Query 033643
Match_columns 114
No_of_seqs 65 out of 67
Neff 2.6
Searched_HMMs 46136
Date Fri Mar 29 04:38:06 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033643.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033643hhsearch_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 4.2E-55 9.2E-60 308.3 9.0 87 13-99 1-87 (87)
2 PF05030 SSXT: SSXT protein (N 88.5 0.43 9.4E-06 32.4 2.5 39 28-70 9-48 (65)
3 PF07011 DUF1313: Protein of u 84.8 1.2 2.6E-05 32.1 3.1 38 54-91 20-65 (87)
4 PF05377 FlaC_arch: Flagella a 80.7 1.7 3.7E-05 28.7 2.5 22 63-84 30-51 (55)
5 PF08056 Trp_leader2: Tryptoph 64.5 1.9 4.1E-05 27.4 -0.3 17 41-57 2-18 (41)
6 PHA02951 Hypothetical protein; 63.8 8.6 0.00019 33.4 3.4 48 15-62 275-330 (337)
7 PF07554 FIVAR: Uncharacterise 62.0 10 0.00022 22.4 2.6 33 14-46 15-50 (51)
8 KOG3227 Calcium-responsive tra 52.9 12 0.00026 31.0 2.4 23 27-49 22-44 (231)
9 PF08649 DASH_Dad1: DASH compl 52.8 14 0.0003 24.6 2.3 30 38-75 8-37 (58)
10 PF11214 Med2: Mediator comple 47.5 36 0.00078 25.2 4.0 29 59-87 43-71 (105)
11 COG3352 FlaC Putative archaeal 45.8 21 0.00045 28.2 2.7 29 63-91 81-109 (157)
12 PF12998 ING: Inhibitor of gro 34.5 1.3E+02 0.0029 19.6 5.4 46 29-76 30-76 (105)
13 PF05130 FlgN: FlgN protein; 33.9 90 0.0019 20.6 4.0 27 17-43 87-113 (143)
14 PF13879 KIAA1430: KIAA1430 ho 33.7 83 0.0018 20.5 3.7 32 20-51 28-59 (98)
15 PF11315 Med30: Mediator compl 32.4 87 0.0019 24.1 4.1 30 17-46 114-143 (150)
16 PF01017 STAT_alpha: STAT prot 32.3 2.2E+02 0.0048 21.5 6.6 34 10-44 114-147 (182)
17 PF07709 SRR: Seven Residue Re 30.9 37 0.00081 16.4 1.3 13 69-81 2-14 (14)
18 PF13949 ALIX_LYPXL_bnd: ALIX 29.1 2.7E+02 0.0058 21.4 6.9 68 18-86 197-266 (296)
19 PF07508 Recombinase: Recombin 28.4 34 0.00074 22.0 1.2 13 25-37 90-102 (102)
20 PF04912 Dynamitin: Dynamitin 27.6 2.9E+02 0.0062 23.1 6.7 47 18-75 336-382 (388)
21 PF13174 TPR_6: Tetratricopept 26.9 96 0.0021 15.5 2.9 29 59-87 5-33 (33)
22 PF14775 NYD-SP28_assoc: Sperm 25.6 2E+02 0.0043 18.7 6.5 30 15-44 13-42 (60)
23 KOG4038 cGMP-phosphodiesterase 25.3 29 0.00062 27.1 0.5 25 45-69 42-66 (150)
24 PF13708 Methyltransf_27: Meth 24.8 3E+02 0.0065 21.0 5.9 69 14-85 5-80 (194)
25 PTZ00065 60S ribosomal protein 22.2 8.1 0.00018 29.3 -3.0 13 30-42 28-40 (130)
26 TIGR01241 FtsH_fam ATP-depende 21.8 1.1E+02 0.0024 26.0 3.3 31 14-44 445-475 (495)
27 PF06143 Baculo_11_kDa: Baculo 21.5 84 0.0018 22.3 2.2 18 26-43 18-35 (84)
28 PF10360 DUF2433: Protein of u 21.0 1E+02 0.0023 23.4 2.7 22 17-41 29-53 (132)
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=4.2e-55 Score=308.30 Aligned_cols=87 Identities=72% Similarity=1.032 Sum_probs=85.0
