Psyllid ID: psy4458

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-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300---

MKEDEGDVTEAANIIQELQVETYGSMEKKEKVTLILEQMRLCLAKKDYIRTQIISKKINTKFFDDEKDDVQELKLKYYRLMIELDQHEGSYLATCKHYRAILTTPCIQSDPVQRHAVLQNVVLYLMLAPYDNEQSDLTHRVLEDKLLNEIPLYKGLLQWFTNPELIKWSGLRQLYEEELFKTSVFNQSTEEGQKCFKMLKHRVVEHNIRVMAKYYTRITLQRMCDLLGLPIEETEEFLSSMVVSKTITAKIDRPAGIINFARNKDPGEILNEWSASLNELMKLVNNTTHLINKEQMIHQRVAA

cccccccHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHccHHHHHHHHHHHcccccccHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHcccHHHHHHHHHHHHHcccEEEEEcccccEEEEccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHc

cccccccHHHHHHHHHHccEcccccccHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHcHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccHcccHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHccHHHHcHHHHHHHHHHccHHHHccHHHHHHHHHHHHHcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHcccHHHHHHHHHHHHHccEEEEEEcccccEEEEcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcc

MKEDEGDVTEAANIIQELQVETYGSMEKKEKVTLILEQMRLCLAKKDYIRTQIISKKintkffddekdDVQELKLKYYRLMIELDQHEGSYLATCKHYRAilttpciqsdpvqrHAVLQNVVLYLMLapydneqsdLTHRVLEDKllneiplykgllqwftnpelikwSGLRQLYEEELFKTSVFNQSTEEGQKCFKMLKHRVVEHNIRVMAKYYTRITLQRMCDllglpieeTEEFLSSMVVSKTitakidrpagiinfarnkdpgeILNEWSASLNELMKLVNNTTHLINKEQMIHQRVAA

mkedegdvteaaniiqelqvetygsmeKKEKVTLILEQMRLCLAKKDYIRTQIiskkintkffddekdDVQELKLKYYRLMIELDQHEGSYLATCKHYRAILTTPCIQSDPVQRHAVLQNVVLYLMLAPYDNEQSDLTHRVLEDKLLNEIPLYKGLLQWFTNPELIKWSGLRQLYEEELFKTSVFNQSTEEGQKCFKMLKHRVVEHNIRVMAKYYTRITLQRMCDLLGLPIEETEEFLSSMVVSKTitakidrpagiinfarnkdpgEILNEWSASLNELMKLVNNTTHLINKEQMIHQRVAA

************NIIQELQVETYGSMEKKEKVTLILEQMRLCLAKKDYIRTQIISKKINTKFFDDEKDDVQELKLKYYRLMIELDQHEGSYLATCKHYRAILTTPCIQSDPVQRHAVLQNVVLYLMLAPYDNEQSDLTHRVLEDKLLNEIPLYKGLLQWFTNPELIKWSGLRQLYEEELFKTSVFNQSTEEGQKCFKMLKHRVVEHNIRVMAKYYTRITLQRMCDLLGLPIEETEEFLSSMVVSKTITAKIDRPAGIINFARNKDPGEILNEWSASLNELMKLVNNTTHLIN***********

MKE**GDVTEAANIIQELQVETYGSMEKKEKVTLILEQMRLCLAKKDYIRTQIISKKINTKFFDDEKDDVQELKLKYYRLMIELDQHEGSYLATCKHYRAILTTPCIQSDPVQRHAVLQNVVLYLMLAPYDN***********DKLLNEIPLYKGLLQWFTNPELIKWSGLRQLYEEELFKTSVFNQSTEEGQKCFKMLKHRVVEHNIRVMAKYYTRITLQRMCDLLGLPIEETEEFLSSMVVSKTITAKIDRPAGIINFARNKDPGEILNEWSASLNELMKLVNNTTHLINKEQMIHQR***

*********EAANIIQELQVETYGSMEKKEKVTLILEQMRLCLAKKDYIRTQIISKKINTKFFDDEKDDVQELKLKYYRLMIELDQHEGSYLATCKHYRAILTTPCIQSDPVQRHAVLQNVVLYLMLAPYDNEQSDLTHRVLEDKLLNEIPLYKGLLQWFTNPELIKWSGLRQLYEEELFKTSVFNQSTEEGQKCFKMLKHRVVEHNIRVMAKYYTRITLQRMCDLLGLPIEETEEFLSSMVVSKTITAKIDRPAGIINFARNKDPGEILNEWSASLNELMKLVNNTTHLINKEQMIHQRVAA

****EGDVTEAANIIQELQVETYGSMEKKEKVTLILEQMRLCLAKKDYIRTQIISKKINTKFFDDEKDDVQELKLKYYRLMIELDQHEGSYLATCKHYRAILTTPCIQSDPVQRHAVLQNVVLYLMLAPYDNEQSDLTHRVLEDKLLNEIPLYKGLLQWFTNPELIKWSGLRQLYEEELFKTSVFNQSTEEGQKCFKMLKHRVVEHNIRVMAKYYTRITLQRMCDLLGLPIEETEEFLSSMVVSKTITAKIDRPAGIINFARNKDPGEILNEWSASLNELMKLVNNTTHLINKEQMIHQRVAA

ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

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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
Query		303	2.2.26 [Sep-21-2011]
O00232		456	26S proteasome non-ATPase	yes	N/A	0.973	0.646	0.659	1e-109
Q5RBI3		456	26S proteasome non-ATPase	yes	N/A	0.973	0.646	0.659	1e-109
Q9D8W5		456	26S proteasome non-ATPase	yes	N/A	0.973	0.646	0.655	1e-109
Q2KJ25		456	26S proteasome non-ATPase	yes	N/A	0.973	0.646	0.655	1e-108
Q54UJ0		447	26S proteasome non-ATPase	yes	N/A	0.966	0.655	0.438	4e-69
Q9UTM3		443	26S proteasome regulatory	yes	N/A	0.990	0.677	0.439	4e-68
Q12250		445	26S proteasome regulatory	yes	N/A	0.973	0.662	0.395	2e-54
Q9V345		407	COP9 signalosome complex	no	N/A	0.861	0.641	0.215	1e-06
Q5R648		406	COP9 signalosome complex	no	N/A	0.537	0.401	0.224	6e-05
O88544		406	COP9 signalosome complex	no	N/A	0.537	0.401	0.224	6e-05

>sp\|O00232\|PSD12_HUMAN 26S proteasome non-ATPase regulatory subunit 12 OS=Homo sapiens GN=PSMD12 PE=1 SV=3	Back alignment and function desciption

 Score =  395 bits (1014), Expect = e-109,   Method: Compositional matrix adjust.
 Identities = 201/305 (65%), Positives = 240/305 (78%), Gaps = 10/305 (3%)

Query: 1   MKEDEGDVTEAANIIQELQVETYGSMEKKEKVTLILEQMRLCLAKKDYIRTQIISKKINT 60
           +KE  GDV EAA+I+QELQVETYGSMEKKE+V  ILEQMRLCLA KDYIRTQIISKKINT
Sbjct: 152 IKEQNGDVKEAASILQELQVETYGSMEKKERVEFILEQMRLCLAVKDYIRTQIISKKINT 211

Query: 61  KFFDDEKDDVQELKLKYYRLMIELDQHEGSYLATCKHYRAILTTPCIQSDPVQRHAVLQN 120
           KFF +E  + ++LKLKYY LMI+LDQHEGSYL+ CKHYRAI  TPCIQ++  +    L++
Sbjct: 212 KFFQEE--NTEKLKLKYYNLMIQLDQHEGSYLSICKHYRAIYDTPCIQAESEKWQQALKS 269

Query: 121 VVLYLMLAPYDNEQSDLTHRVLEDKLLNEIPLYKGLLQWFTNPELIKWSGLRQLYEEELF 180
           VVLY++LAP+DNEQSDL HR+  DK L EIP YK LL+ FT  EL++WS L + Y  EL 
Sbjct: 270 VVLYVILAPFDNEQSDLVHRISGDKKLEEIPKYKDLLKLFTTMELMRWSTLVEDYGMELR 329

Query: 181 K-------TSVFNQSTEEGQKCFKMLKHRVVEHNIRVMAKYYTRITLQRMCDLLGLPIEE 233
           K       T VF  STEEG+K +K LK+RVVEHNIR+MAKYYTRIT++RM  LL L ++E
Sbjct: 330 KGSLESPATDVFG-STEEGEKRWKDLKNRVVEHNIRIMAKYYTRITMKRMAQLLDLSVDE 388

Query: 234 TEEFLSSMVVSKTITAKIDRPAGIINFARNKDPGEILNEWSASLNELMKLVNNTTHLINK 293
           +E FLS++VV+KTI AK+DR AGIINF R KDP  +LN+WS  LN LM LVN TTHLI K
Sbjct: 389 SEAFLSNLVVNKTIFAKVDRLAGIINFQRPKDPNNLLNDWSQKLNSLMSLVNKTTHLIAK 448

Query: 294 EQMIH 298
           E+MIH
Sbjct: 449 EEMIH 453

Acts as a regulatory subunit of the 26S proteasome which is involved in the ATP-dependent degradation of ubiquitinated proteins.
Homo sapiens (taxid: 9606)

>sp\|Q5RBI3\|PSD12_PONAB 26S proteasome non-ATPase regulatory subunit 12 OS=Pongo abelii GN=PSMD12 PE=2 SV=3	Back alignment and function description

>sp\|Q9D8W5\|PSD12_MOUSE 26S proteasome non-ATPase regulatory subunit 12 OS=Mus musculus GN=Psmd12 PE=1 SV=4	Back alignment and function description

>sp\|Q2KJ25\|PSD12_BOVIN 26S proteasome non-ATPase regulatory subunit 12 OS=Bos taurus GN=PSMD12 PE=2 SV=3	Back alignment and function description

>sp\|Q54UJ0\|PSD12_DICDI 26S proteasome non-ATPase regulatory subunit 12 OS=Dictyostelium discoideum GN=psmD12 PE=2 SV=1	Back alignment and function description

>sp\|Q9UTM3\|RPN5_SCHPO 26S proteasome regulatory subunit rpn5 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rpn5a PE=1 SV=1	Back alignment and function description

>sp\|Q12250\|RPN5_YEAST 26S proteasome regulatory subunit RPN5 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RPN5 PE=1 SV=3	Back alignment and function description

>sp\|Q9V345\|CSN4_DROME COP9 signalosome complex subunit 4 OS=Drosophila melanogaster GN=CSN4 PE=1 SV=1	Back alignment and function description

>sp\|Q5R648\|CSN4_PONAB COP9 signalosome complex subunit 4 OS=Pongo abelii GN=COPS4 PE=2 SV=1	Back alignment and function description

>sp\|O88544\|CSN4_MOUSE COP9 signalosome complex subunit 4 OS=Mus musculus GN=Cops4 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
Query		303
242014164		463	26S proteasome non-ATPase regulatory sub	0.986	0.645	0.743	1e-128
91088257		451	PREDICTED: similar to proteasome 26S non	0.990	0.665	0.679	1e-118
332372516		366	unknown [Dendroctonus ponderosae]	0.990	0.819	0.683	1e-116
193594276		461	PREDICTED: 26S proteasome non-ATPase reg	0.993	0.652	0.659	1e-112
392873972		455	26S proteasome non-ATPase regulatory sub	0.973	0.648	0.668	1e-109
54400716		456	26S proteasome non-ATPase regulatory sub	0.973	0.646	0.655	1e-107
4506221		456	26S proteasome non-ATPase regulatory sub	0.973	0.646	0.659	1e-107
351710334		456	26S proteasome non-ATPase regulatory sub	0.976	0.649	0.657	1e-107
296203030		456	PREDICTED: 26S proteasome non-ATPase reg	0.973	0.646	0.659	1e-107
28872765		436	26S proteasome non-ATPase regulatory sub	0.973	0.676	0.659	1e-107

