Citrus Sinensis ID: 029923

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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-----
Protein Sequence
MKKCELCGSPAKMFCESDQASLCWDCDAKVHGANFLVANHSRTLLCHVCQSLTPWNGSGPKLGPTISVCNVCVGNGSGSTSREETNRGETYTDDDYDDANEEEDDDDDDDDGGDEDEDEENQVVPWSSTPPPQVSSSSTSDQEFASKFCNGGEGTYSESQMSFSLKHDYHQGYSSSSQQSKNPYF
Secondary Structure (PSIPRED)
cccccccccccEEEEccccccccHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccccccEEEEEcccccHHcHHHHHHHHHHHHHHHHcccHHHHHHHccccccHHcccccccccEEcHHccccccccccccccccccccccccccccccccccccccccccccccccHccEccccccccccccccccccccHHHHHccccccccccccccccccccccccccccHHHcccccc
Coil and Loop (DISEMBL)
mkkcelcgspakmfcesdqaslcwdcdakvhganflvANHSRTLLCHVcqsltpwngsgpklgptisvcnvcvgngsgstsreetnrgetytdddyddaneeeddddddddggdededeenqvvpwsstpppqvsssstsdQEFASKFcnggegtysesQMSFslkhdyhqgyssssqqsknpyf
Flexible Loop (DISEMBL)
MKKCELCGSPAKMFCESDQASLCWDCDAKVHGANFLVANHSRTLLCHVCQSLTPWNGSGPKLGPTISVCNVCVGNgsgstsreetnrgetytdddyddaneeEDDDDDDDDGGDEDEDeenqvvpwsstpppqvsssstSDQEFASKFCNGGEGTYSESQMSFSLKHDYHqgyssssqqsknpyf
Low Complexity Region (SEG)
MKKCELCGSPAKMFCESDQASLCWDCDAKVHGANFLVANHSRTLLCHVCQSLTPWNGSGPKLGPTISVCNVCVGNGSGSTSREETNRGetytdddyddaneeeddddddddggdededeenqvvpwsstpppqvsssstsDQEFASKFCNGGEGTYSESQMSFSLKHDYHQGYssssqqsKNPYF
Disordered region (IsUnstruct)
**********AKMFCESDQASLCWDCDAKVHGANFLVANHSRTLLCHVCQSLTPWNGSGPKLGPTISVCNVCVG***************************************************************************************************************
Disordered Region (DISOPRED)
MKKCELCGSPAKMFCESDQASLCWDCDAKVHGANFLVANHSRTLLCHVCQSLTPWNGSGPKLGPTISVCNVCV****************************************************************************************************************
Disordered Region (DISEMBL)
MKKCELCGSPAKMFCESDQASLCWDCDAKVHGANFLVANHSRTLLCHVCQSLTPWNGSGPKLGPTISVCNVCVGNG*************TYTDDDYDDA********************************************FASKFCNGGEGTYSESQMSFSLKHD*****************
Disordered Region (DISPRO)
**KCELCGSPAKMFCESDQASLCWDCDAKVHGANFLVANHSRTLLCHVCQSLTPWNGSGPKLGPTISVCNVCVG***************************************************************************************SFSLKHDYHQGYSSS********F
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MKKCELCGSPAKMFCESDQASLCWDCDAKVHGANFLVANHSRTLLCHVCQSLTPWNGSGPKLGPTISVCNVCVGNGSGSTSREETNRGETYTDDDYDDANEEEDDDDDDDDGGDEDEDEENQVVPWSSTPPPQVSSSSTSDQEFASKFCNGGEGTYSESQMSFSLKHDYHQGYSSSSQQSKNPYF
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	185	2.2.26 [Sep-21-2011]
O23379	330	Putative zinc finger prot	no	no	0.275	0.154	0.490	4e-07
Q9SK53	294	Zinc finger protein CONST	no	no	0.264	0.166	0.48	5e-07
Q940T9	362	Zinc finger protein CONST	no	no	0.264	0.135	0.46	1e-06
Q9LUA9	373	Zinc finger protein CONST	no	no	0.259	0.128	0.489	2e-06
Q9SSE5	372	Zinc finger protein CONST	no	no	0.259	0.129	0.489	2e-06
Q96502	347	Zinc finger protein CONST	no	no	0.270	0.144	0.431	3e-06
Q9C9F4	356	Putative zinc finger prot	no	no	0.270	0.140	0.470	3e-06
O22800	402	Zinc finger protein CONST	no	no	0.248	0.114	0.468	1e-05
Q9LJ44	364	Zinc finger protein CONST	no	no	0.264	0.134	0.48	1e-05
Q9FDX8	395	Zinc finger protein HD1 O	no	no	0.264	0.124	0.38	2e-05

>sp|O23379|COL11_ARATH Putative zinc finger protein CONSTANS-LIKE 11 OS=Arabidopsis thaliana GN=COL11 PE=3 SV=2

 Score = 54.7 bits (130), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 26/53 (49%), Positives = 35/53 (66%), Gaps = 2/53 (3%)

Query: 3  KCELCGS-PAKMFCESDQASLCWDCDAKVHGANFLVANHSRTLLCHVCQSLTP 54
          +C+ CG+  A ++C+SD A LC +CD  VH AN L   H+R+LLC  C SL P
Sbjct: 4  RCDFCGTEKALIYCKSDSAKLCLNCDVNVHSANPLSQRHTRSLLCEKC-SLQP 55

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SK53|COL3_ARATH Zinc finger protein CONSTANS-LIKE 3 OS=Arabidopsis thaliana GN=COL3 PE=1 SV=1

 Score = 54.3 bits (129), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 24/50 (48%), Positives = 31/50 (62%), Gaps = 1/50 (2%)

Query: 2  KKCELCGS-PAKMFCESDQASLCWDCDAKVHGANFLVANHSRTLLCHVCQ 50
          + C+ C S  A +FC +D A LC DCD K+H AN L + H R  LC VC+
Sbjct: 6  RLCDSCKSTAATLFCRADAAFLCGDCDGKIHTANKLASRHERVWLCEVCE 55

Arabidopsis thaliana (taxid: 3702)

>sp|Q940T9|COL4_ARATH Zinc finger protein CONSTANS-LIKE 4 OS=Arabidopsis thaliana GN=COL4 PE=2 SV=2

 Score = 52.8 bits (125), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 23/50 (46%), Positives = 31/50 (62%), Gaps = 1/50 (2%)

Query: 2  KKCELCGSP-AKMFCESDQASLCWDCDAKVHGANFLVANHSRTLLCHVCQ 50
          K C+ C S  A ++C  D A LC  CD+KVH AN L + H+R  +C VC+
Sbjct: 4  KLCDSCKSATAALYCRPDAAFLCLSCDSKVHAANKLASRHARVWMCEVCE 53

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LUA9|COL10_ARATH Zinc finger protein CONSTANS-LIKE 10 OS=Arabidopsis thaliana GN=COL10 PE=1 SV=1

 Score = 52.4 bits (124), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 24/49 (48%), Positives = 28/49 (57%), Gaps = 1/49 (2%)

Query: 4  CELCGSPAKM-FCESDQASLCWDCDAKVHGANFLVANHSRTLLCHVCQS 51
          C+ CG    M +C SD A LC  CD  VH AN L   HSRTL+C  C +
Sbjct: 5  CDFCGEQRSMVYCRSDAACLCLSCDRNVHSANALSKRHSRTLVCERCNA 53

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SSE5|COL9_ARATH Zinc finger protein CONSTANS-LIKE 9 OS=Arabidopsis thaliana GN=COL9 PE=2 SV=1

 Score = 52.0 bits (123), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 24/49 (48%), Positives = 28/49 (57%), Gaps = 1/49 (2%)

Query: 4  CELCGSPAKM-FCESDQASLCWDCDAKVHGANFLVANHSRTLLCHVCQS 51
          C+ CG    M +C SD A LC  CD  VH AN L   HSRTL+C  C +
Sbjct: 5  CDFCGEQRSMVYCRSDAACLCLSCDRSVHSANALSKRHSRTLVCERCNA 53

Arabidopsis thaliana (taxid: 3702)

>sp|Q96502|COL2_ARATH Zinc finger protein CONSTANS-LIKE 2 OS=Arabidopsis thaliana GN=COL2 PE=1 SV=1

 Score = 51.6 bits (122), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 22/51 (43%), Positives = 32/51 (62%), Gaps = 1/51 (1%)

Query: 2  KKCELCGSPA-KMFCESDQASLCWDCDAKVHGANFLVANHSRTLLCHVCQS 51
          + C+ C S A  ++CE+D A LC  CDA+VH AN + + H R  +C  C+S
Sbjct: 14 RACDTCRSAACTVYCEADSAYLCTTCDARVHAANRVASRHERVRVCQSCES 64

Putative transcription factor. Does not affect flowering time.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9C9F4|COLX_ARATH Putative zinc finger protein At1g68190 OS=Arabidopsis thaliana GN=At1g68190 PE=2 SV=1

 Score = 51.2 bits (121), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 24/51 (47%), Positives = 33/51 (64%), Gaps = 1/51 (1%)

Query: 2  KKCELCGS-PAKMFCESDQASLCWDCDAKVHGANFLVANHSRTLLCHVCQS 51
          + CE C +  A ++C +D A+LC  CDAKVH AN L   H RT+LC  C++
Sbjct: 12 RVCEFCKAYRAVVYCIADTANLCLTCDAKVHSANSLSGRHLRTVLCDSCKN 62

Arabidopsis thaliana (taxid: 3702)

>sp|O22800|COL14_ARATH Zinc finger protein CONSTANS-LIKE 14 OS=Arabidopsis thaliana GN=COL14 PE=2 SV=2

 Score = 49.7 bits (117), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 22/47 (46%), Positives = 26/47 (55%), Gaps = 1/47 (2%)

Query: 4  CELCG-SPAKMFCESDQASLCWDCDAKVHGANFLVANHSRTLLCHVC 49
          CE CG   A +FC +D A LC  CD  VH AN L   H R+ +C  C
Sbjct: 12 CEFCGERTAVLFCRADTAKLCLPCDQHVHSANLLSRKHVRSQICDNC 58

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LJ44|COL12_ARATH Zinc finger protein CONSTANS-LIKE 12 OS=Arabidopsis thaliana GN=COL12 PE=2 SV=2

 Score = 49.3 bits (116), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 24/50 (48%), Positives = 31/50 (62%), Gaps = 1/50 (2%)

Query: 3  KCELCG-SPAKMFCESDQASLCWDCDAKVHGANFLVANHSRTLLCHVCQS 51
          KC+ C  S A ++C+SD A LC +CD  VH AN L   H R+L+C  C S
Sbjct: 4  KCDHCATSQALIYCKSDLAKLCLNCDVHVHSANPLSHRHIRSLICEKCFS 53

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FDX8|HD1_ORYSJ Zinc finger protein HD1 OS=Oryza sativa subsp. japonica GN=HD1 PE=2 SV=1

 Score = 49.3 bits (116), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 19/50 (38%), Positives = 31/50 (62%), Gaps = 1/50 (2%)

Query: 2  KKCELC-GSPAKMFCESDQASLCWDCDAKVHGANFLVANHSRTLLCHVCQ 50
          + C+ C  +P+ ++C +D A LC  CDA+VH AN + + H R  +C  C+
Sbjct: 33 RPCDGCRAAPSVVYCRADAAYLCASCDARVHAANRVASRHERVRVCEACE 82

Probable transcription factor involved in the regulation of flower development. Required for the promotion of flowering under short day (SD) conditions and the suppression of flowering under long day (LD) conditions. Regulates positively the floral activator HEADING DATE 3a (HD3A) under SD and negatively under LD conditions.

