktK~HKrRvK~l~   90 (129)
T KOG3408|consen   55 GGQFYCIECARYFIDAKALKTHFKTKVHKRRVKELR   90 (129)
T ss_pred             CceeehhhhhhhhcchHHHHHHHhccHHHHHHHhcc
Confidence            378999999999999999999999999999999886

>PLN02748 tRNA dimethylallyltransferase

Probab=92.39  E-value=0.096  Score=56.71  Aligned_cols=37  Identities=30%  Similarity=0.467  Sum_probs=33.3

Q ss_pred             Cceecccccc-ccCCHHHHHHhhhhhhHHHHHHhhhcC
Q 012461          342 FKFWCEDCQV-GTHSAVVMEGHKRGKKHIARSNESKKN  378 (463)
Q Consensus       342 ~~~~C~lCnV-~ctS~~~~~sHL~GkKH~aklk~~~~~  378 (463)
                      ..+.|++|+. ++.++...+.|++|++|+++++...+.
T Consensus       417 ~~~~Ce~C~~~~~~G~~eW~~Hlksr~Hk~~~~~~~k~  454 (468)
T PLN02748        417 TQYVCEACGNKVLRGAHEWEQHKQGRGHRKRVQRLKQK  454 (468)
T ss_pred             ccccccCCCCcccCCHHHHHHHhcchHHHHHHhHHHhh
Confidence            4567999998 899999999999999999999987654

>smart00586 ZnF_DBF Zinc finger in DBF-like proteins

Probab=92.34  E-value=0.057  Score=41.85  Aligned_cols=29  Identities=28%  Similarity=0.450  Sum_probs=25.0

Q ss_pred             CCceeccccccccCCHHHHHHhhcccchHHHH
Q 012461          206 TKEWSCALCQVSATSERGLDEHLQGKKHKAKE  237 (463)
Q Consensus       206 ~k~w~C~LC~Vt~tSe~~L~~HLqGKrHKkk~  237 (463)
                      .+.-||+.|++.+.   .|..|+.+++|++=.
T Consensus         3 ~k~GYCE~Cr~kfd---~l~~Hi~s~~Hr~FA   31 (49)
T smart00586        3 KKPGYCENCREKYD---DLETHLLSEKHRRFA   31 (49)
T ss_pred             CCCcccccHhHHHh---hHHHHhccHHHHHHH
Confidence            35679999999987   799999999999753

>KOG0717 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=92.27  E-value=0.079  Score=57.21  Aligned_cols=37  Identities=22%  Similarity=0.395  Sum_probs=33.8

Q ss_pred             CceeccccccccCCHHHHHHhhhhhhHHHHHHhhhcC
Q 012461          342 FKFWCEDCQVGTHSAVVMEGHKRGKKHIARSNESKKN  378 (463)
Q Consensus       342 ~~~~C~lCnV~ctS~~~~~sHL~GkKH~aklk~~~~~  378 (463)
                      ..++|-+|+.+|-|+.+|..|.+.|||..+|.++..+
T Consensus       291 e~lyC~vCnKsFKseKq~kNHEnSKKHkenv~eLrqe  327 (508)
T KOG0717|consen  291 EVLYCVVCNKSFKSEKQLKNHENSKKHKENVAELRQE  327 (508)
T ss_pred             CceEEeeccccccchHHHHhhHHHHHHHHHHHHHHHH
Confidence            3499999999999999999999999999999888654

>KOG0717 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=92.05  E-value=0.11  Score=56.18  Aligned_cols=37  Identities=35%  Similarity=0.496  Sum_probs=34.1

Q ss_pred             ceeccccccccCCHHHHHHhhcccchHHHHHHHHHHh
Q 012461          208 EWSCALCQVSATSERGLDEHLQGKKHKAKEAGLLRAQ  244 (463)
Q Consensus       208 ~w~C~LC~Vt~tSe~~L~~HLqGKrHKkk~e~L~~a~  244 (463)
                      .+||.+|+-+|-|+..|..|-+.|+|+.+++.|....
T Consensus       292 ~lyC~vCnKsFKseKq~kNHEnSKKHkenv~eLrqem  328 (508)
T KOG0717|consen  292 VLYCVVCNKSFKSEKQLKNHENSKKHKENVAELRQEM  328 (508)
T ss_pred             ceEEeeccccccchHHHHhhHHHHHHHHHHHHHHHHH
Confidence            4999999999999999999999999999999977543

>KOG0227 consensus Splicing factor 3a, subunit 2 [RNA processing and modification]

Probab=92.02  E-value=0.15  Score=49.68  Aligned_cols=39  Identities=28%  Similarity=0.473  Sum_probs=34.2

Q ss_pred             ccccCCCceeccccccccCCHHHHHHhhcccchHHHHHH
Q 012461          201 MSSKKTKEWSCALCQVSATSERGLDEHLQGKKHKAKEAG  239 (463)
Q Consensus       201 ~~kk~~k~w~C~LC~Vt~tSe~~L~~HLqGKrHKkk~e~  239 (463)
                      ..+.--..+.|.||...-.++..+.-|++||||+.|++.
T Consensus        46 ~mkNh~G~yeCkLClT~H~ne~Syl~HtqGKKHq~Nlar   84 (222)
T KOG0227|consen   46 FMKNHLGKYECKLCLTLHNNEGSYLAHTQGKKHQTNLAR   84 (222)
T ss_pred             hhhccCcceeehhhhhhhcchhhhhhhhccchhhHHHHH
Confidence            334455578999999999999999999999999999987

>PLN02748 tRNA dimethylallyltransferase

Probab=91.94  E-value=0.11  Score=56.17  Aligned_cols=37  Identities=19%  Similarity=0.430  Sum_probs=32.3

Q ss_pred             CCceecccccc-ccCCHHHHHHhhcccchHHHHHHHHH
Q 012461          206 TKEWSCALCQV-SATSERGLDEHLQGKKHKAKEAGLLR  242 (463)
Q Consensus       206 ~k~w~C~LC~V-t~tSe~~L~~HLqGKrHKkk~e~L~~  242 (463)
                      -+..+|++|+. ++.++..-+.|+.||+||+++..+.+
T Consensus       416 ~~~~~Ce~C~~~~~~G~~eW~~Hlksr~Hk~~~~~~~k  453 (468)
T PLN02748        416 WTQYVCEACGNKVLRGAHEWEQHKQGRGHRKRVQRLKQ  453 (468)
T ss_pred             cccccccCCCCcccCCHHHHHHHhcchHHHHHHhHHHh
Confidence            34557999998 89999999999999999999988544

>KOG4722 consensus Zn-finger protein [General function prediction only]

Probab=91.80  E-value=0.09  Score=56.34  Aligned_cols=33  Identities=33%  Similarity=0.403  Sum_probs=30.3

Q ss_pred             eeccccccccCCHHHHHHhhhhhhHHHHHHhhh
Q 012461          344 FWCEDCQVGTHSAVVMEGHKRGKKHIARSNESK  376 (463)
Q Consensus       344 ~~C~lCnV~ctS~~~~~sHL~GkKH~aklk~~~  376 (463)
                      --|++|||...|++.|-+|..|+||+..|..+.
T Consensus       494 kqcslcnvlissevylfshvkgrkhqqal~e~~  526 (672)
T KOG4722|consen  494 KQCSLCNVLISSEVYLFSHVKGRKHQQALNELL  526 (672)
T ss_pred             hccchhhhhhhhhhhhhhhhcchhHHHHHHHHh
Confidence            469999999999999999999999999987664

>COG5246 PRP11 Splicing factor 3a, subunit 2 [RNA processing and modification]

Probab=91.65  E-value=0.13  Score=49.77  Aligned_cols=41  Identities=32%  Similarity=0.618  Sum_probs=36.3

Q ss_pred             ccccccCCCceeccccccccCCHHHHHHhhcccchHHHHHH
Q 012461          199 PLMSSKKTKEWSCALCQVSATSERGLDEHLQGKKHKAKEAG  239 (463)
Q Consensus       199 p~~~kk~~k~w~C~LC~Vt~tSe~~L~~HLqGKrHKkk~e~  239 (463)
                      |...+.--..+.|-||+..--++..+..|++||+|+-++..
T Consensus        44 Pyl~knh~Gk~vC~LC~T~H~~e~Sy~~H~~GKKH~~n~~r   84 (222)
T COG5246          44 PYLSKNHTGKYVCLLCKTKHLTEMSYVKHREGKKHKENSSR   84 (222)
T ss_pred             cchhhcCCCcEEeeeeccccccHHHHHHhhccchhhhhHHH
Confidence            45555666789999999999999999999999999999887

>KOG3032 consensus Uncharacterized conserved protein [Function unknown]

Probab=91.53  E-value=0.31  Score=48.69  Aligned_cols=39  Identities=23%  Similarity=0.416  Sum_probs=35.6

Q ss_pred             cccCCCceeccccccccCCHHHHHHhhcccchHHHHHHHH
Q 012461          202 SSKKTKEWSCALCQVSATSERGLDEHLQGKKHKAKEAGLL  241 (463)
Q Consensus       202 ~kk~~k~w~C~LC~Vt~tSe~~L~~HLqGKrHKkk~e~L~  241 (463)
                      ..+......|.||+|-.- +....-|..||+|+.+++.|+
T Consensus        29 kyn~sgql~C~vCn~piK-p~lW~vHvnsKkHre~id~lK   67 (264)
T KOG3032|consen   29 KYNESGQLVCRVCNVPIK-PSLWDVHVNSKKHREAIDSLK   67 (264)
T ss_pred             ccCCCCCeeEEEecCccc-HHHHHHHhccHHHHHHHHHHH
Confidence            346677899999999999 999999999999999999987