>gi\|242014164\|ref\|XP_002427765.1\| 26S proteasome non-ATPase regulatory subunit, putative [Pediculus humanus corporis] gi\|212512219\|gb\|EEB15027.1\| 26S proteasome non-ATPase regulatory subunit, putative [Pediculus humanus corporis]	Back alignment and taxonomy information

 Score =  464 bits (1194), Expect = e-128,   Method: Compositional matrix adjust.
 Identities = 229/308 (74%), Positives = 261/308 (84%), Gaps = 9/308 (2%)

Query: 1   MKEDEGDVTEAANIIQELQVETYGSMEKKEKVTLILEQMRLCLAKKDYIRTQIISKKINT 60
           MKE+EG++TEAANIIQELQVETYGSME+ EKV LILEQMRLCLAKKDYIRTQIISKKINT
Sbjct: 153 MKEEEGNITEAANIIQELQVETYGSMERTEKVELILEQMRLCLAKKDYIRTQIISKKINT 212

Query: 61  KFFDDEKDDVQELKLKYYRLMIELDQHEGSYLATCKHYRAILTTPCIQSDPVQRHAVLQN 120
           KFFDDEK   QELKLKYY LMIELDQHEGS+LATCKHYRA+L+TP IQ+DP QRH +LQN
Sbjct: 213 KFFDDEK--TQELKLKYYLLMIELDQHEGSFLATCKHYRAVLSTPSIQNDPKQRHVILQN 270

Query: 121 VVLYLMLAPYDNEQSDLTHRVLEDKLLNEIPLYKGLLQWFTNPELIKWSGLRQLYEEEL- 179
           V+LYL+LAPYDNEQ+DLTHRV+EDKL++E+P YK LL+ F NPELI+WSGL  +YE  L 
Sbjct: 271 VILYLILAPYDNEQADLTHRVMEDKLIDELPAYKELLKMFINPELIQWSGLVSVYENVLK 330

Query: 180 ------FKTSVFNQSTEEGQKCFKMLKHRVVEHNIRVMAKYYTRITLQRMCDLLGLPIEE 233
                   T VFN +TEEGQ  +K LK++VVEHNIRVMAKYYTRITL RM  LL LPIEE
Sbjct: 331 HGTDDSPPTDVFNPNTEEGQARWKELKNKVVEHNIRVMAKYYTRITLGRMAQLLDLPIEE 390

Query: 234 TEEFLSSMVVSKTITAKIDRPAGIINFARNKDPGEILNEWSASLNELMKLVNNTTHLINK 293
           TEEFLS++VV KTI AK DRP GI+ F R+KDP +ILNEWS  LN LM+LVN TTHLINK
Sbjct: 391 TEEFLSNLVVKKTIEAKTDRPDGIVCFTRSKDPDDILNEWSNHLNSLMQLVNKTTHLINK 450

Query: 294 EQMIHQRV 301
           E+MIH+ +
Sbjct: 451 EEMIHKHL 458

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi\|91088257\|ref\|XP_966746.1\| PREDICTED: similar to proteasome 26S non-ATPase subunit 12 [Tribolium castaneum] gi\|270012153\|gb\|EFA08601.1\| hypothetical protein TcasGA2_TC006260 [Tribolium castaneum]	Back alignment and taxonomy information

>gi\|332372516\|gb\|AEE61400.1\| unknown [Dendroctonus ponderosae]	Back alignment and taxonomy information

>gi\|193594276\|ref\|XP_001945478.1\| PREDICTED: 26S proteasome non-ATPase regulatory subunit 12-like [Acyrthosiphon pisum]	Back alignment and taxonomy information

>gi\|392873972\|gb\|AFM85818.1\| 26S proteasome non-ATPase regulatory subunit 12 [Callorhinchus milii]	Back alignment and taxonomy information

>gi\|54400716\|ref\|NP_001005875.1\| 26S proteasome non-ATPase regulatory subunit 12 [Rattus norvegicus] gi\|53733547\|gb\|AAH83758.1\| Proteasome (prosome, macropain) 26S subunit, non-ATPase, 12 [Rattus norvegicus]	Back alignment and taxonomy information

>gi|4506221|ref|NP_002807.1| 26S proteasome non-ATPase regulatory subunit 12 isoform 1 [Homo sapiens] gi|388453693|ref|NP_001252782.1| 26S proteasome non-ATPase regulatory subunit 12 [Macaca mulatta] gi|114670121|ref|XP_511639.2| PREDICTED: 26S proteasome non-ATPase regulatory subunit 12 isoform 2 [Pan troglodytes] gi|397482379|ref|XP_003812405.1| PREDICTED: 26S proteasome non-ATPase regulatory subunit 12 isoform 1 [Pan paniscus] gi|402900845|ref|XP_003913375.1| PREDICTED: 26S proteasome non-ATPase regulatory subunit 12 isoform 1 [Papio anubis] gi|426347028|ref|XP_004041166.1| PREDICTED: 26S proteasome non-ATPase regulatory subunit 12 isoform 1 [Gorilla gorilla gorilla] gi|441642699|ref|XP_004090469.1| PREDICTED: 26S proteasome non-ATPase regulatory subunit 12 isoform 2 [Nomascus leucogenys] gi|20978544|sp|O00232.3|PSD12_HUMAN RecName: Full=26S proteasome non-ATPase regulatory subunit 12; AltName: Full=26S proteasome regulatory subunit RPN5; AltName: Full=26S proteasome regulatory subunit p55 gi|1945611|dbj|BAA19749.1| 26S proteasome subunit p55 [Homo sapiens] gi|17512153|gb|AAH19062.1| Proteasome (prosome, macropain) 26S subunit, non-ATPase, 12 [Homo sapiens] gi|119609432|gb|EAW89026.1| proteasome (prosome, macropain) 26S subunit, non-ATPase, 12, isoform CRA_a [Homo sapiens] gi|123985956|gb|ABM83747.1| proteasome (prosome, macropain) 26S subunit, non-ATPase, 12 [synthetic construct] gi|123998954|gb|ABM87066.1| proteasome (prosome, macropain) 26S subunit, non-ATPase, 12 [synthetic construct] gi|168275714|dbj|BAG10577.1| 26S proteasome non-ATPase regulatory subunit 12 [synthetic construct] gi|380814946|gb|AFE79347.1| 26S proteasome non-ATPase regulatory subunit 12 isoform 1 [Macaca mulatta] gi|383420191|gb|AFH33309.1| 26S proteasome non-ATPase regulatory subunit 12 isoform 1 [Macaca mulatta] gi|410209240|gb|JAA01839.1| proteasome (prosome, macropain) 26S subunit, non-ATPase, 12 [Pan troglodytes] gi|410250498|gb|JAA13216.1| proteasome (prosome, macropain) 26S subunit, non-ATPase, 12 [Pan troglodytes] gi|410289062|gb|JAA23131.1| proteasome (prosome, macropain) 26S subunit, non-ATPase, 12 [Pan troglodytes]

Back alignment and taxonomy information

>gi\|351710334\|gb\|EHB13253.1\| 26S proteasome non-ATPase regulatory subunit 12 [Heterocephalus glaber]	Back alignment and taxonomy information

>gi\|296203030\|ref\|XP_002748720.1\| PREDICTED: 26S proteasome non-ATPase regulatory subunit 12 isoform 1 [Callithrix jacchus]	Back alignment and taxonomy information

>gi|28872765|ref|NP_777360.1| 26S proteasome non-ATPase regulatory subunit 12 isoform 2 [Homo sapiens] gi|397482381|ref|XP_003812406.1| PREDICTED: 26S proteasome non-ATPase regulatory subunit 12 isoform 2 [Pan paniscus] gi|402900847|ref|XP_003913376.1| PREDICTED: 26S proteasome non-ATPase regulatory subunit 12 isoform 2 [Papio anubis] gi|410052066|ref|XP_003953215.1| PREDICTED: 26S proteasome non-ATPase regulatory subunit 12 isoform 1 [Pan troglodytes] gi|426347030|ref|XP_004041167.1| PREDICTED: 26S proteasome non-ATPase regulatory subunit 12 isoform 2 [Gorilla gorilla gorilla] gi|441642703|ref|XP_003276114.2| PREDICTED: 26S proteasome non-ATPase regulatory subunit 12 isoform 1 [Nomascus leucogenys] gi|119609434|gb|EAW89028.1| proteasome (prosome, macropain) 26S subunit, non-ATPase, 12, isoform CRA_c [Homo sapiens] gi|193787097|dbj|BAG52303.1| unnamed protein product [Homo sapiens]

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
Query		303
RGD\|1359305		456	Psmd12 "proteasome (prosome, m	0.973	0.646	0.655	7.1e-100
UNIPROTKB\|O00232		456	PSMD12 "26S proteasome non-ATP	0.973	0.646	0.659	9.1e-100
UNIPROTKB\|Q5RBI3		456	PSMD12 "26S proteasome non-ATP	0.973	0.646	0.659	9.1e-100
UNIPROTKB\|F1NPQ0		456	LOC100859465 "Uncharacterized	0.973	0.646	0.652	1.2e-99
MGI\|MGI:1914247		456	Psmd12 "proteasome (prosome, m	0.973	0.646	0.655	1.5e-99
UNIPROTKB\|Q2KJ25		456	PSMD12 "26S proteasome non-ATP	0.973	0.646	0.655	3.1e-99
UNIPROTKB\|F1RSM2		456	PSMD12 "Uncharacterized protei	0.973	0.646	0.655	3.1e-99
ZFIN\|ZDB-GENE-030131-617		456	psmd12 "proteasome (prosome, m	0.973	0.646	0.642	5.2e-97
FB\|FBgn0028690		502	Rpn5 "Regulatory particle non-	0.600	0.362	0.461	3.7e-72
ASPGD\|ASPL0000076235		487	AN4775 [Emericella nidulans (t	0.759	0.472	0.468	6.8e-71

RGD\|1359305 Psmd12 "proteasome (prosome, macropain) 26S subunit, non-ATPase, 12" [Rattus norvegicus (taxid:10116)]	Back alignment and assigned GO terms

 Score = 991 (353.9 bits), Expect = 7.1e-100, P = 7.1e-100
 Identities = 200/305 (65%), Positives = 241/305 (79%)

Query:     1 MKEDEGDVTEAANIIQELQVETYGSMEKKEKVTLILEQMRLCLAKKDYIRTQIISKKINT 60
             +KE  GDV EAA+I+QELQVETYGSMEKKE+V  ILEQMRLCLA KDYIRTQIISKKINT
Sbjct:   152 IKEQNGDVKEAASILQELQVETYGSMEKKERVEFILEQMRLCLAVKDYIRTQIISKKINT 211

Query:    61 KFFDDEKDDVQELKLKYYRLMIELDQHEGSYLATCKHYRAILTTPCIQSDPVQRHAVLQN 120
             KFF +E  + ++LKLKYY LMI+LDQHEGSYL+ CKHYRAI  TPCIQ++  +    L++
Sbjct:   212 KFFQEE--NTEKLKLKYYNLMIQLDQHEGSYLSICKHYRAIYDTPCIQAESDKWQQALKS 269

Query:   121 VVLYLMLAPYDNEQSDLTHRVLEDKLLNEIPLYKGLLQWFTNPELIKWSGLRQLYEEELF 180
             VVLY++LAP+DNEQSDL HR+  DK L EIP YK LL+ FT  EL++WS L + Y  EL 
Sbjct:   270 VVLYVILAPFDNEQSDLVHRISSDKKLEEIPKYKDLLKLFTTMELMRWSTLVEDYGVELR 329

