Citrus Sinensis ID: 030471

Local Sequence Feature Prediction

Prediction and (Method)Result
Residue Number Marker
Protein Sequence ?
Secondary Structure (PSIPRED) ?
Secondary Structure Prediction (SSPRO) ?
Coil and Loop (DISEMBL) ?
Flexible Loop (DISEMBL) ?
Low Complexity Region (SEG) ?
Disordered region (IsUnstruct) ?
Disordered Region (DISOPRED) ?
Disordered Region (DISEMBL) ?
Disordered Region (DISPRO) ?
Transmembrane Helix (TMHMM) ?
Transmembrane Helix (HMMTOP) ?
Transmembrane Helix (MEMSAT) ?
TM Helix, Signal Peptide (MEMSAT_SVM) ?
TM Helix, Signal Peptide (Phobius) ?
Signal Peptide (SignalP HMM Mode) ?
Signal Peptide (SignalP NN Mode) ?
Coiled Coils (COILS) ?
Positional Conservation ?
 
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------
MDIEQRQAELIDHFVKQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENSKYLDMLRLFAHGTWSDYKNNAGHLPQLVPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSNW
ccHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHcccccEEcHHHHcccccccccccccHHHHHHHHHHHcccHHHHHHHHcccccccHHHHHHHHHHHHHHHHcccccccHHHHHHHcccccHHHHHHHHHHHHHHHcccEEEEcccccEEEEEEEEcccccccHHHHHHHHHccc
ccHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHccccEEEHHHHHccHHHHHHHccccHHHHHHHHHHHHccHHHHHHcccccccccHHHHHHHHHHHHHHHHHccccccHHHHHHHcccccHHHHHHHHHHHHHHHccEEEEccccccEEEEEEcccccccHHHHHHHHHHHHcc
MDIEQRQAELIDHFVKQASNQKGAALGSVIVEatsqpslfafseilavpniaefegtenskyLDMLRLFAHGtwsdyknnaghlpqlvpdqvLKLKQLTVLTLAetnkvlpydelmeELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFaagrdlrpgqlgsmiQTLSNW
MDIEQRQAELIDHFVKQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENSKYLDMLRLFAHGTWSDYKNNAGHLPQLVPDQVLKLKQLTVLTLaetnkvlpydelMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFaagrdlrpgqlgsmiqtlsnw
MDIEQRQAELIDHFVKQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENSKYLDMLRLFAHGTWSDYKNNAGHLPQLVPDqvlklkqltvltlAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSNW
*************F*********AALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENSKYLDMLRLFAHGTWSDYKNNAGHLPQLVPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDL***************
******Q***IDHFVKQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENSKYLDMLRLFAHGTWSDYKNNAGHLPQLVPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSNW
MDIEQRQAELIDHFVKQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENSKYLDMLRLFAHGTWSDYKNNAGHLPQLVPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSNW
MDIEQRQAELIDHFVKQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENSKYLDMLRLFAHGTWSDYKNNAGHLPQLVPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSNW
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
MDIEQRQAELIDHFVKQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENSKYLDMLRLFAHGTWSDYKNNAGHLPQLVPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSNW
no confident homologs detected

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST ?

Original result of BLAST against SWISS-PROT Database

ID ?Alignment graph ?Length ? Definition ? RBH(Q2H) ? RBH(H2Q) ? Q cover ? H cover ? Identity ? E-value ?
Query177 2.2.26 [Sep-21-2011]
Q94JU3260 COP9 signalosome complex no no 1.0 0.680 0.785 6e-80
Q55BD5259 COP9 signalosome complex yes no 0.937 0.640 0.461 3e-41
Q9H9Q2264 COP9 signalosome complex yes no 0.954 0.640 0.394 2e-32
Q2KI56264 COP9 signalosome complex yes no 0.954 0.640 0.394 2e-32
Q8BV13264 COP9 signalosome complex yes no 0.954 0.640 0.394 3e-32
Q9V4S8278 COP9 signalosome complex yes no 0.943 0.600 0.392 4e-30
Q9CZ04275 COP9 signalosome complex no no 0.932 0.6 0.385 2e-28
Q5R762275 COP9 signalosome complex no no 0.932 0.6 0.379 6e-28
Q9UBW8275 COP9 signalosome complex no no 0.932 0.6 0.379 6e-28
Q7SGS1 417 COP9 signalosome complex N/A no 0.898 0.381 0.336 3e-20
>sp|Q94JU3|CSN7_ARATH COP9 signalosome complex subunit 7 OS=Arabidopsis thaliana GN=CSN7 PE=1 SV=1 Back     alignment and function desciption
 Score =  296 bits (757), Expect = 6e-80,   Method: Compositional matrix adjust.
 Identities = 139/177 (78%), Positives = 155/177 (87%)