>PF07535 zf-DBF: DBF zinc finger; InterPro: IPR006572 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=91.05  E-value=0.13  Score=39.86  Aligned_cols=29  Identities=34%  Similarity=0.591  Sum_probs=24.9

Q ss_pred             CCceeccccccccCCHHHHHHhhcccchHHHH
Q 012461          206 TKEWSCALCQVSATSERGLDEHLQGKKHKAKE  237 (463)
Q Consensus       206 ~k~w~C~LC~Vt~tSe~~L~~HLqGKrHKkk~  237 (463)
                      .+.-||+.|++.+.   .|..|+++++|++=.
T Consensus         3 ~k~GYCE~C~~ky~---~l~~Hi~s~~Hr~FA   31 (49)
T PF07535_consen    3 KKPGYCENCRVKYD---DLEEHIQSEKHRKFA   31 (49)
T ss_pred             CCCccCccccchhh---hHHHHhCCHHHHHHH
Confidence            35679999999998   599999999999753

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. In eukaryotes, initiation of DNA replication requires the assembly of pre-replication complexes (pre-RCs) on chromatin during the G1 phase. In the S phase, pre-RCs are activated by two protein kinases, Cdk2 and Cdc7, which results in the loading of replication factors and the unwinding of replication origins by the MCM helicase complex []. Cdc7 is a serine/threonine kinase that is conserved from yeast to human. It is regulated by its association with a regulatory subunit, the Dbf4 protein. This complex is often referred to as DDK (Dbf4-dependent kinase) []. DBF4 contains an N-terminal BRCT domain and a C-terminal conserved region that could potentially coordinate one zinc atom, the DBF4-type zinc finger. This entry represents the zinc finger, which is important for the interaction with Cdc7 [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding

>KOG3792 consensus Transcription factor NFAT, subunit NF90 [General function prediction only]

Probab=91.02  E-value=0.087  Score=59.28  Aligned_cols=35  Identities=23%  Similarity=0.491  Sum_probs=31.1

Q ss_pred             cCCceeccccccccCCHHHHHHhhhhhhHHHHHHh
Q 012461          340 KKFKFWCEDCQVGTHSAVVMEGHKRGKKHIARSNE  374 (463)
Q Consensus       340 ~~~~~~C~lCnV~ctS~~~~~sHL~GkKH~aklk~  374 (463)
                      +...|.|.+|+-.|+....-..||+|.||.-.-++
T Consensus       356 K~~~f~cKlcdckf~d~nak~mhl~grRhrLQYk~  390 (816)
T KOG3792|consen  356 KLLRFHCKLCDCKFNDPNAKEMHLKGRRHRLQYKQ  390 (816)
T ss_pred             chHhhhhhhhcCCCCCcchHHhhhhcccccceecc
Confidence            45789999999999999999999999999866654

>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A

Probab=90.57  E-value=0.21  Score=30.80  Aligned_cols=21  Identities=29%  Similarity=0.469  Sum_probs=17.6

Q ss_pred             eeccccccccCCHHHHHHhhh
Q 012461          344 FWCEDCQVGTHSAVVMEGHKR  364 (463)
Q Consensus       344 ~~C~lCnV~ctS~~~~~sHL~  364 (463)
                      |.|.+|+..+.+...|..|+.
T Consensus         1 ~~C~~C~~~~~~~~~l~~H~~   21 (24)
T PF13894_consen    1 FQCPICGKSFRSKSELRQHMR   21 (24)
T ss_dssp             EE-SSTS-EESSHHHHHHHHH
T ss_pred             CCCcCCCCcCCcHHHHHHHHH
Confidence            579999999999999999985

...

>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A

Probab=90.28  E-value=0.15  Score=41.47  Aligned_cols=36  Identities=28%  Similarity=0.620  Sum_probs=27.3

Q ss_pred             cCCCceeccccccccCCHHHHHHhhcccchHHHHHH
Q 012461          204 KKTKEWSCALCQVSATSERGLDEHLQGKKHKAKEAG  239 (463)
Q Consensus       204 k~~k~w~C~LC~Vt~tSe~~L~~HLqGKrHKkk~e~  239 (463)
                      +....|.|.+|...+.+...|+.|++.+.|+.....
T Consensus        46 ~~~~~~~C~~C~~~f~s~~~l~~Hm~~~~H~~~~~~   81 (100)
T PF12756_consen   46 KVKESFRCPYCNKTFRSREALQEHMRSKHHKKRNSE   81 (100)
T ss_dssp             ---SSEEBSSSS-EESSHHHHHHHHHHTTTTC-S--
T ss_pred             ccCCCCCCCccCCCCcCHHHHHHHHcCccCCCcccc
Confidence            444479999999999999999999999999986443

>PF07535 zf-DBF: DBF zinc finger; InterPro: IPR006572 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=89.91  E-value=0.23  Score=38.41  Aligned_cols=28  Identities=29%  Similarity=0.478  Sum_probs=24.3

Q ss_pred             CceeccccccccCCHHHHHHhhhhhhHHHHH
Q 012461          342 FKFWCEDCQVGTHSAVVMEGHKRGKKHIARS  372 (463)
Q Consensus       342 ~~~~C~lCnV~ctS~~~~~sHL~GkKH~akl  372 (463)
                      ..-+|+.|.+.+.   +|..|+.+.+|++-.
T Consensus         4 k~GYCE~C~~ky~---~l~~Hi~s~~Hr~FA   31 (49)
T PF07535_consen    4 KPGYCENCRVKYD---DLEEHIQSEKHRKFA   31 (49)
T ss_pred             CCccCccccchhh---hHHHHhCCHHHHHHH
Confidence            4457999999998   699999999999765

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. In eukaryotes, initiation of DNA replication requires the assembly of pre-replication complexes (pre-RCs) on chromatin during the G1 phase. In the S phase, pre-RCs are activated by two protein kinases, Cdk2 and Cdc7, which results in the loading of replication factors and the unwinding of replication origins by the MCM helicase complex []. Cdc7 is a serine/threonine kinase that is conserved from yeast to human. It is regulated by its association with a regulatory subunit, the Dbf4 protein. This complex is often referred to as DDK (Dbf4-dependent kinase) []. DBF4 contains an N-terminal BRCT domain and a C-terminal conserved region that could potentially coordinate one zinc atom, the DBF4-type zinc finger. This entry represents the zinc finger, which is important for the interaction with Cdc7 [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding

>smart00586 ZnF_DBF Zinc finger in DBF-like proteins

Probab=89.47  E-value=0.16  Score=39.32  Aligned_cols=28  Identities=25%  Similarity=0.415  Sum_probs=24.1

Q ss_pred             ceeccccccccCCHHHHHHhhhhhhHHHHHH
Q 012461          343 KFWCEDCQVGTHSAVVMEGHKRGKKHIARSN  373 (463)
Q Consensus       343 ~~~C~lCnV~ctS~~~~~sHL~GkKH~aklk  373 (463)
                      .-+|+.|.+.+.   +|..|+.+.+|++-.+
T Consensus         5 ~GYCE~Cr~kfd---~l~~Hi~s~~Hr~FA~   32 (49)
T smart00586        5 PGYCENCREKYD---DLETHLLSEKHRRFAE   32 (49)
T ss_pred             CcccccHhHHHh---hHHHHhccHHHHHHHc
Confidence            457999999987   8999999999997553

>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A

Probab=89.35  E-value=0.23  Score=30.63  Aligned_cols=21  Identities=29%  Similarity=0.714  Sum_probs=17.7

Q ss_pred             eeccccccccCCHHHHHHhhc
Q 012461          209 WSCALCQVSATSERGLDEHLQ  229 (463)
Q Consensus       209 w~C~LC~Vt~tSe~~L~~HLq  229 (463)
                      |.|.+|...+.+...|+.|+.
T Consensus         1 ~~C~~C~~~~~~~~~l~~H~~   21 (24)
T PF13894_consen    1 FQCPICGKSFRSKSELRQHMR   21 (24)
T ss_dssp             EE-SSTS-EESSHHHHHHHHH
T ss_pred             CCCcCCCCcCCcHHHHHHHHH
Confidence            689999999999999999985

...

>KOG0150 consensus Spliceosomal protein FBP21 [RNA processing and modification]

Probab=89.05  E-value=0.2  Score=51.72  Aligned_cols=36  Identities=25%  Similarity=0.420  Sum_probs=31.6

Q ss_pred             cCCCceecccccccc-CCHHHHHHhhcccchHHHHHH
Q 012461          204 KKTKEWSCALCQVSA-TSERGLDEHLQGKKHKAKEAG  239 (463)
Q Consensus       204 k~~k~w~C~LC~Vt~-tSe~~L~~HLqGKrHKkk~e~  239 (463)
                      +.+...+|++|+|=+ +.......|-+|||||.+++.
T Consensus         6 kS~~kkfCdyCKiWi~dN~~Sv~~He~GkrHke~V~K   42 (336)
T KOG0150|consen    6 KSQPKKFCDYCKIWIKDNPASVRFHERGKRHKENVAK   42 (336)
T ss_pred             hhccchhhhhhhhhhcCChHHHHhHhhhhHHHHHHHH
Confidence            456688999999987 778889999999999999886

>COG5246 PRP11 Splicing factor 3a, subunit 2 [RNA processing and modification]

Probab=88.30  E-value=0.37  Score=46.81  Aligned_cols=37  Identities=24%  Similarity=0.399  Sum_probs=32.7

