Citrus Sinensis ID: 036949

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80-
Protein Sequence
LYTKRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQQQGWTLDPASRMLTVKKQPLVTEQKLDPSKMQCLTEYVFHLEH
Secondary Structure (PSIPRED)
cHHHHHHHHHHHHHccccHHHHHHHHcccHHHHHHHHHHcccEEccccccEEEcccccccccccccHHHHHHHHHHHHccc
Secondary Structure Prediction (SSPRO)
cHHHHHHHHHHHHHHHccHHHHHHHHcccHHHHHHHHHHcccEEHHHHHHHHHccccccccccccHHHHHHHHHHHHHHHc
Coil and Loop (DISEMBL)
LYTKRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQqqgwtldpasrmltvkkqplvteqkldpskmqcLTEYVFHLEH
Flexible Loop (DISEMBL)
LYTKRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQQQGWTLDPASRMLTVKKQPlvteqkldpskmqCLTEYVFHLEH
Low Complexity Region (SEG)
LYTKRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQQQGWTLDPASRMLTVKKQPLVTEQKLDPSKMQCLTEYVFHLEH
Disordered region (IsUnstruct)
*****MFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQQQGWTLDPASRMLTVK**************MQCLTEYVFH***
Disordered Region (DISOPRED)
*YTKRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQQQGWTLDPASRM*********************LTEYVFHLEH
Disordered Region (DISEMBL)
LYTKRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQQQGWTLDPASRMLTVKKQPLVTEQKLDPSKMQCLTEYVFHLEH
Disordered Region (DISPRO)
LYTKRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQQQGWTLDPASRMLTVKKQPLVTEQKLDPSKMQCLTEYVFHLEH
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
LYTKRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQQQGWTLDPASRMLTVKKQPLVTEQKLDPSKMQCLTEYVFHLEH
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	81	2.2.26 [Sep-21-2011]
P43255	197	COP9 signalosome complex	yes	no	1.0	0.411	0.703	6e-27
Q6P637	193	COP9 signalosome complex	yes	no	0.950	0.398	0.4	3e-07
Q7ZUZ0	191	COP9 signalosome complex	yes	no	0.950	0.403	0.362	3e-06
Q6GQA6	195	COP9 signalosome complex	N/A	no	0.950	0.394	0.387	4e-06
Q75K24	196	COP9 signalosome complex	yes	no	0.950	0.392	0.304	0.0001
Q6P4Z9	209	COP9 signalosome complex	yes	no	0.962	0.373	0.294	0.0004
Q8VBV7	209	COP9 signalosome complex	yes	no	0.962	0.373	0.294	0.0004
Q5RF54	209	COP9 signalosome complex	yes	no	0.962	0.373	0.284	0.0005
Q99627	209	COP9 signalosome complex	no	no	0.962	0.373	0.284	0.0005

>sp|P43255|CSN8_ARATH COP9 signalosome complex subunit 8 OS=Arabidopsis thaliana GN=CSN8 PE=1 SV=1

 Score =  119 bits (298), Expect = 6e-27,   Method: Compositional matrix adjust.
 Identities = 57/81 (70%), Positives = 66/81 (81%)

Query: 1   LYTKRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQQQGWTLDPASRMLTVKKQPLVT 60
           LYTKRMFQLL+SAYSTI+  D ALFLGM EDDA  YV + GWT+D AS+M +VKKQ +  
Sbjct: 117 LYTKRMFQLLLSAYSTITIHDLALFLGMTEDDATTYVVENGWTVDAASQMASVKKQAVKR 176

Query: 61  EQKLDPSKMQCLTEYVFHLEH 81
           EQK+D SK+Q LTEYVFHLEH
Sbjct: 177 EQKVDSSKLQRLTEYVFHLEH 197

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|Q6P637|CSN8_XENTR COP9 signalosome complex subunit 8 OS=Xenopus tropicalis GN=csn8 PE=2 SV=1

 Score = 53.9 bits (128), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 32/80 (40%), Positives = 48/80 (60%), Gaps = 3/80 (3%)

Query: 4   KRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQQQGWTLDPASRMLTVKKQPLVTEQK 63
           +R F L+  AY++IS  D A F+G++ ++A   V +QGW  D A+RM+  KK P      
Sbjct: 115 RRAFGLVSQAYTSISADDFAAFVGLSVEEAVKGVIEQGWQADLATRMVMPKK-PDSAPLS 173

Query: 64  LDPSKMQC--LTEYVFHLEH 81
           L P++ Q   LT+YV  LE+
Sbjct: 174 LIPNEQQLARLTDYVAFLEN 193

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.

Xenopus tropicalis (taxid: 8364)

>sp|Q7ZUZ0|CSN8_DANRE COP9 signalosome complex subunit 8 OS=Danio rerio GN=cops8 PE=2 SV=1

 Score = 50.4 bits (119), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 29/80 (36%), Positives = 46/80 (57%), Gaps = 3/80 (3%)

Query: 4   KRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQQQGWTLDPASRMLTVKKQPLVTEQK 63
           +R + L+  AY++IS +D A F+G + ++A   V   GW  DP +RM+  +K P      
Sbjct: 113 RRAYGLVAQAYTSISAEDFAAFVGYSVEEAVKGVVSHGWQADPNTRMIMPQK-PDPPPVS 171

Query: 64  LDPSKMQC--LTEYVFHLEH 81
           L P++ Q   LT+YV  LE+
Sbjct: 172 LVPNEQQLARLTDYVAFLEN 191

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.

Danio rerio (taxid: 7955)

>sp|Q6GQA6|CSN8_XENLA COP9 signalosome complex subunit 8 OS=Xenopus laevis GN=csn8 PE=2 SV=2

 Score = 50.1 bits (118), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 31/80 (38%), Positives = 46/80 (57%), Gaps = 3/80 (3%)

Query: 4   KRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQQQGWTLDPASRMLTVKKQPLVTEQK 63
           +R F L+  AY++IS  D A F+G+  ++A   V +QGW  D A+ M+  KK P      
Sbjct: 117 QRAFGLVSQAYTSISADDFAAFVGLPVEEAVKGVLEQGWQADSATGMVMPKK-PDSAPLS 175

Query: 64  LDPSKMQC--LTEYVFHLEH 81
           L P++ Q   LT+YV  LE+
Sbjct: 176 LIPNEQQLARLTDYVAFLEN 195

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.

Xenopus laevis (taxid: 8355)

>sp|Q75K24|CSN8_DICDI COP9 signalosome complex subunit 8 OS=Dictyostelium discoideum GN=csn8 PE=1 SV=1

 Score = 45.4 bits (106), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 25/82 (30%), Positives = 46/82 (56%), Gaps = 5/82 (6%)

Query: 2   YTKRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQQQGWTLDPASRMLTVKKQPLVTE 61
           + +R F+L+ +AYS+I+  D + +LG++ +D   +   + W  D AS   T+K  P+  +
Sbjct: 114 FQQRTFELISNAYSSITVNDCSSYLGISPEDTIKFTTSKCWEHDKASN--TLKPVPIQKQ 171

Query: 62  QKLDPS---KMQCLTEYVFHLE 80
               P+   +++ LT YV  LE
Sbjct: 172 SSELPTGNQQIRSLTSYVLFLE 193

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|Q6P4Z9|CSN8_RAT COP9 signalosome complex subunit 8 OS=Rattus norvegicus GN=Cops8 PE=2 SV=1

 Score = 43.5 bits (101), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 28/95 (29%), Positives = 45/95 (47%), Gaps = 17/95 (17%)

Query: 4   KRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQQQGWTLDPASRMLTVKKQ------- 56
           +R F L+  AY++I   D A F+G+  ++A   V +QGW  D  +RM+  +K        
Sbjct: 115 RRAFALVSQAYTSIIADDFAAFVGLPVEEAVKGVLEQGWQADSTTRMVLPRKPAPGALDV 174

Query: 57  ------PLVTEQKLDP----SKMQCLTEYVFHLEH 81
                 PL     + P     ++  LT+YV  LE+
Sbjct: 175 SLNRFIPLSEPAPVPPIPNEQQLARLTDYVAFLEN 209

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, c-jun/JUN, IkappaBalpha/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.

Rattus norvegicus (taxid: 10116)

>sp|Q8VBV7|CSN8_MOUSE COP9 signalosome complex subunit 8 OS=Mus musculus GN=Cops8 PE=1 SV=1

 Score = 43.5 bits (101), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 28/95 (29%), Positives = 45/95 (47%), Gaps = 17/95 (17%)

Query: 4   KRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQQQGWTLDPASRMLTVKKQ------- 56
           +R F L+  AY++I   D A F+G+  ++A   V +QGW  D  +RM+  +K        
Sbjct: 115 RRAFALVSQAYTSIIADDFAAFVGLPVEEAVKGVLEQGWQADSTTRMVLPRKPASGTLDV 174

Query: 57  ------PLVTEQKLDP----SKMQCLTEYVFHLEH 81
                 PL     + P     ++  LT+YV  LE+
Sbjct: 175 SLNRFIPLSEPAPVPPIPNEQQLARLTDYVAFLEN 209

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, c-jun/JUN, IkappaBalpha/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|Q5RF54|CSN8_PONAB COP9 signalosome complex subunit 8 OS=Pongo abelii GN=COPS8 PE=2 SV=1

 Score = 43.1 bits (100), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 27/95 (28%), Positives = 45/95 (47%), Gaps = 17/95 (17%)

Query: 4   KRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQQQGWTLDPASRMLTVKKQ------- 56
           +R F L+  AY++I   D A F+G+  ++A   + +QGW  D  +RM+  +K        
Sbjct: 115 RRAFALVSQAYTSIVADDFAAFVGLPVEEAVKGILEQGWQADSTTRMVLPRKPVAGALDV 174

Query: 57  ------PLVTEQKLDP----SKMQCLTEYVFHLEH 81
                 PL     + P     ++  LT+YV  LE+
Sbjct: 175 SFNKFIPLSEPAPVPPIPNEQQLARLTDYVAFLEN 209

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, c-jun/JUN, IkappaBalpha/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|Q99627|CSN8_HUMAN COP9 signalosome complex subunit 8 OS=Homo sapiens GN=COPS8 PE=1 SV=1

 Score = 43.1 bits (100), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 27/95 (28%), Positives = 45/95 (47%), Gaps = 17/95 (17%)

Query: 4   KRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQQQGWTLDPASRMLTVKKQ------- 56
           +R F L+  AY++I   D A F+G+  ++A   + +QGW  D  +RM+  +K        
Sbjct: 115 RRAFALVSQAYTSIIADDFAAFVGLPVEEAVKGILEQGWQADSTTRMVLPRKPVAGALDV 174

Query: 57  ------PLVTEQKLDP----SKMQCLTEYVFHLEH 81
                 PL     + P     ++  LT+YV  LE+
Sbjct: 175 SFNKFIPLSEPAPVPPIPNEQQLARLTDYVAFLEN 209

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, c-jun/JUN, IkappaBalpha/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)

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	81
388514231	197	unknown [Lotus japonicus]	1.0	0.411	0.851	4e-33
351726828	197	uncharacterized protein LOC100500543 [Gl	1.0	0.411	0.839	5e-33
255627935	197	unknown [Glycine max]	1.0	0.411	0.839	1e-32
363808024	155	uncharacterized protein LOC100801424 [Gl	1.0	0.522	0.839	2e-32
147798444	197	hypothetical protein VITISV_002704 [Viti	1.0	0.411	0.827	5e-32
225447785	197	PREDICTED: COP9 signalosome complex subu	1.0	0.411	0.827	5e-32
255574046	176	cop9 signalosome complex subunit 8 (csn	1.0	0.460	0.814	8e-32
29468343	197	CSN8 [Nicotiana benthamiana]	1.0	0.411	0.814	1e-30
224054304	199	predicted protein [Populus trichocarpa]	1.0	0.407	0.802	4e-30
356534795	199	PREDICTED: LOW QUALITY PROTEIN: COP9 sig	1.0	0.407	0.790	5e-30

>gi|388514231|gb|AFK45177.1| unknown [Lotus japonicus]

 Score =  145 bits (365), Expect = 4e-33,   Method: Compositional matrix adjust.
 Identities = 69/81 (85%), Positives = 73/81 (90%)

Query: 1   LYTKRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQQQGWTLDPASRMLTVKKQPLVT 60
           LYTK MFQLL+SAYSTIS  D ALFLGMNEDDA  YVQQQGWT+D ASRMLTVKKQP+VT
Sbjct: 117 LYTKEMFQLLLSAYSTISIADAALFLGMNEDDATSYVQQQGWTVDSASRMLTVKKQPVVT 176

Query: 61  EQKLDPSKMQCLTEYVFHLEH 81
           EQKLDPSK+Q LTEYVFHLEH
Sbjct: 177 EQKLDPSKLQRLTEYVFHLEH 197

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|351726828|ref|NP_001235860.1| uncharacterized protein LOC100500543 [Glycine max] gi|255630595|gb|ACU15657.1| unknown [Glycine max]

 Score =  144 bits (364), Expect = 5e-33,   Method: Compositional matrix adjust.
 Identities = 68/81 (83%), Positives = 74/81 (91%)

Query: 1   LYTKRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQQQGWTLDPASRMLTVKKQPLVT 60
           LYTK MFQLL+SAYSTIS +DTALFLGMNEDDA  Y+ QQGWT+DPASRML VKKQP+VT
Sbjct: 117 LYTKEMFQLLLSAYSTISIKDTALFLGMNEDDATNYLLQQGWTVDPASRMLIVKKQPVVT 176

Query: 61  EQKLDPSKMQCLTEYVFHLEH 81
           EQKLDPSK+Q LTEYVFHLEH
Sbjct: 177 EQKLDPSKLQRLTEYVFHLEH 197

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255627935|gb|ACU14312.1| unknown [Glycine max]

 Score =  143 bits (361), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 68/81 (83%), Positives = 74/81 (91%)

Query: 1   LYTKRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQQQGWTLDPASRMLTVKKQPLVT 60
           LYTK MFQLL+SAYSTIS +DTALFLGMNEDDA  YV QQGWT+DPAS+ML VKKQP+VT
Sbjct: 117 LYTKEMFQLLLSAYSTISIKDTALFLGMNEDDATNYVLQQGWTVDPASQMLIVKKQPVVT 176

Query: 61  EQKLDPSKMQCLTEYVFHLEH 81
           EQKLDPSK+Q LTEYVFHLEH
Sbjct: 177 EQKLDPSKLQRLTEYVFHLEH 197

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|363808024|ref|NP_001242464.1| uncharacterized protein LOC100801424 [Glycine max] gi|255635465|gb|ACU18085.1| unknown [Glycine max]

 Score =  143 bits (360), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 68/81 (83%), Positives = 74/81 (91%)

Query: 1   LYTKRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQQQGWTLDPASRMLTVKKQPLVT 60
           LYTK MFQLL+SAYSTIS +DTALFLGMNEDDA  YV QQGWT+DPAS+ML VKKQP+VT
Sbjct: 75  LYTKEMFQLLLSAYSTISIKDTALFLGMNEDDATNYVLQQGWTVDPASQMLIVKKQPVVT 134

Query: 61  EQKLDPSKMQCLTEYVFHLEH 81
           EQKLDPSK+Q LTEYVFHLEH
Sbjct: 135 EQKLDPSKLQRLTEYVFHLEH 155

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147798444|emb|CAN67908.1| hypothetical protein VITISV_002704 [Vitis vinifera]

 Score =  141 bits (355), Expect = 5e-32,   Method: Compositional matrix adjust.
 Identities = 67/81 (82%), Positives = 74/81 (91%)

Query: 1   LYTKRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQQQGWTLDPASRMLTVKKQPLVT 60
           LYTK+MFQLL+SAYSTIS QDTALFLGM+EDD   YV +QGWT+D ASRMLTVKKQP+VT
Sbjct: 117 LYTKKMFQLLLSAYSTISIQDTALFLGMSEDDVTNYVVEQGWTVDSASRMLTVKKQPIVT 176

Query: 61  EQKLDPSKMQCLTEYVFHLEH 81
           EQKLDPSK+Q LTEYVFHLEH
Sbjct: 177 EQKLDPSKLQRLTEYVFHLEH 197

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225447785|ref|XP_002266060.1| PREDICTED: COP9 signalosome complex subunit 8 [Vitis vinifera] gi|296081479|emb|CBI20002.3| unnamed protein product [Vitis vinifera]

 Score =  141 bits (355), Expect = 5e-32,   Method: Compositional matrix adjust.
 Identities = 67/81 (82%), Positives = 74/81 (91%)

Query: 1   LYTKRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQQQGWTLDPASRMLTVKKQPLVT 60
           LYTK+MFQLL+SAYSTIS QDTALFLGM+EDD   YV +QGWT+D ASRMLTVKKQP+VT
Sbjct: 117 LYTKKMFQLLLSAYSTISIQDTALFLGMSEDDVTNYVVEQGWTVDSASRMLTVKKQPIVT 176

Query: 61  EQKLDPSKMQCLTEYVFHLEH 81
           EQKLDPSK+Q LTEYVFHLEH
Sbjct: 177 EQKLDPSKLQRLTEYVFHLEH 197

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255574046|ref|XP_002527939.1| cop9 signalosome complex subunit 8 (csn complex subunit 8), putative [Ricinus communis] gi|223532643|gb|EEF34428.1| cop9 signalosome complex subunit 8 (csn complex subunit 8), putative [Ricinus communis]

 Score =  140 bits (354), Expect = 8e-32,   Method: Compositional matrix adjust.
 Identities = 66/81 (81%), Positives = 73/81 (90%)

Query: 1   LYTKRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQQQGWTLDPASRMLTVKKQPLVT 60
           LYTKRMFQLL+SAYSTIS QD AL+LGM EDDAA YV QQGW +DPAS+M+TVKKQP+VT
Sbjct: 96  LYTKRMFQLLLSAYSTISIQDAALYLGMTEDDAANYVLQQGWIVDPASQMITVKKQPIVT 155

Query: 61  EQKLDPSKMQCLTEYVFHLEH 81
           EQKLD SK+Q LTEYVFHLEH
Sbjct: 156 EQKLDSSKLQWLTEYVFHLEH 176

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|29468343|gb|AAO85511.1| CSN8 [Nicotiana benthamiana]

 Score =  137 bits (344), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 66/81 (81%), Positives = 72/81 (88%)

Query: 1   LYTKRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQQQGWTLDPASRMLTVKKQPLVT 60
           LY KRMF+LL+SAYSTIS QDTA FLGMNE+DA  YV QQGW LDPAS+MLTVKKQ +VT
Sbjct: 117 LYRKRMFELLLSAYSTISPQDTAQFLGMNENDATNYVLQQGWVLDPASQMLTVKKQAVVT 176

Query: 61  EQKLDPSKMQCLTEYVFHLEH 81
           EQKLDPSK+Q LTEYVFHLEH
Sbjct: 177 EQKLDPSKLQRLTEYVFHLEH 197

Source: Nicotiana benthamiana

Species: Nicotiana benthamiana

Genus: Nicotiana

Family: Solanaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224054304|ref|XP_002298193.1| predicted protein [Populus trichocarpa] gi|222845451|gb|EEE82998.1| predicted protein [Populus trichocarpa]

 Score =  135 bits (339), Expect = 4e-30,   Method: Compositional matrix adjust.
 Identities = 65/81 (80%), Positives = 70/81 (86%)

Query: 1   LYTKRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQQQGWTLDPASRMLTVKKQPLVT 60
           +YTKRMFQLL+SAYSTIS QDTALFLGMNEDDA  YV QQGW +DP SRML VKKQ + T
Sbjct: 119 VYTKRMFQLLLSAYSTISIQDTALFLGMNEDDATSYVLQQGWVVDPDSRMLIVKKQSVKT 178

Query: 61  EQKLDPSKMQCLTEYVFHLEH 81
           EQKLD SK+Q LTEYVFHLEH
Sbjct: 179 EQKLDSSKLQRLTEYVFHLEH 199

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356534795|ref|XP_003535937.1| PREDICTED: LOW QUALITY PROTEIN: COP9 signalosome complex subunit 8-like [Glycine max]

 Score =  134 bits (338), Expect = 5e-30,   Method: Compositional matrix adjust.
 Identities = 64/81 (79%), Positives = 69/81 (85%)

Query: 1   LYTKRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQQQGWTLDPASRMLTVKKQPLVT 60
           LY K MFQLL+SAYS IS +DTALFLGMNEDDA  YV QQGWT+DP SRML VKKQP VT
Sbjct: 119 LYAKEMFQLLLSAYSMISIKDTALFLGMNEDDATNYVLQQGWTVDPTSRMLIVKKQPAVT 178

Query: 61  EQKLDPSKMQCLTEYVFHLEH 81
           +QKLDPSK+Q LTE VFHLEH
Sbjct: 179 QQKLDPSKLQRLTEXVFHLEH 199

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

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	81
TAIR|locus:2129435	197	COP9 "AT4G14110" [Arabidopsis	1.0	0.411	0.703	8.4e-26
ZFIN|ZDB-GENE-040426-982	191	cops8 "COP9 constitutive photo	0.950	0.403	0.362	1.8e-07
UNIPROTKB|F1SM07	209	COPS8 "Uncharacterized protein	0.641	0.248	0.384	7.2e-07
UNIPROTKB|A4FV74	209	COPS8 "COPS8 protein" [Bos tau	0.641	0.248	0.365	1.3e-06
UNIPROTKB|E1C444	209	COPS8 "Uncharacterized protein	0.641	0.248	0.384	2.1e-06
RGD|1311404	209	Cops8 "COP9 signalosome subuni	0.641	0.248	0.365	2.1e-06
UNIPROTKB|Q99627	209	COPS8 "COP9 signalosome comple	0.641	0.248	0.346	2.8e-06
DICTYBASE|DDB_G0275471	196	csn8 "COP9 signalosome complex	0.950	0.392	0.304	3.9e-06
MGI|MGI:1915363	209	Cops8 "COP9 (constitutive phot	0.641	0.248	0.365	0.00012
UNIPROTKB|B8ZZP3	206	COPS8 "COP9 signalosome comple	0.604	0.237	0.365	0.00041

TAIR|locus:2129435 COP9 "AT4G14110" [Arabidopsis thaliana (taxid:3702)]

 Score = 292 (107.8 bits), Expect = 8.4e-26, P = 8.4e-26
 Identities = 57/81 (70%), Positives = 66/81 (81%)

Query:     1 LYTKRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQQQGWTLDPASRMLTVKKQPLVT 60
             LYTKRMFQLL+SAYSTI+  D ALFLGM EDDA  YV + GWT+D AS+M +VKKQ +  
Sbjct:   117 LYTKRMFQLLLSAYSTITIHDLALFLGMTEDDATTYVVENGWTVDAASQMASVKKQAVKR 176

Query:    61 EQKLDPSKMQCLTEYVFHLEH 81
             EQK+D SK+Q LTEYVFHLEH
Sbjct:   177 EQKVDSSKLQRLTEYVFHLEH 197

GO:0005515 "protein binding" evidence=IPI

GO:0008180 "signalosome" evidence=TAS;IPI

GO:0009640 "photomorphogenesis" evidence=RCA;TAS

GO:0009753 "response to jasmonic acid stimulus" evidence=IMP

GO:0000338 "protein deneddylation" evidence=TAS

GO:0004222 "metalloendopeptidase activity" evidence=TAS

GO:0009416 "response to light stimulus" evidence=IMP

GO:0010387 "signalosome assembly" evidence=IMP

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

GO:0006626 "protein targeting to mitochondrion" evidence=RCA

GO:0005634 "nucleus" evidence=IDA

ZFIN|ZDB-GENE-040426-982 cops8 "COP9 constitutive photomorphogenic homolog subunit 8 (Arabidopsis)" [Danio rerio (taxid:7955)]

 Score = 119 (46.9 bits), Expect = 1.8e-07, P = 1.8e-07
 Identities = 29/80 (36%), Positives = 46/80 (57%)

Query:     4 KRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQQQGWTLDPASRMLTVKKQPLVTEQK 63
             +R + L+  AY++IS +D A F+G + ++A   V   GW  DP +RM+  +K P      
Sbjct:   113 RRAYGLVAQAYTSISAEDFAAFVGYSVEEAVKGVVSHGWQADPNTRMIMPQK-PDPPPVS 171

Query:    64 LDPSKMQC--LTEYVFHLEH 81
             L P++ Q   LT+YV  LE+
Sbjct:   172 LVPNEQQLARLTDYVAFLEN 191

GO:0008150 "biological_process" evidence=ND

GO:0003674 "molecular_function" evidence=ND

GO:0008180 "signalosome" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

UNIPROTKB|F1SM07 COPS8 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 100 (40.3 bits), Expect = 7.2e-07, Sum P(2) = 7.2e-07
 Identities = 20/52 (38%), Positives = 32/52 (61%)

