Citrus Sinensis ID: 031131

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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-----
Protein Sequence
MKILEANAGPLTNFEVFDFLRCKGASKDPTRVLVPVTPSEFKVYDYLVESAACNQTRNIINEFLEKSKKFKLAKAEILNIINIRPSSLVEVDSIIEQCDTRFQEEELQELVDLVIEVLPPLPNQPNAAEEVNEDVQGATERMDGEGIKGVNDEKADDEPMTELMG
Secondary Structure (PSIPRED)
ccEEccccccccHHHHHHHHHHHccccccccccccccHHHHHHHHHHHHcccccccHHHHHHHHHHHccccccHHHHHHHHccccccHHHHHHHcccccccccHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHccccccccccccccccccHHHHcc
Secondary Structure Prediction (SSPRO)
ccEHcHHHHHHHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHHHccccccccHHHHHHHHHHHccccccHHHHHHHEccccccHEEEEEEEHcHHHcccHHHHHHHHHHHHHHccccccHcccccccHHcccccHHHcccccccccccccccccccHHHcc
Coil and Loop (DISEMBL)
mkileanagpltnfevfdflrckgaskdptrvlvpvtpsefKVYDYLVESAACNQTRNIINEFLEKSKKFKLAKAEILNIinirpsslvevDSIIEQCDTRFQEEELQELVDLVIEvlpplpnqpnaaeevNEDVQGAtermdgegikgvndekaddepmtelmg
Flexible Loop (DISEMBL)
mkileanagpltnfEVFDFLRCKgaskdptrvlvpvtpSEFKVYDYLVESAACNQTRNIINEFLEKSKKFKLAKAEILNiinirpsslveVDSIIEQCDTRFQEEELQELVDLVIEVLPplpnqpnaaeEVNEDVQGATermdgegikgvndekaddepmtelmg
Low Complexity Region (SEG)
MKILEANAGPLTNFEVFDFLRCKGASKDPTRVLVPVTPSEFKVYDYLVESAACNQTRNIINEFLEKSKKFKLAKAEILNIINIRPSSLVEVDSIIEQCDTRFQeeelqelvdlvievlPPLPNQPNAAEEVNEDVQGATERMDGEGIKGVNDEKADDEPMTELMG
Disordered region (IsUnstruct)
********GPLTNFEVFDFLRCKGASKDPTRVLVPVTPSEFKVYDYLVESAACNQTRNIINEFLEKSKKFKLAKAEILNIINIRPSSLVEVDSIIEQCDTRFQEEELQELVDLVIEVLP**********************************************
Disordered Region (DISOPRED)
MKILEANAGPLTNFEVFD********************SEFKVYDYLVESAACNQTRNIINEFLEKSKKFKLAKAEILNIINIRPSSLVEVDSIIEQCDTRFQEEELQELVDLVIEVL****************************************PMTEL**
Disordered Region (DISEMBL)
MKILEANAGPLTNFEVFDFLRCKGASKDPTRVLVPVTPSEFKVYDYLVESAACNQTRNIINEFLEKSKKFKLAKAEILNIINIRPSSLVEVDSIIEQCDTRFQEEELQELVDLVIEVLPPLPNQPNAAEEVNEDVQGATERMDGEGIKGVNDEKA**********
Disordered Region (DISPRO)
MKILEANAGPLTNFEVFDFLRCKGASKDPTRVLVPVTPSEFKVYDYLVESAACNQTRNIINEFLEKSKKFKLAKAEILNIINIRPSSLVEVDSIIEQCDTRFQEEELQELVDLVIEVLPP*********************************************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MKILEANAGPLTNFEVFDFLRCKGASKDPTRVLVPVTPSEFKVYDYLVESAACNQTRNIINEFLEKSKKFKLAKAEILNIINIRPSSLVEVDSIIEQCDTRFQEEELQELVDLVIEVLPPLPNQPNAAEEVNEDVQGATERMDGEGIKGVNDEKADDEPMTELMG
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	165	2.2.26 [Sep-21-2011]
A0JN61	148	DNA-directed RNA polymera	yes	no	0.793	0.885	0.315	8e-09
Q8VHM6	148	DNA-directed RNA polymera	yes	no	0.721	0.804	0.320	2e-08
O35427	148	DNA-directed RNA polymera	yes	no	0.721	0.804	0.320	3e-08
O75575	148	DNA-directed RNA polymera	yes	no	0.721	0.804	0.305	3e-07
Q60482	146	DNA-directed RNA polymera	yes	no	0.812	0.917	0.307	5e-07
Q9C0Z9	129	DNA-directed RNA polymera	yes	no	0.721	0.922	0.317	1e-06
P47076	161	DNA-directed RNA polymera	yes	no	0.321	0.329	0.415	5e-06
Q54LP2	130	DNA-directed RNA polymera	yes	no	0.612	0.776	0.336	0.0005

>sp|A0JN61|RPC9_BOVIN DNA-directed RNA polymerase III subunit RPC9 OS=Bos taurus GN=CRCP PE=2 SV=1

 Score = 59.7 bits (143), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 46/146 (31%), Positives = 80/146 (54%), Gaps = 15/146 (10%)

Query: 1   MKILEANAGPLTNFEVFDFL-------RCKGASKDPT--RVLVPVTPSEFKVYDYLVESA 51
           M++ +ANA  L+N+EVF  L       +  G +K  +  + L  +T   ++   Y+ ++ 
Sbjct: 1   MEVKDANAALLSNYEVFQLLTDLKEQRKESGKNKHSSGQQNLNTIT---YETLKYISKTP 57

Query: 52  ACNQTRNIINEFLEKSKKFKLAKAEILNIINIRPSSLVEVDSIIEQCDTRFQEEELQELV 111
             +Q+  I+ EFL   K  KL KAE L ++N RP + VE+  ++E+ + R  EE+++ L+
Sbjct: 58  CKHQSPEIVREFLTAMKSHKLTKAEKLQLLNHRPVTAVEIQLMVEESEERLTEEQIEALL 117

Query: 112 DLVIEVLPPLP---NQPNAAEEVNED 134
             V  +LP  P    Q NA+++V  D
Sbjct: 118 HTVTSILPAGPEAEQQQNASDDVAMD 143

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Specific peripheric component of RNA polymerase III which synthesizes small RNAs, such as 5S rRNA and tRNAs. Plays a key role in sensing and limiting infection by intracellular bacteria and DNA viruses. Acts as nuclear and cytosolic DNA sensor involved in innate immune response. Can sense non-self dsDNA that serves as template for transcription into dsRNA. The non-self RNA polymerase III transcripts induce type I interferon and NF- Kappa-B through the RIG-I pathway.
Bos taurus (taxid: 9913)

>sp|Q8VHM6|RPC9_RAT DNA-directed RNA polymerase III subunit RPC9 OS=Rattus norvegicus GN=Crcp PE=2 SV=1

 Score = 58.2 bits (139), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 42/131 (32%), Positives = 71/131 (54%), Gaps = 12/131 (9%)

Query: 1   MKILEANAGPLTNFEVFDFL-------RCKGASKDPT--RVLVPVTPSEFKVYDYLVESA 51
           M++ +ANA  L+N+EVF  L       +  G +K     + L  +T   ++   Y+ ++ 
Sbjct: 1   MEVKDANAALLSNYEVFQLLTDLKEQRKESGKNKHSAGQQNLNAIT---YETLKYISKTP 57

Query: 52  ACNQTRNIINEFLEKSKKFKLAKAEILNIINIRPSSLVEVDSIIEQCDTRFQEEELQELV 111
             NQ+  I+ EFL   K  KL KAE L ++N RP + VE+  ++E+ + R  EE+++ L+
Sbjct: 58  CKNQSPAIVQEFLTAMKSHKLTKAEKLQLLNHRPMTAVEIQLMVEESEERLTEEQIEALL 117

Query: 112 DLVIEVLPPLP 122
             V  +LP  P
Sbjct: 118 HTVTSILPAGP 128

Accessory protein for the calcitonin gene-related peptide (CGRP) receptor. It modulates CGRP responsiveness in a variety of tissues.

Rattus norvegicus (taxid: 10116)

>sp|O35427|RPC9_MOUSE DNA-directed RNA polymerase III subunit RPC9 OS=Mus musculus GN=Crcp PE=2 SV=1

 Score = 57.8 bits (138), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 42/131 (32%), Positives = 71/131 (54%), Gaps = 12/131 (9%)

Query: 1   MKILEANAGPLTNFEVFDFL-------RCKGASKDPT--RVLVPVTPSEFKVYDYLVESA 51
           M++ +ANA  L+N+EVF  L       +  G +K     + L  +T   ++   Y+ ++ 
Sbjct: 1   MEVKDANAALLSNYEVFQLLTDLKEQRKESGKNKHSAGQQNLNAIT---YETLKYISKTP 57

Query: 52  ACNQTRNIINEFLEKSKKFKLAKAEILNIINIRPSSLVEVDSIIEQCDTRFQEEELQELV 111
             NQ+  I+ EFL   K  KL KAE L ++N RP + VE+  ++E+ + R  EE+++ L+
Sbjct: 58  CRNQSPAIVQEFLTAMKSHKLTKAEKLQLLNHRPMTAVEIQLMVEESEERLTEEQIEALL 117

Query: 112 DLVIEVLPPLP 122
             V  +LP  P
Sbjct: 118 HTVTSILPAGP 128

Accessory protein for the calcitonin gene-related peptide (CGRP) receptor. It modulates CGRP responsiveness in a variety of tissues.

Mus musculus (taxid: 10090)

>sp|O75575|RPC9_HUMAN DNA-directed RNA polymerase III subunit RPC9 OS=Homo sapiens GN=CRCP PE=1 SV=1

 Score = 54.7 bits (130), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 40/131 (30%), Positives = 72/131 (54%), Gaps = 12/131 (9%)

Query: 1   MKILEANAGPLTNFEVFDFL-------RCKGASKDPT--RVLVPVTPSEFKVYDYLVESA 51
           M++ +AN+  L+N+EVF  L       +  G +K  +  + L  +T   ++   Y+ ++ 
Sbjct: 1   MEVKDANSALLSNYEVFQLLTDLKEQRKESGKNKHSSGQQNLNTIT---YETLKYISKTP 57

Query: 52  ACNQTRNIINEFLEKSKKFKLAKAEILNIINIRPSSLVEVDSIIEQCDTRFQEEELQELV 111
             +Q+  I+ EFL   K  KL KAE L ++N RP + VE+  ++E+ + R  EE+++ L+
Sbjct: 58  CRHQSPEIVREFLTALKSHKLTKAEKLQLLNHRPVTAVEIQLMVEESEERLTEEQIEALL 117

Query: 112 DLVIEVLPPLP 122
             V  +LP  P
Sbjct: 118 HTVTSILPAEP 128

Accessory protein for the calcitonin gene-related peptide (CGRP) receptor. It modulates CGRP responsiveness in a variety of tissues.

Homo sapiens (taxid: 9606)

>sp|Q60482|RPC9_CAVPO DNA-directed RNA polymerase III subunit RPC9 OS=Cavia porcellus GN=CRCP PE=2 SV=1

 Score = 53.9 bits (128), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 48/156 (30%), Positives = 79/156 (50%), Gaps = 22/156 (14%)

Query: 1   MKILEANAGPLTNFEVFDFL-------RCKGASKDPT--RVLVPVTPSEFKVYDYLVESA 51
           M++ +AN+  L+N+EVF  L       R  G  K     + L  +T   ++   YL ++ 
Sbjct: 1   MEVKDANSALLSNYEVFQLLTDLKDQRRESGKMKHSAGQQNLNTIT---YETLKYLSKTP 57

Query: 52  ACNQTRNIINEFLEKSKKFKLAKAEILNIINIRPSSLVEVDSII-EQCDTRFQEEELQEL 110
             +Q+  I+ EFL   K  KL KAE L ++N RP + VE+  ++ E  +   +EE+++ L
Sbjct: 58  CRHQSPEIVREFLTAMKSHKLTKAEKLQLLNHRPMTAVEIQLMVEETEERFTEEEQIEAL 117

Query: 111 VDLVIEVLPPLPNQPNAAEEVNEDVQGATERMDGEG 146
           +  V  +LP  P       EV +    +TE M+ EG
Sbjct: 118 LHTVTHILPAEP-------EVEQ--MASTEAMEEEG 144

Accessory protein for the calcitonin gene-related peptide (CGRP) receptor. It modulates CGRP responsiveness in a variety of tissues.

Cavia porcellus (taxid: 10141)

>sp|Q9C0Z9|RPC9_SCHPO DNA-directed RNA polymerase III subunit rpc9 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rpc17 PE=1 SV=1

 Score = 52.8 bits (125), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 41/129 (31%), Positives = 67/129 (51%), Gaps = 10/129 (7%)

Query: 1   MKILEANAGPLTNFEVFDFLR-------CKGASKDPTRVLVP--VTPSEFKVYDYLVESA 51
           MK+LEA    LTN EVF  L+        +   +   + LV   +   +F++  YL    
Sbjct: 1   MKVLEARDAYLTNAEVFFHLKEMENEQNARTQERGAAQALVCENLRTIQFEILKYLSSQG 60

Query: 52  AC-NQTRNIINEFLEKSKKFKLAKAEILNIINIRPSSLVEVDSIIEQCDTRFQEEELQEL 110
            C   T+    + +    +F+L KAEIL I+N +PSS+ E+ + IE  + RF+EE++ +L
Sbjct: 61  NCEGLTKERFLDCIAIFNEFELTKAEILVILNNKPSSVPELYACIEGIEERFKEEDIFKL 120

Query: 111 VDLVIEVLP 119
           V+ +    P
Sbjct: 121 VEKINTTFP 129

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Specific peripheric component of RNA polymerase III which synthesizes small RNAs, such as 5S rRNA and tRNAs.

