Citrus Sinensis ID: 032941

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130
Protein Sequence
MSNIVLFEDIFVVEKIDPDGKKFDKVSRIEAHSQNCDMYMLLDVNSELYPMRVGDKFTMALAHTLNLDGTPDTGYYTPGARKTLADKYEYIMHGKLFKIGDEGSGKSLKAYETTTQSIHYYFIWACVIHL
Secondary Structure (PSIPRED)
cccccEEEEEEEEEEEccccccccEEEEEEEEEccccEEEEEEccccEEEcccccEEEEEEEEccccccccccccccccccccccccccEEEEcEEEEEEEcccccEEEEEEEEccEEEEHHHHHHHHcc
Secondary Structure Prediction (SSPRO)
ccccEEHHcEEEEEEccccccEEcEEEEEEEEEccccEEEEEEEccEccccccccEEEEEEEccccccccccccccccccccccccccEEEEEEEEEEEEcccccccEEEEEEcHEEEEEEEEEHHHEcc
Coil and Loop (DISEMBL)
MSNIVLFEDIFVVekidpdgkkfdkVSRIEAHsqncdmymlldvnselypmrvgdkFTMALAHTLnldgtpdtgyytpgarkTLADKYEYIMHGKlfkigdegsgkslkaYETTTQSIHYYFIWACVIHL
Flexible Loop (DISEMBL)
msnivlfedifvvekidpdgkkfdKVSRIEAhsqncdmyMLLDVNSELYPMRVGDKFTMALAHTLnldgtpdtgyyTPGARKTLADKYEYIMHGKLfkigdegsgkSLKAYETTTQSIHYYFIWACVIHL
Low Complexity Region (SEG)
MSNIVLFEDIFVVEKIDPDGKKFDKVSRIEAHSQNCDMYMLLDVNSELYPMRVGDKFTMALAHTLNLDGTPDTGYYTPGARKTLADKYEYIMHGKLFKIGDEGSGKSLKAYETTTQSIHYYFIWACVIHL
Disordered region (IsUnstruct)
***IVLFEDIFVVEKIDPDGKKFDKVSRIEAHSQNCDMYMLLDVNSELYPMRVGDKFTMALAHTLNLDGTPDTGYYTPGARKTLADKYEYIMHGKLFKIGDEGSGKSLKAYETTTQSIHYYFIWACVIH*
Disordered Region (DISOPRED)
**NIVLFEDIFVVEKIDPDGKKFDKVSRIEAHSQNCDMYMLLDVNSELYPMRVGDKFTMALAHTL****************KTLADKYEYIMHGKLFKIGDEGSGKSLKAYETTTQSIHYYFIWACVIHL
Disordered Region (DISEMBL)
MSNIVLFEDIFVVEKIDPDGKKFDKVSRIEAHSQNCDMYMLLDVNSELYPMRVGDKFTMALAHTLNLDGTPDTGYYTPGARKTLADKYEYIMHGKLFKIGDEGSGKSLKAYETTTQSIHYYFIWACVIHL
Disordered Region (DISPRO)
**NIVLFEDIFVVEKIDPDGKKFDKVSRIEAHSQNCDMYMLLDVNSELYPMRVGDKFTMALAHTLNLD***DTGYYTPGARKTLADKYEYIMHGKLFKIGDEGSGKSLKAYETTTQSIHYYFIWACVIHL
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MSNIVLFEDIFVVEKIDPDGKKFDKVSRIEAHSQNCDMYMLLDVNSELYPMRVGDKFTMALAHTLNLDGTPDTGYYTPGARKTLADKYEYIMHGKLFKIGDEGSGKSLKAYETTTQSIHYYFIWACVIHL
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	130	2.2.26 [Sep-21-2011]
Q923G2	150	DNA-directed RNA polymera	yes	no	0.823	0.713	0.5	2e-23
P52434	150	DNA-directed RNA polymera	yes	no	0.823	0.713	0.5	2e-23
A8XT81	148	Probable DNA-directed RNA	N/A	no	0.776	0.682	0.435	1e-21
Q54YW8	142	DNA-directed RNA polymera	yes	no	0.830	0.760	0.431	1e-20
Q19826	148	Probable DNA-directed RNA	yes	no	0.776	0.682	0.415	2e-20
P20436	146	DNA-directed RNA polymera	yes	no	0.730	0.650	0.415	3e-13
Q92399	125	DNA-directed RNA polymera	yes	no	0.723	0.752	0.324	2e-09

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

 Score =  107 bits (267), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 56/112 (50%), Positives = 81/112 (72%), Gaps = 5/112 (4%)

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

Query: 65  LNLDGTPDTGYYTP-GARKTLADKYEYIMHGKLFKI-GDEGSGKS---LKAY 111
           L  DGT D G Y P   R + AD++EY+M+GK+++I GDE S ++   L AY
Sbjct: 64  LYEDGTLDDGEYNPTDDRPSRADQFEYVMYGKVYRIEGDETSTEAATRLSAY 115

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 =  107 bits (267), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 56/112 (50%), Positives = 81/112 (72%), Gaps = 5/112 (4%)

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

Query: 65  LNLDGTPDTGYYTP-GARKTLADKYEYIMHGKLFKI-GDEGSGKS---LKAY 111
           L  DGT D G Y P   R + AD++EY+M+GK+++I GDE S ++   L AY
Sbjct: 64  LYEDGTLDDGEYNPTDDRPSRADQFEYVMYGKVYRIEGDETSTEAATRLSAY 115

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|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 =  101 bits (252), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 44/101 (43%), Positives = 71/101 (70%)

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

Query: 65  LNLDGTPDTGYYTPGARKTLADKYEYIMHGKLFKIGDEGSG 105
           L  DG  D G Y P A      +YEY+M+GK++++ D+ SG
Sbjct: 64  LREDGLADEGEYDPKAEYPRIKQYEYVMYGKVYRLEDDDSG 104

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

 Score = 98.2 bits (243), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 47/109 (43%), Positives = 73/109 (66%), Gaps = 1/109 (0%)

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

Query: 65  LNLDGTPDTGYYTPGARKTLADKYEYIMHGKLFKIGDEGSGKSLKAYET 113
           LNLDG+ D        + +LADKY+Y+M+GK+FK   E S   +  + +
Sbjct: 63  LNLDGSSDNSGSYDTNKPSLADKYDYVMYGKIFKYQKENSSSKVSVFAS 111

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|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 = 97.4 bits (241), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 42/101 (41%), Positives = 70/101 (69%)

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

Query: 65  LNLDGTPDTGYYTPGARKTLADKYEYIMHGKLFKIGDEGSG 105
           L  DG  D G Y P A      +YEY+M+GK++++ D+ +G
Sbjct: 64  LREDGLADEGEYDPKAEYPRIKQYEYVMYGKVYRLEDDDTG 104

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 = 73.9 bits (180), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 44/106 (41%), Positives = 64/106 (60%), Gaps = 11/106 (10%)

