Query 033906
Match_columns 109
No_of_seqs 66 out of 68
Neff 2.6
Searched_HMMs 46136
Date Fri Mar 29 07:38:20 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033906.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033906hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF07011 DUF1313: Protein of u 100.0 1.8E-54 3.9E-59 303.2 8.3 86 14-99 1-86 (87)
2 PF05030 SSXT: SSXT protein (N 88.6 0.44 9.5E-06 32.2 2.5 39 29-71 9-48 (65)
3 PF07011 DUF1313: Protein of u 84.0 1.2 2.5E-05 31.9 2.8 38 56-93 21-66 (87)
4 PF05377 FlaC_arch: Flagella a 81.3 1.7 3.7E-05 28.6 2.6 22 64-85 30-51 (55)
5 PHA02951 Hypothetical protein; 65.0 7.7 0.00017 33.4 3.3 49 15-63 274-330 (337)
6 PF08056 Trp_leader2: Tryptoph 64.4 1.9 4.2E-05 27.2 -0.3 17 42-58 2-18 (41)
7 PF07554 FIVAR: Uncharacterise 58.9 10 0.00022 22.2 2.2 32 15-46 15-49 (51)
8 KOG3227 Calcium-responsive tra 53.4 12 0.00026 30.9 2.4 23 28-50 22-44 (231)
9 PF11214 Med2: Mediator comple 46.1 35 0.00076 25.1 3.7 29 60-88 43-71 (105)
10 COG3352 FlaC Putative archaeal 44.9 23 0.0005 27.7 2.8 28 64-91 81-108 (157)
11 PF13879 KIAA1430: KIAA1430 ho 33.5 83 0.0018 20.4 3.7 32 21-52 28-59 (98)
12 PF07709 SRR: Seven Residue Re 32.6 35 0.00076 16.4 1.4 13 70-82 2-14 (14)
13 PF05130 FlgN: FlgN protein; 32.6 88 0.0019 20.5 3.7 27 18-44 87-113 (143)
14 PF12998 ING: Inhibitor of gro 32.1 1.5E+02 0.0031 19.3 5.4 46 30-77 30-76 (105)
15 PF11315 Med30: Mediator compl 31.0 87 0.0019 24.0 3.9 30 18-47 114-143 (150)
16 PF08649 DASH_Dad1: DASH compl 30.4 56 0.0012 21.6 2.5 30 39-76 8-37 (58)
17 PF07508 Recombinase: Recombin 29.0 33 0.00072 21.9 1.2 13 26-38 90-102 (102)
18 PF13949 ALIX_LYPXL_bnd: ALIX 27.2 2.9E+02 0.0062 21.1 6.2 67 20-87 198-266 (296)
19 PF13174 TPR_6: Tetratricopept 27.0 93 0.002 15.5 3.1 29 60-88 5-33 (33)
20 PF04912 Dynamitin: Dynamitin 26.4 3E+02 0.0066 22.8 6.6 47 19-76 336-382 (388)
21 PF14775 NYD-SP28_assoc: Sperm 26.0 1.9E+02 0.0041 18.7 6.3 30 16-45 13-42 (60)
22 KOG4038 cGMP-phosphodiesterase 25.5 29 0.00064 26.8 0.5 24 46-69 42-65 (150)
23 PF06143 Baculo_11_kDa: Baculo 22.3 81 0.0018 22.3 2.2 18 27-44 18-35 (84)
24 PF12513 SUV3_C: Mitochondrial 22.2 58 0.0013 19.7 1.3 19 71-89 7-25 (49)
25 PF13708 Methyltransf_27: Meth 22.0 3.1E+02 0.0067 20.8 5.5 69 15-86 5-80 (194)
26 PTZ00065 60S ribosomal protein 21.9 7.7 0.00017 29.2 -3.1 13 31-43 28-40 (130)
27 PF10360 DUF2433: Protein of u 20.2 1E+02 0.0022 23.3 2.5 23 18-43 29-54 (132)
28 PF06238 Borrelia_lipo_2: Borr 20.1 99 0.0021 23.1 2.4 44 26-79 59-102 (111)
No 1
>PF07011 DUF1313: Protein of unknown function (DUF1313); InterPro: IPR009741 This family consists of several hypothetical plant proteins of around 100 residues in length. The function of this family is unknown.
