Query 026405
Match_columns 239
No_of_seqs 166 out of 349
Neff 3.8
Searched_HMMs 46136
Date Fri Mar 29 07:36:33 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026405.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026405hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF03479 DUF296: Domain of unk 99.7 6.7E-17 1.5E-21 129.2 6.8 70 153-222 1-72 (120)
2 COG1661 Predicted DNA-binding 99.3 4.3E-12 9.3E-17 106.5 7.5 74 151-224 7-83 (141)
3 PF02178 AT_hook: AT hook moti 96.4 0.0011 2.3E-08 35.7 0.5 12 81-92 1-12 (13)
4 smart00384 AT_hook DNA binding 96.4 0.0018 3.9E-08 40.8 1.3 14 81-94 1-14 (26)
5 PF14621 RFX5_DNA_bdg: RFX5 DN 86.3 0.26 5.6E-06 44.1 0.4 12 79-90 66-77 (219)
6 PF13546 DDE_5: DDE superfamil 81.7 0.79 1.7E-05 40.5 1.5 15 78-92 228-242 (273)
7 COG1710 Uncharacterized protei 76.2 1.2 2.6E-05 37.7 0.9 16 77-92 80-96 (139)
8 COG1777 Predicted transcriptio 56.0 4.8 0.0001 36.7 0.7 14 80-93 63-76 (217)
9 PF14869 DUF4488: Domain of un 50.3 24 0.00053 30.0 4.0 35 179-215 27-61 (133)
10 PF02196 RBD: Raf-like Ras-bin 46.4 71 0.0015 23.6 5.5 44 154-197 11-56 (71)
11 cd01817 RGS12_RBD Ubiquitin do 46.3 59 0.0013 25.0 5.1 45 156-200 12-58 (73)
12 smart00455 RBD Raf-like Ras-bi 43.7 79 0.0017 23.4 5.4 47 154-200 10-58 (70)
13 PF01582 TIR: TIR domain; Int 41.6 23 0.0005 28.2 2.4 36 151-186 27-64 (141)
14 PF13737 DDE_Tnp_1_5: Transpos 34.9 19 0.00041 29.4 1.0 14 78-91 21-34 (112)
15 cd04618 CBS_pair_5 The CBS dom 34.6 1.2E+02 0.0025 22.4 5.1 35 157-191 52-87 (98)
16 KOG4565 E93 protein involved i 32.9 14 0.00031 33.1 -0.0 14 79-92 111-124 (206)
17 PF00571 CBS: CBS domain CBS d 32.2 74 0.0016 20.7 3.4 38 153-190 5-42 (57)
18 cd01760 RBD Ubiquitin-like dom 27.2 1.1E+02 0.0023 23.1 3.8 37 154-190 10-48 (72)
19 PF14252 DUF4347: Domain of un 25.3 1.2E+02 0.0026 26.1 4.3 42 155-197 23-66 (165)
20 PLN03194 putative disease resi 24.6 78 0.0017 28.3 3.1 37 159-195 63-99 (187)
21 PHA00514 dsDNA binding protein 24.5 24 0.00052 28.5 -0.1 25 214-239 34-58 (98)
22 cd04603 CBS_pair_KefB_assoc Th 22.8 1.5E+02 0.0032 21.7 3.9 37 152-188 61-97 (111)
23 PRK08179 prfH peptide chain re 21.7 2.4E+02 0.0051 25.3 5.6 43 157-199 3-60 (200)
24 smart00412 Cu_FIST Copper-Fist 21.4 41 0.0009 23.2 0.6 8 80-87 31-38 (39)
25 PF12736 CABIT: Cell-cycle sus 21.4 59 0.0013 28.7 1.7 62 155-220 2-72 (256)
26 TIGR03072 release_prfH putativ 21.1 2E+02 0.0044 25.7 5.0 43 157-199 2-59 (200)
No 1
>PF03479 DUF296: Domain of unknown function (DUF296); InterPro: IPR005175 This putative conserved domain is found in proteins that contain AT-hook motifs IPR000637 from INTERPRO, suggesting a DNA-binding function for the proteins as a whole, however, the function of this domain is unknown. Overexpression of a protein containing this domain, Q9S7C9 from SWISSPROT, in Arabidopsis thaliana causes late flowering and modified leaf development []. ; PDB: 2DT4_A 2P6Y_A 3HWU_A 3HTN_A 2NMU_A 2H6L_A 2HX0_A.