Query:     4 KRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQQQGWTLDPASRMLTVKK 55
             +R F L+  AY++I   D A F+G+  ++A   V +QGW  D ++RM+  KK
Sbjct:   115 RRAFALVSQAYTSIVADDFAAFVGLPVEEAVKGVLEQGWQADSSTRMVMPKK 166

GO:0010388 "cullin deneddylation" evidence=IEA

GO:0008180 "signalosome" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

UNIPROTKB|A4FV74 COPS8 "COPS8 protein" [Bos taurus (taxid:9913)]

 Score = 98 (39.6 bits), Expect = 1.3e-06, Sum P(2) = 1.3e-06
 Identities = 19/52 (36%), Positives = 31/52 (59%)

Query:     4 KRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQQQGWTLDPASRMLTVKK 55
             +R F L+  AY++I   D A F+G+  ++A   + +QGW  D  +RM+  KK
Sbjct:   115 RRAFALVSQAYTSIIADDFAAFVGLPVEEAVKGILEQGWQADSTTRMVMPKK 166

GO:0010388 "cullin deneddylation" evidence=IEA

GO:0008180 "signalosome" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

UNIPROTKB|E1C444 COPS8 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 96 (38.9 bits), Expect = 2.1e-06, Sum P(2) = 2.1e-06
 Identities = 20/52 (38%), Positives = 32/52 (61%)

Query:     4 KRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQQQGWTLDPASRMLTVKK 55
             +R F L+  AY++I   D A F+G+  ++A   V +QGW  D ++RM+  KK
Sbjct:   115 RRAFGLVSQAYTSIVADDFAAFVGLPVEEAVKGVLEQGWQADFSTRMVMPKK 166

GO:0005737 "cytoplasm" evidence=IEA

GO:0008180 "signalosome" evidence=IEA

GO:0010388 "cullin deneddylation" evidence=IEA

RGD|1311404 Cops8 "COP9 signalosome subunit 8" [Rattus norvegicus (taxid:10116)]

 Score = 96 (38.9 bits), Expect = 2.1e-06, Sum P(2) = 2.1e-06
 Identities = 19/52 (36%), Positives = 31/52 (59%)

Query:     4 KRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQQQGWTLDPASRMLTVKK 55
             +R F L+  AY++I   D A F+G+  ++A   V +QGW  D  +RM+  +K
Sbjct:   115 RRAFALVSQAYTSIIADDFAAFVGLPVEEAVKGVLEQGWQADSTTRMVLPRK 166

GO:0005634 "nucleus" evidence=ISO

GO:0005737 "cytoplasm" evidence=IEA;ISO

GO:0008180 "signalosome" evidence=IEA;ISO

GO:0010388 "cullin deneddylation" evidence=IEA;ISO

GO:0005730 "nucleolus" evidence=ISO

UNIPROTKB|Q99627 COPS8 "COP9 signalosome complex subunit 8" [Homo sapiens (taxid:9606)]

 Score = 95 (38.5 bits), Expect = 2.8e-06, Sum P(2) = 2.8e-06
 Identities = 18/52 (34%), Positives = 31/52 (59%)

Query:     4 KRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQQQGWTLDPASRMLTVKK 55
             +R F L+  AY++I   D A F+G+  ++A   + +QGW  D  +RM+  +K
Sbjct:   115 RRAFALVSQAYTSIIADDFAAFVGLPVEEAVKGILEQGWQADSTTRMVLPRK 166

GO:0008180 "signalosome" evidence=IDA

GO:0010388 "cullin deneddylation" evidence=IDA

GO:0005634 "nucleus" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

DICTYBASE|DDB_G0275471 csn8 "COP9 signalosome complex subunit 8" [Dictyostelium discoideum (taxid:44689)]

 Score = 108 (43.1 bits), Expect = 3.9e-06, P = 3.9e-06
 Identities = 25/82 (30%), Positives = 46/82 (56%)

Query:     2 YTKRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQQQGWTLDPASRMLTVKKQPLVTE 61
             + +R F+L+ +AYS+I+  D + +LG++ +D   +   + W  D AS   T+K  P+  +
Sbjct:   114 FQQRTFELISNAYSSITVNDCSSYLGISPEDTIKFTTSKCWEHDKASN--TLKPVPIQKQ 171

Query:    62 QKLDPS---KMQCLTEYVFHLE 80
                 P+   +++ LT YV  LE
Sbjct:   172 SSELPTGNQQIRSLTSYVLFLE 193

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

MGI|MGI:1915363 Cops8 "COP9 (constitutive photomorphogenic) homolog, subunit 8 (Arabidopsis thaliana)" [Mus musculus (taxid:10090)]

 Score = 96 (38.9 bits), Expect = 0.00012, P = 0.00012
 Identities = 19/52 (36%), Positives = 31/52 (59%)

Query:     4 KRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQQQGWTLDPASRMLTVKK 55
             +R F L+  AY++I   D A F+G+  ++A   V +QGW  D  +RM+  +K
Sbjct:   115 RRAFALVSQAYTSIIADDFAAFVGLPVEEAVKGVLEQGWQADSTTRMVLPRK 166

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IEA

GO:0008180 "signalosome" evidence=ISO;IDA

GO:0010388 "cullin deneddylation" evidence=ISO

UNIPROTKB|B8ZZP3 COPS8 "COP9 signalosome complex subunit 8" [Homo sapiens (taxid:9606)]

 Score = 91 (37.1 bits), Expect = 0.00041, P = 0.00041
 Identities = 19/52 (36%), Positives = 32/52 (61%)

Query:     4 KRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQQQGWTLDPASRMLTVKK 55
             +R F L+  AY++I   D A F+G+  ++A   V++QGW  D  +RM+  +K
Sbjct:   115 RRAFALVSQAYTSIIADDFAAFVGLPVEEA---VKEQGWQADSTTRMVLPRK 163


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.320   0.130   0.380    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0       81        81   0.00091  102 3  11 22  0.38    29
                                                     29  0.42    30


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  10
  No. of states in DFA:  534 (57 KB)
  Total size of DFA:  100 KB (2070 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  8.90u 0.17s 9.07t   Elapsed:  00:00:01
  Total cpu time:  8.91u 0.17s 9.08t   Elapsed:  00:00:01
  Start:  Fri May 10 13:16:55 2013   End:  Fri May 10 13:16:56 2013

GO:0005634 "nucleus" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
P43255	CSN8_ARATH	No assigned EC number	0.7037	1.0	0.4111	yes	no

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	81
pfam10075	144	pfam10075, PCI_Csn8, COP9 signalosome, subunit CSN	2e-12

>gnl|CDD|220553 pfam10075, PCI_Csn8, COP9 signalosome, subunit CSN8

 Score = 57.7 bits (140), Expect = 2e-12
 Identities = 17/58 (29%), Positives = 31/58 (53%), Gaps = 1/58 (1%)

Query: 1   LYTKRMFQLLMSAYSTISTQDTALFLGM-NEDDAAYYVQQQGWTLDPASRMLTVKKQP 57
                +  L+  AYS+IS  D A  LG+ ++++   + +++GWTLD   R+L    + 
Sbjct: 82  TIRDEIAALVGKAYSSISIDDLAELLGLSSDEELEKFAKKRGWTLDSDGRILPPNPEE 139

This PCI_Csn8 domain is conserved from plants to humans. It is a signature protein motif found in components of CSN (COP9 signalosome). It functions as a structural scaffold for subunit-subunit interactions within the complex and is a key regulator of photomorphogenic development. Length = 144

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	81
PF10075	143	PCI_Csn8: COP9 signalosome, subunit CSN8; InterPro	99.68
KOG4414	197	consensus COP9 signalosome, subunit CSN8 [Posttran	99.56
KOG3151	260	consensus 26S proteasome regulatory complex, subun	99.19
KOG3252	217	consensus Uncharacterized conserved protein [Funct	98.36
smart00753	88	PAM PCI/PINT associated module.	97.12
smart00088	88	PINT motif in proteasome subunits, Int-6, Nip-1 an	97.12
PF01399	105	PCI: PCI domain; InterPro: IPR000717 A homology do	97.03
PF03399	204	SAC3_GANP: SAC3/GANP/Nin1/mts3/eIF-3 p25 family; I	96.23
KOG1861	540	consensus Leucine permease transcriptional regulat	96.19
PF03374	111	ANT: Phage antirepressor protein KilAC domain; Int	95.57
smart00071	103	Galanin Galanin. Galanin [1,2,3] is a neuropeptide	94.07
KOG1498	439	consensus 26S proteasome regulatory complex, subun	93.55
COG5071	439	RPN5 26S proteasome regulatory complex component [	93.46
KOG2581	493	consensus 26S proteasome regulatory complex, subun	92.86
PF03683	76	UPF0175: Uncharacterised protein family (UPF0175);	91.75
PF12728	51	HTH_17: Helix-turn-helix domain	91.52
PF10668	60	Phage_terminase: Phage terminase small subunit; In	91.47
PF04800	101	ETC_C1_NDUFA4: ETC complex I subunit conserved reg	91.08
PF04760	54	IF2_N: Translation initiation factor IF-2, N-termi	90.63
PF02042	52	RWP-RK: RWP-RK domain; InterPro: IPR003035 This do	90.58
PRK13503	278	transcriptional activator RhaS; Provisional	89.85
PLN03238	290	probable histone acetyltransferase MYST; Provision	89.08
cd01104	68	HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain	89.02
PF07037	122	DUF1323: Putative transcription regulator (DUF1323	88.99
TIGR01764	49	excise DNA binding domain, excisionase family. An	88.88
PF03484	70	B5: tRNA synthetase B5 domain; InterPro: IPR005147	88.08
PF09339	52	HTH_IclR: IclR helix-turn-helix domain; InterPro:	87.37
PF13404	42	HTH_AsnC-type: AsnC-type helix-turn-helix domain;	87.17
smart00874	71	B5 tRNA synthetase B5 domain. This domain is found	86.96
PF08727	57	P3A: Poliovirus 3A protein like; InterPro: IPR0148	86.8
PF13463	68	HTH_27: Winged helix DNA-binding domain; PDB: 3GFL	86.17
smart00550	68	Zalpha Z-DNA-binding domain in adenosine deaminase	86.11
PF14056	55	DUF4250: Domain of unknown function (DUF4250)	85.71
cd04762	49	HTH_MerR-trunc Helix-Turn-Helix DNA binding domain	85.52
PF12840	61	HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_	85.0
PF00165	42	HTH_AraC: Bacterial regulatory helix-turn-helix pr	84.9
COG2522	119	Predicted transcriptional regulator [General funct	84.87
smart00342	84	HTH_ARAC helix_turn_helix, arabinose operon contro	84.69
PF08279	55	HTH_11: HTH domain; InterPro: IPR013196 Winged hel	84.58
PF01418	77	HTH_6: Helix-turn-helix domain, rpiR family; Inter	84.24
COG3415	138	Transposase and inactivated derivatives [DNA repli	84.11
PRK12686	312	carbamate kinase; Reviewed	83.94
PF05687	150	DUF822: Plant protein of unknown function (DUF822)	83.9
PF08280	59	HTH_Mga: M protein trans-acting positive regulator	83.66
PF01022	47	HTH_5: Bacterial regulatory protein, arsR family;	83.63
PF13412	48	HTH_24: Winged helix-turn-helix DNA-binding; PDB:	83.41
PF12324	77	HTH_15: Helix-turn-helix domain of alkylmercury ly	83.31
smart00497	53	IENR1 Intron encoded nuclease repeat motif. Repeat	83.29
PF08220	57	HTH_DeoR: DeoR-like helix-turn-helix domain; Inter	83.19
PF01296	29	Galanin: Galanin; InterPro: IPR008174 Galanin is a	83.02
KOG3389	178	consensus NADH:ubiquinone oxidoreductase, NDUFS4/1	82.69
smart00418	66	HTH_ARSR helix_turn_helix, Arsenical Resistance Op	82.5
PF09035	67	Tn916-Xis: Excisionase from transposon Tn916; Inte	82.32
PF06627	90	DUF1153: Protein of unknown function (DUF1153); In	82.11
smart00419	48	HTH_CRP helix_turn_helix, cAMP Regulatory protein.	81.7
TIGR02702	203	SufR_cyano iron-sulfur cluster biosynthesis transc	81.36
PF08784	102	RPA_C: Replication protein A C terminal; InterPro:	81.34
COG2886	88	Uncharacterized small protein [Function unknown]	81.03
PF01853	188	MOZ_SAS: MOZ/SAS family; InterPro: IPR002717 Moz i	80.82
PRK10906	252	DNA-binding transcriptional repressor GlpR; Provis	80.81
PRK11511	127	DNA-binding transcriptional activator MarA; Provis	80.75

>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=99.68  E-value=2.8e-17  Score=105.80  Aligned_cols=56  Identities=29%  Similarity=0.577  Sum_probs=41.0

Q ss_pred             ChHHHHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHHhcCCeEeCCCceEeecCC
Q 036949            1 LYTKRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQQQGWTLDPASRMLTVKKQ   56 (81)
Q Consensus         1 ~~R~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~~~GW~~d~~~~~~~p~~~   56 (81)
                      .+|++|+.||++||++|+++++++|||++++++.++++++||++|+++.++.|.+.
T Consensus        82 ~iR~~i~~~i~~aY~sIs~~~la~~Lg~~~~el~~~~~~~gW~~d~~~~~~~~~~~  137 (143)
T PF10075_consen   82 TIRERIAHLISKAYSSISLSDLAEMLGLSEEELEKFIKSRGWTVDGDGVLFPPNPE  137 (143)
T ss_dssp             HHHHHHHHHHHHH-SEE-HHHHHHHTTS-HHHHHHHHHHHT-EE-----EE---HH
T ss_pred             HHHHHHHHHHHHHHhHcCHHHHHHHhCCCHHHHHHHHHHcCCEECCCccEEecCCc
Confidence            37999999999999999999999999999999999999999999988766554433

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.

>KOG4414 consensus COP9 signalosome, subunit CSN8 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]

Probab=99.56  E-value=1.3e-15  Score=100.38  Aligned_cols=79  Identities=44%  Similarity=0.607  Sum_probs=69.4

Q ss_pred             hHHHHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHHhcCCeEeCCCceE-eecCCCCcccCCCChhHHHHHHhHHHhhc
Q 036949            2 YTKRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQQQGWTLDPASRML-TVKKQPLVTEQKLDPSKMQCLTEYVFHLE   80 (81)
Q Consensus         2 ~R~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~~~GW~~d~~~~~~-~p~~~~~~~~~~~~~~~l~~Lt~~v~~LE   80 (81)
                      .|.|.|.|+.+||++|-.+++|.+|||+++|+.+++.+.||+.|+.++|. .|+++...+ ..++-..+..||+++.|||
T Consensus       118 ~~kR~FaLl~qAYssI~~~D~A~FlGl~~ddAtk~ilEnGWqaDaasqMasl~kk~V~~a-~~Vd~nK~~~LsE~a~~~~  196 (197)
T KOG4414|consen  118 TRKRAFALLLQAYSSIIADDFAAFLGLPEDDATKGILENGWQADAASQMASLKKKAVAGA-LDVDFNKFIPLSEPAFHLE  196 (197)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHcccchhhHHHHhhccchhcccc-cccchhhceecCCccCCCC
Confidence            58999999999999999999999999999999999999999999999998 555444443 3337788999999999999


Q ss_pred             C
Q 036949           81 H   81 (81)
Q Consensus        81 ~   81 (81)
                      +
T Consensus       197 ~  197 (197)
T KOG4414|consen  197 H  197 (197)
T ss_pred             C
Confidence            6

>KOG3151 consensus 26S proteasome regulatory complex, subunit RPN12/PSMD8 [Posttranslational modification, protein turnover, chaperones]

Probab=99.19  E-value=5.8e-11  Score=82.78  Aligned_cols=53  Identities=15%  Similarity=0.331  Sum_probs=47.3

Q ss_pred             hHHHHHHHHHHhcccccHHHHHHHhCC-CHHHHHHHHHhcCCeEeCCCceEeec
Q 036949            2 YTKRMFQLLMSAYSTISTQDTALFLGM-NEDDAAYYVQQQGWTLDPASRMLTVK   54 (81)
Q Consensus         2 ~R~~~~~li~~AY~sIs~~~~a~~Lgl-s~~e~~~~~~~~GW~~d~~~~~~~p~   54 (81)
                      ||++|+.|++|+|..|++++++.||+| +++++.+|+++|+|.+++.+.+.+-.
T Consensus       178 iRdEIA~c~EKsYd~l~~s~a~~~L~f~~~~e~~~~~~~r~W~l~~~~~~~~~~  231 (260)
T KOG3151|consen  178 IRDEIAGCIEKSYDKLSASDATQMLLFNNDKELKKFATERQWPLDEKGVFSFAS  231 (260)
T ss_pred             HHHHHHHHHHHHHhhcCHHHHHHHHhcCChHHHHHHHHhcCCcccccccccchh
Confidence            799999999999999999999999999 89999999999999999555444433

>KOG3252 consensus Uncharacterized conserved protein [Function unknown]

Probab=98.36  E-value=1.1e-06  Score=59.86  Aligned_cols=79  Identities=13%  Similarity=0.272  Sum_probs=64.0

Q ss_pred             ChHHHHHHHHHHhcccccHHHHHHHhCC-CHHHHHHHHHhcCCeEeCCCceEeecCCCCcccCCC-ChhHHHHHHhHHHh
Q 036949            1 LYTKRMFQLLMSAYSTISTQDTALFLGM-NEDDAAYYVQQQGWTLDPASRMLTVKKQPLVTEQKL-DPSKMQCLTEYVFH   78 (81)
Q Consensus         1 ~~R~~~~~li~~AY~sIs~~~~a~~Lgl-s~~e~~~~~~~~GW~~d~~~~~~~p~~~~~~~~~~~-~~~~l~~Lt~~v~~   78 (81)
                      ++|.-+...++-.|.+|.-.-+|++||- +..++..++++-||..+.+|.+++|....+-...-. +..+++..++++..
T Consensus       136 svr~yachvv~iTyQkI~k~lLaellG~~sDs~le~~~~~~GW~a~e~G~ifv~~qE~~iKtkNi~EkI~fd~Va~ima~  215 (217)
T KOG3252|consen  136 SVRKYACHVVGITYQKIDKWLLAELLGGLSDSQLEVWMTKYGWIADESGQIFVASQEEEIKTKNIVEKIDFDHVASIMAS  215 (217)
T ss_pred             HHHHHHHHheechHhhchHHHHHHhhCcccHHHHHHHHHHccceecCCceEEEeccccccccCCccccCCcchHHHHHHh
Confidence            4677788899999999999999999998 899999999999999999997777766553321222 77888888887765


Q ss_pred             h
Q 036949           79 L   79 (81)
Q Consensus        79 L   79 (81)
                      +
T Consensus       216 ~  216 (217)
T KOG3252|consen  216 L  216 (217)
T ss_pred             c
Confidence            4

>smart00753 PAM PCI/PINT associated module

Probab=97.12  E-value=0.0013  Score=38.39  Aligned_cols=55  Identities=20%  Similarity=0.267  Sum_probs=44.0

Q ss_pred             hHHHHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHHh------cCCeEeCCCceEeecCC
Q 036949            2 YTKRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQQ------QGWTLDPASRMLTVKKQ   56 (81)
Q Consensus         2 ~R~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~~------~GW~~d~~~~~~~p~~~   56 (81)
                      +|.+.+..+.+.|++|++++++..++++.+++..++.+      ...++|..++++.-...
T Consensus        10 ~~~~~l~~l~~~y~~i~~~~i~~~~~l~~~~vE~~i~~~i~~~~l~~~ID~~~~~v~~~~~   70 (88)
T smart00753       10 IRLTNLLQLSEPYSSISLSDLAKLLGLSVPEVEKLVSKAIRDGEISAKIDQVNGIVEFEEV   70 (88)
T ss_pred             HHHHHHHHHhHHhceeeHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEEcCcCCEEEECCC
Confidence            67888899999999999999999999998888777553      25678876666655543

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

Probab=97.12  E-value=0.0013  Score=38.39  Aligned_cols=55  Identities=20%  Similarity=0.267  Sum_probs=44.0

Q ss_pred             hHHHHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHHh------cCCeEeCCCceEeecCC
Q 036949            2 YTKRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQQ------QGWTLDPASRMLTVKKQ   56 (81)
Q Consensus         2 ~R~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~~------~GW~~d~~~~~~~p~~~   56 (81)
                      +|.+.+..+.+.|++|++++++..++++.+++..++.+      ...++|..++++.-...
T Consensus        10 ~~~~~l~~l~~~y~~i~~~~i~~~~~l~~~~vE~~i~~~i~~~~l~~~ID~~~~~v~~~~~   70 (88)
T smart00088       10 IRLTNLLQLSEPYSSISLSDLAKLLGLSVPEVEKLVSKAIRDGEISAKIDQVNGIVEFEEV   70 (88)
T ss_pred             HHHHHHHHHhHHhceeeHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEEcCcCCEEEECCC
Confidence            67888899999999999999999999998888777553      25678876666655543

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

>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=97.03  E-value=0.0018  Score=38.22  Aligned_cols=38  Identities=24%  Similarity=0.357  Sum_probs=33.0

Q ss_pred             hHHHHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHHh
Q 036949            2 YTKRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQQ   39 (81)
Q Consensus         2 ~R~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~~   39 (81)
                      +|.+.+.-+.+.|++|+++++|..|+++.+++..++.+
T Consensus        46 i~~~~l~~l~~~y~~i~~~~ia~~l~~~~~~vE~~l~~   83 (105)
T PF01399_consen   46 IRRRNLRQLSKPYSSISISEIAKALQLSEEEVESILID   83 (105)
T ss_dssp             HHHHHHHHHHHC-SEEEHHHHHHHHTCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcccchHHHHHHhccchHHHHHHHHH
Confidence            57788889999999999999999999999998887654

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.

>PF03399 SAC3_GANP: SAC3/GANP/Nin1/mts3/eIF-3 p25 family; InterPro: IPR005062 This large family includes diverse proteins involved in large complexes [, , ]

Probab=96.23  E-value=0.0052  Score=40.75  Aligned_cols=27  Identities=30%  Similarity=0.346  Sum_probs=24.4

Q ss_pred             hHHHHHHHHHHhccc-ccHHHHHHHhCC
Q 036949            2 YTKRMFQLLMSAYST-ISTQDTALFLGM   28 (81)
Q Consensus         2 ~R~~~~~li~~AY~s-Is~~~~a~~Lgl   28 (81)
                      +|.+++.++++||.+ |+++.++++|||
T Consensus       177 iR~~al~~i~~ay~~~i~l~~l~~~L~F  204 (204)
T PF03399_consen  177 IRLRALQSISKAYRSSIPLSFLAELLGF  204 (204)
T ss_dssp             HHHHHHHHHHHHS-T-EEHHHHHHHTT-
T ss_pred             HHHHHHHHHHHHcCCCCCHHHHHHHcCC
Confidence            799999999999999 999999999996

The alignment contains one highly conserved negatively charged residue and one highly conserved positively charged residue that are probably important for the function of these proteins. The family includes the yeast nuclear export factor Sac3 [], and mammalian GANP/MCM3-associated proteins, which facilitate the nuclear localisation of MCM3, a protein that associates with chromatin in the G1 phase of the cell-cycle. The 26S protease (or 26S proteasome) is responsible for degrading ubiquitin conjugates. It consists of 19S regulatory complexes associated with the ends of 20S proteasomes. The 19S regulatory complex is composed of about 20 different polypeptides and confers ATP-dependence and substrate specificity to the 26S enzyme. The conserved region occurs at the C-terminal of the Nin1-like regulatory subunit [, , ]. This family includes several eukaryotic translation initiation factor 3 subunit 11 (eIF-3 p25) proteins. Eukaryotic initiation factor 3 (eIF3) is a multisubunit complex that is required for binding of mRNA to 40 S ribosomal subunits, stabilisation of ternary complex binding to 40 S subunits, and dissociation of 40 and 60 S subunits [].; PDB: 3T5V_D.

