Citrus Sinensis ID: 032138

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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------
Protein Sequence
MSNIVLFEDIFVVEKIDPDGKKFDKVSRIEAHSQNCDMYMLLDVNSELYPMRVGDKFTMALAHTLNLDGTPDTGYYTPGARKTLADKYEYIMHGKLFKIGDEGSGKSLKAEIYVSYGGLLMMLKGDPSYVSHFELDQRLFLLMRKL
Secondary Structure (PSIPRED)
cccccEEEEEEEEEEEcccccEEEEEEEEEEEEccccEEEEEEEccccEEcccccEEEEEEEEccccccccccccccccccccccccccEEEEEEEEEEEEcccccccEEEEEEEEcEEEEEEEcccccccccccccEEEEEEEEc
Secondary Structure Prediction (SSPRO)
ccccEHHHcEEEEEEccccccEEcEEEEEEEEEccccEEEEEEEccEccccccccEEEEEEEccccccccccccccccccccccccccEEEEEEEEEEEEEcccccccEEEEEEEcHHHHHHccccHHHccccccccEEEEEEEcc
Coil and Loop (DISEMBL)
MSNIVLFEDIFVVekidpdgkkfdkVSRIEAHsqncdmymlldvnselypmrvgdkFTMALAHTLnldgtpdtgyytpgarkTLADKYEYIMHGKlfkigdegsgkslKAEIYVSYGGLLmmlkgdpsyvshfELDQRLFLLMRKL
Flexible Loop (DISEMBL)
msnivlfedifvvekidpdgkkfdKVSRIEAhsqncdmyMLLDVNSELYPMRVGDKFTMALAHTLnldgtpdtgyyTPGARKTLADKYEYIMHGKLfkigdegsgksLKAEIYVSYGGLLMMLKGDPSYVSHFELDQRLFLLMRKL
Low Complexity Region (SEG)
MSNIVLFEDIFVVEKIDPDGKKFDKVSRIEAHSQNCDMYMLLDVNSELYPMRVGDKFTMALAHTLNLDGTPDTGYYTPGARKTLADKYEYIMHGKLFKIGDEGSGKSLKAEIYVSYGGLLMMLKGDPSYVSHFELDQRLFLLMRKL
Disordered region (IsUnstruct)
***IVLFEDIFVVEKIDPDGKKFDKVSRIEAHSQNCDMYMLLDVNSELYPMRVGDKFTMALAHTLNLDGTPDTGYYTPGARKTLADKYEYIMHGKLFKIGDEGSGKSLKAEIYVSYGGLLMMLKGDPSYVSHFELDQRLFLLM***
Disordered Region (DISOPRED)
**NIVLFEDIFVVEKIDPDGKKFDKVSRIEAHSQNCDMYMLLDVNSELYPMRVGDKFTMALAHTL**************ARKTLADKYEYIMHGKLFKIGDEGSGKSLKAEIYVSYGGLLMMLKGDPSYVSHFELDQRLFLLMRKL
Disordered Region (DISEMBL)
MSNIVLFEDIFVVEKIDPDGKKFDKVSRIEAHSQNCDMYMLLDVNSELYPMRVGDKFTMALAHTLNLDGTPDTGYYTPGARKTLADKYEYIMHGKLFKIGDEGSGKSLKAEIYVSYGGLLMMLKGDPSYVSHFELDQRLFLLMRKL
Disordered Region (DISPRO)
**NIVLFEDIFVVEKIDPDGKKFDKVSRIEAHSQNCDMYMLLDVNSELYPMRVGDKFTMALAHTLNLD**PDTGYYTPGARKTLADKYEYIMHGKLFKIGDEGSGKSLKAEIYVSYGGLLMMLKGDPSYVSHFELDQRLFLLMRKL
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MSNIVLFEDIFVVEKIDPDGKKFDKVSRIEAHSQNCDMYMLLDVNSELYPMRVGDKFTMALAHTLNLDGTPDTGYYTPGARKTLADKYEYIMHGKLFKIGDEGSGKSLKAEIYVSYGGLLMMLKGDPSYVSHFELDQRLFLLMRKL
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	146	2.2.26 [Sep-21-2011]
Q923G2	150	DNA-directed RNA polymera	yes	no	0.972	0.946	0.510	3e-34
P52434	150	DNA-directed RNA polymera	yes	no	0.972	0.946	0.510	3e-34
Q54YW8	142	DNA-directed RNA polymera	yes	no	0.945	0.971	0.468	2e-31
A8XT81	148	Probable DNA-directed RNA	N/A	no	0.965	0.952	0.436	1e-29
Q19826	148	Probable DNA-directed RNA	yes	no	0.965	0.952	0.429	9e-29
P20436	146	DNA-directed RNA polymera	yes	no	0.945	0.945	0.392	1e-18
Q92399	125	DNA-directed RNA polymera	yes	no	0.856	1.0	0.344	3e-16

>sp|Q923G2|RPAB3_MOUSE DNA-directed RNA polymerases I, II, and III subunit RPABC3 OS=Mus musculus GN=Polr2h PE=2 SV=3

 Score =  143 bits (361), Expect = 3e-34,   Method: Compositional matrix adjust.
 Identities = 74/145 (51%), Positives = 107/145 (73%), Gaps = 3/145 (2%)

Query: 5   VLFEDIFVVEKIDPDGKKFDKVSRIEAHSQNCDMYMLLDVNSELYPMRVGDKFTMALAHT 64
           +LFEDIF V+ IDP+GKKFD+VSR+   S++  M ++LDVN ++YP+ +GDKF + +A T
Sbjct: 4   ILFEDIFDVKDIDPEGKKFDRVSRLHCESESFKMDLILDVNIQIYPVDLGDKFRLVIAST 63

Query: 65  LNLDGTPDTGYYTP-GARKTLADKYEYIMHGKLFKI-GDEGSGK-SLKAEIYVSYGGLLM 121
           L  DGT D G Y P   R + AD++EY+M+GK+++I GDE S + + +   YVSYGGLLM
Sbjct: 64  LYEDGTLDDGEYNPTDDRPSRADQFEYVMYGKVYRIEGDETSTEAATRLSAYVSYGGLLM 123

Query: 122 MLKGDPSYVSHFELDQRLFLLMRKL 146
            L+GD + +  FE+D R++LLM+KL
Sbjct: 124 RLQGDANNLHGFEVDSRVYLLMKKL 148

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and small RNAs, such as 5S rRNA and tRNAs, respectively.
Mus musculus (taxid: 10090)

>sp|P52434|RPAB3_HUMAN DNA-directed RNA polymerases I, II, and III subunit RPABC3 OS=Homo sapiens GN=POLR2H PE=1 SV=4

 Score =  143 bits (361), Expect = 3e-34,   Method: Compositional matrix adjust.
 Identities = 74/145 (51%), Positives = 107/145 (73%), Gaps = 3/145 (2%)

Query: 5   VLFEDIFVVEKIDPDGKKFDKVSRIEAHSQNCDMYMLLDVNSELYPMRVGDKFTMALAHT 64
           +LFEDIF V+ IDP+GKKFD+VSR+   S++  M ++LDVN ++YP+ +GDKF + +A T
Sbjct: 4   ILFEDIFDVKDIDPEGKKFDRVSRLHCESESFKMDLILDVNIQIYPVDLGDKFRLVIAST 63

Query: 65  LNLDGTPDTGYYTP-GARKTLADKYEYIMHGKLFKI-GDEGSGK-SLKAEIYVSYGGLLM 121
           L  DGT D G Y P   R + AD++EY+M+GK+++I GDE S + + +   YVSYGGLLM
Sbjct: 64  LYEDGTLDDGEYNPTDDRPSRADQFEYVMYGKVYRIEGDETSTEAATRLSAYVSYGGLLM 123

Query: 122 MLKGDPSYVSHFELDQRLFLLMRKL 146
            L+GD + +  FE+D R++LLM+KL
Sbjct: 124 RLQGDANNLHGFEVDSRVYLLMKKL 148

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and small RNAs, such as 5S rRNA and tRNAs, respectively.

Homo sapiens (taxid: 9606)

>sp|Q54YW8|RPAB3_DICDI DNA-directed RNA polymerases I, II, and III subunit rpabc3 OS=Dictyostelium discoideum GN=polr2h PE=3 SV=1

 Score =  134 bits (338), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 66/141 (46%), Positives = 100/141 (70%), Gaps = 3/141 (2%)

Query: 5   VLFEDIFVVEKIDPDGKKFDKVSRIEAHSQNCDMYMLLDVNSELYPMRVGDKFTMALAHT 64
           +LFED F V++IDPDGKKFD+VSR   +S+N +M + +D+ + +YP+   ++F M LA +
Sbjct: 4   ILFEDTFEVKEIDPDGKKFDRVSRFVCYSENYEMDLQIDIATHIYPLG-HERFKMVLASS 62

Query: 65  LNLDGTPDTGYYTPGARKTLADKYEYIMHGKLFKIGDEGSGKSLKAEIYVSYGGLLMMLK 124
           LNLDG+ D        + +LADKY+Y+M+GK+FK   E S  S K  ++ S+GGLL++L+
Sbjct: 63  LNLDGSSDNSGSYDTNKPSLADKYDYVMYGKIFKYQKENS--SSKVSVFASFGGLLVLLQ 120

Query: 125 GDPSYVSHFELDQRLFLLMRK 145
           GDP Y+   ELD R++LL++K
Sbjct: 121 GDPRYLPGIELDARIYLLIKK 141

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and small RNAs, such as 5S rRNA and tRNAs, respectively.

Dictyostelium discoideum (taxid: 44689)

>sp|A8XT81|RPAB3_CAEBR Probable DNA-directed RNA polymerases I, II, and III subunit RPABC3 OS=Caenorhabditis briggsae GN=rpb-8 PE=3 SV=1

 Score =  128 bits (321), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 62/142 (43%), Positives = 96/142 (67%), Gaps = 1/142 (0%)

Query: 5   VLFEDIFVVEKIDPDGKKFDKVSRIEAHSQNCDMYMLLDVNSELYPMRVGDKFTMALAHT 64
           ++F+D+F V+ +DPDGKKFD+VSR    +++  M +++D+NS++YP++  DKF + LA T
Sbjct: 4   IIFDDMFSVKSVDPDGKKFDRVSRYFCDAESFKMELIIDINSQIYPLKQNDKFRLVLATT 63

Query: 65  LNLDGTPDTGYYTPGARKTLADKYEYIMHGKLFKIGDEGSGK-SLKAEIYVSYGGLLMML 123
           L  DG  D G Y P A      +YEY+M+GK++++ D+ SG    +   Y S+GGLLM L
Sbjct: 64  LREDGLADEGEYDPKAEYPRIKQYEYVMYGKVYRLEDDDSGTDGGQLAAYASFGGLLMRL 123

Query: 124 KGDPSYVSHFELDQRLFLLMRK 145
           KG+   +  FE+D  L+LLM+K
Sbjct: 124 KGEAINLHGFEVDMNLYLLMKK 145

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and small RNAs, such as 5S rRNA and tRNAs, respectively.

Caenorhabditis briggsae (taxid: 6238)

>sp|Q19826|RPAB3_CAEEL Probable DNA-directed RNA polymerases I, II, and III subunit RPABC3 OS=Caenorhabditis elegans GN=rpb-8 PE=1 SV=1

 Score =  125 bits (314), Expect = 9e-29,   Method: Compositional matrix adjust.
 Identities = 61/142 (42%), Positives = 95/142 (66%), Gaps = 1/142 (0%)

Query: 5   VLFEDIFVVEKIDPDGKKFDKVSRIEAHSQNCDMYMLLDVNSELYPMRVGDKFTMALAHT 64
           ++F+D+F V+ +DPDGKKFD+VSR    +++  M +++D+NS++YP++  DK  + LA T
Sbjct: 4   IIFDDMFKVKSVDPDGKKFDRVSRYFCDAESFKMELIIDINSQIYPLKQNDKVRLVLATT 63

Query: 65  LNLDGTPDTGYYTPGARKTLADKYEYIMHGKLFKIGDEGSGK-SLKAEIYVSYGGLLMML 123
           L  DG  D G Y P A      +YEY+M+GK++++ D+ +G    K   Y S+GGLLM L
Sbjct: 64  LREDGLADEGEYDPKAEYPRIKQYEYVMYGKVYRLEDDDTGTDGGKLAAYASFGGLLMRL 123

Query: 124 KGDPSYVSHFELDQRLFLLMRK 145
           KG+   +  FE+D  L+LLM+K
Sbjct: 124 KGEAINLHGFEVDMNLYLLMKK 145

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and small RNAs, such as 5S rRNA and tRNAs, respectively.

