Psyllid ID: psy13378

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270--
Protein Sequence
MADGGVWKLQDDGYLNIDADPDSVIYHPNLNILIVENEFSVSKLCYDYGLSHSELKKRANLLKFYTRNSTPGNPEPIQLEHKLKLAYTCKVCGTRNSHLISKHSYEKGVIKLKHKLKLAYTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNNHLIADNLKWFTDLKPGVTNIEHILAEKGEQGCKGLFCLSHDIKLNTNIVRLMIETCLCHLIRETHGSHHLIADNLKWFSDLKPGVTNIEHILAEKGEQVRRIDSNGAIELIEDEKKLLS
Secondary Structure (PSIPRED)
ccccccEEEEcccccccccccccccccccccEEEEEccEEEEccccccccccccccccccccEEEEcccccccccccccccccccccccccccccccccccccccccccccccccEEEEEEcccccccccEEEccccccccEEEEEcccccccEEEEcccccccccccccccHHHHHHHHcccEEEEEEEccccccccccccEEEEEEccccccccccccccccccccccccccccccccHHHHHHHccccEEEEcccccEEEEccHHcccc
Secondary Structure Prediction (SSPRO)
cccccEEEEcccccEEEccccccEEEccccEEEEEEccEEEcEEEEcccccccEEcccccEEEEEEccccccccccccHHccccccHccccccccccccccccccccccEcccccEEEEEEEcccccccccHEEHHHHcccEEEEEcccccccEEEEcccccccccccccccHHHHHHHcccEEEEEEccccccEEEEccEEEEEEEEcccHHHHHHccccEEEEcccccccccccccccHHHHHHHcccEEEEEEccccEEEEcccHHccc
Coil and Loop (DISEMBL)
madggvwklqddgylnidadpdsviyhpnlniLIVENEFSVSKLCYDYGLSHSELKKRANLLKFYtrnstpgnpepiqlEHKLKLAYTckvcgtrnshliskHSYEKGVIKLKHKLKLAYtckvcgtrnshliskhsYEKGVVIVKcegcsnnhliadnlkwftdlkpgvtNIEHILAekgeqgckglfCLSHDIKLNTNIVRLMIETCLCHLirethgshhliadnlkwfsdlkpgvtNIEHILAEkgeqvrridsngaIELIEDEKKLLS
Flexible Loop (DISEMBL)
MADGGVWKLQDDGYLNIDADPDSVIYHPNLNILIVENEFSVSKLCYDYGLSHSELKKRANLLKFYTrnstpgnpepIQLEHKLKLAYTCKVCGTrnshliskhsYEKGVIKLKHKLKLAYTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNNHLIADNLKWFTDLKPGVTNIEHILAEKGEQGCKGLFCLSHDIKLNTNIVRLMIETCLCHLIRETHGSHHLIADNLKWFSDLKPGVTNIEHilaekgeqvrridsngaieliedekklls
Low Complexity Region (SEG)
MADGGVWKLQDDGYLNIDADPDSVIYHPNLNILIVENEFSVSKLCYDYGLSHSELKKRANLLKFYTRNSTPGNPEPIQLEHKLKLAYTCKVCGTRNSHLISKHSYEKGVIKLKHKLKLAYTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNNHLIADNLKWFTDLKPGVTNIEHILAEKGEQGCKGLFCLSHDIKLNTNIVRLMIETCLCHLIRETHGSHHLIADNLKWFSDLKPGVTNIEHILAEKGEQVRRIDSNGAIELIEDEKKLLS
Disordered region (IsUnstruct)
*****VWKLQDDGYLNIDADPDSVIYHPNLNILIVENEFSVSKLCYDYGLSHSELKKRANLLKFYTR*********IQLEHKLKLAYTCKVCGTRNSHLISKHSYEKGVIKLKHKLKLAYTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNNHLIADNLKWFTDLKPGVTNIEHILAEKGEQGCKGLFCLSHDIKLNTNIVRLMIETCLCHLIRETHGSHHLIADNLKWFSDLKPGVTNIEHILAEKGEQV********************
Disordered Region (DISOPRED)
****GVWKLQDDGYLNIDADPDSVIYHPNLNILIVENEFSVSKLCYDYGL*******************************************************************LAYTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNNHLIADNLKWFTDLKPGVTNIEHILAEKGEQGCKGLFCLSHDIKLNTNIVRLMIETCLCHLIRETHGSHHLIADNLKWFSDLKPGVTNIEHILAE****VRRIDSNGAIELI********
Disordered Region (DISEMBL)
MADGGVWKLQDDGYLNIDADPDSVIYHPNLNILIVENEFSVSKLCYDYGLSHSELKKRANLLKFYTRNSTPGNPEPIQLEHKLKLAYTCKVCGTRNSHLISKHSYEKGVIKLKHKLKLAYTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNNHLIADNLKWFTDLKPGVTNIEHILAEKGEQGCKGLFCLSHDIKLNTNIVRLMIETCLCHLIRETHGSHHLIADNLKWFSDLKPGVTNIEHILAEKGEQVRRIDSNGAIELIEDEKKLLS
Disordered Region (DISPRO)
***GGVWKLQDDGYLNIDADPDSVIYHPNLNILIVENEFSVSKLCYDYGLSHSELKKRANLLKFYTRNSTPGNPEPIQLEHKLKLAYTCKVCGT*************GVIKLKHKLKLAYTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNNHLIADNLKWFTDLKPGVTNIEHILAEKGEQGCKGLFCLSHDIKLNTNIVRLMIETCLCHLIRETHGSHHLIADNLKWFSDLKPGVTNIEHILAEKGEQVRRIDSNGAIELIEDE*****
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MADGGVWKLQDDGYLNIDADPDSVIYHPNLNILIVENEFSVSKLCYDYGLSHSELKKRANLLKFYTRNSTPGNPEPIQLEHKLKLAYTCKVCGTRNSHLISKHSYEKGVIKLKHKLKLAYTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNNHLIADNLKWFTDLKPGVTNIEHILAEKGEQGCKGLFCLSHDIKLNTNIVRLMIETCLCHLIRETHGSHHLIADNLKWFSDLKPGVTNIEHILAEKGEQVRRIDSNGAIELIEDEKKLLS
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	272	2.2.26 [Sep-21-2011]
Q9D113	177	DNL-type zinc finger prot	yes	N/A	0.272	0.418	0.605	6e-19
Q0IH40	188	DNL-type zinc finger prot	N/A	N/A	0.242	0.351	0.671	1e-18
Q5SXM8	178	DNL-type zinc finger prot	yes	N/A	0.272	0.415	0.592	3e-18
A1L1P7	183	DNL-type zinc finger prot	yes	N/A	0.235	0.349	0.676	3e-17
P42844	174	Mitochondrial protein imp	yes	N/A	0.25	0.390	0.464	4e-11
A6ZSH0	174	Mitochondrial protein imp	N/A	N/A	0.25	0.390	0.464	4e-11
B5VQB0	174	Mitochondrial protein imp	N/A	N/A	0.25	0.390	0.464	4e-11
B3LPE4	174	Mitochondrial protein imp	N/A	N/A	0.25	0.390	0.464	4e-11
Q09759	175	Uncharacterized protein C	yes	N/A	0.275	0.428	0.435	5e-11

>sp|Q9D113|DNLZ_MOUSE DNL-type zinc finger protein OS=Mus musculus GN=Dnlz PE=2 SV=1

 Score = 94.7 bits (234), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 46/76 (60%), Positives = 57/76 (75%), Gaps = 2/76 (2%)

Query: 108 GVIKLKHKLKLAYTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNNHLIADNLKWFTDLK 167
           G ++  H  +L YTCKVCGTR+S  ISK +Y +GVVIV C GC N+H+IADNL WF+DLK
Sbjct: 66  GRVEADH-YQLVYTCKVCGTRSSKRISKLAYHQGVVIVTCPGCQNHHIIADNLSWFSDLK 124

Query: 168 PGVTNIEHILAEKGEQ 183
            G  NIE ILA +GE+
Sbjct: 125 -GKRNIEEILAARGEE 139

Mus musculus (taxid: 10090)

>sp|Q0IH40|DNLZ_XENLA DNL-type zinc finger protein OS=Xenopus laevis GN=dnlz PE=2 SV=1

 Score = 94.0 bits (232), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 45/67 (67%), Positives = 53/67 (79%), Gaps = 1/67 (1%)

Query: 117 KLAYTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNNHLIADNLKWFTDLKPGVTNIEHI 176
           +L YTCKVC TR+S  ISK +Y KGVVIV+C GC N+H+IADNL WF+DL+ G  NIE I
Sbjct: 83  RLIYTCKVCATRSSKTISKVAYHKGVVIVRCPGCENHHIIADNLGWFSDLE-GRRNIEEI 141

Query: 177 LAEKGEQ 183
           LA KGEQ
Sbjct: 142 LAAKGEQ 148

Xenopus laevis (taxid: 8355)

>sp|Q5SXM8|DNLZ_HUMAN DNL-type zinc finger protein OS=Homo sapiens GN=DNLZ PE=2 SV=1

 Score = 92.4 bits (228), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 45/76 (59%), Positives = 55/76 (72%), Gaps = 2/76 (2%)

Query: 108 GVIKLKHKLKLAYTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNNHLIADNLKWFTDLK 167
           G ++  H  +L YTCKVCGTR+S  ISK +Y +GVVIV C GC N+H+IADNL WF+DL 
Sbjct: 62  GRVEAAH-YQLVYTCKVCGTRSSKRISKLAYHQGVVIVTCPGCQNHHIIADNLGWFSDLN 120

Query: 168 PGVTNIEHILAEKGEQ 183
            G  NIE IL  +GEQ
Sbjct: 121 -GKRNIEEILTARGEQ 135

Homo sapiens (taxid: 9606)

>sp|A1L1P7|DNLZ_DANRE DNL-type zinc finger protein OS=Danio rerio GN=dnlz PE=2 SV=1

 Score = 89.0 bits (219), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 44/65 (67%), Positives = 50/65 (76%), Gaps = 1/65 (1%)

Query: 118 LAYTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNNHLIADNLKWFTDLKPGVTNIEHIL 177
           L YTCKVC TR+   ISK +Y KGVVIV C GC N+H+IADNLKWF+DL+ G  NIE IL
Sbjct: 83  LVYTCKVCSTRSMKKISKLAYHKGVVIVTCPGCKNHHVIADNLKWFSDLE-GKRNIEEIL 141

Query: 178 AEKGE 182
           A KGE
Sbjct: 142 AAKGE 146

Danio rerio (taxid: 7955)

>sp|P42844|ZIM17_YEAST Mitochondrial protein import protein ZIM17 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=ZIM17 PE=1 SV=2

 Score = 68.6 bits (166), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 33/71 (46%), Positives = 45/71 (63%), Gaps = 3/71 (4%)

Query: 113 KHKLKLAYTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNNHLIADNLKWFTDLKPGVTN 172
           K K+ +A+TCK C TR+SH +SK +YEKG V++ C  C   HLIAD+LK F D       
Sbjct: 66  KPKMMIAFTCKKCNTRSSHTMSKQAYEKGTVLISCPHCKVRHLIADHLKIFHDHH---VT 122

Query: 173 IEHILAEKGEQ 183
           +E ++   GEQ
Sbjct: 123 VEQLMKANGEQ 133

Involved in protein import into mitochondria. Acts as a Hsp70-specific chaperone that prevents self-aggregation of the matrix Hsp70 chaperones SSC1 (mtHSP70) and SSQ1, thereby maintaining their function in mitochondrial protein import and Fe/S protein biosynthesis. May act together with PAM18 as co-chaperone to facilitate recognition and folding of imported proteins by SSC1 in the mitochondrial matrix.

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (taxid: 559292)

>sp|A6ZSH0|ZIM17_YEAS7 Mitochondrial protein import protein ZIM17 OS=Saccharomyces cerevisiae (strain YJM789) GN=ZIM17 PE=3 SV=2

 Score = 68.6 bits (166), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 33/71 (46%), Positives = 45/71 (63%), Gaps = 3/71 (4%)

Query: 113 KHKLKLAYTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNNHLIADNLKWFTDLKPGVTN 172
           K K+ +A+TCK C TR+SH +SK +YEKG V++ C  C   HLIAD+LK F D       
Sbjct: 66  KPKMMIAFTCKKCNTRSSHTMSKQAYEKGTVLISCPHCKVRHLIADHLKIFHDHH---VT 122

Query: 173 IEHILAEKGEQ 183
           +E ++   GEQ
Sbjct: 123 VEQLMKANGEQ 133

Involved in protein import into mitochondria. Acts as a Hsp70-specific chaperone that prevents self-aggregation of the matrix Hsp70 chaperones SSC1 (mtHSP70) and SSQ1, thereby maintaining their function in mitochondrial protein import and Fe/S protein biosynthesis. May act together with PAM18 as co-chaperone to facilitate recognition and folding of imported proteins by SSC1 in the mitochondrial matrix.

Saccharomyces cerevisiae (strain YJM789) (taxid: 307796)

>sp|B5VQB0|ZIM17_YEAS6 Mitochondrial protein import protein ZIM17 OS=Saccharomyces cerevisiae (strain AWRI1631) GN=ZIM17 PE=3 SV=2

 Score = 68.6 bits (166), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 33/71 (46%), Positives = 45/71 (63%), Gaps = 3/71 (4%)

Query: 113 KHKLKLAYTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNNHLIADNLKWFTDLKPGVTN 172
           K K+ +A+TCK C TR+SH +SK +YEKG V++ C  C   HLIAD+LK F D       
Sbjct: 66  KPKMMIAFTCKKCNTRSSHTMSKQAYEKGTVLISCPHCKVRHLIADHLKIFHDHH---VT 122

Query: 173 IEHILAEKGEQ 183
           +E ++   GEQ
Sbjct: 123 VEQLMKANGEQ 133

Involved in protein import into mitochondria. Acts as a Hsp70-specific chaperone that prevents self-aggregation of the matrix Hsp70 chaperones SSC1 (mtHSP70) and SSQ1, thereby maintaining their function in mitochondrial protein import and Fe/S protein biosynthesis. May act together with PAM18 as co-chaperone to facilitate recognition and folding of imported proteins by SSC1 in the mitochondrial matrix.

