Query 028357
Match_columns 210
No_of_seqs 162 out of 288
Neff 3.7
Searched_HMMs 46136
Date Fri Mar 29 10:15:12 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028357.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028357hhsearch_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 98.7 9.6E-09 2.1E-13 80.6 2.9 56 154-209 1-58 (120)
2 PF02178 AT_hook: AT hook moti 96.3 0.0013 2.8E-08 34.9 0.5 12 89-100 1-12 (13)
3 smart00384 AT_hook DNA binding 96.3 0.002 4.4E-08 40.0 1.4 15 89-103 1-15 (26)
4 COG1661 Predicted DNA-binding 93.7 0.12 2.6E-06 43.2 4.7 45 156-200 11-55 (141)
5 PF14621 RFX5_DNA_bdg: RFX5 DN 84.4 0.35 7.6E-06 42.6 0.4 12 87-98 66-77 (219)
6 PF13546 DDE_5: DDE superfamil 80.2 1 2.3E-05 38.9 1.7 16 86-101 228-243 (273)
7 COG1710 Uncharacterized protei 73.1 1.6 3.5E-05 36.4 0.9 16 86-101 81-97 (139)
8 cd04618 CBS_pair_5 The CBS dom 58.1 29 0.00062 25.1 5.0 36 158-193 52-88 (98)
9 COG1777 Predicted transcriptio 51.6 6.3 0.00014 35.3 0.7 23 88-110 63-88 (217)
10 PF01582 TIR: TIR domain; Int 44.5 12 0.00026 29.1 1.2 28 161-188 38-65 (141)
11 cd02955 SSP411 TRX domain, SSP 39.0 99 0.0022 24.6 5.7 50 152-201 49-103 (124)
12 PF00571 CBS: CBS domain CBS d 35.4 68 0.0015 20.5 3.6 40 154-193 5-44 (57)
13 cd04585 CBS_pair_ACT_assoc2 Th 32.8 88 0.0019 22.0 4.1 40 153-192 72-111 (122)
14 cd04595 CBS_pair_DHH_polyA_Pol 32.6 89 0.0019 21.9 4.1 40 153-193 61-100 (110)
15 cd04603 CBS_pair_KefB_assoc Th 30.8 1.1E+02 0.0023 21.9 4.3 40 152-191 60-99 (111)
16 PF13737 DDE_Tnp_1_5: Transpos 30.2 27 0.00059 28.0 1.1 15 86-100 21-35 (112)
17 PF15333 TAF1D: TATA box-bindi 28.8 24 0.00052 31.6 0.7 13 91-103 64-76 (217)
18 PF14869 DUF4488: Domain of un 28.7 67 0.0015 26.9 3.2 27 181-209 28-54 (133)
19 cd04590 CBS_pair_CorC_HlyC_ass 27.8 1.2E+02 0.0025 21.3 4.0 37 157-193 65-101 (111)
20 PF14601 TFX_C: DNA_binding pr 27.4 40 0.00087 25.8 1.6 15 155-169 13-27 (84)
21 cd04596 CBS_pair_DRTGG_assoc T 27.2 1.3E+02 0.0029 21.1 4.2 39 154-192 59-97 (108)
22 cd04587 CBS_pair_CAP-ED_DUF294 27.0 1.1E+02 0.0023 21.4 3.7 40 153-192 63-102 (113)
23 KOG4565 E93 protein involved i 26.7 21 0.00047 31.5 0.0 15 87-101 111-125 (206)
24 cd04610 CBS_pair_ParBc_assoc T 26.6 1.4E+02 0.0031 20.6 4.3 39 154-192 58-96 (107)
25 cd04624 CBS_pair_11 The CBS do 26.5 1.5E+02 0.0032 20.8 4.4 40 153-192 62-101 (112)
26 cd04607 CBS_pair_NTP_transfera 26.1 1.5E+02 0.0032 21.0 4.3 42 153-194 63-104 (113)