Probab=99.68 E-value=6.7e-17 Score=129.15 Aligned_cols=70 Identities=20% Similarity=0.177 Sum_probs=64.4
Q ss_pred ceeEEEEEcCCCchHHHHHHHHHhcCceeEEEeccCeeeeEEEeCCC--CCCCceeEEeeeeeEEeeecccc
Q 026405 153 FTPHVISVAAGEDVGQKIMLFMQQSKREICILSASGSISNASLRQPA--TSGGNITYELRAGPQGVWETVDG 222 (239)
Q Consensus 153 ftpHVIrV~pGEDV~~kI~~Faqq~~rAicILSa~GsVSnVTLRqp~--ssg~tvtyeGrFEILSLsGTl~~ 222 (239)
|++|+|||++||||+++|++||+++++..|+|+++|+|++|+|++++ ..+..++|+|+|||+||+|||..
T Consensus 1 ~r~~~~rl~~Gedl~~~l~~~~~~~~i~~~~is~iGsl~~~~l~~~~~~~~~~~~~~~g~~Ei~sl~G~i~~ 72 (120)
T PF03479_consen 1 GRVFVIRLDPGEDLLESLEAFAREHGIRSGVISGIGSLSNVTLGYYDPPSYYEPLEFEGPFEIISLSGTISP 72 (120)
T ss_dssp EEEEEEEEETTSBHHHHHHHHHHHHT-SSEEEEEEEEEEEEEEEEEETTTEEEEEEEESEEEEEEEEEEEEE
T ss_pred CcEEEEEECCCCHHHHHHHHHHHHCCCcEEEEEEEeEEeEEEEEEecccCCcceEEecccEEEEEeEEEEEC
Confidence 78999999999999999999999999888889999999999999983 34678899999999999999986
No 2
>COG1661 Predicted DNA-binding protein with PD1-like DNA-binding motif [General function prediction only]
Probab=99.32 E-value=4.3e-12 Score=106.46 Aligned_cols=74 Identities=15% Similarity=0.122 Sum_probs=67.5
Q ss_pred CCceeEEEEEcCCCchHHHHHHHHHhcCceeEEEeccCeeeeEEEeCCCCC---CCceeEEeeeeeEEeeecccccc
Q 026405 151 QGFTPHVISVAAGEDVGQKIMLFMQQSKREICILSASGSISNASLRQPATS---GGNITYELRAGPQGVWETVDGVM 224 (239)
Q Consensus 151 ~~ftpHVIrV~pGEDV~~kI~~Faqq~~rAicILSa~GsVSnVTLRqp~ss---g~tvtyeGrFEILSLsGTl~~~~ 224 (239)
..-+-+++||++|||+.+.|.+||+++....+|++|+|++++++||..+.. +..+.+.++||||||.|+|..+.
T Consensus 7 ~~gr~~~~Rld~G~d~~~~l~~~a~~~~i~aa~v~~iGal~~~~l~~~~~~~~~y~~~~~~e~~EvlSL~G~i~~~~ 83 (141)
T COG1661 7 SSGRVIALRLDPGEDLFSELEAFAEQEDIHAAVVTAIGALRDAKLRYFDPEEKEYETIPVNEPLEVLSLLGNIALDD 83 (141)
T ss_pred ccceEEEEEeCCCccHHHHHHHHHHhcCceEEEEEEeeeeeeeEEEEecCCCCceEEEecCCcEEEEEecceeecCC
Confidence 344678999999999999999999999977799999999999999999843 67899999999999999998877
No 3
>PF02178 AT_hook: AT hook motif; InterPro: IPR017956 AT hooks are DNA-binding motifs with a preference for A/T rich regions. These motifs are found in a variety of proteins, including the high mobility group (HMG) proteins [], in DNA-binding proteins from plants [] and in hBRG1 protein, a central ATPase of the human switching/sucrose non-fermenting (SWI/SNF) remodeling complex []. High mobility group (HMG) proteins are a family of relatively low molecular weight non-histone components in chromatin []. HMG-I and HMG-Y (HMGA) are proteins of about 100 amino acid residues which are produced by the alternative splicing of a single gene. HMG-I/Y proteins bind preferentially to the minor groove of AT-rich regions in double-stranded DNA in a non-sequence specific manner [, ]. It is suggested that these proteins could function in nucleosome phasing and in the 3' end processing of mRNA transcripts. They are also involved in the transcription regulation of genes containing, or in close proximity to, AT-rich regions. ; GO: 0003677 DNA binding; PDB: 2EZE_A 2EZD_A 2EZF_A 2EZG_A.
Probab=96.43 E-value=0.0011 Score=35.73 Aligned_cols=12 Identities=67% Similarity=1.104 Sum_probs=4.6
Q ss_pred cccCCCCCCCCC
Q 026405 81 KKKRGRPRKYGT 92 (239)
Q Consensus 81 KkKRGRPRKYg~ 92 (239)
+|+||||+|+..
