Query 033658
Match_columns 114
No_of_seqs 64 out of 66
Neff 2.6
Searched_HMMs 46136
Date Fri Mar 29 04:48:31 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033658.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033658hhsearch_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 4.7E-55 1E-59 308.1 8.8 87 13-99 1-87 (87)
2 PF05030 SSXT: SSXT protein (N 88.6 0.43 9.3E-06 32.4 2.5 39 28-70 9-48 (65)
3 PF07011 DUF1313: Protein of u 85.3 1.1 2.4E-05 32.2 3.2 37 54-90 20-64 (87)
4 PF05377 FlaC_arch: Flagella a 80.5 1.7 3.8E-05 28.7 2.5 22 63-84 30-51 (55)
5 PF08056 Trp_leader2: Tryptoph 64.4 1.9 4.2E-05 27.4 -0.3 17 41-57 2-18 (41)
6 PHA02951 Hypothetical protein; 63.8 8 0.00017 33.6 3.2 48 15-62 275-330 (337)
7 PF07554 FIVAR: Uncharacterise 59.5 11 0.00023 22.3 2.4 34 13-46 14-50 (51)
8 PF08649 DASH_Dad1: DASH compl 54.5 13 0.00027 24.8 2.3 30 38-75 8-37 (58)
9 KOG3227 Calcium-responsive tra 53.4 12 0.00025 31.1 2.4 23 27-49 22-44 (231)
10 PF11214 Med2: Mediator comple 47.7 36 0.00078 25.2 4.0 28 60-87 44-71 (105)
11 COG3352 FlaC Putative archaeal 44.7 24 0.00053 27.8 2.9 29 63-91 81-109 (157)
12 PF12998 ING: Inhibitor of gro 33.9 1.4E+02 0.003 19.6 5.3 46 29-76 30-76 (105)
13 PF13879 KIAA1430: KIAA1430 ho 32.8 84 0.0018 20.5 3.7 32 20-51 28-59 (98)
14 PF05130 FlgN: FlgN protein; 31.9 90 0.002 20.6 3.7 27 17-43 87-113 (143)
15 PF07709 SRR: Seven Residue Re 30.7 39 0.00084 16.4 1.3 13 69-81 2-14 (14)
16 PF11315 Med30: Mediator compl 30.4 89 0.0019 24.1 3.9 30 17-46 114-143 (150)
17 PF07508 Recombinase: Recombin 28.3 35 0.00076 22.0 1.2 13 25-37 90-102 (102)
18 PF13949 ALIX_LYPXL_bnd: ALIX 28.0 2.8E+02 0.0061 21.3 6.7 68 18-86 197-266 (296)
19 PF13174 TPR_6: Tetratricopept 27.1 95 0.002 15.6 3.0 29 59-87 5-33 (33)
20 PF14775 NYD-SP28_assoc: Sperm 25.9 1.9E+02 0.0042 18.8 6.3 30 15-44 13-42 (60)
21 PF04912 Dynamitin: Dynamitin 25.9 2.9E+02 0.0062 23.1 6.4 47 18-75 336-382 (388)
22 KOG4038 cGMP-phosphodiesterase 24.6 30 0.00065 27.0 0.4 25 45-69 42-66 (150)
23 PF06143 Baculo_11_kDa: Baculo 22.0 82 0.0018 22.4 2.2 18 26-43 18-35 (84)
24 PTZ00065 60S ribosomal protein 21.8 8.3 0.00018 29.2 -3.0 13 30-42 28-40 (130)
25 PF13708 Methyltransf_27: Meth 21.7 3.4E+02 0.0074 20.7 5.7 69 14-85 5-80 (194)
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=4.7e-55 Score=308.06 Aligned_cols=87 Identities=76% Similarity=1.057 Sum_probs=85.0
Q ss_pred cccchhhhHHHHHhHHHHHHHHhhhHHHHHHHhhccccCCCCcchhhHHHHHHHhhhHHHHHHHHhhhhhhhhhhhcccC
Q 033658 13 TQVDGKVLQTFRKSFGQVQDILDQNRLLINEINQNHESKVPDNLTRNVGLIKELNNNIRRVVSLYADLSSSFARSVESSS 92 (114)