Saccharomyces cerevisiae (strain AWRI1631) (taxid: 545124)

>sp|B3LPE4|ZIM17_YEAS1 Mitochondrial protein import protein ZIM17 OS=Saccharomyces cerevisiae (strain RM11-1a) GN=ZIM17 PE=3 SV=2

 Score = 68.6 bits (166), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 33/71 (46%), Positives = 45/71 (63%), Gaps = 3/71 (4%)

Query: 113 KHKLKLAYTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNNHLIADNLKWFTDLKPGVTN 172
           K K+ +A+TCK C TR+SH +SK +YEKG V++ C  C   HLIAD+LK F D       
Sbjct: 66  KPKMMIAFTCKKCNTRSSHTMSKQAYEKGTVLISCPHCKVRHLIADHLKIFHDHH---VT 122

Query: 173 IEHILAEKGEQ 183
           +E ++   GEQ
Sbjct: 123 VEQLMKANGEQ 133

Involved in protein import into mitochondria. Acts as a Hsp70-specific chaperone that prevents self-aggregation of the matrix Hsp70 chaperones SSC1 (mtHSP70) and SSQ1, thereby maintaining their function in mitochondrial protein import and Fe/S protein biosynthesis. May act together with PAM18 as co-chaperone to facilitate recognition and folding of imported proteins by SSC1 in the mitochondrial matrix.

Saccharomyces cerevisiae (strain RM11-1a) (taxid: 285006)

>sp|Q09759|YA72_SCHPO Uncharacterized protein C24H6.02c OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=SPAC24H6.02c PE=4 SV=1

 Score = 68.6 bits (166), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 34/78 (43%), Positives = 50/78 (64%), Gaps = 3/78 (3%)

Query: 110 IKLKHKLKLAYTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNNHLIADNLKWFTDLKPG 169
           ++ K    +++TC VC TR++H  SK +Y  G V+V+C  C N HL+AD+LK F++ +  
Sbjct: 70  LQPKPTYNVSFTCTVCNTRSNHNFSKQAYHNGTVLVQCPKCKNRHLMADHLKIFSEER-- 127

Query: 170 VTNIEHILAEKGEQGCKG 187
              IE ILA+KGE   KG
Sbjct: 128 -VTIEDILAKKGETFKKG 144

Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)

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	272
158294079	143	AGAP005377-PA [Anopheles gambiae str. PE	0.459	0.874	0.477	3e-20
194768927	169	GF22240 [Drosophila ananassae] gi|190617	0.264	0.426	0.726	4e-20
270004978	160	hypothetical protein TcasGA2_TC030565 [T	0.286	0.487	0.658	5e-20
42415411	179	LP13032p [Drosophila melanogaster]	0.264	0.402	0.698	6e-20
221329943	174	CG12379 [Drosophila melanogaster] gi|220	0.264	0.413	0.698	7e-20
194894355	121	GG19380 [Drosophila erecta] gi|190649698	0.341	0.768	0.554	7e-20
195355385	119	GM22535 [Drosophila sechellia] gi|194129	0.264	0.605	0.698	9e-20
195566950	119	GD15783 [Drosophila simulans] gi|1942044	0.264	0.605	0.698	1e-19
198471620	178	GA11595 [Drosophila pseudoobscura pseudo	0.264	0.404	0.671	1e-19
157114673	136	hypothetical protein AaeL_AAEL006952 [Ae	0.426	0.852	0.469	1e-19

>gi|158294079|ref|XP_315385.4| AGAP005377-PA [Anopheles gambiae str. PEST] gi|157015398|gb|EAA11296.4| AGAP005377-PA [Anopheles gambiae str. PEST]

 Score =  104 bits (260), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 65/136 (47%), Positives = 79/136 (58%), Gaps = 11/136 (8%)

Query: 60  NLLKFYTRNSTPGNPEPIQLEHKLKLAYTCKVCGTRNSHLI---------SKHSYEKGVI 110
           +LL+   R++      P Q     +LA        RNS            S  + E G I
Sbjct: 6   SLLRLVWRSNVHQLATPAQTRTTYRLASLGWNSSPRNSFCTNVTALEAQQSGPNEEVGRI 65

Query: 111 KLKHKLKLAYTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNNHLIADNLKWFTDLKPGV 170
           + + K+ L YTCKVC  RN H+ISK +YEKGVVIV C+GCSN+HLIADNL WFTDL  G 
Sbjct: 66  QPR-KMNLIYTCKVCNHRNMHMISKQAYEKGVVIVTCDGCSNHHLIADNLNWFTDLN-GK 123

Query: 171 TNIEHILAEKGEQGCK 186
            NIE ILAEKGE+  K
Sbjct: 124 RNIEEILAEKGEKVTK 139

Source: Anopheles gambiae str. PEST

Species: Anopheles gambiae

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|194768927|ref|XP_001966562.1| GF22240 [Drosophila ananassae] gi|190617326|gb|EDV32850.1| GF22240 [Drosophila ananassae]

 Score =  104 bits (260), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 53/73 (72%), Positives = 59/73 (80%), Gaps = 1/73 (1%)

Query: 111 KLKHKLKLAYTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNNHLIADNLKWFTDLKPGV 170
           +L+ KL L YTCKVC TRN   ISK +Y+KGVVIV CEGCSN+HLIADNLKWFTDL  G 
Sbjct: 81  ELQTKLTLIYTCKVCETRNLKTISKVAYQKGVVIVTCEGCSNHHLIADNLKWFTDLD-GK 139

Query: 171 TNIEHILAEKGEQ 183
            NIE ILAEKGE+
Sbjct: 140 RNIEEILAEKGEK 152

Source: Drosophila ananassae

Species: Drosophila ananassae

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|270004978|gb|EFA01426.1| hypothetical protein TcasGA2_TC030565 [Tribolium castaneum]

 Score =  104 bits (259), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 52/79 (65%), Positives = 59/79 (74%), Gaps = 1/79 (1%)

Query: 104 SYEKGVIKLKHKLKLAYTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNNHLIADNLKWF 163
           S    + KL+ KL L +TCKVC  RN+  ISK +Y+KGVVIVKC GC+NNHLIADNL WF
Sbjct: 61  STSTPLAKLEGKLMLGFTCKVCSARNTKFISKVAYQKGVVIVKCSGCNNNHLIADNLNWF 120

Query: 164 TDLKPGVTNIEHILAEKGE 182
           TDL  G  NIE ILAEKGE
Sbjct: 121 TDLN-GKRNIEEILAEKGE 138

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|42415411|gb|AAS15675.1| LP13032p [Drosophila melanogaster]

 Score =  103 bits (258), Expect = 6e-20,   Method: Compositional matrix adjust.
 Identities = 51/73 (69%), Positives = 59/73 (80%), Gaps = 1/73 (1%)

Query: 111 KLKHKLKLAYTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNNHLIADNLKWFTDLKPGV 170
           KL+ K++L YTCKVC TRN   ISK +Y++GVVIV CEGCSN+HLIADNL WFTDL  G 
Sbjct: 92  KLEAKMQLIYTCKVCQTRNMKTISKLAYQRGVVIVTCEGCSNHHLIADNLNWFTDLD-GK 150

Query: 171 TNIEHILAEKGEQ 183
            NIE ILAEKGE+
Sbjct: 151 RNIEEILAEKGEK 163

Source: Drosophila melanogaster

Species: Drosophila melanogaster

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|221329943|ref|NP_573061.2| CG12379 [Drosophila melanogaster] gi|220901782|gb|AAF48497.2| CG12379 [Drosophila melanogaster]

 Score =  103 bits (257), Expect = 7e-20,   Method: Compositional matrix adjust.
 Identities = 51/73 (69%), Positives = 59/73 (80%), Gaps = 1/73 (1%)

Query: 111 KLKHKLKLAYTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNNHLIADNLKWFTDLKPGV 170
           KL+ K++L YTCKVC TRN   ISK +Y++GVVIV CEGCSN+HLIADNL WFTDL  G 
Sbjct: 87  KLEAKMQLIYTCKVCQTRNMKTISKLAYQRGVVIVTCEGCSNHHLIADNLNWFTDLD-GK 145

Query: 171 TNIEHILAEKGEQ 183
            NIE ILAEKGE+
Sbjct: 146 RNIEEILAEKGEK 158

Source: Drosophila melanogaster

Species: Drosophila melanogaster

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|194894355|ref|XP_001978049.1| GG19380 [Drosophila erecta] gi|190649698|gb|EDV46976.1| GG19380 [Drosophila erecta]

 Score =  103 bits (257), Expect = 7e-20,   Method: Compositional matrix adjust.
 Identities = 56/101 (55%), Positives = 69/101 (68%), Gaps = 8/101 (7%)

Query: 90  KVCGTRNSHLISKHSYEKGVI-------KLKHKLKLAYTCKVCGTRNSHLISKHSYEKGV 142
           +V G R +    +   +K V        KL+ K++L YTCKVC TRN   ISK +Y++GV
Sbjct: 6   RVTGYRRNRDFEEDDADKTVATNSIPLAKLEGKMQLIYTCKVCQTRNMKTISKLAYQRGV 65

Query: 143 VIVKCEGCSNNHLIADNLKWFTDLKPGVTNIEHILAEKGEQ 183
           VIV CEGCSN+HLIADNL WFTDL+ G  NIE ILAEKGE+
Sbjct: 66  VIVTCEGCSNHHLIADNLNWFTDLE-GKRNIEEILAEKGEK 105

Source: Drosophila erecta

Species: Drosophila erecta

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195355385|ref|XP_002044172.1| GM22535 [Drosophila sechellia] gi|194129461|gb|EDW51504.1| GM22535 [Drosophila sechellia]

 Score =  103 bits (256), Expect = 9e-20,   Method: Compositional matrix adjust.
 Identities = 51/73 (69%), Positives = 59/73 (80%), Gaps = 1/73 (1%)

Query: 111 KLKHKLKLAYTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNNHLIADNLKWFTDLKPGV 170
           KL+ K++L YTCKVC TRN   ISK +Y++GVVIV CEGCSN+HLIADNL WFTDL  G 
Sbjct: 32  KLEAKMQLIYTCKVCQTRNMKTISKLAYQRGVVIVTCEGCSNHHLIADNLNWFTDL-DGK 90

Query: 171 TNIEHILAEKGEQ 183
            NIE ILAEKGE+
Sbjct: 91  RNIEEILAEKGEK 103

Source: Drosophila sechellia

Species: Drosophila sechellia

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195566950|ref|XP_002107038.1| GD15783 [Drosophila simulans] gi|194204435|gb|EDX18011.1| GD15783 [Drosophila simulans]

 Score =  103 bits (256), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 51/73 (69%), Positives = 59/73 (80%), Gaps = 1/73 (1%)

Query: 111 KLKHKLKLAYTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNNHLIADNLKWFTDLKPGV 170
           KL+ K++L YTCKVC TRN   ISK +Y++GVVIV CEGCSN+HLIADNL WFTDL  G 
Sbjct: 32  KLEAKMQLIYTCKVCQTRNMKTISKLAYQRGVVIVTCEGCSNHHLIADNLNWFTDL-DGK 90

Query: 171 TNIEHILAEKGEQ 183
            NIE ILAEKGE+
Sbjct: 91  RNIEEILAEKGEK 103

Source: Drosophila simulans

Species: Drosophila simulans

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|198471620|ref|XP_001355684.2| GA11595 [Drosophila pseudoobscura pseudoobscura] gi|198145999|gb|EAL32743.2| GA11595 [Drosophila pseudoobscura pseudoobscura]

 Score =  103 bits (256), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 49/73 (67%), Positives = 60/73 (82%), Gaps = 1/73 (1%)

Query: 111 KLKHKLKLAYTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNNHLIADNLKWFTDLKPGV 170
           +L+ K++L YTCK+C TRN   ISK +Y++GVVIV CEGC+N+HLIADNLKWFTDL  G 
Sbjct: 85  ELQTKMQLIYTCKICQTRNMKTISKVAYQRGVVIVTCEGCANHHLIADNLKWFTDLN-GK 143

Query: 171 TNIEHILAEKGEQ 183
            NIE ILAEKGE+
Sbjct: 144 RNIEEILAEKGEK 156

Source: Drosophila pseudoobscura pseudoobscura

Species: Drosophila pseudoobscura

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|157114673|ref|XP_001652366.1| hypothetical protein AaeL_AAEL006952 [Aedes aegypti] gi|108877185|gb|EAT41410.1| AAEL006952-PA [Aedes aegypti]

 Score =  102 bits (255), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 61/130 (46%), Positives = 80/130 (61%), Gaps = 14/130 (10%)

Query: 60  NLLKFYTRNSTPGNPEPIQLEHKLKLAYTCKVCGTRNSHLISKHSYEKGVIKLKH----- 114
           N+L+ Y R + P +P  +   H  +     ++   +N  + S  S E  + + +H     
Sbjct: 9   NVLRQYCR-TIPVSPLGVLNSHIGR-----RIPSLQNQIIRSCASLETHICRGQHLGTIE 62

Query: 115 --KLKLAYTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNNHLIADNLKWFTDLKPGVTN 172
             +L+L YTCK C  RNSH ISK +YEKGVVIV CEGC+N+H+IADNL WFTDL  G  N
Sbjct: 63  SNRLQLTYTCKRCAARNSHFISKQAYEKGVVIVTCEGCNNHHIIADNLNWFTDLN-GKKN 121

