Psyllid ID: psy14375

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200------
Protein Sequence
MVCLGLGQNKEKTVSFLLSTSRISPGDCVVSLFPRKIQPKSNQIKSALSKSVPPRTPYSDRVSIGYIIMTHVLDQVVEEDAGDLQFPKEFENAETLLISEVHMLLQHRKTQNENAEEEQEFSEVFQKTLTYTERFRKFKNRETITSVRNLLTQKKLHKFELAAIANLCPETPEEAKALIPSLECRFEEEELRQILDDIQTKRSLQY
Secondary Structure (PSIPRED)
cccccccccccHHHHHHHHcccccccccccccccccccccccHHHHHHcccccccccccccccccccEEEcccccccccccccccccccccccccccHHHHHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHcccccHHHHHHHHccccccHHHHHHHcccccccccHHHHHHHHHHHHHHHHccc
Secondary Structure Prediction (SSPRO)
cEEEEccccccccEEEEEEcccccccccccccccccccccHHHHHHHHHccccccccccccEEccEEEEEccccccHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHccccHHHHHHHHccccccHHHHHHHHHHHcccccHHHHHHHHHHHHHHHcccc
Coil and Loop (DISEMBL)
mvclglgqnkeKTVSFLLStsrispgdcvvslfprkiqpksnqiksalsksvpprtpysdrvsIGYIIMTHVLDQVveedagdlqfpkefENAETLLISEVHMLLQHRKTQNENAEEEQEFSEVFQKTLTYTERFRKFKNRETITSVRNLLTQKKLHKFELAAIAnlcpetpeeAKALIPSLECRFEEEELRQILDDIQTKRSLQY
Flexible Loop (DISEMBL)
mvclglgqnkEKTVSFLLSTSRISPGDCVVSLFprkiqpksnqiksalsksvpprtpySDRVSIGYIIMTHVLDQVVEEDAGDLQFPKEFENAETLLISEVHMLLQHRKTQNENAEEEQEFSEVFQKTLTYTErfrkfknretitsvRNLLTQKKLHKFELAAIANLCPETPEEAKALIPSLECRFEEEELRQILddiqtkrslqy
Low Complexity Region (SEG)
MVCLGLGQNKEKTVSFLLSTSRISPGDCVVSLFPRKIQPKSNQIKSALSKSVPPRTPYSDRVSIGYIIMTHVLDQVVEEDAGDLQFPKEFENAETLLISEVHMLLQHRKTqnenaeeeqeFSEVFQKTLTYTERFRKFKNRETITSVRNLLTQKKLHKFELAAIANLCPETPEEAKALIPSLECRFEEEELRQILDDIQTKRSLQY
Disordered region (IsUnstruct)
************TVSFLLSTSRISPGDCVVSLFP*************************DRVSIGYIIMTHVLDQVVEEDAGDLQFPKEFENAETLLISEVHMLL******************VFQKTLTYTERFRKFKNRETITSVRNLLTQKKLHKFELAAIANLCPETPEEAKALIPSLECRFE*******************
Disordered Region (DISOPRED)
*********K******************VVSL************************************************AGDLQFPKEFENAETLLISEVHML*********************QKTLTYTERFRKFKNRETITSVRNLLTQKKLHKFELAAIANLCPETPEEAKALIPSLECRFEEEELRQILDDIQTKRSL**
Disordered Region (DISEMBL)
MVCLGLGQNKEKTVSFLLSTSRISPGDCVVSLFPRKIQPK****************PYSDRVSIGYIIMTHVLDQVVEEDAGDLQFPKEFENAETLLISEVHMLLQHR***************VFQKTLTYTERFRKFKNRETITSVRNLLTQKKLHKFELAAIANLCPETPEEAKALIPSLECRFEEEELRQILDDIQTKRSLQY
Disordered Region (DISPRO)
MVCLGLGQNKEKTVSFLLSTSRISPGDCVVSLFPRKIQPKSNQIKSALSKSVPPRTPYSDRVSIGYIIMTHVLDQVVEEDAGDLQFPKEFENAETLLISEVHMLLQHRKTQNENAEEEQEFSEVFQKTLTYTERFRKFKNRETITSVRNLLTQKKLHKFELAAIANLCPETPEEAKALIPSLECRFEEEELRQILDDIQTKRS***
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MVCLGLGQNKEKTVSFLLSTSRISPGDCVVSLFPRKIQPKSNQIKSALSKSVPPRTPYSDRVSIGYIIMTHVLDQVVEEDAGDLQFPKEFENAETLLISEVHMLLQHRKTQNENAEEEQEFSEVFQKTLTYTERFRKFKNRETITSVRNLLTQKKLHKFELAAIANLCPETPEEAKALIPSLECRFEEEELRQILDDIQTKRSLQY
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	206	2.2.26 [Sep-21-2011]
Q9VEA5	139	DNA-directed RNA polymera	yes	N/A	0.635	0.942	0.824	1e-57
Q9D7M8	142	DNA-directed RNA polymera	yes	N/A	0.631	0.915	0.8	5e-53
O15514	142	DNA-directed RNA polymera	yes	N/A	0.631	0.915	0.8	5e-53
Q54S04	155	DNA-directed RNA polymera	yes	N/A	0.601	0.8	0.407	7e-22
O74825	135	DNA-directed RNA polymera	yes	N/A	0.626	0.955	0.358	1e-14
P20433	221	DNA-directed RNA polymera	yes	N/A	0.388	0.361	0.362	2e-08

>sp|Q9VEA5|RPB4_DROME DNA-directed RNA polymerase II 16 kDa polypeptide OS=Drosophila melanogaster GN=Rpb4 PE=2 SV=5

 Score =  222 bits (566), Expect = 1e-57,   Method: Compositional matrix adjust.
 Identities = 108/131 (82%), Positives = 117/131 (89%)

Query: 76  VVEEDAGDLQFPKEFENAETLLISEVHMLLQHRKTQNENAEEEQEFSEVFQKTLTYTERF 135
           +V+EDA DLQFPKEFENAETLLISEVHMLL HRK QNE+A+EEQEFSEVF KT  YT+ F
Sbjct: 9   MVDEDAADLQFPKEFENAETLLISEVHMLLDHRKRQNESADEEQEFSEVFMKTYAYTDSF 68

Query: 136 RKFKNRETITSVRNLLTQKKLHKFELAAIANLCPETPEEAKALIPSLECRFEEEELRQIL 195
           RKFKN+ETI S R+LL QKKLHKFELAA+ NLCPE PEEAKALIPSLE RFE+EELRQIL
Sbjct: 69  RKFKNKETIMSARSLLMQKKLHKFELAALGNLCPEAPEEAKALIPSLEGRFEDEELRQIL 128

Query: 196 DDIQTKRSLQY 206
           DDI TKRSLQY
Sbjct: 129 DDIGTKRSLQY 139

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Associates with POLR2G.
Drosophila melanogaster (taxid: 7227)
EC: 2EC: .EC: 7EC: .EC: 7EC: .EC: 6

>sp|Q9D7M8|RPB4_MOUSE DNA-directed RNA polymerase II subunit RPB4 OS=Mus musculus GN=Polr2d PE=2 SV=2

 Score =  207 bits (526), Expect = 5e-53,   Method: Compositional matrix adjust.
 Identities = 104/130 (80%), Positives = 113/130 (86%)

Query: 77  VEEDAGDLQFPKEFENAETLLISEVHMLLQHRKTQNENAEEEQEFSEVFQKTLTYTERFR 136
           VEEDA  L FPKEFE AETLL SEVHMLL+HRK QNE+AE+EQE SEVF KTL YT RF 
Sbjct: 13  VEEDASQLIFPKEFETAETLLNSEVHMLLEHRKQQNESAEDEQELSEVFMKTLNYTARFS 72

Query: 137 KFKNRETITSVRNLLTQKKLHKFELAAIANLCPETPEEAKALIPSLECRFEEEELRQILD 196
           +FKNRETI SVR+LL QKKLHKFELA +ANLCPET EE+KALIPSLE RFE+EEL+QILD
Sbjct: 73  RFKNRETIASVRSLLLQKKLHKFELACLANLCPETAEESKALIPSLEGRFEDEELQQILD 132

Query: 197 DIQTKRSLQY 206
           DIQTKRS QY
Sbjct: 133 DIQTKRSFQY 142

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Pol II is the central component of the basal RNA polymerase II transcription machinery. It is composed of mobile elements that move relative to each other. RPB4 is part of a subcomplex with RPB7 that binds to a pocket formed by RPB1, RPB2 and RPB6 at the base of the clamp element. The RBP4-RPB7 subcomplex seems to lock the clamp via RPB7 in the closed conformation thus preventing double stranded DNA to enter the active site cleft. The RPB4-RPB7 subcomplex binds single-stranded DNA and RNA.

Mus musculus (taxid: 10090)

>sp|O15514|RPB4_HUMAN DNA-directed RNA polymerase II subunit RPB4 OS=Homo sapiens GN=POLR2D PE=1 SV=1

 Score =  207 bits (526), Expect = 5e-53,   Method: Compositional matrix adjust.
 Identities = 104/130 (80%), Positives = 113/130 (86%)

Query: 77  VEEDAGDLQFPKEFENAETLLISEVHMLLQHRKTQNENAEEEQEFSEVFQKTLTYTERFR 136
           VEEDA  L FPKEFE AETLL SEVHMLL+HRK QNE+AE+EQE SEVF KTL YT RF 
Sbjct: 13  VEEDASQLIFPKEFETAETLLNSEVHMLLEHRKQQNESAEDEQELSEVFMKTLNYTARFS 72

Query: 137 KFKNRETITSVRNLLTQKKLHKFELAAIANLCPETPEEAKALIPSLECRFEEEELRQILD 196
           +FKNRETI SVR+LL QKKLHKFELA +ANLCPET EE+KALIPSLE RFE+EEL+QILD
Sbjct: 73  RFKNRETIASVRSLLLQKKLHKFELACLANLCPETAEESKALIPSLEGRFEDEELQQILD 132

Query: 197 DIQTKRSLQY 206
           DIQTKRS QY
Sbjct: 133 DIQTKRSFQY 142

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Pol II is the central component of the basal RNA polymerase II transcription machinery. It is composed of mobile elements that move relative to each other. RPB4 is part of a subcomplex with RPB7 that binds to a pocket formed by RPB1, RPB2 and RPB6 at the base of the clamp element. The RBP4-RPB7 subcomplex seems to lock the clamp via RPB7 in the closed conformation thus preventing double stranded DNA to enter the active site cleft. The RPB4-RPB7 subcomplex binds single-stranded DNA and RNA.

Homo sapiens (taxid: 9606)

>sp|Q54S04|RPB4_DICDI DNA-directed RNA polymerase II subunit rpb4 OS=Dictyostelium discoideum GN=polr2d PE=3 SV=1

 Score =  103 bits (258), Expect = 7e-22,   Method: Compositional matrix adjust.
 Identities = 57/140 (40%), Positives = 89/140 (63%), Gaps = 16/140 (11%)

Query: 78  EEDAGDLQFPKEFENAETLLISEVHMLLQHRKTQNENAEEE---------------QEFS 122
           EED   L+FP++ ++A+ LL SEV +LL+HRK  +E+   E                +  
Sbjct: 14  EEDLTTLKFPRDLKDAKFLLNSEVAILLEHRKGISESEGTEFPQNTLLIHLYYNSINDII 73

Query: 123 EVFQKTLTYTERFRKFKNRETITSVRNLLTQKKLHKFELAAIANLCPETPEEAKALIPSL 182
             F KTL Y E+F ++KN+ +I  VR  L+++ L +FE+A++ANLCPE  +EAK+LIPSL
Sbjct: 74  RTFHKTLAYAEKFSRYKNKTSIKQVRTALSKQNLEEFEIASLANLCPEISDEAKSLIPSL 133

Query: 183 ECRFEEEELRQILDDIQTKR 202
           + + E++EL+ ILD++   R
Sbjct: 134 K-KMEDDELQAILDELSNLR 152

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Pol II is the central component of the basal RNA polymerase II transcription machinery. It is composed of mobile elements that move relative to each other. RPB4 is part of a subcomplex with RPB7 that binds to a pocket formed by RPB1, RPB2 and RPB6 at the base of the clamp element. The RBP4-RPB7 subcomplex seems to lock the clamp via RPB7 in the closed conformation thus preventing double stranded DNA to enter the active site cleft. The RPB4-RPB7 subcomplex binds single-stranded DNA and RNA.

Dictyostelium discoideum (taxid: 44689)

>sp|O74825|RPB4_SCHPO DNA-directed RNA polymerase II subunit rpb4 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rpb4 PE=1 SV=1

 Score = 79.7 bits (195), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 47/131 (35%), Positives = 71/131 (54%), Gaps = 2/131 (1%)

Query: 76  VVEEDAGDLQFPKEFENAETLLISEVHMLLQHRKTQN-ENAEEEQEFSEVFQKTLTYTER 134
           + EEDA  L+   EFEN + L +SE  +L++    Q       E   ++V +KT+ Y   
Sbjct: 5   IFEEDAAQLKLGPEFENEDMLTVSEAKILIETVLAQRARETNGEIPMTDVMKKTVAYFNV 64

Query: 135 FRKFKNRETITSVRNLLTQKKLHKFELAAIANLCPETPEEAKALIPSLECRFEEEELRQI 194
           F +FK  E   +   +L  +  HKFE A +  LC E  EEA+ LIPSL  + +++ L+ I
Sbjct: 65  FARFKTAEATYACERILGNR-FHKFERAQLGTLCCEDAEEARTLIPSLANKIDDQNLQGI 123

Query: 195 LDDIQTKRSLQ 205
           LD++ T R  Q
Sbjct: 124 LDELSTLRKFQ 134

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Pol II is the central component of the basal RNA polymerase II transcription machinery. It is composed of mobile elements that move relative to each other. RPB4 is part of a subcomplex with RPB7 that binds to a pocket formed by RPB1, RPB2 and RPB6 at the base of the clamp element. The RBP4-RPB7 subcomplex seems to lock the clamp via RPB7 in the closed conformation thus preventing double stranded DNA to enter the active site cleft. The RPB4-RPB7 subcomplex binds single-stranded DNA and RNA.

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

>sp|P20433|RPB4_YEAST DNA-directed RNA polymerase II subunit RPB4 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RPB4 PE=1 SV=1

 Score = 59.7 bits (143), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 29/80 (36%), Positives = 49/80 (61%)

Query: 125 FQKTLTYTERFRKFKNRETITSVRNLLTQKKLHKFELAAIANLCPETPEEAKALIPSLEC 184
            + T+ Y   F +F+++ET+ +V  LL    LH FE+A + +L  +T +EAK LIPSL  
Sbjct: 141 LKNTMQYLTNFSRFRDQETVGAVIQLLKSTGLHPFEVAQLGSLACDTADEAKTLIPSLNN 200

Query: 185 RFEEEELRQILDDIQTKRSL 204
           +  ++EL +IL ++    +L
Sbjct: 201 KISDDELERILKELSNLETL 220

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Pol II is the central component of the basal RNA polymerase II transcription machinery. It is composed of mobile elements that move relative to each other. RPB4 is part of a subcomplex with RPB7 that binds to a pocket formed by RPB1, RPB2 and RPB6 at the base of the clamp element. The RBP4-RPB7 subcomplex seems to lock the clamp via RPB7 in the closed conformation thus preventing double stranded DNA to enter the active site cleft. The RPB4-RPB7 subcomplex binds single-stranded DNA and RNA. The RPB4-RPB7 subcomplex is necessary for promoter-directed transcription initiation but is not required for recruitment of Pol II to active preinitiation complexes and seems to be dispensable for transcription elongation and termination. The RPB4-RPB7 subcomplex recruits FCP1 to Pol II. Involved in DNA repair of damage in the transcribed strand. RPB4 is dispensable under optimal growth conditions, but becomes essential during heat or cold shock and under nutrient depletion. Suppresses the RBP9-mediated transcription-coupled repair (TCR) subpathway of nucleotide excision repair (NER) but facilitates the RAD26-mediated TCR subpathway. Under stress conditions only, involved in mRNA export to the cytoplasm. Involved in mRNA decay. Promotes or enhances the deadenylation process of specific mRNAs and may recruit PAT1 and the LSM1-7 complex to these mRNAs, thus stimulating their decapping and further decay.

