Query 031080
Match_columns 166
No_of_seqs 53 out of 55
Neff 2.0
Searched_HMMs 46136
Date Fri Mar 29 08:56:38 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031080.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031080hhsearch_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 5.6E-49 1.2E-53 290.4 8.5 82 42-123 1-82 (87)
2 PF05030 SSXT: SSXT protein (N 84.3 0.98 2.1E-05 32.3 2.5 39 57-99 9-48 (65)
3 PF07011 DUF1313: Protein of u 77.5 3.3 7.2E-05 31.4 3.5 34 85-118 22-63 (87)
4 PF05377 FlaC_arch: Flagella a 70.0 3.8 8.2E-05 28.6 2.0 21 92-112 30-50 (55)
5 COG5165 POB3 Nucleosome-bindin 62.6 3.2 6.8E-05 39.2 0.7 62 101-165 312-379 (508)
6 PF08512 Rtt106: Histone chape 59.9 3.8 8.2E-05 29.4 0.6 15 145-159 11-25 (95)
7 PF07554 FIVAR: Uncharacterise 58.1 15 0.00032 22.7 3.0 34 42-75 14-50 (51)
8 PHA02951 Hypothetical protein; 57.9 11 0.00025 34.3 3.3 49 43-91 274-330 (337)
9 PF08056 Trp_leader2: Tryptoph 46.4 4.8 0.0001 27.1 -0.6 17 70-86 2-18 (41)
10 KOG0526 Nucleosome-binding fac 42.4 10 0.00023 36.9 0.6 23 143-165 348-370 (615)
11 KOG3227 Calcium-responsive tra 40.7 24 0.00052 30.9 2.5 22 57-78 23-44 (231)
12 COG3352 FlaC Putative archaeal 36.8 39 0.00084 28.1 3.0 34 92-125 81-114 (157)
13 PF11679 DUF3275: Protein of u 34.4 16 0.00034 31.4 0.4 12 144-155 167-178 (214)
14 PF14775 NYD-SP28_assoc: Sperm 28.6 1.1E+02 0.0023 21.0 3.7 32 43-74 12-43 (60)
15 PF15404 PH_4: Pleckstrin homo 28.2 28 0.0006 28.8 0.9 14 150-163 53-66 (185)
16 PF13949 ALIX_LYPXL_bnd: ALIX 25.8 3.5E+02 0.0077 21.8 7.2 40 41-80 191-230 (296)
17 PF07709 SRR: Seven Residue Re 25.0 53 0.0011 16.8 1.3 13 98-110 2-14 (14)
18 PF12998 ING: Inhibitor of gro 23.3 2.4E+02 0.0052 19.3 4.8 46 58-105 30-76 (105)
19 PF05130 FlgN: FlgN protein; 22.6 1.8E+02 0.0038 20.1 4.0 28 45-72 86-113 (143)
20 PF11214 Med2: Mediator comple 22.4 2.5E+02 0.0055 21.9 5.1 44 71-116 27-71 (105)
21 COG1940 NagC Transcriptional r 21.9 45 0.00097 27.0 1.0 21 143-163 118-142 (314)
22 PF13879 KIAA1430: KIAA1430 ho 21.6 1.6E+02 0.0036 20.0 3.6 32 49-80 28-59 (98)
23 PF07508 Recombinase: Recombin 21.4 59 0.0013 21.9 1.3 11 56-66 92-102 (102)
24 PF04912 Dynamitin: Dynamitin 20.3 3.9E+02 0.0085 23.3 6.5 44 49-103 338-381 (388)
25 PHA02110 hypothetical protein 20.2 46 0.00099 25.8 0.7 17 144-160 28-44 (98)
26 PF08649 DASH_Dad1: DASH compl 20.1 1.7E+02 0.0037 20.6 3.4 31 67-105 8-38 (58)
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=5.6e-49 Score=290.39 Aligned_cols=82 Identities=57% Similarity=0.893 Sum_probs=79.5
Q ss_pred cccCHHHHHHHHHhHHHHHHHhhhhHHHHHHHhhhcccCCCCcchhhHHHHHHHhhhHHHHHHHhhhhhhhHHHHHhhhh
Q 031080 42 EEYDAEAWNTLSKSFKQVQTVLDNNRSLIERVNENHLSRIPDNMSKNVELIREINGNISKVVSIYSDLSANFCNIVSQRR 121 (166)
Q Consensus 42 e~~D~kvw~tfqksF~QVQ~ILDqNRlLInEINqNHeSriPDnLsRNV~LIRELN~NIskVV~LYsDLS~sFs~~v~qrr 121 (166)
+++|+|+|++|++||+|||+||||||+||+|||||||||+||+|+|||+||||||+||+|||+||+|||++|+++|++++
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 47999999999999999999999999999999999999999999999999999999999999999999999999999987
Q ss_pred hc
Q 031080 122 RR 123 (166)
Q Consensus 122 ~~ 123 (166)
..
