Query 025938
Match_columns 246
No_of_seqs 194 out of 355
Neff 3.9
Searched_HMMs 46136
Date Fri Mar 29 11:15:12 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025938.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025938hhsearch_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 99.6 6.1E-15 1.3E-19 118.4 7.0 80 156-235 1-98 (120)
2 COG1661 Predicted DNA-binding 99.0 1.9E-09 4.2E-14 91.0 9.7 82 155-236 8-106 (141)
3 PF02178 AT_hook: AT hook moti 96.5 0.00093 2E-08 36.1 0.6 12 88-99 1-12 (13)
4 smart00384 AT_hook DNA binding 96.4 0.0016 3.4E-08 41.2 1.4 15 88-102 1-15 (26)
5 PF14621 RFX5_DNA_bdg: RFX5 DN 85.3 0.3 6.5E-06 43.9 0.4 12 86-97 66-77 (219)
6 PF13546 DDE_5: DDE superfamil 82.3 0.81 1.7E-05 40.6 1.8 17 84-100 227-243 (273)
7 COG1710 Uncharacterized protei 74.8 1.3 2.9E-05 37.6 0.8 16 85-100 81-97 (139)
8 COG1777 Predicted transcriptio 52.5 6 0.00013 36.2 0.7 24 87-110 63-89 (217)
9 cd04618 CBS_pair_5 The CBS dom 47.1 57 0.0012 24.2 5.2 36 160-195 52-88 (98)
10 PF00571 CBS: CBS domain CBS d 37.7 64 0.0014 21.2 3.8 39 156-194 5-43 (57)
11 PF13737 DDE_Tnp_1_5: Transpos 32.0 25 0.00054 28.9 1.2 19 85-104 21-39 (112)
12 KOG4565 E93 protein involved i 28.9 19 0.0004 32.5 0.0 14 86-99 111-124 (206)
13 PF01582 TIR: TIR domain; Int 27.9 47 0.001 26.5 2.1 28 163-190 38-65 (141)
14 cd04595 CBS_pair_DHH_polyA_Pol 26.4 1.5E+02 0.0034 21.3 4.6 39 155-194 61-99 (110)
15 cd04603 CBS_pair_KefB_assoc Th 25.6 1.5E+02 0.0033 21.7 4.5 39 154-192 60-98 (111)
16 PRK08179 prfH peptide chain re 25.1 1.7E+02 0.0038 26.3 5.4 43 160-202 3-60 (200)
17 PF15333 TAF1D: TATA box-bindi 24.7 30 0.00066 31.7 0.6 13 90-102 64-76 (217)
18 cd04802 CBS_pair_3 The CBS dom 22.3 1.2E+02 0.0027 21.8 3.4 35 155-189 63-97 (112)
19 cd04590 CBS_pair_CorC_HlyC_ass 22.1 1.8E+02 0.0039 20.9 4.2 35 159-193 65-99 (111)
20 cd04624 CBS_pair_11 The CBS do 21.9 2E+02 0.0042 20.7 4.4 39 155-193 62-100 (112)
21 cd04610 CBS_pair_ParBc_assoc T 21.3 2.1E+02 0.0046 20.3 4.4 38 156-193 58-95 (107)
22 cd04585 CBS_pair_ACT_assoc2 Th 21.3 1.8E+02 0.0038 21.0 4.0 39 155-193 72-110 (122)
23 cd04615 CBS_pair_2 The CBS dom 20.9 2.3E+02 0.0049 20.4 4.5 38 155-192 63-100 (113)
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=99.56 E-value=6.1e-15 Score=118.42 Aligned_cols=80 Identities=21% Similarity=0.216 Sum_probs=66.9
Q ss_pred ceeEEEEecCCccHHHHHHHHHhhCCceEEEEeccceeeeeEEeCCCC--CCCceEEE--EEEEeeeeeeeec-------
Q 025938 156 FAPHVISIGVGEDIVAKMLSFSQQRPRVVCILSGRGTVSSVTLRQPAT--SVPTVTYE--VEALCLYLFLFWK------- 224 (246)
Q Consensus 156 f~pHvI~V~~GeDV~~kI~~Faqq~~rAicILSa~GsVSnVTLRqp~s--sg~tvtye--FEILSLSGS~l~~------- 224 (246)
||+|+++|.+||||.++|++||++.++..|+++++|+|++|+||+.+. ...+.+++ |||+||+|++.+.
