Query 030207
Match_columns 181
No_of_seqs 48 out of 50
Neff 2.4
Searched_HMMs 46136
Date Fri Mar 29 10:11:35 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030207.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030207hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF13943 WPP: WPP domain 100.0 2.1E-49 4.5E-54 301.1 9.6 96 56-151 1-98 (99)
2 PF02697 DUF217: Uncharacteriz 73.1 5.3 0.00012 29.0 3.5 39 68-106 25-63 (71)
3 PF02172 KIX: KIX domain; Int 52.8 6.7 0.00014 29.3 0.9 49 63-113 11-60 (81)
4 PF07500 TFIIS_M: Transcriptio 47.6 22 0.00047 26.5 2.9 43 64-111 3-45 (115)
5 smart00510 TFS2M Domain in the 37.9 43 0.00093 25.2 3.2 41 65-110 2-42 (102)
6 PRK13696 hypothetical protein; 35.7 44 0.00094 24.2 2.8 36 68-103 26-62 (62)
7 PRK13019 clpS ATP-dependent Cl 32.8 77 0.0017 24.0 3.9 73 48-144 15-87 (94)
8 PF09860 DUF2087: Uncharacteri 27.6 53 0.0011 23.6 2.1 28 57-84 3-30 (71)
9 PF04212 MIT: MIT (microtubule 25.1 1.2E+02 0.0025 20.4 3.4 38 105-143 3-42 (69)
10 KOG4434 Molecular chaperone SE 25.1 33 0.00072 33.2 0.9 27 64-90 6-32 (520)
11 KOG3616 Selective LIM binding 24.6 47 0.001 35.3 1.9 16 115-130 612-627 (1636)
12 PF14261 DUF4351: Domain of un 22.9 43 0.00094 23.2 0.9 15 83-97 15-29 (59)
13 COG1119 ModF ABC-type molybden 21.3 95 0.0021 27.9 2.9 44 56-99 136-180 (257)
14 COG0177 Nth Predicted EndoIII- 20.8 61 0.0013 27.9 1.6 21 63-89 39-59 (211)
No 1
>PF13943 WPP: WPP domain
Probab=100.00 E-value=2.1e-49 Score=301.07 Aligned_cols=96 Identities=52% Similarity=0.888 Sum_probs=93.2
Q ss_pred cEEecCCCchhHHHHHHHHHHhcccchhhhhhcCCCChhhHHHHHhhhHHHHHHhhhhh--cCCCCCchHHHHHHHHHHH
Q 030207 56 TFRIWPPAQRTRDAVIARLIETLTTPSVLSKRYGAMPTDEADFTARFIENDAFSVADAA--ASAEDDGIEVLQVYSKEIS 133 (181)
Q Consensus 56 S~kiWPPsQrTRdaVV~RmienLSt~SilSkrYG~l~~eEAee~Ak~IEe~AFa~An~~--~~pdgDGieavQlYAKE~S 133 (181)
|||||||+|+||||||+||++||+++||||||||+|+++||+++||+|||+||++|++| .+||+|||++||+|+||||
T Consensus 1 s~~lWPpsq~tR~~vv~Rm~~nLss~s~~s~ryg~l~~eeA~~~Ak~IEe~AF~~A~~~~~~~~d~dg~e~vq~YaKE~S 80 (99)
T PF13943_consen 1 SFKLWPPSQRTRDAVVERMTENLSSPSILSKRYGTLPKEEAEEAAKRIEEEAFAAANQHYETEPDGDGIEAVQLYAKEIS 80 (99)
T ss_pred CCCcCCCCchHHHHHHHHHHHhhhhhHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHhhccCCCCCchHHHHHHHHHHHH
Confidence 79999999999999999999999999999999999999999999999999999999997 8899999999999999999
Q ss_pred HHHHHHHhcccccccCCC
Q 030207 134 KRMLEAVKSRSSAAASGI 151 (181)
Q Consensus 134 KrMLE~lK~rs~~a~~~~ 151 (181)
|||||+||+|+.++.++.