Query:   181 K-------TSVFNQSTEEGQKCFKMLKHRVVEHNIRVMAKYYTRITLQRMCDLLGLPIEE 233
             K       T VF+ STEEG+K +K LK+RVVEHNIR+MAKYYTRIT++RM  LL L ++E
Sbjct:   330 KGSSETPATDVFS-STEEGEKRWKDLKNRVVEHNIRIMAKYYTRITMKRMAQLLDLSVDE 388

Query:   234 TEEFLSSMVVSKTITAKIDRPAGIINFARNKDPGEILNEWSASLNELMKLVNNTTHLINK 293
             +E FLS++VV+KTI AK+DR AG+INF R KDP  +LN+WS  LN LM LVN TTHLI K
Sbjct:   389 SEAFLSNLVVNKTIFAKVDRLAGVINFQRPKDPNNLLNDWSQKLNSLMSLVNKTTHLIAK 448

Query:   294 EQMIH 298
             E+MIH
Sbjct:   449 EEMIH 453

GO:0000502 "proteasome complex" evidence=IEA

GO:0005838 "proteasome regulatory particle" evidence=ISS

GO:0022624 "proteasome accessory complex" evidence=ISO

GO:0043161 "proteasomal ubiquitin-dependent protein catabolic process" evidence=ISS

UNIPROTKB\|O00232 PSMD12 "26S proteasome non-ATPase regulatory subunit 12" [Homo sapiens (taxid:9606)]	Back alignment and assigned GO terms

UNIPROTKB\|Q5RBI3 PSMD12 "26S proteasome non-ATPase regulatory subunit 12" [Pongo abelii (taxid:9601)]	Back alignment and assigned GO terms

UNIPROTKB\|F1NPQ0 LOC100859465 "Uncharacterized protein" [Gallus gallus (taxid:9031)]	Back alignment and assigned GO terms

MGI\|MGI:1914247 Psmd12 "proteasome (prosome, macropain) 26S subunit, non-ATPase, 12" [Mus musculus (taxid:10090)]	Back alignment and assigned GO terms

UNIPROTKB\|Q2KJ25 PSMD12 "26S proteasome non-ATPase regulatory subunit 12" [Bos taurus (taxid:9913)]	Back alignment and assigned GO terms

UNIPROTKB\|F1RSM2 PSMD12 "Uncharacterized protein" [Sus scrofa (taxid:9823)]	Back alignment and assigned GO terms

ZFIN\|ZDB-GENE-030131-617 psmd12 "proteasome (prosome, macropain) 26S subunit, non-ATPase, 12" [Danio rerio (taxid:7955)]	Back alignment and assigned GO terms

FB\|FBgn0028690 Rpn5 "Regulatory particle non-ATPase 5" [Drosophila melanogaster (taxid:7227)]	Back alignment and assigned GO terms

ASPGD\|ASPL0000076235 AN4775 [Emericella nidulans (taxid:162425)]	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

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q9UTM3	RPN5_SCHPO	No assigned EC number	0.4393	0.9900	0.6772	yes	N/A
O00232	PSD12_HUMAN	No assigned EC number	0.6590	0.9735	0.6469	yes	N/A
Q54UJ0	PSD12_DICDI	No assigned EC number	0.4381	0.9669	0.6554	yes	N/A
Q9D8W5	PSD12_MOUSE	No assigned EC number	0.6557	0.9735	0.6469	yes	N/A
Q12250	RPN5_YEAST	No assigned EC number	0.3959	0.9735	0.6629	yes	N/A
Q5RBI3	PSD12_PONAB	No assigned EC number	0.6590	0.9735	0.6469	yes	N/A
Q2KJ25	PSD12_BOVIN	No assigned EC number	0.6557	0.9735	0.6469	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Alignment Graph	Length	Definition	E-value
Query		303
COG5071		439	COG5071, RPN5, 26S proteasome regulatory complex c	1e-80
pfam01399		100	pfam01399, PCI, PCI domain	5e-15
smart00753		88	smart00753, PAM, PCI/PINT associated module	6e-14
smart00088		88	smart00088, PINT, motif in proteasome subunits, In	6e-14

>gnl\|CDD\|227403 COG5071, RPN5, 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

 Score =  250 bits (640), Expect = 1e-80
 Identities = 132/297 (44%), Positives = 194/297 (65%), Gaps = 3/297 (1%)

Query: 2   KEDEGDVTEAANIIQELQVETYGSMEKKEKVTLILEQMRLCLAKKDYIRTQIISKKINTK 61
           KE++GD+  A +I+    VETYGS +  EKV  ILEQ+RL L + DY      +KKIN K
Sbjct: 141 KEEQGDIKSAQDILCNEPVETYGSFDLSEKVAFILEQVRLFLLRSDYYMASTYTKKINKK 200

Query: 62  FFDDEKDDVQELKLKYYRLMIELDQHEGSYLATCKHYRAILTTPCIQSDPVQRHAVLQNV 121
           FF  EK+DVQ LKLKYY L + +  H+ +YL  CK+YRA+  T  +Q DP +   VL NV
Sbjct: 201 FF--EKEDVQSLKLKYYELKVRIGLHDRAYLDVCKYYRAVYDTAVVQEDPAKWKEVLSNV 258

Query: 122 VLYLMLAPYDNEQSDLTHRVLEDKLLNEIPLYKGLLQWFTNPELIKWSGLRQLYEEELFK 181
           V + +L PYDNEQ+DL H++  D  LN +PL + L++ F   EL++W  + ++Y   L +
Sbjct: 259 VCFALLTPYDNEQADLLHKINADHKLNSLPLLQQLVKCFIVNELMRWPKVAEIYGSAL-R 317

Query: 182 TSVFNQSTEEGQKCFKMLKHRVVEHNIRVMAKYYTRITLQRMCDLLGLPIEETEEFLSSM 241
           ++VF  + E+G+K +  L+ RV+EHNIRV+A YY+RI   R+  LL +   ETE+F+S +
Sbjct: 318 SNVFAFNDEKGEKRWSDLRKRVIEHNIRVIANYYSRIHCSRLGVLLDMSPSETEQFISDL 377

Query: 242 VVSKTITAKIDRPAGIINFARNKDPGEILNEWSASLNELMKLVNNTTHLINKEQMIH 298
           V      AKI+RPA II+F ++++  E LNEW +++ EL+  +    HLI KE+M++
Sbjct: 378 VNKGHFYAKINRPAQIISFEKSQNVQEQLNEWGSNVTELLGKLEKVRHLIIKEEMMN 434

Length = 439

>gnl\|CDD\|216479 pfam01399, PCI, PCI domain	Back alignment and domain information

>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		303
KOG1498\|consensus		439		100.0
COG5071		439	RPN5 26S proteasome regulatory complex component [	100.0
KOG1497\|consensus		399		100.0
KOG0687\|consensus		393		100.0
COG5187		412	RPN7 26S proteasome regulatory complex component,	99.97
KOG1463\|consensus		411		99.93
KOG1464\|consensus		440		99.91
COG5159		421	RPN6 26S proteasome regulatory complex component [	99.84
KOG2908\|consensus		380		99.79
PF01399		105	PCI: PCI domain; InterPro: IPR000717 A homology do	99.71
smart00088		88	PINT motif in proteasome subunits, Int-6, Nip-1 an	99.58
smart00753		88	PAM PCI/PINT associated module.	99.58
KOG0686\|consensus		466		99.58
PF10602		177	RPN7: 26S proteasome subunit RPN7; InterPro: IPR01	99.48
KOG2581\|consensus		493		99.43
KOG2582\|consensus		422		99.09
KOG2753\|consensus		378		98.3
KOG1076\|consensus		843		98.11
KOG2688\|consensus		394		97.87
KOG2758\|consensus		432		97.59
PF10255		404	Paf67: RNA polymerase I-associated factor PAF67; I	97.38
COG5600		413	Transcription-associated recombination protein [DN	97.07
KOG2072\|consensus		988		97.03
PF10075		143	PCI_Csn8: COP9 signalosome, subunit CSN8; InterPro	96.25
PF09012		69	FeoC: FeoC like transcriptional regulator; InterPr	95.55
PF09756		188	DDRGK: DDRGK domain; InterPro: IPR019153 This is a	94.5
PF09976		145	TPR_21: Tetratricopeptide repeat; InterPro: IPR018	94.31
PF13424		78	TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15	94.17
PF14938		282	SNAP: Soluble NSF attachment protein, SNAP; PDB: 1	93.83
PF08784		102	RPA_C: Replication protein A C terminal; InterPro:	93.45
PF14938		282	SNAP: Soluble NSF attachment protein, SNAP; PDB: 1	92.9
PF12895		84	Apc3: Anaphase-promoting complex, cyclosome, subun	90.94
PF04733		290	Coatomer_E: Coatomer epsilon subunit; InterPro: IP	90.34
TIGR02795		119	tol_pal_ybgF tol-pal system protein YbgF. Members	89.3
PRK11788		389	tetratricopeptide repeat protein; Provisional	89.2
PRK15431		78	ferrous iron transport protein FeoC; Provisional	88.61
PF04348		536	LppC: LppC putative lipoprotein; InterPro: IPR0074	88.58
PF14559		68	TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN	88.55
COG3107		604	LppC Putative lipoprotein [General function predic	88.27
PF12802		62	MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP	87.84
KOG2003\|consensus		840		87.63
PF13432		65	TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL	85.69
PF08220		57	HTH_DeoR: DeoR-like helix-turn-helix domain; Inter	85.56
PF13414		69	TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A	84.64
PF01047		59	MarR: MarR family; InterPro: IPR000835 The MarR-ty	84.33
KOG4414\|consensus		197		84.08
COG3063		250	PilF Tfp pilus assembly protein PilF [Cell motilit	83.71
PF12569		517	NARP1: NMDA receptor-regulated protein 1 ; InterPr	83.67
KOG3081\|consensus		299		82.81
KOG1156\|consensus		700		82.62
KOG0553\|consensus		304		82.23
smart00550		68	Zalpha Z-DNA-binding domain in adenosine deaminase	82.05
KOG3250\|consensus		258		81.6
PF13412		48	HTH_24: Winged helix-turn-helix DNA-binding; PDB:	81.3
TIGR01764		49	excise DNA binding domain, excisionase family. An	80.72
TIGR03879		73	near_KaiC_dom probable regulatory domain. This mod	80.36

>KOG1498\|consensus	Back alignment and domain information

Probab=100.00  E-value=2.8e-70  Score=498.80  Aligned_cols=300  Identities=56%  Similarity=0.909  Sum_probs=291.3

Q ss_pred             CCCccCCHHHHHHHHhccccccccCCchHHHHHHHHHHHHHHHhhcchhHHHHHHHHhhhhccCCCCcchHHHHHHHHHH
Q psy4458           1 MKEDEGDVTEAANIIQELQVETYGSMEKKEKVTLILEQMRLCLAKKDYIRTQIISKKINTKFFDDEKDDVQELKLKYYRL   80 (303)
Q Consensus         1 i~e~~~~~~~Aa~~L~~i~vet~~~~~~~~k~~~~L~~~rL~L~~~D~~~a~~~~~ki~~~~~~~~~~~~~e~k~~y~~~   80 (303)
                      |+|.+|++++||++|+++||||||+|..++|+.|+|+||||||..+||.+|+++++||+.++|++++  ..++|+.||.+
T Consensus       140 ike~~Gdi~~Aa~il~el~VETygsm~~~ekV~fiLEQmrKOG~~~D~vra~i~skKI~~K~F~~~~--~~~lKlkyY~l  217 (439)
T KOG1498|consen  140 IKEEQGDIAEAADILCELQVETYGSMEKSEKVAFILEQMRLCLLRLDYVRAQIISKKINKKFFEKPD--VQELKLKYYEL  217 (439)
T ss_pred             HHHHcCCHHHHHHHHHhcchhhhhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHhhHHhcCCcc--HHHHHHHHHHH
Confidence            5899999999999999999999999999999999999999999999999999999999999998877  99999999999