Caenorhabditis elegans (taxid: 6239)

>sp|P20436|RPAB3_YEAST DNA-directed RNA polymerases I, II, and III subunit RPABC3 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RPB8 PE=1 SV=1

 Score = 92.0 bits (227), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 60/153 (39%), Positives = 92/153 (60%), Gaps = 15/153 (9%)

Query: 1   MSNIVLFEDIFVVEKIDPDGKKFDKVSRIEAHSQNCDMYML-LDVNSELYPMRVGDKFTM 59
           MSN  LF+DIF V ++DP   +++KV RIEA S   D   L LD+N EL+P+   D  T+
Sbjct: 1   MSN-TLFDDIFQVSEVDP--GRYNKVCRIEAASTTQDQCKLTLDINVELFPVAAQDSLTV 57

Query: 60  ALAHTLNLDGTP-----DTGYYTP--GARKTLADKYEYIMHGKLFKIGDEGSGKSLKAEI 112
            +A +LNL+ TP      T  + P     ++LAD Y+Y+M+G  +K   E   K L A +
Sbjct: 58  TIASSLNLEDTPANDSSATRSWRPPQAGDRSLADDYDYVMYGTAYKF--EEVSKDLIA-V 114

Query: 113 YVSYGGLLMMLKGDPSYVSHFELDQRLFLLMRK 145
           Y S+GGLLM L+G+   +++ +  +  +LL+R+
Sbjct: 115 YYSFGGLLMRLEGNYRNLNNLK-QENAYLLIRR 146

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and small RNAs, such as 5S rRNA and tRNAs, respectively.

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

>sp|Q92399|RPAB3_SCHPO DNA-directed RNA polymerases I, II, and III subunit RPABC3 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rpb8 PE=1 SV=2

 Score = 84.0 bits (206), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 50/145 (34%), Positives = 82/145 (56%), Gaps = 20/145 (13%)

Query: 1   MSNIVLFEDIFVVEKIDPDGKKFDKVSRIEAHSQNCDMYMLLDVNSELYPMRVGDKFTMA 60
           MS  VL ++IF V  +D   +K+ +VSRI A S   DM + LD+NS++YP+     F++ 
Sbjct: 1   MSESVLLDEIFTVTSVDK--QKYQRVSRITAVSGQNDMNLTLDINSQIYPLEKDATFSLQ 58

Query: 61  LAHTLNLDGTPDTGYYTPGARKTLADKYEYIMHGKLFKIGDEGSGKSLKAEIYVSYGGLL 120
           +   LN   +PD           L +  +YIM+GK++++ +    K  K  +YVS+GGLL
Sbjct: 59  ITSNLN---SPD-----------LKEAADYIMYGKVYRVEE---AKDEKVSVYVSFGGLL 101

Query: 121 MMLKGDPSYVSHFELDQRLFLLMRK 145
           M ++G    +    LD  ++LL+R+
Sbjct: 102 MAIEGSHRKLYRLSLDH-VYLLLRR 125

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and small RNAs, such as 5S rRNA and tRNAs, respectively.

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

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	146
255578910	146	DNA-directed RNA polymerases I, II, and	1.0	1.0	0.869	6e-70
224135363	148	predicted protein [Populus trichocarpa]	0.993	0.979	0.765	6e-63
297847838	146	ATRPABC16.5 [Arabidopsis lyrata subsp. l	0.986	0.986	0.772	1e-60
15221759	146	RNA polymerase Rpb8 [Arabidopsis thalian	0.986	0.986	0.765	2e-60
15231714	146	RNA polymerase Rpb8 [Arabidopsis thalian	0.986	0.986	0.758	2e-60
192910796	145	RNA polymerase [Elaeis guineensis]	0.972	0.979	0.725	1e-55
53793231	396	putative RNA polymerase I, II and III 16	0.965	0.356	0.711	1e-54
125556620	191	hypothetical protein OsI_24321 [Oryza sa	0.965	0.738	0.711	4e-54
116792470	145	unknown [Picea sitchensis]	0.972	0.979	0.697	4e-53
225434042	145	PREDICTED: DNA-directed RNA polymerases	0.972	0.979	0.683	7e-52

>gi|255578910|ref|XP_002530308.1| DNA-directed RNA polymerases I, II, and III 17.1 kDa polypeptide, putative [Ricinus communis] gi|223530164|gb|EEF32075.1| DNA-directed RNA polymerases I, II, and III 17.1 kDa polypeptide, putative [Ricinus communis]

 Score =  268 bits (684), Expect = 6e-70,   Method: Compositional matrix adjust.
 Identities = 127/146 (86%), Positives = 141/146 (96%)

Query: 1   MSNIVLFEDIFVVEKIDPDGKKFDKVSRIEAHSQNCDMYMLLDVNSELYPMRVGDKFTMA 60
           MSNIVLFEDIFVV+K+DPDGKKFDKVSRIEAHSQNCDM+M LDVN+E+YPM VGDKFTMA
Sbjct: 1   MSNIVLFEDIFVVDKLDPDGKKFDKVSRIEAHSQNCDMFMHLDVNTEIYPMAVGDKFTMA 60

Query: 61  LAHTLNLDGTPDTGYYTPGARKTLADKYEYIMHGKLFKIGDEGSGKSLKAEIYVSYGGLL 120
           LAHTLNLDGTPDTGYYT GARKTLADKYEYIM+GKL+KI +EGSGK++KAE+ VSYGGLL
Sbjct: 61  LAHTLNLDGTPDTGYYTQGARKTLADKYEYIMNGKLYKISEEGSGKAVKAEMLVSYGGLL 120

Query: 121 MMLKGDPSYVSHFELDQRLFLLMRKL 146
           M+L+GDPS+VSHFELDQRLFLLMRKL
Sbjct: 121 MLLRGDPSHVSHFELDQRLFLLMRKL 146

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224135363|ref|XP_002327199.1| predicted protein [Populus trichocarpa] gi|222835569|gb|EEE74004.1| predicted protein [Populus trichocarpa]

 Score =  245 bits (625), Expect = 6e-63,   Method: Compositional matrix adjust.
 Identities = 111/145 (76%), Positives = 133/145 (91%)

Query: 2   SNIVLFEDIFVVEKIDPDGKKFDKVSRIEAHSQNCDMYMLLDVNSELYPMRVGDKFTMAL 61
           SNI++FEDIFVV+K+DPDGKKFDKV+RIEAHSQNCDM+M LDVN+++YPM V DKFTMAL
Sbjct: 4   SNIIMFEDIFVVDKLDPDGKKFDKVTRIEAHSQNCDMFMHLDVNTDVYPMFVNDKFTMAL 63

Query: 62  AHTLNLDGTPDTGYYTPGARKTLADKYEYIMHGKLFKIGDEGSGKSLKAEIYVSYGGLLM 121
           AHTLNLDGTPDTGYYT G RKTLADKYEY+MHGKL++I +EGS ++ + E+ +++GGLLM
Sbjct: 64  AHTLNLDGTPDTGYYTQGGRKTLADKYEYVMHGKLYQIQEEGSRRATRTEMVITFGGLLM 123

Query: 122 MLKGDPSYVSHFELDQRLFLLMRKL 146
           +LKGDPSYVS FELDQRLF L+RKL
Sbjct: 124 LLKGDPSYVSQFELDQRLFCLIRKL 148

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297847838|ref|XP_002891800.1| ATRPABC16.5 [Arabidopsis lyrata subsp. lyrata] gi|297337642|gb|EFH68059.1| ATRPABC16.5 [Arabidopsis lyrata subsp. lyrata]

 Score =  237 bits (605), Expect = 1e-60,   Method: Compositional matrix adjust.
 Identities = 112/145 (77%), Positives = 134/145 (92%), Gaps = 1/145 (0%)

Query: 2   SNIVLFEDIFVVEKIDPDGKKFDKVSRIEAHSQNCDMYMLLDVNSELYPMRVGDKFTMAL 61
           SNI+LFEDIFVV+K+DPDGKKFDKV+R++A S N +M+M LDVN+E+YP+ VGDKFT+AL
Sbjct: 3   SNIILFEDIFVVDKLDPDGKKFDKVTRVQATSHNLEMFMHLDVNTEVYPLAVGDKFTLAL 62

Query: 62  AHTLNLDGTPDTGYYTPGARKTLADKYEYIMHGKLFKIGDEGSGKSLKAEIYVSYGGLLM 121
           A TLNLDGTPDTGY+TPGA+KTLADKYEYIMHGKL+KI  E  GK+ KAE+YVS+GGLLM
Sbjct: 63  APTLNLDGTPDTGYFTPGAKKTLADKYEYIMHGKLYKIS-ERDGKTPKAELYVSFGGLLM 121

Query: 122 MLKGDPSYVSHFELDQRLFLLMRKL 146
           +LKGDP+++SHFELDQRLFLLMRKL
Sbjct: 122 LLKGDPAHISHFELDQRLFLLMRKL 146

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15221759|ref|NP_175827.1| RNA polymerase Rpb8 [Arabidopsis thaliana] gi|4585968|gb|AAD25604.1|AC005287_6 RNA polymerase I, II and III 16.5 kDa subunit [Arabidopsis thaliana] gi|3372230|gb|AAC28252.1| RNA polymerase I, II and III 16.5 kDa subunit [Arabidopsis thaliana] gi|21555812|gb|AAM63939.1| RNA polymerase II subunit, putative [Arabidopsis thaliana] gi|28466897|gb|AAO44057.1| At1g54250 [Arabidopsis thaliana] gi|110735704|dbj|BAE99832.1| RNA polymerase I, II and III 16.5 kDa subunit [Arabidopsis thaliana] gi|332194950|gb|AEE33071.1| RNA polymerase Rpb8 [Arabidopsis thaliana]

 Score =  236 bits (602), Expect = 2e-60,   Method: Compositional matrix adjust.
 Identities = 111/145 (76%), Positives = 134/145 (92%), Gaps = 1/145 (0%)

Query: 2   SNIVLFEDIFVVEKIDPDGKKFDKVSRIEAHSQNCDMYMLLDVNSELYPMRVGDKFTMAL 61
           SNI+LFEDIFVV+++DPDGKKFDKV+R++A S N +M+M LDVN+E+YP+ VGDKFT+AL
Sbjct: 3   SNIILFEDIFVVDQLDPDGKKFDKVTRVQATSHNLEMFMHLDVNTEVYPLAVGDKFTLAL 62

Query: 62  AHTLNLDGTPDTGYYTPGARKTLADKYEYIMHGKLFKIGDEGSGKSLKAEIYVSYGGLLM 121
           A TLNLDGTPDTGY+TPGA+KTLADKYEYIMHGKL+KI  E  GK+ KAE+YVS+GGLLM
Sbjct: 63  APTLNLDGTPDTGYFTPGAKKTLADKYEYIMHGKLYKIS-ERDGKTPKAELYVSFGGLLM 121

Query: 122 MLKGDPSYVSHFELDQRLFLLMRKL 146
           +LKGDP+++SHFELDQRLFLLMRKL
Sbjct: 122 LLKGDPAHISHFELDQRLFLLMRKL 146

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15231714|ref|NP_191519.1| RNA polymerase Rpb8 [Arabidopsis thaliana] gi|297817262|ref|XP_002876514.1| hypothetical protein ARALYDRAFT_907465 [Arabidopsis lyrata subsp. lyrata] gi|6996296|emb|CAB75457.1| putative protein [Arabidopsis thaliana] gi|21554131|gb|AAM63211.1| RNA polymerase II subunit, putative [Arabidopsis thaliana] gi|26453032|dbj|BAC43592.1| unknown protein [Arabidopsis thaliana] gi|30793811|gb|AAP40358.1| unknown protein [Arabidopsis thaliana] gi|297322352|gb|EFH52773.1| hypothetical protein ARALYDRAFT_907465 [Arabidopsis lyrata subsp. lyrata] gi|332646423|gb|AEE79944.1| RNA polymerase Rpb8 [Arabidopsis thaliana]

 Score =  236 bits (602), Expect = 2e-60,   Method: Compositional matrix adjust.
 Identities = 110/145 (75%), Positives = 134/145 (92%), Gaps = 1/145 (0%)

Query: 2   SNIVLFEDIFVVEKIDPDGKKFDKVSRIEAHSQNCDMYMLLDVNSELYPMRVGDKFTMAL 61
           SNI++FEDIFVV+K+DPDGKKFDKV+R+EA S N +M+M LDVN+E+YP+ VGDKFT+A+
Sbjct: 3   SNIIMFEDIFVVDKLDPDGKKFDKVTRVEARSHNLEMFMHLDVNTEVYPLAVGDKFTLAM 62

Query: 62  AHTLNLDGTPDTGYYTPGARKTLADKYEYIMHGKLFKIGDEGSGKSLKAEIYVSYGGLLM 121
           A TLNLDGTPDTGY+TPGA+KTLADKYEYIMHGKL+KI  E  GK+ KAE+YVS+GGLLM
Sbjct: 63  APTLNLDGTPDTGYFTPGAKKTLADKYEYIMHGKLYKIS-ERDGKTPKAELYVSFGGLLM 121

Query: 122 MLKGDPSYVSHFELDQRLFLLMRKL 146
           +L+GDP+++SHFELDQRLFLLMRKL
Sbjct: 122 LLQGDPAHISHFELDQRLFLLMRKL 146

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|192910796|gb|ACF06506.1| RNA polymerase [Elaeis guineensis]

