Psyllid ID: psy8340

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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---
Protein Sequence
SVLRINAWKEEALYTLKDPTNLLAIQKFFSKGEGIEITMSQSQEDINSQNQMQEKLAPKYIFKNPEYEQRKLSRRSTSSNLPTKQWKSLKQILSYEKNIPWPEDTIHYSSIVAPPSFKPSLKYSDISRFECNYKDPQTKLYYYNIEEYKLIRKLPSDIVNGYLALRGALNPLA
Secondary Structure (PSIPRED)
cccEEccccHHHHccccccccHHHccccccccccHHHccccccccccHHHHHHHHccccccccccHHHHHHHccccccccccccccccHHHHHHHHHccccccccccEEcccccccccccccccccccccccccccccccccccHHHHHHHHcccHHHHHHHHHHHccccccc
Secondary Structure Prediction (SSPRO)
cEEEEcHHHHHHHHHcccHHHHHHHHHHHHccccEEEEcccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHcccccccccccEEEEcccccccccccEcccccccccccccccccEEccHHHHHHHccccccHHHHHHHHHccccccc
Coil and Loop (DISEMBL)
SVLRINAWKEEALytlkdptnLLAIQKFFSKGEGIEITMSQSQEDINSQNqmqeklapkyifknpeyeqrklsrrstssnlptkqWKSLKQILSYeknipwpedtihyssivappsfkpslkysdisrfecnykdpqtklyyyNIEEYKLIRKLPSDIVNGYLALRGALNPLA
Flexible Loop (DISEMBL)
svlrinawkeealytlkdptnlLAIQKFFSKGEGIEITMSQSQEDINSQNQMQEKLAPKYIFKNPEYEqrklsrrstssnlptkqwkslKQILSYEKNIPWPEDTIHYSSIVAPPSFKPSLKYSDISRFECNYKDPQTKLYYYNIEEYKLIRKLPSDIVNGYLALRGALNPLA
Low Complexity Region (SEG)
SVLRINAWKEEALYTLKDPTNLLAIQKFFSKGEGIEITMSQSQEDINSQNQMQEKLAPKYIFKNPEYEQRKLSRRSTSSNLPTKQWKSLKQILSYEKNIPWPEDTIHYSSIVAPPSFKPSLKYSDISRFECNYKDPQTKLYYYNIEEYKLIRKLPSDIVNGYLALRGALNPLA
Disordered region (IsUnstruct)
***RINAWKEEALYTLKDPTNLLAIQKFFSKGEGI**************************************************WKSLKQILSYEKNIPWPEDTIHYSSIVAPPSFKPSLKYSDISRFECNYKDPQTKLYYYNIEEYKLIRKLPSDIVNGYLALRGA*****
Disordered Region (DISOPRED)
*VLR**AWKEEA***************************************************************************SLK*IL***********TIHYSSIVAPPSFKPSLKYSDISRFECNYKDPQTKLYYYNIEEYKLIRKLPSDIVNGYLALRGAL****
Disordered Region (DISEMBL)
SVLRINAWKEEALYTLKDPTNLLAIQKFFSKGEGIEITMSQSQEDINSQNQMQEKLAPKYIFKNPEYE****************QWKSLKQILSYEKNIPWPEDTIHYSSIVAPPSFKPSLKYSDISRFECNYKDPQTKLYYYNIEEYKLIRKLPSDIVNGYLALRGALNPLA
Disordered Region (DISPRO)
SVLRINAWKEEALYTLKDPTNLLAIQKFFSKGEGIEITM********************************************KQWKSLKQILSYEKNIPWPEDTIHYSSIVAPPSFKPSLKYSDISRFECNYKDPQTKLYYYNIEEYKLIRKLPSDIVNGYLALRGAL****
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
SVLRINAWKEEALYTLKDPTNLLAIQKFFSKGEGIEITMSQSQEDINSQNQMQEKLAPKYIFKNPEYEQRKLSRRSTSSNLPTKQWKSLKQILSYEKNIPWPEDTIHYSSIVAPPSFKPSLKYSDISRFECNYKDPQTKLYYYNIEEYKLIRKLPSDIVNGYLALRGALNPLA
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

No hits with e-value below 0.001 by BLAST

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Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	173
MGI|MGI:2443014	191	Ino80c "INO80 complex subunit	0.797	0.722	0.421	8.7e-24
RGD|1310199	191	Ino80c "INO80 complex subunit	0.791	0.717	0.425	1.8e-23
UNIPROTKB|Q6PI98	192	INO80C "INO80 complex subunit	0.797	0.718	0.414	3.8e-23
ZFIN|ZDB-GENE-040625-97	210	ino80c "INO80 complex subunit	0.757	0.623	0.388	1.1e-21
CGD|CAL0005227	145	orf19.2889 [Candida albicans (	0.716	0.855	0.340	2.3e-14
UNIPROTKB|Q5A1D0	145	CaO19.10407 "Putative uncharac	0.716	0.855	0.340	2.3e-14
TAIR|locus:1005716392	124	AT4G38495 "AT4G38495" [Arabido	0.612	0.854	0.391	3.4e-13
SGD|S000000770	166	IES6 "Protein that associates	0.352	0.367	0.419	1.5e-11
POMBASE|SPAC222.04c	117	ies6 "Ino80 complex subunit Ie	0.531	0.786	0.385	1.2e-10
UNIPROTKB|G4N5J7	195	MGG_06129 "Uncharacterized pro	0.554	0.492	0.356	4.7e-09

