Query 045300
Match_columns 166
No_of_seqs 62 out of 64
Neff 4.3
Searched_HMMs 46136
Date Fri Mar 29 11:50:18 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/045300.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/045300hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd02584 RNAP_II_Rpb1_C Largest 59.8 11 0.00023 35.0 3.5 61 23-85 10-75 (410)
2 COG4908 Uncharacterized protei 40.9 12 0.00027 35.1 0.8 15 123-137 363-377 (439)
3 cd06528 RNAP_A'' A'' subunit o 38.8 41 0.00089 30.6 3.8 61 23-85 23-88 (363)
4 TIGR02389 RNA_pol_rpoA2 DNA-di 38.8 22 0.00047 32.5 2.1 60 24-85 28-92 (367)
5 PRK04309 DNA-directed RNA poly 31.9 52 0.0011 30.2 3.4 61 23-85 42-107 (383)
6 cd02735 RNAP_I_Rpa1_C Largest 26.8 50 0.0011 29.3 2.3 54 32-87 2-60 (309)
7 PRK14977 bifunctional DNA-dire 24.6 69 0.0015 34.0 3.2 58 24-83 962-1024(1321)
8 PHA02970 hypothetical protein; 23.1 37 0.0008 26.4 0.7 12 127-138 12-23 (115)
9 COG0165 ArgH Argininosuccinate 21.8 54 0.0012 31.1 1.6 65 28-92 232-304 (459)
10 PRK14897 unknown domain/DNA-di 21.0 66 0.0014 30.9 2.0 61 23-85 165-230 (509)
11 cd02736 RNAP_III_Rpc1_C Larges 20.2 78 0.0017 28.1 2.2 52 32-85 2-58 (300)
No 1
>cd02584 RNAP_II_Rpb1_C Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain. RNA polymerase II (RNAP II) is a large multi-subunit complex responsible for the synthesis of mRNA. RNAP II consists of a 10-subunit core enzyme and a peripheral heterodimer of two subunits. The largest core subunit (Rpb1) of yeast RNAP II is the best characterized member of this family. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure. In yeast, Rpb1 and Rpb2, the largest and the second largest subunits, each makes up one clamp, one jaw, and part of the cleft. Rpb1 interacts with Rpb2 to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis. The C-terminal domain of Rpb1 makes up part of the foot and jaw structures.
Probab=59.81 E-value=11 Score=34.98 Aligned_cols=61 Identities=16% Similarity=0.230 Sum_probs=44.6
Q ss_pred HHHHhhhhHHHHhhHhhccCCcc--ccCCCCCCccccccCcccccc---CCCCCCCchhHHHHHHHhh
Q 045300 23 KMLIKARDFYIRSITACSDSVVF--SSAGGVPIGSVNTLPRSYSTN---SSRSSRGDEDFRELVRANS 85 (166)
Q Consensus 23 R~L~kARD~YVRsmt~Ca~~~~~--g~~~g~P~~~~~~lPrSfS~~---ssr~~~~deD~~eLvRAAS 85 (166)
.+|..-++-|.+++..-...++. +-++|.|++|+ || ++|-.+ +.--+-+--.+.|||-|+-
T Consensus 10 ~~~~~~~~~~~~~~~~~ge~vg~~aaQSiGEP~TQm-TL-nTFH~AGVas~NVTlGVPRLkEIInasK 75 (410)
T cd02584 10 WILGEIETRFNRSLVHPGEMVGTIAAQSIGEPATQM-TL-NTFHFAGVSAKNVTLGVPRLKEIINVAK 75 (410)
T ss_pred HHHHHHHHHHHHhhcCCCCCcchhhhhhcCCchhcc-cc-cccccccccccccccCccchHHHhhccc
Confidence 45777888899999888888775 22699999999 88 999653 2111223577899988764
No 2
>COG4908 Uncharacterized protein containing a NRPS condensation (elongation) domain [General function prediction only]
Probab=40.85 E-value=12 Score=35.14 Aligned_cols=15 Identities=40% Similarity=0.399 Sum_probs=13.0
Q ss_pred ceeeccCCCCCcccc
Q 045300 123 AIGRIDEDKPCDFED 137 (166)
Q Consensus 123 gmGRIDED~PCeF~e 137 (166)
-||+|||+.||.+++
T Consensus 363 NiG~id~~~~~f~g~ 377 (439)
T COG4908 363 NIGIIDEEVPPFGGE 377 (439)
T ss_pred cccccccccCCcCce
Confidence 599999999998763
No 3
>cd06528 RNAP_A'' A'' subunit of Archaeal RNA Polymerase (RNAP). Archaeal RNA polymerase (RNAP), like bacterial RNAP, is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. The relative positioning of the RNAP core is highly conserved between archaeal RNAP and the three classes of eukaryotic RNAPs. In archaea, the largest subunit is split into two polypeptides, A' and A'', which are encoded by separate genes in an operon. Sequence alignments reveal that the archaeal A'' subunit corresponds to the C-terminal one-third of the RNAPII largest subunit (Rpb1). In subunit A'', several loops in the jaw domain are shorter. The RNAPII Rpb1 interacts with the second-largest subunit (Rpb2) to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis.