Q ss_pred cccChHHHHHHHHhHHHHHHHHhhhHHHHHHHhhccccCCCCcchhhHHHHHHHhHhHHHHHHHHhhhhhhhhhhhcccc
Q 033643 13 AQVDDKILQIFQKSFGQVQDILDQNRLLINEINQNHESKVPDNLTRNVGLIKELNNNITRVVNLYADLSNSFTRSMEASS 92 (114)
Q Consensus 13 ~~~d~k~~~~f~ksF~qVQ~iLDqNR~LI~EINqNHeSr~PdnL~RNV~LIrELN~NI~rVv~LYsdLS~sF~~~~~~ss 92 (114)
++||+|+|+||+|+|+|||+||||||+||+|||||||||+||+|+|||+||||||+||+|||+||+|||++|+++|++++
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 ccccccc
Q 033643 93 EGESAAT 99 (114)
Q Consensus 93 eg~s~g~ 99 (114)
+|+++|+
T Consensus 81 ~g~~~~~ 87 (87)
T PF07011_consen 81 EGDSSGT 87 (87)
T ss_pred ccCcCCC
Confidence 9999985
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=88.54 E-value=0.43 Score=32.41 Aligned_cols=39 Identities=28% Similarity=0.438 Sum_probs=27.8
Q ss_pred HHHHHHHhhhHHHHHHHhhccc-cCCCCcchhhHHHHHHHhHhH
Q 033643 28 GQVQDILDQNRLLINEINQNHE-SKVPDNLTRNVGLIKELNNNI 70 (114)
Q Consensus 28 ~qVQ~iLDqNR~LI~EINqNHe-Sr~PdnL~RNV~LIrELN~NI 70 (114)
.+||.+||.|.-||+-|.+++. .|.+| =|..-+-|..|+
T Consensus 9 ~~IQk~LdEN~~LI~~I~e~qn~Gr~~E----c~qyq~~LhrNL 48 (65)
T PF05030_consen 9 EQIQKMLDENDQLIQCIQEYQNKGRAQE----CVQYQQILHRNL 48 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCHHH----HHHHHHHHHHHH
Confidence 5799999999999999999875 33333 233455555554
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=84.79 E-value=1.2 Score=32.08 Aligned_cols=38 Identities=32% Similarity=0.472 Sum_probs=28.6
Q ss_pred CcchhhHHHHHHHhH--------hHHHHHHHHhhhhhhhhhhhccc
Q 033643 54 DNLTRNVGLIKELNN--------NITRVVNLYADLSNSFTRSMEAS 91 (114)
Q Consensus 54 dnL~RNV~LIrELN~--------NI~rVv~LYsdLS~sF~~~~~~s 91 (114)
+=|-+|=.||.|+|. |+.|=|.|-++|..+.++.|+-.
T Consensus 20 ~iLDqNR~LI~eINqNHeSr~PdnL~RNV~LIrELN~NI~rVv~lY 65 (87)
T PF07011_consen 20 SILDQNRLLINEINQNHESRIPDNLSRNVGLIRELNGNISRVVDLY 65 (87)
T ss_pred HHHHHhHHHHHHHhhcccccCCchhhHhHHHHHHHHhhHHHHHHHH
Confidence 346778888888885 47788888888888888877643
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=80.72 E-value=1.7 Score=28.75 Aligned_cols=22 Identities=23% Similarity=0.594 Sum_probs=18.3
Q ss_pred HHHHhHhHHHHHHHHhhhhhhh
Q 033643 63 IKELNNNITRVVNLYADLSNSF 84 (114)
Q Consensus 63 IrELN~NI~rVv~LYsdLS~sF 84 (114)
|.+|+.||++|++||.-.|-.+
T Consensus 30 ve~i~envk~ll~lYE~Vs~~i 51 (55)
T PF05377_consen 30 VEKIEENVKDLLSLYEVVSNQI 51 (55)
T ss_pred HHHHHHHHHHHHHHHHHHHccC
Confidence 5678999999999999877543
No 5
>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=64.55 E-value=1.9 Score=27.44 Aligned_cols=17 Identities=35% Similarity=0.571 Sum_probs=13.4
Q ss_pred HHHHhhccccCCCCcch
Q 033643 41 INEINQNHESKVPDNLT 57 (114)
Q Consensus 41 I~EINqNHeSr~PdnL~ 57 (114)
+||+||||..|+..-..