>KOG1861 consensus Leucine permease transcriptional regulator [Transcription]

Probab=96.19  E-value=0.012  Score=45.18  Aligned_cols=58  Identities=19%  Similarity=0.284  Sum_probs=51.8

Q ss_pred             HHHHHHHHHHhcc-cccHHHHHHHhCC-CHHHHHHHHHhcCCeEeCCCceEeecCCCCcc
Q 036949            3 TKRMFQLLMSAYS-TISTQDTALFLGM-NEDDAAYYVQQQGWTLDPASRMLTVKKQPLVT   60 (81)
Q Consensus         3 R~~~~~li~~AY~-sIs~~~~a~~Lgl-s~~e~~~~~~~~GW~~d~~~~~~~p~~~~~~~   60 (81)
                      |-..+..|.|+|. +|+++.++..|.| +.+++..|..+.+|+.|+.|..+.+++.....
T Consensus       464 R~~Al~ii~KsyrP~i~~~fi~~~laf~~~e~c~~~l~~~~~~~~~~g~~~~~~~~~s~~  523 (540)
T KOG1861|consen  464 RKKALTIICKSYRPTITVDFIASELAFDSMEDCVNFLNEQNLTYDSLGPQILDKNASSSN  523 (540)
T ss_pred             HHHHHHHHHHHcCCCccHHHHhhhhhhchHHHHHHHHhccCccccccCCccccccccccc
Confidence            5667889999999 9999999999999 78889999999999999999999888776653

>PF03374 ANT: Phage antirepressor protein KilAC domain; InterPro: IPR005039 This entry is represented by Bacteriophage P1, Ant1 C-terminal domain, which represents the processed Ant2 chain

Probab=95.57  E-value=0.047  Score=33.25  Aligned_cols=49  Identities=10%  Similarity=0.309  Sum_probs=38.3

Q ss_pred             HHHHHHHhcccccHHHHHHHhCCCHHHHHHHHHhcCCeEeCCCceEeec
Q 036949            6 MFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQQQGWTLDPASRMLTVK   54 (81)
Q Consensus         6 ~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~~~GW~~d~~~~~~~p~   54 (81)
                      .++.+..+=..+++.++|..||+++.++.++..+.||-+...+.-..|.
T Consensus        14 ~~d~~~~~~~~~ti~~~AK~L~i~~~~l~~~Lr~~g~l~~~~~~~~~p~   62 (111)
T PF03374_consen   14 FYDAFVDSDGLYTIREAAKLLGIGRNKLFQWLREKGWLYRRGKGRNLPY   62 (111)
T ss_pred             HHHHHHcCCCCccHHHHHHHhCCCHHHHHHHHHhCCceEECCCCCcccC
Confidence            4455555668899999999999999999999999999998322333444

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. Prophages P1 and P7 exist as unit copy DNA plasmids in the bacterial cell. Maintenance of the prophage state requires the continuous expression of two repressors: (i) C1 is a protein which negatively regulates the expression of lytic genes including the C1 inactivator gene coi, and (ii) C4 is an antisense RNA which specifically inhibits the synthesis of an anti-repressor Ant.; GO: 0003677 DNA binding

>smart00071 Galanin Galanin

Probab=94.07  E-value=0.074  Score=32.51  Aligned_cols=21  Identities=29%  Similarity=0.542  Sum_probs=17.2

Q ss_pred             HhcCCeEeCCCceEeecCCCC
Q 036949           38 QQQGWTLDPASRMLTVKKQPL   58 (81)
Q Consensus        38 ~~~GW~~d~~~~~~~p~~~~~   58 (81)
                      .+|||++++.|+.+-|-...+
T Consensus        10 eKRgwtlnsagyllgp~aid~   30 (103)
T smart00071       10 EKRGWTLNSAGYLLGPHAIDN   30 (103)
T ss_pred             cccCceeccCceeeCcccccc
Confidence            578999999999998876443

Galanin [1,2,3] is a neuropeptide that controls various biological activities: it regulates the release growth hormone, inhibits the release of insulin and somatostatin, contracts smooth muscle of the gastrointestinal and genitourinary tract and may be involved in the control of adrenal secretion

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

Probab=93.55  E-value=0.27  Score=37.17  Aligned_cols=33  Identities=15%  Similarity=0.360  Sum_probs=30.2

Q ss_pred             HHHHHHhcccccHHHHHHHhCCCHHHHHHHHHh
Q 036949            7 FQLLMSAYSTISTQDTALFLGMNEDDAAYYVQQ   39 (81)
Q Consensus         7 ~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~~   39 (81)
                      ++-|++=|++|++.+++..|+++.+++.+|...
T Consensus       344 iRiiA~yYSrIt~~rl~eLLdl~~ee~E~~LS~  376 (439)
T KOG1498|consen  344 IRIIAKYYSRITLKRLAELLDLPVEEMEKFLSD  376 (439)
T ss_pred             HHHHHHHHhhccHHHHHHHhCCCHHHHHHHHHH
Confidence            568999999999999999999999999998664

>COG5071 RPN5 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]

Probab=93.46  E-value=0.24  Score=36.79  Aligned_cols=39  Identities=15%  Similarity=0.377  Sum_probs=33.7

Q ss_pred             HHHHHHHhcccccHHHHHHHhCCCHHHHHHHHH---hcCCeE
Q 036949            6 MFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQ---QQGWTL   44 (81)
Q Consensus         6 ~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~---~~GW~~   44 (81)
                      -++.|++-|++|++.++.-.|.+++++..+++.   .+|--+
T Consensus       343 N~RvI~~yYSrI~~~rl~~lld~~~s~te~~ISdlVN~G~~y  384 (439)
T COG5071         343 NIRVIANYYSRIHCSRLGVLLDMSPSETEQFISDLVNKGHFY  384 (439)
T ss_pred             hHhHHHHHhhhhhHHHHHHHHcCCHHHHHHHHHHHHhcCcEE
Confidence            367999999999999999999999999988866   456655

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

Probab=92.86  E-value=0.053  Score=41.25  Aligned_cols=30  Identities=43%  Similarity=0.602  Sum_probs=24.4

Q ss_pred             HHHHHHhcccccHHHHHHHhCC-CHHHHHHH
Q 036949            7 FQLLMSAYSTISTQDTALFLGM-NEDDAAYY   36 (81)
Q Consensus         7 ~~li~~AY~sIs~~~~a~~Lgl-s~~e~~~~   36 (81)
                      .+-||-+|++||+.++|.-||+ |++++.-.
T Consensus       368 IR~ISlsYSRISl~DIA~kL~l~Seed~Eyi  398 (493)
T KOG2581|consen  368 IRKISLSYSRISLQDIAKKLGLNSEEDAEYI  398 (493)
T ss_pred             hhheeeeeeeccHHHHHHHhcCCCchhHHHH
Confidence            4678999999999999999999 55545433

>PF03683 UPF0175: Uncharacterised protein family (UPF0175); InterPro: IPR005368 This entry contains small proteins of unknown function

Probab=91.75  E-value=0.31  Score=28.23  Aligned_cols=30  Identities=20%  Similarity=0.264  Sum_probs=26.9

Q ss_pred             ccccHHHHHHHhCCCHHHHHHHHHhcCCeE
Q 036949           15 STISTQDTALFLGMNEDDAAYYVQQQGWTL   44 (81)
Q Consensus        15 ~sIs~~~~a~~Lgls~~e~~~~~~~~GW~~   44 (81)
                      ..||+..+|.++|+|.-++.++..++|=.+
T Consensus        33 g~iS~gkAAelag~s~~eF~~~L~~~gI~~   62 (76)
T PF03683_consen   33 GKISLGKAAELAGMSRWEFLELLKERGIPI   62 (76)
T ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHHCCCCC
Confidence            579999999999999999999999987543

>PF12728 HTH_17: Helix-turn-helix domain

Probab=91.52  E-value=0.33  Score=25.41  Aligned_cols=23  Identities=17%  Similarity=0.481  Sum_probs=20.5

Q ss_pred             ccHHHHHHHhCCCHHHHHHHHHh
Q 036949           17 ISTQDTALFLGMNEDDAAYYVQQ   39 (81)
Q Consensus        17 Is~~~~a~~Lgls~~e~~~~~~~   39 (81)
                      ++++++|.+||+|..-+..++.+
T Consensus         2 lt~~e~a~~l~is~~tv~~~~~~   24 (51)
T PF12728_consen    2 LTVKEAAELLGISRSTVYRWIRQ   24 (51)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHc
Confidence            47899999999999999998874

>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes

Probab=91.47  E-value=0.62  Score=26.22  Aligned_cols=46  Identities=17%  Similarity=0.325  Sum_probs=37.3

Q ss_pred             HHHHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHHhcCCeEeCCC
Q 036949            3 TKRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQQQGWTLDPAS   48 (81)
Q Consensus         3 R~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~~~GW~~d~~~   48 (81)
                      |++++.+--..=..|.+.++|..||+|+..+..+=..-.|.-.-.|
T Consensus         9 rdkA~e~y~~~~g~i~lkdIA~~Lgvs~~tIr~WK~~dkW~~~~~~   54 (60)
T PF10668_consen    9 RDKAFEIYKESNGKIKLKDIAEKLGVSESTIRKWKSRDKWDEKLKG   54 (60)
T ss_pred             HHHHHHHHHHhCCCccHHHHHHHHCCCHHHHHHHhhhcchhhHhcc
Confidence            6677777666667899999999999999999988887788764343

Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].

>PF04800 ETC_C1_NDUFA4: ETC complex I subunit conserved region; InterPro: IPR006885 This entry represents prokaryotic NADH-ubiquinone oxidoreductase subunits (1

Probab=91.08  E-value=0.17  Score=31.23  Aligned_cols=28  Identities=29%  Similarity=0.630  Sum_probs=18.9

Q ss_pred             hCC-CHHHHHHHHHhcCCeEeCCCceEeecCCC
Q 036949           26 LGM-NEDDAAYYVQQQGWTLDPASRMLTVKKQP   57 (81)
Q Consensus        26 Lgl-s~~e~~~~~~~~GW~~d~~~~~~~p~~~~   57 (81)
                      |-| |.+++++||.+.||.+.    +.-|....
T Consensus        53 l~F~skE~Ai~yaer~G~~Y~----V~~p~~r~   81 (101)
T PF04800_consen   53 LKFDSKEDAIAYAERNGWDYE----VEEPKKRK   81 (101)
T ss_dssp             EEESSHHHHHHHHHHCT-EEE----EE-STT--
T ss_pred             eeeCCHHHHHHHHHHcCCeEE----EeCCCCCc
Confidence            344 89999999999999993    55555443

6.5.3 from EC, 1.6.99.3 from EC) from complex I of the electron transport chain initially identified in Neurospora crassa as a 21 kDa protein [].; GO: 0016651 oxidoreductase activity, acting on NADH or NADPH, 0022900 electron transport chain, 0005743 mitochondrial inner membrane; PDB: 2JYA_A 2LJU_A.

>PF04760 IF2_N: Translation initiation factor IF-2, N-terminal region; InterPro: IPR006847 This region is found in the N-terminal half of translation initiation factor IF-2

Probab=90.63  E-value=0.28  Score=26.30  Aligned_cols=29  Identities=17%  Similarity=0.216  Sum_probs=23.3

Q ss_pred             ccccHHHHHHHhCCCHHHHHHHH-HhcCCe
Q 036949           15 STISTQDTALFLGMNEDDAAYYV-QQQGWT   43 (81)
Q Consensus        15 ~sIs~~~~a~~Lgls~~e~~~~~-~~~GW~   43 (81)
                      ..|++.++|.-||++.+++.+.+ .+.|=.
T Consensus         2 ~~i~V~elAk~l~v~~~~ii~~l~~~~Gi~   31 (54)
T PF04760_consen    2 EKIRVSELAKELGVPSKEIIKKLFKELGIM   31 (54)
T ss_dssp             -EE-TTHHHHHHSSSHHHHHHHH-HHHTS-
T ss_pred             CceEHHHHHHHHCcCHHHHHHHHHHhCCcC
Confidence            35789999999999999999999 557866

It is found in two copies in IF-2 alpha isoforms, and in only one copy in the N-terminally truncated beta and gamma isoforms []. Its function is unknown.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1ND9_A.

>PF02042 RWP-RK: RWP-RK domain; InterPro: IPR003035 This domain is named RWP-RK after a conserved motif at the C terminus of the domain

Probab=90.58  E-value=0.56  Score=25.66  Aligned_cols=29  Identities=17%  Similarity=0.258  Sum_probs=25.4

Q ss_pred             hcccccHHHHHHHhCCCHHHHHHHHHhcC
Q 036949           13 AYSTISTQDTALFLGMNEDDAAYYVQQQG   41 (81)
Q Consensus        13 AY~sIs~~~~a~~Lgls~~e~~~~~~~~G   41 (81)
                      .|=..++.++|.-||++...+...|.+.|
T Consensus        12 ~~fhlp~~eAA~~Lgv~~T~LKr~CR~~G   40 (52)
T PF02042_consen   12 QYFHLPIKEAAKELGVSVTTLKRRCRRLG   40 (52)
T ss_pred             HHhCCCHHHHHHHhCCCHHHHHHHHHHcC
Confidence            46678999999999999999999999876

The domain is found in algal minus dominance proteins as well as plant proteins involved in nitrogen-controlled development [].

>PRK13503 transcriptional activator RhaS; Provisional

Probab=89.85  E-value=0.84  Score=31.24  Aligned_cols=37  Identities=11%  Similarity=0.152  Sum_probs=31.6

Q ss_pred             HHHHHHHHHhcc-cccHHHHHHHhCCCHHHHHHHHHhc
Q 036949            4 KRMFQLLMSAYS-TISTQDTALFLGMNEDDAAYYVQQQ   40 (81)
Q Consensus         4 ~~~~~li~~AY~-sIs~~~~a~~Lgls~~e~~~~~~~~   40 (81)
                      .++.+.|.+.|. .++++++|+.+|+|+.-+...+++.
T Consensus       174 ~~~~~~I~~~~~~~~tl~~lA~~~~lS~~~l~r~Fk~~  211 (278)
T PRK13503        174 NQLLAWLEDHFAEEVNWEALADQFSLSLRTLHRQLKQQ  211 (278)
T ss_pred             HHHHHHHHHhhcCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            357788999998 9999999999999998887777653

>PLN03238 probable histone acetyltransferase MYST; Provisional

Probab=89.08  E-value=1.6  Score=31.69  Aligned_cols=52  Identities=15%  Similarity=0.142  Sum_probs=42.3

Q ss_pred             HHHHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHHhcCCeEeCCCceEeec
Q 036949            3 TKRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQQQGWTLDPASRMLTVK   54 (81)
Q Consensus         3 R~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~~~GW~~d~~~~~~~p~   54 (81)
                      |+.++..+.+...+||+++++...|+..+|+..-.+..|...--.|..++-.
T Consensus       210 ~~~il~~L~~~~~~isi~~is~~T~i~~~Dii~tL~~l~~l~~~~g~~~i~~  261 (290)
T PLN03238        210 TRVLLEQLRDVKGDVSIKDLSLATGIRGEDIVSTLQSLNLIKYWKGQHVIHV  261 (290)
T ss_pred             HHHHHHHHHhcCCCccHHHHHHHhCCCHHHHHHHHHHCCcEEEECCcEEEEe
Confidence            5678888877788999999999999999999999998897654455555544

>cd01104 HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA

Probab=89.02  E-value=2.4  Score=23.06  Aligned_cols=52  Identities=12%  Similarity=0.094  Sum_probs=32.6

Q ss_pred             cHHHHHHHhCCCHHHHHHHHHhcCCeEeCCCceEeecCCCCcccCCC-ChhHHHHHHhHHHhh
Q 036949           18 STQDTALFLGMNEDDAAYYVQQQGWTLDPASRMLTVKKQPLVTEQKL-DPSKMQCLTEYVFHL   79 (81)
Q Consensus        18 s~~~~a~~Lgls~~e~~~~~~~~GW~~d~~~~~~~p~~~~~~~~~~~-~~~~l~~Lt~~v~~L   79 (81)
                      ++.++|+.+|++..-+..+.++.|        ...|.  ........ ++.++.+|-.+....
T Consensus         2 s~~eva~~~gvs~~tlr~w~~~~g--------~~~~~--r~~~~~r~yt~~~v~~l~~i~~l~   54 (68)
T cd01104           2 TIGAVARLTGVSPDTLRAWERRYG--------LPAPQ--RTDGGHRLYSEADVARLRLIRRLT   54 (68)
T ss_pred             CHHHHHHHHCcCHHHHHHHHHhCC--------CCCCC--cCCCCCeecCHHHHHHHHHHHHHH
Confidence            678999999999999998876432        11221  11112222 777777776665443

Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA- and CarA-like proteins in this group appear to lack the long dimerization helix seen i

>PF07037 DUF1323: Putative transcription regulator (DUF1323); InterPro: IPR010749 This family consists of several hypothetical Enterobacterial proteins of around 120 residues in length

Probab=88.99  E-value=0.84  Score=29.13  Aligned_cols=29  Identities=21%  Similarity=0.607  Sum_probs=25.9

Q ss_pred             cHHHHHHHhCCCHHHHHHHHHhcCCeEeC
Q 036949           18 STQDTALFLGMNEDDAAYYVQQQGWTLDP   46 (81)
Q Consensus        18 s~~~~a~~Lgls~~e~~~~~~~~GW~~d~   46 (81)
                      ..+++|..+|++..-+-.++.+.||+-.+
T Consensus         2 T~eELA~~tG~srQTINrWvRkegW~T~p   30 (122)
T PF07037_consen    2 TPEELAELTGYSRQTINRWVRKEGWKTEP   30 (122)
T ss_pred             CHHHHHHHhCccHHHHHHHHHhcCceecc
Confidence            46789999999999999999999999644

The function of this family is unknown.

>TIGR01764 excise DNA binding domain, excisionase family

Probab=88.88  E-value=0.72  Score=23.19  Aligned_cols=23  Identities=17%  Similarity=0.509  Sum_probs=20.4

Q ss_pred             ccHHHHHHHhCCCHHHHHHHHHh
Q 036949           17 ISTQDTALFLGMNEDDAAYYVQQ   39 (81)
Q Consensus        17 Is~~~~a~~Lgls~~e~~~~~~~   39 (81)
                      +++.++|.+||++..-+..++.+
T Consensus         2 lt~~e~a~~lgis~~ti~~~~~~   24 (49)
T TIGR01764         2 LTVEEAAEYLGVSKDTVYRLIHE   24 (49)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHc
Confidence            57899999999999999998864

An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).

>PF03484 B5: tRNA synthetase B5 domain; InterPro: IPR005147 Domain B5 is found in phenylalanine-tRNA synthetase beta subunits

Probab=88.08  E-value=3.1  Score=23.42  Aligned_cols=41  Identities=17%  Similarity=0.353  Sum_probs=30.5

Q ss_pred             cccHHHHHHHhCC--CHHHHHHHHHhcCCeEeC-CCceEeecCC
Q 036949           16 TISTQDTALFLGM--NEDDAAYYVQQQGWTLDP-ASRMLTVKKQ   56 (81)
Q Consensus        16 sIs~~~~a~~Lgl--s~~e~~~~~~~~GW~~d~-~~~~~~p~~~   56 (81)
                      .++.+.+.++||+  +.+++.+.....|-+++. ++..+....|
T Consensus         5 ~~~~~~i~~~lG~~i~~~~i~~~L~~lg~~~~~~~~~~~~v~vP   48 (70)
T PF03484_consen    5 TLSLDKINKLLGIDISPEEIIKILKRLGFKVEKIDGDTLEVTVP   48 (70)
T ss_dssp             EEEHHHHHHHHTS---HHHHHHHHHHTT-EEEE-CTTEEEEEEE
T ss_pred             EecHHHHHHHhCCCCCHHHHHHHHHHCCCEEEECCCCEEEEEcC
Confidence            4678899999998  899999999999999887 5544444433

This domain has been shown to bind DNA through a winged helix-turn-helix motif []. Phenylalanine-tRNA synthetase may influence common cellular processes via DNA binding, in addition to its aminoacylation function.; GO: 0000287 magnesium ion binding, 0003723 RNA binding, 0005524 ATP binding, 0006432 phenylalanyl-tRNA aminoacylation; PDB: 2AKW_B 1B70_B 1B7Y_B 2ALY_B 2IY5_B 2AMC_B 3PCO_D 2CXI_C 1JJC_B 1EIY_B ....

>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=87.37  E-value=1.4  Score=23.22  Aligned_cols=40  Identities=18%  Similarity=0.347  Sum_probs=31.7

Q ss_pred             HHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHH---hcCCeE
Q 036949            5 RMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQ---QQGWTL   44 (81)
Q Consensus         5 ~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~---~~GW~~   44 (81)
                      +|++++..+=..+++.++|+-+|++..-+-.+..   +.||-.
T Consensus         7 ~iL~~l~~~~~~~t~~eia~~~gl~~stv~r~L~tL~~~g~v~   49 (52)
T PF09339_consen    7 RILEALAESGGPLTLSEIARALGLPKSTVHRLLQTLVEEGYVE   49 (52)
T ss_dssp             HHHHCHHCTBSCEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCcCee
Confidence            5778888998999999999999998877655544   568864

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.

>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B

Probab=87.17  E-value=2.8  Score=21.57  Aligned_cols=33  Identities=21%  Similarity=0.299  Sum_probs=23.9

Q ss_pred             HHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHH
Q 036949            5 RMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQ   38 (81)
Q Consensus         5 ~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~   38 (81)
                      +|+.++..- .+++..++|..+|+|+..+..-..
T Consensus         7 ~Il~~Lq~d-~r~s~~~la~~lglS~~~v~~Ri~   39 (42)
T PF13404_consen    7 KILRLLQED-GRRSYAELAEELGLSESTVRRRIR   39 (42)
T ss_dssp             HHHHHHHH--TTS-HHHHHHHHTS-HHHHHHHHH
T ss_pred             HHHHHHHHc-CCccHHHHHHHHCcCHHHHHHHHH
Confidence            566666655 889999999999999998876544

...

>smart00874 B5 tRNA synthetase B5 domain

Probab=86.96  E-value=3.7  Score=22.75  Aligned_cols=32  Identities=13%  Similarity=0.395  Sum_probs=27.9

Q ss_pred             cccHHHHHHHhCC--CHHHHHHHHHhcCCeEeCC
Q 036949           16 TISTQDTALFLGM--NEDDAAYYVQQQGWTLDPA   47 (81)
Q Consensus        16 sIs~~~~a~~Lgl--s~~e~~~~~~~~GW~~d~~   47 (81)
                      +++.+.+.++||+  +.+++.+.....|..++.+
T Consensus         5 ~~~~~~i~~llG~~i~~~ei~~~L~~lg~~~~~~   38 (71)
T smart00874        5 TLRRERINRLLGLDLSAEEIEEILKRLGFEVEVS   38 (71)
T ss_pred             EecHHHHHHHHCCCCCHHHHHHHHHHCCCeEEec
Confidence            4678899999998  7899999999999998653

This domain is found in phenylalanine-tRNA synthetase beta subunits.

>PF08727 P3A: Poliovirus 3A protein like; InterPro: IPR014838 The 3A protein is found in positive-strand RNA viruses

Probab=86.80  E-value=0.43  Score=26.64  Aligned_cols=25  Identities=24%  Similarity=0.522  Sum_probs=14.7

Q ss_pred             HHHHhCC-CHHHHHHHHHhcCCeEeC
Q 036949           22 TALFLGM-NEDDAAYYVQQQGWTLDP   46 (81)
Q Consensus        22 ~a~~Lgl-s~~e~~~~~~~~GW~~d~   46 (81)
                      ++.+|-= ..+|+.+||+++||.+-.
T Consensus        20 I~DLL~SV~~~eV~~YC~~~GWIip~   45 (57)
T PF08727_consen   20 IADLLRSVDSPEVREYCEEQGWIIPA   45 (57)
T ss_dssp             THHHHHHH--HHHHHHHHHHT--TT-
T ss_pred             HHHHHHhcCCHHHHHHHHHCCccccC
Confidence            3444433 568899999999999843

It is a critical component of the poliovirus replication complex, and is also an inhibitor of host cell ER to Golgi transport. ; GO: 0003968 RNA-directed RNA polymerase activity, 0004197 cysteine-type endopeptidase activity, 0017111 nucleoside-triphosphatase activity; PDB: 1NG7_A.

>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A

Probab=86.17  E-value=2.3  Score=23.01  Aligned_cols=39  Identities=15%  Similarity=0.329  Sum_probs=26.5

Q ss_pred             HHHHHHHHhcccccHHHHHHHhCCCHHHHHHH---HHhcCCe
Q 036949            5 RMFQLLMSAYSTISTQDTALFLGMNEDDAAYY---VQQQGWT   43 (81)
Q Consensus         5 ~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~---~~~~GW~   43 (81)
                      .++.+|......++..+++.++|++...+...   ..++||.
T Consensus         7 ~vL~~l~~~~~~~t~~~l~~~~~~~~~~vs~~i~~L~~~glv   48 (68)
T PF13463_consen    7 QVLRALAHSDGPMTQSDLAERLGISKSTVSRIIKKLEEKGLV   48 (68)
T ss_dssp             HHHHHHT--TS-BEHHHHHHHTT--HHHHHHHHHHHHHTTSE
T ss_pred             HHHHHHHccCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCE
Confidence            46667777889999999999999987665444   4567998

>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases

Probab=86.11  E-value=2.6  Score=23.66  Aligned_cols=44  Identities=14%  Similarity=0.225  Sum_probs=35.4

Q ss_pred             hHHHHHHHHHHhcc-cccHHHHHHHhCCCHHHHHHHHH---hcCCeEe
Q 036949            2 YTKRMFQLLMSAYS-TISTQDTALFLGMNEDDAAYYVQ---QQGWTLD   45 (81)
Q Consensus         2 ~R~~~~~li~~AY~-sIs~~~~a~~Lgls~~e~~~~~~---~~GW~~d   45 (81)
                      .+++|+.++...=. .++..++|..||++...+..+..   +.|+..-
T Consensus         7 ~~~~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~~~G~V~~   54 (68)
T smart00550        7 LEEKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLEKKGKVCK   54 (68)
T ss_pred             HHHHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEe
Confidence            57889999998844 49999999999999888877654   5688653

Helix-turn-helix-containing domain. Also known as Zab.