Oryza sativa subsp. japonica (taxid: 39947)

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	185
356554959	152	PREDICTED: uncharacterized protein LOC10	0.805	0.980	0.603	3e-42
147788101	212	hypothetical protein VITISV_015160 [Viti	0.908	0.792	0.574	7e-38
225467580	185	PREDICTED: uncharacterized protein LOC10	0.854	0.854	0.602	3e-37
359495714	188	PREDICTED: uncharacterized protein LOC10	0.854	0.840	0.602	3e-37
351721694	154	uncharacterized protein LOC100306080 [Gl	0.816	0.980	0.571	2e-36
297803370	191	hypothetical protein ARALYDRAFT_913814 [	0.670	0.649	0.558	1e-33
255567473	194	conserved hypothetical protein [Ricinus	0.643	0.613	0.454	2e-32
302398753	144	COL domain class transcription factor [M	0.589	0.756	0.598	3e-30
356543762	221	PREDICTED: uncharacterized protein LOC10	0.675	0.565	0.547	1e-29
147766884	299	hypothetical protein VITISV_004310 [Viti	0.394	0.244	0.794	3e-29

>gi|356554959|ref|XP_003545808.1| PREDICTED: uncharacterized protein LOC100805832 [Glycine max]

 Score =  176 bits (447), Expect = 3e-42,   Method: Compositional matrix adjust.
 Identities = 93/154 (60%), Positives = 114/154 (74%), Gaps = 5/154 (3%)

Query: 1   MKKCELCGSPAKMFCESDQASLCWDCDAKVHGANFLVANHSRTLLCHVCQSLTPWNGSGP 60
           M+KCELC SPAK+FCESDQASLCW+CDAKVH ANFLV  H R LLCHVCQSLT W+G+GP
Sbjct: 1   MRKCELCNSPAKLFCESDQASLCWECDAKVHSANFLVTKHPRILLCHVCQSLTAWHGTGP 60

Query: 61  KLGPTISVCNVCVGNGSGSTSREETNRGETYTDDDYDDANEEEDDDDDDDDGGDEDEDEE 120
           K  PT+SVCN CV N S + S++  N  E + DD++DD   E  D  ++ DGG  ++DEE
Sbjct: 61  KFVPTMSVCNTCVNNNSETCSQQ--NHVEDH-DDNHDDGTGE--DHVENHDGGVSEDDEE 115

Query: 121 NQVVPWSSTPPPQVSSSSTSDQEFASKFCNGGEG 154
           NQVVPW+STPPP  S+SS S    +++F N  EG
Sbjct: 116 NQVVPWTSTPPPPASTSSNSVTTSSTRFSNVEEG 149

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147788101|emb|CAN67068.1| hypothetical protein VITISV_015160 [Vitis vinifera]

 Score =  162 bits (409), Expect = 7e-38,   Method: Compositional matrix adjust.
 Identities = 104/181 (57%), Positives = 126/181 (69%), Gaps = 13/181 (7%)

Query: 1   MKKCELCGSPAKMFCESDQASLCWDCDAKVHGANFLVANHSRTLLCHVCQSLTPWNGSGP 60
           MK CELC SPA ++C+SDQASLC DCDAKVH ANFLVA HSRTLLCHVCQS TPWNGSGP
Sbjct: 1   MKVCELCNSPAVIYCDSDQASLCCDCDAKVHSANFLVAKHSRTLLCHVCQSPTPWNGSGP 60

Query: 61  KLGPTISVCNVCVGNGSGSTSREETNRGETYTDDDYDDANEEEDDDDDDDDGGDEDEDEE 120
           KLG TISVC  CV            NR  T  +    D +E+E+ ++D +D GD++ DEE
Sbjct: 61  KLGTTISVCQRCV------------NRSRTVNETPSTDEDEDEEGEEDGEDEGDDENDEE 108

Query: 121 NQVVPWSSTPPPQVSSSSTSDQEFASKFCNGGEGTYSESQMSFSLKHDYHQGYSSSSQQS 180
           NQVVPWSSTPPP +S SS S++E +S+FCNG EG  S+S+ + SLK    Q     + Q 
Sbjct: 109 NQVVPWSSTPPPPISCSSASEEESSSRFCNGEEGP-SDSKSASSLKPMRQQSSFRPTSQV 167

Query: 181 K 181
           +
Sbjct: 168 R 168

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225467580|ref|XP_002262995.1| PREDICTED: uncharacterized protein LOC100264749 [Vitis vinifera]

 Score =  160 bits (404), Expect = 3e-37,   Method: Compositional matrix adjust.
 Identities = 103/171 (60%), Positives = 123/171 (71%), Gaps = 13/171 (7%)

Query: 1   MKKCELCGSPAKMFCESDQASLCWDCDAKVHGANFLVANHSRTLLCHVCQSLTPWNGSGP 60
           MK CELC SPA ++C+SDQASLC DCDAKVH ANFLVA HSRTLLCHVCQS TPWNGSGP
Sbjct: 1   MKVCELCNSPAVIYCDSDQASLCCDCDAKVHSANFLVAKHSRTLLCHVCQSPTPWNGSGP 60

Query: 61  KLGPTISVCNVCVGNGSGSTSREETNRGETYTDDDYDDANEEEDDDDDDDDGGDEDEDEE 120
           KLG TISVC  CV            NR  T  +    D +E+E+ ++D +D GD++ DEE
Sbjct: 61  KLGTTISVCQRCV------------NRSRTVNETPSTDEDEDEEGEEDGEDEGDDENDEE 108

Query: 121 NQVVPWSSTPPPQVSSSSTSDQEFASKFCNGGEGTYSESQMSFSLKHDYHQ 171
           NQVVPWSSTPPP +S SS S++E +S+FCNG EG  S+S+ + SLK    Q
Sbjct: 109 NQVVPWSSTPPPPISCSSASEEESSSRFCNGEEGP-SDSKSASSLKPMRQQ 158

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359495714|ref|XP_003635069.1| PREDICTED: uncharacterized protein LOC100854750 [Vitis vinifera]

 Score =  159 bits (403), Expect = 3e-37,   Method: Compositional matrix adjust.
 Identities = 103/171 (60%), Positives = 123/171 (71%), Gaps = 13/171 (7%)

Query: 1   MKKCELCGSPAKMFCESDQASLCWDCDAKVHGANFLVANHSRTLLCHVCQSLTPWNGSGP 60
           MK CELC SPA ++C+SDQASLC DCDAKVH ANFLVA HSRTLLCHVCQS TPWNGSGP
Sbjct: 1   MKVCELCNSPAVIYCDSDQASLCCDCDAKVHSANFLVAKHSRTLLCHVCQSPTPWNGSGP 60

Query: 61  KLGPTISVCNVCVGNGSGSTSREETNRGETYTDDDYDDANEEEDDDDDDDDGGDEDEDEE 120
           KLG TISVC  CV            NR  T  +    D +E+E+ ++D +D GD++ DEE
Sbjct: 61  KLGSTISVCQRCV------------NRSRTVNETPSTDEDEDEEGEEDGEDDGDDENDEE 108

Query: 121 NQVVPWSSTPPPQVSSSSTSDQEFASKFCNGGEGTYSESQMSFSLKHDYHQ 171
           NQVVPWSSTPPP +S SS S++E +S+FCNG EG  S+S+ + SLK    Q
Sbjct: 109 NQVVPWSSTPPPPISCSSASEEESSSRFCNGEEGP-SDSKSASSLKPMRQQ 158

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|351721694|ref|NP_001237218.1| uncharacterized protein LOC100306080 [Glycine max] gi|255627475|gb|ACU14082.1| unknown [Glycine max]

 Score =  157 bits (397), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 88/154 (57%), Positives = 107/154 (69%), Gaps = 3/154 (1%)

Query: 1   MKKCELCGSPAKMFCESDQASLCWDCDAKVHGANFLVANHSRTLLCHVCQSLTPWNGSGP 60
           M+KCELC SPAK+FCESDQASLCW CDAKVH ANFLV  H R LLCHVCQSLT W+G+GP
Sbjct: 1   MRKCELCNSPAKLFCESDQASLCWKCDAKVHSANFLVTKHPRILLCHVCQSLTAWHGTGP 60

Query: 61  KLGPTISVCNVCVGNGSGSTSREETNRGETYTDDDYDDANEEEDDDDDDDDGGDEDEDEE 120
           K  PT+SVCN CV N S  T  ++ +  +       D A   E+DD    +  D+D+DEE
Sbjct: 61  KFVPTMSVCNTCVNNNSTETCSQQNHEDDDDDGTGEDHA---ENDDGGVAEDDDDDDDEE 117

Query: 121 NQVVPWSSTPPPQVSSSSTSDQEFASKFCNGGEG 154
           NQVVPW+STPPP  S+SS S    +++F +  EG
Sbjct: 118 NQVVPWTSTPPPPASTSSNSVTTSSTRFSDVEEG 151

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297803370|ref|XP_002869569.1| hypothetical protein ARALYDRAFT_913814 [Arabidopsis lyrata subsp. lyrata] gi|297315405|gb|EFH45828.1| hypothetical protein ARALYDRAFT_913814 [Arabidopsis lyrata subsp. lyrata]