T Consensus 1 ~r~RGRP~k~~~ 12 (13)
T PF02178_consen 1 KRKRGRPRKNAK 12 (13)
T ss_dssp S--SS--TT---
T ss_pred CCcCCCCccccC
Confidence 689999999863
No 4
>smart00384 AT_hook DNA binding domain with preference for A/T rich regions. Small DNA-binding motif first described in the high mobility group non-histone chromosomal protein HMG-I(Y).
Probab=96.35 E-value=0.0018 Score=40.84 Aligned_cols=14 Identities=57% Similarity=0.873 Sum_probs=11.9
Q ss_pred cccCCCCCCCCCCC
Q 026405 81 KKKRGRPRKYGTPE 94 (239)
Q Consensus 81 KkKRGRPRKYg~~~ 94 (239)
|||||||||+..+.
T Consensus 1 kRkRGRPrK~~~~~ 14 (26)
T smart00384 1 KRKRGRPRKAPKDX 14 (26)
T ss_pred CCCCCCCCCCCCcc
Confidence 69999999997554
No 5
>PF14621 RFX5_DNA_bdg: RFX5 DNA-binding domain
Probab=86.28 E-value=0.26 Score=44.12 Aligned_cols=12 Identities=75% Similarity=1.115 Sum_probs=10.6
Q ss_pred cccccCCCCCCC
Q 026405 79 PAKKKRGRPRKY 90 (239)
Q Consensus 79 ~~KkKRGRPRKY 90 (239)
-.|||||||||-
T Consensus 66 dAKRKRGRPRKK 77 (219)
T PF14621_consen 66 DAKRKRGRPRKK 77 (219)
T ss_pred hhhhhcCCCccC
Confidence 579999999976
No 6
>PF13546 DDE_5: DDE superfamily endonuclease
Probab=81.66 E-value=0.79 Score=40.48 Aligned_cols=15 Identities=67% Similarity=1.223 Sum_probs=11.3
Q ss_pred ccccccCCCCCCCCC
Q 026405 78 EPAKKKRGRPRKYGT 92 (239)
Q Consensus 78 ~~~KkKRGRPRKYg~ 92 (239)
.+..+|||||||||.
T Consensus 228 ~~~~~~rGRPr~~g~ 242 (273)
T PF13546_consen 228 PPPPPKRGRPRKYGR 242 (273)
T ss_pred cccCCCCCCCCCCCC
Confidence 344556999999994
No 7
>COG1710 Uncharacterized protein conserved in archaea [Function unknown]
Probab=76.23 E-value=1.2 Score=37.71 Aligned_cols=16 Identities=63% Similarity=1.068 Sum_probs=13.1
Q ss_pred Ccccc-ccCCCCCCCCC
Q 026405 77 LEPAK-KKRGRPRKYGT 92 (239)
Q Consensus 77 ~~~~K-kKRGRPRKYg~ 92 (239)
.-|+| |-|||||||..
T Consensus 80 vIPvk~KgrGrprkyd~ 96 (139)
T COG1710 80 VIPVKLKGRGRPRKYDR 96 (139)
T ss_pred EeeeeecCCCCCcccch
Confidence 35778 88999999974
No 8
>COG1777 Predicted transcriptional regulators [Transcription]
Probab=55.99 E-value=4.8 Score=36.67 Aligned_cols=14 Identities=57% Similarity=0.776 Sum_probs=10.8
Q ss_pred ccccCCCCCCCCCC
Q 026405 80 AKKKRGRPRKYGTP 93 (239)
Q Consensus 80 ~KkKRGRPRKYg~~ 93 (239)
.|.+|||||||=-.
T Consensus 63 e~~~Rg~~rKYY~I 76 (217)
T COG1777 63 EKIPRGRPRKYYMI 76 (217)
T ss_pred cccccCCCcceeec
Confidence 46777999999644
No 9
>PF14869 DUF4488: Domain of unknown function (DUF4488)
Probab=50.31 E-value=24 Score=29.98 Aligned_cols=35 Identities=26% Similarity=0.264 Sum_probs=29.1
Q ss_pred ceeEEEeccCeeeeEEEeCCCCCCCceeEEeeeeeEE
Q 026405 179 REICILSASGSISNASLRQPATSGGNITYELRAGPQG 215 (239)
Q Consensus 179 rAicILSa~GsVSnVTLRqp~ssg~tvtyeGrFEILS 215 (239)
..+=|||.-|...|+++ .+.+ +.++++.|.||+.|
T Consensus 27 ~~lKilS~Dgtf~Ni~~-~~~~-~aiIt~~GtY~~~s 61 (133)
T PF14869_consen 27 NVLKILSDDGTFVNITM-IPKS-GAIITGYGTYEQPS 61 (133)
T ss_pred ccEEEEcCCCcEEEEEE-eCCC-CcEEEEeEEEEEcC
Confidence 34779999999999999 4443 37899999999986
No 10
>PF02196 RBD: Raf-like Ras-binding domain; InterPro: IPR003116 This is the Ras-binding domain found in proteins related to Ras. It is found in association with the PE-bind and pkinase domains.; GO: 0005057 receptor signaling protein activity, 0007165 signal transduction; PDB: 1RFA_A 1C1Y_B 3KUD_B 1GUA_B 3KUC_B 2L05_A 3NY5_D 1RRB_A 1WFY_A 1WXM_A.