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--GARKTLADKYEYIMHGKLFK 98
            +A +LNL+ TP      T  + P     ++LAD Y+Y+M+G  +K
Sbjct: 58  TIASSLNLEDTPANDSSATRSWRPPQAGDRSLADDYDYVMYGTAYK 103

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 = 61.2 bits (147), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 36/111 (32%), Positives = 61/111 (54%), Gaps = 17/111 (15%)

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  LAHTLNLDGTPDTGYYTPGARKTLADKYEYIMHGKLFKIGDEGSGKSLKAY 111
           +   LN   +PD           L +  +YIM+GK++++ +E   + +  Y
Sbjct: 59  ITSNLN---SPD-----------LKEAADYIMYGKVYRV-EEAKDEKVSVY 94

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	130
255578910	146	DNA-directed RNA polymerases I, II, and	0.846	0.753	0.872	8e-51
224135363	148	predicted protein [Populus trichocarpa]	0.838	0.736	0.770	2e-45
15231714	146	RNA polymerase Rpb8 [Arabidopsis thalian	0.830	0.739	0.743	2e-41
297847838	146	ATRPABC16.5 [Arabidopsis lyrata subsp. l	0.830	0.739	0.752	3e-41
15221759	146	RNA polymerase Rpb8 [Arabidopsis thalian	0.830	0.739	0.743	5e-41
192910796	145	RNA polymerase [Elaeis guineensis]	0.815	0.731	0.698	3e-38
53793231	396	putative RNA polymerase I, II and III 16	0.8	0.262	0.695	3e-38
225434042	145	PREDICTED: DNA-directed RNA polymerases	0.807	0.724	0.704	1e-37
116792470	145	unknown [Picea sitchensis]	0.815	0.731	0.679	5e-37
125556620	191	hypothetical protein OsI_24321 [Oryza sa	0.8	0.544	0.695	8e-37

>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 =  204 bits (520), Expect = 8e-51,   Method: Compositional matrix adjust.
 Identities = 96/110 (87%), Positives = 106/110 (96%)

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

Query: 61  LAHTLNLDGTPDTGYYTPGARKTLADKYEYIMHGKLFKIGDEGSGKSLKA 110
           LAHTLNLDGTPDTGYYT GARKTLADKYEYIM+GKL+KI +EGSGK++KA
Sbjct: 61  LAHTLNLDGTPDTGYYTQGARKTLADKYEYIMNGKLYKISEEGSGKAVKA 110

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 =  187 bits (474), Expect = 2e-45,   Method: Compositional matrix adjust.
 Identities = 84/109 (77%), Positives = 100/109 (91%)

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

Query: 62  AHTLNLDGTPDTGYYTPGARKTLADKYEYIMHGKLFKIGDEGSGKSLKA 110
           AHTLNLDGTPDTGYYT G RKTLADKYEY+MHGKL++I +EGS ++ + 
Sbjct: 64  AHTLNLDGTPDTGYYTQGGRKTLADKYEYVMHGKLYQIQEEGSRRATRT 112

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

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 =  173 bits (438), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 81/109 (74%), Positives = 98/109 (89%), Gaps = 1/109 (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  AHTLNLDGTPDTGYYTPGARKTLADKYEYIMHGKLFKIGDEGSGKSLKA 110
           A TLNLDGTPDTGY+TPGA+KTLADKYEYIMHGKL+KI  E  GK+ KA
Sbjct: 63  APTLNLDGTPDTGYFTPGAKKTLADKYEYIMHGKLYKIS-ERDGKTPKA 110

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

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 =  173 bits (438), Expect = 3e-41,   Method: Compositional matrix adjust.
 Identities = 82/109 (75%), Positives = 98/109 (89%), Gaps = 1/109 (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  AHTLNLDGTPDTGYYTPGARKTLADKYEYIMHGKLFKIGDEGSGKSLKA 110
           A TLNLDGTPDTGY+TPGA+KTLADKYEYIMHGKL+KI  E  GK+ KA
Sbjct: 63  APTLNLDGTPDTGYFTPGAKKTLADKYEYIMHGKLYKIS-ERDGKTPKA 110

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 =  172 bits (435), Expect = 5e-41,   Method: Compositional matrix adjust.
 Identities = 81/109 (74%), Positives = 98/109 (89%), Gaps = 1/109 (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  AHTLNLDGTPDTGYYTPGARKTLADKYEYIMHGKLFKIGDEGSGKSLKA 110
           A TLNLDGTPDTGY+TPGA+KTLADKYEYIMHGKL+KI  E  GK+ KA
Sbjct: 63  APTLNLDGTPDTGYFTPGAKKTLADKYEYIMHGKLYKIS-ERDGKTPKA 110

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 =  162 bits (411), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 74/106 (69%), Positives = 90/106 (84%)

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

Query: 65  LNLDGTPDTGYYTPGARKTLADKYEYIMHGKLFKIGDEGSGKSLKA 110
           L+LDGTPD+GYY  G RK+LADK+EY+MHGKL+KI +E SG ++K 
Sbjct: 64  LSLDGTPDSGYYMQGQRKSLADKFEYVMHGKLYKISEESSGPNVKV 109

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 =  162 bits (411), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 73/105 (69%), Positives = 87/105 (82%), Gaps = 1/105 (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-DEGSGKSLK 109
           NLDGTPDTG+YT   RKTLADK++Y+MHGKL+KI  D  SG++ K
Sbjct: 315 NLDGTPDTGFYTQAGRKTLADKFDYVMHGKLYKISEDSSSGQATK 359

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

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 =  160 bits (406), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 74/105 (70%), Positives = 88/105 (83%)

Query: 6   LFEDIFVVEKIDPDGKKFDKVSRIEAHSQNCDMYMLLDVNSELYPMRVGDKFTMALAHTL 65
           LF DIF V +IDPDGKKFDKVSRIEA S+  DMYM LDVN+E+YPM  G+KF M+LA TL
Sbjct: 5   LFGDIFKVIQIDPDGKKFDKVSRIEAQSEQLDMYMQLDVNTEIYPMHAGEKFAMSLASTL 64

Query: 66  NLDGTPDTGYYTPGARKTLADKYEYIMHGKLFKIGDEGSGKSLKA 110
           +LDGTPDTGYYT   RK+LADK+EY+MHGKL+KI +EGSG ++K 
Sbjct: 65  DLDGTPDTGYYTQAGRKSLADKFEYVMHGKLYKISEEGSGPNVKG 109

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  159 bits (401), Expect = 5e-37,   Method: Compositional matrix adjust.
 Identities = 72/106 (67%), Positives = 89/106 (83%)

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

Query: 65  LNLDGTPDTGYYTPGARKTLADKYEYIMHGKLFKIGDEGSGKSLKA 110
           LNLDGTPD GY+  G RK+LADKYEY+M+GKL+ + +EGSG ++K 
Sbjct: 64  LNLDGTPDNGYFIQGGRKSLADKYEYVMYGKLYNLSEEGSGANVKV 109

