Psyllid ID: psy9982

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220--
Protein Sequence
MFTPDFLGLIGGTLTVEIFLLVFLLLNVLSYILIEKFKRKDLEDYLSTDEDEATVYTVSPAYTQVSPAYTQVSPAYTQVSPAYTQVSPAYIPVSPAYTPVSPAYTQVSPAYTQVSPAYTQVSPAYTQVSLAYTQVSLAYTQVSPAYTQVSPAYTQVSPAYTQVSSAYTQVILNKIRPGRESNSRSSAYEAFFHEWVWMSWYPDINPTLPIAMGVHCHDSKDK
Secondary Structure (PSIPRED)
cccccccccccccccccHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccHHccccccccccEEEEEEEEEEEEEEEcccccccccHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEcccccccccc
Coil and Loop (DISEMBL)
mftpdflgligGTLTVEIFLLVFLLLNVLSYILIEKFKrkdledylstdedeatvytvspaytqvspaytqvspaytqvspaytqvspayipvspaytpvspaytqvspaytqvspaytqvspaytQVSLAYTQVSLAYtqvspaytqvspaytqvspaytqVSSAYTQVILNkirpgresnsrsSAYEAFFHEWVWmswypdinptlpiamgvhchdskdk
Flexible Loop (DISEMBL)
mftpdflgLIGGTLTVEIFLLVFLLLNVLSYILIEKFKRKDLEDYLSTDEDEATVYTVSPAYTQVSPAYTQVSPAYTQVSPAYTQVSPAYIPVSPAYTPVSPAYTQVSPAYTQVSPAYTQVSPAYTQVSLAYTQVSLAYTQVSPAYTQVSPAYTQVSPAYTQVSSAYTQVILNKirpgresnsRSSAYEAFFHEWVWMSWYPDINPTLPIAMGVHCHDSKDK
Low Complexity Region (SEG)
MFTPDFLGLIGGTltveifllvflllnvlsyiliEKFKRKDLEDYLSTDEDEATVYTVSPAYTQVSPAYTQVSPAYTQVSPAYTQVSPAYIPVSPAYTPVSPAYTQVSPAYTQVSPAYTQVSPAYTQVSLAYTQVSLAYTQVSPAYTQVSPAYTQVSPAYTQVSSAYTQVILNKIRPGRESNSRSSAYEAFFHEWVWMSWYPDINPTLPIAMGVHCHDSKDK
Disordered region (IsUnstruct)
****DFLGLIGGTLTVEIFLLVFLLLNVLSYILIEKFKRKDLEDYLSTDEDEATVYTVSPAYTQVSPAYTQVSPAYTQVSPAYTQVSPAYIPVSPAYTPVSPAYTQVSPAYTQVSPAYTQVSPAYTQVSLAYTQVSLAYTQVSPAYTQVSPAYTQVSPAYTQVSSAYTQVILNKI***********AYEAFFHEWVWMSWYPDINPTLPIAMGVHC******
Disordered Region (DISOPRED)
**TPD*************************************************************************************************************************************************************************************************************************
Disordered Region (DISEMBL)
MFTPDFLGLIGGTLTVEIFLLVFLLLNVLSYILIEKFKRKDLEDYLSTDEDEATVYTVSPAYTQVSPAYTQVSPAYTQVSPAYTQVSPAYIPVSPAYTPVSPAYTQVSPAYTQVSPAYTQVSPAYTQVSLAYTQVSLAYTQVSPAYTQVSPAYTQVSPAYTQVSSAYTQVILNKIRP********SAYEAFFHEWVWMSWYPDINPTLPIAMGVHCHDSKDK
Disordered Region (DISPRO)
MFTPDFLGLIGGTLTVEIFLLVFLLLNVLSYILIEK***********************************************************************************************************************V*P***************************************MSWYPDINPTLPIAMGVHCH*****
Transmembrane Helix (TMHMM)
oooooooooHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (HMMTOP)
iiiiiHHHHHHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooHHHHHHHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MFTPDFLGLIGGTLTVEIFLLVFLLLNVLSYILIEKFKRKDLEDYLSTDEDEATVYTVSPAYTQVSPAYTQVSPAYTQVSPAYTQVSPAYIPVSPAYTPVSPAYTQVSPAYTQVSPAYTQVSPAYTQVSLAYTQVSLAYTQVSPAYTQVSPAYTQVSPAYTQVSSAYTQVILNKIRPGRESNSRSSAYEAFFHEWVWMSWYPDINPTLPIAMGVHCHDSKDK
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	222	2.2.26 [Sep-21-2011]
P14248	2452	DNA-directed RNA polymera	N/A	N/A	0.472	0.042	0.385	5e-18
P11414	467	DNA-directed RNA polymera	yes	N/A	0.472	0.224	0.425	5e-14
P08775	1970	DNA-directed RNA polymera	yes	N/A	0.481	0.054	0.418	1e-13
P24928	1970	DNA-directed RNA polymera	yes	N/A	0.472	0.053	0.425	2e-13
Q8R0T2	568	Zinc finger protein 768 O	no	N/A	0.707	0.276	0.3	2e-11
P35074	1853	DNA-directed RNA polymera	N/A	N/A	0.486	0.058	0.413	2e-10
P16356	1856	DNA-directed RNA polymera	yes	N/A	0.486	0.058	0.379	1e-09
Q9H5H4	540	Zinc finger protein 768 O	no	N/A	0.518	0.212	0.305	1e-07
O88799	5376	Zonadhesin OS=Mus musculu	no	N/A	0.522	0.021	0.35	7e-06
P04052	1887	DNA-directed RNA polymera	yes	N/A	0.513	0.060	0.298	1e-05

>sp|P14248|RPB1_PLAFD DNA-directed RNA polymerase II subunit RPB1 OS=Plasmodium falciparum (isolate CDC / Honduras) GN=RPII PE=3 SV=1

 Score = 91.3 bits (225), Expect = 5e-18,   Method: Composition-based stats.
 Identities = 42/109 (38%), Positives = 59/109 (54%), Gaps = 4/109 (3%)

Query: 58   VSPAYTQVSPAYTQVSPAYTQVSPAYTQVSPAYIPVSPAYTPVSPAYTQVSPAYTQVSPA 117
            V+  Y  +SP Y+  SP Y+  SP Y+  SP Y P SP Y+P SP Y+  SP Y+  SP 
Sbjct: 2279 VNSQYNVMSPVYSVTSPKYSPTSPKYSPTSPKYSPTSPKYSPTSPKYSPTSPKYSPTSPK 2338

Query: 118  YTQVSPAYTQVSLAYTQVS----LAYTQVSPAYTQVSPAYTQVSPAYTQ 162
            Y+  SP Y+  S     ++      Y+  SP ++  SPAY+  SP Y +
Sbjct: 2339 YSPTSPKYSPTSPVAQNIASPNYSPYSITSPKFSPTSPAYSISSPVYDK 2387

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.
Plasmodium falciparum (isolate CDC / Honduras) (taxid: 5836)
EC: 2EC: .EC: 7EC: .EC: 7EC: .EC: 6

>sp|P11414|RPB1_CRIGR DNA-directed RNA polymerase II subunit RPB1 (Fragment) OS=Cricetulus griseus GN=POLR2A PE=3 SV=1

 Score = 77.8 bits (190), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 46/108 (42%), Positives = 59/108 (54%), Gaps = 3/108 (2%)

Query: 62  YTQVSPAYTQVSPAYTQVSPAYTQVSPAYIPVSPAYTPVSPAYTQVSPAYTQVSPAYTQV 121
           YT  SP Y+  SP Y+  SP Y+  SP Y P +P Y+P SP Y+  SP YT  SP Y+  
Sbjct: 350 YTPTSPKYSPTSPKYSPTSPKYSPTSPTYSPTTPKYSPTSPTYSPTSPVYTPTSPKYSPT 409

Query: 122 SPAYTQVSLAYTQVSLAYTQVSPA---YTQVSPAYTQVSPAYTQVSSA 166
           SP Y+  S  Y+  S  Y+  SP    Y+  SP Y+  SP Y+  S A
Sbjct: 410 SPTYSPTSPKYSPTSPTYSPTSPKGSTYSPTSPGYSPTSPTYSLTSPA 457

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.

Cricetulus griseus (taxid: 10029)

EC: 2

EC: .

EC: 7

EC: .

EC: 7

EC: .

EC: 6

>sp|P08775|RPB1_MOUSE DNA-directed RNA polymerase II subunit RPB1 OS=Mus musculus GN=Polr2a PE=1 SV=3

 Score = 76.6 bits (187), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 46/110 (41%), Positives = 60/110 (54%), Gaps = 3/110 (2%)

Query: 62   YTQVSPAYTQVSPAYTQVSPAYTQVSPAYIPVSPAYTPVSPAYTQVSPAYTQVSPAYTQV 121
            YT  SP Y+  SP Y+  SP Y+  SP Y P +P Y+P SP Y+  SP YT  SP Y+  
Sbjct: 1853 YTPASPKYSPTSPKYSPTSPKYSPTSPTYSPTTPKYSPTSPTYSPTSPVYTPTSPKYSPT 1912

Query: 122  SPAYTQVSLAYTQVSLAYTQVSPA---YTQVSPAYTQVSPAYTQVSSAYT 168
            SP Y+  S  Y+  S  Y+  SP    Y+  SP Y+  SP Y+  S A +
Sbjct: 1913 SPTYSPTSPKYSPTSPTYSPTSPKGSTYSPTSPGYSPTSPTYSLTSPAIS 1962

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.

Mus musculus (taxid: 10090)

EC: 2

EC: .

EC: 7

EC: .

EC: 7

EC: .

EC: 6

>sp|P24928|RPB1_HUMAN DNA-directed RNA polymerase II subunit RPB1 OS=Homo sapiens GN=POLR2A PE=1 SV=2

 Score = 76.3 bits (186), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 46/108 (42%), Positives = 59/108 (54%), Gaps = 3/108 (2%)

Query: 62   YTQVSPAYTQVSPAYTQVSPAYTQVSPAYIPVSPAYTPVSPAYTQVSPAYTQVSPAYTQV 121
            YT  SP Y+  SP Y+  SP Y+  SP Y P +P Y+P SP Y+  SP YT  SP Y+  
Sbjct: 1853 YTPTSPKYSPTSPKYSPTSPKYSPTSPTYSPTTPKYSPTSPTYSPTSPVYTPTSPKYSPT 1912

Query: 122  SPAYTQVSLAYTQVSLAYTQVSPA---YTQVSPAYTQVSPAYTQVSSA 166
            SP Y+  S  Y+  S  Y+  SP    Y+  SP Y+  SP Y+  S A
Sbjct: 1913 SPTYSPTSPKYSPTSPTYSPTSPKGSTYSPTSPGYSPTSPTYSLTSPA 1960

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. Acts as a RNA-dependent RNA polymerase when associated with small delta antigen of Hepatitis delta virus, acting both as a replicate and transcriptase for the viral RNA circular genome.

Homo sapiens (taxid: 9606)

EC: 2

EC: .

EC: 7

EC: .

EC: 7

EC: .

EC: 4

EC: 8

>sp|Q8R0T2|ZN768_MOUSE Zinc finger protein 768 OS=Mus musculus GN=Znf768 PE=2 SV=1

 Score = 69.3 bits (168), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 48/160 (30%), Positives = 63/160 (39%), Gaps = 3/160 (1%)

Query: 59  SPAYTQVSPAYTQVSPAYTQVSPAYTQVSPAYIPVSPAYTPVSPAYTQVSPAYTQVSPAY 118
           SP +   SP +   SP +   SP +   SP ++P SP + P SP     SP +   SP Y
Sbjct: 65  SPEFEPQSPEFESQSPRFEPESPGFESRSPGFVPPSPEFAPRSPESDPQSPEFESQSPKY 124

Query: 119 TQVSPAYTQVSLAYTQVSLAYTQVSPAYTQVSPAYTQVSPAYTQVSSAYTQVILNKIRPG 178
              SP     S      S  Y   SP Y   SP +   SP Y   S  Y           
Sbjct: 125 EPRSPGCHPRSPGCEPGSPRYEPKSPGYGSKSPEFESQSPGYESQSPGYEPQNSGDGVQN 184

Query: 179 RESNSRSSAYE---AFFHEWVWMSWYPDINPTLPIAMGVH 215
            E  + S  +E   + F E   M   P+    L I++GVH
Sbjct: 185 SEFKTHSPEFETQSSKFQEGAEMPLSPEEKNPLSISLGVH 224

May be involved in transcriptional regulation.

Mus musculus (taxid: 10090)

>sp|P35074|RPB1_CAEBR DNA-directed RNA polymerase II subunit RPB1 OS=Caenorhabditis briggsae GN=rpb-1 PE=3 SV=2

 Score = 65.9 bits (159), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 50/121 (41%), Positives = 65/121 (53%), Gaps = 13/121 (10%)

Query: 59   SPAYTQVSPAYTQVSPAYTQVSPAY----------TQVSPAYIPVSPAYTPVSPAYTQVS 108
            SP Y+  SP Y+  SP Y+  SP+Y          +  SP Y P SP+Y+P SP Y+  S
Sbjct: 1690 SPTYSPTSPTYSPTSPTYSPTSPSYEGYSPSSPKYSPSSPTYSPTSPSYSPTSPQYSPTS 1749

Query: 109  PAYTQVSPAYTQVSPAYTQVS-LAYTQVSLAYTQVSPAYTQVSPAYTQVSPAYTQVSSAY 167
            P Y+  SP YT  SP Y   S  A++  S  Y+  SP Y+  SP+YT  SP Y+  S  Y
Sbjct: 1750 PQYSPSSPTYTPSSPTYNPTSPRAFS--SPQYSPTSPTYSPTSPSYTPSSPQYSPTSPTY 1807

Query: 168  T 168
            T
Sbjct: 1808 T 1808

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.

Caenorhabditis briggsae (taxid: 6238)

EC: 2

EC: .

EC: 7

EC: .

EC: 7

EC: .