MGI|MGI:2443014 Ino80c "INO80 complex subunit C" [Mus musculus (taxid:10090)]

 Score = 273 (101.2 bits), Expect = 8.7e-24, P = 8.7e-24
 Identities = 59/140 (42%), Positives = 79/140 (56%)

Query:    29 FSKGEGIEITMSQSQEDINSQNQMQEKLAPKYIFKNPEYEQRKLSRRSTSSNLPTKQWKS 88
             F++G  IE             +   EK A    FK+P +           +    + WK+
Sbjct:    49 FAQGVSIEAMNESKMASSELSSGPVEKAAKPLPFKDPNFVHS--GHGGAVAGKKNRTWKN 106

Query:    89 LKQILSYEKNIPWPEDTIHYSSIVAPPSFKPSLKYSDISRFECNYKDPQTKLYYYNIEEY 148
             LKQIL+ E+ +PW  +  +Y SI APPSFKP+ KYSDIS    NY DPQ+KL +  +EE+
Sbjct:   107 LKQILAAERALPWQLNDPNYFSIDAPPSFKPAKKYSDISGLLANYTDPQSKLRFSTVEEF 166

Query:   149 KLIRKLPSDIVNGYLALRGA 168
               IR+LPSD+V GYLALR A
Sbjct:   167 SYIRRLPSDVVTGYLALRKA 186

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=IEA

GO:0006281 "DNA repair" evidence=IEA

GO:0006310 "DNA recombination" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0006974 "response to DNA damage stimulus" evidence=IEA

GO:0008150 "biological_process" evidence=ND

GO:0031011 "Ino80 complex" evidence=ISO

GO:0071339 "MLL1 complex" evidence=ISO

RGD|1310199 Ino80c "INO80 complex subunit C" [Rattus norvegicus (taxid:10116)]

 Score = 270 (100.1 bits), Expect = 1.8e-23, P = 1.8e-23
 Identities = 60/141 (42%), Positives = 84/141 (59%)

Query:    29 FSKGEGIEITMSQSQEDINSQNQMQ-EKLAPKYIFKNPEYEQRKLSRRSTSSNLPTKQWK 87
             F++G  IE  MS+S+   +  +    EK A    FK+P +           +    + WK
Sbjct:    49 FAQGVSIE-AMSESKMASSELSSGPVEKAAKPLPFKDPNFVHS--GHGGAVAGKKNRTWK 105

Query:    88 SLKQILSYEKNIPWPEDTIHYSSIVAPPSFKPSLKYSDISRFECNYKDPQTKLYYYNIEE 147
             +LKQIL+ E+ +PW  +  +Y SI APPSFKP+ KYSD+S    NY DPQ+KL +  +EE
Sbjct:   106 NLKQILAAERALPWQLNDPNYFSIDAPPSFKPAKKYSDVSGLLANYTDPQSKLRFSTVEE 165

Query:   148 YKLIRKLPSDIVNGYLALRGA 168
             +  IR+LPSD+V GYL LR A
Sbjct:   166 FSYIRRLPSDVVTGYLTLRKA 186

GO:0003674 "molecular_function" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0005730 "nucleolus" evidence=ISO

GO:0006281 "DNA repair" evidence=IEA

GO:0006310 "DNA recombination" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0008150 "biological_process" evidence=ND

GO:0031011 "Ino80 complex" evidence=ISO

GO:0071339 "MLL1 complex" evidence=ISO;ISS

UNIPROTKB|Q6PI98 INO80C "INO80 complex subunit C" [Homo sapiens (taxid:9606)]

 Score = 267 (99.0 bits), Expect = 3.8e-23, P = 3.8e-23
 Identities = 58/140 (41%), Positives = 78/140 (55%)

Query:    29 FSKGEGIEITMSQSQEDINSQNQMQEKLAPKYIFKNPEYEQRKLSRRSTSSNLPTKQWKS 88
             F++G  +E                 EK A    FK+P +           +    + WK+
Sbjct:    50 FAQGISMEAMSENKMVPSEFSTGPVEKAAKPLPFKDPNFVHS--GHGGAVAGKKNRTWKN 107

Query:    89 LKQILSYEKNIPWPEDTIHYSSIVAPPSFKPSLKYSDISRFECNYKDPQTKLYYYNIEEY 148
             LKQIL+ E+ +PW  +  +Y SI APPSFKP+ KYSD+S    NY DPQ+KL +  IEE+
Sbjct:   108 LKQILASERALPWQLNDPNYFSIDAPPSFKPAKKYSDVSGLLANYTDPQSKLRFSTIEEF 167

Query:   149 KLIRKLPSDIVNGYLALRGA 168
               IR+LPSD+V GYLALR A
Sbjct:   168 SYIRRLPSDVVTGYLALRKA 187

GO:0006281 "DNA repair" evidence=IEA

GO:0006310 "DNA recombination" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0003674 "molecular_function" evidence=ND

GO:0008150 "biological_process" evidence=ND

GO:0071339 "MLL1 complex" evidence=IDA

GO:0031011 "Ino80 complex" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

ZFIN|ZDB-GENE-040625-97 ino80c "INO80 complex subunit C" [Danio rerio (taxid:7955)]

 Score = 253 (94.1 bits), Expect = 1.1e-21, P = 1.1e-21
 Identities = 52/134 (38%), Positives = 79/134 (58%)