T Consensus 81 klmLE~vK~~~~~~~~~~ 98 (99)
T PF13943_consen 81 KLMLEVVKSGPKAASAAE 98 (99)
T ss_pred HHHHHHHHhcCCcccccc
Confidence 999999999999887764
No 2
>PF02697 DUF217: Uncharacterized ACR, COG1753; InterPro: IPR003847 This entry is represented by Natrialba phage PhiCh1, Orf96. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=73.06 E-value=5.3 Score=28.96 Aligned_cols=39 Identities=31% Similarity=0.417 Sum_probs=32.5
Q ss_pred HHHHHHHHHhcccchhhhhhcCCCChhhHHHHHhhhHHH
Q 030207 68 DAVIARLIETLTTPSVLSKRYGAMPTDEADFTARFIEND 106 (181)
Q Consensus 68 daVV~RmienLSt~SilSkrYG~l~~eEAee~Ak~IEe~ 106 (181)
.-||.||+..=...-.|..-+|.|+.++|.+..+.|++.
T Consensus 25 SdvI~rli~~~~~~~~l~~~~g~l~deea~~~~~~i~e~ 63 (71)
T PF02697_consen 25 SDVIERLIEKEKKRRDLMDYFGILSDEEADEMEKDIKEE 63 (71)
T ss_pred HHHHHHHHhcccchhHHHHHhccCChhhHHHHHHHHHHH
Confidence 479999999555667788889999999999999888764
No 3
>PF02172 KIX: KIX domain; InterPro: IPR003101 The nuclear factor CREB activates transcription of target genes in part through direct interactions with the KIX domain of the coactivator CBP in a phosphorylation-dependent manner []. This provides a model for activator:coactivator interactions. The KIX domain of CBP also binds to transactivation domains of other nuclear factors including Myb and Jun.; GO: 0003712 transcription cofactor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2KWF_A 1KDX_A 2LQH_A 2LQI_A 1SB0_A 2AGH_B.
Probab=52.79 E-value=6.7 Score=29.26 Aligned_cols=49 Identities=16% Similarity=0.203 Sum_probs=31.7
Q ss_pred CchhHHHHHHHHHHhcccc-hhhhhhcCCCChhhHHHHHhhhHHHHHHhhhh
Q 030207 63 AQRTRDAVIARLIETLTTP-SVLSKRYGAMPTDEADFTARFIENDAFSVADA 113 (181)
Q Consensus 63 sQrTRdaVV~RmienLSt~-SilSkrYG~l~~eEAee~Ak~IEe~AFa~An~ 113 (181)
++.-|..||.+|+..+--. ......-+. -++--+.|+.||..+|..|+.
T Consensus 11 t~~lR~hlV~KLv~aI~P~pdp~a~~d~r--m~~l~~yarkvE~~~fe~A~s 60 (81)
T PF02172_consen 11 TPDLRNHLVHKLVQAIFPTPDPNAMNDPR--MKNLIEYARKVEKDMFETAQS 60 (81)
T ss_dssp -HHHHHHHHHHHHHHHS-SSSCCCCCSHH--HHHHHHHHHHHHHHHHHC-SS
T ss_pred CHHHHHHHHHHHHHhhCCCCChhhhhhHH--HHHHHHHHHHHHHHHHHHhcc
Confidence 4677999999999987632 222111110 134668999999999999875
No 4
>PF07500 TFIIS_M: Transcription factor S-II (TFIIS), central domain; InterPro: IPR003618 Transcription factor S-II (TFIIS) is a eukaryotic protein which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites. TFIIS shows DNA-binding activity only in the presence of RNA polymerase II []. It is widely distributed being found in mammals, Drosophila, yeast and in the archaebacteria Sulfolobus acidocaldarius []. S-II proteins have a relatively conserved C-terminal region but variable N-terminal region, and some members of this family are expressed in a tissue-specific manner [, ]. TFIIS is a modular factor that comprises an N-terminal domain I, a central domain II, and a C-terminal domain III []. The weakly conserved domain I forms a four-helix bundle and is not required for TFIIS activity. Domain II forms a three-helix bundle, and domain III adopts a zinc-ribbon fold with a thin protruding beta-hairpin. Domain II and the linker between domains II and III are required for Pol II binding, whereas domain III is essential for stimulation of RNA cleavage. TFIIS extends from the polymerase surface via a pore to the internal active site, spanning a distance of 100 Angstroms. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. This domain is found in the central region of transcription elongation factor S-II and in several hypothetical proteins.; GO: 0006351 transcription, DNA-dependent; PDB: 3PO3_S 1ENW_A 3GTM_S 1Y1V_S 3NDQ_A 2DME_A.