>PF14056 DUF4250: Domain of unknown function (DUF4250)

Probab=85.71  E-value=2  Score=23.79  Aligned_cols=30  Identities=10%  Similarity=0.216  Sum_probs=28.2

Q ss_pred             cHHHHHHHhCCCHHHHHHHHHhcCCeEeCC
Q 036949           18 STQDTALFLGMNEDDAAYYVQQQGWTLDPA   47 (81)
Q Consensus        18 s~~~~a~~Lgls~~e~~~~~~~~GW~~d~~   47 (81)
                      |+++++..++++.+++.+-...-|..+|+.
T Consensus        22 sLd~Lc~~~~id~~~l~~kL~~~Gy~Y~~~   51 (55)
T PF14056_consen   22 SLDELCYDYDIDKEELEEKLASIGYEYDEE   51 (55)
T ss_pred             CHHHHHHHhCCCHHHHHHHHHHcCCeEchh
Confidence            889999999999999999999999999875

>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins

Probab=85.52  E-value=1.5  Score=21.82  Aligned_cols=22  Identities=23%  Similarity=0.465  Sum_probs=19.6

Q ss_pred             cHHHHHHHhCCCHHHHHHHHHh
Q 036949           18 STQDTALFLGMNEDDAAYYVQQ   39 (81)
Q Consensus        18 s~~~~a~~Lgls~~e~~~~~~~   39 (81)
                      ++.++|.+||++..-+..++.+
T Consensus         2 s~~e~a~~lgvs~~tl~~~~~~   23 (49)
T cd04762           2 TTKEAAELLGVSPSTLRRWVKE   23 (49)
T ss_pred             CHHHHHHHHCcCHHHHHHHHHc
Confidence            6789999999999999988874

Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.

>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B

Probab=85.00  E-value=4.1  Score=22.01  Aligned_cols=36  Identities=19%  Similarity=0.403  Sum_probs=30.2

Q ss_pred             hHHHHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHH
Q 036949            2 YTKRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQ   38 (81)
Q Consensus         2 ~R~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~   38 (81)
                      .|.+|+..+ ......+..++|..||++...+-....
T Consensus        11 ~R~~Il~~L-~~~~~~t~~ela~~l~~~~~t~s~hL~   46 (61)
T PF12840_consen   11 TRLRILRLL-ASNGPMTVSELAEELGISQSTVSYHLK   46 (61)
T ss_dssp             HHHHHHHHH-HHCSTBEHHHHHHHHTS-HHHHHHHHH
T ss_pred             HHHHHHHHH-hcCCCCCHHHHHHHHCCCHHHHHHHHH
Confidence            588899988 788999999999999999988766655

...

>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A

Probab=84.90  E-value=1.7  Score=21.76  Aligned_cols=30  Identities=17%  Similarity=0.217  Sum_probs=21.0

Q ss_pred             cccccHHHHHHHhCCCHHHHHHHHHhc-CCe
Q 036949           14 YSTISTQDTALFLGMNEDDAAYYVQQQ-GWT   43 (81)
Q Consensus        14 Y~sIs~~~~a~~Lgls~~e~~~~~~~~-GW~   43 (81)
                      -+.++++++|..+|+|+.-+....++. |.+
T Consensus         6 ~~~~~l~~iA~~~g~S~~~f~r~Fk~~~g~t   36 (42)
T PF00165_consen    6 QQKLTLEDIAEQAGFSPSYFSRLFKKETGMT   36 (42)
T ss_dssp             -SS--HHHHHHHHTS-HHHHHHHHHHHTSS-
T ss_pred             cCCCCHHHHHHHHCCCHHHHHHHHHHHHCcC
Confidence            457899999999999998888777755 765

>COG2522 Predicted transcriptional regulator [General function prediction only]

Probab=84.87  E-value=2.5  Score=26.83  Aligned_cols=37  Identities=16%  Similarity=0.279  Sum_probs=28.7

Q ss_pred             hHHHHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHHhc
Q 036949            2 YTKRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQQQ   40 (81)
Q Consensus         2 ~R~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~~~   40 (81)
                      ||..++.-+..-  -.|-.++|.+||+++..+-+|..++
T Consensus        10 iRa~lA~~L~ee--G~Sq~~iA~LLGltqaAVS~Yls~k   46 (119)
T COG2522          10 IRALLAKELIEE--GLSQYRIAKLLGLTQAAVSQYLSGK   46 (119)
T ss_pred             HHHHHHHHHHHc--CCcHHHHHHHhCCCHHHHHHHHccC
Confidence            566666644333  6778899999999999999999854

>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein

Probab=84.69  E-value=2.8  Score=22.84  Aligned_cols=28  Identities=21%  Similarity=0.280  Sum_probs=23.9

Q ss_pred             cccHHHHHHHhCC-CHHHHHHHHHhc-CCe
Q 036949           16 TISTQDTALFLGM-NEDDAAYYVQQQ-GWT   43 (81)
Q Consensus        16 sIs~~~~a~~Lgl-s~~e~~~~~~~~-GW~   43 (81)
                      .++++++|..+|+ |...+....++. |.+
T Consensus        50 ~~~~~~ia~~~g~~s~~~f~r~Fk~~~g~s   79 (84)
T smart00342       50 DLSVTEIALRVGFSSQSYFSRAFKKLFGVT   79 (84)
T ss_pred             CCCHHHHHHHhCCCChHHHHHHHHHHHCcC
Confidence            6999999999999 999998887654 655

>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets

Probab=84.58  E-value=4.2  Score=21.28  Aligned_cols=35  Identities=20%  Similarity=0.358  Sum_probs=25.5

Q ss_pred             HHHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHH
Q 036949            4 KRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQ   38 (81)
Q Consensus         4 ~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~   38 (81)
                      .+++.++-.+=..|+..++|..||+|..-+.....
T Consensus         3 ~~il~~L~~~~~~it~~eLa~~l~vS~rTi~~~i~   37 (55)
T PF08279_consen    3 KQILKLLLESKEPITAKELAEELGVSRRTIRRDIK   37 (55)
T ss_dssp             HHHHHHHHHTTTSBEHHHHHHHCTS-HHHHHHHHH
T ss_pred             HHHHHHHHHcCCCcCHHHHHHHhCCCHHHHHHHHH
Confidence            46777775444459999999999999877765554

The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....

>PF01418 HTH_6: Helix-turn-helix domain, rpiR family; InterPro: IPR000281 This domain contains a helix-turn-helix motif []

Probab=84.24  E-value=3.2  Score=23.71  Aligned_cols=39  Identities=10%  Similarity=0.259  Sum_probs=27.7

Q ss_pred             HHHHHHHHhcc---cccHHHHHHHhCCCHHHHHHHHHhcCCe
Q 036949            5 RMFQLLMSAYS---TISTQDTALFLGMNEDDAAYYVQQQGWT   43 (81)
Q Consensus         5 ~~~~li~~AY~---sIs~~~~a~~Lgls~~e~~~~~~~~GW~   43 (81)
                      +|++.|-.-+.   ..++.++|.-+|.|+.-+..||++.|-.
T Consensus        20 ~Ia~yil~~~~~~~~~si~elA~~~~vS~sti~Rf~kkLG~~   61 (77)
T PF01418_consen   20 KIADYILENPDEIAFMSISELAEKAGVSPSTIVRFCKKLGFS   61 (77)
T ss_dssp             HHHHHHHH-HHHHCT--HHHHHHHCTS-HHHHHHHHHHCTTT
T ss_pred             HHHHHHHhCHHHHHHccHHHHHHHcCCCHHHHHHHHHHhCCC
Confidence            45555544443   6789999999999999999999998853

Every member of this family is N-terminal to a SIS domain IPR001347 from INTERPRO. Members of this family are probably regulators of genes involved in phosphosugar metobolism.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2O3F_B 3IWF_B.

>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]

Probab=84.11  E-value=9.1  Score=24.79  Aligned_cols=67  Identities=15%  Similarity=0.096  Sum_probs=44.3

Q ss_pred             HHHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHHhcCCeEeCCCceEeecCCCCcccCCCChhHHHHHHhH
Q 036949            4 KRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQQQGWTLDPASRMLTVKKQPLVTEQKLDPSKMQCLTEY   75 (81)
Q Consensus         4 ~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~~~GW~~d~~~~~~~p~~~~~~~~~~~~~~~l~~Lt~~   75 (81)
                      .|....+.--|.-.|..++|.++|.|..-+..++..  |.  ..|.. .|.++....+..++..|++.|-+.
T Consensus         9 ~R~~~~~~~~~~G~S~re~Ak~~gvs~sTvy~wv~r--~~--e~G~~-l~~~~~~GrP~kl~~~q~~~l~e~   75 (138)
T COG3415           9 LRERVVDAVVGEGLSCREAAKRFGVSISTVYRWVRR--YR--ETGLD-LPPKPRKGRPRKLSEEQLEILLER   75 (138)
T ss_pred             HHHHHHHHHHHcCccHHHHHHHhCccHHHHHHHHHH--hc--ccccc-ccCccCCCCCcccCHHHHHHHHHH
Confidence            455556666788999999999999998888877763  11  12222 355555555555577777766544

>PRK12686 carbamate kinase; Reviewed

Probab=83.94  E-value=2.9  Score=30.49  Aligned_cols=21  Identities=24%  Similarity=0.232  Sum_probs=17.8

Q ss_pred             CCCHHHHHHHHHhcCCeEeCC
Q 036949           27 GMNEDDAAYYVQQQGWTLDPA   47 (81)
Q Consensus        27 gls~~e~~~~~~~~GW~~d~~   47 (81)
                      +++++|+...++++||++-.|
T Consensus       133 ~~~~~~a~~~~~~~g~~~~~d  153 (312)
T PRK12686        133 FYTEEEAKQQAEQPGSTFKED  153 (312)
T ss_pred             ccCHHHHHHHHHHcCCccccc
Confidence            458999999999999987666

>PF05687 DUF822: Plant protein of unknown function (DUF822); InterPro: IPR008540 This group of proteins contains members of the BZR1/LAT61 family of plant transcriptional repressors involved in controlling the response to Brassinosteroids (BRs)

Probab=83.90  E-value=1.2  Score=29.36  Aligned_cols=24  Identities=17%  Similarity=0.587  Sum_probs=18.0

Q ss_pred             CHHHHH-HHHHhcCCeEeCCCceEe
Q 036949           29 NEDDAA-YYVQQQGWTLDPASRMLT   52 (81)
Q Consensus        29 s~~e~~-~~~~~~GW~~d~~~~~~~   52 (81)
                      +-+|+. ++|.+-||++++||..+-
T Consensus        46 D~NeVLkALc~eAGw~Ve~DGTtyr   70 (150)
T PF05687_consen   46 DNNEVLKALCREAGWTVEPDGTTYR   70 (150)
T ss_pred             CHHHHHHHHHHhCCEEEccCCCeec
Confidence            346654 788899999999986643

BRs are plant hormones that play essential roles in growth and development. BZR1 binds directly to DNA repressing the synthesis of genes involved in BR synthesis. Phosphorylation of BZR1 by BIN1 targets BZR1 to the 20S proteosome, while dephosphorylation leads to nuclear accumulation of BZR1 [].

>PF08280 HTH_Mga: M protein trans-acting positive regulator (MGA) HTH domain; InterPro: IPR013199 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions []

Probab=83.66  E-value=4.8  Score=21.87  Aligned_cols=35  Identities=17%  Similarity=0.278  Sum_probs=28.2

Q ss_pred             HHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHHhc
Q 036949            5 RMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQQQ   40 (81)
Q Consensus         5 ~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~~~   40 (81)
                      +++.++-+ -..+++.++|..||+|..-+..++.+.
T Consensus         9 ~Ll~~L~~-~~~~~~~ela~~l~~S~rti~~~i~~L   43 (59)
T PF08280_consen    9 KLLELLLK-NKWITLKELAKKLNISERTIKNDINEL   43 (59)
T ss_dssp             HHHHHHHH-HTSBBHHHHHHHCTS-HHHHHHHHHHH
T ss_pred             HHHHHHHc-CCCCcHHHHHHHHCCCHHHHHHHHHHH
Confidence            45667777 889999999999999998888877754

; PDB: 2WTE_A 3SQN_A.

>PF01022 HTH_5: Bacterial regulatory protein, arsR family; InterPro: IPR001845 Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities

Probab=83.63  E-value=3.8  Score=21.11  Aligned_cols=35  Identities=17%  Similarity=0.306  Sum_probs=29.2

Q ss_pred             hHHHHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHH
Q 036949            2 YTKRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQ   38 (81)
Q Consensus         2 ~R~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~   38 (81)
                      .|-+|+.++.+  ...++.+++..||++...+-.+..
T Consensus         3 ~R~~Il~~L~~--~~~~~~el~~~l~~s~~~vs~hL~   37 (47)
T PF01022_consen    3 TRLRILKLLSE--GPLTVSELAEELGLSQSTVSHHLK   37 (47)
T ss_dssp             HHHHHHHHHTT--SSEEHHHHHHHHTS-HHHHHHHHH
T ss_pred             HHHHHHHHHHh--CCCchhhHHHhccccchHHHHHHH
Confidence            48889999988  889999999999999988876654

One such group, termed arsR, includes several proteins that appear to dissociate from DNA in the presence of metal ions: arsR, which functions as a transcriptional repressor of an arsenic resistance operon; smtB from Synechococcus sp. (strain PCC 7942), which acts as a transcriptional repressor of the smtA gene that codes for a metallothionein; cadC, a protein required for cadmium-resistance; and hypothetical protein yqcJ from Bacillus subtilis. The HTH motif is thought to be located in the central part of these proteins []. The motif is characterised by a number of well-conserved residues: at its N-terminal extremity is a cysteine residue; a second Cys is found in arsR and cadC, but not in smtA; and at the C terminus lie one or two histidines. These residues may be involved in metal-binding (Zn in smtB; metal-oxyanions such as arsenite, antimonite and arsenate for arsR; and cadmium for cadC) []. It is believed that binding of a metal ion could induce a conformational change that would prevent the protein from binding DNA []. The crystal structure of the cyanobacterial smtB shows a fold of five alpha-helices (H) and a pair of antiparallel beta-strands (B) in the topology H1-H2-H3-H4-B1-B2-H5. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing as in other wHTH, such as the dtxR-type or the merR-type. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. Most arsR/smtB-like metalloregulators form homodimers []. The dimer interface is formed by helix 5 and an N-terminal part []. Two distinct metal-binding sites have been identified. The first site comprises cysteine thiolates located in the HTH in helix 3 and for some cases in the N terminus, called the alpha3(N) site []. The second metal-binding site is located in helix 5 (and C terminus) and is called the alpha5(C) site. The alpha3N site binds large thiophilic, toxic metals including Cd, Pb, and Bi, as in S. aureus cadC. ArsR lacks the N-terminal arm and its alpha3 site coordinates smaller thiophilic ions like As and Sb. The alpha5 site contains carboxylate and imidazole ligands and interacts preferentially with biologically required metal ions including Zn, Co, and Ni. ArsR-type metalloregulators contain one of these sites, both, or other potential metal-binding sites [, ]. Binding of metal ions to these sites leads to allosteric changes that can derepress the operator/promotor DNA. The metal-inducible operons contain one or two imperfect 12-2-12 inverted repeats, which can be recognised by multimeric arsR-type metalloregulators. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3CUO_A 1U2W_C 3F72_C 3F6V_A 3JTH_B 2P4W_B 1KU9_B 2LKP_B 1SMT_A 1R22_B ....

>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=83.41  E-value=4.5  Score=20.68  Aligned_cols=40  Identities=18%  Similarity=0.380  Sum_probs=28.9

Q ss_pred             hHHHHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHH---hcCC
Q 036949            2 YTKRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQ---QQGW   42 (81)
Q Consensus         2 ~R~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~---~~GW   42 (81)
                      .+.+|+.++..--. ++..++|..+|+|..-+..+..   +.||
T Consensus         4 ~~~~Il~~l~~~~~-~t~~ela~~~~is~~tv~~~l~~L~~~g~   46 (48)
T PF13412_consen    4 TQRKILNYLRENPR-ITQKELAEKLGISRSTVNRYLKKLEEKGL   46 (48)
T ss_dssp             HHHHHHHHHHHCTT-S-HHHHHHHHTS-HHHHHHHHHHHHHTTS
T ss_pred             HHHHHHHHHHHcCC-CCHHHHHHHhCCCHHHHHHHHHHHHHCcC
Confidence            35678888888444 9999999999999877766655   3465

...

>PF12324 HTH_15: Helix-turn-helix domain of alkylmercury lyase; InterPro: IPR024259 Alkylmercury lyase (EC:4

Probab=83.31  E-value=7.2  Score=22.99  Aligned_cols=45  Identities=16%  Similarity=0.246  Sum_probs=32.9

Q ss_pred             HHHHHHHhcccccHHHHHHHhCCCHHHHHHHHHh-cCCeEeCCCceE
Q 036949            6 MFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQQ-QGWTLDPASRML   51 (81)
Q Consensus         6 ~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~~-~GW~~d~~~~~~   51 (81)
                      +++++.+ =.-+++.++|.-+|.+.+++.+.... -+=++|.+|+++
T Consensus        29 LLr~LA~-G~PVt~~~LA~a~g~~~e~v~~~L~~~p~tEyD~~GrIV   74 (77)
T PF12324_consen   29 LLRLLAK-GQPVTVEQLAAALGWPVEEVRAALAAMPDTEYDDQGRIV   74 (77)
T ss_dssp             HHHHHTT-TS-B-HHHHHHHHT--HHHHHHHHHH-TTSEEETTSEEE
T ss_pred             HHHHHHc-CCCcCHHHHHHHHCCCHHHHHHHHHhCCCceEcCCCCee
Confidence            4555555 56789999999999999999998776 488999888775

99.1.2) cleaves the carbon-mercury bond of organomercurials such as phenylmercuric acetate. This entry represents the N-terminal helix-turn-helix domain.; PDB: 3FN8_B 3F2G_B 3F0P_A 3F2F_B 3F2H_A 3F0O_B 1S6L_A.

>smart00497 IENR1 Intron encoded nuclease repeat motif

Probab=83.29  E-value=3.4  Score=21.39  Aligned_cols=27  Identities=22%  Similarity=0.484  Sum_probs=21.9

Q ss_pred             ccHHHHHHHhCCCHHHHHHHHHhcCCeE
Q 036949           17 ISTQDTALFLGMNEDDAAYYVQQQGWTL   44 (81)
Q Consensus        17 Is~~~~a~~Lgls~~e~~~~~~~~GW~~   44 (81)
                      -|+.+||++||++..-+...+.. |+..
T Consensus        18 ~S~~eAa~~lg~~~~~I~~~~~~-~~~~   44 (53)
T smart00497       18 SSIREAAKYLGISHSSISKYLNT-GKKF   44 (53)
T ss_pred             cCHHHHHHHhCCCHHHHHHHHhC-CCcc
Confidence            37889999999999888888775 5555

Repeat of unknown function, but possibly DNA-binding via helix-turn-helix motif (Ponting, unpublished).

>PF08220 HTH_DeoR: DeoR-like helix-turn-helix domain; InterPro: IPR001034 The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism

Probab=83.19  E-value=4.3  Score=21.93  Aligned_cols=40  Identities=20%  Similarity=0.310  Sum_probs=29.6

Q ss_pred             HHHHHHHHHHhcccccHHHHHHHhCCCHHHHHHHH---HhcCCe
Q 036949            3 TKRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYV---QQQGWT   43 (81)
Q Consensus         3 R~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~---~~~GW~   43 (81)
                      ++.|+.++.. -..+++.++|..||.|..-+..-.   .+.|.-
T Consensus         2 ~~~Il~~l~~-~~~~s~~ela~~~~VS~~TiRRDl~~L~~~g~i   44 (57)
T PF08220_consen    2 QQQILELLKE-KGKVSVKELAEEFGVSEMTIRRDLNKLEKQGLI   44 (57)
T ss_pred             HHHHHHHHHH-cCCEEHHHHHHHHCcCHHHHHHHHHHHHHCCCE
Confidence            4677777755 589999999999999987664433   345664

This family of prokaryotic regulators is named after the Escherichia coli protein DeoR, a repressor of the deo operon, which encodes nucleotide and deoxyribonucleotide catabolic enzymes. DeoR also negatively regulates the expression of nupG and tsx, a nucleoside-specific transport protein and a channel-forming protein, respectively. DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway. The DNA-binding deoR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerisation domain. DeoR occurs as an octamer, whilst glpR and agaR are tetramers. Several operators may be bound simultaneously, which could facilitate DNA looping [, ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular

>PF01296 Galanin: Galanin; InterPro: IPR008174 Galanin is a peptide hormone that controls various biological activities []

Probab=83.02  E-value=0.77  Score=22.06  Aligned_cols=19  Identities=32%  Similarity=0.482  Sum_probs=15.6

Q ss_pred             CCeEeCCCceEeecCCCCc
Q 036949           41 GWTLDPASRMLTVKKQPLV   59 (81)
Q Consensus        41 GW~~d~~~~~~~p~~~~~~   59 (81)
                      ||++++.|..+-|-..++-
T Consensus         1 gwtlnsagyLlGPhaiD~H   19 (29)
T PF01296_consen    1 GWTLNSAGYLLGPHAIDNH   19 (29)
T ss_pred             CccccccceEeccccccCc
Confidence            8999999999888766553

Galanin-like immuno-reactivity has been found in the central and peripheral nervous systems of mammals, with high concentrations demonstrated in discrete regions of the central nervous system, including the median eminence, hypothalamus, arcuate nucleus, septum, neuro-intermediate lobe of the pituitary, and the spinal cord. Its localisation within neurosecretory granules suggests that galanin may function as a neurotransmitter, and it has been shown to coexist with a variety of other peptide and amine neurotransmitters within individual neurons []. Although the precise physiological role of galanin is uncertain, it has a number of pharmacological properties: it stimulates food intake, when injected into the third ventricle of rats; it increases levels of plasma growth hormone and prolactin, and decreases dopamine levels in the median eminence []; and infusion into humans results in hyperglycemia and glucose intolerance, and inhibits pancreatic release of insulin, somatostatin and pancreatic peptide. Galanin also modulates smooth muscle contractility within the gastro-intestinal and genito-urinary tracts, all such activities suggesting that the hormone may play an important role in the nervous modulation of endocrine and smooth muscle function []. Galanin is a 29 amino acid peptide processed from a larger precursor protein. Except in human, galanin is C-terminally amidated. Its sequence is highly conserved and the first 14 residues are identical in all currently known sequences.; GO: 0005179 hormone activity, 0005576 extracellular region

>KOG3389 consensus NADH:ubiquinone oxidoreductase, NDUFS4/18 kDa subunit [Energy production and conversion]

Probab=82.69  E-value=0.71  Score=30.63  Aligned_cols=27  Identities=22%  Similarity=0.634  Sum_probs=20.7

Q ss_pred             HHHHHhCC-CHHHHHHHHHhcCCeEeCC
Q 036949           21 DTALFLGM-NEDDAAYYVQQQGWTLDPA   47 (81)
Q Consensus        21 ~~a~~Lgl-s~~e~~~~~~~~GW~~d~~   47 (81)
                      .+..-|-| +.+++..||.+.||.+|-.
T Consensus       124 Nvgm~L~F~tkEdA~sFaEkngW~ydve  151 (178)
T KOG3389|consen  124 NVGMALAFDTKEDAKSFAEKNGWDYDVE  151 (178)
T ss_pred             ccceeeeeccHHHHHHHHHHcCCccccc
Confidence            33344556 7899999999999999754

>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor

Probab=82.50  E-value=3.7  Score=21.16  Aligned_cols=37  Identities=16%  Similarity=0.313  Sum_probs=27.7

Q ss_pred             HHHHHHHhcccccHHHHHHHhCCCHHHHHHHH---HhcCCeE
Q 036949            6 MFQLLMSAYSTISTQDTALFLGMNEDDAAYYV---QQQGWTL   44 (81)
Q Consensus         6 ~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~---~~~GW~~   44 (81)
                      ++.++.  -..++..+++..||++...+....   .++||-.
T Consensus         2 il~~l~--~~~~~~~~i~~~l~is~~~v~~~l~~L~~~g~i~   41 (66)
T smart00418        2 ILKLLA--EGELCVCELAEILGLSQSTVSHHLKKLREAGLVE   41 (66)
T ss_pred             HHHHhh--cCCccHHHHHHHHCCCHHHHHHHHHHHHHCCCee
Confidence            455665  677899999999999876665554   4678885

>PF09035 Tn916-Xis: Excisionase from transposon Tn916; InterPro: IPR015122 The phage-encoded excisionase protein Tn916-Xis adopts a winged-helix structure that consists of a three-stranded anti-parallel beta-sheet that packs against a helix-turn-helix (HTH) motif and a third C-terminal alpha-helix

Probab=82.32  E-value=3.2  Score=23.76  Aligned_cols=37  Identities=19%  Similarity=0.306  Sum_probs=24.9

Q ss_pred             cccHHHHHHHhCCCHHHHHHHH-H--hcCCeEeCCCceEe
Q 036949           16 TISTQDTALFLGMNEDDAAYYV-Q--QQGWTLDPASRMLT   52 (81)
Q Consensus        16 sIs~~~~a~~Lgls~~e~~~~~-~--~~GW~~d~~~~~~~   52 (81)
                      .+++++||.|.|+..+-+.+.+ .  ..+|.+--++++++
T Consensus        13 ~LTi~EAa~Y~gIG~~klr~l~~~~~~~~f~~~~G~r~lI   52 (67)
T PF09035_consen   13 TLTIEEAAEYFGIGEKKLRELAEENPDCPFVLWIGNRRLI   52 (67)
T ss_dssp             EEEHHHHHHHT-S-HHHHHHHHHH-TT-SSEEEETTEEEE
T ss_pred             ccCHHHHHHHhCccHHHHHHHHHhCCCCCEEEEECCEEEE
Confidence            4688999999999999999999 3  33666543444443

It is encoded for by Tn916, which also codes for the integrase Tn916-Int. The protein interacts with DNA by the insertion of helix alpha-2 into the major groove and the contact of the hairpin that connects strands beta-2 and beta-3 with the adjacent phosphodiester backbone and/or minor groove. Tn916-Xis stimulates phage excision and inhibits viral integration by stabilising distorted DNA structures []. ; PDB: 1Y6U_A.