EC: 6

>sp|P16356|RPB1_CAEEL DNA-directed RNA polymerase II subunit RPB1 OS=Caenorhabditis elegans GN=ama-1 PE=1 SV=3

 Score = 63.5 bits (153), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 47/124 (37%), Positives = 61/124 (49%), Gaps = 16/124 (12%)

Query: 59   SPAYTQVSPAYTQVSPAYTQVSPAYTQVSPA-------------YIPVSPAYTPVSPAYT 105
            SP Y+  SP Y+  SP Y+  SP+Y                   Y P SP+Y+P SP Y+
Sbjct: 1690 SPTYSPTSPTYSPTSPTYSPTSPSYESGGGYSPSSPKYSPSSPTYSPTSPSYSPTSPQYS 1749

Query: 106  QVSPAYTQVSPAYTQVSPAYTQVS-LAYTQVSLAYTQVSPAYTQVSPAYTQVSPAYTQVS 164
              SP Y+  SP YT  SP Y   S   ++  S  Y+  SP Y+  SP+YT  SP Y+  S
Sbjct: 1750 PTSPQYSPSSPTYTPSSPTYNPTSPRGFS--SPQYSPTSPTYSPTSPSYTPSSPQYSPTS 1807

Query: 165  SAYT 168
              YT
Sbjct: 1808 PTYT 1811

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.

Caenorhabditis elegans (taxid: 6239)

EC: 2

EC: .

EC: 7

EC: .

EC: 7

EC: .

EC: 6

>sp|Q9H5H4|ZN768_HUMAN Zinc finger protein 768 OS=Homo sapiens GN=ZNF768 PE=1 SV=2

 Score = 56.2 bits (134), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 36/118 (30%), Positives = 49/118 (41%), Gaps = 3/118 (2%)

Query: 59  SPAYTQVSPAYTQVSPAYTQVSPAYTQVSPAYIPVSPAYTPVSPAYTQVSPAYTQVSPAY 118
           SP +   SP +   SP +   SP +   SP  +P SP + P SP     SP +   SP Y
Sbjct: 62  SPGFEPQSPEFEPQSPRFEPESPGFESRSPGLVPPSPEFAPRSPESDSQSPEFESQSPRY 121

Query: 119 TQVSPAYTQVSLAYTQVSLAYTQVSPAYTQVSPAYTQVSPAYTQVSSAY---TQVILN 173
              SP Y   S  Y   S  Y   S  Y   +      SP +   SS +    +++LN
Sbjct: 122 EPQSPGYEPRSPGYEPRSPGYESESSRYESQNTELKTQSPEFEAQSSKFQEGAEMLLN 179

May be involved in transcriptional regulation.

Homo sapiens (taxid: 9606)

>sp|O88799|ZAN_MOUSE Zonadhesin OS=Mus musculus GN=Zan PE=2 SV=1

 Score = 50.8 bits (120), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 42/120 (35%), Positives = 53/120 (44%), Gaps = 4/120 (3%)

Query: 54  TVYTVSPAYTQVSPAYTQVSPAYTQVSPAYTQVSPAYIPVSPAYTPVSPAYTQVSPAYTQ 113
           T  T+S   T VSP  T +      VS   T VSP    V P  T ++  YT+V    T+
Sbjct: 804 TEETISTEVTTVSPEETTLPTEVPTVSTEVTNVSPEETSVPPEETILTTLYTEVPTVPTE 863

Query: 114 VSPAYTQ---VSPAYTQVSLAYTQVSLAYTQVSPAYTQVSPAYTQVSPAYTQVSSAYTQV 170
           V+  +T+   VSP  T V    T +S   T VSP  T +      VS   T VS   T V
Sbjct: 864 VTGVHTEVTNVSPEETSVPTEET-ISTEVTTVSPEETTLPTEVPTVSTEVTNVSPEETSV 922

Binds in a species-specific manner to the zona pellucida of the egg. May be involved in gamete recognition and/or signaling.

Mus musculus (taxid: 10090)

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

 Score = 50.1 bits (118), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 45/151 (29%), Positives = 63/151 (41%), Gaps = 37/151 (24%)

Query: 56   YTVSPAYTQVSPAYTQV-----------------------SPAYTQVSPAYTQVSPAYIP 92
            Y+ SP Y+  SPAY+Q                        SP YT  SP Y+  SP Y P
Sbjct: 1734 YSASPQYSPASPAYSQTGVKYSPTSPTYSPPSPSYDGSPGSPQYTPGSPQYSPASPKYSP 1793

Query: 93   VSPAY-------------TPVSPAYTQVSPAYTQVSPAYTQVSPAYTQVSLAYTQVSLAY 139
             SP Y             +P    Y+  SP Y+     Y+  S  Y+  S  YT  +  Y
Sbjct: 1794 TSPLYSPSSPQHSPSNQYSPTGSTYSATSPRYSPNMSIYSPSSTKYSPTSPTYTPTARNY 1853

Query: 140  TQVSPAYTQVSPA-YTQVSPAYTQVSSAYTQ 169
            +  SP Y+  +P+ Y+  SPAY+  S  + +
Sbjct: 1854 SPTSPMYSPTAPSHYSPTSPAYSPSSPTFEE 1884

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: 2

EC: .

EC: 7

EC: .

EC: 7

EC: .

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	222
4092885	1553	RNA polymerase II largest subunit [Anton	0.477	0.068	0.518	2e-24
294876120	170	P35 antigen, putative [Perkinsus marinus	0.617	0.805	0.479	3e-23
301090036	1858	DNA-directed RNA polymerase II largest s	0.481	0.057	0.581	7e-23
348676924	1852	RNA polymerase II large subunit [Phytoph	0.481	0.057	0.581	8e-23
3511287	1690	DNA-dependent RNA polymerase II largest	0.472	0.062	0.572	1e-22
255079898	1720	predicted protein [Micromonas sp. RCC299	0.477	0.061	0.572	2e-22
145351142	1646	predicted protein [Ostreococcus lucimari	0.495	0.066	0.572	2e-22
299116996	1904	conserved unknown protein [Ectocarpus si	0.495	0.057	0.572	2e-22
302835796	1879	hypothetical protein VOLCADRAFT_80692 [V	0.463	0.054	0.563	2e-22
412992604	1667	RNA polymerase II largest subunit [Bathy	0.477	0.063	0.563	4e-22

>gi|4092885|gb|AAD12605.1| RNA polymerase II largest subunit [Antonospora locustae]

 Score =  118 bits (296), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 55/106 (51%), Positives = 68/106 (64%)

Query: 57   TVSPAYTQVSPAYTQVSPAYTQVSPAYTQVSPAYIPVSPAYTPVSPAYTQVSPAYTQVSP 116
            T    Y+  SPAY+  SPAY+  SPAY+  SPAY P SPAY+P SPAY+  SPAY+  SP
Sbjct: 1434 TTPSVYSPTSPAYSPTSPAYSPTSPAYSPTSPAYSPTSPAYSPTSPAYSPTSPAYSPTSP 1493

Query: 117  AYTQVSPAYTQVSLAYTQVSLAYTQVSPAYTQVSPAYTQVSPAYTQ 162
            AY+  SPAY+  S AY+  S AY+  SPAY+  SP Y   + A  Q
Sbjct: 1494 AYSPTSPAYSPTSPAYSPTSPAYSPTSPAYSPTSPVYRPSTRAKDQ 1539

Source: Antonospora locustae

Species: Antonospora locustae

Genus: Antonospora

Phylum: Microsporidia

Superkingdom: Eukaryota

>gi|294876120|ref|XP_002767561.1| P35 antigen, putative [Perkinsus marinus ATCC 50983] gi|239869221|gb|EER00279.1| P35 antigen, putative [Perkinsus marinus ATCC 50983]

 Score =  114 bits (285), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 69/144 (47%), Positives = 87/144 (60%), Gaps = 7/144 (4%)

Query: 58  VSPAYTQVSPAYTQVSPAYTQVSPAYTQVSPAYIPVSPAYTPVSPAYTQVSPAYTQVSPA 117
            SPAY+  SPAY+  SPAY+  SPAY+  SPAY P SPAY+P SPAY+  SPAY+  SPA
Sbjct: 11  TSPAYSPTSPAYSPTSPAYSPTSPAYSPTSPAYSPTSPAYSPTSPAYSPTSPAYSPTSPA 70

Query: 118 YTQVSPAYTQVSLAYTQVSLAYTQVSPAYTQVSPAYTQVSPAYTQVSSAY--TQVILNKI 175
           Y+  SPAY+  S AY+  S AY+  SPAY+  SP+Y+  SPAY+  S AY  T    +  
Sbjct: 71  YSPTSPAYSPTSPAYSPTSPAYSPTSPAYSPTSPSYSPTSPAYSPTSPAYSPTSPAYSPT 130

Query: 176 RPGRESNSRSSAYEAFFHEWVWMS 199
            P     S      A++H  V  S
Sbjct: 131 SPAYSPTS-----PAYYHPLVTSS 149

Source: Perkinsus marinus ATCC 50983

Species: Perkinsus marinus

Genus: Perkinsus

Family: Perkinsidae

Order: Perkinsida

Superkingdom: Eukaryota

>gi|301090036|ref|XP_002895253.1| DNA-directed RNA polymerase II largest subunit [Phytophthora infestans T30-4] gi|262101000|gb|EEY59052.1| DNA-directed RNA polymerase II largest subunit [Phytophthora infestans T30-4]

 Score =  113 bits (282), Expect = 7e-23,   Method: Compositional matrix adjust.
 Identities = 64/110 (58%), Positives = 78/110 (70%)

Query: 59   SPAYTQVSPAYTQVSPAYTQVSPAYTQVSPAYIPVSPAYTPVSPAYTQVSPAYTQVSPAY 118
            SPAY+  SPAY+  SPAY+  SPAY+  SPAY P SPAY+P SPAY+  SPAY+  SPAY
Sbjct: 1649 SPAYSPTSPAYSPTSPAYSPTSPAYSPTSPAYSPTSPAYSPTSPAYSPTSPAYSPTSPAY 1708

Query: 119  TQVSPAYTQVSLAYTQVSLAYTQVSPAYTQVSPAYTQVSPAYTQVSSAYT 168
            +  SPAY+  S AY+  S AY+  SPAY+  SPAY+  SPAY+  S AYT
Sbjct: 1709 SPTSPAYSPTSPAYSPTSPAYSPTSPAYSPTSPAYSPTSPAYSPTSPAYT 1758

Source: Phytophthora infestans T30-4

Species: Phytophthora infestans

Genus: Phytophthora

Order: Peronosporales

Superkingdom: Eukaryota

>gi|348676924|gb|EGZ16741.1| RNA polymerase II large subunit [Phytophthora sojae]

 Score =  112 bits (281), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 64/110 (58%), Positives = 78/110 (70%)

Query: 59   SPAYTQVSPAYTQVSPAYTQVSPAYTQVSPAYIPVSPAYTPVSPAYTQVSPAYTQVSPAY 118
            SPAY+  SPAY+  SPAY+  SPAY+  SPAY P SPAY+P SPAY+  SPAY+  SPAY
Sbjct: 1642 SPAYSPTSPAYSPTSPAYSPTSPAYSPTSPAYSPTSPAYSPTSPAYSPTSPAYSPTSPAY 1701

Query: 119  TQVSPAYTQVSLAYTQVSLAYTQVSPAYTQVSPAYTQVSPAYTQVSSAYT 168
            +  SPAY+  S AY+  S AY+  SPAY+  SPAY+  SPAY+  S AYT
Sbjct: 1702 SPTSPAYSPTSPAYSPTSPAYSPTSPAYSPTSPAYSPTSPAYSPTSPAYT 1751

Source: Phytophthora sojae

Species: Phytophthora sojae

Genus: Phytophthora

Order: Peronosporales

Superkingdom: Eukaryota

>gi|3511287|gb|AAC62246.1| DNA-dependent RNA polymerase II largest subunit, partial [Breviata anathema]

 Score =  112 bits (280), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 63/110 (57%), Positives = 78/110 (70%)

Query: 59   SPAYTQVSPAYTQVSPAYTQVSPAYTQVSPAYIPVSPAYTPVSPAYTQVSPAYTQVSPAY 118
            SPAY+  SPAY+  SPAY+  SPAY+  SPAY P SPAY+P SPAY+  SPAY+  SPAY
Sbjct: 1510 SPAYSPASPAYSPASPAYSPASPAYSPASPAYSPASPAYSPASPAYSPASPAYSPASPAY 1569

Query: 119  TQVSPAYTQVSLAYTQVSLAYTQVSPAYTQVSPAYTQVSPAYTQVSSAYT 168
            +  SPAY+  S AY+  S AY+  SPAY+  SPAY+  SPAY+  S AY+
Sbjct: 1570 SPASPAYSPASPAYSPASPAYSPASPAYSPASPAYSPASPAYSPASPAYS 1619

Source: Breviata anathema

Species: Breviata anathema

Genus: Breviata

Superkingdom: Eukaryota

>gi|255079898|ref|XP_002503529.1| predicted protein [Micromonas sp. RCC299] gi|226518796|gb|ACO64787.1| predicted protein [Micromonas sp. RCC299]

 Score =  112 bits (279), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 63/110 (57%), Positives = 78/110 (70%)

Query: 59   SPAYTQVSPAYTQVSPAYTQVSPAYTQVSPAYIPVSPAYTPVSPAYTQVSPAYTQVSPAY 118
            SPAY+  SPAY+  SPAY+  SPAY+  SPAY P SPAY+P SPAY+  SPAY+  SPAY
Sbjct: 1531 SPAYSPTSPAYSPTSPAYSPTSPAYSPTSPAYSPTSPAYSPTSPAYSPTSPAYSPTSPAY 1590

Query: 119  TQVSPAYTQVSLAYTQVSLAYTQVSPAYTQVSPAYTQVSPAYTQVSSAYT 168
            +  SPAY+  S AY+  S AY+  SPAY+  SPAY+  SPAY+  S AY+
Sbjct: 1591 SPTSPAYSPTSPAYSPTSPAYSPTSPAYSPTSPAYSPTSPAYSPTSPAYS 1640

Source: Micromonas sp. RCC299

Species: Micromonas sp. RCC299

Genus: Micromonas

Order: Mamiellales

Class: Mamiellophyceae

Phylum: Chlorophyta

Superkingdom: Eukaryota

>gi|145351142|ref|XP_001419944.1| predicted protein [Ostreococcus lucimarinus CCE9901] gi|144580177|gb|ABO98237.1| predicted protein [Ostreococcus lucimarinus CCE9901]

 Score =  111 bits (278), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 63/110 (57%), Positives = 78/110 (70%)

Query: 59   SPAYTQVSPAYTQVSPAYTQVSPAYTQVSPAYIPVSPAYTPVSPAYTQVSPAYTQVSPAY 118
            SPAY+  SPAY+  SPAY+  SPAY+  SPAY P SPAY+P SPAY+  SPAY+  SPAY
Sbjct: 1527 SPAYSPTSPAYSPTSPAYSPTSPAYSPTSPAYSPTSPAYSPTSPAYSPTSPAYSPTSPAY 1586