 Score =  221 bits (562), Expect = 1e-55,   Method: Compositional matrix adjust.
 Identities = 103/142 (72%), Positives = 123/142 (86%)

Query: 5   VLFEDIFVVEKIDPDGKKFDKVSRIEAHSQNCDMYMLLDVNSELYPMRVGDKFTMALAHT 64
           +LFEDIF + +IDPDGKKFDKVSRIEA S+  DMYM LDVN+E+YP+ VGDKFTM LA T
Sbjct: 4   LLFEDIFTLTRIDPDGKKFDKVSRIEARSEQFDMYMQLDVNTEIYPLHVGDKFTMVLAPT 63

Query: 65  LNLDGTPDTGYYTPGARKTLADKYEYIMHGKLFKIGDEGSGKSLKAEIYVSYGGLLMMLK 124
           L+LDGTPD+GYY  G RK+LADK+EY+MHGKL+KI +E SG ++K EIY S+GGLLMMLK
Sbjct: 64  LSLDGTPDSGYYMQGQRKSLADKFEYVMHGKLYKISEESSGPNVKVEIYASFGGLLMMLK 123

Query: 125 GDPSYVSHFELDQRLFLLMRKL 146
           GDPS  ++FELDQRLFLLMRK+
Sbjct: 124 GDPSNATNFELDQRLFLLMRKV 145

Source: Elaeis guineensis

Species: Elaeis guineensis

Genus: Elaeis

Family: Arecaceae

Order: Arecales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|53793231|dbj|BAD54456.1| putative RNA polymerase I, II and III 16.5 kDa subunit [Oryza sativa Japonica Group]

 Score =  217 bits (553), Expect = 1e-54,   Method: Compositional matrix adjust.
 Identities = 101/142 (71%), Positives = 119/142 (83%), Gaps = 1/142 (0%)

Query: 6   LFEDIFVVEKIDPDGKKFDKVSRIEAHSQNCDMYMLLDVNSELYPMRVGDKFTMALAHTL 65
           LFEDIF V ++DPDGKKFD+VSRIEA S+  DMYM LDV +E+YPMR GD+FTM LA TL
Sbjct: 255 LFEDIFTVTRLDPDGKKFDRVSRIEARSEQFDMYMQLDVATEVYPMRAGDRFTMVLAPTL 314

Query: 66  NLDGTPDTGYYTPGARKTLADKYEYIMHGKLFKIG-DEGSGKSLKAEIYVSYGGLLMMLK 124
           NLDGTPDTG+YT   RKTLADK++Y+MHGKL+KI  D  SG++ K EIY S+GGLLMMLK
Sbjct: 315 NLDGTPDTGFYTQAGRKTLADKFDYVMHGKLYKISEDSSSGQATKVEIYASFGGLLMMLK 374

Query: 125 GDPSYVSHFELDQRLFLLMRKL 146
           GDPS  + FELDQRLFLL+RK+
Sbjct: 375 GDPSSAASFELDQRLFLLIRKV 396

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|125556620|gb|EAZ02226.1| hypothetical protein OsI_24321 [Oryza sativa Indica Group] gi|125598367|gb|EAZ38147.1| hypothetical protein OsJ_22498 [Oryza sativa Japonica Group]

 Score =  215 bits (548), Expect = 4e-54,   Method: Compositional matrix adjust.
 Identities = 101/142 (71%), Positives = 119/142 (83%), Gaps = 1/142 (0%)

Query: 6   LFEDIFVVEKIDPDGKKFDKVSRIEAHSQNCDMYMLLDVNSELYPMRVGDKFTMALAHTL 65
           LFEDIF V ++DPDGKKFD+VSRIEA S+  DMYM LDV +E+YPMR GD+FTM LA TL
Sbjct: 50  LFEDIFTVTRLDPDGKKFDRVSRIEARSEQFDMYMQLDVATEVYPMRAGDRFTMVLAPTL 109

Query: 66  NLDGTPDTGYYTPGARKTLADKYEYIMHGKLFKIG-DEGSGKSLKAEIYVSYGGLLMMLK 124
           NLDGTPDTG+YT   RKTLADK++Y+MHGKL+KI  D  SG++ K EIY S+GGLLMMLK
Sbjct: 110 NLDGTPDTGFYTQAGRKTLADKFDYVMHGKLYKISEDSSSGQATKVEIYASFGGLLMMLK 169

Query: 125 GDPSYVSHFELDQRLFLLMRKL 146
           GDPS  + FELDQRLFLL+RK+
Sbjct: 170 GDPSSAASFELDQRLFLLIRKV 191

Source: Oryza sativa Indica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|116792470|gb|ABK26380.1| unknown [Picea sitchensis]

 Score =  212 bits (539), Expect = 4e-53,   Method: Compositional matrix adjust.
 Identities = 99/142 (69%), Positives = 120/142 (84%)

Query: 5   VLFEDIFVVEKIDPDGKKFDKVSRIEAHSQNCDMYMLLDVNSELYPMRVGDKFTMALAHT 64
           +LFEDIF V +IDPDGKKFDKVSRIEA S+  DMYMLLDVN ++YP+ VG+KF +ALA T
Sbjct: 4   LLFEDIFTVTRIDPDGKKFDKVSRIEARSEQFDMYMLLDVNIDVYPVSVGEKFAVALAPT 63

Query: 65  LNLDGTPDTGYYTPGARKTLADKYEYIMHGKLFKIGDEGSGKSLKAEIYVSYGGLLMMLK 124
           LNLDGTPD GY+  G RK+LADKYEY+M+GKL+ + +EGSG ++K EI  S+GGLLM+LK
Sbjct: 64  LNLDGTPDNGYFIQGGRKSLADKYEYVMYGKLYNLSEEGSGANVKVEINASFGGLLMLLK 123

Query: 125 GDPSYVSHFELDQRLFLLMRKL 146
           GDPS   +FELDQRLFLLMRK+
Sbjct: 124 GDPSNAGNFELDQRLFLLMRKV 145

Source: Picea sitchensis

Species: Picea sitchensis

Genus: Picea

Family: Pinaceae

Order: Coniferales

Class: Coniferopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225434042|ref|XP_002274171.1| PREDICTED: DNA-directed RNA polymerases I, II, and III subunit rpabc3 isoform 1 [Vitis vinifera] gi|359478220|ref|XP_003632088.1| PREDICTED: DNA-directed RNA polymerases I, II, and III subunit rpabc3 isoform 2 [Vitis vinifera] gi|296084252|emb|CBI24640.3| unnamed protein product [Vitis vinifera]

 Score =  208 bits (529), Expect = 7e-52,   Method: Compositional matrix adjust.
 Identities = 97/142 (68%), Positives = 118/142 (83%)

Query: 5   VLFEDIFVVEKIDPDGKKFDKVSRIEAHSQNCDMYMLLDVNSELYPMRVGDKFTMALAHT 64
            LF DIF V +IDPDGKKFDKVSRIEA S+  DMYM LDVN+E+YPM  G+KF M+LA T
Sbjct: 4   TLFGDIFKVIQIDPDGKKFDKVSRIEAQSEQLDMYMQLDVNTEIYPMHAGEKFAMSLAST 63

Query: 65  LNLDGTPDTGYYTPGARKTLADKYEYIMHGKLFKIGDEGSGKSLKAEIYVSYGGLLMMLK 124
           L+LDGTPDTGYYT   RK+LADK+EY+MHGKL+KI +EGSG ++K  IYVS+GGLLMML 
Sbjct: 64  LDLDGTPDTGYYTQAGRKSLADKFEYVMHGKLYKISEEGSGPNVKGVIYVSFGGLLMMLS 123

Query: 125 GDPSYVSHFELDQRLFLLMRKL 146
           GDP+  +  +LDQR+FLL+RK+
Sbjct: 124 GDPANTAKLDLDQRVFLLIRKV 145

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	146
TAIR|locus:2097468	146	NRPB8B "AT3G59600" [Arabidopsi	0.986	0.986	0.758	1.2e-58
TAIR|locus:2020188	146	NRPB8A "AT1G54250" [Arabidopsi	0.986	0.986	0.765	1.5e-58
FB|FBgn0037121	149	Rpb8 "Rpb8" [Drosophila melano	0.972	0.953	0.513	4.4e-36
ZFIN|ZDB-GENE-050417-66	150	zgc:110289 "zgc:110289" [Danio	0.972	0.946	0.517	1.5e-35
UNIPROTKB|E1BSD8	150	POLR2H "Uncharacterized protei	0.972	0.946	0.510	2.2e-34
UNIPROTKB|F2Z4H3	150	POLR2H "Uncharacterized protei	0.972	0.946	0.510	2.2e-34
UNIPROTKB|C9JLU1	149	POLR2H "DNA-directed RNA polym	0.972	0.953	0.510	2.2e-34
UNIPROTKB|P52434	150	POLR2H "DNA-directed RNA polym	0.972	0.946	0.510	2.2e-34
UNIPROTKB|I3LCB2	150	POLR2H "Uncharacterized protei	0.972	0.946	0.510	2.2e-34
MGI|MGI:2384309	150	Polr2h "polymerase (RNA) II (D	0.972	0.946	0.510	2.2e-34

TAIR|locus:2097468 NRPB8B "AT3G59600" [Arabidopsis thaliana (taxid:3702)]

 Score = 602 (217.0 bits), Expect = 1.2e-58, P = 1.2e-58
 Identities = 110/145 (75%), Positives = 134/145 (92%)

Query:     2 SNIVLFEDIFVVEKIDPDGKKFDKVSRIEAHSQNCDMYMLLDVNSELYPMRVGDKFTMAL 61
             SNI++FEDIFVV+K+DPDGKKFDKV+R+EA S N +M+M LDVN+E+YP+ VGDKFT+A+
Sbjct:     3 SNIIMFEDIFVVDKLDPDGKKFDKVTRVEARSHNLEMFMHLDVNTEVYPLAVGDKFTLAM 62

Query:    62 AHTLNLDGTPDTGYYTPGARKTLADKYEYIMHGKLFKIGDEGSGKSLKAEIYVSYGGLLM 121
             A TLNLDGTPDTGY+TPGA+KTLADKYEYIMHGKL+KI  E  GK+ KAE+YVS+GGLLM
Sbjct:    63 APTLNLDGTPDTGYFTPGAKKTLADKYEYIMHGKLYKIS-ERDGKTPKAELYVSFGGLLM 121

Query:   122 MLKGDPSYVSHFELDQRLFLLMRKL 146
             +L+GDP+++SHFELDQRLFLLMRKL
Sbjct:   122 LLQGDPAHISHFELDQRLFLLMRKL 146

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

GO:0005634 "nucleus" evidence=ISM

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

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

TAIR|locus:2020188 NRPB8A "AT1G54250" [Arabidopsis thaliana (taxid:3702)]

 Score = 601 (216.6 bits), Expect = 1.5e-58, P = 1.5e-58
 Identities = 111/145 (76%), Positives = 134/145 (92%)

Query:     2 SNIVLFEDIFVVEKIDPDGKKFDKVSRIEAHSQNCDMYMLLDVNSELYPMRVGDKFTMAL 61
             SNI+LFEDIFVV+++DPDGKKFDKV+R++A S N +M+M LDVN+E+YP+ VGDKFT+AL
Sbjct:     3 SNIILFEDIFVVDQLDPDGKKFDKVTRVQATSHNLEMFMHLDVNTEVYPLAVGDKFTLAL 62

Query:    62 AHTLNLDGTPDTGYYTPGARKTLADKYEYIMHGKLFKIGDEGSGKSLKAEIYVSYGGLLM 121
             A TLNLDGTPDTGY+TPGA+KTLADKYEYIMHGKL+KI  E  GK+ KAE+YVS+GGLLM
Sbjct:    63 APTLNLDGTPDTGYFTPGAKKTLADKYEYIMHGKLYKIS-ERDGKTPKAELYVSFGGLLM 121

Query:   122 MLKGDPSYVSHFELDQRLFLLMRKL 146
             +LKGDP+++SHFELDQRLFLLMRKL
Sbjct:   122 LLKGDPAHISHFELDQRLFLLMRKL 146

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

GO:0005634 "nucleus" evidence=ISM

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

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

FB|FBgn0037121 Rpb8 "Rpb8" [Drosophila melanogaster (taxid:7227)]

 Score = 389 (142.0 bits), Expect = 4.4e-36, P = 4.4e-36
 Identities = 74/144 (51%), Positives = 106/144 (73%)

Query:     5 VLFEDIFVVEKIDPDGKKFDKVSRIEAHSQNCDMYMLLDVNSELYPMRVGDKFTMALAHT 64
             VLFEDIF V+ +DP+GKKFD+VSR+   S++  M ++LD+NS LYPM +GDKF + LA T
Sbjct:     4 VLFEDIFNVKDMDPEGKKFDRVSRLHCESESFKMDLILDINSWLYPMELGDKFRLVLATT 63

