Query 027891
Match_columns 217
No_of_seqs 181 out of 313
Neff 4.0
Searched_HMMs 46136
Date Fri Mar 29 03:02:00 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027891.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027891hhsearch_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 99.4 6.4E-13 1.4E-17 104.9 4.7 63 154-216 1-65 (120)
2 COG1661 Predicted DNA-binding 98.4 8.8E-07 1.9E-11 73.7 7.0 65 152-216 7-74 (141)
3 PF02178 AT_hook: AT hook moti 96.3 0.0014 3.1E-08 34.7 0.5 12 89-100 1-12 (13)
4 smart00384 AT_hook DNA binding 96.3 0.0022 4.8E-08 39.8 1.4 15 89-103 1-15 (26)
5 PF14621 RFX5_DNA_bdg: RFX5 DN 83.9 0.38 8.3E-06 42.5 0.4 12 87-98 66-77 (219)
6 PF14869 DUF4488: Domain of un 80.1 2.8 6E-05 35.1 4.1 35 180-216 27-61 (133)
7 PF13546 DDE_5: DDE superfamil 79.1 1.2 2.5E-05 38.8 1.7 16 86-101 228-243 (273)
8 COG1710 Uncharacterized protei 72.9 1.6 3.6E-05 36.4 0.9 16 86-101 81-97 (139)
9 COG1777 Predicted transcriptio 50.3 6.8 0.00015 35.2 0.7 24 87-110 62-88 (217)
10 cd04618 CBS_pair_5 The CBS dom 48.5 53 0.0011 23.8 5.1 36 158-193 52-88 (98)
11 PF00571 CBS: CBS domain CBS d 37.2 73 0.0016 20.5 4.0 39 154-192 5-43 (57)
12 PF01582 TIR: TIR domain; Int 32.6 34 0.00075 26.8 2.1 28 161-188 38-65 (141)
13 cd04603 CBS_pair_KefB_assoc Th 30.3 94 0.002 22.4 4.0 39 152-190 60-98 (111)
14 PF15333 TAF1D: TATA box-bindi 28.6 24 0.00053 31.7 0.7 13 91-103 64-76 (217)
15 PRK08179 prfH peptide chain re 28.3 1.4E+02 0.0031 26.3 5.4 44 157-200 2-60 (200)
16 PF13737 DDE_Tnp_1_5: Transpos 28.3 30 0.00066 27.8 1.1 19 86-105 21-39 (112)
17 cd04595 CBS_pair_DHH_polyA_Pol 25.6 1.6E+02 0.0035 20.7 4.4 37 154-191 62-98 (110)
18 KOG4565 E93 protein involved i 24.7 25 0.00053 31.2 -0.0 15 87-101 111-125 (206)
19 cd04585 CBS_pair_ACT_assoc2 Th 23.8 1.7E+02 0.0036 20.7 4.2 38 154-191 73-110 (122)
20 TIGR03072 release_prfH putativ 21.6 2.2E+02 0.0048 25.1 5.3 43 158-200 2-59 (200)
21 cd04615 CBS_pair_2 The CBS dom 21.0 2.4E+02 0.0053 19.8 4.6 38 153-190 63-100 (113)
22 cd04610 CBS_pair_ParBc_assoc T 20.9 2.3E+02 0.005 19.6 4.5 38 154-191 58-95 (107)
23 cd04590 CBS_pair_CorC_HlyC_ass 20.8 2E+02 0.0044 20.2 4.2 35 157-191 65-99 (111)
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=99.36 E-value=6.4e-13 Score=104.88 Aligned_cols=63 Identities=27% Similarity=0.283 Sum_probs=56.7