Q ss_pred             HHHHHHHhhhHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHhCCCCchhhHhHHHhhhhhhcCCchHHHHHHHHh
Q psy4458          81 MIELDQHEGSYLATCKHYRAILTTPCIQSDPVQRHAVLQNVVLYLMLAPYDNEQSDLTHRVLEDKLLNEIPLYKGLLQWF  160 (303)
Q Consensus        81 ~~~~~~~~~~f~eaa~~y~e~~~t~~~~~~~~~~~~~L~~~v~~~iLs~~~~~r~~ll~~l~~~~~~~~~p~~~~L~~~f  160 (303)
                      |++++.|.+.|+++|++|+++++|+.++.|+..|...|..+|+|++|||++++++++++++..|+.+.++|.+..+++.|
T Consensus       218 mI~l~lh~~~Yl~v~~~Yraiy~t~~vk~d~~kw~~vL~~iv~f~~LAp~dneQsdll~~is~dKkL~e~p~~k~lLklf  297 (439)
T KOG1498|consen  218 MIRLGLHDRAYLNVCRSYRAIYDTGNVKEDPEKWIEVLRSIVSFCVLAPHDNEQSDLLARISNDKKLSELPDYKELLKLF  297 (439)
T ss_pred             HHHhcccccchhhHHHHHHHHhcccccccChhhhhhhhhhheeEEeecCCCcHHHHHHHHHhcccccccCccHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCcccCchHHHHHHHHhhcccccccccchhHHhHHHHHHHHHHHHHHHHHHhhhceeeHHHHHHHhCCCHHHHHHHHHh
Q psy4458         161 TNPELIKWSGLRQLYEEELFKTSVFNQSTEEGQKCFKMLKHRVVEHNIRVMAKYYTRITLQRMCDLLGLPIEETEEFLSS  240 (303)
Q Consensus       161 ~~~~li~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~~l~~~i~ehNi~~isk~Y~~Itl~~la~ll~ls~~~vE~~l~~  240 (303)
                      .+++|++|+.+...|...|....+| +....|+.||++|+.|++||||+++++||++||+.+||.++|+|++++|..||.
T Consensus       298 v~~EL~rw~s~~~~yg~~l~~~~~~-~~~~~gek~~~dL~~RIiEHNiRiiA~yYSrIt~~rl~eLLdl~~ee~E~~LS~  376 (439)
T KOG1498|consen  298 VTMELIRWVSLVESYGDELRTNDFF-DGGEEGEKRWSDLKLRIIEHNIRIIAKYYSRITLKRLAELLDLPVEEMEKFLSD  376 (439)
T ss_pred             HhcceeeehhHhhhhHHHHhhcccc-cccchhhhHHHHHHHHHHHHHHHHHHHHHhhccHHHHHHHhCCCHHHHHHHHHH
Confidence            9999999998999999999988766 667788999999999999999999999999999999999999999999999999


Q ss_pred             hhhcCceEEEecCCCceEEeccCCChhHHHHHHHHHHHHHHHHHHHHHhhhhHHHHhchhhhC
Q psy4458         241 MVVSKTITAKIDRPAGIINFARNKDPGEILNEWSASLNELMKLVNNTTHLINKEQMIHQRVAA  303 (303)
Q Consensus       241 mI~~~~l~akIDq~~giV~f~~~~~~~~~l~~w~~~i~~l~~~v~~~~~lI~ke~~~~~~~~~  303 (303)
                      ||..|.+.||||||.|+|.|..+++.++.+++|+.++.+|+..++++||+|+||+|||+..++
T Consensus       377 lv~t~ti~aKidrpsgII~F~k~K~~~~~LneW~~nve~L~~ll~K~~HLI~KEemmhsi~~~  439 (439)
T KOG1498|consen  377 LVVTGTIYAKIDRPSGIINFQKVKDSNEILNEWASNVEKLLGLLEKVSHLIHKEEMMHSIQKA  439 (439)
T ss_pred             HHhccceEEEecCCCceEEEEecccHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            999999999999999999999999999999999999999999999999999999999998654

>COG5071 RPN5 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>KOG1497\|consensus	Back alignment and domain information

>KOG0687\|consensus	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

>KOG1463\|consensus	Back alignment and domain information

>KOG1464\|consensus	Back alignment and domain information

>COG5159 RPN6 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>KOG2908\|consensus	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

>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

>KOG0686\|consensus	Back alignment and domain information

>PF10602 RPN7: 26S proteasome subunit RPN7; InterPro: IPR019585 This entry represents the regulatory subunit RPN7 (known as the non-ATPase regulatory subunit 6 in higher eukaryotes) of the 26S proteasome	Back alignment and domain information

>KOG2581\|consensus	Back alignment and domain information

>KOG2582\|consensus	Back alignment and domain information

>KOG2753\|consensus	Back alignment and domain information

>KOG1076\|consensus	Back alignment and domain information

>KOG2688\|consensus	Back alignment and domain information

>KOG2758\|consensus	Back alignment and domain information

>PF10255 Paf67: RNA polymerase I-associated factor PAF67; InterPro: IPR019382 RNA polymerase I is a multi-subunit enzyme and its transcription competence is dependent on the presence of PAF67 []	Back alignment and domain information

>COG5600 Transcription-associated recombination protein [DNA replication, recombination, and repair]	Back alignment and domain information

>KOG2072\|consensus	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

>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

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

>PF09976 TPR_21: Tetratricopeptide repeat; InterPro: IPR018704 This domain, found in various hypothetical prokaryotic proteins, has no known function	Back alignment and domain information

>PF13424 TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 4A1S_B 3CEQ_B 3EDT_H	Back alignment and domain information

>PF14938 SNAP: Soluble NSF attachment protein, SNAP; PDB: 1QQE_A 2IFU_A	Back alignment and domain information

>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)	Back alignment and domain information

>PF14938 SNAP: Soluble NSF attachment protein, SNAP; PDB: 1QQE_A 2IFU_A	Back alignment and domain information

>PF12895 Apc3: Anaphase-promoting complex, cyclosome, subunit 3; PDB: 3KAE_D 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2XPI_A 3ULQ_A	Back alignment and domain information

>PF04733 Coatomer_E: Coatomer epsilon subunit; InterPro: IPR006822 Proteins synthesised on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment	Back alignment and domain information

>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF	Back alignment and domain information

>PRK11788 tetratricopeptide repeat protein; Provisional	Back alignment and domain information

>PRK15431 ferrous iron transport protein FeoC; Provisional	Back alignment and domain information

>PF04348 LppC: LppC putative lipoprotein; InterPro: IPR007443 This entry includes several bacterial outer membrane antigens, whose molecular function is unknown	Back alignment and domain information

>PF14559 TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN_B 3QOU_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 3FP3_A 3LCA_A	Back alignment and domain information

>COG3107 LppC Putative lipoprotein [General function prediction only]	Back alignment and domain information

>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B	Back alignment and domain information

>KOG2003\|consensus	Back alignment and domain information

>PF13432 TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL_A 3CVQ_A 3CV0_A 2GW1_B 3CVN_A 3QKY_A 2PL2_B	Back alignment and domain information

>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	Back alignment and domain information

>PF13414 TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2PL2_B 3IEG_B 2FBN_A	Back alignment and domain information

>PF01047 MarR: MarR family; InterPro: IPR000835 The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance	Back alignment and domain information

>KOG4414\|consensus	Back alignment and domain information

>COG3063 PilF Tfp pilus assembly protein PilF [Cell motility and secretion / Intracellular trafficking and secretion]	Back alignment and domain information

>PF12569 NARP1: NMDA receptor-regulated protein 1 ; InterPro: IPR021183 This group represents N-terminal acetyltransferase A (NatA) auxiliary subunit and represents a non-catalytic component of the NatA N-terminal acetyltransferase, which catalyzes acetylation of proteins beginning with Met-Ser, Met-Gly and Met-Ala	Back alignment and domain information

>KOG3081\|consensus	Back alignment and domain information

>KOG1156\|consensus	Back alignment and domain information

>KOG0553\|consensus	Back alignment and domain information

>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases	Back alignment and domain information

>KOG3250\|consensus	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

>TIGR01764 excise DNA binding domain, excisionase family	Back alignment and domain information

>TIGR03879 near_KaiC_dom probable regulatory domain	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
Query		303
4b4t_P		445	Near-Atomic Resolution Structural Model Of The Yeas		2e-55
1ufm_A		84	Solution Structure Of The Pci Domain Length = 84		2e-04
4b4t_S		523	Near-Atomic Resolution Structural Model Of The Yeas		4e-04

>pdb|4B4T|P Chain P, Near-Atomic Resolution Structural Model Of The Yeast 26s Proteasome Length = 445

Back alignment and structure

Iteration: 1

Score = 212 bits (540), Expect = 2e-55, Method: Compositional matrix adjust. Identities = 118/298 (39%), Positives = 195/298 (65%), Gaps = 3/298 (1%) Query: 1 MKEDEGDVTEAANIIQELQVETYGSMEKKEKVTLILEQMRLCLAKKDYIRTQIISKKINT 60 +K++EG + EAA+I+ ELQVETYGSME EK+ ILEQM L + K DY + ++S+KI Sbjct: 146 IKKEEGKIDEAADILCELQVETYGSMEMSEKIQFILEQMELSILKGDYSQATVLSRKILK 205 Query: 61 KFFDDEKDDVQELKLKYYRLMIELDQHEGSYLATCKHYRAILTTPCIQSDPVQRHAVLQN 120 K F + K + LKL+YY L++++ H+ YL ++ + I T I+SD + VL + Sbjct: 206 KTFKNPK--YESLKLEYYNLLVKISLHKREYLEVAQYLQEIYQTDAIKSDEAKWKPVLSH 263 Query: 121 VVLYLMLAPYDNEQSDLTHRVLEDKLLNEIPLYKGLLQWFTNPELIKWSGLRQLYEEELF 180 +V +L+L+PY N Q+DL H++ D L ++ + L++ FT EL++W +++ YE L Sbjct: 264 IVYFLVLSPYGNLQNDLIHKIQNDNNLKKLESQESLVKLFTTNELMRWPIVQKTYEPVLN 323 Query: 181 KTSVFNQSTEEGQKCFKMLKHRVVEHNIRVMAKYYTRITLQRMCDLLGLPIEETEEFLSS 240 + + E + ++ L+ RV+EHN+RV+++YY+RITL R+ +LL L +TE ++S Sbjct: 324 EDDLAF-GGEANKHHWEDLQKRVIEHNLRVISEYYSRITLLRLNELLDLTESQTETYISD 382 Query: 241 MVVSKTITAKIDRPAGIINFARNKDPGEILNEWSASLNELMKLVNNTTHLINKEQMIH 298 +V I AK++RPA I+NF + K+ ++LNEWS +++EL++ + HLI KE+++H Sbjct: 383 LVNQGIIYAKVNRPAKIVNFEKPKNSSQLLNEWSHNVDELLEHIETIGHLITKEEIMH 440

PyMOL of 4b4t

>pdb|1UFM|A Chain A, Solution Structure Of The Pci Domain Length = 84

Back alignment and structure

>pdb|4B4T|S Chain S, Near-Atomic Resolution Structural Model Of The Yeast 26s Proteasome Length = 523

Back alignment and structure

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Alignment Graph	Length	Definition	E-value
Query		303
1ufm_A		84	COP9 complex subunit 4; helix-turn-helix, structur	2e-28
3txn_A		394	26S proteasome regulatory complex subunit P42B; PC	6e-26
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	8e-10

>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 Length = 84	Back alignment and structure

 Score =  104 bits (260), Expect = 2e-28
 Identities = 21/72 (29%), Positives = 36/72 (50%)