Source: Picea sitchensis

Species: Picea sitchensis

Genus: Picea

Family: Pinaceae

Order: Coniferales

Class: Coniferopsida

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 =  158 bits (399), Expect = 8e-37,   Method: Compositional matrix adjust.
 Identities = 73/105 (69%), Positives = 87/105 (82%), Gaps = 1/105 (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-DEGSGKSLK 109
           NLDGTPDTG+YT   RKTLADK++Y+MHGKL+KI  D  SG++ K
Sbjct: 110 NLDGTPDTGFYTQAGRKTLADKFDYVMHGKLYKISEDSSSGQATK 154

Source: Oryza sativa Indica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

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	130
TAIR|locus:2097468	146	NRPB8B "AT3G59600" [Arabidopsi	0.830	0.739	0.743	1.7e-41
TAIR|locus:2020188	146	NRPB8A "AT1G54250" [Arabidopsi	0.830	0.739	0.743	5.9e-41
FB|FBgn0037121	149	Rpb8 "Rpb8" [Drosophila melano	0.823	0.718	0.522	1.1e-25
ZFIN|ZDB-GENE-050417-66	150	zgc:110289 "zgc:110289" [Danio	0.823	0.713	0.508	3.6e-25
UNIPROTKB|E1BSD8	150	POLR2H "Uncharacterized protei	0.823	0.713	0.5	5.3e-24
UNIPROTKB|F2Z4H3	150	POLR2H "Uncharacterized protei	0.823	0.713	0.5	5.3e-24
UNIPROTKB|C9JLU1	149	POLR2H "DNA-directed RNA polym	0.823	0.718	0.5	5.3e-24
UNIPROTKB|P52434	150	POLR2H "DNA-directed RNA polym	0.823	0.713	0.5	5.3e-24
UNIPROTKB|I3LCB2	150	POLR2H "Uncharacterized protei	0.823	0.713	0.5	5.3e-24
MGI|MGI:2384309	150	Polr2h "polymerase (RNA) II (D	0.823	0.713	0.5	5.3e-24

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

 Score = 440 (159.9 bits), Expect = 1.7e-41, P = 1.7e-41
 Identities = 81/109 (74%), Positives = 98/109 (89%)

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 AHTLNLDGTPDTGYYTPGARKTLADKYEYIMHGKLFKIGDEGSGKSLKA 110
             A TLNLDGTPDTGY+TPGA+KTLADKYEYIMHGKL+KI  E  GK+ KA
Sbjct:    63 APTLNLDGTPDTGYFTPGAKKTLADKYEYIMHGKLYKIS-ERDGKTPKA 110

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 = 435 (158.2 bits), Expect = 5.9e-41, P = 5.9e-41
 Identities = 81/109 (74%), Positives = 98/109 (89%)

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

Query:    62 AHTLNLDGTPDTGYYTPGARKTLADKYEYIMHGKLFKIGDEGSGKSLKA 110
             A TLNLDGTPDTGY+TPGA+KTLADKYEYIMHGKL+KI  E  GK+ KA
Sbjct:    63 APTLNLDGTPDTGYFTPGAKKTLADKYEYIMHGKLYKIS-ERDGKTPKA 110

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 = 291 (107.5 bits), Expect = 1.1e-25, P = 1.1e-25
 Identities = 58/111 (52%), Positives = 80/111 (72%)

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-GDEGSGKS--LKAY 111
             L  DG PD+G Y P   + T AD +EY+M+GK+++I GDE   ++  L AY
Sbjct:    64 LREDGCPDSGEYNPMEHEGTRADSFEYVMYGKIYRIEGDEAHNEASRLSAY 114

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 = 286 (105.7 bits), Expect = 3.6e-25, P = 3.6e-25
 Identities = 57/112 (50%), Positives = 82/112 (73%)

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

Query:    65 LNLDGTPDTGYYTP-GARKTLADKYEYIMHGKLFKI-GDEGSGKS---LKAY 111
             L  DGTPD G Y P   R + AD+++Y+M+GK+++I GDE S ++   L AY
Sbjct:    64 LYEDGTPDDGEYNPQDDRPSRADQFDYVMYGKVYRIEGDETSTEAATRLSAY 115

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

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

 Score = 275 (101.9 bits), Expect = 5.3e-24, P = 5.3e-24
 Identities = 56/112 (50%), Positives = 81/112 (72%)

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

Query:    65 LNLDGTPDTGYYTP-GARKTLADKYEYIMHGKLFKI-GDEGSGKS---LKAY 111
             L  DGT D G Y P   R + AD++EY+M+GK+++I GDE S ++   L AY
Sbjct:    64 LYEDGTLDDGEYNPTDDRPSRADQFEYVMYGKVYRIEGDETSTEAATRLSAY 115

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 = 275 (101.9 bits), Expect = 5.3e-24, P = 5.3e-24
 Identities = 56/112 (50%), Positives = 81/112 (72%)

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

Query:    65 LNLDGTPDTGYYTP-GARKTLADKYEYIMHGKLFKI-GDEGSGKS---LKAY 111
             L  DGT D G Y P   R + AD++EY+M+GK+++I GDE S ++   L AY
Sbjct:    64 LYEDGTLDDGEYNPTDDRPSRADQFEYVMYGKVYRIEGDETSTEAATRLSAY 115

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 = 275 (101.9 bits), Expect = 5.3e-24, P = 5.3e-24
 Identities = 56/112 (50%), Positives = 81/112 (72%)

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

Query:    65 LNLDGTPDTGYYTP-GARKTLADKYEYIMHGKLFKI-GDEGSGKS---LKAY 111
             L  DGT D G Y P   R + AD++EY+M+GK+++I GDE S ++   L AY
Sbjct:    64 LYEDGTLDDGEYNPTDDRPSRADQFEYVMYGKVYRIEGDETSTEAATRLSAY 115

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 = 275 (101.9 bits), Expect = 5.3e-24, P = 5.3e-24
 Identities = 56/112 (50%), Positives = 81/112 (72%)

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

Query:    65 LNLDGTPDTGYYTP-GARKTLADKYEYIMHGKLFKI-GDEGSGKS---LKAY 111
             L  DGT D G Y P   R + AD++EY+M+GK+++I GDE S ++   L AY
Sbjct:    64 LYEDGTLDDGEYNPTDDRPSRADQFEYVMYGKVYRIEGDETSTEAATRLSAY 115

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 = 275 (101.9 bits), Expect = 5.3e-24, P = 5.3e-24
 Identities = 56/112 (50%), Positives = 81/112 (72%)

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

Query:    65 LNLDGTPDTGYYTP-GARKTLADKYEYIMHGKLFKI-GDEGSGKS---LKAY 111
             L  DGT D G Y P   R + AD++EY+M+GK+++I GDE S ++   L AY
Sbjct:    64 LYEDGTLDDGEYNPTDDRPSRADQFEYVMYGKVYRIEGDETSTEAATRLSAY 115