27 PF10623 PilI: Plasmid conjuga 26.0 92 0.002 24.2 3.3 40 153-192 17-56 (83)
28 cd04606 CBS_pair_Mg_transporte 25.9 1.4E+02 0.0031 21.0 4.2 41 152-192 57-97 (109)
29 cd04615 CBS_pair_2 The CBS dom 25.6 1.6E+02 0.0035 20.6 4.4 39 153-191 63-101 (113)
30 cd04588 CBS_pair_CAP-ED_DUF294 25.3 1.7E+02 0.0036 20.4 4.4 40 153-192 60-99 (110)
31 cd04600 CBS_pair_HPP_assoc Thi 25.1 1.5E+02 0.0032 21.2 4.2 43 152-194 73-115 (124)
32 cd04612 CBS_pair_SpoIVFB_EriC_ 24.4 1.6E+02 0.0035 20.4 4.2 40 152-191 60-99 (111)
33 cd04583 CBS_pair_ABC_OpuCA_ass 23.8 1.8E+02 0.0039 20.0 4.4 40 153-192 59-98 (109)
34 cd04611 CBS_pair_PAS_GGDEF_DUF 22.6 2E+02 0.0044 19.9 4.4 39 153-191 61-99 (111)
35 cd04614 CBS_pair_1 The CBS dom 22.1 2.1E+02 0.0046 20.2 4.5 34 158-191 51-84 (96)
36 cd04631 CBS_pair_18 The CBS do 21.6 2E+02 0.0044 20.5 4.4 39 154-192 76-114 (125)
37 cd04630 CBS_pair_17 The CBS do 20.9 2E+02 0.0043 20.4 4.1 41 156-196 1-43 (114)
38 cd04582 CBS_pair_ABC_OpuCA_ass 20.7 2.5E+02 0.0054 19.4 4.6 41 152-192 55-95 (106)
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=98.69 E-value=9.6e-09 Score=80.64 Aligned_cols=56 Identities=25% Similarity=0.258 Sum_probs=47.9
Q ss_pred ceeEEEEeCCCchHHHHHHhhhhcCCceEEEecCCCceeeEEecCCCC--CCCceEEe
Q 028357 154 FTPHVITVAVGEDIAMKLLSFSQQGPRAICVLSANGAISTATLRQPSS--SGGSVTYE 209 (210)
Q Consensus 154 ftPHVItV~~GEDV~~kI~sFaqqg~raICILSA~GaVSnVTLRQP~s--sGgtvTYE 209 (210)
|++++|.+.+||||.++|.+||++.....|+||+.|++++|+|++++. ...+++||
T Consensus 1 ~r~~~~rl~~Gedl~~~l~~~~~~~~i~~~~is~iGsl~~~~l~~~~~~~~~~~~~~~ 58 (120)
T PF03479_consen 1 GRVFVIRLDPGEDLLESLEAFAREHGIRSGVISGIGSLSNVTLGYYDPPSYYEPLEFE 58 (120)
T ss_dssp EEEEEEEEETTSBHHHHHHHHHHHHT-SSEEEEEEEEEEEEEEEEEETTTEEEEEEEE
T ss_pred CcEEEEEECCCCHHHHHHHHHHHHCCCcEEEEEEEeEEeEEEEEEecccCCcceEEec
Confidence 689999999999999999999999999999999999999999999743 23344443
No 2
>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=96.33 E-value=0.0013 Score=34.88 Aligned_cols=12 Identities=75% Similarity=1.140 Sum_probs=4.3
Q ss_pred ccCCCCCCCCCC
Q 028357 89 KRKRGRPRKYGP 100 (210)
Q Consensus 89 KkKRGRPRKY~p 100 (210)
+|+||||+|+..
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 3
>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=96.32 E-value=0.002 Score=39.99 Aligned_cols=15 Identities=67% Similarity=0.948 Sum_probs=13.0
Q ss_pred ccCCCCCCCCCCCCC
Q 028357 89 KRKRGRPRKYGPDGS 103 (210)
Q Consensus 89 KkKRGRPRKY~pdg~ 103 (210)
|||||||||+..+..