Q Consensus 13 ~~~d~~~~~~f~ksF~qVQ~iLDqNR~LI~EINqNHeSr~PdnL~RNV~LIrELN~NI~rVv~LYsdLS~sF~~~~~~~s 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 033658 93 EGESAAA 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=88.58 E-value=0.43 Score=32.43 Aligned_cols=39 Identities=28% Similarity=0.438 Sum_probs=27.8
Q ss_pred HHHHHHHhhhHHHHHHHhhccc-cCCCCcchhhHHHHHHHhhhH
Q 033658 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 233445555554
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=85.30 E-value=1.1 Score=32.21 Aligned_cols=37 Identities=35% Similarity=0.491 Sum_probs=27.9
Q ss_pred CcchhhHHHHHHHhh--------hHHHHHHHHhhhhhhhhhhhcc
Q 033658 54 DNLTRNVGLIKELNN--------NIRRVVSLYADLSSSFARSVES 90 (114)
Q Consensus 54 dnL~RNV~LIrELN~--------NI~rVv~LYsdLS~sF~~~~~~ 90 (114)
+=|-+|=.||.|+|. |+.|=|.|-++|..+.++.|+-
T Consensus 20 ~iLDqNR~LI~eINqNHeSr~PdnL~RNV~LIrELN~NI~rVv~l 64 (87)
T PF07011_consen 20 SILDQNRLLINEINQNHESRIPDNLSRNVGLIRELNGNISRVVDL 64 (87)
T ss_pred HHHHHhHHHHHHHhhcccccCCchhhHhHHHHHHHHhhHHHHHHH
Confidence 346678888888885 4778888888888888877754
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=80.50 E-value=1.7 Score=28.72 Aligned_cols=22 Identities=23% Similarity=0.609 Sum_probs=18.2
Q ss_pred HHHHhhhHHHHHHHHhhhhhhh
Q 033658 63 IKELNNNIRRVVSLYADLSSSF 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=64.40 E-value=1.9 Score=27.41 Aligned_cols=17 Identities=35% Similarity=0.571 Sum_probs=13.4
Q ss_pred HHHHhhccccCCCCcch
Q 033658 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 68999999998864433
No 6
>PHA02951 Hypothetical protein; Provisional
Probab=63.79 E-value=8 Score=33.58 Aligned_cols=48 Identities=23% Similarity=0.345 Sum_probs=41.5
Q ss_pred cchhhhHHHHHhHHHHHHHHhh--------hHHHHHHHhhccccCCCCcchhhHHH
Q 033658 15 VDGKVLQTFRKSFGQVQDILDQ--------NRLLINEINQNHESKVPDNLTRNVGL 62 (114)
Q Consensus 15 ~d~~~~~~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 4578999999999999999999 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=59.46 E-value=11 Score=22.31 Aligned_cols=34 Identities=9% Similarity=0.279 Sum_probs=25.9
Q ss_pred cccchhhhHHHHHhHHHHHHHHhhhH---HHHHHHhh
Q 033658 13 TQVDGKVLQTFRKSFGQVQDILDQNR---LLINEINQ 46 (114)
Q Consensus 13 ~~~d~~~~~~f~ksF~qVQ~iLDqNR---~LI~EINq 46 (114)
...+.+.|.+|++....++.||+... +=-.||++
T Consensus 14 ~~~~~~~~~~y~~Al~~A~~vl~~~~~~~~t~~~V~~ 50 (51)
T PF07554_consen 14 SNATPESKAAYDNALNAAKAVLNNTNNPNATQEEVDQ 50 (51)
T ss_dssp HTS-HHHHHHHHHHHHHHHHHHCCTT---TTHHHHHH
T ss_pred hhcCHHHHHHHHHHHHHHHHHHcCCCCCCCCHHHHhc