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 = 275 (101.9 bits), Expect = 5.3e-24, P = 5.3e-24
 Identities = 56/112 (50%), Positives = 81/112 (72%)

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

Query:    65 LNLDGTPDTGYYTP-GARKTLADKYEYIMHGKLFKI-GDEGSGKS---LKAY 111
             L  DGT D G Y P   R + AD++EY+M+GK+++I GDE S ++   L AY
Sbjct:    64 LYEDGTLDDGEYNPTDDRPSRADQFEYVMYGKVYRIEGDETSTEAATRLSAY 115

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

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

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

Fail to connect to STRING server

---

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	130
smart00658	143	smart00658, RPOL8c, RNA polymerase subunit 8	2e-44
pfam03870	137	pfam03870, RNA_pol_Rpb8, RNA polymerase Rpb8	1e-43
PTZ00167	144	PTZ00167, PTZ00167, RNA polymerase subunit 8c; Pro	5e-19

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

 Score =  141 bits (358), Expect = 2e-44
 Identities = 61/107 (57%), Positives = 82/107 (76%), Gaps = 1/107 (0%)

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

Query: 63  HTLNLDGTPDTGYYTPGA-RKTLADKYEYIMHGKLFKIGDEGSGKSL 108
            TLN DGTPD+G   P A  K+LADKYEY+M+GK+++I ++ +  S 
Sbjct: 61  STLNEDGTPDSGENNPIALIKSLADKYEYVMYGKVYRIEEDKTETSK 107

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

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

 Score =  139 bits (351), Expect = 1e-43
 Identities = 57/105 (54%), Positives = 78/105 (74%), Gaps = 1/105 (0%)

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

Query: 68  DGTPDTGYYTP-GARKTLADKYEYIMHGKLFKIGDEGSGKSLKAY 111
           DGT D G Y P G R +LADKYEY+M+GK+++I +      L AY
Sbjct: 61  DGTADDGSYNPAGDRFSLADKYEYVMYGKVYRIEETSIKTKLSAY 105

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 = 76.7 bits (189), Expect = 5e-19
 Identities = 40/104 (38%), Positives = 63/104 (60%), Gaps = 4/104 (3%)

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  LAHTLNLDGTPDTGYYTPGARKTLADKYEYIMHGKLFKIGDEGS 104
           +  T  L   PD   +     ++L D+YEY+M+GK+FK  ++ S
Sbjct: 58  IGLTNQLSSGPDDNVWESSEPQSLMDQYEYVMYGKIFKFEEKSS 101

Length = 144

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	130
smart00658	143	RPOL8c RNA polymerase subunit 8. subunit of RNA po	100.0
KOG3400	143	consensus RNA polymerase subunit 8 [Transcription]	100.0
PF03870	138	RNA_pol_Rpb8: RNA polymerase Rpb8; InterPro: IPR00	100.0
PTZ00167	144	RNA polymerase subunit 8c; Provisional	100.0
PRK14980	127	DNA-directed RNA polymerase subunit G; Provisional	97.48
PF08530	218	PepX_C: X-Pro dipeptidyl-peptidase C-terminal non-	82.43

>smart00658 RPOL8c RNA polymerase subunit 8

Probab=100.00  E-value=4.5e-53  Score=321.42  Aligned_cols=117  Identities=52%  Similarity=0.847  Sum_probs=107.0

Q ss_pred             ccceeeeEEeeeECCCCCccceEeeEEEEecCCceEEEEEecccccccccCCEEEEEEeeecCCCCCCCCCccCCC-CCC
Q 032941            4 IVLFEDIFVVEKIDPDGKKFDKVSRIEAHSQNCDMYMLLDVNSELYPMRVGDKFTMALAHTLNLDGTPDTGYYTPG-ARK   82 (130)
Q Consensus         4 ~~LFeD~F~V~~iD~dGKkFDrVSRI~a~S~~~~m~l~LDINteLyPl~~gdk~~l~LastL~~dg~~~~~~~~~~-~~~   82 (130)
                      .+||||+|+|++|||+||||||||||.|+|++++|+|+|||||||||+++||+|+|+||+||++||+++++.+++. +.+
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            5799999999999999999999999999999999999999999999999999999999999999999997766554 346


Q ss_pred             CcccccceEEeeeEEEeeecCCC-CeEEEEEecCcceee
Q 032941           83 TLADKYEYIMHGKLFKIGDEGSG-KSLKAYETTTQSIHY  120 (130)
Q Consensus        83 sLaD~ydYVMyGKVYk~e~e~~~-~~~~vYiS~~~~~~~  120 (130)
                      +|||+|||||||||||+|+++++ ++++|||||||+++.
T Consensus        82 ~Lad~ydYVM~GkvYk~e~~~~~~~~~~vy~SFGGLLm~  120 (143)
T smart00658       82 SLADKYEYVMYGKVYRIEEDKTETEKLSVYVSFGGLLMR  120 (143)
T ss_pred             chhhcCCEEeeeEEEEEEecCCCceEEEEEEEeccEeEE
Confidence            79999999999999999975543 499999999999873

subunit of RNA polymerase I, II and III

>KOG3400 consensus RNA polymerase subunit 8 [Transcription]

Probab=100.00  E-value=8.2e-53  Score=317.15  Aligned_cols=118  Identities=52%  Similarity=0.902  Sum_probs=111.2

Q ss_pred             CCcccceeeeEEeeeECCCCCccceEeeEEEEecCCceEEEEEecccccccccCCEEEEEEeeecCCCCCCCCCccCCCC
Q 032941            1 MSNIVLFEDIFVVEKIDPDGKKFDKVSRIEAHSQNCDMYMLLDVNSELYPMRVGDKFTMALAHTLNLDGTPDTGYYTPGA   80 (130)
Q Consensus         1 ms~~~LFeD~F~V~~iD~dGKkFDrVSRI~a~S~~~~m~l~LDINteLyPl~~gdk~~l~LastL~~dg~~~~~~~~~~~   80 (130)
                      |+ ++||||||+|++|||||||||||||+.|.|++++|+|+||||++|||++.||+|+|+||+||++||+|++|||+|.+
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 69999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             CCCcccccceEEeeeEEEeeecC-CCCeEEEEEecCccee
Q 032941           81 RKTLADKYEYIMHGKLFKIGDEG-SGKSLKAYETTTQSIH  119 (130)
Q Consensus        81 ~~sLaD~ydYVMyGKVYk~e~e~-~~~~~~vYiS~~~~~~  119 (130)
                      ..+|||+|||||||||||+|.++ ..+..++|+||+++..
T Consensus        80 ~~~~ad~~eYvMyGkvYriE~~e~~~~~~~~YvSFGGLLM  119 (143)
T KOG3400|consen   80 KKPLADEYEYVMYGKVYRIEYDEGKTEKASAYVSFGGLLM  119 (143)
T ss_pred             cccccceeeEEEeeEEEEEeccCCccceeeEEEeeceEEE
Confidence            77799999999999999999543 5788899999999864