Query:    65 LNLDGTPDTGYYTPGARK-TLADKYEYIMHGKLFKI-GDEGSGKSLKAEIYVSYGGLLMM 122
             L  DG PD+G Y P   + T AD +EY+M+GK+++I GDE   ++ +   YVS+GGLLM 
Sbjct:    64 LREDGCPDSGEYNPMEHEGTRADSFEYVMYGKIYRIEGDEAHNEASRLSAYVSFGGLLMR 123

Query:   123 LKGDPSYVSHFELDQRLFLLMRKL 146
             L+GD + +  FE+DQ ++LLM++L
Sbjct:   124 LQGDANNLHGFEVDQHMYLLMKRL 147

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

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

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

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

ZFIN|ZDB-GENE-050417-66 zgc:110289 "zgc:110289" [Danio rerio (taxid:7955)]

 Score = 384 (140.2 bits), Expect = 1.5e-35, P = 1.5e-35
 Identities = 75/145 (51%), Positives = 108/145 (74%)

Query:     5 VLFEDIFVVEKIDPDGKKFDKVSRIEAHSQNCDMYMLLDVNSELYPMRVGDKFTMALAHT 64
             +LFEDIF V+ IDPDGKKFD+VSR+   S++  M ++LDVN ++YP+ +GDKF + +A T
Sbjct:     4 ILFEDIFDVKDIDPDGKKFDRVSRLHCESESFKMDLILDVNIQIYPVDLGDKFRLVIAST 63

Query:    65 LNLDGTPDTGYYTP-GARKTLADKYEYIMHGKLFKI-GDEGSGKSL-KAEIYVSYGGLLM 121
             L  DGTPD G Y P   R + AD+++Y+M+GK+++I GDE S ++  +   YVSYGGLLM
Sbjct:    64 LYEDGTPDDGEYNPQDDRPSRADQFDYVMYGKVYRIEGDETSTEAATRLSAYVSYGGLLM 123

Query:   122 MLKGDPSYVSHFELDQRLFLLMRKL 146
              L+GD + +  FE+D R++LLM+KL
Sbjct:   124 RLQGDANNLHGFEVDSRVYLLMKKL 148

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

UNIPROTKB|E1BSD8 POLR2H "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 373 (136.4 bits), Expect = 2.2e-34, P = 2.2e-34
 Identities = 74/145 (51%), Positives = 107/145 (73%)

Query:     5 VLFEDIFVVEKIDPDGKKFDKVSRIEAHSQNCDMYMLLDVNSELYPMRVGDKFTMALAHT 64
             +LFEDIF V+ IDP+GKKFD+VSR+   S++  M ++LDVN ++YP+ +GDKF + +A T
Sbjct:     4 ILFEDIFDVKDIDPEGKKFDRVSRLHCESESFKMDLILDVNIQIYPVDLGDKFRLVIAST 63

Query:    65 LNLDGTPDTGYYTP-GARKTLADKYEYIMHGKLFKI-GDEGSGKSL-KAEIYVSYGGLLM 121
             L  DGT D G Y P   R + AD++EY+M+GK+++I GDE S ++  +   YVSYGGLLM
Sbjct:    64 LYEDGTLDDGEYNPTDDRPSRADQFEYVMYGKVYRIEGDETSTEAATRLSAYVSYGGLLM 123

Query:   122 MLKGDPSYVSHFELDQRLFLLMRKL 146
              L+GD + +  FE+D R++LLM+KL
Sbjct:   124 RLQGDANNLHGFEVDSRVYLLMKKL 148

GO:0004672 "protein kinase activity" evidence=IEA

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

GO:0005737 "cytoplasm" evidence=IEA

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

UNIPROTKB|F2Z4H3 POLR2H "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 373 (136.4 bits), Expect = 2.2e-34, P = 2.2e-34
 Identities = 74/145 (51%), Positives = 107/145 (73%)

Query:     5 VLFEDIFVVEKIDPDGKKFDKVSRIEAHSQNCDMYMLLDVNSELYPMRVGDKFTMALAHT 64
             +LFEDIF V+ IDP+GKKFD+VSR+   S++  M ++LDVN ++YP+ +GDKF + +A T
Sbjct:     4 ILFEDIFDVKDIDPEGKKFDRVSRLHCESESFKMDLILDVNIQIYPVDLGDKFRLVIAST 63

Query:    65 LNLDGTPDTGYYTP-GARKTLADKYEYIMHGKLFKI-GDEGSGKSL-KAEIYVSYGGLLM 121
             L  DGT D G Y P   R + AD++EY+M+GK+++I GDE S ++  +   YVSYGGLLM
Sbjct:    64 LYEDGTLDDGEYNPTDDRPSRADQFEYVMYGKVYRIEGDETSTEAATRLSAYVSYGGLLM 123

Query:   122 MLKGDPSYVSHFELDQRLFLLMRKL 146
              L+GD + +  FE+D R++LLM+KL
Sbjct:   124 RLQGDANNLHGFEVDSRVYLLMKKL 148

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

GO:0005737 "cytoplasm" evidence=IEA

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

GO:0004672 "protein kinase activity" evidence=IEA

UNIPROTKB|C9JLU1 POLR2H "DNA-directed RNA polymerases I, II, and III subunit RPABC3" [Homo sapiens (taxid:9606)]

 Score = 373 (136.4 bits), Expect = 2.2e-34, P = 2.2e-34
 Identities = 74/145 (51%), Positives = 107/145 (73%)

Query:     5 VLFEDIFVVEKIDPDGKKFDKVSRIEAHSQNCDMYMLLDVNSELYPMRVGDKFTMALAHT 64
             +LFEDIF V+ IDP+GKKFD+VSR+   S++  M ++LDVN ++YP+ +GDKF + +A T
Sbjct:     4 ILFEDIFDVKDIDPEGKKFDRVSRLHCESESFKMDLILDVNIQIYPVDLGDKFRLVIAST 63

Query:    65 LNLDGTPDTGYYTP-GARKTLADKYEYIMHGKLFKI-GDEGSGKSL-KAEIYVSYGGLLM 121
             L  DGT D G Y P   R + AD++EY+M+GK+++I GDE S ++  +   YVSYGGLLM
Sbjct:    64 LYEDGTLDDGEYNPTDDRPSRADQFEYVMYGKVYRIEGDETSTEAATRLSAYVSYGGLLM 123

Query:   122 MLKGDPSYVSHFELDQRLFLLMRKL 146
              L+GD + +  FE+D R++LLM+KL
Sbjct:   124 RLQGDANNLHGFEVDSRVYLLMKKL 148

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

GO:0005634 "nucleus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

UNIPROTKB|P52434 POLR2H "DNA-directed RNA polymerases I, II, and III subunit RPABC3" [Homo sapiens (taxid:9606)]

 Score = 373 (136.4 bits), Expect = 2.2e-34, P = 2.2e-34
 Identities = 74/145 (51%), Positives = 107/145 (73%)

Query:     5 VLFEDIFVVEKIDPDGKKFDKVSRIEAHSQNCDMYMLLDVNSELYPMRVGDKFTMALAHT 64
             +LFEDIF V+ IDP+GKKFD+VSR+   S++  M ++LDVN ++YP+ +GDKF + +A T
Sbjct:     4 ILFEDIFDVKDIDPEGKKFDRVSRLHCESESFKMDLILDVNIQIYPVDLGDKFRLVIAST 63

Query:    65 LNLDGTPDTGYYTP-GARKTLADKYEYIMHGKLFKI-GDEGSGKSL-KAEIYVSYGGLLM 121
             L  DGT D G Y P   R + AD++EY+M+GK+++I GDE S ++  +   YVSYGGLLM
Sbjct:    64 LYEDGTLDDGEYNPTDDRPSRADQFEYVMYGKVYRIEGDETSTEAATRLSAYVSYGGLLM 123

Query:   122 MLKGDPSYVSHFELDQRLFLLMRKL 146
              L+GD + +  FE+D R++LLM+KL
Sbjct:   124 RLQGDANNLHGFEVDSRVYLLMKKL 148

GO:0003677 "DNA binding" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

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

GO:0008270 "zinc ion binding" evidence=NAS

GO:0004672 "protein kinase activity" evidence=IDA

GO:0005634 "nucleus" evidence=IDA

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

GO:0005665 "DNA-directed RNA polymerase II, core complex" 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:0006360 "transcription from RNA polymerase I promoter" evidence=TAS

GO:0006361 "transcription initiation from RNA polymerase I promoter" evidence=TAS

GO:0006362 "transcription elongation from RNA polymerase I promoter" evidence=TAS

GO:0006363 "termination of RNA polymerase I transcription" 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:0006383 "transcription from RNA polymerase III promoter" evidence=TAS

GO:0006385 "transcription elongation from RNA polymerase III promoter" evidence=TAS

GO:0006386 "termination of RNA polymerase III transcription" evidence=TAS

GO:0008380 "RNA splicing" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

GO:0016032 "viral reproduction" evidence=TAS

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

GO:0006468 "protein phosphorylation" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

UNIPROTKB|I3LCB2 POLR2H "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 373 (136.4 bits), Expect = 2.2e-34, P = 2.2e-34
 Identities = 74/145 (51%), Positives = 107/145 (73%)

Query:     5 VLFEDIFVVEKIDPDGKKFDKVSRIEAHSQNCDMYMLLDVNSELYPMRVGDKFTMALAHT 64
             +LFEDIF V+ IDP+GKKFD+VSR+   S++  M ++LDVN ++YP+ +GDKF + +A T
Sbjct:     4 ILFEDIFDVKDIDPEGKKFDRVSRLHCESESFKMDLILDVNIQIYPVDLGDKFRLVIAST 63

Query:    65 LNLDGTPDTGYYTP-GARKTLADKYEYIMHGKLFKI-GDEGSGKSL-KAEIYVSYGGLLM 121
             L  DGT D G Y P   R + AD++EY+M+GK+++I GDE S ++  +   YVSYGGLLM
Sbjct:    64 LYEDGTLDDGEYNPTDDRPSRADQFEYVMYGKVYRIEGDETSTEAATRLSAYVSYGGLLM 123

Query:   122 MLKGDPSYVSHFELDQRLFLLMRKL 146
              L+GD + +  FE+D R++LLM+KL
Sbjct:   124 RLQGDANNLHGFEVDSRVYLLMKKL 148

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

GO:0005737 "cytoplasm" evidence=IEA

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

GO:0004672 "protein kinase activity" evidence=IEA

MGI|MGI:2384309 Polr2h "polymerase (RNA) II (DNA directed) polypeptide H" [Mus musculus (taxid:10090)]

 Score = 373 (136.4 bits), Expect = 2.2e-34, P = 2.2e-34
 Identities = 74/145 (51%), Positives = 107/145 (73%)

Query:     5 VLFEDIFVVEKIDPDGKKFDKVSRIEAHSQNCDMYMLLDVNSELYPMRVGDKFTMALAHT 64
             +LFEDIF V+ IDP+GKKFD+VSR+   S++  M ++LDVN ++YP+ +GDKF + +A T
Sbjct:     4 ILFEDIFDVKDIDPEGKKFDRVSRLHCESESFKMDLILDVNIQIYPVDLGDKFRLVIAST 63

Query:    65 LNLDGTPDTGYYTP-GARKTLADKYEYIMHGKLFKI-GDEGSGKSL-KAEIYVSYGGLLM 121
             L  DGT D G Y P   R + AD++EY+M+GK+++I GDE S ++  +   YVSYGGLLM
Sbjct:    64 LYEDGTLDDGEYNPTDDRPSRADQFEYVMYGKVYRIEGDETSTEAATRLSAYVSYGGLLM 123

Query:   122 MLKGDPSYVSHFELDQRLFLLMRKL 146
              L+GD + +  FE+D R++LLM+KL
Sbjct:   124 RLQGDANNLHGFEVDSRVYLLMKKL 148

GO:0003674 "molecular_function" evidence=ND

GO:0003677 "DNA binding" evidence=IEA

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

GO:0005634 "nucleus" evidence=ISO

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

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

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

GO:0006468 "protein phosphorylation" evidence=ISO

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
P20436	RPAB3_YEAST	No assigned EC number	0.3921	0.9452	0.9452	yes	no
Q19826	RPAB3_CAEEL	No assigned EC number	0.4295	0.9657	0.9527	yes	no
P52434	RPAB3_HUMAN	No assigned EC number	0.5103	0.9726	0.9466	yes	no
Q92399	RPAB3_SCHPO	No assigned EC number	0.3448	0.8561	1.0	yes	no
Q923G2	RPAB3_MOUSE	No assigned EC number	0.5103	0.9726	0.9466	yes	no
Q54YW8	RPAB3_DICDI	No assigned EC number	0.4680	0.9452	0.9718	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	estExt_Genewise1_v1.C_410025	hypothetical protein (148 aa)
		(Populus trichocarpa)
Predicted Functional Partners:
	gw1.XIII.2192.1	polyribonucleotide nucleotidyltransferase (EC-2.7.7.8) (853 aa)						•			0.899
	gw1.XII.1350.1	hypothetical protein (612 aa)						•			0.899
	gw1.X.1387.1	CTP synthase (EC-6.3.4.2) (589 aa)						•			0.899
	gw1.IX.2629.1	pyruvate kinase (EC-2.7.1.40) (481 aa)						•			0.899
	gw1.II.1445.1	SubName- Full=Putative uncharacterized protein; (164 aa)						•			0.899
	gw1.I.8101.1	CTP synthase (EC-6.3.4.2) (591 aa)						•			0.899
	gw1.I.4193.1	pyruvate kinase (EC-2.7.1.40) (481 aa)						•			0.899
	gw1.I.2477.1	hypothetical protein (950 aa)						•			0.899
	gw1.29.22.1	pyruvate kinase (EC-2.7.1.40) (538 aa)						•			0.899
	gw1.2679.5.1	annotation not avaliable (298 aa)						•			0.899