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

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

Query: 121 VTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSNW 177
           V+NVRELEDFLINECMY GIVRGKLDQL+RCFEV FAAGRDLRPGQLG+M+ TLSNW
Sbjct: 121 VSNVRELEDFLINECMYAGIVRGKLDQLKRCFEVPFAAGRDLRPGQLGNMLHTLSNW 177
Component of the COP9 signalosome complex (CSN), a complex involved in various cellular and developmental processes such as photomorphogenesis and auxin and jasmonate responses. The CSN complex is an essential regulator of the ubiquitin (Ubl) conjugation pathway by mediating the deneddylation of the cullin subunits of SCF-type E3 ligase complexes, leading to decrease the Ubl ligase activity of SCF. It is involved in repression of photomorphogenesis in darkness by regulating the activity of COP1-containing Ubl ligase complexes. The complex is also required for degradation of IAA6 by regulating the activity of the Ubl ligase SCF-TIR complex.
Arabidopsis thaliana (taxid: 3702)
>sp|Q55BD5|CSN7_DICDI COP9 signalosome complex subunit 7 OS=Dictyostelium discoideum GN=csn7 PE=1 SV=1 Back     alignment and function description
>sp|Q9H9Q2|CSN7B_HUMAN COP9 signalosome complex subunit 7b OS=Homo sapiens GN=COPS7B PE=1 SV=1 Back     alignment and function description
>sp|Q2KI56|CSN7B_BOVIN COP9 signalosome complex subunit 7b OS=Bos taurus GN=COPS7B PE=2 SV=1 Back     alignment and function description
>sp|Q8BV13|CSN7B_MOUSE COP9 signalosome complex subunit 7b OS=Mus musculus GN=Cops7b PE=1 SV=1 Back     alignment and function description
>sp|Q9V4S8|CSN7_DROME COP9 signalosome complex subunit 7 OS=Drosophila melanogaster GN=CSN7 PE=1 SV=2 Back     alignment and function description
>sp|Q9CZ04|CSN7A_MOUSE COP9 signalosome complex subunit 7a OS=Mus musculus GN=Cops7a PE=1 SV=2 Back     alignment and function description
>sp|Q5R762|CSN7A_PONAB COP9 signalosome complex subunit 7a OS=Pongo abelii GN=COPS7A PE=2 SV=1 Back     alignment and function description
>sp|Q9UBW8|CSN7A_HUMAN COP9 signalosome complex subunit 7a OS=Homo sapiens GN=COPS7A PE=1 SV=1 Back     alignment and function description
>sp|Q7SGS1|CSN7A_NEUCR COP9 signalosome complex subunit 7a OS=Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987) GN=csn-7a PE=1 SV=1 Back     alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST ?

Original result of BLAST against Nonredundant Database

GI ?Alignment Graph ?Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query177
224067485225 predicted protein [Populus trichocarpa] 1.0 0.786 0.853 4e-87
359489202247 PREDICTED: COP9 signalosome complex subu 1.0 0.716 0.864 2e-86
147788695225 hypothetical protein VITISV_024935 [Viti 1.0 0.786 0.864 2e-86
225453392259 PREDICTED: COP9 signalosome complex subu 1.0 0.683 0.864 6e-86
255541046275 cop9 complex subunit 7a, putative [Ricin 1.0 0.643 0.858 7e-86
224136466223 predicted protein [Populus trichocarpa] 1.0 0.793 0.841 3e-84
118485804259 unknown [Populus trichocarpa] 1.0 0.683 0.841 8e-84
307136429225 cop9 complex subunit 7a [Cucumis melo su 1.0 0.786 0.819 3e-83
449445513259 PREDICTED: COP9 signalosome complex subu 1.0 0.683 0.824 3e-83
329025154247 COP9 complex subunit 7a [Solanum chacoen 1.0 0.716 0.813 9e-81
>gi|224067485|ref|XP_002302493.1| predicted protein [Populus trichocarpa] gi|222844219|gb|EEE81766.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
 Score =  325 bits (833), Expect = 4e-87,   Method: Compositional matrix adjust.
 Identities = 151/177 (85%), Positives = 165/177 (93%)

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

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

Query: 121 VTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSNW 177
           VTNVRELEDFLINECMY GIVRGKLDQLRRCFEVQFAAGRDLRPGQLG+M+QTLSNW
Sbjct: 121 VTNVRELEDFLINECMYAGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGNMLQTLSNW 177

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|359489202|ref|XP_003633896.1| PREDICTED: COP9 signalosome complex subunit 7 isoform 2 [Vitis vinifera] Back     alignment and taxonomy information
>gi|147788695|emb|CAN69751.1| hypothetical protein VITISV_024935 [Vitis vinifera] Back     alignment and taxonomy information
>gi|225453392|ref|XP_002273686.1| PREDICTED: COP9 signalosome complex subunit 7 isoform 1 [Vitis vinifera] gi|297734611|emb|CBI16662.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|255541046|ref|XP_002511587.1| cop9 complex subunit 7a, putative [Ricinus communis] gi|223548767|gb|EEF50256.1| cop9 complex subunit 7a, putative [Ricinus communis] Back     alignment and taxonomy information
>gi|224136466|ref|XP_002326867.1| predicted protein [Populus trichocarpa] gi|222835182|gb|EEE73617.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|118485804|gb|ABK94750.1| unknown [Populus trichocarpa] Back     alignment and taxonomy information
>gi|307136429|gb|ADN34236.1| cop9 complex subunit 7a [Cucumis melo subsp. melo] Back     alignment and taxonomy information
>gi|449445513|ref|XP_004140517.1| PREDICTED: COP9 signalosome complex subunit 7-like [Cucumis sativus] gi|449514708|ref|XP_004164457.1| PREDICTED: COP9 signalosome complex subunit 7-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|329025154|gb|AEB71560.1| COP9 complex subunit 7a [Solanum chacoense] Back     alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST ?