 Score =  147 bits (372), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 76/136 (55%), Positives = 90/136 (66%), Gaps = 12/136 (8%)

Query: 2   KKCELCGSPAKMFCESDQASLCWDCDAKVHGANFLVANHSRTLLCHVCQSLTPWNGSGPK 61
           KKC+LC   A+M+CESDQASLCWDCD KVHGANFLVA H+R LLC  CQSLTPW  SG +
Sbjct: 3   KKCDLCSGVARMYCESDQASLCWDCDGKVHGANFLVAKHTRCLLCSACQSLTPWKASGLR 62

Query: 62  LGPTISVCNVCVG---NGSGSTSREETNRGETYTDDDYDDANEEEDDDDDDDDGGDEDED 118
           LGPT SVC+ CV     G G       +RG+        ++ E E+D   +DDGG  D +
Sbjct: 63  LGPTFSVCDSCVALKNAGGGGNRVSSESRGQEEV-----NSFESEEDRIREDDGG--DGE 115

Query: 119 EENQVVPWSST--PPP 132
            ENQVVPWS+   PPP
Sbjct: 116 AENQVVPWSAAAQPPP 131

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255567473|ref|XP_002524716.1| conserved hypothetical protein [Ricinus communis] gi|223536077|gb|EEF37735.1| conserved hypothetical protein [Ricinus communis]

 Score =  143 bits (361), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 79/174 (45%), Positives = 95/174 (54%), Gaps = 55/174 (31%)

Query: 1   MKKCELCGSPAKMFCESDQASLCWDCDAKVHGANFLVANHSRTLLCHVCQSLTPWNGSGP 60
           MKKCELC S AKM+CESDQASLCWDCDA+VH ANFLVA HSRTLLCH+CQS TPW  SGP
Sbjct: 1   MKKCELCNSLAKMYCESDQASLCWDCDARVHAANFLVAKHSRTLLCHLCQSFTPWTASGP 60

Query: 61  KLGPTISVCNVCVGNGSGSTSREETNRGETYTDDDYDDANEEEDDDDDDDDGGDEDEDEE 120
           +L PT+S+C+ CV                                               
Sbjct: 61  RLRPTVSICDNCV----------------------------------------------- 73

Query: 121 NQVVPWSST-PPPQVSSSSTSDQEFASKFCNGGEGTYSESQMSFSLKHDYHQGY 173
              VPWSST  PP  S+SS SDQE + +     +G  S+S+++FSLK      +
Sbjct: 74  ---VPWSSTSAPPPASTSSNSDQENSCR----SDGGVSQSRIAFSLKRTRESAH 120

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|302398753|gb|ADL36671.1| COL domain class transcription factor [Malus x domestica]

 Score =  137 bits (344), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 76/127 (59%), Positives = 88/127 (69%), Gaps = 18/127 (14%)

Query: 1   MKKCELCGSPAKMFCESDQASLCWDCDAKVHGANFLVANHSRTLLCHVCQSLTPWNGSGP 60
           MKKC+LC S AK++C+SDQASLCWDCD KVHGANFLVA HSRTLLCHVCQS TPW GSG 
Sbjct: 1   MKKCDLCDSAAKVYCDSDQASLCWDCDVKVHGANFLVAKHSRTLLCHVCQSPTPWIGSGL 60

Query: 61  KLGPTISVCNVCVGNGSGSTSREETNRGETYTDDDYDDANEEEDDDDDDDDGGDEDEDEE 120
           KL PT+SVC  CV N  G                  +   +E++DDDD++     +EDEE
Sbjct: 61  KLCPTVSVCESCVNNNEG------------------NHHQDEDEDDDDEEGQDGAEEDEE 102

Query: 121 NQVVPWS 127
           NQVVPWS
Sbjct: 103 NQVVPWS 109

Source: Malus x domestica

Species: Malus x domestica

Genus: Malus

Family: Rosaceae

Order: Rosales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356543762|ref|XP_003540329.1| PREDICTED: uncharacterized protein LOC100809520 [Glycine max]

 Score =  135 bits (339), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 69/126 (54%), Positives = 87/126 (69%), Gaps = 1/126 (0%)

Query: 1   MKKCELCGSPAKMFCESDQASLCWDCDAKVHGANFLVANHSRTLLCHVCQSLTPWNGSGP 60
           MK CELC  PA+ FCESDQASLCWDCDAKVHGANFLVA H+RTLLCH CQSLTPW  SG 
Sbjct: 1   MKNCELCKLPARTFCESDQASLCWDCDAKVHGANFLVARHTRTLLCHACQSLTPWKASGS 60

Query: 61  KLGPTISVCNVCVGNGSGSTSREETNRGETYTDDDYDDANEEEDDDDDDDDGGDEDEDEE 120
            LG T+S+C  C G G+     E     +    D  D+ + ++D + ++++   ++ED +
Sbjct: 61  ALGNTVSLCQSCAG-GTTEQGPESQGGNDDDDIDTDDEDDYDDDGESEENEVAADEEDGD 119

Query: 121 NQVVPW 126
           NQVVPW
Sbjct: 120 NQVVPW 125

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147766884|emb|CAN67529.1| hypothetical protein VITISV_004310 [Vitis vinifera]

 Score =  133 bits (335), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 58/73 (79%), Positives = 63/73 (86%)

Query: 1  MKKCELCGSPAKMFCESDQASLCWDCDAKVHGANFLVANHSRTLLCHVCQSLTPWNGSGP 60
          MK CELCG PA+M+CESDQASLCWDCDAKVHGANFLVA HSR+LLCHVC+S TPW  SG 
Sbjct: 1  MKGCELCGCPARMYCESDQASLCWDCDAKVHGANFLVARHSRSLLCHVCRSPTPWRASGA 60

Query: 61 KLGPTISVCNVCV 73
          KLG T+SVC  CV
Sbjct: 61 KLGHTVSVCERCV 73

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

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	185
TAIR|locus:2131709	223	BBX28 "B-box domain protein 28	0.464	0.385	0.641	1.5e-28
TAIR|locus:2147274	215	BBX29 "B-box domain protein 29	0.432	0.372	0.65	5.7e-27
TAIR|locus:2092940	225	BBX32 "B-box domain protein 32	0.4	0.328	0.467	1.2e-12
TAIR|locus:2095562	121	BBX31 "B-box domain protein 31	0.275	0.421	0.568	1e-11
TAIR|locus:1009023318	117	BBX30 "B-box domain protein 30	0.270	0.427	0.52	9.4e-11
TAIR|locus:2129860	330	BBX9 "B-box domain protein 9"	0.405	0.227	0.392	7.6e-10
TAIR|locus:2091082	372	COL9 "CONSTANS-like 9" [Arabid	0.432	0.215	0.345	9.7e-09
TAIR|locus:2047246	294	COL3 "CONSTANS-like 3" [Arabid	0.254	0.159	0.5	1.2e-08
TAIR|locus:2164718	373	BBX8 "B-box domain protein 8"	0.405	0.201	0.4	1.6e-08
TAIR|locus:2074587	347	COL2 "CONSTANS-like 2" [Arabid	0.270	0.144	0.431	1e-07

TAIR|locus:2131709 BBX28 "B-box domain protein 28" [Arabidopsis thaliana (taxid:3702)]

 Score = 318 (117.0 bits), Expect = 1.5e-28, P = 1.5e-28
 Identities = 59/92 (64%), Positives = 66/92 (71%)

Query:     2 KKCELCGSPAKMFCESDQASLCWDCDAKVHGANFLVANHSRTLLCHVCQSLTPWNGSGPK 61
             KKC+LC   A+M+CESDQASLCWDCD KVHGANFLVA H+R LLC  CQSLTPW  +G +
Sbjct:     3 KKCDLCNGVARMYCESDQASLCWDCDGKVHGANFLVAKHTRCLLCSACQSLTPWKATGLR 62

Query:    62 LGPTISVCNVCV-----GNGSGSTSREETNRG 88
             LGPT SVC  CV     G G G+    E NRG
Sbjct:    63 LGPTFSVCESCVALKNAGGGRGNRVLSE-NRG 93

GO:0005622 "intracellular" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0008270 "zinc ion binding" evidence=IEA;ISS

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS

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

TAIR|locus:2147274 BBX29 "B-box domain protein 29" [Arabidopsis thaliana (taxid:3702)]

 Score = 303 (111.7 bits), Expect = 5.7e-27, P = 5.7e-27
 Identities = 52/80 (65%), Positives = 58/80 (72%)

Query:     2 KKCELCGSPAKMFCESDQASLCWDCDAKVHGANFLVANHSRTLLCHVCQSLTPWNGSGPK 61
             KKCELC   A+M+CESDQASLCWDCD KVHGANFLVA H R LLC  CQS TPW  SG  
Sbjct:     4 KKCELCCGVARMYCESDQASLCWDCDGKVHGANFLVAKHMRCLLCSACQSHTPWKASGLN 63

Query:    62 LGPTISVCNVCVGNGSGSTS 81
             LGPT+S+C  C+     + S
Sbjct:    64 LGPTVSICESCLARKKNNNS 83

GO:0005622 "intracellular" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0008270 "zinc ion binding" evidence=IEA;ISS

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS

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

GO:0009409 "response to cold" evidence=IEP

GO:0009555 "pollen development" evidence=IMP

TAIR|locus:2092940 BBX32 "B-box domain protein 32" [Arabidopsis thaliana (taxid:3702)]

 Score = 168 (64.2 bits), Expect = 1.2e-12, P = 1.2e-12
 Identities = 36/77 (46%), Positives = 45/77 (58%)

Query:     4 CELCGSPAKMFCESDQASLCWDCDAKVHGANFLVANHSRTLLCHVCQSLTPWNGSGPKLG 63
             CELCG+ A + C +D A LC  CDAK H +NFL A H R ++C  C+SLT    SGP L 
Sbjct:     5 CELCGAEADLHCAADSAFLCRSCDAKFHASNFLFARHFRRVICPNCKSLTQNFVSGPLLP 64