Confidence 34678999999999999999998754 55555553
No 8
>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=54.50 E-value=13 Score=24.82 Aligned_cols=30 Identities=27% Similarity=0.458 Sum_probs=15.1
Q ss_pred HHHHHHHhhccccCCCCcchhhHHHHHHHhhhHHHHHH
Q 033658 38 RLLINEINQNHESKVPDNLTRNVGLIKELNNNIRRVVS 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 9
>KOG3227 consensus Calcium-responsive transcription coactivator [Transcription]
Probab=53.38 E-value=12 Score=31.12 Aligned_cols=23 Identities=35% Similarity=0.510 Sum_probs=19.8
Q ss_pred HHHHHHHHhhhHHHHHHHhhccc
Q 033658 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 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=47.71 E-value=36 Score=25.19 Aligned_cols=28 Identities=29% Similarity=0.358 Sum_probs=24.9
Q ss_pred HHHHHHHhhhHHHHHHHHhhhhhhhhhh
Q 033658 60 VGLIKELNNNIRRVVSLYADLSSSFARS 87 (114)
Q Consensus 60 V~LIrELN~NI~rVv~LYsdLS~sF~~~ 87 (114)
-.|++.|+..|...-++--|+-+.|..+
T Consensus 44 ~~l~k~L~eki~~Fh~ILDd~~~~l~~s 71 (105)
T PF11214_consen 44 NQLQKQLSEKIHKFHSILDDTESKLNDS 71 (105)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3569999999999999999999999864
No 11
>COG3352 FlaC Putative archaeal flagellar protein C [Cell motility and secretion]
Probab=44.70 E-value=24 Score=27.78 Aligned_cols=29 Identities=31% Similarity=0.533 Sum_probs=24.2
Q ss_pred HHHHhhhHHHHHHHHhhhhhhhhhhhccc
Q 033658 63 IKELNNNIRRVVSLYADLSSSFARSVESS 91 (114)
Q Consensus 63 IrELN~NI~rVv~LYsdLS~sF~~~~~~~ 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=33.90 E-value=1.4e+02 Score=19.56 Aligned_cols=46 Identities=26% Similarity=0.447 Sum_probs=31.9
Q ss_pred HHHHHHhhhHHHHHHHhhcccc-CCCCcchhhHHHHHHHhhhHHHHHHH
Q 033658 29 QVQDILDQNRLLINEINQNHES-KVPDNLTRNVGLIKELNNNIRRVVSL 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
>PF13879 KIAA1430: KIAA1430 homologue
Probab=32.83 E-value=84 Score=20.48 Aligned_cols=32 Identities=13% Similarity=0.185 Sum_probs=24.8
Q ss_pred hHHHHHhHHHHHHHHhhhHHHHHHHhhccccC
Q 033658 20 LQTFRKSFGQVQDILDQNRLLINEINQNHESK 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 14
>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=31.92 E-value=90 Score=20.61 Aligned_cols=27 Identities=15% Similarity=0.422 Sum_probs=19.7
Q ss_pred hhhhHHHHHhHHHHHHHHhhhHHHHHH
Q 033658 17 GKVLQTFRKSFGQVQDILDQNRLLINE 43 (114)
Q Consensus 17 ~~~~~~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 15
>PF07709 SRR: Seven Residue Repeat; InterPro: IPR011714 This repeat is found in some Plasmodium and Theileria proteins.