Original result of BLAST against Gene Ontology (AMIGO)

ID ? Alignment graph ? Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query177
TAIR|locus:2205593260 FUS5 "FUSCA 5" [Arabidopsis th 1.0 0.680 0.717 2.9e-64
DICTYBASE|DDB_G0271282259 csn7 "proteasome component reg 0.937 0.640 0.419 5.8e-34
UNIPROTKB|Q2KI56264 COPS7B "COP9 signalosome compl 0.977 0.655 0.354 2.2e-27
UNIPROTKB|E2R501264 COPS7B "Uncharacterized protei 0.977 0.655 0.354 2.2e-27
UNIPROTKB|Q9H9Q2264 COPS7B "COP9 signalosome compl 0.977 0.655 0.354 2.2e-27
UNIPROTKB|F1SMV1177 COPS7B "Uncharacterized protei 0.977 0.977 0.354 2.8e-27
MGI|MGI:1349388264 Cops7b "COP9 (constitutive pho 0.977 0.655 0.354 2.8e-27
RGD|1306918322 Cops7b "COP9 signalosome subun 0.977 0.537 0.348 5.7e-27
UNIPROTKB|E1C3R1267 COPS7B "Uncharacterized protei 0.977 0.647 0.342 1.9e-26
FB|FBgn0028836278 CSN7 "COP9 complex homolog sub 0.937 0.597 0.365 1.8e-25
TAIR|locus:2205593 FUS5 "FUSCA 5" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 655 (235.6 bits), Expect = 2.9e-64, P = 2.9e-64
 Identities = 127/177 (71%), Positives = 142/177 (80%)

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

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

Query:   121 VTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSNW 177
             V+NVRELEDFLINECMY GIVRGKLDQL+RCFEV FAAGRDLRPGQLG+M+ TLSNW
Sbjct:   121 VSNVRELEDFLINECMYAGIVRGKLDQLKRCFEVPFAAGRDLRPGQLGNMLHTLSNW 177
GO:0005737 "cytoplasm" evidence=ISM
GO:0004708 "MAP kinase kinase activity" evidence=ISS
GO:0005515 "protein binding" evidence=IPI
GO:0005634 "nucleus" evidence=ISS
GO:0008180 "signalosome" evidence=TAS;IPI
GO:0009640 "photomorphogenesis" evidence=RCA;TAS
GO:0010387 "signalosome assembly" evidence=IMP
GO:0010388 "cullin deneddylation" evidence=RCA;IMP
GO:0005829 "cytosol" evidence=IDA
GO:0016567 "protein ubiquitination" evidence=RCA
GO:0016571 "histone methylation" evidence=RCA
GO:0016579 "protein deubiquitination" evidence=RCA
GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=RCA
DICTYBASE|DDB_G0271282 csn7 "proteasome component region PCI (PINT) domain-containing protein" [Dictyostelium discoideum (taxid:44689)] Back     alignment and assigned GO terms
UNIPROTKB|Q2KI56 COPS7B "COP9 signalosome complex subunit 7b" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms
UNIPROTKB|E2R501 COPS7B "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)] Back     alignment and assigned GO terms
UNIPROTKB|Q9H9Q2 COPS7B "COP9 signalosome complex subunit 7b" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|F1SMV1 COPS7B "Uncharacterized protein" [Sus scrofa (taxid:9823)] Back     alignment and assigned GO terms
MGI|MGI:1349388 Cops7b "COP9 (constitutive photomorphogenic) homolog, subunit 7b (Arabidopsis thaliana)" [Mus musculus (taxid:10090)] Back     alignment and assigned GO terms
RGD|1306918 Cops7b "COP9 signalosome subunit 7B" [Rattus norvegicus (taxid:10116)] Back     alignment and assigned GO terms
UNIPROTKB|E1C3R1 COPS7B "Uncharacterized protein" [Gallus gallus (taxid:9031)] Back     alignment and assigned GO terms
FB|FBgn0028836 CSN7 "COP9 complex homolog subunit 7" [Drosophila melanogaster (taxid:7227)] Back     alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries ?

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server ?

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software ?

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING ?

Original result from the STRING server

Your Input:
fgenesh4_pm.C_LG_II000624
hypothetical protein (225 aa)
(Populus trichocarpa)
Predicted Functional Partners:
grail3.0012044601
SubName- Full=Putative uncharacterized protein; (398 aa)
    • • 0.543
eugene3.01400002
SubName- Full=Putative uncharacterized protein; (306 aa)
    • • 0.464

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database part I

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query177
pfam01399100 pfam01399, PCI, PCI domain 9e-14
smart0075388 smart00753, PAM, PCI/PINT associated module 3e-13
smart0008888 smart00088, PINT, motif in proteasome subunits, In 3e-13
>gnl|CDD|216479 pfam01399, PCI, PCI domain Back     alignment and domain information 
 Score = 63.4 bits (155), Expect = 9e-14
 Identities = 27/102 (26%), Positives = 47/102 (46%), Gaps = 11/102 (10%)