Probab=38.79 E-value=41 Score=30.65 Aligned_cols=61 Identities=21% Similarity=0.302 Sum_probs=43.8
Q ss_pred HHHHhhhhHHHHhhHhhccCCcc--ccCCCCCCccccccCccccccCCCC---CCCchhHHHHHHHhh
Q 045300 23 KMLIKARDFYIRSITACSDSVVF--SSAGGVPIGSVNTLPRSYSTNSSRS---SRGDEDFRELVRANS 85 (166)
Q Consensus 23 R~L~kARD~YVRsmt~Ca~~~~~--g~~~g~P~~~~~~lPrSfS~~ssr~---~~~deD~~eLvRAAS 85 (166)
.+|..-.+-|.+++..=...+|. .-++|.|++|+ || ++|-.+--.+ +.+--.+.|+|-|+.
T Consensus 23 ~~~~~~~~~~~~~~~~~Ge~vG~iaAQSiGEP~TQM-TL-nTFH~AGVas~nVTlGVPRlkEIIna~K 88 (363)
T cd06528 23 EIIKEVLREYLRSLIEPGEAVGIVAAQSIGEPGTQM-TL-RTFHYAGVAEINVTLGLPRLIEIVDARK 88 (363)
T ss_pred HHHHHHHHHHHHHhhccCccccceeeeecCccceec-cc-ccccccccccccCccccccHHHHhhccc
Confidence 34566677799999887777764 33699999999 88 9997652111 223578899998766
No 4
>TIGR02389 RNA_pol_rpoA2 DNA-directed RNA polymerase, subunit A''. This family consists of the archaeal A'' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein.
Probab=38.79 E-value=22 Score=32.50 Aligned_cols=60 Identities=20% Similarity=0.336 Sum_probs=43.5
Q ss_pred HHHhhhhHHHHhhHhhccCCcc--ccCCCCCCccccccCccccccC--C-CCCCCchhHHHHHHHhh
Q 045300 24 MLIKARDFYIRSITACSDSVVF--SSAGGVPIGSVNTLPRSYSTNS--S-RSSRGDEDFRELVRANS 85 (166)
Q Consensus 24 ~L~kARD~YVRsmt~Ca~~~~~--g~~~g~P~~~~~~lPrSfS~~s--s-r~~~~deD~~eLvRAAS 85 (166)
+|..-..-|.|++..=...||. +-++|.|++|+ || ++|-.+- + --+-+--.+.|+|-|+-
T Consensus 28 ~l~~i~~ky~~alv~PGeaVG~IAAQSIGEP~TQM-TL-nTFH~AGVas~nVTlGVPRlkEIINa~k 92 (367)
T TIGR02389 28 IIKRVEEEYLRSLIDPGEAVGIVAAQSIGEPGTQM-TM-RTFHYAGVAELNVTLGLPRLIEIVDARK 92 (367)
T ss_pred HHHHHHHHHHHhcCCCccccchhhhhhcCCccccc-cc-cccccccccccCccccchhHHHHhhccc
Confidence 4566677799999888888875 22699999999 99 9997651 1 11223578899998754
No 5
>PRK04309 DNA-directed RNA polymerase subunit A''; Validated
Probab=31.88 E-value=52 Score=30.19 Aligned_cols=61 Identities=20% Similarity=0.297 Sum_probs=43.2
Q ss_pred HHHHhhhhHHHHhhHhhccCCcc--ccCCCCCCccccccCccccccC--C-CCCCCchhHHHHHHHhh
Q 045300 23 KMLIKARDFYIRSITACSDSVVF--SSAGGVPIGSVNTLPRSYSTNS--S-RSSRGDEDFRELVRANS 85 (166)
Q Consensus 23 R~L~kARD~YVRsmt~Ca~~~~~--g~~~g~P~~~~~~lPrSfS~~s--s-r~~~~deD~~eLvRAAS 85 (166)
.+|..-++-|.+++..=...+|. +-+.|.|++|+ || ++|-.+- + --+-+-..+.|+|-|+.