Probab=47.56 E-value=22 Score=26.48 Aligned_cols=43 Identities=23% Similarity=0.184 Sum_probs=32.9
Q ss_pred chhHHHHHHHHHHhcccchhhhhhcCCCChhhHHHHHhhhHHHHHHhh
Q 030207 64 QRTRDAVIARLIETLTTPSVLSKRYGAMPTDEADFTARFIENDAFSVA 111 (181)
Q Consensus 64 QrTRdaVV~RmienLSt~SilSkrYG~l~~eEAee~Ak~IEe~AFa~A 111 (181)
..+|+.+++-|.+.|...+-. .-...++...|..||+..|..-
T Consensus 3 ~~~R~k~~~~L~~~l~~~~~~-----~~~~~~~~~lA~~IE~~lf~~~ 45 (115)
T PF07500_consen 3 DKVRDKARKLLYKALQKRSDE-----QDDPEDAKELAKEIEEALFDKF 45 (115)
T ss_dssp CHHHHHHHHHHHHHHHHCCCC-----CCCTCCHHHHHHHHHHHHHHHH
T ss_pred cHHHHHHHHHHHHHHHhcCcc-----ccchhHHHHHHHHHHHHHHHHH
Confidence 356888888888877766322 1178889999999999999876
No 5
>smart00510 TFS2M Domain in the central regions of transcription elongation factor S-II (and elsewhere).
Probab=37.87 E-value=43 Score=25.24 Aligned_cols=41 Identities=24% Similarity=0.127 Sum_probs=29.4
Q ss_pred hhHHHHHHHHHHhcccchhhhhhcCCCChhhHHHHHhhhHHHHHHh
Q 030207 65 RTRDAVIARLIETLTTPSVLSKRYGAMPTDEADFTARFIENDAFSV 110 (181)
Q Consensus 65 rTRdaVV~RmienLSt~SilSkrYG~l~~eEAee~Ak~IEe~AFa~ 110 (181)
.+|+.++.-|.+-|.-.+... ....++.+.|..||...|..
T Consensus 2 ~~R~~~~~~L~~al~~~~~~~-----~~~~~~~~lA~~IE~~lf~~ 42 (102)
T smart00510 2 KVRDKCQEMLYKALQKISDPE-----EIELDPTELAVQIEAEMFSE 42 (102)
T ss_pred hHHHHHHHHHHHHHHhcCCCC-----cccccHHHHHHHHHHHHHHH
Confidence 468888888887766444332 13336888999999999985
No 6
>PRK13696 hypothetical protein; Provisional
Probab=35.67 E-value=44 Score=24.25 Aligned_cols=36 Identities=28% Similarity=0.381 Sum_probs=26.2
Q ss_pred HHHHHHHHHhcc-cchhhhhhcCCCChhhHHHHHhhh
Q 030207 68 DAVIARLIETLT-TPSVLSKRYGAMPTDEADFTARFI 103 (181)
Q Consensus 68 daVV~RmienLS-t~SilSkrYG~l~~eEAee~Ak~I 103 (181)
.-||+||++... ....|-+=||.++.+||++..+.|
T Consensus 26 Sevi~~L~~~~~~~~~~l~~~~Gil~dee~~e~~~~~ 62 (62)
T PRK13696 26 SEVIRELIEKKKGNLDKLMKAFGILSEEEAEELKKEL 62 (62)
T ss_pred HHHHHHHHHHhhccHHHHHHHHCCCCHHHHHHHHhhC
Confidence 368999994222 345566679999999999887654
No 7
>PRK13019 clpS ATP-dependent Clp protease adaptor; Reviewed
Probab=32.83 E-value=77 Score=23.99 Aligned_cols=73 Identities=15% Similarity=0.082 Sum_probs=55.8
Q ss_pred hcCCCCCccEEecCCCchhHHHHHHHHHHhcccchhhhhhcCCCChhhHHHHHhhhHHHHHHhhhhhcCCCCCchHHHHH
Q 030207 48 KKLNFSNLTFRIWPPAQRTRDAVIARLIETLTTPSVLSKRYGAMPTDEADFTARFIENDAFSVADAAASAEDDGIEVLQV 127 (181)
Q Consensus 48 ~~~~~~~~S~kiWPPsQrTRdaVV~RmienLSt~SilSkrYG~l~~eEAee~Ak~IEe~AFa~An~~~~pdgDGieavQl 127 (181)
+...|...-+-+|=-.-.|+|.||+.|.+. +-.++.++|...+-.| ...|..+|-+
T Consensus 15 ~~~~p~~ykViL~NDd~~t~dfVi~~vl~~----------vf~~s~~~A~~iml~v--------------H~~G~avv~~ 70 (94)
T PRK13019 15 KLERYPLYKVIVLNDDFNTFEHVVNCLLKA----------IPGMSEDRAWRLMITA--------------HKEGSAVVWV 70 (94)
T ss_pred cccCCCceEEEEEcCCCCCHHHHHHHHHHH----------hcCCCHHHHHHHHHHH--------------hcCCcEEEEE
Confidence 344567788999999999999999887764 2356677776665543 3478889999
Q ss_pred HHHHHHHHHHHHHhccc
Q 030207 128 YSKEISKRMLEAVKSRS 144 (181)
Q Consensus 128 YAKE~SKrMLE~lK~rs 144 (181)
|.+|+-....+-|.+..