Query:    64 -PTISVCNVCVGNGSGS 79
              P  + C  C  + S S
Sbjct:    65 WPPRTTC--CSESSSSS 79

GO:0005634 "nucleus" evidence=ISM;IDA

GO:0008270 "zinc ion binding" evidence=ISS

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS

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

GO:0010200 "response to chitin" evidence=IEP

GO:0005515 "protein binding" evidence=IPI

GO:0009640 "photomorphogenesis" evidence=IMP

GO:0009785 "blue light signaling pathway" evidence=IMP

GO:0010017 "red or far-red light signaling pathway" evidence=IMP

GO:0045892 "negative regulation of transcription, DNA-dependent" evidence=IEP

GO:0005737 "cytoplasm" evidence=IDA

GO:0009909 "regulation of flower development" evidence=IMP

TAIR|locus:2095562 BBX31 "B-box domain protein 31" [Arabidopsis thaliana (taxid:3702)]

 Score = 159 (61.0 bits), Expect = 1.0e-11, P = 1.0e-11
 Identities = 29/51 (56%), Positives = 33/51 (64%)

Query:     3 KCELCGSPAKMFCESDQASLCWDCDAKVHGANFLVANHSRTLLCHVCQSLT 53
             +CELC   A +FCE+D A LC  CD  VHGANFL   H R +LC  CQ LT
Sbjct:    30 RCELCDGDASVFCEADSAFLCRKCDRWVHGANFLAWRHVRRVLCTSCQKLT 80

GO:0005622 "intracellular" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0008270 "zinc ion binding" evidence=IEA;ISS

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS

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

GO:0010224 "response to UV-B" evidence=IEP;RCA

GO:0009744 "response to sucrose stimulus" evidence=RCA

TAIR|locus:1009023318 BBX30 "B-box domain protein 30" [Arabidopsis thaliana (taxid:3702)]

 Score = 150 (57.9 bits), Expect = 9.4e-11, P = 9.4e-11
 Identities = 26/50 (52%), Positives = 32/50 (64%)

Query:     4 CELCGSPAKMFCESDQASLCWDCDAKVHGANFLVANHSRTLLCHVCQSLT 53
             CELCG  A ++CE+D A LC  CD  VH ANFL   H R ++C  C+ LT
Sbjct:    32 CELCGENATVYCEADAAFLCRKCDRWVHSANFLARRHLRRVICTTCRKLT 81

GO:0005622 "intracellular" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0008270 "zinc ion binding" evidence=IEA

TAIR|locus:2129860 BBX9 "B-box domain protein 9" [Arabidopsis thaliana (taxid:3702)]

 Score = 147 (56.8 bits), Expect = 7.6e-10, P = 7.6e-10
 Identities = 31/79 (39%), Positives = 44/79 (55%)

Query:     3 KCELCGSP-AKMFCESDQASLCWDCDAKVHGANFLVANHSRTLLCHVCQSLTPWNGSGPK 61
             +C+ CG+  A ++C+SD A LC +CD  VH AN L   H+R+LLC  C SL P   +   
Sbjct:     4 RCDFCGTEKALIYCKSDSAKLCLNCDVNVHSANPLSQRHTRSLLCEKC-SLQPT--AVHC 60

Query:    62 LGPTISVCNVCVGNGSGST 80
             +   +S+C  C    S  T
Sbjct:    61 MNENVSLCQGCQWTASNCT 79

GO:0005622 "intracellular" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0008270 "zinc ion binding" evidence=IEA;ISS

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS

GO:0006863 "purine nucleobase transport" evidence=RCA

TAIR|locus:2091082 COL9 "CONSTANS-like 9" [Arabidopsis thaliana (taxid:3702)]

 Score = 138 (53.6 bits), Expect = 9.7e-09, P = 9.7e-09
 Identities = 29/84 (34%), Positives = 43/84 (51%)

Query:     4 CELCGSPAKM-FCESDQASLCWDCDAKVHGANFLVANHSRTLLCHVCQSLTPWNGSGPKL 62
             C+ CG    M +C SD A LC  CD  VH AN L   HSRTL+C  C +  P   +   +
Sbjct:     5 CDFCGEQRSMVYCRSDAACLCLSCDRSVHSANALSKRHSRTLVCERCNA-QP--ATVRCV 61

Query:    63 GPTISVCNVCVGNGSGSTSREETN 86
                +S+C  C  +G  +++   ++
Sbjct:    62 EERVSLCQNCDWSGHNNSNNNNSS 85

GO:0005622 "intracellular" evidence=IEA

GO:0005634 "nucleus" evidence=ISM;IDA

GO:0008270 "zinc ion binding" evidence=IEA;ISS

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS

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

GO:0048579 "negative regulation of long-day photoperiodism, flowering" evidence=IMP

GO:0007623 "circadian rhythm" evidence=IEP;RCA

TAIR|locus:2047246 COL3 "CONSTANS-like 3" [Arabidopsis thaliana (taxid:3702)]

 Score = 135 (52.6 bits), Expect = 1.2e-08, P = 1.2e-08
 Identities = 24/48 (50%), Positives = 30/48 (62%)

Query:     4 CELCGSPAK-MFCESDQASLCWDCDAKVHGANFLVANHSRTLLCHVCQ 50
             C+ C S A  +FC +D A LC DCD K+H AN L + H R  LC VC+
Sbjct:     8 CDSCKSTAATLFCRADAAFLCGDCDGKIHTANKLASRHERVWLCEVCE 55

GO:0005622 "intracellular" evidence=IEA

GO:0005634 "nucleus" evidence=ISM;IDA

GO:0008270 "zinc ion binding" evidence=IEA;ISS

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS

GO:0005515 "protein binding" evidence=IPI

GO:0010099 "regulation of photomorphogenesis" evidence=IMP

GO:0010161 "red light signaling pathway" evidence=IMP

GO:0009637 "response to blue light" evidence=RCA

GO:0009644 "response to high light intensity" evidence=RCA

GO:0009744 "response to sucrose stimulus" evidence=RCA

GO:0010114 "response to red light" evidence=RCA

GO:0010155 "regulation of proton transport" evidence=RCA

GO:0010218 "response to far red light" evidence=RCA

GO:0032880 "regulation of protein localization" evidence=RCA

TAIR|locus:2164718 BBX8 "B-box domain protein 8" [Arabidopsis thaliana (taxid:3702)]

 Score = 136 (52.9 bits), Expect = 1.6e-08, P = 1.6e-08
 Identities = 32/80 (40%), Positives = 39/80 (48%)

Query:     4 CELCGSPAKM-FCESDQASLCWDCDAKVHGANFLVANHSRTLLCHVCQSLTPWNGSGPKL 62
             C+ CG    M +C SD A LC  CD  VH AN L   HSRTL+C  C +  P   S    
Sbjct:     5 CDFCGEQRSMVYCRSDAACLCLSCDRNVHSANALSKRHSRTLVCERCNA-QP--ASVRCS 61

Query:    63 GPTISVCNVCVGNG-SGSTS 81
                +S+C  C  +G  G  S
Sbjct:    62 DERVSLCQNCDWSGHDGKNS 81

GO:0005622 "intracellular" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0008270 "zinc ion binding" evidence=IEA;ISS

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS

GO:0005886 "plasma membrane" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

GO:0007623 "circadian rhythm" evidence=RCA

TAIR|locus:2074587 COL2 "CONSTANS-like 2" [Arabidopsis thaliana (taxid:3702)]

 Score = 128 (50.1 bits), Expect = 1.0e-07, P = 1.0e-07
 Identities = 22/51 (43%), Positives = 32/51 (62%)

Query:     2 KKCELCGSPA-KMFCESDQASLCWDCDAKVHGANFLVANHSRTLLCHVCQS 51
             + C+ C S A  ++CE+D A LC  CDA+VH AN + + H R  +C  C+S
Sbjct:    14 RACDTCRSAACTVYCEADSAYLCTTCDARVHAANRVASRHERVRVCQSCES 64

GO:0005622 "intracellular" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0008270 "zinc ion binding" evidence=IEA;ISS

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS

GO:0009909 "regulation of flower development" evidence=IMP

GO:0009658 "chloroplast organization" evidence=IMP

---

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	185
cd00021	39	cd00021, BBOX, B-Box-type zinc finger; zinc bindin	3e-07
smart00336	42	smart00336, BBOX, B-Box-type zinc finger	4e-07
pfam03353	316	pfam03353, Lin-8, Ras-mediated vulval-induction an	2e-05
pfam03066	146	pfam03066, Nucleoplasmin, Nucleoplasmin	1e-04
pfam04147	809	pfam04147, Nop14, Nop14-like family	2e-04
pfam10446	449	pfam10446, DUF2457, Protein of unknown function (D	4e-04
pfam03066	146	pfam03066, Nucleoplasmin, Nucleoplasmin	5e-04
pfam04546	211	pfam04546, Sigma70_ner, Sigma-70, non-essential re	6e-04
pfam04546	211	pfam04546, Sigma70_ner, Sigma-70, non-essential re	0.001
pfam03153	332	pfam03153, TFIIA, Transcription factor IIA, alpha/	0.001
pfam03153	332	pfam03153, TFIIA, Transcription factor IIA, alpha/	0.001
pfam05285	317	pfam05285, SDA1, SDA1	0.002
PHA03346	520	PHA03346, PHA03346, US22 family homolog; Provision	0.002
pfam02724	583	pfam02724, CDC45, CDC45-like protein	0.002
pfam02724	583	pfam02724, CDC45, CDC45-like protein	0.002
PRK05901	509	PRK05901, PRK05901, RNA polymerase sigma factor; P	0.002
PHA02608	80	PHA02608, 67, prohead core protein; Provisional	0.002
pfam04546	211	pfam04546, Sigma70_ner, Sigma-70, non-essential re	0.003
pfam09026	101	pfam09026, Cenp-B_dimeris, Centromere protein B di	0.003
pfam05764	238	pfam05764, YL1, YL1 nuclear protein	0.003
pfam05764	238	pfam05764, YL1, YL1 nuclear protein	0.003
PRK12298	390	PRK12298, obgE, GTPase CgtA; Reviewed	0.003
pfam04889	241	pfam04889, Cwf_Cwc_15, Cwf15/Cwc15 cell cycle cont	0.004
pfam05470	593	pfam05470, eIF-3c_N, Eukaryotic translation initia	0.004

>gnl|CDD|237988 cd00021, BBOX, B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction

 Score = 45.0 bits (107), Expect = 3e-07
 Identities = 18/44 (40%), Positives = 23/44 (52%), Gaps = 7/44 (15%)