>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=3.7e-52  Score=314.81  Aligned_cols=112  Identities=53%  Similarity=0.910  Sum_probs=99.6

Q ss_pred             eeeEEeeeECCCCCccceEeeEEEEecCCceEEEEEecccccccccCCEEEEEEeeecCCCCCCCCC-ccCCCCCCCccc
Q 032941            8 EDIFVVEKIDPDGKKFDKVSRIEAHSQNCDMYMLLDVNSELYPMRVGDKFTMALAHTLNLDGTPDTG-YYTPGARKTLAD   86 (130)
Q Consensus         8 eD~F~V~~iD~dGKkFDrVSRI~a~S~~~~m~l~LDINteLyPl~~gdk~~l~LastL~~dg~~~~~-~~~~~~~~sLaD   86 (130)
                      ||+|+|+++|||||||||||||.|+|++++|+|+|||||||||+++||+|+|+||+||++||+++++ |++..+++||||
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            7999999999999999999999999999999999999999999999999999999999999999876 666557789999


Q ss_pred             ccceEEeeeEEEeeecC-CCCeEEEEEecCccee
Q 032941           87 KYEYIMHGKLFKIGDEG-SGKSLKAYETTTQSIH  119 (130)
Q Consensus        87 ~ydYVMyGKVYk~e~e~-~~~~~~vYiS~~~~~~  119 (130)
                      +|||||||||||+|+.+ .+++++|||||||+++
T Consensus        81 ~ydYVMyGkvYk~ee~~~~~~~~~vY~SFGGLLM  114 (138)
T PF03870_consen   81 DYDYVMYGKVYKFEEGSGGSDKVKVYASFGGLLM  114 (138)
T ss_dssp             SSSEEEEEEEEEEEESSS-TSCEEEEEEETTEEE
T ss_pred             heeeEeeeEEEeeeccCCCCceEEEEEEecceeE
Confidence            99999999999999643 4799999999999986

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=2.2e-50  Score=307.00  Aligned_cols=114  Identities=34%  Similarity=0.614  Sum_probs=103.7

Q ss_pred             CCcccceeeeEEeeeECCCCCccceEeeEEEEecCCceEEEEEecccccccccCCEEEEEEeeecCCCCCCCCC-ccCCC
Q 032941            1 MSNIVLFEDIFVVEKIDPDGKKFDKVSRIEAHSQNCDMYMLLDVNSELYPMRVGDKFTMALAHTLNLDGTPDTG-YYTPG   79 (130)
Q Consensus         1 ms~~~LFeD~F~V~~iD~dGKkFDrVSRI~a~S~~~~m~l~LDINteLyPl~~gdk~~l~LastL~~dg~~~~~-~~~~~   79 (130)
                      |++++||||+|+|+++||+|  |||||||.|+|++++|+|+|||||||||+++||+|+|+||+|| +|| ++++ |++. 
T Consensus         2 ~~~~~LfeD~F~V~~iD~~g--fdrVSRI~a~S~~~~~~l~LDiNtelyPv~~gd~~~l~LastL-~dg-~d~~~~~~~-   76 (144)
T PTZ00167          2 SLPSCLFEDRFVVRSVDNSK--FERVSRIKAKSTGFDAELILDINSDLFPVREKQSLYIGLTNQL-SSG-PDDNVWESS-   76 (144)
T ss_pred             CCCceEEEeeEEEEecCCCC--CceEEEEEEEeCCCceEEEEEecccEEeccCCCEEEEEEeccc-cCC-CCccccccc-
Confidence            45588999999999999976  9999999999999999999999999999999999999999999 999 5554 7665 


Q ss_pred             CCCCcccccceEEeeeEEEeeecCCCCeEEEEEecCcceee
Q 032941           80 ARKTLADKYEYIMHGKLFKIGDEGSGKSLKAYETTTQSIHY  120 (130)
Q Consensus        80 ~~~sLaD~ydYVMyGKVYk~e~e~~~~~~~vYiS~~~~~~~  120 (130)
                      +++||||+|||||||||||||+++ +++++|||||||++..
T Consensus        77 ~~~tLad~ydYVM~GkvYk~ee~~-s~~~~vy~SFGGLLM~  116 (144)
T PTZ00167         77 EPQSLMDQYEYVMYGKIFKFEEKS-SERRTLYASFGGLLMA  116 (144)
T ss_pred             ccccccccCCEEcceEEEEeeecC-CCcEEEEEEcccEeEE
Confidence            588899999999999999999644 5799999999999873

>PRK14980 DNA-directed RNA polymerase subunit G; Provisional

Probab=97.48  E-value=0.0019  Score=48.86  Aligned_cols=94  Identities=10%  Similarity=0.131  Sum_probs=74.6

Q ss_pred             ccceeeeEEeeeECCCCCccceEeeEEEEecCCceEEEEEecccccccccCCEEEEEEeeecCCCCCCCCCccCCCCCCC
Q 032941            4 IVLFEDIFVVEKIDPDGKKFDKVSRIEAHSQNCDMYMLLDVNSELYPMRVGDKFTMALAHTLNLDGTPDTGYYTPGARKT   83 (130)
Q Consensus         4 ~~LFeD~F~V~~iD~dGKkFDrVSRI~a~S~~~~m~l~LDINteLyPl~~gdk~~l~LastL~~dg~~~~~~~~~~~~~s   83 (130)
                      +.-+.-.=+|++|.|  .+.-.-.|+.+.+  .+.++++|+|.+|=+.++||++.+.+.+.-                +.
T Consensus         6 ~~~~~~~cKI~SIEk--g~l~~l~i~~~~C--~~~~v~fDi~~~L~~fsege~v~iiIS~ek----------------P~   65 (127)
T PRK14980          6 AQEIILSCKINSIEK--GSLKNLSIIHMSC--NDFNISFDIIDSINIFSQKEKVKAIISKER----------------PS   65 (127)
T ss_pred             hhheeeEEeeeeecc--cccCCcEEEEEec--CCeEEEEEehhhhheecCCCcEEEEEeccC----------------cc
Confidence            445667789999999  7788888888777  469999999999999999999999997742                22


Q ss_pred             cccccceEEeeeEEEeeecCCCCeEEEEEecCccee
Q 032941           84 LADKYEYIMHGKLFKIGDEGSGKSLKAYETTTQSIH  119 (130)
Q Consensus        84 LaD~ydYVMyGKVYk~e~e~~~~~~~vYiS~~~~~~  119 (130)
                      . .+.|+.=||-|...+. ..+++-.+=+|..|.+.
T Consensus        66 ~-~~~dFCghGyvV~~~k-~~~~~y~~iISl~GlLv   99 (127)
T PRK14980         66 Y-TNDDFCAHGYIVTESS-NNGNRYTTIISLFGLLV   99 (127)
T ss_pred             c-ccceeecCcEEEEEEe-cCCCeEEEEEEeeeEEE
Confidence            3 3378888999988853 45788888888887654