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

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	206
91082085	138	PREDICTED: similar to DNA-directed RNA p	0.669	1.0	0.797	6e-58
357619360	138	putative histone acetyltransferase [Dana	0.669	1.0	0.811	3e-57
390178627	139	GA30251 [Drosophila pseudoobscura pseudo	0.635	0.942	0.832	2e-56
281362019	139	Rpb4 [Drosophila melanogaster] gi|143459	0.635	0.942	0.824	6e-56
27263229	139	RNA polymerase II accessory factor rpb4	0.635	0.942	0.809	7e-55
389609397	151	histone acetyltransferase rpb4 [Papilio	0.660	0.900	0.794	1e-54
321476639	137	hypothetical protein DAPPUDRAFT_306425 [	0.640	0.963	0.795	2e-54
225706322	144	DNA-directed RNA polymerase II 16 kDa po	0.694	0.993	0.765	4e-54
427786429	144	Putative dna-directed rna polymerase ii	0.650	0.930	0.785	8e-54
346469951	144	hypothetical protein [Amblyomma maculatu	0.650	0.930	0.777	8e-54

>gi|91082085|ref|XP_966894.1| PREDICTED: similar to DNA-directed RNA polymerase II 16 kDa polypeptide [Tribolium castaneum] gi|270008323|gb|EFA04771.1| hypothetical protein TcasGA2_TC030678 [Tribolium castaneum]

 Score =  229 bits (583), Expect = 6e-58,   Method: Compositional matrix adjust.
 Identities = 110/138 (79%), Positives = 125/138 (90%)

Query: 69  MTHVLDQVVEEDAGDLQFPKEFENAETLLISEVHMLLQHRKTQNENAEEEQEFSEVFQKT 128
           M +    + EEDA DLQFPKEFENAETLLISEVHMLL+HRK QNE+AE+EQEFS+VF KT
Sbjct: 1   MANANTDLTEEDAADLQFPKEFENAETLLISEVHMLLEHRKAQNESAEDEQEFSDVFMKT 60

Query: 129 LTYTERFRKFKNRETITSVRNLLTQKKLHKFELAAIANLCPETPEEAKALIPSLECRFEE 188
           LTYT+RFRKFKN+ETI++VRNLL QKKLHKFELAAIANLCPET EEAK+LIPSLE RFE+
Sbjct: 61  LTYTDRFRKFKNKETISAVRNLLMQKKLHKFELAAIANLCPETTEEAKSLIPSLEGRFED 120

Query: 189 EELRQILDDIQTKRSLQY 206
           EEL+ +LDDIQTKRS+QY
Sbjct: 121 EELQAVLDDIQTKRSIQY 138

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|357619360|gb|EHJ71970.1| putative histone acetyltransferase [Danaus plexippus]

 Score =  226 bits (577), Expect = 3e-57,   Method: Compositional matrix adjust.
 Identities = 112/138 (81%), Positives = 124/138 (89%)

Query: 69  MTHVLDQVVEEDAGDLQFPKEFENAETLLISEVHMLLQHRKTQNENAEEEQEFSEVFQKT 128
           M+  L  VVEEDA DLQFPKEFENAETLLISEV MLL+HRK QNE+AEEEQEFSEVF KT
Sbjct: 1   MSGPLQDVVEEDAADLQFPKEFENAETLLISEVDMLLEHRKAQNESAEEEQEFSEVFMKT 60

Query: 129 LTYTERFRKFKNRETITSVRNLLTQKKLHKFELAAIANLCPETPEEAKALIPSLECRFEE 188
           LTYT  F+KFKN+ETIT+VRNLL  KKLHKFE+A++ANLCPETPEEAKALIPSLE RFE+
Sbjct: 61  LTYTNMFKKFKNKETITAVRNLLQSKKLHKFEVASLANLCPETPEEAKALIPSLEGRFED 120

Query: 189 EELRQILDDIQTKRSLQY 206
           EELR +LDDIQTKRS+QY
Sbjct: 121 EELRILLDDIQTKRSIQY 138

Source: Danaus plexippus

Species: Danaus plexippus

Genus: Danaus

Family: Nymphalidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|390178627|ref|XP_003736694.1| GA30251 [Drosophila pseudoobscura pseudoobscura] gi|388859523|gb|EIM52767.1| GA30251 [Drosophila pseudoobscura pseudoobscura]

 Score =  224 bits (570), Expect = 2e-56,   Method: Compositional matrix adjust.
 Identities = 109/131 (83%), Positives = 118/131 (90%)

Query: 76  VVEEDAGDLQFPKEFENAETLLISEVHMLLQHRKTQNENAEEEQEFSEVFQKTLTYTERF 135
           +V+EDA DLQFPKEFENAETLLISEVHMLL HRK QNE+A+EEQEFSEVF KT  YT+ F
Sbjct: 9   MVDEDAADLQFPKEFENAETLLISEVHMLLDHRKRQNESADEEQEFSEVFMKTYAYTDSF 68

Query: 136 RKFKNRETITSVRNLLTQKKLHKFELAAIANLCPETPEEAKALIPSLECRFEEEELRQIL 195
           RKFKN+ETI SVR+LL QKKLHKFELAA+ NLCPE PEEAKALIPSLE RFE+EELRQIL
Sbjct: 69  RKFKNKETIMSVRSLLMQKKLHKFELAALGNLCPEAPEEAKALIPSLEGRFEDEELRQIL 128

Query: 196 DDIQTKRSLQY 206
           DDI TKRSLQY
Sbjct: 129 DDIGTKRSLQY 139

Source: Drosophila pseudoobscura pseudoobscura

Species: Drosophila pseudoobscura

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|281362019|ref|NP_001014633.2| Rpb4 [Drosophila melanogaster] gi|143459115|sp|Q9VEA5.5|RPB4_DROME RecName: Full=DNA-directed RNA polymerase II 16 kDa polypeptide; AltName: Full=RNA polymerase II accessory factor rpb4 gi|66571194|gb|AAY51562.1| IP01323p [Drosophila melanogaster] gi|66772825|gb|AAY55724.1| IP02337p [Drosophila melanogaster] gi|66772827|gb|AAY55725.1| IP02340p [Drosophila melanogaster] gi|220943406|gb|ACL84246.1| Rpb4-PF [synthetic construct] gi|220955702|gb|ACL90394.1| Rpb4-PF [synthetic construct] gi|272477037|gb|AAF55522.5| Rpb4 [Drosophila melanogaster]

 Score =  222 bits (566), Expect = 6e-56,   Method: Compositional matrix adjust.
 Identities = 108/131 (82%), Positives = 117/131 (89%)

Query: 76  VVEEDAGDLQFPKEFENAETLLISEVHMLLQHRKTQNENAEEEQEFSEVFQKTLTYTERF 135
           +V+EDA DLQFPKEFENAETLLISEVHMLL HRK QNE+A+EEQEFSEVF KT  YT+ F
Sbjct: 9   MVDEDAADLQFPKEFENAETLLISEVHMLLDHRKRQNESADEEQEFSEVFMKTYAYTDSF 68

Query: 136 RKFKNRETITSVRNLLTQKKLHKFELAAIANLCPETPEEAKALIPSLECRFEEEELRQIL 195
           RKFKN+ETI S R+LL QKKLHKFELAA+ NLCPE PEEAKALIPSLE RFE+EELRQIL
Sbjct: 69  RKFKNKETIMSARSLLMQKKLHKFELAALGNLCPEAPEEAKALIPSLEGRFEDEELRQIL 128

Query: 196 DDIQTKRSLQY 206
           DDI TKRSLQY
Sbjct: 129 DDIGTKRSLQY 139

Source: Drosophila melanogaster

Species: Drosophila melanogaster

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|27263229|gb|AAN88031.1| RNA polymerase II accessory factor rpb4 [Drosophila melanogaster] gi|27263231|gb|AAN88032.1| RNA polymerase II accessory factor rpb4 [Drosophila melanogaster]

 Score =  219 bits (557), Expect = 7e-55,   Method: Compositional matrix adjust.
 Identities = 106/131 (80%), Positives = 116/131 (88%)

Query: 76  VVEEDAGDLQFPKEFENAETLLISEVHMLLQHRKTQNENAEEEQEFSEVFQKTLTYTERF 135
           +V+EDA DLQFPKEFENAETLLISEVHMLL HRK QNE+A+EEQEFSEVF KT  YT+ F
Sbjct: 9   MVDEDAADLQFPKEFENAETLLISEVHMLLDHRKRQNESADEEQEFSEVFMKTYAYTDSF 68

Query: 136 RKFKNRETITSVRNLLTQKKLHKFELAAIANLCPETPEEAKALIPSLECRFEEEELRQIL 195
           RKFKN+ETI S R+LL QKKLHKFELAA+ NLCPE PEEAKALIPSLE RFE+EE R+IL
Sbjct: 69  RKFKNKETIMSARSLLMQKKLHKFELAALGNLCPEAPEEAKALIPSLEGRFEDEEAREIL 128

Query: 196 DDIQTKRSLQY 206
           DDI TKRSLQY
Sbjct: 129 DDIGTKRSLQY 139

Source: Drosophila melanogaster

Species: Drosophila melanogaster

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|389609397|dbj|BAM18310.1| histone acetyltransferase rpb4 [Papilio xuthus]

 Score =  218 bits (555), Expect = 1e-54,   Method: Compositional matrix adjust.
 Identities = 108/136 (79%), Positives = 121/136 (88%)

Query: 69  MTHVLDQVVEEDAGDLQFPKEFENAETLLISEVHMLLQHRKTQNENAEEEQEFSEVFQKT 128
           M+  +  VVEEDA DLQFPKEFENAETLLISEV MLL+HRK QNE+AEEEQEFSEVF KT
Sbjct: 1   MSCPIQDVVEEDAADLQFPKEFENAETLLISEVDMLLEHRKAQNESAEEEQEFSEVFMKT 60

Query: 129 LTYTERFRKFKNRETITSVRNLLTQKKLHKFELAAIANLCPETPEEAKALIPSLECRFEE 188
           LTYT  F+KFKN+ETI +VRNLL  KKLHKFE+A++ANLCPETPEEAKALIPSLE RFE+
Sbjct: 61  LTYTNMFKKFKNKETIAAVRNLLQSKKLHKFEVASLANLCPETPEEAKALIPSLEGRFED 120

Query: 189 EELRQILDDIQTKRSL 204
           EELR +LDDIQTKRS+
Sbjct: 121 EELRILLDDIQTKRSI 136

Source: Papilio xuthus

Species: Papilio xuthus

Genus: Papilio

Family: Papilionidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|321476639|gb|EFX87599.1| hypothetical protein DAPPUDRAFT_306425 [Daphnia pulex]

 Score =  218 bits (554), Expect = 2e-54,   Method: Compositional matrix adjust.
 Identities = 105/132 (79%), Positives = 119/132 (90%)

Query: 75  QVVEEDAGDLQFPKEFENAETLLISEVHMLLQHRKTQNENAEEEQEFSEVFQKTLTYTER 134
           ++ +EDA  LQFPKEFENAETLLISEVHMLL HRK QNE+AE+EQE SEVF KTL YT+R
Sbjct: 6   EISDEDAAVLQFPKEFENAETLLISEVHMLLDHRKLQNESAEDEQELSEVFMKTLNYTQR 65

Query: 135 FRKFKNRETITSVRNLLTQKKLHKFELAAIANLCPETPEEAKALIPSLECRFEEEELRQI 194
           F KFKNRETI ++R+LL QKKLHKFELAA+ANLCPE+PEEAK+LIPSLE RFE+EELRQI
Sbjct: 66  FSKFKNRETIAAIRSLLMQKKLHKFELAALANLCPESPEEAKSLIPSLEGRFEDEELRQI 125

Query: 195 LDDIQTKRSLQY 206
           L+DIQTKRS QY
Sbjct: 126 LEDIQTKRSFQY 137

Source: Daphnia pulex

Species: Daphnia pulex

Genus: Daphnia

Family: Daphniidae

Order: Diplostraca

Class: Branchiopoda

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|225706322|gb|ACO09007.1| DNA-directed RNA polymerase II 16 kDa polypeptide [Osmerus mordax]

 Score =  216 bits (550), Expect = 4e-54,   Method: Compositional matrix adjust.
 Identities = 111/145 (76%), Positives = 120/145 (82%), Gaps = 2/145 (1%)

Query: 62  VSIGYIIMTHVLDQVVEEDAGDLQFPKEFENAETLLISEVHMLLQHRKTQNENAEEEQEF 121
            S G    THV D  VEEDA  L FPKEFENAETLL SEVHMLL+HRK QNE+AE+EQE 
Sbjct: 2   ASGGGSTTTHVGD--VEEDASQLLFPKEFENAETLLNSEVHMLLEHRKQQNESAEDEQEL 59

Query: 122 SEVFQKTLTYTERFRKFKNRETITSVRNLLTQKKLHKFELAAIANLCPETPEEAKALIPS 181
           SEVF KTL YT RF +FKNRETI SVR+LL QKKLHKFELA++ANLCPE  EEAKALIPS
Sbjct: 60  SEVFMKTLNYTARFSRFKNRETIASVRSLLLQKKLHKFELASLANLCPEAAEEAKALIPS 119

Query: 182 LECRFEEEELRQILDDIQTKRSLQY 206
           LE RFE+EEL+QILDDIQTKRS QY
Sbjct: 120 LEGRFEDEELQQILDDIQTKRSFQY 144

Source: Osmerus mordax

Species: Osmerus mordax

Genus: Osmerus

Family: Osmeridae

Order: Osmeriformes

Class: Actinopterygii

Phylum: Chordata

Superkingdom: Eukaryota

>gi|427786429|gb|JAA58666.1| Putative dna-directed rna polymerase ii [Rhipicephalus pulchellus]

 Score =  215 bits (548), Expect = 8e-54,   Method: Compositional matrix adjust.
 Identities = 106/135 (78%), Positives = 121/135 (89%), Gaps = 1/135 (0%)

Query: 72  VLDQVVEEDAGDLQFPKEFENAETLLISEVHMLLQHRKTQNENAEEEQEFSEVFQKTLTY 131
           VLDQV EEDA +LQFPKEFENAETLLISEVHMLL+HRK QNE+AEEEQE SEVF KTL Y
Sbjct: 11  VLDQV-EEDASELQFPKEFENAETLLISEVHMLLEHRKQQNESAEEEQELSEVFMKTLGY 69

Query: 132 TERFRKFKNRETITSVRNLLTQKKLHKFELAAIANLCPETPEEAKALIPSLECRFEEEEL 191
            +RF +FKNRETIT+VR LL QKKLH+FELA +ANLCP+ PEEA+AL+PSLE RFE+++L
Sbjct: 70  CQRFSRFKNRETITAVRQLLAQKKLHRFELAQLANLCPDNPEEARALVPSLEGRFEDDQL 129

Query: 192 RQILDDIQTKRSLQY 206
           RQILDDIQT+RS QY
Sbjct: 130 RQILDDIQTQRSFQY 144

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|346469951|gb|AEO34820.1| hypothetical protein [Amblyomma maculatum]

 Score =  215 bits (548), Expect = 8e-54,   Method: Compositional matrix adjust.
 Identities = 105/135 (77%), Positives = 121/135 (89%), Gaps = 1/135 (0%)

Query: 72  VLDQVVEEDAGDLQFPKEFENAETLLISEVHMLLQHRKTQNENAEEEQEFSEVFQKTLTY 131
           VLDQV EEDA +LQFPKEFENAETLLISEVHMLL+HRK QNE+AEEEQE SEVF KTL Y
Sbjct: 11  VLDQV-EEDASELQFPKEFENAETLLISEVHMLLEHRKQQNESAEEEQELSEVFMKTLGY 69

Query: 132 TERFRKFKNRETITSVRNLLTQKKLHKFELAAIANLCPETPEEAKALIPSLECRFEEEEL 191
            +RF +FKNRETI++VR LL QKKLH+FELA +ANLCP+ PEEA+AL+PSLE RFE+++L
Sbjct: 70  CQRFSRFKNRETISAVRQLLAQKKLHRFELAQLANLCPDNPEEARALVPSLEGRFEDDQL 129

Query: 192 RQILDDIQTKRSLQY 206
           RQILDDIQT+RS QY
Sbjct: 130 RQILDDIQTQRSFQY 144

Source: Amblyomma maculatum

Species: Amblyomma maculatum

Genus: Amblyomma

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	206
FB|FBgn0263757	139	Rpb4 [Drosophila melanogaster	0.635	0.942	0.763	7.7e-48
ZFIN|ZDB-GENE-040714-2	145	polr2d "polymerase (RNA) II (D	0.631	0.896	0.746	1.3e-45
UNIPROTKB|F1P2S1	147	POLR2D "Uncharacterized protei	0.631	0.884	0.746	3.4e-45
UNIPROTKB|Q1JQ91	142	POLR2D "Polymerase (RNA) II (D	0.631	0.915	0.738	9.1e-45
UNIPROTKB|E2RPH1	142	POLR2D "Uncharacterized protei	0.631	0.915	0.738	9.1e-45
UNIPROTKB|O15514	142	POLR2D "DNA-directed RNA polym	0.631	0.915	0.738	9.1e-45
MGI|MGI:1916491	142	Polr2d "polymerase (RNA) II (D	0.631	0.915	0.738	9.1e-45
RGD|1308565	142	Polr2d "polymerase (RNA) II (D	0.631	0.915	0.738	9.1e-45
UNIPROTKB|E9PB93	104	POLR2D "DNA-directed RNA polym	0.504	1.0	0.721	2.8e-34
WB|WBGene00018391	144	rpb-4 [Caenorhabditis elegans	0.640	0.916	0.537	3.2e-33

FB|FBgn0263757 Rpb4 [Drosophila melanogaster (taxid:7227)]

 Score = 500 (181.1 bits), Expect = 7.7e-48, P = 7.7e-48
 Identities = 100/131 (76%), Positives = 107/131 (81%)