Q ss_pred             cCCceeccccccccCCHHHHHHhhhhhhHHHHHHhhh
Q 012461          340 KKFKFWCEDCQVGTHSAVVMEGHKRGKKHIARSNESK  376 (463)
Q Consensus       340 ~~~~~~C~lCnV~ctS~~~~~sHL~GkKH~aklk~~~  376 (463)
                      ....|.|.+|+-.-.++..|..|+.||||+-++-+-.
T Consensus        50 h~Gk~vC~LC~T~H~~e~Sy~~H~~GKKH~~n~~rrs   86 (222)
T COG5246          50 HTGKYVCLLCKTKHLTEMSYVKHREGKKHKENSSRRS   86 (222)
T ss_pred             CCCcEEeeeeccccccHHHHHHhhccchhhhhHHHHH
Confidence            3478999999999999999999999999998876553

>KOG3408 consensus U1-like Zn-finger-containing protein, probabl erole in RNA processing/splicing [RNA processing and modification]

Probab=88.25  E-value=0.29  Score=44.57  Aligned_cols=34  Identities=24%  Similarity=0.430  Sum_probs=32.2

Q ss_pred             ceeccccccccCCHHHHHHhhcccchHHHHHHHH
Q 012461          208 EWSCALCQVSATSERGLDEHLQGKKHKAKEAGLL  241 (463)
Q Consensus       208 ~w~C~LC~Vt~tSe~~L~~HLqGKrHKkk~e~L~  241 (463)
                      .+||-.|---|.++++|+.|+.+|.||..+..|.
T Consensus        57 qfyCi~CaRyFi~~~~l~~H~ktK~HKrRvK~l~   90 (129)
T KOG3408|consen   57 QFYCIECARYFIDAKALKTHFKTKVHKRRVKELR   90 (129)
T ss_pred             eeehhhhhhhhcchHHHHHHHhccHHHHHHHhcc
Confidence            6899999999999999999999999999998864

>KOG3454 consensus U1 snRNP-specific protein C [RNA processing and modification]

Probab=87.53  E-value=0.36  Score=45.83  Aligned_cols=32  Identities=25%  Similarity=0.560  Sum_probs=26.8

Q ss_pred             ceecccccccc--CCHHHHHHhhhhhhHHHHHHh
Q 012461          343 KFWCEDCQVGT--HSAVVMEGHKRGKKHIARSNE  374 (463)
Q Consensus       343 ~~~C~lCnV~c--tS~~~~~sHL~GkKH~aklk~  374 (463)
                      .++|+-|++..  .|..+=..|+.|+||+.+++-
T Consensus         3 RYyCDYCdt~LthDslsvRK~H~~GrkH~~nvk~   36 (165)
T KOG3454|consen    3 RYYCDYCDTYLTHDSLSVRKTHCGGRKHKDNVKD   36 (165)
T ss_pred             cchhhhhhhhhhcccHHHHHhhhhhHHHHHHHHH
Confidence            57899999544  578899999999999988753

>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=86.96  E-value=0.51  Score=29.63  Aligned_cols=22  Identities=23%  Similarity=0.388  Sum_probs=20.1

Q ss_pred             eeccccccccCCHHHHHHhhhh
Q 012461          344 FWCEDCQVGTHSAVVMEGHKRG  365 (463)
Q Consensus       344 ~~C~lCnV~ctS~~~~~sHL~G  365 (463)
                      |.|..|+..|.+...|..|++-
T Consensus         1 y~C~~C~~~f~~~~~l~~H~~~   22 (23)
T PF00096_consen    1 YKCPICGKSFSSKSNLKRHMRR   22 (23)
T ss_dssp             EEETTTTEEESSHHHHHHHHHH
T ss_pred             CCCCCCCCccCCHHHHHHHHhH
Confidence            5699999999999999999874

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. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....

>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B

Probab=85.25  E-value=0.61  Score=30.42  Aligned_cols=21  Identities=33%  Similarity=0.656  Sum_probs=19.7

Q ss_pred             eeccccccccCCHHHHHHhhh
Q 012461          344 FWCEDCQVGTHSAVVMEGHKR  364 (463)
Q Consensus       344 ~~C~lCnV~ctS~~~~~sHL~  364 (463)
                      +.|.+|+..|.+...|..|++
T Consensus         2 ~~C~~C~~~F~~~~~l~~H~~   22 (27)
T PF13912_consen    2 FECDECGKTFSSLSALREHKR   22 (27)
T ss_dssp             EEETTTTEEESSHHHHHHHHC
T ss_pred             CCCCccCCccCChhHHHHHhH
Confidence            679999999999999999984

>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A

Probab=84.58  E-value=0.56  Score=38.09  Aligned_cols=32  Identities=28%  Similarity=0.466  Sum_probs=26.8

Q ss_pred             CceeccccccccCCHHHHHHhhhhhhHHHHHH
Q 012461          342 FKFWCEDCQVGTHSAVVMEGHKRGKKHIARSN  373 (463)
Q Consensus       342 ~~~~C~lCnV~ctS~~~~~sHL~GkKH~aklk  373 (463)
                      ..|.|.+|+..|.+...|..|++.+.|.....
T Consensus        49 ~~~~C~~C~~~f~s~~~l~~Hm~~~~H~~~~~   80 (100)
T PF12756_consen   49 ESFRCPYCNKTFRSREALQEHMRSKHHKKRNS   80 (100)
T ss_dssp             SSEEBSSSS-EESSHHHHHHHHHHTTTTC-S-
T ss_pred             CCCCCCccCCCCcCHHHHHHHHcCccCCCccc
Confidence            36899999999999999999999999987653

>KOG0150 consensus Spliceosomal protein FBP21 [RNA processing and modification]

Probab=82.96  E-value=0.75  Score=47.67  Aligned_cols=34  Identities=24%  Similarity=0.492  Sum_probs=28.0

Q ss_pred             CCceecccccccc-CCHHHHHHhhhhhhHHHHHHh
Q 012461          341 KFKFWCEDCQVGT-HSAVVMEGHKRGKKHIARSNE  374 (463)
Q Consensus       341 ~~~~~C~lCnV~c-tS~~~~~sHL~GkKH~aklk~  374 (463)
                      ....||++|.|.+ +.......|-+|++|+.+|.+
T Consensus         8 ~~kkfCdyCKiWi~dN~~Sv~~He~GkrHke~V~K   42 (336)
T KOG0150|consen    8 QPKKFCDYCKIWIKDNPASVRFHERGKRHKENVAK   42 (336)
T ss_pred             ccchhhhhhhhhhcCChHHHHhHhhhhHHHHHHHH
Confidence            3567899999987 457788999999999988743

>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=82.61  E-value=0.78  Score=28.78  Aligned_cols=22  Identities=27%  Similarity=0.709  Sum_probs=20.0

Q ss_pred             eeccccccccCCHHHHHHhhcc
Q 012461          209 WSCALCQVSATSERGLDEHLQG  230 (463)
Q Consensus       209 w~C~LC~Vt~tSe~~L~~HLqG  230 (463)
                      |.|..|...|++...|+.|++-
T Consensus         1 y~C~~C~~~f~~~~~l~~H~~~   22 (23)
T PF00096_consen    1 YKCPICGKSFSSKSNLKRHMRR   22 (23)
T ss_dssp             EEETTTTEEESSHHHHHHHHHH
T ss_pred             CCCCCCCCccCCHHHHHHHHhH
Confidence            5799999999999999999863

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. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....

>KOG3454 consensus U1 snRNP-specific protein C [RNA processing and modification]

Probab=82.59  E-value=0.68  Score=44.01  Aligned_cols=32  Identities=25%  Similarity=0.465  Sum_probs=27.9

Q ss_pred             ceecccccc--ccCCHHHHHHhhcccchHHHHHH
Q 012461          208 EWSCALCQV--SATSERGLDEHLQGKKHKAKEAG  239 (463)
Q Consensus       208 ~w~C~LC~V--t~tSe~~L~~HLqGKrHKkk~e~  239 (463)
                      .+||+.|++  +=+|.++=+.||.|++|+.++..
T Consensus         3 RYyCDYCdt~LthDslsvRK~H~~GrkH~~nvk~   36 (165)
T KOG3454|consen    3 RYYCDYCDTYLTHDSLSVRKTHCGGRKHKDNVKD   36 (165)
T ss_pred             cchhhhhhhhhhcccHHHHHhhhhhHHHHHHHHH
Confidence            579999984  44899999999999999999874

>KOG2785 consensus C2H2-type Zn-finger protein [General function prediction only]

Probab=81.58  E-value=1.2  Score=47.22  Aligned_cols=39  Identities=26%  Similarity=0.391  Sum_probs=35.2

Q ss_pred             cCCCceeccccccccCCHHHHHHhhcccchHHHHHHHHH
Q 012461          204 KKTKEWSCALCQVSATSERGLDEHLQGKKHKAKEAGLLR  242 (463)
Q Consensus       204 k~~k~w~C~LC~Vt~tSe~~L~~HLqGKrHKkk~e~L~~  242 (463)
                      +.....+|.+|+-.+.|+....+||..|+|+.++....+
T Consensus        64 ~~~~~~~c~~c~k~~~s~~a~~~hl~Sk~h~~~~~~~~r  102 (390)
T KOG2785|consen   64 EAESVVYCEACNKSFASPKAHENHLKSKKHVENLSNHQR  102 (390)
T ss_pred             hcccceehHHhhccccChhhHHHHHHHhhcchhhhhhhc
Confidence            445678999999999999999999999999999998765

>smart00355 ZnF_C2H2 zinc finger

Probab=81.23  E-value=1.3  Score=27.18  Aligned_cols=21  Identities=24%  Similarity=0.548  Sum_probs=19.3