Query: 119  TQVSPAYTQVSLAYTQVSLAYTQVSPAYTQVSPAYTQVSPAYTQVSSAYT 168
            +  SPAY+  S AY+  S AY+  SPAY+  SPAY+  SPAY+  S AY+
Sbjct: 1587 SPTSPAYSPTSPAYSPTSPAYSPTSPAYSPTSPAYSPTSPAYSPTSPAYS 1636

Source: Ostreococcus lucimarinus CCE9901

Species: Ostreococcus 'lucimarinus'

Genus: Ostreococcus

Order: Mamiellales

Class: Mamiellophyceae

Phylum: Chlorophyta

Superkingdom: Eukaryota

>gi|299116996|emb|CBN73767.1| conserved unknown protein [Ectocarpus siliculosus]

 Score =  111 bits (277), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 63/110 (57%), Positives = 78/110 (70%)

Query: 59   SPAYTQVSPAYTQVSPAYTQVSPAYTQVSPAYIPVSPAYTPVSPAYTQVSPAYTQVSPAY 118
            SPAY+  SPAY+  SPAY+  SPAY+  SPAY P SPAY+P SPAY+  SPAY+  SPAY
Sbjct: 1648 SPAYSPTSPAYSPTSPAYSPTSPAYSPTSPAYSPTSPAYSPTSPAYSPTSPAYSPTSPAY 1707

Query: 119  TQVSPAYTQVSLAYTQVSLAYTQVSPAYTQVSPAYTQVSPAYTQVSSAYT 168
            +  SPAY+  S AY+  S AY+  SPAY+  SPAY+  SPAY+  S AY+
Sbjct: 1708 SPTSPAYSPTSPAYSPTSPAYSPTSPAYSPTSPAYSPTSPAYSPTSPAYS 1757

Source: Ectocarpus siliculosus

Species: Ectocarpus siliculosus

Genus: Ectocarpus

Family: Ectocarpaceae

Order: Ectocarpales

Phylum: Phaeophyceae

Superkingdom: Eukaryota

>gi|302835796|ref|XP_002949459.1| hypothetical protein VOLCADRAFT_80692 [Volvox carteri f. nagariensis] gi|300265286|gb|EFJ49478.1| hypothetical protein VOLCADRAFT_80692 [Volvox carteri f. nagariensis]

 Score =  111 bits (277), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 62/110 (56%), Positives = 77/110 (70%)

Query: 59   SPAYTQVSPAYTQVSPAYTQVSPAYTQVSPAYIPVSPAYTPVSPAYTQVSPAYTQVSPAY 118
            SP Y+  SPAY+  SPAY+  SPAY+  SPAY P SPAY+P SPAY+  SPAY+  SPAY
Sbjct: 1557 SPGYSPTSPAYSPTSPAYSPTSPAYSPTSPAYSPTSPAYSPTSPAYSPTSPAYSPTSPAY 1616

Query: 119  TQVSPAYTQVSLAYTQVSLAYTQVSPAYTQVSPAYTQVSPAYTQVSSAYT 168
            +  SPAY+  S AY+  S AY+  SPAY+  SPAY+  SPAY+  S AY+
Sbjct: 1617 SPTSPAYSPTSPAYSPTSPAYSPTSPAYSPTSPAYSPTSPAYSPTSPAYS 1666

Source: Volvox carteri f. nagariensis

Species: Volvox carteri

Genus: Volvox

Family: Volvocaceae

Order: Chlamydomonadales

Class: Chlorophyceae

Phylum: Chlorophyta

Superkingdom: Eukaryota

>gi|412992604|emb|CCO18584.1| RNA polymerase II largest subunit [Bathycoccus prasinos]

 Score =  110 bits (276), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 62/110 (56%), Positives = 77/110 (70%)

Query: 59   SPAYTQVSPAYTQVSPAYTQVSPAYTQVSPAYIPVSPAYTPVSPAYTQVSPAYTQVSPAY 118
            SP Y+  SPAY+  SPAY+  SPAY+  SPAY P SPAY+P SPAY+  SPAY+  SPAY
Sbjct: 1509 SPGYSPTSPAYSPTSPAYSPTSPAYSPTSPAYSPTSPAYSPTSPAYSPTSPAYSPTSPAY 1568

Query: 119  TQVSPAYTQVSLAYTQVSLAYTQVSPAYTQVSPAYTQVSPAYTQVSSAYT 168
            +  SPAY+  S AY+  S AY+  SPAY+  SPAY+  SPAY+  S AY+
Sbjct: 1569 SPTSPAYSPTSPAYSPTSPAYSPTSPAYSPTSPAYSPTSPAYSPTSPAYS 1618

Source: Bathycoccus prasinos

Species: Bathycoccus prasinos

Genus: Bathycoccus

Order: Mamiellales

Class: Mamiellophyceae

Phylum: Chlorophyta

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	222
UNIPROTKB|P11414	467	POLR2A "DNA-directed RNA polym	0.671	0.319	0.364	8.1e-26
UNIPROTKB|I3LQ53	543	I3LQ53 "Uncharacterized protei	0.671	0.274	0.364	1.7e-25
CGD|CAL0000919	1728	RPO21 [Candida albicans (taxid	0.671	0.086	0.390	2.3e-25
UNIPROTKB|Q5ACI7	1728	RPO21 "DNA-directed RNA polyme	0.671	0.086	0.390	2.3e-25
SGD|S000002299	1733	RPO21 "RNA polymerase II large	0.689	0.088	0.382	7.8e-25
UNIPROTKB|J9NW09	1789	POLR2A "DNA-directed RNA polym	0.671	0.083	0.370	8.1e-25
UNIPROTKB|F1PGS0	1969	POLR2A "DNA-directed RNA polym	0.671	0.075	0.370	9.1e-25
ZFIN|ZDB-GENE-041008-78	1965	polr2a "polymerase (RNA) II (D	0.671	0.075	0.364	1.9e-24
UNIPROTKB|P24928	1970	POLR2A "DNA-directed RNA polym	0.671	0.075	0.364	1.9e-24
MGI|MGI:98086	1970	Polr2a "polymerase (RNA) II (D	0.671	0.075	0.364	1.9e-24

UNIPROTKB|P11414 POLR2A "DNA-directed RNA polymerase II subunit RPB1" [Cricetulus griseus (taxid:10029)]

 Score = 295 (108.9 bits), Expect = 8.1e-26, P = 8.1e-26
 Identities = 55/151 (36%), Positives = 90/151 (59%)

Query:    59 SPAYTQVSPAYTQVSPAYTQVSPAYTQVSPAYIPVSPAYTPVSPAYTQVSPAYTQVSPAY 118
             SP+Y+  SP+Y+  SP+Y+  SP+Y+  SP+Y P SP+Y+P SP+Y+  SP+Y+  SP+Y
Sbjct:   137 SPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSY 196

Query:   119 TQVSPAYTQVSLAYTQVSLAYTQVSPAYTQVSPAYTQVSPAYTQVSSAYTQVILNKIRPG 178
             +  SP+Y+  S +Y+  S +Y+  SP+Y+  SP+Y+  SP+Y+  S  Y+    N     
Sbjct:   197 SPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPNYSPTSPNYTPTS 256

Query:   179 RESNSRSSAYEAFFHEWVWMSWYPDINPTLP 209
                +  S +Y      +   S  P+ +PT P
Sbjct:   257 PSYSPTSPSYSPTSPNYTPTS--PNYSPTSP 285

GO:0005634 "nucleus" evidence=ISS

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

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

GO:0006468 "protein phosphorylation" evidence=ISS

GO:0004672 "protein kinase activity" evidence=ISS

UNIPROTKB|I3LQ53 I3LQ53 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 295 (108.9 bits), Expect = 1.7e-25, P = 1.7e-25
 Identities = 55/151 (36%), Positives = 90/151 (59%)

Query:    59 SPAYTQVSPAYTQVSPAYTQVSPAYTQVSPAYIPVSPAYTPVSPAYTQVSPAYTQVSPAY 118
             SP+Y+  SP+Y+  SP+Y+  SP+Y+  SP+Y P SP+Y+P SP+Y+  SP+Y+  SP+Y
Sbjct:   213 SPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSY 272

Query:   119 TQVSPAYTQVSLAYTQVSLAYTQVSPAYTQVSPAYTQVSPAYTQVSSAYTQVILNKIRPG 178
             +  SP+Y+  S +Y+  S +Y+  SP+Y+  SP+Y+  SP+Y+  S  Y+    N     
Sbjct:   273 SPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPNYSPTSPNYTPTS 332

Query:   179 RESNSRSSAYEAFFHEWVWMSWYPDINPTLP 209
                +  S +Y      +   S  P+ +PT P
Sbjct:   333 PSYSPTSPSYSPTSPNYTPTS--PNYSPTSP 361

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

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

GO:0003677 "DNA binding" evidence=IEA

CGD|CAL0000919 RPO21 [Candida albicans (taxid:5476)]

 Score = 303 (111.7 bits), Expect = 2.3e-25, P = 2.3e-25
 Identities = 59/151 (39%), Positives = 88/151 (58%)

Query:    59 SPAYTQVSPAYTQVSPAYTQVSPAYTQVSPAYIPVSPAYTPVSPAYTQVSPAYTQVSPAY 118
             SP+Y   SPAY+  SP+Y   SPAY+  SP+Y P SPAY+P SPAY+  SP+Y+  SP Y
Sbjct:  1554 SPSYAPTSPAYSPTSPSYAPTSPAYSPTSPSYAPTSPAYSPTSPAYSPTSPSYSPTSPQY 1613

Query:   119 TQVSPAYTQVSLAYTQVSLAYTQVSPAYTQVSPAYTQVSPAYTQVSSAYTQVILNKIRPG 178
             +  SP+Y+  S +Y+  S +Y+  SPAY+  SP+Y+  SP+Y+  S  Y+    +     
Sbjct:  1614 SPTSPSYSPTSPSYSPTSPSYSPTSPAYSPTSPSYSPTSPSYSPTSPQYSPTSPSYSPTS 1673

Query:   179 RESNSRSSAYEAFFHEWVWMSWYPDINPTLP 209
              + +  S +Y     ++   S  P  +PT P
Sbjct:  1674 PQYSPTSPSYSPTSPQYSPTS--PQYSPTSP 1702

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

GO:0005829 "cytosol" evidence=IEA

GO:0005739 "mitochondrion" evidence=IEA

GO:0030447 "filamentous growth" evidence=IMP

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

GO:0009267 "cellular response to starvation" evidence=IMP

GO:0036170 "filamentous growth of a population of unicellular organisms in response to starvation" evidence=IMP

GO:0036180 "filamentous growth of a population of unicellular organisms in response to biotic stimulus" evidence=IMP

GO:0071216 "cellular response to biotic stimulus" evidence=IMP

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

GO:0003677 "DNA binding" evidence=IEA

GO:0003968 "RNA-directed RNA polymerase activity" evidence=IEA

UNIPROTKB|Q5ACI7 RPO21 "DNA-directed RNA polymerase" [Candida albicans SC5314 (taxid:237561)]

 Score = 303 (111.7 bits), Expect = 2.3e-25, P = 2.3e-25
 Identities = 59/151 (39%), Positives = 88/151 (58%)

Query:    59 SPAYTQVSPAYTQVSPAYTQVSPAYTQVSPAYIPVSPAYTPVSPAYTQVSPAYTQVSPAY 118
             SP+Y   SPAY+  SP+Y   SPAY+  SP+Y P SPAY+P SPAY+  SP+Y+  SP Y
Sbjct:  1554 SPSYAPTSPAYSPTSPSYAPTSPAYSPTSPSYAPTSPAYSPTSPAYSPTSPSYSPTSPQY 1613

Query:   119 TQVSPAYTQVSLAYTQVSLAYTQVSPAYTQVSPAYTQVSPAYTQVSSAYTQVILNKIRPG 178
             +  SP+Y+  S +Y+  S +Y+  SPAY+  SP+Y+  SP+Y+  S  Y+    +     
Sbjct:  1614 SPTSPSYSPTSPSYSPTSPSYSPTSPAYSPTSPSYSPTSPSYSPTSPQYSPTSPSYSPTS 1673

Query:   179 RESNSRSSAYEAFFHEWVWMSWYPDINPTLP 209
              + +  S +Y     ++   S  P  +PT P
Sbjct:  1674 PQYSPTSPSYSPTSPQYSPTS--PQYSPTSP 1702

GO:0009267 "cellular response to starvation" evidence=IMP

GO:0030447 "filamentous growth" evidence=IMP

GO:0036170 "filamentous growth of a population of unicellular organisms in response to starvation" evidence=IMP

GO:0036180 "filamentous growth of a population of unicellular organisms in response to biotic stimulus" evidence=IMP

GO:0071216 "cellular response to biotic stimulus" evidence=IMP

SGD|S000002299 RPO21 "RNA polymerase II largest subunit B220" [Saccharomyces cerevisiae (taxid:4932)]

 Score = 298 (110.0 bits), Expect = 7.8e-25, P = 7.8e-25
 Identities = 60/157 (38%), Positives = 95/157 (60%)

Query:    54 TVYTVSPAYTQVSPAYTQVSPAYTQVSPAYTQVSPAYIPVSPAYTPVSPAYTQVSPAYTQ 113
             T    SPAY+  SP+Y+  SP+Y+  SP+Y+  SP+Y P SP+Y+P SP+Y+  SP+Y+ 
Sbjct:  1548 TYSPTSPAYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSP 1607

Query:   114 VSPAYTQVSPAYTQVSLAYTQVSLAYTQVSPAYTQVSPAYTQVSPAYTQVSSAYTQVILN 173
              SP+Y+  SP+Y+  S +Y+  S +Y+  SP+Y+  SP+Y+  SP+Y+  S AY+    +
Sbjct:  1608 TSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPAYSPTSPS 1667

Query:   174 KIRPGRESNSRSS-AYEAFFHEWVWMSWYPDINPTLP 209
                P   S S +S +Y      +   S  P+ +PT P
Sbjct:  1668 -YSPTSPSYSPTSPSYSPTSPSYSPTS--PNYSPTSP 1701

GO:0016740 "transferase activity" evidence=IEA

GO:0016779 "nucleotidyltransferase activity" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