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	146
smart00658	143	smart00658, RPOL8c, RNA polymerase subunit 8	5e-62
pfam03870	137	pfam03870, RNA_pol_Rpb8, RNA polymerase Rpb8	1e-59
PTZ00167	144	PTZ00167, PTZ00167, RNA polymerase subunit 8c; Pro	9e-30

>gnl|CDD|197821 smart00658, RPOL8c, RNA polymerase subunit 8

 Score =  186 bits (475), Expect = 5e-62
 Identities = 83/144 (57%), Positives = 109/144 (75%), Gaps = 2/144 (1%)

Query: 3   NIVLFEDIFVVEKIDPDGKKFDKVSRIEAHSQNCDMYMLLDVNSELYPMRVGDKFTMALA 62
            I+LFEDIF V+ +DPDGKKFDKVSRI A S+   M ++LD+NSE+YP+ VGDKF + +A
Sbjct: 1   AIILFEDIFKVKSVDPDGKKFDKVSRIFAESEYLQMELILDINSEIYPLAVGDKFRLVIA 60

Query: 63  HTLNLDGTPDTGYYTPGA-RKTLADKYEYIMHGKLFKIGDEGSGKSLKAEIYVSYGGLLM 121
            TLN DGTPD+G   P A  K+LADKYEY+M+GK+++I ++   ++ K   YVS+GGLLM
Sbjct: 61  STLNEDGTPDSGENNPIALIKSLADKYEYVMYGKVYRIEED-KTETSKLSAYVSFGGLLM 119

Query: 122 MLKGDPSYVSHFELDQRLFLLMRK 145
            LKGD + +  FELD  L+LLMRK
Sbjct: 120 RLKGDANNLKGFELDSNLYLLMRK 143

subunit of RNA polymerase I, II and III. Length = 143

>gnl|CDD|217771 pfam03870, RNA_pol_Rpb8, RNA polymerase Rpb8

 Score =  180 bits (459), Expect = 1e-59
 Identities = 77/139 (55%), Positives = 105/139 (75%), Gaps = 3/139 (2%)

Query: 8   EDIFVVEKIDPDGKKFDKVSRIEAHSQNCDMYMLLDVNSELYPMRVGDKFTMALAHTLNL 67
           +DIF V+ +DPDGKK+D+VSRIEA S++  M ++LD+NS+LYP+ VGDKF + +A TL  
Sbjct: 1   DDIFKVKSVDPDGKKYDRVSRIEAESESFKMELILDINSQLYPLAVGDKFRLVIASTLLE 60

Query: 68  DGTPDTGYYTP-GARKTLADKYEYIMHGKLFKIGDEGSGKSLKAEIYVSYGGLLMMLKGD 126
           DGT D G Y P G R +LADKYEY+M+GK+++I +E S K+ K   YVS+GGLLM L+GD
Sbjct: 61  DGTADDGSYNPAGDRFSLADKYEYVMYGKVYRI-EETSIKT-KLSAYVSFGGLLMRLQGD 118

Query: 127 PSYVSHFELDQRLFLLMRK 145
              +  FE+D  L+LLMR+
Sbjct: 119 ARNLHGFEVDSHLYLLMRR 137

Rpb8 is a subunit common to the three yeast RNA polymerases, pol I, II and III. Rpb8 interacts with the largest subunit Rpb1, and with Rpb3 and Rpb11, two smaller subunits. Length = 137

>gnl|CDD|185493 PTZ00167, PTZ00167, RNA polymerase subunit 8c; Provisional

 Score =  104 bits (262), Expect = 9e-30
 Identities = 57/145 (39%), Positives = 87/145 (60%), Gaps = 7/145 (4%)

Query: 1   MSNIVLFEDIFVVEKIDPDGKKFDKVSRIEAHSQNCDMYMLLDVNSELYPMRVGDKFTMA 60
                LFED FVV  +D    KF++VSRI+A S   D  ++LD+NS+L+P+R  +K ++ 
Sbjct: 2   SLPSCLFEDRFVVRSVD--NSKFERVSRIKAKSTGFDAELILDINSDLFPVR--EKQSLY 57

Query: 61  LAHTLNLDGTPDTGYYTPGARKTLADKYEYIMHGKLFKIGDEGSGKSLKAEIYVSYGGLL 120
           +  T  L   PD   +     ++L D+YEY+M+GK+FK  ++ S +     +Y S+GGLL
Sbjct: 58  IGLTNQLSSGPDDNVWESSEPQSLMDQYEYVMYGKIFKFEEKSSERR---TLYASFGGLL 114

Query: 121 MMLKGDPSYVSHFELDQRLFLLMRK 145
           M L  D   V   ELD R++LL+R+
Sbjct: 115 MALTADKQVVGDLELDMRIYLLVRR 139

Length = 144

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	146
smart00658	143	RPOL8c RNA polymerase subunit 8. subunit of RNA po	100.0
PF03870	138	RNA_pol_Rpb8: RNA polymerase Rpb8; InterPro: IPR00	100.0
PTZ00167	144	RNA polymerase subunit 8c; Provisional	100.0
KOG3400	143	consensus RNA polymerase subunit 8 [Transcription]	100.0
PRK14980	127	DNA-directed RNA polymerase subunit G; Provisional	99.0
PF03459	64	TOBE: TOBE domain; InterPro: IPR005116 The TOBE do	80.38

>smart00658 RPOL8c RNA polymerase subunit 8

Probab=100.00  E-value=5.1e-68  Score=408.90  Aligned_cols=141  Identities=59%  Similarity=0.971  Sum_probs=132.5

Q ss_pred             ccceeeeEEEeeeCCCCCccceEeeEEEEecCCceEEEEEecccceecccCCEEEEEEeeecCCCCCCCCCCCCCCC-Cc
Q 032138            4 IVLFEDIFVVEKIDPDGKKFDKVSRIEAHSQNCDMYMLLDVNSELYPMRVGDKFTMALAHTLNLDGTPDTGYYTPGA-RK   82 (146)
Q Consensus         4 ~~Lfed~F~V~~iD~dgKkfdrVSRi~~~S~~~~~~l~LDiNtelypl~~~d~~~l~LassL~~dg~~d~~~~~~~~-~~   82 (146)
                      .+||||+|+|++|||+||||||||||.|+|++++|+|+|||||||||+++||+|+|+||+||++||+++++.|++.+ .+
T Consensus         2 ~~lfeD~F~V~~iDp~gKkfdrVSRi~~~S~~~~~~l~LDiNtelyPv~~gd~~~l~La~tL~~dg~~d~~~~~~~~~~~   81 (143)
T smart00658        2 IILFDDIFKVKSVDPDGKKFDKVSRIFAESEYLQMELTLDINSEIYPLAVGDKFTLVIASTLNEDGTPDSGENNPIALIK   81 (143)
T ss_pred             ceeeeeEEEEEEECCCCCeEccEEEEEEEcCCCceEEEEEecceEEeccCCCEEEEEEecccccCCCCcccccccccccc
Confidence            57999999999999999999999999999999999999999999999999999999999999999999999998653 36


Q ss_pred             cccccccEEEeeEEEEeecCCCCCcceEEEEEEecceeeEEEcCCCCCCCCCCCCeEEEEEee
Q 032138           83 TLADKYEYIMHGKLFKIGDEGSGKSLKAEIYVSYGGLLMMLKGDPSYVSHFELDQRLFLLMRK  145 (146)
Q Consensus        83 slad~ydYVMyGkVYk~e~~~~~~~~~~~vy~SFGGLLM~L~G~~~~l~~l~~d~~vYLL~rk  145 (146)
                      +|||+|||||||||||||++++ +..+++||||||||||+|+|++++|++|++|++|||||||
T Consensus        82 ~Lad~ydYVM~GkvYk~e~~~~-~~~~~~vy~SFGGLLm~L~G~~~~L~~~~~d~~vYLLirk  143 (143)
T smart00658       82 SLADKYEYVMYGKVYRIEEDKT-ETEKLSVYVSFGGLLMRLKGDANNLKGFELDSNLYLLMRK  143 (143)
T ss_pred             chhhcCCEEeeeEEEEEEecCC-CceEEEEEEEeccEeEEEEeCHHHCccccCCCEEEEEEeC
Confidence            7999999999999999998642 1259999999999999999999999999999999999997

subunit of RNA polymerase I, II and III

>PF03870 RNA_pol_Rpb8: RNA polymerase Rpb8; InterPro: IPR005570 Rpb8 is a subunit common to the three yeast RNA polymerases, pol I, II and III

Probab=100.00  E-value=4.2e-67  Score=401.92  Aligned_cols=137  Identities=58%  Similarity=1.006  Sum_probs=125.7

Q ss_pred             eeeEEEeeeCCCCCccceEeeEEEEecCCceEEEEEecccceecccCCEEEEEEeeecCCCCCCCCCCCCCC-CCccccc
Q 032138            8 EDIFVVEKIDPDGKKFDKVSRIEAHSQNCDMYMLLDVNSELYPMRVGDKFTMALAHTLNLDGTPDTGYYTPG-ARKTLAD   86 (146)
Q Consensus         8 ed~F~V~~iD~dgKkfdrVSRi~~~S~~~~~~l~LDiNtelypl~~~d~~~l~LassL~~dg~~d~~~~~~~-~~~slad   86 (146)
                      ||+|+|++||||||||||||||.|+|++++|+|+|||||||||+++||+|+|+||+||++||+++++.|++. +++||||
T Consensus         1 eD~F~V~~vD~dGkkfdrVSRi~~~S~~~~m~l~LDiNtelyPl~~~d~~~l~La~tL~~dg~~d~~~~~~~~~~~slad   80 (138)
T PF03870_consen    1 EDIFTVTDVDPDGKKFDRVSRIFAKSESFDMELTLDINTELYPLKVGDKFTLALASTLNLDGTPDDGSWRPKGGEPSLAD   80 (138)
T ss_dssp             EEEEEEEEEE---SSSSSEEEEEEEESSSS-EEEEEEETTTSSSTSSEEEEEEECSSS-SSSSSTTTSSSSTTCTTCCCT
T ss_pred             CCeEEEEEECCCCCeeccEEEEEEEeCCCceEEEEEccccEEccCCCCEEEEEEecccccCCCCCccccccCCCCcchhh
Confidence            799999999999999999999999999999999999999999999999999999999999999999999874 5679999


Q ss_pred             cccEEEeeEEEEeecCCCCCcceEEEEEEecceeeEEEcCCCCCCCCCCCCeEEEEEee
Q 032138           87 KYEYIMHGKLFKIGDEGSGKSLKAEIYVSYGGLLMMLKGDPSYVSHFELDQRLFLLMRK  145 (146)
Q Consensus        87 ~ydYVMyGkVYk~e~~~~~~~~~~~vy~SFGGLLM~L~G~~~~l~~l~~d~~vYLL~rk  145 (146)
                      +|||||||||||+++.+ +.+++++||||||||||+|+|++++|++|++|+||||||||
T Consensus        81 ~ydYVMyGkvYk~ee~~-~~~~~~~vY~SFGGLLM~L~G~~~~l~~l~~d~~vYLLirK  138 (138)
T PF03870_consen   81 DYDYVMYGKVYKFEEGS-GGSDKVKVYASFGGLLMRLEGDPRHLSDLEVDSRVYLLIRK  138 (138)
T ss_dssp             SSSEEEEEEEEEEEESS-S-TSCEEEEEEETTEEEEEEESSCCCTSTSTSSTCCEEEEE
T ss_pred             heeeEeeeEEEeeeccC-CCCceEEEEEEecceeEEEEeCHHHCccccCCCEEEEEEeC
Confidence            99999999999999653 35789999999999999999999999999999999999998

Rpb8 interacts with the largest subunit Rpb1, and with Rpb3 and Rpb11, two smaller subunits.; GO: 0006351 transcription, DNA-dependent; PDB: 1TWH_H 1R9T_H 1I3Q_H 2B8K_H 1TWA_H 2NVY_H 4A3E_H 1Y77_H 3GTK_H 2E2J_H ....