T Consensus 1 ~r~~~~rl~~Gedl~~~l~~~~~~~~i~~~~is~iGsl~~~~l~~~~~~~~~~~~~~~g~~Ei~sl~G~i~~~~g~~~~H 80 (120)
T PF03479_consen 1 GRVFVIRLDPGEDLLESLEAFAREHGIRSGVISGIGSLSNVTLGYYDPPSYYEPLEFEGPFEIISLSGTISPEDGKPFVH 80 (120)
T ss_dssp EEEEEEEEETTSBHHHHHHHHHHHHT-SSEEEEEEEEEEEEEEEEEETTTEEEEEEEESEEEEEEEEEEEEEETTEEEEE
T ss_pred CcEEEEEECCCCHHHHHHHHHHHHCCCcEEEEEEEeEEeEEEEEEecccCCcceEEecccEEEEEeEEEEECCCCCCcce
Confidence 789999999999999999999999998777779999999999999743 33356677 9999999999982
Q ss_pred -------CCCCceeeeee
Q 025938 225 -------KKIHQKNFHFC 235 (246)
Q Consensus 225 -------~~~g~~~gh~~ 235 (246)
.++...+|||.
T Consensus 81 lHisl~~~~g~v~gGHl~ 98 (120)
T PF03479_consen 81 LHISLADPDGQVFGGHLL 98 (120)
T ss_dssp EEEEEE-TTSEEEEEEEE
T ss_pred EEEEEECCCCeEEeeEeC
Confidence 33456677776
No 2
>COG1661 Predicted DNA-binding protein with PD1-like DNA-binding motif [General function prediction only]
Probab=99.02 E-value=1.9e-09 Score=90.96 Aligned_cols=82 Identities=15% Similarity=0.176 Sum_probs=68.6
Q ss_pred CceeEEEEecCCccHHHHHHHHHhhCCceEEEEeccceeeeeEEeCCCCCCCc---eEEE--EEEEeeeeeeeecC----
Q 025938 155 AFAPHVISIGVGEDIVAKMLSFSQQRPRVVCILSGRGTVSSVTLRQPATSVPT---VTYE--VEALCLYLFLFWKK---- 225 (246)
Q Consensus 155 ~f~pHvI~V~~GeDV~~kI~~Faqq~~rAicILSa~GsVSnVTLRqp~ssg~t---vtye--FEILSLSGS~l~~~---- 225 (246)
.-+-+++++.+|||+.+.|.+||++......|.+|.|++++++||..+..... +.+. ||||||.|++..++
T Consensus 8 ~gr~~~~Rld~G~d~~~~l~~~a~~~~i~aa~v~~iGal~~~~l~~~~~~~~~y~~~~~~e~~EvlSL~G~i~~~~p~~H 87 (141)
T COG1661 8 SGRVIALRLDPGEDLFSELEAFAEQEDIHAAVVTAIGALRDAKLRYFDPEEKEYETIPVNEPLEVLSLLGNIALDDPFVH 87 (141)
T ss_pred cceEEEEEeCCCccHHHHHHHHHHhcCceEEEEEEeeeeeeeEEEEecCCCCceEEEecCCcEEEEEecceeecCCCcEE
Confidence 45778999999999999999999999986699999999999999999855443 3333 99999999998875
Q ss_pred --------CCCceeeeeee
Q 025938 226 --------KIHQKNFHFCT 236 (246)
Q Consensus 226 --------~~g~~~gh~~~ 236 (246)
++...+|||..
