Citrus Sinensis ID: 031323

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-
Protein Sequence
MDIEQRQAELIDHFVKQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENSKYLDMLRLFAHGTWSDYKNNAGHLPQLVPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVCTVLVRL
Secondary Structure (PSIPRED)
ccHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHccccEEEcHHHHccccHHHccccccHHHHHHHHHHHcccHHHHHHHHcccccccHHHHHHHHHHHHHHHHHccccccHHHHHHHcccccHHHHHHHHHHHHHHHcccEEEEcccccEEEEEEEEccc
Secondary Structure Prediction (SSPRO)
ccHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHccccEEEHHHHHccHHHHHHHccccHHHHHHHHHHHHccHHHHHHcccccccccHHHHHHHHHHHHHHHHHccccccHHHHHHHcccccHHHHHHHHHHHHHHHccEEEEccccccEEEEEEEEEcc
Coil and Loop (DISEMBL)
MDIEQRQAELIDHFVKQASNQKGAALGSVIVEatsqpslfafseilavpniaefegtenskyLDMLRLFAHGtwsdyknnaghlpqlvpdqvLKLKQLTVLTLAetnkvlpydelmeELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVCTVLVRL
Flexible Loop (DISEMBL)
MDIEQRQAELIDHFVKQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENSKYLDMLRLFAHGTWSDYKNNAGHLPQLVPDQVLKLKQLTVLTLaetnkvlpydelMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVCTVLVRL
Low Complexity Region (SEG)
MDIEQRQAELIDHFVKQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENSKYLDMLRLFAHGTWSDYKNNAGHLPQLVPDqvlklkqltvltlAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVCTVLVRL
Disordered region (IsUnstruct)
*************F*********AALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENSKYLDMLRLFAHGTWSDYKNNAGHLPQLVPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVCTVLV**
Disordered Region (DISOPRED)
************HFVKQAS*QKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENSKYLDMLRLFAHGTWSDYKNNAGHLPQLVPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVCTVLVRL
Disordered Region (DISEMBL)
MDIEQRQAELIDHFVKQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENSKYLDMLRLFAHGTWSDYKNNAGHLPQLVPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVCTVLVRL
Disordered Region (DISPRO)
*DI*QRQAELIDHFVKQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENSKYLDMLRLFAHGTWSDYKNNAGHLPQLVPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVCTVLVRL
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MDIEQRQAELIDHFVKQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENSKYLDMLRLFAHGTWSDYKNNAGHLPQLVPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVCTVLVRL
Positional Conservation
no confident homologs detected

---

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	161	2.2.26 [Sep-21-2011]
Q94JU3	260	COP9 signalosome complex	no	no	0.956	0.592	0.779	4e-67
Q55BD5	259	COP9 signalosome complex	yes	no	0.888	0.552	0.444	5e-32
Q2KI56	264	COP9 signalosome complex	yes	no	0.950	0.579	0.4	6e-26
Q9H9Q2	264	COP9 signalosome complex	yes	no	0.950	0.579	0.4	6e-26
Q8BV13	264	COP9 signalosome complex	yes	no	0.950	0.579	0.4	9e-26
Q5R762	275	COP9 signalosome complex	no	no	0.881	0.516	0.391	1e-22
Q9UBW8	275	COP9 signalosome complex	no	no	0.881	0.516	0.391	1e-22
Q9CZ04	275	COP9 signalosome complex	no	no	0.881	0.516	0.391	1e-22
Q9V4S8	278	COP9 signalosome complex	yes	no	0.894	0.517	0.386	4e-22
Q7SGS1	417	COP9 signalosome complex	N/A	no	0.863	0.333	0.349	7e-19

>sp|Q94JU3|CSN7_ARATH COP9 signalosome complex subunit 7 OS=Arabidopsis thaliana GN=CSN7 PE=1 SV=1

 Score =  253 bits (645), Expect = 4e-67,   Method: Compositional matrix adjust.
 Identities = 120/154 (77%), Positives = 134/154 (87%)

Query: 1   MDIEQRQAELIDHFVKQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENS 60
           MDIEQ+QAE+ID  VK+AS  K  ALG +I+EATS PSLFAFSEILA+PN+A+ EGT +S
Sbjct: 1   MDIEQKQAEIIDQLVKRASTCKSEALGPLIIEATSHPSLFAFSEILALPNVAQLEGTTDS 60

Query: 61  KYLDMLRLFAHGTWSDYKNNAGHLPQLVPDQVLKLKQLTVLTLAETNKVLPYDELMEELD 120
            YLD+LRLFAHGTW DYK NA  LP L PDQ+LKLKQLTVLTLAE+NKVLPYD LM ELD
Sbjct: 61  VYLDLLRLFAHGTWGDYKCNATRLPHLSPDQILKLKQLTVLTLAESNKVLPYDTLMVELD 120

Query: 121 VTNVRELEDFLINECMYTGIVRGKLDQLRRCFEV 154
           V+NVRELEDFLINECMY GIVRGKLDQL+RCFEV
Sbjct: 121 VSNVRELEDFLINECMYAGIVRGKLDQLKRCFEV 154

Component of the COP9 signalosome complex (CSN), a complex involved in various cellular and developmental processes such as photomorphogenesis and auxin and jasmonate responses. The CSN complex is an essential regulator of the ubiquitin (Ubl) conjugation pathway by mediating the deneddylation of the cullin subunits of SCF-type E3 ligase complexes, leading to decrease the Ubl ligase activity of SCF. It is involved in repression of photomorphogenesis in darkness by regulating the activity of COP1-containing Ubl ligase complexes. The complex is also required for degradation of IAA6 by regulating the activity of the Ubl ligase SCF-TIR complex.
Arabidopsis thaliana (taxid: 3702)

>sp|Q55BD5|CSN7_DICDI COP9 signalosome complex subunit 7 OS=Dictyostelium discoideum GN=csn7 PE=1 SV=1

 Score =  136 bits (343), Expect = 5e-32,   Method: Compositional matrix adjust.
 Identities = 64/144 (44%), Positives = 98/144 (68%), Gaps = 1/144 (0%)

Query: 11  IDHFVKQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENSKYLDMLRLFA 70
           +  FV  A + KG A+ S+I +A + PS+F F E+L +PN+ + + TE   Y D+L +FA
Sbjct: 14  LKQFVVLAKSSKGRAIVSIIEKALNHPSVFVFGELLDMPNVQQLKETEFKNYYDLLLIFA 73

Query: 71  HGTWSDYKNNAGHLPQLVPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDF 130
           +G++ DYKN    LPQL P  + KLKQLT++ L+ T+ V+PY  L E++++TNVRELED 
Sbjct: 74  YGSFIDYKNKKDSLPQLTPQMITKLKQLTIVFLSSTSNVIPYSVLQEQIEITNVRELEDL 133

Query: 131 LINECMYTGIVRGKLDQLRRCFEV 154
           +I + +Y  I++GKLDQ  +  E+
Sbjct: 134 II-DSIYQNIIKGKLDQKNKHLEI 156

Component of the COP9 signalosome complex (CSN), a complex involved in various cellular and developmental processes. The CSN complex is an essential regulator of the ubiquitin (Ubl) conjugation pathway by mediating the deneddylation of the cullin subunits of E3 ligase complexes, leading to modify the Ubl ligase activity.

Dictyostelium discoideum (taxid: 44689)

>sp|Q2KI56|CSN7B_BOVIN COP9 signalosome complex subunit 7b OS=Bos taurus GN=COPS7B PE=2 SV=1

 Score =  116 bits (291), Expect = 6e-26,   Method: Compositional matrix adjust.
 Identities = 62/155 (40%), Positives = 96/155 (61%), Gaps = 2/155 (1%)

Query: 1   MDIEQR-QAELIDHFVKQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTEN 59
           M  EQ+  + L++ F+  A    G+AL ++I +    P ++ F E+L + N+ E     N
Sbjct: 1   MAGEQKPSSNLLEQFILLAKGTSGSALTALISQVLEAPGVYVFGELLELANVQELAEGAN 60

Query: 60  SKYLDMLRLFAHGTWSDYKNNAGHLPQLVPDQVLKLKQLTVLTLAETNKVLPYDELMEEL 119
           + YL +L LFA+GT+ DY  N   LP+L   Q  KLK LT+++LA   K +PY  L+++L
Sbjct: 61  AAYLQLLNLFAYGTYPDYIANKESLPELSTAQQNKLKHLTIVSLASRMKCIPYSVLLKDL 120

Query: 120 DVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEV 154
           ++ N+RELED +I E +YT I++GKLDQ  +  EV
Sbjct: 121 EMRNLRELEDLII-EAVYTDIIQGKLDQRNQLLEV 154

Component of the COP9 signalosome complex (CSN), a complex involved in various cellular and developmental processes. The CSN complex is an essential regulator of the ubiquitin (Ubl) conjugation pathway by mediating the deneddylation of the cullin subunits of SCF-type E3 ligase complexes, leading to decrease the Ubl ligase activity of SCF-type complexes such as SCF, CSA or DDB2. The complex is also involved in phosphorylation of p53/TP53, JUN, I-kappa-B-alpha/NFKBIA, ITPK1 and IRF8/ICSBP, possibly via its association with CK2 and PKD kinases. CSN-dependent phosphorylation of TP53 and JUN promotes and protects degradation by the Ubl system, respectively.

Bos taurus (taxid: 9913)

>sp|Q9H9Q2|CSN7B_HUMAN COP9 signalosome complex subunit 7b OS=Homo sapiens GN=COPS7B PE=1 SV=1

 Score =  116 bits (291), Expect = 6e-26,   Method: Compositional matrix adjust.
 Identities = 62/155 (40%), Positives = 96/155 (61%), Gaps = 2/155 (1%)

Query: 1   MDIEQR-QAELIDHFVKQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTEN 59
           M  EQ+  + L++ F+  A    G+AL ++I +    P ++ F E+L + N+ E     N
Sbjct: 1   MAGEQKPSSNLLEQFILLAKGTSGSALTALISQVLEAPGVYVFGELLELANVQELAEGAN 60

Query: 60  SKYLDMLRLFAHGTWSDYKNNAGHLPQLVPDQVLKLKQLTVLTLAETNKVLPYDELMEEL 119
           + YL +L LFA+GT+ DY  N   LP+L   Q  KLK LT+++LA   K +PY  L+++L
Sbjct: 61  AAYLQLLNLFAYGTYPDYIANKESLPELSTAQQNKLKHLTIVSLASRMKCIPYSVLLKDL 120

Query: 120 DVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEV 154
           ++ N+RELED +I E +YT I++GKLDQ  +  EV
Sbjct: 121 EMRNLRELEDLII-EAVYTDIIQGKLDQRNQLLEV 154

Component of the COP9 signalosome complex (CSN), a complex involved in various cellular and developmental processes. The CSN complex is an essential regulator of the ubiquitin (Ubl) conjugation pathway by mediating the deneddylation of the cullin subunits of SCF-type E3 ligase complexes, leading to decrease the Ubl ligase activity of SCF-type complexes such as SCF, CSA or DDB2. The complex is also involved in phosphorylation of p53/TP53, JUN, I-kappa-B-alpha/NFKBIA, ITPK1 and IRF8/ICSBP, possibly via its association with CK2 and PKD kinases. CSN-dependent phosphorylation of TP53 and JUN promotes and protects degradation by the Ubl system, respectively.

Homo sapiens (taxid: 9606)

>sp|Q8BV13|CSN7B_MOUSE COP9 signalosome complex subunit 7b OS=Mus musculus GN=Cops7b PE=1 SV=1

 Score =  115 bits (289), Expect = 9e-26,   Method: Compositional matrix adjust.
 Identities = 62/155 (40%), Positives = 96/155 (61%), Gaps = 2/155 (1%)

Query: 1   MDIEQR-QAELIDHFVKQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTEN 59
           M  EQ+  + L++ F+  A    G+AL ++I +    P ++ F E+L + N+ E     N
Sbjct: 1   MAGEQKPSSNLLEQFILLAKGTSGSALTTLISQVLEAPGVYVFGELLELANVQELAEGAN 60

Query: 60  SKYLDMLRLFAHGTWSDYKNNAGHLPQLVPDQVLKLKQLTVLTLAETNKVLPYDELMEEL 119
           + YL +L LFA+GT+ DY  N   LP+L   Q  KLK LT+++LA   K +PY  L+++L
Sbjct: 61  AAYLQLLNLFAYGTYPDYIANKESLPELSVAQQNKLKHLTIVSLASRMKCIPYSVLLKDL 120

Query: 120 DVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEV 154
           ++ N+RELED +I E +YT I++GKLDQ  +  EV
Sbjct: 121 EMRNLRELEDLII-EAVYTDIIQGKLDQRNQLLEV 154

Component of the COP9 signalosome complex (CSN), a complex involved in various cellular and developmental processes. The CSN complex is an essential regulator of the ubiquitin (Ubl) conjugation pathway by mediating the deneddylation of the cullin subunits of SCF-type E3 ligase complexes, leading to decrease the Ubl ligase activity of SCF-type complexes such as SCF, CSA or DDB2. The complex is also involved in phosphorylation of p53/TP53, JUN, I-kappa-B-alpha/NFKBIA, ITPK1 and IRF8/ICSBP, possibly via its association with CK2 and PKD kinases. CSN-dependent phosphorylation of TP53 and JUN promotes and protects degradation by the Ubl system, respectively.

Mus musculus (taxid: 10090)

>sp|Q5R762|CSN7A_PONAB COP9 signalosome complex subunit 7a OS=Pongo abelii GN=COPS7A PE=2 SV=1

 Score =  105 bits (262), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 56/143 (39%), Positives = 88/143 (61%), Gaps = 1/143 (0%)

Query: 12  DHFVKQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENSKYLDMLRLFAH 71
           + F+  A + KGAAL ++I +    P ++ F E+L +PN+ E   ++ +    +L +FA+
Sbjct: 13  EQFLLLAKSAKGAALATLIHQVLEAPGVYVFGELLDMPNVRELAESDFASTFRLLTVFAY 72

Query: 72  GTWSDYKNNAGHLPQLVPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFL 131
           GT++DY   A +LP L   Q  KL+ L+V+TLA   K +PY  L+E L + NVR+LED +
Sbjct: 73  GTYADYLAEARNLPPLTEAQKNKLRHLSVVTLAAKVKCIPYAVLLEALALRNVRQLEDLV 132

Query: 132 INECMYTGIVRGKLDQLRRCFEV 154
           I E +Y  ++RG LDQ  +  EV
Sbjct: 133 I-EAVYADVLRGSLDQRNQRLEV 154

Component of the COP9 signalosome complex (CSN), a complex involved in various cellular and developmental processes. The CSN complex is an essential regulator of the ubiquitin (Ubl) conjugation pathway by mediating the deneddylation of the cullin subunits of SCF-type E3 ligase complexes, leading to decrease the Ubl ligase activity of SCF-type complexes such as SCF, CSA or DDB2. The complex is also involved in phosphorylation of p53/TP53, JUN, I-kappa-B-alpha/NFKBIA, ITPK1 and IRF8/ICSBP, possibly via its association with CK2 and PKD kinases. CSN-dependent phosphorylation of TP53 and JUN promotes and protects degradation by the Ubl system, respectively.

Pongo abelii (taxid: 9601)

>sp|Q9UBW8|CSN7A_HUMAN COP9 signalosome complex subunit 7a OS=Homo sapiens GN=COPS7A PE=1 SV=1

 Score =  105 bits (262), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 56/143 (39%), Positives = 88/143 (61%), Gaps = 1/143 (0%)

Query: 12  DHFVKQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENSKYLDMLRLFAH 71
           + F+  A + KGAAL ++I +    P ++ F E+L +PN+ E   ++ +    +L +FA+
Sbjct: 13  EQFLLLAKSAKGAALATLIHQVLEAPGVYVFGELLDMPNVRELAESDFASTFRLLTVFAY 72

Query: 72  GTWSDYKNNAGHLPQLVPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFL 131
           GT++DY   A +LP L   Q  KL+ L+V+TLA   K +PY  L+E L + NVR+LED +
Sbjct: 73  GTYADYLAEARNLPPLTEAQKNKLRHLSVVTLAAKVKCIPYAVLLEALALRNVRQLEDLV 132

Query: 132 INECMYTGIVRGKLDQLRRCFEV 154
           I E +Y  ++RG LDQ  +  EV
Sbjct: 133 I-EAVYADVLRGSLDQRNQRLEV 154

Component of the COP9 signalosome complex (CSN), a complex involved in various cellular and developmental processes. The CSN complex is an essential regulator of the ubiquitin (Ubl) conjugation pathway by mediating the deneddylation of the cullin subunits of SCF-type E3 ligase complexes, leading to decrease the Ubl ligase activity of SCF-type complexes such as SCF, CSA or DDB2. The complex is also involved in phosphorylation of p53/TP53, JUN, I-kappa-B-alpha/NFKBIA, ITPK1 and IRF8/ICSBP, possibly via its association with CK2 and PKD kinases. CSN-dependent phosphorylation of TP53 and JUN promotes and protects degradation by the Ubl system, respectively.

Homo sapiens (taxid: 9606)

>sp|Q9CZ04|CSN7A_MOUSE COP9 signalosome complex subunit 7a OS=Mus musculus GN=Cops7a PE=1 SV=2

 Score =  105 bits (261), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 56/143 (39%), Positives = 88/143 (61%), Gaps = 1/143 (0%)

Query: 12  DHFVKQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENSKYLDMLRLFAH 71
           + F+  A + KGAAL ++I +    P ++ F E+L +PN+ E   ++ +    +L +FA+
Sbjct: 13  EQFLLLAKSAKGAALATLIHQVLEAPGVYVFGELLDMPNVRELAESDFASTFRLLTVFAY 72

Query: 72  GTWSDYKNNAGHLPQLVPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFL 131
           GT++DY   A +LP L   Q  KL+ L+V+TLA   K +PY  L+E L + NVR+LED +
Sbjct: 73  GTYADYLAEARNLPPLTDAQKNKLRHLSVVTLAAKVKCIPYAVLLEALALRNVRQLEDLV 132

Query: 132 INECMYTGIVRGKLDQLRRCFEV 154
           I E +Y  ++RG LDQ  +  EV
Sbjct: 133 I-EAVYADVLRGSLDQRNQRLEV 154

Component of the COP9 signalosome complex (CSN), a complex involved in various cellular and developmental processes. The CSN complex is an essential regulator of the ubiquitin (Ubl) conjugation pathway by mediating the deneddylation of the cullin subunits of SCF-type E3 ligase complexes, leading to decrease the Ubl ligase activity of SCF-type complexes such as SCF, CSA or DDB2. The complex is also involved in phosphorylation of p53/TP53, JUN, I-kappa-B-alpha/NFKBIA, ITPK1 and IRF8/ICSBP, possibly via its association with CK2 and PKD kinases. CSN-dependent phosphorylation of TP53 and JUN promotes and protects degradation by the Ubl system, respectively.

Mus musculus (taxid: 10090)

>sp|Q9V4S8|CSN7_DROME COP9 signalosome complex subunit 7 OS=Drosophila melanogaster GN=CSN7 PE=1 SV=2

 Score =  103 bits (257), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 56/145 (38%), Positives = 86/145 (59%), Gaps = 1/145 (0%)

Query: 10  LIDHFVKQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENSKYLDMLRLF 69
            ++ F   A +  GAAL  VI +A   P++F F E+LA P++ + +   +SK+ + L LF
Sbjct: 19  FLEKFCVLAKSSTGAALLDVIRQALEAPNVFVFGELLAEPSVLQLKDGPDSKHFETLNLF 78

Query: 70  AHGTWSDYKNNAGHLPQLVPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELED 129
           A+GT+ +Y+       +L P    KL+ LT+++LA   K +PY  L+ EL++ NVR LED
Sbjct: 79  AYGTYKEYRAQPEKFIELTPAMQKKLQHLTIVSLAIKAKSIPYALLLSELEIDNVRHLED 138

Query: 130 FLINECMYTGIVRGKLDQLRRCFEV 154
            +I E +Y  I+ GKL Q  R  EV
Sbjct: 139 III-EAIYADIIHGKLFQNTRILEV 162

Component of the COP9 signalosome complex (CSN), a complex involved in various cellular and developmental processes. The CSN complex is an essential regulator of the ubiquitin (Ubl) conjugation pathway by mediating the deneddylation of the cullin subunits of the SCF-type E3 ligase complexes, leading to decrease the Ubl ligase activity of SCF. The CSN complex plays an essential role in oogenesis and embryogenesis and is required for proper photoreceptor R cell differentiation and promote lamina glial cell migration or axon targeting. It also promotes Ubl-dependent degradation of cyclin E (CycE) during early oogenesis.

Drosophila melanogaster (taxid: 7227)

>sp|Q7SGS1|CSN7A_NEUCR COP9 signalosome complex subunit 7a OS=Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987) GN=csn-7a PE=1 SV=1

 Score = 92.8 bits (229), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 57/163 (34%), Positives = 90/163 (55%), Gaps = 24/163 (14%)

Query: 16  KQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGT-ENSKYLDMLRLFAHGTW 74
           K A++ + AA   ++   TS P+ F F+E+L  P I   E + E S YL +L++F+HGT+
Sbjct: 18  KSATSPRAAA--DLVTRVTSAPNTFIFTELLQTPQIQSLEYSHEFSSYLTLLQIFSHGTY 75

Query: 75  SDYKNNAGHLPQLVPDQVLKLKQLTVLTLA----------------ETNKVLP----YDE 114
           +DY  NA  LP L  DQ LKL+QL++LTL                 E N+  P    Y  
Sbjct: 76  ADYIANASALPALNDDQKLKLRQLSLLTLVANDGSNVPLDYDAMQRENNQAQPPNQSYAS 135

Query: 115 LMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVCTV 157
           L   L++++ RELE+ +I+  +Y G++ G+LD      ++ +V
Sbjct: 136 LTRRLELSSARELEELVIS-AIYAGLIEGQLDPANEMVQINSV 177

Component of the COP9 signalosome (CSN) complex that acts as an regulator of the ubiquitin (Ubl) conjugation pathway by mediating the deneddylation of the cullin subunit of SCF-type E3 ubiquitin-protein ligase complexes (By similarity). The CSN complex is involved in the regulation of the circadian clock through its control of the stability of the SCF(FWD1) complex.

Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987) (taxid: 367110)

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	161
224067485	225	predicted protein [Populus trichocarpa]	0.956	0.684	0.844	4e-73
255541046	275	cop9 complex subunit 7a, putative [Ricin	0.956	0.56	0.857	7e-73
359489202	247	PREDICTED: COP9 signalosome complex subu	0.956	0.623	0.850	3e-72
147788695	225	hypothetical protein VITISV_024935 [Viti	0.956	0.684	0.850	5e-72
225453392	259	PREDICTED: COP9 signalosome complex subu	0.956	0.594	0.850	1e-71
224136466	223	predicted protein [Populus trichocarpa]	0.956	0.690	0.831	3e-70
118485804	259	unknown [Populus trichocarpa]	0.956	0.594	0.831	8e-70
449445513	259	PREDICTED: COP9 signalosome complex subu	0.956	0.594	0.811	3e-69
307136429	225	cop9 complex subunit 7a [Cucumis melo su	0.956	0.684	0.805	4e-69
329025154	247	COP9 complex subunit 7a [Solanum chacoen	0.956	0.623	0.811	4e-67

>gi|224067485|ref|XP_002302493.1| predicted protein [Populus trichocarpa] gi|222844219|gb|EEE81766.1| predicted protein [Populus trichocarpa]

 Score =  278 bits (712), Expect = 4e-73,   Method: Compositional matrix adjust.
 Identities = 130/154 (84%), Positives = 142/154 (92%)

Query: 1   MDIEQRQAELIDHFVKQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENS 60
           MDIEQ+QAELIDHFV QAS  K +AL  +I+EATS PSLFAFSEIL+VP ++E +GTENS
Sbjct: 1   MDIEQKQAELIDHFVNQASTLKASALWPLIIEATSHPSLFAFSEILSVPTVSELQGTENS 60

Query: 61  KYLDMLRLFAHGTWSDYKNNAGHLPQLVPDQVLKLKQLTVLTLAETNKVLPYDELMEELD 120
            YLD+LRLFAHGTW+DYKNNAGHLPQLVPDQVLKLKQLTVLTLAE NKVLPYD+LM+ELD
Sbjct: 61  LYLDVLRLFAHGTWTDYKNNAGHLPQLVPDQVLKLKQLTVLTLAEMNKVLPYDQLMQELD 120

Query: 121 VTNVRELEDFLINECMYTGIVRGKLDQLRRCFEV 154
           VTNVRELEDFLINECMY GIVRGKLDQLRRCFEV
Sbjct: 121 VTNVRELEDFLINECMYAGIVRGKLDQLRRCFEV 154

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255541046|ref|XP_002511587.1| cop9 complex subunit 7a, putative [Ricinus communis] gi|223548767|gb|EEF50256.1| cop9 complex subunit 7a, putative [Ricinus communis]

 Score =  278 bits (710), Expect = 7e-73,   Method: Compositional matrix adjust.
 Identities = 132/154 (85%), Positives = 143/154 (92%)

Query: 1   MDIEQRQAELIDHFVKQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENS 60
           M+IEQ+QAELIDHFVK AS  KG+ALG VIVEATS PSLFAFSEILAVP +AE EG +NS
Sbjct: 1   MEIEQKQAELIDHFVKIASALKGSALGPVIVEATSHPSLFAFSEILAVPTVAELEGVDNS 60

Query: 61  KYLDMLRLFAHGTWSDYKNNAGHLPQLVPDQVLKLKQLTVLTLAETNKVLPYDELMEELD 120
            YLD+LRLFAHGTW+DYKNN+G LPQL+PDQVLKLKQLTVLTLAETNKVLPYD+LM+ELD
Sbjct: 61  VYLDVLRLFAHGTWTDYKNNSGRLPQLIPDQVLKLKQLTVLTLAETNKVLPYDQLMQELD 120

Query: 121 VTNVRELEDFLINECMYTGIVRGKLDQLRRCFEV 154
           VTNVRELEDFLINECMY GIVRGKLDQLRRCFEV
Sbjct: 121 VTNVRELEDFLINECMYAGIVRGKLDQLRRCFEV 154

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359489202|ref|XP_003633896.1| PREDICTED: COP9 signalosome complex subunit 7 isoform 2 [Vitis vinifera]

 Score =  276 bits (705), Expect = 3e-72,   Method: Compositional matrix adjust.
 Identities = 131/154 (85%), Positives = 139/154 (90%)

Query: 1   MDIEQRQAELIDHFVKQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENS 60
           MDIEQRQAELID FVKQAS   G+AL +VI++ATS PSLFAFSEILAVPN+ E  GTENS
Sbjct: 1   MDIEQRQAELIDAFVKQASTHNGSALATVILDATSHPSLFAFSEILAVPNVVELGGTENS 60

Query: 61  KYLDMLRLFAHGTWSDYKNNAGHLPQLVPDQVLKLKQLTVLTLAETNKVLPYDELMEELD 120
            YLDMLRLFAHGTWSDYK+N   LPQLVPDQ LKLKQLTVLTLAETNKVLPYD+LM+ELD
Sbjct: 61  VYLDMLRLFAHGTWSDYKSNVDRLPQLVPDQALKLKQLTVLTLAETNKVLPYDQLMQELD 120

Query: 121 VTNVRELEDFLINECMYTGIVRGKLDQLRRCFEV 154
           VTNVRELEDFLINECMY GIVRGKLDQLRRCFEV
Sbjct: 121 VTNVRELEDFLINECMYAGIVRGKLDQLRRCFEV 154

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147788695|emb|CAN69751.1| hypothetical protein VITISV_024935 [Vitis vinifera]

 Score =  275 bits (703), Expect = 5e-72,   Method: Compositional matrix adjust.
 Identities = 131/154 (85%), Positives = 139/154 (90%)

Query: 1   MDIEQRQAELIDHFVKQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENS 60
           MDIEQRQAELID FVKQAS   G+AL +VI++ATS PSLFAFSEILAVPN+ E  GTENS
Sbjct: 1   MDIEQRQAELIDAFVKQASTHNGSALATVILDATSHPSLFAFSEILAVPNVVELGGTENS 60

Query: 61  KYLDMLRLFAHGTWSDYKNNAGHLPQLVPDQVLKLKQLTVLTLAETNKVLPYDELMEELD 120
            YLDMLRLFAHGTWSDYK+N   LPQLVPDQ LKLKQLTVLTLAETNKVLPYD+LM+ELD
Sbjct: 61  VYLDMLRLFAHGTWSDYKSNVDRLPQLVPDQALKLKQLTVLTLAETNKVLPYDQLMQELD 120

Query: 121 VTNVRELEDFLINECMYTGIVRGKLDQLRRCFEV 154
           VTNVRELEDFLINECMY GIVRGKLDQLRRCFEV
Sbjct: 121 VTNVRELEDFLINECMYAGIVRGKLDQLRRCFEV 154

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225453392|ref|XP_002273686.1| PREDICTED: COP9 signalosome complex subunit 7 isoform 1 [Vitis vinifera] gi|297734611|emb|CBI16662.3| unnamed protein product [Vitis vinifera]

 Score =  273 bits (699), Expect = 1e-71,   Method: Compositional matrix adjust.
 Identities = 131/154 (85%), Positives = 139/154 (90%)

Query: 1   MDIEQRQAELIDHFVKQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENS 60
           MDIEQRQAELID FVKQAS   G+AL +VI++ATS PSLFAFSEILAVPN+ E  GTENS
Sbjct: 1   MDIEQRQAELIDAFVKQASTHNGSALATVILDATSHPSLFAFSEILAVPNVVELGGTENS 60

Query: 61  KYLDMLRLFAHGTWSDYKNNAGHLPQLVPDQVLKLKQLTVLTLAETNKVLPYDELMEELD 120
            YLDMLRLFAHGTWSDYK+N   LPQLVPDQ LKLKQLTVLTLAETNKVLPYD+LM+ELD
Sbjct: 61  VYLDMLRLFAHGTWSDYKSNVDRLPQLVPDQALKLKQLTVLTLAETNKVLPYDQLMQELD 120

Query: 121 VTNVRELEDFLINECMYTGIVRGKLDQLRRCFEV 154
           VTNVRELEDFLINECMY GIVRGKLDQLRRCFEV
Sbjct: 121 VTNVRELEDFLINECMYAGIVRGKLDQLRRCFEV 154

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224136466|ref|XP_002326867.1| predicted protein [Populus trichocarpa] gi|222835182|gb|EEE73617.1| predicted protein [Populus trichocarpa]

 Score =  269 bits (687), Expect = 3e-70,   Method: Compositional matrix adjust.
 Identities = 128/154 (83%), Positives = 139/154 (90%)

Query: 1   MDIEQRQAELIDHFVKQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENS 60
           MDIEQ+QAELIDHFV QAS  K +AL  +I+EATS PSLFAFSEIL+ P ++E EGTENS
Sbjct: 1   MDIEQKQAELIDHFVNQASTLKASALWPLIIEATSHPSLFAFSEILSSPTVSELEGTENS 60

Query: 61  KYLDMLRLFAHGTWSDYKNNAGHLPQLVPDQVLKLKQLTVLTLAETNKVLPYDELMEELD 120
             LD+LRLFAHGTWSDYK+NAG LPQLVPDQVLKLKQLTVLTLAE NKVLPYD+LM+ELD
Sbjct: 61  FCLDVLRLFAHGTWSDYKSNAGRLPQLVPDQVLKLKQLTVLTLAEMNKVLPYDQLMQELD 120

Query: 121 VTNVRELEDFLINECMYTGIVRGKLDQLRRCFEV 154
           VTNVRELEDFLINECMY GIVRGKLDQLRRCFEV
Sbjct: 121 VTNVRELEDFLINECMYAGIVRGKLDQLRRCFEV 154

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|118485804|gb|ABK94750.1| unknown [Populus trichocarpa]

 Score =  267 bits (683), Expect = 8e-70,   Method: Compositional matrix adjust.
 Identities = 128/154 (83%), Positives = 139/154 (90%)

Query: 1   MDIEQRQAELIDHFVKQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENS 60
           MDIEQ+QAELIDHFV QAS  K +AL  +I+EATS PSLFAFSEIL+ P ++E EGTENS
Sbjct: 1   MDIEQKQAELIDHFVNQASTLKASALWPLIIEATSHPSLFAFSEILSSPTVSELEGTENS 60

Query: 61  KYLDMLRLFAHGTWSDYKNNAGHLPQLVPDQVLKLKQLTVLTLAETNKVLPYDELMEELD 120
             LD+LRLFAHGTWSDYK+NAG LPQLVPDQVLKLKQLTVLTLAE NKVLPYD+LM+ELD
Sbjct: 61  FCLDVLRLFAHGTWSDYKSNAGRLPQLVPDQVLKLKQLTVLTLAEMNKVLPYDQLMQELD 120

Query: 121 VTNVRELEDFLINECMYTGIVRGKLDQLRRCFEV 154
           VTNVRELEDFLINECMY GIVRGKLDQLRRCFEV
Sbjct: 121 VTNVRELEDFLINECMYAGIVRGKLDQLRRCFEV 154

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449445513|ref|XP_004140517.1| PREDICTED: COP9 signalosome complex subunit 7-like [Cucumis sativus] gi|449514708|ref|XP_004164457.1| PREDICTED: COP9 signalosome complex subunit 7-like [Cucumis sativus]

 Score =  265 bits (678), Expect = 3e-69,   Method: Compositional matrix adjust.
 Identities = 125/154 (81%), Positives = 139/154 (90%)

Query: 1   MDIEQRQAELIDHFVKQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENS 60
           MDIEQ+Q E IDHFVKQAS+ KG+ALGSV+ +ATS PSLFAFSEILAVPN+ E EGTE+S
Sbjct: 1   MDIEQKQTEFIDHFVKQASSLKGSALGSVVTDATSHPSLFAFSEILAVPNVVELEGTEHS 60

Query: 61  KYLDMLRLFAHGTWSDYKNNAGHLPQLVPDQVLKLKQLTVLTLAETNKVLPYDELMEELD 120
            YLD+LRLFA+GTWSDYK+N+  LP+L  DQ LKLKQLTVLTLAETNKVL YD+LM+ELD
Sbjct: 61  IYLDVLRLFAYGTWSDYKSNSSRLPELSSDQALKLKQLTVLTLAETNKVLAYDQLMQELD 120

Query: 121 VTNVRELEDFLINECMYTGIVRGKLDQLRRCFEV 154
           VTNVRELEDFLINECMY GIVRGKLDQLRRCFEV
Sbjct: 121 VTNVRELEDFLINECMYAGIVRGKLDQLRRCFEV 154

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|307136429|gb|ADN34236.1| cop9 complex subunit 7a [Cucumis melo subsp. melo]

 Score =  265 bits (677), Expect = 4e-69,   Method: Compositional matrix adjust.
 Identities = 124/154 (80%), Positives = 139/154 (90%)

Query: 1   MDIEQRQAELIDHFVKQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENS 60
           MDIEQ+Q E IDHFVKQAS+ KG+ALGSV+ +ATS PSLFAFSEILAVP++ E EGTE+S
Sbjct: 1   MDIEQKQTEFIDHFVKQASSLKGSALGSVVTDATSHPSLFAFSEILAVPSVVELEGTEHS 60

Query: 61  KYLDMLRLFAHGTWSDYKNNAGHLPQLVPDQVLKLKQLTVLTLAETNKVLPYDELMEELD 120
            YLD+LRLFA+GTWSDYK+N+  LP+L  DQ LKLKQLTVLTLAETNKVL YD+LM+ELD
Sbjct: 61  IYLDVLRLFAYGTWSDYKSNSSRLPELSSDQALKLKQLTVLTLAETNKVLAYDQLMQELD 120

Query: 121 VTNVRELEDFLINECMYTGIVRGKLDQLRRCFEV 154
           VTNVRELEDFLINECMY GIVRGKLDQLRRCFEV
Sbjct: 121 VTNVRELEDFLINECMYAGIVRGKLDQLRRCFEV 154

Source: Cucumis melo subsp. melo

Species: Cucumis melo

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|329025154|gb|AEB71560.1| COP9 complex subunit 7a [Solanum chacoense]

 Score =  259 bits (661), Expect = 4e-67,   Method: Compositional matrix adjust.
 Identities = 125/154 (81%), Positives = 138/154 (89%)

Query: 1   MDIEQRQAELIDHFVKQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENS 60
           MDIEQ+QAE I+ FVKQAS  KG+AL SVIVEATS PSLFAFSEIL+VP++ E EGTENS
Sbjct: 1   MDIEQKQAEHIEFFVKQASALKGSALTSVIVEATSHPSLFAFSEILSVPSVLELEGTENS 60

Query: 61  KYLDMLRLFAHGTWSDYKNNAGHLPQLVPDQVLKLKQLTVLTLAETNKVLPYDELMEELD 120
            YLD+LRLFAHGTWSDYK+ A  LPQLV  Q LKLKQLTVLTLA+T+KVLPYD+LM+ELD
Sbjct: 61  VYLDLLRLFAHGTWSDYKSIACRLPQLVSAQALKLKQLTVLTLADTSKVLPYDQLMQELD 120

Query: 121 VTNVRELEDFLINECMYTGIVRGKLDQLRRCFEV 154
           VTNVRELEDFLINECMY GIVRGKLDQL+RCFEV
Sbjct: 121 VTNVRELEDFLINECMYVGIVRGKLDQLKRCFEV 154

Source: Solanum chacoense

Species: Solanum chacoense

Genus: Solanum

Family: Solanaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	161
TAIR|locus:2205593	260	FUS5 "FUSCA 5" [Arabidopsis th	0.956	0.592	0.701	3.8e-53
DICTYBASE|DDB_G0271282	259	csn7 "proteasome component reg	0.888	0.552	0.395	2.5e-26
UNIPROTKB|Q2KI56	264	COPS7B "COP9 signalosome compl	0.931	0.568	0.355	9e-22
UNIPROTKB|E2R501	264	COPS7B "Uncharacterized protei	0.931	0.568	0.355	9e-22
UNIPROTKB|Q9H9Q2	264	COPS7B "COP9 signalosome compl	0.931	0.568	0.355	9e-22
RGD|1306918	322	Cops7b "COP9 signalosome subun	0.931	0.465	0.355	9e-22
UNIPROTKB|F1SMV1	177	COPS7B "Uncharacterized protei	0.931	0.847	0.355	1.1e-21
MGI|MGI:1349388	264	Cops7b "COP9 (constitutive pho	0.931	0.568	0.355	1.1e-21
UNIPROTKB|E1C3R1	267	COPS7B "Uncharacterized protei	0.931	0.561	0.348	3.9e-21
FB|FBgn0028836	278	CSN7 "COP9 complex homolog sub	0.888	0.514	0.354	1.1e-18

TAIR|locus:2205593 FUS5 "FUSCA 5" [Arabidopsis thaliana (taxid:3702)]

 Score = 550 (198.7 bits), Expect = 3.8e-53, P = 3.8e-53
 Identities = 108/154 (70%), Positives = 121/154 (78%)

Query:     1 MDIEQRQAELIDHFVKQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENS 60
             MDIEQ+QAE+ID  VK+AS  K  ALG +I+EATS PSLFAFSEILA+PN+A+ EGT +S
Sbjct:     1 MDIEQKQAEIIDQLVKRASTCKSEALGPLIIEATSHPSLFAFSEILALPNVAQLEGTTDS 60

Query:    61 KYLDMLRLFAHGTWSDYKNNAGHLPQLVPDXXXXXXXXXXXXXAETNKVLPYDELMEELD 120
              YLD+LRLFAHGTW DYK NA  LP L PD             AE+NKVLPYD LM ELD
Sbjct:    61 VYLDLLRLFAHGTWGDYKCNATRLPHLSPDQILKLKQLTVLTLAESNKVLPYDTLMVELD 120

Query:   121 VTNVRELEDFLINECMYTGIVRGKLDQLRRCFEV 154
             V+NVRELEDFLINECMY GIVRGKLDQL+RCFEV
Sbjct:   121 VSNVRELEDFLINECMYAGIVRGKLDQLKRCFEV 154

GO:0005737 "cytoplasm" evidence=ISM

GO:0004708 "MAP kinase kinase activity" evidence=ISS

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=ISS

GO:0008180 "signalosome" evidence=TAS;IPI

GO:0009640 "photomorphogenesis" evidence=RCA;TAS

GO:0010387 "signalosome assembly" evidence=IMP

GO:0010388 "cullin deneddylation" evidence=RCA;IMP

GO:0005829 "cytosol" evidence=IDA

GO:0016567 "protein ubiquitination" evidence=RCA

GO:0016571 "histone methylation" evidence=RCA

GO:0016579 "protein deubiquitination" evidence=RCA

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=RCA

DICTYBASE|DDB_G0271282 csn7 "proteasome component region PCI (PINT) domain-containing protein" [Dictyostelium discoideum (taxid:44689)]

 Score = 297 (109.6 bits), Expect = 2.5e-26, P = 2.5e-26
 Identities = 57/144 (39%), Positives = 88/144 (61%)

Query:    11 IDHFVKQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENSKYLDMLRLFA 70
             +  FV  A + KG A+ S+I +A + PS+F F E+L +PN+ + + TE   Y D+L +FA
Sbjct:    14 LKQFVVLAKSSKGRAIVSIIEKALNHPSVFVFGELLDMPNVQQLKETEFKNYYDLLLIFA 73

Query:    71 HGTWSDYKNNAGHLPQLVPDXXXXXXXXXXXXXAETNKVLPYDELMEELDVTNVRELEDF 130
             +G++ DYKN    LPQL P              + T+ V+PY  L E++++TNVRELED 
Sbjct:    74 YGSFIDYKNKKDSLPQLTPQMITKLKQLTIVFLSSTSNVIPYSVLQEQIEITNVRELEDL 133

Query:   131 LINECMYTGIVRGKLDQLRRCFEV 154
             +I+  +Y  I++GKLDQ  +  E+
Sbjct:   134 IIDS-IYQNIIKGKLDQKNKHLEI 156

GO:0008180 "signalosome" evidence=IEA;ISS;IPI

GO:0005515 "protein binding" evidence=IPI

GO:0005737 "cytoplasm" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0044351 "macropinocytosis" evidence=RCA

UNIPROTKB|Q2KI56 COPS7B "COP9 signalosome complex subunit 7b" [Bos taurus (taxid:9913)]

 Score = 254 (94.5 bits), Expect = 9.0e-22, P = 9.0e-22
 Identities = 54/152 (35%), Positives = 85/152 (55%)

Query:     4 EQR-QAELIDHFVKQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENSKY 62
             EQ+  + L++ F+  A    G+AL ++I +    P ++ F E+L + N+ E     N+ Y
Sbjct:     4 EQKPSSNLLEQFILLAKGTSGSALTALISQVLEAPGVYVFGELLELANVQELAEGANAAY 63

Query:    63 LDMLRLFAHGTWSDYKNNAGHLPQLVPDXXXXXXXXXXXXXAETNKVLPYDELMEELDVT 122
             L +L LFA+GT+ DY  N   LP+L                A   K +PY  L+++L++ 
Sbjct:    64 LQLLNLFAYGTYPDYIANKESLPELSTAQQNKLKHLTIVSLASRMKCIPYSVLLKDLEMR 123

Query:   123 NVRELEDFLINECMYTGIVRGKLDQLRRCFEV 154
             N+RELED +I E +YT I++GKLDQ  +  EV
Sbjct:   124 NLRELEDLII-EAVYTDIIQGKLDQRNQLLEV 154

GO:0005737 "cytoplasm" evidence=IEA

GO:0010388 "cullin deneddylation" evidence=IEA

GO:0008180 "signalosome" evidence=IEA

UNIPROTKB|E2R501 COPS7B "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 254 (94.5 bits), Expect = 9.0e-22, P = 9.0e-22
 Identities = 54/152 (35%), Positives = 85/152 (55%)

Query:     4 EQR-QAELIDHFVKQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENSKY 62
             EQ+  + L++ F+  A    G+AL ++I +    P ++ F E+L + N+ E     N+ Y
Sbjct:     4 EQKPSSNLLEQFILLAKGTSGSALTALISQVLEAPGVYVFGELLELANVQELAEGANAAY 63

Query:    63 LDMLRLFAHGTWSDYKNNAGHLPQLVPDXXXXXXXXXXXXXAETNKVLPYDELMEELDVT 122
             L +L LFA+GT+ DY  N   LP+L                A   K +PY  L+++L++ 
Sbjct:    64 LQLLNLFAYGTYPDYIANKESLPELSTAQQNKLKHLTIVSLASRMKCIPYSVLLKDLEMR 123

Query:   123 NVRELEDFLINECMYTGIVRGKLDQLRRCFEV 154
             N+RELED +I E +YT I++GKLDQ  +  EV
Sbjct:   124 NLRELEDLII-EAVYTDIIQGKLDQRNQLLEV 154

GO:0010388 "cullin deneddylation" evidence=IEA

GO:0008180 "signalosome" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

UNIPROTKB|Q9H9Q2 COPS7B "COP9 signalosome complex subunit 7b" [Homo sapiens (taxid:9606)]

 Score = 254 (94.5 bits), Expect = 9.0e-22, P = 9.0e-22
 Identities = 54/152 (35%), Positives = 85/152 (55%)

Query:     4 EQR-QAELIDHFVKQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENSKY 62
             EQ+  + L++ F+  A    G+AL ++I +    P ++ F E+L + N+ E     N+ Y
Sbjct:     4 EQKPSSNLLEQFILLAKGTSGSALTALISQVLEAPGVYVFGELLELANVQELAEGANAAY 63

Query:    63 LDMLRLFAHGTWSDYKNNAGHLPQLVPDXXXXXXXXXXXXXAETNKVLPYDELMEELDVT 122
             L +L LFA+GT+ DY  N   LP+L                A   K +PY  L+++L++ 
Sbjct:    64 LQLLNLFAYGTYPDYIANKESLPELSTAQQNKLKHLTIVSLASRMKCIPYSVLLKDLEMR 123

Query:   123 NVRELEDFLINECMYTGIVRGKLDQLRRCFEV 154
             N+RELED +I E +YT I++GKLDQ  +  EV
Sbjct:   124 NLRELEDLII-EAVYTDIIQGKLDQRNQLLEV 154

GO:0008180 "signalosome" evidence=IDA

GO:0010388 "cullin deneddylation" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

RGD|1306918 Cops7b "COP9 signalosome subunit 7B" [Rattus norvegicus (taxid:10116)]

 Score = 254 (94.5 bits), Expect = 9.0e-22, P = 9.0e-22
 Identities = 54/152 (35%), Positives = 85/152 (55%)

Query:     4 EQR-QAELIDHFVKQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENSKY 62
             EQ+  + L++ F+  A    G+AL ++I +    P ++ F E+L + N+ E     N+ Y
Sbjct:    62 EQKPSSNLLEQFILLAKGTSGSALTTLISQVLEAPGVYVFGELLELANVQELAEGANAAY 121

Query:    63 LDMLRLFAHGTWSDYKNNAGHLPQLVPDXXXXXXXXXXXXXAETNKVLPYDELMEELDVT 122
             L +L LFA+GT+ DY  N   LP+L                A   K +PY  L+++L++ 
Sbjct:   122 LQLLNLFAYGTYPDYIANKESLPELSAAQQNKLKHLTIVSLASRMKCIPYSVLLKDLEMR 181

Query:   123 NVRELEDFLINECMYTGIVRGKLDQLRRCFEV 154
             N+RELED +I E +YT I++GKLDQ  +  EV
Sbjct:   182 NLRELEDLII-EAVYTDIIQGKLDQRNQLLEV 212

GO:0005737 "cytoplasm" evidence=ISO

GO:0008180 "signalosome" evidence=ISO

GO:0010388 "cullin deneddylation" evidence=ISO

UNIPROTKB|F1SMV1 COPS7B "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 253 (94.1 bits), Expect = 1.1e-21, P = 1.1e-21
 Identities = 54/152 (35%), Positives = 84/152 (55%)

Query:     4 EQR-QAELIDHFVKQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENSKY 62
             EQ+  + L++ F+  A    G+AL ++I +    P ++ F E+L + N+ E     N+ Y
Sbjct:     4 EQKPSSNLLEQFILLAKGTSGSALTALISQVLEAPGVYVFGELLELANVQELAEGANAAY 63

Query:    63 LDMLRLFAHGTWSDYKNNAGHLPQLVPDXXXXXXXXXXXXXAETNKVLPYDELMEELDVT 122
             L +L LFA+GT+ DY  N   LP+L                A   K +PY  L+ +L++ 
Sbjct:    64 LQLLNLFAYGTYPDYIANKESLPELSTAQQNKLKHLTIVSLASRMKCIPYSVLLRDLEMR 123

Query:   123 NVRELEDFLINECMYTGIVRGKLDQLRRCFEV 154
             N+RELED +I E +YT I++GKLDQ  +  EV
Sbjct:   124 NLRELEDLII-EAVYTDIIQGKLDQRNQLLEV 154

GO:0010388 "cullin deneddylation" evidence=IEA

GO:0008180 "signalosome" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

MGI|MGI:1349388 Cops7b "COP9 (constitutive photomorphogenic) homolog, subunit 7b (Arabidopsis thaliana)" [Mus musculus (taxid:10090)]

 Score = 253 (94.1 bits), Expect = 1.1e-21, P = 1.1e-21
 Identities = 54/152 (35%), Positives = 85/152 (55%)

Query:     4 EQR-QAELIDHFVKQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENSKY 62
             EQ+  + L++ F+  A    G+AL ++I +    P ++ F E+L + N+ E     N+ Y
Sbjct:     4 EQKPSSNLLEQFILLAKGTSGSALTTLISQVLEAPGVYVFGELLELANVQELAEGANAAY 63

Query:    63 LDMLRLFAHGTWSDYKNNAGHLPQLVPDXXXXXXXXXXXXXAETNKVLPYDELMEELDVT 122
             L +L LFA+GT+ DY  N   LP+L                A   K +PY  L+++L++ 
Sbjct:    64 LQLLNLFAYGTYPDYIANKESLPELSVAQQNKLKHLTIVSLASRMKCIPYSVLLKDLEMR 123