T Consensus 1 kRkRGRPrK~~~~~~ 15 (26)
T smart00384 1 KRKRGRPRKAPKDXX 15 (26)
T ss_pred CCCCCCCCCCCCccc
Confidence 699999999998764
No 4
>COG1661 Predicted DNA-binding protein with PD1-like DNA-binding motif [General function prediction only]
Probab=93.66 E-value=0.12 Score=43.15 Aligned_cols=45 Identities=29% Similarity=0.353 Sum_probs=40.9
Q ss_pred eEEEEeCCCchHHHHHHhhhhcCCceEEEecCCCceeeEEecCCC
Q 028357 156 PHVITVAVGEDIAMKLLSFSQQGPRAICVLSANGAISTATLRQPS 200 (210)
Q Consensus 156 PHVItV~~GEDV~~kI~sFaqqg~raICILSA~GaVSnVTLRQP~ 200 (210)
=.++-+.+|||+.+.|.+||++..-...|.++-|++++++|+--+
T Consensus 11 ~~~~Rld~G~d~~~~l~~~a~~~~i~aa~v~~iGal~~~~l~~~~ 55 (141)
T COG1661 11 VIALRLDPGEDLFSELEAFAEQEDIHAAVVTAIGALRDAKLRYFD 55 (141)
T ss_pred EEEEEeCCCccHHHHHHHHHHhcCceEEEEEEeeeeeeeEEEEec
Confidence 357788999999999999999999888999999999999999755
No 5
>PF14621 RFX5_DNA_bdg: RFX5 DNA-binding domain
Probab=84.41 E-value=0.35 Score=42.58 Aligned_cols=12 Identities=75% Similarity=1.107 Sum_probs=10.2
Q ss_pred ccccCCCCCCCC
Q 028357 87 PVKRKRGRPRKY 98 (210)
Q Consensus 87 ~~KkKRGRPRKY 98 (210)
-.|||||||||-
T Consensus 66 dAKRKRGRPRKK 77 (219)
T PF14621_consen 66 DAKRKRGRPRKK 77 (219)
T ss_pred hhhhhcCCCccC
Confidence 479999999964
No 6
>PF13546 DDE_5: DDE superfamily endonuclease
Probab=80.20 E-value=1 Score=38.87 Aligned_cols=16 Identities=63% Similarity=1.076 Sum_probs=12.2
Q ss_pred cccccCCCCCCCCCCC
Q 028357 86 EPVKRKRGRPRKYGPD 101 (210)
Q Consensus 86 ~~~KkKRGRPRKY~pd 101 (210)
.+..+|||||||||.-
T Consensus 228 ~~~~~~rGRPr~~g~~ 243 (273)
T PF13546_consen 228 PPPPPKRGRPRKYGRR 243 (273)
T ss_pred cccCCCCCCCCCCCCc
Confidence 3455569999999965
No 7
>COG1710 Uncharacterized protein conserved in archaea [Function unknown]
Probab=73.14 E-value=1.6 Score=36.37 Aligned_cols=16 Identities=63% Similarity=1.120 Sum_probs=13.3
Q ss_pred cccc-cCCCCCCCCCCC
Q 028357 86 EPVK-RKRGRPRKYGPD 101 (210)
Q Consensus 86 ~~~K-kKRGRPRKY~pd 101 (210)
-|+| |-|||||||.-.
T Consensus 81 IPvk~KgrGrprkyd~~ 97 (139)
T COG1710 81 IPVKLKGRGRPRKYDRN 97 (139)
T ss_pred eeeeecCCCCCcccchh
Confidence 3677 889999999874
No 8
>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=58.14 E-value=29 Score=25.10 Aligned_cols=36 Identities=8% Similarity=0.090 Sum_probs=32.2
Q ss_pred EEEeCCCchHHHHHHhhhhcCCceEEEecCC-Cceee
Q 028357 158 VITVAVGEDIAMKLLSFSQQGPRAICVLSAN-GAIST 193 (210)
Q Consensus 158 VItV~~GEDV~~kI~sFaqqg~raICILSA~-GaVSn 193 (210)
+++|.+.+++.+.+-.|.+++-+.++|+..+ |.+..