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

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

This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15). Length = 100
>gnl|CDD|214803 smart00753, PAM, PCI/PINT associated module Back     alignment and domain information
>gnl|CDD|214509 smart00088, PINT, motif in proteasome subunits, Int-6, Nip-1 and TRIP-15 Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 177
KOG3250258 consensus COP9 signalosome, subunit CSN7 [Posttran 100.0
KOG2753378 consensus Uncharacterized conserved protein, conta 100.0
KOG2908380 consensus 26S proteasome regulatory complex, subun 100.0
smart0008888 PINT motif in proteasome subunits, Int-6, Nip-1 an 99.62
smart0075388 PAM PCI/PINT associated module. 99.62
PF01399105 PCI: PCI domain; InterPro: IPR000717 A homology do 99.59
KOG1464440 consensus COP9 signalosome, subunit CSN2 [Posttran 98.04
KOG2581493 consensus 26S proteasome regulatory complex, subun 97.93
KOG2758432 consensus Translation initiation factor 3, subunit 96.54
KOG0686466 consensus COP9 signalosome, subunit CSN1 [Posttran 96.31
KOG2582422 consensus COP9 signalosome, subunit CSN3 [Posttran 95.65
KOG2688394 consensus Transcription-associated recombination p 95.59
COG5600413 Transcription-associated recombination protein [DN 95.28
KOG1497399 consensus COP9 signalosome, subunit CSN4 [Posttran 95.14
PF10075143 PCI_Csn8: COP9 signalosome, subunit CSN8; InterPro 93.74
PF09756188 DDRGK: DDRGK domain; InterPro: IPR019153 This is a 92.87
KOG1463411 consensus 26S proteasome regulatory complex, subun 92.87
PF0208283 Rrf2: Transcriptional regulator; InterPro: IPR0009 91.41
PF0901269 FeoC: FeoC like transcriptional regulator; InterPr 91.2
KOG0687393 consensus 26S proteasome regulatory complex, subun 88.17
KOG1498439 consensus 26S proteasome regulatory complex, subun 88.15
PF1341248 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 87.29
TIGR02010135 IscR iron-sulfur cluster assembly transcription fa 87.21
PRK11179153 DNA-binding transcriptional regulator AsnC; Provis 86.6
PRK14165 217 winged helix-turn-helix domain-containing protein/ 85.75
smart00344108 HTH_ASNC helix_turn_helix ASNC type. AsnC: an auto 85.37
COG5159421 RPN6 26S proteasome regulatory complex component [ 85.09
PF0933952 HTH_IclR: IclR helix-turn-helix domain; InterPro: 85.07
KOG3054299 consensus Uncharacterized conserved protein [Funct 84.98
PRK11169164 leucine-responsive transcriptional regulator; Prov 84.37
PRK10857164 DNA-binding transcriptional regulator IscR; Provis 83.99
TIGR00738132 rrf2_super rrf2 family protein (putative transcrip 83.32
COG1522154 Lrp Transcriptional regulators [Transcription] 83.06
COG1959150 Predicted transcriptional regulator [Transcription 81.47
smart0034691 HTH_ICLR helix_turn_helix isocitrate lyase regulat 81.44
PF0172665 LexA_DNA_bind: LexA DNA binding domain; InterPro: 80.77
COG5187412 RPN7 26S proteasome regulatory complex component, 80.47
>KOG3250 consensus COP9 signalosome, subunit CSN7 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms] Back     alignment and domain information 
Probab=100.00  E-value=1.1e-39  Score=259.26  Aligned_cols=176  Identities=48%  Similarity=0.762  Sum_probs=173.0

Q ss_pred             CchhHHHHHHHHHHHHhccccchHHHHHHHHHHhcCCCceehhhhhcchhhhhccCCCchHHHHHHHHHhcCChhhHhhh
Q 030471            1 MDIEQRQAELIDHFVKQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENSKYLDMLRLFAHGTWSDYKNN   80 (177)
Q Consensus         1 ~~~~~~~~~~~~~~l~~~~~~~~~~a~~~i~~aL~~p~i~~f~eLl~~~~v~~L~~~~~~~l~~LL~if~~G~~~~~~~~   80 (177)
                      ||+|+++++.+++|+.+++..++++...+|..|+.+|++|.|+|||.+|+|..|..+.++.++.||++|++||+.||...
T Consensus         1 m~~ek~~~~~~eqfvllak~~kg~al~~lIsqale~P~vf~F~ELl~l~nv~qlae~~dsa~lrlL~lFa~Gt~~Dy~ae   80 (258)
T KOG3250|consen    1 MDIEKKQAEIIEQFVLLAKTCKGEALEELISQALEAPGVFVFGELLILPNVVQLAEPIDSAYLRLLELFAYGTYRDYSAE   80 (258)
T ss_pred             CCcchhhHHHHHHHHHHHhccchhHHHHHHHHHhcCCCeeeHHHHHhhhhHHHHcccccHHHHHHHHHHhcCchhhhhhh
Confidence            99999999999999999999999999999999999999999999999999999998889999999999999999999999


Q ss_pred             hCCCCCCchHHHHHHHHHHhhccccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeecCC
Q 030471           81 AGHLPQLVPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGR  160 (177)
Q Consensus        81 ~~~~~~L~~~~~~Klr~LtllsL~~~~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~gkIDq~~~~v~v~~~~~R  160 (177)
                      ...+|.|+.+++.||+.+|+.++++..++|+|+.+.+.+.+.+..++|++|| +||+++++.|||||.+|+++|.|+..|
T Consensus        81 a~rlp~Ls~~q~~kLk~ltV~slas~~k~lpy~~Ll~~l~~~nvrelEd~ii-eamya~IlrGkldqr~q~leV~faigR  159 (258)
T KOG3250|consen   81 ALRLPKLSLAQLNKLKHLTVVSLASFEKCLPYLVLLRLLPSRNVRELEDLII-EAMYADILRGKLDQRNQTLEVDFAIGR  159 (258)
T ss_pred             hhcCCCCCHHHHHhhhcceehhhhhhchhhhHHHHHhhccCCchhHHHHHHH-HHHHHHHHHhhHHhhcceEeechhhcc
Confidence            9999999999999999999999999999999999999999999999999999 999999999999999999999999999


Q ss_pred             CCCcchHHHHHHHhccC
Q 030471          161 DLRPGQLGSMIQTLSNW  177 (177)
Q Consensus       161 ~~~~~~~~~L~~~L~~W  177 (177)
                      ++++.++..|...|++|
T Consensus       160 dlr~k~i~nm~~TL~~w  176 (258)
T KOG3250|consen  160 DLRSKDIDNMKYTLDEW  176 (258)
T ss_pred             cccHhHHHHHHHHHHHH
Confidence            99999999999999999