Probab=100.00 E-value=1.8e-54 Score=303.23 Aligned_cols=86 Identities=74% Similarity=1.046 Sum_probs=83.7
Q ss_pred cccchhhhHHHHHhHHHHHHHHhhhHHHHHHHhhccccCCCCchhhhHHHHHHHhhhHHHHHHHHhhhhhhhhhhccCcc
Q 033906 14 TQVNGRVMQTFQRSFGQVQDILDQNRLLINEINQNHESKIPDNLTRNVGLIKELNNNIRRVVNLYADLSTSFSRSVEGSL 93 (109)
Q Consensus 14 ~~~d~~~~~~f~ksF~qVQ~iLDqNR~LI~EINqNHeSr~PdnL~RNV~LIrELN~NI~rVv~LYsdLS~sF~~~~~~ss 93 (109)
++||+|+|+||+|+|+|||+||||||+||+|||||||||+||+|+|||+||||||+||+|||+||+|||++|+++|++++
T Consensus 1 ~~~d~~~~~tf~~sF~qVQ~iLDqNR~LI~eINqNHeSr~PdnL~RNV~LIrELN~NI~rVv~lY~dLs~sFs~~~~~~~ 80 (87)
T PF07011_consen 1 EQGDGKVWQTFQKSFVQVQSILDQNRLLINEINQNHESRIPDNLSRNVGLIRELNGNISRVVDLYSDLSSSFSKSVEQSS 80 (87)
T ss_pred CCccHHHHHHHHHHHHHHHHHHHHhHHHHHHHhhcccccCCchhhHhHHHHHHHHhhHHHHHHHHHHHhHHHHHHHhccc
Confidence 36999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccchhh
Q 033906 94 EDESAG 99 (109)
Q Consensus 94 eg~s~~ 99 (109)
+|++++
T Consensus 81 ~g~~~~ 86 (87)
T PF07011_consen 81 EGDSSG 86 (87)
T ss_pred ccCcCC
Confidence 999874
No 2
>PF05030 SSXT: SSXT protein (N-terminal region); InterPro: IPR007726 SSXT (also known as SYT or SS18) appears to function synergistically with RBM14 as a transcriptional coactivator []. The SSXT protein is involved in synovial sarcoma in humans. A SYT-SSX fusion gene resulting from the chromosomal translocation t(X;18) (p11;q11) is characteristic of synovial sarcomas. This translocation fuses the SSXT (SYT) gene from chromosome 18 to either of two homologous genes at Xp11, SSX1 or SSX2 []. This entry also includes SS18-like protein 1, a transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons [],[].
Probab=88.56 E-value=0.44 Score=32.16 Aligned_cols=39 Identities=28% Similarity=0.430 Sum_probs=27.8
Q ss_pred HHHHHHHhhhHHHHHHHhhccc-cCCCCchhhhHHHHHHHhhhH
Q 033906 29 GQVQDILDQNRLLINEINQNHE-SKIPDNLTRNVGLIKELNNNI 71 (109)
Q Consensus 29 ~qVQ~iLDqNR~LI~EINqNHe-Sr~PdnL~RNV~LIrELN~NI 71 (109)
.+||.+||.|.-||+-|.+++. .|.+|- |..-+-|..|+
T Consensus 9 ~~IQk~LdEN~~LI~~I~e~qn~Gr~~Ec----~qyq~~LhrNL 48 (65)
T PF05030_consen 9 EQIQKMLDENDQLIQCIQEYQNKGRAQEC----VQYQQILHRNL 48 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCHHHH----HHHHHHHHHHH
Confidence 5799999999999999999875 333332 33445555554
No 3
>PF07011 DUF1313: Protein of unknown function (DUF1313); InterPro: IPR009741 This family consists of several hypothetical plant proteins of around 100 residues in length. The function of this family is unknown.
Probab=84.02 E-value=1.2 Score=31.91 Aligned_cols=38 Identities=37% Similarity=0.415 Sum_probs=25.6
Q ss_pred chhhhHHHHHHHhh--------hHHHHHHHHhhhhhhhhhhccCcc
Q 033906 56 NLTRNVGLIKELNN--------NIRRVVNLYADLSTSFSRSVEGSL 93 (109)
Q Consensus 56 nL~RNV~LIrELN~--------NI~rVv~LYsdLS~sF~~~~~~ss 93 (109)
=|-+|=.||.|+|. |+.|=|.|-++|..+.++.|+-.+
T Consensus 21 iLDqNR~LI~eINqNHeSr~PdnL~RNV~LIrELN~NI~rVv~lY~ 66 (87)
T PF07011_consen 21 ILDQNRLLINEINQNHESRIPDNLSRNVGLIRELNGNISRVVDLYS 66 (87)
T ss_pred HHHHhHHHHHHHhhcccccCCchhhHhHHHHHHHHhhHHHHHHHHH
Confidence 35667777777775 366777777777777777665433
No 4
>PF05377 FlaC_arch: Flagella accessory protein C (FlaC); InterPro: IPR008039 Although archaeal flagella appear superficially similar to those of bacteria, they are quite distinct []. In several archaea, the flagellin genes are followed immediately by the flagellar accessory genes flaCDEFGHIJ. The gene products may have a role in translocation, secretion, or assembly of the flagellum. FlaC is a protein whose exact role is unknown but it has been shown to be membrane-associated (by immuno-blotting fractionated cells) [].