Probab=46.36 E-value=71 Score=23.62 Aligned_cols=44 Identities=16% Similarity=0.208 Sum_probs=32.9
Q ss_pred eeEEEEEcCCCchHHHHHHHHHhcC--ceeEEEeccCeeeeEEEeC
Q 026405 154 TPHVISVAAGEDVGQKIMLFMQQSK--REICILSASGSISNASLRQ 197 (239)
Q Consensus 154 tpHVIrV~pGEDV~~kI~~Faqq~~--rAicILSa~GsVSnVTLRq 197 (239)
+.-+|.|.+|+-|.+.|...|++++ -..|.+.-.|.-.-+.+-+
T Consensus 11 q~t~V~vrpg~ti~d~L~~~~~kr~L~~~~~~V~~~~~~k~l~~~~ 56 (71)
T PF02196_consen 11 QRTVVQVRPGMTIRDALSKACKKRGLNPECCDVRLVGEKKPLDWDQ 56 (71)
T ss_dssp EEEEEEE-TTSBHHHHHHHHHHTTT--CCCEEEEEEEEEEEE-TTS
T ss_pred CEEEEEEcCCCCHHHHHHHHHHHcCCCHHHEEEEEcCCCccccCCC
Confidence 5678999999999999999999998 5777777777433333333
No 11
>cd01817 RGS12_RBD Ubiquitin domain of RGS12 and RGS14. RGS12 (regulator of G signalling 12), and RGS14, are members of a family of GTPase-activating proteins (GAP's) specific for the G-alpha subunit, which act as key inhibitors of G-protein-mediated cell responses in eukaryotes. Their domain architecture includes tandem RBD domains as well as PDZ , PTB, and RGS, and GoLoco domains.
Probab=46.29 E-value=59 Score=25.04 Aligned_cols=45 Identities=16% Similarity=0.143 Sum_probs=35.8
Q ss_pred EEEEEcCCCchHHHHHHHHHhcC--ceeEEEeccCeeeeEEEeCCCC
Q 026405 156 HVISVAAGEDVGQKIMLFMQQSK--REICILSASGSISNASLRQPAT 200 (239)
Q Consensus 156 HVIrV~pGEDV~~kI~~Faqq~~--rAicILSa~GsVSnVTLRqp~s 200 (239)
-++.+.||+-|.+.|+..+++++ .+.|.+--.|.=.-+.+-|..+
T Consensus 12 T~V~vrpG~ti~d~L~kllekRgl~~~~~~vf~~g~~k~l~~~qD~~ 58 (73)
T cd01817 12 TVVPTRPGESIRDLLSGLCEKRGINYAAVDLFLVGGDKPLVLDQDSS 58 (73)
T ss_pred EEEEecCCCCHHHHHHHHHHHcCCChhHEEEEEecCCcccccCCccc
Confidence 48999999999999999999998 5667666667666666666553
No 12
>smart00455 RBD Raf-like Ras-binding domain.
Probab=43.74 E-value=79 Score=23.39 Aligned_cols=47 Identities=21% Similarity=0.400 Sum_probs=36.2
Q ss_pred eeEEEEEcCCCchHHHHHHHHHhcC--ceeEEEeccCeeeeEEEeCCCC
Q 026405 154 TPHVISVAAGEDVGQKIMLFMQQSK--REICILSASGSISNASLRQPAT 200 (239)
Q Consensus 154 tpHVIrV~pGEDV~~kI~~Faqq~~--rAicILSa~GsVSnVTLRqp~s 200 (239)
+...|.+.||+-|.+.|...|++++ -.-|.|.-.|.=..+.+.++..