Q ss_pred             eeccccccccCCHHHHHHhhh
Q 012461          344 FWCEDCQVGTHSAVVMEGHKR  364 (463)
Q Consensus       344 ~~C~lCnV~ctS~~~~~sHL~  364 (463)
                      +.|..|...|++...|..|+.
T Consensus         1 ~~C~~C~~~f~~~~~l~~H~~   21 (26)
T smart00355        1 YRCPECGKVFKSKSALKEHMR   21 (26)
T ss_pred             CCCCCCcchhCCHHHHHHHHH
Confidence            359999999999999999987

---

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	463
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-08

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 55.2 bits (132), Expect = 3e-08
 Identities = 71/464 (15%), Positives = 122/464 (26%), Gaps = 158/464 (34%)

Query: 29  FSEQALRVNYSMDPNFMHNPRDFYTIQREIEKERIRHEIITAENLRRRLLEEEVRRELMM 88
           F E+ LR+NY     F+                 I+ E     ++  R+  E+  R    
Sbjct: 82  FVEEVLRINY----KFL--------------MSPIKTEQR-QPSMMTRMYIEQRDR---- 118

Query: 89  EREMARASEMGLSMDERLSMQLH-SRYPLMHQLNNRWLEDRFPFPGSR----GM-GFGHD 142
                      L  D ++  + + SR     +L    LE R   P       G+ G G  
Sbjct: 119 -----------LYNDNQVFAKYNVSRLQPYLKLRQALLELR---PAKNVLIDGVLGSGKT 164

Query: 143 VLPPTL-----PQFSDAMKDEIR--NALEVNKKDKLI-----MLAKPDPNLCGSKRKAST 190
            +   L      +    M  +I   N    N  + ++     +L + DPN       +S 
Sbjct: 165 WV--ALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSN 222

Query: 191 PPAASVELP-----LMSSKKTKEWSCALCQVSATSERGLDEHLQGKKH-KAKEAGLLRAQ 244
                  +      L+ SK  +   C L  V       L  ++Q  K   A         
Sbjct: 223 IKLRIHSIQAELRRLLKSKPYEN--CLL--V-------LL-NVQNAKAWNAFNLS----- 265

Query: 245 KMCNNSISSMSKKSGKKIKLRESKDSSGQEMKTDVEEESTEVNKAVVGSERKAEVVEDSE 304
             C             KI L  ++                 V   +  +      ++   
Sbjct: 266 --C-------------KI-LLTTRFKQ--------------VTDFLSAATTTHISLDHHS 295

Query: 305 IKNEGLPK---KDLTAK-TRKKKNGIPTAEKTKRKPPLRKKFKFWCEDCQVGTHSAVVME 360
                L     K L  K    +   +P   +     P                   + + 
Sbjct: 296 ---MTLTPDEVKSLLLKYLDCRPQDLP--REVLTTNPR-----------------RLSII 333

Query: 361 GHKRGKKHIARSNESKK-NDDAVPATSSMTI-VAPPDPTEKA--------EDEDVVAEEP 410
             +  +  +A  +  K  N D +      ++ V  P    K             +    P
Sbjct: 334 A-ESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHI----P 388

Query: 411 NEKTTGCV---TEKDEDEEVVAKKAKKEMAENVTGDSNGTRPSI 451
                  +     K +   VV K  K  + E        +  SI
Sbjct: 389 -TILLSLIWFDVIKSDVMVVVNKLHKYSLVE---KQPKESTISI 428

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	463
1zu1_A	127	DSRBP-ZFA, RNA binding protein ZFA; zinc finger pr	99.49
1zu1_A	127	DSRBP-ZFA, RNA binding protein ZFA; zinc finger pr	97.94
3cw1_L	77	U1 small nuclear ribonucleoprotein C; PRE-mRNA spl	96.67
1zr9_A	124	Zinc finger protein 593; DNA binding, structural g	96.61
1zr9_A	124	Zinc finger protein 593; DNA binding, structural g	96.48
3cw1_L	77	U1 small nuclear ribonucleoprotein C; PRE-mRNA spl	95.4
4dgw_A	402	PRE-mRNA-splicing factor PRP9; zinc finger; 3.11A	93.92
2yrk_A	55	Zinc finger homeobox protein 4; structure genomics	91.58
3eph_A	409	TRNA isopentenyltransferase; transferase, alternat	91.37
3eph_A	409	TRNA isopentenyltransferase; transferase, alternat	90.36
2d9h_A	78	Zinc finger protein 692; ZF-C2H2 domain, structura	89.4
4dgw_A	402	PRE-mRNA-splicing factor PRP9; zinc finger; 3.11A	89.07
2gqj_A	98	Zinc finger protein KIAA1196; ZF-C2H2 like domain,	87.1
4f9c_B	144	Protein DBF4 homolog A; Ser/Thr protein kinase, tr	85.6
1fu9_A	36	U-shaped transcriptional cofactor; zinc-finger, be	85.49
2yrk_A	55	Zinc finger homeobox protein 4; structure genomics	82.53
1znf_A	27	31ST zinc finger from XFIN; zinc finger DNA bindin	81.25
1ard_A	29	Yeast transcription factor ADR1; transcription reg	80.58
2kvh_A	27	Zinc finger and BTB domain-containing protein 32;	80.48

>1zu1_A DSRBP-ZFA, RNA binding protein ZFA; zinc finger protein, helix-loop-helix, helix-turn-helix; NMR {Xenopus laevis} SCOP: g.37.1.4 g.37.1.4

Probab=99.49  E-value=3.8e-14  Score=124.34  Aligned_cols=98  Identities=22%  Similarity=0.269  Sum_probs=69.0

Q ss_pred             cCCCceeccccccccCCHHHHHHhhcccchHHHHHHHHHHhhhhcCCCcccccccccchhhccccCCCCccccccccccc
Q 012461          204 KKTKEWSCALCQVSATSERGLDEHLQGKKHKAKEAGLLRAQKMCNNSISSMSKKSGKKIKLRESKDSSGQEMKTDVEEES  283 (463)
Q Consensus       204 k~~k~w~C~LC~Vt~tSe~~L~~HLqGKrHKkk~e~L~~a~~~~k~~~as~s~ks~~~tk~~~s~~ts~~e~~~~~~~es  283 (463)
                      ...+.|+|.+|+|+|+|+.++..|++||+|++++..+... . ...  .+++.+                         .
T Consensus        28 ~~~~~~~C~~C~v~~~S~s~~~~H~~gkkH~~~v~~~~~~-~-~~~--~~~~~~-------------------------~   78 (127)
T 1zu1_A           28 HIFSDTQCKVCSAVLISESQKLAHYQSRKHANKVRRYMAI-N-QGE--DSVPAK-------------------------K   78 (127)
T ss_dssp             TTBCSSEETTTTEECCSHHHHHHHHHCHHHHHHHHHHHHH-T-TCC--CCCSCC-------------------------C
T ss_pred             ccCCCCcCcCCCCEeCCHHHHHHHHCcHHHHHHHHHHhcc-c-Ccc--cCCCCC-------------------------c
Confidence            3446799999999999999999999999999999875432 1 000  000000                         0


Q ss_pred             ccccccccCcccchhhhhhhhhhccCCCcchhhhhhhcccCCCcccccccCCCccccCCceeccccccccCCHHHHHHhh
Q 012461          284 TEVNKAVVGSERKAEVVEDSEIKNEGLPKKDLTAKTRKKKNGIPTAEKTKRKPPLRKKFKFWCEDCQVGTHSAVVMEGHK  363 (463)
Q Consensus       284 l~~~~~~~~s~kK~~~~e~~~~kn~~~~~q~~~~~E~~~k~v~~~~~kg~r~~~~k~~~~~~C~lCnV~ctS~~~~~sHL  363 (463)
                      +..      ++.                       +                ........|+|.+|++.|+|+.+|.+|+
T Consensus        79 ~~~------~~~-----------------------~----------------~~~~~~~~~~C~~C~~~f~s~~~~~~H~  113 (127)
T 1zu1_A           79 FKA------APA-----------------------E----------------ISDGEDRSKCCPVCNMTFSSPVVAESHY  113 (127)
T ss_dssp             CSC------CSS-----------------------C----------------CSSCCCTTTEETTTTEECSSHHHHHHHH
T ss_pred             cCC------Ccc-----------------------c----------------cccCCCCCeEcCCCCCEeCCHHHHHHHH
Confidence            000      000                       0                0001246789999999999999999999


Q ss_pred             hhhhHHHHHHhh
Q 012461          364 RGKKHIARSNES  375 (463)
Q Consensus       364 ~GkKH~aklk~~  375 (463)
                      +||+|++++++.
T Consensus       114 ~gk~H~~~~~~~  125 (127)
T 1zu1_A          114 IGKTHIKNLRLR  125 (127)
T ss_dssp             TSHHHHHHHHHH
T ss_pred             CCHHHHHHHHHh
Confidence            999999999876

>1zu1_A DSRBP-ZFA, RNA binding protein ZFA; zinc finger protein, helix-loop-helix, helix-turn-helix; NMR {Xenopus laevis} SCOP: g.37.1.4 g.37.1.4

Probab=97.94  E-value=3.7e-06  Score=73.53  Aligned_cols=37  Identities=19%  Similarity=0.309  Sum_probs=33.9

Q ss_pred             cCCCceeccccccccCCHHHHHHhhcccchHHHHHHH
Q 012461          204 KKTKEWSCALCQVSATSERGLDEHLQGKKHKAKEAGL  240 (463)
Q Consensus       204 k~~k~w~C~LC~Vt~tSe~~L~~HLqGKrHKkk~e~L  240 (463)
                      .....++|.||++.|+|+.+|++|+.||+|++++..+
T Consensus        89 ~~~~~~~C~~C~~~f~s~~~~~~H~~gk~H~~~~~~~  125 (127)
T 1zu1_A           89 GEDRSKCCPVCNMTFSSPVVAESHYIGKTHIKNLRLR  125 (127)
T ss_dssp             CCCTTTEETTTTEECSSHHHHHHHHTSHHHHHHHHHH
T ss_pred             CCCCCeEcCCCCCEeCCHHHHHHHHCCHHHHHHHHHh
Confidence            4567899999999999999999999999999998874