Q ss_pred ceeEEEEecCCccHHHHHHHHhhcCCceEEEecccCeeeeEEeeCCC--CCCCceeEeeeeeeec
Q 027891 154 FTPHVITVAVGEDIAMKLLSFSQQGPRAICVLSANGAISTATLRQPS--SSGGSVTYECPFLEVY 216 (217)
Q Consensus 154 f~pHVI~V~~GEDV~~kI~~Faqq~~raiCILSasGsVSnVTLRqp~--ssg~tvtyeGrFEILS 216 (217)
||+|+|++.+||||.++|.+||++.....|++++.|+|++|+|+++. ....+.+|+|+|||||
T Consensus 1 ~r~~~~rl~~Gedl~~~l~~~~~~~~i~~~~is~iGsl~~~~l~~~~~~~~~~~~~~~g~~Ei~s 65 (120)
T PF03479_consen 1 GRVFVIRLDPGEDLLESLEAFAREHGIRSGVISGIGSLSNVTLGYYDPPSYYEPLEFEGPFEIIS 65 (120)
T ss_dssp EEEEEEEEETTSBHHHHHHHHHHHHT-SSEEEEEEEEEEEEEEEEEETTTEEEEEEEESEEEEEE
T ss_pred CcEEEEEECCCCHHHHHHHHHHHHCCCcEEEEEEEeEEeEEEEEEecccCCcceEEecccEEEEE
Confidence 68999999999999999999999999878888999999999999973 3346789999999997
No 2
>COG1661 Predicted DNA-binding protein with PD1-like DNA-binding motif [General function prediction only]
Probab=98.39 E-value=8.8e-07 Score=73.66 Aligned_cols=65 Identities=22% Similarity=0.223 Sum_probs=57.2
Q ss_pred CCceeEEEEecCCccHHHHHHHHhhcCCceEEEecccCeeeeEEeeCCCCC---CCceeEeeeeeeec
Q 027891 152 MGFTPHVITVAVGEDIAMKLLSFSQQGPRAICVLSANGAISTATLRQPSSS---GGSVTYECPFLEVY 216 (217)
Q Consensus 152 ~~f~pHVI~V~~GEDV~~kI~~Faqq~~raiCILSasGsVSnVTLRqp~ss---g~tvtyeGrFEILS 216 (217)
..-+-+++++.+|||+.+.|.+||++..-..+|.+|.|++++++|+.-+.. -.++++.++|||||
T Consensus 7 ~~gr~~~~Rld~G~d~~~~l~~~a~~~~i~aa~v~~iGal~~~~l~~~~~~~~~y~~~~~~e~~EvlS 74 (141)
T COG1661 7 SSGRVIALRLDPGEDLFSELEAFAEQEDIHAAVVTAIGALRDAKLRYFDPEEKEYETIPVNEPLEVLS 74 (141)
T ss_pred ccceEEEEEeCCCccHHHHHHHHHHhcCceEEEEEEeeeeeeeEEEEecCCCCceEEEecCCcEEEEE
Confidence 345778999999999999999999999966699999999999999998732 34789999999998
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=96.29 E-value=0.0014 Score=34.71 Aligned_cols=12 Identities=75% Similarity=1.140 Sum_probs=4.3
Q ss_pred ccCCCCCCCCCC
Q 027891 89 KRKRGRPRKYGP 100 (217)
Q Consensus 89 KkKRGRPRKY~~ 100 (217)
+|+||||+|+..
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 589999999764
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=96.28 E-value=0.0022 Score=39.82 Aligned_cols=15 Identities=67% Similarity=0.948 Sum_probs=13.0
Q ss_pred ccCCCCCCCCCCCCC
Q 027891 89 KRKRGRPRKYGPDGS 103 (217)
Q Consensus 89 KkKRGRPRKY~~dg~ 103 (217)
|||||||||+..+..