>PF06627 DUF1153: Protein of unknown function (DUF1153); InterPro: IPR009534 This family consists of several short, hypothetical bacterial proteins of unknown function

Probab=82.11  E-value=5.1  Score=24.30  Aligned_cols=37  Identities=11%  Similarity=0.150  Sum_probs=30.4

Q ss_pred             hHHHHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHH
Q 036949            2 YTKRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQ   38 (81)
Q Consensus         2 ~R~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~   38 (81)
                      .|++..-...-.|.-|+.+++++.-|||.+|+..+..
T Consensus        35 a~RKAaVV~aV~~Glis~~EA~~rY~Ls~eEf~~W~~   71 (90)
T PF06627_consen   35 ARRKAAVVRAVRGGLISVEEACRRYGLSEEEFESWQR   71 (90)
T ss_dssp             HHHHHHHHHHHHCTTS-HHHHHHCTTSSHHHHHHHHH
T ss_pred             hhHHHHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHH
Confidence            3566666777789999999999999999999998765

; PDB: 2OA4_A 2JRT_A.

>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein

Probab=81.70  E-value=4.9  Score=19.98  Aligned_cols=35  Identities=17%  Similarity=0.404  Sum_probs=24.5

Q ss_pred             cccHHHHHHHhCCCHHHHHHHH---HhcCCeEeCCCce
Q 036949           16 TISTQDTALFLGMNEDDAAYYV---QQQGWTLDPASRM   50 (81)
Q Consensus        16 sIs~~~~a~~Lgls~~e~~~~~---~~~GW~~d~~~~~   50 (81)
                      .++..++|.++|++...+....   .+.||-.-..+.+
T Consensus         8 ~~s~~~la~~l~~s~~tv~~~l~~L~~~g~l~~~~~~~   45 (48)
T smart00419        8 PLTRQEIAELLGLTRETVSRTLKRLEKEGLISREGGRI   45 (48)
T ss_pred             ccCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeCCEE
Confidence            4678899999999887765554   4679975333333

>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR

Probab=81.36  E-value=5.6  Score=26.64  Aligned_cols=43  Identities=9%  Similarity=0.131  Sum_probs=35.0

Q ss_pred             ChHHHHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHH---hcCCeE
Q 036949            1 LYTKRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQ---QQGWTL   44 (81)
Q Consensus         1 ~~R~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~---~~GW~~   44 (81)
                      +.|++|+..+.+. ..++..++|..||++..-+.....   +.||..
T Consensus         1 ~tr~~IL~~L~~~-~~~t~~eLA~~lgis~~tV~~~L~~Le~~GlV~   46 (203)
T TIGR02702         1 STKEDILSYLLKQ-GQATAAALAEALAISPQAVRRHLKDLETEGLIE   46 (203)
T ss_pred             CHHHHHHHHHHHc-CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeE
Confidence            3588999988764 779999999999999887766654   569985

All members of this cyanobacterial protein family are the transcriptional regulator SufR and regulate the SUF system, which makes possible iron-sulfur cluster biosynthesis despite exposure to oxygen. In all cases, the sufR gene is encoded near SUF system genes but in the opposite direction. This DNA-binding protein belongs to the the DeoR family of helix-loop-helix proteins. All members also have a probable metal-binding motif C-X(12)-C-X(13)-C-X(14)-C near the C-terminus.

>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A)

Probab=81.34  E-value=4  Score=24.34  Aligned_cols=44  Identities=14%  Similarity=0.314  Sum_probs=32.0

Q ss_pred             hHHHHHHHHHHhc---ccccHHHHHHHhCCCHHHHHHHHH---hcCCeEe
Q 036949            2 YTKRMFQLLMSAY---STISTQDTALFLGMNEDDAAYYVQ---QQGWTLD   45 (81)
Q Consensus         2 ~R~~~~~li~~AY---~sIs~~~~a~~Lgls~~e~~~~~~---~~GW~~d   45 (81)
                      ++++|+..|....   .=|+++++++.||++.+++.+.+.   ..|..+.
T Consensus        48 ~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs   97 (102)
T PF08784_consen   48 LQDKVLNFIKQQPNSEEGVHVDEIAQQLGMSENEVRKALDFLSNEGHIYS   97 (102)
T ss_dssp             HHHHHHHHHHC----TTTEEHHHHHHHSTS-HHHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHHHHhcCCCCCcccHHHHHHHhCcCHHHHHHHHHHHHhCCeEec
Confidence            4778888888733   339999999999999988766655   4577763

RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.

>COG2886 Uncharacterized small protein [Function unknown]

Probab=81.03  E-value=5.2  Score=24.14  Aligned_cols=36  Identities=19%  Similarity=0.281  Sum_probs=30.3

Q ss_pred             HHHHHhcccccHHHHHHHhCCCHHHHHHHHHhcCCeEe
Q 036949            8 QLLMSAYSTISTQDTALFLGMNEDDAAYYVQQQGWTLD   45 (81)
Q Consensus         8 ~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~~~GW~~d   45 (81)
                      .++.+  ..||+..+|.+.|++..++.....+||=...
T Consensus        35 ~L~qe--g~vSlg~Aaela~~sl~ef~~eL~~R~i~l~   70 (88)
T COG2886          35 ELFQE--GAVSLGRAAELAGMSLNEFEEELRKRGIPLY   70 (88)
T ss_pred             HHHHH--hhhHHHHHHHHhcCCHHHHHHHHHHhCCCcc
Confidence            34444  7899999999999999999999999986653

>PF01853 MOZ_SAS: MOZ/SAS family; InterPro: IPR002717 Moz is a monocytic leukemia Zn_finger protein and the SAS protein from Saccharomyces cerevisiae (Baker's yeast) is involved in silencing the Hmr locus

Probab=80.82  E-value=7.4  Score=26.58  Aligned_cols=49  Identities=18%  Similarity=0.223  Sum_probs=37.3

Q ss_pred             HHHHHHHHHHhcc--cccHHHHHHHhCCCHHHHHHHHHhcCCeEeCCCceE
Q 036949            3 TKRMFQLLMSAYS--TISTQDTALFLGMNEDDAAYYVQQQGWTLDPASRML   51 (81)
Q Consensus         3 R~~~~~li~~AY~--sIs~~~~a~~Lgls~~e~~~~~~~~GW~~d~~~~~~   51 (81)
                      |..+++.+-..-.  .|++++++...|+..+|+....+..|+-.--.+..+
T Consensus       135 ~~~i~~~L~~~~~~~~isi~~is~~Tgi~~~DIi~tL~~l~~l~~~~~~~~  185 (188)
T PF01853_consen  135 RRVILEYLLEFKGKKSISIKDISQETGIRPEDIISTLQQLGMLKYYKGQHI  185 (188)
T ss_dssp             HHHHHHHHHHTSSE--EEHHHHHHHH-BTHHHHHHHHHHTT-EEEETTEEE
T ss_pred             HHHHHHHHHhcCCCCeEEHHHHHHHHCCCHHHHHHHHHHCCCEEEECCcEE
Confidence            5667777776666  599999999999999999999999999865455443

These proteins were reported to be homologous to acetyltransferases [] but this similarity is not supported by standard sequence analysis.; GO: 0016747 transferase activity, transferring acyl groups other than amino-acyl groups, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3TO6_A 1MJA_A 1MJ9_A 3TO7_A 3TO9_A 1MJB_A 1FY7_A 2OZU_A 2RC4_A 2OU2_A ....

>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional

Probab=80.81  E-value=11  Score=26.18  Aligned_cols=51  Identities=10%  Similarity=0.089  Sum_probs=38.0

Q ss_pred             HHHHHHHHHHhcccccHHHHHHHhCCCHHHHHH---HHHhcCCeEeCCCceEeec
Q 036949            3 TKRMFQLLMSAYSTISTQDTALFLGMNEDDAAY---YVQQQGWTLDPASRMLTVK   54 (81)
Q Consensus         3 R~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~---~~~~~GW~~d~~~~~~~p~   54 (81)
                      |++|..++ +....+++.++|.+||+|..-+..   ...++|--.-.-|....|.
T Consensus         7 ~~~Il~~l-~~~~~~~~~ela~~l~vS~~TiRRdL~~Le~~g~l~r~~GGa~~~~   60 (252)
T PRK10906          7 HDAIIELV-KQQGYVSTEELVEHFSVSPQTIRRDLNDLAEQNKILRHHGGAALPS   60 (252)
T ss_pred             HHHHHHHH-HHcCCEeHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecCCEEecC
Confidence            56777888 779999999999999999987755   4456788654445555554

>PRK11511 DNA-binding transcriptional activator MarA; Provisional

Probab=80.75  E-value=5.4  Score=24.77  Aligned_cols=37  Identities=8%  Similarity=0.114  Sum_probs=29.5

Q ss_pred             HHHHHHHHHhc-ccccHHHHHHHhCCCHHHHHHHHHhc
Q 036949            4 KRMFQLLMSAY-STISTQDTALFLGMNEDDAAYYVQQQ   40 (81)
Q Consensus         4 ~~~~~li~~AY-~sIs~~~~a~~Lgls~~e~~~~~~~~   40 (81)
                      .++...|...| ..++++++|+.+|+|+.-+....++.
T Consensus        12 ~~~~~~I~~~~~~~~sl~~lA~~~g~S~~~l~r~Fk~~   49 (127)
T PRK11511         12 HSILDWIEDNLESPLSLEKVSERSGYSKWHLQRMFKKE   49 (127)
T ss_pred             HHHHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            46777887777 56999999999999998886666543

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

No hit with e-value below 0.005

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	81
1rz4_A	226	Eukaryotic translation initiation factor 3 subuni;	99.69
4b0z_A	229	RPN12, 26S proteasome regulatory subunit RPN12; pr	99.44
4b4t_T	274	26S proteasome regulatory subunit RPN12; hydrolase	99.32
3t5v_A	316	Nuclear mRNA export protein SAC3; PCI, mRNA nuclea	98.18
1ufm_A	84	COP9 complex subunit 4; helix-turn-helix, structur	97.5
3txn_A	394	26S proteasome regulatory complex subunit P42B; PC	96.82
4b4t_P	445	26S proteasome regulatory subunit RPN5; hydrolase,	96.38
4b4t_R	429	RPN7, 26S proteasome regulatory subunit RPN7; hydr	95.85
4b4t_Q	434	26S proteasome regulatory subunit RPN6; hydrolase,	95.49
2heo_A	67	Z-DNA binding protein 1; protein DLM1-Z-DNA comple	95.08
1y6u_A	70	XIS, excisionase from transposon TN916; structure,	93.78
2htj_A	81	P fimbrial regulatory protein KS71A; winged helix-	92.51
2lju_A	108	Putative oxidoreductase; structural genomics, seat	91.71
3lsg_A	103	Two-component response regulator YESN; structural	89.85
2jya_A	106	AGR_C_3324P, uncharacterized protein ATU1810; prot	89.75
2jt1_A	77	PEFI protein; solution structure, winged helix-tur	89.33
2k9s_A	107	Arabinose operon regulatory protein; activator, ar	89.29
4b4t_S	523	RPN3, 26S proteasome regulatory subunit RPN3; hydr	88.47
1nd9_A	49	Translation initiation factor IF-2; NMR {Escherich	87.79
3mn2_A	108	Probable ARAC family transcriptional regulator; st	87.24
3e21_A	45	HFAF1, FAS-associated factor 1; UBA, alternative s	87.16
3oou_A	108	LIN2118 protein; protein structure initiative, PSI	86.66
3oio_A	113	Transcriptional regulator (ARAC-type DNA-binding c	86.57
2krk_A	86	26S protease regulatory subunit 8; structural geno	86.0
1ng7_A	60	Poliovirus 3A-N, genome polyprotein [core protein	85.61
3mkl_A	120	HTH-type transcriptional regulator GADX; PSI2, MCS	85.6
3f2g_A	220	Alkylmercury lyase; MERB, organomercurial lyase, m	85.46
3to7_A	276	Histone acetyltransferase ESA1; MYST family; HET:	85.21
3gbg_A	276	TCP pilus virulence regulatory protein; cupin, hel	84.91
3dkw_A	227	DNR protein; CRP-FNR, HTH, beta barrel, dimerizati	83.96
3dv8_A	220	Transcriptional regulator, CRP/FNR family; cyclic	83.9
4b4t_O	393	26S proteasome regulatory subunit RPN9; hydrolase,	83.53
2gmg_A	105	Hypothetical protein PF0610; winged-helix like pro	83.41
1bl0_A	129	Protein (multiple antibiotic resistance protein),	83.03
3aji_B	83	S6C, proteasome (prosome, macropain) 26S subunit,	82.49
1oyi_A	82	Double-stranded RNA-binding protein; (alpha+beta)	81.09
1z96_A	40	DNA-damage, UBA-domain protein MUD1; ubiquitin, th	80.08

>1rz4_A Eukaryotic translation initiation factor 3 subuni; heat analogous motif, winged-helix, biosynthetic protein; 2.10A {Homo sapiens} SCOP: a.4.5.53 a.118.1.18

Probab=99.69  E-value=2e-17  Score=113.22  Aligned_cols=80  Identities=18%  Similarity=0.305  Sum_probs=64.4

Q ss_pred             ChHHHHHHHHHHhcccccHHHHHHHhC-CCHHHHHHHHHhcCCeEeCCCceEeecCCCCcccCCC--ChhHHHHHHhHH-
Q 036949            1 LYTKRMFQLLMSAYSTISTQDTALFLG-MNEDDAAYYVQQQGWTLDPASRMLTVKKQPLVTEQKL--DPSKMQCLTEYV-   76 (81)
Q Consensus         1 ~~R~~~~~li~~AY~sIs~~~~a~~Lg-ls~~e~~~~~~~~GW~~d~~~~~~~p~~~~~~~~~~~--~~~~l~~Lt~~v-   76 (81)
                      ++|.+|+.|+++||++|+++.+++||| ++++++.+|++++||++|++|.+ +|.++++..++..  +...++.++.++ 
T Consensus       137 sIR~~I~~~i~~aY~sI~~~~la~lLg~~s~~el~~fi~~~GW~vd~~g~I-~~~n~e~~~k~~~~~E~i~~~~~~~~~~  215 (226)
T 1rz4_A          137 SVRKFICHVVGITYQHIDRWLLAEMLGDLSDSQLKVWMSKYGWSADESGQI-FICSQEESIKPKNIVEKIDFDSVSSIMA  215 (226)
T ss_dssp             HHHHHHHHHHHHHCSEECHHHHHHHTTSCCHHHHHHHHHHHTCEECC--CE-ECCCHHHHTSCCCSSCCCCHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHhhCCHHHHHHHHcCCCHHHHHHHHHHCCCEECCCccE-EeCCCcccccceeeeecccHHHHHHHHH
Confidence            379999999999999999999999996 69999999999999999878776 6666666666555  999999999998 


Q ss_pred             -HhhcC
Q 036949           77 -FHLEH   81 (81)
Q Consensus        77 -~~LE~   81 (81)
                       ++|||
T Consensus       216 ~~~~~~  221 (226)
T 1rz4_A          216 SSQLEH  221 (226)
T ss_dssp             C-----
T ss_pred             HHHHhh
Confidence             56664

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

Probab=99.44  E-value=1.4e-13  Score=93.71  Aligned_cols=52  Identities=15%  Similarity=0.312  Sum_probs=49.2

Q ss_pred             hHHHHHHHHHHhcccccHHHHHHHhCC-CHHHHHHHHHhcCCeEeCCCceEeec
Q 036949            2 YTKRMFQLLMSAYSTISTQDTALFLGM-NEDDAAYYVQQQGWTLDPASRMLTVK   54 (81)
Q Consensus         2 ~R~~~~~li~~AY~sIs~~~~a~~Lgl-s~~e~~~~~~~~GW~~d~~~~~~~p~   54 (81)
                      +|.+++.||++||.+|++++++.+||| |++|+.+|++++||+++ ||.++||+
T Consensus       176 vR~~~l~~i~kaY~~i~l~~~~~~L~f~s~~e~~~f~~~~gw~i~-dg~i~F~~  228 (229)
T 4b0z_A          176 VRNEIATCAEKVYSEIPLSNATSLLYLENTKETEKLAEERGWDIR-DGVIYFPK  228 (229)
T ss_dssp             HHHHHHHHHHHHCSEEEHHHHHHHTTCSSHHHHHHHHHHHTCEEE-TTEEECC-
T ss_pred             HHHHHHHHHHHHcCCCCHHHHHHHhCCCCHHHHHHHHHHcCCEEe-CCEEecCC
Confidence            799999999999999999999999999 89999999999999998 88899886

>4b4t_T 26S proteasome regulatory subunit RPN12; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=99.32  E-value=1.7e-12  Score=90.70  Aligned_cols=55  Identities=11%  Similarity=0.239  Sum_probs=46.8

Q ss_pred             hHHHHHHHHHHhcccccHHHHHHHhCC-CHHHHHHHHHhcCCeEeCCCceEeecCCC
Q 036949            2 YTKRMFQLLMSAYSTISTQDTALFLGM-NEDDAAYYVQQQGWTLDPASRMLTVKKQP   57 (81)
Q Consensus         2 ~R~~~~~li~~AY~sIs~~~~a~~Lgl-s~~e~~~~~~~~GW~~d~~~~~~~p~~~~   57 (81)
                      +|.+++.||++||.+|+++.++++||| |++|+.+|++++||+++ +|.++||....
T Consensus       185 iR~~a~~~i~kaY~~i~l~~~~~~L~F~s~~e~~~F~~~~gW~~~-~~~v~F~~~~~  240 (274)
T 4b4t_T          185 IRDEIAKNTELSYDFLPLSNIKALLFFNNEKETEKFALERNWPIV-NSKVYFNNQSK  240 (274)
T ss_dssp             HHHHHHHHHHHHCSSCCHHHHHHHHTCCSHHHHHHHHHHTTCCCC-SSCCCC-----
T ss_pred             HHHHHHHHHHHHHhhcCHHHHHHHhCCCCHHHHHHHHHHcCCEEe-CCEeEECCccc
Confidence            799999999999999999999999999 89999999999999998 45666766543

>3t5v_A Nuclear mRNA export protein SAC3; PCI, mRNA nuclear export, mRNA, nuclear, transcription; 2.90A {Saccharomyces cerevisiae}

Probab=98.18  E-value=3.4e-06  Score=59.91  Aligned_cols=47  Identities=9%  Similarity=-0.004  Sum_probs=43.7

Q ss_pred             hHHHHHHHHHHhcc----cccHHHHHHHhCC-CHHHHHHHHHhcCCeEeCCC
Q 036949            2 YTKRMFQLLMSAYS----TISTQDTALFLGM-NEDDAAYYVQQQGWTLDPAS   48 (81)
Q Consensus         2 ~R~~~~~li~~AY~----sIs~~~~a~~Lgl-s~~e~~~~~~~~GW~~d~~~   48 (81)
                      +|.+++.+|.+||.    .++++.++.+||| +.+|+.+||...||+++.++
T Consensus       206 vR~~AL~~i~kay~~k~~~~pl~~L~~~L~Fds~ee~~~F~~~~gl~~~~~~  257 (316)
T 3t5v_A          206 IRFYALRALSHTLNKKHKPIPFIYLENMLLFNNRQEIIEFCNYYSIEIINGD  257 (316)
T ss_dssp             HHHHHHHHHHHHSCTTCCCEEHHHHHHHTTCSSHHHHHHHHHHTTCCEETTT
T ss_pred             HHHHHHHHHHHHhccCCCCcCHHHHHHHhCCCCHHHHHHHHHHCCCeEeCCC
Confidence            79999999999995    8999999999999 79999999999999998644

>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=97.50  E-value=0.00018  Score=42.04  Aligned_cols=53  Identities=11%  Similarity=0.137  Sum_probs=39.8

Q ss_pred             hHHHHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHHhc------CCeEeCCCceEeec
Q 036949            2 YTKRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQQQ------GWTLDPASRMLTVK   54 (81)
Q Consensus         2 ~R~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~~~------GW~~d~~~~~~~p~   54 (81)
                      +.+.-++.+++-|++|+++.+|.+||++++++..++.+.      -=++|.-..++...
T Consensus        16 v~E~nl~~is~~Y~~Isl~~La~ll~ls~~~vE~~ls~mI~~~~l~akIDq~~g~V~f~   74 (84)
T 1ufm_A           16 VIEHNLLSASKLYNNITFEELGALLEIPAAKAEKIASQMITEGRMNGFIDQIDGIVHFE   74 (84)
T ss_dssp             HHHHHHHHHHHSCSEEEHHHHHHHTTSCHHHHHHHHHHHHHTTSSCEEEETTTTEEEEC
T ss_pred             HHHHHHHHHHHhcCeeeHHHHHHHHCcCHHHHHHHHHHHHhCCcEEEEEeCCCCEEEeC
Confidence            456667789999999999999999999999988775542      22566644454443

>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=96.82  E-value=0.0032  Score=45.71  Aligned_cols=75  Identities=16%  Similarity=0.161  Sum_probs=42.9

Q ss_pred             hHHHHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHHh-------cCCeEeCCCceEeecCCCCcccCCC-ChhHHHHHH
Q 036949            2 YTKRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQQ-------QGWTLDPASRMLTVKKQPLVTEQKL-DPSKMQCLT   73 (81)
Q Consensus         2 ~R~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~~-------~GW~~d~~~~~~~p~~~~~~~~~~~-~~~~l~~Lt   73 (81)
                      +|.+.+.-+.+.|++|+++++|..||++++++...+.+       .| ++|...+++.-..++.....-. ..+.++.++
T Consensus       302 Ir~~~L~~i~~pYsrIsl~~iA~~l~ls~~evE~~L~~lI~dg~I~a-~IDq~~giv~~~~~~~r~~~y~~ale~l~~ls  380 (394)
T 3txn_A          302 MLEQNLCRIIEPYSRVQVAHVAESIQLPMPQVEKKLSQMILDKKFSG-ILDQGEGVLIVFEETPVDKTYERVLETIQSMG  380 (394)
T ss_dssp             HHHHHHHHHHTTCSEEEHHHHHHHHTCCHHHHHHHHHHHHHTTSSCE-EEETTTTEEEECCC------------------
T ss_pred             HHHHHHHHHhHhhceeeHHHHHHHHCcCHHHHHHHHHHHHHCCCeeE-EEcCCCCEEEECCCcchhhHHHHHHHHHHHHH
Confidence            57777888899999999999999999999988777543       24 7888666666554432221111 455666666


Q ss_pred             hHHH
Q 036949           74 EYVF   77 (81)
Q Consensus        74 ~~v~   77 (81)
                      ..|-
T Consensus       381 ~vVd  384 (394)
T 3txn_A          381 KVVD  384 (394)
T ss_dssp             ----
T ss_pred             HHHH
Confidence            6663