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

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

GO:0005739 "mitochondrion" evidence=IDA

GO:0005634 "nucleus" evidence=IEA;IDA

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

GO:0003677 "DNA binding" evidence=IEA

GO:0003968 "RNA-directed RNA polymerase activity" evidence=IDA

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

UNIPROTKB|J9NW09 POLR2A "DNA-directed RNA polymerase" [Canis lupus familiaris (taxid:9615)]

 Score = 298 (110.0 bits), Expect = 8.1e-25, P = 8.1e-25
 Identities = 56/151 (37%), Positives = 91/151 (60%)

Query:    59 SPAYTQVSPAYTQVSPAYTQVSPAYTQVSPAYIPVSPAYTPVSPAYTQVSPAYTQVSPAY 118
             SP+Y+  SP+Y+  SP+Y+  SP+Y+  SP+Y P SP+Y+P SP+Y+  SP+Y+  SP+Y
Sbjct:  1640 SPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSY 1699

Query:   119 TQVSPAYTQVSLAYTQVSLAYTQVSPAYTQVSPAYTQVSPAYTQVSSAYTQVILNKIRPG 178
             +  SP+Y+  S +Y+  S +Y+  SP+Y+  SP+Y+  SP+Y+  S  Y+    N     
Sbjct:  1700 SPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPNYSPSRPNYTPTS 1759

Query:   179 RESNSRSSAYEAFFHEWVWMSWYPDINPTLP 209
                +  S +Y      +  MS  P+ +PT P
Sbjct:  1760 PSYSPTSPSYSPTSPNYTPMS--PNYSPTSP 1788

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

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

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

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|F1PGS0 POLR2A "DNA-directed RNA polymerase" [Canis lupus familiaris (taxid:9615)]

 Score = 298 (110.0 bits), Expect = 9.1e-25, P = 9.1e-25
 Identities = 56/151 (37%), Positives = 91/151 (60%)

Query:    59 SPAYTQVSPAYTQVSPAYTQVSPAYTQVSPAYIPVSPAYTPVSPAYTQVSPAYTQVSPAY 118
             SP+Y+  SP+Y+  SP+Y+  SP+Y+  SP+Y P SP+Y+P SP+Y+  SP+Y+  SP+Y
Sbjct:  1640 SPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSY 1699

Query:   119 TQVSPAYTQVSLAYTQVSLAYTQVSPAYTQVSPAYTQVSPAYTQVSSAYTQVILNKIRPG 178
             +  SP+Y+  S +Y+  S +Y+  SP+Y+  SP+Y+  SP+Y+  S  Y+    N     
Sbjct:  1700 SPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPNYSPSRPNYTPTS 1759

Query:   179 RESNSRSSAYEAFFHEWVWMSWYPDINPTLP 209
                +  S +Y      +  MS  P+ +PT P
Sbjct:  1760 PSYSPTSPSYSPTSPNYTPMS--PNYSPTSP 1788

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

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

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

GO:0003677 "DNA binding" evidence=IEA

ZFIN|ZDB-GENE-041008-78 polr2a "polymerase (RNA) II (DNA directed) polypeptide A" [Danio rerio (taxid:7955)]

 Score = 295 (108.9 bits), Expect = 1.9e-24, P = 1.9e-24
 Identities = 55/151 (36%), Positives = 90/151 (59%)

Query:    59 SPAYTQVSPAYTQVSPAYTQVSPAYTQVSPAYIPVSPAYTPVSPAYTQVSPAYTQVSPAY 118
             SP+Y+  SP+Y+  SP+Y+  SP+Y+  SP+Y P SP+Y+P SP+Y+  SP+Y+  SP+Y
Sbjct:  1637 SPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSY 1696

Query:   119 TQVSPAYTQVSLAYTQVSLAYTQVSPAYTQVSPAYTQVSPAYTQVSSAYTQVILNKIRPG 178
             +  SP+Y+  S +Y+  S +Y+  SP+Y+  SP+Y+  SP+Y+  S +Y+    N     
Sbjct:  1697 SPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPNYTPTS 1756

Query:   179 RESNSRSSAYEAFFHEWVWMSWYPDINPTLP 209
                +  S +Y      +   S  P+  PT P
Sbjct:  1757 PSYSPTSPSYSPTSPSYSPTS--PNYTPTSP 1785

GO:0003677 "DNA binding" evidence=IEA

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

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

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

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

GO:0016740 "transferase activity" evidence=IEA

GO:0016779 "nucleotidyltransferase activity" evidence=IEA

UNIPROTKB|P24928 POLR2A "DNA-directed RNA polymerase II subunit RPB1" [Homo sapiens (taxid:9606)]

 Score = 295 (108.9 bits), Expect = 1.9e-24, P = 1.9e-24
 Identities = 55/151 (36%), Positives = 90/151 (59%)

Query:    59 SPAYTQVSPAYTQVSPAYTQVSPAYTQVSPAYIPVSPAYTPVSPAYTQVSPAYTQVSPAY 118
             SP+Y+  SP+Y+  SP+Y+  SP+Y+  SP+Y P SP+Y+P SP+Y+  SP+Y+  SP+Y
Sbjct:  1640 SPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSY 1699

Query:   119 TQVSPAYTQVSLAYTQVSLAYTQVSPAYTQVSPAYTQVSPAYTQVSSAYTQVILNKIRPG 178
             +  SP+Y+  S +Y+  S +Y+  SP+Y+  SP+Y+  SP+Y+  S  Y+    N     
Sbjct:  1700 SPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPNYSPTSPNYTPTS 1759

Query:   179 RESNSRSSAYEAFFHEWVWMSWYPDINPTLP 209
                +  S +Y      +   S  P+ +PT P
Sbjct:  1760 PSYSPTSPSYSPTSPNYTPTS--PNYSPTSP 1788

GO:0046872 "metal ion binding" evidence=IEA

GO:0003968 "RNA-directed RNA polymerase activity" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0003677 "DNA binding" evidence=NAS

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

GO:0006355 "regulation of transcription, DNA-dependent" evidence=NAS

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

GO:0005634 "nucleus" evidence=IDA;NAS

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

GO:0004672 "protein kinase activity" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

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

GO:0005654 "nucleoplasm" evidence=TAS

GO:0006281 "DNA repair" evidence=TAS

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

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

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

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

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

GO:0008380 "RNA splicing" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

GO:0016032 "viral reproduction" evidence=TAS

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

GO:0031625 "ubiquitin protein ligase binding" evidence=IPI

GO:0006468 "protein phosphorylation" evidence=IDA

MGI|MGI:98086 Polr2a "polymerase (RNA) II (DNA directed) polypeptide A" [Mus musculus (taxid:10090)]

 Score = 295 (108.9 bits), Expect = 1.9e-24, P = 1.9e-24
 Identities = 55/151 (36%), Positives = 90/151 (59%)

Query:    59 SPAYTQVSPAYTQVSPAYTQVSPAYTQVSPAYIPVSPAYTPVSPAYTQVSPAYTQVSPAY 118
             SP+Y+  SP+Y+  SP+Y+  SP+Y+  SP+Y P SP+Y+P SP+Y+  SP+Y+  SP+Y
Sbjct:  1640 SPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSY 1699

Query:   119 TQVSPAYTQVSLAYTQVSLAYTQVSPAYTQVSPAYTQVSPAYTQVSSAYTQVILNKIRPG 178
             +  SP+Y+  S +Y+  S +Y+  SP+Y+  SP+Y+  SP+Y+  S  Y+    N     
Sbjct:  1700 SPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPNYSPTSPNYTPTS 1759

Query:   179 RESNSRSSAYEAFFHEWVWMSWYPDINPTLP 209
                +  S +Y      +   S  P+ +PT P
Sbjct:  1760 PSYSPTSPSYSPTSPNYTPTS--PNYSPTSP 1788

GO:0003677 "DNA binding" evidence=IDA

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

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=ISO

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

GO:0005730 "nucleolus" evidence=ISO

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

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

GO:0006468 "protein phosphorylation" evidence=ISO

GO:0016740 "transferase activity" evidence=IEA

GO:0016779 "nucleotidyltransferase activity" evidence=IEA

GO:0031625 "ubiquitin protein ligase binding" evidence=ISO

GO:0046872 "metal ion 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

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!

---

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	222
PTZ00436	357	PTZ00436, PTZ00436, 60S ribosomal protein L19-like	1e-08
PTZ00436	357	PTZ00436, PTZ00436, 60S ribosomal protein L19-like	1e-08
PTZ00436	357	PTZ00436, PTZ00436, 60S ribosomal protein L19-like	4e-08
PTZ00436	357	PTZ00436, PTZ00436, 60S ribosomal protein L19-like	1e-07
PTZ00436	357	PTZ00436, PTZ00436, 60S ribosomal protein L19-like	1e-07

>gnl|CDD|185616 PTZ00436, PTZ00436, 60S ribosomal protein L19-like protein; Provisional

 Score = 54.2 bits (129), Expect = 1e-08
 Identities = 29/108 (26%), Positives = 36/108 (33%)

Query: 59  SPAYTQVSPAYTQVSPAYTQVSPAYTQVSPAYIPVSPAYTPVSPAYTQVSPAYTQVSPAY 118
           +PA    +PA     PA    +PA    +PA     PA     PA     PA     PA 
Sbjct: 221 APAKAAAAPAKAAAPPAKAAAAPAKAAAAPAKAAAPPAKAAAPPAKAAAPPAKAAAPPAK 280

Query: 119 TQVSPAYTQVSLAYTQVSLAYTQVSPAYTQVSPAYTQVSPAYTQVSSA 166
               PA      A    + A    +PA    +PA     PA      A
Sbjct: 281 AAAPPAKAAAPPAKAAAAPAKAAAAPAKAAAAPAKAAAPPAKAAAPPA 328

Length = 357

>gnl|CDD|185616 PTZ00436, PTZ00436, 60S ribosomal protein L19-like protein; Provisional

 Score = 53.8 bits (128), Expect = 1e-08
 Identities = 29/108 (26%), Positives = 35/108 (32%)

Query: 59  SPAYTQVSPAYTQVSPAYTQVSPAYTQVSPAYIPVSPAYTPVSPAYTQVSPAYTQVSPAY 118
           +PA     PA    +PA    +PA     PA     PA     PA     PA     PA 
Sbjct: 228 APAKAAAPPAKAAAAPAKAAAAPAKAAAPPAKAAAPPAKAAAPPAKAAAPPAKAAAPPAK 287

Query: 119 TQVSPAYTQVSLAYTQVSLAYTQVSPAYTQVSPAYTQVSPAYTQVSSA 166
               PA    + A    + A    +PA     PA     PA      A
Sbjct: 288 AAAPPAKAAAAPAKAAAAPAKAAAAPAKAAAPPAKAAAPPAKAATPPA 335

Length = 357

>gnl|CDD|185616 PTZ00436, PTZ00436, 60S ribosomal protein L19-like protein; Provisional

 Score = 52.3 bits (124), Expect = 4e-08
 Identities = 29/108 (26%), Positives = 34/108 (31%)

Query: 59  SPAYTQVSPAYTQVSPAYTQVSPAYTQVSPAYIPVSPAYTPVSPAYTQVSPAYTQVSPAY 118
            PA    +PA    +PA     PA     PA     PA     PA     PA     PA 
Sbjct: 235 PPAKAAAAPAKAAAAPAKAAAPPAKAAAPPAKAAAPPAKAAAPPAKAAAPPAKAAAPPAK 294

Query: 119 TQVSPAYTQVSLAYTQVSLAYTQVSPAYTQVSPAYTQVSPAYTQVSSA 166
              +PA    + A    + A     PA     PA     PA      A
Sbjct: 295 AAAAPAKAAAAPAKAAAAPAKAAAPPAKAAAPPAKAATPPAKAAAPPA 342

Length = 357

>gnl|CDD|185616 PTZ00436, PTZ00436, 60S ribosomal protein L19-like protein; Provisional

 Score = 51.1 bits (121), Expect = 1e-07
 Identities = 32/138 (23%), Positives = 47/138 (34%), Gaps = 4/138 (2%)

Query: 35  EKFKRKDLEDYLSTDEDEATVYTVSPAYTQ----VSPAYTQVSPAYTQVSPAYTQVSPAY 90
           E+ +R+D     +  +  A     +P+  +     +PA    +PA     PA    +PA 
Sbjct: 186 ERARREDAAAAAAAKQKAAAKKAAAPSGKKSAKAAAPAKAAAAPAKAAAPPAKAAAAPAK 245

Query: 91  IPVSPAYTPVSPAYTQVSPAYTQVSPAYTQVSPAYTQVSLAYTQVSLAYTQVSPAYTQVS 150
              +PA     PA     PA     PA     PA      A      A    +PA    +
Sbjct: 246 AAAAPAKAAAPPAKAAAPPAKAAAPPAKAAAPPAKAAAPPAKAAAPPAKAAAAPAKAAAA 305

Query: 151 PAYTQVSPAYTQVSSAYT 168
           PA    +PA      A  
Sbjct: 306 PAKAAAAPAKAAAPPAKA 323

Length = 357

>gnl|CDD|185616 PTZ00436, PTZ00436, 60S ribosomal protein L19-like protein; Provisional

 Score = 50.7 bits (120), Expect = 1e-07
 Identities = 27/100 (27%), Positives = 32/100 (32%)

Query: 59  SPAYTQVSPAYTQVSPAYTQVSPAYTQVSPAYIPVSPAYTPVSPAYTQVSPAYTQVSPAY 118
           +PA     PA     PA     PA     PA     PA     PA    +PA    +PA 
Sbjct: 249 APAKAAAPPAKAAAPPAKAAAPPAKAAAPPAKAAAPPAKAAAPPAKAAAAPAKAAAAPAK 308

Query: 119 TQVSPAYTQVSLAYTQVSLAYTQVSPAYTQVSPAYTQVSP 158
              +PA      A      A     PA     PA    +P
Sbjct: 309 AAAAPAKAAAPPAKAAAPPAKAATPPAKAAAPPAKAAAAP 348

Length = 357

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	222
KOG0260|consensus	1605		99.96
KOG0260|consensus	1605		99.95
KOG3722|consensus	538		99.34
PF13908	179	Shisa: Wnt and FGF inhibitory regulator	95.31
PF01102	122	Glycophorin_A: Glycophorin A; InterPro: IPR001195	93.84
PF01034	64	Syndecan: Syndecan domain; InterPro: IPR001050 The	92.77
PF06024	101	DUF912: Nucleopolyhedrovirus protein of unknown fu	89.88
PF13908	179	Shisa: Wnt and FGF inhibitory regulator	89.45
PF12273	130	RCR: Chitin synthesis regulation, resistance to Co	84.62
PF02439	38	Adeno_E3_CR2: Adenovirus E3 region protein CR2; In	82.96