T Consensus 81 ~g 82 (87)
T PF07011_consen 81 EG 82 (87)
T ss_pred cc
Confidence 64
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=84.28 E-value=0.98 Score=32.30 Aligned_cols=39 Identities=28% Similarity=0.454 Sum_probs=27.8
Q ss_pred HHHHHHhhhhHHHHHHHhhhcc-cCCCCcchhhHHHHHHHhhhH
Q 031080 57 KQVQTVLDNNRSLIERVNENHL-SRIPDNMSKNVELIREINGNI 99 (166)
Q Consensus 57 ~QVQ~ILDqNRlLInEINqNHe-SriPDnLsRNV~LIRELN~NI 99 (166)
.+||.+||.|.-||+-|.+++. .|.+| =|..-.-|..|+
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 5899999999999999999885 23332 334445555554
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=77.47 E-value=3.3 Score=31.42 Aligned_cols=34 Identities=35% Similarity=0.567 Sum_probs=17.9
Q ss_pred chhhHHHHHHHhh--------hHHHHHHHhhhhhhhHHHHHh
Q 031080 85 MSKNVELIREING--------NISKVVSIYSDLSANFCNIVS 118 (166)
Q Consensus 85 LsRNV~LIRELN~--------NIskVV~LYsDLS~sFs~~v~ 118 (166)
|-+|=.||.|+|. |++|=|.|-.+|..+-++.|+
T Consensus 22 LDqNR~LI~eINqNHeSr~PdnL~RNV~LIrELN~NI~rVv~ 63 (87)
T PF07011_consen 22 LDQNRLLINEINQNHESRIPDNLSRNVGLIRELNGNISRVVD 63 (87)
T ss_pred HHHhHHHHHHHhhcccccCCchhhHhHHHHHHHHhhHHHHHH
Confidence 4455555555554 245555555555555555443
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=69.97 E-value=3.8 Score=28.62 Aligned_cols=21 Identities=24% Similarity=0.547 Sum_probs=17.7
Q ss_pred HHHHhhhHHHHHHHhhhhhhh
Q 031080 92 IREINGNISKVVSIYSDLSAN 112 (166)
Q Consensus 92 IRELN~NIskVV~LYsDLS~s 112 (166)
|.+|+.||.+|++||.-.|..