Probab=81.28 E-value=1.7 Score=28.58 Aligned_cols=22 Identities=18% Similarity=0.584 Sum_probs=18.3
Q ss_pred HHHHhhhHHHHHHHHhhhhhhh
Q 033906 64 IKELNNNIRRVVNLYADLSTSF 85 (109)
Q Consensus 64 IrELN~NI~rVv~LYsdLS~sF 85 (109)
|.+|+.||++|++||.-.|-.+
T Consensus 30 ve~i~envk~ll~lYE~Vs~~i 51 (55)
T PF05377_consen 30 VEKIEENVKDLLSLYEVVSNQI 51 (55)
T ss_pred HHHHHHHHHHHHHHHHHHHccC
Confidence 5678999999999999877644
No 5
>PHA02951 Hypothetical protein; Provisional
Probab=65.00 E-value=7.7 Score=33.43 Aligned_cols=49 Identities=20% Similarity=0.335 Sum_probs=42.2
Q ss_pred ccchhhhHHHHHhHHHHHHHHhh--------hHHHHHHHhhccccCCCCchhhhHHH
Q 033906 15 QVNGRVMQTFQRSFGQVQDILDQ--------NRLLINEINQNHESKIPDNLTRNVGL 63 (109)
Q Consensus 15 ~~d~~~~~~f~ksF~qVQ~iLDq--------NR~LI~EINqNHeSr~PdnL~RNV~L 63 (109)
..+...|.-..+-|..+..+||. |.-+|.+|+.+--++.-|...-|.+|
T Consensus 274 ~~~~~lw~e~t~l~~~i~~lld~n~e~~~~in~yii~~i~~~~~~~~~~eiv~nl~l 330 (337)
T PHA02951 274 TNITTLWNETTKLIKEIKSLLDKNHEDYDIINNYIIKEIKNCEGVKNRDEIVNNLSL 330 (337)
T ss_pred chHHHHHHHHHHHHHHHHHHhccChHHHHHHHHHHHHHHhcccccccHHHHhhhhhh
Confidence 35678999999999999999999 55788999999999988888877765
No 6
>PF08056 Trp_leader2: Tryptophan operon leader peptide; InterPro: IPR012639 This family consists of the tryptophan operon leader peptides. The tryptophan operon is regulated by transcription attenuation in response to changes in the level of tryptophan. The transcript of the leader peptide can adopt alternative mutually-exclusive secondary structures that would either result in termination of transcription of the tryptophan structural genes or in transcription of the entire operon [].
Probab=64.37 E-value=1.9 Score=27.23 Aligned_cols=17 Identities=29% Similarity=0.565 Sum_probs=13.4
Q ss_pred HHHHhhccccCCCCchh
Q 033906 42 INEINQNHESKIPDNLT 58 (109)
Q Consensus 42 I~EINqNHeSr~PdnL~ 58 (109)
+||+||||..|+..-..
T Consensus 2 LQe~n~nqk~kva~~~~ 18 (41)
T PF08056_consen 2 LQEFNQNQKAKVAAHSS 18 (41)
T ss_pred chhhccchhhhhhhhcc
Confidence 68999999998864433
No 7
>PF07554 FIVAR: Uncharacterised Sugar-binding Domain; InterPro: IPR011490 This domain is found in a wide variety of contexts, but mostly occurring in cell wall associated proteins. A lack of conserved catalytic residues suggests that it is a binding domain. From context, possible substrates are hyaluronate or fibronectin. This is further evidenced by []. Possibly the exact substrate is N-acetyl glucosamine. Finding it in the same protein as IPR007781 from INTERPRO further supports this proposal. It is found in the C-terminal part of O82833 from SWISSPROT, which is removed during maturation []. The name FIVAR derives from Found In Various Architectures.; PDB: 1XVH_B 2OZN_B 2JNK_A 2DGJ_A.
Probab=58.92 E-value=10 Score=22.24 Aligned_cols=32 Identities=6% Similarity=0.264 Sum_probs=24.9
Q ss_pred ccchhhhHHHHHhHHHHHHHHhhhH---HHHHHHh
Q 033906 15 QVNGRVMQTFQRSFGQVQDILDQNR---LLINEIN 46 (109)
Q Consensus 15 ~~d~~~~~~f~ksF~qVQ~iLDqNR---~LI~EIN 46 (109)
..+.+.|.+|++....++.||+... +=-.+|+
T Consensus 15 ~~~~~~~~~y~~Al~~A~~vl~~~~~~~~t~~~V~ 49 (51)
T PF07554_consen 15 NATPESKAAYDNALNAAKAVLNNTNNPNATQEEVD 49 (51)
T ss_dssp TS-HHHHHHHHHHHHHHHHHHCCTT---TTHHHHH
T ss_pred hcCHHHHHHHHHHHHHHHHHHcCCCCCCCCHHHHh
Confidence 4688999999999999999998754 4455554
No 8
>KOG3227 consensus Calcium-responsive transcription coactivator [Transcription]
Probab=53.38 E-value=12 Score=30.88 Aligned_cols=23 Identities=35% Similarity=0.510 Sum_probs=19.7
Q ss_pred HHHHHHHHhhhHHHHHHHhhccc
Q 033906 28 FGQVQDILDQNRLLINEINQNHE 50 (109)
Q Consensus 28 F~qVQ~iLDqNR~LI~EINqNHe 50 (109)
-.++|..||.|.-||.-|=+++-
T Consensus 22 ~~~IQk~LdEN~~LI~~I~e~Qn 44 (231)
T KOG3227|consen 22 SEQIQKMLDENKHLIQCIVESQN 44 (231)
T ss_pred HHHHHHHHHhhhHHHHHHHHhhc
Confidence 35899999999999999977764
No 9
>PF11214 Med2: Mediator complex subunit 2; InterPro: IPR021017 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. This family of mediator complex subunit 2 proteins is conserved in fungi. Cyclin-dependent kinase CDK8 or Srb10 interacts with and phosphorylates Med2. Post-translational modifications of Mediator subunits are important for regulation of gene expression [, ].