>KOG2753 consensus Uncharacterized conserved protein, contains PCI domain [General function prediction only] Back     alignment and domain information
>KOG2908 consensus 26S proteasome regulatory complex, subunit RPN9/PSMD13 [Posttranslational modification, protein turnover, chaperones] Back     alignment and domain information
>smart00088 PINT motif in proteasome subunits, Int-6, Nip-1 and TRIP-15 Back     alignment and domain information
>smart00753 PAM PCI/PINT associated module Back     alignment and domain information
>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 Back     alignment and domain information
>KOG1464 consensus COP9 signalosome, subunit CSN2 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms] Back     alignment and domain information
>KOG2581 consensus 26S proteasome regulatory complex, subunit RPN3/PSMD3 [Posttranslational modification, protein turnover, chaperones] Back     alignment and domain information
>KOG2758 consensus Translation initiation factor 3, subunit e (eIF-3e) [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>KOG0686 consensus COP9 signalosome, subunit CSN1 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms] Back     alignment and domain information
>KOG2582 consensus COP9 signalosome, subunit CSN3 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms] Back     alignment and domain information
>KOG2688 consensus Transcription-associated recombination protein - Thp1p [Cell cycle control, cell division, chromosome partitioning] Back     alignment and domain information
>COG5600 Transcription-associated recombination protein [DNA replication, recombination, and repair] Back     alignment and domain information
>KOG1497 consensus COP9 signalosome, subunit CSN4 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms] Back     alignment and domain information
>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 Back     alignment and domain information
>PF09756 DDRGK: DDRGK domain; InterPro: IPR019153 This is a family of proteins of approximately 300 residues Back     alignment and domain information
>KOG1463 consensus 26S proteasome regulatory complex, subunit RPN6/PSMD11 [Posttranslational modification, protein turnover, chaperones] Back     alignment and domain information
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp Back     alignment and domain information
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif Back     alignment and domain information
>KOG0687 consensus 26S proteasome regulatory complex, subunit RPN7/PSMD6 [Posttranslational modification, protein turnover, chaperones] Back     alignment and domain information
>KOG1498 consensus 26S proteasome regulatory complex, subunit RPN5/PSMD12 [Posttranslational modification, protein turnover, chaperones] Back     alignment and domain information
>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 Back     alignment and domain information
>TIGR02010 IscR iron-sulfur cluster assembly transcription factor IscR Back     alignment and domain information
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional Back     alignment and domain information
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional Back     alignment and domain information
>smart00344 HTH_ASNC helix_turn_helix ASNC type Back     alignment and domain information
>COG5159 RPN6 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones] Back     alignment and domain information
>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 Back     alignment and domain information
>KOG3054 consensus Uncharacterized conserved protein [Function unknown] Back     alignment and domain information
>PRK11169 leucine-responsive transcriptional regulator; Provisional Back     alignment and domain information
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional Back     alignment and domain information
>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator) Back     alignment and domain information
>COG1522 Lrp Transcriptional regulators [Transcription] Back     alignment and domain information
>COG1959 Predicted transcriptional regulator [Transcription] Back     alignment and domain information
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation Back     alignment and domain information
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria Back     alignment and domain information
>COG5187 RPN7 26S proteasome regulatory complex component, contains PCI domain [Posttranslational modification, protein turnover, chaperones] Back     alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query177
3chm_A169 Crystal Structure Of Pci Domain From A. Thaliana Co 7e-68
>pdb|3CHM|A Chain A, Crystal Structure Of Pci Domain From A. Thaliana Cop9 Signalosome Subunit 7 (Csn7) Length = 169 Back     alignment and structure 
Iteration: 1

 Score =  252 bits (644), Expect = 7e-68,   Method: Compositional matrix adjust.
 Identities = 120/168 (71%), Positives = 134/168 (79%)
Query: 2   DIEQRQAELIDHFVKQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENSK 61
           DIEQ+QAE+ID  VK+AS  K  ALG +I+EATS PSLFAFSEILA+PN+A+ EGT +S 
Sbjct: 2   DIEQKQAEIIDQLVKRASTCKSEALGPLIIEATSHPSLFAFSEILALPNVAQLEGTTDSV 61
Query: 62  YLDMLRLFAHGTWSDYKNNAGHLPQLVPDXXXXXXXXXXXXXAETNKVLPYDELMEELDV 121
           YLD+LRLFAHGTW DYK NA  LP L PD             AE+NKVLPYD LM ELDV
Sbjct: 62  YLDLLRLFAHGTWGDYKCNATRLPHLSPDQILKLKQLTVLTLAESNKVLPYDTLMVELDV 121
Query: 122 TNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGS 169
           +NVRELEDFLINECMY GIVRGKLDQL+RCFEV FAAGRDLRPGQLG+
Sbjct: 122 SNVRELEDFLINECMYAGIVRGKLDQLKRCFEVPFAAGRDLRPGQLGN 169

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query177
3chm_A169 COP9 signalosome complex subunit 7; heat/ARM repea 3e-62
>3chm_A COP9 signalosome complex subunit 7; heat/ARM repeats, winged helix motif, developmental protein, phosphoprotein; 1.50A {Arabidopsis thaliana} Length = 169 Back     alignment and structure
 Score =  189 bits (481), Expect = 3e-62
 Identities = 132/168 (78%), Positives = 147/168 (87%)

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

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

Query: 122 TNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGS 169
           +NVRELEDFLINECMY GIVRGKLDQL+RCFEV FAAGRDLRPGQLG+
Sbjct: 122 SNVRELEDFLINECMYAGIVRGKLDQLKRCFEVPFAAGRDLRPGQLGN 169