>PTZ00167 RNA polymerase subunit 8c; Provisional

Probab=100.00  E-value=3.4e-66  Score=398.91  Aligned_cols=139  Identities=40%  Similarity=0.736  Sum_probs=131.8

Q ss_pred             CCcccceeeeEEEeeeCCCCCccceEeeEEEEecCCceEEEEEecccceecccCCEEEEEEeeecCCCCCCCCCCCCCCC
Q 032138            1 MSNIVLFEDIFVVEKIDPDGKKFDKVSRIEAHSQNCDMYMLLDVNSELYPMRVGDKFTMALAHTLNLDGTPDTGYYTPGA   80 (146)
Q Consensus         1 ms~~~Lfed~F~V~~iD~dgKkfdrVSRi~~~S~~~~~~l~LDiNtelypl~~~d~~~l~LassL~~dg~~d~~~~~~~~   80 (146)
                      |++++||||+|+|++|||+|  |||||||.|+|++++|+|+|||||||||+++||+|+|+||+|| +|| ++++.|+|.+
T Consensus         2 ~~~~~LfeD~F~V~~iD~~g--fdrVSRI~a~S~~~~~~l~LDiNtelyPv~~gd~~~l~LastL-~dg-~d~~~~~~~~   77 (144)
T PTZ00167          2 SLPSCLFEDRFVVRSVDNSK--FERVSRIKAKSTGFDAELILDINSDLFPVREKQSLYIGLTNQL-SSG-PDDNVWESSE   77 (144)
T ss_pred             CCCceEEEeeEEEEecCCCC--CceEEEEEEEeCCCceEEEEEecccEEeccCCCEEEEEEeccc-cCC-CCcccccccc
Confidence            45689999999999999986  9999999999999999999999999999999999999999999 999 7888899888


Q ss_pred             CccccccccEEEeeEEEEeecCCCCCcceEEEEEEecceeeEEEcCCCCCCCCCCCCeEEEEEeeC
Q 032138           81 RKTLADKYEYIMHGKLFKIGDEGSGKSLKAEIYVSYGGLLMMLKGDPSYVSHFELDQRLFLLMRKL  146 (146)
Q Consensus        81 ~~slad~ydYVMyGkVYk~e~~~~~~~~~~~vy~SFGGLLM~L~G~~~~l~~l~~d~~vYLL~rk~  146 (146)
                      ++||||+|||||||||||||+++   +++++||||||||||+|+|++++|++|++|+||||||||+
T Consensus        78 ~~tLad~ydYVM~GkvYk~ee~~---s~~~~vy~SFGGLLM~L~G~~~~L~~~~~d~~vYLLirk~  140 (144)
T PTZ00167         78 PQSLMDQYEYVMYGKIFKFEEKS---SERRTLYASFGGLLMALTADKQVVGDLELDMRIYLLVRRS  140 (144)
T ss_pred             cccccccCCEEcceEEEEeeecC---CCcEEEEEEcccEeEEEEcCHHHCccccCCCEEEEEEEec
Confidence            99999999999999999999753   4699999999999999999999999999999999999995

>KOG3400 consensus RNA polymerase subunit 8 [Transcription]

Probab=100.00  E-value=8.9e-66  Score=391.34  Aligned_cols=143  Identities=60%  Similarity=1.032  Sum_probs=136.7

Q ss_pred             CCcccceeeeEEEeeeCCCCCccceEeeEEEEecCCceEEEEEecccceecccCCEEEEEEeeecCCCCCCCCCCCCCCC
Q 032138            1 MSNIVLFEDIFVVEKIDPDGKKFDKVSRIEAHSQNCDMYMLLDVNSELYPMRVGDKFTMALAHTLNLDGTPDTGYYTPGA   80 (146)
Q Consensus         1 ms~~~Lfed~F~V~~iD~dgKkfdrVSRi~~~S~~~~~~l~LDiNtelypl~~~d~~~l~LassL~~dg~~d~~~~~~~~   80 (146)
                      || ++||+|||+|++||||||||+||||++|+|++++|+|+||||++|||++.||+|+|+||+||++||+||+++|+|.+
T Consensus         1 Ma-~ilfdDiF~V~~vDpeGkkydrVsR~~~~S~~~~m~l~LDiNt~lyPl~~gdkf~l~iastL~eDgtpd~g~~~p~a   79 (143)
T KOG3400|consen    1 MA-GILFDDIFKVSDVDPEGKKYDRVSRIEAKSESFKMDLILDINTQLYPLATGDKFTLVIASTLNEDGTPDTGEYTPGA   79 (143)
T ss_pred             Cc-chhhhhceeeeecCcccchhhheEeEEeeCCCceEEEEEecccEEEeeccCCEEEEEEecccccCCCccccccCccc
Confidence            55 69999999999999999999999999999999999999999999999999999999999999999999999999887


Q ss_pred             CccccccccEEEeeEEEEeecCCCCCcceEEEEEEecceeeEEEcCCCCCCCCCCCCeEEEEEee
Q 032138           81 RKTLADKYEYIMHGKLFKIGDEGSGKSLKAEIYVSYGGLLMMLKGDPSYVSHFELDQRLFLLMRK  145 (146)
Q Consensus        81 ~~slad~ydYVMyGkVYk~e~~~~~~~~~~~vy~SFGGLLM~L~G~~~~l~~l~~d~~vYLL~rk  145 (146)
                      ...|||+|||||||||||+|.++ +..+..++|+|||||||+|+|++++|.+|++|+++||||||
T Consensus        80 ~~~~ad~~eYvMyGkvYriE~~e-~~~~~~~~YvSFGGLLMrl~G~~~nl~~fe~d~~~yLLmrk  143 (143)
T KOG3400|consen   80 KKPLADEYEYVMYGKVYRIEYDE-GKTEKASAYVSFGGLLMRLQGDARNLHGFELDQRLYLLMRK  143 (143)
T ss_pred             cccccceeeEEEeeEEEEEeccC-CccceeeEEEeeceEEEEecCChhhccccccccEEEEEeeC
Confidence            77799999999999999999764 56788899999999999999999999999999999999997

>PRK14980 DNA-directed RNA polymerase subunit G; Provisional

Probab=99.00  E-value=1.8e-08  Score=76.64  Aligned_cols=118  Identities=13%  Similarity=0.240  Sum_probs=97.0

Q ss_pred             ccceeeeEEEeeeCCCCCccceEeeEEEEecCCceEEEEEecccceecccCCEEEEEEeeecCCCCCCCCCCCCCCCCcc
Q 032138            4 IVLFEDIFVVEKIDPDGKKFDKVSRIEAHSQNCDMYMLLDVNSELYPMRVGDKFTMALAHTLNLDGTPDTGYYTPGARKT   83 (146)
Q Consensus         4 ~~Lfed~F~V~~iD~dgKkfdrVSRi~~~S~~~~~~l~LDiNtelypl~~~d~~~l~LassL~~dg~~d~~~~~~~~~~s   83 (146)
                      +.-+.-.=+|++|.| |+ +-.-.++.+.+  .+.++++|+|.+|-+..+||.+.+.|.+.-                |.
T Consensus         6 ~~~~~~~cKI~SIEk-g~-l~~l~i~~~~C--~~~~v~fDi~~~L~~fsege~v~iiIS~ek----------------P~   65 (127)
T PRK14980          6 AQEIILSCKINSIEK-GS-LKNLSIIHMSC--NDFNISFDIIDSINIFSQKEKVKAIISKER----------------PS   65 (127)
T ss_pred             hhheeeEEeeeeecc-cc-cCCcEEEEEec--CCeEEEEEehhhhheecCCCcEEEEEeccC----------------cc
Confidence            455677789999999 53 77777877777  459999999999999999999999987652                23


Q ss_pred             ccccccEEEeeEEEEeecCCCCCcceEEEEEEecceeeEEEcCCCCC--CCCCCCCeEEEEEee
Q 032138           84 LADKYEYIMHGKLFKIGDEGSGKSLKAEIYVSYGGLLMMLKGDPSYV--SHFELDQRLFLLMRK  145 (146)
Q Consensus        84 lad~ydYVMyGkVYk~e~~~~~~~~~~~vy~SFGGLLM~L~G~~~~l--~~l~~d~~vYLL~rk  145 (146)
                      . .+.|+.-||-|...+-   ..+++..+-+|++|||.++.-..+-|  ++|++=+++|+..||
T Consensus        66 ~-~~~dFCghGyvV~~~k---~~~~~y~~iISl~GlLv~I~sk~~~~~~s~~~~Md~vY~cV~K  125 (127)
T PRK14980         66 Y-TNDDFCAHGYIVTESS---NNGNRYTTIISLFGLLVKIISKESFLKTHQLNVMDHVYFCVKK  125 (127)
T ss_pred             c-ccceeecCcEEEEEEe---cCCCeEEEEEEeeeEEEEEEehhhcccccccccccEEEEEEEc
Confidence            3 3388999999998853   34789999999999999999988744  678877899999997

>PF03459 TOBE: TOBE domain; InterPro: IPR005116 The TOBE domain [] (Transport-associated OB) always occurs as a dimer as the C-terminal strand of each domain is supplied by the partner

Probab=80.38  E-value=7.2  Score=24.78  Aligned_cols=50  Identities=12%  Similarity=0.240  Sum_probs=35.7

Q ss_pred             EEeeEEEEeecCCCCCcceEEEEEEecc---eeeEEEcCCCCCCCCCCCCeEEEEEe
Q 032138           91 IMHGKLFKIGDEGSGKSLKAEIYVSYGG---LLMMLKGDPSYVSHFELDQRLFLLMR  144 (146)
Q Consensus        91 VMyGkVYk~e~~~~~~~~~~~vy~SFGG---LLM~L~G~~~~l~~l~~d~~vYLL~r  144 (146)
                      ...|+|..++..    +....+++-.||   |..+++.+...-=+|+.++.||+.+|
T Consensus         6 ~l~g~V~~ie~~----g~~~~v~~~~~~~~~l~a~it~~~~~~L~L~~G~~V~~~ik   58 (64)
T PF03459_consen    6 QLPGTVESIENL----GSEVEVTLDLGGGETLTARITPESAEELGLKPGDEVYASIK   58 (64)
T ss_dssp             EEEEEEEEEEES----SSEEEEEEEETTSEEEEEEEEHHHHHHCT-STT-EEEEEE-
T ss_pred             EEEEEEEEEEEC----CCeEEEEEEECCCCEEEEEEcHHHHHHcCCCCCCEEEEEEe
Confidence            356999999964    578889999999   66666664443345889999999987

It is probably involved in the recognition of small ligands such as molybdenum (P46930 from SWISSPROT) and sulphate (P16676 from SWISSPROT), and is found in ABC transporters immediately after the ATPase domain.; GO: 0005215 transporter activity, 0005524 ATP binding, 0016820 hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances, 0006810 transport, 0043190 ATP-binding cassette (ABC) transporter complex; PDB: 1G29_2 1H9M_B 1H9J_A 1H9K_A 1H9R_B 1O7L_C 1H9S_A 1B9N_A 1B9M_A 1GUS_C ....

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	146
2f3i_A	150	Solution Structure Of A Subunit Of Rna Polymerase I		3e-35
1i3q_H	146	Rna Polymerase Ii Crystal Form I At 3.1 A Resolutio		1e-19
3h0g_H	125	Rna Polymerase Ii From Schizosaccharomyces Pombe Le		3e-17

>pdb|2F3I|A Chain A, Solution Structure Of A Subunit Of Rna Polymerase Ii Length = 150

Iteration: 1
 Score =  143 bits (361), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 74/145 (51%), Positives = 107/145 (73%), Gaps = 3/145 (2%)
Query: 5   VLFEDIFVVEKIDPDGKKFDKVSRIEAHSQNCDMYMLLDVNSELYPMRVGDKFTMALAHT 64
           +LFEDIF V+ IDP+GKKFD+VSR+   S++  M ++LDVN ++YP+ +GDKF + +A T
Sbjct: 4   ILFEDIFDVKDIDPEGKKFDRVSRLHCESESFKMDLILDVNIQIYPVDLGDKFRLVIAST 63
Query: 65  LNLDGTPDTGYYTP-GARKTLADKYEYIMHGKLFKI-GDEGSGK-SLKAEIYVSYGGLLM 121
           L  DGT D G Y P   R + AD++EY+M+GK+++I GDE S + + +   YVSYGGLLM
Sbjct: 64  LYEDGTLDDGEYNPTDDRPSRADQFEYVMYGKVYRIEGDETSTEAATRLSAYVSYGGLLM 123
Query: 122 MLKGDPSYVSHFELDQRLFLLMRKL 146
            L+GD + +  FE+D R++LLM+KL
Sbjct: 124 RLQGDANNLHGFEVDSRVYLLMKKL 148

>pdb|1I3Q|H Chain H, Rna Polymerase Ii Crystal Form I At 3.1 A Resolution Length = 146