Query:    76 VVEEDAGDLQFPKEFENAETLLISEVHMLLQHRKTXXXXXXXXXXFSEVFQKTLTYTERF 135
             +V+EDA DLQFPKEFENAETLLISEVHMLL HRK           FSEVF KT  YT+ F
Sbjct:     9 MVDEDAADLQFPKEFENAETLLISEVHMLLDHRKRQNESADEEQEFSEVFMKTYAYTDSF 68

Query:   136 RKFKNRETITSVRNLLTQKKLHKFELAAIANLCPETPEEAKALIPSLECRFEEEELRQIL 195
             RKFKN+ETI S R+LL QKKLHKFELAA+ NLCPE PEEAKALIPSLE RFE+EELRQIL
Sbjct:    69 RKFKNKETIMSARSLLMQKKLHKFELAALGNLCPEAPEEAKALIPSLEGRFEDEELRQIL 128

Query:   196 DDIQTKRSLQY 206
             DDI TKRSLQY
Sbjct:   129 DDIGTKRSLQY 139

GO:0003899 "DNA-directed RNA polymerase activity" evidence=ISS;IDA

GO:0005665 "DNA-directed RNA polymerase II, core complex" evidence=ISS;IDA

GO:0006366 "transcription from RNA polymerase II promoter" evidence=ISS;IDA

GO:0016591 "DNA-directed RNA polymerase II, holoenzyme" evidence=ISS

GO:0005700 "polytene chromosome" evidence=IDA

GO:0005634 "nucleus" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

GO:0000166 "nucleotide binding" evidence=IEA

GO:0008283 "cell proliferation" evidence=IDA

GO:0043966 "histone H3 acetylation" evidence=IDA

GO:0043967 "histone H4 acetylation" evidence=IDA

GO:0003682 "chromatin binding" evidence=IDA

GO:0005671 "Ada2/Gcn5/Ada3 transcription activator complex" evidence=IDA

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

GO:0022008 "neurogenesis" evidence=IMP

ZFIN|ZDB-GENE-040714-2 polr2d "polymerase (RNA) II (DNA directed) polypeptide D" [Danio rerio (taxid:7955)]

 Score = 479 (173.7 bits), Expect = 1.3e-45, P = 1.3e-45
 Identities = 97/130 (74%), Positives = 104/130 (80%)

Query:    77 VEEDAGDLQFPKEFENAETLLISEVHMLLQHRKTXXXXXXXXXXFSEVFQKTLTYTERFR 136
             VEEDA  L FPKEFENAETLL SEVHMLL+HRK            SEVF KTL YT RF 
Sbjct:    16 VEEDASQLMFPKEFENAETLLNSEVHMLLEHRKQQNESAEDEQELSEVFMKTLNYTARFS 75

Query:   137 KFKNRETITSVRNLLTQKKLHKFELAAIANLCPETPEEAKALIPSLECRFEEEELRQILD 196
             +FKNRETI SVR+LL QKKLHKFELA++ANLCPE  EEAKALIPSLE RFE+EEL+QILD
Sbjct:    76 RFKNRETIASVRSLLLQKKLHKFELASLANLCPEAAEEAKALIPSLEGRFEDEELQQILD 135

Query:   197 DIQTKRSLQY 206
             DIQTKRS QY
Sbjct:   136 DIQTKRSFQY 145

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003899 "DNA-directed RNA polymerase activity" evidence=IEA

GO:0044237 "cellular metabolic process" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0003824 "catalytic activity" evidence=IEA

UNIPROTKB|F1P2S1 POLR2D "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 475 (172.3 bits), Expect = 3.4e-45, P = 3.4e-45
 Identities = 97/130 (74%), Positives = 103/130 (79%)

Query:    77 VEEDAGDLQFPKEFENAETLLISEVHMLLQHRKTXXXXXXXXXXFSEVFQKTLTYTERFR 136
             VEEDA  L FPKEFE AETLL SEVHMLL+HRK            SEVF KTL YT RF 
Sbjct:    18 VEEDASQLVFPKEFETAETLLNSEVHMLLEHRKQQNESAEDEQELSEVFMKTLNYTARFS 77

Query:   137 KFKNRETITSVRNLLTQKKLHKFELAAIANLCPETPEEAKALIPSLECRFEEEELRQILD 196
             +FKNRETI SVR+LL QKKLHKFELA +ANLCPET EEAKALIPSLE RFE+EEL+QILD
Sbjct:    78 RFKNRETIASVRSLLLQKKLHKFELACLANLCPETAEEAKALIPSLEGRFEDEELQQILD 137

Query:   197 DIQTKRSLQY 206
             DIQTKRS QY
Sbjct:   138 DIQTKRSFQY 147

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003899 "DNA-directed RNA polymerase activity" evidence=IEA

GO:0004672 "protein kinase activity" evidence=IEA

GO:0005665 "DNA-directed RNA polymerase II, core complex" evidence=IEA

GO:0006366 "transcription from RNA polymerase II promoter" evidence=IEA

UNIPROTKB|Q1JQ91 POLR2D "Polymerase (RNA) II (DNA directed) polypeptide D" [Bos taurus (taxid:9913)]

 Score = 471 (170.9 bits), Expect = 9.1e-45, P = 9.1e-45
 Identities = 96/130 (73%), Positives = 103/130 (79%)

Query:    77 VEEDAGDLQFPKEFENAETLLISEVHMLLQHRKTXXXXXXXXXXFSEVFQKTLTYTERFR 136
             VEEDA  L FPKEFE AETLL SEVHMLL+HRK            SEVF KTL YT RF 
Sbjct:    13 VEEDASQLIFPKEFETAETLLNSEVHMLLEHRKQQNESAEDEQELSEVFMKTLNYTARFS 72

Query:   137 KFKNRETITSVRNLLTQKKLHKFELAAIANLCPETPEEAKALIPSLECRFEEEELRQILD 196
             +FKNRETI SVR+LL QKKLHKFELA +ANLCPET EE+KALIPSLE RFE+EEL+QILD
Sbjct:    73 RFKNRETIASVRSLLLQKKLHKFELACLANLCPETAEESKALIPSLEGRFEDEELQQILD 132

Query:   197 DIQTKRSLQY 206
             DIQTKRS QY
Sbjct:   133 DIQTKRSFQY 142

GO:0006366 "transcription from RNA polymerase II promoter" evidence=IEA

GO:0005665 "DNA-directed RNA polymerase II, core complex" evidence=IEA

GO:0004672 "protein kinase activity" evidence=IEA

GO:0003899 "DNA-directed RNA polymerase activity" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|E2RPH1 POLR2D "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 471 (170.9 bits), Expect = 9.1e-45, P = 9.1e-45
 Identities = 96/130 (73%), Positives = 103/130 (79%)

Query:    77 VEEDAGDLQFPKEFENAETLLISEVHMLLQHRKTXXXXXXXXXXFSEVFQKTLTYTERFR 136
             VEEDA  L FPKEFE AETLL SEVHMLL+HRK            SEVF KTL YT RF 
Sbjct:    13 VEEDASQLIFPKEFETAETLLNSEVHMLLEHRKQQNESAEDEQELSEVFMKTLNYTARFS 72

Query:   137 KFKNRETITSVRNLLTQKKLHKFELAAIANLCPETPEEAKALIPSLECRFEEEELRQILD 196
             +FKNRETI SVR+LL QKKLHKFELA +ANLCPET EE+KALIPSLE RFE+EEL+QILD
Sbjct:    73 RFKNRETIASVRSLLLQKKLHKFELACLANLCPETAEESKALIPSLEGRFEDEELQQILD 132

Query:   197 DIQTKRSLQY 206
             DIQTKRS QY
Sbjct:   133 DIQTKRSFQY 142

GO:0006366 "transcription from RNA polymerase II promoter" evidence=IEA

GO:0005665 "DNA-directed RNA polymerase II, core complex" evidence=IEA

GO:0004672 "protein kinase activity" evidence=IEA

GO:0003899 "DNA-directed RNA polymerase activity" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|O15514 POLR2D "DNA-directed RNA polymerase II subunit RPB4" [Homo sapiens (taxid:9606)]

 Score = 471 (170.9 bits), Expect = 9.1e-45, P = 9.1e-45
 Identities = 96/130 (73%), Positives = 103/130 (79%)

Query:    77 VEEDAGDLQFPKEFENAETLLISEVHMLLQHRKTXXXXXXXXXXFSEVFQKTLTYTERFR 136
             VEEDA  L FPKEFE AETLL SEVHMLL+HRK            SEVF KTL YT RF 
Sbjct:    13 VEEDASQLIFPKEFETAETLLNSEVHMLLEHRKQQNESAEDEQELSEVFMKTLNYTARFS 72

Query:   137 KFKNRETITSVRNLLTQKKLHKFELAAIANLCPETPEEAKALIPSLECRFEEEELRQILD 196
             +FKNRETI SVR+LL QKKLHKFELA +ANLCPET EE+KALIPSLE RFE+EEL+QILD
Sbjct:    73 RFKNRETIASVRSLLLQKKLHKFELACLANLCPETAEESKALIPSLEGRFEDEELQQILD 132

Query:   197 DIQTKRSLQY 206
             DIQTKRS QY
Sbjct:   133 DIQTKRSFQY 142

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003899 "DNA-directed RNA polymerase activity" evidence=IMP

GO:0005665 "DNA-directed RNA polymerase II, core complex" evidence=IDA

GO:0006366 "transcription from RNA polymerase II promoter" evidence=IDA;IMP;TAS

GO:0004672 "protein kinase activity" evidence=IDA

GO:0005634 "nucleus" evidence=IDA

GO:0000398 "mRNA splicing, via spliceosome" evidence=TAS

GO:0005654 "nucleoplasm" evidence=TAS

GO:0006281 "DNA repair" evidence=TAS

GO:0006283 "transcription-coupled nucleotide-excision repair" evidence=TAS

GO:0006289 "nucleotide-excision repair" evidence=TAS

GO:0006367 "transcription initiation from RNA polymerase II promoter" evidence=TAS

GO:0006368 "transcription elongation from RNA polymerase II promoter" evidence=TAS

GO:0006370 "7-methylguanosine mRNA capping" evidence=TAS

GO:0008380 "RNA splicing" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

GO:0016032 "viral reproduction" evidence=TAS

GO:0050434 "positive regulation of viral transcription" evidence=TAS

GO:0006468 "protein phosphorylation" evidence=IDA

MGI|MGI:1916491 Polr2d "polymerase (RNA) II (DNA directed) polypeptide D" [Mus musculus (taxid:10090)]

 Score = 471 (170.9 bits), Expect = 9.1e-45, P = 9.1e-45
 Identities = 96/130 (73%), Positives = 103/130 (79%)

Query:    77 VEEDAGDLQFPKEFENAETLLISEVHMLLQHRKTXXXXXXXXXXFSEVFQKTLTYTERFR 136
             VEEDA  L FPKEFE AETLL SEVHMLL+HRK            SEVF KTL YT RF 
Sbjct:    13 VEEDASQLIFPKEFETAETLLNSEVHMLLEHRKQQNESAEDEQELSEVFMKTLNYTARFS 72

Query:   137 KFKNRETITSVRNLLTQKKLHKFELAAIANLCPETPEEAKALIPSLECRFEEEELRQILD 196
             +FKNRETI SVR+LL QKKLHKFELA +ANLCPET EE+KALIPSLE RFE+EEL+QILD
Sbjct:    73 RFKNRETIASVRSLLLQKKLHKFELACLANLCPETAEESKALIPSLEGRFEDEELQQILD 132

Query:   197 DIQTKRSLQY 206
             DIQTKRS QY
Sbjct:   133 DIQTKRSFQY 142

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003824 "catalytic activity" evidence=IEA

GO:0003899 "DNA-directed RNA polymerase activity" evidence=ISO

GO:0005634 "nucleus" evidence=ISO

GO:0005665 "DNA-directed RNA polymerase II, core complex" evidence=ISO

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0006366 "transcription from RNA polymerase II promoter" evidence=ISO

GO:0006468 "protein phosphorylation" evidence=ISO

GO:0044237 "cellular metabolic process" evidence=IEA

RGD|1308565 Polr2d "polymerase (RNA) II (DNA directed) polypeptide D" [Rattus norvegicus (taxid:10116)]

 Score = 471 (170.9 bits), Expect = 9.1e-45, P = 9.1e-45
 Identities = 96/130 (73%), Positives = 103/130 (79%)

Query:    77 VEEDAGDLQFPKEFENAETLLISEVHMLLQHRKTXXXXXXXXXXFSEVFQKTLTYTERFR 136
             VEEDA  L FPKEFE AETLL SEVHMLL+HRK            SEVF KTL YT RF 
Sbjct:    13 VEEDASQLIFPKEFETAETLLNSEVHMLLEHRKQQNESAEDEQELSEVFMKTLNYTARFS 72

Query:   137 KFKNRETITSVRNLLTQKKLHKFELAAIANLCPETPEEAKALIPSLECRFEEEELRQILD 196
             +FKNRETI SVR+LL QKKLHKFELA +ANLCPET EE+KALIPSLE RFE+EEL+QILD
Sbjct:    73 RFKNRETIASVRSLLLQKKLHKFELACLANLCPETAEESKALIPSLEGRFEDEELQQILD 132

Query:   197 DIQTKRSLQY 206
             DIQTKRS QY
Sbjct:   133 DIQTKRSFQY 142

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003899 "DNA-directed RNA polymerase activity" evidence=IEA;ISO

GO:0004672 "protein kinase activity" evidence=IEA;ISO

GO:0005634 "nucleus" evidence=ISO

GO:0005665 "DNA-directed RNA polymerase II, core complex" evidence=IEA;ISO

GO:0006366 "transcription from RNA polymerase II promoter" evidence=IEA;ISO

GO:0006468 "protein phosphorylation" evidence=ISO

UNIPROTKB|E9PB93 POLR2D "DNA-directed RNA polymerase II subunit RPB4" [Homo sapiens (taxid:9606)]

 Score = 372 (136.0 bits), Expect = 2.8e-34, P = 2.8e-34
 Identities = 75/104 (72%), Positives = 82/104 (78%)

Query:   103 MLLQHRKTXXXXXXXXXXFSEVFQKTLTYTERFRKFKNRETITSVRNLLTQKKLHKFELA 162
             MLL+HRK            SEVF KTL YT RF +FKNRETI SVR+LL QKKLHKFELA
Sbjct:     1 MLLEHRKQQNESAEDEQELSEVFMKTLNYTARFSRFKNRETIASVRSLLLQKKLHKFELA 60

Query:   163 AIANLCPETPEEAKALIPSLECRFEEEELRQILDDIQTKRSLQY 206
              +ANLCPET EE+KALIPSLE RFE+EEL+QILDDIQTKRS QY
Sbjct:    61 CLANLCPETAEESKALIPSLEGRFEDEELQQILDDIQTKRSFQY 104

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003899 "DNA-directed RNA polymerase activity" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

WB|WBGene00018391 rpb-4 [Caenorhabditis elegans (taxid:6239)]

 Score = 362 (132.5 bits), Expect = 3.2e-33, P = 3.2e-33
 Identities = 72/134 (53%), Positives = 93/134 (69%)

Query:    74 DQVVEEDAGDLQFPKEFENA--ETLLISEVHMLLQHRKTXXXXXXXXXXFSEVFQKTLTY 131
             D  VEEDA + +FPKEFE    + LL +EV++LL+HR+            SEVF KTL Y
Sbjct:    11 DGQVEEDAAECKFPKEFETTTCDALLTAEVYLLLEHRRQSSESKDEIEEMSEVFIKTLNY 70

Query:   132 TERFRKFKNRETITSVRNLLTQKKLHKFELAAIANLCPETPEEAKALIPSLECRFEEEEL 191
               R  +FKNRETI +VR + ++K LHKFE+A IANLCPE  EEAKAL+PSLE + EE EL
Sbjct:    71 ARRMSRFKNRETIRAVRAIFSEKHLHKFEVAQIANLCPENAEEAKALVPSLENKIEESEL 130

Query:   192 RQILDDIQTKRSLQ 205
              ++L D+Q+KR+ Q
Sbjct:   131 EEVLKDLQSKRTFQ 144

GO:0003899 "DNA-directed RNA polymerase activity" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

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

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q54S04	RPB4_DICDI	No assigned EC number	0.4071	0.6019	0.8	yes	N/A
O15514	RPB4_HUMAN	No assigned EC number	0.8	0.6310	0.9154	yes	N/A
Q9D7M8	RPB4_MOUSE	No assigned EC number	0.8	0.6310	0.9154	yes	N/A
Q9VEA5	RPB4_DROME	2, ., 7, ., 7, ., 6	0.8244	0.6359	0.9424	yes	N/A
O74825	RPB4_SCHPO	No assigned EC number	0.3587	0.6262	0.9555	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	206
smart00657	118	smart00657, RPOL4c, DNA-directed RNA-polymerase II	2e-34
pfam03874	110	pfam03874, RNA_pol_Rpb4, RNA polymerase Rpb4	4e-29
COG5250	138	COG5250, RPB4, RNA polymerase II, fourth largest s	2e-24
PRK14981	112	PRK14981, PRK14981, DNA-directed RNA polymerase su	6e-08
COG1460	114	COG1460, COG1460, Uncharacterized protein conserve	3e-04