T Consensus 52 ~~~v~~~~~l~~a~~~m~~~~~~~lpVvd~~~~~~~g 88 (98)
T cd04618 52 LVSIHPERSLFDAALLLLKNKIHRLPVIDPSTGTGLY 88 (98)
T ss_pred eEEeCCCCcHHHHHHHHHHCCCCEeeEEECCCCCceE
Confidence 8899999999999999999999999999987 76543
No 9
>COG1777 Predicted transcriptional regulators [Transcription]
Probab=51.61 E-value=6.3 Score=35.27 Aligned_cols=23 Identities=52% Similarity=0.745 Sum_probs=16.0
Q ss_pred cccCCCCCCCCC-CCCCccc--ccCC
Q 028357 88 VKRKRGRPRKYG-PDGSVSL--ALSP 110 (210)
Q Consensus 88 ~KkKRGRPRKY~-pdg~~~l--~l~p 110 (210)
.|.+|||||||- ..++++| .++|
T Consensus 63 e~~~Rg~~rKYY~Is~~~rleV~lsp 88 (217)
T COG1777 63 EKIPRGRPRKYYMISRNLRLEVTLSP 88 (217)
T ss_pred cccccCCCcceeeccCCeEEEEEecC
Confidence 577789999997 4565544 4555
No 10
>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=44.51 E-value=12 Score=29.12 Aligned_cols=28 Identities=32% Similarity=0.364 Sum_probs=25.4
Q ss_pred eCCCchHHHHHHhhhhcCCceEEEecCC
Q 028357 161 VAVGEDIAMKLLSFSQQGPRAICVLSAN 188 (210)
Q Consensus 161 V~~GEDV~~kI~sFaqqg~raICILSA~ 188 (210)
..+|+.+.+.|....++..+.|+|||.+
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 5689999999999999999999999964
No 11
>cd02955 SSP411 TRX domain, SSP411 protein family; members of this family are highly conserved proteins present in eukaryotes, bacteria and archaea, about 600-800 amino acids in length, which contain a TRX domain with a redox active CXXC motif. The human/rat protein, called SSP411, is specifically expressed in the testis in an age-dependent manner. The SSP411 mRNA is increased during spermiogenesis and is localized in round and elongated spermatids, suggesting a function in fertility regulation.
Probab=38.99 E-value=99 Score=24.56 Aligned_cols=50 Identities=14% Similarity=0.060 Sum_probs=41.2
Q ss_pred CCceeEEEEeCCCchHHHHHHhh-----hhcCCceEEEecCCCceeeEEecCCCC
Q 028357 152 MGFTPHVITVAVGEDIAMKLLSF-----SQQGPRAICVLSANGAISTATLRQPSS 201 (210)
Q Consensus 152 ~~ftPHVItV~~GEDV~~kI~sF-----aqqg~raICILSA~GaVSnVTLRQP~s 201 (210)
..|.+..+.+....|++.+.+.+ -.+|..++.+|..+|.+-+.+-..|..