Query:    36 EITMSQSQEDINSQNQMQEKLAPKYI-FKNPEYEQRKLSRRSTSSNLPTKQWKSLKQILS 94
             ++   +   ++     +  + A K + FKNP++    +     ++    + WK+LKQIL+
Sbjct:    74 QVAPVEGTSEVKPVGSVDVETATKSLPFKNPDFVHSGIG--GAAAGKKNRTWKNLKQILA 131

Query:    95 YEKNIPWPEDTIHYSSIVAPPSFKPSLKYSDISRFECNYKDPQTKLYYYNIEEYKLIRKL 154
              EK + W  +  +Y +I APPS KP+ KYSDIS    NY DPQTKL + + EE+  IR+L
Sbjct:   132 AEKALLWKINDPNYCNIDAPPSMKPAKKYSDISGLPANYTDPQTKLRFASTEEFSYIRQL 191

Query:   155 PSDIVNGYLALRGA 168
             P+D+V GYL LR A
Sbjct:   192 PTDVVTGYLTLRKA 205

GO:0005575 "cellular_component" evidence=ND

GO:0003674 "molecular_function" evidence=ND

GO:0008150 "biological_process" evidence=ND

CGD|CAL0005227 orf19.2889 [Candida albicans (taxid:5476)]

 Score = 184 (69.8 bits), Expect = 2.3e-14, P = 2.3e-14
 Identities = 45/132 (34%), Positives = 76/132 (57%)

Query:    38 TMSQSQEDINSQNQMQEKLAPKYIFKNPEYEQRKLSRRSTSSNLPTKQWKSLKQILSYEK 97
             T + +Q +++  +++  K  P    +NP  +Q+   R   S  L + +   LK + S + 
Sbjct:    16 TTTTTQVNLHELSEITTK--PHSFKQNPNRKQQSNRRYKPSRQLISDE---LKYLQSKQS 70

Query:    98 NIPWPEDTIHYSSIVAPPSFKPSLKYSDISRFECNYKDPQTKLYYYNIEEYK-LIRKLPS 156
             N+ +  DT  Y+SI++PPS KP++KY DI+    NYK P  +L +YN E Y+ +I+ +P+
Sbjct:    71 NLKF--DTPTYNSIMSPPSLKPTMKYCDITGLPTNYKCPSNQLRFYNSEIYQEVIKNMPA 128

Query:   157 DIVNGYLALRGA 168
              +   YL LRGA
Sbjct:   129 GVDQEYLQLRGA 140

GO:0003674 "molecular_function" evidence=ND

GO:0031011 "Ino80 complex" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0006338 "chromatin remodeling" evidence=IEA

UNIPROTKB|Q5A1D0 CaO19.10407 "Putative uncharacterized protein" [Candida albicans SC5314 (taxid:237561)]

 Score = 184 (69.8 bits), Expect = 2.3e-14, P = 2.3e-14
 Identities = 45/132 (34%), Positives = 76/132 (57%)

Query:    38 TMSQSQEDINSQNQMQEKLAPKYIFKNPEYEQRKLSRRSTSSNLPTKQWKSLKQILSYEK 97
             T + +Q +++  +++  K  P    +NP  +Q+   R   S  L + +   LK + S + 
Sbjct:    16 TTTTTQVNLHELSEITTK--PHSFKQNPNRKQQSNRRYKPSRQLISDE---LKYLQSKQS 70

Query:    98 NIPWPEDTIHYSSIVAPPSFKPSLKYSDISRFECNYKDPQTKLYYYNIEEYK-LIRKLPS 156
             N+ +  DT  Y+SI++PPS KP++KY DI+    NYK P  +L +YN E Y+ +I+ +P+
Sbjct:    71 NLKF--DTPTYNSIMSPPSLKPTMKYCDITGLPTNYKCPSNQLRFYNSEIYQEVIKNMPA 128

Query:   157 DIVNGYLALRGA 168
              +   YL LRGA
Sbjct:   129 GVDQEYLQLRGA 140

GO:0003674 "molecular_function" evidence=ND

TAIR|locus:1005716392 AT4G38495 "AT4G38495" [Arabidopsis thaliana (taxid:3702)]

 Score = 173 (66.0 bits), Expect = 3.4e-13, P = 3.4e-13
 Identities = 45/115 (39%), Positives = 65/115 (56%)

Query:    56 LAPKYIFKNPE-YEQRKLSRRSTSSNLPTKQWKSLKQILSYEKNIP-WPEDTIHYSSIVA 113
             +A +  FK  + YE  K  +  +SS    ++WK LKQIL  E N P  P D   Y +I +
Sbjct:    12 VASRLSFKKKQAYE--KYPKAQSSS----RRWKHLKQILQAE-NFPDLPPDLPTYVNIES 64

Query:   114 PPSFKPSLKYSDISRFECNYKDPQTKLYYYNIEEYKLIRKLPSDIVNGYLALRGA 168
             PPS +P  +  DI+ +E  Y DP+T L Y N   ++ +R L SD V+ YL++R A
Sbjct:    65 PPSTQPCKRLCDITGYEAPYVDPRTNLRYANAHVFQTVRSLSSDQVHQYLSIRNA 119

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

SGD|S000000770 IES6 "Protein that associates with the INO80 chromatin remodeling complex" [Saccharomyces cerevisiae (taxid:4932)]