T Consensus 2 LQe~n~nqk~kva~~~~ 18 (41)
T PF08056_consen 2 LQEFNQNQKAKVAAHSS 18 (41)
T ss_pred chhhccchhhhhhhhcc
Confidence 58999999998864433
No 6
>PHA02951 Hypothetical protein; Provisional
Probab=63.79 E-value=8.6 Score=33.39 Aligned_cols=48 Identities=23% Similarity=0.343 Sum_probs=41.5
Q ss_pred cChHHHHHHHHhHHHHHHHHhh--------hHHHHHHHhhccccCCCCcchhhHHH
Q 033643 15 VDDKILQIFQKSFGQVQDILDQ--------NRLLINEINQNHESKVPDNLTRNVGL 62 (114)
Q Consensus 15 ~d~k~~~~f~ksF~qVQ~iLDq--------NR~LI~EINqNHeSr~PdnL~RNV~L 62 (114)
.+...|.-..+-|..+..+||. |.-+|.+|+.+--++.-|...-|.+|
T Consensus 275 ~~~~lw~e~t~l~~~i~~lld~n~e~~~~in~yii~~i~~~~~~~~~~eiv~nl~l 330 (337)
T PHA02951 275 NITTLWNETTKLIKEIKSLLDKNHEDYDIINNYIIKEIKNCEGVKNRDEIVNNLSL 330 (337)
T ss_pred hHHHHHHHHHHHHHHHHHHhccChHHHHHHHHHHHHHHhcccccccHHHHhhhhhh
Confidence 4668999999999999999999 55788999999999988888877765
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=62.01 E-value=10 Score=22.36 Aligned_cols=33 Identities=9% Similarity=0.271 Sum_probs=25.6
Q ss_pred ccChHHHHHHHHhHHHHHHHHhhhH---HHHHHHhh
Q 033643 14 QVDDKILQIFQKSFGQVQDILDQNR---LLINEINQ 46 (114)
Q Consensus 14 ~~d~k~~~~f~ksF~qVQ~iLDqNR---~LI~EINq 46 (114)
..+.+.|..|++....++.||+... +=-.||++
T Consensus 15 ~~~~~~~~~y~~Al~~A~~vl~~~~~~~~t~~~V~~ 50 (51)
T PF07554_consen 15 NATPESKAAYDNALNAAKAVLNNTNNPNATQEEVDQ 50 (51)
T ss_dssp TS-HHHHHHHHHHHHHHHHHHCCTT---TTHHHHHH
T ss_pred hcCHHHHHHHHHHHHHHHHHHcCCCCCCCCHHHHhc
Confidence 4688999999999999999998754 55555553
No 8
>KOG3227 consensus Calcium-responsive transcription coactivator [Transcription]
Probab=52.92 E-value=12 Score=31.05 Aligned_cols=23 Identities=35% Similarity=0.510 Sum_probs=19.7
Q ss_pred HHHHHHHHhhhHHHHHHHhhccc
Q 033643 27 FGQVQDILDQNRLLINEINQNHE 49 (114)
Q Consensus 27 F~qVQ~iLDqNR~LI~EINqNHe 49 (114)
-.++|..||.|.-||.-|=+++-
T Consensus 22 ~~~IQk~LdEN~~LI~~I~e~Qn 44 (231)
T KOG3227|consen 22 SEQIQKMLDENKHLIQCIVESQN 44 (231)
T ss_pred HHHHHHHHHhhhHHHHHHHHhhc
Confidence 35899999999999999987764
No 9
>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=52.77 E-value=14 Score=24.63 Aligned_cols=30 Identities=23% Similarity=0.438 Sum_probs=15.2
Q ss_pred HHHHHHHhhccccCCCCcchhhHHHHHHHhHhHHHHHH
Q 033643 38 RLLINEINQNHESKVPDNLTRNVGLIKELNNNITRVVN 75 (114)
Q Consensus 38 R~LI~EINqNHeSr~PdnL~RNV~LIrELN~NI~rVv~ 75 (114)
..||+||.++ |..=+.-|..||.|+--|..