T Consensus 30 ve~i~envk~ll~lYE~Vs~~ 50 (55)
T PF05377_consen 30 VEKIEENVKDLLSLYEVVSNQ 50 (55)
T ss_pred HHHHHHHHHHHHHHHHHHHcc
Confidence 567889999999999877754
No 5
>COG5165 POB3 Nucleosome-binding factor SPN, POB3 subunit [Transcription / DNA replication, recombination, and repair / Chromatin structure and dynamics]
Probab=62.55 E-value=3.2 Score=39.18 Aligned_cols=62 Identities=29% Similarity=0.533 Sum_probs=34.1
Q ss_pred HHHHHhhhh-hhhHHHHHhhh---hhc--cccccccchhhhHHHHHHhhhhccccccCcceeeeeeecccc
Q 031080 101 KVVSIYSDL-SANFCNIVSQR---RRR--MRMRMNNGHRRRAQRIRREKMAFGELWPLRDCFIYITLSTLQ 165 (166)
Q Consensus 101 kVV~LYsDL-S~sFs~~v~qr---r~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 165 (166)
||-.-|..+ +-=|+..++.- +.. +-.--..|||.- +- .-|.-=|.|+||.+||.||+-.||-
T Consensus 312 klK~~Yd~~~~ev~s~v~~gLt~rkvv~p~ef~S~~g~~av--~C-s~KAnEGqLYpLD~~flFlpKptl~ 379 (508)
T COG5165 312 KLKGEYDGLLSEVFSEVMEGLTVRKVVRPSEFESRDGMRAV--RC-SMKANEGQLYPLDDCFLFLPKPTLR 379 (508)
T ss_pred hhhhhccchHHHHHHHHHHhhcceeeecchhhcccCCceee--ee-eeeccCceEeeccceEEeccCceEE
Confidence 666667654 44566666552 111 112223344321 10 1233458999999999999876663
No 6
>PF08512 Rtt106: Histone chaperone Rttp106-like; InterPro: IPR013719 This is a domain of unknown function that is associated with a number of different protein families. It is found in Rtt106p, which is a histone chaperone involved in heterochromatin-mediated silencing []. It is also found in genes annotated as transcription factors/regulators. This domain is the C-terminal domain of yeast Spt16p P32558 from SWISSPROT, which is a subunit of the heterodimeric yeast FACT complex (Spt16p-Pob3p, IPR000969 from INTERPRO) []. In addition Spt16p and its relatives, in this entry, are described as non-peptidase homologues belonging to the MEROPS peptidase family M24. The FACT complex facilitates RNA Polymerase II transcription elongation through nucleosomes by destabilising and then reassembling nucleosome structure [, ]. ; PDB: 3TW1_A 3GYO_A 3TO1_A 3FSS_A 3TVV_B 3GYP_A 2GCJ_D 2GCL_A.
Probab=59.91 E-value=3.8 Score=29.45 Aligned_cols=15 Identities=33% Similarity=0.800 Sum_probs=12.7
Q ss_pred hccccccCcceeeee
Q 031080 145 AFGELWPLRDCFIYI 159 (166)
Q Consensus 145 ~~~~~~~~~~~~~~~ 159 (166)
.=|-||||.+||+++
T Consensus 11 ~~g~L~pl~~~l~f~ 25 (95)
T PF08512_consen 11 NEGFLYPLEKCLLFG 25 (95)
T ss_dssp EEEEEEEESSEEEEE
T ss_pred cCEEEEEccceEEEe
Confidence 447899999999984
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=58.09 E-value=15 Score=22.73 Aligned_cols=34 Identities=18% Similarity=0.308 Sum_probs=26.2
Q ss_pred cccCHHHHHHHHHhHHHHHHHhhhhH---HHHHHHhh
Q 031080 42 EEYDAEAWNTLSKSFKQVQTVLDNNR---SLIERVNE 75 (166)
Q Consensus 42 e~~D~kvw~tfqksF~QVQ~ILDqNR---lLInEINq 75 (166)
...+++.|..|......++.||+... +=-.+|++
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 45689999999999999999998754 55555553
No 8
>PHA02951 Hypothetical protein; Provisional
Probab=57.87 E-value=11 Score=34.32 Aligned_cols=49 Identities=22% Similarity=0.422 Sum_probs=41.8
Q ss_pred ccCHHHHHHHHHhHHHHHHHhhh--------hHHHHHHHhhhcccCCCCcchhhHHH
Q 031080 43 EYDAEAWNTLSKSFKQVQTVLDN--------NRSLIERVNENHLSRIPDNMSKNVEL 91 (166)
Q Consensus 43 ~~D~kvw~tfqksF~QVQ~ILDq--------NRlLInEINqNHeSriPDnLsRNV~L 91 (166)
..+...|.-..+-|..|..+||. |.-+|.+|+.+--++.-|...-|.+|
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 34678999999999999999999 45688899999888888888777765
No 9
>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=46.38 E-value=4.8 Score=27.09 Aligned_cols=17 Identities=18% Similarity=0.438 Sum_probs=13.5
Q ss_pred HHHHhhhcccCCCCcch
Q 031080 70 IERVNENHLSRIPDNMS 86 (166)
Q Consensus 70 InEINqNHeSriPDnLs 86 (166)
+||+||||..++.....