 Score = 123 (48.4 bits), Expect = 1.5e-11, Sum P(2) = 1.5e-11
 Identities = 26/62 (41%), Positives = 37/62 (59%)

Query:   108 YSSIVAPPSFKPSLKYSDISRFECNYKDPQTKLYYYNIEEYKLIRK-LPSDIVNGYLALR 166
             Y S+ APPS +P+ KY D++  +  YK P   + Y+N E Y+LI K +   +   YL LR
Sbjct:   100 YFSVEAPPSIRPAKKYCDVTGLKGFYKSPTNNIRYHNAEIYQLIVKPMAPGVDQEYLKLR 159

Query:   167 GA 168
             GA
Sbjct:   160 GA 161

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0005634 "nucleus" evidence=IEA;IDA

GO:0003674 "molecular_function" evidence=ND

GO:0008150 "biological_process" evidence=ND

POMBASE|SPAC222.04c ies6 "Ino80 complex subunit Ies6" [Schizosaccharomyces pombe (taxid:4896)]

 Score = 149 (57.5 bits), Expect = 1.2e-10, P = 1.2e-10
 Identities = 42/109 (38%), Positives = 59/109 (54%)

Query:    62 FKNPEYEQRKLSRRSTSSNLPTKQWKSLKQILSYE--KNIPWPEDTIHYSSIVAPPSFKP 119
             F+NP Y+ +   RR+          ++L+QI+  +  +N P       YSSI APPS  P
Sbjct:    19 FRNPNYKAQP--RRN----------RNLRQIIQNDPVQNEP---SKFSYSSIEAPPSVLP 63

Query:   120 SLKYSDISRFECNYKDPQTKLYYYNIEEYKLIRKLPSDIVNGYLALRGA 168
               KY D++     Y DP+T+L Y+N E Y LIR+LPS     YL LR +
Sbjct:    64 QPKYCDVTGLLAIYTDPKTRLRYHNKEIYGLIRELPSGADQEYLKLRSS 112

GO:0003674 "molecular_function" evidence=ND

GO:0005737 "cytoplasm" evidence=IDA

GO:0006338 "chromatin remodeling" evidence=IPI

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0031011 "Ino80 complex" evidence=IDA

UNIPROTKB|G4N5J7 MGG_06129 "Uncharacterized protein" [Magnaporthe oryzae 70-15 (taxid:242507)]

 Score = 134 (52.2 bits), Expect = 4.7e-09, P = 4.7e-09
 Identities = 36/101 (35%), Positives = 54/101 (53%)

Query:    69 QRKLSRRSTS-SNLPTKQWKSLKQILSYEKNIPWPEDTIHYSSIVAPPSFKPSLKYSDIS 127
             Q  L++ S S S L  +  K+L+   S +     P  T  Y++I + PS  P  +Y DI+
Sbjct:    94 QPNLAQASRSLSKLVLE--KNLRSAASGQPGPSAPSAT--YTNIESAPSMAPMKRYCDIT 149

Query:   128 RFECNYKDPQTKLYYYNIEEYKLIRKLPSDIVNGYLALRGA 168
                  Y DP+T+L Y+N E + +IR LPS +   +L  RGA
Sbjct:   150 GLPAPYNDPKTRLRYHNKEVFGIIRGLPSGVAEQFLEARGA 190

GO:0003674 "molecular_function" evidence=ND

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Prediction of Enzyme Commission (EC) Number

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

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Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	173
COG5195	118	COG5195, COG5195, Uncharacterized conserved protei	2e-17
pfam08265	30	pfam08265, YL1_C, YL1 nuclear protein C-terminal d	1e-09
smart00993	30	smart00993, YL1_C, YL1 nuclear protein C-terminal	9e-09

>gnl|CDD|227522 COG5195, COG5195, Uncharacterized conserved protein [Function unknown]

 Score = 73.5 bits (180), Expect = 2e-17
 Identities = 39/125 (31%), Positives = 56/125 (44%), Gaps = 13/125 (10%)

Query: 44  EDINSQNQMQEKLAPKYIFKNPEYEQRKLSRRSTSSNLPTKQWKSLKQILSYEKNIPWPE 103
            + N+ +    KL  +  FK   Y+               +++K+L+Q++          
Sbjct: 2   NNNNNNDGGDMKLLKRPWFKKSTYKG------------KNRRFKTLRQLIPRLTIENESS 49

Query: 104 DTIHYSSIVAPPSFKPSLKYSDISRFECNYKDPQTKLYYYNIEEYKLIRKLPSDIVNGYL 163
               Y SI APPS KP +KY D++     Y  P T L Y+N E YKLI +LPS     YL
Sbjct: 50  KH-RYLSIEAPPSVKPRMKYCDVTGLPAPYTCPNTGLRYHNSEIYKLICELPSGRDQEYL 108

Query: 164 ALRGA 168
            LR  
Sbjct: 109 KLREF 113

Length = 118

>gnl|CDD|191983 pfam08265, YL1_C, YL1 nuclear protein C-terminal domain

 Score = 50.5 bits (122), Expect = 1e-09
 Identities = 15/30 (50%), Positives = 20/30 (66%)

Query: 122 KYSDISRFECNYKDPQTKLYYYNIEEYKLI 151
           KY DI+     YKDP+T L Y N+E +K+I
Sbjct: 1   KYCDITGLPAKYKDPKTGLPYSNVEAFKVI 30