T Consensus 49 ~~fv~VkvD~~~~~~~~~~~~~~~~~~~~~~G~Pt~vfl~~~G~~~~~~~~~~~~ 103 (124)
T cd02955 49 ENFVPIKVDREERPDVDKIYMNAAQAMTGQGGWPLNVFLTPDLKPFFGGTYFPPE 103 (124)
T ss_pred CCEEEEEEeCCcCcHHHHHHHHHHHHhcCCCCCCEEEEECCCCCEEeeeeecCCC
Confidence 47888888888888999888774 456788999999999999988777654
No 12
>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=35.40 E-value=68 Score=20.50 Aligned_cols=40 Identities=23% Similarity=0.355 Sum_probs=33.5
Q ss_pred ceeEEEEeCCCchHHHHHHhhhhcCCceEEEecCCCceee
Q 028357 154 FTPHVITVAVGEDIAMKLLSFSQQGPRAICVLSANGAIST 193 (210)
Q Consensus 154 ftPHVItV~~GEDV~~kI~sFaqqg~raICILSA~GaVSn 193 (210)
|++-++.|...+.+.+.+-.|.+.+-+.+.|+..+|.+--
T Consensus 5 m~~~~~~v~~~~~l~~~~~~~~~~~~~~~~V~d~~~~~~G 44 (57)
T PF00571_consen 5 MTPPPITVSPDDSLEEALEIMRKNGISRLPVVDEDGKLVG 44 (57)
T ss_dssp SBSSSEEEETTSBHHHHHHHHHHHTSSEEEEESTTSBEEE
T ss_pred CcCCCEEEcCcCcHHHHHHHHHHcCCcEEEEEecCCEEEE
Confidence 5566788999999999999999999999999977776543
No 13
>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=32.78 E-value=88 Score=21.98 Aligned_cols=40 Identities=15% Similarity=0.124 Sum_probs=32.4
Q ss_pred CceeEEEEeCCCchHHHHHHhhhhcCCceEEEecCCCcee
Q 028357 153 GFTPHVITVAVGEDIAMKLLSFSQQGPRAICVLSANGAIS 192 (210)
Q Consensus 153 ~ftPHVItV~~GEDV~~kI~sFaqqg~raICILSA~GaVS 192 (210)
.++..++.|...+.+.+-+..|.+.+...+.|+..+|.+-
T Consensus 72 ~~~~~~~~v~~~~~l~~~~~~~~~~~~~~~~Vv~~~~~~~ 111 (122)
T cd04585 72 IMTRDPITVSPDASVEEAAELMLERKISGLPVVDDQGRLV 111 (122)
T ss_pred hccCCCeEeCCCCcHHHHHHHHHHcCCCceeEECCCCcEE
Confidence 3456788899999998888889989888899998877643
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=32.64 E-value=89 Score=21.92 Aligned_cols=40 Identities=13% Similarity=0.145 Sum_probs=32.5
Q ss_pred CceeEEEEeCCCchHHHHHHhhhhcCCceEEEecCCCceee
Q 028357 153 GFTPHVITVAVGEDIAMKLLSFSQQGPRAICVLSANGAIST 193 (210)
Q Consensus 153 ~ftPHVItV~~GEDV~~kI~sFaqqg~raICILSA~GaVSn 193 (210)
.+..+++.|...+.+.+.+..|.+.+-..++|+. +|.+.-
T Consensus 61 ~~~~~~~~v~~~~~l~~~~~~~~~~~~~~~~V~~-~~~~~G 100 (110)
T cd04595 61 YMSTDVVTVPPDTPLSEVQELMVEHDIGRVPVVE-DGRLVG 100 (110)
T ss_pred HhcCCCEEECCCCcHHHHHHHHHHcCCCeeEEEe-CCEEEE
Confidence 3456788999999999888889888888899988 666543
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=30.78 E-value=1.1e+02 Score=21.90 Aligned_cols=40 Identities=18% Similarity=0.255 Sum_probs=33.3
Q ss_pred CCceeEEEEeCCCchHHHHHHhhhhcCCceEEEecCCCce
Q 028357 152 MGFTPHVITVAVGEDIAMKLLSFSQQGPRAICVLSANGAI 191 (210)
Q Consensus 152 ~~ftPHVItV~~GEDV~~kI~sFaqqg~raICILSA~GaV 191 (210)
..++..+..|...+++.+.+..|.+++...++|+..+|.+
T Consensus 60 ~~~~~~~~~v~~~~~l~~al~~m~~~~~~~lpVvd~~~~~ 99 (111)
T cd04603 60 EVYIVPVPIVYCDSKVTDLLRIFRETEPPVVAVVDKEGKL 99 (111)
T ss_pred heeecCCcEECCCCcHHHHHHHHHHcCCCeEEEEcCCCeE
Confidence 3456677899999999999999999998999999887643
No 16
>PF13737 DDE_Tnp_1_5: Transposase DDE domain
Probab=30.17 E-value=27 Score=27.99 Aligned_cols=15 Identities=47% Similarity=0.968 Sum_probs=11.9
Q ss_pred cccccCCCCCCCCCC
Q 028357 86 EPVKRKRGRPRKYGP 100 (210)
Q Consensus 86 ~~~KkKRGRPRKY~p 100 (210)
++...|||||++|-.