Query:   123 NVRELEDFLINECMYTGIVRGKLDQLRRCFEV 154
             N+RELED +I E +YT I++GKLDQ  +  EV
Sbjct:   124 NLRELEDLII-EAVYTDIIQGKLDQRNQLLEV 154

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0008180 "signalosome" evidence=ISO

GO:0010388 "cullin deneddylation" evidence=ISO

UNIPROTKB|E1C3R1 COPS7B "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 248 (92.4 bits), Expect = 3.9e-21, P = 3.9e-21
 Identities = 54/155 (34%), Positives = 85/155 (54%)

Query:     4 EQRQA-ELIDHFVKQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENSKY 62
             EQ+ +  L++ F+  A    G+AL ++I +    P ++ F E+L + N+ E     N+ Y
Sbjct:     4 EQKPSCNLLEQFILLAKGTSGSALTALINQVLEAPGVYVFGELLELTNVQELAEGSNAAY 63

Query:    63 LDMLRLFAHGTWSDY---KNNAGHLPQLVPDXXXXXXXXXXXXXAETNKVLPYDELMEEL 119
               +L LFA+GT+ DY     N  +LP+L                A   K +PY  L+++L
Sbjct:    64 FQLLNLFAYGTYPDYVALTANKDNLPELTATQKNKLKHLTIVSLASRMKCIPYSVLLKDL 123

Query:   120 DVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEV 154
             D+ N+RELED +I E +YT I++GKLDQ  +  EV
Sbjct:   124 DMRNLRELEDLII-EAVYTDIIQGKLDQRNQMLEV 157

GO:0005737 "cytoplasm" evidence=IEA

GO:0008180 "signalosome" evidence=IEA

GO:0010388 "cullin deneddylation" evidence=IEA

FB|FBgn0028836 CSN7 "COP9 complex homolog subunit 7" [Drosophila melanogaster (taxid:7227)]

 Score = 225 (84.3 bits), Expect = 1.1e-18, P = 1.1e-18
 Identities = 51/144 (35%), Positives = 77/144 (53%)

Query:    11 IDHFVKQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENSKYLDMLRLFA 70
             ++ F   A +  GAAL  VI +A   P++F F E+LA P++ + +   +SK+ + L LFA
Sbjct:    20 LEKFCVLAKSSTGAALLDVIRQALEAPNVFVFGELLAEPSVLQLKDGPDSKHFETLNLFA 79

Query:    71 HGTWSDYKNNAGHLPQLVPDXXXXXXXXXXXXXAETNKVLPYDELMEELDVTNVRELEDF 130
             +GT+ +Y+       +L P              A   K +PY  L+ EL++ NVR LED 
Sbjct:    80 YGTYKEYRAQPEKFIELTPAMQKKLQHLTIVSLAIKAKSIPYALLLSELEIDNVRHLEDI 139

Query:   131 LINECMYTGIVRGKLDQLRRCFEV 154
             +I E +Y  I+ GKL Q  R  EV
Sbjct:   140 II-EAIYADIIHGKLFQNTRILEV 162

GO:0005515 "protein binding" evidence=IPI

GO:0008180 "signalosome" evidence=ISS;IDA;IPI

GO:0050821 "protein stabilization" evidence=IMP

GO:0007095 "mitotic G2 DNA damage checkpoint" evidence=IGI

GO:0046331 "lateral inhibition" evidence=IMP

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	161
pfam01399	100	pfam01399, PCI, PCI domain	3e-13
smart00753	88	smart00753, PAM, PCI/PINT associated module	4e-09
smart00088	88	smart00088, PINT, motif in proteasome subunits, In	4e-09

>gnl|CDD|216479 pfam01399, PCI, PCI domain

 Score = 61.5 bits (150), Expect = 3e-13
 Identities = 27/102 (26%), Positives = 47/102 (46%), Gaps = 11/102 (10%)

Query: 62  YLDMLRLFAHGTWSDYKNNAG---------HLPQLVPDQVLKLKQLTVLTLAETNKVLPY 112
           Y D+LR F  G  SD++              L +L+ D   K+++L +  LA+    +  
Sbjct: 1   YRDLLRAFYSGDLSDFEEILADNEDELLDDGLAELLEDLRRKIRELNLRRLAKPYSSISL 60

Query: 113 DELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEV 154
            +L + L ++ V E+E  L    +  G +RGK+DQ+      
Sbjct: 61  SDLAKLLGLS-VDEVEKILSK-LIRDGRIRGKIDQVNGIVVF 100

This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15). Length = 100

>gnl|CDD|214803 smart00753, PAM, PCI/PINT associated module

 Score = 50.7 bits (122), Expect = 4e-09
 Identities = 16/69 (23%), Positives = 31/69 (44%), Gaps = 2/69 (2%)

Query: 86  QLVPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKL 145
           QLV     K++   +L L+E    +   +L + L ++   E+E  +    +  G +  K+
Sbjct: 1   QLVERLQRKIRLTNLLQLSEPYSSISLSDLAKLLGLSVP-EVEKLVSK-AIRDGEISAKI 58

Query: 146 DQLRRCFEV 154
           DQ+    E 
Sbjct: 59  DQVNGIVEF 67

Length = 88

>gnl|CDD|214509 smart00088, PINT, motif in proteasome subunits, Int-6, Nip-1 and TRIP-15

 Score = 50.7 bits (122), Expect = 4e-09
 Identities = 16/69 (23%), Positives = 31/69 (44%), Gaps = 2/69 (2%)

Query: 86  QLVPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKL 145
           QLV     K++   +L L+E    +   +L + L ++   E+E  +    +  G +  K+
Sbjct: 1   QLVERLQRKIRLTNLLQLSEPYSSISLSDLAKLLGLSVP-EVEKLVSK-AIRDGEISAKI 58

Query: 146 DQLRRCFEV 154
           DQ+    E 
Sbjct: 59  DQVNGIVEF 67

Also called the PCI (Proteasome, COP9, Initiation factor 3) domain. Unknown function. Length = 88

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	161
KOG3250	258	consensus COP9 signalosome, subunit CSN7 [Posttran	100.0
KOG2753	378	consensus Uncharacterized conserved protein, conta	100.0
KOG2908	380	consensus 26S proteasome regulatory complex, subun	99.97
PF01399	105	PCI: PCI domain; InterPro: IPR000717 A homology do	99.62
smart00753	88	PAM PCI/PINT associated module.	99.42
smart00088	88	PINT motif in proteasome subunits, Int-6, Nip-1 an	99.42
KOG1464	440	consensus COP9 signalosome, subunit CSN2 [Posttran	97.72
KOG2581	493	consensus 26S proteasome regulatory complex, subun	97.58
KOG2688	394	consensus Transcription-associated recombination p	95.99
KOG2758	432	consensus Translation initiation factor 3, subunit	95.79
KOG0686	466	consensus COP9 signalosome, subunit CSN1 [Posttran	95.34
KOG1497	399	consensus COP9 signalosome, subunit CSN4 [Posttran	95.34
COG5600	413	Transcription-associated recombination protein [DN	95.0
KOG2582	422	consensus COP9 signalosome, subunit CSN3 [Posttran	93.09
PF09012	69	FeoC: FeoC like transcriptional regulator; InterPr	92.46
PF09756	188	DDRGK: DDRGK domain; InterPro: IPR019153 This is a	92.3
PF10075	143	PCI_Csn8: COP9 signalosome, subunit CSN8; InterPro	91.47
PF02082	83	Rrf2: Transcriptional regulator; InterPro: IPR0009	90.69
KOG1463	411	consensus 26S proteasome regulatory complex, subun	88.77
PRK14165	217	winged helix-turn-helix domain-containing protein/	87.96
PF13412	48	HTH_24: Winged helix-turn-helix DNA-binding; PDB:	87.45
TIGR02010	135	IscR iron-sulfur cluster assembly transcription fa	86.71
KOG1498	439	consensus 26S proteasome regulatory complex, subun	86.71
KOG0687	393	consensus 26S proteasome regulatory complex, subun	86.12
PF13730	55	HTH_36: Helix-turn-helix domain	84.87
PF07389	100	DUF1500: Protein of unknown function (DUF1500); In	84.57
PRK11179	153	DNA-binding transcriptional regulator AsnC; Provis	84.46
smart00346	91	HTH_ICLR helix_turn_helix isocitrate lyase regulat	83.6
TIGR00738	132	rrf2_super rrf2 family protein (putative transcrip	83.4
PF09339	52	HTH_IclR: IclR helix-turn-helix domain; InterPro:	82.83
KOG3054	299	consensus Uncharacterized conserved protein [Funct	82.57
smart00344	108	HTH_ASNC helix_turn_helix ASNC type. AsnC: an auto	82.49
PRK10857	164	DNA-binding transcriptional regulator IscR; Provis	82.43
COG1522	154	Lrp Transcriptional regulators [Transcription]	80.26

>KOG3250 consensus COP9 signalosome, subunit CSN7 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]

Probab=100.00  E-value=2.6e-36  Score=239.71  Aligned_cols=159  Identities=47%  Similarity=0.714  Sum_probs=156.0

Q ss_pred             CcHhHHHHHHHHHHHHHhcccchHHHHHHHHHHhcCCCcccchhhhcCcccccccCCCchhHHHHHHHHhcCCHhHHhhc
Q 031323            1 MDIEQRQAELIDHFVKQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENSKYLDMLRLFAHGTWSDYKNN   80 (161)
Q Consensus         1 ~~~~~~~~~~l~~~l~~~~~~~~~~a~~~i~~aL~~p~i~~f~eLl~~~~v~~L~~s~~~~l~~LL~iF~~G~~~dy~~~   80 (161)
                      ||+++.+.+-+|.|+.+++..++++...+|..|+.+|++|.|+|||.+|+|..|..+.++.++.||++|++|||.||.++
T Consensus         1 m~~ek~~~~~~eqfvllak~~kg~al~~lIsqale~P~vf~F~ELl~l~nv~qlae~~dsa~lrlL~lFa~Gt~~Dy~ae   80 (258)
T KOG3250|consen    1 MDIEKKQAEIIEQFVLLAKTCKGEALEELISQALEAPGVFVFGELLILPNVVQLAEPIDSAYLRLLELFAYGTYRDYSAE   80 (258)
T ss_pred             CCcchhhHHHHHHHHHHHhccchhHHHHHHHHHhcCCCeeeHHHHHhhhhHHHHcccccHHHHHHHHHHhcCchhhhhhh
Confidence            99999999999999999999999999999999999999999999999999999998888999999999999999999998


Q ss_pred             cCCCCCCCHHHHHHHHHHHHHHhhhcCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEEecCCCCEEEEEeeecc
Q 031323           81 AGHLPQLVPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVCTVLVR  160 (161)
Q Consensus        81 ~~~~~~L~~~~~~KlrlLtL~sLa~~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gkIDq~~~~v~V~~~~~R  160 (161)
                      ...+|.|++.++.||+.||+.++|+..+.++|+.+.+.+...+..++|+++| +||+++++.|||||.+|+++|.|+.+|
T Consensus        81 a~rlp~Ls~~q~~kLk~ltV~slas~~k~lpy~~Ll~~l~~~nvrelEd~ii-eamya~IlrGkldqr~q~leV~faigR  159 (258)
T KOG3250|consen   81 ALRLPKLSLAQLNKLKHLTVVSLASFEKCLPYLVLLRLLPSRNVRELEDLII-EAMYADILRGKLDQRNQTLEVDFAIGR  159 (258)
T ss_pred             hhcCCCCCHHHHHhhhcceehhhhhhchhhhHHHHHhhccCCchhHHHHHHH-HHHHHHHHHhhHHhhcceEeechhhcc
Confidence            8899999999999999999999999999999999999999998999999999 999999999999999999999999998

>KOG2753 consensus Uncharacterized conserved protein, contains PCI domain [General function prediction only]

Probab=100.00  E-value=1.9e-33  Score=235.06  Aligned_cols=149  Identities=28%  Similarity=0.541  Sum_probs=133.9

Q ss_pred             HHHHHHHHHHhcccc----hHHHHHHHHHHhcCCCcccchhhhcCcccccccCCCchhHHHHHHHHhcCCHhHHhh----
Q 031323            8 AELIDHFVKQASNQK----GAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENSKYLDMLRLFAHGTWSDYKN----   79 (161)
Q Consensus         8 ~~~l~~~l~~~~~~~----~~~a~~~i~~aL~~p~i~~f~eLl~~~~v~~L~~s~~~~l~~LL~iF~~G~~~dy~~----   79 (161)
                      ..++-+||.++...+    -++|.+||+.|+.+|++|.|++|+++|+|+.|+++.   +|+||+||.+|.+++|.+    
T Consensus       185 ~kvmt~lLgtyt~dnas~AredA~rcV~~av~dP~~F~fD~Ll~L~pV~qLE~d~---i~qLL~IF~s~~L~aYveF~~~  261 (378)
T KOG2753|consen  185 SKVMTELLGTYTEDNASEAREDAMRCVVEAVKDPKIFLFDHLLTLPPVKQLEGDL---IHQLLKIFVSGKLDAYVEFVAA  261 (378)
T ss_pred             HHHHHHHHHHhcccchhHHHHHHHHHHHHHHcCCceeccchhccCchHHHhccch---HHHHHHHHHhcchHHHHHHHHh
Confidence            456678888887643    356999999999999999999999999999999865   899999999999999997    


Q ss_pred             ccCCCCC--CC-HHHHHHHHHHHHHHhhhcCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEEecCCCCEEEEEe
Q 031323           80 NAGHLPQ--LV-PDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVCT  156 (161)
Q Consensus        80 ~~~~~~~--L~-~~~~~KlrlLtL~sLa~~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gkIDq~~~~v~V~~  156 (161)
                      |++++..  +. +.++.|||+||+|+||+.+++|||+++++.|+|+ .+|||.||| +||++|+|+|||||.+++|+|++
T Consensus       262 N~~Fvqs~gl~~E~~~~KMRLLTlm~LA~es~eisy~~l~k~LqI~-edeVE~fVI-daI~aklV~~kidq~~~~viVs~  339 (378)
T KOG2753|consen  262 NSGFVQSQGLVHEQNMAKMRLLTLMSLAEESNEISYDTLAKELQIN-EDEVELFVI-DAIRAKLVEGKIDQMNRTVIVSS  339 (378)
T ss_pred             ChHHHHHhcccHHHHHHHHHHHHHHHHhccCCCCCHHHHHHHhccC-HHHHHHHHH-HHHHHHHHHhhHHhhcceEEeeh
Confidence            4444433  33 7789999999999999999999999999999998 999999999 99999999999999999999999


Q ss_pred             eeccC
Q 031323          157 VLVRL  161 (161)
Q Consensus       157 ~~~Rv  161 (161)
                      +++|.
T Consensus       340 ~~hR~  344 (378)
T KOG2753|consen  340 STHRT  344 (378)
T ss_pred             hhhhh
Confidence            99984

>KOG2908 consensus 26S proteasome regulatory complex, subunit RPN9/PSMD13 [Posttranslational modification, protein turnover, chaperones]

Probab=99.97  E-value=8.3e-32  Score=226.03  Aligned_cols=147  Identities=20%  Similarity=0.382  Sum_probs=134.1

Q ss_pred             HHHHHh------cccchHHHHHHHHHHhcCCCcccchhhhcCcccccccCCCchhHHHHHHHHhcCCHhHHhhcc---CC
Q 031323           13 HFVKQA------SNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENSKYLDMLRLFAHGTWSDYKNNA---GH   83 (161)
Q Consensus        13 ~~l~~~------~~~~~~~a~~~i~~aL~~p~i~~f~eLl~~~~v~~L~~s~~~~l~~LL~iF~~G~~~dy~~~~---~~   83 (161)
                      .||...      .+++.+.|..+..+||.+.++||||||+.||+...|+|+++.|++++|..|+.||+..|++..   +.
T Consensus       182 ~YL~~~d~~~l~~se~~~lA~~L~~aALLGe~iyNfGELL~HPilesL~gT~~eWL~dll~Afn~Gdl~~f~~l~~~~~~  261 (380)
T KOG2908|consen  182 LYLGCSDIDDLSESEKQDLAFDLSLAALLGENIYNFGELLAHPILESLKGTNREWLKDLLIAFNSGDLKRFESLKGVWGK  261 (380)
T ss_pred             HHhccccccccCHHHHHHHHHHHHHHHHhccccccHHHHHhhHHHHHhcCCcHHHHHHHHHHhccCCHHHHHHHHHHhcc
Confidence            566666      444668899999999999999999999999999999999999999999999999999999843   34


Q ss_pred             CCCCC--H-HHHHHHHHHHHHHhhh----cCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEEecCCCCEEEEEe
Q 031323           84 LPQLV--P-DQVLKLKQLTVLTLAE----TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVCT  156 (161)
Q Consensus        84 ~~~L~--~-~~~~KlrlLtL~sLa~----~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gkIDq~~~~v~V~~  156 (161)
                      .|.|.  + -..+|+++|+|+.+|+    +.|.+||++||++++|| .++||.+|| +|++.|||+|.|||++|+|+++|
T Consensus       262 ~p~L~~~e~~L~qKI~LmaLiEi~F~rpa~~R~lsf~~Ia~~tkip-~~eVE~LVM-KAlslgLikG~Idqv~~~v~~sw  339 (380)
T KOG2908|consen  262 QPDLASNEDFLLQKIRLLALIEITFSRPANERTLSFKEIAEATKIP-NKEVELLVM-KALSLGLIKGSIDQVEGVVYMSW  339 (380)
T ss_pred             CchHHHHHHHHHHHHHHHHHHHHHhcCcchhccccHHHHHHHhCCC-HHHHHHHHH-HHHhccceeeeecccccEEEEec
Confidence            67774  3 3689999999999998    46999999999999999 999999999 99999999999999999999999


Q ss_pred             eeccC
Q 031323          157 VLVRL  161 (161)
Q Consensus       157 ~~~Rv  161 (161)
                      ++|||
T Consensus       340 vqPRv  344 (380)
T KOG2908|consen  340 VQPRV  344 (380)
T ss_pred             ccccc
Confidence            99997

>PF01399 PCI: PCI domain; InterPro: IPR000717 A homology domain of unclear function, occurs in the C-terminal region of several regulatory components of the 26S proteasome as well as in other proteins

Probab=99.62  E-value=1.5e-15  Score=106.72  Aligned_cols=95  Identities=21%  Similarity=0.433  Sum_probs=80.9

Q ss_pred             hhHHHHHHHHhcCCHhHHhhccCC-----C--CCC---CHHHHHHHHHHHHHHhhhcCCccCHHHHHHhcCCCChhhHHH
Q 031323           60 SKYLDMLRLFAHGTWSDYKNNAGH-----L--PQL---VPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELED  129 (161)
Q Consensus        60 ~~l~~LL~iF~~G~~~dy~~~~~~-----~--~~L---~~~~~~KlrlLtL~sLa~~~~~isy~~I~~~l~i~~~~evE~  129 (161)
                      .|+.+++++|..|++.+|.+.-..     +  +.+   .+.+.+|++..++.+++...+.+++++|++.++++ .++||.
T Consensus         1 ~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~~~~l~~~i~~~~l~~l~~~y~~i~~~~ia~~l~~~-~~~vE~   79 (105)
T PF01399_consen    1 PPYSELLRAFRSGDLQEFEEFLEKHSESLFKDPFLAEYVEQLKEKIRRRNLRQLSKPYSSISISEIAKALQLS-EEEVES   79 (105)
T ss_dssp             HHHHHHHHHHHCT-HHHHHHHHHHTCHHHHHCTTHHHHHHHHHHHHHHHHHHHHHHC-SEEEHHHHHHHHTCC-HHHHHH
T ss_pred             CHHHHHHHHHHhCCHHHHHHHHHHHHHHHHcCccHHHHHHHHHHHHHHHHHHHHHHHhcccchHHHHHHhccc-hHHHHH
Confidence            378999999999999999862111     1  222   26678999999999999999999999999999999 999999


Q ss_pred             HHHHHhHhcCCcEEEecCCCCEEEEEe
Q 031323          130 FLINECMYTGIVRGKLDQLRRCFEVCT  156 (161)
Q Consensus       130 lvI~~ai~~gLi~gkIDq~~~~v~V~~  156 (161)
                      +++ ++|..|.|.|+|||.+|+|+++|
T Consensus        80 ~l~-~~I~~~~i~~~ID~~~~~v~~~k  105 (105)
T PF01399_consen   80 ILI-DLISNGLIKAKIDQVNGVVVFSK  105 (105)
T ss_dssp             HHH-HHHHTTSSEEEEETTTTEEEE-S
T ss_pred             HHH-HHHHCCCEEEEEECCCCEEEecC
Confidence            999 99999999999999999999986

This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15) []. Apparently, all of the characterised proteins containing PCI domains are parts of larger multi-protein complexes. Proteins with PCI domains include budding yeast proteasome regulatory components Rpn3(Sun2), Rpn5, Rpn6, Rpn7and Rpn9 []; mammalian proteasome regulatory components p55, p58 and p44.5, and translation initiation factor 3 complex subunits p110 and INT6 [, ]; Arabidopsis COP9 and FUS6/COP11 []; mammalian G-protein pathway suppressor GPS1, and several uncharacterised ORFs from plant, nematodes and mammals. The complete homology domain comprises approx. 200 residues, the highest conservation is found in the C-terminal half. Several of the proteins mentioned above have no detectable homology to the N-terminal half of the domain.; GO: 0005515 protein binding; PDB: 3TXM_A 3TXN_A 1UFM_A 3CHM_A 3T5X_A 3T5V_B.

>smart00753 PAM PCI/PINT associated module

Probab=99.42  E-value=6.8e-13  Score=91.65  Aligned_cols=70  Identities=23%  Similarity=0.326  Sum_probs=67.0

Q ss_pred             HHHHHHHHHHHHHHhhhcCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEEecCCCCEEEEEeeecc
Q 031323           89 PDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVCTVLVR  160 (161)
Q Consensus        89 ~~~~~KlrlLtL~sLa~~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gkIDq~~~~v~V~~~~~R  160 (161)
                      +...+|+|.+++..++...+.++|++|++.++++ .+++|.+++ ++|..|.+.|+|||.+++|.+++..+|
T Consensus         4 ~~l~~~~~~~~l~~l~~~y~~i~~~~i~~~~~l~-~~~vE~~i~-~~i~~~~l~~~ID~~~~~v~~~~~~~r   73 (88)
T smart00753        4 ERLQRKIRLTNLLQLSEPYSSISLSDLAKLLGLS-VPEVEKLVS-KAIRDGEISAKIDQVNGIVEFEEVDPR   73 (88)
T ss_pred             HHHHHHHHHHHHHHHhHHhceeeHHHHHHHhCcC-HHHHHHHHH-HHHHCCCeEEEEcCcCCEEEECCCchh
Confidence            4578999999999999999999999999999999 889999999 999999999999999999999999887

>smart00088 PINT motif in proteasome subunits, Int-6, Nip-1 and TRIP-15

Probab=99.42  E-value=6.8e-13  Score=91.65  Aligned_cols=70  Identities=23%  Similarity=0.326  Sum_probs=67.0

Q ss_pred             HHHHHHHHHHHHHHhhhcCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEEecCCCCEEEEEeeecc
Q 031323           89 PDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVCTVLVR  160 (161)
Q Consensus        89 ~~~~~KlrlLtL~sLa~~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gkIDq~~~~v~V~~~~~R  160 (161)
                      +...+|+|.+++..++...+.++|++|++.++++ .+++|.+++ ++|..|.+.|+|||.+++|.+++..+|
T Consensus         4 ~~l~~~~~~~~l~~l~~~y~~i~~~~i~~~~~l~-~~~vE~~i~-~~i~~~~l~~~ID~~~~~v~~~~~~~r   73 (88)
T smart00088        4 ERLQRKIRLTNLLQLSEPYSSISLSDLAKLLGLS-VPEVEKLVS-KAIRDGEISAKIDQVNGIVEFEEVDPR   73 (88)
T ss_pred             HHHHHHHHHHHHHHHhHHhceeeHHHHHHHhCcC-HHHHHHHHH-HHHHCCCeEEEEcCcCCEEEECCCchh
Confidence            4578999999999999999999999999999999 889999999 999999999999999999999999887

Also called the PCI (Proteasome, COP9, Initiation factor 3) domain. Unknown function.

