Query 034007
Match_columns 106
No_of_seqs 124 out of 564
Neff 5.0
Searched_HMMs 46136
Date Fri Mar 29 08:45:42 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034007.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034007hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00018 histone H3; Provision 100.0 2.6E-36 5.7E-41 218.7 6.1 95 1-106 1-95 (136)
2 PLN00161 histone H3; Provision 100.0 3.8E-36 8.3E-41 217.6 6.1 89 1-106 1-89 (135)
3 PLN00121 histone H3; Provision 100.0 3.9E-36 8.5E-41 217.8 6.0 95 1-106 1-95 (136)
4 KOG1745 Histones H3 and H4 [Ch 100.0 4.1E-31 8.8E-36 191.7 4.7 95 1-106 1-96 (137)
5 smart00428 H3 Histone H3. 100.0 1.6E-29 3.5E-34 176.5 4.6 63 44-106 2-64 (105)
6 PLN00160 histone H3; Provision 99.9 2.5E-27 5.3E-32 163.6 3.6 55 51-106 1-55 (97)
7 COG2036 HHT1 Histones H3 and H 99.1 5.1E-11 1.1E-15 81.6 2.3 47 53-106 1-47 (91)
8 PF00125 Histone: Core histone 97.9 3.6E-06 7.8E-11 53.7 1.0 38 67-106 1-38 (75)
9 KOG0870 DNA polymerase epsilon 47.0 8.4 0.00018 29.3 0.6 33 69-105 8-40 (172)
10 PF07789 DUF1627: Protein of u 35.0 21 0.00046 26.8 1.2 10 57-66 141-150 (155)
11 PF10788 DUF2603: Protein of u 30.3 54 0.0012 24.1 2.6 32 55-87 97-128 (137)
12 cd07981 TAF12 TATA Binding Pro 29.5 28 0.0006 22.2 0.9 24 77-106 7-30 (72)
13 KOG1071 Mitochondrial translat 23.4 42 0.0009 28.1 1.1 33 54-89 114-146 (340)
No 1
>PTZ00018 histone H3; Provisional
Probab=100.00 E-value=2.6e-36 Score=218.74 Aligned_cols=95 Identities=43% Similarity=0.563 Sum_probs=81.9
Q ss_pred CCcccccccccCCcccccccCCCCCCCCccchhhhhcCCCCCCccccccccCCCchhhHHHHhhhcccccccccCchHHH
Q 034007 1 MARTKHMARRSSRLQAAVKATPPTSSPGTSRQRRSEAGEGTPTAQRKRQRLRPGTKALREIRRFQKSVDLLIPRMSFIRE 80 (106)
Q Consensus 1 MARtK~ta~kst~~k~~~k~~~~~~~~~~~~k~~~~~~~~~~~~~kk~~r~rpgt~alrEIr~yQkst~lLI~k~pF~RL 80 (106)
||||||++++++++++|+++++ .+...++.+.. ++.++++||+||++||+|||+||+||+|||+|+||+||
T Consensus 1 MaRtk~~~~k~~~~~~prk~~~--------~~~~~~~~~~~-~~~~~~~r~rpGt~aLrEIr~yQkst~lLI~k~pF~RL 71 (136)
T PTZ00018 1 MARTKQTARKSTGGKAPRKQLA--------SKAARKSAPVT-GGIKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRL 71 (136)
T ss_pred CCCCCcCccCCCCCCCCccccc--------ccccccCCCCC-CCCCCCcccCCchhHHHHHHHHcccchhccccccHHHH
Confidence 9999999999999998888765 22222222222 67889999999999999999999999999999999999
Q ss_pred HHHHhhhcCCCCcccccHHHHhhccC
Q 034007 81 VRTITYRVAPPDVNRWTPEALIALQE 106 (106)
Q Consensus 81 VreI~~~~~~~~~lRfq~~Al~ALQE 106 (106)
||||+++| .+++|||++||+||||
T Consensus 72 VREI~~~~--~~~~rf~~~al~aLQe 95 (136)
T PTZ00018 72 VREIAQDF--KTDLRFQSSAVLALQE 95 (136)
T ss_pred HHHHHHHc--CCcceeeHHHHHHHHH
Confidence 99999994 5689999999999997
No 2
>PLN00161 histone H3; Provisional