Query: 3  KCELCGS-PAKMFCESDQASLCWDCDAKVHGANFLVANHSRTLL 45
           C+  G  P  +FCE+D+A LC DCD  VH      + H R  L
Sbjct: 2  LCDEHGEEPLSLFCETDRALLCVDCDLSVH------SGHRRVPL 39

Length = 39

>gnl|CDD|197662 smart00336, BBOX, B-Box-type zinc finger

 Score = 44.6 bits (106), Expect = 4e-07
 Identities = 17/46 (36%), Positives = 20/46 (43%), Gaps = 7/46 (15%)

Query: 1  MKKCELCGS-PAKMFCESDQASLCWDCDAKVHGANFLVANHSRTLL 45
            KC+  G  PA+ FCE   A LC  CD   H        H+  LL
Sbjct: 3  APKCDSHGDEPAEFFCEECGALLCRTCDEAEH------RGHTVVLL 42

Length = 42

>gnl|CDD|217509 pfam03353, Lin-8, Ras-mediated vulval-induction antagonist

 Score = 43.1 bits (102), Expect = 2e-05
 Identities = 23/109 (21%), Positives = 37/109 (33%), Gaps = 19/109 (17%)

Query: 82  REETNRGETYTDDDYDD--------ANEEEDDDDDDDDGGDEDEDEENQVVPWSSTPPPQ 133
           R+E   GE    DD DD            E  D +++D  DE E EE      ++    +
Sbjct: 127 RKEPWTGEDQEADDEDDIIYDGIFEDRTRESQDMEENDEVDEVEVEEVPDDYGANLAVDE 186

Query: 134 VSSSSTSDQEFASKFCNGGEGTYSESQMSFSLKHDYHQGYSSSSQQSKN 182
              S+ S  +              +S  +     +  Q   S+S +S  
Sbjct: 187 PEQSTMSRPQ-----------EVKQSVPAQQAPPNPQQPMPSASSESAT 224

LIN-8 is a nuclear protein, present at the sites of transcriptional repressor complexes, which interacts with LIN-35 Rb.Lin35 Rb is a product of the class B synMuv gene lin-35 which silences genes required for vulval specification through chromatin modification and remodelling. The biological role of the interaction has not yet been determined however predictions have been made. The interaction shows that class A synMuv genes control vulval induction through the transcriptional regulation of gene expression. LIN-8 normally functions as part of a protein complex however when the complex is absent, other family members can partially replace LIN-8 activity. Length = 316

>gnl|CDD|145949 pfam03066, Nucleoplasmin, Nucleoplasmin

 Score = 40.0 bits (94), Expect = 1e-04
 Identities = 12/33 (36%), Positives = 24/33 (72%)

Query: 91  YTDDDYDDANEEEDDDDDDDDGGDEDEDEENQV 123
            +++D  D +EE+++++DD++  DEDE EE + 
Sbjct: 108 ASEEDESDDDEEDEEEEDDEEDDDEDESEEEES 140

Nucleoplasmins are also known as chromatin decondensation proteins. They bind to core histones and transfer DNA to them in a reaction that requires ATP. This is thought to play a role in the assembly of regular nucleosomal arrays. Length = 146

>gnl|CDD|217927 pfam04147, Nop14, Nop14-like family

 Score = 40.4 bits (95), Expect = 2e-04
 Identities = 13/48 (27%), Positives = 22/48 (45%)

Query: 77  SGSTSREETNRGETYTDDDYDDANEEEDDDDDDDDGGDEDEDEENQVV 124
                    +  E   DDD ++  E+ D  D+++D  DED D+E+   
Sbjct: 323 EEEEEDGVDDEDEEDDDDDLEEEEEDVDLSDEEEDEEDEDSDDEDDEE 370

Emg1 and Nop14 are novel proteins whose interaction is required for the maturation of the 18S rRNA and for 40S ribosome production. Length = 809

>gnl|CDD|220759 pfam10446, DUF2457, Protein of unknown function (DUF2457)

 Score = 39.6 bits (92), Expect = 4e-04
 Identities = 20/36 (55%), Positives = 27/36 (75%)

Query: 93  DDDYDDANEEEDDDDDDDDGGDEDEDEENQVVPWSS 128
           +DD DD +E+EDDDDDDDD  DEDED+++  +   S
Sbjct: 58  EDDDDDDDEDEDDDDDDDDEDDEDEDDDDSTLHDDS 93

This is a family of uncharacterized proteins. Length = 449

>gnl|CDD|145949 pfam03066, Nucleoplasmin, Nucleoplasmin

 Score = 38.1 bits (89), Expect = 5e-04
 Identities = 15/33 (45%), Positives = 23/33 (69%)

Query: 93  DDDYDDANEEEDDDDDDDDGGDEDEDEENQVVP 125
           D+  DD  +EE++DD++DD  DE E+EE+ V  
Sbjct: 112 DESDDDEEDEEEEDDEEDDDEDESEEEESPVKK 144

Nucleoplasmins are also known as chromatin decondensation proteins. They bind to core histones and transfer DNA to them in a reaction that requires ATP. This is thought to play a role in the assembly of regular nucleosomal arrays. Length = 146

>gnl|CDD|203043 pfam04546, Sigma70_ner, Sigma-70, non-essential region

 Score = 38.7 bits (91), Expect = 6e-04
 Identities = 12/29 (41%), Positives = 19/29 (65%)

Query: 93  DDDYDDANEEEDDDDDDDDGGDEDEDEEN 121
            +   D  + EDDDDDD+D  ++DE+E +
Sbjct: 44  IESELDEEDLEDDDDDDEDEDEDDEEEAD 72

The domain is found in the primary vegetative sigma factor. The function of this domain is unclear and can be removed without loss of function. Length = 211

>gnl|CDD|203043 pfam04546, Sigma70_ner, Sigma-70, non-essential region

 Score = 38.3 bits (90), Expect = 0.001
 Identities = 14/37 (37%), Positives = 22/37 (59%)

Query: 89  ETYTDDDYDDANEEEDDDDDDDDGGDEDEDEENQVVP 125
            T    + +   E+ +DDDDDD+  DED++EE  + P
Sbjct: 39  ATAAAIESELDEEDLEDDDDDDEDEDEDDEEEADLGP 75

The domain is found in the primary vegetative sigma factor. The function of this domain is unclear and can be removed without loss of function. Length = 211

>gnl|CDD|217392 pfam03153, TFIIA, Transcription factor IIA, alpha/beta subunit

 Score = 38.6 bits (90), Expect = 0.001
 Identities = 14/31 (45%), Positives = 17/31 (54%)

Query: 93  DDDYDDANEEEDDDDDDDDGGDEDEDEENQV 123
           DDD D+   E D DD DDD  DED ++    
Sbjct: 257 DDDDDEDAIESDLDDSDDDVSDEDGEDLFDT 287

Transcription initiation factor IIA (TFIIA) is a heterotrimer, the three subunits being known as alpha, beta, and gamma, in order of molecular weight. The N and C-terminal domains of the gamma subunit are represented in pfam02268 and pfam02751, respectively. This family represents the precursor that yields both the alpha and beta subunits. The TFIIA heterotrimer is an essential general transcription initiation factor for the expression of genes transcribed by RNA polymerase II. Together with TFIID, TFIIA binds to the promoter region; this is the first step in the formation of a pre-initiation complex (PIC). Binding of the rest of the transcription machinery follows this step. After initiation, the PIC does not completely dissociate from the promoter. Some components, including TFIIA, remain attached and re-initiate a subsequent round of transcription. Length = 332

>gnl|CDD|217392 pfam03153, TFIIA, Transcription factor IIA, alpha/beta subunit

 Score = 38.2 bits (89), Expect = 0.001
 Identities = 16/39 (41%), Positives = 22/39 (56%), Gaps = 2/39 (5%)

Query: 88  GETYTDDDYDDANEEEDDDDDDD--DGGDEDEDEENQVV 124
           G+   DDD +DA E + DD DDD  D   ED  + + V+
Sbjct: 253 GDGSDDDDDEDAIESDLDDSDDDVSDEDGEDLFDTDNVM 291

Transcription initiation factor IIA (TFIIA) is a heterotrimer, the three subunits being known as alpha, beta, and gamma, in order of molecular weight. The N and C-terminal domains of the gamma subunit are represented in pfam02268 and pfam02751, respectively. This family represents the precursor that yields both the alpha and beta subunits. The TFIIA heterotrimer is an essential general transcription initiation factor for the expression of genes transcribed by RNA polymerase II. Together with TFIID, TFIIA binds to the promoter region; this is the first step in the formation of a pre-initiation complex (PIC). Binding of the rest of the transcription machinery follows this step. After initiation, the PIC does not completely dissociate from the promoter. Some components, including TFIIA, remain attached and re-initiate a subsequent round of transcription. Length = 332

>gnl|CDD|218538 pfam05285, SDA1, SDA1

 Score = 37.7 bits (88), Expect = 0.002
 Identities = 11/28 (39%), Positives = 18/28 (64%)

Query: 93  DDDYDDANEEEDDDDDDDDGGDEDEDEE 120
           DDD ++  E E+D+D DD+G   D + +
Sbjct: 97  DDDEEEEWEVEEDEDSDDEGEWIDVESD 124

This family consists of several SDA1 protein homologues. SDA1 is a Saccharomyces cerevisiae protein which is involved in the control of the actin cytoskeleton. The protein is essential for cell viability and is localised in the nucleus. Length = 317

>gnl|CDD|223052 PHA03346, PHA03346, US22 family homolog; Provisional

 Score = 37.8 bits (88), Expect = 0.002
 Identities = 20/68 (29%), Positives = 27/68 (39%), Gaps = 3/68 (4%)

Query: 94  DDYDDANEEEDDDDDDDDGGDEDEDEEN---QVVPWSSTPPPQVSSSSTSDQEFASKFCN 150
            D DD  ++EDDDD +D G D DED+      V  W        +      Q     +  
Sbjct: 426 PDDDDEGDDEDDDDWEDLGFDLDEDDVYDLKDVDEWRLERRIATAERWELGQRLLDAYMT 485

Query: 151 GGEGTYSE 158
             E T +E
Sbjct: 486 EAEVTEAE 493

Length = 520

>gnl|CDD|217203 pfam02724, CDC45, CDC45-like protein

 Score = 37.7 bits (88), Expect = 0.002
 Identities = 22/78 (28%), Positives = 32/78 (41%), Gaps = 16/78 (20%)