>KOG1464 consensus COP9 signalosome, subunit CSN2 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]

Probab=97.72  E-value=0.00012  Score=61.70  Aligned_cols=92  Identities=14%  Similarity=0.413  Sum_probs=78.1

Q ss_pred             hHHHHHHHHhcCCHhHHhh----ccCCCCC---C---CHHHHHHHHHHHHHHhhhcCCccCHHHHHHhcCCCChhhHHHH
Q 031323           61 KYLDMLRLFAHGTWSDYKN----NAGHLPQ---L---VPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDF  130 (161)
Q Consensus        61 ~l~~LL~iF~~G~~~dy~~----~~~~~~~---L---~~~~~~KlrlLtL~sLa~~~~~isy~~I~~~l~i~~~~evE~l  130 (161)
                      .+-+|+..+...++.+|+.    |++.+-+   +   .++.++++|.-.|+.|......|...-|+++|.++ ..+||.+
T Consensus       306 AMTnlv~aYQ~NdI~eFE~Il~~~~~~IM~DpFIReh~EdLl~niRTQVLlkLIkPYt~i~Ipfis~~Lnv~-~~dV~~L  384 (440)
T KOG1464|consen  306 AMTNLVAAYQNNDIIEFERILKSNRSNIMDDPFIREHIEDLLRNIRTQVLLKLIKPYTNIGIPFISKELNVP-EADVESL  384 (440)
T ss_pred             HHHHHHHHHhcccHHHHHHHHHhhhccccccHHHHHHHHHHHHHHHHHHHHHHhccccccCchhhHhhcCCC-HHHHHHH
Confidence            3678999999999999996    3333211   1   27789999999999999987788888899999999 9999999


Q ss_pred             HHHHhHhcCCcEEEecCCCCEEEE
Q 031323          131 LINECMYTGIVRGKLDQLRRCFEV  154 (161)
Q Consensus       131 vI~~ai~~gLi~gkIDq~~~~v~V  154 (161)
                      ++ +||-..-|+|+|||+++.+..
T Consensus       385 LV-~~ILD~~i~g~Ide~n~~l~~  407 (440)
T KOG1464|consen  385 LV-SCILDDTIDGRIDEVNQYLEL  407 (440)
T ss_pred             HH-HHHhccccccchHHhhhHhcc
Confidence            99 999999999999999987654

>KOG2581 consensus 26S proteasome regulatory complex, subunit RPN3/PSMD3 [Posttranslational modification, protein turnover, chaperones]

Probab=97.58  E-value=0.00026  Score=62.06  Aligned_cols=92  Identities=9%  Similarity=0.295  Sum_probs=65.2

Q ss_pred             hhHHHHHHHHhcCCHhHHhhccCCCCC-C----CHHHHHHHHH----HHHHHhhhcCCccCHHHHHHhcCCCChhhHHHH
Q 031323           60 SKYLDMLRLFAHGTWSDYKNNAGHLPQ-L----VPDQVLKLKQ----LTVLTLAETNKVLPYDELMEELDVTNVRELEDF  130 (161)
Q Consensus        60 ~~l~~LL~iF~~G~~~dy~~~~~~~~~-L----~~~~~~Klrl----LtL~sLa~~~~~isy~~I~~~l~i~~~~evE~l  130 (161)
                      .++|+|=...-.||++-|...-+.+.+ +    +-...-.||.    =.+-.+.-..+-||+.+||+.|+++|.+++|-+
T Consensus       319 ~~Yf~Lt~AVr~gdlkkF~~~leq~k~~f~~D~ty~LivRLR~NVIkTgIR~ISlsYSRISl~DIA~kL~l~Seed~Eyi  398 (493)
T KOG2581|consen  319 RPYFKLTQAVRLGDLKKFNETLEQFKDKFQADGTYTLIVRLRHNVIKTGIRKISLSYSRISLQDIAKKLGLNSEEDAEYI  398 (493)
T ss_pred             HHHHHHHHHHHHhhHHHHHHHHHHHHHHHhhCCcchHHHHHHHHHHHHhhhheeeeeeeccHHHHHHHhcCCCchhHHHH
Confidence            458999999999999999964322211 1    1111222221    111111113678999999999999988999999


Q ss_pred             HHHHhHhcCCcEEEecCCCCEE
Q 031323          131 LINECMYTGIVRGKLDQLRRCF  152 (161)
Q Consensus       131 vI~~ai~~gLi~gkIDq~~~~v  152 (161)
                      |= +||+.|+|+|+||..++.+
T Consensus       399 Va-kAIRDGvIea~Id~~~g~m  419 (493)
T KOG2581|consen  399 VA-KAIRDGVIEAKIDHEDGFM  419 (493)
T ss_pred             HH-HHHHhccceeeeccccCce
Confidence            99 9999999999999998844

>KOG2688 consensus Transcription-associated recombination protein - Thp1p [Cell cycle control, cell division, chromosome partitioning]

Probab=95.99  E-value=0.019  Score=50.34  Aligned_cols=97  Identities=15%  Similarity=0.200  Sum_probs=73.7

Q ss_pred             hHHHHHHHHhcCCHhHHhh----ccCCCCCCC-HHHHHHHHHHHHHHhhh-------cCCccCHHHHHHhcCCCC-----
Q 031323           61 KYLDMLRLFAHGTWSDYKN----NAGHLPQLV-PDQVLKLKQLTVLTLAE-------TNKVLPYDELMEELDVTN-----  123 (161)
Q Consensus        61 ~l~~LL~iF~~G~~~dy~~----~~~~~~~L~-~~~~~KlrlLtL~sLa~-------~~~~isy~~I~~~l~i~~-----  123 (161)
                      .+-.++.....||+..|..    |...+.... =-.+.|+++++.-.|..       ....+|++.+..+++..+     
T Consensus       273 ~~~~lv~aVr~Gnl~~f~~al~~~E~~f~~~gi~l~l~~l~lv~yrnL~kkv~~~~~~~~~lpls~~~~al~~~~~~~~~  352 (394)
T KOG2688|consen  273 KYSPLVQAVRSGNLRLFDLALADNERFFIRSGIYLTLEKLPLVVYRNLFKKVIQLWGKTSQLPLSRFLTALQFSGVTDVD  352 (394)
T ss_pred             hHHHHHHHHHhccHHHHHHHHhhhHHHHHHhccHHHhhhhhHHHHHHHHHHHHHHhCCCCCCCHHHHHHHHhhcCCCCCc
Confidence            5677899999999999985    222222211 11245566666665554       457899999999998764     


Q ss_pred             hhhHHHHHHHHhHhcCCcEEEecCCCCEEEEEeee
Q 031323          124 VRELEDFLINECMYTGIVRGKLDQLRRCFEVCTVL  158 (161)
Q Consensus       124 ~~evE~lvI~~ai~~gLi~gkIDq~~~~v~V~~~~  158 (161)
                      .+|||-.+. .+|+.|.|+|.|+...+++.++.--
T Consensus       353 ~deveciLa-~lI~~G~ikgYish~~~~~V~sK~~  386 (394)
T KOG2688|consen  353 LDEVECILA-NLIDLGRIKGYISHQLQTLVFSKKD  386 (394)
T ss_pred             hhhHHHHHH-hhhhhccccchhchhhheEEEecCC
Confidence            789999999 9999999999999999999988643

>KOG2758 consensus Translation initiation factor 3, subunit e (eIF-3e) [Translation, ribosomal structure and biogenesis]

Probab=95.79  E-value=0.016  Score=49.90  Aligned_cols=66  Identities=15%  Similarity=0.232  Sum_probs=59.1

Q ss_pred             HHHHHHHHHHHHHHhhhcCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEEecCCCCEEEEEe
Q 031323           89 PDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVCT  156 (161)
Q Consensus        89 ~~~~~KlrlLtL~sLa~~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gkIDq~~~~v~V~~  156 (161)
                      ++-++--|++-.-..|.-+..|+.+-+|+.|.++ .+|.|.|++ +.|+...+++|||..-|+|.+..
T Consensus       329 ~~F~E~ARl~ifEtfCRIHqcIti~mLA~kLnm~-~eeaErwiv-nlIr~~rl~AkidSklg~Vvmg~  394 (432)
T KOG2758|consen  329 DEFLENARLLIFETFCRIHQCITIDMLADKLNMD-PEEAERWIV-NLIRTARLDAKIDSKLGHVVMGH  394 (432)
T ss_pred             HHHHHHHHHHHHHHHHHHHHheeHHHHHHHhcCC-HHHHHHHHH-HHHHHhhhhhhhccccCceeecC
Confidence            3346777888888889888999999999999998 999999999 99999999999999999987753

>KOG0686 consensus COP9 signalosome, subunit CSN1 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]

Probab=95.34  E-value=0.14  Score=45.19  Aligned_cols=97  Identities=14%  Similarity=0.198  Sum_probs=78.2

Q ss_pred             hHHHHHHHHhcCCHhHHhh----ccCCC---CCCC---HHHHHHHHHHHHHHhhhcCCccCHHHHHHhcCCCChhhHHHH
Q 031323           61 KYLDMLRLFAHGTWSDYKN----NAGHL---PQLV---PDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDF  130 (161)
Q Consensus        61 ~l~~LL~iF~~G~~~dy~~----~~~~~---~~L~---~~~~~KlrlLtL~sLa~~~~~isy~~I~~~l~i~~~~evE~l  130 (161)
                      .+.++|.-|..+.++.-..    .++.+   +-|.   +....|+|.=+++..-....++.+..+|.+.+.+ ...+|.=
T Consensus       307 qlr~il~~fy~sky~~cl~~L~~~k~~llLD~yLaphVd~Ly~~IR~r~llqy~~py~s~~m~~mA~af~~s-v~~le~~  385 (466)
T KOG0686|consen  307 QLREILFKFYSSKYASCLELLREIKPRLLLDMYLAPHVDNLYSLIRNRALLQYLSPYSSADMSKMAEAFNTS-VAILESE  385 (466)
T ss_pred             HHHHHHHHHhhhhHHHHHHHHHHhccceeechhcchhHHHHHHHHHHhhHHHhcCccccchHHHHHHHhccc-HHHHHHH
Confidence            3777888888887775554    22221   1122   5568999999999988888999999999999998 9999999


Q ss_pred             HHHHhHhcCCcEEEecCCCCEEEEEeeec
Q 031323          131 LINECMYTGIVRGKLDQLRRCFEVCTVLV  159 (161)
Q Consensus       131 vI~~ai~~gLi~gkIDq~~~~v~V~~~~~  159 (161)
                      |. +.|-.|-|.||||+-++.+++.-.-.
T Consensus       386 l~-~LI~~~~i~~rIDs~~ki~~~~~~~~  413 (466)
T KOG0686|consen  386 LL-ELILEGKISGRIDSHNKILYARDADS  413 (466)
T ss_pred             HH-HHHHccchheeeccccceeeeccccc
Confidence            99 99999999999999999999876543

>KOG1497 consensus COP9 signalosome, subunit CSN4 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]

Probab=95.34  E-value=0.075  Score=45.74  Aligned_cols=127  Identities=10%  Similarity=0.105  Sum_probs=84.7

Q ss_pred             HHHHHHHHhcCCCcccc-hhhhcCcccccccCCC-chhHHHHHHHHhcC-CHhHHhhc-cC----CCCCCCHHHHHHHHH
Q 031323           26 LGSVIVEATSQPSLFAF-SEILAVPNIAEFEGTE-NSKYLDMLRLFAHG-TWSDYKNN-AG----HLPQLVPDQVLKLKQ   97 (161)
Q Consensus        26 a~~~i~~aL~~p~i~~f-~eLl~~~~v~~L~~s~-~~~l~~LL~iF~~G-~~~dy~~~-~~----~~~~L~~~~~~Klrl   97 (161)
                      |..|.+-|.-+|..-.| ..|...|.++.+..=. -+++|  |+-|..+ .++.|... .+    +.+.=+...-+-+.-
T Consensus       228 a~~CtlLA~~gpqrsr~Latlfkder~~~l~~y~ileKmy--l~riI~k~el~ef~~~L~pHQka~~~dgssil~ra~~E  305 (399)
T KOG1497|consen  228 ALQCTLLASAGPQRSRMLATLFKDERCQKLPAYGILEKMY--LERIIRKEELQEFEAFLQPHQKAHTMDGSSILDRAVIE  305 (399)
T ss_pred             hHhheeecCCChHHHHHHHHHhcCcccccccchHHHHHHH--HHHHhcchhHHHHHHHhcchhhhcccCcchhhhhHHHH
Confidence            66666777778887765 5677778777765311 12233  4555555 57777752 11    111111111122333


Q ss_pred             HHHHHhhhcCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEEecCCCCEEEEEe
Q 031323           98 LTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVCT  156 (161)
Q Consensus        98 LtL~sLa~~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gkIDq~~~~v~V~~  156 (161)
                      -.|+++..-...+||+++.+.++|+ ...+|..+= ++|..|=+.|.|||.++.+|...
T Consensus       306 hNlls~Skly~nisf~~Lg~ll~i~-~ekaekiaa-~MI~qeRmng~IDQ~egiihFe~  362 (399)
T KOG1497|consen  306 HNLLSASKLYNNISFEELGALLKID-AEKAEKIAA-QMITQERMNGSIDQIEGIIHFED  362 (399)
T ss_pred             HhHHHHHHHHHhccHHHHHHHhCCC-HHHHHHHHH-HHHhHHHhccchHhhcceEeecc
Confidence            3445555545579999999999999 999999999 99999999999999999999764

>COG5600 Transcription-associated recombination protein [DNA replication, recombination, and repair]

Probab=95.00  E-value=0.059  Score=47.05  Aligned_cols=99  Identities=19%  Similarity=0.307  Sum_probs=61.2

Q ss_pred             hhHHHHHHHHhcCCHhHHhh----ccCCCCC--CCHHHHHHHHHHH-------HHHhhhcCCccCHHHHHHhcCCC--C-
Q 031323           60 SKYLDMLRLFAHGTWSDYKN----NAGHLPQ--LVPDQVLKLKQLT-------VLTLAETNKVLPYDELMEELDVT--N-  123 (161)
Q Consensus        60 ~~l~~LL~iF~~G~~~dy~~----~~~~~~~--L~~~~~~KlrlLt-------L~sLa~~~~~isy~~I~~~l~i~--~-  123 (161)
                      +.+--|.++..+|++++|..    |...+.+  |---+..+.+.++       ...++.....+|++-+...++++  + 
T Consensus       289 s~~~~LvkavrsGni~~~~~~l~~ner~~~~~~l~ltl~~~~~~V~~RNL~rk~w~~~~~qsrlp~sil~~~~qls~~dn  368 (413)
T COG5600         289 SVYSPLVKAVRSGNIEDFDLALSRNERKFAKRGLYLTLLAHYPLVCFRNLFRKIWRLHGKQSRLPLSILLIVLQLSAIDN  368 (413)
T ss_pred             chhHHHHHHHHcCCHHHHHHHHHHhHHHHHHcchHHHHHhhccHHHHHHHHHHHHhhccccccCcHHHHHHHHHccCCCc
Confidence            34556889999999999985    2111111  0000111111121       12222233445566555555443  3 


Q ss_pred             ---hhhHHHHHHHHhHhcCCcEEEecCCCCEEEEEeeec
Q 031323          124 ---VRELEDFLINECMYTGIVRGKLDQLRRCFEVCTVLV  159 (161)
Q Consensus       124 ---~~evE~lvI~~ai~~gLi~gkIDq~~~~v~V~~~~~  159 (161)
                         .++||-.+. .+|+.|+++|.|....++|.+++-.|
T Consensus       369 ~~~~~~VEciL~-tlI~~G~lrgYis~s~~~vV~sk~~p  406 (413)
T COG5600         369 FHSFKEVECILV-TLIGLGLLRGYISHSRRTVVFSKKDP  406 (413)
T ss_pred             ccChHHHHHHHH-HHHhhhhhhheecccceEEEEecCCC
Confidence               578999999 99999999999999999999987543

>KOG2582 consensus COP9 signalosome, subunit CSN3 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]

Probab=93.09  E-value=0.4  Score=41.96  Aligned_cols=90  Identities=11%  Similarity=0.277  Sum_probs=67.4

Q ss_pred             hHHHHHHHHhcCCHhHHhh----ccCCC-CCCC----HHHHHHHHHHHHHHhhhcCCccCHHHHHHhcCCCChhhHHHHH
Q 031323           61 KYLDMLRLFAHGTWSDYKN----NAGHL-PQLV----PDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFL  131 (161)
Q Consensus        61 ~l~~LL~iF~~G~~~dy~~----~~~~~-~~L~----~~~~~KlrlLtL~sLa~~~~~isy~~I~~~l~i~~~~evE~lv  131 (161)
                      ++.+++++...+.-.+...    +.+.+ .+-+    -..+.-+.+-+|.++...-.+++.++||+..++.+..|||..|
T Consensus       260 pY~ef~~~Y~~~~~~eLr~lVk~~~~rF~kDnnt~l~k~av~sl~k~nI~rltktF~sLsL~dIA~~vQLa~~qevek~I  339 (422)
T KOG2582|consen  260 PYHEFLNVYLKDSSTELRTLVKKHSERFTKDNNTGLAKQAVSSLYKKNIQRLTKTFLSLSLSDIASRVQLASAQEVEKYI  339 (422)
T ss_pred             hHHHHHHHHhcCCcHHHHHHHHHHHHHHhhcCcHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHhcchHHHHHHH
Confidence            5788999999888776654    22222 2222    2235556666677777777789999999988888889999999


Q ss_pred             HHHhHhcCCcEEEecCCCCEEEE
Q 031323          132 INECMYTGIVRGKLDQLRRCFEV  154 (161)
Q Consensus       132 I~~ai~~gLi~gkIDq~~~~v~V  154 (161)
                      + +.|..|=|-+.||   |-|..
T Consensus       340 l-qmie~~~i~a~iN---G~v~f  358 (422)
T KOG2582|consen  340 L-QMIEDGEIFASIN---GMVFF  358 (422)
T ss_pred             H-HHhccCceEEEec---ceEEE
Confidence            9 9999999999999   55544

>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif

Probab=92.46  E-value=0.17  Score=33.19  Aligned_cols=47  Identities=15%  Similarity=0.203  Sum_probs=36.1

Q ss_pred             HHHHhhhcCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEEecC
Q 031323           99 TVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQ  147 (161)
Q Consensus        99 tL~sLa~~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gkIDq  147 (161)
                      .|.+....++.+|+++||.+++++ ...||.++= ..++.|-|+-.-++
T Consensus         4 ~i~~~l~~~~~~S~~eLa~~~~~s-~~~ve~mL~-~l~~kG~I~~~~~~   50 (69)
T PF09012_consen    4 EIRDYLRERGRVSLAELAREFGIS-PEAVEAMLE-QLIRKGYIRKVDMS   50 (69)
T ss_dssp             HHHHHHHHS-SEEHHHHHHHTT---HHHHHHHHH-HHHCCTSCEEEEEE
T ss_pred             HHHHHHHHcCCcCHHHHHHHHCcC-HHHHHHHHH-HHHHCCcEEEecCC
Confidence            445555578899999999999999 999999988 99999999844433

FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.

>PF09756 DDRGK: DDRGK domain; InterPro: IPR019153 This is a family of proteins of approximately 300 residues

Probab=92.30  E-value=0.4  Score=38.11  Aligned_cols=59  Identities=14%  Similarity=0.246  Sum_probs=41.3

Q ss_pred             HHHHHHHhhhcCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEEecCCCCEEEEEe
Q 031323           96 KQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVCT  156 (161)
Q Consensus        96 rlLtL~sLa~~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gkIDq~~~~v~V~~  156 (161)
                      -+-.+++....++.+..+++|.++++. ..++-+-|- +....|.|.|-||...+=|+||.
T Consensus       100 lL~~Fi~yIK~~Kvv~ledla~~f~l~-t~~~i~ri~-~L~~~g~ltGv~DdrGkfIyIs~  158 (188)
T PF09756_consen  100 LLQEFINYIKEHKVVNLEDLAAEFGLR-TQDVINRIQ-ELEAEGRLTGVIDDRGKFIYISE  158 (188)
T ss_dssp             HHHHHHHHHHH-SEE-HHHHHHHH-S--HHHHHHHHH-HHHHHSSS-EEE-TT--EEE---
T ss_pred             HHHHHHHHHHHcceeeHHHHHHHcCCC-HHHHHHHHH-HHHHCCCceeeEcCCCCeEEecH
Confidence            455667777789999999999999998 777777777 89999999999999988888874

They contain a highly conserved DDRGK motif. The function is unknown. ; PDB: 1WI9_A.

>PF10075 PCI_Csn8: COP9 signalosome, subunit CSN8; InterPro: IPR019280 The photomorphogenic 9 (COP9) signalosome or CSN complex is composed of eight subunits: Cops1/GPS1, Cops2, Cops3, Cops4, Cops5, Cop6, Cops7 (Cops7A or Cops7B) and Cops8

Probab=91.47  E-value=1.4  Score=32.67  Aligned_cols=108  Identities=15%  Similarity=0.205  Sum_probs=69.7

Q ss_pred             HHHHHHHHHHhcCCCcccchhhhcCcccccccC-CCchhHHHHHHHHhcCCHhHHhhc-cCC-C-CC---CCHHHHHHHH
Q 031323           24 AALGSVIVEATSQPSLFAFSEILAVPNIAEFEG-TENSKYLDMLRLFAHGTWSDYKNN-AGH-L-PQ---LVPDQVLKLK   96 (161)
Q Consensus        24 ~~a~~~i~~aL~~p~i~~f~eLl~~~~v~~L~~-s~~~~l~~LL~iF~~G~~~dy~~~-~~~-~-~~---L~~~~~~Klr   96 (161)
                      .........+|..-.+-+|.-+|..-+-...+. .+-..+..|.+.+-.|++.+|.+. ++. . +.   +-+....++|
T Consensus         5 ~~~~~~Ll~~L~~~~~~df~~~~~rip~~~~~~~~~i~~i~~l~~~L~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~iR   84 (143)
T PF10075_consen    5 EIYALILLKYLMQNDLSDFRLLWKRIPEELKQSDPEIKAIWSLGQALWEGDYSKFWQALRSNPWSPDYKPFVPGFEDTIR   84 (143)
T ss_dssp             HHHHHHHHHHHHTTTSTHHHHHHHTS-HHHHTS-TTHHHHHHHHHHHHTT-HHHHHHHS-TT----HHHHTSTTHHHHHH
T ss_pred             hHHHHHHHHHHHcCCchHHHHHHHcCCHHHHhhhHHHHHHHHHHHHHHCCCHHHHHHHHHhccchHHHHHHHHHHHHHHH
Confidence            344455556666656678887775443333332 345668899999999999999872 221 1 11   1244577788


Q ss_pred             HHHHHHhhhcCCccCHHHHHHhcCCCChhhHHHHHH
Q 031323           97 QLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLI  132 (161)
Q Consensus        97 lLtL~sLa~~~~~isy~~I~~~l~i~~~~evE~lvI  132 (161)
                      .=.+-.+......|+-+.+++-||++ .++++.++.
T Consensus        85 ~~i~~~i~~aY~sIs~~~la~~Lg~~-~~el~~~~~  119 (143)
T PF10075_consen   85 ERIAHLISKAYSSISLSDLAEMLGLS-EEELEKFIK  119 (143)
T ss_dssp             HHHHHHHHHH-SEE-HHHHHHHTTS--HHHHHHHHH
T ss_pred             HHHHHHHHHHHhHcCHHHHHHHhCCC-HHHHHHHHH
Confidence            66666666678899999999999999 999999877

In the complex, Cops8, which is the smallest subunit, probably interacts directly with Cops3, Cops4 and Cops7 (Cops7A or Cops7B). This signalosome is homologous to the lid subcomplex of the 26S proteasome and regulates the ubiquitin-proteasome pathway. It functions as a structural scaffold for subunit-subunit interactions within the complex and is a key regulator of photomorphogenic development [].; PDB: 1RZ4_A.

>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp

Probab=90.69  E-value=0.8  Score=30.94  Aligned_cols=37  Identities=19%  Similarity=0.312  Sum_probs=30.7

Q ss_pred             cCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEE
Q 031323          106 TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGK  144 (161)
Q Consensus       106 ~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gk  144 (161)
                      +++.++-++||+.++++ ...++..+= +....|+|+.+
T Consensus        22 ~~~~~s~~eiA~~~~i~-~~~l~kil~-~L~~~Gli~s~   58 (83)
T PF02082_consen   22 DGKPVSSKEIAERLGIS-PSYLRKILQ-KLKKAGLIESS   58 (83)
T ss_dssp             TSC-BEHHHHHHHHTS--HHHHHHHHH-HHHHTTSEEEE
T ss_pred             CCCCCCHHHHHHHHCcC-HHHHHHHHH-HHhhCCeeEec
Confidence            34459999999999999 999999877 99999998764

(strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.