T Consensus 1 kRkRGRPrK~~~~~~ 15 (26)
T smart00384 1 KRKRGRPRKAPKDXX 15 (26)
T ss_pred CCCCCCCCCCCCccc
Confidence 699999999998764
No 5
>PF14621 RFX5_DNA_bdg: RFX5 DNA-binding domain
Probab=83.90 E-value=0.38 Score=42.45 Aligned_cols=12 Identities=75% Similarity=1.107 Sum_probs=10.3
Q ss_pred ccccCCCCCCCC
Q 027891 87 PVKRKRGRPRKY 98 (217)
Q Consensus 87 ~~KkKRGRPRKY 98 (217)
-.|||||||||-
T Consensus 66 dAKRKRGRPRKK 77 (219)
T PF14621_consen 66 DAKRKRGRPRKK 77 (219)
T ss_pred hhhhhcCCCccC
Confidence 489999999964
No 6
>PF14869 DUF4488: Domain of unknown function (DUF4488)
Probab=80.06 E-value=2.8 Score=35.06 Aligned_cols=35 Identities=20% Similarity=0.250 Sum_probs=29.5
Q ss_pred ceEEEecccCeeeeEEeeCCCCCCCceeEeeeeeeec
Q 027891 180 RAICVLSANGAISTATLRQPSSSGGSVTYECPFLEVY 216 (217)
Q Consensus 180 raiCILSasGsVSnVTLRqp~ssg~tvtyeGrFEILS 216 (217)
...=|||.-|+..|+++.. .+ +.++|+.|-||+.|
T Consensus 27 ~~lKilS~Dgtf~Ni~~~~-~~-~aiIt~~GtY~~~s 61 (133)
T PF14869_consen 27 NVLKILSDDGTFVNITMIP-KS-GAIITGYGTYEQPS 61 (133)
T ss_pred ccEEEEcCCCcEEEEEEeC-CC-CcEEEEeEEEEEcC
Confidence 3577999999999999944 33 58999999999986
No 7
>PF13546 DDE_5: DDE superfamily endonuclease
Probab=79.13 E-value=1.2 Score=38.85 Aligned_cols=16 Identities=63% Similarity=1.076 Sum_probs=12.2
Q ss_pred cccccCCCCCCCCCCC
Q 027891 86 EPVKRKRGRPRKYGPD 101 (217)
Q Consensus 86 ~~~KkKRGRPRKY~~d 101 (217)
.+..+|||||||||.-
T Consensus 228 ~~~~~~rGRPr~~g~~ 243 (273)
T PF13546_consen 228 PPPPPKRGRPRKYGRR 243 (273)
T ss_pred cccCCCCCCCCCCCCc
Confidence 3455569999999965
No 8
>COG1710 Uncharacterized protein conserved in archaea [Function unknown]
Probab=72.86 E-value=1.6 Score=36.35 Aligned_cols=16 Identities=63% Similarity=1.120 Sum_probs=13.4
Q ss_pred cccc-cCCCCCCCCCCC
Q 027891 86 EPVK-RKRGRPRKYGPD 101 (217)
Q Consensus 86 ~~~K-kKRGRPRKY~~d 101 (217)
-|+| |-|||||||.-.
T Consensus 81 IPvk~KgrGrprkyd~~ 97 (139)
T COG1710 81 IPVKLKGRGRPRKYDRN 97 (139)
T ss_pred eeeeecCCCCCcccchh
Confidence 4778 889999999864
No 9
>COG1777 Predicted transcriptional regulators [Transcription]
Probab=50.25 E-value=6.8 Score=35.18 Aligned_cols=24 Identities=50% Similarity=0.678 Sum_probs=16.5
Q ss_pred ccccCCCCCCCCC-CCCCccc--ccCC
Q 027891 87 PVKRKRGRPRKYG-PDGSVSL--ALSP 110 (217)
Q Consensus 87 ~~KkKRGRPRKY~-~dg~~~l--~l~p 110 (217)
-.|.+|||||||- ..++++| .++|
T Consensus 62 ie~~~Rg~~rKYY~Is~~~rleV~lsp 88 (217)
T COG1777 62 IEKIPRGRPRKYYMISRNLRLEVTLSP 88 (217)
T ss_pred ccccccCCCcceeeccCCeEEEEEecC
Confidence 3577889999997 4566554 4555
No 10
>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=48.54 E-value=53 Score=23.84 Aligned_cols=36 Identities=8% Similarity=0.090 Sum_probs=31.6
Q ss_pred EEEecCCccHHHHHHHHhhcCCceEEEeccc-Ceeee
Q 027891 158 VITVAVGEDIAMKLLSFSQQGPRAICVLSAN-GAIST 193 (217)
Q Consensus 158 VI~V~~GEDV~~kI~~Faqq~~raiCILSas-GsVSn 193 (217)
++++.+.+++.+.+..|.+.+-+.++|+... |.+..