Query: 173 IEHILAEKGE 182
           IE ILAEKGE
Sbjct: 122 IEEILAEKGE 131

Source: Aedes aegypti

Species: Aedes aegypti

Genus: Aedes

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

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	272
FB|FBgn0030676	174	CG12379 [Drosophila melanogast	0.264	0.413	0.698	1.3e-22
RGD|1308635	173	Dnlz "DNL-type zinc finger" [R	0.459	0.722	0.470	1.5e-21
MGI|MGI:106559	177	Dnlz "DNL-type zinc finger" [M	0.272	0.418	0.605	5.7e-20
ZFIN|ZDB-GENE-070112-1482	183	zgc:158228 "zgc:158228" [Danio	0.268	0.398	0.613	5.1e-19
UNIPROTKB|Q5SXM8	178	DNLZ "DNL-type zinc finger pro	0.272	0.415	0.592	4e-19
UNIPROTKB|E1BGR3	169	LOC100848156 "Uncharacterized	0.242	0.390	0.641	1.1e-18
UNIPROTKB|F1PCL0	171	DNLZ "Uncharacterized protein"	0.253	0.403	0.6	1.7e-18
UNIPROTKB|F1NF52	178	DNLZ "Uncharacterized protein"	0.272	0.415	0.539	1.4e-16
WB|WBGene00018723	119	F53A3.7 [Caenorhabditis elegan	0.257	0.588	0.547	2.6e-15
TAIR|locus:1006230204	223	ZR3 "zinc ribbon 3" [Arabidops	0.272	0.331	0.474	5.4e-15

FB|FBgn0030676 CG12379 [Drosophila melanogaster (taxid:7227)]

 Score = 262 (97.3 bits), Expect = 1.3e-22, P = 1.3e-22
 Identities = 51/73 (69%), Positives = 59/73 (80%)

Query:   111 KLKHKLKLAYTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNNHLIADNLKWFTDLKPGV 170
             KL+ K++L YTCKVC TRN   ISK +Y++GVVIV CEGCSN+HLIADNL WFTDL  G 
Sbjct:    87 KLEAKMQLIYTCKVCQTRNMKTISKLAYQRGVVIVTCEGCSNHHLIADNLNWFTDLD-GK 145

Query:   171 TNIEHILAEKGEQ 183
              NIE ILAEKGE+
Sbjct:   146 RNIEEILAEKGEK 158

GO:0008270 "zinc ion binding" evidence=IEA

RGD|1308635 Dnlz "DNL-type zinc finger" [Rattus norvegicus (taxid:10116)]

 Score = 252 (93.8 bits), Expect = 1.5e-21, P = 1.5e-21
 Identities = 63/134 (47%), Positives = 82/134 (61%)

Query:    55 LKKRANLLKFY-TRNSTPGNPEPIQLEHKLKLAYTCK--VCGTRNSHLI--SKHSYEKGV 109
             L +   LL+   TR+S P   +   L  +LK A   +    G R+S     S+H+   G 
Sbjct:     6 LSRMPTLLRSVRTRDSGPR--QLWDLGARLKTAKRLRGWAWGWRSSSSAPGSEHAAALGR 63

Query:   110 IKLKHKLKLAYTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNNHLIADNLKWFTDLKPG 169
             +K  H  +L YTCKVCGTR+S  ISK +Y +GVVIV C GC N+H+IADNL WF+DLK G
Sbjct:    64 VKADH-YQLVYTCKVCGTRSSKHISKLAYHQGVVIVTCPGCQNHHIIADNLSWFSDLK-G 121

Query:   170 VTNIEHILAEKGEQ 183
               NIE ILA +GE+
Sbjct:   122 KRNIEEILAARGEE 135

GO:0005739 "mitochondrion" evidence=IEA;ISO

GO:0008270 "zinc ion binding" evidence=IEA

MGI|MGI:106559 Dnlz "DNL-type zinc finger" [Mus musculus (taxid:10090)]

 Score = 237 (88.5 bits), Expect = 5.7e-20, P = 5.7e-20
 Identities = 46/76 (60%), Positives = 57/76 (75%)

Query:   108 GVIKLKHKLKLAYTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNNHLIADNLKWFTDLK 167
             G ++  H  +L YTCKVCGTR+S  ISK +Y +GVVIV C GC N+H+IADNL WF+DLK
Sbjct:    66 GRVEADH-YQLVYTCKVCGTRSSKRISKLAYHQGVVIVTCPGCQNHHIIADNLSWFSDLK 124

Query:   168 PGVTNIEHILAEKGEQ 183
              G  NIE ILA +GE+
Sbjct:   125 -GKRNIEEILAARGEE 139

GO:0003674 "molecular_function" evidence=ND

GO:0005739 "mitochondrion" evidence=IDA

GO:0008150 "biological_process" evidence=ND

GO:0008270 "zinc ion binding" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

ZFIN|ZDB-GENE-070112-1482 zgc:158228 "zgc:158228" [Danio rerio (taxid:7955)]

 Score = 228 (85.3 bits), Expect = 5.1e-19, P = 5.1e-19
 Identities = 46/75 (61%), Positives = 54/75 (72%)

Query:   108 GVIKLKHKLKLAYTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNNHLIADNLKWFTDLK 167
             G ++  H   L YTCKVC TR+   ISK +Y KGVVIV C GC N+H+IADNLKWF+DL+
Sbjct:    74 GQLQSTH-YHLVYTCKVCSTRSMKKISKLAYHKGVVIVTCPGCKNHHVIADNLKWFSDLE 132

Query:   168 PGVTNIEHILAEKGE 182
              G  NIE ILA KGE
Sbjct:   133 -GKRNIEEILAAKGE 146

GO:0008270 "zinc ion binding" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

GO:0046872 "metal ion binding" evidence=IEA

UNIPROTKB|Q5SXM8 DNLZ "DNL-type zinc finger protein" [Homo sapiens (taxid:9606)]

 Score = 229 (85.7 bits), Expect = 4.0e-19, P = 4.0e-19
 Identities = 45/76 (59%), Positives = 55/76 (72%)

Query:   108 GVIKLKHKLKLAYTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNNHLIADNLKWFTDLK 167
             G ++  H  +L YTCKVCGTR+S  ISK +Y +GVVIV C GC N+H+IADNL WF+DL 
Sbjct:    62 GRVEAAH-YQLVYTCKVCGTRSSKRISKLAYHQGVVIVTCPGCQNHHIIADNLGWFSDLN 120

Query:   168 PGVTNIEHILAEKGEQ 183
              G  NIE IL  +GEQ
Sbjct:   121 -GKRNIEEILTARGEQ 135

GO:0008270 "zinc ion binding" evidence=IEA

GO:0005739 "mitochondrion" evidence=IEA

UNIPROTKB|E1BGR3 LOC100848156 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 225 (84.3 bits), Expect = 1.1e-18, P = 1.1e-18
 Identities = 43/67 (64%), Positives = 52/67 (77%)

Query:   117 KLAYTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNNHLIADNLKWFTDLKPGVTNIEHI 176
             +L YTCKVCGTR+S  ISK +Y +GVVIV C GC N+H+IADNL WF+DL  G  NIE I
Sbjct:    61 QLVYTCKVCGTRSSKRISKLAYHQGVVIVTCPGCQNHHIIADNLGWFSDLD-GKRNIEEI 119

Query:   177 LAEKGEQ 183
             LA +GE+
Sbjct:   120 LAARGEK 126

GO:0005739 "mitochondrion" evidence=IEA

GO:0043565 "sequence-specific DNA binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

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

UNIPROTKB|F1PCL0 DNLZ "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 223 (83.6 bits), Expect = 1.7e-18, P = 1.7e-18
 Identities = 42/70 (60%), Positives = 53/70 (75%)

Query:   117 KLAYTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNNHLIADNLKWFTDLKPGVTNIEHI 176
             +L YTCKVCG+R+S  ISK +Y +GVVIV C GC  +H+IADNL WF+DL  G  NIE I
Sbjct:    63 QLVYTCKVCGSRSSKRISKLAYHRGVVIVTCPGCQKHHVIADNLGWFSDLD-GKRNIEEI 121

Query:   177 LAEKGEQGCK 186
             LA +GE+ C+
Sbjct:   122 LAARGEKVCR 131

GO:0005739 "mitochondrion" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

UNIPROTKB|F1NF52 DNLZ "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 205 (77.2 bits), Expect = 1.4e-16, P = 1.4e-16
 Identities = 41/76 (53%), Positives = 54/76 (71%)

Query:   108 GVIKLKHKLKLAYTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNNHLIADNLKWFTDLK 167
             G ++  H  +L YTCKVC  R +  IS+ +Y +GVVIV C GC ++H+IADNL WF+DL+
Sbjct:    60 GRLQPSH-YRLVYTCKVCRRRTAQNISRLAYSRGVVIVTCPGCHSHHVIADNLGWFSDLQ 118

Query:   168 PGVTNIEHILAEKGEQ 183
              G  NIE ILA KGE+
Sbjct:   119 -GKRNIEEILAAKGEK 133

GO:0008270 "zinc ion binding" evidence=IEA

GO:0005739 "mitochondrion" evidence=IEA

WB|WBGene00018723 F53A3.7 [Caenorhabditis elegans (taxid:6239)]

 Score = 193 (73.0 bits), Expect = 2.6e-15, P = 2.6e-15
 Identities = 40/73 (54%), Positives = 49/73 (67%)

Query:   111 KLKHKLKLAYTCKVCGTRNS-HLISKHSYEKGVVIVKCEGCSNNHLIADNLKWFTDLKPG 169
             K + +L L+YTCKVC +R      +K SYEKGVVIV C GC N+H+IADN+ WF D K G
Sbjct:    30 KQEPQLSLSYTCKVCNSREGPKTFAKSSYEKGVVIVTCSGCHNHHIIADNIGWFEDFK-G 88

Query:   170 VTNIEHILAEKGE 182
               NIE  L  +GE
Sbjct:    89 -KNIEDHLKTRGE 100

GO:0008270 "zinc ion binding" evidence=IEA

GO:0009792 "embryo development ending in birth or egg hatching" evidence=IMP

GO:0000003 "reproduction" evidence=IMP

GO:0010171 "body morphogenesis" evidence=IMP

TAIR|locus:1006230204 ZR3 "zinc ribbon 3" [Arabidopsis thaliana (taxid:3702)]

 Score = 190 (71.9 bits), Expect = 5.4e-15, P = 5.4e-15
 Identities = 37/78 (47%), Positives = 50/78 (64%)

Query:   110 IKLKHKLKLAYTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNNHLIADNLKWFTDLKPG 169
             I  +H   + +TCKVC TR+  + S+ SYE GVV+V+C GC N HLIAD   WF +  PG
Sbjct:   130 INPRHDFMMVFTCKVCDTRSMKMASRESYENGVVVVRCGGCDNLHLIADRRGWFGE--PG 187

Query:   170 VTNIEHILAEKGEQGCKG 187
               ++E  LA +GE+  KG
Sbjct:   188 --SVEDFLASQGEEFKKG 203

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0008270 "zinc ion binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q5SXM8	DNLZ_HUMAN	No assigned EC number	0.5921	0.2720	0.4157	yes	N/A
Q9D113	DNLZ_MOUSE	No assigned EC number	0.6052	0.2720	0.4180	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

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	272
pfam05180	66	pfam05180, zf-DNL, DNL zinc finger	9e-30
pfam05180	66	pfam05180, zf-DNL, DNL zinc finger	3e-07

>gnl|CDD|191217 pfam05180, zf-DNL, DNL zinc finger

 Score =  106 bits (267), Expect = 9e-30
 Identities = 44/68 (64%), Positives = 50/68 (73%), Gaps = 3/68 (4%)

Query: 116 LKLAYTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNNHLIADNLKWFTDLKPGVTNIEH 175
            +L +TCKVCGTR++  ISK +YEKG VIV+C GC N HLIADNL WF D K    NIE 
Sbjct: 1   YQLTFTCKVCGTRSTKTISKQAYEKGTVIVQCPGCKNRHLIADNLGWFGDGK---VNIED 57

Query: 176 ILAEKGEQ 183
           ILAEKGE 
Sbjct: 58  ILAEKGES 65

The domain is named after a short C-terminal motif of D(N/H)L. This domain is a novel zinc-finger protein essential for protein import into mitochondria. Length = 66

>gnl|CDD|191217 pfam05180, zf-DNL, DNL zinc finger

 Score = 46.4 bits (111), Expect = 3e-07
 Identities = 22/33 (66%), Positives = 23/33 (69%), Gaps = 3/33 (9%)

Query: 220 SHHLIADNLKWFSDLKPGVTNIEHILAEKGEQV 252
           + HLIADNL WF D K    NIE ILAEKGE V
Sbjct: 37  NRHLIADNLGWFGDGK---VNIEDILAEKGESV 66

The domain is named after a short C-terminal motif of D(N/H)L. This domain is a novel zinc-finger protein essential for protein import into mitochondria. Length = 66

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	272
PF05180	66	zf-DNL: DNL zinc finger; InterPro: IPR007853 Zinc	100.0
KOG3277|consensus	165		100.0
KOG3277|consensus	165		99.84
PF05180	66	zf-DNL: DNL zinc finger; InterPro: IPR007853 Zinc	99.78
PF13719	37	zinc_ribbon_5: zinc-ribbon domain	94.4
PF13717	36	zinc_ribbon_4: zinc-ribbon domain	93.37
PF01096	39	TFIIS_C: Transcription factor S-II (TFIIS); InterP	91.85
smart00440	40	ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding mo	91.43
TIGR02098	38	MJ0042_CXXC MJ0042 family finger-like domain. This	91.24
PF01096	39	TFIIS_C: Transcription factor S-II (TFIIS); InterP	90.14
smart00440	40	ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding mo	89.22
PF05207	55	zf-CSL: CSL zinc finger; InterPro: IPR007872 Zinc	88.35
PRK00398	46	rpoP DNA-directed RNA polymerase subunit P; Provis	88.01
KOG2923|consensus	67		87.99
PF03367	161	zf-ZPR1: ZPR1 zinc-finger domain; InterPro: IPR004	87.96
TIGR00340	163	zpr1_rel ZPR1-related zinc finger protein. A model	87.17
TIGR01206	54	lysW lysine biosynthesis protein LysW. This very s	85.91
COG3478	68	Predicted nucleic-acid-binding protein containing	85.69
COG5216	67	Uncharacterized conserved protein [Function unknow	83.61
PRK03564	309	formate dehydrogenase accessory protein FdhE; Prov	81.47
TIGR01385	299	TFSII transcription elongation factor S-II. This m	80.7
PF09723	42	Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR0134	80.59
PF05907	161	DUF866: Eukaryotic protein of unknown function (DU	80.59