Query: 47  HVCQSLTPWNGSGPKLGPTISVCNVCVGNGS----GSTSREETNRGETYTDDDYDDANEE 102
           +V  S  PWN           + NV  G+           EE  + E   DD Y D  E+
Sbjct: 79  YVIDSHRPWN-----------LDNVF-GSDQVVIFDDGDIEEELQDEPRYDDAYRDLEED 126

Query: 103 EDDDDDDDDGGDEDEDEE 120
           +DDD++ D+  +E    E
Sbjct: 127 DDDDEESDEEDEESSKSE 144

CDC45 is an essential gene required for initiation of DNA replication in S. cerevisiae, forming a complex with MCM5/CDC46. Homologues of CDC45 have been identified in human, mouse and smut fungus among others. Length = 583

>gnl|CDD|217203 pfam02724, CDC45, CDC45-like protein

 Score = 37.7 bits (88), Expect = 0.002
 Identities = 13/38 (34%), Positives = 25/38 (65%)

Query: 82  REETNRGETYTDDDYDDANEEEDDDDDDDDGGDEDEDE 119
            EE +  +  +D++ +++++ EDD+DDDDD  D+D   
Sbjct: 123 LEEDDDDDEESDEEDEESSKSEDDEDDDDDDDDDDIAT 160

CDC45 is an essential gene required for initiation of DNA replication in S. cerevisiae, forming a complex with MCM5/CDC46. Homologues of CDC45 have been identified in human, mouse and smut fungus among others. Length = 583

>gnl|CDD|235640 PRK05901, PRK05901, RNA polymerase sigma factor; Provisional

 Score = 37.7 bits (88), Expect = 0.002
 Identities = 18/28 (64%), Positives = 23/28 (82%)

Query: 93  DDDYDDANEEEDDDDDDDDGGDEDEDEE 120
           DDD DD +++EDDD+DDDD   +DEDEE
Sbjct: 144 DDDIDDDDDDEDDDEDDDDDDVDDEDEE 171

Length = 509

>gnl|CDD|177433 PHA02608, 67, prohead core protein; Provisional

 Score = 35.1 bits (81), Expect = 0.002
 Identities = 18/34 (52%), Positives = 25/34 (73%), Gaps = 1/34 (2%)

Query: 88  GETYTDDDYDDANEEEDDDDD-DDDGGDEDEDEE 120
           GE   DDD D+ ++++DD DD DDD  D+DED+E
Sbjct: 47  GEEPEDDDDDEDDDDDDDKDDKDDDDDDDDEDDE 80

Length = 80

>gnl|CDD|203043 pfam04546, Sigma70_ner, Sigma-70, non-essential region

 Score = 36.8 bits (86), Expect = 0.003
 Identities = 8/29 (27%), Positives = 19/29 (65%)

Query: 93  DDDYDDANEEEDDDDDDDDGGDEDEDEEN 121
            D+ D  ++++DD+D+D+D  +E +   +
Sbjct: 48  LDEEDLEDDDDDDEDEDEDDEEEADLGPD 76

The domain is found in the primary vegetative sigma factor. The function of this domain is unclear and can be removed without loss of function. Length = 211

>gnl|CDD|117592 pfam09026, Cenp-B_dimeris, Centromere protein B dimerisation domain

 Score = 35.5 bits (81), Expect = 0.003
 Identities = 18/36 (50%), Positives = 27/36 (75%)

Query: 93  DDDYDDANEEEDDDDDDDDGGDEDEDEENQVVPWSS 128
           +D   D++EEEDDDD+D++  DED+DE++  VP  S
Sbjct: 10  EDSDSDSDEEEDDDDEDEEDDDEDDDEDDDEVPVPS 45

The centromere protein B (CENP-B) dimerisation domain is composed of two alpha-helices, which are folded into an antiparallel configuration. Dimerisation of CENP-B is mediated by this domain, in which monomers dimerise to form a symmetrical, antiparallel, four-helix bundle structure with a large hydrophobic patch in which 23 residues of one monomer form van der Waals contacts with the other monomer. This CENP-B dimer configuration may be suitable for capturing two distant CENP-B boxes during centromeric heterochromatin formation. Length = 101

>gnl|CDD|218737 pfam05764, YL1, YL1 nuclear protein

 Score = 36.6 bits (85), Expect = 0.003
 Identities = 9/30 (30%), Positives = 19/30 (63%)

Query: 93  DDDYDDANEEEDDDDDDDDGGDEDEDEENQ 122
           D++++   EEE+++ D D    ED++ E+ 
Sbjct: 40  DEEFEIEEEEEEEEVDSDFDDSEDDEPESD 69

The proteins in this family are designated YL1. These proteins have been shown to be DNA-binding and may be a transcription factor. Length = 238

>gnl|CDD|218737 pfam05764, YL1, YL1 nuclear protein

 Score = 36.6 bits (85), Expect = 0.003
 Identities = 10/29 (34%), Positives = 19/29 (65%)

Query: 93  DDDYDDANEEEDDDDDDDDGGDEDEDEEN 121
           +DD +   EEE+++++ D   D+ ED+E 
Sbjct: 38  EDDEEFEIEEEEEEEEVDSDFDDSEDDEP 66

The proteins in this family are designated YL1. These proteins have been shown to be DNA-binding and may be a transcription factor. Length = 238

>gnl|CDD|237047 PRK12298, obgE, GTPase CgtA; Reviewed

 Score = 36.8 bits (86), Expect = 0.003
 Identities = 13/37 (35%), Positives = 19/37 (51%)

Query: 89  ETYTDDDYDDANEEEDDDDDDDDGGDEDEDEENQVVP 125
           + Y  +  ++  EE+DDD DDD   D+DE  E     
Sbjct: 354 DDYHREQLEEVEEEDDDDWDDDWDEDDDEGVEVIYKR 390

Length = 390

>gnl|CDD|218312 pfam04889, Cwf_Cwc_15, Cwf15/Cwc15 cell cycle control protein

 Score = 36.6 bits (85), Expect = 0.004
 Identities = 11/27 (40%), Positives = 15/27 (55%)

Query: 94  DDYDDANEEEDDDDDDDDGGDEDEDEE 120
           DD D +++ +  DDD DD   EDE   
Sbjct: 120 DDSDSSSDSDSSDDDSDDDDSEDETAA 146

This family represents Cwf15/Cwc15 (from Schizosaccharomyces pombe and Saccharomyces cerevisiae respectively) and their homologues. The function of these proteins is unknown, but they form part of the spliceosome and are thus thought to be involved in mRNA splicing. Length = 241

>gnl|CDD|218598 pfam05470, eIF-3c_N, Eukaryotic translation initiation factor 3 subunit 8 N-terminus

 Score = 36.7 bits (85), Expect = 0.004
 Identities = 17/78 (21%), Positives = 31/78 (39%)

Query: 91  YTDDDYDDANEEEDDDDDDDDGGDEDEDEENQVVPWSSTPPPQVSSSSTSDQEFASKFCN 150
           Y +D   +  EEE+D+DDDDDG D+++++E+ V           S      ++       
Sbjct: 131 YREDPESEDEEEEEDEDDDDDGSDDEDEDEDGVGATEEVAASSESGVDRVKEDDEEDEDA 190

Query: 151 GGEGTYSESQMSFSLKHD 168
                    +     K +
Sbjct: 191 DLSKKDVLEEPKMFKKPE 208

The largest of the mammalian translation initiation factors, eIF3, consists of at least eight subunits ranging in mass from 35 to 170 kDa. eIF3 binds to the 40 S ribosome in an early step of translation initiation and promotes the binding of methionyl-tRNAi and mRNA. Length = 593

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	185
cd00021	39	BBOX B-Box-type zinc finger; zinc binding domain (	97.65
smart00336	42	BBOX B-Box-type zinc finger.	97.13
PF00643	42	zf-B_box: B-box zinc finger; InterPro: IPR000315 Z	97.1
PF10446	458	DUF2457: Protein of unknown function (DUF2457); In	95.06
PF10446	458	DUF2457: Protein of unknown function (DUF2457); In	94.07
PF09026	101	CENP-B_dimeris: Centromere protein B dimerisation	92.0
KOG4367	699	consensus Predicted Zn-finger protein [Function un	91.13
PTZ00415	2849	transmission-blocking target antigen s230; Provisi	88.77
PF03066	149	Nucleoplasmin: Nucleoplasmin; InterPro: IPR004301	85.78
smart00336	42	BBOX B-Box-type zinc finger.	84.11
PF14812	81	PBP1_TM: Transmembrane domain of transglycosylase	82.8

>cd00021 BBOX B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction

Probab=97.65  E-value=4e-05  Score=47.20  Aligned_cols=38  Identities=47%  Similarity=0.982  Sum_probs=32.9

Q ss_pred             CCCCCCC-CCceEEeccCccccChhhccccccCCcCCCCceeeee
Q 029923            2 KKCELCG-SPAKMFCESDQASLCWDCDAKVHGANFLVANHSRTLL   45 (185)
Q Consensus         2 ~~Cd~C~-apA~vyC~aD~A~LC~~CDa~VHsAN~La~rH~RvpL   45 (185)
                      .+|..++ +++.|||..|++.||..|+...|.      .|.|++|
T Consensus         1 ~~C~~H~~~~~~~fC~~~~~~iC~~C~~~~H~------~H~~~~i   39 (39)
T cd00021           1 RLCDEHGEEPLSLFCETDRALLCVDCDLSVHS------GHRRVPL   39 (39)
T ss_pred             CCCCccCCcceEEEeCccChhhhhhcChhhcC------CCCEeeC
Confidence            3688898 699999999999999999988773      7888875

>smart00336 BBOX B-Box-type zinc finger

Probab=97.13  E-value=0.00043  Score=43.04  Aligned_cols=39  Identities=44%  Similarity=0.821  Sum_probs=33.3

Q ss_pred             CCCCCCCC-CCceEEeccCccccChhhccccccCCcCCCCceeeee
Q 029923            1 MKKCELCG-SPAKMFCESDQASLCWDCDAKVHGANFLVANHSRTLL   45 (185)
Q Consensus         1 m~~Cd~C~-apA~vyC~aD~A~LC~~CDa~VHsAN~La~rH~RvpL   45 (185)
                      ++.|..+. .++.+||..+++.||..|....|      +.|.+++|
T Consensus         3 ~~~C~~h~~~~~~~~C~~c~~~iC~~C~~~~H------~~H~~~~l   42 (42)
T smart00336        3 PPKCDSHGDEPAEFFCEECGALLCRTCDEAEH------RGHTVVLL   42 (42)
T ss_pred             CCcCCCCCCCceEEECCCCCcccccccChhhc------CCCceecC
Confidence            35799999 89999999999999999998766      57877764