This domain is found in proteins of the YL1 family. These proteins have been shown to be DNA-binding and may be a transcription factor. This domain is found in proteins that are not YL1 proteins. Length = 30

>gnl|CDD|198061 smart00993, YL1_C, YL1 nuclear protein C-terminal domain

 Score = 48.3 bits (116), Expect = 9e-09
 Identities = 15/30 (50%), Positives = 19/30 (63%)

Query: 122 KYSDISRFECNYKDPQTKLYYYNIEEYKLI 151
           KY DI+     Y+DP+T L Y N E YK+I
Sbjct: 1   KYCDITGLPARYRDPKTGLRYANAEAYKVI 30

This domain is found in proteins of the YL1 family. These proteins have been shown to be DNA-binding and may be a transcription factor. This domain is found in proteins that are not YL1 proteins. Length = 30

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	173
KOG4137|consensus	102		100.0
COG5195	118	Uncharacterized conserved protein [Function unknow	100.0
PF08265	30	YL1_C: YL1 nuclear protein C-terminal domain; Inte	99.54
KOG3362|consensus	156		99.42
PF04438	30	zf-HIT: HIT zinc finger; InterPro: IPR007529 Zinc	98.3
KOG2897|consensus	390		98.17
KOG4317|consensus	383		96.6
PF13824	55	zf-Mss51: Zinc-finger of mitochondrial splicing su	91.86
KOG2857|consensus	157		90.01

>KOG4137|consensus

Probab=100.00  E-value=2.2e-37  Score=234.88  Aligned_cols=101  Identities=42%  Similarity=0.592  Sum_probs=95.2

Q ss_pred             CCCCchhhHhhhhcccCCCCCCCcccccHHHHHHHhhcCCCCCCCCcccccccCCCCCCCcccccccCCCccccCCCCCC
Q psy8340          61 IFKNPEYEQRKLSRRSTSSNLPTKQWKSLKQILSYEKNIPWPEDTIHYSSIVAPPSFKPSLKYSDISRFECNYKDPQTKL  140 (173)
Q Consensus        61 ~FKnp~~~~~~~~~~~~~~~~k~R~~KnlKQLL~~E~~~~~~~d~ptY~sI~APPSlkP~kkyCdITGlpA~YtDP~TgL  140 (173)
                      +||+|.+..            +.++.||+||++..|+.+...+..++|++|+||||++|++||||||||||.|+||.|||
T Consensus         2 ~fk~p~~kk------------~t~~~kn~rq~~~~e~~q~l~~~k~tYfsi~appSv~PakKycDvTGLpapYtdP~t~L   69 (102)
T KOG4137|consen    2 KFQKPWYKK------------STRRGKNMRQKILKELLQRLIEKKHTYFSIEAPPSVKPAKKYCDVTGLPAPYTDPNTGL   69 (102)
T ss_pred             CccCccccC------------CcccCccHHHHHhhhhhhhcccccCceEEecCCCccccchhhccccCCcccccCCCccc
Confidence            489998852            56999999999999998777788899999999999999999999999999999999999


Q ss_pred             cccCHHHHHHHhcCChhHHHHHHHhhCCCCCCC
Q psy8340         141 YYYNIEEYKLIRKLPSDIVNGYLALRGALNPLA  173 (173)
Q Consensus       141 RY~n~~~y~~Ir~lp~~~~q~YL~LRga~~iv~  173 (173)
                      ||||+++|+.|++||+|+||+||.|||++++|+
T Consensus        70 ry~naeiY~~i~empsd~vq~ylklRg~~~~l~  102 (102)
T KOG4137|consen   70 RYHNAEIYKLICEMPSDRVQEYLKLRGFGKVLK  102 (102)
T ss_pred             eeccHHHHHHHHHCCchHhhhHHhhhccccccC
Confidence            999999999999999999999999999999986

>COG5195 Uncharacterized conserved protein [Function unknown]

Probab=100.00  E-value=1.9e-34  Score=222.54  Aligned_cols=113  Identities=35%  Similarity=0.505  Sum_probs=98.4

Q ss_pred             chhhhhhhccCCCCCCCCchhhHhhhhcccCCCCCCCcccccHHHHHHHhhcCCCCCCCCcccccccCCCCCCCcccccc
Q psy8340          47 NSQNQMQEKLAPKYIFKNPEYEQRKLSRRSTSSNLPTKQWKSLKQILSYEKNIPWPEDTIHYSSIVAPPSFKPSLKYSDI  126 (173)
Q Consensus        47 ~~~~~~~~~~~~~~~FKnp~~~~~~~~~~~~~~~~k~R~~KnlKQLL~~E~~~~~~~d~ptY~sI~APPSlkP~kkyCdI  126 (173)
                      ++.+..++.+..+|-||+++|..            +.|++|++||||..+.... .....+|++|+||||++|+++||||
T Consensus         5 nn~d~~d~~ll~rP~fk~~~Yk~------------~~rr~ktlrQli~~~~i~n-e~sk~~Y~sieappSv~P~~KyCDv   71 (118)
T COG5195           5 NNNDGGDMKLLKRPWFKKSTYKG------------KNRRFKTLRQLIPRLTIEN-ESSKHRYLSIEAPPSVKPRMKYCDV   71 (118)
T ss_pred             CCCcccchhhhhcccccCccccC------------cccchhhHHHHcccccccc-ccccceeEeecCCCccccccccccc
Confidence            33444566666666799999953            5699999999999875443 2335799999999999999999999