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 3456666543 33334445556665555443
No 10
>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=47.55 E-value=36 Score=25.18 Aligned_cols=29 Identities=24% Similarity=0.359 Sum_probs=25.3
Q ss_pred hHHHHHHHhHhHHHHHHHHhhhhhhhhhh
Q 033643 59 NVGLIKELNNNITRVVNLYADLSNSFTRS 87 (114)
Q Consensus 59 NV~LIrELN~NI~rVv~LYsdLS~sF~~~ 87 (114)
|-.|++-|+..|...-++--|+-+.|..+
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 11
>COG3352 FlaC Putative archaeal flagellar protein C [Cell motility and secretion]
Probab=45.82 E-value=21 Score=28.15 Aligned_cols=29 Identities=31% Similarity=0.528 Sum_probs=24.4
Q ss_pred HHHHhHhHHHHHHHHhhhhhhhhhhhccc
Q 033643 63 IKELNNNITRVVNLYADLSNSFTRSMEAS 91 (114)
Q Consensus 63 IrELN~NI~rVv~LYsdLS~sF~~~~~~s 91 (114)
|-+|=+||.+++.+|+-+|..|.--+...
T Consensus 81 lerLe~~iKdl~~lye~Vs~d~Npf~s~~ 109 (157)
T COG3352 81 LERLEENIKDLVSLYELVSRDFNPFMSKT 109 (157)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhhhHHhhh
Confidence 45688999999999999999998766543
No 12
>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=34.50 E-value=1.3e+02 Score=19.61 Aligned_cols=46 Identities=26% Similarity=0.448 Sum_probs=31.9
Q ss_pred HHHHHHhhhHHHHHHHhhcccc-CCCCcchhhHHHHHHHhHhHHHHHHH
Q 033643 29 QVQDILDQNRLLINEINQNHES-KVPDNLTRNVGLIKELNNNITRVVNL 76 (114)
Q Consensus 29 qVQ~iLDqNR~LI~EINqNHeS-r~PdnL~RNV~LIrELN~NI~rVv~L 76 (114)
++|+++.+-.-.+++.-+++.+ .+|.+ .-..++++|+..+.++..+
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 3567777777788887777776 23333 6677888888888877654
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=33.87 E-value=90 Score=20.61 Aligned_cols=27 Identities=11% Similarity=0.387 Sum_probs=19.7
Q ss_pred hHHHHHHHHhHHHHHHHHhhhHHHHHH
Q 033643 17 DKILQIFQKSFGQVQDILDQNRLLINE 43 (114)
Q Consensus 17 ~k~~~~f~ksF~qVQ~iLDqNR~LI~E 43 (114)
...|..+.....+++.+=+.|+.||+.
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 346777777777777777777777764
No 14
>PF13879 KIAA1430: KIAA1430 homologue
Probab=33.65 E-value=83 Score=20.49 Aligned_cols=32 Identities=16% Similarity=0.175 Sum_probs=24.9
Q ss_pred HHHHHHhHHHHHHHHhhhHHHHHHHhhccccC
Q 033643 20 LQIFQKSFGQVQDILDQNRLLINEINQNHESK 51 (114)
Q Consensus 20 ~~~f~ksF~qVQ~iLDqNR~LI~EINqNHeSr 51 (114)
|..++....+++.|..+|+.|.+.|..=+..+
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 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=32.36 E-value=87 Score=24.14 Aligned_cols=30 Identities=30% Similarity=0.472 Sum_probs=24.9
Q ss_pred hHHHHHHHHhHHHHHHHHhhhHHHHHHHhh
Q 033643 17 DKILQIFQKSFGQVQDILDQNRLLINEINQ 46 (114)
Q Consensus 17 ~k~~~~f~ksF~qVQ~iLDqNR~LI~EINq 46 (114)
.++.+.+...=.|...|+||=|.+|.|||.