Probab=100.00 E-value=3.8e-36 Score=217.55 Aligned_cols=89 Identities=43% Similarity=0.609 Sum_probs=77.4
Q ss_pred CCcccccccccCCcccccccCCCCCCCCccchhhhhcCCCCCCccccccccCCCchhhHHHHhhhcccccccccCchHHH
Q 034007 1 MARTKHMARRSSRLQAAVKATPPTSSPGTSRQRRSEAGEGTPTAQRKRQRLRPGTKALREIRRFQKSVDLLIPRMSFIRE 80 (106)
Q Consensus 1 MARtK~ta~kst~~k~~~k~~~~~~~~~~~~k~~~~~~~~~~~~~kk~~r~rpgt~alrEIr~yQkst~lLI~k~pF~RL 80 (106)
||||||+ +++++|+.|.+++. . + ..++++++++||+||+|||+|||+||+||+|||||+||+||
T Consensus 1 mar~k~~-~~~~~~~~~~~~~~--------~----~---~~~~~~kk~~r~rpGtvaLrEIR~yQkst~lLIpklPF~RL 64 (135)
T PLN00161 1 MARRLQG-KRFRKGKKPQKEAS--------G----V---TRQELDKKPHRYRPGTVALREIRKYQKSTELLIRKLPFARL 64 (135)
T ss_pred CCccccc-ccccCCCCCcccCC--------C----C---CCCCCCCCCccCCCcchHHHHHHHHccccccccccccHHHH
Confidence 9999999 77778877766554 1 0 11178899999999999999999999999999999999999
Q ss_pred HHHHhhhcCCCCcccccHHHHhhccC
Q 034007 81 VRTITYRVAPPDVNRWTPEALIALQE 106 (106)
Q Consensus 81 VreI~~~~~~~~~lRfq~~Al~ALQE 106 (106)
||||+++| ..+++|||++||+||||
T Consensus 65 VREI~~~~-~~~~~Rfq~~Al~ALQE 89 (135)
T PLN00161 65 VREISNEM-LREPFRWTAEALLALQE 89 (135)
T ss_pred HHHHHHhc-CCCCcEeeHHHHHHHHH
Confidence 99999996 34689999999999997
No 3
>PLN00121 histone H3; Provisional
Probab=100.00 E-value=3.9e-36 Score=217.82 Aligned_cols=95 Identities=42% Similarity=0.571 Sum_probs=82.2
Q ss_pred CCcccccccccCCcccccccCCCCCCCCccchhhhhcCCCCCCccccccccCCCchhhHHHHhhhcccccccccCchHHH
Q 034007 1 MARTKHMARRSSRLQAAVKATPPTSSPGTSRQRRSEAGEGTPTAQRKRQRLRPGTKALREIRRFQKSVDLLIPRMSFIRE 80 (106)
Q Consensus 1 MARtK~ta~kst~~k~~~k~~~~~~~~~~~~k~~~~~~~~~~~~~kk~~r~rpgt~alrEIr~yQkst~lLI~k~pF~RL 80 (106)
||||||++++++++++|+++++ .+...++.+.. ++.++++||+||++||+|||+||+||+|||+|+||+||
T Consensus 1 MaRtk~~~~k~~~~~~p~~~~~--------~~~~~~~~~~~-~~~~~~~r~rpGt~aLrEIr~yQkst~lLI~k~pF~RL 71 (136)
T PLN00121 1 MARTKQTARKSTGGKAPRKQLA--------TKAARKSAPAT-GGVKKPHRYRPGTVALREIRKYQKSTELLIRKLPFQRL 71 (136)
T ss_pred CCCCCcCccCCCCCCCCccccc--------ccccccCCCCC-CCCCCCcccCchhHHHHHHHHhccccccccccccHHHH
Confidence 9999999999999999888765 22222222222 67899999999999999999999999999999999999
Q ss_pred HHHHhhhcCCCCcccccHHHHhhccC
Q 034007 81 VRTITYRVAPPDVNRWTPEALIALQE 106 (106)
Q Consensus 81 VreI~~~~~~~~~lRfq~~Al~ALQE 106 (106)
||||+++| .+++|||++||+||||
T Consensus 72 VREI~~~~--~~~~Rf~~~Al~ALQe 95 (136)
T PLN00121 72 VREIAQDF--KTDLRFQSSAVLALQE 95 (136)
T ss_pred HHHHHHHh--CccceeeHHHHHHHHH
Confidence 99999994 5789999999999997
No 4
>KOG1745 consensus Histones H3 and H4 [Chromatin structure and dynamics]
Probab=99.97 E-value=4.1e-31 Score=191.66 Aligned_cols=95 Identities=43% Similarity=0.543 Sum_probs=82.1