T Consensus 2 LQe~n~nqk~kva~~~~ 18 (41)
T PF08056_consen 2 LQEFNQNQKAKVAAHSS 18 (41)
T ss_pred chhhccchhhhhhhhcc
Confidence 68999999998875443
No 10
>KOG0526 consensus Nucleosome-binding factor SPN, POB3 subunit [Transcription; Replication, recombination and repair; Chromatin structure and dynamics]
Probab=42.45 E-value=10 Score=36.85 Aligned_cols=23 Identities=30% Similarity=0.569 Sum_probs=18.1
Q ss_pred hhhccccccCcceeeeeeecccc
Q 031080 143 KMAFGELWPLRDCFIYITLSTLQ 165 (166)
Q Consensus 143 ~~~~~~~~~~~~~~~~~~~~~~~ 165 (166)
|..-|-|+||.+||+||.=.++-
T Consensus 348 KAneG~LYPLekgFlFl~KP~l~ 370 (615)
T KOG0526|consen 348 KANEGLLYPLEKGFLFLPKPPLY 370 (615)
T ss_pred cccCceEeecccceEeecCCceE
Confidence 34568999999999999865553
No 11
>KOG3227 consensus Calcium-responsive transcription coactivator [Transcription]
Probab=40.69 E-value=24 Score=30.88 Aligned_cols=22 Identities=36% Similarity=0.582 Sum_probs=19.5
Q ss_pred HHHHHHhhhhHHHHHHHhhhcc
Q 031080 57 KQVQTVLDNNRSLIERVNENHL 78 (166)
Q Consensus 57 ~QVQ~ILDqNRlLInEINqNHe 78 (166)
.++|..||.|.-||.-|=+++-
T Consensus 23 ~~IQk~LdEN~~LI~~I~e~Qn 44 (231)
T KOG3227|consen 23 EQIQKMLDENKHLIQCIVESQN 44 (231)
T ss_pred HHHHHHHHhhhHHHHHHHHhhc
Confidence 5899999999999999987764
No 12
>COG3352 FlaC Putative archaeal flagellar protein C [Cell motility and secretion]
Probab=36.78 E-value=39 Score=28.07 Aligned_cols=34 Identities=26% Similarity=0.485 Sum_probs=27.5
Q ss_pred HHHHhhhHHHHHHHhhhhhhhHHHHHhhhhhccc
Q 031080 92 IREINGNISKVVSIYSDLSANFCNIVSQRRRRMR 125 (166)
Q Consensus 92 IRELN~NIskVV~LYsDLS~sFs~~v~qrr~~~~ 125 (166)
|-+|=.||..++.+|+-+|..|.-.+++--.-++
T Consensus 81 lerLe~~iKdl~~lye~Vs~d~Npf~s~~~qes~ 114 (157)
T COG3352 81 LERLEENIKDLVSLYELVSRDFNPFMSKTPQESR 114 (157)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhhhHHhhhHHHHH
Confidence 4568899999999999999999888777544444
No 13
>PF11679 DUF3275: Protein of unknown function (DUF3275); InterPro: IPR021693 This family of proteins with unknown function appear to be restricted to Proteobacteria.