T Consensus 42 ~~~~~i~~~y~~~~v~pGe~VG~iaAQsIGEP~TQM-TL-~TFH~AGva~~nVTlGvPRlkEIina~K 107 (383)
T PRK04309 42 EIIEEVVREYLRSLVEPGEAVGVVAAQSIGEPGTQM-TM-RTFHYAGVAEINVTLGLPRLIEIVDARK 107 (383)
T ss_pred HHHHHHHHHHHHhhcCCCCccchhhhhhccchhhhc-cc-ccccccCccccCcccCchhHHHHHhccc
Confidence 45667777899998876666664 33699999999 99 9997652 1 11223688999997654
No 6
>cd02735 RNAP_I_Rpa1_C Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain. RNA polymerase I (RNAP I) is a multi-subunit protein complex responsible for the synthesis of rRNA precursor. It consists of at least 14 different subunits, and the largest one is homologous to subunit Rpb1 of yeast RNAP II and subunit beta' of bacterial RNAP. Rpa1 is also known as Rpa190 in yeast. Structure studies suggest that different RNAP complexes share a similar crab-claw-shape structure. The C-terminal domain of Rpb1, the largest subunit of RNAP II, makes up part of the foot and jaw structures of RNAP II. The similarity between this domain and the C-terminal domain of Rpb1, its counterpart in RNAP II, suggests a similar functional and structural role.
Probab=26.77 E-value=50 Score=29.32 Aligned_cols=54 Identities=22% Similarity=0.353 Sum_probs=35.8
Q ss_pred HHHhhHhhccCCcc--ccCCCCCCccccccCccccccCC--C-CCCCchhHHHHHHHhhhh
Q 045300 32 YIRSITACSDSVVF--SSAGGVPIGSVNTLPRSYSTNSS--R-SSRGDEDFRELVRANSMK 87 (166)
Q Consensus 32 YVRsmt~Ca~~~~~--g~~~g~P~~~~~~lPrSfS~~ss--r-~~~~deD~~eLvRAAS~R 87 (166)
|.|++..=...||. +-++|.|++|+ || ++|-.+-- - -+-+--+++|+|=.||+.
T Consensus 2 y~~slv~PGE~VG~iaAQSIGEPsTQM-TL-nTFH~AGv~~~nVTlGvPRL~EIi~~Ask~ 60 (309)
T cd02735 2 YMRSLVEPGEAVGLLAAQSIGEPSTQM-TL-NTFHFAGRGEMNVTLGIPRLREILMTASKN 60 (309)
T ss_pred chhccCCCCcccchhhhhccCCccccc-cc-ccccccCccccccccccccHHHHHhhhccC
Confidence 56666655555654 33699999999 99 99977511 1 111257899999777644
No 7
>PRK14977 bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
Probab=24.62 E-value=69 Score=34.04 Aligned_cols=58 Identities=19% Similarity=0.275 Sum_probs=40.8
Q ss_pred HHHhhhhHHHHhhHhhccCCcc--ccCCCCCCccccccCccccccCC---CCCCCchhHHHHHHH
Q 045300 24 MLIKARDFYIRSITACSDSVVF--SSAGGVPIGSVNTLPRSYSTNSS---RSSRGDEDFRELVRA 83 (166)
Q Consensus 24 ~L~kARD~YVRsmt~Ca~~~~~--g~~~g~P~~~~~~lPrSfS~~ss---r~~~~deD~~eLvRA 83 (166)
++.+.++.|.+++..=+..||. +-++|.|++|+ || ++|-.+-- --+-+-..++|+|-|
T Consensus 962 ~~~~~~~~~~~~~~~pGe~VG~iaAQSiGEP~TQm-TL-nTFH~AGv~~~nvt~GvpRl~Eii~a 1024 (1321)
T PRK14977 962 ICAEGKEGFEKAKVEPGQAIGIISAQSIAEPGTQM-TL-RTFHAAGIKAMDVTHGLERFIELVDA 1024 (1321)
T ss_pred HHHHHHHHHHhcccCCcccchhhhhhhccCceeee-cc-cccccccccccCcccCccchHHhhhc
Confidence 4555688899999877777764 33699999999 99 99965421 112235889999953
No 8
>PHA02970 hypothetical protein; Provisional
Probab=23.12 E-value=37 Score=26.44 Aligned_cols=12 Identities=33% Similarity=0.537 Sum_probs=9.5
Q ss_pred ccCCCCCccccc
Q 045300 127 IDEDKPCDFEDD 138 (166)
Q Consensus 127 IDED~PCeF~ed 138 (166)
-|-++||+|++=
T Consensus 12 ydgispCYFG~C 23 (115)
T PHA02970 12 YDGISPCYFGKC 23 (115)
T ss_pred cCCCCCceeccc
Confidence 477899999854
No 9
>COG0165 ArgH Argininosuccinate lyase [Amino acid transport and metabolism]