>PF05180 zf-DNL: DNL zinc finger; InterPro: IPR007853 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=100.00  E-value=3.6e-35  Score=221.34  Aligned_cols=66  Identities=58%  Similarity=1.065  Sum_probs=51.8

Q ss_pred             eEEEEEcCCCCcccccccchhcccceEEEEEcCCCCcceeeeccccccccCCCCCCCHHHHHHHhCCee
Q psy13378        116 LKLAYTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNNHLIADNLKWFTDLKPGVTNIEHILAEKGEQG  184 (272)
Q Consensus       116 ~~L~FTCk~C~tRS~h~ISK~AY~kGvViVqC~gC~n~HLIADnLgwF~d~~~g~~tIEdil~~kGE~V  184 (272)
                      |+|.|||++|++||+|+|||+||++|+||||||||+|+||||||||||.|.   +.||||||++|||+|
T Consensus         1 ~~l~FTC~~C~~Rs~~~~sk~aY~~GvViv~C~gC~~~HlIaDnLg~f~e~---~~~iE~~l~~kge~v   66 (66)
T PF05180_consen    1 YQLTFTCNKCGTRSAKMFSKQAYHKGVVIVQCPGCKNRHLIADNLGWFGEN---KRNIEDILKEKGEKV   66 (66)
T ss_dssp             EEEEEEETTTTEEEEEEEEHHHHHTSEEEEE-TTS--EEES--SS-SGGGS------HHHHHHHH----
T ss_pred             CeEEEEcCCCCCccceeeCHHHHhCCeEEEECCCCcceeeehhhhcccccC---CCCHHHHHHHcCCcC
Confidence            789999999999999999999999999999999999999999999999985   479999999999986

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The DNL-type zinc finger is found in Tim15, a zinc finger protein essential for protein import into mitochondria. Mitochondrial functions rely on the correct transport of resident proteins synthesized in the cytosol to mitochondria. Protein import into mitochondria is mediated by membrane protein complexes, protein translocators, in the outer and inner mitochondrial membranes, in cooperation with their assistant proteins in the cytosol, intermembrane space and matrix. Proteins destined to the mitochondrial matrix cross the outer membrane with the aid of the outer membrane translocator, the tOM40 complex, and then the inner membrane with the aid of the inner membrane translocator, the TIM23 complex, and mitochondrial motor and chaperone (MMC) proteins including mitochondrial heat- shock protein 70 (mtHsp70), and translocase in the inner mitochondrial membrane (Tim)15. Tim15 is also known as zinc finger motif (Zim)17 or mtHsp70 escort protein (Hep)1. Tim15 contains a zinc-finger motif (CXXC and CXXC) of ~100 residues, which has been named DNL after a short C-terminal motif of D(N/H)L [, , ]. The DNL-type zinc finger is an L-shaped molecule. The two CXXC motifs are located at the end of the L, and are sandwiched by two- stranded antiparallel beta-sheets. Two short alpha-helices constitute another leg of the L. The outer (convex) face of the L has a large acidic groove, which is lined with five acidic residues, whereas the inner (concave) face of the L has two positively charged residues, next to the CXXC motifs []. This entry represents the DNL-type zinc finger.; GO: 0008270 zinc ion binding; PDB: 2E2Z_A.

>KOG3277|consensus

Probab=100.00  E-value=8.4e-34  Score=244.02  Aligned_cols=80  Identities=63%  Similarity=1.003  Sum_probs=76.3

Q ss_pred             ccccccceEEEEEcCCCCcccccccchhcccceEEEEEcCCCCcceeeeccccccccCCCCCCCHHHHHHHhCCeeeece
Q psy13378        109 VIKLKHKLKLAYTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNNHLIADNLKWFTDLKPGVTNIEHILAEKGEQGCKGL  188 (272)
Q Consensus       109 v~~~~~~~~L~FTCk~C~tRS~h~ISK~AY~kGvViVqC~gC~n~HLIADnLgwF~d~~~g~~tIEdil~~kGE~V~kg~  188 (272)
                      +..++|+|+|.|||++|++|++|.|||+||++||||||||||+|+||||||||||.|.+ |++||||||++|||+|+++.
T Consensus        69 ~~~~kp~m~l~yTCkvCntRs~ktisk~AY~~GvVivqC~gC~~~HliaDnL~~F~d~~-~~~nied~l~~kge~v~~~~  147 (165)
T KOG3277|consen   69 FKVPKPRMQLAYTCKVCNTRSTKTISKQAYEKGVVIVQCPGCKNHHLIADNLGWFHDLK-GKRNIEDILAAKGEQVKRNL  147 (165)
T ss_pred             ccCCCcceEEEEEeeccCCccccccChhhhhCceEEEECCCCccceeehhhhccccccc-ccccHHHHHHhccceeeeec
Confidence            36788999999999999999999999999999999999999999999999999999986 87899999999999999987


Q ss_pred             e
Q psy13378        189 F  189 (272)
Q Consensus       189 ~  189 (272)
                      .
T Consensus       148 g  148 (165)
T KOG3277|consen  148 G  148 (165)
T ss_pred             c
Confidence            4

>KOG3277|consensus

Probab=99.84  E-value=1.7e-21  Score=168.17  Aligned_cols=91  Identities=42%  Similarity=0.609  Sum_probs=78.5

Q ss_pred             hhcccceEEEEEcCCCCcceeeeccccccccCCCCCCCHHHHHHHhCCeeeeceeeeccceeccccceeEEEEeecchhh
Q psy13378        135 KHSYEKGVVIVKCEGCSNNHLIADNLKWFTDLKPGVTNIEHILAEKGEQGCKGLFCLSHDIKLNTNIVRLMIETCLCHLI  214 (272)
Q Consensus       135 K~AY~kGvViVqC~gC~n~HLIADnLgwF~d~~~g~~tIEdil~~kGE~V~kg~~~~~~die~~~~~~~~vi~~C~~~~~  214 (272)
                      +.---+..|..+|.-|+.|-.               +||.+.      .+.+|+                |||+|||   
T Consensus        70 ~~~kp~m~l~yTCkvCntRs~---------------ktisk~------AY~~Gv----------------VivqC~g---  109 (165)
T KOG3277|consen   70 KVPKPRMQLAYTCKVCNTRST---------------KTISKQ------AYEKGV----------------VIVQCPG---  109 (165)
T ss_pred             cCCCcceEEEEEeeccCCccc---------------cccChh------hhhCce----------------EEEECCC---
Confidence            445567889999999999865               588884      477777                8999997   


Q ss_pred             hcccccceeeecccCCccCCCCCcCCHHHHHHhcCCcEEEecCCCcEEEeccccc
Q psy13378        215 RETHGSHHLIADNLKWFSDLKPGVTNIEHILAEKGEQVRRIDSNGAIELIEDEKK  269 (272)
Q Consensus       215 ~~~C~n~HlIADnLGwF~d~~~g~~nIE~iL~~kGE~V~r~~~~~~lE~~~~~~~  269 (272)
                         |.|+||||||||||.|.+ |++||||||++|||+|++..+|+..|.+.+.+|
T Consensus       110 ---C~~~HliaDnL~~F~d~~-~~~nied~l~~kge~v~~~~g~~~~e~i~~~~~  160 (165)
T KOG3277|consen  110 ---CKNHHLIADNLGWFHDLK-GKRNIEDILAAKGEQVKRNLGDGEDEDIPEDSK  160 (165)
T ss_pred             ---Cccceeehhhhccccccc-ccccHHHHHHhccceeeeecccccccccccccc
Confidence               999999999999999998 688999999999999999988888888766543

>PF05180 zf-DNL: DNL zinc finger; InterPro: IPR007853 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=99.78  E-value=5.3e-20  Score=139.13  Aligned_cols=65  Identities=38%  Similarity=0.636  Sum_probs=41.2

Q ss_pred             EEEEEcCCCCcceeeeccccccccCCCCCCCHHHHHHHhCCeeeeceeeeccceeccccceeEEEEeecchhhhcccccc
Q psy13378        142 VVIVKCEGCSNNHLIADNLKWFTDLKPGVTNIEHILAEKGEQGCKGLFCLSHDIKLNTNIVRLMIETCLCHLIRETHGSH  221 (272)
Q Consensus       142 vViVqC~gC~n~HLIADnLgwF~d~~~g~~tIEdil~~kGE~V~kg~~~~~~die~~~~~~~~vi~~C~~~~~~~~C~n~  221 (272)
                      .+.-+|..|..|-.               ++|...+      +.+|+                |||+||+      |+|+
T Consensus         2 ~l~FTC~~C~~Rs~---------------~~~sk~a------Y~~Gv----------------Viv~C~g------C~~~   38 (66)
T PF05180_consen    2 QLTFTCNKCGTRSA---------------KMFSKQA------YHKGV----------------VIVQCPG------CKNR   38 (66)
T ss_dssp             EEEEEETTTTEEEE---------------EEEEHHH------HHTSE----------------EEEE-TT------S--E
T ss_pred             eEEEEcCCCCCccc---------------eeeCHHH------HhCCe----------------EEEECCC------Ccce
Confidence            45678999987765               3444433      55555                8999997      9999


Q ss_pred             eeeecccCCccCCCCCcCCHHHHHHhcCCcE
Q psy13378        222 HLIADNLKWFSDLKPGVTNIEHILAEKGEQV  252 (272)
Q Consensus       222 HlIADnLGwF~d~~~g~~nIE~iL~~kGE~V  252 (272)
                      ||||||||||.|.   ++||||||++|||+|
T Consensus        39 HlIaDnLg~f~e~---~~~iE~~l~~kge~v   66 (66)
T PF05180_consen   39 HLIADNLGWFGEN---KRNIEDILKEKGEKV   66 (66)
T ss_dssp             EES--SS-SGGGS------HHHHHHHH----
T ss_pred             eeehhhhcccccC---CCCHHHHHHHcCCcC
Confidence            9999999999984   689999999999987

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The DNL-type zinc finger is found in Tim15, a zinc finger protein essential for protein import into mitochondria. Mitochondrial functions rely on the correct transport of resident proteins synthesized in the cytosol to mitochondria. Protein import into mitochondria is mediated by membrane protein complexes, protein translocators, in the outer and inner mitochondrial membranes, in cooperation with their assistant proteins in the cytosol, intermembrane space and matrix. Proteins destined to the mitochondrial matrix cross the outer membrane with the aid of the outer membrane translocator, the tOM40 complex, and then the inner membrane with the aid of the inner membrane translocator, the TIM23 complex, and mitochondrial motor and chaperone (MMC) proteins including mitochondrial heat- shock protein 70 (mtHsp70), and translocase in the inner mitochondrial membrane (Tim)15. Tim15 is also known as zinc finger motif (Zim)17 or mtHsp70 escort protein (Hep)1. Tim15 contains a zinc-finger motif (CXXC and CXXC) of ~100 residues, which has been named DNL after a short C-terminal motif of D(N/H)L [, , ]. The DNL-type zinc finger is an L-shaped molecule. The two CXXC motifs are located at the end of the L, and are sandwiched by two- stranded antiparallel beta-sheets. Two short alpha-helices constitute another leg of the L. The outer (convex) face of the L has a large acidic groove, which is lined with five acidic residues, whereas the inner (concave) face of the L has two positively charged residues, next to the CXXC motifs []. This entry represents the DNL-type zinc finger.; GO: 0008270 zinc ion binding; PDB: 2E2Z_A.

>PF13719 zinc_ribbon_5: zinc-ribbon domain

Probab=94.40  E-value=0.032  Score=37.57  Aligned_cols=34  Identities=26%  Similarity=0.565  Sum_probs=26.6

Q ss_pred             EEEEcCCCCcccccccchhcccceEEEEEcCCCCcc
Q psy13378        118 LAYTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNN  153 (272)
Q Consensus       118 L~FTCk~C~tRS~h~ISK~AY~kGvViVqC~gC~n~  153 (272)
                      |..+|+.|+++  ..|.+.....+-..++|+.|+..
T Consensus         1 M~i~CP~C~~~--f~v~~~~l~~~~~~vrC~~C~~~   34 (37)
T PF13719_consen    1 MIITCPNCQTR--FRVPDDKLPAGGRKVRCPKCGHV   34 (37)
T ss_pred             CEEECCCCCce--EEcCHHHcccCCcEEECCCCCcE
Confidence            46789999976  88888776666668999999853

>PF13717 zinc_ribbon_4: zinc-ribbon domain

Probab=93.37  E-value=0.07  Score=35.94  Aligned_cols=33  Identities=21%  Similarity=0.469  Sum_probs=24.4

Q ss_pred             EEEEcCCCCcccccccchhcccceEEEEEcCCCCc
Q psy13378        118 LAYTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSN  152 (272)
Q Consensus       118 L~FTCk~C~tRS~h~ISK~AY~kGvViVqC~gC~n  152 (272)
                      |.++|+.|+++  ..|++...-..-+-+||+.|..
T Consensus         1 M~i~Cp~C~~~--y~i~d~~ip~~g~~v~C~~C~~   33 (36)
T PF13717_consen    1 MIITCPNCQAK--YEIDDEKIPPKGRKVRCSKCGH   33 (36)
T ss_pred             CEEECCCCCCE--EeCCHHHCCCCCcEEECCCCCC
Confidence            35788888866  7777776666666888888874

>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=91.85  E-value=0.1  Score=35.55  Aligned_cols=12  Identities=42%  Similarity=1.018  Sum_probs=6.0

Q ss_pred             eEEEEEcCCCCc
Q psy13378        116 LKLAYTCKVCGT  127 (272)
Q Consensus       116 ~~L~FTCk~C~t  127 (272)
                      +.+-|+|..|++
T Consensus        25 ~T~fy~C~~C~~   36 (39)
T PF01096_consen   25 MTLFYVCCNCGH   36 (39)
T ss_dssp             SEEEEEESSSTE
T ss_pred             CeEEEEeCCCCC
Confidence            344555555553

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 a zinc finger motif found in transcription factor IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....