>PF00643 zf-B_box: B-box zinc finger; InterPro: IPR000315 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=97.10  E-value=0.00041  Score=43.91  Aligned_cols=39  Identities=28%  Similarity=0.589  Sum_probs=33.0

Q ss_pred             CCCCCCCC-CCceEEeccCccccChhhccccccCCcCCCCceeeee
Q 029923            1 MKKCELCG-SPAKMFCESDQASLCWDCDAKVHGANFLVANHSRTLL   45 (185)
Q Consensus         1 m~~Cd~C~-apA~vyC~aD~A~LC~~CDa~VHsAN~La~rH~RvpL   45 (185)
                      +++|..+. .++.+||..+...||..|....|..      |..++|
T Consensus         3 ~~~C~~H~~~~~~~~C~~C~~~~C~~C~~~~H~~------H~~~~i   42 (42)
T PF00643_consen    3 EPKCPEHPEEPLSLFCEDCNEPLCSECTVSGHKG------HKIVPI   42 (42)
T ss_dssp             SSB-SSTTTSBEEEEETTTTEEEEHHHHHTSTTT------SEEEEC
T ss_pred             CccCccCCccceEEEecCCCCccCccCCCCCCCC------CEEeEC
Confidence            46899999 6699999999999999999999843      887765

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 B-box-type zinc finger domains, which are around 40 residues in length. B-box zinc fingers can be divided into two groups, where types 1 and 2 B-box domains differ in their consensus sequence and in the spacing of the 7-8 zinc-binding residues. Several proteins contain both types 1 and 2 B-boxes, suggesting some level of cooperativity between these two domains. B-box domains are found in over 1500 proteins from a variety of organisms. They are found in TRIM (tripartite motif) proteins that consist of an N-terminal RING finger (originally called an A-box), followed by 1-2 B-box domains and a coiled-coil domain (also called RBCC for Ring, B-box, Coiled-Coil). TRIM proteins contain a type 2 B-box domain, and may also contain a type 1 B-box. In proteins that do not contain RING or coiled-coil domains, the B-box domain is primarily type 2. Many type 2 B-box proteins are involved in ubiquitinylation. Proteins containing a B-box zinc finger domain include transcription factors, ribonucleoproteins and proto-oncoproteins; for example, MID1, MID2, TRIM9, TNL, TRIM36, TRIM63, TRIFIC, NCL1 and CONSTANS-like proteins []. The microtubule-associated E3 ligase MID1 (6.3.2 from EC) contains a type 1 B-box zinc finger domain. MID1 specifically binds Alpha-4, which in turn recruits the catalytic subunit of phosphatase 2A (PP2Ac). This complex is required for targeting of PP2Ac for proteasome-mediated degradation. The MID1 B-box coordinates two zinc ions and adopts a beta/beta/alpha cross-brace structure similar to that of ZZ, PHD, RING and FYVE zinc fingers [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 3DDT_B 2D8U_A 3Q1D_A 2EGM_A 2YVR_B 2DJA_A 2DQ5_A 2JUN_A 2YRG_A 2DID_A ....

>PF10446 DUF2457: Protein of unknown function (DUF2457); InterPro: IPR018853 This entry represents a family of uncharacterised proteins

Probab=95.06  E-value=0.009  Score=56.72  Aligned_cols=10  Identities=10%  Similarity=0.308  Sum_probs=5.6

Q ss_pred             CcceeeCCCC
Q 029923          120 ENQVVPWSST  129 (185)
Q Consensus       120 enqvVP~s~~  129 (185)
                      +.-.+=|+..
T Consensus       119 ~sd~~~WtP~  128 (458)
T PF10446_consen  119 GSDYEFWTPG  128 (458)
T ss_pred             cccceeeccc
Confidence            3456667643

>PF10446 DUF2457: Protein of unknown function (DUF2457); InterPro: IPR018853 This entry represents a family of uncharacterised proteins

Probab=94.07  E-value=0.034  Score=52.90  Aligned_cols=8  Identities=13%  Similarity=-0.022  Sum_probs=3.2

Q ss_pred             CcceeeCC
Q 029923          120 ENQVVPWS  127 (185)
Q Consensus       120 enqvVP~s  127 (185)
                      +...|=|.
T Consensus        87 ~d~~~~~~   94 (458)
T PF10446_consen   87 DDSTVHDF   94 (458)
T ss_pred             cccccccc
Confidence            33344443

>PF09026 CENP-B_dimeris: Centromere protein B dimerisation domain; InterPro: IPR015115 Centromere protein B (CENP-B) interacts with centromeric heterochromatin in chromosomes and binds to a specific subset of alphoid satellite DNA, called the CENP-B box

Probab=92.00  E-value=0.045  Score=42.85  Aligned_cols=10  Identities=40%  Similarity=0.790  Sum_probs=0.0

Q ss_pred             CCCcCCCcce
Q 029923          114 DEDEDEENQV  123 (185)
Q Consensus       114 ~e~ed~enqv  123 (185)
                      ++++++++-|
T Consensus        34 ddee~de~p~   43 (101)
T PF09026_consen   34 DDEEEDEVPV   43 (101)
T ss_dssp             ----------
T ss_pred             cccccccccc
Confidence            3333335544

CENP-B may organise arrays of centromere satellite DNA into a higher order structure, which then directs centromere formation and kinetochore assembly in mammalian chromosomes. The CENP-B dimerisation domain is composed of two alpha-helices, which are folded into an antiparallel configuration. Dimerisation of CENP-B is mediated by this domain, in which monomers dimerise to form a symmetrical, antiparallel, four-helix bundle structure with a large hydrophobic patch in which 23 residues of one monomer form van der Waals contacts with the other monomer. This CENP-B dimer configuration may be suitable for capturing two distant CENP-B boxes during centromeric heterochromatin formation []. ; GO: 0003677 DNA binding, 0003682 chromatin binding, 0006355 regulation of transcription, DNA-dependent, 0000775 chromosome, centromeric region, 0005634 nucleus; PDB: 1UFI_A.

>KOG4367 consensus Predicted Zn-finger protein [Function unknown]

Probab=91.13  E-value=0.042  Score=53.09  Aligned_cols=74  Identities=26%  Similarity=0.454  Sum_probs=60.2

Q ss_pred             CCCCCC-C--CceEEeccCccccChhhccccccCCcCCCCceeeeecc-------------cccCCCCCcccCCCCCCcc
Q 029923            3 KCELCG-S--PAKMFCESDQASLCWDCDAKVHGANFLVANHSRTLLCH-------------VCQSLTPWNGSGPKLGPTI   66 (185)
Q Consensus         3 ~Cd~C~-a--pA~vyC~aD~A~LC~~CDa~VHsAN~La~rH~RvpLC~-------------~C~~~~A~~~sg~C~~daa   66 (185)
                      .|.+|+ +  .|.|+|..+..+.|.-|..+.|-+--.+++|.-+|-.+             .|..++..-.+..|+.+.+
T Consensus       164 kcqlce~a~k~a~v~ceqcdv~yc~pc~~~~hp~rgplakh~l~~~~~grvs~~~s~r~~~~ct~h~~e~~smyc~~ck~  243 (699)
T KOG4367|consen  164 KCQLCEKAPKEATVMCEQCDVFYCDPCRLRCHPPRGPLAKHRLVPPAQGRVSRRLSPRKVSTCTDHELENHSMYCVQCKM  243 (699)
T ss_pred             hhhhhcCChhhhhhhHhhCceEEechHHhccCCCCCchhhcccCCcccCceeeccchhhhhhccCCCCCCceEEEEecCC
Confidence            689998 4  69999999999999999999998777778887665432             4666666666778999999


Q ss_pred             ccccccccCC
Q 029923           67 SVCNVCVGNG   76 (185)
Q Consensus        67 sLC~sCd~~~   76 (185)
                      .+|-.|....
T Consensus       244 pvc~~clee~  253 (699)
T KOG4367|consen  244 PVCYQCLEEG  253 (699)
T ss_pred             hHHHHHHHhh
Confidence            9999996554

>PTZ00415 transmission-blocking target antigen s230; Provisional

Probab=88.77  E-value=0.22  Score=54.50  Aligned_cols=32  Identities=41%  Similarity=0.859  Sum_probs=20.1

Q ss_pred             CCcCCCCCCCCCCCCCCCCCcCCCcceeeCCC
Q 029923           97 DDANEEEDDDDDDDDGGDEDEDEENQVVPWSS  128 (185)
Q Consensus        97 ~d~d~~d~~~~~~~~~~~e~ed~enqvVP~s~  128 (185)
                      ||+||++++|||+++|++|+|+++.||-|+--
T Consensus       154 d~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~d  185 (2849)
T PTZ00415        154 DDDDEDEDEDDDDEEDDEEEEEEEEEIKGFDD  185 (2849)
T ss_pred             CCccccccccccccccccccccccccccCCCc
Confidence            34444444455555556667777788999874

>PF03066 Nucleoplasmin: Nucleoplasmin; InterPro: IPR004301 The nucleophosmin/nucleoplasmin family of chaperones includes nucleophosmin, nucleoplasmin and nucleoplasmin-like proteins

Probab=85.78  E-value=0.24  Score=40.32  Aligned_cols=6  Identities=17%  Similarity=0.257  Sum_probs=2.9

Q ss_pred             eeeecc
Q 029923           42 RTLLCH   47 (185)
Q Consensus        42 RvpLC~   47 (185)
                      +++|+-
T Consensus        63 kv~lAt   68 (149)
T PF03066_consen   63 KVPLAT   68 (149)
T ss_dssp             EEEEEE
T ss_pred             EEEEEE
Confidence            455543

They function as nuclear chaperones which are needed for the proper assembly of nucleosomes and the attainment of proper higher order chromatin structures [].; GO: 0003676 nucleic acid binding; PDB: 2P1B_E 1XB9_I 1XE0_C 1NLQ_A 2VTX_E 1K5J_D 1EJY_N 1EE5_B 3T30_J.