Probab=46.15 E-value=35 Score=25.07 Aligned_cols=29 Identities=24% Similarity=0.381 Sum_probs=25.3
Q ss_pred hHHHHHHHhhhHHHHHHHHhhhhhhhhhh
Q 033906 60 NVGLIKELNNNIRRVVNLYADLSTSFSRS 88 (109)
Q Consensus 60 NV~LIrELN~NI~rVv~LYsdLS~sF~~~ 88 (109)
|-.|++-|+..|...-++--|+-+.|..+
T Consensus 43 n~~l~k~L~eki~~Fh~ILDd~~~~l~~s 71 (105)
T PF11214_consen 43 NNQLQKQLSEKIHKFHSILDDTESKLNDS 71 (105)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33569999999999999999999999864
No 10
>COG3352 FlaC Putative archaeal flagellar protein C [Cell motility and secretion]
Probab=44.87 E-value=23 Score=27.70 Aligned_cols=28 Identities=29% Similarity=0.519 Sum_probs=23.7
Q ss_pred HHHHhhhHHHHHHHHhhhhhhhhhhccC
Q 033906 64 IKELNNNIRRVVNLYADLSTSFSRSVEG 91 (109)
Q Consensus 64 IrELN~NI~rVv~LYsdLS~sF~~~~~~ 91 (109)
|-+|=+||.+++.+|+-+|..|.--+..
T Consensus 81 lerLe~~iKdl~~lye~Vs~d~Npf~s~ 108 (157)
T COG3352 81 LERLEENIKDLVSLYELVSRDFNPFMSK 108 (157)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhhhHHhh
Confidence 4568899999999999999999876644
No 11
>PF13879 KIAA1430: KIAA1430 homologue
Probab=33.55 E-value=83 Score=20.35 Aligned_cols=32 Identities=16% Similarity=0.204 Sum_probs=24.7
Q ss_pred hHHHHHhHHHHHHHHhhhHHHHHHHhhccccC
Q 033906 21 MQTFQRSFGQVQDILDQNRLLINEINQNHESK 52 (109)
Q Consensus 21 ~~~f~ksF~qVQ~iLDqNR~LI~EINqNHeSr 52 (109)
+..++....+++.|..+|+.|.+.|..=+..+
T Consensus 28 ~kk~~~~~er~~~I~reN~~LL~ki~~I~~~~ 59 (98)
T PF13879_consen 28 RKKLQFEEERQREIERENQILLRKIMEIMRKP 59 (98)
T ss_pred HHHHHhhHHHHHHHHHHHHHHHHHHHHHHcCC
Confidence 44556667889999999999999998765443
No 12
>PF07709 SRR: Seven Residue Repeat; InterPro: IPR011714 This repeat is found in some Plasmodium and Theileria proteins.
Probab=32.60 E-value=35 Score=16.38 Aligned_cols=13 Identities=38% Similarity=0.618 Sum_probs=10.1
Q ss_pred hHHHHHHHHhhhh
Q 033906 70 NIRRVVNLYADLS 82 (109)
Q Consensus 70 NI~rVv~LYsdLS 82 (109)
|-.+|.+.|..|+
T Consensus 2 ~~~~V~~aY~~l~ 14 (14)
T PF07709_consen 2 KFEKVKNAYEQLS 14 (14)
T ss_pred cHHHHHHHHHhcC
Confidence 4568999998875
No 13
>PF05130 FlgN: FlgN protein; InterPro: IPR007809 Flagella synthesis protein FlgN is an export chaperone involved in flagellar synthesis []. This entry represents a FlgN-like domain, consisting of a 4 long helices bundle, where the last helix is shorter than the three others.; GO: 0009296 flagellum assembly, 0019861 flagellum; PDB: 2FUP_A 3OPC_A.