>smart00440 ZnF_C2C2 C2C2 Zinc finger

Probab=91.43  E-value=0.17  Score=34.78  Aligned_cols=31  Identities=26%  Similarity=0.611  Sum_probs=14.5

Q ss_pred             EcCCCCcccccccch---hcccceEEEEEcCCCC
Q psy13378        121 TCKVCGTRNSHLISK---HSYEKGVVIVKCEGCS  151 (272)
Q Consensus       121 TCk~C~tRS~h~ISK---~AY~kGvViVqC~gC~  151 (272)
                      .|+.|+++.+..+..   .|-+-.+++..|..|.
T Consensus         2 ~Cp~C~~~~a~~~q~Q~RsaDE~mT~fy~C~~C~   35 (40)
T smart00440        2 PCPKCGNREATFFQLQTRSADEPMTVFYVCTKCG   35 (40)
T ss_pred             cCCCCCCCeEEEEEEcccCCCCCCeEEEEeCCCC
Confidence            455555544444432   2334445555555554

Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.

>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain

Probab=91.24  E-value=0.17  Score=33.39  Aligned_cols=33  Identities=21%  Similarity=0.524  Sum_probs=20.2

Q ss_pred             EEEEcCCCCcccccccchhcc-cceEEEEEcCCCCcc
Q psy13378        118 LAYTCKVCGTRNSHLISKHSY-EKGVVIVKCEGCSNN  153 (272)
Q Consensus       118 L~FTCk~C~tRS~h~ISK~AY-~kGvViVqC~gC~n~  153 (272)
                      |.++|+.|++.  -.|..... ..|. -++||.|+..
T Consensus         1 M~~~CP~C~~~--~~v~~~~~~~~~~-~v~C~~C~~~   34 (38)
T TIGR02098         1 MRIQCPNCKTS--FRVVDSQLGANGG-KVRCGKCGHV   34 (38)
T ss_pred             CEEECCCCCCE--EEeCHHHcCCCCC-EEECCCCCCE
Confidence            35788888865  44554333 3343 7788888753

This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.

>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=90.14  E-value=0.17  Score=34.43  Aligned_cols=34  Identities=18%  Similarity=0.468  Sum_probs=25.9

Q ss_pred             EEcCCCCcccccccch---hcccceEEEEEcCCCCcc
Q psy13378        120 YTCKVCGTRNSHLISK---HSYEKGVVIVKCEGCSNN  153 (272)
Q Consensus       120 FTCk~C~tRS~h~ISK---~AY~kGvViVqC~gC~n~  153 (272)
                      |+|+.|+++.+..+..   .|-+..+++..|..|..+
T Consensus         1 ~~Cp~Cg~~~a~~~~~Q~rsaDE~~T~fy~C~~C~~~   37 (39)
T PF01096_consen    1 IKCPKCGHNEAVFFQIQTRSADEPMTLFYVCCNCGHR   37 (39)
T ss_dssp             S--SSS-SSEEEEEEESSSSSSSSSEEEEEESSSTEE
T ss_pred             CCCcCCCCCeEEEEEeeccCCCCCCeEEEEeCCCCCe
Confidence            4799999999888854   477888999999999854

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 a zinc finger motif found in transcription factor IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....

>smart00440 ZnF_C2C2 C2C2 Zinc finger

Probab=89.22  E-value=0.32  Score=33.35  Aligned_cols=37  Identities=24%  Similarity=0.665  Sum_probs=26.5

Q ss_pred             eecCCcCCcccccccCCcccccccccccceEEEEEcCCCCcc
Q psy13378         87 YTCKVCGTRNSHLISKHSYEKGVIKLKHKLKLAYTCKVCGTR  128 (272)
Q Consensus        87 fTCkvC~TRSSh~ISK~Sy~kGv~~~~~~~~L~FTCk~C~tR  128 (272)
                      +.|+.|+.+.+.-+..|     +......+.+-|+|..|+++
T Consensus         1 ~~Cp~C~~~~a~~~q~Q-----~RsaDE~mT~fy~C~~C~~~   37 (40)
T smart00440        1 APCPKCGNREATFFQLQ-----TRSADEPMTVFYVCTKCGHR   37 (40)
T ss_pred             CcCCCCCCCeEEEEEEc-----ccCCCCCCeEEEEeCCCCCE
Confidence            47999997776644333     33445567799999999976

Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.

>PF05207 zf-CSL: CSL zinc finger; InterPro: IPR007872 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=88.35  E-value=0.4  Score=35.00  Aligned_cols=33  Identities=42%  Similarity=0.856  Sum_probs=28.0

Q ss_pred             EEEEcCCCCcccccccchhcccceEEEEEcCCCCcc
Q psy13378        118 LAYTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNN  153 (272)
Q Consensus       118 L~FTCk~C~tRS~h~ISK~AY~kGvViVqC~gC~n~  153 (272)
                      ..|.| .||..  -.|++...+.|.++|+|++|.-+
T Consensus        17 ~~y~C-RCG~~--f~i~e~~l~~~~~iv~C~sCSL~   49 (55)
T PF05207_consen   17 YSYPC-RCGGE--FEISEEDLEEGEVIVQCDSCSLW   49 (55)
T ss_dssp             EEEEE-TTSSE--EEEEHHHHHCT--EEEETTTTEE
T ss_pred             EEEcC-CCCCE--EEEcchhccCcCEEEECCCCccE
Confidence            68999 99966  99999999999999999999864

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 a probable zinc binding motif that contains four cysteines and may chelate zinc, known as the DPH-type after the diphthamide (DPH) biosynthesis protein in which it was first characterised, including the proteins DPH3 and DPH4. This domain is also found associated with N-terminal domain of heat shock protein DnaJ IPR001623 from INTERPRO domain. Diphthamide is a unique post-translationally modified histidine residue found only in translation elongation factor 2 (eEF-2). It is conserved from archaea to humans and serves as the target for diphteria toxin and Pseudomonas exotoxin A. These two toxins catalyse the transfer of ADP-ribose to diphtamide on eEF-2, thus inactivating eEF-2, halting cellular protein synthesis, and causing cell death []. The biosynthesis of diphtamide is dependent on at least five proteins, DPH1 to -5, and a still unidentified amidating enzyme. DPH3 and DPH4 share a conserved region, which encode a putative zinc finger, the DPH-type or CSL-type (after the conserved motif of the final cysteine) zinc finger [, ]. The function of this motif is unknown. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2L6L_A 1WGE_A 2JR7_A 1YOP_A 1YWS_A.

>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional

Probab=88.01  E-value=0.4  Score=33.13  Aligned_cols=35  Identities=23%  Similarity=0.510  Sum_probs=19.7

Q ss_pred             EEEEcCCCCcccccccchhcccceEEEEEcCCCCcceeeecc
Q psy13378        118 LAYTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNNHLIADN  159 (272)
Q Consensus       118 L~FTCk~C~tRS~h~ISK~AY~kGvViVqC~gC~n~HLIADn  159 (272)
                      +.|.|+.|+..  -.+     ...+..++||.|.++=++.|+
T Consensus         2 ~~y~C~~CG~~--~~~-----~~~~~~~~Cp~CG~~~~~~~~   36 (46)
T PRK00398          2 AEYKCARCGRE--VEL-----DEYGTGVRCPYCGYRILFKER   36 (46)
T ss_pred             CEEECCCCCCE--EEE-----CCCCCceECCCCCCeEEEccC
Confidence            46777777754  222     122225677777776665444

>KOG2923|consensus

Probab=87.99  E-value=0.34  Score=37.59  Aligned_cols=32  Identities=31%  Similarity=0.659  Sum_probs=28.6

Q ss_pred             EEEcC-CCCcccccccchhcccceEEEEEcCCCCc
Q psy13378        119 AYTCK-VCGTRNSHLISKHSYEKGVVIVKCEGCSN  152 (272)
Q Consensus       119 ~FTCk-~C~tRS~h~ISK~AY~kGvViVqC~gC~n  152 (272)
                      +|+++ +||-|  -.|++.-.+.|-.+++||+|.-
T Consensus        20 ~y~yPCpCGDr--f~It~edL~~ge~Va~CpsCSL   52 (67)
T KOG2923|consen   20 TYYYPCPCGDR--FQITLEDLENGEDVARCPSCSL   52 (67)
T ss_pred             eEEcCCCCCCe--eeecHHHHhCCCeeecCCCceE
Confidence            57776 79988  9999999999999999999963

>PF03367 zf-ZPR1: ZPR1 zinc-finger domain; InterPro: IPR004457 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=87.96  E-value=0.52  Score=40.85  Aligned_cols=53  Identities=26%  Similarity=0.546  Sum_probs=32.4

Q ss_pred             ecCCcCCcccccccCCcccccccccccceEEEEEcCCCCcccccccchhcc-cceEEE
Q psy13378         88 TCKVCGTRNSHLISKHSYEKGVIKLKHKLKLAYTCKVCGTRNSHLISKHSY-EKGVVI  144 (272)
Q Consensus        88 TCkvC~TRSSh~ISK~Sy~kGv~~~~~~~~L~FTCk~C~tRS~h~ISK~AY-~kGvVi  144 (272)
                      .|++|+......+    +...+--.+.-+.+.|.|+.|+.|+.-..+--+. .+|+.+
T Consensus         3 ~Cp~C~~~~~~~~----~~~~IP~F~evii~sf~C~~CGyk~~ev~~~~~~~~~G~r~   56 (161)
T PF03367_consen    3 LCPNCGENGTTRI----LLTDIPYFKEVIIMSFECEHCGYKNNEVKSGGQIQPKGVRI   56 (161)
T ss_dssp             E-TTTSSCCEEEE----EEEEETTTEEEEEEEEE-TTT--EEEEEEEECSS-SSEEEE
T ss_pred             cCCCCCCCcEEEE----EEEcCCCCceEEEEEeECCCCCCEeeeEEECccCCCCceEE
Confidence            6999997643322    2222333456688999999999999888877777 455554

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 ZPR1-type zinc finger domains. An orthologous protein found once in each of the completed archaeal genomes corresponds to a zinc finger-containing domain repeated as the N-terminal and C-terminal halves of the mouse protein ZPR1. ZPR1 is an experimentally proven zinc-binding protein that binds the tyrosine kinase domain of the epidermal growth factor receptor (EGFR); binding is inhibited by EGF stimulation and tyrosine phosphorylation, and activation by EGF is followed by some redistribution of ZPR1 to the nucleus. By analogy, other proteins with the ZPR1 zinc finger domain may be regulatory proteins that sense protein phosphorylation state and/or participate in signal transduction (see also IPR004470 from INTERPRO). Deficiencies in ZPR1 may contribute to neurodegenerative disorders. ZPR1 appears to be down-regulated in patients with spinal muscular atrophy (SMA), a disease characterised by degeneration of the alpha-motor neurons in the spinal cord that can arise from mutations affecting the expression of Survival Motor Neurons (SMN) []. ZPR1 interacts with complexes formed by SMN [], and may act as a modifier that effects the severity of SMA. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2QKD_A.

>TIGR00340 zpr1_rel ZPR1-related zinc finger protein

Probab=87.17  E-value=0.57  Score=41.06  Aligned_cols=46  Identities=26%  Similarity=0.526  Sum_probs=30.8

Q ss_pred             cCCcCCccccc---ccCCcccccccccccceEEEEEcCCCCcccccccchhcccc
Q psy13378         89 CKVCGTRNSHL---ISKHSYEKGVIKLKHKLKLAYTCKVCGTRNSHLISKHSYEK  140 (272)
Q Consensus        89 CkvC~TRSSh~---ISK~Sy~kGv~~~~~~~~L~FTCk~C~tRS~h~ISK~AY~k  140 (272)
                      |++|++.....   .-+-+|-      +.-+.+.|+|+.||.|++-..+--+.+.
T Consensus         1 CP~Cg~~~~~~~~~~~~IP~F------~evii~sf~C~~CGyr~~ev~~~~~~~p   49 (163)
T TIGR00340         1 CPVCGSRTLKAVTYDYDIPYF------GKIMLSTYICEKCGYRSTDVYQLEEKEP   49 (163)
T ss_pred             CCCCCCcceEeeeEeccCCCc------ceEEEEEEECCCCCCchhheeEcCCcCC
Confidence            89999763222   1334443      3446789999999999887766665544

A model ZPR1_znf (TIGR00310) has been created to describe the domain shared by this protein and ZPR1.

>TIGR01206 lysW lysine biosynthesis protein LysW

Probab=85.91  E-value=0.59  Score=34.52  Aligned_cols=34  Identities=24%  Similarity=0.612  Sum_probs=20.9

Q ss_pred             EEEcCCCCcccccccchhcccceEEEEEcCCCCcceeee
Q psy13378        119 AYTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNNHLIA  157 (272)
Q Consensus       119 ~FTCk~C~tRS~h~ISK~AY~kGvViVqC~gC~n~HLIA  157 (272)
                      +|+|+.|+..  =.+.  .-..|. ++.||.|....=+.
T Consensus         2 ~~~CP~CG~~--iev~--~~~~Ge-iV~Cp~CGaeleVv   35 (54)
T TIGR01206         2 QFECPDCGAE--IELE--NPELGE-LVICDECGAELEVV   35 (54)
T ss_pred             ccCCCCCCCE--EecC--CCccCC-EEeCCCCCCEEEEE
Confidence            6888888853  2332  222255 55888888776553

This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.