T Consensus 71 ~~~E~AE~~~~~l~~~g 87 (94)
T PRK13019 71 GPLEQAELYHQQLTDAG 87 (94)
T ss_pred ecHHHHHHHHHHHHHcc
Confidence 99999998888877654
No 8
>PF09860 DUF2087: Uncharacterized protein conserved in bacteria (DUF2087); InterPro: IPR018656 This domain, found in various hypothetical prokaryotic proteins and transcriptional activators, has no known function.
Probab=27.55 E-value=53 Score=23.65 Aligned_cols=28 Identities=14% Similarity=0.415 Sum_probs=22.9
Q ss_pred EEecCCCchhHHHHHHHHHHhcccchhh
Q 030207 57 FRIWPPAQRTRDAVIARLIETLTTPSVL 84 (181)
Q Consensus 57 ~kiWPPsQrTRdaVV~RmienLSt~Sil 84 (181)
+.-||..+..|..|+..|+..+...-.+
T Consensus 3 L~~~P~k~~~r~~iL~~l~~~f~~g~~y 30 (71)
T PF09860_consen 3 LKRWPSKRKKRLVILEYLASRFEPGREY 30 (71)
T ss_pred ccccCccHHHHHHHHHHHHHhCCCCCcc
Confidence 5679999999999999999988544333
No 9
>PF04212 MIT: MIT (microtubule interacting and transport) domain; InterPro: IPR007330 The MIT domain is found in vacuolar sorting proteins, spastin (probable ATPase involved in the assembly or function of nuclear protein complexes), and a sorting nexin, which may play a role in intracellular trafficking.; PDB: 2DL1_A 2JQK_A 1WR0_A 2CPT_A 2JQH_A 2V6Y_A 2JQ9_A 2K3W_A 1YXR_A 3EAB_E ....
Probab=25.13 E-value=1.2e+02 Score=20.41 Aligned_cols=38 Identities=29% Similarity=0.424 Sum_probs=25.3
Q ss_pred HHHHHhhhhh--cCCCCCchHHHHHHHHHHHHHHHHHHhcc
Q 030207 105 NDAFSVADAA--ASAEDDGIEVLQVYSKEISKRMLEAVKSR 143 (181)
Q Consensus 105 e~AFa~An~~--~~pdgDGieavQlYAKE~SKrMLE~lK~r 143 (181)
+.||..++.+ ....|+=-+|++.| ++....|+..++.-
T Consensus 3 ~~A~~~~~~Av~~D~~g~~~~A~~~Y-~~ai~~l~~~~~~~ 42 (69)
T PF04212_consen 3 DKAIELIKKAVEADEAGNYEEALELY-KEAIEYLMQALKSE 42 (69)
T ss_dssp HHHHHHHHHHHHHHHTTSHHHHHHHH-HHHHHHHHHHHHHS
T ss_pred HHHHHHHHHHHHHHHCCCHHHHHHHH-HHHHHHHHHHhccC
Confidence 4566666666 33466778999999 55666666666543
No 10
>KOG4434 consensus Molecular chaperone SEC63, endoplasmic reticulum translocon component [Intracellular trafficking, secretion, and vesicular transport; Posttranslational modification, protein turnover, chaperones]
Probab=25.09 E-value=33 Score=33.19 Aligned_cols=27 Identities=30% Similarity=0.389 Sum_probs=24.6
Q ss_pred chhHHHHHHHHHHhcccchhhhhhcCC
Q 030207 64 QRTRDAVIARLIETLTTPSVLSKRYGA 90 (181)
Q Consensus 64 QrTRdaVV~RmienLSt~SilSkrYG~ 90 (181)
-+||.|.+.|||-.|+..+=|+++|..