T Consensus 52 ~~~v~~~~~l~~a~~~m~~~~~~~lpVvd~~~~~~~g 88 (98)
T cd04618 52 LVSIHPERSLFDAALLLLKNKIHRLPVIDPSTGTGLY 88 (98)
T ss_pred eEEeCCCCcHHHHHHHHHHCCCCEeeEEECCCCCceE
Confidence 7899999999999999999999999999887 75443
No 11
>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=37.17 E-value=73 Score=20.46 Aligned_cols=39 Identities=23% Similarity=0.373 Sum_probs=32.4
Q ss_pred ceeEEEEecCCccHHHHHHHHhhcCCceEEEecccCeee
Q 027891 154 FTPHVITVAVGEDIAMKLLSFSQQGPRAICVLSANGAIS 192 (217)
Q Consensus 154 f~pHVI~V~~GEDV~~kI~~Faqq~~raiCILSasGsVS 192 (217)
|++-++.|.+.+.+.+.+..|.+.+-+.+.|+...|.+-
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 556678899999999999889999989999997666653
No 12
>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=32.56 E-value=34 Score=26.75 Aligned_cols=28 Identities=32% Similarity=0.364 Sum_probs=25.2
Q ss_pred ecCCccHHHHHHHHhhcCCceEEEeccc
Q 027891 161 VAVGEDIAMKLLSFSQQGPRAICVLSAN 188 (217)
Q Consensus 161 V~~GEDV~~kI~~Faqq~~raiCILSas 188 (217)
+.+|+.+.+.|....++..+.|+|||.+
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 6789999999999999988999999853
No 13
>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=30.30 E-value=94 Score=22.38 Aligned_cols=39 Identities=18% Similarity=0.238 Sum_probs=32.0
Q ss_pred CCceeEEEEecCCccHHHHHHHHhhcCCceEEEecccCe
Q 027891 152 MGFTPHVITVAVGEDIAMKLLSFSQQGPRAICVLSANGA 190 (217)
Q Consensus 152 ~~f~pHVI~V~~GEDV~~kI~~Faqq~~raiCILSasGs 190 (217)
..|...+..+.+.+++.+.+..+.+++...++|+...|.
T Consensus 60 ~~~~~~~~~v~~~~~l~~al~~m~~~~~~~lpVvd~~~~ 98 (111)
T cd04603 60 EVYIVPVPIVYCDSKVTDLLRIFRETEPPVVAVVDKEGK 98 (111)
T ss_pred heeecCCcEECCCCcHHHHHHHHHHcCCCeEEEEcCCCe
Confidence 346666788999999999998888888888999987554
No 14
>PF15333 TAF1D: TATA box-binding protein-associated factor 1D
Probab=28.63 E-value=24 Score=31.70 Aligned_cols=13 Identities=46% Similarity=0.912 Sum_probs=9.9
Q ss_pred CCCCCCCCCCCCC
Q 027891 91 KRGRPRKYGPDGS 103 (217)
Q Consensus 91 KRGRPRKY~~dg~ 103 (217)
|+-+.|||-+-|.
