Query 040778
Match_columns 262
No_of_seqs 96 out of 98
Neff 2.6
Searched_HMMs 46136
Date Fri Mar 29 11:43:44 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/040778.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/040778hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF00642 zf-CCCH: Zinc finger 97.2 4.6E-05 9.9E-10 47.7 -0.9 25 227-251 2-26 (27)
2 smart00356 ZnF_C3H1 zinc finge 97.0 0.00061 1.3E-08 40.7 2.2 22 229-251 5-26 (27)
3 KOG2135 Proteins containing th 96.7 0.00043 9.2E-09 68.9 0.3 33 226-258 210-242 (526)
4 COG5152 Uncharacterized conser 92.5 0.044 9.5E-07 50.6 0.5 28 226-253 139-166 (259)
5 KOG1677 CCCH-type Zn-finger pr 90.9 0.16 3.4E-06 45.8 2.3 31 225-255 174-204 (332)
6 KOG1813 Predicted E3 ubiquitin 87.6 0.16 3.5E-06 48.5 -0.2 24 227-250 185-208 (313)
7 KOG1595 CCCH-type Zn-finger pr 85.8 0.37 8E-06 48.8 1.3 23 229-252 237-259 (528)
8 PF14608 zf-CCCH_2: Zinc finge 84.5 0.68 1.5E-05 27.3 1.5 18 231-251 2-19 (19)
9 KOG1677 CCCH-type Zn-finger pr 83.0 0.56 1.2E-05 42.3 1.1 31 226-256 130-161 (332)
10 COG5063 CTH1 CCCH-type Zn-fing 82.9 0.64 1.4E-05 45.0 1.5 33 226-258 272-304 (351)
11 KOG1040 Polyadenylation factor 74.1 1.9 4.1E-05 41.2 1.8 27 226-252 103-129 (325)
12 COG5063 CTH1 CCCH-type Zn-fing 55.6 18 0.00039 35.4 4.4 27 226-252 113-139 (351)
13 KOG1492 C3H1-type Zn-finger pr 45.8 7.4 0.00016 37.1 0.2 24 230-253 208-231 (377)
14 KOG2494 C3H1-type Zn-finger pr 38.0 11 0.00024 36.6 0.2 29 229-258 38-67 (331)
15 COG5084 YTH1 Cleavage and poly 36.8 19 0.00041 34.2 1.4 24 229-252 135-158 (285)
16 KOG2333 Uncharacterized conser 34.0 20 0.00042 37.3 1.1 22 227-248 113-134 (614)
17 KOG4791 Uncharacterized conser 26.1 59 0.0013 34.0 2.9 51 193-254 93-143 (667)
18 PF11942 Spt5_N: Spt5 transcri 26.0 31 0.00068 27.1 0.8 33 35-68 40-74 (97)
19 PF11705 RNA_pol_3_Rpc31: DNA- 22.5 1.7E+02 0.0037 25.9 4.8 14 168-181 31-44 (233)
20 KOG0153 Predicted RNA-binding 20.8 43 0.00094 33.2 0.8 24 229-253 162-185 (377)
No 1
>PF00642 zf-CCCH: Zinc finger C-x8-C-x5-C-x3-H type (and similar); InterPro: IPR000571 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents C-x8-C-x5-C-x3-H (CCCH) type Zinc finger (Znf) domains. Proteins containing CCCH Znf domains include Znf proteins from eukaryotes involved in cell cycle or growth phase-related regulation, e.g. human TIS11B (butyrate response factor 1), a probable regulatory protein involved in regulating the response to growth factors, and the mouse TTP growth factor-inducible nuclear protein, which has the same function. The mouse TTP protein is induced by growth factors. Another protein containing this domain is the human splicing factor U2AF 35kDa subunit, which plays a critical role in both constitutive and enhancer-dependent splicing by mediating essential protein-protein interactions and protein-RNA interactions required for 3' splice site selection. It has been shown that different CCCH-type Znf proteins interact with the 3'-untranslated region of various mRNA [, ]. This type of Znf is very often present in two copies. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding; PDB: 1M9O_A 1RGO_A 2CQE_A 2FC6_A 2D9M_A 2E5S_A 2RHK_C 2D9N_A 3D2S_A 3D2Q_C ....