>KOG1463 consensus 26S proteasome regulatory complex, subunit RPN6/PSMD11 [Posttranslational modification, protein turnover, chaperones]

Probab=88.77  E-value=0.66  Score=40.36  Aligned_cols=101  Identities=18%  Similarity=0.301  Sum_probs=70.9

Q ss_pred             ccCCCchhHHHHHHHHhcCCHhHHhhc-cCCCCCCC--H---HHHH----HHHHHHHHHhhhcCCccCHHHHHHhcCCCC
Q 031323           54 FEGTENSKYLDMLRLFAHGTWSDYKNN-AGHLPQLV--P---DQVL----KLKQLTVLTLAETNKVLPYDELMEELDVTN  123 (161)
Q Consensus        54 L~~s~~~~l~~LL~iF~~G~~~dy~~~-~~~~~~L~--~---~~~~----KlrlLtL~sLa~~~~~isy~~I~~~l~i~~  123 (161)
                      ..+..-..+...=+.|..-++.||+.- .+.-++|.  +   ...+    -|--=-|+.+.+..+.+..+-||+-.|++ 
T Consensus       280 y~g~~i~AmkavAeA~~nRSLkdF~~AL~~yk~eL~~D~ivr~Hl~~Lyd~lLEknl~riIEPyS~Vei~hIA~~IGl~-  358 (411)
T KOG1463|consen  280 YAGRDIDAMKAVAEAFGNRSLKDFEKALADYKKELAEDPIVRSHLQSLYDNLLEKNLCRIIEPYSRVEISHIAEVIGLD-  358 (411)
T ss_pred             ccCcchHHHHHHHHHhcCCcHHHHHHHHHHhHHHHhcChHHHHHHHHHHHHHHHHhHHHHcCchhhhhHHHHHHHHCCC-
Confidence            444444557778888999999999962 21112232  1   1111    11112344555566777888899999999 


Q ss_pred             hhhHHHHHHHHhHhcCCcEEEecCCCCEEEEEe
Q 031323          124 VRELEDFLINECMYTGIVRGKLDQLRRCFEVCT  156 (161)
Q Consensus       124 ~~evE~lvI~~ai~~gLi~gkIDq~~~~v~V~~  156 (161)
                      ...||.=+= ++|-.+-+.|.+||-++++.|.-
T Consensus       359 ~~~VEkKLs-qMILDKkf~G~LDQg~g~Liv~~  390 (411)
T KOG1463|consen  359 VPQVEKKLS-QMILDKKFYGTLDQGEGCLIVFE  390 (411)
T ss_pred             cHHHHHHHH-HHHHHHHhhcccccCCCeEEEeC
Confidence            999999988 99999999999999999999854

>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional

Probab=87.96  E-value=2.4  Score=34.37  Aligned_cols=62  Identities=11%  Similarity=0.145  Sum_probs=50.2

Q ss_pred             HHHHHHHHHHhhhcCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEEecCCCCEEEEEe
Q 031323           93 LKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVCT  156 (161)
Q Consensus        93 ~KlrlLtL~sLa~~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gkIDq~~~~v~V~~  156 (161)
                      .=|+.|.++....+...+|..+|++.++++ ...+=..+- +.-..|+|+-+.+...+.+++|.
T Consensus         5 ~~Lk~iallg~l~~~~~IS~~eLA~~L~iS-~~Tvsr~Lk-~LEe~GlI~R~~~~r~~~v~LTe   66 (217)
T PRK14165          5 EALKKLALLGAVNNTVKISSSEFANHTGTS-SKTAARILK-QLEDEGYITRTIVPRGQLITITE   66 (217)
T ss_pred             HHHHHHHHHhccCCCCCcCHHHHHHHHCcC-HHHHHHHHH-HHHHCCCEEEEEcCCceEEEECH
Confidence            445566666655566789999999999998 888888888 99999999999998877777763

>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A

Probab=87.45  E-value=2.2  Score=25.53  Aligned_cols=41  Identities=20%  Similarity=0.368  Sum_probs=30.7

Q ss_pred             HHHhhhcCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcE
Q 031323          100 VLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVR  142 (161)
Q Consensus       100 L~sLa~~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~  142 (161)
                      ++.....+..+|..+||+.++++ ...|-..+= +....|+|+
T Consensus         8 Il~~l~~~~~~t~~ela~~~~is-~~tv~~~l~-~L~~~g~I~   48 (48)
T PF13412_consen    8 ILNYLRENPRITQKELAEKLGIS-RSTVNRYLK-KLEEKGLIE   48 (48)
T ss_dssp             HHHHHHHCTTS-HHHHHHHHTS--HHHHHHHHH-HHHHTTSEE
T ss_pred             HHHHHHHcCCCCHHHHHHHhCCC-HHHHHHHHH-HHHHCcCcC
Confidence            33444456679999999999998 888888766 888899875

...

>TIGR02010 IscR iron-sulfur cluster assembly transcription factor IscR

Probab=86.71  E-value=2.1  Score=31.59  Aligned_cols=45  Identities=18%  Similarity=0.300  Sum_probs=37.6

Q ss_pred             HHHHHHhhh--cCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEE
Q 031323           97 QLTVLTLAE--TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRG  143 (161)
Q Consensus        97 lLtL~sLa~--~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~g  143 (161)
                      +..++.||.  +++.++-++|++.+++| ...++..+= ..-..|+|..
T Consensus        11 l~~l~~La~~~~~~~~s~~~ia~~~~ip-~~~l~kil~-~L~~~glv~s   57 (135)
T TIGR02010        11 VTAMLDLALNAETGPVTLADISERQGIS-LSYLEQLFA-KLRKAGLVKS   57 (135)
T ss_pred             HHHHHHHHhCCCCCcCcHHHHHHHHCcC-HHHHHHHHH-HHHHCCceEE
Confidence            455666664  45579999999999999 999999887 8999999975

This model describes IscR, an iron-sulfur binding transcription factor of the ISC iron-sulfur cluster assembly system.

>KOG1498 consensus 26S proteasome regulatory complex, subunit RPN5/PSMD12 [Posttranslational modification, protein turnover, chaperones]

Probab=86.71  E-value=1.7  Score=38.38  Aligned_cols=124  Identities=20%  Similarity=0.248  Sum_probs=78.0

Q ss_pred             HHHhcCCCcccchhhhcCccc-ccccCCCchhHHHHHHHHhcCCHhHHhhc---------cCCCCC---CCHHH----HH
Q 031323           31 VEATSQPSLFAFSEILAVPNI-AEFEGTENSKYLDMLRLFAHGTWSDYKNN---------AGHLPQ---LVPDQ----VL   93 (161)
Q Consensus        31 ~~aL~~p~i~~f~eLl~~~~v-~~L~~s~~~~l~~LL~iF~~G~~~dy~~~---------~~~~~~---L~~~~----~~   93 (161)
                      ..++..|..---.+|++.-.. +.|+  +.+..-.+|.+|..|-+--|...         .+.+-.   ..+..    ..
T Consensus       260 ~f~~LAp~dneQsdll~~is~dKkL~--e~p~~k~lLklfv~~EL~rw~s~~~~yg~~l~~~~~~~~~~~gek~~~dL~~  337 (439)
T KOG1498|consen  260 SFCVLAPHDNEQSDLLARISNDKKLS--ELPDYKELLKLFVTMELIRWVSLVESYGDELRTNDFFDGGEEGEKRWSDLKL  337 (439)
T ss_pred             eEEeecCCCcHHHHHHHHHhcccccc--cCccHHHHHHHHHhcceeeehhHhhhhHHHHhhcccccccchhhhHHHHHHH
Confidence            344555554434455533321 1132  33446789999999976655521         111111   11111    11


Q ss_pred             HHHHHHHHHhhhcCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEEecCCCCEEEEEeee
Q 031323           94 KLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVCTVL  158 (161)
Q Consensus        94 KlrlLtL~sLa~~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gkIDq~~~~v~V~~~~  158 (161)
                      .+--.-+-=+|.-...||+.++++-++.+ .++.|.++= ..+..|-+.+|||+..+.+....+.
T Consensus       338 RIiEHNiRiiA~yYSrIt~~rl~eLLdl~-~ee~E~~LS-~lv~t~ti~aKidrpsgII~F~k~K  400 (439)
T KOG1498|consen  338 RIIEHNIRIIAKYYSRITLKRLAELLDLP-VEEMEKFLS-DLVVTGTIYAKIDRPSGIINFQKVK  400 (439)
T ss_pred             HHHHHHHHHHHHHHhhccHHHHHHHhCCC-HHHHHHHHH-HHHhccceEEEecCCCceEEEEecc
Confidence            12223333334446789999999999999 999999999 9999999999999999999877653

>KOG0687 consensus 26S proteasome regulatory complex, subunit RPN7/PSMD6 [Posttranslational modification, protein turnover, chaperones]

Probab=86.12  E-value=1.4  Score=38.30  Aligned_cols=109  Identities=18%  Similarity=0.289  Sum_probs=75.7

Q ss_pred             hhcCcccccccCCCchhHHHHHHHHhcCCHhHHhhcc-----CCC-CC--CCHH---HHHHHHHHHHHHhhhcCCccCHH
Q 031323           45 ILAVPNIAEFEGTENSKYLDMLRLFAHGTWSDYKNNA-----GHL-PQ--LVPD---QVLKLKQLTVLTLAETNKVLPYD  113 (161)
Q Consensus        45 Ll~~~~v~~L~~s~~~~l~~LL~iF~~G~~~dy~~~~-----~~~-~~--L~~~---~~~KlrlLtL~sLa~~~~~isy~  113 (161)
                      .+..|-|...-.. -..+.+++..+-.-++++|-..-     ..+ ++  +.+.   -.+-||...-..+-+..|.++.+
T Consensus       243 Vi~~~Evl~vl~~-l~~~~q~l~SLY~C~Y~~Ff~~L~~~~~~~lk~D~~l~~h~~yyvREMR~rvY~QlLESYrsl~l~  321 (393)
T KOG0687|consen  243 VIKCPEVLEVLHK-LPSVSQLLNSLYECDYSDFFNDLAAVEAKQLKDDRYLGPHYRYYVREMRRRVYAQLLESYRSLTLE  321 (393)
T ss_pred             hcCcHHHHHHhhc-CchHHHHHHHHHhccHHHHHHHHHHHHHHhhccchhcchHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4445555432211 12355666666666777666421     111 11  2332   25777777777777788999999


Q ss_pred             HHHHhcCCCChhhHHHHHHHHhHhcCCcEEEecCCCCEEEEEe
Q 031323          114 ELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVCT  156 (161)
Q Consensus       114 ~I~~~l~i~~~~evE~lvI~~ai~~gLi~gkIDq~~~~v~V~~  156 (161)
                      -.|++.|++ .+-+++=+= +-|-.|=+.++||-+++.|.+++
T Consensus       322 ~MA~aFgVS-VefiDreL~-rFI~~grL~ckIDrVnGVVEtNr  362 (393)
T KOG0687|consen  322 SMAKAFGVS-VEFIDRELG-RFIAAGRLHCKIDRVNGVVETNR  362 (393)
T ss_pred             HHHHHhCch-HHHHHhHHH-HhhccCceeeeeecccceeecCC
Confidence            999999998 888888887 88889999999999999999875

>PF13730 HTH_36: Helix-turn-helix domain

Probab=84.87  E-value=4.2  Score=24.86  Aligned_cols=47  Identities=21%  Similarity=0.277  Sum_probs=38.0

Q ss_pred             HHHHHHHHHHhhhc-CCc-cCHHHHHHhcCCCChhhHHHHHHHHhHhcCCc
Q 031323           93 LKLKQLTVLTLAET-NKV-LPYDELMEELDVTNVRELEDFLINECMYTGIV  141 (161)
Q Consensus        93 ~KlrlLtL~sLa~~-~~~-isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi  141 (161)
                      .|+-.+.|.+.+.+ +.. -|++.||+.++++ ...|-..+= +....|+|
T Consensus         7 ~~~v~~~l~~~~~~~~~~~pS~~~la~~~g~s-~~Tv~~~i~-~L~~~G~I   55 (55)
T PF13730_consen    7 AKLVYLYLASYANKNGGCFPSQETLAKDLGVS-RRTVQRAIK-ELEEKGLI   55 (55)
T ss_pred             HHHHHHHHHHhcCCCCCCCcCHHHHHHHHCcC-HHHHHHHHH-HHHHCcCC
Confidence            67788888888853 223 3799999999998 999999877 88888875

>PF07389 DUF1500: Protein of unknown function (DUF1500); InterPro: IPR009974 This family consists of several Orthopoxvirus specific proteins, which include Vaccinia virus, B6 protein, they are around 100 residues in length

Probab=84.57  E-value=1.5  Score=30.80  Aligned_cols=35  Identities=17%  Similarity=0.467  Sum_probs=26.7

Q ss_pred             hhhcCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCC
Q 031323          103 LAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGI  140 (161)
Q Consensus       103 La~~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gL  140 (161)
                      +.+.-..++|++|-+.  +|+.+.||+||| +.+..+.
T Consensus        42 lftr~~vi~Fd~iVr~--mpNes~v~qWV~-dtln~i~   76 (100)
T PF07389_consen   42 LFTRCAVIPFDDIVRT--MPNESRVKQWVI-DTLNDIM   76 (100)
T ss_pred             HHHhhccccHHHHHHh--CCCHHHHHHHHH-HHHHhHh
Confidence            3334457899999999  667899999999 8765443

The function of this family is unknown.

>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional

Probab=84.46  E-value=2.4  Score=31.89  Aligned_cols=45  Identities=22%  Similarity=0.349  Sum_probs=36.1

Q ss_pred             HHhhhcCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEE---EecC
Q 031323          101 LTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRG---KLDQ  147 (161)
Q Consensus       101 ~sLa~~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~g---kIDq  147 (161)
                      +..-..+.-.||.+||+.+|++ ...|-.-+= +....|+|+|   .+|+
T Consensus        15 l~~Lq~d~R~s~~eiA~~lglS-~~tV~~Ri~-rL~~~GvI~~~~~~v~~   62 (153)
T PRK11179         15 LEALMENARTPYAELAKQFGVS-PGTIHVRVE-KMKQAGIITGTRVDVNP   62 (153)
T ss_pred             HHHHHHcCCCCHHHHHHHHCcC-HHHHHHHHH-HHHHCCCeeeEEEEECH
Confidence            3333456789999999999998 999888877 9999999984   4554

>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation

Probab=83.60  E-value=3.8  Score=27.42  Aligned_cols=47  Identities=23%  Similarity=0.231  Sum_probs=37.3

Q ss_pred             HHHHHHHhhhcC-CccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEE
Q 031323           96 KQLTVLTLAETN-KVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGK  144 (161)
Q Consensus        96 rlLtL~sLa~~~-~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gk  144 (161)
                      |.+.++...... +.++..+|++.++++ ...|-..+- .....|++...
T Consensus         6 r~~~Il~~l~~~~~~~t~~~ia~~l~i~-~~tv~r~l~-~L~~~g~l~~~   53 (91)
T smart00346        6 RGLAVLRALAEEPGGLTLAELAERLGLS-KSTAHRLLN-TLQELGYVEQD   53 (91)
T ss_pred             HHHHHHHHHHhCCCCcCHHHHHHHhCCC-HHHHHHHHH-HHHHCCCeeec
Confidence            345555544443 689999999999999 999999888 88899999763

>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator)

Probab=83.40  E-value=3.4  Score=29.83  Aligned_cols=48  Identities=23%  Similarity=0.277  Sum_probs=37.1

Q ss_pred             HHHHHHHHhhhcCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEE
Q 031323           95 LKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGK  144 (161)
Q Consensus        95 lrlLtL~sLa~~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gk  144 (161)
                      ++.|..+....++..+|-++|++.++++ ...|.+.+= .....|+|...
T Consensus        11 l~~l~~la~~~~~~~~s~~eia~~~~i~-~~~v~~il~-~L~~~gli~~~   58 (132)
T TIGR00738        11 LRALLDLALNPDEGPVSVKEIAERQGIS-RSYLEKILR-TLRRAGLVESV   58 (132)
T ss_pred             HHHHHHHHhCCCCCcCcHHHHHHHHCcC-HHHHHHHHH-HHHHCCcEEec
Confidence            4444444433234589999999999999 999999887 89999999753

This model represents a superfamily of probable transcriptional regulators. One member, RRF2 of Desulfovibrio vulgaris is an apparent regulatory protein experimentally (MEDLINE:97293189). The N-terminal region appears related to the DNA-binding biotin repressor region of the BirA bifunctional according to results after three rounds of PSI-BLAST with a fairly high stringency.

>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities

Probab=82.83  E-value=3.8  Score=25.04  Aligned_cols=45  Identities=18%  Similarity=0.279  Sum_probs=34.8

Q ss_pred             HHHHHHHhhh-cCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcE
Q 031323           96 KQLTVLTLAE-TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVR  142 (161)
Q Consensus        96 rlLtL~sLa~-~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~  142 (161)
                      |-+.+++.-. .+..++..+|++.++++ ...+-.++- .....|+++
T Consensus         4 ral~iL~~l~~~~~~~t~~eia~~~gl~-~stv~r~L~-tL~~~g~v~   49 (52)
T PF09339_consen    4 RALRILEALAESGGPLTLSEIARALGLP-KSTVHRLLQ-TLVEEGYVE   49 (52)
T ss_dssp             HHHHHHHCHHCTBSCEEHHHHHHHHTS--HHHHHHHHH-HHHHTTSEE
T ss_pred             HHHHHHHHHHcCCCCCCHHHHHHHHCcC-HHHHHHHHH-HHHHCcCee
Confidence            4566666554 45568999999999999 999999887 888888875

One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1MKM_A 3MQ0_A 3R4K_A 2G7U_C 2O0Y_C 2XRO_F 2XRN_B 2IA2_D.

>KOG3054 consensus Uncharacterized conserved protein [Function unknown]

Probab=82.57  E-value=3.4  Score=34.37  Aligned_cols=54  Identities=19%  Similarity=0.425  Sum_probs=42.3

Q ss_pred             HHHhhhcCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEEecCCCCEEEEE
Q 031323          100 VLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVC  155 (161)
Q Consensus       100 L~sLa~~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gkIDq~~~~v~V~  155 (161)
                      ++....++++++.++++.+.++-+.+.+-. += +.+..|++.|-||...+-++|+
T Consensus       205 Fv~YIk~nKvV~ledLas~f~Lrtqd~inr-iq-~~l~eg~ltGVmDDRGKfIYIS  258 (299)
T KOG3054|consen  205 FVEYIKKNKVVPLEDLASEFGLRTQDSINR-IQ-ELLAEGLLTGVMDDRGKFIYIS  258 (299)
T ss_pred             HHHHHHhcCeeeHHHHHHHhCccHHHHHHH-HH-HHHHhhhheeeecCCCceEEec
Confidence            456666889999999999999974433332 23 5556899999999999999987

>smart00344 HTH_ASNC helix_turn_helix ASNC type

Probab=82.49  E-value=3.3  Score=28.84  Aligned_cols=36  Identities=11%  Similarity=0.301  Sum_probs=31.7

Q ss_pred             cCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEE
Q 031323          106 TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRG  143 (161)
Q Consensus       106 ~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~g  143 (161)
                      .+..+|+.+|++.++++ ...|-..+- +....|+|++
T Consensus        14 ~~~~~~~~~la~~l~~s-~~tv~~~l~-~L~~~g~i~~   49 (108)
T smart00344       14 KDARISLAELAKKVGLS-PSTVHNRVK-RLEEEGVIKG   49 (108)
T ss_pred             HhCCCCHHHHHHHHCcC-HHHHHHHHH-HHHHCCCeec
Confidence            44579999999999999 999999888 9999999884

AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli

>PRK10857 DNA-binding transcriptional regulator IscR; Provisional

Probab=82.43  E-value=3.5  Score=31.79  Aligned_cols=45  Identities=18%  Similarity=0.298  Sum_probs=37.2

Q ss_pred             HHHHHHhhh--cCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEE
Q 031323           97 QLTVLTLAE--TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRG  143 (161)
Q Consensus        97 lLtL~sLa~--~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~g  143 (161)
                      +..++-+|+  +++.+|-++||+.+++| ..-+++.+- ..-..|||..
T Consensus        11 l~~l~~lA~~~~~~~vs~~eIA~~~~ip-~~~l~kIl~-~L~~aGLv~s   57 (164)
T PRK10857         11 VTAMLDVALNSEAGPVPLADISERQGIS-LSYLEQLFS-RLRKNGLVSS   57 (164)
T ss_pred             HHHHHHHHhCCCCCcCcHHHHHHHHCcC-HHHHHHHHH-HHHHCCCEEe
Confidence            444555554  45689999999999999 999999888 9999999986

>COG1522 Lrp Transcriptional regulators [Transcription]

Probab=80.26  E-value=4.1  Score=29.99  Aligned_cols=37  Identities=14%  Similarity=0.232  Sum_probs=31.3

Q ss_pred             cCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEE
Q 031323          106 TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGK  144 (161)
Q Consensus       106 ~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gk  144 (161)
                      .+..+||.+||+.++++ ...|=.-+= +....|+|+|.
T Consensus        19 ~d~r~~~~eia~~lglS-~~~v~~Ri~-~L~~~GiI~~~   55 (154)
T COG1522          19 EDARISNAELAERVGLS-PSTVLRRIK-RLEEEGVIKGY   55 (154)
T ss_pred             HhCCCCHHHHHHHHCCC-HHHHHHHHH-HHHHCCceeeE
Confidence            44459999999999998 888887777 88999998874

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	161
3chm_A	169	Crystal Structure Of Pci Domain From A. Thaliana Co		2e-59

>pdb|3CHM|A Chain A, Crystal Structure Of Pci Domain From A. Thaliana Cop9 Signalosome Subunit 7 (Csn7) Length = 169

Iteration: 1
 Score =  224 bits (571), Expect = 2e-59,   Method: Compositional matrix adjust.
 Identities = 107/153 (69%), Positives = 120/153 (78%)
Query: 2   DIEQRQAELIDHFVKQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENSK 61
           DIEQ+QAE+ID  VK+AS  K  ALG +I+EATS PSLFAFSEILA+PN+A+ EGT +S 
Sbjct: 2   DIEQKQAEIIDQLVKRASTCKSEALGPLIIEATSHPSLFAFSEILALPNVAQLEGTTDSV 61
Query: 62  YLDMLRLFAHGTWSDYKNNAGHLPQLVPDXXXXXXXXXXXXXAETNKVLPYDELMEELDV 121
           YLD+LRLFAHGTW DYK NA  LP L PD             AE+NKVLPYD LM ELDV
Sbjct: 62  YLDLLRLFAHGTWGDYKCNATRLPHLSPDQILKLKQLTVLTLAESNKVLPYDTLMVELDV 121
Query: 122 TNVRELEDFLINECMYTGIVRGKLDQLRRCFEV 154
           +NVRELEDFLINECMY GIVRGKLDQL+RCFEV
Sbjct: 122 SNVRELEDFLINECMYAGIVRGKLDQLKRCFEV 154
  Database: pdbaa

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	161
3chm_A	169	COP9 signalosome complex subunit 7; heat/ARM repea	4e-55

>3chm_A COP9 signalosome complex subunit 7; heat/ARM repeats, winged helix motif, developmental protein, phosphoprotein; 1.50A {Arabidopsis thaliana} Length = 169

 Score =  170 bits (431), Expect = 4e-55
 Identities = 120/159 (75%), Positives = 134/159 (84%)

Query: 2   DIEQRQAELIDHFVKQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENSK 61
           DIEQ+QAE+ID  VK+AS  K  ALG +I+EATS PSLFAFSEILA+PN+A+ EGT +S 
Sbjct: 2   DIEQKQAEIIDQLVKRASTCKSEALGPLIIEATSHPSLFAFSEILALPNVAQLEGTTDSV 61

Query: 62  YLDMLRLFAHGTWSDYKNNAGHLPQLVPDQVLKLKQLTVLTLAETNKVLPYDELMEELDV 121
           YLD+LRLFAHGTW DYK NA  LP L PDQ+LKLKQLTVLTLAE+NKVLPYD LM ELDV
Sbjct: 62  YLDLLRLFAHGTWGDYKCNATRLPHLSPDQILKLKQLTVLTLAESNKVLPYDTLMVELDV 121

Query: 122 TNVRELEDFLINECMYTGIVRGKLDQLRRCFEVCTVLVR 160
           +NVRELEDFLINECMY GIVRGKLDQL+RCFEV     R
Sbjct: 122 SNVRELEDFLINECMYAGIVRGKLDQLKRCFEVPFAAGR 160

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	161
3chm_A	169	COP9 signalosome complex subunit 7; heat/ARM repea	100.0
4b4t_O	393	26S proteasome regulatory subunit RPN9; hydrolase,	99.96
3txn_A	394	26S proteasome regulatory complex subunit P42B; PC	99.43
4b4t_R	429	RPN7, 26S proteasome regulatory subunit RPN7; hydr	98.88
3t5x_A	203	PCI domain-containing protein 2; PCI, mRNA nuclear	98.72
4b4t_P	445	26S proteasome regulatory subunit RPN5; hydrolase,	98.71
4b4t_Q	434	26S proteasome regulatory subunit RPN6; hydrolase,	98.41
1ufm_A	84	COP9 complex subunit 4; helix-turn-helix, structur	98.4
3t5v_B	455	Nuclear mRNA export protein THP1; PCI, mRNA nuclea	97.94
4b4t_S	523	RPN3, 26S proteasome regulatory subunit RPN3; hydr	97.87
1wi9_A	72	Protein C20ORF116 homolog; helix-turn-helix motif,	94.52
4b0z_A	229	RPN12, 26S proteasome regulatory subunit RPN12; pr	93.92
1qgp_A	77	Protein (double stranded RNA adenosine deaminase);	90.99
1qbj_A	81	Protein (double-stranded RNA specific adenosine D	90.38
3lwf_A	159	LIN1550 protein, putative transcriptional regulato	87.57
2hzt_A	107	Putative HTH-type transcriptional regulator YTCD;	87.31
2y75_A	129	HTH-type transcriptional regulator CYMR; DNA bindi	86.99
3t8r_A	143	Staphylococcus aureus CYMR; transcriptional regula	86.83
1xn7_A	78	Hypothetical protein YHGG; alpha+beta, GFT structu	84.49
3cuo_A	99	Uncharacterized HTH-type transcriptional regulato;	84.39
1oyi_A	82	Double-stranded RNA-binding protein; (alpha+beta)	84.32
2heo_A	67	Z-DNA binding protein 1; protein DLM1-Z-DNA comple	83.84
2v79_A	135	DNA replication protein DNAD; primosome, DNA-bindi	82.79
1sfx_A	109	Conserved hypothetical protein AF2008; structural	82.51
1z7u_A	112	Hypothetical protein EF0647; winged-helix-turn-hel	80.88
1ylf_A	149	RRF2 family protein; structural genomics, transcri	80.77
2p5v_A	162	Transcriptional regulator, LRP/ASNC family; NMB057	80.74
1xd7_A	145	YWNA; structural genomics, protein structure initi	80.63
3k69_A	162	Putative transcription regulator; putative transcr	80.47
2pg4_A	95	Uncharacterized protein; structural genomics, join	80.26
1yyv_A	131	Putative transcriptional regulator; reductive meth	80.18