Iteration: 1
 Score = 92.0 bits (227), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 60/153 (39%), Positives = 92/153 (60%), Gaps = 15/153 (9%)
Query: 1   MSNIVLFEDIFVVEKIDPDGKKFDKVSRIEAHSQNCDMYML-LDVNSELYPMRVGDKFTM 59
           MSN  LF+DIF V ++DP   +++KV RIEA S   D   L LD+N EL+P+   D  T+
Sbjct: 1   MSN-TLFDDIFQVSEVDP--GRYNKVCRIEAASTTQDQCKLTLDINVELFPVAAQDSLTV 57
Query: 60  ALAHTLNLDGTP-----DTGYYTP--GARKTLADKYEYIMHGKLFKIGDEGSGKSLKAEI 112
            +A +LNL+ TP      T  + P     ++LAD Y+Y+M+G  +K   E   K L A +
Sbjct: 58  TIASSLNLEDTPANDSSATRSWRPPQAGDRSLADDYDYVMYGTAYKF--EEVSKDLIA-V 114
Query: 113 YVSYGGLLMMLKGDPSYVSHFELDQRLFLLMRK 145
           Y S+GGLLM L+G+   +++ +  +  +LL+R+
Sbjct: 115 YYSFGGLLMRLEGNYRNLNNLK-QENAYLLIRR 146

>pdb|3H0G|H Chain H, Rna Polymerase Ii From Schizosaccharomyces Pombe Length = 125

Iteration: 1
 Score = 84.0 bits (206), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 50/145 (34%), Positives = 82/145 (56%), Gaps = 20/145 (13%)
Query: 1   MSNIVLFEDIFVVEKIDPDGKKFDKVSRIEAHSQNCDMYMLLDVNSELYPMRVGDKFTMA 60
           MS  VL ++IF V  +D   +K+ +VSRI A S   DM + LD+NS++YP+     F++ 
Sbjct: 1   MSESVLLDEIFTVTSVDK--QKYQRVSRITAVSGQNDMNLTLDINSQIYPLEKDATFSLQ 58
Query: 61  LAHTLNLDGTPDTGYYTPGARKTLADKYEYIMHGKLFKIGDEGSGKSLKAEIYVSYGGLL 120
           +   LN   +PD           L +  +YIM+GK++++ +    K  K  +YVS+GGLL
Sbjct: 59  ITSNLN---SPD-----------LKEAADYIMYGKVYRVEE---AKDEKVSVYVSFGGLL 101
Query: 121 MMLKGDPSYVSHFELDQRLFLLMRK 145
           M ++G    +    LD  ++LL+R+
Sbjct: 102 MAIEGSHRKLYRLSLDH-VYLLLRR 125

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	146
2f3i_A	150	DNA-directed RNA polymerases I, II, and III 17.1 k	5e-62
1a1d_A	146	RNA polymerase; RPB8, OB fold, eukaryotic, yeast,	2e-50
3h0g_H	125	DNA-directed RNA polymerases I, II, and III subuni	9e-48

>2f3i_A DNA-directed RNA polymerases I, II, and III 17.1 kDa polypeptide; RNA polymerase II, transferase; NMR {Homo sapiens} Length = 150

 Score =  186 bits (474), Expect = 5e-62
 Identities = 72/149 (48%), Positives = 106/149 (71%), Gaps = 4/149 (2%)

Query: 1   MSNIVLFEDIFVVEKIDPDGKKFDKVSRIEAHSQNCDMYMLLDVNSELYPMRVGDKFTMA 60
           M+ I LFEDIF V+ IDP+GKKFD+VSR+   S++  M ++LDVN ++YP+ +GDKF + 
Sbjct: 1   MAGI-LFEDIFDVKDIDPEGKKFDRVSRLHCESESFKMDLILDVNIQIYPVDLGDKFRLV 59

Query: 61  LAHTLNLDGTPDTGYYTP-GARKTLADKYEYIMHGKLFKI--GDEGSGKSLKAEIYVSYG 117
           +A TL  DGT D G Y P   R + AD++EY+M+GK+++I   +  +  + +   YVSYG
Sbjct: 60  IASTLYEDGTLDDGEYNPTDDRPSRADQFEYVMYGKVYRIEGDETSTEAATRLSAYVSYG 119

Query: 118 GLLMMLKGDPSYVSHFELDQRLFLLMRKL 146
           GLLM L+GD + +  FE+D R++LLM+KL
Sbjct: 120 GLLMRLQGDANNLHGFEVDSRVYLLMKKL 148

>1a1d_A RNA polymerase; RPB8, OB fold, eukaryotic, yeast, nucleotidyltransferase; NMR {Saccharomyces cerevisiae} SCOP: b.40.4.8 PDB: 1i3q_H 1i50_H 1i6h_H 1k83_H* 1nik_H 1nt9_H 1pqv_H 1r5u_H 1r9s_H* 1r9t_H* 1sfo_H* 1twa_H* 1twc_H* 1twf_H* 1twg_H* 1twh_H* 1wcm_H 1y1v_H 1y1w_H 1y1y_H ... Length = 146

 Score =  157 bits (397), Expect = 2e-50
 Identities = 52/153 (33%), Positives = 86/153 (56%), Gaps = 15/153 (9%)

Query: 1   MSNIVLFEDIFVVEKIDPDGKKFDKVSRIEAHSQNC-DMYMLLDVNSELYPMRVGDKFTM 59
           MSN  LF+DIF V ++DP   +++KV RIEA S       + LD+N EL+P+   D  T+
Sbjct: 1   MSNT-LFDDIFQVSEVDPG--RYNKVCRIEAASTTQDQCKLTLDINVELFPVAAQDSLTV 57

Query: 60  ALAHTLNLDGTPDTGYYTPGA-------RKTLADKYEYIMHGKLFKIGDEGSGKSLKAEI 112
            +A +LNL+ TP        +        ++LAD Y+Y+M+G  +K  +          +
Sbjct: 58  TIASSLNLEDTPANDSSATRSWRPPQAGDRSLADDYDYVMYGTAYKFEEVSKD---LIAV 114

Query: 113 YVSYGGLLMMLKGDPSYVSHFELDQRLFLLMRK 145
           Y S+GGLLM L+G+   +++ +  +  +LL+R+
Sbjct: 115 YYSFGGLLMRLEGNYRNLNNLK-QENAYLLIRR 146

>3h0g_H DNA-directed RNA polymerases I, II, and III subunit rpabc3; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 125

 Score =  149 bits (378), Expect = 9e-48
 Identities = 47/145 (32%), Positives = 78/145 (53%), Gaps = 20/145 (13%)

Query: 1   MSNIVLFEDIFVVEKIDPDGKKFDKVSRIEAHSQNCDMYMLLDVNSELYPMRVGDKFTMA 60
           MS  VL ++IF V  +D   +K+ +VSRI A S   DM + LD+NS++YP+     F++ 
Sbjct: 1   MSESVLLDEIFTVTSVDK--QKYQRVSRITAVSGQNDMNLTLDINSQIYPLEKDATFSLQ 58

Query: 61  LAHTLNLDGTPDTGYYTPGARKTLADKYEYIMHGKLFKIGDEGSGKSLKAEIYVSYGGLL 120
           +   LN                 L +  +YIM+GK++++ +    K     +YVS+GGLL
Sbjct: 59  ITSNLNSPD--------------LKEAADYIMYGKVYRVEEAKDEKV---SVYVSFGGLL 101

Query: 121 MMLKGDPSYVSHFELDQRLFLLMRK 145
           M ++G    +    LD  ++LL+R+
Sbjct: 102 MAIEGSHRKLYRLSLDH-VYLLLRR 125

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	146
2f3i_A	150	DNA-directed RNA polymerases I, II, and III 17.1 k	100.0
1a1d_A	146	RNA polymerase; RPB8, OB fold, eukaryotic, yeast,	100.0
3h0g_H	125	DNA-directed RNA polymerases I, II, and III subuni	100.0
4ayb_G	132	DNA-directed RNA polymerase; transferase, multi-su	98.97

>2f3i_A DNA-directed RNA polymerases I, II, and III 17.1 kDa polypeptide; RNA polymerase II, transferase; NMR {Homo sapiens}

Probab=100.00  E-value=1.9e-70  Score=424.00  Aligned_cols=145  Identities=49%  Similarity=0.887  Sum_probs=137.2

Q ss_pred             CCcccceeeeEEEeeeCCCCCccceEeeEEEEecCCceEEEEEecccceecccCCEEEEEEeeecCCCCCCCCCCCCCC-
Q 032138            1 MSNIVLFEDIFVVEKIDPDGKKFDKVSRIEAHSQNCDMYMLLDVNSELYPMRVGDKFTMALAHTLNLDGTPDTGYYTPG-   79 (146)
Q Consensus         1 ms~~~Lfed~F~V~~iD~dgKkfdrVSRi~~~S~~~~~~l~LDiNtelypl~~~d~~~l~LassL~~dg~~d~~~~~~~-   79 (146)
                      || ++||||+|+|++|||+||||||||||.|+|++++|+|+|||||||||+++||+|+|+||+||++||+|+++.|+|. 
T Consensus         1 Ms-~~LfeD~F~V~~iDp~GKkfdrVSRi~~~S~~~~~~l~LDiNtelyP~~~gd~~~l~LastL~~dg~~d~~~~~~~~   79 (150)
T 2f3i_A            1 MA-GILFEDIFDVKDIDPEGKKFDRVSRLHCESESFKMDLILDVNIQIYPVDLGDKFRLVIASTLYEDGTLDDGEYNPTD   79 (150)
T ss_dssp             CC-CCCCEEEEEEEEEECCCCSSTTEEEEEEEESSSCCEEEEEEECTTSSSTTCCCEEEECSCCCCSSSSSTTTCSSSTT
T ss_pred             CC-CceeeeeEEEEEECCCCCeeeeEEEEEEEeCCCceEEEEEecccEeccCCCCEEEEEEecccccCCCCCCCcccccc
Confidence            66 8999999999999999999999999999999999999999999999999999999999999999999999999886 


Q ss_pred             CCccccccccEEEeeEEEEeecCCCCC--cceEEEEEEecceeeEEEcCCCCCCCCCCCCeEEEEEeeC
Q 032138           80 ARKTLADKYEYIMHGKLFKIGDEGSGK--SLKAEIYVSYGGLLMMLKGDPSYVSHFELDQRLFLLMRKL  146 (146)
Q Consensus        80 ~~~slad~ydYVMyGkVYk~e~~~~~~--~~~~~vy~SFGGLLM~L~G~~~~l~~l~~d~~vYLL~rk~  146 (146)
                      ++++|||+|||||||||||||+++++.  .++++||||||||||+|+|++++|++|++|++|||||||+
T Consensus        80 ~~~slad~ydYVM~GkvYk~e~~~~~~~~~~~~~vY~SFGGLLM~L~G~~~~L~~l~~d~~vYLLirk~  148 (150)
T 2f3i_A           80 DRPSRADQFEYVMYGKVYRIEGDETSTEAATRLSAYVSYGGLLMRLQGDANNLHGFEVDSRVYLLMKKL  148 (150)
T ss_dssp             STTSCTTTTSEEECEEEECCSSCCSSSSCCSSEEEEEEETTEEEEEEECHHHHTCCSTTSTTSEEEEEC
T ss_pred             CCcccccccCEEEeeEEEEEeecCCCccccceEEEEEEcceEeEEEEcCHHHCccccCCCEEEEEEEec
Confidence            688999999999999999999864211  2899999999999999999999999999999999999995

>1a1d_A RNA polymerase; RPB8, OB fold, eukaryotic, yeast, nucleotidyltransferase; NMR {Saccharomyces cerevisiae} SCOP: b.40.4.8 PDB: 1i3q_H 1i50_H 1i6h_H 1k83_H* 1nik_H 1nt9_H 1pqv_H 1r5u_H 1r9s_H* 1r9t_H* 1sfo_H* 1twa_H* 1twc_H* 1twf_H* 1twg_H* 1twh_H* 1wcm_H 1y1v_H 1y1w_H 1y1y_H ...