Probab=97.24 E-value=4.6e-05 Score=47.72 Aligned_cols=25 Identities=40% Similarity=0.816 Sum_probs=20.2
Q ss_pred CCCCCCCccccccccCCCCCCCCCC
Q 040778 227 SRQRCRDFEERGFCLRGDMCPMEHG 251 (262)
Q Consensus 227 ~r~RCrDydekGyC~rGd~CpydHG 251 (262)
++..|++|.+.|+|.+|+.|.|.|+
T Consensus 2 k~~~C~~f~~~g~C~~G~~C~f~H~ 26 (27)
T PF00642_consen 2 KTKLCRFFMRTGTCPFGDKCRFAHG 26 (27)
T ss_dssp TSSB-HHHHHTS--TTGGGSSSBSS
T ss_pred ccccChhhccCCccCCCCCcCccCC
Confidence 4568999999999999999999997
No 2
>smart00356 ZnF_C3H1 zinc finger.
Probab=96.95 E-value=0.00061 Score=40.74 Aligned_cols=22 Identities=41% Similarity=1.025 Sum_probs=20.5
Q ss_pred CCCCCccccccccCCCCCCCCCC
Q 040778 229 QRCRDFEERGFCLRGDMCPMEHG 251 (262)
Q Consensus 229 ~RCrDydekGyC~rGd~CpydHG 251 (262)
..|++| ++|.|.+|+.|+|.|.
T Consensus 5 ~~C~~~-~~g~C~~g~~C~~~H~ 26 (27)
T smart00356 5 ELCKFF-KRGYCPYGDRCKFAHP 26 (27)
T ss_pred CcCcCc-cCCCCCCCCCcCCCCc
Confidence 479999 9999999999999996
No 3
>KOG2135 consensus Proteins containing the RNA recognition motif [General function prediction only]
Probab=96.71 E-value=0.00043 Score=68.89 Aligned_cols=33 Identities=39% Similarity=0.672 Sum_probs=30.7
Q ss_pred CCCCCCCCccccccccCCCCCCCCCCCCccccc
Q 040778 226 ISRQRCRDFEERGFCLRGDMCPMEHGVNRIVVE 258 (262)
Q Consensus 226 ~~r~RCrDydekGyC~rGd~CpydHG~Dpvvv~ 258 (262)
....||.+|++.|||.+|++|||+||.++||++
T Consensus 210 ~s~~r~k~fee~g~~~r~el~p~~hg~~~vv~~ 242 (526)
T KOG2135|consen 210 NSENRRKFFEEFGVLERGELCPTHHGCVPVVSK 242 (526)
T ss_pred ccHHhhhhhHhhceeeeccccccccccceeEee
Confidence 456789999999999999999999999999987
No 4
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=92.45 E-value=0.044 Score=50.55 Aligned_cols=28 Identities=32% Similarity=0.807 Sum_probs=23.9
Q ss_pred CCCCCCCCccccccccCCCCCCCCCCCC
Q 040778 226 ISRQRCRDFEERGFCLRGDMCPMEHGVN 253 (262)
Q Consensus 226 ~~r~RCrDydekGyC~rGd~CpydHG~D 253 (262)
...-.|.||.+-|||-.||+|.|-|.-+
T Consensus 139 ~qpdVCKdyk~TGYCGYGDsCKflH~R~ 166 (259)
T COG5152 139 TQPDVCKDYKETGYCGYGDSCKFLHDRS 166 (259)
T ss_pred cCcccccchhhcccccCCchhhhhhhhh
Confidence 3445799999999999999999999544
No 5
>KOG1677 consensus CCCH-type Zn-finger protein [General function prediction only]
Probab=90.90 E-value=0.16 Score=45.80 Aligned_cols=31 Identities=26% Similarity=0.599 Sum_probs=27.3
Q ss_pred CCCCCCCCCccccccccCCCCCCCCCCCCcc
Q 040778 225 GISRQRCRDFEERGFCLRGDMCPMEHGVNRI 255 (262)
Q Consensus 225 ~~~r~RCrDydekGyC~rGd~CpydHG~Dpv 255 (262)
..+..-|..|.+-|+|..|..|.|-|+.+-.