>gnl|CDD|128904 smart00657, RPOL4c, DNA-directed RNA-polymerase II subunit

 Score =  118 bits (297), Expect = 2e-34
 Identities = 60/118 (50%), Positives = 80/118 (67%)

Query: 88  KEFENAETLLISEVHMLLQHRKTQNENAEEEQEFSEVFQKTLTYTERFRKFKNRETITSV 147
            EF+NA  L  SEV +LL+ ++   E+ EE+Q  S V +KTL Y  +F +FKNRE + +V
Sbjct: 1   PEFKNATCLTNSEVQLLLELKRQSKESEEEQQPLSTVMKKTLKYLSKFARFKNREIVRAV 60

Query: 148 RNLLTQKKLHKFELAAIANLCPETPEEAKALIPSLECRFEEEELRQILDDIQTKRSLQ 205
           R LL  KKLHKFE+A + NL PET EEA+ LIPSLE R +EEEL ++LDD+ +     
Sbjct: 61  RTLLKSKKLHKFEIAQLGNLRPETAEEAQLLIPSLEERIDEEELEELLDDLSSLLPFY 118

Length = 118

>gnl|CDD|217775 pfam03874, RNA_pol_Rpb4, RNA polymerase Rpb4

 Score =  104 bits (261), Expect = 4e-29
 Identities = 41/109 (37%), Positives = 62/109 (56%), Gaps = 2/109 (1%)

Query: 96  LLISEVHMLLQHR--KTQNENAEEEQEFSEVFQKTLTYTERFRKFKNRETITSVRNLLTQ 153
           L  SEV  +L+    + + E+   E+  + + +KTL Y  +F + KN E+   +   L +
Sbjct: 2   LTNSEVLEILKKELEERRRESRYVEENLNTILRKTLEYLNKFSRLKNPESARELVEELKE 61

Query: 154 KKLHKFELAAIANLCPETPEEAKALIPSLECRFEEEELRQILDDIQTKR 202
            +L KFE   I NL PET +E +A+I SLE RF EE+L +ILD +   R
Sbjct: 62  FELTKFEALQIVNLLPETADELRAIIESLESRFSEEQLEEILDILSKYR 110

This family includes the Rpb4 protein. This family also includes C17 (aka CGRP-RCP) is an essential subunit of RNA polymerase III. C17 forms a subcomplex with C25 which is likely to be the counterpart of subcomplex Rpb4/7 in Pol II. Length = 110

>gnl|CDD|227575 COG5250, RPB4, RNA polymerase II, fourth largest subunit [Transcription]

 Score = 93.1 bits (231), Expect = 2e-24
 Identities = 45/132 (34%), Positives = 74/132 (56%), Gaps = 4/132 (3%)

Query: 78  EEDAGDLQFPKEFENAETLLISEVHMLLQHRKTQNENAEEEQEF----SEVFQKTLTYTE 133
           EEDA  L+   EFEN + L++SE   L++ +  +        EF     +VF+ TL Y +
Sbjct: 7   EEDAAQLKLGPEFENEDMLMLSEARYLIEGQLERRRRETNGAEFRSNDVKVFKSTLGYLD 66

Query: 134 RFRKFKNRETITSVRNLLTQKKLHKFELAAIANLCPETPEEAKALIPSLECRFEEEELRQ 193
            F +FK++E   ++R  L+    H+FE+A + +L  ++ EEAK LIPSL  + ++  L+ 
Sbjct: 67  DFCRFKDKEVAEALRTTLSGLGFHEFEIAQLGSLFCQSAEEAKTLIPSLGNKIDDAILQA 126

Query: 194 ILDDIQTKRSLQ 205
           IL ++   R  Q
Sbjct: 127 ILKELSLLRKFQ 138

Length = 138

>gnl|CDD|184943 PRK14981, PRK14981, DNA-directed RNA polymerase subunit F; Provisional

 Score = 48.7 bits (117), Expect = 6e-08
 Identities = 33/110 (30%), Positives = 51/110 (46%), Gaps = 9/110 (8%)

Query: 88  KEFENAETLLISEVHMLLQHRKTQNENAEEEQEFSEVFQKTLTYTERFRKFKNRETITSV 147
           K+    E + I+E   +L          EEE+E S   ++TL Y  RF K  + E    +
Sbjct: 4   KKILEEEYITIAEAKEIL-------SEIEEERELSYELRRTLDYLNRFSKL-DPEDAEEL 55

Query: 148 RNLLTQKKLHKFELAA-IANLCPETPEEAKALIPSLECRFEEEELRQILD 196
              L + +  K + A  IA++ PET +E +A+          EEL +ILD
Sbjct: 56  VEELLELEKMKEKTAVKIADILPETRDELRAIFAKERYTLSPEELDEILD 105

Length = 112

>gnl|CDD|224377 COG1460, COG1460, Uncharacterized protein conserved in archaea [Function unknown]

 Score = 38.5 bits (90), Expect = 3e-04
 Identities = 24/84 (28%), Positives = 42/84 (50%)

Query: 113 ENAEEEQEFSEVFQKTLTYTERFRKFKNRETITSVRNLLTQKKLHKFELAAIANLCPETP 172
              E E+E +   ++ L Y E+F K    +    V  LL+  K+ +     IA++ P TP
Sbjct: 23  SKVEREEELTYEQREALEYAEKFAKLDPEKARELVEELLSIVKMSEKIAVKIADIMPRTP 82

Query: 173 EEAKALIPSLECRFEEEELRQILD 196
           +E ++++        +EEL +ILD
Sbjct: 83  DELRSILAKERVMLSDEELDKILD 106

Length = 114

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	206
KOG2351|consensus	134		100.0
COG5250	138	RPB4 RNA polymerase II, fourth largest subunit [Tr	99.97
smart00657	118	RPOL4c DNA-directed RNA-polymerase II subunit.	99.96
PRK14981	112	DNA-directed RNA polymerase subunit F; Provisional	99.96
PF03874	117	RNA_pol_Rpb4: RNA polymerase Rpb4; InterPro: IPR00	99.92
COG1460	114	Uncharacterized protein conserved in archaea [Func	99.84
KOG4168|consensus	149		98.71

>KOG2351|consensus

Probab=100.00  E-value=2.8e-40  Score=261.72  Aligned_cols=132  Identities=53%  Similarity=0.875  Sum_probs=126.8

Q ss_pred             CcccccccccCCCcccccccccccHHHHHHHHHHHHhhch-hhhhhhhhHHHHHHHHHHHHhcccCCChHHHHHHHHHHh
Q psy14375         74 DQVVEEDAGDLQFPKEFENAETLLISEVHMLLQHRKTQNE-NAEEEQEFSEVFQKTLTYTERFRKFKNRETITSVRNLLT  152 (206)
Q Consensus        74 ~~~~eEda~~LklG~eF~~a~~LT~sEV~~IL~~~~~~~~-~~d~~~els~v~~kTleYl~rFsk~~~~ea~e~vrelL~  152 (206)
                      .+++||||++|+||++|+.+.||++|||+.||+++..+.+ +.|++.++++||.+|+.|+++|++|++++++.+||.+|.
T Consensus         2 ~g~~EEdAa~lk~g~EFe~~~~L~~sEa~lllE~~~~q~~rs~d~~~~~s~Vf~kTl~Y~~~FsRfKn~etv~avr~iLs   81 (134)
T KOG2351|consen    2 RGEEEEDAAELKLGKEFETADALMLSEARLLLEHRLEQRRRSEDDESEMSDVFKKTLQYLDRFSRFKNRETVRAVRTILS   81 (134)
T ss_pred             cchhhccHHhccccHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccchHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHh
Confidence            4678999999999999999999999999999999988765 467889999999999999999999999999999999999


Q ss_pred             cCCCChhhhHhhcccCCCCHHHHhhhhcccccCCCHHHHHHHHHHHHHhhhcc
Q psy14375        153 QKKLHKFELAAIANLCPETPEEAKALIPSLECRFEEEELRQILDDIQTKRSLQ  205 (206)
Q Consensus       153 ~~~L~kfEia~IaNL~P~t~eEaraLIPSLe~r~sdeeLe~ILd~L~k~R~fq  205 (206)
                      ..+||+||+|+|+||||+|+||||+|||||+.+++|++|++||+.|+..|+||
T Consensus        82 ~~~lhkFE~A~lgnLcpetaEEAkaLvPSL~nkidD~~le~iL~dls~lr~fq  134 (134)
T KOG2351|consen   82 GKGLHKFEVAQLGNLCPETAEEAKALVPSLENKIDDDELEQILKDLSTLRTFQ  134 (134)
T ss_pred             hCCcchhhHHHHhccCcccHHHHHHhccccccccCHHHHHHHHHHHHHHHhcC
Confidence            99999999999999999999999999999999999999999999999999998

>COG5250 RPB4 RNA polymerase II, fourth largest subunit [Transcription]

Probab=99.97  E-value=3.2e-31  Score=208.92  Aligned_cols=131  Identities=34%  Similarity=0.580  Sum_probs=118.8

Q ss_pred             cccccccccCCCcccccccccccHHHHHHHHHHHHhhchhhh--hhhhhHH--HHHHHHHHHHhcccCCChHHHHHHHHH
Q psy14375         75 QVVEEDAGDLQFPKEFENAETLLISEVHMLLQHRKTQNENAE--EEQEFSE--VFQKTLTYTERFRKFKNRETITSVRNL  150 (206)
Q Consensus        75 ~~~eEda~~LklG~eF~~a~~LT~sEV~~IL~~~~~~~~~~d--~~~els~--v~~kTleYl~rFsk~~~~ea~e~vrel  150 (206)
                      +.+||||++||||++|+|...|+++|++.+++....++.++.  .+-+.++  ++++|+.|++.|++|++.+++.+++.+
T Consensus         4 ~~~ee~aa~lklg~efe~ed~l~lsEAr~lie~~l~~rrretn~~e~~s~dvk~~k~T~~Yl~~F~Rfkd~e~~~a~~~~   83 (138)
T COG5250           4 AIFEEDAAQLKLGPEFENEDMLMLSEARYLIEGQLERRRRETNGAEFRSNDVKVFKSTLGYLDDFCRFKDKEVAEALRTT   83 (138)
T ss_pred             hHhhhhHHHhhcCccccchHHHHHHHHHHHHHHHHHHHHHhcccccccchhHHHHHHHHHHHHHHHHhhhHHHHHHHHHH
Confidence            467899999999999999999999999999998876654321  1233344  599999999999999999999999999


Q ss_pred             HhcCCCChhhhHhhcccCCCCHHHHhhhhcccccCCCHHHHHHHHHHHHHhhhcc
Q psy14375        151 LTQKKLHKFELAAIANLCPETPEEAKALIPSLECRFEEEELRQILDDIQTKRSLQ  205 (206)
Q Consensus       151 L~~~~L~kfEia~IaNL~P~t~eEaraLIPSLe~r~sdeeLe~ILd~L~k~R~fq  205 (206)
                      |...|+|+||+||+++|||+++||||+|||||..+++|..++.||++++.+|+||
T Consensus        84 L~~~gfh~fEiAqlGsL~c~saeEAktLiPSL~nkidD~~lq~ilkels~l~~~~  138 (138)
T COG5250          84 LSGLGFHEFEIAQLGSLFCQSAEEAKTLIPSLGNKIDDAILQAILKELSLLRKFQ  138 (138)
T ss_pred             HccCCcchhhHHHhhccccccHHHHHhhcccccccccHHHHHHHHHHHHHHHhhC
Confidence            9999999999999999999999999999999999999999999999999999998

>smart00657 RPOL4c DNA-directed RNA-polymerase II subunit

Probab=99.96  E-value=6.7e-30  Score=200.87  Aligned_cols=118  Identities=51%  Similarity=0.774  Sum_probs=108.5

Q ss_pred             ccccccccccHHHHHHHHHHHHhhchhhhhhhhhHHHHHHHHHHHHhcccCCChHHHHHHHHHHhcCCCChhhhHhhccc
Q psy14375         88 KEFENAETLLISEVHMLLQHRKTQNENAEEEQEFSEVFQKTLTYTERFRKFKNRETITSVRNLLTQKKLHKFELAAIANL  167 (206)
Q Consensus        88 ~eF~~a~~LT~sEV~~IL~~~~~~~~~~d~~~els~v~~kTleYl~rFsk~~~~ea~e~vrelL~~~~L~kfEia~IaNL  167 (206)
                      ++|.|++||||+||+.||+.++......++..+++.++++|++|+++|+++++++++..++++|..++|++||++||+||
T Consensus         1 ~~f~~a~~L~n~Ev~~ll~~k~~~~~~~~~~~~l~~v~~~tl~Yl~~~~~~~~~e~i~~~~~~L~~~~L~k~E~~~i~Nl   80 (118)
T smart00657        1 PEFKNATCLTNSEVQLLLELKRQSKESEEEQQPLSTVMKKTLKYLSKFARFKNREIVRAVRTLLKSKKLHKFEIAQLGNL   80 (118)
T ss_pred             CCccchhHhHHHHHHHHHHHHHHhhccccccchHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCCHHHHHHHhCC
Confidence            48999999999999999997655433333456789999999999999999999999999999999999999999999999


Q ss_pred             CCCCHHHHhhhhcccccCCCHHHHHHHHHHHHHhhhcc
Q psy14375        168 CPETPEEAKALIPSLECRFEEEELRQILDDIQTKRSLQ  205 (206)
Q Consensus       168 ~P~t~eEaraLIPSLe~r~sdeeLe~ILd~L~k~R~fq  205 (206)
                      ||+|++||++|||+++.||+++++++||++|+++|+|+
T Consensus        81 ~P~s~~E~~~lI~sl~~r~~ee~l~~iL~~i~~~~~~~  118 (118)
T smart00657       81 RPETAEEAQLLIPSLEERIDEEELEELLDDLSSLLPFY  118 (118)
T ss_pred             CCCCHHHHHHHhhhhhccCCHHHHHHHHHHHHHhcCCC
Confidence            99999999999999998999999999999999999985

>PRK14981 DNA-directed RNA polymerase subunit F; Provisional

Probab=99.96  E-value=2.3e-29  Score=196.89  Aligned_cols=112  Identities=28%  Similarity=0.418  Sum_probs=105.8

Q ss_pred             CCcccccccccccHHHHHHHHHHHHhhchhhhhhhhhHHHHHHHHHHHHhcccCCChHHHHHHHHHHhcCCCChhhhHhh
Q psy14375         85 QFPKEFENAETLLISEVHMLLQHRKTQNENAEEEQEFSEVFQKTLTYTERFRKFKNRETITSVRNLLTQKKLHKFELAAI  164 (206)
Q Consensus        85 klG~eF~~a~~LT~sEV~~IL~~~~~~~~~~d~~~els~v~~kTleYl~rFsk~~~~ea~e~vrelL~~~~L~kfEia~I  164 (206)
                      ++|++..+.+|||++||+.||+++...       .++++++++|++|+++|++++++++.+++++++..++|++|++|+|
T Consensus         1 mi~k~i~~e~~lt~sEa~~iL~~~~~~-------~els~~~~ktl~y~~kFsk~~~e~a~elve~L~~~~~l~e~~a~~I   73 (112)
T PRK14981          1 MIGKKILEEEYITIAEAKEILSEIEEE-------RELSYELRRTLDYLNRFSKLDPEDAEELVEELLELEKMKEKTAVKI   73 (112)
T ss_pred             CchhhhhhcccccHHHHHHHHHHHHhc-------cchhHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHccCCCHHHHHHH
Confidence            578899999999999999999998764       2789999999999999999999999999999999888999999999


Q ss_pred             cccCCCCHHHHhhhhcccccCCCHHHHHHHHHHHHHhhh
Q psy14375        165 ANLCPETPEEAKALIPSLECRFEEEELRQILDDIQTKRS  203 (206)
Q Consensus       165 aNL~P~t~eEaraLIPSLe~r~sdeeLe~ILd~L~k~R~  203 (206)
                      +||||+|+||||+|||+++.++++++|++||++|++||.
T Consensus        74 ~nL~P~~~dElrai~~~~~~~~~~e~l~~ILd~l~k~~~  112 (112)
T PRK14981         74 ADILPETRDELRAIFAKERYTLSPEELDEILDIVKKYRE  112 (112)
T ss_pred             HhcCCCCHHHHHHHHHHhccCCCHHHHHHHHHHHHHhhC
Confidence            999999999999999999999999999999999999984

>PF03874 RNA_pol_Rpb4: RNA polymerase Rpb4; InterPro: IPR005574 The eukaryotic RNA polymerase subunits RPB4 and RPB7 form a heterodimer that reversibly associates with the RNA polymerase II core

Probab=99.92  E-value=2.7e-25  Score=172.38  Aligned_cols=108  Identities=39%  Similarity=0.584  Sum_probs=94.0