Probab=21.79 E-value=54 Score=31.09 Aligned_cols=65 Identities=25% Similarity=0.328 Sum_probs=39.3
Q ss_pred hhhHHHHhhHhhccCCc---ccc----CCCCCCccccccCccccccCCC-CCCCchhHHHHHHHhhhhhcccc
Q 045300 28 ARDFYIRSITACSDSVV---FSS----AGGVPIGSVNTLPRSYSTNSSR-SSRGDEDFRELVRANSMKILASQ 92 (166)
Q Consensus 28 ARD~YVRsmt~Ca~~~~---~g~----~~g~P~~~~~~lPrSfS~~ssr-~~~~deD~~eLvRAAS~R~~g~~ 92 (166)
.|||=+-.+..|+.-+. .=+ .+..|--.+-.||.+|+.+||= .---+-|+.||||+-+.|..|+-
T Consensus 232 ~Rdf~le~l~~~s~~~~~LSRlaedlI~wss~EfgfI~l~D~~sTGSSIMPQKKNPD~~ELiRgk~grv~G~l 304 (459)
T COG0165 232 DRDFILEFLSAAALIMVHLSRLAEDLILWSSPEFGFIELPDEFSTGSSIMPQKKNPDVLELIRGKAGRVIGAL 304 (459)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccCceEeCCcccccccccCCCCCCCcHHHHHHHhhhhhHHHH
Confidence 56776665555554321 000 1222322233899999998751 01127899999999999988854
No 10
>PRK14897 unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional
Probab=20.97 E-value=66 Score=30.92 Aligned_cols=61 Identities=21% Similarity=0.276 Sum_probs=41.6
Q ss_pred HHHHhhhhHHHHhhHhhccCCcc--ccCCCCCCccccccCccccccCCC---CCCCchhHHHHHHHhh
Q 045300 23 KMLIKARDFYIRSITACSDSVVF--SSAGGVPIGSVNTLPRSYSTNSSR---SSRGDEDFRELVRANS 85 (166)
Q Consensus 23 R~L~kARD~YVRsmt~Ca~~~~~--g~~~g~P~~~~~~lPrSfS~~ssr---~~~~deD~~eLvRAAS 85 (166)
.+|..-+.-|.+++..=...+|. .-++|.|++|+ || ++|-.+--. -+-+--.+.|||-|+-
T Consensus 165 ~i~~ei~~~y~~~~v~pGE~VG~IAAQSIGEP~TQM-TL-nTFH~AGVas~NVTlGVPRLkEIINa~K 230 (509)
T PRK14897 165 EILRRIREEYERARVDPYEAVGIVAAQSIGEPGTQM-TM-RTFHYAGVAEMNVTLGLPRLIEIVDARK 230 (509)
T ss_pred HHHHHHHHHHHHhccCCCCCcchhhhhhhCCccccc-cc-cccccccccccccccCcchhHHHhhccc
Confidence 34555666799998887777775 22699999999 99 999764211 1113567888887743
No 11
>cd02736 RNAP_III_Rpc1_C Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain. Eukaryotic RNA polymerase III (RNAP III) is a large multi-subunit complex responsible for the synthesis of tRNAs, 5SrRNA, Alu-RNA, U6 snRNA, among others. Rpc1 is also known as C160 in yeast. Structure studies suggest that different RNA polymerase complexes share a similar crab-claw-shape structure. The C-terminal domain of Rpb1, the largest subunit of RNAP II, makes up part of the foot and jaw structures of RNAP II. The similarity between this domain and the C-terminal domain of Rpb1, its counterpart in RNAP II, suggests a similar functional and structural role.
Probab=20.16 E-value=78 Score=28.11 Aligned_cols=52 Identities=19% Similarity=0.301 Sum_probs=33.7
Q ss_pred HHHhhHhhccCCcc--ccCCCCCCccccccCccccccCC---CCCCCchhHHHHHHHhh
Q 045300 32 YIRSITACSDSVVF--SSAGGVPIGSVNTLPRSYSTNSS---RSSRGDEDFRELVRANS 85 (166)
Q Consensus 32 YVRsmt~Ca~~~~~--g~~~g~P~~~~~~lPrSfS~~ss---r~~~~deD~~eLvRAAS 85 (166)
|.|++..=...++. +-++|.|++|+ || ++|-.+-- --+-+--++.|||-|+-
T Consensus 2 y~~~~v~pGe~vG~iaaQsiGEp~TQm-TL-~TFH~aGv~~~nvtlGvPRlkEIinasK 58 (300)
T cd02736 2 YMRAKVEPGTAVGAIAAQSIGEPGTQM-TL-KTFHFAGVASMNITLGVPRIKEIINASK 58 (300)
T ss_pred chhhccCCCccchhhhhhhcCCccccc-cc-cccccccccccccccCchHHHHHHhccc
Confidence 55666555555553 33699999999 88 99976421 11123578999996644
Done!