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 456666777778999999999999999995
No 16
>PF01017 STAT_alpha: STAT protein, all-alpha domain; InterPro: IPR013800 The STAT protein (Signal Transducers and Activators of Transcription) family contains transcription factors that are specifically activated to regulate gene transcription when cells encounter cytokines and growth factors, hence they act as signal transducers in the cytoplasm and transcription activators in the nucleus []. Binding of these factors to cell-surface receptors leads to receptor autophosphorylation at a tyrosine, the phosphotyrosine being recognised by the STAT SH2 domain, which mediates the recruitment of STAT proteins from the cytosol and their association with the activated receptor. The STAT proteins are then activated by phosphorylation via members of the JAK family of protein kinases, causing them to dimerise and translocated to the nucleus, where they bind to specific promoter sequences in target genes. In mammals, STATs comprise a family of seven structurally and functionally related proteins: Stat1, Stat2, Stat3, Stat4, Stat5a and Stat5b, Stat6. STAT proteins play a critical role in regulating innate and acquired host immune responses. Dysregulation of at least two STAT signalling cascades (i.e. Stat3 and Stat5) is associated with cellular transformation. Signalling through the JAK/STAT pathway is initiated when a cytokine binds to its corresponding receptor. This leads to conformational changes in the cytoplasmic portion of the receptor, initiating activation of receptor associated members of the JAK family of kinases. The JAKs, in turn, mediate phosphorylation at the specific receptor tyrosine residues, which then serve as docking sites for STATs and other signalling molecules. Once recruited to the receptor, STATs also become phosphorylated by JAKs, on a single tyrosine residue. Activated STATs dissociate from the receptor, dimerise, translocate to the nucleus and bind to members of the GAS (gamma activated site) family of enhancers. The seven STAT proteins identified in mammals range in size from 750 and 850 amino acids. The chromosomal distribution of these STATs, as well as the identification of STATs in more primitive eukaryotes, suggest that this family arose from a single primordial gene. STATs share structurally and functionally conserved domains including: an N-terminal domain that strengthens interactions between STAT dimers on adjacent DNA-binding sites; a coiled-coil STAT domain that is implicated in protein-protein interactions; a DNA-binding domain with an immunoglobulin-like fold similar to p53 tumour suppressor protein; an EF-hand-like linker domain connecting the DNA-binding and SH2 domains; an SH2 domain (IPR000980 from INTERPRO) that acts as a phosphorylation-dependent switch to control receptor recognition and DNA-binding; and a C-terminal transactivation domain []. The crystal structure of the N terminus of Stat4 reveals a dimer. The interface of this dimer is formed by a ring-shaped element consisting of five short helices. Several studies suggest that this N-terminal dimerisation promotes cooperativity of binding to tandem GAS elements and with the transcriptional coactivator CBP/p300. This entry represents the all-alpha helical domain, which consists of four long helices arranged in a bundle with a left-handed twist (coiled-coil), which in turn forms a right-handed superhelix.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0004871 signal transducer activity, 0006355 regulation of transcription, DNA-dependent, 0007165 signal transduction, 0005634 nucleus; PDB: 1YVL_A 1BF5_A 3CWG_B 1BG1_A 1Y1U_B.
Probab=32.27 E-value=2.2e+02 Score=21.45 Aligned_cols=34 Identities=26% Similarity=0.232 Sum_probs=27.3
Q ss_pred CCccccChHHHHHHHHhHHHHHHHHhhhHHHHHHH
Q 033643 10 GNDAQVDDKILQIFQKSFGQVQDILDQNRLLINEI 44 (114)
Q Consensus 10 g~~~~~d~k~~~~f~ksF~qVQ~iLDqNR~LI~EI 44 (114)
|+|.+ ...-++.+|+-|..+-.+|=|+|-.|.++
T Consensus 114 ~iG~P-~~~~LD~LQ~wfe~LAe~l~qlrqqlk~l 147 (182)
T PF01017_consen 114 CIGAP-FDSSLDQLQNWFESLAEILWQLRQQLKKL 147 (182)
T ss_dssp HTTSS-----THHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred cCCCC-ChhhhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45666 57789999999999999999999999998
No 17
>PF07709 SRR: Seven Residue Repeat; InterPro: IPR011714 This repeat is found in some Plasmodium and Theileria proteins.
Probab=30.88 E-value=37 Score=16.40 Aligned_cols=13 Identities=38% Similarity=0.606 Sum_probs=10.0
Q ss_pred hHHHHHHHHhhhh
Q 033643 69 NITRVVNLYADLS 81 (114)
Q Consensus 69 NI~rVv~LYsdLS 81 (114)
|-.+|.+.|..|+
T Consensus 2 ~~~~V~~aY~~l~ 14 (14)
T PF07709_consen 2 KFEKVKNAYEQLS 14 (14)
T ss_pred cHHHHHHHHHhcC
Confidence 4568899998875
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=29.06 E-value=2.7e+02 Score=21.44 Aligned_cols=68 Identities=16% Similarity=0.226 Sum_probs=37.4
Q ss_pred HHHHHHHHhHHHHHHHHhhhHHHHHHHhhccccCCCCc--chhhHHHHHHHhHhHHHHHHHHhhhhhhhhh
Q 033643 18 KILQIFQKSFGQVQDILDQNRLLINEINQNHESKVPDN--LTRNVGLIKELNNNITRVVNLYADLSNSFTR 86 (114)
Q Consensus 18 k~~~~f~ksF~qVQ~iLDqNR~LI~EINqNHeSr~Pdn--L~RNV~LIrELN~NI~rVv~LYsdLS~sF~~ 86 (114)
+-++-|..-..+|+.-+.+...||++|-..++.-.+.. .... .-....-..+....+.|.+|..+...