>KOG0260|consensus

Probab=99.96  E-value=7.2e-29  Score=252.69  Aligned_cols=51  Identities=45%  Similarity=0.985  Sum_probs=23.7

Q ss_pred             ecCCCcccCCCCccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q psy9982          57 TVSPAYTQVSPAYTQVSPAYTQVSPAYTQVSPAYIPVSPAYTPVSPAYTQV  107 (222)
Q Consensus        57 ~iS~~lc~~Sp~ysPtSP~ySPtSP~ysPtSP~ysPtSP~YsPtSP~ysp~  107 (222)
                      --|++|.+.||.|+|+||.|+|++|+|+|+||+|+|+||.|+|++|.|+|+
T Consensus      1447 ~ssp~~s~tsp~ysptsp~ys~tsp~~sptspsysptspsysptspsyspt 1497 (1605)
T KOG0260|consen 1447 SSSPGYSPTSPNYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPT 1497 (1605)
T ss_pred             CCCCCCCCCCCCCCCCCCccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Confidence            355555555555555555444444444444444444444443333333333

>KOG0260|consensus

Probab=99.95  E-value=5e-28  Score=246.59  Aligned_cols=108  Identities=42%  Similarity=0.912  Sum_probs=60.7

Q ss_pred             CcccCCCCccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccCCCCCC
Q psy9982          61 AYTQVSPAYTQVSPAYTQVSPAYTQVSPAYIPVSPAYTPVSPAYTQVSPAYTQVSPAYTQVSPAYTQVSLAYTQVSLAYT  140 (222)
Q Consensus        61 ~lc~~Sp~ysPtSP~ySPtSP~ysPtSP~ysPtSP~YsPtSP~ysp~SP~ysPsSPsySP~SP~YSP~SP~ysP~SPsys  140 (222)
                      .|.+.||+|+|+||.|+|+||.|+|+||.|+|+||.|+|+||.|+|++|+|+|+||+|+|+||+|+|++|+|+|++|+|+
T Consensus      1472 ~~sptspsysptspsysptspsysptspsysptspsysptspsysptspsysptspsysptspsysptspsysptspsys 1551 (1605)
T KOG0260|consen 1472 SYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYS 1551 (1605)
T ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Confidence            34444444444444444444444444444555555555555555555555555555555555566666666666666666


Q ss_pred             CCCCCCcCCCCCCCCCCCCCCCCCcccc
Q psy9982         141 QVSPAYTQVSPAYTQVSPAYTQVSSAYT  168 (222)
Q Consensus       141 PtSP~ysPtSP~ysPsSP~~sp~ss~~s  168 (222)
                      |+||.|+|+||.|+|++|.|+|+|+.|+
T Consensus      1552 ptspsysptsp~ysptspsysptspsys 1579 (1605)
T KOG0260|consen 1552 PTSPSYSPTSPSYSPTSPSYSPTSPSYS 1579 (1605)
T ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCcc
Confidence            6666666666666666666666666666

>KOG3722|consensus

Probab=99.34  E-value=2.7e-13  Score=129.00  Aligned_cols=57  Identities=33%  Similarity=0.486  Sum_probs=52.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhcccccccccccCCccccceeecCCCcccCCCCccCCC
Q psy9982          16 VEIFLLVFLLLNVLSYILIEKFKRKDLEDYLSTDEDEATVYTVSPAYTQVSPAYTQVS   73 (222)
Q Consensus        16 ~iI~lLLF~~LYi~Sy~ii~~fkk~~~~~~~~~d~~da~V~~iS~~lc~~Sp~ysPtS   73 (222)
                      .|||++||++||+.+|++|.|||||+|++ ++.||||+.|||||+|+|+|+.|-+=++
T Consensus        24 ~ii~~~l~~lLy~~sy~~isr~krk~~~~-ly~~dED~~Vyris~wl~tftlAvs~Ga   80 (538)
T KOG3722|consen   24 QIICMLLFMLLYVFSYWLISRLKRKTERE-LYAGDEDAFVYRISLWLSTFTLAVSIGA   80 (538)
T ss_pred             HHHHHHHHHHHHHHHhhhHHHHhhcCccc-cccCccceeeeeehhhHHHHHHHHHhcc
Confidence            57999999999999999999999999987 8888999999999999999998865443

>PF13908 Shisa: Wnt and FGF inhibitory regulator

Probab=95.31  E-value=0.089  Score=44.06  Aligned_cols=23  Identities=13%  Similarity=0.296  Sum_probs=10.0

Q ss_pred             ccchhhHHHHHHHHHHHHHHHHH
Q psy9982          10 IGGTLTVEIFLLVFLLLNVLSYI   32 (222)
Q Consensus        10 ~~~~~~~iI~lLLF~~LYi~Sy~   32 (222)
                      +.+++..||++++|+++-|+.++
T Consensus        77 ~~~iivgvi~~Vi~Iv~~Iv~~~   99 (179)
T PF13908_consen   77 ITGIIVGVICGVIAIVVLIVCFC   99 (179)
T ss_pred             eeeeeeehhhHHHHHHHhHhhhe
Confidence            33344444444444444444443

>PF01102 Glycophorin_A: Glycophorin A; InterPro: IPR001195 Proteins in this group are responsible for the molecular basis of the blood group antigens, surface markers on the outside of the red blood cell membrane

Probab=93.84  E-value=0.054  Score=44.41  Aligned_cols=33  Identities=21%  Similarity=0.398  Sum_probs=13.0

Q ss_pred             ccchhhHHHHHHHHHHHHHHHHHHHhhcccccccc
Q psy9982          10 IGGTLTVEIFLLVFLLLNVLSYILIEKFKRKDLED   44 (222)
Q Consensus        10 ~~~~~~~iI~lLLF~~LYi~Sy~ii~~fkk~~~~~   44 (222)
                      |.|.++++++-++.++| +|.|+| +|.|||...+
T Consensus        66 i~~Ii~gv~aGvIg~Il-li~y~i-rR~~Kk~~~~   98 (122)
T PF01102_consen   66 IIGIIFGVMAGVIGIIL-LISYCI-RRLRKKSSSD   98 (122)
T ss_dssp             HHHHHHHHHHHHHHHHH-HHHHHH-HHHS------
T ss_pred             eeehhHHHHHHHHHHHH-HHHHHH-HHHhccCCCC
Confidence            34444444444444444 455666 4455555543

Most of these markers are proteins, but some are carbohydrates attached to lipids or proteins [Reid M.E., Lomas-Francis C. The Blood Group Antigen FactsBook Academic Press, London / San Diego, (1997)]. Glycophorin A (PAS-2) and glycophorin B (PAS-3) belong to the MNS blood group system and are associated with antigens that include M/N, S/s, U, He, Mi(a), M(c), Vw, Mur, M(g), Vr, M(e), Mt(a), St(a), Ri(a), Cl(a), Ny(a), Hut, Hil, M(v), Far, Mit, Dantu, Hop, Nob, En(a), ENKT, amongst others. Glycophorin A is the major sialoglycoprotein of the erythrocyte membrane []. Structurally, glycophorin A consists of an N-terminal extracellular domain, heavily glycosylated on serine and threonine residues, followed by a transmembrane region and a C-terminal cytoplasmic domain. Other glycophorins in this entry such as Glycophorin B and Glycophorin E represent minor sialoglycoproteins in the erythrocyte membrane.; GO: 0016021 integral to membrane; PDB: 2KPF_B 1AFO_B 2KPE_A.

>PF01034 Syndecan: Syndecan domain; InterPro: IPR001050 The syndecans are transmembrane proteoglycans which are involved in the organisation of cytoskeleton and/or actin microfilaments, and have important roles as cell surface receptors during cell-cell and/or cell-matrix interactions [, ]

Probab=92.77  E-value=0.038  Score=41.05  Aligned_cols=32  Identities=25%  Similarity=0.533  Sum_probs=0.9

Q ss_pred             chhhccchhhHHHHHHHHHHHHHHHHHHHhhccccccc
Q psy9982           6 FLGLIGGTLTVEIFLLVFLLLNVLSYILIEKFKRKDLE   43 (222)
Q Consensus         6 ~~~~~~~~~~~iI~lLLF~~LYi~Sy~ii~~fkk~~~~   43 (222)
                      +.|+|+|.|..++|.+|.++      ++|.|+|||+|-
T Consensus        11 laavIaG~Vvgll~ailLIl------f~iyR~rkkdEG   42 (64)
T PF01034_consen   11 LAAVIAGGVVGLLFAILLIL------FLIYRMRKKDEG   42 (64)
T ss_dssp             --------------------------------S-----
T ss_pred             HHHHHHHHHHHHHHHHHHHH------HHHHHHHhcCCC
Confidence            35788887766666555443      356688888884

Structurally, these proteins consist of four separate domains: A signal sequence; An extracellular domain (ectodomain) of variable length whose sequence is not evolutionary conserved in the various forms of syndecans. The ectodomain contains the sites of attachment of the heparan sulphate glycosaminoglycan side chains; A transmembrane region; A highly conserved cytoplasmic domain of about 30 to 35 residues, which could interact with cytoskeletal proteins. The proteins known to belong to this family are: Syndecan 1. Syndecan 2 or fibroglycan. Syndecan 3 or neuroglycan or N-syndecan. Syndecan 4 or amphiglycan or ryudocan. Drosophila syndecan. Caenorhabditis elegans probable syndecan (F57C7.3). Syndecan-4, a transmembrane heparan sulphate proteoglycan, is a coreceptor with integrins in cell adhesion. It has been suggested to form a ternary signalling complex with protein kinase Calpha and phosphatidylinositol 4,5-bisphosphate (PIP2). Structural studies have demonstrated that the cytoplasmic domain undergoes a conformational transition and forms a symmetric dimer in the presence of phospholipid activator PIP2, and whose overall structure in solution exhibits a twisted clamp shape having a cavity in the centre of dimeric interface. In addition, it has been observed that the syndecan-4 variable domain interacts, strongly, not only with fatty acyl groups but also the anionic head group of PIP2. These findings indicate that PIP2 promotes oligomerisation of the syndecan-4 cytoplasmic domain for transmembrane signalling and cell-matrix adhesion [, ].; GO: 0008092 cytoskeletal protein binding, 0016020 membrane; PDB: 1EJQ_B 1EJP_B 1YBO_C 1OBY_Q.

>PF06024 DUF912: Nucleopolyhedrovirus protein of unknown function (DUF912); InterPro: IPR009261 This entry is represented by Autographa californica nuclear polyhedrosis virus (AcMNPV), Orf78; it is a family of uncharacterised viral proteins

Probab=89.88  E-value=0.11  Score=40.72  Aligned_cols=27  Identities=19%  Similarity=0.483  Sum_probs=20.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhcccccc
Q psy9982          16 VEIFLLVFLLLNVLSYILIEKFKRKDL   42 (222)
Q Consensus        16 ~iI~lLLF~~LYi~Sy~ii~~fkk~~~   42 (222)
                      .+.|+.++++||+|.|+||.|=|++..
T Consensus        68 lls~v~IlVily~IyYFVILRer~~~~   94 (101)
T PF06024_consen   68 LLSFVCILVILYAIYYFVILRERQKSI   94 (101)
T ss_pred             HHHHHHHHHHHhhheEEEEEecccccc
Confidence            345666777889999999997666554

>PF13908 Shisa: Wnt and FGF inhibitory regulator

Probab=89.45  E-value=2.6  Score=35.27  Aligned_cols=31  Identities=19%  Similarity=0.260  Sum_probs=22.5

Q ss_pred             chhhccchhhHHHHHHHHHHHHHHHHHHHhh
Q psy9982           6 FLGLIGGTLTVEIFLLVFLLLNVLSYILIEK   36 (222)
Q Consensus         6 ~~~~~~~~~~~iI~lLLF~~LYi~Sy~ii~~   36 (222)
                      ..|+|+|.+..||++++.+++++.|-..+.|
T Consensus        77 ~~~iivgvi~~Vi~Iv~~Iv~~~Cc~c~~~K  107 (179)
T PF13908_consen   77 ITGIIVGVICGVIAIVVLIVCFCCCCCCLYK  107 (179)
T ss_pred             eeeeeeehhhHHHHHHHhHhhheeccccccc
Confidence            4577888777777778888888876765444

>PF12273 RCR: Chitin synthesis regulation, resistance to Congo red; InterPro: IPR020999 RCR proteins are ER membrane proteins that regulate chitin deposition in fungal cell walls

Probab=84.62  E-value=0.95  Score=36.32  Aligned_cols=19  Identities=26%  Similarity=0.424  Sum_probs=7.9

Q ss_pred             HHHHHHHHHHHHHHHHHhh
Q psy9982          18 IFLLVFLLLNVLSYILIEK   36 (222)
Q Consensus        18 I~lLLF~~LYi~Sy~ii~~   36 (222)
                      |++++|+++.++++++-+|
T Consensus         7 iii~~i~l~~~~~~~~~rR   25 (130)
T PF12273_consen    7 IIIVAILLFLFLFYCHNRR   25 (130)
T ss_pred             HHHHHHHHHHHHHHHHHHH
Confidence            3334444444444444443

Although chitin, a linear polymer of beta-1,4-linked N-acetylglucosamine, constitutes only 2% of the cell wall it plays a vital role in the overall protection of the cell wall against stress, noxious chemicals and osmotic pressure changes. Congo red is a cell wall-disrupting benzidine-type dye extensively used in many cell wall mutant studies that specifically targets chitin in yeast cells and inhibits growth. RCR proteins render the yeasts resistant to Congo red by diminishing the content of chitin in the cell wall []. RCR proteins are probably regulating chitin synthase III interact directly with ubiquitin ligase Rsp5, and the VPEY motif is necessary for this, via interaction with the WW domains of Rsp5 [].