T Consensus 174 ~~kt~lC~~f~~tG~C~yG~rC~F~H~~~~~ 204 (332)
T KOG1677|consen 174 KYKTKLCPKFQKTGLCKYGSRCRFIHGEPED 204 (332)
T ss_pred CCCCcCCCccccCCCCCCCCcCeecCCCccc
Confidence 3677889999999999999999999998733
No 6
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=87.57 E-value=0.16 Score=48.53 Aligned_cols=24 Identities=38% Similarity=0.958 Sum_probs=21.6
Q ss_pred CCCCCCCccccccccCCCCCCCCC
Q 040778 227 SRQRCRDFEERGFCLRGDMCPMEH 250 (262)
Q Consensus 227 ~r~RCrDydekGyC~rGd~CpydH 250 (262)
..-.|.||+|-|||-.|+.|.|-|
T Consensus 185 qpDicKdykeTgycg~gdSckFlh 208 (313)
T KOG1813|consen 185 QPDICKDYKETGYCGYGDSCKFLH 208 (313)
T ss_pred CchhhhhhHhhCcccccchhhhhh
Confidence 345799999999999999999987
No 7
>KOG1595 consensus CCCH-type Zn-finger protein [General function prediction only]
Probab=85.82 E-value=0.37 Score=48.83 Aligned_cols=23 Identities=48% Similarity=1.084 Sum_probs=20.2
Q ss_pred CCCCCccccccccCCCCCCCCCCC
Q 040778 229 QRCRDFEERGFCLRGDMCPMEHGV 252 (262)
Q Consensus 229 ~RCrDydekGyC~rGd~CpydHG~ 252 (262)
.-|.+|.. |-|-+||+|.|-||.
T Consensus 237 tpCPefrk-G~C~rGD~CEyaHgv 259 (528)
T KOG1595|consen 237 TPCPEFRK-GSCERGDSCEYAHGV 259 (528)
T ss_pred ccCccccc-CCCCCCCccccccce
Confidence 34999876 999999999999984
No 8
>PF14608 zf-CCCH_2: Zinc finger C-x8-C-x5-C-x3-H type
Probab=84.49 E-value=0.68 Score=27.30 Aligned_cols=18 Identities=39% Similarity=0.922 Sum_probs=14.7
Q ss_pred CCCccccccccCCCCCCCCCC
Q 040778 231 CRDFEERGFCLRGDMCPMEHG 251 (262)
Q Consensus 231 CrDydekGyC~rGd~CpydHG 251 (262)
|+.+-. |..++.|+|.|.