T Consensus 21 ~~~~~kRGr~~~ySD 35 (112)
T PF13737_consen 21 APPRGKRGRPPRYSD 35 (112)
T ss_pred cCCCCCCCCCcccch
Confidence 355789999999954
No 17
>PF15333 TAF1D: TATA box-binding protein-associated factor 1D
Probab=28.84 E-value=24 Score=31.65 Aligned_cols=13 Identities=46% Similarity=0.912 Sum_probs=9.9
Q ss_pred CCCCCCCCCCCCC
Q 028357 91 KRGRPRKYGPDGS 103 (210)
Q Consensus 91 KRGRPRKY~pdg~ 103 (210)
|+-+.|||-+-|.
T Consensus 64 KkrkkrKYk~tgr 76 (217)
T PF15333_consen 64 KKRKKRKYKPTGR 76 (217)
T ss_pred HHhhhhccCccCC
Confidence 5666799998764
No 18
>PF14869 DUF4488: Domain of unknown function (DUF4488)
Probab=28.74 E-value=67 Score=26.88 Aligned_cols=27 Identities=26% Similarity=0.340 Sum_probs=20.2
Q ss_pred eEEEecCCCceeeEEecCCCCCCCceEEe
Q 028357 181 AICVLSANGAISTATLRQPSSSGGSVTYE 209 (210)
Q Consensus 181 aICILSA~GaVSnVTLRQP~ssGgtvTYE 209 (210)
..=|||.+|++.|+++.+ . ++.++|++
T Consensus 28 ~lKilS~Dgtf~Ni~~~~-~-~~aiIt~~ 54 (133)
T PF14869_consen 28 VLKILSDDGTFVNITMIP-K-SGAIITGY 54 (133)
T ss_pred cEEEEcCCCcEEEEEEeC-C-CCcEEEEe
Confidence 477999999999999943 2 33666653
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=27.77 E-value=1.2e+02 Score=21.25 Aligned_cols=37 Identities=11% Similarity=0.099 Sum_probs=30.4
Q ss_pred EEEEeCCCchHHHHHHhhhhcCCceEEEecCCCceee
Q 028357 157 HVITVAVGEDIAMKLLSFSQQGPRAICVLSANGAIST 193 (210)
Q Consensus 157 HVItV~~GEDV~~kI~sFaqqg~raICILSA~GaVSn 193 (210)
++..|...+++.+.+-.|.+++...++|+..+|.+--
T Consensus 65 ~~~~v~~~~~l~~~~~~~~~~~~~~~~Vv~~~~~~~G 101 (111)
T cd04590 65 PPLFVPESTPLDDLLEEMRKERSHMAIVVDEYGGTAG 101 (111)
T ss_pred CCeecCCCCcHHHHHHHHHhcCCcEEEEEECCCCEEE
Confidence 4678899999988888888888889999998876543
No 20
>PF14601 TFX_C: DNA_binding protein, TFX, C-term; PDB: 1NR3_A.