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query177
3chm_A169 COP9 signalosome complex subunit 7; heat/ARM repea 100.0
4b4t_O393 26S proteasome regulatory subunit RPN9; hydrolase, 100.0
3txn_A394 26S proteasome regulatory complex subunit P42B; PC 99.39
4b4t_R429 RPN7, 26S proteasome regulatory subunit RPN7; hydr 98.81
3t5x_A203 PCI domain-containing protein 2; PCI, mRNA nuclear 98.75
4b4t_P445 26S proteasome regulatory subunit RPN5; hydrolase, 98.72
1ufm_A84 COP9 complex subunit 4; helix-turn-helix, structur 98.47
4b4t_Q434 26S proteasome regulatory subunit RPN6; hydrolase, 98.34
4b4t_S523 RPN3, 26S proteasome regulatory subunit RPN3; hydr 98.1
3t5v_B455 Nuclear mRNA export protein THP1; PCI, mRNA nuclea 97.97
4b0z_A229 RPN12, 26S proteasome regulatory subunit RPN12; pr 94.91
1wi9_A72 Protein C20ORF116 homolog; helix-turn-helix motif, 94.9
1qgp_A77 Protein (double stranded RNA adenosine deaminase); 89.9
3lwf_A159 LIN1550 protein, putative transcriptional regulato 87.81
3t8r_A143 Staphylococcus aureus CYMR; transcriptional regula 87.61
2hzt_A107 Putative HTH-type transcriptional regulator YTCD; 87.6
1qbj_A81 Protein (double-stranded RNA specific adenosine D 87.47
1i1g_A141 Transcriptional regulator LRPA; helix-turn-helix, 87.03
2dbb_A151 Putative HTH-type transcriptional regulator PH006; 86.81
2p5v_A162 Transcriptional regulator, LRP/ASNC family; NMB057 86.68
2cg4_A152 Regulatory protein ASNC; DNA binding, FFRP, LRP fa 85.87
2ia0_A171 Putative HTH-type transcriptional regulator PF086; 85.83
2cfx_A144 HTH-type transcriptional regulator LRPC; transcrip 85.36
3cuo_A99 Uncharacterized HTH-type transcriptional regulato; 84.91
2y75_A129 HTH-type transcriptional regulator CYMR; DNA bindi 84.14
2pn6_A150 ST1022, 150AA long hypothetical transcriptional re 83.69
1xn7_A78 Hypothetical protein YHGG; alpha+beta, GFT structu 83.61
2htj_A81 P fimbrial regulatory protein KS71A; winged helix- 82.93
2e1c_A171 Putative HTH-type transcriptional regulator PH151; 81.95
1oyi_A82 Double-stranded RNA-binding protein; (alpha+beta) 81.95
3i4p_A162 Transcriptional regulator, ASNC family; PSI, struc 81.7
1ylf_A149 RRF2 family protein; structural genomics, transcri 81.21
1sfx_A109 Conserved hypothetical protein AF2008; structural 81.1
2cyy_A151 Putative HTH-type transcriptional regulator PH151; 80.78
>3chm_A COP9 signalosome complex subunit 7; heat/ARM repeats, winged helix motif, developmental protein, phosphoprotein; 1.50A {Arabidopsis thaliana} Back     alignment and structure
Probab=100.00  E-value=3.2e-50  Score=313.58  Aligned_cols=168  Identities=79%  Similarity=1.223  Sum_probs=157.5

Q ss_pred             chhHHHHHHHHHHHHhccccchHHHHHHHHHHhcCCCceehhhhhcchhhhhccCCCchHHHHHHHHHhcCChhhHhhhh
Q 030471            2 DIEQRQAELIDHFVKQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENSKYLDMLRLFAHGTWSDYKNNA   81 (177)
Q Consensus         2 ~~~~~~~~~~~~~l~~~~~~~~~~a~~~i~~aL~~p~i~~f~eLl~~~~v~~L~~~~~~~l~~LL~if~~G~~~~~~~~~   81 (177)
                      ++++++.+.|++|+.+++++++++|.+++.+||.+|++|+||||+.+|+|++|++++++|+++||++|++||+++|.+++
T Consensus         2 ~~~~~~~~~l~~f~~la~~~~~~~a~~li~~Al~~p~vf~F~eLL~~p~v~~L~~~~~~~~~~LL~iF~~G~~~~y~~~~   81 (169)
T 3chm_A            2 DIEQKQAEIIDQLVKRASTCKSEALGPLIIEATSHPSLFAFSEILALPNVAQLEGTTDSVYLDLLRLFAHGTWGDYKCNA   81 (169)
T ss_dssp             --CCCHHHHHHHHHHHHTTSCGGGHHHHHHHHHHCTTCCCCHHHHTCHHHHTTTTSTTHHHHHHHHHHHHCCHHHHHHHG
T ss_pred             chhHHHHHHHHHHHHHHhcCcHHHHHHHHHHHhcCCCeeehHHHhCChHHHHhcCCChhHHHHHHHHHhcCCHHHHHHhH
Confidence            47899999999999999999999999999999999999999999999999999988899999999999999999999999


Q ss_pred             CCCCCCchHHHHHHHHHHhhccccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeecCCC
Q 030471           82 GHLPQLVPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRD  161 (177)
Q Consensus        82 ~~~~~L~~~~~~Klr~LtllsL~~~~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~gkIDq~~~~v~v~~~~~R~  161 (177)
                      +.+|.|++.+.+|||+|||++||..++++||++|+++|+++|.++||.|||++||+.|||+|+|||++++|+|+|++||+
T Consensus        82 ~~~p~L~~~~~~KlrlLtL~sLa~~~~~lsy~~I~~~l~i~~~~evE~lvI~~ai~~gLI~gkiDQ~~~~v~V~~~~~R~  161 (169)
T 3chm_A           82 TRLPHLSPDQILKLKQLTVLTLAESNKVLPYDTLMVELDVSNVRELEDFLINECMYAGIVRGKLDQLKRCFEVPFAAGRD  161 (169)
T ss_dssp             GGSCCCCHHHHHHHHHHHHHHHHHHCSEEEHHHHHHHHTCCSHHHHHHHHHHTHHHHTSEEEEEETTTTEEEEEEECCTT
T ss_pred             HhCcchHHHHHHHHHHHHHHHHHHhCCCcCHHHHHHHhCCCCHHHHHHHHHHHHHHhCCeEEEEcCcCCEEEEEeecCCc
Confidence            88999999999999999999999999999999999999999899999999977999999999999999999999999999