>3cw1_L U1 small nuclear ribonucleoprotein C; PRE-mRNA splicing, spliceosome, RNA-binding domain, SM fold, finger, RNA recognition motif, 5' splice site; 5.49A {Homo sapiens} PDB: 1uw2_A 2vrd_A

Probab=96.67  E-value=0.00094  Score=54.74  Aligned_cols=33  Identities=30%  Similarity=0.574  Sum_probs=29.6

Q ss_pred             ceecccccccc--CCHHHHHHhhhhhhHHHHHHhh
Q 012461          343 KFWCEDCQVGT--HSAVVMEGHKRGKKHIARSNES  375 (463)
Q Consensus       343 ~~~C~lCnV~c--tS~~~~~sHL~GkKH~aklk~~  375 (463)
                      .|||+.|++.+  .|..+...|++|+||+.+++..
T Consensus         3 kYyCdYCd~~lt~Ds~s~Rk~H~~G~kH~~nv~~y   37 (77)
T 3cw1_L            3 KFYCDYCDTYLTHDSPSVRKTHCSGRKHKENVKDY   37 (77)
T ss_pred             CcccccCCceecCCCHHHHHHHHccHHHHHHHHHH
Confidence            58999999998  5688899999999999998776

>1zr9_A Zinc finger protein 593; DNA binding, structural genomics, PSI, protein structure initiative, center for eukaryotic structural genomics, CESG; NMR {Homo sapiens} SCOP: g.37.1.4

Probab=96.61  E-value=0.0011  Score=58.69  Aligned_cols=36  Identities=19%  Similarity=0.178  Sum_probs=33.8

Q ss_pred             CceeccccccccCCHHHHHHhhhhhhHHHHHHhhhc
Q 012461          342 FKFWCEDCQVGTHSAVVMEGHKRGKKHIARSNESKK  377 (463)
Q Consensus       342 ~~~~C~lCnV~ctS~~~~~sHL~GkKH~aklk~~~~  377 (463)
                      ..|+|..|+..|.+...|..|+++|+|+++++.+..
T Consensus        49 kpfyC~~C~K~F~~~~~L~~H~rsK~HKrrvk~l~~   84 (124)
T 1zr9_A           49 GLHRCLACARYFIDSTNLKTHFRSKDHKKRLKQLSV   84 (124)
T ss_dssp             GCSEETTTTEECSSHHHHHHHTTCHHHHHHHHHHTS
T ss_pred             cceEcccCcchhCCHHHHHHHHhhhhhhHHHHHhcc
Confidence            579999999999999999999999999999999864

>1zr9_A Zinc finger protein 593; DNA binding, structural genomics, PSI, protein structure initiative, center for eukaryotic structural genomics, CESG; NMR {Homo sapiens} SCOP: g.37.1.4

Probab=96.48  E-value=0.0012  Score=58.33  Aligned_cols=34  Identities=24%  Similarity=0.383  Sum_probs=32.3

Q ss_pred             CceeccccccccCCHHHHHHhhcccchHHHHHHH
Q 012461          207 KEWSCALCQVSATSERGLDEHLQGKKHKAKEAGL  240 (463)
Q Consensus       207 k~w~C~LC~Vt~tSe~~L~~HLqGKrHKkk~e~L  240 (463)
                      +.++|.+|...|.+...|+.|+++|+|+.++..|
T Consensus        49 kpfyC~~C~K~F~~~~~L~~H~rsK~HKrrvk~l   82 (124)
T 1zr9_A           49 GLHRCLACARYFIDSTNLKTHFRSKDHKKRLKQL   82 (124)
T ss_dssp             GCSEETTTTEECSSHHHHHHHTTCHHHHHHHHHH
T ss_pred             cceEcccCcchhCCHHHHHHHHhhhhhhHHHHHh
Confidence            4799999999999999999999999999999985

>3cw1_L U1 small nuclear ribonucleoprotein C; PRE-mRNA splicing, spliceosome, RNA-binding domain, SM fold, finger, RNA recognition motif, 5' splice site; 5.49A {Homo sapiens} PDB: 1uw2_A 2vrd_A

Probab=95.40  E-value=0.0066  Score=49.75  Aligned_cols=36  Identities=22%  Similarity=0.392  Sum_probs=31.3

Q ss_pred             ceecccccccc--CCHHHHHHhhcccchHHHHHHHHHH
Q 012461          208 EWSCALCQVSA--TSERGLDEHLQGKKHKAKEAGLLRA  243 (463)
Q Consensus       208 ~w~C~LC~Vt~--tSe~~L~~HLqGKrHKkk~e~L~~a  243 (463)
                      .++|+.|++..  +|..+-..|++|++|+.+++.....
T Consensus         3 kYyCdYCd~~lt~Ds~s~Rk~H~~G~kH~~nv~~yy~~   40 (77)
T 3cw1_L            3 KFYCDYCDTYLTHDSPSVRKTHCSGRKHKENVKDYYCK   40 (77)
T ss_pred             CcccccCCceecCCCHHHHHHHHccHHHHHHHHHHHHH
Confidence            58999999998  7788899999999999999875443

>4dgw_A PRE-mRNA-splicing factor PRP9; zinc finger; 3.11A {Saccharomyces cerevisiae}

Probab=93.92  E-value=0.026  Score=58.44  Aligned_cols=35  Identities=23%  Similarity=0.354  Sum_probs=31.3

Q ss_pred             CCceeccccccccCCHHHHHHhhhhhhHHHHHHhh
Q 012461          341 KFKFWCEDCQVGTHSAVVMEGHKRGKKHIARSNES  375 (463)
Q Consensus       341 ~~~~~C~lCnV~ctS~~~~~sHL~GkKH~aklk~~  375 (463)
                      ...+||..|+..|.++.+|..||.||||.+.+.+.
T Consensus       290 ~~~l~C~~c~K~Fs~~~v~~~hL~GKkh~K~~~~~  324 (402)
T 4dgw_A          290 AKGIYCPFCSRWFKTSSVFESHLVGKIHKKNESKR  324 (402)
T ss_dssp             TTEECBTTTTBCBSSHHHHHTTSSSHHHHHHHHHS
T ss_pred             CcCeeehhhhhhhccccccHHHhcccccchhHHHH
Confidence            35789999999999999999999999999987553

>2yrk_A Zinc finger homeobox protein 4; structure genomics, ZF-C2H2 domain, ZFH-4, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: g.37.1.4

Probab=91.58  E-value=0.065  Score=41.31  Aligned_cols=35  Identities=23%  Similarity=0.348  Sum_probs=31.8

Q ss_pred             eeccccccccCCHHHHHHhhhhhhHHHHHHhhhcC
Q 012461          344 FWCEDCQVGTHSAVVMEGHKRGKKHIARSNESKKN  378 (463)
Q Consensus       344 ~~C~lCnV~ctS~~~~~sHL~GkKH~aklk~~~~~  378 (463)
                      ..|++|+|.++....+..|+--+.|..+|+.+-..
T Consensus        14 ~eC~lC~vkYs~r~slqDHIFs~qHI~~vk~~v~~   48 (55)
T 2yrk_A           14 PECTLCGVKYSARLSIRDHIFSKQHISKVRETVGS   48 (55)
T ss_dssp             SCCTTTTCCCCSSSCHHHHHTSHHHHHHHHHTTCS
T ss_pred             ccccccCcccccccchhhhhccHHHHHHHHHHHHh
Confidence            47999999999999999999999999999976543

>3eph_A TRNA isopentenyltransferase; transferase, alternative initiation, ATP-binding, cytoplasm, mitochondrion, nucleotide-binding, nucleus; 2.95A {Saccharomyces cerevisiae} PDB: 3epj_A 3epk_A* 3epl_A*

Probab=91.37  E-value=0.071  Score=55.26  Aligned_cols=37  Identities=11%  Similarity=0.238  Sum_probs=32.7

Q ss_pred             Cceecccccc------ccCCHHHHHHhhhhhhHHHHHHhhhcC
Q 012461          342 FKFWCEDCQV------GTHSAVVMEGHKRGKKHIARSNESKKN  378 (463)
Q Consensus       342 ~~~~C~lCnV------~ctS~~~~~sHL~GkKH~aklk~~~~~  378 (463)
                      ..+.|++|+.      .+.++.....|++|++|+++++...+.
T Consensus       359 ~~~~Ce~C~~~~~~~~~~~ge~~W~~H~ksr~Hk~~~~~~~k~  401 (409)
T 3eph_A          359 THYTCNVCRNADGKNVVAIGEKYWKIHLGSRRHKSNLKRNTRQ  401 (409)
T ss_dssp             CEEEEEEEECTTSCEEEEESHHHHHHHHTSHHHHHHHHHHHHH
T ss_pred             cceeCCCCCCCCCCcceEEcHHHHHHHhhhhHHHHHHHHHHHH
Confidence            4578999998      899999999999999999999877543

>3eph_A TRNA isopentenyltransferase; transferase, alternative initiation, ATP-binding, cytoplasm, mitochondrion, nucleotide-binding, nucleus; 2.95A {Saccharomyces cerevisiae} PDB: 3epj_A 3epk_A* 3epl_A*

Probab=90.36  E-value=0.12  Score=53.47  Aligned_cols=36  Identities=25%  Similarity=0.488  Sum_probs=31.4