Query: 197 KMLKHRVVEHNIRVMAKYYTRITLQRMCDLLGLPIEETEEFLSSMVVSKTITAKIDRPAG 256
            +L   V+EHN+   +K Y  IT + +  LL +P  + E+  S M+    +   ID+  G
Sbjct: 10  SILDRAVIEHNLLSASKLYNNITFEELGALLEIPAAKAEKIASQMITEGRMNGFIDQIDG 69

Query: 257 IINFARNKDPGE 268
           I++F   +  G 
Sbjct: 70  IVHFETREASGP 81

PyMOL of 1ufm

>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 Length = 394	Back alignment and structure

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221	Back alignment and structure

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		303
4b4t_P		445	26S proteasome regulatory subunit RPN5; hydrolase,	100.0
4b4t_R		429	RPN7, 26S proteasome regulatory subunit RPN7; hydr	100.0
3txn_A		394	26S proteasome regulatory complex subunit P42B; PC	100.0
4b4t_Q		434	26S proteasome regulatory subunit RPN6; hydrolase,	99.98
4b4t_O		393	26S proteasome regulatory subunit RPN9; hydrolase,	99.91
4b4t_S		523	RPN3, 26S proteasome regulatory subunit RPN3; hydr	99.86
1ufm_A		84	COP9 complex subunit 4; helix-turn-helix, structur	99.85
3t5x_A		203	PCI domain-containing protein 2; PCI, mRNA nuclear	99.55
3t5v_B		455	Nuclear mRNA export protein THP1; PCI, mRNA nuclea	99.46
3chm_A		169	COP9 signalosome complex subunit 7; heat/ARM repea	98.52
4b0z_A		229	RPN12, 26S proteasome regulatory subunit RPN12; pr	98.3
4ga2_A		150	E3 SUMO-protein ligase ranbp2; TPR motif, nuclear	95.72
3ro3_A		164	PINS homolog, G-protein-signaling modulator 2; asy	95.66
3ulq_A		383	Response regulator aspartate phosphatase F; tetrat	95.27
3ro3_A		164	PINS homolog, G-protein-signaling modulator 2; asy	95.25
3q15_A		378	PSP28, response regulator aspartate phosphatase H;	95.08
1elr_A		131	TPR2A-domain of HOP; HOP, TPR-domain, peptide-comp	94.92
3uq3_A		258	Heat shock protein STI1; HSP90, peptide binding, c	94.77
3gw4_A		203	Uncharacterized protein; structural genomics, PSI-	94.45
1wi9_A		72	Protein C20ORF116 homolog; helix-turn-helix motif,	94.2
1qqe_A		292	Vesicular transport protein SEC17; helix-turn-heli	94.11
4gcn_A		127	Protein STI-1; structural genomics, PSI-biology, m	93.9
3sf4_A		406	G-protein-signaling modulator 2; tetratricopeptide	93.67
4b4t_T		274	26S proteasome regulatory subunit RPN12; hydrolase	93.52
2qfc_A		293	PLCR protein; TPR, HTH, transcription regulation;	93.48
3u3w_A		293	Transcriptional activator PLCR protein; ternary co	93.35
4b4t_Q		434	26S proteasome regulatory subunit RPN6; hydrolase,	93.29
3ro2_A		338	PINS homolog, G-protein-signaling modulator 2; TPR	93.16
3ro2_A		338	PINS homolog, G-protein-signaling modulator 2; TPR	93.08
3vtx_A		184	MAMA; tetratricopeptide repeats (TPR) containing p	92.93
1qqe_A		292	Vesicular transport protein SEC17; helix-turn-heli	92.92
3vtx_A		184	MAMA; tetratricopeptide repeats (TPR) containing p	92.91
3gw4_A		203	Uncharacterized protein; structural genomics, PSI-	92.83
3u3w_A		293	Transcriptional activator PLCR protein; ternary co	92.52
3sf4_A		406	G-protein-signaling modulator 2; tetratricopeptide	92.45
4a1s_A		411	PINS, partner of inscuteable; cell cycle, LGN, mit	92.43
4a1s_A		411	PINS, partner of inscuteable; cell cycle, LGN, mit	91.87
3mkr_A		291	Coatomer subunit epsilon; tetratricopeptide repeat	91.85
3qky_A		261	Outer membrane assembly lipoprotein YFIO; membrane	91.81
1elw_A		118	TPR1-domain of HOP; HOP, TPR-domain, peptide-compl	91.45
2dba_A		148	Smooth muscle cell associated protein-1, isoform 2	91.24
3as5_A		186	MAMA; tetratricopeptide repeats (TPR) containing p	91.12
3q15_A		378	PSP28, response regulator aspartate phosphatase H;	91.0
4i17_A		228	Hypothetical protein; TPR repeats protein, structu	90.87
3mv2_B		310	Coatomer subunit epsilon; vesicular membrane coat	90.78
2qfc_A		293	PLCR protein; TPR, HTH, transcription regulation;	90.73
3u4t_A		272	TPR repeat-containing protein; structural genomics	90.66
2lni_A		133	Stress-induced-phosphoprotein 1; structural genomi	90.56
2ifu_A		307	Gamma-SNAP; membrane fusion, snare complex disasse	90.51
2xev_A		129	YBGF; tetratricopeptide, alpha-helical, metal bind	90.39
2vyi_A		131	SGTA protein; chaperone, TPR repeat, phosphoprotei	90.28
2ho1_A		252	Type 4 fimbrial biogenesis protein PILF; type IV p	90.02
1sfx_A		109	Conserved hypothetical protein AF2008; structural	89.96
2vq2_A		225	PILW, putative fimbrial biogenesis and twitching m	89.77
1xnf_A		275	Lipoprotein NLPI; TPR, tetratricopeptide, structur	89.67
2pzi_A		681	Probable serine/threonine-protein kinase PKNG; ATP	89.59
2ifu_A		307	Gamma-SNAP; membrane fusion, snare complex disasse	89.3
2k02_A		87	Ferrous iron transport protein C; FEOC, iron-sulfu	88.89
3edt_B		283	KLC 2, kinesin light chain 2; superhelical, struct	88.85
1xn7_A		78	Hypothetical protein YHGG; alpha+beta, GFT structu	88.8
3ulq_A		383	Response regulator aspartate phosphatase F; tetrat	88.66
3nf1_A		311	KLC 1, kinesin light chain 1; TPR, structural geno	88.2
1na0_A		125	Designed protein CTPR3; de novo protein; HET: IPT;	88.09
1a17_A		166	Serine/threonine protein phosphatase 5; hydrolase,	88.07
3sz7_A		164	HSC70 cochaperone (SGT); TPR domain, GET4, GET5, G	88.05
3ieg_A		359	DNAJ homolog subfamily C member 3; TPR motif, chap	88.02
4gco_A		126	Protein STI-1; structural genomics, PSI-biology, m	88.02
3q49_B		137	STIP1 homology and U box-containing protein 1; E3	87.95
1qgp_A		77	Protein (double stranded RNA adenosine deaminase);	87.88
3upv_A		126	Heat shock protein STI1; TPR-fold, adaptor protein	87.79
3edt_B		283	KLC 2, kinesin light chain 2; superhelical, struct	87.73
1na3_A		91	Designed protein CTPR2; de novo protein; HET: IPT;	87.64
2kck_A		112	TPR repeat; tetratricopeptide repeat, structural g	87.58
3k9i_A		117	BH0479 protein; putative protein binding protein,	87.53
2q7f_A		243	YRRB protein; TPR, protein binding; 2.49A {Bacillu	87.44
4i17_A		228	Hypothetical protein; TPR repeats protein, structu	87.41
3mkr_A		291	Coatomer subunit epsilon; tetratricopeptide repeat	87.18
2ho1_A		252	Type 4 fimbrial biogenesis protein PILF; type IV p	87.17
2xcb_A		142	PCRH, regulatory protein PCRH; protein transport,	87.15
2q7f_A		243	YRRB protein; TPR, protein binding; 2.49A {Bacillu	86.85
2pl2_A		217	Hypothetical conserved protein TTC0263; TPR, prote	86.78
3nf1_A		311	KLC 1, kinesin light chain 1; TPR, structural geno	86.71
3ieg_A		359	DNAJ homolog subfamily C member 3; TPR motif, chap	86.64
2v5f_A		104	Prolyl 4-hydroxylase subunit alpha-1; endoplasmic	86.61
1ub9_A		100	Hypothetical protein PH1061; helix-turn-helix moti	86.37
2fo7_A		136	Synthetic consensus TPR protein; tetratricopeptide	86.0
1w3b_A		388	UDP-N-acetylglucosamine--peptide N-acetylglucosami	85.94
4eqf_A		365	PEX5-related protein; accessory protein, tetratric	85.72
1rz4_A		226	Eukaryotic translation initiation factor 3 subuni;	85.68
2y4t_A		450	DNAJ homolog subfamily C member 3; chaperone, endo	85.49
1qbj_A		81	Protein (double-stranded RNA specific adenosine D	85.4
2vgx_A		148	Chaperone SYCD; alternative dimer assembly, tetrat	85.26
1hxi_A		121	PEX5, peroxisome targeting signal 1 receptor PEX5;	84.97
3uq3_A		258	Heat shock protein STI1; HSP90, peptide binding, c	84.88
2vgx_A		148	Chaperone SYCD; alternative dimer assembly, tetrat	84.63
2fbn_A		198	70 kDa peptidylprolyl isomerase, putative; sulfur	84.63
1hh8_A		213	P67PHOX, NCF-2, neutrophil cytosol factor 2; cell	84.23
2xcb_A		142	PCRH, regulatory protein PCRH; protein transport,	84.2
3rkv_A		162	Putative peptidylprolyl isomerase; structural geno	84.0
3qky_A		261	Outer membrane assembly lipoprotein YFIO; membrane	83.82
3r0a_A		123	Putative transcriptional regulator; structural gen	83.7
4b4t_P		445	26S proteasome regulatory subunit RPN5; hydrolase,	83.36
2jt1_A		77	PEFI protein; solution structure, winged helix-tur	83.27
3sz7_A		164	HSC70 cochaperone (SGT); TPR domain, GET4, GET5, G	82.92
2vsy_A		568	XCC0866; transferase, glycosyl transferase, GT-B,	82.89
4gyw_A		723	UDP-N-acetylglucosamine--peptide N- acetylglucosam	82.65
3hym_B		330	Cell division cycle protein 16 homolog; APC, anaph	82.54
2y4t_A		450	DNAJ homolog subfamily C member 3; chaperone, endo	82.48
2fbi_A		142	Probable transcriptional regulator; MARR, APC5816,	82.25
3urz_A		208	Uncharacterized protein; tetratricopeptide repeats	81.81
3upv_A		126	Heat shock protein STI1; TPR-fold, adaptor protein	81.75
3qou_A		287	Protein YBBN; thioredoxin-like fold, tetratricopep	81.46
2vq2_A		225	PILW, putative fimbrial biogenesis and twitching m	81.4
3n71_A		490	Histone lysine methyltransferase SMYD1; heart deve	81.35
2fbh_A		146	Transcriptional regulator PA3341; MARR, transcript	81.27
1hz4_A		373	MALT regulatory protein; two-helix bundles, helix	81.26
3qww_A		433	SET and MYND domain-containing protein 2; methyltr	81.1
2heo_A		67	Z-DNA binding protein 1; protein DLM1-Z-DNA comple	81.06
2e2e_A		177	Formate-dependent nitrite reductase complex NRFG;	80.97
2a61_A		145	Transcriptional regulator TM0710; APC4350, MCSG, m	80.57
1ku9_A		152	Hypothetical protein MJ223; putative transcription	80.52
3txn_A		394	26S proteasome regulatory complex subunit P42B; PC	80.46
1elw_A		118	TPR1-domain of HOP; HOP, TPR-domain, peptide-compl	80.4
2nnn_A		140	Probable transcriptional regulator; structural gen	80.27
1s3j_A		155	YUSO protein; structural genomics, MARR transcript	80.11