T Consensus 197 ~eL~k~~~~~~~i~~~~~~Q~~ll~~i~~~~~~~~~~~~~~~~~-~~r~~~~~~l~~a~~~y~el~~~l~e 266 (296)
T PF13949_consen 197 EELKKFDPLQNRIQQNLSKQEELLQEIQEANEEFAQSRKSDQEQ-KERESALQRLEAAYDAYKELSSNLEE 266 (296)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS--SHHH-HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccHHH-HHHHHHHHHHHHHHHHHHHHHHhHHH
Confidence 33444555556677777778899999988775443322 1111 22333334444455555555555443
No 19
>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=28.42 E-value=34 Score=22.03 Aligned_cols=13 Identities=38% Similarity=0.624 Sum_probs=11.1
Q ss_pred HhHHHHHHHHhhh
Q 033643 25 KSFGQVQDILDQN 37 (114)
Q Consensus 25 ksF~qVQ~iLDqN 37 (114)
.-|.+||.+|++|
T Consensus 90 ~~f~~vq~~l~~r 102 (102)
T PF07508_consen 90 EEFERVQKKLDER 102 (102)
T ss_pred HHHHHHHHHHhcC
Confidence 3599999999986
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=27.56 E-value=2.9e+02 Score=23.08 Aligned_cols=47 Identities=17% Similarity=0.345 Sum_probs=35.1
Q ss_pred HHHHHHHHhHHHHHHHHhhhHHHHHHHhhccccCCCCcchhhHHHHHHHhHhHHHHHH
Q 033643 18 KILQIFQKSFGQVQDILDQNRLLINEINQNHESKVPDNLTRNVGLIKELNNNITRVVN 75 (114)
Q Consensus 18 k~~~~f~ksF~qVQ~iLDqNR~LI~EINqNHeSr~PdnL~RNV~LIrELN~NI~rVv~ 75 (114)
..+..+...=.+++.-|.+++.++++++++ +..|...| ++||..+-+
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 445666666778889999999999999998 77777654 456665543
No 21
>PF13174 TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_A 3URZ_B 2Q7F_A.
Probab=26.91 E-value=96 Score=15.55 Aligned_cols=29 Identities=7% Similarity=0.120 Sum_probs=22.5
Q ss_pred hHHHHHHHhHhHHHHHHHHhhhhhhhhhh
Q 033643 59 NVGLIKELNNNITRVVNLYADLSNSFTRS 87 (114)
Q Consensus 59 NV~LIrELN~NI~rVv~LYsdLS~sF~~~ 87 (114)
+.+.+....++..+-+..|..+-..|.+|
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 45677777888888899998888777653
No 22
>PF14775 NYD-SP28_assoc: Sperm tail C-terminal domain
Probab=25.62 E-value=2e+02 Score=18.72 Aligned_cols=30 Identities=13% Similarity=0.186 Sum_probs=27.1
Q ss_pred cChHHHHHHHHhHHHHHHHHhhhHHHHHHH
Q 033643 15 VDDKILQIFQKSFGQVQDILDQNRLLINEI 44 (114)
Q Consensus 15 ~d~k~~~~f~ksF~qVQ~iLDqNR~LI~EI 44 (114)
-.-++|.+|.+.+.+=-.||-+-..||+|+
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 346899999999999999999999999997
No 23
>KOG4038 consensus cGMP-phosphodiesterase, delta subunit [Signal transduction mechanisms]
Probab=25.34 E-value=29 Score=27.10 Aligned_cols=25 Identities=28% Similarity=0.575 Sum_probs=21.8
Q ss_pred hhccccCCCCcchhhHHHHHHHhHh
Q 033643 45 NQNHESKVPDNLTRNVGLIKELNNN 69 (114)
Q Consensus 45 NqNHeSr~PdnL~RNV~LIrELN~N 69 (114)
.+.||.|+|.++-+=-+.-||||=-
T Consensus 42 ~~ehearvpkkilkcravsreinfs 66 (150)
T KOG4038|consen 42 DQEHEARVPKKILKCRAVSREINFS 66 (150)
T ss_pred cchhhhcccHHHHhhHhhhhhcccc
Confidence 4789999999999999999999843