T Consensus 10 ~~~~V~vrpg~tl~e~L~~~~~kr~l~~~~~~v~~~g~~k~ldl~~~~~ 58 (70)
T smart00455 10 QRTVVKVRPGKTVRDALAKALKKRGLNPECCVVRLRGEKKPLDLNQPIS 58 (70)
T ss_pred CEEEEEECCCCCHHHHHHHHHHHcCCCHHHEEEEEcCCCcceecCCccc
Confidence 4568999999999999999999998 4666666667445556666553
No 13
>PF01582 TIR: TIR domain; InterPro: IPR000157 In Drosophila melanogaster the Toll protein is involved in establishment of dorso-ventral polarity in the embryo. In addition, members of the Toll family play a key role in innate antibacterial and antifungal immunity in insects as well as in mammals. These proteins are type-I transmembrane receptors that share an intracellular 200 residue domain with the interleukin-1 receptor (IL-1R), the Toll/IL-1R homologous region (TIR). The similarity between Toll-like receptors (LTRs) and IL-1R is not restricted to sequence homology since these proteins also share a similar signalling pathway. They both induce the activation of a Rel type transcription factor via an adaptor protein and a protein kinase []. Interestingly, MyD88, a cytoplasmic adaptor protein found in mammals, contains a TIR domain associated to a DEATH domain (see IPR000488 from INTERPRO) [, , ]. Besides the mammalian and Drosophila melanogaster proteins, a TIR domain is also found in a number of plant proteins implicated in host defence []. As MyD88, these proteins are cytoplasmic. Site directed mutagenesis and deletion analysis have shown that the TIR domain is essential for Toll and IL-1R activities. Sequence analysis have revealed the presence of three highly conserved regions among the different members of the family: box 1 (FDAFISY), box 2 (GYKLC-RD-PG), and box 3 (a conserved W surrounded by basic residues). It has been proposed that boxes 1 and 2 are involved in the binding of proteins involved in signalling, whereas box 3 is primarily involved in directing localization of receptor, perhaps through interactions with cytoskeletal elements [].; GO: 0005515 protein binding, 0007165 signal transduction, 0005622 intracellular; PDB: 3J0A_A 2J67_B 3JRN_A 1FYV_A 1O77_D 1FYX_A 1FYW_A 3OZI_B 1T3G_B 2JS7_A ....
Probab=41.60 E-value=23 Score=28.19 Aligned_cols=36 Identities=25% Similarity=0.379 Sum_probs=28.4
Q ss_pred CCceeEEEE--EcCCCchHHHHHHHHHhcCceeEEEec
Q 026405 151 QGFTPHVIS--VAAGEDVGQKIMLFMQQSKREICILSA 186 (239)
Q Consensus 151 ~~ftpHVIr--V~pGEDV~~kI~~Faqq~~rAicILSa 186 (239)
.+++.-+-. +.+|+.+.+.|.+..++..+.|+|||.
T Consensus 27 ~g~~~c~~~rD~~~G~~~~~~i~~~i~~Sr~~I~VlS~ 64 (141)
T PF01582_consen 27 YGYKLCLDERDFLPGESILDNIQEAIERSRRTIVVLSR 64 (141)
T ss_dssp STS-EEEHHHCTSSSSCHHHHHHHHHHTEEEEEEEESH
T ss_pred CCeEEEEechhhcccccccchhhHhhhhceeeEEEeec
Confidence 345543333 679999999999999999999999995
No 14
>PF13737 DDE_Tnp_1_5: Transposase DDE domain
Probab=34.95 E-value=19 Score=29.42 Aligned_cols=14 Identities=50% Similarity=1.101 Sum_probs=11.9
Q ss_pred ccccccCCCCCCCC
Q 026405 78 EPAKKKRGRPRKYG 91 (239)
Q Consensus 78 ~~~KkKRGRPRKYg 91 (239)
++...|||||++|-
T Consensus 21 ~~~~~kRGr~~~yS 34 (112)
T PF13737_consen 21 APPRGKRGRPPRYS 34 (112)
T ss_pred cCCCCCCCCCcccc
Confidence 45679999999995
No 15
>cd04618 CBS_pair_5 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic genera
Probab=34.60 E-value=1.2e+02 Score=22.36 Aligned_cols=35 Identities=11% Similarity=0.278 Sum_probs=30.5
Q ss_pred EEEEcCCCchHHHHHHHHHhcCceeEEEecc-Ceee
Q 026405 157 VISVAAGEDVGQKIMLFMQQSKREICILSAS-GSIS 191 (239)
Q Consensus 157 VIrV~pGEDV~~kI~~Faqq~~rAicILSa~-GsVS 191 (239)
++.+.+.+++.+.+..|.+.+-+.++|+... |-+.
T Consensus 52 ~~~v~~~~~l~~a~~~m~~~~~~~lpVvd~~~~~~~ 87 (98)
T cd04618 52 LVSIHPERSLFDAALLLLKNKIHRLPVIDPSTGTGL 87 (98)
T ss_pred eEEeCCCCcHHHHHHHHHHCCCCEeeEEECCCCCce
Confidence 7899999999999999999888999999876 6543
No 16
>KOG4565 consensus E93 protein involved in programmed cell death, putative transcription regulator [Transcription]
Probab=32.92 E-value=14 Score=33.11 Aligned_cols=14 Identities=50% Similarity=0.864 Sum_probs=11.9
Q ss_pred cccccCCCCCCCCC
Q 026405 79 PAKKKRGRPRKYGT 92 (239)
Q Consensus 79 ~~KkKRGRPRKYg~ 92 (239)
.-+|||||=|+|..