T Consensus 88 lHa~l~~~~G~~~GGHL~~ 106 (141)
T COG1661 88 LHAALGDENGITLGGHLLE 106 (141)
T ss_pred EEEEEecCCCcEEeeeecc
Confidence 45666777753
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=96.50 E-value=0.00093 Score=36.08 Aligned_cols=12 Identities=75% Similarity=1.138 Sum_probs=4.4
Q ss_pred cCCCCCCCCCCC
Q 025938 88 KKKRGRPRKYAP 99 (246)
Q Consensus 88 KkKRGRPRKY~p 99 (246)
+||||||+|+..
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 689999999864
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=96.45 E-value=0.0016 Score=41.24 Aligned_cols=15 Identities=60% Similarity=0.933 Sum_probs=13.1
Q ss_pred cCCCCCCCCCCCCCc
Q 025938 88 KKKRGRPRKYAPDGQ 102 (246)
Q Consensus 88 KkKRGRPRKY~pdg~ 102 (246)
|||||||||+..+..
T Consensus 1 kRkRGRPrK~~~~~~ 15 (26)
T smart00384 1 KRKRGRPRKAPKDXX 15 (26)
T ss_pred CCCCCCCCCCCCccc
Confidence 699999999988764
No 5
>PF14621 RFX5_DNA_bdg: RFX5 DNA-binding domain
Probab=85.28 E-value=0.3 Score=43.87 Aligned_cols=12 Identities=67% Similarity=1.052 Sum_probs=10.4
Q ss_pred cCcCCCCCCCCC
Q 025938 86 PVKKKRGRPRKY 97 (246)
Q Consensus 86 ~~KkKRGRPRKY 97 (246)
-.|||||||||-
T Consensus 66 dAKRKRGRPRKK 77 (219)
T PF14621_consen 66 DAKRKRGRPRKK 77 (219)
T ss_pred hhhhhcCCCccC
Confidence 489999999964
No 6
>PF13546 DDE_5: DDE superfamily endonuclease
Probab=82.33 E-value=0.81 Score=40.62 Aligned_cols=17 Identities=53% Similarity=0.903 Sum_probs=12.6
Q ss_pred CCcCcCCCCCCCCCCCC
Q 025938 84 SDPVKKKRGRPRKYAPD 100 (246)
Q Consensus 84 ~~~~KkKRGRPRKY~pd 100 (246)
..+..+|||||||||.-
T Consensus 227 ~~~~~~~rGRPr~~g~~ 243 (273)
T PF13546_consen 227 PPPPPPKRGRPRKYGRR 243 (273)
T ss_pred ccccCCCCCCCCCCCCc
Confidence 34455569999999965
No 7
>COG1710 Uncharacterized protein conserved in archaea [Function unknown]
Probab=74.76 E-value=1.3 Score=37.56 Aligned_cols=16 Identities=69% Similarity=1.099 Sum_probs=13.2
Q ss_pred CcCc-CCCCCCCCCCCC
Q 025938 85 DPVK-KKRGRPRKYAPD 100 (246)
Q Consensus 85 ~~~K-kKRGRPRKY~pd 100 (246)
-|+| |-|||||||.-.
T Consensus 81 IPvk~KgrGrprkyd~~ 97 (139)
T COG1710 81 IPVKLKGRGRPRKYDRN 97 (139)
T ss_pred eeeeecCCCCCcccchh
Confidence 4778 889999999764
No 8
>COG1777 Predicted transcriptional regulators [Transcription]
Probab=52.49 E-value=6 Score=36.19 Aligned_cols=24 Identities=46% Similarity=0.647 Sum_probs=15.6
Q ss_pred CcCCCCCCCCCCC-CCccc--cccCCC
Q 025938 87 VKKKRGRPRKYAP-DGQVS--LGLSPL 110 (246)
Q Consensus 87 ~KkKRGRPRKY~p-dg~~~--l~l~p~ 110 (246)
.|.+|||||||-- .++++ +-++|.