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

Probab=100.00  E-value=1.2e-65  Score=496.57  Aligned_cols=299  Identities=40%  Similarity=0.699  Sum_probs=243.8

Q ss_pred             CCCccCCHHHHHHHHhccccccccCCchHHHHHHHHHHHHHHHhhcchhHHHHHHHHhhhhccCCCCcchHHHHHHHHHH
Q psy4458           1 MKEDEGDVTEAANIIQELQVETYGSMEKKEKVTLILEQMRLCLAKKDYIRTQIISKKINTKFFDDEKDDVQELKLKYYRL   80 (303)
Q Consensus         1 i~e~~~~~~~Aa~~L~~i~vet~~~~~~~~k~~~~L~~~rL~L~~~D~~~a~~~~~ki~~~~~~~~~~~~~e~k~~y~~~   80 (303)
                      |+|++|++.+|+++|+++++||+++|+..+|++++|+|+|+|++.+||.+|+.+++||+.+.+...+  +++++.+|+.|
T Consensus       146 i~e~~g~~~eA~~iL~~l~~Et~~~~~~~~kve~~l~q~rl~l~~~d~~~a~~~~~ki~~~~~~~~~--~~~lk~~~~~~  223 (445)
T 4b4t_P          146 IKKEEGKIDEAADILCELQVETYGSMEMSEKIQFILEQMELSILKGDYSQATVLSRKILKKTFKNPK--YESLKLEYYNL  223 (445)
T ss_dssp             HHHHHTCHHHHHHHHHHHHHHHCSSSCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHSSC--CHHHHHHHHHH
T ss_pred             HHHHccCHHHHHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhhcccCC--cHHHHHHHHHH
Confidence            4688999999999999999999999999999999999999999999999999999999988876666  78999999999


Q ss_pred             HHHHHHHhhhHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHhCCCCchhhHhHHHhhhhhhcCCchHHHHHHHHh
Q psy4458          81 MIELDQHEGSYLATCKHYRAILTTPCIQSDPVQRHAVLQNVVLYLMLAPYDNEQSDLTHRVLEDKLLNEIPLYKGLLQWF  160 (303)
Q Consensus        81 ~~~~~~~~~~f~eaa~~y~e~~~t~~~~~~~~~~~~~L~~~v~~~iLs~~~~~r~~ll~~l~~~~~~~~~p~~~~L~~~f  160 (303)
                      +|+++.+.++|.+||++|++++.++.+.+++..+..+|+++|+|.||+|+++++++++++++.+++++++|.|+.|+++|
T Consensus       224 ~~~~~~~e~~y~~a~~~y~e~~~~~~~~~d~~~~~~~L~~~v~~~iLa~~~~~~~~ll~~~~~~~~~~~l~~~~~L~k~f  303 (445)
T 4b4t_P          224 LVKISLHKREYLEVAQYLQEIYQTDAIKSDEAKWKPVLSHIVYFLVLSPYGNLQNDLIHKIQNDNNLKKLESQESLVKLF  303 (445)
T ss_dssp             HHHHHHHHCCHHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHSSCSSTTHHHHHSHHHHSSCHHHHHHHHHHHHH
T ss_pred             HHHHHHHhhhHHHHHHHHHHHHhcccccCCHHHHHHHHHHHHHHHHhCCCCchHHHHHHHHhhcccccccHHHHHHHHHH
Confidence            99999999999999999999999998888888888999999999999999999999999999999999999999999999


Q ss_pred             cCCcccCchHHHHHHHHhhcccccccccchhHHhHHHHHHHHHHHHHHHHHHhhhceeeHHHHHHHhCCCHHHHHHHHHh
Q psy4458         161 TNPELIKWSGLRQLYEEELFKTSVFNQSTEEGQKCFKMLKHRVVEHNIRVMAKYYTRITLQRMCDLLGLPIEETEEFLSS  240 (303)
Q Consensus       161 ~~~~li~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~~l~~~i~ehNi~~isk~Y~~Itl~~la~ll~ls~~~vE~~l~~  240 (303)
                      .+++|++|+.+...|...|.+|+++ ...+.+..||..|+++++|||++++++||++|+|++||++||+|++++|..+++
T Consensus       304 ~~~~L~~~~~~~~~~~~~L~~~~~~-~~~~~~~~~~~~L~~~v~ehnl~~i~k~Ys~I~l~~la~lL~l~~~evE~~ls~  382 (445)
T 4b4t_P          304 TTNELMRWPIVQKTYEPVLNEDDLA-FGGEANKHHWEDLQKRVIEHNLRVISEYYSRITLLRLNELLDLTESQTETYISD  382 (445)
T ss_dssp             HHCCSSSHHHHHHHTCSSTTTCCSS-CCCSCSSHHHHHHHHHHHHHHHHHHHHHEEEEEHHHHHHHHTSCHHHHHHHHHH
T ss_pred             HhchHhhhHHHHHHHHHHhcccchh-hhcchhhHHHHHHHHHHHHHHHHHHHHHhceeeHHHHHHHhCcCHHHHHHHHHH
Confidence            9999999999889999999999986 233344678999999999999999999999999999999999999999999999


Q ss_pred             hhhcCceEEEecCCCceEEeccCCChhHHHHHHHHHHHHHHHHHHHHHhhhhHHHHhchhhh
Q psy4458         241 MVVSKTITAKIDRPAGIINFARNKDPGEILNEWSASLNELMKLVNNTTHLINKEQMIHQRVA  302 (303)
Q Consensus       241 mI~~~~l~akIDq~~giV~f~~~~~~~~~l~~w~~~i~~l~~~v~~~~~lI~ke~~~~~~~~  302 (303)
                      ||.+|+|+|+|||++|+|+|++++++++.+++|+.+|.+||+.|++++|+|+||+|||++++
T Consensus       383 mI~~g~i~akIDq~~giV~F~~~~~~~~~l~~W~~~i~~l~~~v~k~~~lI~kE~m~~~~~~  444 (445)
T 4b4t_P          383 LVNQGIIYAKVNRPAKIVNFEKPKNSSQLLNEWSHNVDELLEHIETIGHLITKEEIMHGLQA  444 (445)
T ss_dssp             HHHHTSSCCEEETTTTEEEC------------------------------------------
T ss_pred             HHHCCCEEEEEcCCCCEEEECCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence            99999999999999999999999989999999999999999999999999999999999864

PyMOL of 4b4t

>4b4t_R RPN7, 26S proteasome regulatory subunit RPN7; 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_Q 26S proteasome regulatory subunit RPN6; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}	Back alignment and structure

>4b4t_O 26S proteasome regulatory subunit RPN9; 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

>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

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

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

>4ga2_A E3 SUMO-protein ligase ranbp2; TPR motif, nuclear pore complex component nucleocytoplasmic transport, transport protein; 0.95A {Pan troglodytes} PDB: 4ga0_A 4ga1_A*	Back alignment and structure

>3ro3_A PINS homolog, G-protein-signaling modulator 2; asymmetric cell division, protein binding; 1.10A {Mus musculus}	Back alignment and structure

>3ulq_A Response regulator aspartate phosphatase F; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis}	Back alignment and structure

>3ro3_A PINS homolog, G-protein-signaling modulator 2; asymmetric cell division, protein binding; 1.10A {Mus musculus}	Back alignment and structure

>3q15_A PSP28, response regulator aspartate phosphatase H; tetratricopeptide repeat, 3-helix bundle, phosphorelay signa transduction, phosphatase; 2.19A {Bacillus subtilis}	Back alignment and structure

>1elr_A TPR2A-domain of HOP; HOP, TPR-domain, peptide-complex, helical repeat, protein binding, chaperone; 1.90A {Homo sapiens} SCOP: a.118.8.1 PDB: 3esk_A 3fwv_A	Back alignment and structure

>3uq3_A Heat shock protein STI1; HSP90, peptide binding, chaperone; 2.60A {Saccharomyces cerevisiae}	Back alignment and structure

>3gw4_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, no structural genomics consortium, NESG, DRR162B; 2.49A {Deinococcus radiodurans R1}	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

>1qqe_A Vesicular transport protein SEC17; helix-turn-helix TPR-like repeat, protein transport; 2.90A {Saccharomyces cerevisiae} SCOP: a.118.8.1	Back alignment and structure

>4gcn_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; HET: PGE; 1.85A {Caenorhabditis elegans}	Back alignment and structure

>3sf4_A G-protein-signaling modulator 2; tetratricopeptide repeat, TPR, cell polarity, asymmetric CEL division, mitotic spindle orientation; 2.60A {Homo sapiens}	Back alignment and structure

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

>2qfc_A PLCR protein; TPR, HTH, transcription regulation; 2.60A {Bacillus thuringiensis serovar ISRAELE35646}	Back alignment and structure

>3u3w_A Transcriptional activator PLCR protein; ternary complex, PLCR-PAPR7-DNA, HTH DNA-binding domain, QUO sensing; 2.40A {Bacillus thuringiensis} PDB: 2qfc_A	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

>3ro2_A PINS homolog, G-protein-signaling modulator 2; TPR repeat, protein-protein interaction, protein-binding, PR binding; 2.30A {Mus musculus}	Back alignment and structure

>3ro2_A PINS homolog, G-protein-signaling modulator 2; TPR repeat, protein-protein interaction, protein-binding, PR binding; 2.30A {Mus musculus}	Back alignment and structure

>3vtx_A MAMA; tetratricopeptide repeats (TPR) containing protein, peptide protein, protein binding; 1.75A {Candidatus magnetobacterium bavaricum} PDB: 3vty_A	Back alignment and structure

>1qqe_A Vesicular transport protein SEC17; helix-turn-helix TPR-like repeat, protein transport; 2.90A {Saccharomyces cerevisiae} SCOP: a.118.8.1	Back alignment and structure

>3vtx_A MAMA; tetratricopeptide repeats (TPR) containing protein, peptide protein, protein binding; 1.75A {Candidatus magnetobacterium bavaricum} PDB: 3vty_A	Back alignment and structure

>3gw4_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, no structural genomics consortium, NESG, DRR162B; 2.49A {Deinococcus radiodurans R1}	Back alignment and structure

>3u3w_A Transcriptional activator PLCR protein; ternary complex, PLCR-PAPR7-DNA, HTH DNA-binding domain, QUO sensing; 2.40A {Bacillus thuringiensis} PDB: 2qfc_A	Back alignment and structure

>3sf4_A G-protein-signaling modulator 2; tetratricopeptide repeat, TPR, cell polarity, asymmetric CEL division, mitotic spindle orientation; 2.60A {Homo sapiens}	Back alignment and structure

>4a1s_A PINS, partner of inscuteable; cell cycle, LGN, mitotic spindle orientation, asymmetric CEL divisions; 2.10A {Drosophila melanogaster}	Back alignment and structure

>4a1s_A PINS, partner of inscuteable; cell cycle, LGN, mitotic spindle orientation, asymmetric CEL divisions; 2.10A {Drosophila melanogaster}	Back alignment and structure

>3mkr_A Coatomer subunit epsilon; tetratricopeptide repeats (TPR), beta-hairpin, alpha-solenoi transport protein; 2.60A {Bos taurus}	Back alignment and structure

>3qky_A Outer membrane assembly lipoprotein YFIO; membrane protein; 2.15A {Rhodothermus marinus}	Back alignment and structure

>1elw_A TPR1-domain of HOP; HOP, TPR-domain, peptide-complex, helical repeat, HSP70, protein binding, chaperone; 1.60A {Homo sapiens} SCOP: a.118.8.1	Back alignment and structure

>2dba_A Smooth muscle cell associated protein-1, isoform 2; tetratricopeptide repeat, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>3as5_A MAMA; tetratricopeptide repeats (TPR) containing protein, TPR PROT protein-protein interactions, protein binding; 2.00A {Magnetospirillum magnetotacticum} PDB: 3as4_A 3asd_A 3asg_A 3ash_A 3as8_A 3asf_A	Back alignment and structure