Q ss_pred             cccHHHHHHHHHHHHhhchh---------hhhhhhhHHHHHHHHHHHHhcccCCChHHHHHHHHHHhcCCCChhhhHhhc
Q psy14375         95 TLLISEVHMLLQHRKTQNEN---------AEEEQEFSEVFQKTLTYTERFRKFKNRETITSVRNLLTQKKLHKFELAAIA  165 (206)
Q Consensus        95 ~LT~sEV~~IL~~~~~~~~~---------~d~~~els~v~~kTleYl~rFsk~~~~ea~e~vrelL~~~~L~kfEia~Ia  165 (206)
                      ||||+||..+|+++......         .....+++.++++|++|+++|+++.+++++..+++.|..++|+++|++||+
T Consensus         1 ~Lsn~EV~~iL~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Yl~~~~~~~~~e~~~~l~~~L~~~~L~~~E~~qi~   80 (117)
T PF03874_consen    1 LLSNYEVLQILEKRREEQKNKSKKKQKNKEDPPENLNTIQYKTLEYLEKFSKFQNPESIKELREELKKFGLTEFEILQII   80 (117)
T ss_dssp             EE-HHHHHHHHHHHHHHHHCHCHHHHHHHHHCSSCHCHHHHHHHHHHHHH-SSSSHHHHHHHHHHHTTSTS-HHHHHHHH
T ss_pred             CCcHHHHHHHHHHHHHHHHhhhccccccccccccchHHHHHHHHHHHHccccCCCHHHHHHHHHHHhcccCCHHHHHHHh
Confidence            79999999999966554322         234577899999999999999999999999999999999999999999999


Q ss_pred             ccCCCCHHHHhhhhcccccCCCHHHHHHHHHHHHHhh
Q psy14375        166 NLCPETPEEAKALIPSLECRFEEEELRQILDDIQTKR  202 (206)
Q Consensus       166 NL~P~t~eEaraLIPSLe~r~sdeeLe~ILd~L~k~R  202 (206)
                      ||||+|++|+++|||+++.||++++|++||++|++||
T Consensus        81 Nl~P~~~~El~~ii~~~~~r~~ee~l~~iL~~v~~~~  117 (117)
T PF03874_consen   81 NLRPTTAVELRAIIESLESRFSEEDLEEILDLVSKYR  117 (117)
T ss_dssp             HH--SSHHHHHHHSTTGTTTSTHHHHHHHHHHHHHHT
T ss_pred             cCCCCCHHHHHHHHHHhccCCCHHHHHHHHHHHHHhC
Confidence            9999999999999999999999999999999999997

Archaeal cells contain a single RNAP made up of about 12 subunits, displaying considerable homology to the eukaryotic RNAPII subunits. The RPB4 and RPB7 homologs are called subunits F and E, respectively, and have been shown to form a stable heterodimer. While the RPB7 homologue is reasonably well conserved, the similarity between the eukaryotic RPB4 and the archaeal F subunit is barely detectable [].; GO: 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3AYH_A 3H3V_E 4A3C_D 3PO3_D 3HOX_D 2R92_D 3HOU_D 1Y77_D 2R7Z_D 3QT1_D ....

>COG1460 Uncharacterized protein conserved in archaea [Function unknown]

Probab=99.84  E-value=1.3e-20  Score=147.74  Aligned_cols=112  Identities=26%  Similarity=0.410  Sum_probs=103.0

Q ss_pred             CCcccccccccccHHHHHHHHHHHHhhchhhhhhhhhHHHHHHHHHHHHhcccCCChHHHHHHHHHHhcCCCChhhhHhh
Q psy14375         85 QFPKEFENAETLLISEVHMLLQHRKTQNENAEEEQEFSEVFQKTLTYTERFRKFKNRETITSVRNLLTQKKLHKFELAAI  164 (206)
Q Consensus        85 klG~eF~~a~~LT~sEV~~IL~~~~~~~~~~d~~~els~v~~kTleYl~rFsk~~~~ea~e~vrelL~~~~L~kfEia~I  164 (206)
                      ++|++.-+.+++|++||+.||.++.       ++.++++.+++||+|+++|+++.++.+.+.+.++++..++.+.-++.|
T Consensus         2 mi~k~~le~~yiti~Eak~il~~~~-------~~~eL~y~~~~al~y~~kFakldpe~a~e~veEL~~i~~~~e~~avkI   74 (114)
T COG1460           2 MIGKKILEEKYITISEAKKILSKVE-------REEELTYEQREALEYAEKFAKLDPEKARELVEELLSIVKMSEKIAVKI   74 (114)
T ss_pred             chHHHHhhccCccHHHHHHHHHHhc-------ccccchHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhhccccHHHHHHH
Confidence            5788888899999999999999982       347789999999999999999999999999999999888766667779


Q ss_pred             cccCCCCHHHHhhhhcccccCCCHHHHHHHHHHHHHhhh
Q psy14375        165 ANLCPETPEEAKALIPSLECRFEEEELRQILDDIQTKRS  203 (206)
Q Consensus       165 aNL~P~t~eEaraLIPSLe~r~sdeeLe~ILd~L~k~R~  203 (206)
                      ++|||+|.+|+|+|+.+.+.++++|++++|||++++||.
T Consensus        75 adI~P~t~~ElRsIla~e~~~~s~E~l~~Ildiv~Ky~~  113 (114)
T COG1460          75 ADIMPRTPDELRSILAKERVMLSDEELDKILDIVDKYRE  113 (114)
T ss_pred             HHhCCCCHHHHHHHHHHccCCCCHHHHHHHHHHHHHHhc
Confidence            999999999999999999999999999999999999985

>KOG4168|consensus

Probab=98.71  E-value=4.4e-08  Score=80.05  Aligned_cols=110  Identities=25%  Similarity=0.346  Sum_probs=86.1

Q ss_pred             ccccccHHHHHHHHHHHHhhc-----hh-hhhhh-----hhHHHHHHHHHHHHhcccCC--ChHHHHHHHHHHhcCCCCh
Q psy14375         92 NAETLLISEVHMLLQHRKTQN-----EN-AEEEQ-----EFSEVFQKTLTYTERFRKFK--NRETITSVRNLLTQKKLHK  158 (206)
Q Consensus        92 ~a~~LT~sEV~~IL~~~~~~~-----~~-~d~~~-----els~v~~kTleYl~rFsk~~--~~ea~e~vrelL~~~~L~k  158 (206)
                      ..-+||+.||...|.+.....     .+ +...+     +++.+.+.|+.|+..-..+.  +++.+-.+---+..++|++
T Consensus         7 r~a~LtnyEVl~fL~el~~~n~~~~k~s~r~~~Q~~~~~~l~ti~~et~kYls~~~n~~~qt~E~i~el~~k~~~fkLtK   86 (149)
T KOG4168|consen    7 RNAALTNYEVLQFLNELECMNEEADKSSHRLGAQNILQNDLPTITYETLKYLSDNKNASTQTNESIIELITKLKSFKLTK   86 (149)
T ss_pred             hHHHhhhHHHHHHHHHhhhhhhhhhhhhhhhhcccccccccchhHHHHHHHHhcCcccccccHHHHHHHHHHhccccchH
Confidence            456899999999999887211     11 11112     37899999999999876333  3444444444556689999


Q ss_pred             hhhHhhcccCCCCHHHHhhhhcccccCC-CHHHHHHHHHHHHHh
Q psy14375        159 FELAAIANLCPETPEEAKALIPSLECRF-EEEELRQILDDIQTK  201 (206)
Q Consensus       159 fEia~IaNL~P~t~eEaraLIPSLe~r~-sdeeLe~ILd~L~k~  201 (206)
                      .|+.+|.|+.|.+.-|+..+|...+.|| ++++|.+++..+.++
T Consensus        87 AE~LqiiN~rPss~vel~~~iE~~eeRf~~ee~i~elv~~i~~~  130 (149)
T KOG4168|consen   87 AEILQIINLRPSSSVELYLIIEEVEERFQDEEDIEELVETISKT  130 (149)
T ss_pred             HHHHHHhccCcchHHHHHHHHHHHHHhccchhcHHHHHHhcccc
Confidence            9999999999999999999999999999 999999999988765

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	206
2c35_A	152	Subunits Rpb4 And Rpb7 Of Human Rna Polymerase Ii L		2e-49
3h0g_D	135	Rna Polymerase Ii From Schizosaccharomyces Pombe Le		1e-14
1y14_A	187	Crystal Structure Of Yeast Subcomplex Of Rpb4 And R		1e-09
1nt9_D	221	Complete 12-Subunit Rna Polymerase Ii Length = 221		2e-09
3qt1_D	219	Rna Polymerase Ii Variant Containing A Chimeric Rpb		2e-09
1pqv_D	221	Rna Polymerase Ii-Tfiis Complex Length = 221		2e-09
1wcm_D	177	Complete 12-Subunit Rna Polymerase Ii At 3.8 Ang Le		2e-09

>pdb|2C35|A Chain A, Subunits Rpb4 And Rpb7 Of Human Rna Polymerase Ii Length = 152

Iteration: 1
 Score =  191 bits (485), Expect = 2e-49,   Method: Compositional matrix adjust.
 Identities = 101/151 (66%), Positives = 110/151 (72%), Gaps = 3/151 (1%)
Query: 59  SDRVSIGYIIMTHVLD---QVVEEDAGDLQFPKEFENAETLLISEVHMLLQHRKTXXXXX 115
           S R S+G  +     D     VEEDA  L FPKEFE AETLL SEVHMLL+HRK      
Sbjct: 2   SRRASVGSQMAAGGSDPRAGDVEEDASQLIFPKEFETAETLLNSEVHMLLEHRKQQNESA 61
Query: 116 XXXXXFSEVFQKTLTYTERFRKFKNRETITSVRNLLTQKKLHKFELAAIANLCPETPEEA 175
                 SEVF KTL YT RF +FKNRETI SVR+LL QKKLHKFELA +ANLCPET EE+
Sbjct: 62  EDEQELSEVFMKTLNYTARFSRFKNRETIASVRSLLLQKKLHKFELACLANLCPETAEES 121
Query: 176 KALIPSLECRFEEEELRQILDDIQTKRSLQY 206
           KALIPSLE RFE+EEL+QILDDIQTKRS QY
Sbjct: 122 KALIPSLEGRFEDEELQQILDDIQTKRSFQY 152

>pdb|3H0G|D Chain D, Rna Polymerase Ii From Schizosaccharomyces Pombe Length = 135

Iteration: 1
 Score = 76.6 bits (187), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 45/131 (34%), Positives = 69/131 (52%), Gaps = 2/131 (1%)
Query: 76  VVEEDAGDLQFPKEFENAETLLISEVHMLLQHRKTXXXXXXXXXX-FSEVFQKTLTYTER 134
           + EEDA  L+   EFEN + L +SE  +L++                ++V +KT+ Y   
Sbjct: 5   IFEEDAAQLKLGPEFENEDMLTVSEAKILIETVLAQRARETNGEIPMTDVMKKTVAYFNV 64
Query: 135 FRKFKNRETITSVRNLLTQKKLHKFELAAIANLCPETPEEAKALIPSLECRFEEEELRQI 194
           F +FK  E   +   +L  +  HKFE A +  LC E  EEA+ LIPSL  + +++ L+ I
Sbjct: 65  FARFKTAEATYACERILGNR-FHKFERAQLGTLCCEDAEEARTLIPSLANKIDDQNLQGI 123
Query: 195 LDDIQTKRSLQ 205
           LD++ T R  Q
Sbjct: 124 LDELSTLRKFQ 134

>pdb|1Y14|A Chain A, Crystal Structure Of Yeast Subcomplex Of Rpb4 And Rpb7 Length = 187

Iteration: 1
 Score = 59.7 bits (143), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 29/80 (36%), Positives = 49/80 (61%)
Query: 125 FQKTLTYTERFRKFKNRETITSVRNLLTQKKLHKFELAAIANLCPETPEEAKALIPSLEC 184
            + T+ Y   F +F+++ET+ +V  LL    LH FE+A + +L  +T +EAK LIPSL  
Sbjct: 107 LKNTMQYLTNFSRFRDQETVGAVIQLLKSTGLHPFEVAQLGSLACDTADEAKTLIPSLNN 166
Query: 185 RFEEEELRQILDDIQTKRSL 204
           +  ++EL +IL ++    +L
Sbjct: 167 KISDDELERILKELSNLETL 186

>pdb|1NT9|D Chain D, Complete 12-Subunit Rna Polymerase Ii Length = 221

Iteration: 1
 Score = 58.9 bits (141), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 29/80 (36%), Positives = 49/80 (61%)
Query: 125 FQKTLTYTERFRKFKNRETITSVRNLLTQKKLHKFELAAIANLCPETPEEAKALIPSLEC 184
            + T+ Y   F +F+++ET+ +V  LL    LH FE+A + +L  +T +EAK LIPSL  
Sbjct: 141 LKNTMQYLTNFSRFRDQETVGAVIQLLKSTGLHPFEVAQLGSLACDTADEAKTLIPSLNN 200
Query: 185 RFEEEELRQILDDIQTKRSL 204
           +  ++EL +IL ++    +L
Sbjct: 201 KISDDELERILKELSNLETL 220

>pdb|3QT1|D Chain D, Rna Polymerase Ii Variant Containing A Chimeric Rpb9-C11 Subunit Length = 219

Iteration: 1
 Score = 58.9 bits (141), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 28/74 (37%), Positives = 47/74 (63%)
Query: 125 FQKTLTYTERFRKFKNRETITSVRNLLTQKKLHKFELAAIANLCPETPEEAKALIPSLEC 184
            + T+ Y   F +F+++ET+ +V  LL    LH FE+A + +L  +T +EAK LIPSL  
Sbjct: 139 LKNTMQYLTNFSRFRDQETVGAVIQLLKSTGLHPFEVAQLGSLACDTADEAKTLIPSLNN 198
Query: 185 RFEEEELRQILDDI 198
           +  ++EL +IL ++
Sbjct: 199 KISDDELERILKEL 212

>pdb|1PQV|D Chain D, Rna Polymerase Ii-Tfiis Complex Length = 221

Iteration: 1
 Score = 58.9 bits (141), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 28/74 (37%), Positives = 47/74 (63%)
Query: 125 FQKTLTYTERFRKFKNRETITSVRNLLTQKKLHKFELAAIANLCPETPEEAKALIPSLEC 184
            + T+ Y   F +F+++ET+ +V  LL    LH FE+A + +L  +T +EAK LIPSL  
Sbjct: 141 LKNTMQYLTNFSRFRDQETVGAVIQLLKSTGLHPFEVAQLGSLACDTADEAKTLIPSLNN 200
Query: 185 RFEEEELRQILDDI 198
           +  ++EL +IL ++
Sbjct: 201 KISDDELERILKEL 214

>pdb|1WCM|D Chain D, Complete 12-Subunit Rna Polymerase Ii At 3.8 Ang Length = 177

Iteration: 1
 Score = 58.5 bits (140), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 28/74 (37%), Positives = 47/74 (63%)
Query: 125 FQKTLTYTERFRKFKNRETITSVRNLLTQKKLHKFELAAIANLCPETPEEAKALIPSLEC 184
            + T+ Y   F +F+++ET+ +V  LL    LH FE+A + +L  +T +EAK LIPSL  
Sbjct: 97  LKNTMQYLTNFSRFRDQETVGAVIQLLKSTGLHPFEVAQLGSLACDTADEAKTLIPSLNN 156
Query: 185 RFEEEELRQILDDI 198
           +  ++EL +IL ++
Sbjct: 157 KISDDELERILKEL 170

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	206
2c35_A	152	Human RPB4, DNA-directed RNA polymerase II 16 kDa	9e-49
3h0g_D	135	DNA-directed RNA polymerase II subunit RPB4; trans	4e-43
1y14_A	187	B32, RPB4, DNA-directed RNA polymerase II 32 kDa p	1e-28
3hou_D	221	DNA-directed RNA polymerase II subunit RPB4; RNA p	2e-28
3ayh_A	136	DNA-directed RNA polymerase III subunit RPC9; tran	5e-13
1go3_F	107	DNA-directed RNA polymerase subunit F; transferase	2e-08
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-06
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	7e-04
4ayb_F	113	DNA-directed RNA polymerase; transferase, multi-su	1e-06
2ckz_A	161	DNA-directed RNA polymerase III 18 KD polypeptide;	3e-05

>2c35_A Human RPB4, DNA-directed RNA polymerase II 16 kDa polypeptide; transcription, nucleotidyltransferase; 2.70A {Homo sapiens} SCOP: a.60.8.2 Length = 152

 Score =  155 bits (392), Expect = 9e-49
 Identities = 104/130 (80%), Positives = 113/130 (86%)

Query: 77  VEEDAGDLQFPKEFENAETLLISEVHMLLQHRKTQNENAEEEQEFSEVFQKTLTYTERFR 136
           VEEDA  L FPKEFE AETLL SEVHMLL+HRK QNE+AE+EQE SEVF KTL YT RF 
Sbjct: 23  VEEDASQLIFPKEFETAETLLNSEVHMLLEHRKQQNESAEDEQELSEVFMKTLNYTARFS 82

Query: 137 KFKNRETITSVRNLLTQKKLHKFELAAIANLCPETPEEAKALIPSLECRFEEEELRQILD 196
           +FKNRETI SVR+LL QKKLHKFELA +ANLCPET EE+KALIPSLE RFE+EEL+QILD
Sbjct: 83  RFKNRETIASVRSLLLQKKLHKFELACLANLCPETAEESKALIPSLEGRFEDEELQQILD 142