Q ss_pred             cCCCccccCCCCCCcccCHHHHHHHhcCChhHHHHHHHhhCCCCCC
Q psy8340         127 SRFECNYKDPQTKLYYYNIEEYKLIRKLPSDIVNGYLALRGALNPL  172 (173)
Q Consensus       127 TGlpA~YtDP~TgLRY~n~~~y~~Ir~lp~~~~q~YL~LRga~~iv  172 (173)
                      |||||.||||.|||||||+++|+.|+.||+|.+|+||.||+++.||
T Consensus        72 TGL~a~Yt~P~t~lrYhn~eiY~lI~elpsg~dQeylkLR~~~~vL  117 (118)
T COG5195          72 TGLPAPYTCPNTGLRYHNSEIYKLICELPSGRDQEYLKLREFGKVL  117 (118)
T ss_pred             cCCcccccCCCcCceeccHHHHHHhhcCCCchhHHHHHhhhcCccc
Confidence            9999999999999999999999999999999999999999999987

>PF08265 YL1_C: YL1 nuclear protein C-terminal domain; InterPro: IPR013272 This domain is found at the C terminus in proteins of the YL1 family []

Probab=99.54  E-value=1.9e-15  Score=93.32  Aligned_cols=30  Identities=50%  Similarity=0.868  Sum_probs=28.8

Q ss_pred             ccccccCCCccccCCCCCCcccCHHHHHHH
Q psy8340         122 KYSDISRFECNYKDPQTKLYYYNIEEYKLI  151 (173)
Q Consensus       122 kyCdITGlpA~YtDP~TgLRY~n~~~y~~I  151 (173)
                      |+|||||+||+|+||+|||+|+|.++|++|
T Consensus         1 k~C~iTglpA~Y~DP~T~l~Y~n~~ayk~i   30 (30)
T PF08265_consen    1 KYCDITGLPARYRDPKTGLPYANSEAYKII   30 (30)
T ss_pred             CcccccCCCccccCCCCCCcccCHHHhhcC
Confidence            689999999999999999999999999976

These proteins have been shown to be DNA-binding and may be transcription factors []. This domain is also found in proteins that do not belong to the YL1 family.

>KOG3362|consensus

Probab=99.42  E-value=4.1e-14  Score=114.76  Aligned_cols=68  Identities=19%  Similarity=0.294  Sum_probs=60.1

Q ss_pred             CCCcccccHHHHHHHhhcCCCCCCCCcccccccCCCCCCCcccccccCCCccccCCCCCCcccCHHHHHH
Q psy8340          81 LPTKQWKSLKQILSYEKNIPWPEDTIHYSSIVAPPSFKPSLKYSDISRFECNYKDPQTKLYYYNIEEYKL  150 (173)
Q Consensus        81 ~k~R~~KnlKQLL~~E~~~~~~~d~ptY~sI~APPSlkP~kkyCdITGlpA~YtDP~TgLRY~n~~~y~~  150 (173)
                      .+.+++|||+++|++.... +. ..++|.++-||||.+|.++||.|||++++|.|..||.+||++.|+++
T Consensus        80 ~~~~~RKnf~~~Ldea~~~-~~-k~~~Y~~~~a~p~~KP~r~fCaVCG~~S~ysC~~CG~kyCsv~C~~~  147 (156)
T KOG3362|consen   80 FKLRFRKNFQALLDEALLN-LM-KNPNYHTAYAKPSFKPLRKFCAVCGYDSKYSCVNCGTKYCSVRCLKT  147 (156)
T ss_pred             hhhhHHHHHHHHHHccchh-hh-hccchhhcccCCCCCCcchhhhhcCCCchhHHHhcCCceeechhhhh
Confidence            3578899999999865432 22 67999999999999999999999999999999999999999999986

>PF04438 zf-HIT: HIT zinc finger; InterPro: IPR007529 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=98.30  E-value=2.5e-07  Score=56.88  Aligned_cols=30  Identities=20%  Similarity=0.365  Sum_probs=23.9

Q ss_pred             CcccccccCCCccccCCCCCCcccCHHHHH
Q psy8340         120 SLKYSDISRFECNYKDPQTKLYYYNIEEYK  149 (173)
Q Consensus       120 ~kkyCdITGlpA~YtDP~TgLRY~n~~~y~  149 (173)
                      ++++|.|+|.+|+|+||+|+++|++.++|+
T Consensus         1 ~~~~C~vC~~~~kY~Cp~C~~~~CSl~C~k   30 (30)
T PF04438_consen    1 PRKLCSVCGNPAKYRCPRCGARYCSLACYK   30 (30)
T ss_dssp             --EEETSSSSEESEE-TTT--EESSHHHHH
T ss_pred             CcCCCccCcCCCEEECCCcCCceeCcEeEC
Confidence            367999999999999999999999999985

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the HIT-type zinc finger, which contains 7 conserved cysteines and one histidine that can potentially coordinate two zinc atoms. It has been named after the first protein that originally defined the domain: the yeast HIT1 protein (P46973 from SWISSPROT) []. The HIT-type zinc finger displays some sequence similarities to the MYND-type zinc finger. The function of this domain is unknown but it is mainly found in nuclear proteins involved in gene regulation and chromatin remodeling. This domain is also found in the thyroid receptor interacting protein 3 (TRIP-3) Q15649 from SWISSPROT, that specifically interacts with the ligand binding domain of the thyroid receptor. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2YQP_A 2YQQ_A 1X4S_A.