Probab=32.58 E-value=88 Score=20.49 Aligned_cols=27 Identities=11% Similarity=0.367 Sum_probs=21.6
Q ss_pred hhhhHHHHHhHHHHHHHHhhhHHHHHH
Q 033906 18 GRVMQTFQRSFGQVQDILDQNRLLINE 44 (109)
Q Consensus 18 ~~~~~~f~ksF~qVQ~iLDqNR~LI~E 44 (109)
...|..+.....+++.+=+.|+.||+.
T Consensus 87 ~~~~~~l~~~~~~~~~~n~~N~~ll~~ 113 (143)
T PF05130_consen 87 QALWRELRELLEELQELNERNQQLLEQ 113 (143)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 456888888888888888888888865
No 14
>PF12998 ING: Inhibitor of growth proteins N-terminal histone-binding; InterPro: IPR024610 Histones undergo numerous post-translational modifications, including acetylation and methylation, at residues which are then probable docking sites for various chromatin remodelling complexes. Inhibitor of growth proteins (INGs) specifically bind to residues that have been thus modified. INGs carry a well-characterised C-terminal PHD-type zinc-finger domain, binding with lysine 4-tri-methylated histone H3 (H3K4me3), as well as this N-terminal domain that binds unmodified H3 tails. Although these two regions can bind histones independently, together they increase the apparent association of the ING for the H3 tail. This entry represents the N-terminal histone binding domain found in inhibitor proteins.; PDB: 4AFL_A.
Probab=32.06 E-value=1.5e+02 Score=19.29 Aligned_cols=46 Identities=26% Similarity=0.459 Sum_probs=31.9
Q ss_pred HHHHHHhhhHHHHHHHhhcccc-CCCCchhhhHHHHHHHhhhHHHHHHH
Q 033906 30 QVQDILDQNRLLINEINQNHES-KIPDNLTRNVGLIKELNNNIRRVVNL 77 (109)
Q Consensus 30 qVQ~iLDqNR~LI~EINqNHeS-r~PdnL~RNV~LIrELN~NI~rVv~L 77 (109)
++|+++.+-...+++.-+++.+ ..|.+ .-..++++|...+.++..+
T Consensus 30 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~I~~~~~~~~~l 76 (105)
T PF12998_consen 30 KSQDLLEELDQQIQKFIKNHGSPSLSPE--KRRELLKEIQEEYERALEL 76 (105)
T ss_dssp HHHHHHHHHHHHHHHHHTCTTS--S-HH--HHHHHHHHHHHHHHHHHHH
T ss_pred hHHHHHHHHHHHHHHHHhhcccccCChH--HHHHHHHHHHHHHHHHHHH
Confidence 3567777777788888777776 23333 6677888888888877654
No 15
>PF11315 Med30: Mediator complex subunit 30; InterPro: IPR021019 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. Med30 is a metazoan-specific subunit of Mediator [], having no homologues in yeasts.
Probab=31.00 E-value=87 Score=23.96 Aligned_cols=30 Identities=30% Similarity=0.452 Sum_probs=24.4
Q ss_pred hhhhHHHHHhHHHHHHHHhhhHHHHHHHhh
Q 033906 18 GRVMQTFQRSFGQVQDILDQNRLLINEINQ 47 (109)
Q Consensus 18 ~~~~~~f~ksF~qVQ~iLDqNR~LI~EINq 47 (109)
.++.+.+...=.|...|+||=|.+|.|||.
T Consensus 114 ~el~e~v~~KN~qLk~iid~lR~~iweIN~ 143 (150)
T PF11315_consen 114 KELIEQVKQKNQQLKEIIDQLRNIIWEINT 143 (150)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 356666666778899999999999999995
No 16
>PF08649 DASH_Dad1: DASH complex subunit Dad1; InterPro: IPR013958 The DASH complex is a ~10 subunit microtubule-binding complex that is transferred to the kinetochore prior to mitosis []. In Saccharomyces cerevisiae (Baker's yeast) DASH forms both rings and spiral structures on microtubules in vitro [, ]. Components of the DASH complex, including Dam1, Duo1, Spc34, Dad1 and Ask1, are essential and connect the centromere to the plus end of spindle microtubules []. Throughout the cell cycle Dad1 remains bound to kinetochores and its association is dependent on the Mis6 and Mal2 [].
Probab=30.38 E-value=56 Score=21.58 Aligned_cols=30 Identities=23% Similarity=0.443 Sum_probs=18.4
Q ss_pred HHHHHHHhhccccCCCCchhhhHHHHHHHhhhHHHHHH
Q 033906 39 RLLINEINQNHESKIPDNLTRNVGLIKELNNNIRRVVN 76 (109)
Q Consensus 39 R~LI~EINqNHeSr~PdnL~RNV~LIrELN~NI~rVv~ 76 (109)
..||+||.++ |..=+.-|..||.|+--|.+
T Consensus 8 ~~Li~eI~~~--------~e~vl~nlN~LNRsLE~~i~ 37 (58)
T PF08649_consen 8 DRLIQEISES--------MESVLNNLNALNRSLESVIS 37 (58)
T ss_pred HHHHHHHHHH--------HHHHHHHHHHHHHhHHHHHH
Confidence 4577777643 44445566677777666554
No 17
>PF07508 Recombinase: Recombinase; InterPro: IPR011109 This domain is usually found associated with IPR006119 from INTERPRO in putative integrases/recombinases of mobile genetic elements of diverse bacteria and phages.