Probab=34.36 E-value=16 Score=31.45 Aligned_cols=12 Identities=58% Similarity=1.176 Sum_probs=8.9
Q ss_pred hhccccccCcce
Q 031080 144 MAFGELWPLRDC 155 (166)
Q Consensus 144 ~~~~~~~~~~~~ 155 (166)
--||+||||.+-
T Consensus 167 ~Lfg~lWplge~ 178 (214)
T PF11679_consen 167 ELFGELWPLGEP 178 (214)
T ss_pred hhhhhcccCCCc
Confidence 458899988764
No 14
>PF14775 NYD-SP28_assoc: Sperm tail C-terminal domain
Probab=28.58 E-value=1.1e+02 Score=21.04 Aligned_cols=32 Identities=22% Similarity=0.420 Sum_probs=28.1
Q ss_pred ccCHHHHHHHHHhHHHHHHHhhhhHHHHHHHh
Q 031080 43 EYDAEAWNTLSKSFKQVQTVLDNNRSLIERVN 74 (166)
Q Consensus 43 ~~D~kvw~tfqksF~QVQ~ILDqNRlLInEIN 74 (166)
+..-++|.+|.+.+.+=-.||-+-..||+|+.
T Consensus 12 ~~~~~~W~~L~~~l~rY~~vL~~R~~l~~e~~ 43 (60)
T PF14775_consen 12 DEKIRLWDALENFLKRYNKVLLDRAALIQEKE 43 (60)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34568999999999999999999999999983
No 15
>PF15404 PH_4: Pleckstrin homology domain
Probab=28.21 E-value=28 Score=28.83 Aligned_cols=14 Identities=57% Similarity=1.146 Sum_probs=11.1
Q ss_pred ccCcceeeeeeecc
Q 031080 150 WPLRDCFIYITLST 163 (166)
Q Consensus 150 ~~~~~~~~~~~~~~ 163 (166)
-||+||+||--+.|
T Consensus 53 I~L~dcYvYSG~lt 66 (185)
T PF15404_consen 53 IPLRDCYVYSGLLT 66 (185)
T ss_pred eccCCceEEeccch
Confidence 59999999965544
No 16
>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=25.82 E-value=3.5e+02 Score=21.75 Aligned_cols=40 Identities=15% Similarity=0.169 Sum_probs=30.4
Q ss_pred CcccCHHHHHHHHHhHHHHHHHhhhhHHHHHHHhhhcccC
Q 031080 41 EEEYDAEAWNTLSKSFKQVQTVLDNNRSLIERVNENHLSR 80 (166)
Q Consensus 41 ~e~~D~kvw~tfqksF~QVQ~ILDqNRlLInEINqNHeSr 80 (166)
.+.+=.+.+.-|..-..+|+.-+.+...||++|-..++.-
T Consensus 191 ~~~lf~~eL~k~~~~~~~i~~~~~~Q~~ll~~i~~~~~~~ 230 (296)
T PF13949_consen 191 FEALFEEELKKFDPLQNRIQQNLSKQEELLQEIQEANEEF 230 (296)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4555566667777777788888888899999998877544
No 17
>PF07709 SRR: Seven Residue Repeat; InterPro: IPR011714 This repeat is found in some Plasmodium and Theileria proteins.