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

Probab=96.38  E-value=0.01  Score=43.14  Aligned_cols=52  Identities=15%  Similarity=0.226  Sum_probs=38.8

Q ss_pred             hHHHHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHHh-----c--CCeEeC-CCceEeec
Q 036949            2 YTKRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQQ-----Q--GWTLDP-ASRMLTVK   54 (81)
Q Consensus         2 ~R~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~~-----~--GW~~d~-~~~~~~p~   54 (81)
                      +++.-+.-+++-|++|+++++|..||++++++..++.+     +  | ++|. +|.+.|-.
T Consensus       345 v~ehnl~~i~k~Ys~I~l~~la~lL~l~~~evE~~ls~mI~~g~i~a-kIDq~~giV~F~~  404 (445)
T 4b4t_P          345 VIEHNLRVISEYYSRITLLRLNELLDLTESQTETYISDLVNQGIIYA-KVNRPAKIVNFEK  404 (445)
T ss_dssp             HHHHHHHHHHHHEEEEEHHHHHHHHTSCHHHHHHHHHHHHHHTSSCC-EEETTTTEEEC--
T ss_pred             HHHHHHHHHHHHhceeeHHHHHHHhCcCHHHHHHHHHHHHHCCCEEE-EEcCCCCEEEECC
Confidence            45666778999999999999999999999999888653     2  4 5665 45444433

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

Probab=95.85  E-value=0.012  Score=42.45  Aligned_cols=58  Identities=14%  Similarity=0.250  Sum_probs=43.6

Q ss_pred             hHHHHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHHh-----c-CCeEeCCCceEeecCCCCc
Q 036949            2 YTKRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQQ-----Q-GWTLDPASRMLTVKKQPLV   59 (81)
Q Consensus         2 ~R~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~~-----~-GW~~d~~~~~~~p~~~~~~   59 (81)
                      +|.+.+.-+.+.|++|+++.+|..||+|++++.+.+.+     + .=++|.-.+++.-..|+..
T Consensus       333 ir~~~l~q~~~~Ys~I~l~~mA~~l~~s~~~~E~~L~~lI~~g~l~akID~~~giv~~~~~d~~  396 (429)
T 4b4t_R          333 MRRKVYAQLLESYKTLSLKSMASAFGVSVAFLDNDLGKFIPNKQLNCVIDRVNGIVETNRPDNK  396 (429)
T ss_dssp             HHHHHHHHHHHTCSEEEHHHHHHHHTSCHHHHHHHHHHHHHHTSSCEEEETTTTEEEECC----
T ss_pred             HHHHHHHHHhHHhceeeHHHHHHHhCcCHHHHHHHHHHHHHcCCeEEEEcCCCCEEEECCCCch
Confidence            78999999999999999999999999999887665432     2 4467876677766655443

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

Probab=95.49  E-value=0.041  Score=37.55  Aligned_cols=75  Identities=8%  Similarity=0.051  Sum_probs=37.4

Q ss_pred             hHHHHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHHhc------CCeEeCC-CceEeecCCCCcccCCC-ChhHHHHHH
Q 036949            2 YTKRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQQQ------GWTLDPA-SRMLTVKKQPLVTEQKL-DPSKMQCLT   73 (81)
Q Consensus         2 ~R~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~~~------GW~~d~~-~~~~~p~~~~~~~~~~~-~~~~l~~Lt   73 (81)
                      +|...+.-+.+.|++|+++++|..||++++++...+.+.      -=++|.. |.+.+-.++.... .-. .-+.+++|+
T Consensus       342 ~~~~~l~~~~~~y~~i~l~~la~~l~~~~~~~E~~l~~lI~~~~i~a~id~~~g~v~~~~~~~~~~-~~~~~l~~~~~l~  420 (434)
T 4b4t_Q          342 LLESNLCKIIEPFECVEISHISKIIGLDTQQVEGKLSQMILDKIFYGVLDQGNGWLYVYETPNQDA-TYDSALELVGQLN  420 (434)
T ss_dssp             HHHHHHHHHHSSCSCEEHHHHHHHHTCCHHHHHHHHHHHHHHTSSCCEEETTTTEEECC---------------------
T ss_pred             HHHHHHHHHHHHHHhcCHHHHHHHhCcCHHHHHHHHHHHHhCCCcceecccccCeEeeCCCcchhH-HHHHHHHHHHHHH
Confidence            466777889999999999999999999999887765431      1234543 3333322222211 111 445566677


Q ss_pred             hHHH
Q 036949           74 EYVF   77 (81)
Q Consensus        74 ~~v~   77 (81)
                      ++|.
T Consensus       421 ~~vd  424 (434)
T 4b4t_Q          421 KVVD  424 (434)
T ss_dssp             ----
T ss_pred             HHHH
Confidence            6664

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

Probab=95.08  E-value=0.12  Score=28.12  Aligned_cols=43  Identities=5%  Similarity=0.026  Sum_probs=34.6

Q ss_pred             hHHHHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHH---hcCCeE
Q 036949            2 YTKRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQ---QQGWTL   44 (81)
Q Consensus         2 ~R~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~---~~GW~~   44 (81)
                      .|++|+.++...=..++..++|..||+|...+...+.   +.|+..
T Consensus        11 ~~~~IL~~L~~~~~~~s~~eLA~~lglsr~tv~~~l~~L~~~G~I~   56 (67)
T 2heo_A           11 LEQKILQVLSDDGGPVAIFQLVKKCQVPKKTLNQVLYRLKKEDRVS   56 (67)
T ss_dssp             HHHHHHHHHHHHCSCEEHHHHHHHHCSCHHHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHHHcCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEe
Confidence            4788999998754569999999999999888766655   468854

>1y6u_A XIS, excisionase from transposon TN916; structure, DNA architectural protein, tyrosine recombinase, winged-helix protein; NMR {Enterococcus faecalis}

Probab=93.78  E-value=0.14  Score=28.58  Aligned_cols=39  Identities=10%  Similarity=0.384  Sum_probs=31.3

Q ss_pred             cccHHHHHHHhCCCHHHHHHHHHh---cCCeEeCCCceEeec
Q 036949           16 TISTQDTALFLGMNEDDAAYYVQQ---QGWTLDPASRMLTVK   54 (81)
Q Consensus        16 sIs~~~~a~~Lgls~~e~~~~~~~---~GW~~d~~~~~~~p~   54 (81)
                      .++++++|.|||++.+-+.+++.+   ..|.+--++.+.+++
T Consensus        16 ~LTi~EaAeylgIg~~~l~~L~~~~~~~~~~~~iG~~~lI~r   57 (70)
T 1y6u_A           16 TLTIEEASKYFRIGENKLRRLAEENKNANWLIMNGNRIQIKR   57 (70)
T ss_dssp             EEEHHHHHHHTCSCHHHHHHHHHHCTTCSSEEEETTEEEEES
T ss_pred             eeCHHHHHHHHCcCHHHHHHHHHcCCCCCcEEEeCCEEEEEH
Confidence            467899999999999999999987   378764456666665

>2htj_A P fimbrial regulatory protein KS71A; winged helix-turn-helix, PAP PILI, transcription activator; NMR {Escherichia coli} SCOP: a.4.5.73

Probab=92.51  E-value=0.28  Score=27.14  Aligned_cols=42  Identities=19%  Similarity=0.325  Sum_probs=33.6

Q ss_pred             hHHHHHHHHHHhcccccHHHHHHHhCCCHHHHHHHH---HhcCCeE
Q 036949            2 YTKRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYV---QQQGWTL   44 (81)
Q Consensus         2 ~R~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~---~~~GW~~   44 (81)
                      +|++|+.++... ..++..++|..||+|..-+....   .+.|+-.
T Consensus         1 ~r~~Il~~L~~~-~~~s~~eLa~~lgvs~~tv~r~L~~L~~~GlI~   45 (81)
T 2htj_A            1 MKNEILEFLNRH-NGGKTAEIAEALAVTDYQARYYLLLLEKAGMVQ   45 (81)
T ss_dssp             CHHHHHHHHHHS-CCCCHHHHHHHHTSCHHHHHHHHHHHHHHTSEE
T ss_pred             CHHHHHHHHHHc-CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence            478899998764 67999999999999987765554   4569876

>2lju_A Putative oxidoreductase; structural genomics, seattle structural GENO center for infectious disease, ssgcid; NMR {Ehrlichia chaffeensis}

Probab=91.71  E-value=0.13  Score=31.25  Aligned_cols=20  Identities=15%  Similarity=0.160  Sum_probs=17.2

Q ss_pred             hCC-CHHHHHHHHHhcCCeEe
Q 036949           26 LGM-NEDDAAYYVQQQGWTLD   45 (81)
Q Consensus        26 Lgl-s~~e~~~~~~~~GW~~d   45 (81)
                      |.| |.+++++||++.||.+.
T Consensus        64 L~F~skE~AiayAek~G~~y~   84 (108)
T 2lju_A           64 LSFTTRELAIAYAVAHKIDYT   84 (108)
T ss_dssp             EEESSHHHHHHHHHHTTCEEE
T ss_pred             EecCCHHHHHHHHHHcCCEEE
Confidence            344 89999999999999983

>3lsg_A Two-component response regulator YESN; structural genomics, PSI-2, protein structure initiative, MCSG; 2.05A {Fusobacterium nucleatum}

Probab=89.85  E-value=0.65  Score=26.47  Aligned_cols=42  Identities=7%  Similarity=0.136  Sum_probs=34.2

Q ss_pred             hHHHHHHHHHHhcc--cccHHHHHHHhCCCHHHHHHHHHhc-CCe
Q 036949            2 YTKRMFQLLMSAYS--TISTQDTALFLGMNEDDAAYYVQQQ-GWT   43 (81)
Q Consensus         2 ~R~~~~~li~~AY~--sIs~~~~a~~Lgls~~e~~~~~~~~-GW~   43 (81)
                      +-+++...|..-|.  .++++++|..+|+|+..+.....+. |=+
T Consensus         3 ~~~~i~~~i~~~~~~~~~~~~~lA~~~~~S~~~l~r~fk~~~g~s   47 (103)
T 3lsg_A            3 AKELIQNIIEESYTDSQFTLSVLSEKLDLSSGYLSIMFKKNFGIP   47 (103)
T ss_dssp             HHHHHHHHHHHHTTCTTCCHHHHHHHTTCCHHHHHHHHHHHHSSC
T ss_pred             HHHHHHHHHHHHccCCCCCHHHHHHHHCcCHHHHHHHHHHHHCcC
Confidence            34678888999986  6999999999999999887777655 544

>2jya_A AGR_C_3324P, uncharacterized protein ATU1810; protein with unknown function ATU1810, ontario centre for ST proteomics, OCSP; NMR {Agrobacterium tumefaciens str}

Probab=89.75  E-value=0.14  Score=31.09  Aligned_cols=20  Identities=25%  Similarity=0.476  Sum_probs=17.2

Q ss_pred             hCC-CHHHHHHHHHhcCCeEe
Q 036949           26 LGM-NEDDAAYYVQQQGWTLD   45 (81)
Q Consensus        26 Lgl-s~~e~~~~~~~~GW~~d   45 (81)
                      |.| |.+++++||++.||.+.
T Consensus        56 L~F~skE~AiayAek~G~~y~   76 (106)
T 2jya_A           56 LTFETQEQAEAYAQRKGIEYR   76 (106)
T ss_dssp             EEESSHHHHHHHHHHHTCEEE
T ss_pred             EecCCHHHHHHHHHHcCCEEE
Confidence            444 89999999999999984

>2jt1_A PEFI protein; solution structure, winged helix-turn-helix, transcripti regulatory protein, structural genomics, PSI-2; NMR {Salmonella typhimurium LT2}

Probab=89.33  E-value=0.99  Score=25.41  Aligned_cols=41  Identities=15%  Similarity=0.259  Sum_probs=31.5

Q ss_pred             hHHHHHHHHHHh------cccccHHHHHHHhCCCHHHHHHHHH---hcCCe
Q 036949            2 YTKRMFQLLMSA------YSTISTQDTALFLGMNEDDAAYYVQ---QQGWT   43 (81)
Q Consensus         2 ~R~~~~~li~~A------Y~sIs~~~~a~~Lgls~~e~~~~~~---~~GW~   43 (81)
                      .+++|+++|...      | .+++.++|..||+|..-+.....   ++|.-
T Consensus         5 r~~~IL~~I~~~i~~~~g~-~psv~EIa~~lgvS~~TVrr~L~~Le~kG~I   54 (77)
T 2jt1_A            5 IVTKIISIVQERQNMDDGA-PVKTRDIADAAGLSIYQVRLYLEQLHDVGVL   54 (77)
T ss_dssp             HHHHHHHHHHHHHHHHTTS-CEEHHHHHHHHTCCHHHHHHHHHHHHHTTSE
T ss_pred             HHHHHHHHHHHHHhhccCC-CcCHHHHHHHHCCCHHHHHHHHHHHHHCCcE
Confidence            467888888877      5 49999999999999876655543   45665

>2k9s_A Arabinose operon regulatory protein; activator, arabinose catabolism, carbohydrate metabolism, cytoplasm, DNA-binding, repressor, transcription; NMR {Escherichia coli}

Probab=89.29  E-value=0.83  Score=26.23  Aligned_cols=40  Identities=13%  Similarity=0.194  Sum_probs=32.7

Q ss_pred             HHHHHHHHHhcc--cccHHHHHHHhCCCHHHHHHHHHhc-CCe
Q 036949            4 KRMFQLLMSAYS--TISTQDTALFLGMNEDDAAYYVQQQ-GWT   43 (81)
Q Consensus         4 ~~~~~li~~AY~--sIs~~~~a~~Lgls~~e~~~~~~~~-GW~   43 (81)
                      .++.+.|..-|.  .++++++|..+|+|...+.....+. |=+
T Consensus         6 ~~~~~~i~~~~~~~~~~~~~lA~~~~~S~~~l~r~fk~~~G~s   48 (107)
T 2k9s_A            6 REACQYISDHLADSNFDIASVAQHVCLSPSRLSHLFRQQLGIS   48 (107)
T ss_dssp             HHHHHHHHHTSSCSSCCHHHHHHHTTSCHHHHHHHHHHHHSSC
T ss_pred             HHHHHHHHHHhccCCCCHHHHHHHHCCCHHHHHHHHHHHHCcC
Confidence            467788888885  8999999999999999888777754 644

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

Probab=88.47  E-value=0.054  Score=40.82  Aligned_cols=36  Identities=28%  Similarity=0.443  Sum_probs=28.3

Q ss_pred             HHHHHHHHHHhcccccHHHHHHHhCC-CHHHHHHHHH
Q 036949            3 TKRMFQLLMSAYSTISTQDTALFLGM-NEDDAAYYVQ   38 (81)
Q Consensus         3 R~~~~~li~~AY~sIs~~~~a~~Lgl-s~~e~~~~~~   38 (81)
                      .+.-++-|+++|++||+.++|..||+ |++++.-++.
T Consensus       388 ir~~irkis~~YsrIsL~dIa~kL~L~s~eeaE~iVA  424 (523)
T 4b4t_S          388 IKTGIRIISLTYKKISLRDICLKLNLDSEQTVEYMVS  424 (523)
T ss_dssp             HHHHHHHSCCCSSEECHHHHHHHHHHHHSSCHHHHHH
T ss_pred             HHHHHHHHHHHHhcccHHHHHHHhCCCCHHHHHHHHH
Confidence            44567788999999999999999999 4555655444

>1nd9_A Translation initiation factor IF-2; NMR {Escherichia coli} SCOP: a.6.1.6

Probab=87.79  E-value=0.43  Score=23.84  Aligned_cols=27  Identities=7%  Similarity=0.003  Sum_probs=23.8

Q ss_pred             cccHHHHHHHhCCCHHHHHHHHHhcCC
Q 036949           16 TISTQDTALFLGMNEDDAAYYVQQQGW   42 (81)
Q Consensus        16 sIs~~~~a~~Lgls~~e~~~~~~~~GW   42 (81)
                      .+.+.++|.-||++.+++.++..+.|=
T Consensus         2 k~rv~~lAkel~~~~k~l~~~l~~~g~   28 (49)
T 1nd9_A            2 DVTIKTLAAERQTSVERLVQQFADAGI   28 (49)
T ss_dssp             EECTTHHHHHHSSSHHHHHHHHHHHTS
T ss_pred             cccHHHHHHHHCcCHHHHHHHHHHcCC
Confidence            467889999999999999999998773

>3mn2_A Probable ARAC family transcriptional regulator; structural genomics, PSI-2, protein structure initiative; 1.80A {Rhodopseudomonas palustris}

Probab=87.24  E-value=1.4  Score=25.18  Aligned_cols=37  Identities=8%  Similarity=0.202  Sum_probs=29.6

Q ss_pred             HHHHHHHHHhc-ccccHHHHHHHhCCCHHHHHHHHHhc
Q 036949            4 KRMFQLLMSAY-STISTQDTALFLGMNEDDAAYYVQQQ   40 (81)
Q Consensus         4 ~~~~~li~~AY-~sIs~~~~a~~Lgls~~e~~~~~~~~   40 (81)
                      +++...|..-| ..++++++|..+|+|+..+.....+.
T Consensus         5 ~~~~~~i~~~~~~~~~~~~lA~~~~~s~~~l~r~fk~~   42 (108)
T 3mn2_A            5 RQVEEYIEANWMRPITIEKLTALTGISSRGIFKAFQRS   42 (108)
T ss_dssp             HHHHHHHHHHTTSCCCHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHcccCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            45667777776 56999999999999999887777654

>3e21_A HFAF1, FAS-associated factor 1; UBA, alternative splicing, apoptosis, nucleus, phosphoprotein; 1.73A {Homo sapiens}

Probab=87.16  E-value=0.11  Score=26.81  Aligned_cols=29  Identities=28%  Similarity=0.429  Sum_probs=24.6

Q ss_pred             HHHHHHHhCCC-HHHHHHHHHhcCCeEeCC
Q 036949           19 TQDTALFLGMN-EDDAAYYVQQQGWTLDPA   47 (81)
Q Consensus        19 ~~~~a~~Lgls-~~e~~~~~~~~GW~~d~~   47 (81)
                      +.+++.+.|.+ ++++..|...-+|-++..
T Consensus         9 ia~F~~iTG~~d~~~A~~~Lea~nWDLe~A   38 (45)
T 3e21_A            9 LADFQACTGIENIDEAITLLEQNNWDLVAA   38 (45)
T ss_dssp             HHHHHHHHCCCCHHHHHHHHHHTTTCHHHH
T ss_pred             HHHHHHHHCCCCHHHHHHHHHHcCCcHHHH
Confidence            45688999997 599999999999998754

>3oou_A LIN2118 protein; protein structure initiative, PSI-2, structural genomics, MI center for structural genomics, MCSG, unknown function; HET: BTB; 1.57A {Listeria innocua}

Probab=86.66  E-value=1.5  Score=25.07  Aligned_cols=40  Identities=13%  Similarity=0.142  Sum_probs=31.7

Q ss_pred             HHHHHHHHHhcc-cccHHHHHHHhCCCHHHHHHHHHhc-CCe
Q 036949            4 KRMFQLLMSAYS-TISTQDTALFLGMNEDDAAYYVQQQ-GWT   43 (81)
Q Consensus         4 ~~~~~li~~AY~-sIs~~~~a~~Lgls~~e~~~~~~~~-GW~   43 (81)
                      .++...|..-|. .++++++|..+|+|+..+.....+. |=+
T Consensus         8 ~~~~~~i~~~~~~~~~~~~lA~~~~~S~~~l~r~fk~~~G~s   49 (108)
T 3oou_A            8 QNVLSYITEHFSEGMSLKTLGNDFHINAVYLGQLFQKEMGEH   49 (108)
T ss_dssp             HHHHHHHHHHTTSCCCHHHHHHHHTSCHHHHHHHHHHHHSSC
T ss_pred             HHHHHHHHHHhcCCCCHHHHHHHHCcCHHHHHHHHHHHHCcC
Confidence            466777777775 6999999999999999887777654 544

>3oio_A Transcriptional regulator (ARAC-type DNA-binding containing proteins); PSI-2, midwest center for structural genomics; 1.65A {Chromobacterium violaceum}

Probab=86.57  E-value=1.2  Score=25.70  Aligned_cols=40  Identities=20%  Similarity=0.334  Sum_probs=31.8

Q ss_pred             HHHHHHHHHhcc-cccHHHHHHHhCCCHHHHHHHHHhc-CCe
Q 036949            4 KRMFQLLMSAYS-TISTQDTALFLGMNEDDAAYYVQQQ-GWT   43 (81)
Q Consensus         4 ~~~~~li~~AY~-sIs~~~~a~~Lgls~~e~~~~~~~~-GW~   43 (81)
                      .++...|..-|. .++++++|..+|+|+..+...+.+. |=+
T Consensus        10 ~~~~~~i~~~~~~~~~~~~lA~~~~~S~~~l~r~fk~~~G~s   51 (113)
T 3oio_A           10 TEAVSLMEANIEEPLSTDDIAYYVGVSRRQLERLFKQYLGTV   51 (113)
T ss_dssp             HHHHHHHHTCSSSCCCHHHHHHHHTSCHHHHHHHHHHHTSSC
T ss_pred             HHHHHHHHhhhcCCCCHHHHHHHHCcCHHHHHHHHHHHHCcC
Confidence            356777777764 5999999999999999988877765 644

>2krk_A 26S protease regulatory subunit 8; structural genomics, northeast structural genomics consortium (NESG), target HR3102A, PSI-2; NMR {Homo sapiens}

Probab=86.00  E-value=0.99  Score=25.61  Aligned_cols=37  Identities=8%  Similarity=0.136  Sum_probs=29.7

Q ss_pred             HHHHHHHHHHhc---ccccHHHHHHHh-CCCHHHHHHHHHh
Q 036949            3 TKRMFQLLMSAY---STISTQDTALFL-GMNEDDAAYYVQQ   39 (81)
Q Consensus         3 R~~~~~li~~AY---~sIs~~~~a~~L-gls~~e~~~~~~~   39 (81)
                      |.+|++...+-.   ..+.++.+|... |+|+.|+...|.+
T Consensus        16 R~~IL~~~l~~~~l~~dvdl~~LA~~T~G~SGADL~~l~~e   56 (86)
T 2krk_A           16 RLDILKIHSRKMNLTRGINLRKIAELMPGASGAEVKGVCTE   56 (86)
T ss_dssp             HHHHHHHHTTTSEECTTCCCHHHHHTCSSCCHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCCCcccCHHHHHHHcCCCCHHHHHHHHHH
Confidence            778888777655   368888999888 9999999888774

>1ng7_A Poliovirus 3A-N, genome polyprotein [core protein P3A]; helical hairpin, unfolded domain, symmetric dimer, viral protein; NMR {Human poliovirus 1} SCOP: a.178.1.1

Probab=85.61  E-value=0.33  Score=26.61  Aligned_cols=23  Identities=17%  Similarity=0.531  Sum_probs=17.1

Q ss_pred             HHHHhCC-CHHHHHHHHHhcCCeE
Q 036949           22 TALFLGM-NEDDAAYYVQQQGWTL   44 (81)
Q Consensus        22 ~a~~Lgl-s~~e~~~~~~~~GW~~   44 (81)
                      ++.+|-= ..+++++||+++||.+
T Consensus        22 I~DLLksvds~eV~~YC~~kGwIi   45 (60)
T 1ng7_A           22 INDLLQAVDSQEVRDYCEKKGWIV   45 (60)
T ss_dssp             THHHHHHHCCHHHHHHHHHHTCCC
T ss_pred             HHHHHHcCCCHHHHHHHHHCCcee
Confidence            3444433 4488999999999997

>3mkl_A HTH-type transcriptional regulator GADX; PSI2, MCSG, structural genomics, protein structure initiativ midwest center for structural genomics; 2.15A {Escherichia coli}

Probab=85.60  E-value=2.2  Score=24.92  Aligned_cols=41  Identities=10%  Similarity=0.003  Sum_probs=32.6

Q ss_pred             HHHHHHHHHHhc-ccccHHHHHHHhCCCHHHHHHHHHhcCCe
Q 036949            3 TKRMFQLLMSAY-STISTQDTALFLGMNEDDAAYYVQQQGWT   43 (81)
Q Consensus         3 R~~~~~li~~AY-~sIs~~~~a~~Lgls~~e~~~~~~~~GW~   43 (81)
                      -+++...|..-| ..++++++|..+|+|+.-+.....+.|=+
T Consensus         9 ~~~~~~~i~~~~~~~~~~~~lA~~~~~S~~~l~r~fk~~G~s   50 (120)
T 3mkl_A            9 RTRVCTVINNNIAHEWTLARIASELLMSPSLLKKKLREEETS   50 (120)
T ss_dssp             HHHHHHHHHTSTTSCCCHHHHHHHTTCCHHHHHHHHHHTTCC
T ss_pred             HHHHHHHHHHhccCCCCHHHHHHHHCcCHHHHHHHHHHcCCC
Confidence            456777787776 47899999999999999998887765543