Q ss_pred CCcccccccccCCcccccccCCCCCCCCccchhhhhc-CCCCCCccccccccCCCchhhHHHHhhhcccccccccCchHH
Q 034007 1 MARTKHMARRSSRLQAAVKATPPTSSPGTSRQRRSEA-GEGTPTAQRKRQRLRPGTKALREIRRFQKSVDLLIPRMSFIR 79 (106)
Q Consensus 1 MARtK~ta~kst~~k~~~k~~~~~~~~~~~~k~~~~~-~~~~~~~~kk~~r~rpgt~alrEIr~yQkst~lLI~k~pF~R 79 (106)
|+|+++++++++++++++++.+ .+..... .+.. +.+++.+||+||+++|+|||+||+||||||+|+||+|
T Consensus 1 m~r~~~t~~k~~~~~~~r~~~a--------~~~~~~~~~~~~-~~~~k~~r~rpg~~al~eirkyQkstdLlI~K~PFqR 71 (137)
T KOG1745|consen 1 MARTKQTARKSTGGKAPRKQLA--------GKAARKSAAPRT-GRVKKPHRYRPGTVALREIRKYQKSTDLLIRKLPFQR 71 (137)
T ss_pred CCCCCcccccccCCCCCccccc--------cccccccccccc-cccCccccccCchHHHHHHHHHHhhhHHHhhcCcHHH
Confidence 8999999999999999988776 2222221 1112 5778899999999999999999999999999999999
Q ss_pred HHHHHhhhcCCCCcccccHHHHhhccC
Q 034007 80 EVRTITYRVAPPDVNRWTPEALIALQE 106 (106)
Q Consensus 80 LVreI~~~~~~~~~lRfq~~Al~ALQE 106 (106)
|||||+++ |..|+|||+.||.||||
T Consensus 72 lvrei~q~--f~~dLrfqs~Ai~ALQe 96 (137)
T KOG1745|consen 72 LVREIAQD--FKTDLRFQSSAIAALQE 96 (137)
T ss_pred HhHHHHhc--ccccceehHHHHHHHHH
Confidence 99999999 57899999999999997
No 5
>smart00428 H3 Histone H3.
Probab=99.96 E-value=1.6e-29 Score=176.46 Aligned_cols=63 Identities=46% Similarity=0.671 Sum_probs=58.4
Q ss_pred ccccccccCCCchhhHHHHhhhcccccccccCchHHHHHHHhhhcCCCCcccccHHHHhhccC
Q 034007 44 AQRKRQRLRPGTKALREIRRFQKSVDLLIPRMSFIREVRTITYRVAPPDVNRWTPEALIALQE 106 (106)
Q Consensus 44 ~~kk~~r~rpgt~alrEIr~yQkst~lLI~k~pF~RLVreI~~~~~~~~~lRfq~~Al~ALQE 106 (106)
++++++||+||++||+|||+||+||+|||||+||+||||||+++|....++|||++||+||||
T Consensus 2 ~~~~~~r~rpg~~aLrEIr~yQkst~lLI~k~pF~RLVREI~~~~~~~~~~R~~~~Al~aLQe 64 (105)
T smart00428 2 GKTKHRRYRPGQVALREIRKYQKSTDLLIRKAPFQRLVREIAQKFTTGVDLRFQSSAIMALQE 64 (105)
T ss_pred CCCCCcCCCCcchHHHHHHHHccCcccccccccHHHHHHHHHHHcCCCCCceeeHHHHHHHHH
Confidence 578899999999999999999999999999999999999999996423489999999999997
No 6
>PLN00160 histone H3; Provisional
Probab=99.93 E-value=2.5e-27 Score=163.59 Aligned_cols=55 Identities=51% Similarity=0.851 Sum_probs=52.1
Q ss_pred cCCCchhhHHHHhhhcccccccccCchHHHHHHHhhhcCCCCcccccHHHHhhccC
Q 034007 51 LRPGTKALREIRRFQKSVDLLIPRMSFIREVRTITYRVAPPDVNRWTPEALIALQE 106 (106)
Q Consensus 51 ~rpgt~alrEIr~yQkst~lLI~k~pF~RLVreI~~~~~~~~~lRfq~~Al~ALQE 106 (106)
|+||++||+|||+||+||+|||||+||+||||||+++| ..+++|||++||+||||
T Consensus 1 ~rpGt~aLrEIR~yQkst~lLI~k~pF~RLVREI~~~~-~~~~~Rfq~~Al~ALQe 55 (97)
T PLN00160 1 MRPGEKALKEIKMYQKSTDLLIRRLPFARLVREIQMEM-SREAYRWQGSAILALQE 55 (97)
T ss_pred CCCccHHHHHHHHHccchhhhhccccHHHHHHHHHHHc-CCCCcEeeHHHHHHHHH
Confidence 78999999999999999999999999999999999995 35679999999999997
No 7
>COG2036 HHT1 Histones H3 and H4 [Chromatin structure and dynamics]