T Consensus 111 qpRkKRGrYRqYd~ 124 (206)
T KOG4565|consen 111 QPRKKRGRYRQYDK 124 (206)
T ss_pred CccccccchhhhhH
Confidence 56899999999963
No 17
>PF00571 CBS: CBS domain CBS domain web page. Mutations in the CBS domain of Swiss:P35520 lead to homocystinuria.; InterPro: IPR000644 CBS (cystathionine-beta-synthase) domains are small intracellular modules, mostly found in two or four copies within a protein, that occur in a variety of proteins in bacteria, archaea, and eukaryotes [, ]. Tandem pairs of CBS domains can act as binding domains for adenosine derivatives and may regulate the activity of attached enzymatic or other domains []. In some cases, CBS domains may act as sensors of cellular energy status by being activated by AMP and inhibited by ATP []. In chloride ion channels, the CBS domains have been implicated in intracellular targeting and trafficking, as well as in protein-protein interactions, but results vary with different channels: in the CLC-5 channel, the CBS domain was shown to be required for trafficking [], while in the CLC-1 channel, the CBS domain was shown to be critical for channel function, but not necessary for trafficking []. Recent experiments revealing that CBS domains can bind adenosine-containing ligands such ATP, AMP, or S-adenosylmethionine have led to the hypothesis that CBS domains function as sensors of intracellular metabolites [, ]. Crystallographic studies of CBS domains have shown that pairs of CBS sequences form a globular domain where each CBS unit adopts a beta-alpha-beta-beta-alpha pattern []. Crystal structure of the CBS domains of the AMP-activated protein kinase in complexes with AMP and ATP shows that the phosphate groups of AMP/ATP lie in a surface pocket at the interface of two CBS domains, which is lined with basic residues, many of which are associated with disease-causing mutations []. In humans, mutations in conserved residues within CBS domains cause a variety of human hereditary diseases, including (with the gene mutated in parentheses): homocystinuria (cystathionine beta-synthase); Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase); retinitis pigmentosa (IMP dehydrogenase-1); congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members).; GO: 0005515 protein binding; PDB: 3JTF_A 3TE5_C 3TDH_C 3T4N_C 2QLV_C 3OI8_A 3LV9_A 2QH1_B 1PVM_B 3LQN_A ....
Probab=32.19 E-value=74 Score=20.75 Aligned_cols=38 Identities=13% Similarity=0.387 Sum_probs=30.0
Q ss_pred ceeEEEEEcCCCchHHHHHHHHHhcCceeEEEeccCee
Q 026405 153 FTPHVISVAAGEDVGQKIMLFMQQSKREICILSASGSI 190 (239)
Q Consensus 153 ftpHVIrV~pGEDV~~kI~~Faqq~~rAicILSa~GsV 190 (239)
|++-++.|.+.+.+.+.+..|.+.+-..+.|+...|-+
T Consensus 5 m~~~~~~v~~~~~l~~~~~~~~~~~~~~~~V~d~~~~~ 42 (57)
T PF00571_consen 5 MTPPPITVSPDDSLEEALEIMRKNGISRLPVVDEDGKL 42 (57)
T ss_dssp SBSSSEEEETTSBHHHHHHHHHHHTSSEEEEESTTSBE
T ss_pred CcCCCEEEcCcCcHHHHHHHHHHcCCcEEEEEecCCEE
Confidence 45567889999999999888888887889998655544
No 18
>cd01760 RBD Ubiquitin-like domain of RBD-like S/T kinases. The ras-binding domain (RBD) of the serine/threonine kinase raf is structurally quite similar to the beta-grasp fold of ubiquitin. A raf-like RBD is also present in RGS12 and other members of a family of GTPase activating proteins and TIAM1, a guanine nucleotide exchange protein.
Probab=27.25 E-value=1.1e+02 Score=23.10 Aligned_cols=37 Identities=19% Similarity=0.179 Sum_probs=29.0
Q ss_pred eeEEEEEcCCCchHHHHHHHHHhcC--ceeEEEeccCee
Q 026405 154 TPHVISVAAGEDVGQKIMLFMQQSK--REICILSASGSI 190 (239)
Q Consensus 154 tpHVIrV~pGEDV~~kI~~Faqq~~--rAicILSa~GsV 190 (239)
+..++.|.||+-|.+.|+..|++++ -+.|.|--.|.-
T Consensus 10 ~~t~V~vrpg~ti~d~L~~~c~kr~l~~~~~~v~~~~~~ 48 (72)
T cd01760 10 QRTVVPVRPGMSVRDVLAKACKKRGLNPECCDVFLLGLD 48 (72)
T ss_pred CeEEEEECCCCCHHHHHHHHHHHcCCCHHHEEEEEecCC
Confidence 4568999999999999999999998 455555544443
No 19
>PF14252 DUF4347: Domain of unknown function (DUF4347)
Probab=25.29 E-value=1.2e+02 Score=26.08 Aligned_cols=42 Identities=19% Similarity=0.193 Sum_probs=32.3
Q ss_pred eEEEEEcCCCchHHHHHHHHHhcC--ceeEEEeccCeeeeEEEeC
Q 026405 155 PHVISVAAGEDVGQKIMLFMQQSK--REICILSASGSISNASLRQ 197 (239)
Q Consensus 155 pHVIrV~pGEDV~~kI~~Faqq~~--rAicILSa~GsVSnVTLRq 197 (239)
-+|+.|++++|-++.|.++.++++ .++-|+|= |+=-.+.|..