T Consensus 63 e~~~Rg~~rKYY~Is~~~rleV~lsp~ 89 (217)
T COG1777 63 EKIPRGRPRKYYMISRNLRLEVTLSPN 89 (217)
T ss_pred cccccCCCcceeeccCCeEEEEEecCc
Confidence 5777799999964 44544 345553
No 9
>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=47.12 E-value=57 Score=24.16 Aligned_cols=36 Identities=14% Similarity=0.162 Sum_probs=31.7
Q ss_pred EEEecCCccHHHHHHHHHhhCCceEEEEecc-ceeee
Q 025938 160 VISIGVGEDIVAKMLSFSQQRPRVVCILSGR-GTVSS 195 (246)
Q Consensus 160 vI~V~~GeDV~~kI~~Faqq~~rAicILSa~-GsVSn 195 (246)
++.+.+.+++.+.+..|.+.+.+.++|+... |.+..
T Consensus 52 ~~~v~~~~~l~~a~~~m~~~~~~~lpVvd~~~~~~~g 88 (98)
T cd04618 52 LVSIHPERSLFDAALLLLKNKIHRLPVIDPSTGTGLY 88 (98)
T ss_pred eEEeCCCCcHHHHHHHHHHCCCCEeeEEECCCCCceE
Confidence 7899999999999999999999999999887 76543
No 10
>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=37.70 E-value=64 Score=21.18 Aligned_cols=39 Identities=8% Similarity=0.210 Sum_probs=32.8
Q ss_pred ceeEEEEecCCccHHHHHHHHHhhCCceEEEEeccceee
Q 025938 156 FAPHVISIGVGEDIVAKMLSFSQQRPRVVCILSGRGTVS 194 (246)
Q Consensus 156 f~pHvI~V~~GeDV~~kI~~Faqq~~rAicILSa~GsVS 194 (246)
|++-++.|.+.+.+.+.+..|.+.+-+.+.|+...|.+-
T Consensus 5 m~~~~~~v~~~~~l~~~~~~~~~~~~~~~~V~d~~~~~~ 43 (57)
T PF00571_consen 5 MTPPPITVSPDDSLEEALEIMRKNGISRLPVVDEDGKLV 43 (57)
T ss_dssp SBSSSEEEETTSBHHHHHHHHHHHTSSEEEEESTTSBEE
T ss_pred CcCCCEEEcCcCcHHHHHHHHHHcCCcEEEEEecCCEEE
Confidence 566688899999999999999999989999997666554
No 11
>PF13737 DDE_Tnp_1_5: Transposase DDE domain
Probab=32.03 E-value=25 Score=28.88 Aligned_cols=19 Identities=42% Similarity=0.915 Sum_probs=14.3
Q ss_pred CcCcCCCCCCCCCCCCCccc
Q 025938 85 DPVKKKRGRPRKYAPDGQVS 104 (246)
Q Consensus 85 ~~~KkKRGRPRKY~pdg~~~ 104 (246)
++...|||||++| +|-.|.
T Consensus 21 ~~~~~kRGr~~~y-SD~aI~ 39 (112)
T PF13737_consen 21 APPRGKRGRPPRY-SDAAIQ 39 (112)
T ss_pred cCCCCCCCCCccc-chHHHH
Confidence 4566899999999 565544
No 12
>KOG4565 consensus E93 protein involved in programmed cell death, putative transcription regulator [Transcription]
Probab=28.89 E-value=19 Score=32.50 Aligned_cols=14 Identities=50% Similarity=0.788 Sum_probs=12.3
Q ss_pred cCcCCCCCCCCCCC
Q 025938 86 PVKKKRGRPRKYAP 99 (246)
Q Consensus 86 ~~KkKRGRPRKY~p 99 (246)
.-+|||||=|+|..