>COG3478 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]

Probab=85.69  E-value=0.71  Score=35.94  Aligned_cols=43  Identities=30%  Similarity=0.604  Sum_probs=28.7

Q ss_pred             eeeeecCCcCCcccccccCCcccc--ccc---ccccceEEEEEcCCCCcc
Q psy13378         84 KLAYTCKVCGTRNSHLISKHSYEK--GVI---KLKHKLKLAYTCKVCGTR  128 (272)
Q Consensus        84 ~i~fTCkvC~TRSSh~ISK~Sy~k--Gv~---~~~~~~~L~FTCk~C~tR  128 (272)
                      ..+|.|+.|+-++-.  .|+=..+  ++.   .++..-.++.||+.|+-.
T Consensus         2 ~~~~kCpKCgn~~~~--ekei~~tg~~lskifdvq~n~f~~itCk~CgYt   49 (68)
T COG3478           2 KNAFKCPKCGNTNYE--EKEIAATGGGLSKIFDVQNNKFIVITCKNCGYT   49 (68)
T ss_pred             CccccCCCcCCcchh--hceeeccCCCcceeEEecccEEEEEEeccCCch
Confidence            356889999977643  2322222  222   566778889999999955

>COG5216 Uncharacterized conserved protein [Function unknown]

Probab=83.61  E-value=1  Score=34.76  Aligned_cols=31  Identities=39%  Similarity=0.918  Sum_probs=26.8

Q ss_pred             EEEEcCCCCcccccccchhcccceEEEEEcCCCC
Q psy13378        118 LAYTCKVCGTRNSHLISKHSYEKGVVIVKCEGCS  151 (272)
Q Consensus       118 L~FTCk~C~tRS~h~ISK~AY~kGvViVqC~gC~  151 (272)
                      ..|-| +|+-|  -.||-.-...|-|..+||+|.
T Consensus        21 ftyPC-PCGDR--FeIsLeDl~~GE~VArCPSCS   51 (67)
T COG5216          21 FTYPC-PCGDR--FEISLEDLRNGEVVARCPSCS   51 (67)
T ss_pred             EEecC-CCCCE--eEEEHHHhhCCceEEEcCCce
Confidence            35556 59988  899999999999999999996

>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional

Probab=81.47  E-value=1.2  Score=42.73  Aligned_cols=51  Identities=29%  Similarity=0.740  Sum_probs=30.6

Q ss_pred             ecCCcCCccccccc--CCcccccccccccceEEEEEcCCCCcccccccchhcccceEEEEEcCCCCcceeeecccccc
Q psy13378         88 TCKVCGTRNSHLIS--KHSYEKGVIKLKHKLKLAYTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNNHLIADNLKWF  163 (272)
Q Consensus        88 TCkvC~TRSSh~IS--K~Sy~kGv~~~~~~~~L~FTCk~C~tRS~h~ISK~AY~kGvViVqC~gC~n~HLIADnLgwF  163 (272)
                      +|+|||..-  .+|  ..+...|..        -..|..|++.         |  .+|-++|+.|.+    .+.|..|
T Consensus       189 ~CPvCGs~P--~~s~v~~~~~~G~R--------yL~CslC~te---------W--~~~R~~C~~Cg~----~~~l~y~  241 (309)
T PRK03564        189 FCPVCGSMP--VSSVVQIGTTQGLR--------YLHCNLCESE---------W--HVVRVKCSNCEQ----SGKLHYW  241 (309)
T ss_pred             CCCCCCCcc--hhheeeccCCCCce--------EEEcCCCCCc---------c--cccCccCCCCCC----CCceeee
Confidence            899999543  222  111223442        4578889876         2  245678888887    3556655

>TIGR01385 TFSII transcription elongation factor S-II

Probab=80.70  E-value=1.2  Score=42.25  Aligned_cols=33  Identities=27%  Similarity=0.663  Sum_probs=14.5

Q ss_pred             EEcCCCCccccccc---chhcccceEEEEEcCCCCc
Q psy13378        120 YTCKVCGTRNSHLI---SKHSYEKGVVIVKCEGCSN  152 (272)
Q Consensus       120 FTCk~C~tRS~h~I---SK~AY~kGvViVqC~gC~n  152 (272)
                      |+|+.|+++..-.+   .+.|=+-.+++++|..|.+
T Consensus       259 ~~C~~C~~~~~~~~q~QtrsaDEpmT~f~~C~~Cg~  294 (299)
T TIGR01385       259 FTCGKCKQKKCTYYQLQTRSADEPMTTFVTCEECGN  294 (299)
T ss_pred             ccCCCCCCccceEEEecccCCCCCCeEEEEcCCCCC
Confidence            55555554433222   2223334455555555543

This model represents eukaryotic transcription elongation factor S-II. This protein allows stalled RNA transcription complexes to perform a cleavage of the nascent RNA and restart at the newly generated 3-prime end.

>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria

Probab=80.59  E-value=1.1  Score=30.70  Aligned_cols=14  Identities=36%  Similarity=0.850  Sum_probs=8.6

Q ss_pred             eeecCCcCCccccc
Q psy13378         86 AYTCKVCGTRNSHL   99 (272)
Q Consensus        86 ~fTCkvC~TRSSh~   99 (272)
                      .|.|..||+.....
T Consensus         5 ey~C~~Cg~~fe~~   18 (42)
T PF09723_consen    5 EYRCEECGHEFEVL   18 (42)
T ss_pred             EEEeCCCCCEEEEE
Confidence            46777777665443

The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.

>PF05907 DUF866: Eukaryotic protein of unknown function (DUF866); InterPro: IPR008584 This family consists of a number of hypothetical eukaryotic proteins of unknown function with an average length of around 165 residues

Probab=80.59  E-value=1.7  Score=37.82  Aligned_cols=75  Identities=16%  Similarity=0.372  Sum_probs=40.7

Q ss_pred             cceeeeeecCCcCCccccc--ccCCcccccccccccceEEEEEcCCCCcccccccch---hccc-------ceEEEEEcC
Q psy13378         81 HKLKLAYTCKVCGTRNSHL--ISKHSYEKGVIKLKHKLKLAYTCKVCGTRNSHLISK---HSYE-------KGVVIVKCE  148 (272)
Q Consensus        81 ~k~~i~fTCkvC~TRSSh~--ISK~Sy~kGv~~~~~~~~L~FTCk~C~tRS~h~ISK---~AY~-------kGvViVqC~  148 (272)
                      ..+.+...|..|++.+.+.  |+..- ...+.--|+..-++++|+.|+..++-.|.+   .+|.       .-++..-|.
T Consensus        25 ~~~~fkvkCt~CgE~~~k~V~i~~~e-~~e~~gsrG~aNfv~KCk~C~re~si~i~~~~~~~~~~e~~~~~~~i~~fdCR  103 (161)
T PF05907_consen   25 FEWFFKVKCTSCGEVHPKWVYINRFE-KHEIPGSRGTANFVMKCKFCKRESSIDIIPGKGKPYTAEDSGKFVPILAFDCR  103 (161)
T ss_dssp             --EEEEEEETTSS--EEEEEEE-TT--BEE-TTSS-EESEEE--SSSS--EEEEEE--TTTEEEGGGTTS-EEEEEEEEE
T ss_pred             CEEEEEEEECCCCCccCcceEeecce-EEecCCCccceEeEecCcCcCCccEEEEEecCccccccccccCCceEEEEECC
Confidence            4588888999999877544  33321 112223456667899999999776655544   4565       446778899


Q ss_pred             CCCcceee
Q psy13378        149 GCSNNHLI  156 (272)
Q Consensus       149 gC~n~HLI  156 (272)
                      ||.----.
T Consensus       104 G~e~~~f~  111 (161)
T PF05907_consen  104 GLEPVEFS  111 (161)
T ss_dssp             SEEEEEE-
T ss_pred             CcEeEEEe
Confidence            98654443

; PDB: 1ZSO_B.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	272
2e2z_A	100	Solution Nmr Structure Of Yeast Tim15, Co-Chaperone		4e-12

>pdb|2E2Z|A Chain A, Solution Nmr Structure Of Yeast Tim15, Co-Chaperone Of Mitochondrial Hsp70 Length = 100

Iteration: 1
 Score = 68.2 bits (165), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 33/71 (46%), Positives = 45/71 (63%), Gaps = 3/71 (4%)
Query: 113 KHKLKLAYTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNNHLIADNLKWFTDLKPGVTN 172
           K K+ +A+TCK C TR+SH +SK +YEKG V++ C  C   HLIAD+LK F D       
Sbjct: 7   KPKMMIAFTCKKCNTRSSHTMSKQAYEKGTVLISCPHCKVRHLIADHLKIFHDHH---VT 63
Query: 173 IEHILAEKGEQ 183
           +E ++   GEQ
Sbjct: 64  VEQLMKANGEQ 74

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	272
2e2z_A	100	TIM15; protein import, zinc finger, protein transp	1e-28
2e2z_A	100	TIM15; protein import, zinc finger, protein transp	6e-09
3k1f_M	197	Transcription initiation factor IIB; RNA polymeras	3e-05

>2e2z_A TIM15; protein import, zinc finger, protein transport, chaperone regulator; NMR {Saccharomyces cerevisiae} Length = 100

 Score =  103 bits (259), Expect = 1e-28
 Identities = 33/75 (44%), Positives = 46/75 (61%), Gaps = 3/75 (4%)

Query: 113 KHKLKLAYTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNNHLIADNLKWFTDLKPGVTN 172
           K K+ +A+TCK C TR+SH +SK +YEKG V++ C  C   HLIAD+LK F D       
Sbjct: 7   KPKMMIAFTCKKCNTRSSHTMSKQAYEKGTVLISCPHCKVRHLIADHLKIFHDHH---VT 63

Query: 173 IEHILAEKGEQGCKG 187
           +E ++   GEQ  + 
Sbjct: 64  VEQLMKANGEQVSQD 78

>2e2z_A TIM15; protein import, zinc finger, protein transport, chaperone regulator; NMR {Saccharomyces cerevisiae} Length = 100

 Score = 51.6 bits (123), Expect = 6e-09
 Identities = 17/48 (35%), Positives = 23/48 (47%), Gaps = 3/48 (6%)

Query: 220 SHHLIADNLKWFSDLKPGVTNIEHILAEKGEQVRRIDSNGAIELIEDE 267
             HLIAD+LK F D       +E ++   GEQV +   +   E I D 
Sbjct: 46  VRHLIADHLKIFHDHH---VTVEQLMKANGEQVSQDVGDLEFEDIPDS 90

>3k1f_M Transcription initiation factor IIB; RNA polymerase II, TFIIB, transcription factor, DNA-binding, DNA-directed RNA polymerase; 4.30A {Saccharomyces cerevisiae} Length = 197

 Score = 43.1 bits (101), Expect = 3e-05
 Identities = 13/72 (18%), Positives = 31/72 (43%), Gaps = 9/72 (12%)

Query: 99  LISKHSYEKGVIKLKHKLKLAYTCKVCGTRNSHLISKHSYEKGVVIVKCEGCS---NNHL 155
           ++++ S +K   +    L +  TC  C      ++    + +G V+  C  C    ++ L
Sbjct: 1   MMTRESIDKRAGRRGPNLNIVLTCPECKVYPPKIV--ERFSEGDVV--CALCGLVLSDKL 56

Query: 156 IADNLKW--FTD 165
           +    +W  F++
Sbjct: 57  VDTRSEWRTFSN 68

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	272
2e2z_A	100	TIM15; protein import, zinc finger, protein transp	100.0
2e2z_A	100	TIM15; protein import, zinc finger, protein transp	99.82
2jr7_A	89	DPH3 homolog; DESR1, CSL zinc finger, metal bindin	91.01
1yop_A	83	KTI11P; zinc finger, metal binding protein; NMR {S	90.87
1wge_A	83	Hypothetical protein 2610018L09RIK; diphthamide,CS	90.23
1twf_I	122	B12.6, DNA-directed RNA polymerase II 14.2 kDa pol	87.52
1qyp_A	57	RNA polymerase II; transcription, RPB9, Zn ribbon,	86.15
1tfi_A	50	Transcriptional elongation factor SII; transcripti	83.41
1tfi_A	50	Transcriptional elongation factor SII; transcripti	83.3
2l6l_A	155	DNAJ homolog subfamily C member 24; DPH4, Zn-CSL,	81.93

>2e2z_A TIM15; protein import, zinc finger, protein transport, chaperone regulator; NMR {Saccharomyces cerevisiae}

Probab=100.00  E-value=2e-36  Score=242.64  Aligned_cols=82  Identities=41%  Similarity=0.748  Sum_probs=77.1

Q ss_pred             ccccceEEEEEcCCCCcccccccchhcccceEEEEEcCCCCcceeeeccccccccCCCCCCCHHHHHHHhCCeeeeceee
Q psy13378        111 KLKHKLKLAYTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNNHLIADNLKWFTDLKPGVTNIEHILAEKGEQGCKGLFC  190 (272)
Q Consensus       111 ~~~~~~~L~FTCk~C~tRS~h~ISK~AY~kGvViVqC~gC~n~HLIADnLgwF~d~~~g~~tIEdil~~kGE~V~kg~~~  190 (272)
                      ..+|+|+|+|||++|++||+|+|||+||++|+||||||||+|+||||||||||.|.   ++||||||++|||+|+++   
T Consensus         5 ~~~~~~~l~FTC~~C~tRs~k~iSk~aY~~GvViv~C~gC~n~HlIaDnLgwF~d~---~~~IEdil~~kGe~V~~~---   78 (100)
T 2e2z_A            5 VDKPKMMIAFTCKKCNTRSSHTMSKQAYEKGTVLISCPHCKVRHLIADHLKIFHDH---HVTVEQLMKANGEQVSQD---   78 (100)
T ss_dssp             SCCCEEEEEEEETTTTEEEEEEEEHHHHHTSEEEEECTTTCCEEESCCSSCSGGGS---CCCHHHHHHHHCCCCSSS---
T ss_pred             CCCCcEEEEEEccCCCCcchhhcCHHHhhCCEEEEEcCCCccceEeehhhhhhccC---CCCHHHHHHHcCCEeeec---
Confidence            45799999999999999999999999999999999999999999999999999985   489999999999999986   