T Consensus 23 ~~v~~ld~~~d~~~qI~~~L~~~~~i~~lhivsH-G~~G~l~LG~ 66 (165)
T PF14252_consen 23 VEVVILDPSRDGLEQIAQALAGYQNIDALHIVSH-GSPGALQLGN 66 (165)
T ss_pred CEEEEEeCCCchHHHHHHHHhcCCCCceEEEEcC-CCcceEEECC
Confidence 368999999999999999999987 67888774 5444444433
No 20
>PLN03194 putative disease resistance protein; Provisional
Probab=24.64 E-value=78 Score=28.26 Aligned_cols=37 Identities=19% Similarity=0.204 Sum_probs=30.3
Q ss_pred EEcCCCchHHHHHHHHHhcCceeEEEeccCeeeeEEE
Q 026405 159 SVAAGEDVGQKIMLFMQQSKREICILSASGSISNASL 195 (239)
Q Consensus 159 rV~pGEDV~~kI~~Faqq~~rAicILSa~GsVSnVTL 195 (239)
++..|++|...|..-.++-..+|+|||-.=+-|.-+|
T Consensus 63 el~~G~~i~~~L~~AIeeSri~IvVfS~~Ya~S~WCL 99 (187)
T PLN03194 63 NMKPGDKLFDKINSAIRNCKVGVAVFSPRYCESYFCL 99 (187)
T ss_pred cccCCCcHHHHHHHHHHhCeEEEEEECCCcccchhHH
Confidence 4779999999999999999999999998655444433
No 21
>PHA00514 dsDNA binding protein
Probab=24.54 E-value=24 Score=28.47 Aligned_cols=25 Identities=32% Similarity=0.473 Sum_probs=21.9
Q ss_pred EEeeeccccccccccccccccccCCC
Q 026405 214 QGVWETVDGVMSQRRLSTTYDEHGSV 239 (239)
Q Consensus 214 LSLsGTl~~~~~~~~~~~~~~~~~~~ 239 (239)
..|.|+|+-+-+||+|+..| .||.|
T Consensus 34 ~Tl~GNLtiEqAQ~e~~k~~-k~~pv 58 (98)
T PHA00514 34 QTLLGNLTIEQAQKELSKQY-KHGPV 58 (98)
T ss_pred ceeecceeHHHHHHHHhhcc-cCCCe
Confidence 58999999999999999999 66654
No 22
>cd04603 CBS_pair_KefB_assoc This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the KefB (Kef-type K+ transport systems) domain which is involved in inorganic ion transport and metabolism. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide range of different proteins. CBS domains usually come in tandem repeats, which associate to form a so-called Bateman domain or a CBS pair which is reflected in this model. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown.