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

>sp|P47076|RPC9_YEAST DNA-directed RNA polymerase III subunit RPC9 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RPC17 PE=1 SV=2

 Score = 50.4 bits (119), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 22/53 (41%), Positives = 38/53 (71%)

Query: 62  EFLEKSKKFKLAKAEILNIINIRPSSLVEVDSIIEQCDTRFQEEELQELVDLV 114
           E + K   FKL KAE L I+N  P+++V + SI+E+CD RF E+ ++E+++++
Sbjct: 105 ELMTKLNSFKLFKAEKLQIVNQLPANMVHLYSIVEECDARFDEKTIEEMLEII 157

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Specific peripheric component of RNA polymerase III which synthesizes small RNAs, such as 5S rRNA and tRNAs. The RPC25/RPC8-RPC17/RPC9 subcomplex may bind Pol III transcripts emerging from the adjacent exit pore during elongation.

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

>sp|Q54LP2|RPC9_DICDI DNA-directed RNA polymerase III subunit rpc9 OS=Dictyostelium discoideum GN=rpc9 PE=3 SV=1

 Score = 43.9 bits (102), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 39/116 (33%), Positives = 55/116 (47%), Gaps = 15/116 (12%)

Query: 1   MKILEANAGPL-TNFEVFDFLRCKGASKDPTRVLVPVTPSEF--KVYDYLVESAACNQTR 57
           MKI++ +   + TNFEV   L      K   R+   V  +EF   V  YL  + A  QT 
Sbjct: 1   MKIIKKDKEEIITNFEVLQLL------KHKRRIEEQVLLNEFVNNVIRYLETTPASKQTI 54

Query: 58  NIINEFLEKSKKF------KLAKAEILNIINIRPSSLVEVDSIIEQCDTRFQEEEL 107
             + E  +   K       K+   E+L I+NI PSS VEV  +IE C+ R   +E+
Sbjct: 55  ESVKECKKSVTKLADTSGCKILTGEMLQILNIAPSSEVEVHLVIEDCEDRIDAKEV 110

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Specific component of RNA polymerase III which synthesizes small RNAs, such as 5S rRNA and tRNAs.

Dictyostelium discoideum (taxid: 44689)

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	165
225465821	156	PREDICTED: DNA-directed RNA polymerase I	0.848	0.897	0.659	1e-43
147801996	388	hypothetical protein VITISV_004802 [Viti	0.812	0.345	0.659	7e-41
388498384	162	unknown [Lotus japonicus]	0.781	0.796	0.643	1e-39
388504500	162	unknown [Lotus japonicus]	0.781	0.796	0.627	7e-38
449455302	160	PREDICTED: DNA-directed RNA polymerase I	0.933	0.962	0.552	6e-37
351721416	161	uncharacterized protein LOC100526847 [Gl	0.957	0.981	0.537	8e-35
356569570	161	PREDICTED: DNA-directed RNA polymerase I	0.721	0.739	0.638	9e-35
15242004	139	RNA polymerase II, Rpb4, core protein [A	0.824	0.978	0.565	1e-34
388509714	170	unknown [Medicago truncatula]	0.866	0.841	0.517	1e-33
224081032	159	predicted protein [Populus trichocarpa]	0.624	0.647	0.679	7e-33

>gi|225465821|ref|XP_002263648.1| PREDICTED: DNA-directed RNA polymerase III subunit RPC9 [Vitis vinifera] gi|296087853|emb|CBI35109.3| unnamed protein product [Vitis vinifera]

 Score =  181 bits (458), Expect = 1e-43,   Method: Compositional matrix adjust.
 Identities = 95/144 (65%), Positives = 111/144 (77%), Gaps = 4/144 (2%)

Query: 1   MKILEANAGPLTNFEVFDFLRCKGASKDPTRVLVPVTPSEFKVYDYLVESAACNQTRNII 60
           MKI +ANAG LTNFEV DFLR +GA+KDPTRV+ P+  SEFKVYDYLVESAACNQTR  I
Sbjct: 1   MKIKKANAGALTNFEVLDFLRSRGAAKDPTRVIAPIAASEFKVYDYLVESAACNQTRESI 60

Query: 61  NEFLEKSKKFKLAKAEILNIINIRPSSLVEVDSIIEQCDTRFQEEELQELVDLVIEVLPP 120
           NE LEK KK+ LAKAEILNIINIRP+S VE+D IIE+ + R   E +++L+++VI VLPP
Sbjct: 61  NELLEKCKKYDLAKAEILNIINIRPASPVEIDPIIEESEKRMG-EGIEDLIEMVITVLPP 119

Query: 121 LPNQPNAAEEVNEDVQGATERMDG 144
            PNQ N  EEV   V G  E  DG
Sbjct: 120 PPNQMNTEEEV---VAGDEEIADG 140

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147801996|emb|CAN72759.1| hypothetical protein VITISV_004802 [Vitis vinifera]

 Score =  171 bits (434), Expect = 7e-41,   Method: Compositional matrix adjust.
 Identities = 89/135 (65%), Positives = 105/135 (77%), Gaps = 1/135 (0%)

Query: 5   EANAGPLTNFEVFDFLRCKGASKDPTRVLVPVTPSEFKVYDYLVESAACNQTRNIINEFL 64
           +ANAG LTNFEV DFLR +GA+KD TRV+ P+  SEFKVYDYLVESAACNQTR  INE L
Sbjct: 26  KANAGALTNFEVLDFLRSRGAAKDXTRVIAPIAASEFKVYDYLVESAACNQTRESINELL 85

Query: 65  EKSKKFKLAKAEILNIINIRPSSLVEVDSIIEQCDTRFQEEELQELVDLVIEVLPPLPNQ 124
           EK KK+ LAKAEILNIINIRP+S VE+D IIE+ + R   E +++L+++VI VLPP PNQ
Sbjct: 86  EKCKKYDLAKAEILNIINIRPASPVEIDPIIEESEKRMG-EGIEDLIEMVITVLPPPPNQ 144

Query: 125 PNAAEEVNEDVQGAT 139
            N  EEV  D Q  T
Sbjct: 145 MNTEEEVIMDKQVHT 159

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388498384|gb|AFK37258.1| unknown [Lotus japonicus]

 Score =  167 bits (423), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 83/129 (64%), Positives = 100/129 (77%)

Query: 1   MKILEANAGPLTNFEVFDFLRCKGASKDPTRVLVPVTPSEFKVYDYLVESAACNQTRNII 60
           MKILEANAG LTNFEV DFLR KGASKDPTRV+  V  SE+KVYDYLV +AA NQTR  I
Sbjct: 1   MKILEANAGALTNFEVLDFLRGKGASKDPTRVIAKVAQSEYKVYDYLVNTAASNQTRESI 60

Query: 61  NEFLEKSKKFKLAKAEILNIINIRPSSLVEVDSIIEQCDTRFQEEELQELVDLVIEVLPP 120
           NEF+   KK  LAKAE+LNIINIRP++ VE+  IIE+C++RF +EE+ E+V+LV + LP 
Sbjct: 61  NEFMASVKKHDLAKAEVLNIINIRPAAAVEMFPIIEECESRFPDEEVTEIVELVKKTLPA 120

Query: 121 LPNQPNAAE 129
            P + N  E
Sbjct: 121 PPAKKNVVE 129

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388504500|gb|AFK40316.1| unknown [Lotus japonicus]

 Score =  161 bits (408), Expect = 7e-38,   Method: Compositional matrix adjust.
 Identities = 81/129 (62%), Positives = 97/129 (75%)

Query: 1   MKILEANAGPLTNFEVFDFLRCKGASKDPTRVLVPVTPSEFKVYDYLVESAACNQTRNII 60
           MKILEANAG LTNFEV DFLR KGASKDPTRV+  V  SE+KVYDYLV +AA NQTR  I
Sbjct: 1   MKILEANAGALTNFEVLDFLRGKGASKDPTRVIAKVAQSEYKVYDYLVNTAASNQTRESI 60

Query: 61  NEFLEKSKKFKLAKAEILNIINIRPSSLVEVDSIIEQCDTRFQEEELQELVDLVIEVLPP 120
           NEF+   KK  LAKAE+LNIINI P++ VE+  IIE+C+ RF +EE+ E+V+L  + LP 
Sbjct: 61  NEFMASVKKHDLAKAEVLNIINITPAAAVEMFPIIEECEPRFPDEEVTEIVELAKKTLPA 120

Query: 121 LPNQPNAAE 129
            P + N  E
Sbjct: 121 PPAKKNVVE 129

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449455302|ref|XP_004145392.1| PREDICTED: DNA-directed RNA polymerase III subunit rpc9-like [Cucumis sativus] gi|449523065|ref|XP_004168545.1| PREDICTED: DNA-directed RNA polymerase III subunit rpc9-like [Cucumis sativus]

 Score =  158 bits (400), Expect = 6e-37,   Method: Compositional matrix adjust.
 Identities = 90/163 (55%), Positives = 112/163 (68%), Gaps = 9/163 (5%)

Query: 1   MKILEANAGPLTNFEVFDFLRCKGASKDPTRVLVPVTPSEFKVYDYLVESAACNQTRNII 60
           MKILEANAGPLTNFEV DFLR KGA+KDPTRVL  V PSE+KV+DYL +++ACNQTR  I
Sbjct: 1   MKILEANAGPLTNFEVLDFLRSKGAAKDPTRVLAKVLPSEYKVFDYLNQTSACNQTREAI 60

Query: 61  NEFLEKSKKFKLAKAEILNIINIRPSSLVEVDSIIEQCDTRFQE---EELQELVDLVIEV 117
             F EKSK++ LAKAEILNIIN+RP++ VE+  +IE CD R  E   E ++E+  +V  V
Sbjct: 61  INFAEKSKEYDLAKAEILNIINLRPTTPVELFPVIENCDARMGEGATERMEEIGLMVEHV 120

Query: 118 LPPLPNQPNAAEEVNEDVQGATERMDGEGIKGVNDEKADDEPM 160
            P   N+P    EV        E M+ +  +G  D  AD+EPM
Sbjct: 121 FPTPQNEPTF--EVTPKEGNEAEAMEVQ--EGAGD--ADEEPM 157

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|351721416|ref|NP_001238744.1| uncharacterized protein LOC100526847 [Glycine max] gi|255630978|gb|ACU15853.1| unknown [Glycine max]

 Score =  151 bits (382), Expect = 8e-35,   Method: Compositional matrix adjust.
 Identities = 86/160 (53%), Positives = 109/160 (68%), Gaps = 2/160 (1%)

Query: 1   MKILEANAGPLTNFEVFDFLRCKGASKDPTRVLVPVTPSEFKVYDYLVESAACNQTRNII 60
           MKILE NAG LTNFEV DFLR KGASKDPTRV+  V+ SE+KVYDYLV++AA  QTR  I
Sbjct: 1   MKILEGNAGALTNFEVLDFLRAKGASKDPTRVIAKVSQSEYKVYDYLVDTAASVQTRESI 60

Query: 61  NEFLEKSKKFKLAKAEILNIINIRPSSLVEVDSIIEQCDTRFQEEELQELVDLVIEVLPP 120
           NEFL   K+  LAKAE+LNI+NI P++ VE+  I+E+ D RF +E + E+V+LV + L P
Sbjct: 61  NEFLRSVKQHDLAKAEVLNILNIGPAAEVELYPILEESDERFGDEGVTEIVELVKKAL-P 119

Query: 121 LPNQPNAAEEVNEDVQGATERMDGEGIKGVNDEKADDEPM 160
           LP      E    D + AT + + +G K   D+  D E M
Sbjct: 120 LPLNMKKEEITKGDEETATLKNE-KGNKIRQDQNEDGEEM 158

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356569570|ref|XP_003552972.1| PREDICTED: DNA-directed RNA polymerase III subunit rpc9-like [Glycine max]

 Score =  151 bits (381), Expect = 9e-35,   Method: Compositional matrix adjust.
 Identities = 76/119 (63%), Positives = 91/119 (76%)

Query: 1   MKILEANAGPLTNFEVFDFLRCKGASKDPTRVLVPVTPSEFKVYDYLVESAACNQTRNII 60
           MKILE NAG LTNFEV DFLR KGASKDPTRV+  V  SE+KVYDYLV++AA  QTR  I
Sbjct: 1   MKILECNAGALTNFEVLDFLRAKGASKDPTRVIAKVAQSEYKVYDYLVDTAASVQTRESI 60

Query: 61  NEFLEKSKKFKLAKAEILNIINIRPSSLVEVDSIIEQCDTRFQEEELQELVDLVIEVLP 119
           NEFL   K+  LAKAE+LNI+NI P++ VE+  IIE CD RF +E + E+V+LV + LP
Sbjct: 61  NEFLTSVKQHDLAKAEVLNILNIGPAAEVELYPIIEDCDERFGDEGVLEIVELVKKTLP 119

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15242004|ref|NP_201100.1| RNA polymerase II, Rpb4, core protein [Arabidopsis thaliana] gi|334188590|ref|NP_001190602.1| RNA polymerase II, Rpb4, core protein [Arabidopsis thaliana] gi|32815911|gb|AAP88340.1| At5g62950 [Arabidopsis thaliana] gi|110743157|dbj|BAE99470.1| hypothetical protein [Arabidopsis thaliana] gi|332010294|gb|AED97677.1| RNA polymerase II, Rpb4, core protein [Arabidopsis thaliana] gi|332010296|gb|AED97679.1| RNA polymerase II, Rpb4, core protein [Arabidopsis thaliana]

 Score =  150 bits (380), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 78/138 (56%), Positives = 101/138 (73%), Gaps = 2/138 (1%)

Query: 1   MKILEANAGPLTNFEVFDFLRCKGASKDPTRVLVPVTPSEFKVYDYLVESAACNQTRNII 60
           MKI++ANAG LTNFEV DFL  +GASKD TRV+ P+  SE+KVYDYLVE+AA  QTR  I
Sbjct: 1   MKIVKANAGALTNFEVLDFLNSRGASKDTTRVIAPIARSEYKVYDYLVETAASTQTRESI 60

Query: 61  NEFLEKSKKFKLAKAEILNIINIRPSSLVEVDSIIEQCDTRFQEEELQELVDLVIEVLPP 120
           N+F +K K FKLAKAEILNIIN+RPSS+VE+  IIE  D R  E +   +++LV ++LPP
Sbjct: 61  NKFADKCKDFKLAKAEILNIINLRPSSIVELLPIIENLDDR--EIDTDGILELVKDLLPP 118

Query: 121 LPNQPNAAEEVNEDVQGA 138
           LP   +  ++  E+ +  
Sbjct: 119 LPTTASPKDDDEEETENG 136

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388509714|gb|AFK42923.1| unknown [Medicago truncatula]

 Score =  147 bits (372), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 74/143 (51%), Positives = 99/143 (69%)

Query: 1   MKILEANAGPLTNFEVFDFLRCKGASKDPTRVLVPVTPSEFKVYDYLVESAACNQTRNII 60
           MKILE NAG LTNFEV DFLR KGASKDP+RVL  V  SE+KVYDYLV++ A +QTR  +
Sbjct: 12  MKILEENAGALTNFEVLDFLRAKGASKDPSRVLAKVAMSEYKVYDYLVKTPAGSQTRESV 71

Query: 61  NEFLEKSKKFKLAKAEILNIINIRPSSLVEVDSIIEQCDTRFQEEELQELVDLVIEVLPP 120
            E+    K+  L++AE+LN++NIRP+S VE+  IIE C+ RF +EE+ E+V+ V   LP 
Sbjct: 72  KEYFTAIKQHDLSEAEVLNVLNIRPASEVEIYHIIEDCEERFPDEEVTEIVEKVGNTLPA 131

Query: 121 LPNQPNAAEEVNEDVQGATERMD 143
            P++    E    D +  T++ D
Sbjct: 132 PPDKATPEEITKGDEETETQKHD 154

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224081032|ref|XP_002306270.1| predicted protein [Populus trichocarpa] gi|222855719|gb|EEE93266.1| predicted protein [Populus trichocarpa]

 Score =  145 bits (365), Expect = 7e-33,   Method: Compositional matrix adjust.
 Identities = 70/103 (67%), Positives = 83/103 (80%)

Query: 1   MKILEANAGPLTNFEVFDFLRCKGASKDPTRVLVPVTPSEFKVYDYLVESAACNQTRNII 60
           MKI   NAG LTNFEV DFLR +GAS+D +RVL PV  SE+KVYDYLVE+ ACN TR  I
Sbjct: 1   MKIKNPNAGALTNFEVLDFLRSRGASRDVSRVLAPVAASEYKVYDYLVETPACNLTREKI 60

Query: 61  NEFLEKSKKFKLAKAEILNIINIRPSSLVEVDSIIEQCDTRFQ 103
           NEFLE+ KK+ LAKAE+LNIINIRPS  VE+ +IIE+ D+RF+
Sbjct: 61  NEFLERCKKYDLAKAELLNIINIRPSQTVEIYTIIEEMDSRFE 103

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	165
TAIR|locus:2170768	139	AT5G62950 [Arabidopsis thalian	0.836	0.992	0.528	4.7e-32
TAIR|locus:504955773	137	AT3G28956 [Arabidopsis thalian	0.8	0.963	0.514	3.1e-28
UNIPROTKB|Q60482	146	CRCP "DNA-directed RNA polymer	0.836	0.945	0.282	3.6e-09
UNIPROTKB|A0JN61	148	CRCP "DNA-directed RNA polymer	0.812	0.905	0.272	4.7e-09
WB|WBGene00044924	128	M106.7 [Caenorhabditis elegans	0.618	0.796	0.323	9.7e-09
MGI|MGI:1100818	148	Crcp "calcitonin gene-related	0.806	0.898	0.258	1.6e-08
RGD|620753	148	Crcp "CGRP receptor component"	0.806	0.898	0.258	1.6e-08
UNIPROTKB|Q8VHM6	148	Crcp "DNA-directed RNA polymer	0.806	0.898	0.258	1.6e-08
UNIPROTKB|O75575	148	CRCP "DNA-directed RNA polymer	0.848	0.945	0.255	2e-08
UNIPROTKB|F1PM57	147	CRCP "Uncharacterized protein"	0.612	0.687	0.299	3.3e-08

TAIR|locus:2170768 AT5G62950 [Arabidopsis thaliana (taxid:3702)]

 Score = 351 (128.6 bits), Expect = 4.7e-32, P = 4.7e-32
 Identities = 74/140 (52%), Positives = 92/140 (65%)

Query:     1 MKILEANAGPLTNFEVFDFLRCKGASKDPTRVLVPVTPSEFKVYDYLVESAACNQTRNII 60
             MKI++ANAG LTNFEV DFL  +GASKD TRV+ P+  SE+KVYDYLVE+AA  QTR  I
Sbjct:     1 MKIVKANAGALTNFEVLDFLNSRGASKDTTRVIAPIARSEYKVYDYLVETAASTQTRESI 60

Query:    61 NEFLEKSKKFKLAKAEILNIINIRPSSLVEVDSIIEQCDTRFQXXXXXXXXXXXXXXXPP 120
             N+F +K K FKLAKAEILNIIN+RPSS+VE+  IIE  D R                 PP
Sbjct:    61 NKFADKCKDFKLAKAEILNIINLRPSSIVELLPIIENLDDR--EIDTDGILELVKDLLPP 118

Query:   121 LPNQPNAAEEVNEDVQGATE 140
             LP   +  ++  E+ +   +
Sbjct:   119 LPTTASPKDDDEEETENGEQ 138

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003824 "catalytic activity" evidence=IEA

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

GO:0005886 "plasma membrane" evidence=ISM

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

GO:0044237 "cellular metabolic process" evidence=IEA

TAIR|locus:504955773 AT3G28956 [Arabidopsis thaliana (taxid:3702)]

 Score = 315 (115.9 bits), Expect = 3.1e-28, P = 3.1e-28
 Identities = 70/136 (51%), Positives = 85/136 (62%)

Query:     4 LEANAGPLTNFEVFDFLRCKGASKDPTRVLVPVTPSEFKVYDYLVESAACNQTRNIINEF 63
             ++ANAG LTNFE+ DFL  +GASKD TRV+ P+  SE+KVYDYLVE+AA  QTR  +N+ 
Sbjct:     1 MKANAGALTNFELLDFLNSRGASKDTTRVIAPIARSEYKVYDYLVETAASTQTRESVNKS 60

Query:    64 LEKSKKFKLAKAEILNIINIRPSSLVEVDSIIEQCDTRFQXXXXXXXXXXXXXXXPPLPN 123
              +K K FKLAKAEILNIIN+ PSS+VE+  IIE  D R                 PPLP 
Sbjct:    61 ADKCKDFKLAKAEILNIINLWPSSIVELLPIIENLDDR--EIDTDGILELVKDLLPPLPT 118

Query:   124 --QPNAAEEVNEDVQG 137
                P   +E  E   G
Sbjct:   119 AESPKDNDEEEETENG 134

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003824 "catalytic activity" evidence=IEA

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

GO:0005886 "plasma membrane" evidence=ISM

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

GO:0044237 "cellular metabolic process" evidence=IEA

UNIPROTKB|Q60482 CRCP "DNA-directed RNA polymerase III subunit RPC9" [Cavia porcellus (taxid:10141)]

 Score = 135 (52.6 bits), Expect = 3.6e-09, P = 3.6e-09
 Identities = 43/152 (28%), Positives = 71/152 (46%)

Query:     1 MKILEANAGPLTNFEVFDFLR-CKGASKDPTRVLVPVTPSEFKV--YD---YLVESAACN 54
             M++ +AN+  L+N+EVF  L   K   ++  ++             Y+   YL ++   +
Sbjct:     1 MEVKDANSALLSNYEVFQLLTDLKDQRRESGKMKHSAGQQNLNTITYETLKYLSKTPCRH 60

Query:    55 QTRNIINEFLEKSKKFKLAKAEILNIINIRPSSLVEVDSIIEQCDTRFQXXXXXXXXXXX 114
             Q+  I+ EFL   K  KL KAE L ++N RP + VE+  ++E+ + RF            
Sbjct:    61 QSPEIVREFLTAMKSHKLTKAEKLQLLNHRPMTAVEIQLMVEETEERFTEEEQIEALLHT 120

Query:   115 XXXXPPLPNQPNAAEEVNEDVQGATERMDGEG 146
                   LP +P    EV +    +TE M+ EG
Sbjct:   121 VTHI--LPAEP----EVEQ--MASTEAMEEEG 144

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

GO:0006383 "transcription from RNA polymerase III promoter" evidence=ISS

GO:0009360 "DNA polymerase III complex" evidence=ISS

UNIPROTKB|A0JN61 CRCP "DNA-directed RNA polymerase III subunit RPC9" [Bos taurus (taxid:9913)]

 Score = 134 (52.2 bits), Expect = 4.7e-09, P = 4.7e-09
 Identities = 39/143 (27%), Positives = 68/143 (47%)

Query:     1 MKILEANAGPLTNFEVFDFL-----RCKGASKDP-TRVLVPVTPSEFKVYDYLVESAACN 54
             M++ +ANA  L+N+EVF  L     + K + K+  +     +    ++   Y+ ++   +
Sbjct:     1 MEVKDANAALLSNYEVFQLLTDLKEQRKESGKNKHSSGQQNLNTITYETLKYISKTPCKH 60

Query:    55 QTRNIINEFLEKSKKFKLAKAEILNIINIRPSSLVEVDSIIEQCDTRF---QXXXXXXXX 111
             Q+  I+ EFL   K  KL KAE L ++N RP + VE+  ++E+ + R    Q        
Sbjct:    61 QSPEIVREFLTAMKSHKLTKAEKLQLLNHRPVTAVEIQLMVEESEERLTEEQIEALLHTV 120

Query:   112 XXXXXXXPPLPNQPNAAEEVNED 134
                    P    Q NA+++V  D
Sbjct:   121 TSILPAGPEAEQQQNASDDVAMD 143

GO:0009360 "DNA polymerase III complex" evidence=ISS

GO:0006383 "transcription from RNA polymerase III promoter" evidence=ISS

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

GO:0005886 "plasma membrane" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0007218 "neuropeptide signaling pathway" evidence=IEA

GO:0001669 "acrosomal vesicle" evidence=IEA

GO:0001635 "calcitonin gene-related polypeptide receptor activity" evidence=IEA

GO:0051607 "defense response to virus" evidence=IEA

GO:0045087 "innate immune response" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

WB|WBGene00044924 M106.7 [Caenorhabditis elegans (taxid:6239)]

 Score = 131 (51.2 bits), Expect = 9.7e-09, P = 9.7e-09
 Identities = 34/105 (32%), Positives = 51/105 (48%)

Query:     1 MKILEANAGPLTNFEVFDFLRCKGASKDPTRVLVPVTPSEFKVYD---YLVESAACNQTR 57
             M++L+     LTN EV  FL      +D  +           +Y+   YL  S A  Q  
Sbjct:     1 MEVLKTRETMLTNQEVLSFLNALKKEEDNKQQHERCKQLSTVIYETKKYLNTSPAVTQNE 60

Query:    58 NIINEFLEKSKKFKLAKAEILNIINIRPSSLVEVDSIIEQCDTRF 102
              +I E + K   FKL  AE L +IN+RPS+  ++  +IE+ + RF
Sbjct:    61 AVICELIPKLAPFKLTGAETLQVINLRPSTTADIQLLIEETEERF 105

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

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

MGI|MGI:1100818 Crcp "calcitonin gene-related peptide-receptor component protein" [Mus musculus (taxid:10090)]

 Score = 129 (50.5 bits), Expect = 1.6e-08, P = 1.6e-08
 Identities = 36/139 (25%), Positives = 62/139 (44%)

Query:     1 MKILEANAGPLTNFEVFDFL-----RCKGASKDPTRV-LVPVTPSEFKVYDYLVESAACN 54
             M++ +ANA  L+N+EVF  L     + K + K+        +    ++   Y+ ++   N
Sbjct:     1 MEVKDANAALLSNYEVFQLLTDLKEQRKESGKNKHSAGQQNLNAITYETLKYISKTPCRN 60

Query:    55 QTRNIINEFLEKSKKFKLAKAEILNIINIRPSSLVEVDSIIEQCDTRFQXXXXXXXXXXX 114
             Q+  I+ EFL   K  KL KAE L ++N RP + VE+  ++E+ + R             
Sbjct:    61 QSPAIVQEFLTAMKSHKLTKAEKLQLLNHRPMTAVEIQLMVEESEERLTEEQIEALLHTV 120

Query:   115 XXXXPPLPNQPNAAEEVNE 133
                 P  P    +    N+
Sbjct:   121 TSILPAGPEDEQSKSTSND 139

GO:0000166 "nucleotide binding" evidence=IEA

GO:0001635 "calcitonin gene-related polypeptide receptor activity" evidence=IDA

GO:0001669 "acrosomal vesicle" evidence=IDA

GO:0003824 "catalytic activity" evidence=IEA

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

GO:0005634 "nucleus" evidence=IEA

GO:0005886 "plasma membrane" evidence=IEA

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

GO:0006383 "transcription from RNA polymerase III promoter" evidence=ISO

GO:0006954 "inflammatory response" evidence=ISO

GO:0007218 "neuropeptide signaling pathway" evidence=IDA

GO:0009360 "DNA polymerase III complex" evidence=ISO

GO:0016020 "membrane" evidence=IEA

GO:0044237 "cellular metabolic process" evidence=IEA

GO:0045087 "innate immune response" evidence=IEA

GO:0051607 "defense response to virus" evidence=IEA

RGD|620753 Crcp "CGRP receptor component" [Rattus norvegicus (taxid:10116)]

 Score = 129 (50.5 bits), Expect = 1.6e-08, P = 1.6e-08
 Identities = 36/139 (25%), Positives = 62/139 (44%)

Query:     1 MKILEANAGPLTNFEVFDFL-----RCKGASKDPTRV-LVPVTPSEFKVYDYLVESAACN 54
             M++ +ANA  L+N+EVF  L     + K + K+        +    ++   Y+ ++   N
Sbjct:     1 MEVKDANAALLSNYEVFQLLTDLKEQRKESGKNKHSAGQQNLNAITYETLKYISKTPCKN 60

Query:    55 QTRNIINEFLEKSKKFKLAKAEILNIINIRPSSLVEVDSIIEQCDTRFQXXXXXXXXXXX 114
             Q+  I+ EFL   K  KL KAE L ++N RP + VE+  ++E+ + R             
Sbjct:    61 QSPAIVQEFLTAMKSHKLTKAEKLQLLNHRPMTAVEIQLMVEESEERLTEEQIEALLHTV 120

Query:   115 XXXXPPLPNQPNAAEEVNE 133
                 P  P    +    N+
Sbjct:   121 TSILPAGPEDEQSKSTSND 139

GO:0000166 "nucleotide binding" evidence=IEA

GO:0001635 "calcitonin gene-related polypeptide receptor activity" evidence=IEA;ISO

GO:0001669 "acrosomal vesicle" evidence=IEA;ISO

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

GO:0005634 "nucleus" evidence=IEA

GO:0005886 "plasma membrane" evidence=IEA

GO:0006383 "transcription from RNA polymerase III promoter" evidence=IEA;ISO;ISS

GO:0006950 "response to stress" evidence=IEP

GO:0006954 "inflammatory response" evidence=IDA

GO:0007218 "neuropeptide signaling pathway" evidence=IEA;ISO

GO:0009360 "DNA polymerase III complex" evidence=IEA;ISO;ISS

GO:0045087 "innate immune response" evidence=IEA

GO:0051607 "defense response to virus" evidence=IEA

UNIPROTKB|Q8VHM6 Crcp "DNA-directed RNA polymerase III subunit RPC9" [Rattus norvegicus (taxid:10116)]

 Score = 129 (50.5 bits), Expect = 1.6e-08, P = 1.6e-08
 Identities = 36/139 (25%), Positives = 62/139 (44%)

Query:     1 MKILEANAGPLTNFEVFDFL-----RCKGASKDPTRV-LVPVTPSEFKVYDYLVESAACN 54
             M++ +ANA  L+N+EVF  L     + K + K+        +    ++   Y+ ++   N
Sbjct:     1 MEVKDANAALLSNYEVFQLLTDLKEQRKESGKNKHSAGQQNLNAITYETLKYISKTPCKN 60

Query:    55 QTRNIINEFLEKSKKFKLAKAEILNIINIRPSSLVEVDSIIEQCDTRFQXXXXXXXXXXX 114
             Q+  I+ EFL   K  KL KAE L ++N RP + VE+  ++E+ + R             
Sbjct:    61 QSPAIVQEFLTAMKSHKLTKAEKLQLLNHRPMTAVEIQLMVEESEERLTEEQIEALLHTV 120

Query:   115 XXXXPPLPNQPNAAEEVNE 133
                 P  P    +    N+
Sbjct:   121 TSILPAGPEDEQSKSTSND 139

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|O75575 CRCP "DNA-directed RNA polymerase III subunit RPC9" [Homo sapiens (taxid:9606)]

 Score = 128 (50.1 bits), Expect = 2.0e-08, P = 2.0e-08
 Identities = 38/149 (25%), Positives = 70/149 (46%)

Query:     1 MKILEANAGPLTNFEVFDFL-----RCKGASKDP-TRVLVPVTPSEFKVYDYLVESAACN 54
             M++ +AN+  L+N+EVF  L     + K + K+  +     +    ++   Y+ ++   +
Sbjct:     1 MEVKDANSALLSNYEVFQLLTDLKEQRKESGKNKHSSGQQNLNTITYETLKYISKTPCRH 60

Query:    55 QTRNIINEFLEKSKKFKLAKAEILNIINIRPSSLVEVDSIIEQCDTRFQXXXXXXXXXXX 114
             Q+  I+ EFL   K  KL KAE L ++N RP + VE+  ++E+ + R             
Sbjct:    61 QSPEIVREFLTALKSHKLTKAEKLQLLNHRPVTAVEIQLMVEESEERLTEEQIEALLHTV 120

Query:   115 XXXXPPLPNQPNAAEEVNEDVQGATERMD 143
                   LP +P A ++ N +   A +  D
Sbjct:   121 TSI---LPAEPEAEQKKNTNSNVAMDEED 146

GO:0000166 "nucleotide binding" evidence=IEA

GO:0045087 "innate immune response" evidence=IEA

GO:0051607 "defense response to virus" evidence=IEA

GO:0001635 "calcitonin gene-related polypeptide receptor activity" evidence=IEA

GO:0001669 "acrosomal vesicle" evidence=IEA

GO:0007218 "neuropeptide signaling pathway" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005886 "plasma membrane" evidence=IEA

GO:0004948 "calcitonin receptor activity" evidence=NAS

GO:0007340 "acrosome reaction" evidence=NAS

GO:0009360 "DNA polymerase III complex" evidence=IDA

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

GO:0006383 "transcription from RNA polymerase III promoter" evidence=IDA

UNIPROTKB|F1PM57 CRCP "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 126 (49.4 bits), Expect = 3.3e-08, P = 3.3e-08
 Identities = 32/107 (29%), Positives = 58/107 (54%)

Query:     1 MKILEANAGPLTNFEVFDFL-----RCKGASKDP-TRVLVPVTPSEFKVYDYLVESAACN 54
             M++ +AN+  L+N+EVF  L     + K + K+  +     +    ++   Y+ ++   +
Sbjct:     1 MEVKDANSALLSNYEVFQLLTDLKEQRKESGKNKHSSGQQNLNTITYETLKYISKTPCRH 60

Query:    55 QTRNIINEFLEKSKKFKLAKAEILNIINIRPSSLVEVDSIIEQCDTR 101
             QT  I+ EFL   K  KL KAE L ++N RP + VE+  ++E+ + R
Sbjct:    61 QTPEIVREFLTAMKSHKLTKAEKLQLLNHRPMTAVEIQLMVEESEER 107

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

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

GO:0000166 "nucleotide binding" evidence=IEA

---

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)
Q60482	RPC9_CAVPO	No assigned EC number	0.3076	0.8121	0.9178	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: GSVIVG00030898001 SubName- Full=Chromosome undetermined scaffold_53, whole genome shotgun sequence; (157 aa) (Vitis vinifera)

Predicted Functional Partners:

Sorry, there are no predicted associations at the current settings.

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	165
pfam03874	110	pfam03874, RNA_pol_Rpb4, RNA polymerase Rpb4	5e-21
smart00657	118	smart00657, RPOL4c, DNA-directed RNA-polymerase II	5e-21

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

 Score = 82.2 bits (204), Expect = 5e-21
 Identities = 32/111 (28%), Positives = 58/111 (52%), Gaps = 3/111 (2%)

Query: 10  PLTNFEVFDFLRCKGASKD--PTRVLVPVTPSEFKVYDYLVESAACNQTRNIINEFLEKS 67
            LTN EV + L+ +   +      V   +     K  +YL    +  +      E +E+ 
Sbjct: 1   YLTNSEVLEILKKELEERRRESRYVEENLNTILRKTLEYL-NKFSRLKNPESARELVEEL 59

Query: 68  KKFKLAKAEILNIINIRPSSLVEVDSIIEQCDTRFQEEELQELVDLVIEVL 118
           K+F+L K E L I+N+ P +  E+ +IIE  ++RF EE+L+E++D++ +  
Sbjct: 60  KEFELTKFEALQIVNLLPETADELRAIIESLESRFSEEQLEEILDILSKYR 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|128904 smart00657, RPOL4c, DNA-directed RNA-polymerase II subunit

 Score = 82.4 bits (204), Expect = 5e-21
 Identities = 39/116 (33%), Positives = 54/116 (46%), Gaps = 1/116 (0%)

Query: 5   EANAGPLTNFEVFDFLRCKGASKDPTRVLVPVTPSEFKVYDYLVESAACNQTRNIINEFL 64
             NA  LTN EV   L  K  SK+      P++    K   YL + A   + R I+    
Sbjct: 3   FKNATCLTNSEVQLLLELKRQSKESEEEQQPLSTVMKKTLKYLSKFAR-FKNREIVRAVR 61

Query: 65  EKSKKFKLAKAEILNIINIRPSSLVEVDSIIEQCDTRFQEEELQELVDLVIEVLPP 120
              K  KL K EI  + N+RP +  E   +I   + R  EEEL+EL+D +  +LP 
Sbjct: 62  TLLKSKKLHKFEIAQLGNLRPETAEEAQLLIPSLEERIDEEELEELLDDLSSLLPF 117

Length = 118

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	165
KOG4168	149	consensus Predicted RNA polymerase III subunit C17	100.0
smart00657	118	RPOL4c DNA-directed RNA-polymerase II subunit.	99.95
PF03874	117	RNA_pol_Rpb4: RNA polymerase Rpb4; InterPro: IPR00	99.94
PRK14981	112	DNA-directed RNA polymerase subunit F; Provisional	99.57
KOG2351	134	consensus RNA polymerase II, fourth largest subuni	99.3
COG1460	114	Uncharacterized protein conserved in archaea [Func	98.75
COG5250	138	RPB4 RNA polymerase II, fourth largest subunit [Tr	97.41
KOG4168	149	consensus Predicted RNA polymerase III subunit C17	84.35
KOG0030	152	consensus Myosin essential light chain, EF-Hand pr	80.84

>KOG4168 consensus Predicted RNA polymerase III subunit C17 [Transcription]

Probab=100.00  E-value=2.4e-34  Score=224.40  Aligned_cols=124  Identities=43%  Similarity=0.656  Sum_probs=112.7

Q ss_pred             CeeecCCcccCcHHHHHHHHHhhc-----CCCCCCC------CCcccccchHHHHHHHhhCc-ccccCHHHHHHHHHHhh
Q 031131            1 MKILEANAGPLTNFEVFDFLRCKG-----ASKDPTR------VLVPVTPSEFKVYDYLVESA-ACNQTRNIINEFLEKSK   68 (165)
Q Consensus         1 MkIl~~~~a~LSN~EVl~~L~~~~-----~~~~~~~------~~~~l~~~e~e~l~YL~~~p-~~~qt~e~i~~l~~~L~   68 (165)
                      |||+++|++.|||||||+||.+.+     +.+...+      ..+++.+++|+|++||..+| |+.|++|+|.+|+..|+
T Consensus         1 MKvl~ar~a~LtnyEVl~fL~el~~~n~~~~k~s~r~~~Q~~~~~~l~ti~~et~kYls~~~n~~~qt~E~i~el~~k~~   80 (149)
T KOG4168|consen    1 MKVLKARNAALTNYEVLQFLNELECMNEEADKSSHRLGAQNILQNDLPTITYETLKYLSDNKNASTQTNESIIELITKLK   80 (149)
T ss_pred             CchhhhhHHHhhhHHHHHHHHHhhhhhhhhhhhhhhhhcccccccccchhHHHHHHHHhcCcccccccHHHHHHHHHHhc
Confidence            999999999999999999999876     2222222      23568899999999999999 89999999999999999


Q ss_pred             cCCCCHHHHHHHhcCCCCcHHHHHHhhcccccCC-CHHHHHHHHHHHHHhCCCCCCC
Q 031131           69 KFKLAKAEILNIINIRPSSLVEVDSIIEQCDTRF-QEEELQELVDLVIEVLPPLPNQ  124 (165)
Q Consensus        69 ~f~LTk~E~LQIvNl~Pts~veL~~iIEe~e~Rf-sEeqieeIL~iI~e~L~~~~~~  124 (165)
                      .|+|||+|+|||+|++|++.|+||+|||+||+|| +++++.++++.|..+||+.|..
T Consensus        81 ~fkLtKAE~LqiiN~rPss~vel~~~iE~~eeRf~~ee~i~elv~~i~~~~P~~P~~  137 (149)
T KOG4168|consen   81 SFKLTKAEILQIINLRPSSSVELYLIIEEVEERFQDEEDIEELVETISKTLPATPKN  137 (149)
T ss_pred             cccchHHHHHHHhccCcchHHHHHHHHHHHHHhccchhcHHHHHHhccccCCCCccc
Confidence            9999999999999999999999999999999999 9999999999999999977754

>smart00657 RPOL4c DNA-directed RNA-polymerase II subunit

Probab=99.95  E-value=7.4e-28  Score=182.42  Aligned_cols=113  Identities=35%  Similarity=0.376  Sum_probs=101.8

Q ss_pred             CcccCcHHHHHHHHHhhcCCCCCCCCCcccccchHHHHHHHhhCcccccCHHHHHHHHHHhhcCCCCHHHHHHHhcCCCC
Q 031131            7 NAGPLTNFEVFDFLRCKGASKDPTRVLVPVTPSEFKVYDYLVESAACNQTRNIINEFLEKSKKFKLAKAEILNIINIRPS   86 (165)
Q Consensus         7 ~~a~LSN~EVl~~L~~~~~~~~~~~~~~~l~~~e~e~l~YL~~~p~~~qt~e~i~~l~~~L~~f~LTk~E~LQIvNl~Pt   86 (165)
                      ++..|||+||+.+|++++..+.+.+...++.++.+++++||+++| ..+++++|.+|++.|++|+|||+|++||+|+||+
T Consensus         5 ~a~~L~n~Ev~~ll~~k~~~~~~~~~~~~l~~v~~~tl~Yl~~~~-~~~~~e~i~~~~~~L~~~~L~k~E~~~i~Nl~P~   83 (118)
T smart00657        5 NATCLTNSEVQLLLELKRQSKESEEEQQPLSTVMKKTLKYLSKFA-RFKNREIVRAVRTLLKSKKLHKFEIAQLGNLRPE   83 (118)
T ss_pred             chhHhHHHHHHHHHHHHHHhhccccccchHHHHHHHHHHHHHHcC-CCCCHHHHHHHHHHHHhcCCCHHHHHHHhCCCCC
Confidence            457899999999999876555444445566777799999999998 6889999999999999999999999999999999


Q ss_pred             cHHHHHHhhcccccCCCHHHHHHHHHHHHHhCCC
Q 031131           87 SLVEVDSIIEQCDTRFQEEELQELVDLVIEVLPP  120 (165)
Q Consensus        87 s~veL~~iIEe~e~RfsEeqieeIL~iI~e~L~~  120 (165)
                      |++|+++||++|++||+|+++++||++|++++|.
T Consensus        84 s~~E~~~lI~sl~~r~~ee~l~~iL~~i~~~~~~  117 (118)
T smart00657       84 TAEEAQLLIPSLEERIDEEELEELLDDLSSLLPF  117 (118)
T ss_pred             CHHHHHHHhhhhhccCCHHHHHHHHHHHHHhcCC
Confidence            9999999999999999999999999999999874

>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=99.94  E-value=3.1e-27  Score=176.64  Aligned_cols=108  Identities=35%  Similarity=0.546  Sum_probs=89.2

Q ss_pred             cCcHHHHHHHHHhhcCCC-CC--------CCCCcccccchHHHHHHHhhCcccccCHHHHHHHHHHhhcCCCCHHHHHHH
Q 031131           10 PLTNFEVFDFLRCKGASK-DP--------TRVLVPVTPSEFKVYDYLVESAACNQTRNIINEFLEKSKKFKLAKAEILNI   80 (165)
Q Consensus        10 ~LSN~EVl~~L~~~~~~~-~~--------~~~~~~l~~~e~e~l~YL~~~p~~~qt~e~i~~l~~~L~~f~LTk~E~LQI   80 (165)
                      +|||+||+++|+++.+.+ ..        .+...++.++.+++++||++ |+..++++.+.+|++.|+.|+||++|++||
T Consensus         1 ~Lsn~EV~~iL~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Yl~~-~~~~~~~e~~~~l~~~L~~~~L~~~E~~qi   79 (117)
T PF03874_consen    1 LLSNYEVLQILEKRREEQKNKSKKKQKNKEDPPENLNTIQYKTLEYLEK-FSKFQNPESIKELREELKKFGLTEFEILQI   79 (117)
T ss_dssp             EE-HHHHHHHHHHHHHHHHCHCHHHHHHHHHCSSCHCHHHHHHHHHHHH-H-SSSSHHHHHHHHHHHTTSTS-HHHHHHH
T ss_pred             CCcHHHHHHHHHHHHHHHHhhhccccccccccccchHHHHHHHHHHHHc-cccCCCHHHHHHHHHHHhcccCCHHHHHHH
Confidence            589999999999543321 11        12334666777999999999 888889999999999999999999999999


Q ss_pred             hcCCCCcHHHHHHhhcccccCCCHHHHHHHHHHHHHhC
Q 031131           81 INIRPSSLVEVDSIIEQCDTRFQEEELQELVDLVIEVL  118 (165)
Q Consensus        81 vNl~Pts~veL~~iIEe~e~RfsEeqieeIL~iI~e~L  118 (165)
                      +|++|+|++|+++||++|+.||+|+++++||++|+++.
T Consensus        80 ~Nl~P~~~~El~~ii~~~~~r~~ee~l~~iL~~v~~~~  117 (117)
T PF03874_consen   80 INLRPTTAVELRAIIESLESRFSEEDLEEILDLVSKYR  117 (117)
T ss_dssp             HHH--SSHHHHHHHSTTGTTTSTHHHHHHHHHHHHHHT
T ss_pred             hcCCCCCHHHHHHHHHHhccCCCHHHHHHHHHHHHHhC
Confidence            99999999999999999999999999999999999863

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 ....

>PRK14981 DNA-directed RNA polymerase subunit F; Provisional

Probab=99.57  E-value=2.3e-14  Score=108.18  Aligned_cols=102  Identities=20%  Similarity=0.240  Sum_probs=88.7

Q ss_pred             cccCcHHHHHHHHHhhcCCCCCCCCCcccccchHHHHHHHhhCcccccCHHHHHHHHHHhhcC-CCCHHHHHHHhcCCCC
Q 031131            8 AGPLTNFEVFDFLRCKGASKDPTRVLVPVTPSEFKVYDYLVESAACNQTRNIINEFLEKSKKF-KLAKAEILNIINIRPS   86 (165)
Q Consensus         8 ~a~LSN~EVl~~L~~~~~~~~~~~~~~~l~~~e~e~l~YL~~~p~~~qt~e~i~~l~~~L~~f-~LTk~E~LQIvNl~Pt   86 (165)
                      ...|||.||..+|.++...+       .++....++++|++++.  +.+++...++++.|... +|++.+..||+|+||.
T Consensus         9 e~~lt~sEa~~iL~~~~~~~-------els~~~~ktl~y~~kFs--k~~~e~a~elve~L~~~~~l~e~~a~~I~nL~P~   79 (112)
T PRK14981          9 EEYITIAEAKEILSEIEEER-------ELSYELRRTLDYLNRFS--KLDPEDAEELVEELLELEKMKEKTAVKIADILPE   79 (112)
T ss_pred             cccccHHHHHHHHHHHHhcc-------chhHHHHHHHHHHHHHh--CCCHHHHHHHHHHHHHccCCCHHHHHHHHhcCCC
Confidence            35899999999999887664       34444589999999995  45788888999998664 5799999999999999


Q ss_pred             cHHHHHHhhcccccCCCHHHHHHHHHHHHHhC
Q 031131           87 SLVEVDSIIEQCDTRFQEEELQELVDLVIEVL  118 (165)
Q Consensus        87 s~veL~~iIEe~e~RfsEeqieeIL~iI~e~L  118 (165)
                      |+.|+.+|+.....+|+++++++||++|+++.
T Consensus        80 ~~dElrai~~~~~~~~~~e~l~~ILd~l~k~~  111 (112)
T PRK14981         80 TRDELRAIFAKERYTLSPEELDEILDIVKKYR  111 (112)
T ss_pred             CHHHHHHHHHHhccCCCHHHHHHHHHHHHHhh
Confidence            99999999999988999999999999999873

>KOG2351 consensus RNA polymerase II, fourth largest subunit [Transcription]

Probab=99.30  E-value=8.2e-12  Score=96.23  Aligned_cols=108  Identities=14%  Similarity=0.150  Sum_probs=91.7

Q ss_pred             ccCcHHHHHHHHHhhcCCCC-CCCCCcccccchHHHHHHHhhCcccccCHHHHHHHHHHhhcCCCCHHHHHHHhcCCCCc
Q 031131            9 GPLTNFEVFDFLRCKGASKD-PTRVLVPVTPSEFKVYDYLVESAACNQTRNIINEFLEKSKKFKLAKAEILNIINIRPSS   87 (165)
Q Consensus         9 a~LSN~EVl~~L~~~~~~~~-~~~~~~~l~~~e~e~l~YL~~~p~~~qt~e~i~~l~~~L~~f~LTk~E~LQIvNl~Pts   87 (165)
                      ..|.|.||.-+|.++..+.+ .....+.+..+-.+++.|+..+. +.-+++.+..+..-|...+|+|.|+-||-|+||.|
T Consensus        22 ~~L~~sEa~lllE~~~~q~~rs~d~~~~~s~Vf~kTl~Y~~~Fs-RfKn~etv~avr~iLs~~~lhkFE~A~lgnLcpet  100 (134)
T KOG2351|consen   22 DALMLSEARLLLEHRLEQRRRSEDDESEMSDVFKKTLQYLDRFS-RFKNRETVRAVRTILSGKGLHKFEVAQLGNLCPET  100 (134)
T ss_pred             HHHHHHHHHHHHHHHHHHHhhcccccchHHHHHHHHHHHHHHHH-HhcCHHHHHHHHHHHhhCCcchhhHHHHhccCccc
Confidence            35789999999998765443 33333344444489999999874 55689999999999999999999999999999999


Q ss_pred             HHHHHHhhcccccCCCHHHHHHHHHHHHHh
Q 031131           88 LVEVDSIIEQCDTRFQEEELQELVDLVIEV  117 (165)
Q Consensus        88 ~veL~~iIEe~e~RfsEeqieeIL~iI~e~  117 (165)
                      +.|-.++|..++.|++|+.+++||+-|+..
T Consensus       101 aEEAkaLvPSL~nkidD~~le~iL~dls~l  130 (134)
T KOG2351|consen  101 AEEAKALVPSLENKIDDDELEQILKDLSTL  130 (134)
T ss_pred             HHHHHHhccccccccCHHHHHHHHHHHHHH
Confidence            999999999999999999999999999864

>COG1460 Uncharacterized protein conserved in archaea [Function unknown]

Probab=98.75  E-value=1.5e-07  Score=71.67  Aligned_cols=102  Identities=20%  Similarity=0.221  Sum_probs=87.7

Q ss_pred             cccCcHHHHHHHHHhhcCCCCCCCCCcccccchHHHHHHHhhCcccccCHHHHHHHHHHhhc-CCCCHHHHHHHhcCCCC
Q 031131            8 AGPLTNFEVFDFLRCKGASKDPTRVLVPVTPSEFKVYDYLVESAACNQTRNIINEFLEKSKK-FKLAKAEILNIINIRPS   86 (165)
Q Consensus         8 ~a~LSN~EVl~~L~~~~~~~~~~~~~~~l~~~e~e~l~YL~~~p~~~qt~e~i~~l~~~L~~-f~LTk~E~LQIvNl~Pt   86 (165)
                      ...+|=.||..+|.++....       .++..++.+++|+.++.  +..++..+++++.|.. +++.+.-..-|+.++|+
T Consensus        10 ~~yiti~Eak~il~~~~~~~-------eL~y~~~~al~y~~kFa--kldpe~a~e~veEL~~i~~~~e~~avkIadI~P~   80 (114)
T COG1460          10 EKYITISEAKKILSKVEREE-------ELTYEQREALEYAEKFA--KLDPEKARELVEELLSIVKMSEKIAVKIADIMPR   80 (114)
T ss_pred             ccCccHHHHHHHHHHhcccc-------cchHHHHHHHHHHHHHh--cCCHHHHHHHHHHHHhhccccHHHHHHHHHhCCC
Confidence            45788999999998873332       56666789999999994  5779999999999976 45788888999999999


Q ss_pred             cHHHHHHhhcccccCCCHHHHHHHHHHHHHhC
Q 031131           87 SLVEVDSIIEQCDTRFQEEELQELVDLVIEVL  118 (165)
Q Consensus        87 s~veL~~iIEe~e~RfsEeqieeIL~iI~e~L  118 (165)
                      |..||++|..--..++|+|++++||++|..+.
T Consensus        81 t~~ElRsIla~e~~~~s~E~l~~Ildiv~Ky~  112 (114)
T COG1460          81 TPDELRSILAKERVMLSDEELDKILDIVDKYR  112 (114)
T ss_pred             CHHHHHHHHHHccCCCCHHHHHHHHHHHHHHh
Confidence            99999999999889999999999999998763

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

Probab=97.41  E-value=0.00079  Score=52.07  Aligned_cols=76  Identities=12%  Similarity=0.121  Sum_probs=68.6

Q ss_pred             hHHHHHHHhhCcccccCHHHHHHHHHHhhcCCCCHHHHHHHhcCCCCcHHHHHHhhcccccCCCHHHHHHHHHHHHH
Q 031131           40 EFKVYDYLVESAACNQTRNIINEFLEKSKKFKLAKAEILNIINIRPSSLVEVDSIIEQCDTRFQEEELQELVDLVIE  116 (165)
Q Consensus        40 e~e~l~YL~~~p~~~qt~e~i~~l~~~L~~f~LTk~E~LQIvNl~Pts~veL~~iIEe~e~RfsEeqieeIL~iI~e  116 (165)
                      -+.|+.||..+ |..-+.+....+..-|+.-||.+.|+-|+=-++|.|+.|...+|..+-.|.+|...+.|++.++.
T Consensus        58 ~k~T~~Yl~~F-~Rfkd~e~~~a~~~~L~~~gfh~fEiAqlGsL~c~saeEAktLiPSL~nkidD~~lq~ilkels~  133 (138)
T COG5250          58 FKSTLGYLDDF-CRFKDKEVAEALRTTLSGLGFHEFEIAQLGSLFCQSAEEAKTLIPSLGNKIDDAILQAILKELSL  133 (138)
T ss_pred             HHHHHHHHHHH-HHhhhHHHHHHHHHHHccCCcchhhHHHhhccccccHHHHHhhcccccccccHHHHHHHHHHHHH
Confidence            37899999986 34556788999999999999999999999999999999999999999999999999999988764

>KOG4168 consensus Predicted RNA polymerase III subunit C17 [Transcription]

Probab=84.35  E-value=1.4  Score=35.23  Aligned_cols=65  Identities=18%  Similarity=0.249  Sum_probs=47.8

Q ss_pred             chHHHHHHHhhCcccccCHHHHHHHHHHhhcCCCCHHHHHHHhcCCCCcHHHHHHhhccccc--CCCHHHHHHHHHH
Q 031131           39 SEFKVYDYLVESAACNQTRNIINEFLEKSKKFKLAKAEILNIINIRPSSLVEVDSIIEQCDT--RFQEEELQELVDL  113 (165)
Q Consensus        39 ~e~e~l~YL~~~p~~~qt~e~i~~l~~~L~~f~LTk~E~LQIvNl~Pts~veL~~iIEe~e~--RfsEeqieeIL~i  113 (165)
                      ..|+|++||...+|  +      .......++.+-+-+++|  |..|++.-+.+..|.+--.  -.+.|-|-+++.+
T Consensus        12 tnyEVl~fL~el~~--~------n~~~~k~s~r~~~Q~~~~--~~l~ti~~et~kYls~~~n~~~qt~E~i~el~~k   78 (149)
T KOG4168|consen   12 TNYEVLQFLNELEC--M------NEEADKSSHRLGAQNILQ--NDLPTITYETLKYLSDNKNASTQTNESIIELITK   78 (149)
T ss_pred             hhHHHHHHHHHhhh--h------hhhhhhhhhhhhcccccc--cccchhHHHHHHHHhcCcccccccHHHHHHHHHH
Confidence            35999999999998  3      333455778888999999  9999999999988887662  2455544444433

>KOG0030 consensus Myosin essential light chain, EF-Hand protein superfamily [Cytoskeleton]

Probab=80.84  E-value=2.1  Score=34.21  Aligned_cols=86  Identities=20%  Similarity=0.302  Sum_probs=53.2

Q ss_pred             ccCcHHHHHHHHHhhcCCCCCCCCCcccccchHH----HHHHHhhCcccccCHHHHHHHHHHhhcCCCCHHHHHHHhcCC
Q 031131            9 GPLTNFEVFDFLRCKGASKDPTRVLVPVTPSEFK----VYDYLVESAACNQTRNIINEFLEKSKKFKLAKAEILNIINIR   84 (165)
Q Consensus         9 a~LSN~EVl~~L~~~~~~~~~~~~~~~l~~~e~e----~l~YL~~~p~~~qt~e~i~~l~~~L~~f~LTk~E~LQIvNl~   84 (165)
                      ..=||.||.+.|.+-++.+-      ++..+.++    ++.-+.+.  .  ..-....|++-|+.|+=-..=.+      
T Consensus        42 ~nPT~aeV~k~l~~~~~~~~------~~~rl~FE~fLpm~q~vakn--k--~q~t~edfvegLrvFDkeg~G~i------  105 (152)
T KOG0030|consen   42 QNPTNAEVLKVLGQPKRREM------NVKRLDFEEFLPMYQQVAKN--K--DQGTYEDFVEGLRVFDKEGNGTI------  105 (152)
T ss_pred             CCCcHHHHHHHHcCcccchh------hhhhhhHHHHHHHHHHHHhc--c--ccCcHHHHHHHHHhhcccCCcce------
Confidence            34589999999976555431      11112232    23334443  1  22466778888888853222221      


Q ss_pred             CCcHHHHHHhhcccccCCCHHHHHHHHH
Q 031131           85 PSSLVEVDSIIEQCDTRFQEEELQELVD  112 (165)
Q Consensus        85 Pts~veL~~iIEe~e~RfsEeqieeIL~  112 (165)
                        ..++|+-|+=-+-+|+|+++++++|+
T Consensus       106 --~~aeLRhvLttlGekl~eeEVe~Lla  131 (152)
T KOG0030|consen  106 --MGAELRHVLTTLGEKLTEEEVEELLA  131 (152)
T ss_pred             --eHHHHHHHHHHHHhhccHHHHHHHHc
Confidence              24678888888899999999999986

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	165
3ayh_A	136	Crystal Structure Of The C1725 SUBCOMPLEX FROM S. P		1e-05
2ckz_A	161	X-Ray Structure Of Rna Polymerase Iii Subcomplex C1		4e-05

>pdb|3AYH|A Chain A, Crystal Structure Of The C1725 SUBCOMPLEX FROM S. POMBE RNA Polymerase Iii Length = 136

Iteration: 1
 Score = 45.8 bits (107), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 36/113 (31%), Positives = 57/113 (50%), Gaps = 10/113 (8%)
Query: 1   MKILEANAGPLTNFEVFDFLR-------CKGASKDPTRVLVP--VTPSEFKVYDYLVESA 51
           MK+LEA    LTN EVF  L+        +   +   + LV   +   +F++  YL    
Sbjct: 8   MKVLEARDAYLTNAEVFFHLKEMENEQNARTQERGAAQALVCENLRTIQFEILKYLSSQG 67
Query: 52  AC-NQTRNIINEFLEKSKKFKLAKAEILNIINIRPSSLVEVDSIIEQCDTRFQ 103
            C   T+    + +    +F+L KAEIL I+N +PSS+ E+ + IE  + RF+
Sbjct: 68  NCEGLTKERFLDCIAIFNEFELTKAEILVILNNKPSSVPELYACIEGIEERFK 120

>pdb|2CKZ|A Chain A, X-Ray Structure Of Rna Polymerase Iii Subcomplex C17-C25. Length = 161

Iteration: 1
 Score = 43.9 bits (102), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 20/41 (48%), Positives = 28/41 (68%)
Query: 62  EFLEKSKKFKLAKAEILNIINIRPSSLVEVDSIIEQCDTRF 102
           E + K   FKL KAE L I+N  P+++V + SI+E+CD RF
Sbjct: 105 ELMTKLNSFKLFKAEKLQIVNQLPANMVHLYSIVEECDARF 145

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	165
3ayh_A	136	DNA-directed RNA polymerase III subunit RPC9; tran	3e-31
2ckz_A	161	DNA-directed RNA polymerase III 18 KD polypeptide;	5e-26
2c35_A	152	Human RPB4, DNA-directed RNA polymerase II 16 kDa	3e-08
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-06

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

 Score =  108 bits (271), Expect = 3e-31
 Identities = 40/129 (31%), Positives = 65/129 (50%), Gaps = 10/129 (7%)

Query: 1   MKILEANAGPLTNFEVFDFLRCKGASKDPT---------RVLVPVTPSEFKVYDYLVESA 51
           MK+LEA    LTN EVF  L+     ++            V   +   +F++  YL    
Sbjct: 8   MKVLEARDAYLTNAEVFFHLKEMENEQNARTQERGAAQALVCENLRTIQFEILKYLSSQG 67

Query: 52  ACN-QTRNIINEFLEKSKKFKLAKAEILNIINIRPSSLVEVDSIIEQCDTRFQEEELQEL 110
            C   T+    + +    +F+L KAEIL I+N +PSS+ E+ + IE  + RF+EE++ +L
Sbjct: 68  NCEGLTKERFLDCIAIFNEFELTKAEILVILNNKPSSVPELYACIEGIEERFKEEDIFKL 127

Query: 111 VDLVIEVLP 119
           V+ +    P
Sbjct: 128 VEKINTTFP 136

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

 Score = 96.1 bits (238), Expect = 5e-26
 Identities = 34/159 (21%), Positives = 58/159 (36%), Gaps = 43/159 (27%)

Query: 1   MKILEANAGPLTNFEVFDFLR--------------------------------------- 21
           MK+LE     L+++EV  FL                                        
Sbjct: 1   MKVLEERNAFLSDYEVLKFLTDLEKKHLWDQKSLAALKKSRSKGKQNRPYNHPELQGITR 60

Query: 22  ----CKGASKDPTRVLVPVTPSEFKVYDYLVESAACNQTRNIINEFLEKSKKFKLAKAEI 77
                   +K+           E        +S     +     E + K   FKL KAE 
Sbjct: 61  NVVNYLSINKNFINQEDEGEERESSGAKDAEKSGISKMSDESFAELMTKLNSFKLFKAEK 120

Query: 78  LNIINIRPSSLVEVDSIIEQCDTRFQEEELQELVDLVIE 116
           L I+N  P+++V + SI+E+CD RF E+ ++E+++++  
Sbjct: 121 LQIVNQLPANMVHLYSIVEECDARFDEKTIEEMLEIISA 159

>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 = 49.3 bits (117), Expect = 3e-08
 Identities = 25/109 (22%), Positives = 46/109 (42%), Gaps = 1/109 (0%)

Query: 6   ANAGPLTNFEVFDFLRCKGASKDPTRVLVPVTPSEFKVYDYLVESAACNQTRNIINEFLE 65
             A  L N EV   L  +    +       ++    K  +Y    +   + R  I     
Sbjct: 37  ETAETLLNSEVHMLLEHRKQQNESAEDEQELSEVFMKTLNYTARFSRF-KNRETIASVRS 95

Query: 66  KSKKFKLAKAEILNIINIRPSSLVEVDSIIEQCDTRFQEEELQELVDLV 114
              + KL K E+  + N+ P +  E  ++I   + RF++EELQ+++D +
Sbjct: 96  LLLQKKLHKFELACLANLCPETAEESKALIPSLEGRFEDEELQQILDDI 144

>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 = 46.0 bits (108), Expect = 2e-06
 Identities = 24/125 (19%), Positives = 46/125 (36%), Gaps = 33/125 (26%)

Query: 14  FEVFDFLRCKGASKDPTRVLVPVTPSEFKVYDYLVESAACNQTRNIINEFLEKSKKFKLA 73
           +  F+   CK        +L+  T    +V D+L  +   + + +  +  L   +   L 
Sbjct: 259 WNAFNL-SCK--------ILL--TTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSL- 306

Query: 74  KAEILNIINIRPSSL-VEVD-------SII-----EQCDT-----RFQEEELQELVDLVI 115
              +L  ++ RP  L  EV        SII     +   T         ++L  +++  +
Sbjct: 307 ---LLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSL 363

Query: 116 EVLPP 120
            VL P
Sbjct: 364 NVLEP 368

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	165
3ayh_A	136	DNA-directed RNA polymerase III subunit RPC9; tran	100.0
2ckz_A	161	DNA-directed RNA polymerase III 18 KD polypeptide;	100.0
2c35_A	152	Human RPB4, DNA-directed RNA polymerase II 16 kDa	99.88
3h0g_D	135	DNA-directed RNA polymerase II subunit RPB4; trans	99.8
1y14_A	187	B32, RPB4, DNA-directed RNA polymerase II 32 kDa p	99.64
1go3_F	107	DNA-directed RNA polymerase subunit F; transferase	99.5
4ayb_F	113	DNA-directed RNA polymerase; transferase, multi-su	99.5
3hou_D	221	DNA-directed RNA polymerase II subunit RPB4; RNA p	99.27
4h62_V	31	Mediator of RNA polymerase II transcription subun;	80.25

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

Probab=100.00  E-value=7.8e-41  Score=258.23  Aligned_cols=119  Identities=34%  Similarity=0.507  Sum_probs=108.5

Q ss_pred             CeeecCCcccCcHHHHHHHHHhhcCCCC-------CC--CCCcccccchHHHHHHHhhCcccc-cCHHHHHHHHHHhhcC
Q 031131            1 MKILEANAGPLTNFEVFDFLRCKGASKD-------PT--RVLVPVTPSEFKVYDYLVESAACN-QTRNIINEFLEKSKKF   70 (165)
Q Consensus         1 MkIl~~~~a~LSN~EVl~~L~~~~~~~~-------~~--~~~~~l~~~e~e~l~YL~~~p~~~-qt~e~i~~l~~~L~~f   70 (165)
                      |||+++++++|||||||+||+++++++.       ++  ....++.++.+++++||+++||+. |++++|.+|+++|++|
T Consensus         8 Mkil~~~~a~LsN~EVl~~L~~~~~~~~~~~~~~~~~~~~~~~~l~ti~~e~l~YL~~~p~~~~q~~e~i~~l~~~L~~~   87 (136)
T 3ayh_A            8 MKVLEARDAYLTNAEVFFHLKEMENEQNARTQERGAAQALVCENLRTIQFEILKYLSSQGNCEGLTKERFLDCIAIFNEF   87 (136)
T ss_dssp             CEEEEEEEEEECHHHHHHHHHHHHHHHHHHHHHHGGGGCCCCHHHHHHHHHHHHHHHTTTCCTTCCHHHHHHHHHTTTTT
T ss_pred             ceEeccccccccHHHHHHHHHHHHhhhcccccccCCccccccchHHHHHHHHHHHHHhCCCccccCHHHHHHHHHHHHhc
Confidence            9999999999999999999998765321       11  123567778899999999999987 9999999999999999


Q ss_pred             CCCHHHHHHHhcCCCCcHHHHHHhhcccccCCCHHHHHHHHHHHHHhCC
Q 031131           71 KLAKAEILNIINIRPSSLVEVDSIIEQCDTRFQEEELQELVDLVIEVLP  119 (165)
Q Consensus        71 ~LTk~E~LQIvNl~Pts~veL~~iIEe~e~RfsEeqieeIL~iI~e~L~  119 (165)
                      +|||+|+|||||+||+|+||||+|||+||+||||||+++||++|+++||
T Consensus        88 ~Ltk~E~LqivNl~P~t~vel~~iIEe~e~Rfsee~ie~IL~~i~~~lp  136 (136)
T 3ayh_A           88 ELTKAEILVILNNKPSSVPELYACIEGIEERFKEEDIFKLVEKINTTFP  136 (136)
T ss_dssp             CCCHHHHHHHHHHCCCSHHHHHHHSTTHHHHHTTTTHHHHHHHHHHHCC
T ss_pred             CCCHHHHHHHhccCCCCHHHHHHHHHhcccCCCHHHHHHHHHHHHHhCc
Confidence            9999999999999999999999999999999999999999999999997

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

Probab=100.00  E-value=1.4e-37  Score=246.57  Aligned_cols=117  Identities=29%  Similarity=0.462  Sum_probs=39.2

Q ss_pred             CeeecCCcccCcHHHHHHHHHhhcCCCC-------------------CCCCCcccccchHHHHHHHhhCcc---------
Q 031131            1 MKILEANAGPLTNFEVFDFLRCKGASKD-------------------PTRVLVPVTPSEFKVYDYLVESAA---------   52 (165)
Q Consensus         1 MkIl~~~~a~LSN~EVl~~L~~~~~~~~-------------------~~~~~~~l~~~e~e~l~YL~~~p~---------   52 (165)
                      |||+++|+++|||||||+||++++.++.                   +.....++.++.+++++||+++|+         
T Consensus         1 MkIl~~~~a~LSN~EVl~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~ti~~e~~~YL~~~p~~~~~~~~~~   80 (161)
T 2ckz_A            1 MKVLEERNAFLSDYEVLKFLTDLEKKHLWDQKSLAALKKSRSKGKQNRPYNHPELQGITRNVVNYLSINKNFINQEDEGE   80 (161)
T ss_dssp             CEEEEEEEEEECHHHHHHHHHHHHHHTTCSHHHHHCC----------CCCCCHHHHHHHHHHHHHHTC------------
T ss_pred             CcccchhhhhhhHHHHHHHHHHhhhhccccccchhhhhcccccccccCCCCCccHHHHHHHHHHHHHhCCcccccccccc
Confidence            9999999999999999999998654321                   111235677888999999999998         


Q ss_pred             ---------------cccCHHHHHHHHHHhhcCCCCHHHHHHHhcCCCCcHHHHHHhhcccccCCCHHHHHHHHHHHHHh
Q 031131           53 ---------------CNQTRNIINEFLEKSKKFKLAKAEILNIINIRPSSLVEVDSIIEQCDTRFQEEELQELVDLVIEV  117 (165)
Q Consensus        53 ---------------~~qt~e~i~~l~~~L~~f~LTk~E~LQIvNl~Pts~veL~~iIEe~e~RfsEeqieeIL~iI~e~  117 (165)
                                     +.+++++|++|+++|++|+|||+|+|||||+||+|+||||+|||+||+|||||++++||++|+++
T Consensus        81 ~~~~~~~~~~~~~~~~~~~~e~i~~l~~~L~~~~Ltk~E~lqivNl~P~s~vel~~iIEe~e~Rfsee~ie~IL~ii~~~  160 (161)
T 2ckz_A           81 ERESSGAKDAEKSGISKMSDESFAELMTKLNSFKLFKAEKLQIVNQLPANMVHLYSIVEECDARFDEKTIEEMLEIISAY  160 (161)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             ccccccccccccccccccCHHHHHHHHHHHHhcCCCHHHHHHHhccCCCCHHHHHHHHHhcccCCCHHHHHHHHHHHHHh
Confidence                           56889999999999999999999999999999999999999999999999999999999999875

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

Probab=99.88  E-value=1e-22  Score=159.72  Aligned_cols=113  Identities=22%  Similarity=0.262  Sum_probs=96.7

Q ss_pred             CCcccCcHHHHHHHHHhhcCCCCCCCCCcccccchHHHHHHHhhCcccccCHHHHHHHHHHhhcCCCCHHHHHHHhcCCC
Q 031131            6 ANAGPLTNFEVFDFLRCKGASKDPTRVLVPVTPSEFKVYDYLVESAACNQTRNIINEFLEKSKKFKLAKAEILNIINIRP   85 (165)
Q Consensus         6 ~~~a~LSN~EVl~~L~~~~~~~~~~~~~~~l~~~e~e~l~YL~~~p~~~qt~e~i~~l~~~L~~f~LTk~E~LQIvNl~P   85 (165)
                      .+...|||+||..+|.+++..+...+...++..+.+++++||.+++ ..++++++.+|++.|.+|+|++.|++||+|+||
T Consensus        37 ~~~~~Lt~sEV~~lL~~~~~~~~~~~~~~els~v~~kTl~Yl~~F~-k~k~~e~~~~l~e~L~~~~L~~~E~a~L~NL~P  115 (152)
T 2c35_A           37 ETAETLLNSEVHMLLEHRKQQNESAEDEQELSEVFMKTLNYTARFS-RFKNRETIASVRSLLLQKKLHKFELACLANLCP  115 (152)
T ss_dssp             SSCEECCHHHHHHHHHHHHHHHHSSCSSCCCCHHHHHHHHHHHHTC-SCCSHHHHHHHHHHHHTSSCCHHHHHHHHHHCC
T ss_pred             cccccccHHHHHHHHHHHHHhhcccccccchHHHHHHHHHHHHHcc-CCCCHHHHHHHHHHHHhcCCCHHHHHHhccCCC
Confidence            4678999999999999876432111111345555699999999998 346999999999999999999999999999999


Q ss_pred             CcHHHHHHhhcccccCCCHHHHHHHHHHHHHhCC
Q 031131           86 SSLVEVDSIIEQCDTRFQEEELQELVDLVIEVLP  119 (165)
Q Consensus        86 ts~veL~~iIEe~e~RfsEeqieeIL~iI~e~L~  119 (165)
                      .|++|+++||+.++.||+++++++||++|+++..
T Consensus       116 ~t~dEar~lipsl~~r~sdEeLe~ILd~l~k~r~  149 (152)
T 2c35_A          116 ETAEESKALIPSLEGRFEDEELQQILDDIQTKRS  149 (152)
T ss_dssp             SSHHHHHHHCGGGTTTSCHHHHHHHHHHHHHHCC
T ss_pred             CCHHHHHHHHHhhccCCCHHHHHHHHHHHHHHHh
Confidence            9999999999999999999999999999998764

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

Probab=99.80  E-value=2.9e-19  Score=137.77  Aligned_cols=108  Identities=16%  Similarity=0.086  Sum_probs=91.3

Q ss_pred             CcccCcHHHHHHHHHhhc----CCCCCCCCCcccccchHHHHHHHhhCcccccCHHHHHHHHHHhhcCCCCHHHHHHHhc
Q 031131            7 NAGPLTNFEVFDFLRCKG----ASKDPTRVLVPVTPSEFKVYDYLVESAACNQTRNIINEFLEKSKKFKLAKAEILNIIN   82 (165)
Q Consensus         7 ~~a~LSN~EVl~~L~~~~----~~~~~~~~~~~l~~~e~e~l~YL~~~p~~~qt~e~i~~l~~~L~~f~LTk~E~LQIvN   82 (165)
                      +...|||+||..+|++..    .......   ++..+-++|++|+.+++ ...+++++..+.+.|+. +|++.|+.||+|
T Consensus        21 ~a~~Ls~sEv~~lL~~~~~~r~~~~~~~~---~~~~v~~kTl~Yl~~Fs-k~~~~e~~~~v~~lL~~-~L~~fEia~L~N   95 (135)
T 3h0g_D           21 NEDMLTVSEAKILIETVLAQRARETNGEI---PMTDVMKKTVAYFNVFA-RFKTAEATYACERILGN-RFHKFERAQLGT   95 (135)
T ss_dssp             HSCBCCHHHHHHHHHHHHHHHHTTCCSCC---CCTTHHHHHHHHHHTTC-TTCSHHHHHHHHHHCCC-CSCHHHHHHHHH
T ss_pred             CcccccHHHHHHHHHHHHHHHHhcccCCc---chhHHHHHHHHHHHHcc-CCCCHHHHHHHHHHHHh-cCCHHHHHHHcc
Confidence            457899999999999642    2111112   33444599999999997 55689999999999999 999999999999


Q ss_pred             CCCCcHHHHHHhhcccccCCCHHHHHHHHHHHHHhCC
Q 031131           83 IRPSSLVEVDSIIEQCDTRFQEEELQELVDLVIEVLP  119 (165)
Q Consensus        83 l~Pts~veL~~iIEe~e~RfsEeqieeIL~iI~e~L~  119 (165)
                      +||.|++|+++||+.+++||+++++++||++|+.+-.
T Consensus        96 L~P~t~dEak~LIpsL~~r~~de~L~~IL~~l~~~r~  132 (135)
T 3h0g_D           96 LCCEDAEEARTLIPSLANKIDDQNLQGILDELSTLRK  132 (135)
T ss_dssp             HCCCCHHHHHHHCGGGTTTSCSHHHHHHHHHHHHHTT
T ss_pred             CCCCCHHHHHHHHHHhcccCCHHHHHHHHHHHHHHhc
Confidence            9999999999999999999999999999999998753

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

Probab=99.64  E-value=6e-16  Score=125.03  Aligned_cols=84  Identities=11%  Similarity=0.185  Sum_probs=77.9

Q ss_pred             ccccchHHHHHHHhhCcccccCHHHHHHHHHHhhcCCCCHHHHHHHhcCCCCcHHHHHHhhcccccCCCHHHHHHHHHHH
Q 031131           35 PVTPSEFKVYDYLVESAACNQTRNIINEFLEKSKKFKLAKAEILNIINIRPSSLVEVDSIIEQCDTRFQEEELQELVDLV  114 (165)
Q Consensus        35 ~l~~~e~e~l~YL~~~p~~~qt~e~i~~l~~~L~~f~LTk~E~LQIvNl~Pts~veL~~iIEe~e~RfsEeqieeIL~iI  114 (165)
                      ++..+.+++++|+.++++. ++++++.+|++.|..|+|+++|++||+|+||.|++|+++||+.++.||+++++++||++|
T Consensus       102 ~ls~v~~KTLeYl~rFsk~-kn~Esa~elre~L~~~kL~efE~aqLaNL~PeTadEaraLIpSle~rlsdEeLeeILd~L  180 (187)
T 1y14_A          102 GNNKDLKNTMQYLTNFSRF-RDQETVGAVIQLLKSTGLHPFEVAQLGSLACDTADEAKTLIPSLNNKISDDELERILKEL  180 (187)
T ss_dssp             SCCHHHHHHHHHHHHHCSC-CSHHHHHHHHHHHHTTTCCHHHHHHHHHSCCSSHHHHHHHSGGGTTTSCHHHHHHHHHHH
T ss_pred             cccHHHHHHHHHHHHccCC-CCHHHHHHHHHHHHhcCCCHHHHHHcCcCCCCCHHHHHHHHHhhccCCCHHHHHHHHHHH
Confidence            4555679999999999764 799999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHhCC
Q 031131          115 IEVLP  119 (165)
Q Consensus       115 ~e~L~  119 (165)
                      +++..
T Consensus       181 ~k~r~  185 (187)
T 1y14_A          181 SNLET  185 (187)
T ss_dssp             HHHCC
T ss_pred             HHhhc
Confidence            98753

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

Probab=99.50  E-value=1.7e-14  Score=107.10  Aligned_cols=99  Identities=15%  Similarity=0.227  Sum_probs=85.4

Q ss_pred             CcccCcHHHHHHHHHhhcCCCCCCCCCcccccchHHHHHHHhhCcccccCHHHHHHHHHHhhcCCCCHHHHHHHhcCCCC
Q 031131            7 NAGPLTNFEVFDFLRCKGASKDPTRVLVPVTPSEFKVYDYLVESAACNQTRNIINEFLEKSKKFKLAKAEILNIINIRPS   86 (165)
Q Consensus         7 ~~a~LSN~EVl~~L~~~~~~~~~~~~~~~l~~~e~e~l~YL~~~p~~~qt~e~i~~l~~~L~~f~LTk~E~LQIvNl~Pt   86 (165)
                      ....|||.||..+|.++....       .++.....+++|+.++.  +.+++...++++.|..++|++.+..||+|+||.
T Consensus         8 ~~~~lt~sEa~~iL~~~~~~~-------e~s~~~~ktl~y~~kFs--k~~~e~a~~l~e~L~~~~l~e~~a~~I~nl~P~   78 (107)
T 1go3_F            8 GERYVTVSEAAEIMYNRAQIG-------ELSYEQGCALDYLQKFA--KLDKEEAKKLVEELISLGIDEKTAVKIADILPE   78 (107)
T ss_dssp             EEEEECHHHHHHHHHHHHHHS-------CCCHHHHHHHHHHHHHC--CSCHHHHHHHHHHHHHTTCCHHHHHHHHHHCCC
T ss_pred             cccccCHHHHHHHHHHHHhcc-------cccHHHHHHHHHHHHHh--CCCHHHHHHHHHHHHhCCCCHHHHHHHHHhCCC
Confidence            345799999999999876531       33334489999999985  458899999999999999999999999999999


Q ss_pred             cHHHHHHhhcccccCCCHHHHHHHHHHHHHh
Q 031131           87 SLVEVDSIIEQCDTRFQEEELQELVDLVIEV  117 (165)
Q Consensus        87 s~veL~~iIEe~e~RfsEeqieeIL~iI~e~  117 (165)
                      |+.|+++||....  + ++++++||++|+++
T Consensus        79 t~dElraii~~~~--~-~eel~~ILd~l~k~  106 (107)
T 1go3_F           79 DLDDLRAIYYKRE--L-PENAEEILEIVRKY  106 (107)
T ss_dssp             SHHHHHHHSTTSC--C-CTTHHHHHHHHTTC
T ss_pred             CHHHHHHHHhccc--C-cHHHHHHHHHHHHc
Confidence            9999999999974  4 99999999999875

>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=99.50  E-value=3e-15  Score=112.05  Aligned_cols=106  Identities=18%  Similarity=0.188  Sum_probs=87.3

Q ss_pred             eeecCCcccCcHHHHHHHHHhhcCCCCCCCCCcccccchHHHHHHHhhCcccccCHHHHHHHHHHhhcCCCCHHHHHHHh
Q 031131            2 KILEANAGPLTNFEVFDFLRCKGASKDPTRVLVPVTPSEFKVYDYLVESAACNQTRNIINEFLEKSKKFKLAKAEILNII   81 (165)
Q Consensus         2 kIl~~~~a~LSN~EVl~~L~~~~~~~~~~~~~~~l~~~e~e~l~YL~~~p~~~qt~e~i~~l~~~L~~f~LTk~E~LQIv   81 (165)
                      +|++  ..++|+.||..+|.++....       .+..+...+++|++++.  +.+++...++++.|..++|++.++.||+
T Consensus         5 ~ii~--e~~it~~eakeiL~~~~~~~-------~~s~~~~ktl~y~~~Fs--k~~~e~a~~l~e~L~~~~l~~~~~a~Ia   73 (113)
T 4ayb_F            5 YIVE--EHYIPYSVAKKLLSDVIKSG-------SSSNLLQRTYDYLNSVE--KCDAESAQKVVEELSSIISREDVRAVLA   73 (113)
T ss_dssp             EEEE--EEEECTTGGGGTTTTTSSSS-------CCCTTHHHHHHHTTTTC--SSCHHHHHHHHHHHHTTCCCHHHHHHHH
T ss_pred             eeec--ccccCHHHHHHHHHHHHhcc-------cccHHHHHHHHHHHHHc--CCCHHHHHHHHHHHHHcCCCHHHHHHHH
Confidence            4443  46799999999998764432       22334589999999994  4688999999999999999999999999


Q ss_pred             cCCCCcHHHHHHhhcccccC-CCHHHHHHHHHHHHHhC
Q 031131           82 NIRPSSLVEVDSIIEQCDTR-FQEEELQELVDLVIEVL  118 (165)
Q Consensus        82 Nl~Pts~veL~~iIEe~e~R-fsEeqieeIL~iI~e~L  118 (165)
                      |+||.++.|+.+||...+.| |+++++++||++|++|.
T Consensus        74 nL~P~~~dElrali~s~e~~~~~deeL~~IL~~l~ky~  111 (113)
T 4ayb_F           74 SICPITPDEVRSILIMDSNRTYTSEDIQKIIDIIRKYI  111 (113)
T ss_dssp             HHCCCSSCCCCTTTTTTCCCCCCCTHHHHHHHHC----
T ss_pred             HcCCCCHHHHHHHHHhhccCCCCHHHHHHHHHHHHHHh
Confidence            99999999999999998877 89999999999999885

>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=99.27  E-value=1.7e-11  Score=100.84  Aligned_cols=78  Identities=12%  Similarity=0.204  Sum_probs=71.2

Q ss_pred             hHHHHHHHhhCcccccCHHHHHHHHHHhhcCCCCHHHHHHHhcCCCCcHHHHHHhhcccccCCCHHHHHHHHHHHHHhC
Q 031131           40 EFKVYDYLVESAACNQTRNIINEFLEKSKKFKLAKAEILNIINIRPSSLVEVDSIIEQCDTRFQEEELQELVDLVIEVL  118 (165)
Q Consensus        40 e~e~l~YL~~~p~~~qt~e~i~~l~~~L~~f~LTk~E~LQIvNl~Pts~veL~~iIEe~e~RfsEeqieeIL~iI~e~L  118 (165)
                      -.++++|+.++.. .-+++++..+.+.|..++|++.|+.||+|+||.++.|+.+||..+..||+++++++||+.|+.+-
T Consensus       141 f~KTLdYl~rFSK-fkn~EAv~aVrELL~~~gLheFEiAqLANLcPeTaDEARALIPSL~~k~sDEeLqeILdeLskyR  218 (221)
T 3hou_D          141 LKNTMQYLTNFSR-FRDQETVGAVIQLLKSTGLHPFEVAQLGSLACDTADEAKTLIPSLNNKISDDELERILKELSNLE  218 (221)
T ss_dssp             HHHHHHHHHHSCS-CCCHHHHHHHHHHHTTSCCCHHHHHHHHHSCCCSHHHHHHHCTTCTTSSCHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHhcC-CCcHHHHHHHHHHHHhcCCChHHhheecccCCCCHHHHHHHHHhhcccCCHHHHHHHHHHHHHhh
Confidence            4899999999864 33678888888888999999999999999999999999999999999999999999999999874

>4h62_V Mediator of RNA polymerase II transcription subun; mediator complex, nucleus; HET: MES; 3.00A {Saccharomyces cerevisiae}

Probab=80.25  E-value=0.98  Score=25.69  Aligned_cols=20  Identities=45%  Similarity=0.750  Sum_probs=14.7

Q ss_pred             cCCCHHHHHHHHHHHHHhCC
Q 031131          100 TRFQEEELQELVDLVIEVLP  119 (165)
Q Consensus       100 ~RfsEeqieeIL~iI~e~L~  119 (165)
                      .||+|.||+++|+-+-++|-
T Consensus         7 trfdekqieelldncietfv   26 (31)
T 4h62_V            7 TRFDEKQIEELLDNCIETFV   26 (31)
T ss_dssp             ---CHHHHHHHHHHHHHHHH
T ss_pred             ccccHHHHHHHHHHHHHHHH
Confidence            49999999999998877663

---

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	165
d2c35a1	129	a.60.8.2 (A:14-142) RNA polymerase II subunit RBP4	4e-20
d1y14a_	176	a.60.8.2 (A:) RNA polymerase II subunit RBP4 (RpoF	3e-04
d1go3f_	107	a.60.8.2 (F:) RNA polymerase II subunit RBP4 (RpoF	0.001

>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 = 78.7 bits (194), Expect = 4e-20
 Identities = 25/108 (23%), Positives = 46/108 (42%), Gaps = 1/108 (0%)

Query: 7   NAGPLTNFEVFDFLRCKGASKDPTRVLVPVTPSEFKVYDYLVESAACNQTRNIINEFLEK 66
            A  L N EV   L  +    +       ++    K  +Y     +  + R  I      
Sbjct: 15  TAETLLNSEVHMLLEHRKQQNESAEDEQELSEVFMKTLNYT-ARFSRFKNRETIASVRSL 73

Query: 67  SKKFKLAKAEILNIINIRPSSLVEVDSIIEQCDTRFQEEELQELVDLV 114
             + KL K E+  + N+ P +  E  ++I   + RF++EELQ+++D +
Sbjct: 74  LLQKKLHKFELACLANLCPETAEESKALIPSLEGRFEDEELQQILDDI 121

>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 = 37.2 bits (86), Expect = 3e-04
 Identities = 9/73 (12%), Positives = 31/73 (42%), Gaps = 1/73 (1%)

Query: 42  KVYDYLVESAACNQTRNIINEFLEKSKKFKLAKAEILNIINIRPSSLVEVDSIIEQCDTR 101
               YL  + +  + +  +   ++  K   L   E+  + ++   +  E  ++I   + +
Sbjct: 98  NTMQYL-TNFSRFRDQETVGAVIQLLKSTGLHPFEVAQLGSLACDTADEAKTLIPSLNNK 156

Query: 102 FQEEELQELVDLV 114
             ++EL+ ++  +
Sbjct: 157 ISDDELERILKEL 169

>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 = 34.7 bits (80), Expect = 0.001
 Identities = 14/71 (19%), Positives = 31/71 (43%), Gaps = 2/71 (2%)

Query: 42  KVYDYLVESAACNQTRNIINEFLEKSKKFKLAKAEILNIINIRPSSLVEVDSIIEQCDTR 101
              DYL + A  +  +    + +E+     + +   + I +I P  L ++ +I  + +  
Sbjct: 36  CALDYLQKFAKLD--KEEAKKLVEELISLGIDEKTAVKIADILPEDLDDLRAIYYKRELP 93

Query: 102 FQEEELQELVD 112
              EE+ E+V 
Sbjct: 94  ENAEEILEIVR 104

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	165
d2c35a1	129	RNA polymerase II subunit RBP4 (RpoF) {Human (Homo	99.92
d1y14a_	176	RNA polymerase II subunit RBP4 (RpoF) {Baker's yea	99.35
d1go3f_	107	RNA polymerase II subunit RBP4 (RpoF) {Archaeon Me	99.28

>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=99.92  E-value=1.4e-25  Score=169.53  Aligned_cols=113  Identities=22%  Similarity=0.262  Sum_probs=97.9

Q ss_pred             CCcccCcHHHHHHHHHhhcCCCCCCCCCcccccchHHHHHHHhhCcccccCHHHHHHHHHHhhcCCCCHHHHHHHhcCCC
Q 031131            6 ANAGPLTNFEVFDFLRCKGASKDPTRVLVPVTPSEFKVYDYLVESAACNQTRNIINEFLEKSKKFKLAKAEILNIINIRP   85 (165)
Q Consensus         6 ~~~a~LSN~EVl~~L~~~~~~~~~~~~~~~l~~~e~e~l~YL~~~p~~~qt~e~i~~l~~~L~~f~LTk~E~LQIvNl~P   85 (165)
                      .+...|||+||+.+|++++..+...+.-.++.++.+++++|++++ |+.++++++..+.+.|+.|+|+++|++||+|+||
T Consensus        14 ~~~~~Lt~~Ev~~iL~~~~~~~~~~~~~~~l~~~~~ktl~Yl~~f-ak~~~~es~~~~~~ll~~~~L~~~E~~~i~Nl~P   92 (129)
T d2c35a1          14 ETAETLLNSEVHMLLEHRKQQNESAEDEQELSEVFMKTLNYTARF-SRFKNRETIASVRSLLLQKKLHKFELACLANLCP   92 (129)
T ss_dssp             SSCEECCHHHHHHHHHHHHHHHHSSCSSCCCCHHHHHHHHHHHHT-CSCCSHHHHHHHHHHHHTSSCCHHHHHHHHHHCC
T ss_pred             cchhhhhHHHHHHHHHHHHHHHhcccccccHHHHHHHHHHHHHHh-ccCCCHHHHHHHHHHhcccCCCHHHHHHHhCCCC
Confidence            467899999999999876543322222345666679999999886 5678999999999999999999999999999999


Q ss_pred             CcHHHHHHhhcccccCCCHHHHHHHHHHHHHhCC
Q 031131           86 SSLVEVDSIIEQCDTRFQEEELQELVDLVIEVLP  119 (165)
Q Consensus        86 ts~veL~~iIEe~e~RfsEeqieeIL~iI~e~L~  119 (165)
                      +|++|+++||++|+.|||++++++||++|+++.+
T Consensus        93 ~~~~El~~li~~l~~r~see~l~~iLd~l~~~r~  126 (129)
T d2c35a1          93 ETAEESKALIPSLEGRFEDEELQQILDDIQTKRS  126 (129)
T ss_dssp             SSHHHHHHHCGGGTTTSCHHHHHHHHHHHHHHCC
T ss_pred             CCHHHHHHHHHHhccCCCHHHHHHHHHHHHHHhc
Confidence            9999999999999999999999999999999865

>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=99.35  E-value=1.4e-12  Score=102.52  Aligned_cols=76  Identities=12%  Similarity=0.233  Sum_probs=71.0

Q ss_pred             HHHHHHHhhCcccccCHHHHHHHHHHhhcCCCCHHHHHHHhcCCCCcHHHHHHhhcccccCCCHHHHHHHHHHHHHh
Q 031131           41 FKVYDYLVESAACNQTRNIINEFLEKSKKFKLAKAEILNIINIRPSSLVEVDSIIEQCDTRFQEEELQELVDLVIEV  117 (165)
Q Consensus        41 ~e~l~YL~~~p~~~qt~e~i~~l~~~L~~f~LTk~E~LQIvNl~Pts~veL~~iIEe~e~RfsEeqieeIL~iI~e~  117 (165)
                      .+|++|+.++.. ..+++++..+.+.|+.++|++.|+.||+|+||.|+.|+.++|..++.||+++++++||+.|+++
T Consensus        97 ~kTldYl~~Fsk-~k~~es~~~vrelL~~~~L~~fE~a~L~NLcPet~eEAkaLiPSL~~k~~de~Lq~IL~~L~~~  172 (176)
T d1y14a_          97 KNTMQYLTNFSR-FRDQETVGAVIQLLKSTGLHPFEVAQLGSLACDTADEAKTLIPSLNNKISDDELERILKELSNL  172 (176)
T ss_dssp             HHHHHHHHHHCS-CCSHHHHHHHHHHHHTTTCCHHHHHHHHHSCCSSHHHHHHHSGGGTTTSCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcc-CCCHHHHHHHHHHHHhcCCCHHHHHHhhccCCCCHHHHHHHhhhhcccCCHHHHHHHHHHHHHh
Confidence            799999999853 3478999999999999999999999999999999999999999999999999999999999876

>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=99.28  E-value=4.2e-12  Score=92.52  Aligned_cols=99  Identities=14%  Similarity=0.193  Sum_probs=80.7

Q ss_pred             CcccCcHHHHHHHHHhhcCCCCCCCCCcccccchHHHHHHHhhCcccccCHHHHHHHHHHhhcCCCCHHHHHHHhcCCCC
Q 031131            7 NAGPLTNFEVFDFLRCKGASKDPTRVLVPVTPSEFKVYDYLVESAACNQTRNIINEFLEKSKKFKLAKAEILNIINIRPS   86 (165)
Q Consensus         7 ~~a~LSN~EVl~~L~~~~~~~~~~~~~~~l~~~e~e~l~YL~~~p~~~qt~e~i~~l~~~L~~f~LTk~E~LQIvNl~Pt   86 (165)
                      ...++|++||..+|.++....       .++.....+++|++++.  +.+++.+.++++.|..++|++.++.||+|+||.
T Consensus         8 ~e~~lt~ae~keiL~~~~~~~-------elsye~~~tL~y~~~fa--k~~~e~~~~l~~~L~~~~~~~~~aakIanL~P~   78 (107)
T d1go3f_           8 GERYVTVSEAAEIMYNRAQIG-------ELSYEQGCALDYLQKFA--KLDKEEAKKLVEELISLGIDEKTAVKIADILPE   78 (107)
T ss_dssp             EEEEECHHHHHHHHHHHHHHS-------CCCHHHHHHHHHHHHHC--CSCHHHHHHHHHHHHHTTCCHHHHHHHHHHCCC
T ss_pred             hccccCHHHHHHHHHHhhccc-------cccHHHHHHHHHHHHHH--cCCHHHHHHHHHHHHhcCCCHHHHHHHHHhCCC
Confidence            356899999999998764332       34434588999999984  458999999999999999999999999999999


Q ss_pred             cHHHHHHhhcccccCCCHHHHHHHHHHHHHh
Q 031131           87 SLVEVDSIIEQCDTRFQEEELQELVDLVIEV  117 (165)
Q Consensus        87 s~veL~~iIEe~e~RfsEeqieeIL~iI~e~  117 (165)
                      |+.|+++|+......++.   ++|+++|.+|
T Consensus        79 ~~dElrai~~~~~~~~~~---eeIl~il~~y  106 (107)
T d1go3f_          79 DLDDLRAIYYKRELPENA---EEILEIVRKY  106 (107)
T ss_dssp             SHHHHHHHSTTSCCCTTH---HHHHHHHTTC
T ss_pred             CHHHHHHHHHHhccCCCH---HHHHHHHHHh
Confidence            999999999875444544   5678887765