>PF08530 PepX_C: X-Pro dipeptidyl-peptidase C-terminal non-catalytic domain; InterPro: IPR013736 This domain is found at the C terminus of cocaine esterase CocE, several glutaryl-7-ACA acylases, and the putative diester hydrolase NonD of Streptomyces griseus (all hydrolases)

Probab=82.43  E-value=4.7  Score=31.10  Aligned_cols=54  Identities=13%  Similarity=0.315  Sum_probs=38.8

Q ss_pred             EEeeeECCCCCccceEeeEEEEe-------------cCCceEEEEEecccccccccCCEEEEEEeeec
Q 032941           11 FVVEKIDPDGKKFDKVSRIEAHS-------------QNCDMYMLLDVNSELYPMRVGDKFTMALAHTL   65 (130)
Q Consensus        11 F~V~~iD~dGKkFDrVSRI~a~S-------------~~~~m~l~LDINteLyPl~~gdk~~l~LastL   65 (130)
                      -.+.+++|||+. ..|++-.++-             .+--.++.+.++---|-+++|.+++|.|+++=
T Consensus       115 v~L~dv~pdG~~-~~it~G~l~~s~r~~~~~~~~~~pg~~~~~~i~L~p~~~~~~~GhrLrl~I~~~d  181 (218)
T PF08530_consen  115 VRLSDVDPDGTS-TLITRGWLRASHRESDEKPEPLEPGEPYDVTIELQPTAYVFPAGHRLRLSISSSD  181 (218)
T ss_dssp             EEEEEEETTSSE-EEEEEEEEEGGGSSCSSST----TT-EEEEEEEEEEEEEEE-TT-EEEEEEESSB
T ss_pred             EEEEEeCCCCCE-EEccceEEEcccccCccccccCCCCcEEEEEEEEchhccEECCCCEEEEEEEecC
Confidence            356799999875 4566655553             13235889999999999999999999999873

The domain, which is a beta sandwich, is also found in serine peptidases belonging to MEROPS peptidase family S15: Xaa-Pro dipeptidyl-peptidases. Members of this entry, that are not characterised as peptidases, show extensive low-level similarity to the Xaa-Pro dipeptidyl-peptidases. ; GO: 0008239 dipeptidyl-peptidase activity; PDB: 2B4K_D 1RYY_F 2B9V_O 1NX9_B 3PUH_B 3I2I_A 3I2G_A 1JU4_A 3I2K_A 1L7R_A ....

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	130
2f3i_A	150	Solution Structure Of A Subunit Of Rna Polymerase I		2e-24
1i3q_H	146	Rna Polymerase Ii Crystal Form I At 3.1 A Resolutio		3e-14
3h0g_H	125	Rna Polymerase Ii From Schizosaccharomyces Pombe Le		2e-10

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

Iteration: 1
 Score =  107 bits (267), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 56/112 (50%), Positives = 81/112 (72%), Gaps = 5/112 (4%)
Query: 5   VLFEDIFVVEKIDPDGKKFDKVSRIEAHSQNCDMYMLLDVNSELYPMRVGDKFTMALAHT 64
           +LFEDIF V+ IDP+GKKFD+VSR+   S++  M ++LDVN ++YP+ +GDKF + +A T
Sbjct: 4   ILFEDIFDVKDIDPEGKKFDRVSRLHCESESFKMDLILDVNIQIYPVDLGDKFRLVIAST 63
Query: 65  LNLDGTPDTGYYTP-GARKTLADKYEYIMHGKLFKI-GDEGSGKS---LKAY 111
           L  DGT D G Y P   R + AD++EY+M+GK+++I GDE S ++   L AY
Sbjct: 64  LYEDGTLDDGEYNPTDDRPSRADQFEYVMYGKVYRIEGDETSTEAATRLSAY 115

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

Iteration: 1
 Score = 73.9 bits (180), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 44/106 (41%), Positives = 64/106 (60%), Gaps = 11/106 (10%)
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--GARKTLADKYEYIMHGKLFK 98
            +A +LNL+ TP      T  + P     ++LAD Y+Y+M+G  +K
Sbjct: 58  TIASSLNLEDTPANDSSATRSWRPPQAGDRSLADDYDYVMYGTAYK 103

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

Iteration: 1
 Score = 61.2 bits (147), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 36/111 (32%), Positives = 61/111 (54%), Gaps = 17/111 (15%)
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  LAHTLNLDGTPDTGYYTPGARKTLADKYEYIMHGKLFKIGDEGSGKSLKAY 111
           +   LN   +PD           L +  +YIM+GK++++ +E   + +  Y
Sbjct: 59  ITSNLN---SPD-----------LKEAADYIMYGKVYRV-EEAKDEKVSVY 94

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	130
2f3i_A	150	DNA-directed RNA polymerases I, II, and III 17.1 k	3e-44
1a1d_A	146	RNA polymerase; RPB8, OB fold, eukaryotic, yeast,	7e-37
3h0g_H	125	DNA-directed RNA polymerases I, II, and III subuni	1e-33

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

 Score =  140 bits (355), Expect = 3e-44
 Identities = 51/106 (48%), Positives = 76/106 (71%), Gaps = 2/106 (1%)

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

Query: 61  LAHTLNLDGTPDTGYYTP-GARKTLADKYEYIMHGKLFKIGDEGSG 105
           +A TL  DGT D G Y P   R + AD++EY+M+GK+++I  + + 
Sbjct: 60  IASTLYEDGTLDDGEYNPTDDRPSRADQFEYVMYGKVYRIEGDETS 105

>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 =  121 bits (306), Expect = 7e-37
 Identities = 43/119 (36%), Positives = 66/119 (55%), Gaps = 12/119 (10%)

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-------RKTLADKYEYIMHGKLFKIGDEGSGKSLKAY 111
            +A +LNL+ TP        +        ++LAD Y+Y+M+G  +K  +E S   +  Y
Sbjct: 58  TIASSLNLEDTPANDSSATRSWRPPQAGDRSLADDYDYVMYGTAYKF-EEVSKDLIAVY 115

>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 =  113 bits (284), Expect = 1e-33
 Identities = 34/111 (30%), Positives = 57/111 (51%), Gaps = 17/111 (15%)

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  LAHTLNLDGTPDTGYYTPGARKTLADKYEYIMHGKLFKIGDEGSGKSLKAY 111
           +   LN                 L +  +YIM+GK++++ +    K +  Y
Sbjct: 59  ITSNLNSPD--------------LKEAADYIMYGKVYRVEEAKDEK-VSVY 94

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	130
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	97.47

>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=8.7e-56  Score=337.40  Aligned_cols=118  Identities=43%  Similarity=0.759  Sum_probs=110.3