>3f2g_A Alkylmercury lyase; MERB, organomercurial lyase, mercury resistance, mercuric resistance, plasmid; 1.78A {Escherichia coli} PDB: 3f2h_A 3fn8_A 1s6l_A 3f0o_A 3f0p_A 3f2f_A

Probab=85.46  E-value=3.2  Score=27.94  Aligned_cols=47  Identities=15%  Similarity=0.140  Sum_probs=36.8

Q ss_pred             HHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHHhc-CCeEeCCCceEe
Q 036949            5 RMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQQQ-GWTLDPASRMLT   52 (81)
Q Consensus         5 ~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~~~-GW~~d~~~~~~~   52 (81)
                      -+++++. -=+-++++++|.-+|.+.+++.+...+. +..+|.+|+++-
T Consensus        26 ~llr~la-~Grpv~~~~LA~~~g~~~~~v~~~L~~l~~~~~D~~G~Ivg   73 (220)
T 3f2g_A           26 PLLRELA-KGRPVSRTTLAGILDWPAERVAAVLEQATSTEYDKDGNIIG   73 (220)
T ss_dssp             HHHHHHT-TTSCBCHHHHHHHHTCCHHHHHHHHHHCTTCEECTTSCEEE
T ss_pred             HHHHHHh-cCCCCCHHHHHHHhCcCHHHHHHHHHhCCcEEECCCCCEEE
Confidence            3444444 3356789999999999999999999877 899999887643

>3to7_A Histone acetyltransferase ESA1; MYST family; HET: ALY COA; 1.90A {Saccharomyces cerevisiae} SCOP: d.108.1.1 PDB: 3to6_A* 1fy7_A* 1mja_A* 1mjb_A* 3to9_A* 1mj9_A*

Probab=85.21  E-value=1.8  Score=30.17  Aligned_cols=52  Identities=10%  Similarity=0.088  Sum_probs=42.5

Q ss_pred             HHHHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHHhcCCeEeCCCceEeec
Q 036949            3 TKRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQQQGWTLDPASRMLTVK   54 (81)
Q Consensus         3 R~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~~~GW~~d~~~~~~~p~   54 (81)
                      +..++..+...-..|++++++...|+..+|+..-.+..|+..--.|+.++-.
T Consensus       195 ~~~i~~~L~~~~~~isi~~is~~Tgi~~~Dii~tL~~l~~l~~~kg~~~i~~  246 (276)
T 3to7_A          195 SDTLITLLVEHQKEITIDEISSMTSMTTTDILHTAKTLNILRYYKGQHIIFL  246 (276)
T ss_dssp             HHHHHHHHHHTCSEEEHHHHHHHHCBCHHHHHHHHHHTTCEEEETTEEEEEC
T ss_pred             HHHHHHHHHhcCCceeHHHHHHHhCCCHHHHHHHHHHCCCEEEeCCcEEEEE
Confidence            4567777776667899999999999999999999999999865566665544

>3gbg_A TCP pilus virulence regulatory protein; cupin, helix-turn-helix, ARAC family, activator, DNA-binding transcription, transcription regulation; HET: PAM; 1.90A {Vibrio cholerae}

Probab=84.91  E-value=1.8  Score=28.39  Aligned_cols=40  Identities=15%  Similarity=0.014  Sum_probs=33.3

Q ss_pred             HHHHHHHHHhccc-ccHHHHHHHhCCCHHHHHHHHHhcCCe
Q 036949            4 KRMFQLLMSAYST-ISTQDTALFLGMNEDDAAYYVQQQGWT   43 (81)
Q Consensus         4 ~~~~~li~~AY~s-Is~~~~a~~Lgls~~e~~~~~~~~GW~   43 (81)
                      .++.+.|..-|.. ++++++|..+|+|+.-+...+++.|=+
T Consensus       172 ~~~~~~i~~~~~~~~sl~~lA~~~~~S~~~l~r~fk~~G~t  212 (276)
T 3gbg_A          172 EKISCLVKSDITRNWRWADICGELRTNRMILKKELESRGVK  212 (276)
T ss_dssp             HHHHHHHHHTTTSCCCHHHHHHHHTCCHHHHHHHHHTTTCC
T ss_pred             HHHHHHHHHhhcCCCCHHHHHHHHCcCHHHHHHHHHHcCCC
Confidence            4677888888876 999999999999999998888655544

>3dkw_A DNR protein; CRP-FNR, HTH, beta barrel, dimerization helix, homodimer, transcription regulator; 3.60A {Pseudomonas aeruginosa}

Probab=83.96  E-value=4.1  Score=25.41  Aligned_cols=54  Identities=13%  Similarity=0.177  Sum_probs=35.0

Q ss_pred             hHHHHHHHHHHhcc-----------cccHHHHHHHhCCCHHHHHHH---HHhcCCeEeCCCceEeecC
Q 036949            2 YTKRMFQLLMSAYS-----------TISTQDTALFLGMNEDDAAYY---VQQQGWTLDPASRMLTVKK   55 (81)
Q Consensus         2 ~R~~~~~li~~AY~-----------sIs~~~~a~~Lgls~~e~~~~---~~~~GW~~d~~~~~~~p~~   55 (81)
                      .++|++..+-.-+.           .++..++|.|||++.+-+-..   ..+.||---..+.+.+...
T Consensus       153 ~~~Rl~~~L~~~~~~~~~~~~~~~~~~t~~~lA~~lg~sr~tvsR~l~~l~~~g~I~~~~~~i~i~d~  220 (227)
T 3dkw_A          153 ATHRVVRYLLTLAAHAPGENCRVEIPVAKQLVAGHLSIQPETFSRIMHRLGDEGIIHLDGREISILDR  220 (227)
T ss_dssp             HHHHHHHHHHHHHCSSSSSCCCCCCCSCTHHHHHHTTSCHHHHHHHHHHHHHHTSEEESSSCEEESCS
T ss_pred             HHHHHHHHHHHhhhhcCCCCeEEEecCCHHHHHHHhCCCHHHHHHHHHHHHHCCcEEecCCEEEEeCH
Confidence            35777776544332           356789999999988765444   4467996444556655543

>3dv8_A Transcriptional regulator, CRP/FNR family; cyclic nucleotide-binding domain, structural genomics, joint for structural genomics; 2.55A {Eubacterium rectale atcc 33656}

Probab=83.90  E-value=4.6  Score=25.04  Aligned_cols=51  Identities=20%  Similarity=0.244  Sum_probs=33.1

Q ss_pred             hHHHHHHHHHHhcc-------cccHHHHHHHhCCCHHHHHHH---HHhcCCeEeCCCceEe
Q 036949            2 YTKRMFQLLMSAYS-------TISTQDTALFLGMNEDDAAYY---VQQQGWTLDPASRMLT   52 (81)
Q Consensus         2 ~R~~~~~li~~AY~-------sIs~~~~a~~Lgls~~e~~~~---~~~~GW~~d~~~~~~~   52 (81)
                      .++|++..+-.-..       .++..++|.|||++.+-+-..   ..+.|+---..+.+.+
T Consensus       148 ~~~Rl~~~L~~~~~~~~~~~~~~t~~~lA~~lg~sr~tvsR~l~~L~~~g~I~~~~~~i~i  208 (220)
T 3dv8_A          148 LDKRVASFLLEETSIEGTNELKITHETIANHLGSHREVITRMLRYFQVEGLVKLSRGKITI  208 (220)
T ss_dssp             HHHHHHHHHHHHHHHHTSSEECCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEETTEEEE
T ss_pred             HHHHHHHHHHHhhhhcCCceecCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEeCCCEEEE
Confidence            45677666654332       678899999999988776444   4467886433444433

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

Probab=83.53  E-value=1.7  Score=30.94  Aligned_cols=42  Identities=17%  Similarity=0.298  Sum_probs=29.9

Q ss_pred             HhcccccHHHHHHHhCCCHHHHHHHHHh---cCC---eEeCCCceEee
Q 036949           12 SAYSTISTQDTALFLGMNEDDAAYYVQQ---QGW---TLDPASRMLTV   53 (81)
Q Consensus        12 ~AY~sIs~~~~a~~Lgls~~e~~~~~~~---~GW---~~d~~~~~~~p   53 (81)
                      +.|++|+.+.+|..||++.+++..++.+   .|-   ++|.-.+++..
T Consensus       303 ~~~~~i~f~~ia~~l~i~~~evE~lli~aI~~glI~GkIDQv~~~v~v  350 (393)
T 4b4t_O          303 KNIRMLSFEDISKATHLPKDNVEHLVMRAISLGLLKGSIDQVNELVTI  350 (393)
T ss_dssp             SSCCCEEHHHHHHHHTCCHHHHHHHHHHHHHHSCSSSCEETTTTEECC
T ss_pred             CCCCcCcHHHHHHHhCcCHHHHHHHHHHHHHcCCEEEEEcCCCCEEEE
Confidence            3478899999999999999998877654   122   45654444433

>2gmg_A Hypothetical protein PF0610; winged-helix like protein with metal binding site, structura genomics, PSI, protein structure initiative; NMR {Pyrococcus furiosus} SCOP: a.4.5.82

Probab=83.41  E-value=0.51  Score=28.53  Aligned_cols=29  Identities=21%  Similarity=0.379  Sum_probs=25.7

Q ss_pred             hHHHHHHHHHHhcccccHHHHHHHhCC---CHHH
Q 036949            2 YTKRMFQLLMSAYSTISTQDTALFLGM---NEDD   32 (81)
Q Consensus         2 ~R~~~~~li~~AY~sIs~~~~a~~Lgl---s~~e   32 (81)
                      +|++|+.++..  .-++..+++..||+   ++.+
T Consensus        12 ~Re~Ii~lL~~--~plta~ei~~~l~i~~~~~ke   43 (105)
T 2gmg_A           12 RREKIIELLLE--GDYSPSELARILDMRGKGSKK   43 (105)
T ss_dssp             HHHHHHHHTTT--SCBCTTHHHHSSCCCSSCCHH
T ss_pred             HHHHHHHHHHc--CCCCHHHHHHHhCCCCCChHH
Confidence            69999999984  88899999999999   6677

>1bl0_A Protein (multiple antibiotic resistance protein), DNA (5'- D(*CP*CP*GP*AP*TP*GP*CP*CP*AP*CP*GP*TP*TP*TP*TP*GP*CP*TP*AP *AP*AP*TP* CP*C)-3')...; transcriptional activator; HET: DNA; 2.30A {Escherichia coli} SCOP: a.4.1.8 a.4.1.8 PDB: 1xs9_A

Probab=83.03  E-value=1.7  Score=25.81  Aligned_cols=37  Identities=5%  Similarity=0.096  Sum_probs=29.6

Q ss_pred             HHHHHHHHHhcc-cccHHHHHHHhCCCHHHHHHHHHhc
Q 036949            4 KRMFQLLMSAYS-TISTQDTALFLGMNEDDAAYYVQQQ   40 (81)
Q Consensus         4 ~~~~~li~~AY~-sIs~~~~a~~Lgls~~e~~~~~~~~   40 (81)
                      .++...|..-|. .++++++|..+|+|...+.....+.
T Consensus        14 ~~~~~~i~~~~~~~~sl~~lA~~~~~S~~~l~r~fk~~   51 (129)
T 1bl0_A           14 HSILDWIEDNLESPLSLEKVSERSGYSKWHLQRMFKKE   51 (129)
T ss_dssp             HHHHHHHHTTTTSCCCCHHHHHHSSSCHHHHHHHHHHH
T ss_pred             HHHHHHHHHccCCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            456777777765 6999999999999998887776654

>3aji_B S6C, proteasome (prosome, macropain) 26S subunit, ATPA; gankyrin, S6 ATPase, P-benzoyl-L-phenylalanine, PBPA, amber suppression; HET: PBF; 2.05A {Mus musculus} PDB: 2dwz_B* 2dvw_B*

Probab=82.49  E-value=1.9  Score=23.72  Aligned_cols=37  Identities=14%  Similarity=0.179  Sum_probs=29.8

Q ss_pred             HHHHHHHHHHhc---ccccHHHHHHHh-CCCHHHHHHHHHh
Q 036949            3 TKRMFQLLMSAY---STISTQDTALFL-GMNEDDAAYYVQQ   39 (81)
Q Consensus         3 R~~~~~li~~AY---~sIs~~~~a~~L-gls~~e~~~~~~~   39 (81)
                      |.+|++...+-+   ..+.++.+|... |+|+.|+...|.+
T Consensus         6 R~~Il~~~l~~~~~~~~vdl~~la~~t~G~SGADi~~l~~e   46 (83)
T 3aji_B            6 KRLIFSTITSKMNLSEEVDLEDYVARPDKISGADINSICQE   46 (83)
T ss_dssp             HHHHHHHHHTTSCBCTTCCTHHHHTSSCCCCHHHHHHHHHH
T ss_pred             HHHHHHHHhCCCCCCcccCHHHHHHHcCCCCHHHHHHHHHH
Confidence            778888777655   367888888888 9999999998875

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

Probab=81.09  E-value=1.8  Score=24.85  Aligned_cols=43  Identities=5%  Similarity=-0.002  Sum_probs=34.3

Q ss_pred             hHHHHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHHh---cCCeEeC
Q 036949            2 YTKRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQQ---QGWTLDP   46 (81)
Q Consensus         2 ~R~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~~---~GW~~d~   46 (81)
                      ++++|+.++.+ -. ++..++|+-||+|...+..+..+   .|-....
T Consensus        18 ~~~~IL~lL~~-~g-~sa~eLAk~LgiSk~aVr~~L~~Le~eG~I~~~   63 (82)
T 1oyi_A           18 IVCEAIKTIGI-EG-ATAAQLTRQLNMEKREVNKALYDLQRSAMVYSS   63 (82)
T ss_dssp             HHHHHHHHHSS-ST-EEHHHHHHHSSSCHHHHHHHHHHHHHHTSSEEC
T ss_pred             HHHHHHHHHHH-cC-CCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeC
Confidence            57889988884 44 99999999999999998888664   3776643

>1z96_A DNA-damage, UBA-domain protein MUD1; ubiquitin, three-helix bundle, protein transport; 1.80A {Schizosaccharomyces pombe} SCOP: a.5.2.1

Probab=80.08  E-value=1.5  Score=20.97  Aligned_cols=26  Identities=19%  Similarity=0.198  Sum_probs=21.1

Q ss_pred             HHHHHHHhCCCHHHHHHHHHhcCCeEe
Q 036949           19 TQDTALFLGMNEDDAAYYVQQQGWTLD   45 (81)
Q Consensus        19 ~~~~a~~Lgls~~e~~~~~~~~GW~~d   45 (81)
                      +..+..| |++.+++.......+|-++
T Consensus         8 i~~L~~m-Gf~~~~a~~AL~~~~~n~e   33 (40)
T 1z96_A            8 IAQLVSM-GFDPLEAAQALDAANGDLD   33 (40)
T ss_dssp             HHHHHHT-TCCHHHHHHHHHHTTTCHH
T ss_pred             HHHHHHc-CCCHHHHHHHHHHcCCCHH
Confidence            5678887 9999999888888888654

---

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	81
d1rz4a1	85	Eukaryotic translation initiation factor 3 subunit	99.55
d1ufma_	84	COP9 signalosome complex subunit 4, GSN4 {Mouse (M	97.53
d1mkma1	75	Transcriptional regulator IclR, N-terminal domain	91.58
d1ng7a_	60	Soluble domain of poliovirus core protein 3a {Poli	91.18
d1z05a1	71	Transcriptional regulator VC2007 N-terminal domain	90.8
d1z6ra1	70	Mlc protein N-terminal domain {Escherichia coli [T	89.56
d1zyba1	73	Probable transcription regulator BT4300, C-termina	89.03
d1jjcb2	75	Domains B1 and B5 of PheRS-beta, PheT {Thermus the	88.99
d1jhfa1	71	LexA repressor, N-terminal DNA-binding domain {Esc	88.48
d1i1ga1	60	LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}	88.0
d2ev0a1	61	Manganese transport regulator MntR {Bacillus subti	87.17
d1jt6a1	71	Multidrug binding protein QacR {Staphylococcus aur	85.29
d2cfxa1	63	Transcriptional regulator LrpC {Bacillus subtilis	85.13
d1j5ya1	65	Putative transcriptional regulator TM1602, N-termi	84.77
d1s6la1	60	Alkylmercury lyase MerB {Escherichia coli [TaxId:	84.28
d2cg4a1	63	Regulatory protein AsnC {Escherichia coli [TaxId:	84.18
d2isya1	63	Iron-dependent regulator IdeR {Mycobacterium tuber	84.02
d1v92a_	46	NSFL1 (p97 ATPase) cofactor p47, UBA-like domain {	83.55
d2cyya1	60	Putative transcriptional regulator PH1519 {Archaeo	82.62
d2fbqa1	79	Transcriptional regulator PsrA {Pseudomonas aerugi	82.31
d1k78a1	63	Pax-5 {Human (Homo sapiens) [TaxId: 9606]}	81.79
d2gaua1	81	Transcriptional regulator PG0396, C-terminal domai	81.65
d3e11a1	113	Uncharacterized protein Acel_2062 {Acidothermus ce	81.31
d1biaa1	63	Biotin repressor, N-terminal domain {Escherichia c	80.85
d1d5ya1	54	Rob transcription factor, N-terminal domain {Esche	80.65
d1rp3a1	77	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	80.04

>d1rz4a1 a.4.5.53 (A:132-216) Eukaryotic translation initiation factor 3 subunit 12, eIF3k, C-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Eukaryotic translation initiation factor 3 subunit 12, eIF3k, C-terminal domain
domain: Eukaryotic translation initiation factor 3 subunit 12, eIF3k, C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.55  E-value=2e-15  Score=88.41  Aligned_cols=76  Identities=14%  Similarity=0.217  Sum_probs=66.5

Q ss_pred             ChHHHHHHHHHHhcccccHHHHHHHhCC-CHHHHHHHHHhcCCeEeCCCceEeecCCCCcccCCC--ChhHHHHHHhHHH
Q 036949            1 LYTKRMFQLLMSAYSTISTQDTALFLGM-NEDDAAYYVQQQGWTLDPASRMLTVKKQPLVTEQKL--DPSKMQCLTEYVF   77 (81)
Q Consensus         1 ~~R~~~~~li~~AY~sIs~~~~a~~Lgl-s~~e~~~~~~~~GW~~d~~~~~~~p~~~~~~~~~~~--~~~~l~~Lt~~v~   77 (81)
                      +||..|...|+.+|.+|+.+.++.|||+ +++++..++++.||+.+.+ ..++|.|+++.+++..  +...+++++.+++
T Consensus         6 sIR~~i~~vv~iTyq~I~~~~L~e~LG~~~d~~L~~~i~~~gW~~~~~-g~v~v~nqe~~iK~kni~EkI~fe~v~~ima   84 (85)
T d1rz4a1           6 SVRKFICHVVGITYQHIDRWLLAEMLGDLSDSQLKVWMSKYGWSADES-GQIFICSQEESIKPKNIVEKIDFDSVSSIMA   84 (85)
T ss_dssp             HHHHHHHHHHHHHCSEECHHHHHHHTTSCCHHHHHHHHHHHTCEECC---CEECCCHHHHTSCCCSSCCCCHHHHHHHHC
T ss_pred             HHHHHHHhheeeeeeEEcHHHHHHHhCCCCHHHHHHHHHHcCCEEcCC-CEEEecChhhhcCccceeeeccHHHHHHHhc
Confidence            4899999999999999999999999998 7899999999999999855 5669999988887766  8889999988874

>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=97.53  E-value=7.4e-05  Score=42.30  Aligned_cols=55  Identities=11%  Similarity=0.142  Sum_probs=41.4

Q ss_pred             hHHHHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHHh------cCCeEeCCCceEeecCC
Q 036949            2 YTKRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQQ------QGWTLDPASRMLTVKKQ   56 (81)
Q Consensus         2 ~R~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~~------~GW~~d~~~~~~~p~~~   56 (81)
                      +++.-+..+++.|++|+++++|..||++.+++..++.+      ..=++|....++....+
T Consensus        16 i~Ehni~~is~~Y~~Isl~~la~~l~l~~~evE~~l~~mI~~~~i~akIDq~~g~V~F~~~   76 (84)
T d1ufma_          16 VIEHNLLSASKLYNNITFEELGALLEIPAAKAEKIASQMITEGRMNGFIDQIDGIVHFETR   76 (84)
T ss_dssp             HHHHHHHHHHHSCSEEEHHHHHHHTTSCHHHHHHHHHHHHHTTSSCEEEETTTTEEEECCS
T ss_pred             HHHHHHHHHHHhhceeeHHHHHHHHCCCHHHHHHHHHHHHhcCeEEEEEeCCCCEEEECCC
Confidence            56777889999999999999999999999998777553      14456765455544333

>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=91.58  E-value=0.47  Score=24.93  Aligned_cols=46  Identities=17%  Similarity=0.358  Sum_probs=35.7

Q ss_pred             HHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHH---hcCCeE-eCCCce
Q 036949            5 RMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQ---QQGWTL-DPASRM   50 (81)
Q Consensus         5 ~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~---~~GW~~-d~~~~~   50 (81)
                      +|+++++..=..+++.++|..+|++..-+-.+..   +.||-. |+++.+
T Consensus         9 ~IL~~~a~~~~~~s~~eia~~~~~~~st~~rll~tL~~~g~l~~~~~g~y   58 (75)
T d1mkma1           9 EILDFIVKNPGDVSVSEIAEKFNMSVSNAYKYMVVLEEKGFVLRKKDKRY   58 (75)
T ss_dssp             HHHHHHHHCSSCBCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEECTTSCE
T ss_pred             HHHHHHHhCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEECCCCCE
Confidence            4677788887889999999999998877665544   679987 455543

>d1ng7a_ a.178.1.1 (A:) Soluble domain of poliovirus core protein 3a {Poliovirus type 1, strain Mahoney [TaxId: 12080]}

class: All alpha proteins
fold: Soluble domain of poliovirus core protein 3a
superfamily: Soluble domain of poliovirus core protein 3a
family: Soluble domain of poliovirus core protein 3a
domain: Soluble domain of poliovirus core protein 3a
species: Poliovirus type 1, strain Mahoney [TaxId: 12080]

Probab=91.18  E-value=0.048  Score=28.53  Aligned_cols=24  Identities=17%  Similarity=0.540  Sum_probs=18.4

Q ss_pred             HHHHhCC-CHHHHHHHHHhcCCeEe
Q 036949           22 TALFLGM-NEDDAAYYVQQQGWTLD   45 (81)
Q Consensus        22 ~a~~Lgl-s~~e~~~~~~~~GW~~d   45 (81)
                      ++.+|-= ..+|+.+||+++||.+.
T Consensus        22 I~DLLkSVDSeEVReYCk~kgWii~   46 (60)
T d1ng7a_          22 INDLLQAVDSQEVRDYCEKKGWIVN   46 (60)
T ss_dssp             THHHHHHHCCHHHHHHHHHHTCCCC
T ss_pred             HHHHHHhcCcHHHHHHHHHCCeeec
Confidence            3444433 67999999999999984

>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=90.80  E-value=0.27  Score=25.51  Aligned_cols=42  Identities=12%  Similarity=0.113  Sum_probs=32.9

Q ss_pred             HHHHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHH---hcCCeEe
Q 036949            3 TKRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQ---QQGWTLD   45 (81)
Q Consensus         3 R~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~---~~GW~~d   45 (81)
                      +.+|+.+|-. ...++..++|..+|+|..-+...+.   +.||-..
T Consensus         8 ~~~Il~~l~~-~g~~sr~eLa~~~glS~~Tv~~~l~~L~~~Glv~e   52 (71)
T d1z05a1           8 AGRVYKLIDQ-KGPISRIDLSKESELAPASITKITRELIDAHLIHE   52 (71)
T ss_dssp             HHHHHHHHHH-HCSBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHHHH-cCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence            4678888854 7899999999999998877655544   5688753

>d1z6ra1 a.4.5.63 (A:12-81) Mlc protein 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: ROK associated domain
domain: Mlc protein N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=89.56  E-value=0.44  Score=24.74  Aligned_cols=42  Identities=10%  Similarity=0.167  Sum_probs=33.2

Q ss_pred             HHHHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHH---hcCCeEe
Q 036949            3 TKRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQ---QQGWTLD   45 (81)
Q Consensus         3 R~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~---~~GW~~d   45 (81)
                      +..|+++|- ....++..++|..+|||..-+-..+.   +.||-..
T Consensus         7 ~~~Il~~i~-~~g~~sr~eLa~~~gLS~~Tvs~iv~~L~~~glv~e   51 (70)
T d1z6ra1           7 AGAVYRLID-QLGPVSRIDLSRLAQLAPASITKIVHEMLEAHLVQE   51 (70)
T ss_dssp             HHHHHHHHH-SSCSCCHHHHHHHTTCCHHHHHHHHHHHHHHTSEEE
T ss_pred             HHHHHHHHH-HcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEe
Confidence            456777777 58999999999999998877666555   5699875