Q ss_pred             CCcchHHH
Q 030471          162 LRPGQLGS  169 (177)
Q Consensus       162 ~~~~~~~~  169 (177)
                      |+++||..
T Consensus       162 l~~~qi~~  169 (169)
T 3chm_A          162 LRPGQLGN  169 (169)
T ss_dssp             CCC-----
T ss_pred             cCHHhccC
Confidence            99999963
>4b4t_O 26S proteasome regulatory subunit RPN9; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae} Back     alignment and structure
>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 Back     alignment and structure
>4b4t_R RPN7, 26S proteasome regulatory subunit RPN7; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae} Back     alignment and structure
>3t5x_A PCI domain-containing protein 2; PCI, mRNA nuclear export, transcription; 2.12A {Homo sapiens} Back     alignment and structure
>4b4t_P 26S proteasome regulatory subunit RPN5; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae} Back     alignment and structure
>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 Back     alignment and structure
>4b4t_Q 26S proteasome regulatory subunit RPN6; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae} Back     alignment and structure
>4b4t_S RPN3, 26S proteasome regulatory subunit RPN3; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae} Back     alignment and structure
>3t5v_B Nuclear mRNA export protein THP1; PCI, mRNA nuclear export, mRNA, nuclear, transcription; 2.90A {Saccharomyces cerevisiae} Back     alignment and structure
>4b0z_A RPN12, 26S proteasome regulatory subunit RPN12; protein binding, proteasome ubitquitin; HET: SGM GOL; 1.58A {Schizosaccharomyces pombe} Back     alignment and structure
>1wi9_A Protein C20ORF116 homolog; helix-turn-helix motif, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Mus musculus} SCOP: a.4.5.47 Back     alignment and structure
>1qgp_A Protein (double stranded RNA adenosine deaminase); Z-alpha-Z-DNA binding domain, RNA-editing, Z-DNA recognition, ADAR1, helix- turn-helix; NMR {Homo sapiens} SCOP: a.4.5.19 Back     alignment and structure
>3lwf_A LIN1550 protein, putative transcriptional regulator; structural genomics, JOI for structural genomics, JCSG; HET: SO4; 2.06A {Listeria innocua} Back     alignment and structure
>3t8r_A Staphylococcus aureus CYMR; transcriptional regulator protein, dimer, sulfenic acid, UNK function; 1.70A {Staphylococcus aureus} PDB: 3t8t_A Back     alignment and structure
>2hzt_A Putative HTH-type transcriptional regulator YTCD; DNA-binding protein, HTH-type transcription regulators, structural genomics, PSI-2; HET: CSU MSE; 2.00A {Bacillus subtilis} SCOP: a.4.5.69 Back     alignment and structure
>1qbj_A Protein (double-stranded RNA specific adenosine D (ADAR1)); protein-Z-DNA complex, hydrolase-DNA complex; HET: DNA; 2.10A {Homo sapiens} SCOP: a.4.5.19 PDB: 3f21_A* 3f22_A* 3f23_A* 3irr_A* 3irq_D* 2gxb_A 2acj_A 2l54_A Back     alignment and structure
>1i1g_A Transcriptional regulator LRPA; helix-turn-helix, LRP/ASNC family; 2.90A {Pyrococcus furiosus} SCOP: a.4.5.32 d.58.4.2 Back     alignment and structure
>2dbb_A Putative HTH-type transcriptional regulator PH006; ASNC family, helix-turn-helix (HTH) domain, structural genom NPPSFA; 2.00A {Pyrococcus horikoshii} Back     alignment and structure
>2p5v_A Transcriptional regulator, LRP/ASNC family; NMB0573, structu genomics; 1.99A {Neisseria meningitidis} PDB: 2p6s_A 2p6t_A Back     alignment and structure
>2cg4_A Regulatory protein ASNC; DNA binding, FFRP, LRP family, transcription, DNA- binding, transcription regulation; 2.4A {Escherichia coli} SCOP: a.4.5.32 d.58.4.2 Back     alignment and structure
>2ia0_A Putative HTH-type transcriptional regulator PF086; ASNC, PSI, structural genomics, southeast collaboratory for structural genomics; 2.37A {Pyrococcus furiosus} Back     alignment and structure
>2cfx_A HTH-type transcriptional regulator LRPC; transcriptional regulation, DNA binding, FFRP; 2.4A {Bacillus subtilis} SCOP: a.4.5.32 d.58.4.2 Back     alignment and structure
>3cuo_A Uncharacterized HTH-type transcriptional regulato; DNA-binding transcriptional regulator, structural genomics, MCSG; 2.00A {Escherichia coli K12} Back     alignment and structure
>2y75_A HTH-type transcriptional regulator CYMR; DNA binding protein; 2.00A {Bacillus subtilis} Back     alignment and structure
>2pn6_A ST1022, 150AA long hypothetical transcriptional regulator; LRP/ASNC family Gln binding, structural genomics, NPPSFA; HET: GLN; 1.44A {Sulfolobus tokodaii} PDB: 2efn_A* 2e7x_A* 2e7w_A* 2yx4_A* 2efq_A* 2pmh_A* 2yx7_A* 2efp_A* 2efo_A* Back     alignment and structure
>1xn7_A Hypothetical protein YHGG; alpha+beta, GFT structural genomics, protein structure initiative, PSI, NESG; NMR {Escherichia coli} SCOP: a.4.5.62 Back     alignment and structure
>2htj_A P fimbrial regulatory protein KS71A; winged helix-turn-helix, PAP PILI, transcription activator; NMR {Escherichia coli} SCOP: a.4.5.73 Back     alignment and structure
>1oyi_A Double-stranded RNA-binding protein; (alpha+beta) helix-turn-helix, viral protein; NMR {Vaccinia virus} SCOP: a.4.5.19 Back     alignment and structure
>3i4p_A Transcriptional regulator, ASNC family; PSI, structural genom protein structure initiative, midwest center for structural genomics; 2.30A {Agrobacterium tumefaciens str} Back     alignment and structure
>1ylf_A RRF2 family protein; structural genomics, transcription regulator, P protein structure initiative; 2.50A {Bacillus cereus atcc 14579} SCOP: a.4.5.55 Back     alignment and structure
>1sfx_A Conserved hypothetical protein AF2008; structural genomics, HTH MOT protein structure initiative, midwest center for structural genomics; 1.55A {Archaeoglobus fulgidus} SCOP: a.4.5.50 Back     alignment and structure
>2cyy_A Putative HTH-type transcriptional regulator PH151; structural genomics, pyrococcus horikosii OT3, NPPSFA; HET: MSE GLN; 1.80A {Pyrococcus horikoshii} SCOP: a.4.5.32 d.58.4.2 Back     alignment and structure