>KOG2897|consensus

Probab=98.17  E-value=1.1e-06  Score=80.28  Aligned_cols=46  Identities=26%  Similarity=0.360  Sum_probs=38.6

Q ss_pred             CcccccccCCCccccCCCCCCcccCHHHHHHHhcCChhHHHHHHHhhCC
Q psy8340         120 SLKYSDISRFECNYKDPQTKLYYYNIEEYKLIRKLPSDIVNGYLALRGA  168 (173)
Q Consensus       120 ~kkyCdITGlpA~YtDP~TgLRY~n~~~y~~Ir~lp~~~~q~YL~LRga  168 (173)
                      .+-.|.|||+||+|.||.|||+|+++.+|++||.   ..-+.|+.+||-
T Consensus       292 ~~~~C~iTg~PA~Y~DPVT~lPy~ta~AFKviRe---~y~~~~~~~~~~  337 (390)
T KOG2897|consen  292 ERVVCVITGRPARYLDPVTGLPYSTAQAFKVIRE---RYKKHLRSIRGN  337 (390)
T ss_pred             ccccccccCCcccccCcccCCcchhHHHHHHHHH---HHHHHhhhcccc
Confidence            5569999999999999999999999999999994   344556666653

>KOG4317|consensus

Probab=96.60  E-value=0.00059  Score=62.15  Aligned_cols=33  Identities=21%  Similarity=0.390  Sum_probs=28.7

Q ss_pred             CcccccccCC-CccccCCCCCCcccCHHHHHHHh
Q psy8340         120 SLKYSDISRF-ECNYKDPQTKLYYYNIEEYKLIR  152 (173)
Q Consensus       120 ~kkyCdITGl-pA~YtDP~TgLRY~n~~~y~~Ir  152 (173)
                      +.-+|.|||. ++.||||+|.++||+..||..=.
T Consensus         6 ~~~~C~ic~vq~~~YtCPRCn~~YCsl~CYr~h~   39 (383)
T KOG4317|consen    6 SFLACGICGVQKREYTCPRCNLLYCSLKCYRNHK   39 (383)
T ss_pred             ceeeccccccccccccCCCCCccceeeeeecCCC
Confidence            3568999996 78999999999999999998644

>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51

Probab=91.86  E-value=0.11  Score=36.26  Aligned_cols=25  Identities=16%  Similarity=0.207  Sum_probs=21.5

Q ss_pred             cccccCC----CccccCCCCCCcccCHHH
Q psy8340         123 YSDISRF----ECNYKDPQTKLYYYNIEE  147 (173)
Q Consensus       123 yCdITGl----pA~YtDP~TgLRY~n~~~  147 (173)
                      +|.+|+-    ..+|+||.||++++.++.
T Consensus         1 ~Cpv~~~~~~~~v~~~Cp~cGipthcS~e   29 (55)
T PF13824_consen    1 LCPVCKKDLPAHVNFECPDCGIPTHCSEE   29 (55)
T ss_pred             CCCCCccccccccCCcCCCCCCcCccCHH
Confidence            5899998    999999999999876554

>KOG2857|consensus

Probab=90.01  E-value=0.16  Score=41.94  Aligned_cols=34  Identities=24%  Similarity=0.368  Sum_probs=28.7

Q ss_pred             ccccccCC-CccccCCCCCCcccCHHHHHHHhcCC
Q psy8340         122 KYSDISRF-ECNYKDPQTKLYYYNIEEYKLIRKLP  155 (173)
Q Consensus       122 kyCdITGl-pA~YtDP~TgLRY~n~~~y~~Ir~lp  155 (173)
                      ..|.||-- +.+|+||+|..+||+.-||++=+.-|
T Consensus         6 ~tC~ic~e~~~KYKCpkC~vPYCSl~CfKiHk~tP   40 (157)
T KOG2857|consen    6 TTCVICLESEIKYKCPKCSVPYCSLPCFKIHKSTP   40 (157)
T ss_pred             eeehhhhcchhhccCCCCCCccccchhhhhccCCc
Confidence            46888865 66999999999999999999877633

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

No hit with e-value below 0.005

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	173
2yqq_A	56	Zinc finger HIT domain-containing protein 3; struc	98.23
1x4s_A	59	Protein FON, zinc finger HIT domain containing pro	98.14

>2yqq_A Zinc finger HIT domain-containing protein 3; structure genomics, ZF-HIT domain, TRIP-3, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.23  E-value=6.4e-07  Score=61.32  Aligned_cols=38  Identities=16%  Similarity=0.206  Sum_probs=33.3

Q ss_pred             CCCCCCcccccccCCCccccCCCCCCcccCHHHHHHHh
Q psy8340         115 PSFKPSLKYSDISRFECNYKDPQTKLYYYNIEEYKLIR  152 (173)
Q Consensus       115 PSlkP~kkyCdITGlpA~YtDP~TgLRY~n~~~y~~Ir  152 (173)
                      .++.-...+|.|||.+++|+||+|++|||+.+||+.-+
T Consensus         6 ~~~~~~~~~C~vC~~~~kY~CPrC~~~yCSl~C~k~Hk   43 (56)
T 2yqq_A            6 SGLKCSTVVCVICLEKPKYRCPACRVPYCSVVCFRKHK   43 (56)
T ss_dssp             CCCCCCCCCCTTTCSCCSEECTTTCCEESSHHHHHHHH
T ss_pred             cccCCCCCccCcCcCCCeeeCCCCCCCeeCHHHHHHHH
Confidence            35666667999999999999999999999999998754