Q ss_pred             eccceeccc
Q psy13378        191 LSHDIKLNT  199 (272)
Q Consensus       191 ~~~die~~~  199 (272)
                       .+|++|++
T Consensus        79 -~~d~~~ed   86 (100)
T 2e2z_A           79 -VGDLEFED   86 (100)
T ss_dssp             -SCEEEESS
T ss_pred             -CCCccHhh
Confidence             48999987

>2e2z_A TIM15; protein import, zinc finger, protein transport, chaperone regulator; NMR {Saccharomyces cerevisiae}

Probab=99.82  E-value=3.2e-21  Score=154.69  Aligned_cols=82  Identities=27%  Similarity=0.443  Sum_probs=66.5

Q ss_pred             ceEEEEEcCCCCcceeeeccccccccCCCCCCCHHHHHHHhCCeeeeceeeeccceeccccceeEEEEeecchhhhcccc
Q psy13378        140 KGVVIVKCEGCSNNHLIADNLKWFTDLKPGVTNIEHILAEKGEQGCKGLFCLSHDIKLNTNIVRLMIETCLCHLIRETHG  219 (272)
Q Consensus       140 kGvViVqC~gC~n~HLIADnLgwF~d~~~g~~tIEdil~~kGE~V~kg~~~~~~die~~~~~~~~vi~~C~~~~~~~~C~  219 (272)
                      +-.+..+|..|..|-.               ++|...+      +.+|+                |||+||+      |+
T Consensus         9 ~~~l~FTC~~C~tRs~---------------k~iSk~a------Y~~Gv----------------Viv~C~g------C~   45 (100)
T 2e2z_A            9 KMMIAFTCKKCNTRSS---------------HTMSKQA------YEKGT----------------VLISCPH------CK   45 (100)
T ss_dssp             EEEEEEEETTTTEEEE---------------EEEEHHH------HHTSE----------------EEEECTT------TC
T ss_pred             cEEEEEEccCCCCcch---------------hhcCHHH------hhCCE----------------EEEEcCC------Cc
Confidence            4568889999998765               3555543      56666                8999997      99


Q ss_pred             cceeeecccCCccCCCCCcCCHHHHHHhcCCcEEEecCCCcEEEeccccc
Q psy13378        220 SHHLIADNLKWFSDLKPGVTNIEHILAEKGEQVRRIDSNGAIELIEDEKK  269 (272)
Q Consensus       220 n~HlIADnLGwF~d~~~g~~nIE~iL~~kGE~V~r~~~~~~lE~~~~~~~  269 (272)
                      |+||||||||||+|.   ++||||||++|||+|++.  .+++||++-.+.
T Consensus        46 n~HlIaDnLgwF~d~---~~~IEdil~~kGe~V~~~--~~d~~~ed~pe~   90 (100)
T 2e2z_A           46 VRHLIADHLKIFHDH---HVTVEQLMKANGEQVSQD--VGDLEFEDIPDS   90 (100)
T ss_dssp             CEEESCCSSCSGGGS---CCCHHHHHHHHCCCCSSS--SCEEEESSCCHH
T ss_pred             cceEeehhhhhhccC---CCCHHHHHHHcCCEeeec--CCCccHhhChHH
Confidence            999999999999985   689999999999999874  567888765443

>2jr7_A DPH3 homolog; DESR1, CSL zinc finger, metal binding protein; NMR {Homo sapiens}

Probab=91.01  E-value=0.093  Score=41.15  Aligned_cols=37  Identities=30%  Similarity=0.631  Sum_probs=31.6

Q ss_pred             EEEEEcCCCCcccccccchhcccceEEEEEcCCCCcceee
Q psy13378        117 KLAYTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNNHLI  156 (272)
Q Consensus       117 ~L~FTCk~C~tRS~h~ISK~AY~kGvViVqC~gC~n~HLI  156 (272)
                      ...|.|+ ||-+  -.|++...+.|.++++|++|.-+=.+
T Consensus        21 ~y~ypCr-CGd~--F~IteedLe~ge~iv~C~sCSL~IkV   57 (89)
T 2jr7_A           21 TYFYPCP-CGDN--FSITKEDLENGEDVATCPSCSLIIKV   57 (89)
T ss_dssp             EEEEECT-TSSE--EEEEHHHHHHTCCEEECTTTCCEEEE
T ss_pred             EEEEcCC-CCCE--EEECHHHHhCCCEEEECCCCccEEEE
Confidence            3679997 9977  89999999999999999999876443

>1yop_A KTI11P; zinc finger, metal binding protein; NMR {Saccharomyces cerevisiae} SCOP: g.41.17.1 PDB: 1yws_A

Probab=90.87  E-value=0.092  Score=40.60  Aligned_cols=36  Identities=28%  Similarity=0.531  Sum_probs=30.7

Q ss_pred             EEEEEcCCCCcccccccchhcccceEEEEEcCCCCccee
Q psy13378        117 KLAYTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNNHL  155 (272)
Q Consensus       117 ~L~FTCk~C~tRS~h~ISK~AY~kGvViVqC~gC~n~HL  155 (272)
                      ...|.|+ ||-+  -.|++...+.|.++++|++|.-+=.
T Consensus        21 ~y~ypCr-CGd~--F~it~edL~~ge~iv~C~sCSL~I~   56 (83)
T 1yop_A           21 MFTYPCP-CGDR--FQIYLDDMFEGEKVAVCPSCSLMID   56 (83)
T ss_dssp             EEEEEET-TTEE--EEEEHHHHHTTCCEEECSSSCCEEE
T ss_pred             EEEEeCC-CCCe--EEECHHHHhCCCEEEECCCCccEEE
Confidence            3679997 9944  8999999999999999999997544

>1wge_A Hypothetical protein 2610018L09RIK; diphthamide,CSL zinc finger, ADP-ribosylating toxin, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: g.41.17.1

Probab=90.23  E-value=0.13  Score=39.83  Aligned_cols=36  Identities=31%  Similarity=0.628  Sum_probs=31.3

Q ss_pred             EEEEEcCCCCcccccccchhcccceEEEEEcCCCCccee
Q psy13378        117 KLAYTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNNHL  155 (272)
Q Consensus       117 ~L~FTCk~C~tRS~h~ISK~AY~kGvViVqC~gC~n~HL  155 (272)
                      ...|.|+ |+-+  -.|++...+.|.++++|++|.-+=.
T Consensus        28 ~y~y~Cr-CGd~--F~it~edL~~ge~iv~C~sCSL~I~   63 (83)
T 1wge_A           28 TYFYPCP-CGDN--FAITKEDLENGEDVATCPSCSLIIK   63 (83)
T ss_dssp             EEEECCS-SSSC--EEEEHHHHHTTCCEEECTTTCCEEE
T ss_pred             EEEEeCC-CCCE--EEECHHHHhCCCEEEECCCCceEEE
Confidence            4679997 9977  8999999999999999999987544

>1twf_I B12.6, DNA-directed RNA polymerase II 14.2 kDa polypepti; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: g.41.3.1 g.41.3.1 PDB: 1i3q_I 1i6h_I 1k83_I* 1nik_I 1nt9_I 1pqv_I 1r5u_I 1r9s_I* 1r9t_I* 1sfo_I* 1twa_I* 1twc_I* 1i50_I* 1twg_I* 1twh_I* 1wcm_I 1y1v_I 1y1w_I 1y1y_I 1y77_I* ...

Probab=87.52  E-value=0.44  Score=38.14  Aligned_cols=35  Identities=20%  Similarity=0.445  Sum_probs=28.9

Q ss_pred             EEEcCCCCcccccccch---hcccceEEEEEcCCCCcc
Q psy13378        119 AYTCKVCGTRNSHLISK---HSYEKGVVIVKCEGCSNN  153 (272)
Q Consensus       119 ~FTCk~C~tRS~h~ISK---~AY~kGvViVqC~gC~n~  153 (272)
                      .++|+.|+++.+..+-.   .|-+-.+++.+|..|..+
T Consensus        72 ~~~Cp~C~~~~a~~~q~q~rsade~~t~fy~C~~C~~~  109 (122)
T 1twf_I           72 DRECPKCHSRENVFFQSQQRRKDTSMVLFFVCLSCSHI  109 (122)
T ss_dssp             CCCCTTTCCCCEEEEECSSCCTTCCCCEEEEETTTCCE
T ss_pred             CCCCCCCCCCEEEEEEecCccCCCCceEEEEeCCCCCE
Confidence            58999999987766654   477889999999999865

>1qyp_A RNA polymerase II; transcription, RPB9, Zn ribbon, hyperthermophilic, extremophIle; NMR {Thermococcus celer} SCOP: g.41.3.1

Probab=86.15  E-value=0.5  Score=32.91  Aligned_cols=35  Identities=23%  Similarity=0.543  Sum_probs=17.5

Q ss_pred             EEEcCCCCcccccccchh---cccceEEEEEcCCCCcc
Q psy13378        119 AYTCKVCGTRNSHLISKH---SYEKGVVIVKCEGCSNN  153 (272)
Q Consensus       119 ~FTCk~C~tRS~h~ISK~---AY~kGvViVqC~gC~n~  153 (272)
                      .++|+.|+++....+..|   |-+-.+++.+|..|..+
T Consensus        15 ~~~Cp~Cg~~~~~~~q~Q~rsadep~T~fy~C~~Cg~~   52 (57)
T 1qyp_A           15 KITCPKCGNDTAYWWEMQTRAGDEPSTIFYKCTKCGHT   52 (57)
T ss_dssp             ECCCTTTCCSEEEEEEECCSSSSCSSEEEEEESSSCCE
T ss_pred             EeECCCCCCCEEEEEEeecccCCCCCcEEEEcCCCCCE
Confidence            355666665443333322   33444566666666543

>1tfi_A Transcriptional elongation factor SII; transcription regulation; NMR {Homo sapiens} SCOP: g.41.3.1

Probab=83.41  E-value=0.53  Score=32.84  Aligned_cols=37  Identities=22%  Similarity=0.549  Sum_probs=17.1

Q ss_pred             eecCCcCCcccccccCCcccccccccccceEEEEEcCCCCcc
Q psy13378         87 YTCKVCGTRNSHLISKHSYEKGVIKLKHKLKLAYTCKVCGTR  128 (272)
Q Consensus        87 fTCkvC~TRSSh~ISK~Sy~kGv~~~~~~~~L~FTCk~C~tR  128 (272)
                      ++|+.|+.+.+.-...|     +......|.+-|+|..|++|
T Consensus        10 ~~Cp~Cg~~~a~f~q~Q-----~RsaDE~mT~Fy~C~~Cg~~   46 (50)
T 1tfi_A           10 FTCGKCKKKNCTYTQVQ-----TRSADEPMTTFVVCNECGNR   46 (50)
T ss_dssp             SCCSSSCSSCEEEEEEC-----SSSSSSCCEEEEEESSSCCE
T ss_pred             cCCCCCCCCEEEEEEec-----CcCCCCCceEEEEcCCCCCe
Confidence            45666665543321111     22222334556666666654

>1tfi_A Transcriptional elongation factor SII; transcription regulation; NMR {Homo sapiens} SCOP: g.41.3.1

Probab=83.30  E-value=0.69  Score=32.25  Aligned_cols=35  Identities=26%  Similarity=0.563  Sum_probs=28.8

Q ss_pred             EEEcCCCCcccccccchh---cccceEEEEEcCCCCcc
Q psy13378        119 AYTCKVCGTRNSHLISKH---SYEKGVVIVKCEGCSNN  153 (272)
Q Consensus       119 ~FTCk~C~tRS~h~ISK~---AY~kGvViVqC~gC~n~  153 (272)
                      .++|+.|+++.+..+-.|   |-+-.++++.|..|..+
T Consensus         9 ~~~Cp~Cg~~~a~f~q~Q~RsaDE~mT~Fy~C~~Cg~~   46 (50)
T 1tfi_A            9 LFTCGKCKKKNCTYTQVQTRSADEPMTTFVVCNECGNR   46 (50)
T ss_dssp             CSCCSSSCSSCEEEEEECSSSSSSCCEEEEEESSSCCE
T ss_pred             ccCCCCCCCCEEEEEEecCcCCCCCceEEEEcCCCCCe
Confidence            478999999987666544   77888999999999865

>2l6l_A DNAJ homolog subfamily C member 24; DPH4, Zn-CSL, J-domain, chaperone; NMR {Homo sapiens}

Probab=81.93  E-value=0.84  Score=36.91  Aligned_cols=35  Identities=26%  Similarity=0.601  Sum_probs=28.2

Q ss_pred             EEEEcCCCCcccccccchhcccceEEEEEcCCCCcceee
Q psy13378        118 LAYTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNNHLI  156 (272)
Q Consensus       118 L~FTCk~C~tRS~h~ISK~AY~kGvViVqC~gC~n~HLI  156 (272)
                      ..+.|. |+.+  -.|++.-.+.| ++++|++|..+-.+
T Consensus       111 f~~~Cr-CG~~--f~i~~~~l~~~-~~v~C~sCSl~~~v  145 (155)
T 2l6l_A          111 FYLSCR-CGGK--YSVSKDEAEEV-SLISCDTCSLIIEL  145 (155)
T ss_dssp             EEEECS-SSCE--EEEETTHHHHC-CEEECSSSSCEEEE
T ss_pred             EEEcCC-CCCe--EEecHHHhCCC-CEEECCCCceEEEE
Confidence            568897 9976  77888877778 88999999976554