Q ss_pred             Cceecccccc------ccCCHHHHHHhhcccchHHHHHHHHH
Q 012461          207 KEWSCALCQV------SATSERGLDEHLQGKKHKAKEAGLLR  242 (463)
Q Consensus       207 k~w~C~LC~V------t~tSe~~L~~HLqGKrHKkk~e~L~~  242 (463)
                      +..+|++|+.      ++.++..-+.|+.||+|++++....+
T Consensus       359 ~~~~Ce~C~~~~~~~~~~~ge~~W~~H~ksr~Hk~~~~~~~k  400 (409)
T 3eph_A          359 THYTCNVCRNADGKNVVAIGEKYWKIHLGSRRHKSNLKRNTR  400 (409)
T ss_dssp             CEEEEEEEECTTSCEEEEESHHHHHHHHTSHHHHHHHHHHHH
T ss_pred             cceeCCCCCCCCCCcceEEcHHHHHHHhhhhHHHHHHHHHHH
Confidence            4458999998      89999999999999999999887433

>2d9h_A Zinc finger protein 692; ZF-C2H2 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=89.40  E-value=0.31  Score=36.52  Aligned_cols=23  Identities=17%  Similarity=0.501  Sum_probs=20.2

Q ss_pred             CCceeccccccccCCHHHHHHhh
Q 012461          206 TKEWSCALCQVSATSERGLDEHL  228 (463)
Q Consensus       206 ~k~w~C~LC~Vt~tSe~~L~~HL  228 (463)
                      .+.+.|.+|...|.....|..|+
T Consensus         5 ~k~~~C~~C~k~f~~~~~L~~H~   27 (78)
T 2d9h_A            5 SSGLQCEICGFTCRQKASLNWHQ   27 (78)
T ss_dssp             CCCEECSSSCCEESSHHHHHHHH
T ss_pred             CcCeECCCCCCeeCCHHHHHHHH
Confidence            35789999999999999999886

>4dgw_A PRE-mRNA-splicing factor PRP9; zinc finger; 3.11A {Saccharomyces cerevisiae}

Probab=89.07  E-value=0.17  Score=52.51  Aligned_cols=33  Identities=30%  Similarity=0.498  Sum_probs=30.1

Q ss_pred             CceeccccccccCCHHHHHHhhcccchHHHHHH
Q 012461          207 KEWSCALCQVSATSERGLDEHLQGKKHKAKEAG  239 (463)
Q Consensus       207 k~w~C~LC~Vt~tSe~~L~~HLqGKrHKkk~e~  239 (463)
                      ...+|..|+--|.++.++..||.||+|+++.+.
T Consensus       291 ~~l~C~~c~K~Fs~~~v~~~hL~GKkh~K~~~~  323 (402)
T 4dgw_A          291 KGIYCPFCSRWFKTSSVFESHLVGKIHKKNESK  323 (402)
T ss_dssp             TEECBTTTTBCBSSHHHHHTTSSSHHHHHHHHH
T ss_pred             cCeeehhhhhhhccccccHHHhcccccchhHHH
Confidence            467899999999999999999999999998654

>2gqj_A Zinc finger protein KIAA1196; ZF-C2H2 like domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=87.10  E-value=0.68  Score=36.76  Aligned_cols=23  Identities=30%  Similarity=0.595  Sum_probs=20.7

Q ss_pred             CCceeccccccccC-CHHHHHHhh
Q 012461          206 TKEWSCALCQVSAT-SERGLDEHL  228 (463)
Q Consensus       206 ~k~w~C~LC~Vt~t-Se~~L~~HL  228 (463)
                      .+.+.|.+|...|. ....|..|+
T Consensus        22 ~~~~~C~~C~k~f~~~~~~L~~H~   45 (98)
T 2gqj_A           22 RGEAVCPTCNVVTRKTLVGLKKHM   45 (98)
T ss_dssp             TSCCCCTTTCCCCSSCSHHHHHHH
T ss_pred             CCCcCCCCCCCChhhhHHHHHHHH
Confidence            46789999999999 999999996

>4f9c_B Protein DBF4 homolog A; Ser/Thr protein kinase, transferase, phosphorylation, cell C cell division, mitosis, S phase; HET: 0SX; 2.08A {Homo sapiens} PDB: 4f99_B* 4f9b_B* 4f9a_B*

Probab=85.60  E-value=0.51  Score=42.38  Aligned_cols=30  Identities=27%  Similarity=0.478  Sum_probs=22.6

Q ss_pred             cCCCceeccccccccCCHHHHHHhhcccchHHH
Q 012461          204 KKTKEWSCALCQVSATSERGLDEHLQGKKHKAK  236 (463)
Q Consensus       204 k~~k~w~C~LC~Vt~tSe~~L~~HLqGKrHKkk  236 (463)
                      ...+.-||++|++.+..   |..|+...+|+.=
T Consensus        83 ~~~k~GyCE~C~~~y~~---l~~H~~s~~Hr~f  112 (144)
T 4f9c_B           83 EKKKKGYCECCLQKYED---LETHLLSEQHRNF  112 (144)
T ss_dssp             -----CEETTTTEECSC---HHHHHHSHHHHHH
T ss_pred             ccCCCCCccchhhhhhh---HHHHcCCHHHHHH
Confidence            33456799999999985   8899999999864

>1fu9_A U-shaped transcriptional cofactor; zinc-finger, beta-hairpin + alpha-helix; NMR {Drosophila melanogaster} SCOP: g.37.1.2 PDB: 1jn7_A

Probab=85.49  E-value=0.5  Score=33.60  Aligned_cols=23  Identities=22%  Similarity=0.489  Sum_probs=20.6

Q ss_pred             CCceeccccccccCCHHHHHHhh
Q 012461          341 KFKFWCEDCQVGTHSAVVMEGHK  363 (463)
Q Consensus       341 ~~~~~C~lCnV~ctS~~~~~sHL  363 (463)
                      ...+.|+.|+|+|++-.+|..|.
T Consensus         6 ~~~~~C~~C~IsF~~l~ty~aHK   28 (36)
T 1fu9_A            6 VMKKYCSTCDISFNYVKTYLAHK   28 (36)
T ss_dssp             CCCSEETTTTEECSSHHHHHHHH
T ss_pred             cCcCeeccccceehhhHHHhhhh
Confidence            35678999999999999999995

>2yrk_A Zinc finger homeobox protein 4; structure genomics, ZF-C2H2 domain, ZFH-4, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: g.37.1.4

Probab=82.53  E-value=0.47  Score=36.60  Aligned_cols=31  Identities=26%  Similarity=0.532  Sum_probs=29.3

Q ss_pred             eccccccccCCHHHHHHhhcccchHHHHHHH
Q 012461          210 SCALCQVSATSERGLDEHLQGKKHKAKEAGL  240 (463)
Q Consensus       210 ~C~LC~Vt~tSe~~L~~HLqGKrHKkk~e~L  240 (463)
                      -|.+|.|.++....+++|+--+.|-+++..+
T Consensus        15 eC~lC~vkYs~r~slqDHIFs~qHI~~vk~~   45 (55)
T 2yrk_A           15 ECTLCGVKYSARLSIRDHIFSKQHISKVRET   45 (55)
T ss_dssp             CCTTTTCCCCSSSCHHHHHTSHHHHHHHHHT
T ss_pred             cccccCcccccccchhhhhccHHHHHHHHHH
Confidence            6999999999999999999999999998873

>1znf_A 31ST zinc finger from XFIN; zinc finger DNA binding domain; NMR {Xenopus laevis} SCOP: g.37.1.1

Probab=81.25  E-value=1.1  Score=26.24  Aligned_cols=21  Identities=19%  Similarity=0.458  Sum_probs=19.2

Q ss_pred             eeccccccccCCHHHHHHhhh
Q 012461          344 FWCEDCQVGTHSAVVMEGHKR  364 (463)
Q Consensus       344 ~~C~lCnV~ctS~~~~~sHL~  364 (463)
                      +.|.+|...|.+...|..|++
T Consensus         2 ~~C~~C~k~f~~~~~l~~H~~   22 (27)
T 1znf_A            2 YKCGLCERSFVEKSALSRHQR   22 (27)
T ss_dssp             CBCSSSCCBCSSHHHHHHHGG
T ss_pred             ccCCCCCCcCCCHHHHHHHHH
Confidence            579999999999999999974

>1ard_A Yeast transcription factor ADR1; transcription regulation; NMR {Saccharomyces cerevisiae} SCOP: g.37.1.1 PDB: 1arf_A 1are_A

Probab=80.58  E-value=1.1  Score=26.49  Aligned_cols=22  Identities=27%  Similarity=0.471  Sum_probs=19.8

Q ss_pred             ceeccccccccCCHHHHHHhhh
Q 012461          343 KFWCEDCQVGTHSAVVMEGHKR  364 (463)
Q Consensus       343 ~~~C~lCnV~ctS~~~~~sHL~  364 (463)
                      .+.|.+|...|.....|..|+.
T Consensus         2 ~~~C~~C~~~f~~~~~l~~H~~   23 (29)
T 1ard_A            2 SFVCEVCTRAFARQEHLKRHYR   23 (29)
T ss_dssp             CCBCTTTCCBCSSHHHHHHHHH
T ss_pred             CeECCCCCcccCCHHHHHHHHH
Confidence            3679999999999999999975

>2kvh_A Zinc finger and BTB domain-containing protein 32; protein/DNA, metal-binding, transcription; NMR {Mus musculus}

Probab=80.48  E-value=1.1  Score=26.39  Aligned_cols=22  Identities=27%  Similarity=0.466  Sum_probs=20.0