Probab=30.74 E-value=39 Score=16.35 Aligned_cols=13 Identities=31% Similarity=0.544 Sum_probs=10.1
Q ss_pred hHHHHHHHHhhhh
Q 033658 69 NIRRVVSLYADLS 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 16
>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=30.42 E-value=89 Score=24.09 Aligned_cols=30 Identities=30% Similarity=0.478 Sum_probs=24.8
Q ss_pred hhhhHHHHHhHHHHHHHHhhhHHHHHHHhh
Q 033658 17 GKVLQTFRKSFGQVQDILDQNRLLINEINQ 46 (114)
Q Consensus 17 ~~~~~~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 456666777778899999999999999995
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=28.28 E-value=35 Score=22.01 Aligned_cols=13 Identities=38% Similarity=0.624 Sum_probs=11.1
Q ss_pred HhHHHHHHHHhhh
Q 033658 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 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=27.98 E-value=2.8e+02 Score=21.33 Aligned_cols=68 Identities=18% Similarity=0.236 Sum_probs=37.6
Q ss_pred hhhHHHHHhHHHHHHHHhhhHHHHHHHhhccccCCCCc--chhhHHHHHHHhhhHHHHHHHHhhhhhhhhh
Q 033658 18 KVLQTFRKSFGQVQDILDQNRLLINEINQNHESKVPDN--LTRNVGLIKELNNNIRRVVSLYADLSSSFAR 86 (114)
Q Consensus 18 ~~~~~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 34444555556677777778899999988775443322 1111 23333334444555555566555544
No 19
>PF13174 TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_A 3URZ_B 2Q7F_A.
Probab=27.13 E-value=95 Score=15.57 Aligned_cols=29 Identities=7% Similarity=0.103 Sum_probs=22.6
Q ss_pred hHHHHHHHhhhHHHHHHHHhhhhhhhhhh
Q 033658 59 NVGLIKELNNNIRRVVSLYADLSSSFARS 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 45677777888889999998888777653
No 20
>PF14775 NYD-SP28_assoc: Sperm tail C-terminal domain
Probab=25.94 E-value=1.9e+02 Score=18.75 Aligned_cols=30 Identities=13% Similarity=0.169 Sum_probs=27.1
Q ss_pred cchhhhHHHHHhHHHHHHHHhhhHHHHHHH
Q 033658 15 VDGKVLQTFRKSFGQVQDILDQNRLLINEI 44 (114)
Q Consensus 15 ~d~~~~~~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 21
>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=25.92 E-value=2.9e+02 Score=23.07 Aligned_cols=47 Identities=17% Similarity=0.372 Sum_probs=35.1
Q ss_pred hhhHHHHHhHHHHHHHHhhhHHHHHHHhhccccCCCCcchhhHHHHHHHhhhHHHHHH
Q 033658 18 KVLQTFRKSFGQVQDILDQNRLLINEINQNHESKVPDNLTRNVGLIKELNNNIRRVVS 75 (114)
Q Consensus 18 ~~~~~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 77777655 456665543
No 22
>KOG4038 consensus cGMP-phosphodiesterase, delta subunit [Signal transduction mechanisms]
Probab=24.63 E-value=30 Score=27.00 Aligned_cols=25 Identities=28% Similarity=0.575 Sum_probs=21.8
Q ss_pred hhccccCCCCcchhhHHHHHHHhhh
Q 033658 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 4689999999999999999999843
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=21.96 E-value=82 Score=22.39 Aligned_cols=18 Identities=22% Similarity=0.645 Sum_probs=16.2
Q ss_pred hHHHHHHHHhhhHHHHHH
Q 033658 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 24
>PTZ00065 60S ribosomal protein L14; Provisional
Probab=21.80 E-value=8.3 Score=29.21 Aligned_cols=13 Identities=31% Similarity=0.723 Sum_probs=10.3
Q ss_pred HHHHHhhhHHHHH
Q 033658 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 4468999999984
No 25
>PF13708 Methyltransf_27: Methyltransferase domain
Probab=21.73 E-value=3.4e+02 Score=20.70 Aligned_cols=69 Identities=17% Similarity=0.358 Sum_probs=52.4
Q ss_pred ccchhhhHHHHHhHHHHHHHHhhhHHHHHHHhhccc-cCCCCcchhhH-HHHHHHhhhH-----HHHHHHHhhhhhhhh
Q 033658 14 QVDGKVLQTFRKSFGQVQDILDQNRLLINEINQNHE-SKVPDNLTRNV-GLIKELNNNI-----RRVVSLYADLSSSFA 85 (114)
Q Consensus 14 ~~d~~~~~~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 888888775 355555544 46777777787 5778888885 568999999988875
Done!