>3q15_A PSP28, response regulator aspartate phosphatase H; tetratricopeptide repeat, 3-helix bundle, phosphorelay signa transduction, phosphatase; 2.19A {Bacillus subtilis}	Back alignment and structure

>4i17_A Hypothetical protein; TPR repeats protein, structural genomics, joint center for S genomics, JCSG, protein structure initiative; HET: MSE; 1.83A {Bacteroides fragilis}	Back alignment and structure

>3mv2_B Coatomer subunit epsilon; vesicular membrane coat COAT protein complex I, protein TRAN; 2.90A {Saccharomyces cerevisiae} PDB: 3mv3_B	Back alignment and structure

>2qfc_A PLCR protein; TPR, HTH, transcription regulation; 2.60A {Bacillus thuringiensis serovar ISRAELE35646}	Back alignment and structure

>3u4t_A TPR repeat-containing protein; structural genomics, PSI- protein structure initiative, northeast structural genomics consortium, NESG; 2.28A {Cytophaga hutchinsonii}	Back alignment and structure

>2lni_A Stress-induced-phosphoprotein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, chaperone; NMR {Homo sapiens}	Back alignment and structure

>2ifu_A Gamma-SNAP; membrane fusion, snare complex disassembly, protein structure initiative, PSI, center for eukaryotic structural genomics, CESG; HET: MSE; 2.60A {Danio rerio}	Back alignment and structure

>2xev_A YBGF; tetratricopeptide, alpha-helical, metal binding; 1.57A {Xanthomonas campestris}	Back alignment and structure

>2vyi_A SGTA protein; chaperone, TPR repeat, phosphoprotein, tetratricopeptide repeat protein, HOST-virus interaction; 2.4A {Homo sapiens} SCOP: k.38.1.1	Back alignment and structure

>2ho1_A Type 4 fimbrial biogenesis protein PILF; type IV pilus biogenesis, TPR, superhelix, protein binding; HET: MSE; 2.00A {Pseudomonas aeruginosa} PDB: 2fi7_A	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

>2vq2_A PILW, putative fimbrial biogenesis and twitching motility protein; secretin, TPR repeat, type IV pilus, bacterail virulence; 1.54A {Neisseria meningitidis}	Back alignment and structure

>1xnf_A Lipoprotein NLPI; TPR, tetratricopeptide, structural genomi unknown function; 1.98A {Escherichia coli} SCOP: a.118.8.1	Back alignment and structure

>2pzi_A Probable serine/threonine-protein kinase PKNG; ATP-recognition, kinase-INH complex, rubredoxin fold, TPR domain, transferase; HET: AXX; 2.40A {Mycobacterium tuberculosis}	Back alignment and structure

>2ifu_A Gamma-SNAP; membrane fusion, snare complex disassembly, protein structure initiative, PSI, center for eukaryotic structural genomics, CESG; HET: MSE; 2.60A {Danio rerio}	Back alignment and structure

>2k02_A Ferrous iron transport protein C; FEOC, iron-sulfur, metal-binding, metal binding protein; NMR {Klebsiella pneumoniae subsp}	Back alignment and structure

>3edt_B KLC 2, kinesin light chain 2; superhelical, structural genomics, structural genomics conso SGC, microtubule, motor protein, phosphoprotein; 2.70A {Homo sapiens} PDB: 3ceq_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

>3ulq_A Response regulator aspartate phosphatase F; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis}	Back alignment and structure

>3nf1_A KLC 1, kinesin light chain 1; TPR, structural genomics consortium (SGC), motor PR transport protein; 2.80A {Homo sapiens}	Back alignment and structure

>1na0_A Designed protein CTPR3; de novo protein; HET: IPT; 1.60A {Unidentified} SCOP: k.38.1.1 PDB: 2wqh_A 3kd7_A	Back alignment and structure

>1a17_A Serine/threonine protein phosphatase 5; hydrolase, protein-protein interactions, TPR, S helix; 2.45A {Homo sapiens} SCOP: a.118.8.1 PDB: 2bug_A	Back alignment and structure

>3sz7_A HSC70 cochaperone (SGT); TPR domain, GET4, GET5, GET3, MDY2, SSA1, SSE1, chaperone regulator; 1.72A {Aspergillus fumigatus}	Back alignment and structure

>3ieg_A DNAJ homolog subfamily C member 3; TPR motif, chaperone, endoplasmic reticulum, TPR repeat, UNF protein response; 2.51A {Mus musculus}	Back alignment and structure

>4gco_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; 1.60A {Caenorhabditis elegans}	Back alignment and structure

>3q49_B STIP1 homology and U box-containing protein 1; E3 ubiquitin ligase, ligase-chaperone complex; 1.54A {Mus musculus} PDB: 3q47_B 3q4a_B*	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

>3upv_A Heat shock protein STI1; TPR-fold, adaptor protein for HSP70 and HSP90, C-terminal PA HSP70, peptide binding protein; 1.60A {Saccharomyces cerevisiae}	Back alignment and structure

>3edt_B KLC 2, kinesin light chain 2; superhelical, structural genomics, structural genomics conso SGC, microtubule, motor protein, phosphoprotein; 2.70A {Homo sapiens} PDB: 3ceq_A	Back alignment and structure

>1na3_A Designed protein CTPR2; de novo protein; HET: IPT; 1.55A {Unidentified} SCOP: k.38.1.1 PDB: 2avp_A	Back alignment and structure

>2kck_A TPR repeat; tetratricopeptide repeat, structural genomics, unknown function, PSI-2, protein structure initiative; NMR {Methanococcus maripaludis}	Back alignment and structure

>3k9i_A BH0479 protein; putative protein binding protein, structural genomics, joint for structural genomics, JCSG; 2.71A {Bacillus halodurans}	Back alignment and structure

>2q7f_A YRRB protein; TPR, protein binding; 2.49A {Bacillus subtilis} SCOP: k.38.1.1	Back alignment and structure

>4i17_A Hypothetical protein; TPR repeats protein, structural genomics, joint center for S genomics, JCSG, protein structure initiative; HET: MSE; 1.83A {Bacteroides fragilis}	Back alignment and structure

>3mkr_A Coatomer subunit epsilon; tetratricopeptide repeats (TPR), beta-hairpin, alpha-solenoi transport protein; 2.60A {Bos taurus}	Back alignment and structure

>2ho1_A Type 4 fimbrial biogenesis protein PILF; type IV pilus biogenesis, TPR, superhelix, protein binding; HET: MSE; 2.00A {Pseudomonas aeruginosa} PDB: 2fi7_A	Back alignment and structure

>2xcb_A PCRH, regulatory protein PCRH; protein transport, bacterial toxin, type III secretion, protein binding; 1.85A {Pseudomonas aeruginosa} PDB: 2xcc_A	Back alignment and structure

>2q7f_A YRRB protein; TPR, protein binding; 2.49A {Bacillus subtilis} SCOP: k.38.1.1	Back alignment and structure

>2pl2_A Hypothetical conserved protein TTC0263; TPR, protein binding; 2.50A {Thermus thermophilus}	Back alignment and structure

>3nf1_A KLC 1, kinesin light chain 1; TPR, structural genomics consortium (SGC), motor PR transport protein; 2.80A {Homo sapiens}	Back alignment and structure

>3ieg_A DNAJ homolog subfamily C member 3; TPR motif, chaperone, endoplasmic reticulum, TPR repeat, UNF protein response; 2.51A {Mus musculus}	Back alignment and structure

>2v5f_A Prolyl 4-hydroxylase subunit alpha-1; endoplasmic reticulum, metal-binding, oxidoreductase; 2.03A {Homo sapiens} PDB: 1tjc_A	Back alignment and structure

>1ub9_A Hypothetical protein PH1061; helix-turn-helix motif, winged helix motif, structural genom transcription; 2.05A {Pyrococcus horikoshii} SCOP: a.4.5.28	Back alignment and structure

>2fo7_A Synthetic consensus TPR protein; tetratricopeptide repeat, consensus protein, superhelix, de novo protein; 2.30A {Synthetic} SCOP: k.38.1.1 PDB: 2hyz_A	Back alignment and structure

>1w3b_A UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110; OGT, glcnac, nucleoporin, O-linked glycosylation, TPR repeat, protein binding; 2.85A {Homo sapiens} SCOP: a.118.8.1	Back alignment and structure

>4eqf_A PEX5-related protein; accessory protein, tetratricopeptide repeat, TPR; 3.00A {Mus musculus}	Back alignment and structure

>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	Back alignment and structure

>2y4t_A DNAJ homolog subfamily C member 3; chaperone, endoplasmic reticulum, protein folding, tetratricopeptiderepeat, J domain, unfolded protein respons; 3.00A {Homo sapiens} PDB: 2y4u_A	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

>2vgx_A Chaperone SYCD; alternative dimer assembly, tetratricopeptide repeat, type III secretion; HET: MLY; 1.95A {Yersinia enterocolitica} SCOP: k.38.1.1 PDB: 2vgx_B* 2vgy_A*	Back alignment and structure

>1hxi_A PEX5, peroxisome targeting signal 1 receptor PEX5; alpha helical, transport protein; 1.60A {Trypanosoma brucei} SCOP: a.118.8.1	Back alignment and structure

>3uq3_A Heat shock protein STI1; HSP90, peptide binding, chaperone; 2.60A {Saccharomyces cerevisiae}	Back alignment and structure

>2vgx_A Chaperone SYCD; alternative dimer assembly, tetratricopeptide repeat, type III secretion; HET: MLY; 1.95A {Yersinia enterocolitica} SCOP: k.38.1.1 PDB: 2vgx_B* 2vgy_A*	Back alignment and structure

>2fbn_A 70 kDa peptidylprolyl isomerase, putative; sulfur SAD, PFL2275C, TPR-containing domain, structural genomics; 1.63A {Plasmodium falciparum} SCOP: a.118.8.1	Back alignment and structure

>1hh8_A P67PHOX, NCF-2, neutrophil cytosol factor 2; cell cycle, phagocyte oxidase factor, SH3 domain, repeat, TPR repeat cell cycle; HET: FLC; 1.8A {Homo sapiens} SCOP: a.118.8.1 PDB: 1wm5_A 1e96_B*	Back alignment and structure

>2xcb_A PCRH, regulatory protein PCRH; protein transport, bacterial toxin, type III secretion, protein binding; 1.85A {Pseudomonas aeruginosa} PDB: 2xcc_A	Back alignment and structure

>3rkv_A Putative peptidylprolyl isomerase; structural genomics, APC102156, PSI-biology, midwest center structural genomics, MCSG; 2.41A {Caenorhabditis elegans}	Back alignment and structure

>3qky_A Outer membrane assembly lipoprotein YFIO; membrane protein; 2.15A {Rhodothermus marinus}	Back alignment and structure

>3r0a_A Putative transcriptional regulator; structural genomics, PSI-biology, midwest center for structu genomics, MCSG; 2.31A {Methanosarcina mazei}	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

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

>3sz7_A HSC70 cochaperone (SGT); TPR domain, GET4, GET5, GET3, MDY2, SSA1, SSE1, chaperone regulator; 1.72A {Aspergillus fumigatus}	Back alignment and structure

>2vsy_A XCC0866; transferase, glycosyl transferase, GT-B, OGT, protein O-GLCN; HET: NHE; 2.10A {Xanthomonas campestris PV} PDB: 2jlb_A* 2xgm_A* 2xgo_A* 2xgs_A* 2vsn_A*	Back alignment and structure