>3chm_A COP9 signalosome complex subunit 7; heat/ARM repeats, winged helix motif, developmental protein, phosphoprotein; 1.50A {Arabidopsis thaliana}

Probab=100.00  E-value=5e-51  Score=316.01  Aligned_cols=160  Identities=75%  Similarity=1.131  Sum_probs=155.1

Q ss_pred             cHhHHHHHHHHHHHHHhcccchHHHHHHHHHHhcCCCcccchhhhcCcccccccCCCchhHHHHHHHHhcCCHhHHhhcc
Q 031323            2 DIEQRQAELIDHFVKQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENSKYLDMLRLFAHGTWSDYKNNA   81 (161)
Q Consensus         2 ~~~~~~~~~l~~~l~~~~~~~~~~a~~~i~~aL~~p~i~~f~eLl~~~~v~~L~~s~~~~l~~LL~iF~~G~~~dy~~~~   81 (161)
                      |+++++.++||+|+.+++++++++|.+++++||.+|++|+|||||.+|+|++|++++++|+++||++|++||+++|.+++
T Consensus         2 ~~~~~~~~~l~~f~~la~~~~~~~a~~li~~Al~~p~vf~F~eLL~~p~v~~L~~~~~~~~~~LL~iF~~G~~~~y~~~~   81 (169)
T 3chm_A            2 DIEQKQAEIIDQLVKRASTCKSEALGPLIIEATSHPSLFAFSEILALPNVAQLEGTTDSVYLDLLRLFAHGTWGDYKCNA   81 (169)
T ss_dssp             --CCCHHHHHHHHHHHHTTSCGGGHHHHHHHHHHCTTCCCCHHHHTCHHHHTTTTSTTHHHHHHHHHHHHCCHHHHHHHG
T ss_pred             chhHHHHHHHHHHHHHHhcCcHHHHHHHHHHHhcCCCeeehHHHhCChHHHHhcCCChhHHHHHHHHHhcCCHHHHHHhH
Confidence            78999999999999999999999999999999999999999999999999999998899999999999999999999988


Q ss_pred             CCCCCCCHHHHHHHHHHHHHHhhhcCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEEecCCCCEEEEEeeeccC
Q 031323           82 GHLPQLVPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVCTVLVRL  161 (161)
Q Consensus        82 ~~~~~L~~~~~~KlrlLtL~sLa~~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gkIDq~~~~v~V~~~~~Rv  161 (161)
                      +.+|.|++.+.+|||+|||++||++++++||++|+++|++++.++||+||||+||+.|||+|||||++++|+|+|++||+
T Consensus        82 ~~~p~L~~~~~~KlrlLtL~sLa~~~~~lsy~~I~~~l~i~~~~evE~lvI~~ai~~gLI~gkiDQ~~~~v~V~~~~~R~  161 (169)
T 3chm_A           82 TRLPHLSPDQILKLKQLTVLTLAESNKVLPYDTLMVELDVSNVRELEDFLINECMYAGIVRGKLDQLKRCFEVPFAAGRD  161 (169)
T ss_dssp             GGSCCCCHHHHHHHHHHHHHHHHHHCSEEEHHHHHHHHTCCSHHHHHHHHHHTHHHHTSEEEEEETTTTEEEEEEECCTT
T ss_pred             HhCcchHHHHHHHHHHHHHHHHHHhCCCcCHHHHHHHhCCCCHHHHHHHHHHHHHHhCCeEEEEcCcCCEEEEEeecCCc
Confidence            88999999999999999999999999999999999999999899999999999999999999999999999999999996

>4b4t_O 26S proteasome regulatory subunit RPN9; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=99.96  E-value=2.5e-30  Score=221.82  Aligned_cols=137  Identities=14%  Similarity=0.307  Sum_probs=117.8

Q ss_pred             hHHHHHHHHHHhcCCCcccchhhhcCcccccccC-CCchhHHHHHHHHhcCCHhHHhhc----cCCCCCCC---HHHHHH
Q 031323           23 GAALGSVIVEATSQPSLFAFSEILAVPNIAEFEG-TENSKYLDMLRLFAHGTWSDYKNN----AGHLPQLV---PDQVLK   94 (161)
Q Consensus        23 ~~~a~~~i~~aL~~p~i~~f~eLl~~~~v~~L~~-s~~~~l~~LL~iF~~G~~~dy~~~----~~~~~~L~---~~~~~K   94 (161)
                      ...|+.+++.||.+|++|+||+|+++|.++.|++ +++.|+++||++|++|++.+|.+.    .+..|.++   ....+|
T Consensus       211 ~~~a~~l~~~all~~~i~~f~eLL~~p~i~~L~~~~~~~~l~~Ll~~f~~g~~~~f~~~~~~~~~~~~~l~~~~~~l~~k  290 (393)
T 4b4t_O          211 QQLAYDLSISALLGDKIYNFGELLHHPIMETIVNDSNYDWLFQLLNALTVGDFDKFDSLIKVQISKIPILAQHESFLRQK  290 (393)
T ss_dssp             HHHHHHHHHHHHHCCSSCSTHHHHHSCCTTSSCSSSSTTHHHHHHHHHHHTCHHHHHHHCCHHHHHSHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCCCChHHHhCChHHHHhhcCCchHHHHHHHHHHhcCCHHHHHHHHHHhhhhCcchhhhHHHHHHH
Confidence            4668999999999999999999999999999975 579999999999999999999863    34456664   346899


Q ss_pred             HHHHHHHHhhh--cCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEEecCCCCEEEEEeeeccC
Q 031323           95 LKQLTVLTLAE--TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVCTVLVRL  161 (161)
Q Consensus        95 lrlLtL~sLa~--~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gkIDq~~~~v~V~~~~~Rv  161 (161)
                      ||+++++++++  ..+.|||++|+++|+++ .++||.||| +||+.|+|+|+|||++|+|+|+|++||+
T Consensus       291 irll~l~~l~~~~~~~~i~f~~ia~~l~i~-~~evE~lli-~aI~~glI~GkIDQv~~~v~v~~~~pR~  357 (393)
T 4b4t_O          291 ICLMTLIETVFVKNIRMLSFEDISKATHLP-KDNVEHLVM-RAISLGLLKGSIDQVNELVTISWVQPRI  357 (393)
T ss_dssp             HHHHHHHHHHCSSSCCCEEHHHHHHHHTCC-HHHHHHHHH-HHHHHSCSSSCEETTTTEECC-------
T ss_pred             HHHHHHHHHhccCCCCcCcHHHHHHHhCcC-HHHHHHHHH-HHHHcCCEEEEEcCCCCEEEEEeccCCC
Confidence            99999999996  46899999999999998 999999999 9999999999999999999999999996

>3txn_A 26S proteasome regulatory complex subunit P42B; PCI domain, alpha solenoid, regulatory PART LID, hydrolase, protein binding; 2.50A {Drosophila melanogaster} PDB: 3txm_A

Probab=99.43  E-value=7.6e-13  Score=113.73  Aligned_cols=135  Identities=10%  Similarity=0.089  Sum_probs=112.6

Q ss_pred             HHHHHHHHHHhcCCCcccchhhhcCcccccccCCCchhHHHHHHHHhcCCHhHHhh----ccCCCCC---CC---HHHHH
Q 031323           24 AALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENSKYLDMLRLFAHGTWSDYKN----NAGHLPQ---LV---PDQVL   93 (161)
Q Consensus        24 ~~a~~~i~~aL~~p~i~~f~eLl~~~~v~~L~~s~~~~l~~LL~iF~~G~~~dy~~----~~~~~~~---L~---~~~~~   93 (161)
                      +.++-++..+|..-+.+.+++++..|......+++..|+.+|+..|..|++.+|.+    +.+.+..   +.   +...+
T Consensus       221 ~~lkYlvL~aLl~~~r~el~~~l~~~~~~~~~~pei~~l~~L~~a~~~~dl~~f~~iL~~~~~~l~~D~~l~~h~~~L~~  300 (394)
T 3txn_A          221 TSLKYMLLCKIMLGQSDDVNQLVSGKLAITYSGRDIDAMKSVAEASHKRSLADFQAALKEYKKELAEDVIVQAHLGTLYD  300 (394)
T ss_dssp             HHHHHHHHHHHHTTCGGGHHHHHHSHHHHTTCSHHHHHHHHHHHHHHTTCHHHHHHHHHHSTTTTTTSHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHhccccccccCCccHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhcChHHHHHHHHHHH
Confidence            45778899999999999999999888765555556789999999999999999986    3332221   11   34578


Q ss_pred             HHHHHHHHHhhhcCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEEecCCCCEEEEEeeecc
Q 031323           94 KLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVCTVLVR  160 (161)
Q Consensus        94 KlrlLtL~sLa~~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gkIDq~~~~v~V~~~~~R  160 (161)
                      ++|...+..+....+.|+++.||+.++++ .++||.+++ ++|..|.|.|+|||++|+|++++.-+|
T Consensus       301 ~Ir~~~L~~i~~pYsrIsl~~iA~~l~ls-~~evE~~L~-~lI~dg~I~a~IDq~~giv~~~~~~~r  365 (394)
T 3txn_A          301 TMLEQNLCRIIEPYSRVQVAHVAESIQLP-MPQVEKKLS-QMILDKKFSGILDQGEGVLIVFEETPV  365 (394)
T ss_dssp             HHHHHHHHHHHTTCSEEEHHHHHHHHTCC-HHHHHHHHH-HHHHTTSSCEEEETTTTEEEECCC---
T ss_pred             HHHHHHHHHHhHhhceeeHHHHHHHHCcC-HHHHHHHHH-HHHHCCCeeEEEcCCCCEEEECCCcch
Confidence            99999999999999999999999999997 999999999 999999999999999999999775443

>4b4t_R RPN7, 26S proteasome regulatory subunit RPN7; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=98.88  E-value=1.3e-08  Score=87.45  Aligned_cols=153  Identities=13%  Similarity=0.082  Sum_probs=112.0

Q ss_pred             HHHHHHHHHHHHhccc-------chHHHHHHHHHHhcCCCcccch-hhhcCcccccc-cCCC-chhHHHHHHHHhcCCHh
Q 031323            6 RQAELIDHFVKQASNQ-------KGAALGSVIVEATSQPSLFAFS-EILAVPNIAEF-EGTE-NSKYLDMLRLFAHGTWS   75 (161)
Q Consensus         6 ~~~~~l~~~l~~~~~~-------~~~~a~~~i~~aL~~p~i~~f~-eLl~~~~v~~L-~~s~-~~~l~~LL~iF~~G~~~   75 (161)
                      +|..+-..|+..+...       ....+..+++.++..++.-++. .++.-|.+... ...+ ..++.+++..|..+.+.
T Consensus       223 ~f~~Aa~~f~e~~~t~~~~e~~~~~~~~~y~~l~al~~~~r~~l~~~v~~~~~~~~~l~~~p~~~~~~~l~~~~~~~~~~  302 (429)
T 4b4t_R          223 NFKEAAKLLVDSLATFTSIELTSYESIATYASVTGLFTLERTDLKSKVIDSPELLSLISTTAALQSISSLTISLYASDYA  302 (429)
T ss_dssp             CHHHHHHHHHHHHHHSCCSCHHHHHHHHHHHHHHHHHTTCHHHHHHSSSSSHHHHHGGGSHHHHHHHHHHHHHHHHTCHH
T ss_pred             hHHHHHHHHHHHhccCCccchhhHHHHHHHHHHHHHhcCCHHHHHHHHhcCHHHHhhccCChhHHHHHHHHHHHHhccHH
Confidence            4555556676665432       1245777777888877765543 36666665543 3322 34577888889999988


Q ss_pred             HHhh-----ccCCC---CCCC---HHHHHHHHHHHHHHhhhcCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEE
Q 031323           76 DYKN-----NAGHL---PQLV---PDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGK  144 (161)
Q Consensus        76 dy~~-----~~~~~---~~L~---~~~~~KlrlLtL~sLa~~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gk  144 (161)
                      .|..     ....+   +-+.   +...+.||...+..++.-.+.|+++.+|+.++++ .+++|.++. ++|..|-|.||
T Consensus       303 ~~~~~~l~~~~~~l~~d~~l~~h~~~l~~~ir~~~l~q~~~~Ys~I~l~~mA~~l~~s-~~~~E~~L~-~lI~~g~l~ak  380 (429)
T 4b4t_R          303 SYFPYLLETYANVLIPCKYLNRHADFFVREMRRKVYAQLLESYKTLSLKSMASAFGVS-VAFLDNDLG-KFIPNKQLNCV  380 (429)
T ss_dssp             HHHHHHHHHHSTTTTTCTTSTTTHHHHHHHHHHHHHHHHHHTCSEEEHHHHHHHHTSC-HHHHHHHHH-HHHHHTSSCEE
T ss_pred             HHHHHHHHHHHhhhccCHHHHHHHHHHHHHHHHHHHHHHhHHhceeeHHHHHHHhCcC-HHHHHHHHH-HHHHcCCeEEE
Confidence            8754     12211   1232   5678999999999999999999999999999998 999999999 99999999999


Q ss_pred             ecCCCCEEEEEeeecc
Q 031323          145 LDQLRRCFEVCTVLVR  160 (161)
Q Consensus       145 IDq~~~~v~V~~~~~R  160 (161)
                      |||++|+|+.++.-+|
T Consensus       381 ID~~~giv~~~~~d~~  396 (429)
T 4b4t_R          381 IDRVNGIVETNRPDNK  396 (429)
T ss_dssp             EETTTTEEEECC----
T ss_pred             EcCCCCEEEECCCCch
Confidence            9999999998776544

>3t5x_A PCI domain-containing protein 2; PCI, mRNA nuclear export, transcription; 2.12A {Homo sapiens}

Probab=98.72  E-value=4.7e-09  Score=82.51  Aligned_cols=96  Identities=18%  Similarity=0.269  Sum_probs=76.4

Q ss_pred             hHHHHHHHHhcCCHhHHhh----ccCCCCC-CCHHHHHHHHHHHHHHhhh------cCCccCHHHHHHhcCCC-----Ch
Q 031323           61 KYLDMLRLFAHGTWSDYKN----NAGHLPQ-LVPDQVLKLKQLTVLTLAE------TNKVLPYDELMEELDVT-----NV  124 (161)
Q Consensus        61 ~l~~LL~iF~~G~~~dy~~----~~~~~~~-L~~~~~~KlrlLtL~sLa~------~~~~isy~~I~~~l~i~-----~~  124 (161)
                      .+.+|.+.+..||+..|++    +.+.+.. -.-..++|+|.+.+.++..      ....||+++|+.+++++     +.
T Consensus        82 ~y~~L~~Avr~Gdl~~f~~~l~~~~~~f~~~~~~lll~rlr~~v~r~l~rkv~~~~~~~rI~l~~i~~~l~~~~~~~~~~  161 (203)
T 3t5x_A           82 QFAEVTRAVSEGNLLLLHEALAKHEAFFIRCGIFLILEKLKIITYRNLFKKVYLLLKTHQLSLDAFLVALKFMQVEDVDI  161 (203)
T ss_dssp             GGHHHHHHHHHTCHHHHHHHHHHTHHHHHHHTCHHHHHTHHHHHHHHHHHHHHHHHCCSEEEHHHHHHHHHHTTCTTCCH
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHhHHHHHHCChHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHHhcCCCCCCH
Confidence            4779999999999999996    2211100 0123578899888877765      46799999999999752     48


Q ss_pred             hhHHHHHHHHhHhcCCcEEEecCCCCEEEEEee
Q 031323          125 RELEDFLINECMYTGIVRGKLDQLRRCFEVCTV  157 (161)
Q Consensus       125 ~evE~lvI~~ai~~gLi~gkIDq~~~~v~V~~~  157 (161)
                      +|||.++. ++|..|.|+|+||+.++++.++..
T Consensus       162 ~evE~ila-~lI~~G~Ikg~I~~~~~~lVlsk~  193 (203)
T 3t5x_A          162 DEVQCILA-NLIYMGHVKGYISHQHQKLVVSKQ  193 (203)
T ss_dssp             HHHHHHHH-HHHHHTSSCEEEETTTTEEEECSS
T ss_pred             HHHHHHHH-HHHHcCceEEEEcccccEEEECCC
Confidence            99999999 999999999999999999988764

>4b4t_P 26S proteasome regulatory subunit RPN5; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=98.71  E-value=5e-08  Score=84.37  Aligned_cols=148  Identities=11%  Similarity=0.099  Sum_probs=104.6

Q ss_pred             HHHHHHHHHHHHhccc--------chHHHHHHHHHHhcCCCcccchhhhcCcccccccCCCchhHHHHHHHHhcCCHhHH
Q 031323            6 RQAELIDHFVKQASNQ--------KGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENSKYLDMLRLFAHGTWSDY   77 (161)
Q Consensus         6 ~~~~~l~~~l~~~~~~--------~~~~a~~~i~~aL~~p~i~~f~eLl~~~~v~~L~~s~~~~l~~LL~iF~~G~~~dy   77 (161)
                      +|..+=..|...++..        ...+-...+...+.+|..-....+++-+.... ..++-.++..|++.|..+.+..|
T Consensus       233 ~y~~a~~~y~e~~~~~~~~~d~~~~~~~L~~~v~~~iLa~~~~~~~~ll~~~~~~~-~~~~l~~~~~L~k~f~~~~L~~~  311 (445)
T 4b4t_P          233 EYLEVAQYLQEIYQTDAIKSDEAKWKPVLSHIVYFLVLSPYGNLQNDLIHKIQNDN-NLKKLESQESLVKLFTTNELMRW  311 (445)
T ss_dssp             CHHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHSSCSSTTHHHHHSHHHHS-SCHHHHHHHHHHHHHHHCCSSSH
T ss_pred             hHHHHHHHHHHHHhcccccCCHHHHHHHHHHHHHHHHhCCCCchHHHHHHHHhhcc-cccccHHHHHHHHHHHhchHhhh
Confidence            3444445555555432        12334556667777887777777876543221 11234668899999999998877


Q ss_pred             hh----ccCCC---CC-----C-C---HHHHHHHHHHHHHHhhhcCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCc
Q 031323           78 KN----NAGHL---PQ-----L-V---PDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIV  141 (161)
Q Consensus        78 ~~----~~~~~---~~-----L-~---~~~~~KlrlLtL~sLa~~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi  141 (161)
                      ..    +...+   +.     . .   ....+.++...+..++.-.+.|+++.|++.++++ .++||.++. ++|..|.|
T Consensus       312 ~~~~~~~~~~L~~~~~~~~~~~~~~~~~~L~~~v~ehnl~~i~k~Ys~I~l~~la~lL~l~-~~evE~~ls-~mI~~g~i  389 (445)
T 4b4t_P          312 PIVQKTYEPVLNEDDLAFGGEANKHHWEDLQKRVIEHNLRVISEYYSRITLLRLNELLDLT-ESQTETYIS-DLVNQGII  389 (445)
T ss_dssp             HHHHHHTCSSTTTCCSSCCCSCSSHHHHHHHHHHHHHHHHHHHHHEEEEEHHHHHHHHTSC-HHHHHHHHH-HHHHHTSS
T ss_pred             HHHHHHHHHHhcccchhhhcchhhHHHHHHHHHHHHHHHHHHHHHhceeeHHHHHHHhCcC-HHHHHHHHH-HHHHCCCE
Confidence            64    22211   11     1 1   3356777778888888888999999999999998 999999999 99999999


Q ss_pred             EEEecCCCCEEEEEe
Q 031323          142 RGKLDQLRRCFEVCT  156 (161)
Q Consensus       142 ~gkIDq~~~~v~V~~  156 (161)
                      .|+|||++|.|+..+
T Consensus       390 ~akIDq~~giV~F~~  404 (445)
T 4b4t_P          390 YAKVNRPAKIVNFEK  404 (445)
T ss_dssp             CCEEETTTTEEEC--
T ss_pred             EEEEcCCCCEEEECC
Confidence            999999999998764

>4b4t_Q 26S proteasome regulatory subunit RPN6; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=98.41  E-value=1.5e-06  Score=71.18  Aligned_cols=99  Identities=12%  Similarity=0.103  Sum_probs=79.6

Q ss_pred             CchhHHHHHHHHhcCCHhHHhhcc----CCCCC---CC---HHHHHHHHHHHHHHhhhcCCccCHHHHHHhcCCCChhhH
Q 031323           58 ENSKYLDMLRLFAHGTWSDYKNNA----GHLPQ---LV---PDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVREL  127 (161)
Q Consensus        58 ~~~~l~~LL~iF~~G~~~dy~~~~----~~~~~---L~---~~~~~KlrlLtL~sLa~~~~~isy~~I~~~l~i~~~~ev  127 (161)
                      +..++..+...|..+++.+|....    ..+..   +.   ....+.++...+..++...+.++++.|++.++++ .+++
T Consensus       295 ~~~~~~~l~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~l~~~~~~y~~i~l~~la~~l~~~-~~~~  373 (434)
T 4b4t_Q          295 GIDAMKAVAEAYNNRSLLDFNTALKQYEKELMGDELTRSHFNALYDTLLESNLCKIIEPFECVEISHISKIIGLD-TQQV  373 (434)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHTHHHHTCSHHHHHHHHHHHHHHHHHHHHHHHSSCSCEEHHHHHHHHTCC-HHHH
T ss_pred             hhhHHHHHHHHHHhhhHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHhCcC-HHHH
Confidence            356788899999999999998621    11111   11   3346778888888999888999999999999998 9999


Q ss_pred             HHHHHHHhHhcCCcEEEecCCCCEEEEEeee
Q 031323          128 EDFLINECMYTGIVRGKLDQLRRCFEVCTVL  158 (161)
Q Consensus       128 E~lvI~~ai~~gLi~gkIDq~~~~v~V~~~~  158 (161)
                      |.++. ++|..|.+.|+|||.+|.|.+....
T Consensus       374 E~~l~-~lI~~~~i~a~id~~~g~v~~~~~~  403 (434)
T 4b4t_Q          374 EGKLS-QMILDKIFYGVLDQGNGWLYVYETP  403 (434)
T ss_dssp             HHHHH-HHHHHTSSCCEEETTTTEEECC---
T ss_pred             HHHHH-HHHhCCCcceecccccCeEeeCCCc
Confidence            99999 9999999999999999999886543

>1ufm_A COP9 complex subunit 4; helix-turn-helix, structural genomics, riken structural genomics/proteomics initiative, RSGI, signaling protein; NMR {Mus musculus} SCOP: a.4.5.47

Probab=98.40  E-value=8.3e-07  Score=60.65  Aligned_cols=58  Identities=17%  Similarity=0.265  Sum_probs=51.4

Q ss_pred             HHHHHhhhcCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEEecCCCCEEEEEee
Q 031323           98 LTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVCTV  157 (161)
Q Consensus        98 LtL~sLa~~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gkIDq~~~~v~V~~~  157 (161)
                      -.|..++.-...|+++.+|+.++++ .++||.++. ++|..|-+.|+|||++++|...+.
T Consensus        19 ~nl~~is~~Y~~Isl~~La~ll~ls-~~~vE~~ls-~mI~~~~l~akIDq~~g~V~f~~~   76 (84)
T 1ufm_A           19 HNLLSASKLYNNITFEELGALLEIP-AAKAEKIAS-QMITEGRMNGFIDQIDGIVHFETR   76 (84)
T ss_dssp             HHHHHHHHSCSEEEHHHHHHHTTSC-HHHHHHHHH-HHHHTTSSCEEEETTTTEEEECCS
T ss_pred             HHHHHHHHhcCeeeHHHHHHHHCcC-HHHHHHHHH-HHHhCCcEEEEEeCCCCEEEeCCc
Confidence            3333566678999999999999999 999999999 999999999999999999987654

>3t5v_B Nuclear mRNA export protein THP1; PCI, mRNA nuclear export, mRNA, nuclear, transcription; 2.90A {Saccharomyces cerevisiae}

Probab=97.94  E-value=5.3e-06  Score=72.39  Aligned_cols=95  Identities=18%  Similarity=0.208  Sum_probs=73.2