Probab=99.08 E-value=5.1e-11 Score=81.59 Aligned_cols=47 Identities=43% Similarity=0.675 Sum_probs=44.2
Q ss_pred CCchhhHHHHhhhcccccccccCchHHHHHHHhhhcCCCCcccccHHHHhhccC
Q 034007 53 PGTKALREIRRFQKSVDLLIPRMSFIREVRTITYRVAPPDVNRWTPEALIALQE 106 (106)
Q Consensus 53 pgt~alrEIr~yQkst~lLI~k~pF~RLVreI~~~~~~~~~lRfq~~Al~ALQE 106 (106)
||.++++|||+||++++++||++||+|++|+...+ ||+.+|+++|||
T Consensus 1 ~~~~~~~~~r~~~~~~~~~Lp~apv~Ri~r~~~~~-------Rvs~~A~~~l~~ 47 (91)
T COG2036 1 PGAVGLKEIRRYQRSTDLLLPKAPVRRILRKAGAE-------RVSSSAIEELQE 47 (91)
T ss_pred CCcchHHHHHhhhhhhhhhcCchHHHHHHHHHhHH-------HhhHHHHHHHHH
Confidence 68899999999999999999999999999998865 999999999986
No 8
>PF00125 Histone: Core histone H2A/H2B/H3/H4 histone h2a signature histone h2b signature histone h3 signature histone h4 signature; InterPro: IPR007125 The core histones together with some other DNA binding proteins appear to form a superfamily defined by a common fold and distant sequence similarities [, ]. Some proteins contain local homology domains related to the histone fold [].; GO: 0003677 DNA binding; PDB: 2YFW_D 2YFV_B 1U35_H 2F8N_D 2PYO_D 2NQB_D 3AN2_C 3AZJ_C 3AV1_G 3AZM_G ....
Probab=97.91 E-value=3.6e-06 Score=53.68 Aligned_cols=38 Identities=37% Similarity=0.511 Sum_probs=32.9
Q ss_pred ccccccccCchHHHHHHHhhhcCCCCcccccHHHHhhccC
Q 034007 67 SVDLLIPRMSFIREVRTITYRVAPPDVNRWTPEALIALQE 106 (106)
Q Consensus 67 st~lLI~k~pF~RLVreI~~~~~~~~~lRfq~~Al~ALQE 106 (106)
+++++|+++||.|+++||..++. ..+||+++|+.+||+
T Consensus 1 ~~~~~~~~~~~~r~~r~i~~~~~--~~~ris~~a~~~L~~ 38 (75)
T PF00125_consen 1 RTRRLIPKFPFSRLLREIGEEIL--SKYRISSEALVALQS 38 (75)
T ss_dssp HHSHSSSHHHHHHHHHHHHHTTS--SSSEECHHHHHHHHH
T ss_pred CcccccCceEEeeeeehhhcccc--cccccccccchhhhh
Confidence 46789999999999999999953 348999999999874
No 9
>KOG0870 consensus DNA polymerase epsilon, subunit D [Transcription]
Probab=46.99 E-value=8.4 Score=29.34 Aligned_cols=33 Identities=24% Similarity=0.268 Sum_probs=28.6
Q ss_pred ccccccCchHHHHHHHhhhcCCCCcccccHHHHhhcc
Q 034007 69 DLLIPRMSFIREVRTITYRVAPPDVNRWTPEALIALQ 105 (106)
Q Consensus 69 ~lLI~k~pF~RLVreI~~~~~~~~~lRfq~~Al~ALQ 105 (106)
+|++|++-..|||+|+..++ +.-.+.+|+.|++
T Consensus 8 dl~lP~AiI~rlvke~l~E~----~vsisKeA~~Ai~ 40 (172)
T KOG0870|consen 8 DLNLPNAIITRLVKEVLPES----NVSISKEARLAIA 40 (172)
T ss_pred HhhccHHHHHHHHHHhCccc----cccccHHHHHHHH
Confidence 68899999999999999883 5778999999876
No 10
>PF07789 DUF1627: Protein of unknown function (DUF1627); InterPro: IPR012432 This is a group of sequences found in hypothetical proteins predicted to be expressed in a number of bacterial species. The region in question is approximately 150 amino acid residues long.