Query: 197 DIQTKRSLQY 206
           DIQTKRS QY
Sbjct: 143 DIQTKRSFQY 152

>3h0g_D DNA-directed RNA polymerase II subunit RPB4; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 135

 Score =  140 bits (354), Expect = 4e-43
 Identities = 47/132 (35%), Positives = 71/132 (53%), Gaps = 2/132 (1%)

Query: 75  QVVEEDAGDLQFPKEFENAETLLISEVHMLLQHRKTQNEN-AEEEQEFSEVFQKTLTYTE 133
            + EEDA  L+   EFEN + L +SE  +L++    Q       E   ++V +KT+ Y  
Sbjct: 4   AIFEEDAAQLKLGPEFENEDMLTVSEAKILIETVLAQRARETNGEIPMTDVMKKTVAYFN 63

Query: 134 RFRKFKNRETITSVRNLLTQKKLHKFELAAIANLCPETPEEAKALIPSLECRFEEEELRQ 193
            F +FK  E   +   +L   + HKFE A +  LC E  EEA+ LIPSL  + +++ L+ 
Sbjct: 64  VFARFKTAEATYACERIL-GNRFHKFERAQLGTLCCEDAEEARTLIPSLANKIDDQNLQG 122

Query: 194 ILDDIQTKRSLQ 205
           ILD++ T R  Q
Sbjct: 123 ILDELSTLRKFQ 134

>1y14_A B32, RPB4, DNA-directed RNA polymerase II 32 kDa polypeptide; transferase; 2.30A {Saccharomyces cerevisiae} SCOP: a.60.8.2 Length = 187

 Score =  105 bits (262), Expect = 1e-28
 Identities = 35/129 (27%), Positives = 62/129 (48%), Gaps = 12/129 (9%)

Query: 88  KEFENAETLLISEVHMLLQHRKTQNENAEEEQEF------------SEVFQKTLTYTERF 135
              E+ +  L  +           +E  E+E E             ++  + T+ Y   F
Sbjct: 58  TAVEDEDDDLDEDDVNADDDDFMHSETREKELESIDVLLEQTTGGNNKDLKNTMQYLTNF 117

Query: 136 RKFKNRETITSVRNLLTQKKLHKFELAAIANLCPETPEEAKALIPSLECRFEEEELRQIL 195
            +F+++ET+ +V  LL    LH FE+A + +L  +T +EAK LIPSL  +  ++EL +IL
Sbjct: 118 SRFRDQETVGAVIQLLKSTGLHPFEVAQLGSLACDTADEAKTLIPSLNNKISDDELERIL 177

Query: 196 DDIQTKRSL 204
            ++    +L
Sbjct: 178 KELSNLETL 186

>3hou_D DNA-directed RNA polymerase II subunit RPB4; RNA polymerase II, metal-binding, transcription bubble; HET: BRU; 3.20A {Saccharomyces cerevisiae} PDB: 1nt9_D 1y1w_D 1y1y_D 1y77_D* 2b63_D* 2b8k_D 2ja5_D* 2ja6_D* 2ja7_D* 2ja8_D* 2r7z_D 2r92_D 2r93_D 1y1v_D* 3fki_D 3h3v_E 2vum_D* 3hov_D* 3how_D* 3hox_D* ... Length = 221

 Score =  105 bits (262), Expect = 2e-28
 Identities = 35/127 (27%), Positives = 62/127 (48%), Gaps = 12/127 (9%)

Query: 90  FENAETLLISEVHMLLQHRKTQNENAEEEQEF------------SEVFQKTLTYTERFRK 137
            E+ +  L  +           +E  E+E E             ++  + T+ Y   F +
Sbjct: 94  VEDEDDDLDEDDVNADDDDFMHSETREKELESIDVLLEQTTGGNNKDLKNTMQYLTNFSR 153

Query: 138 FKNRETITSVRNLLTQKKLHKFELAAIANLCPETPEEAKALIPSLECRFEEEELRQILDD 197
           F+++ET+ +V  LL    LH FE+A + +L  +T +EAK LIPSL  +  ++EL +IL +
Sbjct: 154 FRDQETVGAVIQLLKSTGLHPFEVAQLGSLACDTADEAKTLIPSLNNKISDDELERILKE 213

Query: 198 IQTKRSL 204
           +    +L
Sbjct: 214 LSNLETL 220

>3ayh_A DNA-directed RNA polymerase III subunit RPC9; transcription; 2.19A {Schizosaccharomyces pombe} Length = 136

 Score = 62.8 bits (152), Expect = 5e-13
 Identities = 23/113 (20%), Positives = 46/113 (40%), Gaps = 2/113 (1%)

Query: 90  FENAETLLISEVHMLLQHRKTQNENAEEEQEFSEVFQKTLTY--TERFRKFKNRETITSV 147
            E    L   E     + ++     A   +    +  + L Y  ++   +   +E     
Sbjct: 21  AEVFFHLKEMENEQNARTQERGAAQALVCENLRTIQFEILKYLSSQGNCEGLTKERFLDC 80

Query: 148 RNLLTQKKLHKFELAAIANLCPETPEEAKALIPSLECRFEEEELRQILDDIQT 200
             +  + +L K E+  I N  P +  E  A I  +E RF+EE++ ++++ I T
Sbjct: 81  IAIFNEFELTKAEILVILNNKPSSVPELYACIEGIEERFKEEDIFKLVEKINT 133

>1go3_F DNA-directed RNA polymerase subunit F; transferase, transferase, transcription; 1.75A {Methanococcus jannaschii} SCOP: a.60.8.2 Length = 107

 Score = 49.4 bits (118), Expect = 2e-08
 Identities = 21/110 (19%), Positives = 43/110 (39%), Gaps = 8/110 (7%)

Query: 88  KEFENAETLLISEVHMLLQHRKTQNENAEEEQEFSEVFQKTLTYTERFRKFKNRETITSV 147
           K+      + +SE   ++        N  +  E S      L Y ++F K  ++E    +
Sbjct: 4   KKILGERYVTVSEAAEIM-------YNRAQIGELSYEQGCALDYLQKFAKL-DKEEAKKL 55

Query: 148 RNLLTQKKLHKFELAAIANLCPETPEEAKALIPSLECRFEEEELRQILDD 197
              L    + +     IA++ PE  ++ +A+    E     EE+ +I+  
Sbjct: 56  VEELISLGIDEKTAVKIADILPEDLDDLRAIYYKRELPENAEEILEIVRK 105

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

 Score = 47.5 bits (112), Expect = 1e-06
 Identities = 49/299 (16%), Positives = 85/299 (28%), Gaps = 108/299 (36%)

Query: 1   MVCLGLGQNKEKTVSFLLSTSRISPGD-----C-----VVSLFPRKI-----------QP 39
           +    +    ++  S LL      P D            +S+    I             
Sbjct: 291 LDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHV 350

Query: 40  KSNQIKSALSKSVPPRTPYSDR-----VSI---GYIIMTHVL--------DQVVEEDAGD 83
             +++ + +  S+    P   R     +S+      I T +L           V      
Sbjct: 351 NCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNK 410

Query: 84  L-------QFPKEFENAETLLISEVHMLLQ---------HRK------------------ 109
           L       + PKE     T+ I  +++ L+         HR                   
Sbjct: 411 LHKYSLVEKQPKES----TISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIP 466

Query: 110 ---------------TQNENAEEEQEFSEVFQKTLTYTERFRKFKNRETIT------SVR 148
                             E+ E    F  VF   L +  RF + K R   T      S+ 
Sbjct: 467 PYLDQYFYSHIGHHLKNIEHPERMTLFRMVF---LDF--RFLEQKIRHDSTAWNASGSIL 521

Query: 149 NLLTQKKLHKFELAAIANLCPETPEEAKALIPSLECRFEEEELR-QILDDIQTKRSLQY 206
           N L Q K +K     I +  P+      A++  L  + EE  +  +  D ++   +L  
Sbjct: 522 NTLQQLKFYK---PYICDNDPKYERLVNAILDFLP-KIEENLICSKYTDLLR--IALMA 574

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

 Score = 39.1 bits (90), Expect = 7e-04
 Identities = 45/228 (19%), Positives = 69/228 (30%), Gaps = 55/228 (24%)

Query: 1   MVCLGLGQNKEKTVSFL-LSTSRISPGDCVVSLFPRKI---------QPKS--NQIKSAL 48
           +  LG G    KT   + L          V      KI          P++    ++  L
Sbjct: 158 V--LGSG----KTW--VALDVCLSYK---VQCKMDFKIFWLNLKNCNSPETVLEMLQKLL 206

Query: 49  SKSVPPRTPYSDRVSIGYIIMTHVLDQVVEEDAGDLQFPKEFENAETLLI-SEVHMLLQH 107
            +  P  T  SD  S    +  H +   +      L   K +EN   LL+   V      
Sbjct: 207 YQIDPNWTSRSDH-SSNIKLRIHSIQAELR----RLLKSKPYENC--LLVLLNV------ 253

Query: 108 RKTQNENAEEEQEFSEVFQ-KTLTYTERFRK---FKNRETITSVRNLLTQKKLHKFE--- 160
                +NA+    F+     K L  T RF++   F +  T T +        L   E   
Sbjct: 254 -----QNAKAWNAFN--LSCKILL-TTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKS 305

Query: 161 -LAAIANLCPET-PEEAKALIPSLECRFEEEELRQILDDIQTKRSLQY 206
            L    +  P+  P E     P        E +R  L      + +  
Sbjct: 306 LLLKYLDCRPQDLPREVLTTNP-RRLSIIAESIRDGLATWDNWKHVNC 352

>4ayb_F DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2wb1_F 2y0s_F 2waq_F 4b1o_F 4b1p_U 2pmz_F 3hkz_F Length = 113

 Score = 44.5 bits (105), Expect = 1e-06
 Identities = 22/110 (20%), Positives = 45/110 (40%), Gaps = 9/110 (8%)

Query: 88  KEFENAETLLISEVHMLLQHRKTQNENAEEEQEFSEVFQKTLTYTERFRKFKNRETITSV 147
                   +  S    LL        +  +    S + Q+T  Y     K  + E+   V
Sbjct: 4   VYIVEEHYIPYSVAKKLL-------SDVIKSGSSSNLLQRTYDYLNSVEKC-DAESAQKV 55

Query: 148 RNLLTQKKLHKFELAAIANLCPETPEEAKALIPSLECR-FEEEELRQILD 196
              L+     +   A +A++CP TP+E ++++     R +  E++++I+D
Sbjct: 56  VEELSSIISREDVRAVLASICPITPDEVRSILIMDSNRTYTSEDIQKIID 105

>2ckz_A DNA-directed RNA polymerase III 18 KD polypeptide; multiprotein complex, nucleotidyltransferase, nuclear protein, hypothetical protein; 3.2A {Saccharomyces cerevisiae} Length = 161

 Score = 41.8 bits (97), Expect = 3e-05
 Identities = 16/93 (17%), Positives = 34/93 (36%)

Query: 108 RKTQNENAEEEQEFSEVFQKTLTYTERFRKFKNRETITSVRNLLTQKKLHKFELAAIANL 167
              +N   +E++             +      + E+   +   L   KL K E   I N 
Sbjct: 67  SINKNFINQEDEGEERESSGAKDAEKSGISKMSDESFAELMTKLNSFKLFKAEKLQIVNQ 126

Query: 168 CPETPEEAKALIPSLECRFEEEELRQILDDIQT 200
            P       +++   + RF+E+ + ++L+ I  
Sbjct: 127 LPANMVHLYSIVEECDARFDEKTIEEMLEIISA 159

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	206
3h0g_D	135	DNA-directed RNA polymerase II subunit RPB4; trans	100.0
2c35_A	152	Human RPB4, DNA-directed RNA polymerase II 16 kDa	100.0
3hou_D	221	DNA-directed RNA polymerase II subunit RPB4; RNA p	99.97
1go3_F	107	DNA-directed RNA polymerase subunit F; transferase	99.96
1y14_A	187	B32, RPB4, DNA-directed RNA polymerase II 32 kDa p	99.95
4ayb_F	113	DNA-directed RNA polymerase; transferase, multi-su	99.92
3ayh_A	136	DNA-directed RNA polymerase III subunit RPC9; tran	99.8
2ckz_A	161	DNA-directed RNA polymerase III 18 KD polypeptide;	99.72

>3h0g_D DNA-directed RNA polymerase II subunit RPB4; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}

Probab=100.00  E-value=2.7e-41  Score=270.92  Aligned_cols=131  Identities=36%  Similarity=0.616  Sum_probs=120.0

Q ss_pred             cccccccccCCCcccccccccccHHHHHHHHHHHHhhchh-hhhhhhhHHHHHHHHHHHHhcccCCChHHHHHHHHHHhc
Q psy14375         75 QVVEEDAGDLQFPKEFENAETLLISEVHMLLQHRKTQNEN-AEEEQEFSEVFQKTLTYTERFRKFKNRETITSVRNLLTQ  153 (206)
Q Consensus        75 ~~~eEda~~LklG~eF~~a~~LT~sEV~~IL~~~~~~~~~-~d~~~els~v~~kTleYl~rFsk~~~~ea~e~vrelL~~  153 (206)
                      +.+||||++|+||++|++++|||||||+.||++..+++.. ..+..++++++++|++|+++|+++++++++..|+++|+.
T Consensus         4 ~~~ee~a~~L~lg~eF~~a~~Ls~sEv~~lL~~~~~~r~~~~~~~~~~~~v~~kTl~Yl~~Fsk~~~~e~~~~v~~lL~~   83 (135)
T 3h0g_D            4 AIFEEDAAQLKLGPEFENEDMLTVSEAKILIETVLAQRARETNGEIPMTDVMKKTVAYFNVFARFKTAEATYACERILGN   83 (135)
T ss_dssp             --CCCCCTTTCSCHHHHHSCBCCHHHHHHHHHHHHHHHHTTCCSCCCCTTHHHHHHHHHHTTCTTCSHHHHHHHHHHCCC
T ss_pred             hHHHHhHHhhCCCHhhcCcccccHHHHHHHHHHHHHHHHhcccCCcchhHHHHHHHHHHHHccCCCCHHHHHHHHHHHHh
Confidence            5688999999999999999999999999999988665432 123467899999999999999999999999999999998


Q ss_pred             CCCChhhhHhhcccCCCCHHHHhhhhcccccCCCHHHHHHHHHHHHHhhhccC
Q psy14375        154 KKLHKFELAAIANLCPETPEEAKALIPSLECRFEEEELRQILDDIQTKRSLQY  206 (206)
Q Consensus       154 ~~L~kfEia~IaNL~P~t~eEaraLIPSLe~r~sdeeLe~ILd~L~k~R~fq~  206 (206)
                       +||+||+|+|+||||+|+||||+|||||+.++++++|++||++|++||+||.
T Consensus        84 -~L~~fEia~L~NL~P~t~dEak~LIpsL~~r~~de~L~~IL~~l~~~r~f~~  135 (135)
T 3h0g_D           84 -RFHKFERAQLGTLCCEDAEEARTLIPSLANKIDDQNLQGILDELSTLRKFQD  135 (135)
T ss_dssp             -CSCHHHHHHHHHHCCCCHHHHHHHCGGGTTTSCSHHHHHHHHHHHHHTTTCC
T ss_pred             -cCCHHHHHHHccCCCCCHHHHHHHHHHhcccCCHHHHHHHHHHHHHHhcccC
Confidence             9999999999999999999999999999888999999999999999999995

>2c35_A Human RPB4, DNA-directed RNA polymerase II 16 kDa polypeptide; transcription, nucleotidyltransferase; 2.70A {Homo sapiens} SCOP: a.60.8.2

Probab=100.00  E-value=9.3e-41  Score=272.25  Aligned_cols=135  Identities=77%  Similarity=1.059  Sum_probs=121.2

Q ss_pred             cCCcccccccccCCCcccccccccccHHHHHHHHHHHHhhchhhhhhhhhHHHHHHHHHHHHhcccCCChHHHHHHHHHH
Q psy14375         72 VLDQVVEEDAGDLQFPKEFENAETLLISEVHMLLQHRKTQNENAEEEQEFSEVFQKTLTYTERFRKFKNRETITSVRNLL  151 (206)
Q Consensus        72 ~~~~~~eEda~~LklG~eF~~a~~LT~sEV~~IL~~~~~~~~~~d~~~els~v~~kTleYl~rFsk~~~~ea~e~vrelL  151 (206)
                      +..+.+||||++|+||++|++++||||+||+.||++++......++..++++++++|++||++|++++++++++.++++|
T Consensus        18 ~~~~~~ee~a~~l~~gkef~~~~~Lt~sEV~~lL~~~~~~~~~~~~~~els~v~~kTl~Yl~~F~k~k~~e~~~~l~e~L   97 (152)
T 2c35_A           18 PRAGDVEEDASQLIFPKEFETAETLLNSEVHMLLEHRKQQNESAEDEQELSEVFMKTLNYTARFSRFKNRETIASVRSLL   97 (152)
T ss_dssp             ------CCBGGGTBCCSSSSSCEECCHHHHHHHHHHHHHHHHSSCSSCCCCHHHHHHHHHHHHTCSCCSHHHHHHHHHHH
T ss_pred             CCCCCccccHHHHhcchhhcccccccHHHHHHHHHHHHHhhcccccccchHHHHHHHHHHHHHccCCCCHHHHHHHHHHH
Confidence            56677889999999999999999999999999999998754433445788999999999999999999999999999999


Q ss_pred             hcCCCChhhhHhhcccCCCCHHHHhhhhcccccCCCHHHHHHHHHHHHHhhhccC
Q psy14375        152 TQKKLHKFELAAIANLCPETPEEAKALIPSLECRFEEEELRQILDDIQTKRSLQY  206 (206)
Q Consensus       152 ~~~~L~kfEia~IaNL~P~t~eEaraLIPSLe~r~sdeeLe~ILd~L~k~R~fq~  206 (206)
                      ..++||+||+|+|+||||+|++|||+|||+++.++++++|++||++|++||+|||
T Consensus        98 ~~~~L~~~E~a~L~NL~P~t~dEar~lipsl~~r~sdEeLe~ILd~l~k~r~f~~  152 (152)
T 2c35_A           98 LQKKLHKFELACLANLCPETAEESKALIPSLEGRFEDEELQQILDDIQTKRSFQY  152 (152)
T ss_dssp             HTSSCCHHHHHHHHHHCCSSHHHHHHHCGGGTTTSCHHHHHHHHHHHHHHCCCC-
T ss_pred             HhcCCCHHHHHHhccCCCCCHHHHHHHHHhhccCCCHHHHHHHHHHHHHHHhhcC
Confidence            9999999999999999999999999999999999999999999999999999997

>3hou_D DNA-directed RNA polymerase II subunit RPB4; RNA polymerase II, metal-binding, transcription bubble; HET: BRU; 3.20A {Saccharomyces cerevisiae} PDB: 1nt9_D 1y1w_D 1y1y_D 1y77_D* 2b63_D* 2b8k_D 2ja5_D* 2ja6_D* 2ja7_D* 2ja8_D* 2r7z_D 2r92_D 2r93_D 1y1v_D* 3fki_D 3h3v_E 2vum_D* 3hov_D* 3how_D* 3hox_D* ...