Probab=25.04 E-value=53 Score=16.85 Aligned_cols=13 Identities=38% Similarity=0.567 Sum_probs=10.1
Q ss_pred hHHHHHHHhhhhh
Q 031080 98 NISKVVSIYSDLS 110 (166)
Q Consensus 98 NIskVV~LYsDLS 110 (166)
|-.+|.+.|..|+
T Consensus 2 ~~~~V~~aY~~l~ 14 (14)
T PF07709_consen 2 KFEKVKNAYEQLS 14 (14)
T ss_pred cHHHHHHHHHhcC
Confidence 4568999998875
No 18
>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=23.31 E-value=2.4e+02 Score=19.27 Aligned_cols=46 Identities=24% Similarity=0.400 Sum_probs=30.2
Q ss_pred HHHHHhhhhHHHHHHHhhhcccC-CCCcchhhHHHHHHHhhhHHHHHHH
Q 031080 58 QVQTVLDNNRSLIERVNENHLSR-IPDNMSKNVELIREINGNISKVVSI 105 (166)
Q Consensus 58 QVQ~ILDqNRlLInEINqNHeSr-iPDnLsRNV~LIRELN~NIskVV~L 105 (166)
++|+++.+-...+++.-+++.+. +|.+ .-..++.+|...+.++..+
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 35667777777777777777662 3333 5667888888887776654
No 19
>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=22.63 E-value=1.8e+02 Score=20.08 Aligned_cols=28 Identities=21% Similarity=0.482 Sum_probs=23.6
Q ss_pred CHHHHHHHHHhHHHHHHHhhhhHHHHHH
Q 031080 45 DAEAWNTLSKSFKQVQTVLDNNRSLIER 72 (166)
Q Consensus 45 D~kvw~tfqksF~QVQ~ILDqNRlLInE 72 (166)
-.+.|..+.....+++.+=+.|..||+.
T Consensus 86 l~~~~~~l~~~~~~~~~~n~~N~~ll~~ 113 (143)
T PF05130_consen 86 LQALWRELRELLEELQELNERNQQLLEQ 113 (143)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4567888999999999999999998875
No 20
>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=22.43 E-value=2.5e+02 Score=21.90 Aligned_cols=44 Identities=23% Similarity=0.378 Sum_probs=31.3
Q ss_pred HHHhhhc-ccCCCCcchhhHHHHHHHhhhHHHHHHHhhhhhhhHHHH
Q 031080 71 ERVNENH-LSRIPDNMSKNVELIREINGNISKVVSIYSDLSANFCNI 116 (166)
Q Consensus 71 nEINqNH-eSriPDnLsRNV~LIRELN~NIskVV~LYsDLS~sFs~~ 116 (166)
++|+.|. +|.+-.+. |-.|++.|+..|...-++--|+-+.|..+
T Consensus 27 eqik~~ql~s~vi~G~--n~~l~k~L~eki~~Fh~ILDd~~~~l~~s 71 (105)
T PF11214_consen 27 EQIKNNQLQSNVITGF--NNQLQKQLSEKIHKFHSILDDTESKLNDS 71 (105)
T ss_pred HHHHHHhhhhhhhccc--cHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4444443 33344443 33569999999999999999999998875
No 21
>COG1940 NagC Transcriptional regulator/sugar kinase [Transcription / Carbohydrate transport and metabolism]
Probab=21.94 E-value=45 Score=27.02 Aligned_cols=21 Identities=43% Similarity=0.567 Sum_probs=16.0
Q ss_pred hhhcccccc----Ccceeeeeeecc
Q 031080 143 KMAFGELWP----LRDCFIYITLST 163 (166)
Q Consensus 143 ~~~~~~~~~----~~~~~~~~~~~~ 163 (166)
-+|.||.|- -.+.|+||+++|
T Consensus 118 ~aalaE~~~g~~~~~~~~~~i~~gt 142 (314)
T COG1940 118 AAALAEAWFGAGRGIDDVVYITLGT 142 (314)
T ss_pred HHHHHHHHhCCCCCCCCEEEEEEcc
Confidence 367888883 356799999987
No 22
>PF13879 KIAA1430: KIAA1430 homologue
Probab=21.64 E-value=1.6e+02 Score=20.00 Aligned_cols=32 Identities=13% Similarity=0.115 Sum_probs=25.4
Q ss_pred HHHHHHhHHHHHHHhhhhHHHHHHHhhhcccC
Q 031080 49 WNTLSKSFKQVQTVLDNNRSLIERVNENHLSR 80 (166)
Q Consensus 49 w~tfqksF~QVQ~ILDqNRlLInEINqNHeSr 80 (166)
+..++....+++.|...|+.|.+.|..=+...