Probab=34.97 E-value=21 Score=26.77 Aligned_cols=10 Identities=40% Similarity=0.747 Sum_probs=5.9
Q ss_pred hhHHHHhhhc
Q 034007 57 ALREIRRFQK 66 (106)
Q Consensus 57 alrEIr~yQk 66 (106)
|||||++|+.
T Consensus 141 AlRELnKhRd 150 (155)
T PF07789_consen 141 ALRELNKHRD 150 (155)
T ss_pred HHHHHHHHHH
Confidence 5666666643
No 11
>PF10788 DUF2603: Protein of unknown function (DUF2603); InterPro: IPR019724 This entry represents a conserved protein in epsilon-Proteobacteria. The function is not known.
Probab=30.33 E-value=54 Score=24.08 Aligned_cols=32 Identities=22% Similarity=0.394 Sum_probs=26.6
Q ss_pred chhhHHHHhhhcccccccccCchHHHHHHHhhh
Q 034007 55 TKALREIRRFQKSVDLLIPRMSFIREVRTITYR 87 (106)
Q Consensus 55 t~alrEIr~yQkst~lLI~k~pF~RLVreI~~~ 87 (106)
.||+.||+++-.+..-+ +..-+-+||.+|=.+
T Consensus 97 ~VAm~ei~~~~~~~~~~-~~id~~~lvk~IKk~ 128 (137)
T PF10788_consen 97 AVAMDEIKKMRQKDGNL-PNIDLDKLVKNIKKE 128 (137)
T ss_pred HHHHHHHHHHHhcCCCc-CCCCHHHHHHHHHHh
Confidence 68999999996555444 899999999999876
No 12
>cd07981 TAF12 TATA Binding Protein (TBP) Associated Factor 12 (TAF12) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 12 (TAF12) is one of several TAFs that bind TBP and are involved in forming the TFIID complex. TFIID is one of the seven General Transcription Factors (GTFs) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs are named after their electrophoretic mobility in polyacrylamide gels in different species. A new, unified nomenclature has been suggested for the pol II TAFs to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs function such as serving as activator-bind
Probab=29.51 E-value=28 Score=22.15 Aligned_cols=24 Identities=17% Similarity=0.174 Sum_probs=16.7
Q ss_pred hHHHHHHHhhhcCCCCcccccHHHHhhccC
Q 034007 77 FIREVRTITYRVAPPDVNRWTPEALIALQE 106 (106)
Q Consensus 77 F~RLVreI~~~~~~~~~lRfq~~Al~ALQE 106 (106)
-+.||++|.. ..|+..+|.++|||
T Consensus 7 l~~lv~~id~------~~~~~~da~~~l~~ 30 (72)
T cd07981 7 LQELLKEIDP------REQLDPDVEELLLE 30 (72)
T ss_pred HHHHHHhhCC------CCCcCHHHHHHHHH
Confidence 3456665532 37999999999875
No 13
>KOG1071 consensus Mitochondrial translation elongation factor EF-Tsmt, catalyzes nucleotide exchange on EF-Tumt [Translation, ribosomal structure and biogenesis]
Probab=23.44 E-value=42 Score=28.12 Aligned_cols=33 Identities=24% Similarity=0.277 Sum_probs=27.5
Q ss_pred CchhhHHHHhhhcccccccccCchHHHHHHHhhhcC
Q 034007 54 GTKALREIRRFQKSVDLLIPRMSFIREVRTITYRVA 89 (106)
Q Consensus 54 gt~alrEIr~yQkst~lLI~k~pF~RLVreI~~~~~ 89 (106)
|+.++-|+.+ .|||.-+-.+|+.||..|+..++
T Consensus 114 ~r~vlvElNC---ETDFVARn~~Fq~Lv~~iA~~~l 146 (340)
T KOG1071|consen 114 GRTVLVELNC---ETDFVARNDIFQDLVDQIALSVL 146 (340)
T ss_pred CeEEEEEeec---ccchhhccchHHHHHHHHHHHHH
Confidence 5567777765 68999999999999999998854
Done!