Q ss_pred             ceeccccccccCCHHHHHHhhh
Q 012461          343 KFWCEDCQVGTHSAVVMEGHKR  364 (463)
Q Consensus       343 ~~~C~lCnV~ctS~~~~~sHL~  364 (463)
                      .+.|.+|...|.....|..|++
T Consensus         3 ~~~C~~C~k~f~~~~~l~~H~~   24 (27)
T 2kvh_A            3 PFSCSLCPQRSRDFSAMTKHLR   24 (27)
T ss_dssp             CEECSSSSCEESSHHHHHHHHH
T ss_pred             CccCCCcChhhCCHHHHHHHHH
Confidence            5789999999999999999974

---

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	463
d1zu1a2	55	dsRNA-binding protein ZFa (ZNF346, JAZ) {African c	98.5
d1zu1a2	55	dsRNA-binding protein ZFa (ZNF346, JAZ) {African c	98.07
d1zr9a1	67	Zinc finger protein 593, ZNF593 {Human (Homo sapie	97.38
d1zr9a1	67	Zinc finger protein 593, ZNF593 {Human (Homo sapie	97.22
d1zu1a1	72	dsRNA-binding protein ZFa (ZNF346, JAZ) {African c	96.11
d1zu1a1	72	dsRNA-binding protein ZFa (ZNF346, JAZ) {African c	95.62
d2vrda1	61	Spliceosomal protein U1C {Human (Homo sapiens) [Ta	94.84
d2vrda1	61	Spliceosomal protein U1C {Human (Homo sapiens) [Ta	93.0
d2yrka1	48	Zinc finger homeobox protein 4, ZFHX4 {Human (Homo	87.97
d1fu9a_	36	U-shaped transcription factor, different fingers {	85.49
d1srka_	35	Zinc finger protein ZFPM1 (FOG-1) {Mouse (Mus musc	83.94
d1bboa2	29	Enhancer binding protein {Human (Homo sapiens) [Ta	83.08
d1bboa2	29	Enhancer binding protein {Human (Homo sapiens) [Ta	82.59

>d1zu1a2 g.37.1.4 (A:74-128) dsRNA-binding protein ZFa (ZNF346, JAZ) {African clawed frog (Xenopus laevis) [TaxId: 8355]}

class: Small proteins
fold: beta-beta-alpha zinc fingers
superfamily: beta-beta-alpha zinc fingers
family: HkH motif-containing C2H2 finger
domain: dsRNA-binding protein ZFa (ZNF346, JAZ)
species: African clawed frog (Xenopus laevis) [TaxId: 8355]

Probab=98.50  E-value=4.6e-08  Score=73.53  Aligned_cols=50  Identities=20%  Similarity=0.309  Sum_probs=39.5

Q ss_pred             CCCCCCCCCCCCCcccccccccCCCceeccccccccCCHHHHHHhhcccchHHHHHH
Q 012461          183 GSKRKASTPPAASVELPLMSSKKTKEWSCALCQVSATSERGLDEHLQGKKHKAKEAG  239 (463)
Q Consensus       183 G~KRKa~~~~~~t~elp~~~kk~~k~w~C~LC~Vt~tSe~~L~~HLqGKrHKkk~e~  239 (463)
                      ++||...+....+.       ..+...+|.||+++|+|+...++||.||.|++++..
T Consensus         3 p~k~~~~~~~~~~~-------~~d~nk~C~lCn~~Fns~~~AqsHY~GK~H~K~lk~   52 (55)
T d1zu1a2           3 PAKKFKAAPAEISD-------GEDRSKCCPVCNMTFSSPVVAESHYIGKTHIKNLRL   52 (55)
T ss_dssp             SCCCCSCCSSCCSS-------CCCTTTEETTTTEECSSHHHHHHHHTSHHHHHHHHH
T ss_pred             CcccccCCcccccC-------CCCchhhhhhhhcccCCHHHHHHHhhhhHHHHHHHH
Confidence            44565555433222       556777999999999999999999999999999875

>d1zu1a2 g.37.1.4 (A:74-128) dsRNA-binding protein ZFa (ZNF346, JAZ) {African clawed frog (Xenopus laevis) [TaxId: 8355]}

class: Small proteins
fold: beta-beta-alpha zinc fingers
superfamily: beta-beta-alpha zinc fingers
family: HkH motif-containing C2H2 finger
domain: dsRNA-binding protein ZFa (ZNF346, JAZ)
species: African clawed frog (Xenopus laevis) [TaxId: 8355]

Probab=98.07  E-value=9.1e-07  Score=66.38  Aligned_cols=33  Identities=33%  Similarity=0.449  Sum_probs=30.7

Q ss_pred             eeccccccccCCHHHHHHhhhhhhHHHHHHhhh
Q 012461          344 FWCEDCQVGTHSAVVMEGHKRGKKHIARSNESK  376 (463)
Q Consensus       344 ~~C~lCnV~ctS~~~~~sHL~GkKH~aklk~~~  376 (463)
                      .+|.|||.+|+|..+..+|..||+|.++|++..
T Consensus        22 k~C~lCn~~Fns~~~AqsHY~GK~H~K~lk~~~   54 (55)
T d1zu1a2          22 KCCPVCNMTFSSPVVAESHYIGKTHIKNLRLRE   54 (55)
T ss_dssp             TEETTTTEECSSHHHHHHHHTSHHHHHHHHHHH
T ss_pred             hhhhhhhcccCCHHHHHHHhhhhHHHHHHHHhc
Confidence            379999999999999999999999999998754

>d1zr9a1 g.37.1.4 (A:28-94) Zinc finger protein 593, ZNF593 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: beta-beta-alpha zinc fingers
superfamily: beta-beta-alpha zinc fingers
family: HkH motif-containing C2H2 finger
domain: Zinc finger protein 593, ZNF593
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.38  E-value=4.2e-05  Score=59.30  Aligned_cols=37  Identities=19%  Similarity=0.181  Sum_probs=34.4

Q ss_pred             CceeccccccccCCHHHHHHhhhhhhHHHHHHhhhcC
Q 012461          342 FKFWCEDCQVGTHSAVVMEGHKRGKKHIARSNESKKN  378 (463)
Q Consensus       342 ~~~~C~lCnV~ctS~~~~~sHL~GkKH~aklk~~~~~  378 (463)
                      ..|+|-.|+..|.|+.+|..|+++|+|+++|+.+...
T Consensus        14 gqfYCv~C~K~F~se~~l~~H~ksKkHKrrvk~L~~~   50 (67)
T d1zr9a1          14 GLHRCLACARYFIDSTNLKTHFRSKDHKKRLKQLSVE   50 (67)
T ss_dssp             GCSEETTTTEECSSHHHHHHHTTCHHHHHHHHHHTSC
T ss_pred             CEEecccccCccCCHHHHHHHHcccHHHHHHHHhccC
Confidence            5699999999999999999999999999999998653

>d1zr9a1 g.37.1.4 (A:28-94) Zinc finger protein 593, ZNF593 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: beta-beta-alpha zinc fingers
superfamily: beta-beta-alpha zinc fingers
family: HkH motif-containing C2H2 finger
domain: Zinc finger protein 593, ZNF593
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.22  E-value=7e-05  Score=58.03  Aligned_cols=33  Identities=24%  Similarity=0.405  Sum_probs=31.8

Q ss_pred             ceeccccccccCCHHHHHHhhcccchHHHHHHH
Q 012461          208 EWSCALCQVSATSERGLDEHLQGKKHKAKEAGL  240 (463)
Q Consensus       208 ~w~C~LC~Vt~tSe~~L~~HLqGKrHKkk~e~L  240 (463)
                      .|||.+|...|.++..|+.|+.+|+||+++..|
T Consensus        15 qfYCv~C~K~F~se~~l~~H~ksKkHKrrvk~L   47 (67)
T d1zr9a1          15 LHRCLACARYFIDSTNLKTHFRSKDHKKRLKQL   47 (67)
T ss_dssp             CSEETTTTEECSSHHHHHHHTTCHHHHHHHHHH
T ss_pred             EEecccccCccCCHHHHHHHHcccHHHHHHHHh
Confidence            599999999999999999999999999999986

>d1zu1a1 g.37.1.4 (A:2-73) dsRNA-binding protein ZFa (ZNF346, JAZ) {African clawed frog (Xenopus laevis) [TaxId: 8355]}

class: Small proteins
fold: beta-beta-alpha zinc fingers
superfamily: beta-beta-alpha zinc fingers
family: HkH motif-containing C2H2 finger
domain: dsRNA-binding protein ZFa (ZNF346, JAZ)
species: African clawed frog (Xenopus laevis) [TaxId: 8355]

Probab=96.11  E-value=0.0012  Score=51.18  Aligned_cols=36  Identities=25%  Similarity=0.391  Sum_probs=32.6

Q ss_pred             CceeccccccccCCHHHHHHhhcccchHHHHHHHHH
Q 012461          207 KEWSCALCQVSATSERGLDEHLQGKKHKAKEAGLLR  242 (463)
Q Consensus       207 k~w~C~LC~Vt~tSe~~L~~HLqGKrHKkk~e~L~~  242 (463)
                      ...+|.||++...|++.-..|++||+|.+|+..+..
T Consensus        31 td~~CkvC~a~L~seSQriaHYeskkHa~kvr~yf~   66 (72)
T d1zu1a1          31 SDTQCKVCSAVLISESQKLAHYQSRKHANKVRRYMA   66 (72)
T ss_dssp             CSSEETTTTEECCSHHHHHHHHHCHHHHHHHHHHHH
T ss_pred             chhhHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            467999999999999999999999999999987543