>1x4s_A Protein FON, zinc finger HIT domain containing protein 2; structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.85.1.2

Probab=98.14  E-value=9.7e-07  Score=61.16  Aligned_cols=38  Identities=13%  Similarity=0.109  Sum_probs=33.0

Q ss_pred             CCCCCCCcccccccC----CCccccCCCCCCcccCHHHHHHH
Q psy8340         114 PPSFKPSLKYSDISR----FECNYKDPQTKLYYYNIEEYKLI  151 (173)
Q Consensus       114 PPSlkP~kkyCdITG----lpA~YtDP~TgLRY~n~~~y~~I  151 (173)
                      .+|-.++...|.||+    .+++|+||+|++|||+..||+.=
T Consensus         4 ~~s~m~~~~~C~vC~~~~~~~akY~CPrC~~rYCSl~C~k~H   45 (59)
T 1x4s_A            4 GSSGMEPAGPCGFCPAGEVQPARYTCPRCNAPYCSLRCYRTH   45 (59)
T ss_dssp             CCSSCCCCEEECSSCTTCCEEECEECTTTCCEESSHHHHHHH
T ss_pred             CCCCCCCCCcCcCCCCCcCCCccccCcCCCCCccChHHHHHH
Confidence            455566778999999    69999999999999999999953

---

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	173
d1x4sa1	46	Zinc finger HIT domain containing protein 2, ZNHIT	96.33
d2dana1	47	Zinc finger MYND domain-containing protein 10, ZMY	88.15
d1y0jb1	36	U-shaped transcription factor, different fingers {	86.07

>d1x4sa1 g.85.1.2 (A:8-53) Zinc finger HIT domain containing protein 2, ZNHIT2 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: HIT/MYND zinc finger-like
superfamily: HIT/MYND zinc finger-like
family: HIT zinc finger
domain: Zinc finger HIT domain containing protein 2, ZNHIT2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.33  E-value=0.00058  Score=43.56  Aligned_cols=28  Identities=14%  Similarity=0.354  Sum_probs=25.2

Q ss_pred             cccccC-CCccccCCCCCCcccCHHHHHH
Q psy8340         123 YSDISR-FECNYKDPQTKLYYYNIEEYKL  150 (173)
Q Consensus       123 yCdITG-lpA~YtDP~TgLRY~n~~~y~~  150 (173)
                      +|.|+. -+++|+||+|+.+||+..||+.
T Consensus         9 lC~vC~~~~~KY~CP~C~~~yCSL~CyK~   37 (46)
T d1x4sa1           9 FCPAGEVQPARYTCPRCNAPYCSLRCYRT   37 (46)
T ss_dssp             SSCTTCCEEECEECTTTCCEESSHHHHHH
T ss_pred             cChhhhCccccccCCCCCCceechHHHhh
Confidence            688887 5789999999999999999985

>d2dana1 g.85.1.1 (A:8-54) Zinc finger MYND domain-containing protein 10, ZMYND10 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: HIT/MYND zinc finger-like
superfamily: HIT/MYND zinc finger-like
family: MYND zinc finger
domain: Zinc finger MYND domain-containing protein 10, ZMYND10
species: Human (Homo sapiens) [TaxId: 9606]

Probab=88.15  E-value=0.17  Score=31.13  Aligned_cols=34  Identities=12%  Similarity=0.077  Sum_probs=28.6

Q ss_pred             CCCCCcccccccCCCccccCCCCC-CcccCHHHHH
Q psy8340         116 SFKPSLKYSDISRFECNYKDPQTK-LYYYNIEEYK  149 (173)
Q Consensus       116 SlkP~kkyCdITGlpA~YtDP~Tg-LRY~n~~~y~  149 (173)
                      .+.|.+..|+.||-++..+|..|+ .+||+.++-.
T Consensus         3 ~~~p~~~~C~~Cg~~~~~~Cs~C~~~~YCs~~CQ~   37 (47)
T d2dana1           3 AVAPERPRCAYCSAEASKRCSRCQNEWYCCRECQV   37 (47)
T ss_dssp             CCCCCCCCCSSSCCCCCEECTTTSCSEESSHHHHH
T ss_pred             ccCCCCCcCcCCCChhhccCCCCCCEeeCCHHHHH
Confidence            355666789999999999999998 6899988864

>d1y0jb1 g.37.1.2 (B:1-36) 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=86.07  E-value=0.23  Score=29.53  Aligned_cols=20  Identities=0%  Similarity=0.004  Sum_probs=17.4

Q ss_pred             CccccCCCCCCcccCHHHHH
Q psy8340         130 ECNYKDPQTKLYYYNIEEYK  149 (173)
Q Consensus       130 pA~YtDP~TgLRY~n~~~y~  149 (173)
                      ||+|.|+-||+||.+....+
T Consensus         6 parf~c~pcgirfss~stle   25 (36)
T d1y0jb1           6 PARFMCLPCGIAFSSPSTLE   25 (36)
T ss_dssp             CCCCBCTTTCCBCSCHHHHH
T ss_pred             ccceeccccceeecChhHHH
Confidence            78899999999999987654