>d1zyba1 a.4.5.4 (A:148-220) Probable transcription regulator BT4300, C-terminal domain {Bacteroides thetaiotaomicron [TaxId: 818]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: Probable transcription regulator BT4300, C-terminal domain
species: Bacteroides thetaiotaomicron [TaxId: 818]

Probab=89.03  E-value=0.56  Score=24.57  Aligned_cols=54  Identities=13%  Similarity=0.142  Sum_probs=36.9

Q ss_pred             ChHHHHHHHHHHhcc--------cccHHHHHHHhCCCHHHHH---HHHHhcCCeEeCCCceEeec
Q 036949            1 LYTKRMFQLLMSAYS--------TISTQDTALFLGMNEDDAA---YYVQQQGWTLDPASRMLTVK   54 (81)
Q Consensus         1 ~~R~~~~~li~~AY~--------sIs~~~~a~~Lgls~~e~~---~~~~~~GW~~d~~~~~~~p~   54 (81)
                      ++++|+++.+-....        .++-+++|.|+|++.+-+-   ....+.||---..+.+.++.
T Consensus         4 dv~~Rla~~Ll~~~~~~~~~~~i~lt~~elA~~lg~sr~tvsr~l~~l~~~g~I~~~~~~i~I~d   68 (73)
T d1zyba1           4 DLKSKIIRFFLSHCEKPQGEKTFKVKMDDLARCLDDTRLNISKTLNELQDNGLIELHRKEILIPD   68 (73)
T ss_dssp             SHHHHHHHHHHTTCSSSSSCEEEECCHHHHHHHHTSCHHHHHHHHHHHHHTTSCEEETTEEEESC
T ss_pred             CHHHHHHHHHHHhhhhhCCCeEeecCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecCCEEEEcc
Confidence            467888886654333        3688999999999876654   44556799754455655543

>d1jjcb2 a.6.1.1 (B:400-474) Domains B1 and B5 of PheRS-beta, PheT {Thermus thermophilus [TaxId: 274]}

class: All alpha proteins
fold: Putative DNA-binding domain
superfamily: Putative DNA-binding domain
family: Domains B1 and B5 of PheRS-beta, PheT
domain: Domains B1 and B5 of PheRS-beta, PheT
species: Thermus thermophilus [TaxId: 274]

Probab=88.99  E-value=0.88  Score=24.01  Aligned_cols=39  Identities=13%  Similarity=0.215  Sum_probs=31.6

Q ss_pred             cccHHHHHHHhCC--CHHHHHHHHHhcCCeEeCCCceEeec
Q 036949           16 TISTQDTALFLGM--NEDDAAYYVQQQGWTLDPASRMLTVK   54 (81)
Q Consensus        16 sIs~~~~a~~Lgl--s~~e~~~~~~~~GW~~d~~~~~~~p~   54 (81)
                      +++.+.+.++||+  +.+++.+.....|-+++.++..+...
T Consensus         6 ~l~~~~i~~~lG~~i~~~~i~~~L~~Lg~~~~~~~~~~~V~   46 (75)
T d1jjcb2           6 PFRPEYANRLLGTSYPEAEQIAILKRLGCRVEGEGPTYRVT   46 (75)
T ss_dssp             EECHHHHHHHHTCCCCHHHHHHHHHHTTCEEECSSSSEEEE
T ss_pred             EECHHHHHHHhCCCCCHHHHHHHHHHcCCceEecCCcEEEe
Confidence            3677889999998  89999999999999998765544443

>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=88.48  E-value=0.57  Score=24.53  Aligned_cols=43  Identities=19%  Similarity=0.229  Sum_probs=33.6

Q ss_pred             HHHHHHHHHHhccc----ccHHHHHHHhCC-CHHHHHHH---HHhcCCeEe
Q 036949            3 TKRMFQLLMSAYST----ISTQDTALFLGM-NEDDAAYY---VQQQGWTLD   45 (81)
Q Consensus         3 R~~~~~li~~AY~s----Is~~~~a~~Lgl-s~~e~~~~---~~~~GW~~d   45 (81)
                      +.++++.|..-|..    -+..++|..+|+ |..-+..+   ..++||---
T Consensus         7 Q~~vL~~I~~~~~~~G~~Ps~rei~~~~g~~S~stv~~~l~~Le~kG~I~r   57 (71)
T d1jhfa1           7 QQEVFDLIRDHISQTGMPPTRAEIAQRLGFRSPNAAEEHLKALARKGVIEI   57 (71)
T ss_dssp             HHHHHHHHHHHHHHHSSCCCHHHHHHHTTCSSHHHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCCHHHHHHHHHHHHHCcCeec
Confidence            46788888888875    899999999999 77766555   446799853

>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=88.00  E-value=0.62  Score=23.51  Aligned_cols=34  Identities=21%  Similarity=0.266  Sum_probs=27.8

Q ss_pred             HHHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHH
Q 036949            4 KRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQ   38 (81)
Q Consensus         4 ~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~   38 (81)
                      .+|+.++.+= .++|..++|..+|+|++.+..-..
T Consensus         6 ~kIl~~L~~n-~r~s~~~lA~~~gls~~~v~~Ri~   39 (60)
T d1i1ga1           6 KIILEILEKD-ARTPFTEIAKKLGISETAVRKRVK   39 (60)
T ss_dssp             HHHHHHHHHC-TTCCHHHHHHHHTSCHHHHHHHHH
T ss_pred             HHHHHHHHHc-CCCCHHHHHHHHCcCHHHHHHHHH
Confidence            4677777754 899999999999999998876655

>d2ev0a1 a.4.5.24 (A:2-62) Manganese transport regulator MntR {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Iron-dependent repressor protein
domain: Manganese transport regulator MntR
species: Bacillus subtilis [TaxId: 1423]

Probab=87.17  E-value=0.69  Score=23.61  Aligned_cols=39  Identities=10%  Similarity=0.212  Sum_probs=27.9

Q ss_pred             HHHHHHHHhcccccHHHHHHHhCCCH---HHHHHHHHhcCCeE
Q 036949            5 RMFQLLMSAYSTISTQDTALFLGMNE---DDAAYYVQQQGWTL   44 (81)
Q Consensus         5 ~~~~li~~AY~sIs~~~~a~~Lgls~---~e~~~~~~~~GW~~   44 (81)
                      .|+.|...- ..++..++|.+||+++   .++.+-..++||.-
T Consensus        11 ~I~~l~~~~-~~v~~~~iA~~L~vs~~SVs~mikrL~~~GlV~   52 (61)
T d2ev0a1          11 QIYMLIEEK-GYARVSDIAEALAVHPSSVTKMVQKLDKDEYLI   52 (61)
T ss_dssp             HHHHHHHHH-SSCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHhcC-CCccHHHHHHHhCCCchhHHHHHHHHHHCCCEE
Confidence            455555443 6899999999999965   45555566789964

>d1jt6a1 a.4.1.9 (A:2-72) Multidrug binding protein QacR {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Multidrug binding protein QacR
species: Staphylococcus aureus [TaxId: 1280]

Probab=85.29  E-value=0.85  Score=23.25  Aligned_cols=34  Identities=6%  Similarity=0.189  Sum_probs=27.4

Q ss_pred             ChHHHHHH-----HHHHhcccccHHHHHHHhCCCHHHHH
Q 036949            1 LYTKRMFQ-----LLMSAYSTISTQDTALFLGMNEDDAA   34 (81)
Q Consensus         1 ~~R~~~~~-----li~~AY~sIs~~~~a~~Lgls~~e~~   34 (81)
                      +.|++|++     +..+.|..+++.++|.-.|+|..-+-
T Consensus         1 d~r~~Il~aa~~l~~~~G~~~~s~~~Ia~~agvs~~~~y   39 (71)
T d1jt6a1           1 NLKDKILGVAKELFIKNGYNATTTGEIVKLSESSKGNLY   39 (71)
T ss_dssp             CHHHHHHHHHHHHHHHHCTTTCCHHHHHHHTTCCHHHHH
T ss_pred             CHHHHHHHHHHHHHHHhCccccCHHHHHHHHCcCHhHHH
Confidence            45777776     46788999999999999999885543

>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=85.13  E-value=1.1  Score=22.70  Aligned_cols=34  Identities=12%  Similarity=0.130  Sum_probs=27.2

Q ss_pred             HHHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHH
Q 036949            4 KRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQ   38 (81)
Q Consensus         4 ~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~   38 (81)
                      .+|+..+.+- .+++..++|+.+|+|+..+..-..
T Consensus         8 ~~IL~~L~~n-~r~s~~~iA~~lgis~~tv~~Ri~   41 (63)
T d2cfxa1           8 LNIIEELKKD-SRLSMRELGRKIKLSPPSVTERVR   41 (63)
T ss_dssp             HHHHHHHHHC-SCCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHHHc-CCCCHHHHHHHHCcCHHHHHHHHH
Confidence            4566666653 789999999999999999877655

>d1j5ya1 a.4.5.1 (A:3-67) Putative transcriptional regulator TM1602, 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: Biotin repressor-like
domain: Putative transcriptional regulator TM1602, N-terminal domain
species: Thermotoga maritima [TaxId: 2336]

Probab=84.77  E-value=1.3  Score=22.46  Aligned_cols=42  Identities=14%  Similarity=0.188  Sum_probs=31.7

Q ss_pred             HHHHHHHHHhcccccHHHHHHHhCCCHHHHHHH---HHhcCCeEe
Q 036949            4 KRMFQLLMSAYSTISTQDTALFLGMNEDDAAYY---VQQQGWTLD   45 (81)
Q Consensus         4 ~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~---~~~~GW~~d   45 (81)
                      .+|+.++.++=..|+.+++|..||+|..-+...   ..+.|+.+.
T Consensus        10 ~~Il~~L~~~~~~vs~~~La~~l~VS~~TI~rdi~~L~~~G~~I~   54 (65)
T d1j5ya1          10 KSIVRILERSKEPVSGAQLAEELSVSRQVIVQDIAYLRSLGYNIV   54 (65)
T ss_dssp             HHHHHHHHHCSSCBCHHHHHHHHTSCHHHHHHHHHHHHHHTCCCE
T ss_pred             HHHHHHHHHcCCCCcHHHHHHHHCCCHHHHHHHHHHHHHCCCeEE
Confidence            467888877656799999999999998766443   345688654

>d1s6la1 a.4.5.79 (A:21-80) Alkylmercury lyase MerB {Escherichia coli [TaxId: 562]}

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

Probab=84.28  E-value=0.84  Score=23.58  Aligned_cols=37  Identities=16%  Similarity=0.174  Sum_probs=31.3

Q ss_pred             ccccHHHHHHHhCCCHHHHHHHHHhc-CCeEeCCCceE
Q 036949           15 STISTQDTALFLGMNEDDAAYYVQQQ-GWTLDPASRML   51 (81)
Q Consensus        15 ~sIs~~~~a~~Lgls~~e~~~~~~~~-GW~~d~~~~~~   51 (81)
                      .-+++..+|.-||-+.+++.....+. .=++|.+|+++
T Consensus        15 ~PVs~~~LA~alg~~~~eV~~aL~~~p~tEyD~~G~iv   52 (60)
T d1s6la1          15 RPVSRTTLAGILDWPAERVAAVLEQATSTEYDKDGNII   52 (60)
T ss_dssp             CCBCHHHHHHHHTCCHHHHHHHHTTCCSSCEETTTEEC
T ss_pred             CCcCHHHHHHHhCCCHHHHHHHHHhCCCceecCCCCEE
Confidence            35789999999999999999888876 77888888764

>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=84.18  E-value=1.2  Score=22.42  Aligned_cols=34  Identities=15%  Similarity=0.270  Sum_probs=27.7

Q ss_pred             HHHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHH
Q 036949            4 KRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQ   38 (81)
Q Consensus         4 ~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~   38 (81)
                      .+|+..+.+- .++|..++|+.+|+|...+..-..
T Consensus         8 ~~IL~~L~~~-~r~s~~eiA~~l~ls~~~v~~Ri~   41 (63)
T d2cg4a1           8 RGILEALMGN-ARTAYAELAKQFGVSPETIHVRVE   41 (63)
T ss_dssp             HHHHHHHHHC-TTSCHHHHHHHHTSCHHHHHHHHH
T ss_pred             HHHHHHHHHc-CCCCHHHHHHHHCcCHHHHHHHHH
Confidence            4667777766 889999999999999998866554

>d2isya1 a.4.5.24 (A:2-64) Iron-dependent regulator IdeR {Mycobacterium tuberculosis [TaxId: 1773]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Iron-dependent repressor protein
domain: Iron-dependent regulator IdeR
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=84.02  E-value=1.1  Score=23.04  Aligned_cols=34  Identities=12%  Similarity=-0.059  Sum_probs=25.5

Q ss_pred             HHhcccccHHHHHHHhCCCHHH---HHHHHHhcCCeE
Q 036949           11 MSAYSTISTQDTALFLGMNEDD---AAYYVQQQGWTL   44 (81)
Q Consensus        11 ~~AY~sIs~~~~a~~Lgls~~e---~~~~~~~~GW~~   44 (81)
                      ...=..++..++|.+||+++.-   +.+-..++||--
T Consensus        18 ~~~~~~v~~~~iA~~L~vs~~SVt~mvkrL~~~Glv~   54 (63)
T d2isya1          18 EEEGVTPLRARIAERLDQSGPTVSQTVSRMERDGLLR   54 (63)
T ss_dssp             HHTTCCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEE
T ss_pred             HhcCCCCcHHHHHHHhCCCchhHHHHHHHHHHCCCEE
Confidence            4445779999999999997654   555555789975

>d1v92a_ a.5.2.3 (A:) NSFL1 (p97 ATPase) cofactor p47, UBA-like domain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: RuvA C-terminal domain-like
superfamily: UBA-like
family: TAP-C domain-like
domain: NSFL1 (p97 ATPase) cofactor p47, UBA-like domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=83.55  E-value=0.58  Score=22.73  Aligned_cols=28  Identities=25%  Similarity=0.661  Sum_probs=24.7

Q ss_pred             cHHHHHHHhCCCHHHHHHHHHhcCCeEe
Q 036949           18 STQDTALFLGMNEDDAAYYVQQQGWTLD   45 (81)
Q Consensus        18 s~~~~a~~Lgls~~e~~~~~~~~GW~~d   45 (81)
                      -++.+....|.+++.+..|...-+|.++
T Consensus         8 lI~qF~~iTg~~~~~A~~~Le~~~w~Le   35 (46)
T d1v92a_           8 ALREFVAVTGAEEDRARFFLESAGWDLQ   35 (46)
T ss_dssp             HHHHHHHHTCCCHHHHHHHHHHTTSCSH
T ss_pred             HHHHHHHHHCcCHHHHHHHHHHcCCcHH
Confidence            3567888999999999999999999885

>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=82.62  E-value=1.6  Score=21.67  Aligned_cols=34  Identities=12%  Similarity=0.297  Sum_probs=27.7

Q ss_pred             HHHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHH
Q 036949            4 KRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQ   38 (81)
Q Consensus         4 ~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~   38 (81)
                      .+|+.++.+- .+++..++|..||+|+..+..-.+
T Consensus         6 ~~Il~~L~~n-~r~s~~eiA~~l~ls~~~v~~Ri~   39 (60)
T d2cyya1           6 KKIIKILQND-GKAPLREISKITGLAESTIHERIR   39 (60)
T ss_dssp             HHHHHHHHHC-TTCCHHHHHHHHCSCHHHHHHHHH
T ss_pred             HHHHHHHHHc-CCCCHHHHHHHHCcCHHHHHHHHH
Confidence            4677777775 788999999999999998876654

>d2fbqa1 a.4.1.9 (A:2-80) Transcriptional regulator PsrA {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Transcriptional regulator PsrA
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=82.31  E-value=0.8  Score=23.77  Aligned_cols=31  Identities=13%  Similarity=0.182  Sum_probs=24.8

Q ss_pred             HHHHHH-----HHHHhcccccHHHHHHHhCCCHHHH
Q 036949            3 TKRMFQ-----LLMSAYSTISTQDTALFLGMNEDDA   33 (81)
Q Consensus         3 R~~~~~-----li~~AY~sIs~~~~a~~Lgls~~e~   33 (81)
                      |++|++     +.++-|..+++.++|+..|+|..-+
T Consensus         6 re~Il~aa~~~~~~~G~~~~ti~~Ia~~agvs~~s~   41 (79)
T d2fbqa1           6 VERILDAAEQLFAEKGFAETSLRLITSKAGVNLAAV   41 (79)
T ss_dssp             HHHHHHHHHHHHHHHCSTTCCHHHHHHHHTSCHHHH
T ss_pred             HHHHHHHHHHHHHHhCcccccHHHHHHHHCcChhHH
Confidence            555555     5668999999999999999987544

>d1k78a1 a.4.1.5 (A:19-81) Pax-5 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Paired domain
domain: Pax-5
species: Human (Homo sapiens) [TaxId: 9606]

Probab=81.79  E-value=1.5  Score=22.64  Aligned_cols=36  Identities=11%  Similarity=0.151  Sum_probs=30.0

Q ss_pred             ChHHHHHHHHHHhcccccHHHHHHHhCCCHHHHHHHHHh
Q 036949            1 LYTKRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYVQQ   39 (81)
Q Consensus         1 ~~R~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~~~   39 (81)
                      ++|+||+.++.   .-.|.-++|+.|++|..=+.++...
T Consensus        18 DLR~Riv~~~~---~G~s~r~aA~rf~VS~s~v~k~l~r   53 (63)
T d1k78a1          18 VVRQRIVELAH---QGVRPCDISRQLRVSHGCVSKILGR   53 (63)
T ss_dssp             HHHHHHHHHHH---TTCCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHH---cCCCHHHHHHHhCCCHHHHHHHHHH
Confidence            36999998875   5689999999999999888877653

>d2gaua1 a.4.5.4 (A:152-232) Transcriptional regulator PG0396, C-terminal domain {Porphyromonas gingivalis [TaxId: 837]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: Transcriptional regulator PG0396, C-terminal domain
species: Porphyromonas gingivalis [TaxId: 837]

Probab=81.65  E-value=2.2  Score=21.99  Aligned_cols=52  Identities=13%  Similarity=0.070  Sum_probs=32.2

Q ss_pred             ChHHHHHHHHHHhcc-------------cccHHHHHHHhCCCHHHHHHH---HHhcCCeEeCCCceEe
Q 036949            1 LYTKRMFQLLMSAYS-------------TISTQDTALFLGMNEDDAAYY---VQQQGWTLDPASRMLT   52 (81)
Q Consensus         1 ~~R~~~~~li~~AY~-------------sIs~~~~a~~Lgls~~e~~~~---~~~~GW~~d~~~~~~~   52 (81)
                      .+|+|++..+-.-+.             .++-.++|.|+|++.+-+-..   ..+.||---..+.+.+
T Consensus         1 ~v~~Rla~~Ll~l~~~~g~~~~~~~i~~~lt~~eLA~~~G~sretvsr~L~~l~~~glI~~~~~~i~I   68 (81)
T d2gaua1           1 HVRGRLAETLLILKENFGFENDGATLSIYLSREELATLSNMTVSNAIRTLSTFVSERMLALDGKRIKI   68 (81)
T ss_dssp             CHHHHHHHHHHHHHHHHCBCTTSSBBSCCCCHHHHHHHTTSCHHHHHHHHHHHHHTTSEEEETTEEEE
T ss_pred             CHHHHHHHHHHHHHHHhCCCCCCCEEeecCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecCCEEEE
Confidence            367788764432221             356778999999988766444   4467987533444433

>d3e11a1 d.92.1.17 (A:1-113) Uncharacterized protein Acel_2062 {Acidothermus cellulolyticus [TaxId: 28049]}

class: Alpha and beta proteins (a+b)
fold: Zincin-like
superfamily: Metalloproteases ("zincins"), catalytic domain
family: TTHA0227-like
domain: Uncharacterized protein Acel 2062
species: Acidothermus cellulolyticus [TaxId: 28049]

Probab=81.31  E-value=0.46  Score=27.35  Aligned_cols=21  Identities=14%  Similarity=0.406  Sum_probs=17.8

Q ss_pred             cHHHHHHHhCCCHHHHHHHHHhcCC
Q 036949           18 STQDTALFLGMNEDDAAYYVQQQGW   42 (81)
Q Consensus        18 s~~~~a~~Lgls~~e~~~~~~~~GW   42 (81)
                      =+.++|.|+|+|++++.+    .||
T Consensus        93 lvhEiah~fG~~de~l~~----~Gw  113 (113)
T d3e11a1          93 VVHEIAHHFGIDDERLHE----LGY  113 (113)
T ss_dssp             HHHHHHHHTTCCHHHHHT----TTC
T ss_pred             HHHHHHHHcCCCHHHHHh----cCC
Confidence            356799999999999974    788

>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=80.85  E-value=2.1  Score=21.54  Aligned_cols=43  Identities=16%  Similarity=0.112  Sum_probs=32.8

Q ss_pred             hHHHHHHHHHHhcccccHHHHHHHhCCCHHHHHHHH---HhcCCeEe
Q 036949            2 YTKRMFQLLMSAYSTISTQDTALFLGMNEDDAAYYV---QQQGWTLD   45 (81)
Q Consensus         2 ~R~~~~~li~~AY~sIs~~~~a~~Lgls~~e~~~~~---~~~GW~~d   45 (81)
                      .+.+|+.++. .-..+|.+++|..||+|..-+....   .+.|+.+.
T Consensus         6 ~~~~iL~~L~-~~~~~s~~eLa~~l~vS~~ti~r~i~~L~~~G~~I~   51 (63)
T d1biaa1           6 VPLKLIALLA-NGEFHSGEQLGETLGMSRAAINKHIQTLRDWGVDVF   51 (63)
T ss_dssp             HHHHHHHHHT-TSSCBCHHHHHHHHTSCHHHHHHHHHHHHHTTCCCE
T ss_pred             HHHHHHHHHH-HCCcCCHHHHHHHHCcCHHHHHHHHHHHHHCCCcEE
Confidence            4667888885 4678999999999999987765544   45688654

>d1d5ya1 a.4.1.8 (A:3-56) Rob transcription factor, N-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: AraC type transcriptional activator
domain: Rob transcription factor, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=80.65  E-value=0.99  Score=21.86  Aligned_cols=36  Identities=11%  Similarity=0.095  Sum_probs=27.3

Q ss_pred             HHHHHHHHHh-cccccHHHHHHHhCCCHHHHHHHHHh
Q 036949            4 KRMFQLLMSA-YSTISTQDTALFLGMNEDDAAYYVQQ   39 (81)
Q Consensus         4 ~~~~~li~~A-Y~sIs~~~~a~~Lgls~~e~~~~~~~   39 (81)
                      +++.+-|..- ...|+++++|+.+|+|+.-+....++
T Consensus         6 ~~i~~yi~~~~~~~itl~~lA~~~~~S~~~l~r~Fk~   42 (54)
T d1d5ya1           6 RDLLIWLEGHLDQPLSLDNVAAKAGYSKWHLQRMFKD   42 (54)
T ss_dssp             HHHHHHHHTTSSSSCCCHHHHTTTSSCHHHHHHHHHH
T ss_pred             HHHHHHHHHccCCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            3455555544 46799999999999999988777664

>d1rp3a1 a.4.13.1 (A:87-163) Sigma factor sigma-28 (FliA) {Aquifex aeolicus [TaxId: 63363]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma3 domain
domain: Sigma factor sigma-28 (FliA)
species: Aquifex aeolicus [TaxId: 63363]

Probab=80.04  E-value=2.2  Score=22.10  Aligned_cols=30  Identities=13%  Similarity=0.106  Sum_probs=22.6

Q ss_pred             HHHHHhcccccHHHHHHHhCCCHHHHHHHH
Q 036949            8 QLLMSAYSTISTQDTALFLGMNEDDAAYYV   37 (81)
Q Consensus         8 ~li~~AY~sIs~~~~a~~Lgls~~e~~~~~   37 (81)
                      .|..+--..-+..++|..||++.+++.++.
T Consensus        18 ~L~~~lGR~Pt~~EiA~~lg~s~~e~~~~l   47 (77)
T d1rp3a1          18 KLKEKLGREPTDEEVAKELGISTEELFKTL   47 (77)
T ss_dssp             HHHHHHSSCCCHHHHHHHHTSCHHHHHHHH
T ss_pred             HHHHHHCcCCCHHHHHHHHCcCHHHHHHHH
Confidence            344444556688899999999999987764