T Consensus 64 KkrkkrKYk~tgr 76 (217)
T PF15333_consen 64 KKRKKRKYKPTGR 76 (217)
T ss_pred HHhhhhccCccCC
Confidence 5666799998774
No 15
>PRK08179 prfH peptide chain release factor-like protein; Reviewed
Probab=28.28 E-value=1.4e+02 Score=26.27 Aligned_cols=44 Identities=11% Similarity=0.187 Sum_probs=35.8
Q ss_pred EEEEecCCc----------cHHHHHHHHhhcCCceEEEeccc-----CeeeeEEeeCCC
Q 027891 157 HVITVAVGE----------DIAMKLLSFSQQGPRAICVLSAN-----GAISTATLRQPS 200 (217)
Q Consensus 157 HVI~V~~GE----------DV~~kI~~Faqq~~raiCILSas-----GsVSnVTLRqp~ 200 (217)
.+|+|.+|. |+..-...||++....+.|++.+ |.+.+|+|.--+
T Consensus 2 ~~leI~aG~Gg~Ea~~fa~~L~~my~~~a~~~g~~~~ii~~~~~~~~gg~ksa~~~i~G 60 (200)
T PRK08179 2 ILLQLSSAQGPAECCLAVAKALERLLKEAARQGVRVTVLETETGRYPDTLRSALVSLDG 60 (200)
T ss_pred EEEEEeCCCChHHHHHHHHHHHHHHHHHHHHcCCeEEEEeCCCCCCCCceEEEEEEEEc
Confidence 378888885 77788888999999999999874 678998887654
No 16
>PF13737 DDE_Tnp_1_5: Transposase DDE domain
Probab=28.27 E-value=30 Score=27.81 Aligned_cols=19 Identities=42% Similarity=0.945 Sum_probs=13.9
Q ss_pred cccccCCCCCCCCCCCCCcc
Q 027891 86 EPVKRKRGRPRKYGPDGSVS 105 (217)
Q Consensus 86 ~~~KkKRGRPRKY~~dg~~~ 105 (217)
++...|||||++|- |-.|.
T Consensus 21 ~~~~~kRGr~~~yS-D~aI~ 39 (112)
T PF13737_consen 21 APPRGKRGRPPRYS-DAAIQ 39 (112)
T ss_pred cCCCCCCCCCcccc-hHHHH
Confidence 35678999999996 54443
No 17
>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=25.57 E-value=1.6e+02 Score=20.75 Aligned_cols=37 Identities=14% Similarity=0.212 Sum_probs=30.2
Q ss_pred ceeEEEEecCCccHHHHHHHHhhcCCceEEEecccCee
Q 027891 154 FTPHVITVAVGEDIAMKLLSFSQQGPRAICVLSANGAI 191 (217)
Q Consensus 154 f~pHVI~V~~GEDV~~kI~~Faqq~~raiCILSasGsV 191 (217)
+..+++.|...+.+.+.+..|.+.....++|+. .|.+
T Consensus 62 ~~~~~~~v~~~~~l~~~~~~~~~~~~~~~~V~~-~~~~ 98 (110)
T cd04595 62 MSTDVVTVPPDTPLSEVQELMVEHDIGRVPVVE-DGRL 98 (110)
T ss_pred hcCCCEEECCCCcHHHHHHHHHHcCCCeeEEEe-CCEE
Confidence 556788999999999999888888778888887 5554
No 18
>KOG4565 consensus E93 protein involved in programmed cell death, putative transcription regulator [Transcription]
Probab=24.67 E-value=25 Score=31.18 Aligned_cols=15 Identities=40% Similarity=0.793 Sum_probs=12.8
Q ss_pred ccccCCCCCCCCCCC
Q 027891 87 PVKRKRGRPRKYGPD 101 (217)
Q Consensus 87 ~~KkKRGRPRKY~~d 101 (217)
.-+|||||=|+|...