>smart00336 BBOX B-Box-type zinc finger

Probab=84.11  E-value=0.58  Score=28.75  Aligned_cols=34  Identities=12%  Similarity=0.004  Sum_probs=25.7

Q ss_pred             eeeecccccCCCCCcccCCCCCCccccccccccCCCC
Q 029923           42 RTLLCHVCQSLTPWNGSGPKLGPTISVCNVCVGNGSG   78 (185)
Q Consensus        42 RvpLC~~C~~~~A~~~sg~C~~daasLC~sCd~~~h~   78 (185)
                      |.++|..+...+..++   |..+...||..|....|.
T Consensus         2 ~~~~C~~h~~~~~~~~---C~~c~~~iC~~C~~~~H~   35 (42)
T smart00336        2 RPPKCDSHGDEPAEFF---CEECGALLCRTCDEAEHR   35 (42)
T ss_pred             cCCcCCCCCCCceEEE---CCCCCcccccccChhhcC
Confidence            5677888775444443   999999999999877664

>PF14812 PBP1_TM: Transmembrane domain of transglycosylase PBP1 at N-terminal; PDB: 3FWL_A 3VMA_A

Probab=82.80  E-value=0.39  Score=36.27  Aligned_cols=9  Identities=22%  Similarity=0.464  Sum_probs=0.0

Q ss_pred             CcceeeCCC
Q 029923          120 ENQVVPWSS  128 (185)
Q Consensus       120 enqvVP~s~  128 (185)
                      |++.+|+-.
T Consensus        49 eee~m~rK~   57 (81)
T PF14812_consen   49 EEEPMPRKG   57 (81)
T ss_dssp             ---------
T ss_pred             hcccccccc
Confidence            445667653

---

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	185
2ayu_A	417	Nucleosome assembly protein; histone chaperone; 3.	3e-04

>2ayu_A Nucleosome assembly protein; histone chaperone; 3.00A {Saccharomyces cerevisiae} SCOP: d.305.1.1 PDB: 2z2r_A Length = 417

 Score = 39.5 bits (91), Expect = 3e-04
 Identities = 12/49 (24%), Positives = 26/49 (53%)

Query: 85  TNRGETYTDDDYDDANEEEDDDDDDDDGGDEDEDEENQVVPWSSTPPPQ 133
           T     +  ++ ++  +E++D+++DDD G ED+D E+          P+
Sbjct: 361 TGAALEFEFEEDEEEADEDEDEEEDDDHGLEDDDGESAEEQDDFAGRPE 409

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	185
2jun_A	101	Midline-1; B-BOX, TRIM, ring finger, alternative s	97.9
2ffw_A	78	Midline-1; B-BOX, ring finger, zinc-finger, ligase	87.39
2did_A	53	Tripartite motif protein 39; ZF-B-box domian, Zn b	84.32
2yrg_A	59	Tripartite motif-containing protein 5; B-box domai	84.13
1fre_A	42	Nuclear factor XNF7; zinc-binding protein, BBOX, d	82.03

>2jun_A Midline-1; B-BOX, TRIM, ring finger, alternative splicing, coiled coil, cytoplasm, cytoskeleton, disease mutation, ligase, metal-binding; NMR {Homo sapiens}

Probab=97.90  E-value=5.2e-06  Score=59.53  Aligned_cols=77  Identities=16%  Similarity=0.242  Sum_probs=61.2

Q ss_pred             CCCCCCC----CCceEEeccCccccChhhccccccCCcCCCCceee-eec------ccccCCCCCcccCCCCCCcccccc
Q 029923            2 KKCELCG----SPAKMFCESDQASLCWDCDAKVHGANFLVANHSRT-LLC------HVCQSLTPWNGSGPKLGPTISVCN   70 (185)
Q Consensus         2 ~~Cd~C~----apA~vyC~aD~A~LC~~CDa~VHsAN~La~rH~Rv-pLC------~~C~~~~A~~~sg~C~~daasLC~   70 (185)
                      ..|.+|.    .+|+++|..+.+.||..|...+|..++.+++|..+ ++-      ..|..++...+...|..+...+|.
T Consensus         4 ~~C~~C~~~~~~~av~~C~~C~~~~C~~Cl~~~h~~~~~~~~h~l~~~~~~~~~~~~~C~~H~~e~l~~fC~~~~~~iC~   83 (101)
T 2jun_A            4 VLCQFCDQDPAQDAVKTCVTCEVSYCDECLKATHPNKKPFTGHRLIEPIPDSHIRGLMCLEHEDEKVNMYCVTDDQLICA   83 (101)
T ss_dssp             CBCTTCCSSSCCBCCEEETTTTEEECHHHHHHHSCSCSSSTTCCBSSCCCSCCSSCCCCSSCSSSCCCEEETTTTEEECH
T ss_pred             CCCcCCCCCCCCCceEECCcCChHHhHHHCHHHhccCCccCCCeeeccccccCccCCcCcCcCCCcceEECCCCCCccch
Confidence            3699997    37999999999999999999999888888899876 332      247766433334469999999999


Q ss_pred             cccc-CCCC
Q 029923           71 VCVG-NGSG   78 (185)
Q Consensus        71 sCd~-~~h~   78 (185)
                      .|.. ..|.
T Consensus        84 ~C~~~~~H~   92 (101)
T 2jun_A           84 LCKLVGRHR   92 (101)
T ss_dssp             HHHHHTTTS
T ss_pred             hcCCCCCcC
Confidence            9986 6775

>2ffw_A Midline-1; B-BOX, ring finger, zinc-finger, ligase; NMR {Homo sapiens}

Probab=87.39  E-value=0.32  Score=34.04  Aligned_cols=41  Identities=22%  Similarity=0.417  Sum_probs=34.0

Q ss_pred             CCCCCCC----CCceEEeccCccccChhhccccccCCcCCCCcee
Q 029923            2 KKCELCG----SPAKMFCESDQASLCWDCDAKVHGANFLVANHSR   42 (185)
Q Consensus         2 ~~Cd~C~----apA~vyC~aD~A~LC~~CDa~VHsAN~La~rH~R   42 (185)
                      ..|++|.    .+|+..|....+.||..|=...|...+.+++|.=
T Consensus        31 v~C~~C~~~~~~~A~ksCl~C~~s~C~~hl~~~H~~~~~~~~H~L   75 (78)
T 2ffw_A           31 VLCQFCDQDPAQDAVKTCVTCEVSYCDECLKATHPNKKPFTGHRL   75 (78)
T ss_dssp             CBCSSCCSSSCCBCCEEETTTTEEECHHHHHHHSCCCSSSCSCCC
T ss_pred             ccCCcCCCCCCCCCeeEccCccchhhhhhhHhhcCCCCCCCCCcc
Confidence            3799996    3699999999999999998877877777778863

>2did_A Tripartite motif protein 39; ZF-B-box domian, Zn binding, one sequence two fold, NPPSFA; NMR {Homo sapiens} SCOP: g.43.1.1 PDB: 2dif_A

Probab=84.32  E-value=0.97  Score=28.71  Aligned_cols=39  Identities=26%  Similarity=0.532  Sum_probs=28.4

Q ss_pred             CCCCCCCCceEEeccCccccChhhcc-ccccCCcCCCCceeeeecc
Q 029923            3 KCELCGSPAKMFCESDQASLCWDCDA-KVHGANFLVANHSRTLLCH   47 (185)
Q Consensus         3 ~Cd~C~apA~vyC~aD~A~LC~~CDa-~VHsAN~La~rH~RvpLC~   47 (185)
                      +|..-+.+-.|||..|...+|..|-. .-|      +.|..++|-.
T Consensus        10 ~C~~H~e~l~lfC~~d~~~iC~~C~~~~~H------~~H~~~~l~e   49 (53)
T 2did_A           10 LCPQHHEALSLFCYEDQEAVCLICAISHTH------RAHTVVPLSG   49 (53)
T ss_dssp             BCTTTCCBCCEEESSSCSEECHHHHTSSTT------TTSCEEECCC
T ss_pred             cChhhCCeeeEEeCCCCeEEeccccCCCCC------CCCcEeeHHH
Confidence            45555567789999999999999976 455      3566666543

>2yrg_A Tripartite motif-containing protein 5; B-box domain, ring finger protein 88, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=84.13  E-value=0.76  Score=30.28  Aligned_cols=38  Identities=26%  Similarity=0.705  Sum_probs=27.7

Q ss_pred             CCCCCCCCceEEeccCccccChhhcc-ccccCCcCCCCceeeeec
Q 029923            3 KCELCGSPAKMFCESDQASLCWDCDA-KVHGANFLVANHSRTLLC   46 (185)
Q Consensus         3 ~Cd~C~apA~vyC~aD~A~LC~~CDa-~VHsAN~La~rH~RvpLC   46 (185)
                      +|..-+.+-.|||..|.+.+|..|-. .-|      +.|..++|-
T Consensus        16 ~C~~H~e~L~lfC~~d~~~iC~~C~~s~eH------~~H~~~~l~   54 (59)
T 2yrg_A           16 HCARHGEKLLLFCQEDGKVICWLCERSQEH------RGHHTFPTS   54 (59)
T ss_dssp             BCTTTCCBCCEEETTTCSEECHHHHTSTTT------TTCCEEECC
T ss_pred             cChhhCceeeeecCCCCcEEecccCCCCcC------CCCcEeeHH
Confidence            45555567789999999999999976 445      245555554

>1fre_A Nuclear factor XNF7; zinc-binding protein, BBOX, development, MID-blastula- transition; NMR {Xenopus laevis} SCOP: g.43.1.1

Probab=82.03  E-value=0.86  Score=27.54  Aligned_cols=29  Identities=28%  Similarity=0.594  Sum_probs=23.0

Q ss_pred             CCCCCCCCceEEeccCccccChhhcc-ccc
Q 029923            3 KCELCGSPAKMFCESDQASLCWDCDA-KVH   31 (185)
Q Consensus         3 ~Cd~C~apA~vyC~aD~A~LC~~CDa-~VH   31 (185)
                      +|..-+.+-.|||..|.+.+|..|-. .-|
T Consensus         5 ~C~~H~e~l~lfC~~d~~~iC~~C~~~~~H   34 (42)
T 1fre_A            5 KCSEHDERLKLYCKDDGTLSCVICRDSLKH   34 (42)
T ss_dssp             CCCSSCSSCCCCCCSSSSSSCCTTSSCSSC
T ss_pred             cchhhCCeeeEEeCCCCeEEeccCCCCCCC
Confidence            45555567789999999999999976 445

---

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

No hit with probability above 80.00