T Consensus 6 ~kTp~M~~kR~imVLags~EFdkqyNk 32 (520)
T KOG4434|consen 6 NRTPRMEIKRMIMVLAGSFEFDKQYNK 32 (520)
T ss_pred ccCchhHHHHHHHHHhcccccChhhch
Confidence 379999999999999999999999953
No 11
>KOG3616 consensus Selective LIM binding factor [Transcription]
Probab=24.62 E-value=47 Score=35.26 Aligned_cols=16 Identities=31% Similarity=0.717 Sum_probs=14.7
Q ss_pred cCCCCCchHHHHHHHH
Q 030207 115 ASAEDDGIEVLQVYSK 130 (181)
Q Consensus 115 ~~pdgDGieavQlYAK 130 (181)
++++|||.+|+|+|-|
T Consensus 612 k~sdgd~laaiqlyik 627 (1636)
T KOG3616|consen 612 KESDGDGLAAIQLYIK 627 (1636)
T ss_pred ccccCccHHHHHHHHH
Confidence 7899999999999966
No 12
>PF14261 DUF4351: Domain of unknown function (DUF4351)
Probab=22.92 E-value=43 Score=23.19 Aligned_cols=15 Identities=27% Similarity=0.875 Sum_probs=11.8
Q ss_pred hhhhhcCCCChhhHH
Q 030207 83 VLSKRYGAMPTDEAD 97 (181)
Q Consensus 83 ilSkrYG~l~~eEAe 97 (181)
.|.||||.||++-..
T Consensus 15 lL~rrFG~lp~~~~~ 29 (59)
T PF14261_consen 15 LLTRRFGELPPEIQE 29 (59)
T ss_pred HHHHHcCCCCHHHHH
Confidence 478999999997543
No 13
>COG1119 ModF ABC-type molybdenum transport system, ATPase component/photorepair protein PhrA [Inorganic ion transport and metabolism]
Probab=21.26 E-value=95 Score=27.91 Aligned_cols=44 Identities=16% Similarity=0.253 Sum_probs=39.8
Q ss_pred cEEecC-CCchhHHHHHHHHHHhcccchhhhhhcCCCChhhHHHH
Q 030207 56 TFRIWP-PAQRTRDAVIARLIETLTTPSVLSKRYGAMPTDEADFT 99 (181)
Q Consensus 56 S~kiWP-PsQrTRdaVV~RmienLSt~SilSkrYG~l~~eEAee~ 99 (181)
||-+|. +.-..+...++-|.+.+-..++..|.|++|+..|...+
T Consensus 136 siG~y~~~~~~~~~~~a~~lle~~g~~~la~r~~~~LS~Ge~rrv 180 (257)
T COG1119 136 SIGIYQEDLTAEDLAAAQWLLELLGAKHLADRPFGSLSQGEQRRV 180 (257)
T ss_pred cccccccCCCHHHHHHHHHHHHHcchhhhccCchhhcCHhHHHHH
Confidence 678898 88888999999999999999999999999999988764
No 14
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=20.76 E-value=61 Score=27.88 Aligned_cols=21 Identities=33% Similarity=0.507 Sum_probs=17.6
Q ss_pred CchhHHHHHHHHHHhcccchhhhhhcC
Q 030207 63 AQRTRDAVIARLIETLTTPSVLSKRYG 89 (181)
Q Consensus 63 sQrTRdaVV~RmienLSt~SilSkrYG 89 (181)
||+|+|.+|++.+.+| -++|+
T Consensus 39 SaqttD~~vn~at~~L------f~~~~ 59 (211)
T COG0177 39 SAQTTDEVVNKATPAL------FKRYP 59 (211)
T ss_pred hccCchHHHHHHHHHH------HHHcC
Confidence 8999999999999876 35566
Done!