Probab=99.97  E-value=1.5e-30  Score=221.75  Aligned_cols=130  Identities=32%  Similarity=0.537  Sum_probs=111.0

Q ss_pred             cccccccccCCCcccccc-----------cccccHHHHHHHH----HHHHhhchh-------------------------
Q psy14375         75 QVVEEDAGDLQFPKEFEN-----------AETLLISEVHMLL----QHRKTQNEN-------------------------  114 (206)
Q Consensus        75 ~~~eEda~~LklG~eF~~-----------a~~LT~sEV~~IL----~~~~~~~~~-------------------------  114 (206)
                      -.+||+|+.|+||++|+-           --+|++||++.|+    .+|+...++                         
T Consensus        18 ~~~eenaa~l~lg~efql~q~~~~g~~~~lialnlsearl~i~~al~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   97 (221)
T 3hou_D           18 VEEEENAATLQLGQEFQLKQINHQGEEEELIALNLSEARLVIKEALVERRRAFKRSQKKHKKKHLKHENANDETTAVEDE   97 (221)
T ss_dssp             CCCCCCCSSSCCCGGGCSEEECTTSCEEECCBCCTTHHHHHHHHHHHHHHHHHHHTTCC---------------------
T ss_pred             ccchhhhHHhhcCcccceeecccCCchhHhHhhhhHHHHHHHHHHHHHHHHHhhcccccccccccccccccccccccccc
Confidence            378899999999999975           4579999999985    334331000                         


Q ss_pred             ---h-------h---------hhh--------------hhHHHHHHHHHHHHhcccCCChHHHHHHHHHHhcCCCChhhh
Q psy14375        115 ---A-------E---------EEQ--------------EFSEVFQKTLTYTERFRKFKNRETITSVRNLLTQKKLHKFEL  161 (206)
Q Consensus       115 ---~-------d---------~~~--------------els~v~~kTleYl~rFsk~~~~ea~e~vrelL~~~~L~kfEi  161 (206)
                         .       +         .+.              ..+.+|++||+||++|++|++++++++|+++|...+||+||+
T Consensus        98 ~~~~~~~~~~~~~~~~~~~~~~e~e~~~~~~~~~~~~g~~seVf~KTLdYl~rFSKfkn~EAv~aVrELL~~~gLheFEi  177 (221)
T 3hou_D           98 DDDLDEDDVNADDDDFMHSETREKELESIDVLLEQTTGGNNKDLKNTMQYLTNFSRFRDQETVGAVIQLLKSTGLHPFEV  177 (221)
T ss_dssp             --------------------CTHHHHHHHHHHHHHHSCSCCHHHHHHHHHHHHSCSCCCHHHHHHHHHHHTTSCCCHHHH
T ss_pred             cccccccccccccchhhhccchHHHHHHHHHHHhhcCCCccHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHhcCCChHHh
Confidence               0       0         001              235889999999999999999999999999999999999999


Q ss_pred             HhhcccCCCCHHHHhhhhcccccCCCHHHHHHHHHHHHHhhhc
Q psy14375        162 AAIANLCPETPEEAKALIPSLECRFEEEELRQILDDIQTKRSL  204 (206)
Q Consensus       162 a~IaNL~P~t~eEaraLIPSLe~r~sdeeLe~ILd~L~k~R~f  204 (206)
                      |+|+||||+|+||||+|||||+.++++++|++||++|++||.|
T Consensus       178 AqLANLcPeTaDEARALIPSL~~k~sDEeLqeILdeLskyR~~  220 (221)
T 3hou_D          178 AQLGSLACDTADEAKTLIPSLNNKISDDELERILKELSNLETL  220 (221)
T ss_dssp             HHHHHSCCCSHHHHHHHCTTCTTSSCHHHHHHHHHHHHHHSCC
T ss_pred             heecccCCCCHHHHHHHHHhhcccCCHHHHHHHHHHHHHhhcc
Confidence            9999999999999999999999899999999999999999976

>1go3_F DNA-directed RNA polymerase subunit F; transferase, transferase, transcription; 1.75A {Methanococcus jannaschii} SCOP: a.60.8.2

Probab=99.96  E-value=1.8e-29  Score=195.08  Aligned_cols=107  Identities=21%  Similarity=0.269  Sum_probs=97.1

Q ss_pred             CCcccccccccccHHHHHHHHHHHHhhchhhhhhhhhHHHHHHHHHHHHhcccCCChHHHHHHHHHHhcCCCChhhhHhh
Q psy14375         85 QFPKEFENAETLLISEVHMLLQHRKTQNENAEEEQEFSEVFQKTLTYTERFRKFKNRETITSVRNLLTQKKLHKFELAAI  164 (206)
Q Consensus        85 klG~eF~~a~~LT~sEV~~IL~~~~~~~~~~d~~~els~v~~kTleYl~rFsk~~~~ea~e~vrelL~~~~L~kfEia~I  164 (206)
                      ++|++|.+++|||+|||+.||+++...       .++++++++|++|+++|++++++++.+.+++++ ..+|++|++++|
T Consensus         1 mi~kei~~~~~lt~sEa~~iL~~~~~~-------~e~s~~~~ktl~y~~kFsk~~~e~a~~l~e~L~-~~~l~e~~a~~I   72 (107)
T 1go3_F            1 MIGKKILGERYVTVSEAAEIMYNRAQI-------GELSYEQGCALDYLQKFAKLDKEEAKKLVEELI-SLGIDEKTAVKI   72 (107)
T ss_dssp             CCSSEEEEEEEECHHHHHHHHHHHHHH-------SCCCHHHHHHHHHHHHHCCSCHHHHHHHHHHHH-HTTCCHHHHHHH
T ss_pred             CchHHHhcccccCHHHHHHHHHHHHhc-------ccccHHHHHHHHHHHHHhCCCHHHHHHHHHHHH-hCCCCHHHHHHH
Confidence            589999999999999999999998752       567899999999999999998777777776666 567999999999


Q ss_pred             cccCCCCHHHHhhhhcccccCCCHHHHHHHHHHHHHhh
Q psy14375        165 ANLCPETPEEAKALIPSLECRFEEEELRQILDDIQTKR  202 (206)
Q Consensus       165 aNL~P~t~eEaraLIPSLe~r~sdeeLe~ILd~L~k~R  202 (206)
                      +||||+|+||||+|||+++.   +++|++||++|++||
T Consensus        73 ~nl~P~t~dElraii~~~~~---~eel~~ILd~l~k~~  107 (107)
T 1go3_F           73 ADILPEDLDDLRAIYYKREL---PENAEEILEIVRKYI  107 (107)
T ss_dssp             HHHCCCSHHHHHHHSTTSCC---CTTHHHHHHHHTTCC
T ss_pred             HHhCCCCHHHHHHHHhcccC---cHHHHHHHHHHHHcC
Confidence            99999999999999999953   999999999999986

>1y14_A B32, RPB4, DNA-directed RNA polymerase II 32 kDa polypeptide; transferase; 2.30A {Saccharomyces cerevisiae} SCOP: a.60.8.2

Probab=99.95  E-value=1e-27  Score=201.07  Aligned_cols=86  Identities=34%  Similarity=0.611  Sum_probs=83.4

Q ss_pred             hhhHHHHHHHHHHHHhcccCCChHHHHHHHHHHhcCCCChhhhHhhcccCCCCHHHHhhhhcccccCCCHHHHHHHHHHH
Q psy14375        119 QEFSEVFQKTLTYTERFRKFKNRETITSVRNLLTQKKLHKFELAAIANLCPETPEEAKALIPSLECRFEEEELRQILDDI  198 (206)
Q Consensus       119 ~els~v~~kTleYl~rFsk~~~~ea~e~vrelL~~~~L~kfEia~IaNL~P~t~eEaraLIPSLe~r~sdeeLe~ILd~L  198 (206)
                      .++++++++|++||++|++++++++++.|+++|..++|++||+|+|+||||+|++|||+|||+++.++++++|++||++|
T Consensus       101 ~~ls~v~~KTLeYl~rFsk~kn~Esa~elre~L~~~kL~efE~aqLaNL~PeTadEaraLIpSle~rlsdEeLeeILd~L  180 (187)
T 1y14_A          101 GGNNKDLKNTMQYLTNFSRFRDQETVGAVIQLLKSTGLHPFEVAQLGSLACDTADEAKTLIPSLNNKISDDELERILKEL  180 (187)
T ss_dssp             CSCCHHHHHHHHHHHHHCSCCSHHHHHHHHHHHHTTTCCHHHHHHHHHSCCSSHHHHHHHSGGGTTTSCHHHHHHHHHHH
T ss_pred             ccccHHHHHHHHHHHHccCCCCHHHHHHHHHHHHhcCCCHHHHHHcCcCCCCCHHHHHHHHHhhccCCCHHHHHHHHHHH
Confidence            46889999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHhhhc
Q psy14375        199 QTKRSL  204 (206)
Q Consensus       199 ~k~R~f  204 (206)
                      ++||+|
T Consensus       181 ~k~r~~  186 (187)
T 1y14_A          181 SNLETL  186 (187)
T ss_dssp             HHHCCC
T ss_pred             HHhhcc
Confidence            999998

>4ayb_F DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2wb1_F 2y0s_F 2waq_F 4b1o_F 4b1p_U 2pmz_F 3hkz_F

Probab=99.92  E-value=1.2e-27  Score=186.25  Aligned_cols=111  Identities=20%  Similarity=0.256  Sum_probs=92.6

Q ss_pred             CCcccccccccccHHHHHHHHHHHHhhchhhhhhhhhHHHHHHHHHHHHhcccCCChHHHHHHHHHHhcCCCChhhhHhh
Q psy14375         85 QFPKEFENAETLLISEVHMLLQHRKTQNENAEEEQEFSEVFQKTLTYTERFRKFKNRETITSVRNLLTQKKLHKFELAAI  164 (206)
Q Consensus        85 klG~eF~~a~~LT~sEV~~IL~~~~~~~~~~d~~~els~v~~kTleYl~rFsk~~~~ea~e~vrelL~~~~L~kfEia~I  164 (206)
                      ++|++..+.+++|++||+.||.++...       .++++++++|++|+++|++++++++.+++++++. .++++|++|+|
T Consensus         1 m~~~~ii~e~~it~~eakeiL~~~~~~-------~~~s~~~~ktl~y~~~Fsk~~~e~a~~l~e~L~~-~~l~~~~~a~I   72 (113)
T 4ayb_F            1 MSSVYIVEEHYIPYSVAKKLLSDVIKS-------GSSSNLLQRTYDYLNSVEKCDAESAQKVVEELSS-IISREDVRAVL   72 (113)
T ss_dssp             --CCEEEEEEEECTTGGGGTTTTTSSS-------SCCCTTHHHHHHHTTTTCSSCHHHHHHHHHHHHT-TCCCHHHHHHH
T ss_pred             CCcceeecccccCHHHHHHHHHHHHhc-------ccccHHHHHHHHHHHHHcCCCHHHHHHHHHHHHH-cCCCHHHHHHH
Confidence            578899999999999999999887432       4567899999999999999987777776666665 68999999999


Q ss_pred             cccCCCCHHHHhhhhcccccC-CCHHHHHHHHHHHHHhhh
Q psy14375        165 ANLCPETPEEAKALIPSLECR-FEEEELRQILDDIQTKRS  203 (206)
Q Consensus       165 aNL~P~t~eEaraLIPSLe~r-~sdeeLe~ILd~L~k~R~  203 (206)
                      +||||+|+||||+||||++++ +++++|++||++|++|++
T Consensus        73 anL~P~~~dElrali~s~e~~~~~deeL~~IL~~l~ky~~  112 (113)
T 4ayb_F           73 ASICPITPDEVRSILIMDSNRTYTSEDIQKIIDIIRKYIK  112 (113)
T ss_dssp             HHHCCCSSCCCCTTTTTTCCCCCCCTHHHHHHHHC-----
T ss_pred             HHcCCCCHHHHHHHHHhhccCCCCHHHHHHHHHHHHHHhc
Confidence            999999999999999999754 899999999999999975

>3ayh_A DNA-directed RNA polymerase III subunit RPC9; transcription; 2.19A {Schizosaccharomyces pombe}

Probab=99.80  E-value=8.6e-20  Score=145.82  Aligned_cols=109  Identities=21%  Similarity=0.272  Sum_probs=95.8

Q ss_pred             cccccHHHHHHHHHHHHhhchh---hhh------hhhhHHHHHHHHHHHHhccc--CCChHHHHHHHHHHhcCCCChhhh
Q psy14375         93 AETLLISEVHMLLQHRKTQNEN---AEE------EQEFSEVFQKTLTYTERFRK--FKNRETITSVRNLLTQKKLHKFEL  161 (206)
Q Consensus        93 a~~LT~sEV~~IL~~~~~~~~~---~d~------~~els~v~~kTleYl~rFsk--~~~~ea~e~vrelL~~~~L~kfEi  161 (206)
                      +.+|||+||..+|++++.+...   ...      ..+++.++++|++|+++|.+  +.+++++..+.+.|+.++|+++|+
T Consensus        15 ~a~LsN~EVl~~L~~~~~~~~~~~~~~~~~~~~~~~~l~ti~~e~l~YL~~~p~~~~q~~e~i~~l~~~L~~~~Ltk~E~   94 (136)
T 3ayh_A           15 DAYLTNAEVFFHLKEMENEQNARTQERGAAQALVCENLRTIQFEILKYLSSQGNCEGLTKERFLDCIAIFNEFELTKAEI   94 (136)
T ss_dssp             EEEECHHHHHHHHHHHHHHHHHHHHHHGGGGCCCCHHHHHHHHHHHHHHHTTTCCTTCCHHHHHHHHHTTTTTCCCHHHH
T ss_pred             cccccHHHHHHHHHHHHhhhcccccccCCccccccchHHHHHHHHHHHHHhCCCccccCHHHHHHHHHHHHhcCCCHHHH
Confidence            6899999999999998764421   111      16789999999999999964  357888888888899999999999


Q ss_pred             HhhcccCCCCHHHHhhhhcccccCCCHHHHHHHHHHHHHh
Q psy14375        162 AAIANLCPETPEEAKALIPSLECRFEEEELRQILDDIQTK  201 (206)
Q Consensus       162 a~IaNL~P~t~eEaraLIPSLe~r~sdeeLe~ILd~L~k~  201 (206)
                      +||+|+||.++.|+++||+..+.||+||++++||++|+++
T Consensus        95 LqivNl~P~t~vel~~iIEe~e~Rfsee~ie~IL~~i~~~  134 (136)
T 3ayh_A           95 LVILNNKPSSVPELYACIEGIEERFKEEDIFKLVEKINTT  134 (136)
T ss_dssp             HHHHHHCCCSHHHHHHHSTTHHHHHTTTTHHHHHHHHHHH
T ss_pred             HHHhccCCCCHHHHHHHHHhcccCCCHHHHHHHHHHHHHh
Confidence            9999999999999999999999999999999999999986