T Consensus 111 qpRkKRGrYRqYd~ 124 (206)
T KOG4565|consen 111 QPRKKRGRYRQYDK 124 (206)
T ss_pred CccccccchhhhhH
Confidence 57899999999975
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=27.88 E-value=47 Score=26.53 Aligned_cols=28 Identities=21% Similarity=0.326 Sum_probs=25.3
Q ss_pred ecCCccHHHHHHHHHhhCCceEEEEecc
Q 025938 163 IGVGEDIVAKMLSFSQQRPRVVCILSGR 190 (246)
Q Consensus 163 V~~GeDV~~kI~~Faqq~~rAicILSa~ 190 (246)
+.+|+.+.+.|....++..+.|+|||.+
T Consensus 38 ~~~G~~~~~~i~~~i~~Sr~~I~VlS~~ 65 (141)
T PF01582_consen 38 FLPGESILDNIQEAIERSRRTIVVLSRN 65 (141)
T ss_dssp TSSSSCHHHHHHHHHHTEEEEEEEESHH
T ss_pred hcccccccchhhHhhhhceeeEEEeecc
Confidence 6799999999999999988999999954
No 14
>cd04595 CBS_pair_DHH_polyA_Pol_assoc This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with an upstream DHH domain which performs a phosphoesterase function and a downstream polyA polymerase domain. 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=26.41 E-value=1.5e+02 Score=21.25 Aligned_cols=39 Identities=8% Similarity=0.106 Sum_probs=31.3
Q ss_pred CceeEEEEecCCccHHHHHHHHHhhCCceEEEEeccceee
Q 025938 155 AFAPHVISIGVGEDIVAKMLSFSQQRPRVVCILSGRGTVS 194 (246)
Q Consensus 155 ~f~pHvI~V~~GeDV~~kI~~Faqq~~rAicILSa~GsVS 194 (246)
.|+.+++.|...+.+.+.+..|.+.....++|+. .|.+.
T Consensus 61 ~~~~~~~~v~~~~~l~~~~~~~~~~~~~~~~V~~-~~~~~ 99 (110)
T cd04595 61 YMSTDVVTVPPDTPLSEVQELMVEHDIGRVPVVE-DGRLV 99 (110)
T ss_pred HhcCCCEEECCCCcHHHHHHHHHHcCCCeeEEEe-CCEEE
Confidence 4566788999999999999889888777888887 55543
No 15
>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=25.62 E-value=1.5e+02 Score=21.68 Aligned_cols=39 Identities=15% Similarity=0.271 Sum_probs=32.2
Q ss_pred CCceeEEEEecCCccHHHHHHHHHhhCCceEEEEeccce
Q 025938 154 IAFAPHVISIGVGEDIVAKMLSFSQQRPRVVCILSGRGT 192 (246)
Q Consensus 154 ~~f~pHvI~V~~GeDV~~kI~~Faqq~~rAicILSa~Gs 192 (246)
..|...+..+.+.+++.+.+..+.+++...++|+...|.
T Consensus 60 ~~~~~~~~~v~~~~~l~~al~~m~~~~~~~lpVvd~~~~ 98 (111)
T cd04603 60 EVYIVPVPIVYCDSKVTDLLRIFRETEPPVVAVVDKEGK 98 (111)
T ss_pred heeecCCcEECCCCcHHHHHHHHHHcCCCeEEEEcCCCe
Confidence 346666788999999999999999988888999987554
No 16
>PRK08179 prfH peptide chain release factor-like protein; Reviewed
Probab=25.13 E-value=1.7e+02 Score=26.28 Aligned_cols=43 Identities=12% Similarity=0.228 Sum_probs=35.5
Q ss_pred EEEecCCc----------cHHHHHHHHHhhCCceEEEEecc-----ceeeeeEEeCCC
Q 025938 160 VISIGVGE----------DIVAKMLSFSQQRPRVVCILSGR-----GTVSSVTLRQPA 202 (246)
Q Consensus 160 vI~V~~Ge----------DV~~kI~~Faqq~~rAicILSa~-----GsVSnVTLRqp~ 202 (246)
+|+|.+|. ||..-...||++....+.|++.+ |.+..|+|.--+
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 78888885 78888889999999999999874 678888887654
No 17
>PF15333 TAF1D: TATA box-binding protein-associated factor 1D
Probab=24.69 E-value=30 Score=31.69 Aligned_cols=13 Identities=46% Similarity=0.974 Sum_probs=9.9
Q ss_pred CCCCCCCCCCCCc
Q 025938 90 KRGRPRKYAPDGQ 102 (246)
Q Consensus 90 KRGRPRKY~pdg~ 102 (246)
|+-+.|||-+-|.