---

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	272
d1wgea1	70	DelGEF-interacting protein 1, DelGIP1 {Mouse (Mus	91.29
d1tfia_	50	Transcriptional factor SII, C-terminal domain {Hum	91.07
d1qypa_	57	RBP9 subunit of RNA polymerase II {Archaeon Thermo	90.84
d1tfia_	50	Transcriptional factor SII, C-terminal domain {Hum	90.43
d1ywsa1	82	Diphthamide biosynthesis protein 3, DPH3 {Baker's	89.24
d1qypa_	57	RBP9 subunit of RNA polymerase II {Archaeon Thermo	88.66
d1twfi2	72	RBP9 subunit of RNA polymerase II {Baker's yeast (	85.28
d1twfi2	72	RBP9 subunit of RNA polymerase II {Baker's yeast (	83.55
d1wiia_	85	Hypothetical UPF0222 protein MGC4549 {Mouse (Mus m	83.3

>d1wgea1 g.41.17.1 (A:8-77) DelGEF-interacting protein 1, DelGIP1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: Rubredoxin-like
superfamily: CSL zinc finger
family: CSL zinc finger
domain: DelGEF-interacting protein 1, DelGIP1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=91.29  E-value=0.042  Score=39.74  Aligned_cols=36  Identities=31%  Similarity=0.628  Sum_probs=31.2

Q ss_pred             EEEEEcCCCCcccccccchhcccceEEEEEcCCCCccee
Q psy13378        117 KLAYTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNNHL  155 (272)
Q Consensus       117 ~L~FTCk~C~tRS~h~ISK~AY~kGvViVqC~gC~n~HL  155 (272)
                      ...|.|+ ||-+  -.|++.-.+.|-++++||+|.-+=.
T Consensus        21 ~~~ypCp-CGd~--F~it~~dLe~ge~V~~C~sCSL~ik   56 (70)
T d1wgea1          21 TYFYPCP-CGDN--FAITKEDLENGEDVATCPSCSLIIK   56 (70)
T ss_dssp             EEEECCS-SSSC--EEEEHHHHHTTCCEEECTTTCCEEE
T ss_pred             EEEeCCC-CCCe--EEECHHHHhCCCeEEeCCCCceEEE
Confidence            4678999 9965  8999999999999999999987644

>d1tfia_ g.41.3.1 (A:) Transcriptional factor SII, C-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: Transcriptional factor domain
domain: Transcriptional factor SII, C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.07  E-value=0.045  Score=37.17  Aligned_cols=37  Identities=22%  Similarity=0.529  Sum_probs=16.1

Q ss_pred             eecCCcCCcccccccCCcccccccccccceEEEEEcCCCCcc
Q psy13378         87 YTCKVCGTRNSHLISKHSYEKGVIKLKHKLKLAYTCKVCGTR  128 (272)
Q Consensus        87 fTCkvC~TRSSh~ISK~Sy~kGv~~~~~~~~L~FTCk~C~tR  128 (272)
                      |+|+.|+.+......     ..+......+.+-|+|..|++|
T Consensus        10 ~~C~kC~~~~~~~~~-----~QtRSADEp~T~F~~C~~Cg~~   46 (50)
T d1tfia_          10 FTCGKCKKKNCTYTQ-----VQTRSADEPMTTFVVCNECGNR   46 (50)
T ss_dssp             SCCSSSCSSCEEEEE-----ECSSSSSSCCEEEEEESSSCCE
T ss_pred             EECCCCCCCccEEEE-----EEccCCCCCceEEEEccccCCe
Confidence            555555555443221     1222223334445555555543

>d1qypa_ g.41.3.1 (A:) RBP9 subunit of RNA polymerase II {Archaeon Thermococcus celer [TaxId: 2264]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: Transcriptional factor domain
domain: RBP9 subunit of RNA polymerase II
species: Archaeon Thermococcus celer [TaxId: 2264]

Probab=90.84  E-value=0.068  Score=36.95  Aligned_cols=33  Identities=24%  Similarity=0.574  Sum_probs=19.1

Q ss_pred             EEcCCCCcccccccchh---cccceEEEEEcCCCCc
Q psy13378        120 YTCKVCGTRNSHLISKH---SYEKGVVIVKCEGCSN  152 (272)
Q Consensus       120 FTCk~C~tRS~h~ISK~---AY~kGvViVqC~gC~n  152 (272)
                      ++|+.|+++.+..+..|   |-+-.+++..|..|..
T Consensus        16 ~~CpkC~~~~a~~~~~QtRsaDE~~T~fy~C~~Cg~   51 (57)
T d1qypa_          16 ITCPKCGNDTAYWWEMQTRAGDEPSTIFYKCTKCGH   51 (57)
T ss_dssp             CCCTTTCCSEEEEEEECCSSSSCSSEEEEEESSSCC
T ss_pred             CCCCCCCCCceEEEEeecccccCCCeEEEEeCCCCC
Confidence            45666666655555444   3555666666666654

>d1tfia_ g.41.3.1 (A:) Transcriptional factor SII, C-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: Transcriptional factor domain
domain: Transcriptional factor SII, C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.43  E-value=0.071  Score=36.14  Aligned_cols=36  Identities=25%  Similarity=0.540  Sum_probs=30.5

Q ss_pred             EEEcCCCCcccccccchh---cccceEEEEEcCCCCcce
Q psy13378        119 AYTCKVCGTRNSHLISKH---SYEKGVVIVKCEGCSNNH  154 (272)
Q Consensus       119 ~FTCk~C~tRS~h~ISK~---AY~kGvViVqC~gC~n~H  154 (272)
                      .|+|+.|++++......|   |=|--+++++|..|.++-
T Consensus         9 ~~~C~kC~~~~~~~~~~QtRSADEp~T~F~~C~~Cg~~W   47 (50)
T d1tfia_           9 LFTCGKCKKKNCTYTQVQTRSADEPMTTFVVCNECGNRW   47 (50)
T ss_dssp             CSCCSSSCSSCEEEEEECSSSSSSCCEEEEEESSSCCEE
T ss_pred             CEECCCCCCCccEEEEEEccCCCCCceEEEEccccCCee
Confidence            599999999987777665   678889999999999763

>d1ywsa1 g.41.17.1 (A:1-82) Diphthamide biosynthesis protein 3, DPH3 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Small proteins
fold: Rubredoxin-like
superfamily: CSL zinc finger
family: CSL zinc finger
domain: Diphthamide biosynthesis protein 3, DPH3
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=89.24  E-value=0.072  Score=39.48  Aligned_cols=57  Identities=23%  Similarity=0.438  Sum_probs=42.8

Q ss_pred             EEEEEcCCCCcccccccchhcccceEEEEEcCCCCcceeeeccccccccCCCCCCCHHHHHHHhCCeeee
Q psy13378        117 KLAYTCKVCGTRNSHLISKHSYEKGVVIVKCEGCSNNHLIADNLKWFTDLKPGVTNIEHILAEKGEQGCK  186 (272)
Q Consensus       117 ~L~FTCk~C~tRS~h~ISK~AY~kGvViVqC~gC~n~HLIADnLgwF~d~~~g~~tIEdil~~kGE~V~k  186 (272)
                      ...|.|+ ||-+  -.|++.-.+.|.++++||+|.-+=.|     .|..     -..++...++|+.+..
T Consensus        20 ~~~ypCr-CGd~--F~it~~dLe~ge~v~~C~sCSL~IrV-----if~~-----ed~~~~~~~~~~~~~~   76 (82)
T d1ywsa1          20 MFTYPCP-CGDR--FQIYLDDMFEGEKVAVCPSCSLMIDV-----VFDK-----EDLAEYYEEAGIHPPE   76 (82)
T ss_dssp             EEEECCS-SSSC--EEEEHHHHHTTCCEEEETTTTEEEEE-----ECCH-----HHHHHHHHHHTCCCCC
T ss_pred             EEEeccc-cCCe--EEEcHHHHhCCCeEEeCCCCceEEEE-----Eech-----hHhhhhhhhhcCCCCc
Confidence            3568888 9966  89999999999999999999876543     2322     2567777777776653

>d1qypa_ g.41.3.1 (A:) RBP9 subunit of RNA polymerase II {Archaeon Thermococcus celer [TaxId: 2264]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: Transcriptional factor domain
domain: RBP9 subunit of RNA polymerase II
species: Archaeon Thermococcus celer [TaxId: 2264]

Probab=88.66  E-value=0.21  Score=34.33  Aligned_cols=38  Identities=21%  Similarity=0.464  Sum_probs=28.1

Q ss_pred             eeecCCcCCcccccccCCcccccccccccceEEEEEcCCCCcc
Q psy13378         86 AYTCKVCGTRNSHLISKHSYEKGVIKLKHKLKLAYTCKVCGTR  128 (272)
Q Consensus        86 ~fTCkvC~TRSSh~ISK~Sy~kGv~~~~~~~~L~FTCk~C~tR  128 (272)
                      .++|+.|+.+.+.....|     +......+.+.|+|..|+++
T Consensus        15 ~~~CpkC~~~~a~~~~~Q-----tRsaDE~~T~fy~C~~Cg~~   52 (57)
T d1qypa_          15 KITCPKCGNDTAYWWEMQ-----TRAGDEPSTIFYKCTKCGHT   52 (57)
T ss_dssp             ECCCTTTCCSEEEEEEEC-----CSSSSCSSEEEEEESSSCCE
T ss_pred             cCCCCCCCCCceEEEEee-----cccccCCCeEEEEeCCCCCc
Confidence            458999998887754444     33344566799999999976

>d1twfi2 g.41.3.1 (I:50-121) RBP9 subunit of RNA polymerase II {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: Transcriptional factor domain
domain: RBP9 subunit of RNA polymerase II
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=85.28  E-value=0.17  Score=36.30  Aligned_cols=33  Identities=21%  Similarity=0.509  Sum_probs=17.0

Q ss_pred             EEcCCCCcccccccchh---cccceEEEEEcCCCCc
Q psy13378        120 YTCKVCGTRNSHLISKH---SYEKGVVIVKCEGCSN  152 (272)
Q Consensus       120 FTCk~C~tRS~h~ISK~---AY~kGvViVqC~gC~n  152 (272)
                      ..|+.|+++....+..|   |.+..++++.|..|..
T Consensus        24 ~~CpkCg~~~a~~~q~QtRsaDE~mT~Fy~C~~C~h   59 (72)
T d1twfi2          24 RECPKCHSRENVFFQSQQRRKDTSMVLFFVCLSCSH   59 (72)
T ss_dssp             CCCTTTCCCCEEEEECSSCCTTCCCCEEEEETTTCC
T ss_pred             CCCCCCCCCeEEEEEeecCccCCCceEEEEcCCCCC
Confidence            34555555554444443   3455555555555543

>d1twfi2 g.41.3.1 (I:50-121) RBP9 subunit of RNA polymerase II {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: Transcriptional factor domain
domain: RBP9 subunit of RNA polymerase II
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=83.55  E-value=0.24  Score=35.58  Aligned_cols=38  Identities=16%  Similarity=0.440  Sum_probs=27.8

Q ss_pred             eeecCCcCCcccccccCCcccccccccccceEEEEEcCCCCcc
Q psy13378         86 AYTCKVCGTRNSHLISKHSYEKGVIKLKHKLKLAYTCKVCGTR  128 (272)
Q Consensus        86 ~fTCkvC~TRSSh~ISK~Sy~kGv~~~~~~~~L~FTCk~C~tR  128 (272)
                      .+.|+.|+.+.+.....|     .......|.+-|+|..|+++
T Consensus        23 ~~~CpkCg~~~a~~~q~Q-----tRsaDE~mT~Fy~C~~C~h~   60 (72)
T d1twfi2          23 DRECPKCHSRENVFFQSQ-----QRRKDTSMVLFFVCLSCSHI   60 (72)
T ss_dssp             CCCCTTTCCCCEEEEECS-----SCCTTCCCCEEEEETTTCCE
T ss_pred             CCCCCCCCCCeEEEEEee-----cCccCCCceEEEEcCCCCCC
Confidence            358999998877654444     33344567799999999976

>d1wiia_ g.41.3.4 (A:) Hypothetical UPF0222 protein MGC4549 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: Putative zinc binding domain
domain: Hypothetical UPF0222 protein MGC4549
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=83.30  E-value=0.32  Score=36.09  Aligned_cols=44  Identities=18%  Similarity=0.414  Sum_probs=25.2

Q ss_pred             ccccceeeeeecCCcCCcccccccCCcccccccccccceEEEEEcCCCCcccc
Q psy13378         78 QLEHKLKLAYTCKVCGTRNSHLISKHSYEKGVIKLKHKLKLAYTCKVCGTRNS  130 (272)
Q Consensus        78 q~~~k~~i~fTCkvC~TRSSh~ISK~Sy~kGv~~~~~~~~L~FTCk~C~tRS~  130 (272)
                      +...++--.|+|+.|++..+-.+. ---..+++        ..+|..|+.+-.
T Consensus        15 k~~~kL~t~F~CPfCnh~~sV~vk-~dkk~~~g--------~l~C~vCg~~~~   58 (85)
T d1wiia_          15 KMTGTLETQFTCPFCNHEKSCDVK-MDRARNTG--------VISCTVCLEEFQ   58 (85)
T ss_dssp             CCCCCCSSCCCCTTTCCSSCEEEE-EETTTTEE--------EEEESSSCCEEE
T ss_pred             cccCCCCceEcCCCCCCCCeEEEE-EEecCCEE--------EEEEecCCCeEE
Confidence            445677778888888865433211 11111332        577888886633