>2ckz_A DNA-directed RNA polymerase III 18 KD polypeptide; multiprotein complex, nucleotidyltransferase, nuclear protein, hypothetical protein; 3.2A {Saccharomyces cerevisiae}

Probab=99.72  E-value=1.8e-18  Score=142.04  Aligned_cols=111  Identities=18%  Similarity=0.219  Sum_probs=33.0

Q ss_pred             ccccccHHHHHHHHHHHHhhchh-----------------hh--hhhhhHHHHHHHHHHHHhccc---------------
Q psy14375         92 NAETLLISEVHMLLQHRKTQNEN-----------------AE--EEQEFSEVFQKTLTYTERFRK---------------  137 (206)
Q Consensus        92 ~a~~LT~sEV~~IL~~~~~~~~~-----------------~d--~~~els~v~~kTleYl~rFsk---------------  137 (206)
                      ++.+|||.||..+|+++......                 ..  ...+++.+++.|++||.++++               
T Consensus         7 ~~a~LSN~EVl~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~ti~~e~~~YL~~~p~~~~~~~~~~~~~~~~   86 (161)
T 2ckz_A            7 RNAFLSDYEVLKFLTDLEKKHLWDQKSLAALKKSRSKGKQNRPYNHPELQGITRNVVNYLSINKNFINQEDEGEERESSG   86 (161)
T ss_dssp             EEEEECHHHHHHHHHHHHHHTTCSHHHHHCC----------CCCCCHHHHHHHHHHHHHHTC------------------
T ss_pred             hhhhhhHHHHHHHHHHhhhhccccccchhhhhcccccccccCCCCCccHHHHHHHHHHHHHhCCcccccccccccccccc
Confidence            35789999999999998765320                 00  125688999999999999987               


Q ss_pred             ----------CCChHHHHHHHHHHhcCCCChhhhHhhcccCCCCHHHHhhhhcccccCCCHHHHHHHHHHHHHhh
Q psy14375        138 ----------FKNRETITSVRNLLTQKKLHKFELAAIANLCPETPEEAKALIPSLECRFEEEELRQILDDIQTKR  202 (206)
Q Consensus       138 ----------~~~~ea~e~vrelL~~~~L~kfEia~IaNL~P~t~eEaraLIPSLe~r~sdeeLe~ILd~L~k~R  202 (206)
                                ..+++++..+.+.|..++|+++|++||+||||.++.|+++||+..+.||++|++++||++|+.||
T Consensus        87 ~~~~~~~~~~~~~~e~i~~l~~~L~~~~Ltk~E~lqivNl~P~s~vel~~iIEe~e~Rfsee~ie~IL~ii~~~~  161 (161)
T 2ckz_A           87 AKDAEKSGISKMSDESFAELMTKLNSFKLFKAEKLQIVNQLPANMVHLYSIVEECDARFDEKTIEEMLEIISAYA  161 (161)
T ss_dssp             ---------------------------------------------------------------------------
T ss_pred             ccccccccccccCHHHHHHHHHHHHhcCCCHHHHHHHhccCCCCHHHHHHHHHhcccCCCHHHHHHHHHHHHHhC
Confidence                      23466667777777889999999999999999999999999999999999999999999999886

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Length	Definition	E-value
Query	206
d2c35a1	129	a.60.8.2 (A:14-142) RNA polymerase II subunit RBP4	9e-50
d1y14a_	176	a.60.8.2 (A:) RNA polymerase II subunit RBP4 (RpoF	9e-36
d1go3f_	107	a.60.8.2 (F:) RNA polymerase II subunit RBP4 (RpoF	2e-26

>d2c35a1 a.60.8.2 (A:14-142) RNA polymerase II subunit RBP4 (RpoF) {Human (Homo sapiens) [TaxId: 9606]} Length = 129

class: All alpha proteins
fold: SAM domain-like
superfamily: HRDC-like
family: RNA polymerase II subunit RBP4 (RpoF)
domain: RNA polymerase II subunit RBP4 (RpoF)
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  156 bits (395), Expect = 9e-50
 Identities = 103/129 (79%), Positives = 112/129 (86%)

Query: 78  EEDAGDLQFPKEFENAETLLISEVHMLLQHRKTQNENAEEEQEFSEVFQKTLTYTERFRK 137
           EEDA  L FPKEFE AETLL SEVHMLL+HRK QNE+AE+EQE SEVF KTL YT RF +
Sbjct: 1   EEDASQLIFPKEFETAETLLNSEVHMLLEHRKQQNESAEDEQELSEVFMKTLNYTARFSR 60

Query: 138 FKNRETITSVRNLLTQKKLHKFELAAIANLCPETPEEAKALIPSLECRFEEEELRQILDD 197
           FKNRETI SVR+LL QKKLHKFELA +ANLCPET EE+KALIPSLE RFE+EEL+QILDD
Sbjct: 61  FKNRETIASVRSLLLQKKLHKFELACLANLCPETAEESKALIPSLEGRFEDEELQQILDD 120

Query: 198 IQTKRSLQY 206
           IQTKRS QY
Sbjct: 121 IQTKRSFQY 129

>d1y14a_ a.60.8.2 (A:) RNA polymerase II subunit RBP4 (RpoF) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 176

class: All alpha proteins
fold: SAM domain-like
superfamily: HRDC-like
family: RNA polymerase II subunit RBP4 (RpoF)
domain: RNA polymerase II subunit RBP4 (RpoF)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score =  121 bits (306), Expect = 9e-36
 Identities = 32/121 (26%), Positives = 64/121 (52%), Gaps = 3/121 (2%)

Query: 87  PKEFENAETLLISEVHMLLQHRKTQNENAEEEQ---EFSEVFQKTLTYTERFRKFKNRET 143
             + ++        +H   + ++ ++ +   EQ     ++  + T+ Y   F +F+++ET
Sbjct: 55  DLDEDDVNADDDDFMHSETREKELESIDVLLEQTTGGNNKDLKNTMQYLTNFSRFRDQET 114

Query: 144 ITSVRNLLTQKKLHKFELAAIANLCPETPEEAKALIPSLECRFEEEELRQILDDIQTKRS 203
           + +V  LL    LH FE+A + +L  +T +EAK LIPSL  +  ++EL +IL ++    +
Sbjct: 115 VGAVIQLLKSTGLHPFEVAQLGSLACDTADEAKTLIPSLNNKISDDELERILKELSNLET 174

Query: 204 L 204
           L
Sbjct: 175 L 175

>d1go3f_ a.60.8.2 (F:) RNA polymerase II subunit RBP4 (RpoF) {Archaeon Methanococcus jannaschii [TaxId: 2190]} Length = 107

class: All alpha proteins
fold: SAM domain-like
superfamily: HRDC-like
family: RNA polymerase II subunit RBP4 (RpoF)
domain: RNA polymerase II subunit RBP4 (RpoF)
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

 Score = 95.6 bits (238), Expect = 2e-26
 Identities = 19/101 (18%), Positives = 41/101 (40%), Gaps = 1/101 (0%)

Query: 97  LISEVHMLLQHRKTQNENAEEEQEFSEVFQKTLTYTERFRKFKNRETITSVRNLLTQKKL 156
           ++ E ++ +        N  +  E S      L Y ++F K  ++E    +   L    +
Sbjct: 6   ILGERYVTVSEAAEIMYNRAQIGELSYEQGCALDYLQKFAKL-DKEEAKKLVEELISLGI 64

Query: 157 HKFELAAIANLCPETPEEAKALIPSLECRFEEEELRQILDD 197
            +     IA++ PE  ++ +A+    E     EE+ +I+  
Sbjct: 65  DEKTAVKIADILPEDLDDLRAIYYKRELPENAEEILEIVRK 105

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	206
d2c35a1	129	RNA polymerase II subunit RBP4 (RpoF) {Human (Homo	100.0
d1y14a_	176	RNA polymerase II subunit RBP4 (RpoF) {Baker's yea	99.93
d1go3f_	107	RNA polymerase II subunit RBP4 (RpoF) {Archaeon Me	99.9

>d2c35a1 a.60.8.2 (A:14-142) RNA polymerase II subunit RBP4 (RpoF) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: SAM domain-like
superfamily: HRDC-like
family: RNA polymerase II subunit RBP4 (RpoF)
domain: RNA polymerase II subunit RBP4 (RpoF)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=1.2e-39  Score=256.84  Aligned_cols=129  Identities=80%  Similarity=1.120  Sum_probs=122.3

Q ss_pred             ccccccCCCcccccccccccHHHHHHHHHHHHhhchhhhhhhhhHHHHHHHHHHHHhcccCCChHHHHHHHHHHhcCCCC
Q psy14375         78 EEDAGDLQFPKEFENAETLLISEVHMLLQHRKTQNENAEEEQEFSEVFQKTLTYTERFRKFKNRETITSVRNLLTQKKLH  157 (206)
Q Consensus        78 eEda~~LklG~eF~~a~~LT~sEV~~IL~~~~~~~~~~d~~~els~v~~kTleYl~rFsk~~~~ea~e~vrelL~~~~L~  157 (206)
                      ||||++|+||++|+|++||||+||+.||++++......++..++++++++|++|+++|++++++++++.+++++..++|+
T Consensus         1 ee~a~~l~~~~ef~~~~~Lt~~Ev~~iL~~~~~~~~~~~~~~~l~~~~~ktl~Yl~~fak~~~~es~~~~~~ll~~~~L~   80 (129)
T d2c35a1           1 EEDASQLIFPKEFETAETLLNSEVHMLLEHRKQQNESAEDEQELSEVFMKTLNYTARFSRFKNRETIASVRSLLLQKKLH   80 (129)
T ss_dssp             CCBGGGTBCCSSSSSCEECCHHHHHHHHHHHHHHHHSSCSSCCCCHHHHHHHHHHHHTCSCCSHHHHHHHHHHHHTSSCC
T ss_pred             CcchhhhcccHhhcchhhhhHHHHHHHHHHHHHHHhcccccccHHHHHHHHHHHHHHhccCCCHHHHHHHHHHhcccCCC
Confidence            69999999999999999999999999999887765555566889999999999999999999999999999999999999


Q ss_pred             hhhhHhhcccCCCCHHHHhhhhcccccCCCHHHHHHHHHHHHHhhhccC
Q psy14375        158 KFELAAIANLCPETPEEAKALIPSLECRFEEEELRQILDDIQTKRSLQY  206 (206)
Q Consensus       158 kfEia~IaNL~P~t~eEaraLIPSLe~r~sdeeLe~ILd~L~k~R~fq~  206 (206)
                      ++|+++|+||||+|++||++|||+++.+|++++|++||+.|++||+|||
T Consensus        81 ~~E~~~i~Nl~P~~~~El~~li~~l~~r~see~l~~iLd~l~~~r~f~~  129 (129)
T d2c35a1          81 KFELACLANLCPETAEESKALIPSLEGRFEDEELQQILDDIQTKRSFQY  129 (129)
T ss_dssp             HHHHHHHHHHCCSSHHHHHHHCGGGTTTSCHHHHHHHHHHHHHHCCCC-
T ss_pred             HHHHHHHhCCCCCCHHHHHHHHHHhccCCCHHHHHHHHHHHHHHhcccC
Confidence            9999999999999999999999999999999999999999999999997

>d1y14a_ a.60.8.2 (A:) RNA polymerase II subunit RBP4 (RpoF) {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: SAM domain-like
superfamily: HRDC-like
family: RNA polymerase II subunit RBP4 (RpoF)
domain: RNA polymerase II subunit RBP4 (RpoF)
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.93  E-value=3.6e-27  Score=194.21  Aligned_cols=114  Identities=27%  Similarity=0.482  Sum_probs=84.3

Q ss_pred             cccccccHHHHHHHHHHHHhhchh-------hhhhhhhHHHHHHHHHHHHhcccCCChHHHHHHHHHHhcCCCChhhhHh
Q psy14375         91 ENAETLLISEVHMLLQHRKTQNEN-------AEEEQEFSEVFQKTLTYTERFRKFKNRETITSVRNLLTQKKLHKFELAA  163 (206)
Q Consensus        91 ~~a~~LT~sEV~~IL~~~~~~~~~-------~d~~~els~v~~kTleYl~rFsk~~~~ea~e~vrelL~~~~L~kfEia~  163 (206)
                      .++.++..+|....++........       +.+....+.+|++|++|+++|++|+++++++.|+++|+.++||+||+|+
T Consensus        55 ~~~~~~~~~~~~~~~~~~~~e~~l~~~~~~~e~~sg~~~~v~~kTldYl~~Fsk~k~~es~~~vrelL~~~~L~~fE~a~  134 (176)
T d1y14a_          55 DLDEDDVNADDDDFMHSETREKELESIDVLLEQTTGGNNKDLKNTMQYLTNFSRFRDQETVGAVIQLLKSTGLHPFEVAQ  134 (176)
T ss_dssp             ------------------CHHHHHHHHHHHHHHHSCSCCHHHHHHHHHHHHHCSCCSHHHHHHHHHHHHTTTCCHHHHHH
T ss_pred             hhhhhhccchhhhhhhhhhhHHHHHhhhhhcccCCCCchHHHHHHHHHHHHhccCCCHHHHHHHHHHHHhcCCCHHHHHH
Confidence            334555555555554433222111       1222345789999999999999999999999999999999999999999


Q ss_pred             hcccCCCCHHHHhhhhcccccCCCHHHHHHHHHHHHHhhhc
Q psy14375        164 IANLCPETPEEAKALIPSLECRFEEEELRQILDDIQTKRSL  204 (206)
Q Consensus       164 IaNL~P~t~eEaraLIPSLe~r~sdeeLe~ILd~L~k~R~f  204 (206)
                      |+||||+|+||||+|||||+.++++++|++||+.|++||..
T Consensus       135 L~NLcPet~eEAkaLiPSL~~k~~de~Lq~IL~~L~~~r~~  175 (176)
T d1y14a_         135 LGSLACDTADEAKTLIPSLNNKISDDELERILKELSNLETL  175 (176)
T ss_dssp             HHHSCCSSHHHHHHHSGGGTTTSCHHHHHHHHHHHHHHCCC
T ss_pred             hhccCCCCHHHHHHHhhhhcccCCHHHHHHHHHHHHHhhcc
Confidence            99999999999999999999899999999999999999963

>d1go3f_ a.60.8.2 (F:) RNA polymerase II subunit RBP4 (RpoF) {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: All alpha proteins
fold: SAM domain-like
superfamily: HRDC-like
family: RNA polymerase II subunit RBP4 (RpoF)
domain: RNA polymerase II subunit RBP4 (RpoF)
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=99.90  E-value=1.9e-24  Score=165.20  Aligned_cols=106  Identities=20%  Similarity=0.260  Sum_probs=90.1

Q ss_pred             CCcccccccccccHHHHHHHHHHHHhhchhhhhhhhhHHHHHHHHHHHHhcccCCChHHHHHHHHHHhcCCCChhhhHhh
Q psy14375         85 QFPKEFENAETLLISEVHMLLQHRKTQNENAEEEQEFSEVFQKTLTYTERFRKFKNRETITSVRNLLTQKKLHKFELAAI  164 (206)
Q Consensus        85 klG~eF~~a~~LT~sEV~~IL~~~~~~~~~~d~~~els~v~~kTleYl~rFsk~~~~ea~e~vrelL~~~~L~kfEia~I  164 (206)
                      ++|+++.+.+++|++||++||.++.+       +.++++++++|++|+++|++++++.+.+.++++++ .+++++++|+|
T Consensus         1 Mi~keii~e~~lt~ae~keiL~~~~~-------~~elsye~~~tL~y~~~fak~~~e~~~~l~~~L~~-~~~~~~~aakI   72 (107)
T d1go3f_           1 MIGKKILGERYVTVSEAAEIMYNRAQ-------IGELSYEQGCALDYLQKFAKLDKEEAKKLVEELIS-LGIDEKTAVKI   72 (107)
T ss_dssp             CCSSEEEEEEEECHHHHHHHHHHHHH-------HSCCCHHHHHHHHHHHHHCCSCHHHHHHHHHHHHH-TTCCHHHHHHH
T ss_pred             CcchhhhhccccCHHHHHHHHHHhhc-------cccccHHHHHHHHHHHHHHcCCHHHHHHHHHHHHh-cCCCHHHHHHH
Confidence            58999999999999999999988643       35789999999999999999976666666666654 79999999999


Q ss_pred             cccCCCCHHHHhhhhcccccCCCHHHHHHHHHHHHHh
Q psy14375        165 ANLCPETPEEAKALIPSLECRFEEEELRQILDDIQTK  201 (206)
Q Consensus       165 aNL~P~t~eEaraLIPSLe~r~sdeeLe~ILd~L~k~  201 (206)
                      +||||+|+||+|+|+|+++..++.   ++||++|++|
T Consensus        73 anL~P~~~dElrai~~~~~~~~~~---eeIl~il~~y  106 (107)
T d1go3f_          73 ADILPEDLDDLRAIYYKRELPENA---EEILEIVRKY  106 (107)
T ss_dssp             HHHCCCSHHHHHHHSTTSCCCTTH---HHHHHHHTTC
T ss_pred             HHhCCCCHHHHHHHHHHhccCCCH---HHHHHHHHHh
Confidence            999999999999999999766655   4567777665