T Consensus 64 KkrkkrKYk~tgr 76 (217)
T PF15333_consen 64 KKRKKRKYKPTGR 76 (217)
T ss_pred HHhhhhccCccCC
Confidence 5566799999775
No 18
>cd04802 CBS_pair_3 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=22.26 E-value=1.2e+02 Score=21.79 Aligned_cols=35 Identities=6% Similarity=0.138 Sum_probs=28.7
Q ss_pred CceeEEEEecCCccHHHHHHHHHhhCCceEEEEec
Q 025938 155 AFAPHVISIGVGEDIVAKMLSFSQQRPRVVCILSG 189 (246)
Q Consensus 155 ~f~pHvI~V~~GeDV~~kI~~Faqq~~rAicILSa 189 (246)
.++.+++.+.+++.+.+.+..|.+.....++|+..
T Consensus 63 ~~~~~~~~v~~~~~l~~~~~~~~~~~~~~~~Vv~~ 97 (112)
T cd04802 63 VMSTPLITIDPNASLNEAAKLMAKHGIKRLPVVDD 97 (112)
T ss_pred hcCCCcEEECCCCCHHHHHHHHHHcCCCeeEEeeC
Confidence 35678899999999998888888888777888864
No 19
>cd04590 CBS_pair_CorC_HlyC_assoc This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the CorC_HlyC domain. CorC_HlyC is a transporter associated domain. This small domain is found in Na+/H+ antiporters, in proteins involved in magnesium and cobalt efflux, and in association with some proteins of unknown function. The function of the CorC_HlyC domain is uncertain but it might be involved in modulating transport of ion substrates. 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,
Probab=22.08 E-value=1.8e+02 Score=20.86 Aligned_cols=35 Identities=6% Similarity=0.128 Sum_probs=28.9
Q ss_pred EEEEecCCccHHHHHHHHHhhCCceEEEEecccee
Q 025938 159 HVISIGVGEDIVAKMLSFSQQRPRVVCILSGRGTV 193 (246)
Q Consensus 159 HvI~V~~GeDV~~kI~~Faqq~~rAicILSa~GsV 193 (246)
++..+...+++.+.+..|.+.+...++|+...|.+
T Consensus 65 ~~~~v~~~~~l~~~~~~~~~~~~~~~~Vv~~~~~~ 99 (111)
T cd04590 65 PPLFVPESTPLDDLLEEMRKERSHMAIVVDEYGGT 99 (111)
T ss_pred CCeecCCCCcHHHHHHHHHhcCCcEEEEEECCCCE
Confidence 46788999999888888888888899999886654
No 20
>cd04624 CBS_pair_11 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 gener
Probab=21.95 E-value=2e+02 Score=20.71 Aligned_cols=39 Identities=8% Similarity=0.187 Sum_probs=29.7
Q ss_pred CceeEEEEecCCccHHHHHHHHHhhCCceEEEEecccee
Q 025938 155 AFAPHVISIGVGEDIVAKMLSFSQQRPRVVCILSGRGTV 193 (246)
Q Consensus 155 ~f~pHvI~V~~GeDV~~kI~~Faqq~~rAicILSa~GsV 193 (246)
.|+..++.+...+++.+.+..|.++....+.|+...|.+
T Consensus 62 ~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~Vv~~~g~~ 100 (112)
T cd04624 62 IMTRDLVTVDPDEPVAEAAKLMRKNNIRHHLVVDKGGEL 100 (112)
T ss_pred hccCCCEEECCCCcHHHHHHHHHHcCccEEEEEcCCCcE
Confidence 355678889999999887777766665678888876654
No 21