Q ss_pred             CCcccceeeeEEeeeECCCCCccceEeeEEEEecCCceEEEEEecccccccccCCEEEEEEeeecCCCCCCCC-CccCCC
Q 032941            1 MSNIVLFEDIFVVEKIDPDGKKFDKVSRIEAHSQNCDMYMLLDVNSELYPMRVGDKFTMALAHTLNLDGTPDT-GYYTPG   79 (130)
Q Consensus         1 ms~~~LFeD~F~V~~iD~dGKkFDrVSRI~a~S~~~~m~l~LDINteLyPl~~gdk~~l~LastL~~dg~~~~-~~~~~~   79 (130)
                      || ++||||+|+|++||||||||||||||.|+|++++|+|+|||||||||+++||+|+|+||+||++||++++ +|+++.
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 8999999999999999999999999999999999999999999999999999999999999999999876 577765


Q ss_pred             CCCCcccccceEEeeeEEEeeecCCC----CeEEEEEecCccee
Q 032941           80 ARKTLADKYEYIMHGKLFKIGDEGSG----KSLKAYETTTQSIH  119 (130)
Q Consensus        80 ~~~sLaD~ydYVMyGKVYk~e~e~~~----~~~~vYiS~~~~~~  119 (130)
                      ++++|||+|||||||||||||+++++    ++++|||||||++.
T Consensus        80 ~~~slad~ydYVM~GkvYk~e~~~~~~~~~~~~~vY~SFGGLLM  123 (150)
T 2f3i_A           80 DRPSRADQFEYVMYGKVYRIEGDETSTEAATRLSAYVSYGGLLM  123 (150)
T ss_dssp             STTSCTTTTSEEECEEEECCSSCCSSSSCCSSEEEEEEETTEEE
T ss_pred             CCcccccccCEEEeeEEEEEeecCCCccccceEEEEEEcceEeE
Confidence            68899999999999999999976555    79999999999986

>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=4.6e-51  Score=310.22  Aligned_cols=115  Identities=38%  Similarity=0.677  Sum_probs=107.7

Q ss_pred             CCcccceeeeEEeeeECCCCCccceEeeEEEEecCCceE-EEEEecccccccccCCEEEEEEeeecCCCCCC-----CC-
Q 032941            1 MSNIVLFEDIFVVEKIDPDGKKFDKVSRIEAHSQNCDMY-MLLDVNSELYPMRVGDKFTMALAHTLNLDGTP-----DT-   73 (130)
Q Consensus         1 ms~~~LFeD~F~V~~iD~dGKkFDrVSRI~a~S~~~~m~-l~LDINteLyPl~~gdk~~l~LastL~~dg~~-----~~-   73 (130)
                      || ++||||+|+|++|||+  ||||||||.|+|++++|+ |+|||||||||+++||+|+|+||+||++||++     ++ 
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 8999999999999996  999999999999999999 99999999999999999999999999999987     54 


Q ss_pred             CccCCC-CCCCcccccceEEeeeEEEeeecCCCCeEEEEEecCccee
Q 032941           74 GYYTPG-ARKTLADKYEYIMHGKLFKIGDEGSGKSLKAYETTTQSIH  119 (130)
Q Consensus        74 ~~~~~~-~~~sLaD~ydYVMyGKVYk~e~e~~~~~~~vYiS~~~~~~  119 (130)
                      +|+++. ++++|||+|||||||||||||+ +++++++|||||||++.
T Consensus        78 ~~~~~~~~~~slad~ydYVM~GkvYk~e~-~~~~~~~vy~SFGGLLM  123 (146)
T 1a1d_A           78 SWRPPQAGDRSLADDYDYVMYGTAYKFEE-VSKDLIAVYYSFGGLLM  123 (146)
T ss_pred             cccccccCCcccccccCEEEeeEEEEEee-cCCceEEEEEEcceEeE
Confidence            688754 6889999999999999999997 66899999999999986

>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=1.9e-47  Score=284.11  Aligned_cols=102  Identities=32%  Similarity=0.619  Sum_probs=94.7

Q ss_pred             CCcccceeeeEEeeeECCCCCccceEeeEEEEecCCceEEEEEecccccccccCCEEEEEEeeecCCCCCCCCCccCCCC
Q 032941            1 MSNIVLFEDIFVVEKIDPDGKKFDKVSRIEAHSQNCDMYMLLDVNSELYPMRVGDKFTMALAHTLNLDGTPDTGYYTPGA   80 (130)
Q Consensus         1 ms~~~LFeD~F~V~~iD~dGKkFDrVSRI~a~S~~~~m~l~LDINteLyPl~~gdk~~l~LastL~~dg~~~~~~~~~~~   80 (130)
                      ||+++||||+|+|++|||+  ||||||||.|+|++++|+|+|||||||||+++||+|+|+||+||+++   +  |     
T Consensus         1 m~~~~LfeD~F~V~~id~~--kfdrVSRi~~~S~~~~~~l~LDiNtelyP~~~gd~~~l~LassL~~~---d--~-----   68 (125)
T 3h0g_H            1 MSESVLLDEIFTVTSVDKQ--KYQRVSRITAVSGQNDMNLTLDINSQIYPLEKDATFSLQITSNLNSP---D--L-----   68 (125)
T ss_dssp             -CCCCCCCBCCCCCCEECS--SCSSCCEEECCCSSSCCCBEEECCTTTSCCCSSCCCCEECCCCCCCS---H--H-----
T ss_pred             CCCcEEEEeEEEEeeCChh--hCCcEEEEEEEeCCCceEEEEEecceEEecCCCCEEEEEEeccCCch---h--h-----
Confidence            8899999999999999995  99999999999999999999999999999999999999999999972   1  4     


Q ss_pred             CCCcccccceEEeeeEEEeeecCCCCeEEEEEecCccee
Q 032941           81 RKTLADKYEYIMHGKLFKIGDEGSGKSLKAYETTTQSIH  119 (130)
Q Consensus        81 ~~sLaD~ydYVMyGKVYk~e~e~~~~~~~vYiS~~~~~~  119 (130)
                          ||+|||||||||||+|+ +++++++|||||||+..
T Consensus        69 ----ad~ydYVMyGkvYk~e~-~~~~~~~vy~SFGGLLM  102 (125)
T 3h0g_H           69 ----KEAADYIMYGKVYRVEE-AKDEKVSVYVSFGGLLM  102 (125)
T ss_dssp             ----HHSSSEEECCCCCCEEC-CSSSCEEECCEETTEEC
T ss_pred             ----hccccEEEEeEEEEEee-cCCceEEEEEEecCEEE
Confidence                89999999999999985 46899999999999875

>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=97.47  E-value=0.00012  Score=54.57  Aligned_cols=86  Identities=10%  Similarity=0.190  Sum_probs=67.9