>4gyw_A UDP-N-acetylglucosamine--peptide N- acetylglucosaminyltransferase 110 kDa subunit...; GT-B, glycosyltransferase, glcnacylation, transferase-peptid; HET: UDP NAG; 1.70A {Homo sapiens} PDB: 3pe3_A* 3pe4_A* 4ay5_A* 4ay6_A* 3tax_A* 4gyy_A* 4gz3_A* 4gz5_A* 4gz6_A*	Back alignment and structure

>3hym_B Cell division cycle protein 16 homolog; APC, anaphase promoting complex, cell cycle, mitosis, cyclosome, TPR, ubiquitin, ubiquitin ligase, twinning; 2.80A {Homo sapiens}	Back alignment and structure

>2y4t_A DNAJ homolog subfamily C member 3; chaperone, endoplasmic reticulum, protein folding, tetratricopeptiderepeat, J domain, unfolded protein respons; 3.00A {Homo sapiens} PDB: 2y4u_A	Back alignment and structure

>2fbi_A Probable transcriptional regulator; MARR, APC5816, structural genomic protein structure initiative; 2.10A {Pseudomonas aeruginosa} SCOP: a.4.5.28	Back alignment and structure

>3urz_A Uncharacterized protein; tetratricopeptide repeats (TPR) containing protein, structur genomics, joint center for structural genomics, JCSG; HET: PG4; 2.19A {Bacteroides ovatus}	Back alignment and structure

>3upv_A Heat shock protein STI1; TPR-fold, adaptor protein for HSP70 and HSP90, C-terminal PA HSP70, peptide binding protein; 1.60A {Saccharomyces cerevisiae}	Back alignment and structure

>3qou_A Protein YBBN; thioredoxin-like fold, tetratricopeptide repeat, lysine dimethylation, protein binding; HET: MLY; 1.80A {Escherichia coli} PDB: 3qdn_A*	Back alignment and structure

>2vq2_A PILW, putative fimbrial biogenesis and twitching motility protein; secretin, TPR repeat, type IV pilus, bacterail virulence; 1.54A {Neisseria meningitidis}	Back alignment and structure

>3n71_A Histone lysine methyltransferase SMYD1; heart development, transcription; HET: SFG MES; 2.30A {Mus musculus}	Back alignment and structure

>2fbh_A Transcriptional regulator PA3341; MARR, transcription regulator, APC5857, structural genomics, protein structure initiative; 1.80A {Pseudomonas aeruginosa} SCOP: a.4.5.28	Back alignment and structure

>1hz4_A MALT regulatory protein; two-helix bundles, helix repeats, protein superhelix, transc activator; 1.45A {Escherichia coli} SCOP: a.118.8.2	Back alignment and structure

>3qww_A SET and MYND domain-containing protein 2; methyltransferase, HSP90, transferase-transferase inhibitor; HET: SFG; 1.80A {Mus musculus} PDB: 3qwv_A* 3s7d_A* 3s7b_A* 3s7f_A* 3s7j_A* 3tg4_A* 3tg5_A* 3rib_A*	Back alignment and structure

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

>2e2e_A Formate-dependent nitrite reductase complex NRFG; TPR, cytochrome C biogenesis, O157:H7 EDL933, formate- nitrite reductase complex, lyase; 2.05A {Escherichia coli}	Back alignment and structure

>2a61_A Transcriptional regulator TM0710; APC4350, MCSG, midwest center for structural genomics, PSI, protein structure initiative, MARR; 1.80A {Thermotoga maritima} SCOP: a.4.5.28	Back alignment and structure

>1ku9_A Hypothetical protein MJ223; putative transcription factor, homodimeric winged-helix fold, structural genomics, PSI; 2.80A {Methanocaldococcus jannaschii} SCOP: a.4.5.36	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

>1elw_A TPR1-domain of HOP; HOP, TPR-domain, peptide-complex, helical repeat, HSP70, protein binding, chaperone; 1.60A {Homo sapiens} SCOP: a.118.8.1	Back alignment and structure

>2nnn_A Probable transcriptional regulator; structural genomics, PSI-2, protein structure initiative, M center for structural genomics, MCSG; 2.40A {Pseudomonas aeruginosa}	Back alignment and structure

>1s3j_A YUSO protein; structural genomics, MARR transcriptional regulator family, PSI, protein structure initiative; HET: MSE; 2.25A {Bacillus subtilis} SCOP: a.4.5.28	Back alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Alignment Graph	Length	Definition	E-value
Query		303
d1ufma_		84	a.4.5.47 (A:) COP9 signalosome complex subunit 4,	4e-23

>d1ufma_ a.4.5.47 (A:) COP9 signalosome complex subunit 4, GSN4 {Mouse (Mus musculus) [TaxId: 10090]} Length = 84	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]

 Score = 88.7 bits (220), Expect = 4e-23
 Identities = 20/68 (29%), Positives = 35/68 (51%)

Query: 198 MLKHRVVEHNIRVMAKYYTRITLQRMCDLLGLPIEETEEFLSSMVVSKTITAKIDRPAGI 257
           +L   V+EHN+   +K Y  IT + +  LL +P  + E+  S M+    +   ID+  GI
Sbjct: 11  ILDRAVIEHNLLSASKLYNNITFEELGALLEIPAAKAEKIASQMITEGRMNGFIDQIDGI 70

Query: 258 INFARNKD 265
           ++F   + 
Sbjct: 71  VHFETREA 78

PyMOL of d1ufma_

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Alignment Graph	Length	Definition	Probability
Query		303
d1ufma_		84	COP9 signalosome complex subunit 4, GSN4 {Mouse (M	99.82
d1qqea_		290	Vesicular transport protein sec17 {Baker's yeast (	95.35
d1wi9a_		72	Hypothetical protein C20orf116 homolog {Mouse (Mus	94.36
d1tjca_		95	Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human	93.02
d1sfxa_		109	Hypothetical protein AF2008 {Archaeoglobus fulgidu	92.93
d1ub9a_		100	Hypothetical protein PH1061 {Archaeon Pyrococcus h	91.9
d1hz4a_		366	Transcription factor MalT domain III {Escherichia	91.68
d1dpua_		69	C-terminal domain of RPA32 {Human (Homo sapiens) [	91.46
d1qqea_		290	Vesicular transport protein sec17 {Baker's yeast (	91.01
d1z05a1		71	Transcriptional regulator VC2007 N-terminal domain	90.4
d2cfxa1		63	Transcriptional regulator LrpC {Bacillus subtilis	89.98
d1p5qa1		170	FKBP52 (FKBP4), C-terminal domain {Human (Homo sap	89.4
d1elra_		128	Hop {Human (Homo sapiens) [TaxId: 9606]}	89.28
d1z6ra1		70	Mlc protein N-terminal domain {Escherichia coli [T	88.92
d1hxia_		112	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	87.49
d2cg4a1		63	Regulatory protein AsnC {Escherichia coli [TaxId:	86.58
d2c2la1		201	STIP1 homology and U box-containing protein 1, STU	86.4
d1a17a_		159	Protein phosphatase 5 {Human (Homo sapiens) [TaxId	86.27
d1xnfa_		259	Lipoprotein NlpI {Escherichia coli [TaxId: 562]}	85.23
d1a17a_		159	Protein phosphatase 5 {Human (Homo sapiens) [TaxId	85.22
d1i1ga1		60	LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}	84.48
d1hh8a_		192	Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {H	83.46
d2cyya1		60	Putative transcriptional regulator PH1519 {Archaeo	82.57
d1w3ba_		388	O-GlcNAc transferase p110 subunit, OGT {Human (Hom	82.49
d2fbha1		137	Transcriptional regulator PA3341 {Pseudomonas aeru	81.14
d1elwa_		117	Hop {Human (Homo sapiens) [TaxId: 9606]}	80.32
d1p5qa1		170	FKBP52 (FKBP4), C-terminal domain {Human (Homo sap	80.18

>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=99.82  E-value=7.7e-21  Score=139.64  Aligned_cols=69  Identities=29%  Similarity=0.543  Sum_probs=66.2

Q ss_pred             HHHHHHHHHHHHHHHHhhhceeeHHHHHHHhCCCHHHHHHHHHhhhhcCceEEEecCCCceEEeccCCC
Q psy4458         197 KMLKHRVVEHNIRVMAKYYTRITLQRMCDLLGLPIEETEEFLSSMVVSKTITAKIDRPAGIINFARNKD  265 (303)
Q Consensus       197 ~~l~~~i~ehNi~~isk~Y~~Itl~~la~ll~ls~~~vE~~l~~mI~~~~l~akIDq~~giV~f~~~~~  265 (303)
                      ..|+++++||||++++++|++|+|++||++|++|++++|..|++||.+|+|+|+|||++|+|+|+.++.
T Consensus        10 t~L~~~i~Ehni~~is~~Y~~Isl~~la~~l~l~~~evE~~l~~mI~~~~i~akIDq~~g~V~F~~~e~   78 (84)
T d1ufma_          10 SILDRAVIEHNLLSASKLYNNITFEELGALLEIPAAKAEKIASQMITEGRMNGFIDQIDGIVHFETREA   78 (84)
T ss_dssp             CCCCHHHHHHHHHHHHHSCSEEEHHHHHHHTTSCHHHHHHHHHHHHHTTSSCEEEETTTTEEEECCSSC
T ss_pred             HHHHHHHHHHHHHHHHHhhceeeHHHHHHHHCCCHHHHHHHHHHHHhcCeEEEEEeCCCCEEEECCCCc
Confidence            568899999999999999999999999999999999999999999999999999999999999998754

PyMOL of d1ufma_

>d1qqea_ a.118.8.1 (A:) Vesicular transport protein sec17 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}	Back information, alignment and structure

>d1wi9a_ a.4.5.47 (A:) Hypothetical protein C20orf116 homolog {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1tjca_ a.118.8.1 (A:) Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1sfxa_ a.4.5.50 (A:) Hypothetical protein AF2008 {Archaeoglobus fulgidus [TaxId: 2234]}	Back information, alignment and structure

>d1ub9a_ a.4.5.28 (A:) Hypothetical protein PH1061 {Archaeon Pyrococcus horikoshii [TaxId: 53953]}	Back information, alignment and structure

>d1hz4a_ a.118.8.2 (A:) Transcription factor MalT domain III {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

>d1dpua_ a.4.5.16 (A:) C-terminal domain of RPA32 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1qqea_ a.118.8.1 (A:) Vesicular transport protein sec17 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}	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

>d2cfxa1 a.4.5.32 (A:1-63) Transcriptional regulator LrpC {Bacillus subtilis [TaxId: 1423]}	Back information, alignment and structure

>d1p5qa1 a.118.8.1 (A:258-427) FKBP52 (FKBP4), C-terminal domain {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1elra_ a.118.8.1 (A:) Hop {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1z6ra1 a.4.5.63 (A:12-81) Mlc protein N-terminal domain {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

>d1hxia_ a.118.8.1 (A:) Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor) {Trypanosoma brucei [TaxId: 5691]}	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

>d2c2la1 a.118.8.1 (A:24-224) STIP1 homology and U box-containing protein 1, STUB1 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1a17a_ a.118.8.1 (A:) Protein phosphatase 5 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1xnfa_ a.118.8.1 (A:) Lipoprotein NlpI {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

>d1a17a_ a.118.8.1 (A:) Protein phosphatase 5 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1i1ga1 a.4.5.32 (A:2-61) LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}	Back information, alignment and structure

>d1hh8a_ a.118.8.1 (A:) Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {Human (Homo sapiens) [TaxId: 9606]}	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

>d1w3ba_ a.118.8.1 (A:) O-GlcNAc transferase p110 subunit, OGT {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2fbha1 a.4.5.28 (A:8-144) Transcriptional regulator PA3341 {Pseudomonas aeruginosa [TaxId: 287]}	Back information, alignment and structure

>d1elwa_ a.118.8.1 (A:) Hop {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1p5qa1 a.118.8.1 (A:258-427) FKBP52 (FKBP4), C-terminal domain {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure