Psyllid ID: psy6966

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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-----
Protein Sequence
MLPLHPLILPPSSPYSCTSTPLILPRTTHLILNAHSPSGIRSYPSPPTPHPSSTSKGPPHWTPYIRPDPSPFILPLTGVSHPLDLHPSVLLLEGTTGSYGPEGTWIHDPLYGLRGGVILDYHLLVLETTIVLGIEAVRKSVEKEMNTVLQFYGLY
Secondary Structure (PSIPRED)
cccccccccccccccccccccEEcccccEEEEccccccccccccccccccccccccccccccccccccccccEEEcccccccccccccEEEEEcccccccccccEEccccccccccEEEEccccHHHHHHHHHHHHHHHHHHHHHccEEEccccc
Secondary Structure Prediction (SSPRO)
ccccccccccccccccccccccccccccHHEEccccccccccccccccccccccccccccccccccccccccEEccccccccccccccEEEEEcccccccccccEEcccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccc
Coil and Loop (DISEMBL)
mlplhplilppsspysctstplilprtthlilnahspsgirsypspptphpsstskgpphwtpyirpdpspfilpltgvshpldlhpsvlllegttgsygpegtwihdplyglrggviLDYHLLVLETTIVLGIEAVRKSVEKEMNTVLQFYGLY
Flexible Loop (DISEMBL)
mlplhplilppsspyscTSTPLILPRTTHLILNAHSPSGIRSYPSPPTPHPSSTSKGPPHWTPYIRPDPSPFILPLTGVSHPLDLHPSVLLLEGTTGSYGPEGTWIHDPLYGLRGGVILDYHLLVLETTIVLGIEAVRKSVEKEMNtvlqfygly
Low Complexity Region (SEG)
MlplhplilppsspysctstpLILPRTTHLILNAHSPSGIRsypspptphpsstskgpphWTPYIRPDPSPFILPLTGVSHPLDLHPSVLLLEGTTGSYGPEGTWIHDPLYGLRGGVILDYHLLVLETTIVLGIEAVRKSVEKEMNTVLQFYGLY
Disordered region (IsUnstruct)
****************CTSTPLILPRTTHLILN*****************************PYIRPDPSPFILPLTGVSHPLDLHPSVLLLEGTTGSYGPEGTWIHDPLYGLRGGVILDYHLLVLETTIVLGIEAVRKSVEKEMNTVLQFYG**
Disordered Region (DISOPRED)
**PLHPLILPPSSPYSCTSTPLILPRTTHLILNAHSP************************TPYIRPDPSPFILPLTGVSHPLDLHPSVLLLEGTTGSYGPEGTWIHDPLYGLRGGVILDYHLLVLETTIVLGIEAVRKSVEKEMNTVLQFYGLY
Disordered Region (DISEMBL)
MLPLHPLILPPSSPYSCTSTPLILPRTTHLILNAHSPSGIRS****************PHWTPYIRPDPSPFILPLTGVSHPLDLHPSVLLLEGTTGSYGPEGTWIHDPLYGLRGGVILDYHLLVLETTIVLGIEAVRKSVEKEMNTVLQFYGLY
Disordered Region (DISPRO)
*LPLHPLILPPSSPYSCTSTPLILPRTTHLILNAHSPSG**S**S************PPHWTPYIRPDPSPFILPLTGVSHPLDLHPSVLLLEGTTGSYGPEGTWIHDPLYGLRGGVILDYHLLVLETTIVLGIEAVRKSVEKEMNTVLQFYGLY
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MLPLHPLILPPSSPYSCTSTPLILPRTTHLILNAHSPSGIRSYPSPPTPHPSSTSKGPPHWTPYIRPDPSPFILPLTGVSHPLDLHPSVLLLEGTTGSYGPEGTWIHDPLYGLRGGVILDYHLLVLETTIVLGIEAVRKSVEKEMNTVLQFYGLY
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	155	2.2.26 [Sep-21-2011]
P04052	1887	DNA-directed RNA polymera	yes	N/A	0.2	0.016	0.806	2e-07

>sp|P04052|RPB1_DROME DNA-directed RNA polymerase II subunit RPB1 OS=Drosophila melanogaster GN=RpII215 PE=3 SV=4

 Score = 54.7 bits (130), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 25/31 (80%), Positives = 26/31 (83%)

Query: 125  VLETTIVLGIEAVRKSVEKEMNTVLQFYGLY 155
            + E   VLGIEAVRKSVEKEMN VLQFYGLY
Sbjct: 1354 ICEIFQVLGIEAVRKSVEKEMNAVLQFYGLY 1384

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Largest and catalytic component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Forms the polymerase active center together with the second largest subunit. 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. RPB1 is part of the core element with the central large cleft, the clamp element that moves to open and close the cleft and the jaws that are thought to grab the incoming DNA template. At the start of transcription, a single stranded DNA template strand of the promoter is positioned within the central active site cleft of Pol II. A bridging helix emanates from RPB1 and crosses the cleft near the catalytic site and is thought to promote translocation of Pol II by acting as a ratchet that moves the RNA-DNA hybrid through the active site by switching from straight to bent conformations at each step of nucleotide addition. During transcription elongation, Pol II moves on the template as the transcript elongates. Elongation is influenced by the phosphorylation status of the C-terminal domain (CTD) of Pol II largest subunit (RPB1), which serves as a platform for assembly of factors that regulate transcription initiation, elongation, termination and mRNA processing.
Drosophila melanogaster (taxid: 7227)
EC: 2EC: .EC: 7EC: .EC: 7EC: .EC: 6

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	155
321464303	1895	hypothetical protein DAPPUDRAFT_306846 [	0.225	0.018	0.771	3e-06
324120512	1882	RNA polymerase II largest subunit [Petro	0.2	0.016	0.838	3e-06
324120588	1754	RNA polymerase II largest subunit [Steno	0.2	0.017	0.838	5e-06
328722767	1958	PREDICTED: DNA-directed RNA polymerase I	0.2	0.015	0.838	5e-06
324120560	1803	RNA polymerase II largest subunit [Crypt	0.2	0.017	0.838	5e-06
324120534	1907	RNA polymerase II largest subunit [Karoo	0.2	0.016	0.838	5e-06
324120520	1922	RNA polymerase II largest subunit [Epiop	0.2	0.016	0.838	5e-06
324120548	1862	RNA polymerase II largest subunit [Zorot	0.2	0.016	0.838	6e-06
324120532	1904	RNA polymerase II largest subunit [Gallo	0.2	0.016	0.838	6e-06
195566225	552	RNA polymerase II 215kD subunit [Drosoph	0.2	0.056	0.806	6e-06

>gi|321464303|gb|EFX75312.1| hypothetical protein DAPPUDRAFT_306846 [Daphnia pulex]

 Score = 57.0 bits (136), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 27/35 (77%), Positives = 28/35 (80%)

Query: 121  YHLLVLETTIVLGIEAVRKSVEKEMNTVLQFYGLY 155
            Y   + E   VLGIEAVRKSVEKEMNTVLQFYGLY
Sbjct: 1352 YSNDICEIFAVLGIEAVRKSVEKEMNTVLQFYGLY 1386

Source: Daphnia pulex

Species: Daphnia pulex

Genus: Daphnia

Family: Daphniidae

Order: Diplostraca

Class: Branchiopoda

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|324120512|dbj|BAJ78647.1| RNA polymerase II largest subunit [Petrobiellus takunagae]

 Score = 56.6 bits (135), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 26/31 (83%), Positives = 27/31 (87%)

Query: 125  VLETTIVLGIEAVRKSVEKEMNTVLQFYGLY 155
            + E   VLGIEAVRKSVEKEMNTVLQFYGLY
Sbjct: 1336 ICEIFAVLGIEAVRKSVEKEMNTVLQFYGLY 1366

Source: Petrobiellus takunagae

Species: Petrobiellus takunagae

Genus: Petrobiellus

Family: Machilidae

Order: Archaeognatha

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|324120588|dbj|BAJ78685.1| RNA polymerase II largest subunit [Stenopsyche marmorata]

 Score = 56.2 bits (134), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 26/31 (83%), Positives = 27/31 (87%)

Query: 125  VLETTIVLGIEAVRKSVEKEMNTVLQFYGLY 155
            + E   VLGIEAVRKSVEKEMNTVLQFYGLY
Sbjct: 1356 ICEIFQVLGIEAVRKSVEKEMNTVLQFYGLY 1386

Source: Stenopsyche marmorata

Species: Stenopsyche marmorata

Genus: Stenopsyche

Family: Stenopsychidae

Order: Trichoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328722767|ref|XP_001943949.2| PREDICTED: DNA-directed RNA polymerase II subunit RPB1-like [Acyrthosiphon pisum]

 Score = 56.2 bits (134), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 26/31 (83%), Positives = 27/31 (87%)

Query: 125  VLETTIVLGIEAVRKSVEKEMNTVLQFYGLY 155
            + E   VLGIEAVRKSVEKEMNTVLQFYGLY
Sbjct: 1357 ICEIFSVLGIEAVRKSVEKEMNTVLQFYGLY 1387

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|324120560|dbj|BAJ78671.1| RNA polymerase II largest subunit [Cryptotympana facialis]

 Score = 55.8 bits (133), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 26/31 (83%), Positives = 27/31 (87%)

Query: 125  VLETTIVLGIEAVRKSVEKEMNTVLQFYGLY 155
            + E   VLGIEAVRKSVEKEMNTVLQFYGLY
Sbjct: 1355 ICEIFSVLGIEAVRKSVEKEMNTVLQFYGLY 1385

Source: Cryptotympana facialis

Species: Cryptotympana facialis

Genus: Cryptotympana

Family: Cicadidae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|324120534|dbj|BAJ78658.1| RNA polymerase II largest subunit [Karoophasma biedouwense]

 Score = 55.8 bits (133), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 26/31 (83%), Positives = 27/31 (87%)

Query: 125  VLETTIVLGIEAVRKSVEKEMNTVLQFYGLY 155
            + E   VLGIEAVRKSVEKEMNTVLQFYGLY
Sbjct: 1356 ICEIFSVLGIEAVRKSVEKEMNTVLQFYGLY 1386

Source: Karoophasma biedouwense

Species: Karoophasma biedouwense

Genus: Karoophasma

Family: Austrophasmatidae

Order: Mantophasmatodea

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|324120520|dbj|BAJ78651.1| RNA polymerase II largest subunit [Epiophlebia superstes]

 Score = 55.8 bits (133), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 26/31 (83%), Positives = 27/31 (87%)

Query: 125  VLETTIVLGIEAVRKSVEKEMNTVLQFYGLY 155
            + E   VLGIEAVRKSVEKEMNTVLQFYGLY
Sbjct: 1343 ICEIFSVLGIEAVRKSVEKEMNTVLQFYGLY 1373

Source: Epiophlebia superstes

Species: Epiophlebia superstes

Genus: Epiophlebia

Family: Epiophlebiidae

Order: Odonata

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|324120548|dbj|BAJ78665.1| RNA polymerase II largest subunit [Zorotypus sp. 154-1]

 Score = 55.8 bits (133), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 26/31 (83%), Positives = 27/31 (87%)

Query: 125  VLETTIVLGIEAVRKSVEKEMNTVLQFYGLY 155
            + E   VLGIEAVRKSVEKEMNTVLQFYGLY
Sbjct: 1354 ICEIFSVLGIEAVRKSVEKEMNTVLQFYGLY 1384

Source: Zorotypus sp. 154-1

Species: Zorotypus sp. 154-1

Genus: Zorotypus

Family: Zorotypidae

Order: Zoraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|324120532|dbj|BAJ78657.1| RNA polymerase II largest subunit [Galloisiana yuasai]

 Score = 55.8 bits (133), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 26/31 (83%), Positives = 27/31 (87%)

Query: 125  VLETTIVLGIEAVRKSVEKEMNTVLQFYGLY 155
            + E   VLGIEAVRKSVEKEMNTVLQFYGLY
Sbjct: 1356 ICEIFSVLGIEAVRKSVEKEMNTVLQFYGLY 1386

Source: Galloisiana yuasai

Species: Galloisiana yuasai

Genus: Galloisiana

Family: Grylloblattidae

Order: Grylloblattodea

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195566225|ref|XP_002106688.1| RNA polymerase II 215kD subunit [Drosophila simulans] gi|194204073|gb|EDX17649.1| RNA polymerase II 215kD subunit [Drosophila simulans]

 Score = 55.8 bits (133), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 25/31 (80%), Positives = 26/31 (83%)

Query: 125 VLETTIVLGIEAVRKSVEKEMNTVLQFYGLY 155
           + E   VLGIEAVRKSVEKEMN VLQFYGLY
Sbjct: 19  ICEIFQVLGIEAVRKSVEKEMNAVLQFYGLY 49

Source: Drosophila simulans

Species: Drosophila simulans

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

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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	155
FB|FBgn0003277	1887	RpII215 "RNA polymerase II 215	0.2	0.016	0.806	9.4e-06

FB|FBgn0003277 RpII215 "RNA polymerase II 215kD subunit" [Drosophila melanogaster (taxid:7227)]

 Score = 119 (46.9 bits), Expect = 9.4e-06, P = 9.4e-06
 Identities = 25/31 (80%), Positives = 26/31 (83%)

Query:   125 VLETTIVLGIEAVRKSVEKEMNTVLQFYGLY 155
             + E   VLGIEAVRKSVEKEMN VLQFYGLY
Sbjct:  1354 ICEIFQVLGIEAVRKSVEKEMNAVLQFYGLY 1384


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.322   0.144   0.452    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0      155       116   0.00091  102 3  11 22  0.49    30
                                                     29  0.45    32


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  1
  No. of states in DFA:  516 (55 KB)
  Total size of DFA:  113 KB (2076 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  12.86u 0.10s 12.96t   Elapsed:  00:00:24
  Total cpu time:  12.86u 0.10s 12.96t   Elapsed:  00:00:24
  Start:  Thu Aug 15 14:15:45 2013   End:  Thu Aug 15 14:16:09 2013

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

GO:0005703 "polytene chromosome puff" evidence=IDA

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

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

GO:0005634 "nucleus" evidence=IDA

GO:0003677 "DNA binding" evidence=IEA

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

GO:0005700 "polytene chromosome" evidence=IDA

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Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

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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	155
cd02584	410	cd02584, RNAP_II_Rpb1_C, Largest subunit (Rpb1) of	8e-08
pfam04998	447	pfam04998, RNA_pol_Rpb1_5, RNA polymerase Rpb1, do	2e-05

>gnl|CDD|132720 cd02584, RNAP_II_Rpb1_C, Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain

 Score = 49.9 bits (120), Expect = 8e-08
 Identities = 15/31 (48%), Positives = 21/31 (67%)

Query: 125 VLETTIVLGIEAVRKSVEKEMNTVLQFYGLY 155
           ++E   VLGIEA RK++ KE+  V+ F G Y
Sbjct: 296 IVEIFEVLGIEAARKALLKELRNVISFDGSY 326

RNA polymerase II (RNAP II) is a large multi-subunit complex responsible for the synthesis of mRNA. RNAP II consists of a 10-subunit core enzyme and a peripheral heterodimer of two subunits. The largest core subunit (Rpb1) of yeast RNAP II is the best characterized member of this family. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure. In yeast, Rpb1 and Rpb2, the largest and the second largest subunits, each makes up one clamp, one jaw, and part of the cleft. Rpb1 interacts with Rpb2 to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis. The C-terminal domain of Rpb1 makes up part of the foot and jaw structures. Length = 410

>gnl|CDD|147266 pfam04998, RNA_pol_Rpb1_5, RNA polymerase Rpb1, domain 5

 Score = 43.1 bits (102), Expect = 2e-05
 Identities = 18/56 (32%), Positives = 27/56 (48%), Gaps = 3/56 (5%)

Query: 102 EGTWIHDPLYGLRGGVILDYH--LLVLETTIVLGIEAVRKSVEKEMNTVLQFYGLY 155
           EG  +   +  L+G +  D      + E    LGIEA R S+  E+  V +F G+Y
Sbjct: 356 EGNNLQA-VMRLQGVIDNDKTYSNDIREMLKKLGIEAARDSILLEIRNVFKFDGIY 410

RNA polymerases catalyze the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 5, represents the discontinuous cleft domain that is required to from the central cleft or channel where the DNA is bound. Length = 447

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	155
cd02737	381	RNAP_IV_NRPD1_C Largest subunit (NRPD1) of Higher	99.72
cd02584	410	RNAP_II_Rpb1_C Largest subunit (Rpb1) of Eukaryoti	99.71
cd02736	300	RNAP_III_Rpc1_C Largest subunit (Rpc1) of Eukaryot	99.71
TIGR02389	367	RNA_pol_rpoA2 DNA-directed RNA polymerase, subunit	99.68
PRK14897	509	unknown domain/DNA-directed RNA polymerase subunit	99.68
cd02735	309	RNAP_I_Rpa1_C Largest subunit (Rpa1) of Eukaryotic	99.67
cd06528	363	RNAP_A'' A'' subunit of Archaeal RNA Polymerase (R	99.65
PRK04309	383	DNA-directed RNA polymerase subunit A''; Validated	99.64
PRK14977	1321	bifunctional DNA-directed RNA polymerase A'/A'' su	99.57
PRK14898	858	DNA-directed RNA polymerase subunit A''; Provision	99.57
KOG0262|consensus	1640		99.56
KOG0260|consensus	1605		99.47
KOG0261|consensus	1386		99.27
PF04998	277	RNA_pol_Rpb1_5: RNA polymerase Rpb1, domain 5; Int	99.23
cd00630	158	RNAP_largest_subunit_C Largest subunit of RNA poly	98.79
cd02655	204	RNAP_beta'_C Largest subunit (beta') of Bacterial	97.96
COG0086	808	RpoC DNA-directed RNA polymerase, beta' subunit/16	96.0
PRK00566	1156	DNA-directed RNA polymerase subunit beta'; Provisi	95.84
TIGR02386	1140	rpoC_TIGR DNA-directed RNA polymerase, beta' subun	95.66
PRK14844	2836	bifunctional DNA-directed RNA polymerase subunit b	93.69
PRK02597	1331	rpoC2 DNA-directed RNA polymerase subunit beta'; P	87.37

>cd02737 RNAP_IV_NRPD1_C Largest subunit (NRPD1) of Higher plant RNA polymerase IV, C-terminal domain

Probab=99.72  E-value=7.4e-18  Score=148.79  Aligned_cols=83  Identities=11%  Similarity=0.012  Sum_probs=67.6

Q ss_pred             EEeecccccc--cccC--CcceEEEcCCCCcCCccceEEecc---------cc-------------ceeeeceeeccCHH
Q psy6966          73 ILPLTGVSHP--LDLH--PSVLLLEGTTGSYGPEGTWIHDPL---------YG-------------LRGGVILDYHLLVL  126 (155)
Q Consensus        73 ~LpL~g~~~i--~dl~--~~~RavI~edg~~~~~~e~~LeTe---------Gt-------------~gVD~~RTySNDI~  126 (155)
                      .+.|+|..+|  +++.  +..+..+.+++.++..+||+|+|+         |.             ++||.+|++||||.
T Consensus       184 ~~~lkG~~~I~kv~i~~~~~~~~~~~~~~~~~~~~E~vLe~~~~~~~~~t~G~~~~~vl~~c~~~~~~ID~~rt~sNdI~  263 (381)
T cd02737         184 ETVIKGDERIKSVNILWEDSPSTSWVKSVGKSSRGELVLEVTVEESCKKTRGNAWNVVMDACIPVMDLIDWERSMPYSIQ  263 (381)
T ss_pred             heeecccCCeeEEEEEecCCCcccccccccccccceEEEEEEeccccccccchhHHHHHHhhhcccccCcCCCcEECCHH
Confidence            3778888776  5554  444444444444566689999988         75             78999999999999


Q ss_pred             HHHHHHhHHHHHHHHHHHHHHHhhhcCCC
Q psy6966         127 ETTIVLGIEAVRKSVEKEMNTVLQFYGLY  155 (155)
Q Consensus       127 EI~~VLGIEAAR~aIIkEI~~Vf~~yGsY  155 (155)
                      ||+++|||||||++|++||++||++||+|
T Consensus       264 ev~~~lGIEAAR~~ii~El~~v~~~~G~~  292 (381)
T cd02737         264 QIKSVLGIDAAFEQFVQRLESAVSMTGKS  292 (381)
T ss_pred             HHHHHHhHHHHHHHHHHHHHHHHHhcCCc
Confidence            99999999999999999999999999986

Higher plants have five multi-subunit nuclear RNA polymerases: RNAP I, RNAP II and RNAP III, which are essential for viability; plus the two isoforms of the non-essential polymerase RNAP IV (IVa and IVb), which specialize in small RNA-mediated gene silencing pathways. RNAP IVa and/or RNAP IVb might be involved in RNA-directed DNA methylation of endogenous repetitive elements, silencing of transgenes, regulation of flowering-time genes, inducible regulation of adjacent gene pairs, and spreading of mobile silencing signals. NRPD1a is the largest subunit of RNAP IVa, whereas NRPD1b is the largest subunit of RNAP IVb. The full subunit compositions of RNAP IVa and RNAP IVb are not known, nor are their templates or enzymatic products. However, it has been shown that RNAP IVa and, to a lesser extent, RNAP IVb are crucial for several RNA-mediated gene silencing phenomena.

>cd02584 RNAP_II_Rpb1_C Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain

Probab=99.71  E-value=1.3e-17  Score=148.32  Aligned_cols=77  Identities=26%  Similarity=0.318  Sum_probs=63.6

Q ss_pred             EEeecccccccccCCcceEEEcC---------CCCcCCccceEEecccc--------ceeeeceeeccCHHHHHHHHhHH
Q psy6966          73 ILPLTGVSHPLDLHPSVLLLEGT---------TGSYGPEGTWIHDPLYG--------LRGGVILDYHLLVLETTIVLGIE  135 (155)
Q Consensus        73 ~LpL~g~~~i~dl~~~~RavI~e---------dg~~~~~~e~~LeTeGt--------~gVD~~RTySNDI~EI~~VLGIE  135 (155)
                      .+.|.|.++      .+|+++.+         .|.++...+|+|+|+|+        ++||.+||+||||+||+++||||
T Consensus       233 ~i~l~Gi~~------I~r~~i~~~~~~~~~~~~g~~~~~~~~~l~teG~nl~~v~~~~~Vd~~rt~sNdI~ei~~~lGIE  306 (410)
T cd02584         233 DMTLKGIEG------IRKVFIREENKKKVDIETGEFKKREEWVLETDGVNLREVLSHPGVDPTRTTSNDIVEIFEVLGIE  306 (410)
T ss_pred             CcEEeCCCC------ceEEEEEcCCceEecCCCCcccCCcceEEEecCcCHHHHhCCCCCccccCEeCCHHHHHHhcCHH
Confidence            466777665      34444432         34444456899999998        78999999999999999999999


Q ss_pred             HHHHHHHHHHHHHhhhcCCC
Q psy6966         136 AVRKSVEKEMNTVLQFYGLY  155 (155)
Q Consensus       136 AAR~aIIkEI~~Vf~~yGsY  155 (155)
                      |||++|++||++||+.||+|
T Consensus       307 AaR~~ii~Ei~~v~~~~Gi~  326 (410)
T cd02584         307 AARKALLKELRNVISFDGSY  326 (410)
T ss_pred             HHHHHHHHHHHHHHHhcCCc
Confidence            99999999999999999986

RNA polymerase II (RNAP II) is a large multi-subunit complex responsible for the synthesis of mRNA. RNAP II consists of a 10-subunit core enzyme and a peripheral heterodimer of two subunits. The largest core subunit (Rpb1) of yeast RNAP II is the best characterized member of this family. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure. In yeast, Rpb1 and Rpb2, the largest and the second largest subunits, each makes up one clamp, one jaw, and part of the cleft. Rpb1 interacts with Rpb2 to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis. The C-terminal domain of Rpb1 makes up part of the foot and jaw structures.

>cd02736 RNAP_III_Rpc1_C Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain

Probab=99.71  E-value=1.7e-17  Score=142.40  Aligned_cols=65  Identities=17%  Similarity=0.052  Sum_probs=58.0

Q ss_pred             cceEEEcCCCCcCCccceEEecccc--------ceeeeceeeccCHHHHHHHHhHHHHHHHHHHHHHHHhhhcCCC
Q psy6966          88 SVLLLEGTTGSYGPEGTWIHDPLYG--------LRGGVILDYHLLVLETTIVLGIEAVRKSVEKEMNTVLQFYGLY  155 (155)
Q Consensus        88 ~~RavI~edg~~~~~~e~~LeTeGt--------~gVD~~RTySNDI~EI~~VLGIEAAR~aIIkEI~~Vf~~yGsY  155 (155)
                      .+|+++.+++   ..++|.|+|+|+        ++||.+|++||||.||+++|||||||++|++||++||+.||++
T Consensus       149 I~r~~i~~~~---~~~~~~l~teG~nl~~v~~~~~Vd~~rt~sNdI~ei~~~lGIEAaR~~ii~Ei~~v~~~~Gi~  221 (300)
T cd02736         149 VKRAVINKDK---KKGKYKLLVEGYGLRAVMNTPGVIGTRTTSNHIMEVEKVLGIEAARSTIINEIQYTMKSHGMS  221 (300)
T ss_pred             ceEEEEecCC---CCCcEEEEEecccHHHHhcCCcEeccCCccCCHHHHHHhcCHHHHHHHHHHHHHHHHHhcCCc
Confidence            5588886543   135799999998        8899999999999999999999999999999999999999975

Eukaryotic RNA polymerase III (RNAP III) is a large multi-subunit complex responsible for the synthesis of tRNAs, 5SrRNA, Alu-RNA, U6 snRNA, among others. Rpc1 is also known as C160 in yeast. Structure studies suggest that different RNA polymerase complexes share a similar crab-claw-shape structure. The C-terminal domain of Rpb1, the largest subunit of RNAP II, makes up part of the foot and jaw structures of RNAP II. The similarity between this domain and the C-terminal domain of Rpb1, its counterpart in RNAP II, suggests a similar functional and structural role.

>TIGR02389 RNA_pol_rpoA2 DNA-directed RNA polymerase, subunit A''

Probab=99.68  E-value=4.1e-17  Score=143.51  Aligned_cols=71  Identities=20%  Similarity=0.151  Sum_probs=61.3

Q ss_pred             EeecccccccccCCcceEEEcCCCCcCCccceEEecccc--------ceeeeceeeccCHHHHHHHHhHHHHHHHHHHHH
Q psy6966          74 LPLTGVSHPLDLHPSVLLLEGTTGSYGPEGTWIHDPLYG--------LRGGVILDYHLLVLETTIVLGIEAVRKSVEKEM  145 (155)
Q Consensus        74 LpL~g~~~i~dl~~~~RavI~edg~~~~~~e~~LeTeGt--------~gVD~~RTySNDI~EI~~VLGIEAAR~aIIkEI  145 (155)
                      +.+.|.++      .+||++.++     .++|+|+|+|+        ++||.+||+||||+||+++|||||||++|++||
T Consensus       205 ~~v~Gi~g------I~r~~i~~~-----~~~~~l~teG~nl~~v~~~~~VD~~rt~sNdI~ei~~~lGIEAaR~~Ii~Ei  273 (367)
T TIGR02389       205 LHIKGIKG------IKRVVIRKE-----GDEYVIYTEGSNLKEVLKLEGVDKTRTTTNDIHEIAEVLGIEAARNAIIEEI  273 (367)
T ss_pred             ceEeCCCC------ceEEEEECC-----CCeEEEEEeccCHHHHHcCCCCccccCccCCHHHHHHhcCHHHHHHHHHHHH
Confidence            44555554      668888643     24799999998        889999999999999999999999999999999


Q ss_pred             HHHhhhcCCC
Q psy6966         146 NTVLQFYGLY  155 (155)
Q Consensus       146 ~~Vf~~yGsY  155 (155)
                      ++||+.||++
T Consensus       274 ~~v~~~~Gi~  283 (367)
T TIGR02389       274 KRTLEEQGLD  283 (367)
T ss_pred             HHHHHHcCCe
Confidence            9999999985

This family consists of the archaeal A'' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein.

>PRK14897 unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional

Probab=99.68  E-value=4.5e-17  Score=148.74  Aligned_cols=74  Identities=24%  Similarity=0.278  Sum_probs=64.3

Q ss_pred             EEeecccccccccCCcceEEEcCCCCcCCccceEEecccc--------ceeeeceeeccCHHHHHHHHhHHHHHHHHHHH
Q psy6966          73 ILPLTGVSHPLDLHPSVLLLEGTTGSYGPEGTWIHDPLYG--------LRGGVILDYHLLVLETTIVLGIEAVRKSVEKE  144 (155)
Q Consensus        73 ~LpL~g~~~i~dl~~~~RavI~edg~~~~~~e~~LeTeGt--------~gVD~~RTySNDI~EI~~VLGIEAAR~aIIkE  144 (155)
                      .+.|.|+++      ..||++++++   ...+|+|+|+|+        ++||.+||+||||+||+++|||||||++|++|
T Consensus       338 ~i~I~Gipg------I~r~~i~~~~---~~~~~~L~TeG~NL~~vl~~~~VD~~rt~SNdI~eI~~vlGIEAAR~~Ii~E  408 (509)
T PRK14897        338 SLTIKGIKG------IKRAIARKEN---DERRWVIYTQGSNLKDVLEIDEVDPTRTYTNDIIEIATVLGIEAARNAIIHE  408 (509)
T ss_pred             ccEEeCCCC------ccEEEEecCC---CCceeEEEeeccCHHHHhcCCCcccccCccCCHHHHHHhcCHHHHHHHHHHH
Confidence            466667665      7788887543   234699999998        88999999999999999999999999999999


Q ss_pred             HHHHhhhcCCC
Q psy6966         145 MNTVLQFYGLY  155 (155)
Q Consensus       145 I~~Vf~~yGsY  155 (155)
                      |++||+.||+|
T Consensus       409 i~~V~~~~Gi~  419 (509)
T PRK14897        409 AKRTLQEQGLN  419 (509)
T ss_pred             HHHHHHhcCCc
Confidence            99999999986

>cd02735 RNAP_I_Rpa1_C Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain

Probab=99.67  E-value=9.8e-17  Score=137.80  Aligned_cols=67  Identities=18%  Similarity=0.087  Sum_probs=58.4

Q ss_pred             cceEEEcCCCCcCCccceEEecccc---------ceeeeceeeccCHHHHHHHHhHHHHHHHHHHHHHHHhhhcCCC
Q psy6966          88 SVLLLEGTTGSYGPEGTWIHDPLYG---------LRGGVILDYHLLVLETTIVLGIEAVRKSVEKEMNTVLQFYGLY  155 (155)
Q Consensus        88 ~~RavI~edg~~~~~~e~~LeTeGt---------~gVD~~RTySNDI~EI~~VLGIEAAR~aIIkEI~~Vf~~yGsY  155 (155)
                      .+||++++++.. ...+|+|+|+|+         ++||.+|++||||+||+++|||||||++|++|+++||+.||.+
T Consensus       153 I~r~~i~~~~~~-~~~~~~l~teG~nl~~v~~~~~~vd~~r~~sNdi~ei~~~lGIEAar~~ii~Ei~~v~~~~Gi~  228 (309)
T cd02735         153 ITRCFVVEEDKG-GKTKYLVITEGVNLAALWKFSDILDVNRIYTNDIHAMLNTYGIEAARRAIVKEISNVFKVYGIA  228 (309)
T ss_pred             ccEEEEecCcCC-CceEEEEEeccccHHHHHhccCccccccceeCCHHHHHHhhCHHHHHHHHHHHHHHHHHhcCCe
Confidence            678888754321 234799999998         5799999999999999999999999999999999999999975

RNA polymerase I (RNAP I) is a multi-subunit protein complex responsible for the synthesis of rRNA precursor. It consists of at least 14 different subunits, and the largest one is homologous to subunit Rpb1 of yeast RNAP II and subunit beta' of bacterial RNAP. Rpa1 is also known as Rpa190 in yeast. Structure studies suggest that different RNAP complexes share a similar crab-claw-shape structure. The C-terminal domain of Rpb1, the largest subunit of RNAP II, makes up part of the foot and jaw structures of RNAP II. The similarity between this domain and the C-terminal domain of Rpb1, its counterpart in RNAP II, suggests a similar functional and structural role.

>cd06528 RNAP_A'' A'' subunit of Archaeal RNA Polymerase (RNAP)

Probab=99.65  E-value=1.5e-16  Score=139.62  Aligned_cols=72  Identities=18%  Similarity=0.122  Sum_probs=62.8

Q ss_pred             EEeecccccccccCCcceEEEcCCCCcCCccceEEecccc--------ceeeeceeeccCHHHHHHHHhHHHHHHHHHHH
Q psy6966          73 ILPLTGVSHPLDLHPSVLLLEGTTGSYGPEGTWIHDPLYG--------LRGGVILDYHLLVLETTIVLGIEAVRKSVEKE  144 (155)
Q Consensus        73 ~LpL~g~~~i~dl~~~~RavI~edg~~~~~~e~~LeTeGt--------~gVD~~RTySNDI~EI~~VLGIEAAR~aIIkE  144 (155)
                      .+.|.|.++      .+|+++.++.     ++|+|+|+|+        ++||.+||+||||.||+++|||||||++|++|
T Consensus       199 ~~~v~Gi~g------I~r~~i~~~~-----~~~~l~teG~nl~~v~~~~~Vd~~rt~sNdI~ei~~~lGIEAaR~~ii~E  267 (363)
T cd06528         199 NTKIKGIKG------IKRVIVRKEE-----DEYVIYTEGSNLKAVLKVEGVDPTRTTTNNIHEIEEVLGIEAARNAIINE  267 (363)
T ss_pred             ccEEeCCCC------ceEEEEecCC-----ceEEEEecCcCHHHHhcCCCCcccccccCCHHHHHHhCCHHHHHHHHHHH
Confidence            455666665      6788886542     3799999998        78999999999999999999999999999999


Q ss_pred             HHHHhhhcCCC
Q psy6966         145 MNTVLQFYGLY  155 (155)
Q Consensus       145 I~~Vf~~yGsY  155 (155)
                      |++||+.||.+
T Consensus       268 i~~v~~~~Gi~  278 (363)
T cd06528         268 IKRTLEEQGLD  278 (363)
T ss_pred             HHHHHHhcCCe
Confidence            99999999975

Archaeal RNA polymerase (RNAP), like bacterial RNAP, is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. The relative positioning of the RNAP core is highly conserved between archaeal RNAP and the three classes of eukaryotic RNAPs. In archaea, the largest subunit is split into two polypeptides, A' and A'', which are encoded by separate genes in an operon. Sequence alignments reveal that the archaeal A'' subunit corresponds to the C-terminal one-third of the RNAPII largest subunit (Rpb1). In subunit A'', several loops in the jaw domain are shorter. The RNAPII Rpb1 interacts with the second-largest subunit (Rpb2) to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis.

>PRK04309 DNA-directed RNA polymerase subunit A''; Validated

Probab=99.64  E-value=2.8e-16  Score=138.71  Aligned_cols=64  Identities=19%  Similarity=0.105  Sum_probs=57.9

Q ss_pred             CcceEEEcCCCCcCCccceEEecccc--------ceeeeceeeccCHHHHHHHHhHHHHHHHHHHHHHHHhhhcCCC
Q psy6966          87 PSVLLLEGTTGSYGPEGTWIHDPLYG--------LRGGVILDYHLLVLETTIVLGIEAVRKSVEKEMNTVLQFYGLY  155 (155)
Q Consensus        87 ~~~RavI~edg~~~~~~e~~LeTeGt--------~gVD~~RTySNDI~EI~~VLGIEAAR~aIIkEI~~Vf~~yGsY  155 (155)
                      ..+|+++.++     .++|.|+|+|+        ++||.+||+||||+||+++|||||||++|++||++||+.||++
T Consensus       224 gI~r~~i~~~-----~~~~~l~teG~nl~~v~~~~~VD~~rt~sNdI~ei~~vlGIEAAR~~ii~Ei~~v~~~~Gi~  295 (383)
T PRK04309        224 GIKRVIIRKE-----GDEYVIYTEGSNLKEVLKVEGVDATRTTTNNIHEIEEVLGIEAARNAIIEEIKNTLEEQGLD  295 (383)
T ss_pred             CceEEEEecC-----CCeEEEEEcccCHHHHhcCCCEeeccccCCCHHHHHHHcCHHHHHHHHHHHHHHHHHHcCCe
Confidence            3678888754     24799999998        8899999999999999999999999999999999999999975

>PRK14977 bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional

Probab=99.57  E-value=3.2e-15  Score=147.89  Aligned_cols=75  Identities=21%  Similarity=0.202  Sum_probs=62.1

Q ss_pred             EeecccccccccCCcceEEEcCCCCcCCccceEEecccc--------ceeeeceeeccCHHHHHHHHhHHHHHHHHHHHH
Q psy6966          74 LPLTGVSHPLDLHPSVLLLEGTTGSYGPEGTWIHDPLYG--------LRGGVILDYHLLVLETTIVLGIEAVRKSVEKEM  145 (155)
Q Consensus        74 LpL~g~~~i~dl~~~~RavI~edg~~~~~~e~~LeTeGt--------~gVD~~RTySNDI~EI~~VLGIEAAR~aIIkEI  145 (155)
                      +.+.|.++      .+|++++.... ....+|+|+|+|+        ++||..||+||||+||+++|||||||++|++||
T Consensus      1144 ~~i~Gi~~------I~r~~i~~~~~-~~~~e~~l~teG~nl~~vl~~~~Vd~~rt~sN~i~ei~~~lGIEAaR~~ii~Ei 1216 (1321)
T PRK14977       1144 KPVKGVPD------IERAWVELVEK-DGRDEWIIQTSGSNLAAVLEMKCIDIANTITNDCFEIAGTLGIEAARNAIFNEL 1216 (1321)
T ss_pred             cEEecCCC------ceEEEEEeecc-CCCeeEEEEecCcCHHHHhCCCCCcccccEECCHHHHHHhhhHHHHHHHHHHHH
Confidence            45556554      67877753211 1225899999998        889999999999999999999999999999999


Q ss_pred             HHHhhhcCCC
Q psy6966         146 NTVLQFYGLY  155 (155)
Q Consensus       146 ~~Vf~~yGsY  155 (155)
                      ++||++||+|
T Consensus      1217 ~~v~~~~G~~ 1226 (1321)
T PRK14977       1217 ASILEDQGLE 1226 (1321)
T ss_pred             HHHHHHcCCc
Confidence            9999999986

>PRK14898 DNA-directed RNA polymerase subunit A''; Provisional

Probab=99.57  E-value=4.1e-15  Score=141.50  Aligned_cols=75  Identities=21%  Similarity=0.187  Sum_probs=62.8

Q ss_pred             EeecccccccccCCcceEEEcCCCCcCCccceEEecccc--------ceeeeceeeccCHHHHHHHHhHHHHHHHHHHHH
Q psy6966          74 LPLTGVSHPLDLHPSVLLLEGTTGSYGPEGTWIHDPLYG--------LRGGVILDYHLLVLETTIVLGIEAVRKSVEKEM  145 (155)
Q Consensus        74 LpL~g~~~i~dl~~~~RavI~edg~~~~~~e~~LeTeGt--------~gVD~~RTySNDI~EI~~VLGIEAAR~aIIkEI  145 (155)
                      +.|.|+++      ..||++.++.. +...+|+|+|+|+        ++||.+||+||||+||+++|||||||++|++||
T Consensus       683 ~~i~gi~g------I~~~~i~~~~~-~~~~~~~l~teG~nl~~~~~~~~vd~~~~~sN~i~~i~~~lGIEAar~~ii~Ei  755 (858)
T PRK14898        683 IVLKGIPG------IERVLVKKEEH-ENDEEYVLYTQGSNLREVFKIEGVDTSRTTTNNIIEIQEVLGIEAARNAIINEM  755 (858)
T ss_pred             cEEECCCC------ccEEEEecCCC-CCCceEEEEecCcCHHHHhcCCCCcccccccCCHHHHHHhhCHHHHHHHHHHHH
Confidence            44555554      67888875431 1235899999998        789999999999999999999999999999999


Q ss_pred             HHHhhhcCCC
Q psy6966         146 NTVLQFYGLY  155 (155)
Q Consensus       146 ~~Vf~~yGsY  155 (155)
                      ++||+.||++
T Consensus       756 ~~v~~~~gi~  765 (858)
T PRK14898        756 MNTLEQQGLE  765 (858)
T ss_pred             HHHHHhcCCc
Confidence            9999999975

>KOG0262|consensus

Probab=99.56  E-value=2e-15  Score=148.89  Aligned_cols=81  Identities=22%  Similarity=0.187  Sum_probs=66.8

Q ss_pred             ceEEeecccccccccCCcc----------------eEEEcCCCCcCCccceEEecccc---------ceeeeceeeccCH
Q psy6966          71 PFILPLTGVSHPLDLHPSV----------------LLLEGTTGSYGPEGTWIHDPLYG---------LRGGVILDYHLLV  125 (155)
Q Consensus        71 ~f~LpL~g~~~i~dl~~~~----------------RavI~edg~~~~~~e~~LeTeGt---------~gVD~~RTySNDI  125 (155)
                      .|.+|+...+  +||.+.+                ||++.+.+...+... +|.|+|+         +.+|++++|||||
T Consensus      1446 ~~~lp~~~~k--~~mssiVe~~~~~~vI~q~~gIeRc~~~~~~~~~k~~~-~l~TeGVnl~a~~~~~d~LDv~~lySNDI 1522 (1640)
T KOG0262|consen 1446 ELKLPLDKEK--LDMSSIVESIAPKSVIHQVPGIERCVVSEPQDDVKEKS-VLLTEGVNLPALFDHADILDVNRLYSNDI 1522 (1640)
T ss_pred             EEEecCCCcc--hHHHHHHHHHhcceeeeccCCceeeeccCCcccccccc-eehhcCccHHHHHHHHhhhhhhhhccchH
Confidence            5778887666  8885544                787765443333334 8999998         5699999999999


Q ss_pred             HHHHHHHhHHHHHHHHHHHHHHHhhhcCC
Q psy6966         126 LETTIVLGIEAVRKSVEKEMNTVLQFYGL  154 (155)
Q Consensus       126 ~EI~~VLGIEAAR~aIIkEI~~Vf~~yGs  154 (155)
                      ++|+++|||||||++|++||++||++||+
T Consensus      1523 ~ail~tyGVEAar~~Iv~Ev~~VF~vYGI 1551 (1640)
T KOG0262|consen 1523 HAILNTYGVEAARNAIVNEVNNVFKVYGI 1551 (1640)
T ss_pred             HHHHHHhhHHHHHHHHHHHHHHhhhheee
Confidence            99999999999999999999999999996

>KOG0260|consensus

Probab=99.47  E-value=2.1e-14  Score=141.41  Aligned_cols=76  Identities=26%  Similarity=0.341  Sum_probs=66.9

Q ss_pred             EeecccccccccCCcceEEE--cCCCCcCCccceEEecccc--------ceeeeceeeccCHHHHHHHHhHHHHHHHHHH
Q psy6966          74 LPLTGVSHPLDLHPSVLLLE--GTTGSYGPEGTWIHDPLYG--------LRGGVILDYHLLVLETTIVLGIEAVRKSVEK  143 (155)
Q Consensus        74 LpL~g~~~i~dl~~~~RavI--~edg~~~~~~e~~LeTeGt--------~gVD~~RTySNDI~EI~~VLGIEAAR~aIIk  143 (155)
                      |+|+|..+|      .|+++  .++|.+....+|+|+|+|+        ++||..||+|||+.||+++|||||+|+++++
T Consensus      1250 ~~l~G~~~i------~kV~m~~~~~G~f~~~~ew~LeTdg~~l~~v~s~~~vD~~rt~sn~l~ei~~vlgIea~r~a~~~ 1323 (1605)
T KOG0260|consen 1250 MTLRGIPDI------FKVYMSPTEDGEFKPVDEWDLETDGVNLRRVLSEPDVDPARTTSNDLVEIAEVLGIEAVRKALLR 1323 (1605)
T ss_pred             cccCCcccc------ceEEEeecCCCceeecceeEEecCchhHHhhhccCCCCcccccccchhhhhhhhcHHHHHhhhhh
Confidence            777777764      34443  4578787778999999998        7899999999999999999999999999999


Q ss_pred             HHHHHhhhcCCC
Q psy6966         144 EMNTVLQFYGLY  155 (155)
Q Consensus       144 EI~~Vf~~yGsY  155 (155)
                      |+.+|+.++|+|
T Consensus      1324 e~~~vi~f~gsy 1335 (1605)
T KOG0260|consen 1324 ELLNVISFDGSY 1335 (1605)
T ss_pred             hhhheEeecccc
Confidence            999999999998

>KOG0261|consensus

Probab=99.27  E-value=1.3e-12  Score=127.41  Aligned_cols=66  Identities=20%  Similarity=0.032  Sum_probs=54.4

Q ss_pred             CCcceEEEcCCCCcCCccceEEecccc--------ceeeeceeeccCHHHHHHHHhHHHHHHHHHHHHHHHhhhcCC
Q psy6966          86 HPSVLLLEGTTGSYGPEGTWIHDPLYG--------LRGGVILDYHLLVLETTIVLGIEAVRKSVEKEMNTVLQFYGL  154 (155)
Q Consensus        86 ~~~~RavI~edg~~~~~~e~~LeTeGt--------~gVD~~RTySNDI~EI~~VLGIEAAR~aIIkEI~~Vf~~yGs  154 (155)
                      -+.+|++|+.|+.-   +-|-|-+||+        +||+++||.||++.||.+||||||||.+||+||.++|+.||+
T Consensus      1203 p~vnr~vi~~de~~---~~y~L~vEG~gLr~Vm~t~GV~g~~TtsNnv~Ev~~vLGIEAAR~~II~EI~ytM~~HGm 1276 (1386)
T KOG0261|consen 1203 PEVNRAVINIDEKR---GLYKLLVEGTGLRAVMNTDGVKGRRTTSNNVLEVEKVLGIEAARTTIISEIGYTMSNHGM 1276 (1386)
T ss_pred             cchhhhheeecccC---CceEEEEeccchHHHhccCCccccccccCceEEeehhhchHHHHHHHHHHHHHHHHhcCc
Confidence            45678988765321   1144445553        899999999999999999999999999999999999999997

>PF04998 RNA_pol_Rpb1_5: RNA polymerase Rpb1, domain 5; InterPro: IPR007081 RNA polymerases catalyse the DNA dependent polymerisation of RNA

Probab=99.23  E-value=7.7e-12  Score=99.04  Aligned_cols=54  Identities=22%  Similarity=0.199  Sum_probs=50.6

Q ss_pred             ccceEEecccc--------ce-eeeceeeccCHHHHHHHHhHHHHHHHHHHHHHHHhhhcCCC
Q psy6966         102 EGTWIHDPLYG--------LR-GGVILDYHLLVLETTIVLGIEAVRKSVEKEMNTVLQFYGLY  155 (155)
Q Consensus       102 ~~e~~LeTeGt--------~g-VD~~RTySNDI~EI~~VLGIEAAR~aIIkEI~~Vf~~yGsY  155 (155)
                      ..+|+++++|.        ++ +|.+|+++|||.+|+++|||||||++|++|++.||..||.+
T Consensus       178 ~~~~~l~~~g~~l~~v~~~qgvid~~k~~sn~I~qm~~~~GIeaar~~i~~e~~~v~~~~g~~  240 (277)
T PF04998_consen  178 SKEYVLQTEGSNLQEVYSSQGVIDNDKHISNDIRQMLSKLGIEAARNSIIKELKNVFESYGIE  240 (277)
T ss_dssp             CCCCEEECCSHHHHHHTCSTT-EETCHHECSHHHHHHHHHEHHHHHHHHHHHHHCHHHHCTSC
T ss_pred             hHHHHHHHHhhhchhheecccccCCCEEEeceeEeeeeeEEEEECCCceeecCcEeeHHHHHH
Confidence            35899999997        77 99999999999999999999999999999999999999964

Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial and chloroplast polymerases). This domain, domain 5, represents the discontinuous cleft domain that is required to form the central cleft or channel where the DNA is bound [, ].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 1ZYR_D 1SMY_D 2A68_N 2O5J_D 3AOH_N 2O5I_D 2CW0_N 2A6H_N 2A69_D 3EQL_D ....

>cd00630 RNAP_largest_subunit_C Largest subunit of RNA polymerase (RNAP), C-terminal domain

Probab=98.79  E-value=4.9e-09  Score=83.45  Aligned_cols=32  Identities=34%  Similarity=0.475  Sum_probs=31.0

Q ss_pred             CHHHHHHHHhHHHHHHHHHHHHHHHhhhcCCC
Q psy6966         124 LVLETTIVLGIEAVRKSVEKEMNTVLQFYGLY  155 (155)
Q Consensus       124 DI~EI~~VLGIEAAR~aIIkEI~~Vf~~yGsY  155 (155)
                      ||.+|+++|||||||+.|++||++||+.||.+
T Consensus        49 dI~~i~~~lGIEAaR~~iv~El~~v~~~~Gi~   80 (158)
T cd00630          49 SIHEMLEALGIEAARETIIREIQKVLASQGVS   80 (158)
T ss_pred             cHHHHHHHhCHHHHHHHHHHHHHHHHHhcCce
Confidence            99999999999999999999999999999974

RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is the final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei, RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. Structure studies revealed that prokaryotic and eukaryotic RNAPs share a conserved crab-claw-shape structure. The largest and the second largest subunits each make up one clamp, one jaw, and part of the cleft. The largest RNAP subunit (Rpb1) interacts with the second-largest RNAP subunit (Rpb2) to form the DNA entry and RNA exit channe

>cd02655 RNAP_beta'_C Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain

Probab=97.96  E-value=9.1e-06  Score=67.37  Aligned_cols=38  Identities=21%  Similarity=0.142  Sum_probs=34.6

Q ss_pred             eeeceeeccCHHHHHHHH--hHHHHHHHHHHHHHHHhhhcCCC
Q psy6966         115 GGVILDYHLLVLETTIVL--GIEAVRKSVEKEMNTVLQFYGLY  155 (155)
Q Consensus       115 VD~~RTySNDI~EI~~VL--GIEAAR~aIIkEI~~Vf~~yGsY  155 (155)
                      ++..+   ||++++++++  ||||||+.|++||++|+..||.+
T Consensus        49 ~e~r~---~~~~~il~~~~~Giea~r~~iv~EIq~Vy~~qGV~   88 (204)
T cd02655          49 FEARK---INPHDLLRIKFLGPEAVQKYLVEEIQKVYRSQGVN   88 (204)
T ss_pred             HHhhc---CCHHHHHHHHhHHHHHHHHHHHHHHHHHHHhcCee
Confidence            55555   9999999999  99999999999999999999975

Bacterial RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. This family also includes the eukaryotic plastid-encoded RNAP beta" subunit. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure with two pincers defining a central cleft. Beta' and beta, the largest and the second largest subunits of bacterial RNAP, each makes up one pincer and part of the base of the cleft. The C-terminal domain includes a G loop that forms part of the floor of the downstream DNA-binding cavity. The position of the G loop may determine the switch of the bridge helix between flipped-out and normal alpha-helical conformations.

>COG0086 RpoC DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]

Probab=96.00  E-value=0.0012  Score=63.99  Aligned_cols=52  Identities=25%  Similarity=0.300  Sum_probs=46.6

Q ss_pred             cceEEecccc--------ceeeeceeeccCHHHHHHHHhHHHHHHHHHHHHHHHhhhcCC
Q psy6966         103 GTWIHDPLYG--------LRGGVILDYHLLVLETTIVLGIEAVRKSVEKEMNTVLQFYGL  154 (155)
Q Consensus       103 ~e~~LeTeGt--------~gVD~~RTySNDI~EI~~VLGIEAAR~aIIkEI~~Vf~~yGs  154 (155)
                      .+|+.+++|.        +++|.+++.+||+.|++.++|+||+|+++++|+..+++..|.
T Consensus       601 ~e~v~~ae~~v~~~i~~~~~g~lt~~~~~~i~e~~e~~~~e~l~~ai~~~~~~~~~~~g~  660 (808)
T COG0086         601 DEIVIEAEGSVLKLILQYEEGDLTRTERNNIVEIIEVLGIEALRNAIIEEIKITLEEQGL  660 (808)
T ss_pred             HHHHHHHHHHHHHHHHHhhcCCccccCCCCeEEEeehHHHHHHHHHHHHHHhhhHHhcCC
Confidence            3688888886        679999999999999999999999999999999998876664

>PRK00566 DNA-directed RNA polymerase subunit beta'; Provisional

Probab=95.84  E-value=0.0088  Score=60.37  Aligned_cols=33  Identities=27%  Similarity=0.391  Sum_probs=30.5

Q ss_pred             cCHHHHHHHHhHHHHHHHHHHHHHHHhhhcCCC
Q psy6966         123 LLVLETTIVLGIEAVRKSVEKEMNTVLQFYGLY  155 (155)
Q Consensus       123 NDI~EI~~VLGIEAAR~aIIkEI~~Vf~~yGsY  155 (155)
                      =|++||++++||||+|+.|++||++|+..+|.+
T Consensus       989 ~~~~~il~v~G~~~~~~~lv~eiq~vY~~QGv~ 1021 (1156)
T PRK00566        989 IDPHDILRVLGVEAVQNYLVNEVQKVYRLQGVK 1021 (1156)
T ss_pred             CCHHHHHHhcCHHHHHHHHHHHHHHHHHhCCcc
Confidence            359999999999999999999999999999963

>TIGR02386 rpoC_TIGR DNA-directed RNA polymerase, beta' subunit, predominant form

Probab=95.66  E-value=0.011  Score=59.53  Aligned_cols=34  Identities=24%  Similarity=0.320  Sum_probs=31.3

Q ss_pred             ccCHHHHHHHHhHHHHHHHHHHHHHHHhhhcCCC
Q psy6966         122 HLLVLETTIVLGIEAVRKSVEKEMNTVLQFYGLY  155 (155)
Q Consensus       122 SNDI~EI~~VLGIEAAR~aIIkEI~~Vf~~yGsY  155 (155)
                      +-|++||++++||||+|+.|++||++|+..+|.+
T Consensus       986 ~~~~~~il~v~G~~a~~~~lv~evq~vY~~QGv~ 1019 (1140)
T TIGR02386       986 SIDPHDLLRIKGIQAVQEYLVKEVQKVYRLQGVE 1019 (1140)
T ss_pred             CCCHHHHHHhcCHHHHHHHHHHHHHHHHHhCCcc
Confidence            4579999999999999999999999999999853

Bacteria have a single DNA-directed RNA polymerase, with required subunits that include alpha, beta, and beta-prime. This model describes the predominant architecture of the beta-prime subunit in most bacteria. This model excludes from among the bacterial mostly sequences from the cyanobacteria, where RpoC is replaced by two tandem genes homologous to it but also encoding an additional domain.

>PRK14844 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional

Probab=93.69  E-value=0.064  Score=58.37  Aligned_cols=33  Identities=24%  Similarity=0.350  Sum_probs=31.2

Q ss_pred             ccCHHHHHHHHhHHHHHHHHHHHHHHHhhhcCC
Q psy6966         122 HLLVLETTIVLGIEAVRKSVEKEMNTVLQFYGL  154 (155)
Q Consensus       122 SNDI~EI~~VLGIEAAR~aIIkEI~~Vf~~yGs  154 (155)
                      +.|.++|++++||||+|+.|++||+.|+..+|.
T Consensus      2635 ~~~p~dil~v~G~ea~~~ylv~Evq~VYr~QGV 2667 (2836)
T PRK14844       2635 DPDLHDILRVLGLEALAHYMISEIQQVYRLQGV 2667 (2836)
T ss_pred             CCCHHHHHHhhCHHHHHHHHHHHHHHHHHhcCe
Confidence            568999999999999999999999999999985

>PRK02597 rpoC2 DNA-directed RNA polymerase subunit beta'; Provisional

Probab=87.37  E-value=0.65  Score=48.08  Aligned_cols=33  Identities=15%  Similarity=0.172  Sum_probs=30.2

Q ss_pred             cCHHHHHHH----------------HhHHHHHHHHHHHHHHHhhhcCCC
Q psy6966         123 LLVLETTIV----------------LGIEAVRKSVEKEMNTVLQFYGLY  155 (155)
Q Consensus       123 NDI~EI~~V----------------LGIEAAR~aIIkEI~~Vf~~yGsY  155 (155)
                      .|.++++++                +|+||+|..+++|+++|++++|.|
T Consensus      1059 ~~ph~iL~~~f~~~~~~~g~~~aa~~~~~~~~~~lv~evq~Vy~~QGv~ 1107 (1331)
T PRK02597       1059 INPHELLEIFFEDLRDRKGLYEAALEALQKLQRFLVNEVQNVYQSQGVD 1107 (1331)
T ss_pred             CCHHHHHhhhhhhhcccchhhHHHHHhHHHHHHHHHHHHHHHHHhcCeE
Confidence            677888888                899999999999999999999975

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	155
1twf_A	1733	B220, DNA-directed RNA polymerase II largest subun	5e-05
3h0g_A	1752	DNA-directed RNA polymerase II subunit RPB1; trans	2e-04

>1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A 1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A* 1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A* 1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ... Length = 1733

 Score = 41.6 bits (97), Expect = 5e-05
 Identities = 12/31 (38%), Positives = 18/31 (58%)

Query: 125  VLETTIVLGIEAVRKSVEKEMNTVLQFYGLY 155
             ++   VLGIEA R ++ KE+  V+   G Y
Sbjct: 1332 FIDIMEVLGIEAGRAALYKEVYNVIASDGSY 1362

>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 1752

 Score = 39.7 bits (92), Expect = 2e-04
 Identities = 13/31 (41%), Positives = 20/31 (64%)

Query: 125  VLETTIVLGIEAVRKSVEKEMNTVLQFYGLY 155
             +E   +LGIEA R ++ KE+  V++F G Y
Sbjct: 1338 FVEILQILGIEATRSALLKELRNVIEFDGSY 1368

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	155
3h0g_A	1752	DNA-directed RNA polymerase II subunit RPB1; trans	99.72
1twf_A	1733	B220, DNA-directed RNA polymerase II largest subun	99.7
4ayb_C	395	DNA-directed RNA polymerase; transferase, multi-su	99.41
2a6h_D	1524	DNA-directed RNA polymerase beta' chain; RNA polym	97.3
1hqm_D	1265	DNA-directed RNA polymerase; transferase, transcri	96.67
3lu0_D	1407	DNA-directed RNA polymerase subunit beta'; E. coli	95.56

>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}

Probab=99.72  E-value=1.1e-18  Score=174.06  Aligned_cols=82  Identities=23%  Similarity=0.362  Sum_probs=66.7

Q ss_pred             Eeecccccc--cccCCcceEEEcCCCCcCCccceEEecccc--------ceeeeceeeccCHHHHHHHHhHHHHHHHHHH
Q psy6966          74 LPLTGVSHP--LDLHPSVLLLEGTTGSYGPEGTWIHDPLYG--------LRGGVILDYHLLVLETTIVLGIEAVRKSVEK  143 (155)
Q Consensus        74 LpL~g~~~i--~dl~~~~RavI~edg~~~~~~e~~LeTeGt--------~gVD~~RTySNDI~EI~~VLGIEAAR~aIIk  143 (155)
                      +.|+|+++|  +.+.+.++.+++++|++....+|+|+|+|+        +|||.+||+||||+||++||||||||++|++
T Consensus      1277 ~~i~Gi~~I~rv~i~~~~~~~~~~~g~~~~~~~~~l~teG~nL~~v~~~~gVD~~rt~sNdI~ei~~vlGIEAAR~~Ii~ 1356 (1752)
T 3h0g_A         1277 ISLRGVPNITRVYMMEHKIVRQIEDGTFERADEWVLETDGINLTEAMTVEGVDATRTYSNSFVEILQILGIEATRSALLK 1356 (1752)
T ss_dssp             CCSSCCTTCCCCCEEEEEEEEECSSSCEEEEEEEEEECCSCCCSTTTSSSSCCTTTCCCSCHHHHHHHSCHHHHHHHHHH
T ss_pred             eEEecCCCccEEEEecccceeecCCCcccccceEEEEecccCHHHHhCcCCCccccCeeCCHHHHHHHHhHHHHHHHHHH
Confidence            566677765  444444444444455444456899999998        8999999999999999999999999999999


Q ss_pred             HHHHHhhhcCCC
Q psy6966         144 EMNTVLQFYGLY  155 (155)
Q Consensus       144 EI~~Vf~~yGsY  155 (155)
                      ||++||++||+|
T Consensus      1357 Ei~~v~~~~G~~ 1368 (1752)
T 3h0g_A         1357 ELRNVIEFDGSY 1368 (1752)
T ss_dssp             HHHTTSCSSSCC
T ss_pred             HHHHHHHhcCCC
Confidence            999999999987

>1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A 1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A* 1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A* 1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ...

Probab=99.70  E-value=6.4e-18  Score=168.39  Aligned_cols=82  Identities=26%  Similarity=0.259  Sum_probs=67.3

Q ss_pred             Eeecccccc--cccCCcceEEEcCCCCcCCccceEEecccc--------ceeeeceeeccCHHHHHHHHhHHHHHHHHHH
Q psy6966          74 LPLTGVSHP--LDLHPSVLLLEGTTGSYGPEGTWIHDPLYG--------LRGGVILDYHLLVLETTIVLGIEAVRKSVEK  143 (155)
Q Consensus        74 LpL~g~~~i--~dl~~~~RavI~edg~~~~~~e~~LeTeGt--------~gVD~~RTySNDI~EI~~VLGIEAAR~aIIk  143 (155)
                      +.|.|+++|  +.+...+|.+++++|.+...++|+|+|+|+        ++||.+||+||||+||++||||||||++|++
T Consensus      1271 ~~v~Gi~~I~r~~i~~~~~~~~~~~g~~~~~~~~~L~teG~nL~~vl~~~~VD~~rt~SNdI~eI~~vlGIEAAR~~Ii~ 1350 (1733)
T 1twf_A         1271 ITLRGVENIERVVMMKYDRKVPSPTGEYVKEPEWVLETDGVNLSEVMTVPGIDPTRIYTNSFIDIMEVLGIEAGRAALYK 1350 (1733)
T ss_dssp             CEEESCTTCCCEEEEEEEEEEECTTSSEEEEEEEEEEEESCCHHHHTTSTTBCTTTCBCSCHHHHHHHHCHHHHHHHHHH
T ss_pred             eEEecCCCccEEEEecccceeecCCCccccCcceEEEeecccHHHHhccCCcccccceeccHHHHHHHhhHHHHHHHHHH
Confidence            566777765  344333455556666554456899999998        6799999999999999999999999999999


Q ss_pred             HHHHHhhhcCCC
Q psy6966         144 EMNTVLQFYGLY  155 (155)
Q Consensus       144 EI~~Vf~~yGsY  155 (155)
                      ||++||++||+|
T Consensus      1351 Ei~~V~~~~Gi~ 1362 (1733)
T 1twf_A         1351 EVYNVIASDGSY 1362 (1733)
T ss_dssp             HHHHHHHTTTCC
T ss_pred             HHHHHHhhcCcc
Confidence            999999999986

>4ayb_C DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2y0s_C 4b1o_C 4b1p_Y 2waq_C 2wb1_C 3hkz_C 2pmz_C

Probab=99.41  E-value=1.3e-13  Score=117.39  Aligned_cols=63  Identities=22%  Similarity=0.124  Sum_probs=55.9

Q ss_pred             cceEEEcCCCCcCCccceEEecccc--------ceeeeceeeccCHHHHHHHHhHHHHHHHHHHHHHHHhhhcCCC
Q psy6966          88 SVLLLEGTTGSYGPEGTWIHDPLYG--------LRGGVILDYHLLVLETTIVLGIEAVRKSVEKEMNTVLQFYGLY  155 (155)
Q Consensus        88 ~~RavI~edg~~~~~~e~~LeTeGt--------~gVD~~RTySNDI~EI~~VLGIEAAR~aIIkEI~~Vf~~yGsY  155 (155)
                      ..|+++.+.+     .+|++.|+|.        +++|.++++|||++||+++|||||||+.|++|+++||..||.+
T Consensus       237 i~r~~~~~~~-----~~~~~~t~g~~l~~~~~~~~vd~~~~~sn~i~eI~~vlGiEAar~~iv~Ei~~V~~~~Gv~  307 (395)
T 4ayb_C          237 IKRAIVQKKG-----DEYIILTDGSNLSGVLSVKGVDIAKVETNNIREIEEVFGIEAAREIIIREISKVLAEQGLD  307 (395)
T ss_dssp             CCEEEEEEET-----TEEEEEEESCCHHHHTTSTTCCTTTCEESCTTHHHHHHCHHHHHHHHHHHHHHHHHTTSCC
T ss_pred             eeEEEEeccC-----CEEEEEecCCCceeeeEeecccccccccCcchhhhhhhhHHHHHHHHHHhHHHHHhccCce
Confidence            4577765433     4799999997        7899999999999999999999999999999999999999975

>2a6h_D DNA-directed RNA polymerase beta' chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: e.29.1.2 PDB: 1smy_D* 1zyr_D* 1iw7_D* 2a69_D* 2a6e_D 2a68_D* 2be5_D* 2cw0_D 2o5i_D 2o5j_D* 2ppb_D* 3aoh_D* 3aoi_D* 3dxj_D* 3eql_D* 1ynj_D* 1l9z_D 1l9u_D* 1ynn_D* 2auj_D

Probab=97.30  E-value=0.00017  Score=72.53  Aligned_cols=34  Identities=21%  Similarity=0.183  Sum_probs=32.1

Q ss_pred             ccCHHHHHHHHhHHHHHHHHHHHHHHHhhhcCCC
Q psy6966         122 HLLVLETTIVLGIEAVRKSVEKEMNTVLQFYGLY  155 (155)
Q Consensus       122 SNDI~EI~~VLGIEAAR~aIIkEI~~Vf~~yGsY  155 (155)
                      +||++||++++||||||+.|++||++|+..+|..
T Consensus      1329 ~~~~~dil~v~Giea~~~~iv~Eiq~Vyr~QGv~ 1362 (1524)
T 2a6h_D         1329 AIDPHQLLEAKGPEAVERYLVEEIQKVYRAQGVK 1362 (1524)
T ss_dssp             BCCHHHHHHHHCHHHHHHHHHHHHHHHHHTTTCC
T ss_pred             CCCchhheeecCHHHHHHHHHHHHHHHHHhcCcc
Confidence            4999999999999999999999999999999963

>1hqm_D DNA-directed RNA polymerase; transferase, transcription, 3D- structure; 3.30A {Thermus aquaticus} SCOP: i.8.1.1 PDB: 1i6v_D* 2gho_D

Probab=96.67  E-value=0.00096  Score=66.03  Aligned_cols=33  Identities=21%  Similarity=0.203  Sum_probs=31.7

Q ss_pred             ccCHHHHHHHHhHHHHHHHHHHHHHHHhhhcCC
Q psy6966         122 HLLVLETTIVLGIEAVRKSVEKEMNTVLQFYGL  154 (155)
Q Consensus       122 SNDI~EI~~VLGIEAAR~aIIkEI~~Vf~~yGs  154 (155)
                      +||++||++++||||||+.|++||++|+..+|.
T Consensus      1070 ~~~~~eil~v~Giea~~~~lv~EIq~vyr~QGv 1102 (1265)
T 1hqm_D         1070 AIDPHQLLEAKGPEAVERYLVDEIQKVYRAQGV 1102 (1265)
T ss_dssp             BSHHHHHHHTTHHHHHHHHHHHHHHHHHHTTSC
T ss_pred             CccHHHHHHHhhHHHHHHHHHHHHHHHHHHcCc
Confidence            599999999999999999999999999999996

>3lu0_D DNA-directed RNA polymerase subunit beta'; E. coli RNA polymerase, nucleotidyltransferase, transcription, transferase; 11.20A {Escherichia coli} PDB: 3iyd_D*

Probab=95.56  E-value=0.0033  Score=63.03  Aligned_cols=34  Identities=18%  Similarity=0.248  Sum_probs=31.9

Q ss_pred             ccCHHHHHHHHhHHHHHHHHHHHHHHHhhhcCCC
Q psy6966         122 HLLVLETTIVLGIEAVRKSVEKEMNTVLQFYGLY  155 (155)
Q Consensus       122 SNDI~EI~~VLGIEAAR~aIIkEI~~Vf~~yGsY  155 (155)
                      +.|.++|++++||||+|+.|++||++|+..+|.+
T Consensus      1214 ~~~p~dil~v~Giea~~~ylv~Evq~VYr~QGV~ 1247 (1407)
T 3lu0_D         1214 PEAPHDILRLRGVHAVTRYIVNEVQDVYRLQGVK 1247 (1407)
T ss_dssp             CCCHHHHHHHSCHHHHHHHTTTTTHHHHHHHTCC
T ss_pred             CCCHHHHHHhhCHHHHHHHHHHHHHHHHHhcCcc
Confidence            6789999999999999999999999999999963

---

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	155
d1twfa_	1449	e.29.1.2 (A:) RBP1 {Baker's yeast (Saccharomyces c	2e-05

>d1twfa_ e.29.1.2 (A:) RBP1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 1449

class: Multi-domain proteins (alpha and beta)
fold: beta and beta-prime subunits of DNA dependent RNA-polymerase
superfamily: beta and beta-prime subunits of DNA dependent RNA-polymerase
family: RNA-polymerase beta-prime
domain: RBP1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 41.4 bits (96), Expect = 2e-05
 Identities = 18/79 (22%), Positives = 28/79 (35%), Gaps = 8/79 (10%)

Query: 85   LHPSVLLLEGTTGSYGPEGTWIHDPLYGLRGGVILDYHLLVLETTI--------VLGIEA 136
            +      +   TG Y  E  W+ +        V+    +               VLGIEA
Sbjct: 1283 MMKYDRKVPSPTGEYVKEPEWVLETDGVNLSEVMTVPGIDPTRIYTNSFIDIMEVLGIEA 1342

Query: 137  VRKSVEKEMNTVLQFYGLY 155
             R ++ KE+  V+   G Y
Sbjct: 1343 GRAALYKEVYNVIASDGSY 1361

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	155
d1twfa_	1449	RBP1 {Baker's yeast (Saccharomyces cerevisiae) [Ta	99.51

>d1twfa_ e.29.1.2 (A:) RBP1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Multi-domain proteins (alpha and beta)
fold: beta and beta-prime subunits of DNA dependent RNA-polymerase
superfamily: beta and beta-prime subunits of DNA dependent RNA-polymerase
family: RNA-polymerase beta-prime
domain: RBP1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.51  E-value=3.7e-15  Score=142.32  Aligned_cols=82  Identities=26%  Similarity=0.259  Sum_probs=65.0

Q ss_pred             Eeecccccc--cccCCcceEEEcCCCCcCCccceEEecccc--------ceeeeceeeccCHHHHHHHHhHHHHHHHHHH
Q psy6966          74 LPLTGVSHP--LDLHPSVLLLEGTTGSYGPEGTWIHDPLYG--------LRGGVILDYHLLVLETTIVLGIEAVRKSVEK  143 (155)
Q Consensus        74 LpL~g~~~i--~dl~~~~RavI~edg~~~~~~e~~LeTeGt--------~gVD~~RTySNDI~EI~~VLGIEAAR~aIIk  143 (155)
                      +.+.|+.+|  +.+...+|.+....+.+....+|+|+|+|+        ++||..|++||||++|+++|||||||+.|++
T Consensus      1270 ~~v~Gi~~I~rv~i~~~~~~~~~~~~~~~~~~~~vl~teG~nl~~~l~~~~iD~~~~~sNdI~dil~~lGIEAar~~ii~ 1349 (1449)
T d1twfa_        1270 ITLRGVENIERVVMMKYDRKVPSPTGEYVKEPEWVLETDGVNLSEVMTVPGIDPTRIYTNSFIDIMEVLGIEAGRAALYK 1349 (1449)
T ss_dssp             CEEESCTTCCCEEEEEEEEEEECTTSSEEEEEEEEEEEESCCHHHHTTSTTBCTTTCBCSCHHHHHHHHCHHHHHHHHHH
T ss_pred             cEEeCCCCeEEEEEecccceeeCCCCcCccCCcEEEEcCcCCHHHHhccCCcccccCccCcHHHHHHHHhHHHHHHHHHH
Confidence            456666654  333344444444455554556899999998        5699999999999999999999999999999


Q ss_pred             HHHHHhhhcCCC
Q psy6966         144 EMNTVLQFYGLY  155 (155)
Q Consensus       144 EI~~Vf~~yGsY  155 (155)
                      ||++||+.||.+
T Consensus      1350 EI~~V~~~~Gi~ 1361 (1449)
T d1twfa_        1350 EVYNVIASDGSY 1361 (1449)
T ss_dssp             HHHHHHHTTTCC
T ss_pred             HHHHHHHhcCcE
Confidence            999999999975