Probab=29.02 E-value=33 Score=21.92 Aligned_cols=13 Identities=38% Similarity=0.603 Sum_probs=11.1
Q ss_pred HhHHHHHHHHhhh
Q 033906 26 RSFGQVQDILDQN 38 (109)
Q Consensus 26 ksF~qVQ~iLDqN 38 (109)
.-|.+||.+|++|
T Consensus 90 ~~f~~vq~~l~~r 102 (102)
T PF07508_consen 90 EEFERVQKKLDER 102 (102)
T ss_pred HHHHHHHHHHhcC
Confidence 3599999999986
No 18
>PF13949 ALIX_LYPXL_bnd: ALIX V-shaped domain binding to HIV ; PDB: 2XS1_A 2XS8_A 2R03_A 2R02_A 2OEX_B 2OEV_A 2OJQ_A 2R05_A.
Probab=27.24 E-value=2.9e+02 Score=21.14 Aligned_cols=67 Identities=15% Similarity=0.233 Sum_probs=35.7
Q ss_pred hhHHHHHhHHHHHHHHhhhHHHHHHHhhccccCCCCc--hhhhHHHHHHHhhhHHHHHHHHhhhhhhhhh
Q 033906 20 VMQTFQRSFGQVQDILDQNRLLINEINQNHESKIPDN--LTRNVGLIKELNNNIRRVVNLYADLSTSFSR 87 (109)
Q Consensus 20 ~~~~f~ksF~qVQ~iLDqNR~LI~EINqNHeSr~Pdn--L~RNV~LIrELN~NI~rVv~LYsdLS~sF~~ 87 (109)
-++-|..-..+|+.-+.+...||++|-..++.-.+.. .... .-....=..+....+.|.+|..+...
T Consensus 198 eL~k~~~~~~~i~~~~~~Q~~ll~~i~~~~~~~~~~~~~~~~~-~~r~~~~~~l~~a~~~y~el~~~l~e 266 (296)
T PF13949_consen 198 ELKKFDPLQNRIQQNLSKQEELLQEIQEANEEFAQSRKSDQEQ-KERESALQRLEAAYDAYKELSSNLEE 266 (296)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS--SHHH-HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccHHH-HHHHHHHHHHHHHHHHHHHHHHhHHH
Confidence 3444544455667777777889999988775433222 1111 22233334444445555555555443
No 19
>PF13174 TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_A 3URZ_B 2Q7F_A.
Probab=27.04 E-value=93 Score=15.47 Aligned_cols=29 Identities=7% Similarity=0.112 Sum_probs=22.8
Q ss_pred hHHHHHHHhhhHHHHHHHHhhhhhhhhhh
Q 033906 60 NVGLIKELNNNIRRVVNLYADLSTSFSRS 88 (109)
Q Consensus 60 NV~LIrELN~NI~rVv~LYsdLS~sF~~~ 88 (109)
+.+.+....++..+-+..|..+-..|.+|
T Consensus 5 ~~a~~~~~~g~~~~A~~~~~~~~~~~P~s 33 (33)
T PF13174_consen 5 RLARCYYKLGDYDEAIEYFQRLIKRYPDS 33 (33)
T ss_dssp HHHHHHHHHCHHHHHHHHHHHHHHHSTTS
T ss_pred HHHHHHHHccCHHHHHHHHHHHHHHCcCC
Confidence 45677777888899999999888877653
No 20
>PF04912 Dynamitin: Dynamitin ; InterPro: IPR006996 Dynamitin is a subunit of the microtubule-dependent motor complex, it is also implicated in cell adhesion by binding to macrophage-enriched myristoylated alanine-rice C kinase substrate (MacMARCKS) []. It is also thought to modulate cytoplasmic dynein binding to an organelle, and plays a role in prometaphase chromosome alignment and spindle organisation during mitosis. Dynamitin is also involved in anchoring microtubules to centrosomes and may play a role in synapse formation during brain development []. ; GO: 0007017 microtubule-based process, 0005869 dynactin complex
Probab=26.35 E-value=3e+02 Score=22.75 Aligned_cols=47 Identities=15% Similarity=0.376 Sum_probs=34.9
Q ss_pred hhhHHHHHhHHHHHHHHhhhHHHHHHHhhccccCCCCchhhhHHHHHHHhhhHHHHHH