>PF02439 Adeno_E3_CR2: Adenovirus E3 region protein CR2; InterPro: IPR003470 Early region 3 (E3) of human adenoviruses (Ads) codes for proteins that appear to control viral interactions with the host []

Probab=82.96  E-value=1.2  Score=30.09  Aligned_cols=26  Identities=8%  Similarity=0.253  Sum_probs=20.9

Q ss_pred             chhhccchhhHHHHHHHHHHHHHHHH
Q psy9982           6 FLGLIGGTLTVEIFLLVFLLLNVLSY   31 (222)
Q Consensus         6 ~~~~~~~~~~~iI~lLLF~~LYi~Sy   31 (222)
                      ..|.|+|.+..++.+.|.+++|+++|
T Consensus         5 ~IaIIv~V~vg~~iiii~~~~YaCcy   30 (38)
T PF02439_consen    5 TIAIIVAVVVGMAIIIICMFYYACCY   30 (38)
T ss_pred             hhhHHHHHHHHHHHHHHHHHHHHHHH
Confidence            35778888888888888888888887

This region called CR1 (conserved region 1) [] is found three times in Human adenovirus 19 (a subgroup D adenovirus) 49 kDa protein in the E3 region. CR1 is also found in the 20.1 Kd protein of subgroup B adenoviruses. The function of this 80 amino acid region is unknown. This region is probably a divergent immunoglobulin domain.

---

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	222
1twf_A	1733	B220, DNA-directed RNA polymerase II largest subun	5e-30
1twf_A	1733	B220, DNA-directed RNA polymerase II largest subun	2e-29
1twf_A	1733	B220, DNA-directed RNA polymerase II largest subun	5e-28
1twf_A	1733	B220, DNA-directed RNA polymerase II largest subun	8e-28
1twf_A	1733	B220, DNA-directed RNA polymerase II largest subun	1e-27
1twf_A	1733	B220, DNA-directed RNA polymerase II largest subun	1e-27
1twf_A	1733	B220, DNA-directed RNA polymerase II largest subun	1e-27
1twf_A	1733	B220, DNA-directed RNA polymerase II largest subun	2e-27
1twf_A	1733	B220, DNA-directed RNA polymerase II largest subun	4e-27
1twf_A	1733	B220, DNA-directed RNA polymerase II largest subun	5e-27
1twf_A	1733	B220, DNA-directed RNA polymerase II largest subun	8e-27
1twf_A	1733	B220, DNA-directed RNA polymerase II largest subun	1e-26
1twf_A	1733	B220, DNA-directed RNA polymerase II largest subun	1e-26
1twf_A	1733	B220, DNA-directed RNA polymerase II largest subun	1e-26
1twf_A	1733	B220, DNA-directed RNA polymerase II largest subun	2e-24
1twf_A	1733	B220, DNA-directed RNA polymerase II largest subun	1e-22
1twf_A	1733	B220, DNA-directed RNA polymerase II largest subun	9e-22
1twf_A	1733	B220, DNA-directed RNA polymerase II largest subun	8e-10
3h0g_A	1752	DNA-directed RNA polymerase II subunit RPB1; trans	5e-29
3h0g_A	1752	DNA-directed RNA polymerase II subunit RPB1; trans	2e-28
3h0g_A	1752	DNA-directed RNA polymerase II subunit RPB1; trans	4e-28
3h0g_A	1752	DNA-directed RNA polymerase II subunit RPB1; trans	6e-28
3h0g_A	1752	DNA-directed RNA polymerase II subunit RPB1; trans	8e-28
3h0g_A	1752	DNA-directed RNA polymerase II subunit RPB1; trans	1e-27
3h0g_A	1752	DNA-directed RNA polymerase II subunit RPB1; trans	2e-27
3h0g_A	1752	DNA-directed RNA polymerase II subunit RPB1; trans	9e-27
3h0g_A	1752	DNA-directed RNA polymerase II subunit RPB1; trans	1e-26
3h0g_A	1752	DNA-directed RNA polymerase II subunit RPB1; trans	1e-26
3h0g_A	1752	DNA-directed RNA polymerase II subunit RPB1; trans	2e-26
3h0g_A	1752	DNA-directed RNA polymerase II subunit RPB1; trans	2e-26
3h0g_A	1752	DNA-directed RNA polymerase II subunit RPB1; trans	9e-26
3h0g_A	1752	DNA-directed RNA polymerase II subunit RPB1; trans	4e-25
3h0g_A	1752	DNA-directed RNA polymerase II subunit RPB1; trans	6e-24
3h0g_A	1752	DNA-directed RNA polymerase II subunit RPB1; trans	7e-22
3h0g_A	1752	DNA-directed RNA polymerase II subunit RPB1; trans	1e-19
3h0g_A	1752	DNA-directed RNA polymerase II subunit RPB1; trans	8e-15

>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 =  115 bits (290), Expect = 5e-30
 Identities = 47/111 (42%), Positives = 72/111 (64%)

Query: 59   SPAYTQVSPAYTQVSPAYTQVSPAYTQVSPAYIPVSPAYTPVSPAYTQVSPAYTQVSPAY 118
            SP+Y+  SP+Y+  SP+Y+  SP+Y+  SP+Y P SP+Y+P SPAY+  SP+Y+  SP+Y
Sbjct: 1616 SPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPAYSPTSPSYSPTSPSY 1675

Query: 119  TQVSPAYTQVSLAYTQVSLAYTQVSPAYTQVSPAYTQVSPAYTQVSSAYTQ 169
            +  SP+Y+  S +Y+  S  Y+  SP+Y+  SP Y+  SPAY+        
Sbjct: 1676 SPTSPSYSPTSPSYSPTSPNYSPTSPSYSPTSPGYSPGSPAYSPKQDEQKH 1726

>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 =  114 bits (286), Expect = 2e-29
 Identities = 49/110 (44%), Positives = 76/110 (69%)

Query: 59   SPAYTQVSPAYTQVSPAYTQVSPAYTQVSPAYIPVSPAYTPVSPAYTQVSPAYTQVSPAY 118
            SP+Y+  SP+Y+  SP+Y+  SP+Y+  SP+Y P SP+Y+P SP+Y+  SPAY+  SP+Y
Sbjct: 1609 SPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPAYSPTSPSY 1668

Query: 119  TQVSPAYTQVSLAYTQVSLAYTQVSPAYTQVSPAYTQVSPAYTQVSSAYT 168
            +  SP+Y+  S +Y+  S +Y+  SP Y+  SP+Y+  SP Y+  S AY+
Sbjct: 1669 SPTSPSYSPTSPSYSPTSPSYSPTSPNYSPTSPSYSPTSPGYSPGSPAYS 1718

>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 =  110 bits (275), Expect = 5e-28
 Identities = 48/111 (43%), Positives = 78/111 (70%)

Query: 58   VSPAYTQVSPAYTQVSPAYTQVSPAYTQVSPAYIPVSPAYTPVSPAYTQVSPAYTQVSPA 117
             SP+Y+  SP+Y+  SP+Y+  SP+Y+  SP+Y P SP+Y+P SP+Y+  SP+Y+  SP+
Sbjct: 1580 TSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPS 1639

Query: 118  YTQVSPAYTQVSLAYTQVSLAYTQVSPAYTQVSPAYTQVSPAYTQVSSAYT 168
            Y+  SP+Y+  S +Y+  S AY+  SP+Y+  SP+Y+  SP+Y+  S +Y+
Sbjct: 1640 YSPTSPSYSPTSPSYSPTSPAYSPTSPSYSPTSPSYSPTSPSYSPTSPSYS 1690

>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 =  109 bits (274), Expect = 8e-28
 Identities = 48/110 (43%), Positives = 78/110 (70%)

Query: 59   SPAYTQVSPAYTQVSPAYTQVSPAYTQVSPAYIPVSPAYTPVSPAYTQVSPAYTQVSPAY 118
            SP+Y+  SP+Y+  SP+Y+  SP+Y+  SP+Y P SP+Y+P SP+Y+  SP+Y+  SP+Y
Sbjct: 1574 SPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSY 1633

Query: 119  TQVSPAYTQVSLAYTQVSLAYTQVSPAYTQVSPAYTQVSPAYTQVSSAYT 168
            +  SP+Y+  S +Y+  S +Y+  SPAY+  SP+Y+  SP+Y+  S +Y+
Sbjct: 1634 SPTSPSYSPTSPSYSPTSPSYSPTSPAYSPTSPSYSPTSPSYSPTSPSYS 1683

>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 =  109 bits (273), Expect = 1e-27
 Identities = 50/130 (38%), Positives = 82/130 (63%)

Query: 59   SPAYTQVSPAYTQVSPAYTQVSPAYTQVSPAYIPVSPAYTPVSPAYTQVSPAYTQVSPAY 118
            SP+Y+  SP+Y+  SP+Y+  SP+Y+  SP+Y P SP+Y+P SP+Y+  SP+Y+  SP+Y
Sbjct: 1567 SPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSY 1626

Query: 119  TQVSPAYTQVSLAYTQVSLAYTQVSPAYTQVSPAYTQVSPAYTQVSSAYTQVILNKIRPG 178
            +  SP+Y+  S +Y+  S +Y+  SP+Y+  SPAY+  SP+Y+  S +Y+    +     
Sbjct: 1627 SPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPAYSPTSPSYSPTSPSYSPTSPSYSPTS 1686

Query: 179  RESNSRSSAY 188
               +  S  Y
Sbjct: 1687 PSYSPTSPNY 1696

>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 =  109 bits (272), Expect = 1e-27
 Identities = 46/109 (42%), Positives = 73/109 (66%)

Query: 59   SPAYTQVSPAYTQVSPAYTQVSPAYTQVSPAYIPVSPAYTPVSPAYTQVSPAYTQVSPAY 118
            SP +   SP ++  SP Y+  SPAY+  SP+Y P SP+Y+P SP+Y+  SP+Y+  SP+Y
Sbjct: 1532 SPGFGVSSPGFSPTSPTYSPTSPAYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSY 1591

Query: 119  TQVSPAYTQVSLAYTQVSLAYTQVSPAYTQVSPAYTQVSPAYTQVSSAY 167
            +  SP+Y+  S +Y+  S +Y+  SP+Y+  SP+Y+  SP+Y+  S +Y
Sbjct: 1592 SPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSY 1640

>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 =  109 bits (272), Expect = 1e-27
 Identities = 48/110 (43%), Positives = 76/110 (69%)

Query: 59   SPAYTQVSPAYTQVSPAYTQVSPAYTQVSPAYIPVSPAYTPVSPAYTQVSPAYTQVSPAY 118
            SP+Y+  SP+Y+  SP+Y+  SP+Y+  SP+Y P SP+Y+P SP+Y+  SP+Y+  SPAY
Sbjct: 1602 SPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPAY 1661

Query: 119  TQVSPAYTQVSLAYTQVSLAYTQVSPAYTQVSPAYTQVSPAYTQVSSAYT 168
            +  SP+Y+  S +Y+  S +Y+  SP+Y+  SP Y+  SP+Y+  S  Y+
Sbjct: 1662 SPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPNYSPTSPSYSPTSPGYS 1711

>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 =  108 bits (270), Expect = 2e-27
 Identities = 48/112 (42%), Positives = 77/112 (68%)

Query: 58   VSPAYTQVSPAYTQVSPAYTQVSPAYTQVSPAYIPVSPAYTPVSPAYTQVSPAYTQVSPA 117
             SP+Y+  SP+Y+  SP+Y+  SP+Y+  SP+Y P SP+Y+P SP+Y+  SP+Y+  SP+
Sbjct: 1594 TSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPS 1653

Query: 118  YTQVSPAYTQVSLAYTQVSLAYTQVSPAYTQVSPAYTQVSPAYTQVSSAYTQ 169
            Y+  SPAY+  S +Y+  S +Y+  SP+Y+  SP+Y+  SP Y+  S +Y+ 
Sbjct: 1654 YSPTSPAYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPNYSPTSPSYSP 1705

>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 =  107 bits (269), Expect = 4e-27
 Identities = 47/110 (42%), Positives = 76/110 (69%)

Query: 59   SPAYTQVSPAYTQVSPAYTQVSPAYTQVSPAYIPVSPAYTPVSPAYTQVSPAYTQVSPAY 118
            SP ++  SP Y+  SPAY+  SP+Y+  SP+Y P SP+Y+P SP+Y+  SP+Y+  SP+Y
Sbjct: 1539 SPGFSPTSPTYSPTSPAYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSY 1598

Query: 119  TQVSPAYTQVSLAYTQVSLAYTQVSPAYTQVSPAYTQVSPAYTQVSSAYT 168
            +  SP+Y+  S +Y+  S +Y+  SP+Y+  SP+Y+  SP+Y+  S +Y+
Sbjct: 1599 SPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYS 1648

>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 =  107 bits (268), Expect = 5e-27
 Identities = 48/111 (43%), Positives = 77/111 (69%)

Query: 59   SPAYTQVSPAYTQVSPAYTQVSPAYTQVSPAYIPVSPAYTPVSPAYTQVSPAYTQVSPAY 118
            SP Y+  SPAY+  SP+Y+  SP+Y+  SP+Y P SP+Y+P SP+Y+  SP+Y+  SP+Y
Sbjct: 1546 SPTYSPTSPAYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSY 1605

Query: 119  TQVSPAYTQVSLAYTQVSLAYTQVSPAYTQVSPAYTQVSPAYTQVSSAYTQ 169
            +  SP+Y+  S +Y+  S +Y+  SP+Y+  SP+Y+  SP+Y+  S +Y+ 
Sbjct: 1606 SPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSP 1656

>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 =  106 bits (266), Expect = 8e-27
 Identities = 48/110 (43%), Positives = 78/110 (70%)

Query: 59   SPAYTQVSPAYTQVSPAYTQVSPAYTQVSPAYIPVSPAYTPVSPAYTQVSPAYTQVSPAY 118
            SP+Y+  SP+Y+  SP+Y+  SP+Y+  SP+Y P SP+Y+P SP+Y+  SP+Y+  SP+Y
Sbjct: 1560 SPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSY 1619

Query: 119  TQVSPAYTQVSLAYTQVSLAYTQVSPAYTQVSPAYTQVSPAYTQVSSAYT 168
            +  SP+Y+  S +Y+  S +Y+  SP+Y+  SP+Y+  SPAY+  S +Y+
Sbjct: 1620 SPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPAYSPTSPSYS 1669

>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 =  106 bits (266), Expect = 1e-26
 Identities = 48/125 (38%), Positives = 75/125 (60%)

Query: 44   DYLSTDEDEATVYTVSPAYTQVSPAYTQVSPAYTQVSPAYTQVSPAYIPVSPAYTPVSPA 103
             Y   D  EAT    +      SP +   SP ++  SP Y+  SPAY P SP+Y+P SP+
Sbjct: 1510 AYGGADYGEATSPFGAYGEAPTSPGFGVSSPGFSPTSPTYSPTSPAYSPTSPSYSPTSPS 1569