T Consensus 2 Ck~~~~---C~~~~~C~f~HP 19 (19)
T PF14608_consen 2 CKFGPN---CTNGDNCPFSHP 19 (19)
T ss_pred CcCcCC---CCCCCcCccCCc
Confidence 776544 999999999994
No 9
>KOG1677 consensus CCCH-type Zn-finger protein [General function prediction only]
Probab=83.03 E-value=0.56 Score=42.28 Aligned_cols=31 Identities=29% Similarity=0.762 Sum_probs=27.4
Q ss_pred CCCCCCCCccccccccC-CCCCCCCCCCCccc
Q 040778 226 ISRQRCRDFEERGFCLR-GDMCPMEHGVNRIV 256 (262)
Q Consensus 226 ~~r~RCrDydekGyC~r-Gd~CpydHG~Dpvv 256 (262)
.+...|+.|.+.|+|.. |+.|.|.||.+-+-
T Consensus 130 ~kt~lc~~~~~~g~c~y~ge~crfah~~~e~r 161 (332)
T KOG1677|consen 130 YKTPLCRSFRKSGTCKYRGEQCRFAHGLEELR 161 (332)
T ss_pred ccCCcceeeecCccccccCchhhhcCCccccc
Confidence 56778999999999999 99999999887554
No 10
>COG5063 CTH1 CCCH-type Zn-finger protein [General function prediction only]
Probab=82.95 E-value=0.64 Score=45.03 Aligned_cols=33 Identities=24% Similarity=0.598 Sum_probs=28.5
Q ss_pred CCCCCCCCccccccccCCCCCCCCCCCCccccc
Q 040778 226 ISRQRCRDFEERGFCLRGDMCPMEHGVNRIVVE 258 (262)
Q Consensus 226 ~~r~RCrDydekGyC~rGd~CpydHG~Dpvvv~ 258 (262)
-+.+-|.+|+.-|||..|--|+|-||.|-.|-.
T Consensus 272 frTePcinwe~sGyc~yg~Rc~F~hgd~~~ie~ 304 (351)
T COG5063 272 FRTEPCINWEKSGYCPYGLRCCFKHGDDSDIEM 304 (351)
T ss_pred cccCCccchhhcccCccccccccccCChhhccc
Confidence 456789999999999999999999999976543
No 11
>KOG1040 consensus Polyadenylation factor I complex, subunit, Yth1 (CPSF subunit) [RNA processing and modification]
Probab=74.14 E-value=1.9 Score=41.20 Aligned_cols=27 Identities=33% Similarity=0.663 Sum_probs=24.2
Q ss_pred CCCCCCCCccccccccCCCCCCCCCCC
Q 040778 226 ISRQRCRDFEERGFCLRGDMCPMEHGV 252 (262)
Q Consensus 226 ~~r~RCrDydekGyC~rGd~CpydHG~ 252 (262)
.+...|..|...|+|..+..|+|-|+.
T Consensus 103 ~k~rec~ff~~~g~c~~~~~c~y~h~d 129 (325)
T KOG1040|consen 103 TKMRECKFFSLFGECTNGKDCPYLHGD 129 (325)
T ss_pred cccccccccccccccccccCCcccCCC
Confidence 455689999999999999999999986
No 12
>COG5063 CTH1 CCCH-type Zn-finger protein [General function prediction only]
Probab=55.64 E-value=18 Score=35.42 Aligned_cols=27 Identities=22% Similarity=0.322 Sum_probs=22.7
Q ss_pred CCCCCCCCccccccccCCCCCCCCCCC
Q 040778 226 ISRQRCRDFEERGFCLRGDMCPMEHGV 252 (262)
Q Consensus 226 ~~r~RCrDydekGyC~rGd~CpydHG~ 252 (262)
.+...|++--+.+||..++.|||.|..