Probab=100.00  E-value=1.1e-65  Score=395.94  Aligned_cols=138  Identities=39%  Similarity=0.732  Sum_probs=132.2

Q ss_pred             CCcccceeeeEEEeeeCCCCCccceEeeEEEEecCCceE-EEEEecccceecccCCEEEEEEeeecCCCCCC-----CCC
Q 032138            1 MSNIVLFEDIFVVEKIDPDGKKFDKVSRIEAHSQNCDMY-MLLDVNSELYPMRVGDKFTMALAHTLNLDGTP-----DTG   74 (146)
Q Consensus         1 ms~~~Lfed~F~V~~iD~dgKkfdrVSRi~~~S~~~~~~-l~LDiNtelypl~~~d~~~l~LassL~~dg~~-----d~~   74 (146)
                      || ++||||+|+|++|||+  ||||||||.|+|++++|+ |+|||||||||+++||+|+|+||+||++||++     +++
T Consensus         1 Ms-~~LfeD~F~V~~iDp~--kfdrVSRi~~~S~~~~~~~l~LDiNtelyPv~~gd~l~l~LastL~~dg~~~~~~~d~~   77 (146)
T 1a1d_A            1 MS-NTLFDDIFQVSEVDPG--RYNKVCRIEAASTTQDQCKLTLDINVELFPVAAQDSLTVTIASSLNLEDTPANDSSATR   77 (146)
T ss_pred             CC-CceeeeeEEEEecChh--HCceeEEEEEEeCCCCceEEEEEecccEeccCCCCEEEEEEecccCcCCCcccccccCc
Confidence            66 8999999999999998  799999999999999999 99999999999999999999999999999999     899


Q ss_pred             CCCC--CCCccccccccEEEeeEEEEeecCCCCCcceEEEEEEecceeeEEEcCCCCCCCCCCCCeEEEEEee
Q 032138           75 YYTP--GARKTLADKYEYIMHGKLFKIGDEGSGKSLKAEIYVSYGGLLMMLKGDPSYVSHFELDQRLFLLMRK  145 (146)
Q Consensus        75 ~~~~--~~~~slad~ydYVMyGkVYk~e~~~~~~~~~~~vy~SFGGLLM~L~G~~~~l~~l~~d~~vYLL~rk  145 (146)
                      .|++  +++++|||+|||||||||||||+ +  ++++++||||||||||+|+|++++|++|++| +|||||||
T Consensus        78 ~~~~~~~~~~slad~ydYVM~GkvYk~e~-~--~~~~~~vy~SFGGLLM~L~G~~~~L~~l~~d-~vYLLirk  146 (146)
T 1a1d_A           78 SWRPPQAGDRSLADDYDYVMYGTAYKFEE-V--SKDLIAVYYSFGGLLMRLEGNYRNLNNLKQE-NAYLLIRR  146 (146)
T ss_pred             cccccccCCcccccccCEEEeeEEEEEee-c--CCceEEEEEEcceEeEEEecCHHHCCcCccC-eEEEEEeC
Confidence            9987  57889999999999999999997 3  3699999999999999999999999999999 99999997

>3h0g_H DNA-directed RNA polymerases I, II, and III subunit rpabc3; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}

Probab=100.00  E-value=1.6e-61  Score=364.57  Aligned_cols=125  Identities=38%  Similarity=0.733  Sum_probs=117.6

Q ss_pred             CCcccceeeeEEEeeeCCCCCccceEeeEEEEecCCceEEEEEecccceecccCCEEEEEEeeecCCCCCCCCCCCCCCC
Q 032138            1 MSNIVLFEDIFVVEKIDPDGKKFDKVSRIEAHSQNCDMYMLLDVNSELYPMRVGDKFTMALAHTLNLDGTPDTGYYTPGA   80 (146)
Q Consensus         1 ms~~~Lfed~F~V~~iD~dgKkfdrVSRi~~~S~~~~~~l~LDiNtelypl~~~d~~~l~LassL~~dg~~d~~~~~~~~   80 (146)
                      ||+++||||+|+|++|||+  ||||||||.|+|++++|+|+|||||||||+++||+|+|+||+||++   ++   |    
T Consensus         1 m~~~~LfeD~F~V~~id~~--kfdrVSRi~~~S~~~~~~l~LDiNtelyP~~~gd~~~l~LassL~~---~d---~----   68 (125)
T 3h0g_H            1 MSESVLLDEIFTVTSVDKQ--KYQRVSRITAVSGQNDMNLTLDINSQIYPLEKDATFSLQITSNLNS---PD---L----   68 (125)
T ss_dssp             -CCCCCCCBCCCCCCEECS--SCSSCCEEECCCSSSCCCBEEECCTTTSCCCSSCCCCEECCCCCCC---SH---H----
T ss_pred             CCCcEEEEeEEEEeeCChh--hCCcEEEEEEEeCCCceEEEEEecceEEecCCCCEEEEEEeccCCc---hh---h----
Confidence            8899999999999999998  7999999999999999999999999999999999999999999996   22   4    


Q ss_pred             CccccccccEEEeeEEEEeecCCCCCcceEEEEEEecceeeEEEcCCCCCCCCCCCCeEEEEEee
Q 032138           81 RKTLADKYEYIMHGKLFKIGDEGSGKSLKAEIYVSYGGLLMMLKGDPSYVSHFELDQRLFLLMRK  145 (146)
Q Consensus        81 ~~slad~ydYVMyGkVYk~e~~~~~~~~~~~vy~SFGGLLM~L~G~~~~l~~l~~d~~vYLL~rk  145 (146)
                          ||+|||||||||||+|++   +++++++|||||||||+|+|++++|++|+ |++|||||||
T Consensus        69 ----ad~ydYVMyGkvYk~e~~---~~~~~~vy~SFGGLLM~L~G~~~~l~~l~-~~~vYLLirk  125 (125)
T 3h0g_H           69 ----KEAADYIMYGKVYRVEEA---KDEKVSVYVSFGGLLMAIEGSHRKLYRLS-LDHVYLLLRR  125 (125)
T ss_dssp             ----HHSSSEEECCCCCCEECC---SSSCEEECCEETTEECCEEECSSSCSCCC-CSCCCEEECC
T ss_pred             ----hccccEEEEeEEEEEeec---CCceEEEEEEecCEEEEEEeCHHHCcccC-CCEEEEEEeC
Confidence                899999999999999863   57999999999999999999999999999 9999999997

>4ayb_G DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2wb1_G 2y0s_G 2waq_G 4b1o_G 4b1p_V 3hkz_G

Probab=98.97  E-value=1.1e-10  Score=88.26  Aligned_cols=113  Identities=12%  Similarity=0.256  Sum_probs=79.4

Q ss_pred             EEeeeCCCCCccceEeeEEEEecCCceEEEEEecccceecccCCEEEEEEeeecCCCCCCCCCCCCCCCCccccccccEE
Q 032138           12 VVEKIDPDGKKFDKVSRIEAHSQNCDMYMLLDVNSELYPMRVGDKFTMALAHTLNLDGTPDTGYYTPGARKTLADKYEYI   91 (146)
Q Consensus        12 ~V~~iD~dgKkfdrVSRi~~~S~~~~~~l~LDiNtelypl~~~d~~~l~LassL~~dg~~d~~~~~~~~~~slad~ydYV   91 (146)
                      +|++|.| | +.-.+.|+.+++.+  .++++|+|.+|.++.+||++++.|..+.-                ...+. |++
T Consensus        14 kI~sIek-g-~l~~l~i~~~~C~d--~~I~~Di~~~i~~f~~gekV~i~ISrekp----------------~~~~~-dFC   72 (132)
T 4ayb_G           14 EINSIER-G-SLKNLSIIHMSCND--FNISFDIIDSINIFSQKEKVKAFISKNRL----------------SYTND-DFC   72 (132)
T ss_dssp             CCCCEEE-C-SSTTEEEEECCBSS--EEEEEEEESTTCCCCSSCCCEEEEESSCC----------------CCCTT-SEE
T ss_pred             EEeeEcc-c-ccCCeEEEEEecCC--EEEEEEhhhhhhcccCCCeEEEEEecCCc----------------ccccC-ccc
Confidence            4778888 4 48889999998855  99999999999999999999999987642                33343 788


Q ss_pred             EeeEEEEeecCC-CCCcceEEEEEEecceeeEEEcCCCCC---CCCCCCCeEEEEEee
Q 032138           92 MHGKLFKIGDEG-SGKSLKAEIYVSYGGLLMMLKGDPSYV---SHFELDQRLFLLMRK  145 (146)
Q Consensus        92 MyGkVYk~e~~~-~~~~~~~~vy~SFGGLLM~L~G~~~~l---~~l~~d~~vYLL~rk  145 (146)
                      =||-|......+ +..+++..+.+|+||||..|.-+.+.+   .+|++.+++|+.+||
T Consensus        73 GhGYvVt~~k~~~~~~~~~~~~iISl~GlLvvi~s~k~~f~~~~~lk~MdkvY~cv~K  130 (132)
T 4ayb_G           73 GHGYIVTELKDSSSNNGNRYITIISLFGLLVKIISNKESFLKIHQLNVMDHIYFCVKK  130 (132)
T ss_dssp             BCEEEEETTTTEEEETTEEEEEEESCCHHHHHHSCSSEEEEEEEC-------------
T ss_pred             cceEEEEEeecccccCCceeEEEEEeeeEEEEEEccccccccccCCccccEEEEEEEc
Confidence            899998764332 124678999999999999999987633   568988999999997

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Length	Definition	E-value
Query	146
d1twfh_	145	b.40.4.8 (H:) RNA polymerase subunit RBP8 {Baker's	3e-59

>d1twfh_ b.40.4.8 (H:) RNA polymerase subunit RBP8 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 145

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: RNA polymerase subunit RBP8
domain: RNA polymerase subunit RBP8
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score =  177 bits (452), Expect = 3e-59
 Identities = 50/149 (33%), Positives = 84/149 (56%), Gaps = 14/149 (9%)

Query: 5   VLFEDIFVVEKIDPDGKKFDKVSRIEAHSQNCD-MYMLLDVNSELYPMRVGDKFTMALAH 63
            LF+DIF V ++DP   +++KV RIEA S   D   + LD+N EL+P+   D  T+ +A 
Sbjct: 3   TLFDDIFQVSEVDP--GRYNKVCRIEAASTTQDQCKLTLDINVELFPVAAQDSLTVTIAS 60

Query: 64  TLNLDGTPDTGYYTPGA-------RKTLADKYEYIMHGKLFKIGDEGSGKSLKAEIYVSY 116
           +LNL+ TP        +        ++LAD Y+Y+M+G  +K  +          +Y S+
Sbjct: 61  SLNLEDTPANDSSATRSWRPPQAGDRSLADDYDYVMYGTAYKFEEVSKD---LIAVYYSF 117

Query: 117 GGLLMMLKGDPSYVSHFELDQRLFLLMRK 145
           GGLLM L+G+   +++ + +   +LL+R+
Sbjct: 118 GGLLMRLEGNYRNLNNLKQE-NAYLLIRR 145

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	146
d1twfh_	145	RNA polymerase subunit RBP8 {Baker's yeast (Saccha	100.0

>d1twfh_ b.40.4.8 (H:) RNA polymerase subunit RBP8 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: RNA polymerase subunit RBP8
domain: RNA polymerase subunit RBP8
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=100.00  E-value=3.3e-65  Score=391.11  Aligned_cols=137  Identities=36%  Similarity=0.688  Sum_probs=119.4

Q ss_pred             cccceeeeEEEeeeCCCCCccceEeeEEEEecCC-ceEEEEEecccceecccCCEEEEEEeeecCCCCCCCC-----CCC
Q 032138            3 NIVLFEDIFVVEKIDPDGKKFDKVSRIEAHSQNC-DMYMLLDVNSELYPMRVGDKFTMALAHTLNLDGTPDT-----GYY   76 (146)
Q Consensus         3 ~~~Lfed~F~V~~iD~dgKkfdrVSRi~~~S~~~-~~~l~LDiNtelypl~~~d~~~l~LassL~~dg~~d~-----~~~   76 (146)
                      |++||||+|+|++|||  |||||||||+|+|+++ +|+|+|||||||||+++||+|+|+||+||++||+|++     +.|
T Consensus         1 s~~LFED~F~V~~vd~--kKfdrVSRi~~~S~~~~~~~l~LDINtelyPv~~gd~~~l~LastL~ldg~~~~~~~~~~~~   78 (145)
T d1twfh_           1 SNTLFDDIFQVSEVDP--GRYNKVCRIEAASTTQDQCKLTLDINVELFPVAAQDSLTVTIASSLNLEDTPANDSSATRSW   78 (145)
T ss_dssp             CCCCCEEEEEEEEEEC--TTCSSEEEEEEEESSCSSCEEEEEEEGGGSCCCTTCEEEEECCCCC------------CCCC
T ss_pred             CCcceeEEEEEEecCC--CccceEEEEEEEeCCCCceEEEEEeccceeeccCCCEEEEEEeceeccCCCccccccccccc
Confidence            4789999999999999  6899999999999987 6999999999999999999999999999999998764     356


Q ss_pred             C--CCCCccccccccEEEeeEEEEeecCCCCCcceEEEEEEecceeeEEEcCCCCCCCCCCCCeEEEEEee
Q 032138           77 T--PGARKTLADKYEYIMHGKLFKIGDEGSGKSLKAEIYVSYGGLLMMLKGDPSYVSHFELDQRLFLLMRK  145 (146)
Q Consensus        77 ~--~~~~~slad~ydYVMyGkVYk~e~~~~~~~~~~~vy~SFGGLLM~L~G~~~~l~~l~~d~~vYLL~rk  145 (146)
                      +  +.+++||||+|||||||||||||++   ++++++||||||||||+|+|++++|++|++| +|||||||
T Consensus        79 ~~~~~~~~slad~yeYVM~GkvYk~ee~---~~~~~~vy~SFGGLLM~L~G~~~~L~~l~~d-~vYLLirK  145 (145)
T d1twfh_          79 RPPQAGDRSLADDYDYVMYGTAYKFEEV---SKDLIAVYYSFGGLLMRLEGNYRNLNNLKQE-NAYLLIRR  145 (145)
T ss_dssp             CCSSTTTSSCCCCSSEEEEEEECCCCCC---CTTCEEEEEEETTEEEEEEESTTTTTSCSSS-CEEEEEEC
T ss_pred             ccccCCccchhhcCCEEeeeEEEEeeec---CCCcEEEEEEecceeEEEecCHHHccccccc-eEEEEEcC
Confidence            4  4578999999999999999999864   4678999999999999999999999999975 99999998