Query: 104  YTQVSPAYTQVSPAYTQVSPAYTQVSLAYTQVSLAYTQVSPAYTQVSPAYTQVSPAYTQV 163
            Y+  SP+Y+  SP+Y+  SP+Y+  S +Y+  S +Y+  SP+Y+  SP+Y+  SP+Y+  
Sbjct: 1570 YSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPT 1629

Query: 164  SSAYT 168
            S +Y+
Sbjct: 1630 SPSYS 1634

>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 =  106 bits (265), Expect = 1e-26
 Identities = 56/151 (37%), Positives = 91/151 (60%), Gaps = 2/151 (1%)

Query: 59   SPAYTQVSPAYTQVSPAYTQVSPAYTQVSPAYIPVSPAYTPVSPAYTQVSPAYTQVSPAY 118
            SPAY+  SP+Y+  SP+Y+  SP+Y+  SP+Y P SP+Y+P SP+Y+  SP+Y+  SP+Y
Sbjct: 1553 SPAYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSY 1612

Query: 119  TQVSPAYTQVSLAYTQVSLAYTQVSPAYTQVSPAYTQVSPAYTQVSSAYTQVILNKIRPG 178
            +  SP+Y+  S +Y+  S +Y+  SP+Y+  SP+Y+  SP+Y+  S AY+    +     
Sbjct: 1613 SPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPAYSPTSPSYSPTS 1672

Query: 179  RESNSRSSAYEAFFHEWVWMSWYPDINPTLP 209
               +  S +Y      +   S  P+ +PT P
Sbjct: 1673 PSYSPTSPSYSPTSPSYSPTS--PNYSPTSP 1701

>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 =  105 bits (264), Expect = 1e-26
 Identities = 44/111 (39%), Positives = 70/111 (63%)

Query: 59   SPAYTQVSPAYTQVSPAYTQVSPAYTQVSPAYIPVSPAYTPVSPAYTQVSPAYTQVSPAY 118
            SP+Y+  SP+Y+  SP+Y+  SP+Y+  SP+Y P SPAY+P SP+Y+  SP+Y+  SP+Y
Sbjct: 1623 SPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPAYSPTSPSYSPTSPSYSPTSPSY 1682

Query: 119  TQVSPAYTQVSLAYTQVSLAYTQVSPAYTQVSPAYTQVSPAYTQVSSAYTQ 169
            +  SP+Y+  S  Y+  S +Y+  SP Y+  SPAY+          +  ++
Sbjct: 1683 SPTSPSYSPTSPNYSPTSPSYSPTSPGYSPGSPAYSPKQDEQKHNENENSR 1733

>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 =  100 bits (249), Expect = 2e-24
 Identities = 40/104 (38%), Positives = 65/104 (62%)

Query: 66   SPAYTQVSPAYTQVSPAYTQVSPAYIPVSPAYTPVSPAYTQVSPAYTQVSPAYTQVSPAY 125
            +      SP +   SP ++  SP Y P SPAY+P SP+Y+  SP+Y+  SP+Y+  SP+Y
Sbjct: 1525 AYGEAPTSPGFGVSSPGFSPTSPTYSPTSPAYSPTSPSYSPTSPSYSPTSPSYSPTSPSY 1584

Query: 126  TQVSLAYTQVSLAYTQVSPAYTQVSPAYTQVSPAYTQVSSAYTQ 169
            +  S +Y+  S +Y+  SP+Y+  SP+Y+  SP+Y+  S +Y+ 
Sbjct: 1585 SPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSP 1628

>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 = 94.8 bits (235), Expect = 1e-22
 Identities = 38/102 (37%), Positives = 60/102 (58%)

Query: 54   TVYTVSPAYTQVSPAYTQVSPAYTQVSPAYTQVSPAYIPVSPAYTPVSPAYTQVSPAYTQ 113
            +    SP+Y+  SP+Y+  SP+Y+  SPAY+  SP+Y P SP+Y+P SP+Y+  SP+Y+ 
Sbjct: 1632 SYSPTSPSYSPTSPSYSPTSPSYSPTSPAYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSP 1691

Query: 114  VSPAYTQVSPAYTQVSLAYTQVSLAYTQVSPAYTQVSPAYTQ 155
             SP Y+  SP+Y+  S  Y+  S AY+             ++
Sbjct: 1692 TSPNYSPTSPSYSPTSPGYSPGSPAYSPKQDEQKHNENENSR 1733

>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 = 92.1 bits (228), Expect = 9e-22
 Identities = 39/122 (31%), Positives = 66/122 (54%)

Query: 47   STDEDEATVYTVSPAYTQVSPAYTQVSPAYTQVSPAYTQVSPAYIPVSPAYTPVSPAYTQ 106
             +++  A  +T               +      SP +   SP + P SP Y+P SPAY+ 
Sbjct: 1499 GSNDAMAGGFTAYGGADYGEATSPFGAYGEAPTSPGFGVSSPGFSPTSPTYSPTSPAYSP 1558

Query: 107  VSPAYTQVSPAYTQVSPAYTQVSLAYTQVSLAYTQVSPAYTQVSPAYTQVSPAYTQVSSA 166
             SP+Y+  SP+Y+  SP+Y+  S +Y+  S +Y+  SP+Y+  SP+Y+  SP+Y+  S +
Sbjct: 1559 TSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPS 1618

Query: 167  YT 168
            Y+
Sbjct: 1619 YS 1620

>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 = 57.0 bits (137), Expect = 8e-10
 Identities = 31/150 (20%), Positives = 61/150 (40%), Gaps = 10/150 (6%)

Query: 24   LLLNVLSYILIEKFKRKDLEDYLSTDEDEATVYTVSPAYTQ---VSPAYTQVSPAYTQVS 80
            ++++  S  L++    + + +     +   T Y+                  SP     S
Sbjct: 1443 VMIDEES--LVKYMPEQKITEIEDGQDGGVTPYSNESGLVNADLDVKDELMFSPLVD--S 1498

Query: 81   PAYTQVSPAYIPVSPA-YTPVSPAYTQVSPAYTQVSPAYTQVSPAYTQVSLAYTQVSLAY 139
             +   ++  +     A Y   +  +     A T  SP +   SP ++  S  Y+  S AY
Sbjct: 1499 GSNDAMAGGFTAYGGADYGEATSPFGAYGEAPT--SPGFGVSSPGFSPTSPTYSPTSPAY 1556

Query: 140  TQVSPAYTQVSPAYTQVSPAYTQVSSAYTQ 169
            +  SP+Y+  SP+Y+  SP+Y+  S +Y+ 
Sbjct: 1557 SPTSPSYSPTSPSYSPTSPSYSPTSPSYSP 1586

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

 Score =  113 bits (283), Expect = 5e-29
 Identities = 48/112 (42%), Positives = 77/112 (68%)

Query: 56   YTVSPAYTQVSPAYTQVSPAYTQVSPAYTQVSPAYIPVSPAYTPVSPAYTQVSPAYTQVS 115
            Y+ SPAY   SP+Y+  SP+Y+  SP+Y+  SP+Y P SP+Y+  SP+Y+  SP+Y+  S
Sbjct: 1565 YSTSPAYMPSSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSATSPSYSPTSPSYSPTS 1624

Query: 116  PAYTQVSPAYTQVSLAYTQVSLAYTQVSPAYTQVSPAYTQVSPAYTQVSSAY 167
            P+Y+  SP+Y+  S +Y+  S +Y+  SP+Y+  SP+Y+  SP+Y+  S +Y
Sbjct: 1625 PSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSY 1676

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

 Score =  111 bits (279), Expect = 2e-28
 Identities = 47/110 (42%), Positives = 78/110 (70%)

Query: 59   SPAYTQVSPAYTQVSPAYTQVSPAYTQVSPAYIPVSPAYTPVSPAYTQVSPAYTQVSPAY 118
            SP+Y+  SP+Y+  SP+Y+  SP+Y+  SP+Y P SP+Y+P SP+Y+  SP+Y+  SP+Y
Sbjct: 1582 SPSYSPTSPSYSPTSPSYSPTSPSYSATSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSY 1641

Query: 119  TQVSPAYTQVSLAYTQVSLAYTQVSPAYTQVSPAYTQVSPAYTQVSSAYT 168
            +  SP+Y+  S +Y+  S +Y+  SP+Y+  SP+Y+  SP+Y+  S +Y+
Sbjct: 1642 SPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYS 1691

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

 Score =  110 bits (276), Expect = 4e-28
 Identities = 47/110 (42%), Positives = 78/110 (70%)

Query: 59   SPAYTQVSPAYTQVSPAYTQVSPAYTQVSPAYIPVSPAYTPVSPAYTQVSPAYTQVSPAY 118
            SP+Y+  SP+Y+  SP+Y+  SP+Y+  SP+Y P SP+Y+P SP+Y+  SP+Y+  SP+Y
Sbjct: 1589 SPSYSPTSPSYSPTSPSYSATSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSY 1648

Query: 119  TQVSPAYTQVSLAYTQVSLAYTQVSPAYTQVSPAYTQVSPAYTQVSSAYT 168
            +  SP+Y+  S +Y+  S +Y+  SP+Y+  SP+Y+  SP+Y+  S +Y+
Sbjct: 1649 SPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYS 1698

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

 Score =  110 bits (275), Expect = 6e-28
 Identities = 46/110 (41%), Positives = 77/110 (70%)

Query: 59   SPAYTQVSPAYTQVSPAYTQVSPAYTQVSPAYIPVSPAYTPVSPAYTQVSPAYTQVSPAY 118
            SP+Y+  SP+Y+  SP+Y+  SP+Y+  SP+Y   SP+Y+P SP+Y+  SP+Y+  SP+Y
Sbjct: 1575 SPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSATSPSYSPTSPSYSPTSPSYSPTSPSY 1634

Query: 119  TQVSPAYTQVSLAYTQVSLAYTQVSPAYTQVSPAYTQVSPAYTQVSSAYT 168
            +  SP+Y+  S +Y+  S +Y+  SP+Y+  SP+Y+  SP+Y+  S +Y+
Sbjct: 1635 SPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYS 1684

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

 Score =  109 bits (274), Expect = 8e-28
 Identities = 50/130 (38%), Positives = 81/130 (62%), Gaps = 1/130 (0%)

Query: 59   SPAYTQVSPAYTQVSPAYTQVSPAYTQVSPAYIPVSPAYTPVSPAYTQVSPAYTQVSPAY 118
            SP Y+  SPAY   SP+Y+  SP+Y+  SP+Y P SP+Y+P SP+Y+  SP+Y+  SP+Y
Sbjct: 1562 SPGYST-SPAYMPSSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSATSPSYSPTSPSY 1620

Query: 119  TQVSPAYTQVSLAYTQVSLAYTQVSPAYTQVSPAYTQVSPAYTQVSSAYTQVILNKIRPG 178
            +  SP+Y+  S +Y+  S +Y+  SP+Y+  SP+Y+  SP+Y+  S +Y+    +     
Sbjct: 1621 SPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTS 1680

Query: 179  RESNSRSSAY 188
               +  S +Y
Sbjct: 1681 PSYSPTSPSY 1690

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

 Score =  109 bits (273), Expect = 1e-27
 Identities = 47/110 (42%), Positives = 78/110 (70%)

Query: 59   SPAYTQVSPAYTQVSPAYTQVSPAYTQVSPAYIPVSPAYTPVSPAYTQVSPAYTQVSPAY 118
            SP+Y+  SP+Y+  SP+Y+  SP+Y+  SP+Y P SP+Y+P SP+Y+  SP+Y+  SP+Y
Sbjct: 1596 SPSYSPTSPSYSATSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSY 1655

Query: 119  TQVSPAYTQVSLAYTQVSLAYTQVSPAYTQVSPAYTQVSPAYTQVSSAYT 168
            +  SP+Y+  S +Y+  S +Y+  SP+Y+  SP+Y+  SP+Y+  S +Y+
Sbjct: 1656 SPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYS 1705

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

 Score =  108 bits (270), Expect = 2e-27
 Identities = 47/110 (42%), Positives = 78/110 (70%)

Query: 59   SPAYTQVSPAYTQVSPAYTQVSPAYTQVSPAYIPVSPAYTPVSPAYTQVSPAYTQVSPAY 118
            SP+Y+  SP+Y+  SP+Y+  SP+Y+  SP+Y P SP+Y+P SP+Y+  SP+Y+  SP+Y
Sbjct: 1631 SPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSY 1690

Query: 119  TQVSPAYTQVSLAYTQVSLAYTQVSPAYTQVSPAYTQVSPAYTQVSSAYT 168
            +  SP+Y+  S +Y+  S +Y+  SP+Y+  SP+Y+  SP+Y+  S +Y+
Sbjct: 1691 SPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYS 1740

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

 Score =  106 bits (266), Expect = 9e-27
 Identities = 47/111 (42%), Positives = 78/111 (70%)

Query: 59   SPAYTQVSPAYTQVSPAYTQVSPAYTQVSPAYIPVSPAYTPVSPAYTQVSPAYTQVSPAY 118
            SP+Y+  SP+Y+  SP+Y+  SP+Y+  SP+Y P SP+Y+P SP+Y+  SP+Y+  SP+Y
Sbjct: 1610 SPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSY 1669

Query: 119  TQVSPAYTQVSLAYTQVSLAYTQVSPAYTQVSPAYTQVSPAYTQVSSAYTQ 169
            +  SP+Y+  S +Y+  S +Y+  SP+Y+  SP+Y+  SP+Y+  S +Y+ 
Sbjct: 1670 SPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSP 1720

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

 Score =  106 bits (265), Expect = 1e-26
 Identities = 47/109 (43%), Positives = 77/109 (70%)

Query: 59   SPAYTQVSPAYTQVSPAYTQVSPAYTQVSPAYIPVSPAYTPVSPAYTQVSPAYTQVSPAY 118
            SP+Y+  SP+Y+  SP+Y+  SP+Y+  SP+Y P SP+Y+P SP+Y+  SP+Y+  SP+Y
Sbjct: 1603 SPSYSATSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSY 1662

Query: 119  TQVSPAYTQVSLAYTQVSLAYTQVSPAYTQVSPAYTQVSPAYTQVSSAY 167
            +  SP+Y+  S +Y+  S +Y+  SP+Y+  SP+Y+  SP+Y+  S +Y
Sbjct: 1663 SPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSY 1711