Probab=27.45 E-value=40 Score=25.84 Aligned_cols=15 Identities=33% Similarity=0.510 Sum_probs=9.5
Q ss_pred eeEEEEeCCCchHHH
Q 028357 155 TPHVITVAVGEDIAM 169 (210)
Q Consensus 155 tPHVItV~~GEDV~~ 169 (210)
.|+.|+|++|+|+.+
T Consensus 13 Apv~i~i~~GtDl~d 27 (84)
T PF14601_consen 13 APVRITIPAGTDLFD 27 (84)
T ss_dssp --EEEEE--GGGHHH
T ss_pred CCEEEEEcCCCcHHH
Confidence 599999999998754
No 21
>cd04596 CBS_pair_DRTGG_assoc This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with a DRTGG domain upstream. The function of the DRTGG domain, named after its conserved residues, is unknown. 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=27.16 E-value=1.3e+02 Score=21.11 Aligned_cols=39 Identities=21% Similarity=0.160 Sum_probs=31.9
Q ss_pred ceeEEEEeCCCchHHHHHHhhhhcCCceEEEecCCCcee
Q 028357 154 FTPHVITVAVGEDIAMKLLSFSQQGPRAICVLSANGAIS 192 (210)
Q Consensus 154 ftPHVItV~~GEDV~~kI~sFaqqg~raICILSA~GaVS 192 (210)
++.+++.|...+.+.+-+-.|.+.+...++|+..+|-+-
T Consensus 59 ~~~~~~~v~~~~~l~~~~~~~~~~~~~~~~Vv~~~~~~~ 97 (108)
T cd04596 59 MTKNPITVNPKTSVASVAHMMIWEGIEMLPVVDDNKKLL 97 (108)
T ss_pred hcCCCeEECCCCCHHHHHHHHHHcCCCeeeEEcCCCCEE
Confidence 456788999999998888888888889999998777543
No 22
>cd04587 CBS_pair_CAP-ED_DUF294_PBI_assoc This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with either the CAP_ED (cAMP receptor protein effector domain) family of transcription factors and the DUF294 domain or the PB1 (Phox and Bem1p) domain. Members of CAP_ED, include CAP which binds cAMP, FNR (fumarate and nitrate reductase) which uses an iron-sulfur cluster to sense oxygen, and CooA a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. DUF294 is a putative nucleotidyltransferase with a conserved DxD motif. The PB1 domain adopts a beta-grasp fold, similar to that found in ubiquitin and Ras-binding domains. A motif, variously termed OPR, PC and AID, represents the most conserved region of the majority of PB1 domains, and is necessary for PB1 domain function. This function is the formation of PB1 domain heterodimers, although not all PB1 domain pai
Probab=26.97 E-value=1.1e+02 Score=21.43 Aligned_cols=40 Identities=18% Similarity=0.207 Sum_probs=32.5
Q ss_pred CceeEEEEeCCCchHHHHHHhhhhcCCceEEEecCCCcee
Q 028357 153 GFTPHVITVAVGEDIAMKLLSFSQQGPRAICVLSANGAIS 192 (210)
Q Consensus 153 ~ftPHVItV~~GEDV~~kI~sFaqqg~raICILSA~GaVS 192 (210)
-+.++++.|...+.+.+.+-.|.+++...+.|+..+|.+.
T Consensus 63 i~~~~~~~v~~~~~l~~~~~~~~~~~~~~l~Vv~~~~~~~ 102 (113)
T cd04587 63 VMTPNPVCATSDTPVLEALHLMVQGKFRHLPVVDKSGQVV 102 (113)
T ss_pred hcCCCCeEEcCCCCHHHHHHHHHHcCCCcccEECCCCCEE
Confidence 3567788999999998888888888888888998877643
No 23
>KOG4565 consensus E93 protein involved in programmed cell death, putative transcription regulator [Transcription]
Probab=26.68 E-value=21 Score=31.47 Aligned_cols=15 Identities=40% Similarity=0.793 Sum_probs=12.8
Q ss_pred ccccCCCCCCCCCCC
Q 028357 87 PVKRKRGRPRKYGPD 101 (210)
Q Consensus 87 ~~KkKRGRPRKY~pd 101 (210)
.-+|||||=|+|...