Probab=22.76 E-value=1.5e+02 Score=21.68 Aligned_cols=37 Identities=14% Similarity=0.218 Sum_probs=29.9
Q ss_pred CceeEEEEEcCCCchHHHHHHHHHhcCceeEEEeccC
Q 026405 152 GFTPHVISVAAGEDVGQKIMLFMQQSKREICILSASG 188 (239)
Q Consensus 152 ~ftpHVIrV~pGEDV~~kI~~Faqq~~rAicILSa~G 188 (239)
-|...++.+.+.+.+.+.+..+.+.+...++|+...|
T Consensus 61 ~~~~~~~~v~~~~~l~~al~~m~~~~~~~lpVvd~~~ 97 (111)
T cd04603 61 VYIVPVPIVYCDSKVTDLLRIFRETEPPVVAVVDKEG 97 (111)
T ss_pred eeecCCcEECCCCcHHHHHHHHHHcCCCeEEEEcCCC
Confidence 3566678899999999998888888778889987644
No 23
>PRK08179 prfH peptide chain release factor-like protein; Reviewed
Probab=21.74 E-value=2.4e+02 Score=25.32 Aligned_cols=43 Identities=5% Similarity=0.197 Sum_probs=35.9
Q ss_pred EEEEcCCC----------chHHHHHHHHHhcCceeEEEecc-----CeeeeEEEeCCC
Q 026405 157 VISVAAGE----------DVGQKIMLFMQQSKREICILSAS-----GSISNASLRQPA 199 (239)
Q Consensus 157 VIrV~pGE----------DV~~kI~~Faqq~~rAicILSa~-----GsVSnVTLRqp~ 199 (239)
+|+|.+|. ||+.-...||++.+..+.||+.. |.+..|+|..-+
T Consensus 3 ~leI~aG~Gg~Ea~~fa~~L~~my~~~a~~~g~~~~ii~~~~~~~~gg~ksa~~~i~G 60 (200)
T PRK08179 3 LLQLSSAQGPAECCLAVAKALERLLKEAARQGVRVTVLETETGRYPDTLRSALVSLDG 60 (200)
T ss_pred EEEEeCCCChHHHHHHHHHHHHHHHHHHHHcCCeEEEEeCCCCCCCCceEEEEEEEEc
Confidence 67888885 78889999999999999999874 678988887754
No 24
>smart00412 Cu_FIST Copper-Fist. binds DNA only in present of copper or silver
Probab=21.38 E-value=41 Score=23.18 Aligned_cols=8 Identities=50% Similarity=1.012 Sum_probs=6.2
Q ss_pred ccccCCCC
Q 026405 80 AKKKRGRP 87 (239)
Q Consensus 80 ~KkKRGRP 87 (239)
.=||||||
T Consensus 31 ~i~kkGRP 38 (39)
T smart00412 31 PVRPRGRP 38 (39)
T ss_pred eecCCCCC
Confidence 45788998
No 25
>PF12736 CABIT: Cell-cycle sustaining, positive selection,
Probab=21.36 E-value=59 Score=28.73 Aligned_cols=62 Identities=11% Similarity=0.057 Sum_probs=40.6
Q ss_pred eEEEEEcCCCchHHHHHHHHHhcCceeEEEeccCeeeeEEEeCCCCCC---------CceeEEeeeeeEEeeecc
Q 026405 155 PHVISVAAGEDVGQKIMLFMQQSKREICILSASGSISNASLRQPATSG---------GNITYELRAGPQGVWETV 220 (239)
Q Consensus 155 pHVIrV~pGEDV~~kI~~Faqq~~rAicILSa~GsVSnVTLRqp~ssg---------~tvtyeGrFEILSLsGTl 220 (239)
|-|++|..|..-...+.++. -..|.|+..-.+..|.++--.... -...|.|.|+++.=.+-|
T Consensus 2 P~vv~V~~g~y~~~~~~~l~----G~~l~l~~~~~~k~i~a~~~~~~~~~~~g~~~~IP~~y~G~F~~~~~~~~f 72 (256)
T PF12736_consen 2 PRVVKVQSGVYFQGSVYELS----GQELCLHTGDQIKKILAQSVESEKGRKVGPHFLIPLNYPGKFKRLPRPGPF 72 (256)
T ss_pred CeEEEEecCCCCCCccccCC----CCEEEEEecCEeeEEEEEEEeccCccccCCEEEECCcccceEEECCCcccc
Confidence 67889999988877776666 345666666666655533322221 246799999998765533
No 26
>TIGR03072 release_prfH putative peptide chain release factor H. Members of this protein family are bacterial proteins homologous to peptide chain release factors 1 (RF-1, product of the prfA gene), and 2 (RF-2, product of the prfB gene). The member from Escherichia coli K-12, designated prfH, appears to be a pseudogene. This class I release factor is always found as the downstream gene of a two-gene operon.
Probab=21.09 E-value=2e+02 Score=25.74 Aligned_cols=43 Identities=7% Similarity=0.166 Sum_probs=35.1
Q ss_pred EEEEcCC----------CchHHHHHHHHHhcCceeEEEecc-----CeeeeEEEeCCC
Q 026405 157 VISVAAG----------EDVGQKIMLFMQQSKREICILSAS-----GSISNASLRQPA 199 (239)
Q Consensus 157 VIrV~pG----------EDV~~kI~~Faqq~~rAicILSa~-----GsVSnVTLRqp~ 199 (239)
+|+|.+| +||+.-...||++.+..+.||... |.+..|+|..-+
T Consensus 2 ~leI~aG~GG~Ea~lfa~~L~~my~~~a~~~g~~~eii~~~~~~~~gg~ksa~~~i~G 59 (200)
T TIGR03072 2 LLQLSSAQGPAECCLAVAKALERLTREAAARGVRVEVLEQEPGEVPGTLRSALVSLDG 59 (200)
T ss_pred EEEEECCCCcHHHHHHHHHHHHHHHHHHHHcCCeEEEEeCCCCCCCCceEEEEEEEEc
Confidence 5777777 479999999999999999999874 678888887754
Done!