T Consensus 28 ~kk~~~~~er~~~I~reN~~LL~ki~~I~~~~ 59 (98)
T PF13879_consen 28 RKKLQFEEERQREIERENQILLRKIMEIMRKP 59 (98)
T ss_pred HHHHHhhHHHHHHHHHHHHHHHHHHHHHHcCC
Confidence 55566677889999999999999998766443
No 23
>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=21.39 E-value=59 Score=21.91 Aligned_cols=11 Identities=45% Similarity=0.730 Sum_probs=8.0
Q ss_pred HHHHHHHhhhh
Q 031080 56 FKQVQTVLDNN 66 (166)
Q Consensus 56 F~QVQ~ILDqN 66 (166)
|.+||.+|++|
T Consensus 92 f~~vq~~l~~r 102 (102)
T PF07508_consen 92 FERVQKKLDER 102 (102)
T ss_pred HHHHHHHHhcC
Confidence 66677788765
No 24
>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=20.28 E-value=3.9e+02 Score=23.34 Aligned_cols=44 Identities=25% Similarity=0.406 Sum_probs=29.5
Q ss_pred HHHHHHhHHHHHHHhhhhHHHHHHHhhhcccCCCCcchhhHHHHHHHhhhHHHHH
Q 031080 49 WNTLSKSFKQVQTVLDNNRSLIERVNENHLSRIPDNMSKNVELIREINGNISKVV 103 (166)
Q Consensus 49 w~tfqksF~QVQ~ILDqNRlLInEINqNHeSriPDnLsRNV~LIRELN~NIskVV 103 (166)
+..|...=.+++.-|.++..+++.|+++ |..|...| ++||+.+-
T Consensus 338 l~~le~~q~~l~~~l~~~~~~L~~ve~~--------~~~N~~~i---~~n~~~le 381 (388)
T PF04912_consen 338 LSELESQQSDLQSQLKKWEELLNKVEEK--------FKENMETI---EKNVKKLE 381 (388)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH--------HHHHHHHH---HHHHHHHH
Confidence 3344444556777788888899998887 77776654 45665543
No 25
>PHA02110 hypothetical protein
Probab=20.25 E-value=46 Score=25.80 Aligned_cols=17 Identities=35% Similarity=0.813 Sum_probs=14.4
Q ss_pred hhccccccCcceeeeee
Q 031080 144 MAFGELWPLRDCFIYIT 160 (166)
Q Consensus 144 ~~~~~~~~~~~~~~~~~ 160 (166)
--|.+.|-.||-||||.
T Consensus 28 eifk~~w~i~dgfvf~~ 44 (98)
T PHA02110 28 EIFKSHWMIRDGFVFIG 44 (98)
T ss_pred eeeeeeeEeecCEEEeC
Confidence 35788999999999984
No 26
>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=20.08 E-value=1.7e+02 Score=20.57 Aligned_cols=31 Identities=23% Similarity=0.482 Sum_probs=20.5
Q ss_pred HHHHHHHhhhcccCCCCcchhhHHHHHHHhhhHHHHHHH
Q 031080 67 RSLIERVNENHLSRIPDNMSKNVELIREINGNISKVVSI 105 (166)
Q Consensus 67 RlLInEINqNHeSriPDnLsRNV~LIRELN~NIskVV~L 105 (166)
..||+||.++ |..=+.-|..||.|+--|+++
T Consensus 8 ~~Li~eI~~~--------~e~vl~nlN~LNRsLE~~i~V 38 (58)
T PF08649_consen 8 DRLIQEISES--------MESVLNNLNALNRSLESVISV 38 (58)
T ss_pred HHHHHHHHHH--------HHHHHHHHHHHHHhHHHHHHH
Confidence 4678888754 444556677788887766643
Done!