>cd04610 CBS_pair_ParBc_assoc This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with a ParBc (ParB-like nuclease) domain downstream. 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=21.34 E-value=2.1e+02 Score=20.27 Aligned_cols=38 Identities=5% Similarity=0.042 Sum_probs=29.7
Q ss_pred ceeEEEEecCCccHHHHHHHHHhhCCceEEEEecccee
Q 025938 156 FAPHVISIGVGEDIVAKMLSFSQQRPRVVCILSGRGTV 193 (246)
Q Consensus 156 f~pHvI~V~~GeDV~~kI~~Faqq~~rAicILSa~GsV 193 (246)
+...++.+.+.+.+.+.+..|.+.....++|+...|.+
T Consensus 58 ~~~~~~~v~~~~~l~~~~~~~~~~~~~~~~Vv~~~g~~ 95 (107)
T cd04610 58 MSKDLVVAVPEMDIMDAARVMFRTGISKLPVVDENNNL 95 (107)
T ss_pred CCCCCeEECCCCCHHHHHHHHHHhCCCeEeEECCCCeE
Confidence 55667889999999988888877776788898876643
No 22
>cd04585 CBS_pair_ACT_assoc2 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in the acetoin utilization proteins in bacteria. Acetoin is a product of fermentative metabolism in many prokaryotic and eukaryotic microorganisms. They produce acetoin as an external carbon storage compound and then later reuse it as a carbon and energy source during their stationary phase and sporulation. In addition these CBS domains are associated with a downstream ACT domain, which is linked to a wide range of metabolic enzymes that are regulated by amino acid concentration. Pairs of ACT domains bind specifically to a particular amino acid leading to regulation of the linked enzyme. 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 i
Probab=21.32 E-value=1.8e+02 Score=21.00 Aligned_cols=39 Identities=5% Similarity=0.133 Sum_probs=30.9
Q ss_pred CceeEEEEecCCccHHHHHHHHHhhCCceEEEEecccee
Q 025938 155 AFAPHVISIGVGEDIVAKMLSFSQQRPRVVCILSGRGTV 193 (246)
Q Consensus 155 ~f~pHvI~V~~GeDV~~kI~~Faqq~~rAicILSa~GsV 193 (246)
.|+..++.+.+.+.+.+.+..|.+.+...+.|+...|.+
T Consensus 72 ~~~~~~~~v~~~~~l~~~~~~~~~~~~~~~~Vv~~~~~~ 110 (122)
T cd04585 72 IMTRDPITVSPDASVEEAAELMLERKISGLPVVDDQGRL 110 (122)
T ss_pred hccCCCeEeCCCCcHHHHHHHHHHcCCCceeEECCCCcE
Confidence 355567889999999988888888888888888875543
No 23
>cd04615 CBS_pair_2 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=20.86 E-value=2.3e+02 Score=20.39 Aligned_cols=38 Identities=18% Similarity=0.288 Sum_probs=29.6
Q ss_pred CceeEEEEecCCccHHHHHHHHHhhCCceEEEEeccce
Q 025938 155 AFAPHVISIGVGEDIVAKMLSFSQQRPRVVCILSGRGT 192 (246)
Q Consensus 155 ~f~pHvI~V~~GeDV~~kI~~Faqq~~rAicILSa~Gs 192 (246)
.|+.+++.+...+.+.+.+..|.+.....++|+...|-
T Consensus 63 ~~~~~~~~v~~~~~l~~~~~~~~~~~~~~~~Vvd~~g~ 100 (113)
T cd04615 63 VMNSPVITIDANDSIAKARWLMSNNNISRLPVLDDKGK 100 (113)
T ss_pred hccCCceEECCCCcHHHHHHHHHHcCCCeeeEECCCCe
Confidence 45678899999999988887887776677888876654
Done!