Q 033906 19 RVMQTFQRSFGQVQDILDQNRLLINEINQNHESKIPDNLTRNVGLIKELNNNIRRVVN 76 (109)
Q Consensus 19 ~~~~~f~ksF~qVQ~iLDqNR~LI~EINqNHeSr~PdnL~RNV~LIrELN~NI~rVv~ 76 (109)
..+..+...=.+++.-|.+++.++++++++ +..|...| ++||..+-+
T Consensus 336 ~~l~~le~~q~~l~~~l~~~~~~L~~ve~~--------~~~N~~~i---~~n~~~le~ 382 (388)
T PF04912_consen 336 QTLSELESQQSDLQSQLKKWEELLNKVEEK--------FKENMETI---EKNVKKLEE 382 (388)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--------HHHHHHHH---HHHHHHHHH
Confidence 345566666777888999999999999998 77777655 456665543
No 21
>PF14775 NYD-SP28_assoc: Sperm tail C-terminal domain
Probab=25.97 E-value=1.9e+02 Score=18.65 Aligned_cols=30 Identities=17% Similarity=0.200 Sum_probs=27.3
Q ss_pred cchhhhHHHHHhHHHHHHHHhhhHHHHHHH
Q 033906 16 VNGRVMQTFQRSFGQVQDILDQNRLLINEI 45 (109)
Q Consensus 16 ~d~~~~~~f~ksF~qVQ~iLDqNR~LI~EI 45 (109)
-.-++|.+|.+.+.+=-.||-+-..||+|+
T Consensus 13 ~~~~~W~~L~~~l~rY~~vL~~R~~l~~e~ 42 (60)
T PF14775_consen 13 EKIRLWDALENFLKRYNKVLLDRAALIQEK 42 (60)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 456899999999999999999999999997
No 22
>KOG4038 consensus cGMP-phosphodiesterase, delta subunit [Signal transduction mechanisms]
Probab=25.45 E-value=29 Score=26.84 Aligned_cols=24 Identities=25% Similarity=0.583 Sum_probs=21.4
Q ss_pred hhccccCCCCchhhhHHHHHHHhh
Q 033906 46 NQNHESKIPDNLTRNVGLIKELNN 69 (109)
Q Consensus 46 NqNHeSr~PdnL~RNV~LIrELN~ 69 (109)
.+.||.|+|.++-+=-+.-||||=
T Consensus 42 ~~ehearvpkkilkcravsreinf 65 (150)
T KOG4038|consen 42 DQEHEARVPKKILKCRAVSREINF 65 (150)
T ss_pred cchhhhcccHHHHhhHhhhhhccc
Confidence 468999999999999999999984
No 23
>PF06143 Baculo_11_kDa: Baculovirus 11 kDa family; InterPro: IPR009313 This is a family of uncharacterised Baculovirus proteins that are all about 11 kDa in size.
Probab=22.31 E-value=81 Score=22.26 Aligned_cols=18 Identities=22% Similarity=0.645 Sum_probs=16.1
Q ss_pred hHHHHHHHHhhhHHHHHH
Q 033906 27 SFGQVQDILDQNRLLINE 44 (109)
Q Consensus 27 sF~qVQ~iLDqNR~LI~E 44 (109)
.|+|.+.++-+||.+|.+
T Consensus 18 d~DQL~qlVsrN~sfird 35 (84)
T PF06143_consen 18 DYDQLEQLVSRNRSFIRD 35 (84)
T ss_pred cHHHHHHHHHhChHHHHH
Confidence 489999999999999876
No 24
>PF12513 SUV3_C: Mitochondrial degradasome RNA helicase subunit C terminal; InterPro: IPR022192 This domain family is found in bacteria and eukaryotes, and is approximately 50 amino acids in length. The family is found in association with PF00271 from PFAM. The yeast mitochondrial degradosome (mtEXO) is an NTP-dependent exoribonuclease involved in mitochondrial RNA metabolism. mtEXO is made up of two subunits: an RNase (DSS1) and an RNA helicase (SUV3). These co-purify with mitochondrial ribosomes. ; GO: 0016817 hydrolase activity, acting on acid anhydrides; PDB: 3RC8_A 3RC3_A.