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

 Score =  106 bits (265), Expect = 1e-26
 Identities = 47/110 (42%), Positives = 78/110 (70%)

Query: 59   SPAYTQVSPAYTQVSPAYTQVSPAYTQVSPAYIPVSPAYTPVSPAYTQVSPAYTQVSPAY 118
            SP+Y+  SP+Y+  SP+Y+  SP+Y+  SP+Y P SP+Y+P SP+Y+  SP+Y+  SP+Y
Sbjct: 1638 SPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSY 1697

Query: 119  TQVSPAYTQVSLAYTQVSLAYTQVSPAYTQVSPAYTQVSPAYTQVSSAYT 168
            +  SP+Y+  S +Y+  S +Y+  SP+Y+  SP+Y+  SP+Y+  S +Y+
Sbjct: 1698 SPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYS 1747

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

 Score =  105 bits (264), Expect = 2e-26
 Identities = 47/110 (42%), Positives = 78/110 (70%)

Query: 59   SPAYTQVSPAYTQVSPAYTQVSPAYTQVSPAYIPVSPAYTPVSPAYTQVSPAYTQVSPAY 118
            SP+Y+  SP+Y+  SP+Y+  SP+Y+  SP+Y P SP+Y+P SP+Y+  SP+Y+  SP+Y
Sbjct: 1617 SPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSY 1676

Query: 119  TQVSPAYTQVSLAYTQVSLAYTQVSPAYTQVSPAYTQVSPAYTQVSSAYT 168
            +  SP+Y+  S +Y+  S +Y+  SP+Y+  SP+Y+  SP+Y+  S +Y+
Sbjct: 1677 SPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYS 1726

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

 Score =  105 bits (263), Expect = 2e-26
 Identities = 47/110 (42%), Positives = 78/110 (70%)

Query: 59   SPAYTQVSPAYTQVSPAYTQVSPAYTQVSPAYIPVSPAYTPVSPAYTQVSPAYTQVSPAY 118
            SP+Y+  SP+Y+  SP+Y+  SP+Y+  SP+Y P SP+Y+P SP+Y+  SP+Y+  SP+Y
Sbjct: 1624 SPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSY 1683

Query: 119  TQVSPAYTQVSLAYTQVSLAYTQVSPAYTQVSPAYTQVSPAYTQVSSAYT 168
            +  SP+Y+  S +Y+  S +Y+  SP+Y+  SP+Y+  SP+Y+  S +Y+
Sbjct: 1684 SPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYS 1733

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

 Score =  104 bits (259), Expect = 9e-26
 Identities = 47/116 (40%), Positives = 74/116 (63%), Gaps = 8/116 (6%)

Query: 59   SPAYTQVSPAYTQVSPAYTQVSPAYTQVSPA------YIPVSPAYTPVSPAYTQVSPAYT 112
            SP YT  SP  + +SP Y   SP+Y+  SP       Y+P SP+Y+P SP+Y+  SP+Y+
Sbjct: 1536 SPGYT--SPFSSAMSPGYGLTSPSYSPSSPGYSTSPAYMPSSPSYSPTSPSYSPTSPSYS 1593

Query: 113  QVSPAYTQVSPAYTQVSLAYTQVSLAYTQVSPAYTQVSPAYTQVSPAYTQVSSAYT 168
              SP+Y+  SP+Y+  S +Y+  S +Y+  SP+Y+  SP+Y+  SP+Y+  S +Y+
Sbjct: 1594 PTSPSYSPTSPSYSATSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYS 1649

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

 Score =  101 bits (253), Expect = 4e-25
 Identities = 46/106 (43%), Positives = 75/106 (70%)

Query: 59   SPAYTQVSPAYTQVSPAYTQVSPAYTQVSPAYIPVSPAYTPVSPAYTQVSPAYTQVSPAY 118
            SP+Y+  SP+Y+  SP+Y+  SP+Y+  SP+Y P SP+Y+P SP+Y+  SP+Y+  SP+Y
Sbjct: 1645 SPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSY 1704

Query: 119  TQVSPAYTQVSLAYTQVSLAYTQVSPAYTQVSPAYTQVSPAYTQVS 164
            +  SP+Y+  S +Y+  S +Y+  SP+Y+  SP+Y+  SP+Y+  S
Sbjct: 1705 SPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTS 1750

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

 Score = 98.6 bits (245), Expect = 6e-24
 Identities = 44/101 (43%), Positives = 72/101 (71%)

Query: 59   SPAYTQVSPAYTQVSPAYTQVSPAYTQVSPAYIPVSPAYTPVSPAYTQVSPAYTQVSPAY 118
            SP+Y+  SP+Y+  SP+Y+  SP+Y+  SP+Y P SP+Y+P SP+Y+  SP+Y+  SP+Y
Sbjct: 1652 SPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSY 1711

Query: 119  TQVSPAYTQVSLAYTQVSLAYTQVSPAYTQVSPAYTQVSPA 159
            +  SP+Y+  S +Y+  S +Y+  SP+Y+  SP+Y+  SP+
Sbjct: 1712 SPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPS 1752

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

 Score = 92.4 bits (229), Expect = 7e-22
 Identities = 43/113 (38%), Positives = 65/113 (57%), Gaps = 3/113 (2%)

Query: 56   YTVSPAYTQVSPAYTQVSPAYTQVSPAYTQVSPAYIPVSPAYTPVSPAYTQVSPAYTQVS 115
            +         SP     SP YT  SP  + +SP Y   SP+Y+P SP Y+  SPAY   S
Sbjct: 1519 FGDYGLLGAASPYKGVQSPGYT--SPFSSAMSPGYGLTSPSYSPSSPGYST-SPAYMPSS 1575

Query: 116  PAYTQVSPAYTQVSLAYTQVSLAYTQVSPAYTQVSPAYTQVSPAYTQVSSAYT 168
            P+Y+  SP+Y+  S +Y+  S +Y+  SP+Y+  SP+Y+  SP+Y+  S +Y+
Sbjct: 1576 PSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSATSPSYSPTSPSYSPTSPSYS 1628

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

 Score = 85.9 bits (212), Expect = 1e-19
 Identities = 40/99 (40%), Positives = 63/99 (63%), Gaps = 4/99 (4%)

Query: 54   TVYTVSPAYTQVSPAYTQVSPAYTQVSPAYTQVSPAYIPVSPAYTPVSPAYTQVSPAYTQ 113
            T  + SP     SP     SP+Y+  SP+Y+  SP+Y P SP+Y+P SP+Y+  SP+Y+ 
Sbjct: 1658 TSPSYSPTSPSYSPT----SPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSP 1713

Query: 114  VSPAYTQVSPAYTQVSLAYTQVSLAYTQVSPAYTQVSPA 152
             SP+Y+  SP+Y+  S +Y+  S +Y+  SP+Y+  SP+
Sbjct: 1714 TSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPS 1752

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

 Score = 72.0 bits (176), Expect = 8e-15
 Identities = 38/115 (33%), Positives = 54/115 (46%), Gaps = 5/115 (4%)

Query: 56   YTVSPAYTQVSPAYTQVSPAYTQVSPAY--TQVSPAYIPVSPAYTPVSPAYTQVSPAYTQ 113
            +  SP     SP     S               SP     SP YT  SP  + +SP Y  
Sbjct: 1496 FVGSPDAAAFSPLVQGGSEGREGFGDYGLLGAASPYKGVQSPGYT--SPFSSAMSPGYGL 1553

Query: 114  VSPAYTQVSPAYTQVSLAYTQVSLAYTQVSPAYTQVSPAYTQVSPAYTQVSSAYT 168
             SP+Y+  SP Y+  S AY   S +Y+  SP+Y+  SP+Y+  SP+Y+  S +Y+
Sbjct: 1554 TSPSYSPSSPGYST-SPAYMPSSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYS 1607

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	222
1twf_A	1733	B220, DNA-directed RNA polymerase II largest subun	99.8
1twf_A	1733	B220, DNA-directed RNA polymerase II largest subun	99.79
3h0g_A	1752	DNA-directed RNA polymerase II subunit RPB1; trans	99.55
3h0g_A	1752	DNA-directed RNA polymerase II subunit RPB1; trans	99.53
4gwq_H	35	DNA-directed RNA polymerase II subunit RPB1; bindi	98.61
2rdd_B	37	UPF0092 membrane protein YAJC; drug resistance, mu	82.69

>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=99.80  E-value=2.5e-21  Score=204.60  Aligned_cols=60  Identities=48%  Similarity=1.060  Sum_probs=0.0

Q ss_pred             CCCccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q psy9982          66 SPAYTQVSPAYTQVSPAYTQVSPAYIPVSPAYTPVSPAYTQVSPAYTQVSPAYTQVSPAY  125 (222)
Q Consensus        66 Sp~ysPtSP~ySPtSP~ysPtSP~ysPtSP~YsPtSP~ysp~SP~ysPsSPsySP~SP~Y  125 (222)
                      ||+|+|+||.|+|+||.|+|++|.|+|+||.|+|++|.|++++|.|+|++|+|+|++|.|
T Consensus      1595 s~~~~ptsp~ysp~sp~~sptsp~~sptsp~ysP~sp~~sptsp~ysp~sp~~sp~sp~y 1654 (1733)
T 1twf_A         1595 SPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSY 1654 (1733)
T ss_dssp             ------------------------------------------------------------
T ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Confidence            333333333344333333333443333333333333333333333333333333333333

>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=99.79  E-value=7.1e-21  Score=201.14  Aligned_cols=62  Identities=39%  Similarity=0.787  Sum_probs=0.0

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCccCCCCCCCCCCCCcCCCCCCCCCCCCCCCCCcc
Q psy9982         105 TQVSPAYTQVSPAYTQVSPAYTQVSLAYTQVSLAYTQVSPAYTQVSPAYTQVSPAYTQVSSA  166 (222)
Q Consensus       105 sp~SP~ysPsSPsySP~SP~YSP~SP~ysP~SPsysPtSP~ysPtSP~ysPsSP~~sp~ss~  166 (222)
                      +|++|.|+|++|.|+|++|.|+|++|.|+|++|+|+|++|.|+|++|.|+|++|.|+|+++.
T Consensus      1627 sP~sp~~sptsp~ysp~sp~~sp~sp~y~p~sp~~sp~sp~~~p~sp~y~p~sp~y~p~sp~ 1688 (1733)
T 1twf_A         1627 SPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPAYSPTSPSYSPTSPSYSPTSPSYSPTSPS 1688 (1733)
T ss_dssp             --------------------------------------------------------------
T ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Confidence            33333333333344444444444444444444444444444444433333333333333333

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

Probab=99.55  E-value=3.6e-16  Score=165.69  Aligned_cols=23  Identities=48%  Similarity=1.011  Sum_probs=0.0

Q ss_pred             CCCcccCCCCccCCCCCCCCCCC
Q psy9982          59 SPAYTQVSPAYTQVSPAYTQVSP   81 (222)
Q Consensus        59 S~~lc~~Sp~ysPtSP~ySPtSP   81 (222)
                      |+.++..+|+|+|++|.|+|++|
T Consensus      1582 SP~~s~tsP~ysptspaysptsp 1604 (1752)
T 3h0g_A         1582 SPSYSPTSPSYSPTSPSYSPTSP 1604 (1752)
T ss_dssp             -----------------------
T ss_pred             CCCCCCCCCCCCCCCCCCCCCCC
Confidence            33444444444444444443333

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

Probab=99.53  E-value=7.2e-16  Score=163.44  Aligned_cols=22  Identities=45%  Similarity=0.942  Sum_probs=0.0

Q ss_pred             CCCccCCCCCCCCCCCCCCCCC
Q psy9982          66 SPAYTQVSPAYTQVSPAYTQVS   87 (222)
Q Consensus        66 Sp~ysPtSP~ySPtSP~ysPtS   87 (222)
                      +|.|+++||.|++++|+|++++
T Consensus      1575 sP~ysptSP~~s~tsP~yspts 1596 (1752)
T 3h0g_A         1575 SPSYSPTSPSYSPTSPSYSPTS 1596 (1752)
T ss_dssp             ----------------------
T ss_pred             CCCCCCCCCCCCCCCCCCCCCC
Confidence            3334333443433333333333

>4gwq_H DNA-directed RNA polymerase II subunit RPB1; binding sites, mediator complex, models, molecular, phosphor protein structure, tertiary; 4.50A {Saccharomyces cerevisiae}

Probab=98.61  E-value=2.3e-08  Score=64.97  Aligned_cols=26  Identities=46%  Similarity=0.968  Sum_probs=8.3

Q ss_pred             cCCCCCCCCCCCCCCCCCCCCCCCCC
Q psy9982          70 TQVSPAYTQVSPAYTQVSPAYIPVSP   95 (222)
Q Consensus        70 sPtSP~ySPtSP~ysPtSP~ysPtSP   95 (222)
                      +|+||.|+|++|+|++++|.|+|+||
T Consensus         2 sPtSP~ysPtSP~YsPtSP~YsPtSP   27 (35)
T 4gwq_H            2 SPTSPSYSPTSPSYSPTSPSYSPTSP   27 (35)
T ss_dssp             ----CCSSSCCCCCCSSSSCSCCCCC
T ss_pred             CCCCCCcCCCCCCcCCCCCCcCCCCC
Confidence            33444444333333333333333333

>2rdd_B UPF0092 membrane protein YAJC; drug resistance, multidrug efflux, transporter, antiporter, novel transmembrane helix, ACRB, inner membrane; HET: AIC; 3.50A {Escherichia coli}

Probab=82.69  E-value=0.43  Score=30.34  Aligned_cols=25  Identities=4%  Similarity=0.329  Sum_probs=14.8

Q ss_pred             hHHHHHHHHHHHHHHHHHHHhhcccccc
Q psy9982          15 TVEIFLLVFLLLNVLSYILIEKFKRKDL   42 (222)
Q Consensus        15 ~~iI~lLLF~~LYi~Sy~ii~~fkk~~~   42 (222)
                      ..++.+++|++.|   +++|+..|||..
T Consensus         5 ~~l~~v~~~~ifY---Fl~iRPQ~Kr~K   29 (37)
T 2rdd_B            5 LILMLVVFGLIFY---FMILRPQQKRTK   29 (37)
T ss_dssp             HHHHHHHHHHHHH---HHTHHHHHHHHH
T ss_pred             HHHHHHHHHHHHH---HHHhhhHHHHHH
Confidence            3344445555544   567888887764

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

No hit with probability above 80.00