>d1zu1a1 g.37.1.4 (A:2-73) dsRNA-binding protein ZFa (ZNF346, JAZ) {African clawed frog (Xenopus laevis) [TaxId: 8355]}

class: Small proteins
fold: beta-beta-alpha zinc fingers
superfamily: beta-beta-alpha zinc fingers
family: HkH motif-containing C2H2 finger
domain: dsRNA-binding protein ZFa (ZNF346, JAZ)
species: African clawed frog (Xenopus laevis) [TaxId: 8355]

Probab=95.62  E-value=0.0032  Score=48.74  Aligned_cols=33  Identities=18%  Similarity=0.239  Sum_probs=30.6

Q ss_pred             ceeccccccccCCHHHHHHhhhhhhHHHHHHhh
Q 012461          343 KFWCEDCQVGTHSAVVMEGHKRGKKHIARSNES  375 (463)
Q Consensus       343 ~~~C~lCnV~ctS~~~~~sHL~GkKH~aklk~~  375 (463)
                      ..+|.+|++...|+++-.+|..|+||..+++..
T Consensus        32 d~~CkvC~a~L~seSQriaHYeskkHa~kvr~y   64 (72)
T d1zu1a1          32 DTQCKVCSAVLISESQKLAHYQSRKHANKVRRY   64 (72)
T ss_dssp             SSEETTTTEECCSHHHHHHHHHCHHHHHHHHHH
T ss_pred             hhhHHHhHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            457999999999999999999999999999865

>d2vrda1 g.37.1.4 (A:1-61) Spliceosomal protein U1C {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: beta-beta-alpha zinc fingers
superfamily: beta-beta-alpha zinc fingers
family: HkH motif-containing C2H2 finger
domain: Spliceosomal protein U1C
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.84  E-value=0.0071  Score=45.70  Aligned_cols=35  Identities=29%  Similarity=0.529  Sum_probs=30.3

Q ss_pred             ceeccccccccC--CHHHHHHhhhhhhHHHHHHhhhc
Q 012461          343 KFWCEDCQVGTH--SAVVMEGHKRGKKHIARSNESKK  377 (463)
Q Consensus       343 ~~~C~lCnV~ct--S~~~~~sHL~GkKH~aklk~~~~  377 (463)
                      .++|+-|++.++  |..+=..|++|+||+.+++..=.
T Consensus         3 ryyCdYC~~~lt~ds~s~RK~H~~G~kH~~n~~~yy~   39 (61)
T d2vrda1           3 KFYCDYCDTYLTHDSPSVRKTHCSGRKHKENVKDYYQ   39 (61)
T ss_dssp             SCEETTTTEECSCCSHHHHHHHTCCTHHHHHHHHHTS
T ss_pred             chhhhhhcchhccCChhHHHHHhccHHHHHHHHHHHH
Confidence            589999999995  56777899999999999988754

>d2vrda1 g.37.1.4 (A:1-61) Spliceosomal protein U1C {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: beta-beta-alpha zinc fingers
superfamily: beta-beta-alpha zinc fingers
family: HkH motif-containing C2H2 finger
domain: Spliceosomal protein U1C
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.00  E-value=0.026  Score=42.48  Aligned_cols=32  Identities=28%  Similarity=0.494  Sum_probs=28.3

Q ss_pred             ceeccccccccC--CHHHHHHhhcccchHHHHHH
Q 012461          208 EWSCALCQVSAT--SERGLDEHLQGKKHKAKEAG  239 (463)
Q Consensus       208 ~w~C~LC~Vt~t--Se~~L~~HLqGKrHKkk~e~  239 (463)
                      ..+|+-|++-++  +.++=..|++|++|+.++..
T Consensus         3 ryyCdYC~~~lt~ds~s~RK~H~~G~kH~~n~~~   36 (61)
T d2vrda1           3 KFYCDYCDTYLTHDSPSVRKTHCSGRKHKENVKD   36 (61)
T ss_dssp             SCEETTTTEECSCCSHHHHHHHTCCTHHHHHHHH
T ss_pred             chhhhhhcchhccCChhHHHHHhccHHHHHHHHH
Confidence            579999999994  67777999999999999886

>d2yrka1 g.37.1.4 (A:8-55) Zinc finger homeobox protein 4, ZFHX4 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: beta-beta-alpha zinc fingers
superfamily: beta-beta-alpha zinc fingers
family: HkH motif-containing C2H2 finger
domain: Zinc finger homeobox protein 4, ZFHX4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=87.97  E-value=0.083  Score=37.90  Aligned_cols=34  Identities=24%  Similarity=0.395  Sum_probs=31.1

Q ss_pred             eccccccccCCHHHHHHhhhhhhHHHHHHhhhcC
Q 012461          345 WCEDCQVGTHSAVVMEGHKRGKKHIARSNESKKN  378 (463)
Q Consensus       345 ~C~lCnV~ctS~~~~~sHL~GkKH~aklk~~~~~  378 (463)
                      -|.+|+|..++......|+-.+.|.++|+.+-..
T Consensus         8 eC~lC~vKYs~~~SvrdHiFskqHI~~Vk~~v~~   41 (48)
T d2yrka1           8 ECTLCGVKYSARLSIRDHIFSKQHISKVRETVGS   41 (48)
T ss_dssp             CCTTTTCCCCSSSCHHHHHTSHHHHHHHHHTTCS
T ss_pred             cCcccceeeeeecchHhhhhhHHHHHHHHHHHHh
Confidence            4999999999999999999999999999987543

>d1fu9a_ g.37.1.2 (A:) U-shaped transcription factor, different fingers {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: Small proteins
fold: beta-beta-alpha zinc fingers
superfamily: beta-beta-alpha zinc fingers
family: C2HC finger
domain: U-shaped transcription factor, different fingers
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=85.49  E-value=0.24  Score=33.43  Aligned_cols=22  Identities=23%  Similarity=0.537  Sum_probs=19.8

Q ss_pred             CceeccccccccCCHHHHHHhh
Q 012461          342 FKFWCEDCQVGTHSAVVMEGHK  363 (463)
Q Consensus       342 ~~~~C~lCnV~ctS~~~~~sHL  363 (463)
                      ...+|..|+|.|++-.+|.+|.
T Consensus         7 ~~rYC~~CDI~Fn~~~T~~aHK   28 (36)
T d1fu9a_           7 MKKYCSTCDISFNYVKTYLAHK   28 (36)
T ss_dssp             CCSEETTTTEECSSHHHHHHHH
T ss_pred             hhhHHhhCCceehhHHHHHHHH
Confidence            4568999999999999999995

>d1srka_ g.37.1.1 (A:) Zinc finger protein ZFPM1 (FOG-1) {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: beta-beta-alpha zinc fingers
superfamily: beta-beta-alpha zinc fingers
family: Classic zinc finger, C2H2
domain: Zinc finger protein ZFPM1 (FOG-1)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=83.94  E-value=0.31  Score=32.46  Aligned_cols=23  Identities=17%  Similarity=0.281  Sum_probs=21.2

Q ss_pred             CceeccccccccCCHHHHHHhhh
Q 012461          342 FKFWCEDCQVGTHSAVVMEGHKR  364 (463)
Q Consensus       342 ~~~~C~lCnV~ctS~~~~~sHL~  364 (463)
                      ..|.|.+|+..|+....|..|++
T Consensus         6 kPy~C~~C~k~F~~~~~L~~H~r   28 (35)
T d1srka_           6 RPFVCRICLSAFTTKANCARHLK   28 (35)
T ss_dssp             SCEECSSSCCEESSHHHHHHHHG
T ss_pred             ccccCCCCCCcccChHHHHHHcc
Confidence            56889999999999999999984

>d1bboa2 g.37.1.1 (A:29-57) Enhancer binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: beta-beta-alpha zinc fingers
superfamily: beta-beta-alpha zinc fingers
family: Classic zinc finger, C2H2
domain: Enhancer binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=83.08  E-value=0.1  Score=33.57  Aligned_cols=28  Identities=18%  Similarity=0.417  Sum_probs=25.1

Q ss_pred             ceeccccccccCCHHHHHHhhhhhhHHH
Q 012461          343 KFWCEDCQVGTHSAVVMEGHKRGKKHIA  370 (463)
Q Consensus       343 ~~~C~lCnV~ctS~~~~~sHL~GkKH~a  370 (463)
                      .+.|..||-.|-....|.-|+..|-|.+
T Consensus         1 py~C~~CnF~FKTKGNLTKHmkSKaH~k   28 (29)
T d1bboa2           1 PYHCTYCNFSFKTKGNLTKHMKSKAHSK   28 (29)
T ss_dssp             CEECSSSSCEESSHHHHHHHHHSSSSCC
T ss_pred             CcccceeeeeEeeccchhHhhhhhhhcc
Confidence            3789999999999999999999998853

>d1bboa2 g.37.1.1 (A:29-57) Enhancer binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: beta-beta-alpha zinc fingers
superfamily: beta-beta-alpha zinc fingers
family: Classic zinc finger, C2H2
domain: Enhancer binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=82.59  E-value=0.13  Score=33.09  Aligned_cols=27  Identities=26%  Similarity=0.677  Sum_probs=25.2

Q ss_pred             eeccccccccCCHHHHHHhhcccchHH
Q 012461          209 WSCALCQVSATSERGLDEHLQGKKHKA  235 (463)
Q Consensus       209 w~C~LC~Vt~tSe~~L~~HLqGKrHKk  235 (463)
                      +.|.-|+.+|.....|-.|+..|-|.+
T Consensus         2 y~C~~CnF~FKTKGNLTKHmkSKaH~k   28 (29)
T d1bboa2           2 YHCTYCNFSFKTKGNLTKHMKSKAHSK   28 (29)
T ss_dssp             EECSSSSCEESSHHHHHHHHHSSSSCC
T ss_pred             cccceeeeeEeeccchhHhhhhhhhcc
Confidence            689999999999999999999999964