Q ss_pred             HHHHHHHHhcCCHhHHhh----ccCCCC-CCC-HHHHHHHHHHHHHHhhh----------cCCccCHHHHHHhcCC----
Q 031323           62 YLDMLRLFAHGTWSDYKN----NAGHLP-QLV-PDQVLKLKQLTVLTLAE----------TNKVLPYDELMEELDV----  121 (161)
Q Consensus        62 l~~LL~iF~~G~~~dy~~----~~~~~~-~L~-~~~~~KlrlLtL~sLa~----------~~~~isy~~I~~~l~i----  121 (161)
                      +..|.+....||+..|++    |...+. .=. -..+.|+|.+.+-++..          +...||++.|+.++++    
T Consensus       299 y~~L~~AVr~Gdl~~F~~~L~~~~~~f~~~gily~LlerLr~~v~RnLirkv~~~~~~~~~~srI~l~~i~~aL~~~~~~  378 (455)
T 3t5v_B          299 WSVLYKHVRYGNIQGVSLWLRQNERHLCARQLLIVLLEKLPMVTYRNLIKTVIKSWTTEWGQNKLPYSLIERVLQLSIGP  378 (455)
T ss_dssp             HHHHHHHHHHTCHHHHHHHHHHTHHHHHHTTCHHHHHHHHHHHHHHHHHHHHHHHHTTTTCCCEEEHHHHHHHHHHHHCC
T ss_pred             HHHHHHHHHhCCHHHHHHHHHHhHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCeeeHHHHHHHHhhccCc
Confidence            667999999999999996    222111 112 34578888775544432          2368999999999984    


Q ss_pred             ----------------CChhhHHHHHHHHhHhcCCcEEEecCCCCEEEEEee
Q 031323          122 ----------------TNVRELEDFLINECMYTGIVRGKLDQLRRCFEVCTV  157 (161)
Q Consensus       122 ----------------~~~~evE~lvI~~ai~~gLi~gkIDq~~~~v~V~~~  157 (161)
                                      .+.+|||-++. .+|+.|+|+|+||+.++++.+++.
T Consensus       379 ~~~~~~~~~~~~~~~~~~~devEcIlA-~LI~~G~IkGyIsh~~~~lVlSK~  429 (455)
T 3t5v_B          379 TFEDPGAQEITIYNGIHSPKNVENVLV-TLINLGLLRANCFPQLQLCVVKKT  429 (455)
T ss_dssp             CTTSTTCCCCCTTTSSCCSSCHHHHHH-HHHHHTSCCEEEETTTTEEEECCC
T ss_pred             cccccccccccccccCCCHHHHHHHHH-HHHHcCCeEEEEecCCCEEEECCC
Confidence                            14889999999 999999999999999999998875

>4b4t_S RPN3, 26S proteasome regulatory subunit RPN3; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=97.87  E-value=8.4e-06  Score=72.18  Aligned_cols=94  Identities=12%  Similarity=0.232  Sum_probs=69.7

Q ss_pred             hhHHHHHHHHhcCCHhHHhh----ccCCC-CCCCHHHHHHHHHH----HHHHhhhcCCccCHHHHHHhcCCCChhhHHHH
Q 031323           60 SKYLDMLRLFAHGTWSDYKN----NAGHL-PQLVPDQVLKLKQL----TVLTLAETNKVLPYDELMEELDVTNVRELEDF  130 (161)
Q Consensus        60 ~~l~~LL~iF~~G~~~dy~~----~~~~~-~~L~~~~~~KlrlL----tL~sLa~~~~~isy~~I~~~l~i~~~~evE~l  130 (161)
                      .++++|...|..|++..|.+    |...+ .+=+-..+.|+|.-    -+..+......||+++|+..+++++.+++|.+
T Consensus       343 ~pY~~Lv~Avr~GdL~~F~~~L~~h~~~F~~Dgty~LI~rLr~~vir~~irkis~~YsrIsL~dIa~kL~L~s~eeaE~i  422 (523)
T 4b4t_S          343 LPYYHLTKAVKLGDLKKFTSTITKYKQLLLKDDTYQLCVRLRSNVIKTGIRIISLTYKKISLRDICLKLNLDSEQTVEYM  422 (523)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHTHHHHHHTTCTHHHHHHHHHHHHHHHHHSCCCSSEECHHHHHHHHHHHHSSCHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHhcceeccCChhHHHHHHHHHHHHHHHHHHHHHHhcccHHHHHHHhCCCCHHHHHHH
Confidence            45889999999999999996    22111 11112234444433    23334445678999999999999878899999


Q ss_pred             HHHHhHhcCCcEEEecCCCCEEEE
Q 031323          131 LINECMYTGIVRGKLDQLRRCFEV  154 (161)
Q Consensus       131 vI~~ai~~gLi~gkIDq~~~~v~V  154 (161)
                      |- +||..|.|+|+||+.+|.|.-
T Consensus       423 VA-kmI~dG~I~A~Idh~~g~v~s  445 (523)
T 4b4t_S          423 VS-RAIRDGVIEAKINHEDGFIET  445 (523)
T ss_dssp             HH-HHHHHTSSCCEECTTTCCEEC
T ss_pred             HH-HHHHcCCceEEEecCCCEEEe
Confidence            99 999999999999999997753

>1wi9_A Protein C20ORF116 homolog; helix-turn-helix motif, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Mus musculus} SCOP: a.4.5.47

Probab=94.52  E-value=0.089  Score=34.58  Aligned_cols=55  Identities=11%  Similarity=0.273  Sum_probs=46.4

Q ss_pred             HHHhhhcCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEEecCCCCEEEEEe
Q 031323          100 VLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVCT  156 (161)
Q Consensus       100 L~sLa~~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gkIDq~~~~v~V~~  156 (161)
                      +++....++.++.+++|.++++. ..++-+-+- +....|-+.|-||...+=++|+.
T Consensus        12 Fi~yIk~~Kvv~LedLA~~F~l~-t~~~i~RI~-~Le~~g~ltGViDDRGKfIyIs~   66 (72)
T 1wi9_A           12 FINYIKKSKVVLLEDLAFQMGLR-TQDAINRIQ-DLLTEGTLTGVIDDRGKFIYITP   66 (72)
T ss_dssp             HHHHHHHCSEECHHHHHHHHCSC-HHHHHHHHH-HHHHHSSSCEEECTTCCEEECCC
T ss_pred             HHHHHHHcCeeeHHHHHHHhCCC-hHHHHHHHH-HHHHCCCeEEEEeCCCCEEEecH
Confidence            45566678999999999999999 666656566 88899999999999999998874

>4b0z_A RPN12, 26S proteasome regulatory subunit RPN12; protein binding, proteasome ubitquitin; HET: SGM GOL; 1.58A {Schizosaccharomyces pombe}

Probab=93.92  E-value=0.12  Score=40.63  Aligned_cols=74  Identities=9%  Similarity=0.059  Sum_probs=59.0

Q ss_pred             hhHHHHHHHHhcCCHhHHhhccCCCCCC-----CHHHHHHHHHHHHHHhhhcCCccCHHHHHHhcCCCChhhHHHHHHHH
Q 031323           60 SKYLDMLRLFAHGTWSDYKNNAGHLPQL-----VPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINE  134 (161)
Q Consensus        60 ~~l~~LL~iF~~G~~~dy~~~~~~~~~L-----~~~~~~KlrlLtL~sLa~~~~~isy~~I~~~l~i~~~~evE~lvI~~  134 (161)
                      ...+++-+.+..|++..|.+.....|..     -+....++|.-.+-.++.....||.+++++.|+++|.++++.++- +
T Consensus       136 ~~al~l~~al~~GnY~kff~l~~~~p~~~~~~~~~~l~~~vR~~~l~~i~kaY~~i~l~~~~~~L~f~s~~e~~~f~~-~  214 (229)
T 4b0z_A          136 EWVISLEQNVMEGAFDKVASMIRSCNFPEFSYFMKIVMSMVRNEIATCAEKVYSEIPLSNATSLLYLENTKETEKLAE-E  214 (229)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHTCCCGGGHHHHHHHHHHHHHHHHHHHHHHCSEEEHHHHHHHTTCSSHHHHHHHHH-H
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHhcCccchHHHHHHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHhCCCCHHHHHHHHH-H
Confidence            3457888899999999998643333322     244578899888888888888999999999999998999999987 6

>1qgp_A Protein (double stranded RNA adenosine deaminase); Z-alpha-Z-DNA binding domain, RNA-editing, Z-DNA recognition, ADAR1, helix- turn-helix; NMR {Homo sapiens} SCOP: a.4.5.19

Probab=90.99  E-value=0.6  Score=30.40  Aligned_cols=49  Identities=16%  Similarity=0.186  Sum_probs=39.6

Q ss_pred             HHHHHHHHhhhcCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEEe
Q 031323           95 LKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKL  145 (161)
Q Consensus        95 lrlLtL~sLa~~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gkI  145 (161)
                      .++|.++.-...+..+|+.+||+.++++ ...|...+= +....|+|.+.-
T Consensus        17 ~~IL~~L~~~~~~~~~t~~eLA~~Lgvs-~~tV~~~L~-~L~~~G~I~~~g   65 (77)
T 1qgp_A           17 QRILKFLEELGEGKATTAHDLSGKLGTP-KKEINRVLY-SLAKKGKLQKEA   65 (77)
T ss_dssp             HHHHHHHHHHCSSSCEEHHHHHHHHCCC-HHHHHHHHH-HHHHHTSEEEEC
T ss_pred             HHHHHHHHHcCCCCCcCHHHHHHHHCcC-HHHHHHHHH-HHHHCCCEEecC
Confidence            4455555544445689999999999999 899999877 888999998874

>1qbj_A Protein (double-stranded RNA specific adenosine D (ADAR1)); protein-Z-DNA complex, hydrolase-DNA complex; HET: DNA; 2.10A {Homo sapiens} SCOP: a.4.5.19 PDB: 3f21_A* 3f22_A* 3f23_A* 3irr_A* 3irq_D* 2gxb_A 2acj_A 2l54_A

Probab=90.38  E-value=1.2  Score=29.45  Aligned_cols=58  Identities=14%  Similarity=0.183  Sum_probs=41.6

Q ss_pred             HHHHHHHHHhhhcCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEEecCCCCEEEE
Q 031323           94 KLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEV  154 (161)
Q Consensus        94 KlrlLtL~sLa~~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gkIDq~~~~v~V  154 (161)
                      ..++|.++.-...+..+++.+||+.|+++ ...|...+- +....|+|.-. ....+.-.|
T Consensus        12 ~~~IL~~L~~~~pg~~~t~~eLA~~Lgvs-r~tV~~~L~-~Le~~G~I~~~-g~~~~~W~i   69 (81)
T 1qbj_A           12 EQRILKFLEELGEGKATTAHDLSGKLGTP-KKEINRVLY-SLAKKGKLQKE-AGTPPLWKI   69 (81)
T ss_dssp             HHHHHHHHHHHCTTCCBCHHHHHHHHTCC-HHHHHHHHH-HHHHTTSEEEE-SSSSCEEEE
T ss_pred             HHHHHHHHHHcCCCCCcCHHHHHHHHCcC-HHHHHHHHH-HHHHCCCEEec-CCCCCeeEE
Confidence            34455555533234589999999999999 899999988 99999999643 343444443

>3lwf_A LIN1550 protein, putative transcriptional regulator; structural genomics, JOI for structural genomics, JCSG; HET: SO4; 2.06A {Listeria innocua}

Probab=87.57  E-value=1.4  Score=32.66  Aligned_cols=46  Identities=17%  Similarity=0.252  Sum_probs=37.0

Q ss_pred             HHHHHHhhh--cCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEE
Q 031323           97 QLTVLTLAE--TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGK  144 (161)
Q Consensus        97 lLtL~sLa~--~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gk  144 (161)
                      +-.|+-||.  +++.+|-++||+.++++ ..-|++.+- +.-.+|+|..+
T Consensus        30 lr~L~~LA~~~~~~~~s~~eIA~~~~i~-~~~l~kil~-~L~~aGlv~s~   77 (159)
T 3lwf_A           30 LTITLELAKRIGDGPISLRSIAQDKNLS-EHYLEQLIG-PLRNAGIVKSI   77 (159)
T ss_dssp             HHHHHHHHHTTTSCCBCHHHHHHHHTCC-HHHHHHHHH-HHHHTTSEEEE
T ss_pred             HHHHHHHHhcCCCCCcCHHHHHHHHCcC-HHHHHHHHH-HHHHCCeEEEe
Confidence            333444443  45679999999999999 999999988 99999999865

>2hzt_A Putative HTH-type transcriptional regulator YTCD; DNA-binding protein, HTH-type transcription regulators, structural genomics, PSI-2; HET: CSU MSE; 2.00A {Bacillus subtilis} SCOP: a.4.5.69

Probab=87.31  E-value=2.7  Score=28.37  Aligned_cols=50  Identities=14%  Similarity=0.025  Sum_probs=39.9

Q ss_pred             CCccCHHHHHHhc-CCCChhhHHHHHHHHhHhcCCcEEEecCCCCEEEEEeee
Q 031323          107 NKVLPYDELMEEL-DVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVCTVL  158 (161)
Q Consensus       107 ~~~isy~~I~~~l-~i~~~~evE~lvI~~ai~~gLi~gkIDq~~~~v~V~~~~  158 (161)
                      .+..++.+|++.+ +++ ...+=..+= +....|+|+.+-+...+....-..+
T Consensus        25 ~~~~~~~eLa~~l~~is-~~tls~~L~-~Le~~GlI~r~~~~~d~r~~~y~LT   75 (107)
T 2hzt_A           25 HGKKRTSELKRLMPNIT-QKMLTQQLR-ELEADGVINRIVYNQVPPKVEYELS   75 (107)
T ss_dssp             TCCBCHHHHHHHCTTSC-HHHHHHHHH-HHHHTTSEEEEEECSSSCEEEEEEC
T ss_pred             hCCCCHHHHHHHhcCCC-HHHHHHHHH-HHHHCCCEEEeecCCCCCeEEEEEC
Confidence            3579999999999 998 888888766 8899999999998776654444443

>2y75_A HTH-type transcriptional regulator CYMR; DNA binding protein; 2.00A {Bacillus subtilis}

Probab=86.99  E-value=1.5  Score=30.63  Aligned_cols=48  Identities=13%  Similarity=0.167  Sum_probs=37.5

Q ss_pred             HHHHHHHHhhhcCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEE
Q 031323           95 LKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGK  144 (161)
Q Consensus        95 lrlLtL~sLa~~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gk  144 (161)
                      ++.|..+.-..+++.+|-.+||+.++++ ...|+..+- .....|+|+.+
T Consensus        12 l~iL~~la~~~~~~~~s~~ela~~~~i~-~~~v~~il~-~L~~~Glv~~~   59 (129)
T 2y75_A           12 LTIMIELAKKHGEGPTSLKSIAQTNNLS-EHYLEQLVS-PLRNAGLVKSI   59 (129)
T ss_dssp             HHHHHHHHHTTTSCCBCHHHHHHHTTSC-HHHHHHHHH-HHHHTTSEEEC
T ss_pred             HHHHHHHHhCCCCCcCCHHHHHHHHCcC-HHHHHHHHH-HHHHCCceEec
Confidence            4444444333345789999999999999 999999888 99999998753

>3t8r_A Staphylococcus aureus CYMR; transcriptional regulator protein, dimer, sulfenic acid, UNK function; 1.70A {Staphylococcus aureus} PDB: 3t8t_A

Probab=86.83  E-value=1.1  Score=32.35  Aligned_cols=44  Identities=18%  Similarity=0.288  Sum_probs=35.8

Q ss_pred             HHHHhhh--cCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEE
Q 031323           99 TVLTLAE--TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGK  144 (161)
Q Consensus        99 tL~sLa~--~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gk  144 (161)
                      .|+-|+.  +++.+|-++||+.++++ ...|+..+- +.-.+|+|+.+
T Consensus        16 ~L~~La~~~~~~~~s~~~IA~~~~i~-~~~l~kil~-~L~~aGlv~s~   61 (143)
T 3t8r_A           16 LMISLAKKEGQGCISLKSIAEENNLS-DLYLEQLVG-PLRNAGLIRSV   61 (143)
T ss_dssp             HHHHHHTTTTSCCEEHHHHHHHTTCC-HHHHHHHHH-HHHHTTSEEEC
T ss_pred             HHHHHHhCCCCCCcCHHHHHHHHCcC-HHHHHHHHH-HHHHCCEEEec
Confidence            3444443  34579999999999999 999999988 99999998864

>1xn7_A Hypothetical protein YHGG; alpha+beta, GFT structural genomics, protein structure initiative, PSI, NESG; NMR {Escherichia coli} SCOP: a.4.5.62

Probab=84.49  E-value=2  Score=28.08  Aligned_cols=44  Identities=11%  Similarity=0.100  Sum_probs=36.9

Q ss_pred             HHHHHHhhhcCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcE
Q 031323           97 QLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVR  142 (161)
Q Consensus        97 lLtL~sLa~~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~  142 (161)
                      +..|+++...++.++.++|++.++++ ...|..-+- +....|++.
T Consensus         4 L~~Il~~L~~~g~vsv~eLa~~l~VS-~~TIRrdL~-~Le~~G~l~   47 (78)
T 1xn7_A            4 LIQVRDLLALRGRMEAAQISQTLNTP-QPMINAMLQ-QLESMGKAV   47 (78)
T ss_dssp             HHHHHHHHHHSCSBCHHHHHHHTTCC-HHHHHHHHH-HHHHHTSEE
T ss_pred             HHHHHHHHHHcCCCcHHHHHHHHCcC-HHHHHHHHH-HHHHCCCEE
Confidence            34456666678899999999999998 999999888 888899874

>3cuo_A Uncharacterized HTH-type transcriptional regulato; DNA-binding transcriptional regulator, structural genomics, MCSG; 2.00A {Escherichia coli K12}

Probab=84.39  E-value=4  Score=26.33  Aligned_cols=42  Identities=12%  Similarity=0.101  Sum_probs=35.0

Q ss_pred             hcCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEEecCC
Q 031323          105 ETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQL  148 (161)
Q Consensus       105 ~~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gkIDq~  148 (161)
                      ..++.++..+|++.++++ ...|-..+= .....|+|...-+..
T Consensus        34 ~~~~~~s~~ela~~l~is-~~tvs~~l~-~L~~~glv~~~~~~r   75 (99)
T 3cuo_A           34 SGSPGTSAGELTRITGLS-ASATSQHLA-RMRDEGLIDSQRDAQ   75 (99)
T ss_dssp             TTCCSEEHHHHHHHHCCC-HHHHHHHHH-HHHHTTSEEEEECSS
T ss_pred             HhCCCcCHHHHHHHHCcC-HHHHHHHHH-HHHHCCCEEEEecCC
Confidence            345689999999999998 888988877 888999998876543

>1oyi_A Double-stranded RNA-binding protein; (alpha+beta) helix-turn-helix, viral protein; NMR {Vaccinia virus} SCOP: a.4.5.19

Probab=84.32  E-value=1.5  Score=29.22  Aligned_cols=46  Identities=13%  Similarity=0.204  Sum_probs=37.6

Q ss_pred             HHHHHHHHHHHhhhcCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEE
Q 031323           92 VLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRG  143 (161)
Q Consensus        92 ~~KlrlLtL~sLa~~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~g  143 (161)
                      -.+.++|.++.  .++  +|+.+||++++++ ...|-..+- +.-..|+|.-
T Consensus        17 ~~~~~IL~lL~--~~g--~sa~eLAk~LgiS-k~aVr~~L~-~Le~eG~I~~   62 (82)
T 1oyi_A           17 EIVCEAIKTIG--IEG--ATAAQLTRQLNME-KREVNKALY-DLQRSAMVYS   62 (82)
T ss_dssp             HHHHHHHHHHS--SST--EEHHHHHHHSSSC-HHHHHHHHH-HHHHHTSSEE
T ss_pred             HHHHHHHHHHH--HcC--CCHHHHHHHHCcC-HHHHHHHHH-HHHHCCCEEe
Confidence            35667777766  333  9999999999998 899999888 8889999875

>2heo_A Z-DNA binding protein 1; protein DLM1-Z-DNA complex, immune system-DNA complex; 1.70A {Mus musculus} PDB: 1j75_A

Probab=83.84  E-value=2.4  Score=26.54  Aligned_cols=46  Identities=20%  Similarity=0.221  Sum_probs=35.9

Q ss_pred             HHHHHHHHHhhhcCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEE
Q 031323           94 KLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRG  143 (161)
Q Consensus        94 KlrlLtL~sLa~~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~g  143 (161)
                      +.++|.++.  .+++.+|..+||+.++++ ...|...+= ..-..|+|..
T Consensus        12 ~~~IL~~L~--~~~~~~s~~eLA~~lgls-r~tv~~~l~-~L~~~G~I~~   57 (67)
T 2heo_A           12 EQKILQVLS--DDGGPVAIFQLVKKCQVP-KKTLNQVLY-RLKKEDRVSS   57 (67)
T ss_dssp             HHHHHHHHH--HHCSCEEHHHHHHHHCSC-HHHHHHHHH-HHHHTTSEEE
T ss_pred             HHHHHHHHH--HcCCCcCHHHHHHHHCcC-HHHHHHHHH-HHHHCCcEec
Confidence            444555553  345679999999999999 999999876 8888899754

>2v79_A DNA replication protein DNAD; primosome, DNA-binding protein; HET: DNA; 2.00A {Bacillus subtilis}

Probab=82.79  E-value=6.2  Score=28.24  Aligned_cols=62  Identities=19%  Similarity=0.127  Sum_probs=46.2

Q ss_pred             HHHHHHHHHhhhcC-CccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEE--EecCCCCEEEEEee
Q 031323           94 KLKQLTVLTLAETN-KVLPYDELMEELDVTNVRELEDFLINECMYTGIVRG--KLDQLRRCFEVCTV  157 (161)
Q Consensus        94 KlrlLtL~sLa~~~-~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~g--kIDq~~~~v~V~~~  157 (161)
                      =+-+|-|......+ .-.|.++||+.++++ ..+|...+= ..+..|+|+-  +.|..++....-+.
T Consensus        35 ~~lLl~L~~~~~~g~~~ps~~~LA~~~~~s-~~~v~~~L~-~L~~KGlI~i~~~~d~~g~~~~~ydL   99 (135)
T 2v79_A           35 LILLLKIKMHLEKGSYFPTPNQLQEGMSIS-VEECTNRLR-MFIQKGFLFIEECEDQNGIKFEKYSL   99 (135)
T ss_dssp             HHHHHHHHHHHTTTCCSCCHHHHHTTSSSC-HHHHHHHHH-HHHHHTSCEEEEEECTTCCEEEEEEC
T ss_pred             HHHHHHHHHHHhcCCCCCCHHHHHHHHCcC-HHHHHHHHH-HHHHCCCEEEEeEecCCCceEEEeeH
Confidence            34455555554443 568999999999998 999999888 9999999987  66776655544443

>1sfx_A Conserved hypothetical protein AF2008; structural genomics, HTH MOT protein structure initiative, midwest center for structural genomics; 1.55A {Archaeoglobus fulgidus} SCOP: a.4.5.50

Probab=82.51  E-value=5  Score=25.93  Aligned_cols=38  Identities=26%  Similarity=0.350  Sum_probs=34.1

Q ss_pred             CccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEEecC
Q 031323          108 KVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQ  147 (161)
Q Consensus       108 ~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gkIDq  147 (161)
                      ..++..+|++.++++ ...|-..+= .....|+|...-+.
T Consensus        33 ~~~s~~ela~~l~is-~~tv~~~l~-~L~~~glv~~~~~~   70 (109)
T 1sfx_A           33 GGMRVSEIARELDLS-ARFVRDRLK-VLLKRGFVRREIVE   70 (109)
T ss_dssp             CCBCHHHHHHHHTCC-HHHHHHHHH-HHHHTTSEEEEEEE
T ss_pred             CCCCHHHHHHHHCCC-HHHHHHHHH-HHHHCCCEEEEeec
Confidence            469999999999998 999999877 99999999988776

>1z7u_A Hypothetical protein EF0647; winged-helix-turn-helix, MARR, structural genomics, PSI, Pro structure initiative; 2.20A {Enterococcus faecalis} SCOP: a.4.5.69

Probab=80.88  E-value=5.9  Score=26.79  Aligned_cols=49  Identities=27%  Similarity=0.123  Sum_probs=39.6

Q ss_pred             CccCHHHHHHhc-CCCChhhHHHHHHHHhHhcCCcEEEecCCCCEEEEEeee
Q 031323          108 KVLPYDELMEEL-DVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVCTVL  158 (161)
Q Consensus       108 ~~isy~~I~~~l-~i~~~~evE~lvI~~ai~~gLi~gkIDq~~~~v~V~~~~  158 (161)
                      +.+++.+|++.+ +++ ...|=..+= +....|+|+.+-+...+....-..+
T Consensus        34 ~~~~~~eLa~~l~~is-~~tvs~~L~-~Le~~GlI~r~~~~~d~r~~~~~LT   83 (112)
T 1z7u_A           34 GTKRNGELMRALDGIT-QRVLTDRLR-EMEKDGLVHRESFNELPPRVEYTLT   83 (112)
T ss_dssp             SCBCHHHHHHHSTTCC-HHHHHHHHH-HHHHHTSEEEEEECCSSCEEEEEEC
T ss_pred             CCCCHHHHHHHhccCC-HHHHHHHHH-HHHHCCCEEEeecCCCCCeEEEEEC
Confidence            468999999999 998 888888777 8999999999998766554444433

>1ylf_A RRF2 family protein; structural genomics, transcription regulator, P protein structure initiative; 2.50A {Bacillus cereus atcc 14579} SCOP: a.4.5.55

Probab=80.77  E-value=2.7  Score=30.24  Aligned_cols=43  Identities=12%  Similarity=0.123  Sum_probs=35.3