No 24
>PF13708 Methyltransf_27: Methyltransferase domain
Probab=24.76 E-value=3e+02 Score=21.01 Aligned_cols=69 Identities=16% Similarity=0.342 Sum_probs=52.5
Q ss_pred ccChHHHHHHHHhHHHHHHHHhhhHHHHHHHhhccc-cCCCCcchhhH-HHHHHHhHhH-----HHHHHHHhhhhhhhh
Q 033643 14 QVDDKILQIFQKSFGQVQDILDQNRLLINEINQNHE-SKVPDNLTRNV-GLIKELNNNI-----TRVVNLYADLSNSFT 85 (114)
Q Consensus 14 ~~d~k~~~~f~ksF~qVQ~iLDqNR~LI~EINqNHe-Sr~PdnL~RNV-~LIrELN~NI-----~rVv~LYsdLS~sF~ 85 (114)
.+|.+.|+-+=+... +.+.+++.+ .+|+++.=+ -..|+==..|| +...+|..|- +.|+++|..||..|-
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 478999998887666 888888875 355555544 46777777787 5778888885 568999999988875
No 25
>PTZ00065 60S ribosomal protein L14; Provisional
Probab=22.18 E-value=8.1 Score=29.27 Aligned_cols=13 Identities=31% Similarity=0.723 Sum_probs=10.2
Q ss_pred HHHHHhhhHHHHH
Q 033643 30 VQDILDQNRLLIN 42 (114)
Q Consensus 30 VQ~iLDqNR~LI~ 42 (114)
|=+|+||||.||.
T Consensus 28 IVDIID~nRvLVD 40 (130)
T PTZ00065 28 IVDIVTPTRVLVD 40 (130)
T ss_pred EEEEEcCCeEEEe
Confidence 3468999999984
No 26
>TIGR01241 FtsH_fam ATP-dependent metalloprotease FtsH. HflB(FtsH) is a pleiotropic protein required for correct cell division in bacteria. It has ATP-dependent zinc metalloprotease activity. It was formerly designated cell division protein FtsH.
Probab=21.76 E-value=1.1e+02 Score=26.02 Aligned_cols=31 Identities=19% Similarity=0.517 Sum_probs=27.5
Q ss_pred ccChHHHHHHHHhHHHHHHHHhhhHHHHHHH
Q 033643 14 QVDDKILQIFQKSFGQVQDILDQNRLLINEI 44 (114)
Q Consensus 14 ~~d~k~~~~f~ksF~qVQ~iLDqNR~LI~EI 44 (114)
.+|.++-+.+...+.++..+|.+||..+..|
T Consensus 445 ~id~~v~~lL~~a~~ra~~lL~~~~~~l~~l 475 (495)
T TIGR01241 445 EIDEEVKRIIEEAYKRAKQILTENRDELELL 475 (495)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhHHHHHHH
Confidence 3578888899999999999999999998876
No 27
>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=21.53 E-value=84 Score=22.33 Aligned_cols=18 Identities=22% Similarity=0.645 Sum_probs=16.0
Q ss_pred hHHHHHHHHhhhHHHHHH
Q 033643 26 SFGQVQDILDQNRLLINE 43 (114)
Q Consensus 26 sF~qVQ~iLDqNR~LI~E 43 (114)
.|+|.+.++-+||.+|.+
T Consensus 18 d~DQL~qlVsrN~sfird 35 (84)
T PF06143_consen 18 DYDQLEQLVSRNRSFIRD 35 (84)
T ss_pred cHHHHHHHHHhChHHHHH
Confidence 489999999999999876
No 28
>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=20.97 E-value=1e+02 Score=23.36 Aligned_cols=22 Identities=27% Similarity=0.525 Sum_probs=14.8
Q ss_pred hHHHHHHHHhHHHHHHHHhhh---HHHH
Q 033643 17 DKILQIFQKSFGQVQDILDQN---RLLI 41 (114)
Q Consensus 17 ~k~~~~f~ksF~qVQ~iLDqN---R~LI 41 (114)
.++|++..- ||..+||.| |.||
T Consensus 29 ~~vW~~VK~---~ve~~i~~~~~q~~LL 53 (132)
T PF10360_consen 29 GEVWETVKG---QVEEAIDPNEAQRNLL 53 (132)
T ss_pred HHHHHHHHH---HHHHHhCCCHHHHHHH
Confidence 467777764 777788877 5554
Done!