Probab=22.24 E-value=58 Score=19.72 Aligned_cols=19 Identities=32% Similarity=0.513 Sum_probs=15.3
Q ss_pred HHHHHHHHhhhhhhhhhhc
Q 033906 71 IRRVVNLYADLSTSFSRSV 89 (109)
Q Consensus 71 I~rVv~LYsdLS~sF~~~~ 89 (109)
.-+++++|--||--|...+
T Consensus 7 ~hk~l~lYlWLs~Rfp~~F 25 (49)
T PF12513_consen 7 LHKVLDLYLWLSYRFPDVF 25 (49)
T ss_dssp HHHHHHHHHHHHCC-TTTS
T ss_pred HHHHHHHHHHHHHHccccc
Confidence 4689999999999997665
No 25
>PF13708 Methyltransf_27: Methyltransferase domain
Probab=21.95 E-value=3.1e+02 Score=20.76 Aligned_cols=69 Identities=16% Similarity=0.348 Sum_probs=52.4
Q ss_pred ccchhhhHHHHHhHHHHHHHHhhhHHHHHHHhhccc-cCCCCchhhhH-HHHHHHhhhH-----HHHHHHHhhhhhhhh
Q 033906 15 QVNGRVMQTFQRSFGQVQDILDQNRLLINEINQNHE-SKIPDNLTRNV-GLIKELNNNI-----RRVVNLYADLSTSFS 86 (109)
Q Consensus 15 ~~d~~~~~~f~ksF~qVQ~iLDqNR~LI~EINqNHe-Sr~PdnL~RNV-~LIrELN~NI-----~rVv~LYsdLS~sF~ 86 (109)
.+|.+.|+-+=+... +.+.+++.+ .+|+++.=+ -..|+==..|| +...+|..|- +.|+++|..||..|-
T Consensus 5 ~ld~~~W~~l~~~t~-~~~~m~~~~--r~~~~~~l~~~~~p~ft~~NI~~t~~~l~~~r~~~~~~~v~~vF~~Ls~~yK 80 (194)
T PF13708_consen 5 NLDRSYWRRLMDKTG-MRSFMSAQA--RDEWDKQLEEDDPPEFTEENIYSTFEQLHANRGEIFERGVIDVFRSLSWDYK 80 (194)
T ss_pred HHHHHHHHHHHHhhC-cHhHhCHHH--HHHHHHHHhcCCCCCccHHHHHHHHHHHHHCHHHHHHHHHHHHHHHhchhhc
Confidence 578999998887666 888888775 355555544 46777777787 5778888885 568999999988875
No 26
>PTZ00065 60S ribosomal protein L14; Provisional
Probab=21.87 E-value=7.7 Score=29.18 Aligned_cols=13 Identities=31% Similarity=0.723 Sum_probs=10.3
Q ss_pred HHHHHhhhHHHHH
Q 033906 31 VQDILDQNRLLIN 43 (109)
Q Consensus 31 VQ~iLDqNR~LI~ 43 (109)
|=+|+||||.||.
T Consensus 28 IVDIID~nRvLVD 40 (130)
T PTZ00065 28 IVDIVTPTRVLVD 40 (130)
T ss_pred EEEEEcCCeEEEe
Confidence 3468999999984
No 27
>PF10360 DUF2433: Protein of unknown function (DUF2433); InterPro: IPR018829 This entry represents a conserved domain of 120 residues from a family fungal proteins. Their function is not known.
Probab=20.24 E-value=1e+02 Score=23.28 Aligned_cols=23 Identities=39% Similarity=0.644 Sum_probs=15.7
Q ss_pred hhhhHHHHHhHHHHHHHHhhh---HHHHH
Q 033906 18 GRVMQTFQRSFGQVQDILDQN---RLLIN 43 (109)
Q Consensus 18 ~~~~~~f~ksF~qVQ~iLDqN---R~LI~ 43 (109)
.++|++..- ||..+||.| |.||.
T Consensus 29 ~~vW~~VK~---~ve~~i~~~~~q~~LL~ 54 (132)
T PF10360_consen 29 GEVWETVKG---QVEEAIDPNEAQRNLLE 54 (132)
T ss_pred HHHHHHHHH---HHHHHhCCCHHHHHHHH
Confidence 467777764 777888877 55553
No 28
>PF06238 Borrelia_lipo_2: Borrelia burgdorferi BBR25 lipoprotein; InterPro: IPR009358 This entry consists of a number of lipoproteins conserved in Borrelia species [].
Probab=20.15 E-value=99 Score=23.12 Aligned_cols=44 Identities=25% Similarity=0.463 Sum_probs=31.4
Q ss_pred HhHHHHHHHHhhhHHHHHHHhhccccCCCCchhhhHHHHHHHhhhHHHHHHHHh
Q 033906 26 RSFGQVQDILDQNRLLINEINQNHESKIPDNLTRNVGLIKELNNNIRRVVNLYA 79 (109)
Q Consensus 26 ksF~qVQ~iLDqNR~LI~EINqNHeSr~PdnL~RNV~LIrELN~NI~rVv~LYs 79 (109)
|-|..+|+||.-|--+|.-||+. ||-..|-.|=.-=-++|.-|-
T Consensus 59 KIl~eIq~Ilk~nieiIeai~~~----------k~~~iIs~LkakRNkiMkeyi 102 (111)
T PF06238_consen 59 KILEEIQDILKYNIEIIEAISTD----------KNKRIISSLKAKRNKIMKEYI 102 (111)
T ss_pred HHHHHHHHHHHHHHHHHHHHccc----------hhhhHHHHHHHHHHHHHHHHH
Confidence 46889999999999999999885 455555555444445555554
Done!