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 ?Alignment Graph ?Length ? Definition ? Probability ?
Query177
d1ufma_84 COP9 signalosome complex subunit 4, GSN4 {Mouse (M 98.63
d1wi9a_72 Hypothetical protein C20orf116 homolog {Mouse (Mus 94.72
d2cfxa163 Transcriptional regulator LrpC {Bacillus subtilis 93.46
d2cg4a163 Regulatory protein AsnC {Escherichia coli [TaxId: 93.36
d2cyya160 Putative transcriptional regulator PH1519 {Archaeo 92.95
d1i1ga160 LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]} 92.92
d1z05a171 Transcriptional regulator VC2007 N-terminal domain 89.36
d1ub9a_100 Hypothetical protein PH1061 {Archaeon Pyrococcus h 84.1
d1biaa163 Biotin repressor, N-terminal domain {Escherichia c 83.97
d1jhfa171 LexA repressor, N-terminal DNA-binding domain {Esc 83.94
d1mkma175 Transcriptional regulator IclR, N-terminal domain 82.24
d3ctaa185 Ta1064 (RFK), N-terminal domain {Thermoplasma acid 81.18
>d1ufma_ a.4.5.47 (A:) COP9 signalosome complex subunit 4, GSN4 {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: PCI domain (PINT motif)
domain: COP9 signalosome complex subunit 4, GSN4
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.63  E-value=3.4e-08  Score=66.31  Aligned_cols=62  Identities=15%  Similarity=0.261  Sum_probs=55.0

Q ss_pred             HHHHHHhhccccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEee
Q 030471           94 KLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFA  157 (177)
Q Consensus        94 Klr~LtllsL~~~~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~gkIDq~~~~v~v~~~  157 (177)
                      .++...|..+++....|+++.+|+.++++ .+++|.+|. ++|..|-|.|+|||.+++|++..-
T Consensus        15 ~i~Ehni~~is~~Y~~Isl~~la~~l~l~-~~evE~~l~-~mI~~~~i~akIDq~~g~V~F~~~   76 (84)
T d1ufma_          15 AVIEHNLLSASKLYNNITFEELGALLEIP-AAKAEKIAS-QMITEGRMNGFIDQIDGIVHFETR   76 (84)
T ss_dssp             HHHHHHHHHHHHSCSEEEHHHHHHHTTSC-HHHHHHHHH-HHHHTTSSCEEEETTTTEEEECCS
T ss_pred             HHHHHHHHHHHHhhceeeHHHHHHHHCCC-HHHHHHHHH-HHHhcCeEEEEEeCCCCEEEECCC
Confidence            44556666777889999999999999997 999999999 999999999999999999988653
>d1wi9a_ a.4.5.47 (A:) Hypothetical protein C20orf116 homolog {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d2cfxa1 a.4.5.32 (A:1-63) Transcriptional regulator LrpC {Bacillus subtilis [TaxId: 1423]} Back     information, alignment and structure
>d2cg4a1 a.4.5.32 (A:4-66) Regulatory protein AsnC {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d2cyya1 a.4.5.32 (A:5-64) Putative transcriptional regulator PH1519 {Archaeon Pyrococcus horikoshii [TaxId: 53953]} Back     information, alignment and structure
>d1i1ga1 a.4.5.32 (A:2-61) LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]} Back     information, alignment and structure
>d1z05a1 a.4.5.63 (A:10-80) Transcriptional regulator VC2007 N-terminal domain {Vibrio cholerae [TaxId: 666]} Back     information, alignment and structure
>d1ub9a_ a.4.5.28 (A:) Hypothetical protein PH1061 {Archaeon Pyrococcus horikoshii [TaxId: 53953]} Back     information, alignment and structure
>d1biaa1 a.4.5.1 (A:1-63) Biotin repressor, N-terminal domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1jhfa1 a.4.5.2 (A:2-72) LexA repressor, N-terminal DNA-binding domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1mkma1 a.4.5.33 (A:1-75) Transcriptional regulator IclR, N-terminal domain {Thermotoga maritima [TaxId: 2336]} Back     information, alignment and structure
>d3ctaa1 a.4.5.28 (A:5-89) Ta1064 (RFK), N-terminal domain {Thermoplasma acidophilum [TaxId: 2303]} Back     information, alignment and structure