Q ss_pred             HHHhhh-cCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEE
Q 031323          100 VLTLAE-TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGK  144 (161)
Q Consensus       100 L~sLa~-~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gk  144 (161)
                      |+.|+. .++.++-++||+.++++ ...|++.+- ..-..|+|+.+
T Consensus        20 L~~La~~~~~~~~~~~iA~~~~i~-~~~l~kil~-~L~~~Glv~s~   63 (149)
T 1ylf_A           20 LSILKNNPSSLCTSDYMAESVNTN-PVVIRKIMS-YLKQAGFVYVN   63 (149)
T ss_dssp             HHHHHHSCGGGCCHHHHHHHHTSC-HHHHHHHHH-HHHHTTSEEEC
T ss_pred             HHHHHhCCCCCcCHHHHHHHHCcC-HHHHHHHHH-HHHHCCcEEEc
Confidence            333443 34679999999999999 999999988 99999998854

>2p5v_A Transcriptional regulator, LRP/ASNC family; NMB0573, structu genomics; 1.99A {Neisseria meningitidis} PDB: 2p6s_A 2p6t_A

Probab=80.74  E-value=3.6  Score=29.68  Aligned_cols=36  Identities=28%  Similarity=0.194  Sum_probs=31.8

Q ss_pred             cCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEE
Q 031323          106 TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRG  143 (161)
Q Consensus       106 ~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~g  143 (161)
                      .+..+|+.+||+.++++ ...|-..+- +....|+|++
T Consensus        21 ~~~~~s~~ela~~lg~s-~~tv~~~l~-~L~~~G~i~~   56 (162)
T 2p5v_A           21 ENGRLTNVELSERVALS-PSPCLRRLK-QLEDAGIVRQ   56 (162)
T ss_dssp             HCTTCCHHHHHHHHTSC-HHHHHHHHH-HHHHTTSEEE
T ss_pred             HcCCCCHHHHHHHHCcC-HHHHHHHHH-HHHHCCCEee
Confidence            44569999999999998 999998888 9999999986

>1xd7_A YWNA; structural genomics, protein structure initiative, winged HE binding, hypothetical protein, PSI; 2.30A {Bacillus subtilis subsp} SCOP: a.4.5.55

Probab=80.63  E-value=3.1  Score=29.80  Aligned_cols=45  Identities=4%  Similarity=0.065  Sum_probs=35.6

Q ss_pred             HHHHHHhhhcCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEE
Q 031323           97 QLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGK  144 (161)
Q Consensus        97 lLtL~sLa~~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gk  144 (161)
                      +..|+.||..... |-++||+.+++| ..-+++++- +.-.+|||+..
T Consensus        12 l~~L~~La~~~~~-s~~~IA~~~~i~-~~~l~kIl~-~L~~aGlv~s~   56 (145)
T 1xd7_A           12 IHILSLISMDEKT-SSEIIADSVNTN-PVVVRRMIS-LLKKADILTSR   56 (145)
T ss_dssp             HHHHHHHHTCSCC-CHHHHHHHHTSC-HHHHHHHHH-HHHHTTSEECC
T ss_pred             HHHHHHHHhCCCC-CHHHHHHHHCcC-HHHHHHHHH-HHHHCCceEee
Confidence            3444555543234 999999999999 999999998 99999999754

>3k69_A Putative transcription regulator; putative transcriptional regulator, structural genomics, JOI for structural genomics, JCSG; HET: MSE; 1.95A {Lactobacillus plantarum} SCOP: a.4.5.0

Probab=80.47  E-value=4  Score=30.04  Aligned_cols=36  Identities=17%  Similarity=0.241  Sum_probs=32.5

Q ss_pred             CCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEE
Q 031323          107 NKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGK  144 (161)
Q Consensus       107 ~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gk  144 (161)
                      ++.+|-++||+.++++ ..-|+..+- +.-.+|+|+.+
T Consensus        26 ~~~~s~~~IA~~~~is-~~~l~kil~-~L~~aGlv~s~   61 (162)
T 3k69_A           26 DSKVASRELAQSLHLN-PVMIRNILS-VLHKHGYLTGT   61 (162)
T ss_dssp             TSCBCHHHHHHHHTSC-GGGTHHHHH-HHHHTTSSEEE
T ss_pred             CCCcCHHHHHHHHCcC-HHHHHHHHH-HHHHCCCEEee
Confidence            5679999999999999 999999888 99999999764

>2pg4_A Uncharacterized protein; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2, DNA binding protein; HET: MSE CIT; 2.21A {Aeropyrum pernix} SCOP: a.4.5.48

Probab=80.26  E-value=2.6  Score=27.54  Aligned_cols=45  Identities=13%  Similarity=0.187  Sum_probs=33.9

Q ss_pred             HHHHHHHh-hhcCCccCHHHHHHhcCCCChhh-HHHHHHHHhHhcCCcE
Q 031323           96 KQLTVLTL-AETNKVLPYDELMEELDVTNVRE-LEDFLINECMYTGIVR  142 (161)
Q Consensus        96 rlLtL~sL-a~~~~~isy~~I~~~l~i~~~~e-vE~lvI~~ai~~gLi~  142 (161)
                      |.+.++.. ...+..++..+|++.++++ ... |=..+= +....|+|.
T Consensus        16 ~~l~~L~~l~~~~~~~t~~eLa~~l~is-~~t~vs~~l~-~Le~~Glv~   62 (95)
T 2pg4_A           16 RILPTLLEFEKKGYEPSLAEIVKASGVS-EKTFFMGLKD-RLIRAGLVK   62 (95)
T ss_dssp             HHHHHHHHHHHTTCCCCHHHHHHHHCCC-HHHHHTTHHH-HHHHTTSEE
T ss_pred             HHHHHHHHHHhcCCCCCHHHHHHHHCCC-chHHHHHHHH-HHHHCCCee
Confidence            33443333 3344479999999999998 888 877766 888999999

>1yyv_A Putative transcriptional regulator; reductive methylation, D lysine, structural genomics, PSI; HET: MLY; 2.35A {Salmonella typhimurium} SCOP: a.4.5.69

Probab=80.18  E-value=6.5  Score=27.68  Aligned_cols=61  Identities=11%  Similarity=0.097  Sum_probs=44.0

Q ss_pred             HHHHHHHHHHhhhcCCccCHHHHHHhc-CCCChhhHHHHHHHHhHhcCCcEEEecCCCCEEEEEee
Q 031323           93 LKLKQLTVLTLAETNKVLPYDELMEEL-DVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVCTV  157 (161)
Q Consensus        93 ~KlrlLtL~sLa~~~~~isy~~I~~~l-~i~~~~evE~lvI~~ai~~gLi~gkIDq~~~~v~V~~~  157 (161)
                      .|.+.+-|..|.  .+..+|.+|++.+ +++ ..-+=..+= +....|+|+-+-+...+....-+.
T Consensus        34 ~~w~l~IL~~L~--~g~~~~~eLa~~l~gis-~~tls~~L~-~Le~~GlV~r~~~~~d~r~~~y~L   95 (131)
T 1yyv_A           34 SRWGVLILVALR--DGTHRFSDLRRXMGGVS-EXMLAQSLQ-ALEQDGFLNRVSYPVVPPHVEYSL   95 (131)
T ss_dssp             SHHHHHHHHHGG--GCCEEHHHHHHHSTTCC-HHHHHHHHH-HHHHHTCEEEEEECSSSCEEEEEE
T ss_pred             CCcHHHHHHHHH--cCCCCHHHHHHHhccCC-HHHHHHHHH-HHHHCCcEEEEecCCCCCeEEEEE
Confidence            344444444454  3579999999999 698 888888777 888999999998876655444433

---

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	161
d1ufma_	84	COP9 signalosome complex subunit 4, GSN4 {Mouse (M	98.58
d1wi9a_	72	Hypothetical protein C20orf116 homolog {Mouse (Mus	93.23
d2cfxa1	63	Transcriptional regulator LrpC {Bacillus subtilis	93.14
d2cg4a1	63	Regulatory protein AsnC {Escherichia coli [TaxId:	93.08
d2cyya1	60	Putative transcriptional regulator PH1519 {Archaeo	92.6
d1i1ga1	60	LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}	92.46
d1z05a1	71	Transcriptional regulator VC2007 N-terminal domain	90.1
d1ub9a_	100	Hypothetical protein PH1061 {Archaeon Pyrococcus h	85.5
d1mkma1	75	Transcriptional regulator IclR, N-terminal domain	84.49
d1jhfa1	71	LexA repressor, N-terminal DNA-binding domain {Esc	84.31
d1biaa1	63	Biotin repressor, N-terminal domain {Escherichia c	81.72
d1l0oc_	57	SigmaF {Bacillus stearothermophilus [TaxId: 1422]}	80.67
d3ctaa1	85	Ta1064 (RFK), N-terminal domain {Thermoplasma acid	80.6

>d1ufma_ a.4.5.47 (A:) COP9 signalosome complex subunit 4, GSN4 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: PCI domain (PINT motif)
domain: COP9 signalosome complex subunit 4, GSN4
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.58  E-value=7.1e-08  Score=64.39  Aligned_cols=62  Identities=16%  Similarity=0.252  Sum_probs=54.3

Q ss_pred             HHHHHHHHHHhhhcCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEEecCCCCEEEEEe
Q 031323           93 LKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVCT  156 (161)
Q Consensus        93 ~KlrlLtL~sLa~~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gkIDq~~~~v~V~~  156 (161)
                      +.++...+..++.-...|+++.+++.++++ .+++|.++. ++|..|-|.|+|||.+++|+...
T Consensus        14 ~~i~Ehni~~is~~Y~~Isl~~la~~l~l~-~~evE~~l~-~mI~~~~i~akIDq~~g~V~F~~   75 (84)
T d1ufma_          14 RAVIEHNLLSASKLYNNITFEELGALLEIP-AAKAEKIAS-QMITEGRMNGFIDQIDGIVHFET   75 (84)
T ss_dssp             HHHHHHHHHHHHHSCSEEEHHHHHHHTTSC-HHHHHHHHH-HHHHTTSSCEEEETTTTEEEECC
T ss_pred             HHHHHHHHHHHHHhhceeeHHHHHHHHCCC-HHHHHHHHH-HHHhcCeEEEEEeCCCCEEEECC
Confidence            344555556677778899999999999998 999999999 99999999999999999998765

>d1wi9a_ a.4.5.47 (A:) Hypothetical protein C20orf116 homolog {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: PCI domain (PINT motif)
domain: Hypothetical protein C20orf116 homolog
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=93.23  E-value=0.11  Score=32.44  Aligned_cols=58  Identities=10%  Similarity=0.224  Sum_probs=46.3

Q ss_pred             HHHhhhcCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEEecCCCCEEEEEeeec
Q 031323          100 VLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVCTVLV  159 (161)
Q Consensus       100 L~sLa~~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gkIDq~~~~v~V~~~~~  159 (161)
                      ++......+.+..+++|.+.++...+-+ +-+- +....|.|.|-||...+-++|+-.-|
T Consensus        12 FI~~Ik~~Kvv~LedLAa~F~lktqd~i-~RIq-~Le~~g~ltGViDDRGKfIyIS~s~~   69 (72)
T d1wi9a_          12 FINYIKKSKVVLLEDLAFQMGLRTQDAI-NRIQ-DLLTEGTLTGVIDDRGKFIYITPSGP   69 (72)
T ss_dssp             HHHHHHHCSEECHHHHHHHHCSCHHHHH-HHHH-HHHHHSSSCEEECTTCCEEECCCSSC
T ss_pred             HHHHHHHCCEeeHHHHHHHcCCcHHHHH-HHHH-HHHHCCCeeeEEcCCCCEEEEcCCCC
Confidence            3445557899999999999999844444 4455 78889999999999999999986544

>d2cfxa1 a.4.5.32 (A:1-63) Transcriptional regulator LrpC {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: Transcriptional regulator LrpC
species: Bacillus subtilis [TaxId: 1423]

Probab=93.14  E-value=0.084  Score=31.81  Aligned_cols=36  Identities=14%  Similarity=0.226  Sum_probs=32.5

Q ss_pred             cCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEE
Q 031323          106 TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRG  143 (161)
Q Consensus       106 ~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~g  143 (161)
                      .+..+||.+||+.++++ ...|..-+= +....|+|+|
T Consensus        16 ~n~r~s~~~iA~~lgis-~~tv~~Ri~-~L~~~giI~~   51 (63)
T d2cfxa1          16 KDSRLSMRELGRKIKLS-PPSVTERVR-QLESFGIIKQ   51 (63)
T ss_dssp             HCSCCCHHHHHHHHTCC-HHHHHHHHH-HHHHTTSEEE
T ss_pred             HcCCCCHHHHHHHHCcC-HHHHHHHHH-HHHHCCCeee
Confidence            45678999999999999 999999887 9999999987

>d2cg4a1 a.4.5.32 (A:4-66) Regulatory protein AsnC {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: Regulatory protein AsnC
species: Escherichia coli [TaxId: 562]

Probab=93.08  E-value=0.078  Score=31.89  Aligned_cols=43  Identities=21%  Similarity=0.299  Sum_probs=35.3

Q ss_pred             HHHhhhcCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEE
Q 031323          100 VLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGK  144 (161)
Q Consensus       100 L~sLa~~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gk  144 (161)
                      +++.-..+..+||.+||+.++++ ...|-.-+= +....|+|.|.
T Consensus        10 IL~~L~~~~r~s~~eiA~~l~ls-~~~v~~Ri~-rL~~~GiI~~~   52 (63)
T d2cg4a1          10 ILEALMGNARTAYAELAKQFGVS-PETIHVRVE-KMKQAGIITGA   52 (63)
T ss_dssp             HHHHHHHCTTSCHHHHHHHHTSC-HHHHHHHHH-HHHHHTSEEEE
T ss_pred             HHHHHHHcCCCCHHHHHHHHCcC-HHHHHHHHH-HHHHCCCeEeE
Confidence            33433456788999999999998 999999887 99999999863

>d2cyya1 a.4.5.32 (A:5-64) Putative transcriptional regulator PH1519 {Archaeon Pyrococcus horikoshii [TaxId: 53953]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: Putative transcriptional regulator PH1519
species: Archaeon Pyrococcus horikoshii [TaxId: 53953]

Probab=92.60  E-value=0.082  Score=31.42  Aligned_cols=41  Identities=7%  Similarity=0.238  Sum_probs=33.5

Q ss_pred             HHhhhcCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEE
Q 031323          101 LTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRG  143 (161)
Q Consensus       101 ~sLa~~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~g  143 (161)
                      +..-..+..+||.+||+.++++ ...|..-+= +....|+|.+
T Consensus         9 l~~L~~n~r~s~~eiA~~l~ls-~~~v~~Ri~-~L~~~giI~~   49 (60)
T d2cyya1           9 IKILQNDGKAPLREISKITGLA-ESTIHERIR-KLRESGVIKK   49 (60)
T ss_dssp             HHHHHHCTTCCHHHHHHHHCSC-HHHHHHHHH-HHHHHTSSCC
T ss_pred             HHHHHHcCCCCHHHHHHHHCcC-HHHHHHHHH-HHHHCCCeEe
Confidence            3333456788999999999998 999988876 8889999874

>d1i1ga1 a.4.5.32 (A:2-61) LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: LprA
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=92.46  E-value=0.086  Score=31.43  Aligned_cols=41  Identities=20%  Similarity=0.399  Sum_probs=33.7

Q ss_pred             HHhhhcCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEE
Q 031323          101 LTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRG  143 (161)
Q Consensus       101 ~sLa~~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~g  143 (161)
                      +.+-..+..+||.+||+.++++ ...|-.-+= +....|+|.+
T Consensus         9 l~~L~~n~r~s~~~lA~~~gls-~~~v~~Ri~-~L~~~giI~~   49 (60)
T d1i1ga1           9 LEILEKDARTPFTEIAKKLGIS-ETAVRKRVK-ALEEKGIIEG   49 (60)
T ss_dssp             HHHHHHCTTCCHHHHHHHHTSC-HHHHHHHHH-HHHHHTSSCC
T ss_pred             HHHHHHcCCCCHHHHHHHHCcC-HHHHHHHHH-HHHHCCCeEe
Confidence            3333356789999999999998 999988877 8999999874

>d1z05a1 a.4.5.63 (A:10-80) Transcriptional regulator VC2007 N-terminal domain {Vibrio cholerae [TaxId: 666]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ROK associated domain
domain: Transcriptional regulator VC2007 N-terminal domain
species: Vibrio cholerae [TaxId: 666]

Probab=90.10  E-value=0.3  Score=29.55  Aligned_cols=49  Identities=10%  Similarity=0.173  Sum_probs=39.9

Q ss_pred             HHHHHHHHHHHhhhcCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcE
Q 031323           92 VLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVR  142 (161)
Q Consensus        92 ~~KlrlLtL~sLa~~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~  142 (161)
                      +++...-.++.+...+..+|-.+||+.++++ ...|-..+= +.+..|+|.
T Consensus         3 ir~~N~~~Il~~l~~~g~~sr~eLa~~~glS-~~Tv~~~l~-~L~~~Glv~   51 (71)
T d1z05a1           3 IKQINAGRVYKLIDQKGPISRIDLSKESELA-PASITKITR-ELIDAHLIH   51 (71)
T ss_dssp             HHHHHHHHHHHHHHHHCSBCHHHHHHHHTCC-HHHHHHHHH-HHHHTTSEE
T ss_pred             HHHHHHHHHHHHHHHcCCcCHHHHHHHHCCC-HHHHHHHHH-HHHHCCCEE
Confidence            4455555566666666789999999999998 999999877 999999996

>d1ub9a_ a.4.5.28 (A:) Hypothetical protein PH1061 {Archaeon Pyrococcus horikoshii [TaxId: 53953]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Hypothetical protein PH1061
species: Archaeon Pyrococcus horikoshii [TaxId: 53953]

Probab=85.50  E-value=1.1  Score=28.26  Aligned_cols=50  Identities=18%  Similarity=0.237  Sum_probs=39.6

Q ss_pred             CCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEEecCCCCEEEEEeee
Q 031323          107 NKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVCTVL  158 (161)
Q Consensus       107 ~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gkIDq~~~~v~V~~~~  158 (161)
                      ....++.+|++.++++ ...|=..+= +....|+|+.+-++.++...+-+.+
T Consensus        28 ~~~~~~~eLa~~l~is-~~~vs~~l~-~L~~~glV~~~~~~~d~r~~~~~LT   77 (100)
T d1ub9a_          28 RRKAPFSQIQKVLDLT-PGNLDSHIR-VLERNGLVKTYKVIADRPRTVVEIT   77 (100)
T ss_dssp             HSEEEHHHHHHHTTCC-HHHHHHHHH-HHHHTTSEEEEEECSSSCEEEEEEC
T ss_pred             CCCeeHHHHHHHHhhc-cccccHHHH-HHhhhceeEEEEcCcCCccccccCC
Confidence            4579999999999998 777766554 8888999999988877765555544

>d1mkma1 a.4.5.33 (A:1-75) Transcriptional regulator IclR, N-terminal domain {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Transcriptional regulator IclR, N-terminal domain
domain: Transcriptional regulator IclR, N-terminal domain
species: Thermotoga maritima [TaxId: 2336]

Probab=84.49  E-value=1.3  Score=26.84  Aligned_cols=46  Identities=15%  Similarity=0.298  Sum_probs=37.9

Q ss_pred             HHHHHHHhh-hcCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEE
Q 031323           96 KQLTVLTLA-ETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRG  143 (161)
Q Consensus        96 rlLtL~sLa-~~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~g  143 (161)
                      |-+.+++.. ..++.++..+|++.++++ ...+=.++- .....|++.=
T Consensus         6 r~l~IL~~~a~~~~~~s~~eia~~~~~~-~st~~rll~-tL~~~g~l~~   52 (75)
T d1mkma1           6 KAFEILDFIVKNPGDVSVSEIAEKFNMS-VSNAYKYMV-VLEEKGFVLR   52 (75)
T ss_dssp             HHHHHHHHHHHCSSCBCHHHHHHHTTCC-HHHHHHHHH-HHHHTTSEEE
T ss_pred             HHHHHHHHHHhCCCCCCHHHHHHHHCcC-HHHHHHHHH-HHHHCCCEEE
Confidence            345566544 456789999999999999 999999988 9999999984

>d1jhfa1 a.4.5.2 (A:2-72) LexA repressor, N-terminal DNA-binding domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: LexA repressor, N-terminal DNA-binding domain
domain: LexA repressor, N-terminal DNA-binding domain
species: Escherichia coli [TaxId: 562]

Probab=84.31  E-value=1.2  Score=26.97  Aligned_cols=47  Identities=15%  Similarity=0.148  Sum_probs=36.9

Q ss_pred             cCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEEecCCCCEEEE
Q 031323          106 TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEV  154 (161)
Q Consensus       106 ~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gkIDq~~~~v~V  154 (161)
                      ++..-||.+|++.+|+.|...|-..|- ..-..|+|+=. .-..+.+.|
T Consensus        21 ~G~~Ps~rei~~~~g~~S~stv~~~l~-~Le~kG~I~r~-~~~~R~i~i   67 (71)
T d1jhfa1          21 TGMPPTRAEIAQRLGFRSPNAAEEHLK-ALARKGVIEIV-SGASRGIRL   67 (71)
T ss_dssp             HSSCCCHHHHHHHTTCSSHHHHHHHHH-HHHHTTSEEEC-SSSSSCEEE
T ss_pred             hCCCCCHHHHHHHcCCCCHHHHHHHHH-HHHHCcCeecC-CCCCceeEe
Confidence            578999999999999977899999888 88899998753 333344444

>d1biaa1 a.4.5.1 (A:1-63) Biotin repressor, N-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Biotin repressor-like
domain: Biotin repressor, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=81.72  E-value=2.6  Score=24.73  Aligned_cols=42  Identities=17%  Similarity=0.232  Sum_probs=31.7

Q ss_pred             HHHHHHHHHhhhcCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCC
Q 031323           94 KLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGI  140 (161)
Q Consensus        94 KlrlLtL~sLa~~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gL  140 (161)
                      .+++|.++   .++..+|.+++|+.++++ ...|=.-+- ..-..|+
T Consensus         7 ~~~iL~~L---~~~~~~s~~eLa~~l~vS-~~ti~r~i~-~L~~~G~   48 (63)
T d1biaa1           7 PLKLIALL---ANGEFHSGEQLGETLGMS-RAAINKHIQ-TLRDWGV   48 (63)
T ss_dssp             HHHHHHHH---TTSSCBCHHHHHHHHTSC-HHHHHHHHH-HHHHTTC
T ss_pred             HHHHHHHH---HHCCcCCHHHHHHHHCcC-HHHHHHHHH-HHHHCCC
Confidence            34555555   467889999999999998 777777665 6666776

>d1l0oc_ a.4.13.2 (C:) SigmaF {Bacillus stearothermophilus [TaxId: 1422]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: SigmaF
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=80.67  E-value=1.7  Score=25.17  Aligned_cols=24  Identities=8%  Similarity=0.170  Sum_probs=21.3

Q ss_pred             cCCccCHHHHHHhcCCCChhhHHHH
Q 031323          106 TNKVLPYDELMEELDVTNVRELEDF  130 (161)
Q Consensus       106 ~~~~isy~~I~~~l~i~~~~evE~l  130 (161)
                      .+++-|.++||++|+++ .++|...
T Consensus        28 lgRePT~~EiA~~l~~~-~e~V~~~   51 (57)
T d1l0oc_          28 RGRAPTVTEIADHLGIS-PEDVVLA   51 (57)
T ss_dssp             HTSCCBHHHHHHHHTSC-HHHHHHH
T ss_pred             cCCCCCHHHHHHHHCcC-HHHHHHH
Confidence            58999999999999999 8888664

>d3ctaa1 a.4.5.28 (A:5-89) Ta1064 (RFK), N-terminal domain {Thermoplasma acidophilum [TaxId: 2303]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Ta1064 (RFK), N-terminal domain
species: Thermoplasma acidophilum [TaxId: 2303]

Probab=80.60  E-value=2.3  Score=26.43  Aligned_cols=59  Identities=12%  Similarity=0.238  Sum_probs=43.2

Q ss_pred             HHHHHHHHhhhcCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEEecCCCCEEEEE
Q 031323           95 LKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVC  155 (161)
Q Consensus        95 lrlLtL~sLa~~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gkIDq~~~~v~V~  155 (161)
                      |+.+..+.-.+++..+|..+|++.++++ ...|=.+|= +.-..|+|.=.-|.....+++|
T Consensus         7 l~~l~~~~~~~~~~~lt~~eLa~~l~i~-~~~vs~~l~-~Le~~GlV~r~~D~R~~~i~LT   65 (85)
T d3ctaa1           7 IKKIKEAAEASNRAYLTSSKLADMLGIS-QQSASRIII-DLEKNGYITRTVTKRGQILNIT   65 (85)
T ss_dssp             HHHHHHHTTTSSEEECCHHHHHHHHTSC-HHHHHHHHH-HHHHTTSEEEEEETTEEEEEEC
T ss_pred             HHHHHHhhhccCCCCCCHHHHHHHHCCC-HHHHHHHHH-HHHHCCCeeeecccccccceEC
Confidence            3444444444456789999999999998 888888777 8899999998776544444443