T Consensus 111 qpRkKRGrYRqYd~e 125 (206)
T KOG4565|consen 111 QPRKKRGRYRQYDKE 125 (206)
T ss_pred CccccccchhhhhHH
Confidence 578999999999864
No 19
>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=23.76 E-value=1.7e+02 Score=20.72 Aligned_cols=38 Identities=16% Similarity=0.178 Sum_probs=30.4
Q ss_pred ceeEEEEecCCccHHHHHHHHhhcCCceEEEecccCee
Q 027891 154 FTPHVITVAVGEDIAMKLLSFSQQGPRAICVLSANGAI 191 (217)
Q Consensus 154 f~pHVI~V~~GEDV~~kI~~Faqq~~raiCILSasGsV 191 (217)
++..++.|.+.+.+.+.+..|.+.+...+.|+...|.+
T Consensus 73 ~~~~~~~v~~~~~l~~~~~~~~~~~~~~~~Vv~~~~~~ 110 (122)
T cd04585 73 MTRDPITVSPDASVEEAAELMLERKISGLPVVDDQGRL 110 (122)
T ss_pred ccCCCeEeCCCCcHHHHHHHHHHcCCCceeEECCCCcE
Confidence 45567889999999888888888888889998876643
No 20
>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=21.57 E-value=2.2e+02 Score=25.09 Aligned_cols=43 Identities=12% Similarity=0.176 Sum_probs=35.1
Q ss_pred EEEecCCc----------cHHHHHHHHhhcCCceEEEeccc-----CeeeeEEeeCCC
Q 027891 158 VITVAVGE----------DIAMKLLSFSQQGPRAICVLSAN-----GAISTATLRQPS 200 (217)
Q Consensus 158 VI~V~~GE----------DV~~kI~~Faqq~~raiCILSas-----GsVSnVTLRqp~ 200 (217)
+|+|.+|. |+..-...||.+....+.|++.+ |.+..|+|.--+
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 67888874 78888889999999999999874 678888887643
No 21
>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=20.98 E-value=2.4e+02 Score=19.82 Aligned_cols=38 Identities=24% Similarity=0.270 Sum_probs=29.3
Q ss_pred CceeEEEEecCCccHHHHHHHHhhcCCceEEEecccCe
Q 027891 153 GFTPHVITVAVGEDIAMKLLSFSQQGPRAICVLSANGA 190 (217)
Q Consensus 153 ~f~pHVI~V~~GEDV~~kI~~Faqq~~raiCILSasGs 190 (217)
.|+.+++.|...+.+.+.+-.|.+.....++|+...|-
T Consensus 63 ~~~~~~~~v~~~~~l~~~~~~~~~~~~~~~~Vvd~~g~ 100 (113)
T cd04615 63 VMNSPVITIDANDSIAKARWLMSNNNISRLPVLDDKGK 100 (113)
T ss_pred hccCCceEECCCCcHHHHHHHHHHcCCCeeeEECCCCe
Confidence 35677899999988888777777777678888876654
No 22
>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=20.89 E-value=2.3e+02 Score=19.62 Aligned_cols=38 Identities=13% Similarity=0.172 Sum_probs=29.1
Q ss_pred ceeEEEEecCCccHHHHHHHHhhcCCceEEEecccCee
Q 027891 154 FTPHVITVAVGEDIAMKLLSFSQQGPRAICVLSANGAI 191 (217)
Q Consensus 154 f~pHVI~V~~GEDV~~kI~~Faqq~~raiCILSasGsV 191 (217)
+...++.|.+.+.+.+.+..|.+.....++|+...|.+
T Consensus 58 ~~~~~~~v~~~~~l~~~~~~~~~~~~~~~~Vv~~~g~~ 95 (107)
T cd04610 58 MSKDLVVAVPEMDIMDAARVMFRTGISKLPVVDENNNL 95 (107)
T ss_pred CCCCCeEECCCCCHHHHHHHHHHhCCCeEeEECCCCeE
Confidence 45567889999998888877777666788999877753
No 23
>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=20.76 E-value=2e+02 Score=20.17 Aligned_cols=35 Identities=11% Similarity=0.104 Sum_probs=28.3
Q ss_pred EEEEecCCccHHHHHHHHhhcCCceEEEecccCee
Q 027891 157 HVITVAVGEDIAMKLLSFSQQGPRAICVLSANGAI 191 (217)
Q Consensus 157 HVI~V~~GEDV~~kI~~Faqq~~raiCILSasGsV 191 (217)
++..|...+++.+.+..|.+.+...++|+...|.+
T Consensus 65 ~~~~v~~~~~l~~~~~~~~~~~~~~~~Vv~~~~~~ 99 (111)
T cd04590 65 PPLFVPESTPLDDLLEEMRKERSHMAIVVDEYGGT 99 (111)
T ss_pred CCeecCCCCcHHHHHHHHHhcCCcEEEEEECCCCE
Confidence 46778999999888877888788899999886653
Done!