T Consensus 113 ~kt~~l~ss~~~~~~~~p~~n~fahs~ 139 (351)
T COG5063 113 YKTEMLRSSTEIPYCRYPDKNPFAHSK 139 (351)
T ss_pred ccchhhhccccccccccCCCCcCCCcc
Confidence 456678888899999999999999965
No 13
>KOG1492 consensus C3H1-type Zn-finger protein [General function prediction only]
Probab=45.79 E-value=7.4 Score=37.14 Aligned_cols=24 Identities=29% Similarity=0.765 Sum_probs=22.0
Q ss_pred CCCCccccccccCCCCCCCCCCCC
Q 040778 230 RCRDFEERGFCLRGDMCPMEHGVN 253 (262)
Q Consensus 230 RCrDydekGyC~rGd~CpydHG~D 253 (262)
-||-|...|+|-.|+.|.|-|.+-
T Consensus 208 ycryynangicgkgaacrfvhept 231 (377)
T KOG1492|consen 208 YCRYYNANGICGKGAACRFVHEPT 231 (377)
T ss_pred EEEEecCCCcccCCceeeeecccc
Confidence 699999999999999999999654
No 14
>KOG2494 consensus C3H1-type Zn-finger protein [Transcription]
Probab=38.03 E-value=11 Score=36.59 Aligned_cols=29 Identities=38% Similarity=0.765 Sum_probs=22.9
Q ss_pred CCCCCccccccccCCCC-CCCCCCCCccccc
Q 040778 229 QRCRDFEERGFCLRGDM-CPMEHGVNRIVVE 258 (262)
Q Consensus 229 ~RCrDydekGyC~rGd~-CpydHG~Dpvvv~ 258 (262)
+.|||| -||.|.|||. |.|-|=.--+=|+
T Consensus 38 eVCReF-~rn~C~R~d~~CkfaHP~~~~~V~ 67 (331)
T KOG2494|consen 38 EVCREF-LRNTCSRGDRECKFAHPPKNCQVS 67 (331)
T ss_pred HHHHHH-HhccccCCCccccccCCCCCCCcc
Confidence 569997 5899999999 9999965544343
No 15
>COG5084 YTH1 Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin family Zn-finger proteins [General function prediction only]
Probab=36.79 E-value=19 Score=34.22 Aligned_cols=24 Identities=33% Similarity=0.677 Sum_probs=21.9
Q ss_pred CCCCCccccccccCCCCCCCCCCC
Q 040778 229 QRCRDFEERGFCLRGDMCPMEHGV 252 (262)
Q Consensus 229 ~RCrDydekGyC~rGd~CpydHG~ 252 (262)
--|+.|-.+|.|..|..|+|-|..
T Consensus 135 ~~c~~Fs~~G~cs~g~~c~~~h~d 158 (285)
T COG5084 135 PPCRSFSLKGSCSSGPSCGYSHID 158 (285)
T ss_pred CCcccccccceeccCCCCCccccC
Confidence 469999999999999999999974
No 16
>KOG2333 consensus Uncharacterized conserved protein [General function prediction only]
Probab=33.96 E-value=20 Score=37.29 Aligned_cols=22 Identities=36% Similarity=0.712 Sum_probs=20.2
Q ss_pred CCCCCCCccccccccCCCCCCC
Q 040778 227 SRQRCRDFEERGFCLRGDMCPM 248 (262)
Q Consensus 227 ~r~RCrDydekGyC~rGd~Cpy 248 (262)
....|.-|+..|||..|-.|.|
T Consensus 113 ig~~Cp~f~s~G~Cp~G~~CRF 134 (614)
T KOG2333|consen 113 IGPSCPVFESLGFCPYGFKCRF 134 (614)
T ss_pred cCCccceeeccccCCccceeeh
Confidence 3468999999999999999999
No 17
>KOG4791 consensus Uncharacterized conserved protein [Function unknown]
Probab=26.10 E-value=59 Score=33.95 Aligned_cols=51 Identities=10% Similarity=-0.013 Sum_probs=30.9
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCcCCCCCCCCCCCCCccccccccCCCCCCCCCCCCc
Q 040778 193 LIPGVPNGGLDTLPSIGLQGTLRPPLNSSLNMGISRQRCRDFEERGFCLRGDMCPMEHGVNR 254 (262)
Q Consensus 193 ~mPGMppm~l~~~h~~g~qG~lqp~~~~~~~~~~~r~RCrDydekGyC~rGd~CpydHG~Dp 254 (262)
.||+-|.|.+-++|-.. -+++|+.. .--| ++.-||||+.+|+|-+-|-+-+
T Consensus 93 ~~p~~pe~ev~~~~~SA----q~~sV~~~------p~P~-l~~~K~~e~~~D~~s~Lh~P~A 143 (667)
T KOG4791|consen 93 TVPESPEEEVKASQLSA----QQNSVQSN------PSPQ-LRSVKKVESSEDVPSPLHPPVA 143 (667)
T ss_pred CCCCCcccccccccccC----CCcccccC------CchH-HHHhhhhhhhccccccCCCCcc
Confidence 45555666666555432 12233221 1123 5678999999999999886533
No 18
>PF11942 Spt5_N: Spt5 transcription elongation factor, acidic N-terminal; InterPro: IPR022581 This is the very acidic N-terminal domain of the early transcription elongation factor Spt5 []. The Spt5-Spt4 complex regulates early transcription elongation by RNA polymerase II and has an imputed role in pre-mRNA processing via its physical association with mRNA capping enzymes. The actual function of this N-terminal domain is not known although it is dispensable for binding to Spt4 [], nor is it essential for RNA polymerase II binding [].