Q ss_pred             EeeeECCCCCccceEeeEEEEecCCceEEEEEecccccccccCCEEEEEEeeecCCCCCCCCCccCCCCCCCcccccceE
Q 032941           12 VVEKIDPDGKKFDKVSRIEAHSQNCDMYMLLDVNSELYPMRVGDKFTMALAHTLNLDGTPDTGYYTPGARKTLADKYEYI   91 (130)
Q Consensus        12 ~V~~iD~dGKkFDrVSRI~a~S~~~~m~l~LDINteLyPl~~gdk~~l~LastL~~dg~~~~~~~~~~~~~sLaD~ydYV   91 (130)
                      +|++|.|  .+.-.+.|+.+++.  +.++++|+|.+|.++.+||++++.++.+.-                ...+. |++
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--GSLKNLSIIHMSCN--DFNISFDIIDSINIFSQKEKVKAFISKNRL----------------SYTND-DFC   72 (132)
T ss_dssp             CCCCEEE--CSSTTEEEEECCBS--SEEEEEEEESTTCCCCSSCCCEEEEESSCC----------------CCCTT-SEE
T ss_pred             EEeeEcc--cccCCeEEEEEecC--CEEEEEEhhhhhhcccCCCeEEEEEecCCc----------------ccccC-ccc
Confidence            5778888  78899999999885  499999999999999999999999987532                23344 688


Q ss_pred             EeeeEEEeeec---CCCCeEEEEEecCcce
Q 032941           92 MHGKLFKIGDE---GSGKSLKAYETTTQSI  118 (130)
Q Consensus        92 MyGKVYk~e~e---~~~~~~~vYiS~~~~~  118 (130)
                      =||-|......   .++++-.+.+|..|.+
T Consensus        73 GhGYvVt~~k~~~~~~~~~~~~iISl~GlL  102 (132)
T 4ayb_G           73 GHGYIVTELKDSSSNNGNRYITIISLFGLL  102 (132)
T ss_dssp             BCEEEEETTTTEEEETTEEEEEEESCCHHH
T ss_pred             cceEEEEEeecccccCCceeEEEEEeeeEE
Confidence            88988755321   2467888999988764

---

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	130
d1twfh_	145	b.40.4.8 (H:) RNA polymerase subunit RBP8 {Baker's	5e-44

>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 =  139 bits (351), Expect = 5e-44
 Identities = 39/115 (33%), Positives = 62/115 (53%), Gaps = 11/115 (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-------RKTLADKYEYIMHGKLFKIGDEGSGKSLKAY 111
           +LNL+ TP        +        ++LAD Y+Y+M+G  +K  +      +  Y
Sbjct: 61  SLNLEDTPANDSSATRSWRPPQAGDRSLADDYDYVMYGTAYKFEEVSKDL-IAVY 114

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	130
d1twfh_	145	RNA polymerase subunit RBP8 {Baker's yeast (Saccha	100.0
d1mpxa1	233	Alpha-amino acid ester hydrolase {Xanthomonas citr	82.21

>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=7.1e-52  Score=312.56  Aligned_cols=115  Identities=35%  Similarity=0.629  Sum_probs=99.6

Q ss_pred             cccceeeeEEeeeECCCCCccceEeeEEEEecCC-ceEEEEEecccccccccCCEEEEEEeeecCCCCCCC------CCc
Q 032941            3 NIVLFEDIFVVEKIDPDGKKFDKVSRIEAHSQNC-DMYMLLDVNSELYPMRVGDKFTMALAHTLNLDGTPD------TGY   75 (130)
Q Consensus         3 ~~~LFeD~F~V~~iD~dGKkFDrVSRI~a~S~~~-~m~l~LDINteLyPl~~gdk~~l~LastL~~dg~~~------~~~   75 (130)
                      |++||||+|+|++|||  |||||||||.|+|+++ +|+|+|||||||||+++||+|+|+||+||++||+|+      ..|
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  9999999999999987 599999999999999999999999999999999864      358


Q ss_pred             cCCC-CCCCcccccceEEeeeEEEeeecCCCCeEEEEEecCcceee
Q 032941           76 YTPG-ARKTLADKYEYIMHGKLFKIGDEGSGKSLKAYETTTQSIHY  120 (130)
Q Consensus        76 ~~~~-~~~sLaD~ydYVMyGKVYk~e~e~~~~~~~vYiS~~~~~~~  120 (130)
                      +++. +++||||+|||||||||||||+ .++++++|||||||++..
T Consensus        79 ~~~~~~~~slad~yeYVM~GkvYk~ee-~~~~~~~vy~SFGGLLM~  123 (145)
T d1twfh_          79 RPPQAGDRSLADDYDYVMYGTAYKFEE-VSKDLIAVYYSFGGLLMR  123 (145)
T ss_dssp             CCSSTTTSSCCCCSSEEEEEEECCCCC-CCTTCEEEEEEETTEEEE
T ss_pred             ccccCCccchhhcCCEEeeeEEEEeee-cCCCcEEEEEEecceeEE
Confidence            8654 7899999999999999999985 567899999999999874

>d1mpxa1 b.18.1.13 (A:405-637) Alpha-amino acid ester hydrolase {Xanthomonas citri [TaxId: 346]}

class: All beta proteins
fold: Galactose-binding domain-like
superfamily: Galactose-binding domain-like
family: PepX C-terminal domain-like
domain: Alpha-amino acid ester hydrolase
species: Xanthomonas citri [TaxId: 346]

Probab=82.21  E-value=2.5  Score=30.59  Aligned_cols=54  Identities=9%  Similarity=0.078  Sum_probs=40.3

Q ss_pred             EEeeeECCCCCcc--------ceEeeEEEE-e------------cCCceEEEEEecccccccccCCEEEEEEeee
Q 032941           11 FVVEKIDPDGKKF--------DKVSRIEAH-S------------QNCDMYMLLDVNSELYPMRVGDKFTMALAHT   64 (130)
Q Consensus        11 F~V~~iD~dGKkF--------DrVSRI~a~-S------------~~~~m~l~LDINteLyPl~~gdk~~l~Last   64 (130)
                      -++.+++|||+..        .+|++-... |            .+.-+++.+++..--+-+++|++++|.|+++
T Consensus       113 v~L~dv~pdg~~~~~~~g~~~~~i~~g~lr~~~r~~~~~~~~l~pG~~~~~~i~L~p~~~~f~~GhrLrl~Is~s  187 (233)
T d1mpxa1         113 VKLIDVYPEEMASNPKMGGYELPVSLAIFRGRYRESFSTPKPLTSNQPLAFQFGLPTANHTFQPGHRVMVQVQSS  187 (233)
T ss_dssp             EEEEEECCSCCTTSGGGTTCEEEEEEEEEEGGGSSCSSSCCCCCTTCCEEEEEECCCEEEEECTTCEEEEEEESC
T ss_pred             EEEEEECCCCcEEEecCCceeEEeecccccccccCcccCccccCCCCEEEEEEEEhhheEEECCCCEEEEEEECC
Confidence            3677899998864        245554444 1            2334788899999999999999999999987