Probab=26.01 E-value=31 Score=27.10 Aligned_cols=33 Identities=18% Similarity=0.393 Sum_probs=15.8
Q ss_pred ccchhhhhhhccccccccchhhhhchhhh--hcCCC
Q 040778 35 RNHKHRRRETRSQSLERDSLDQVYMRSYR--KRNKP 68 (262)
Q Consensus 35 RNHKHRRRe~rsqs~~rd~~e~~~~r~~k--kr~~~ 68 (262)
+.+.||+...+-+-...-..+.+ ...|| ||+..
T Consensus 40 ~d~~~r~~d~~r~~~~~~dae~l-ae~~k~~~RY~~ 74 (97)
T PF11942_consen 40 DDRRHRRLDRRREMEEEEDAEEL-AEYLKLSERYAR 74 (97)
T ss_pred hHhhhhhhhhhHHHHhccCHHHH-HHHHHHHHHhcc
Confidence 45566665444333333222333 44667 66543
No 19
>PF11705 RNA_pol_3_Rpc31: DNA-directed RNA polymerase III subunit Rpc31; InterPro: IPR024661 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. RNA polymerase III contains seventeen subunits in yeasts and in human cells. Twelve of these are akin to RNA polymerase I or II and the other five are RNA polymerase III-specific, and form the functionally distinct groups: (i) Rpc31-Rpc34-Rpc82, and (ii) Rpc37-Rpc53. Rpc31, Rpc34 and Rpc82 form a cluster of enzyme-specific subunits that contribute to transcription initiation in Saccharomyces cerevisiae and Homo sapiens. There is evidence that these subunits are anchored at or near the N-terminal Zn-fold of Rpc1, itself prolonged by a highly conserved but RNA polymerase III-specific domain []. This entry represents the Rpc31 subunit.
Probab=22.52 E-value=1.7e+02 Score=25.92 Aligned_cols=14 Identities=36% Similarity=0.550 Sum_probs=7.3
Q ss_pred CCCCCCCCCCCCCC
Q 040778 168 MPPSRFAGRGLPNI 181 (262)
Q Consensus 168 ~ppg~fpg~gp~~~ 181 (262)
-|+.|||.-.+|-+
T Consensus 31 ~P~~lfP~~~~P~~ 44 (233)
T PF11705_consen 31 QPPPLFPPLNLPVP 44 (233)
T ss_pred CCCCCCCCCCCCCC
Confidence 44667764444433
No 20
>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]
Probab=20.81 E-value=43 Score=33.23 Aligned_cols=24 Identities=38% Similarity=0.783 Sum_probs=19.1
Q ss_pred CCCCCccccccccCCCCCCCCCCCC
Q 040778 229 QRCRDFEERGFCLRGDMCPMEHGVN 253 (262)
Q Consensus 229 ~RCrDydekGyC~rGd~CpydHG~D 253 (262)
..|..| .+|=|-||+.|+|-|.-.
T Consensus 162 ~Icsf~-v~geckRG~ec~yrhEkp 185 (377)
T KOG0153|consen 162 HICSFF-VKGECKRGAECPYRHEKP 185 (377)
T ss_pred ccccce-eeccccccccccccccCC
Confidence 457765 577999999999999653
Done!