T Consensus 111 qpRkKRGrYRqYd~e 125 (206)
T KOG4565|consen 111 QPRKKRGRYRQYDKE 125 (206)
T ss_pred CccccccchhhhhHH
Confidence 468999999999864
No 24
>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=26.60 E-value=1.4e+02 Score=20.56 Aligned_cols=39 Identities=13% Similarity=0.159 Sum_probs=30.5
Q ss_pred ceeEEEEeCCCchHHHHHHhhhhcCCceEEEecCCCcee
Q 028357 154 FTPHVITVAVGEDIAMKLLSFSQQGPRAICVLSANGAIS 192 (210)
Q Consensus 154 ftPHVItV~~GEDV~~kI~sFaqqg~raICILSA~GaVS 192 (210)
+...++.|...+.+.+-+-.|-+.....++|+..+|.+-
T Consensus 58 ~~~~~~~v~~~~~l~~~~~~~~~~~~~~~~Vv~~~g~~~ 96 (107)
T cd04610 58 MSKDLVVAVPEMDIMDAARVMFRTGISKLPVVDENNNLV 96 (107)
T ss_pred CCCCCeEECCCCCHHHHHHHHHHhCCCeEeEECCCCeEE
Confidence 456678899999888877777777777899999888643
No 25
>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=26.53 E-value=1.5e+02 Score=20.77 Aligned_cols=40 Identities=20% Similarity=0.204 Sum_probs=30.4
Q ss_pred CceeEEEEeCCCchHHHHHHhhhhcCCceEEEecCCCcee
Q 028357 153 GFTPHVITVAVGEDIAMKLLSFSQQGPRAICVLSANGAIS 192 (210)
Q Consensus 153 ~ftPHVItV~~GEDV~~kI~sFaqqg~raICILSA~GaVS 192 (210)
.+...++.|...+++..-+-.|.+++...+.|+..+|.+.
T Consensus 62 ~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~Vv~~~g~~~ 101 (112)
T cd04624 62 IMTRDLVTVDPDEPVAEAAKLMRKNNIRHHLVVDKGGELV 101 (112)
T ss_pred hccCCCEEECCCCcHHHHHHHHHHcCccEEEEEcCCCcEE
Confidence 3456788899998887766667777777889999887653
No 26
>cd04607 CBS_pair_NTP_transferase_assoc This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domain associated with the NTP (Nucleotidyl transferase) 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=26.14 E-value=1.5e+02 Score=20.96 Aligned_cols=42 Identities=19% Similarity=0.230 Sum_probs=34.2
Q ss_pred CceeEEEEeCCCchHHHHHHhhhhcCCceEEEecCCCceeeE
Q 028357 153 GFTPHVITVAVGEDIAMKLLSFSQQGPRAICVLSANGAISTA 194 (210)
Q Consensus 153 ~ftPHVItV~~GEDV~~kI~sFaqqg~raICILSA~GaVSnV 194 (210)
.+.+.++.|...+++.+.+-.|...+.+.++|+-.+|.+-.+
T Consensus 63 ~~~~~~~~v~~~~~l~~~~~~~~~~~~~~~~Vv~~~~~~~Gv 104 (113)
T cd04607 63 VMNRNPITAKVGSSREEILALMRERSIRHLPILDEEGRVVGL 104 (113)
T ss_pred hhcCCCEEEcCCCCHHHHHHHHHHCCCCEEEEECCCCCEEEE
Confidence 456778899999999988888999888889999887765433
No 27
>PF10623 PilI: Plasmid conjugative transfer protein PilI; InterPro: IPR018897 The thin pilus of plasmid R64 belongs to the type IV family and is required for liquid matings. PilI is one of 14 genes that have been identified as being involved in biogenesis of the R64 thin pilus [].
Probab=25.97 E-value=92 Score=24.25 Aligned_cols=40 Identities=15% Similarity=0.159 Sum_probs=33.5
Q ss_pred CceeEEEEeCCCchHHHHHHhhhhcCCceEEEecCCCcee
Q 028357 153 GFTPHVITVAVGEDIAMKLLSFSQQGPRAICVLSANGAIS 192 (210)
Q Consensus 153 ~ftPHVItV~~GEDV~~kI~sFaqqg~raICILSA~GaVS 192 (210)
.=.=-+|..++-+|+..-|+.|+--..+=||||--|=-|-
T Consensus 17 ~c~~kL~~~~~~~D~~~i~r~f~TpdN~lV~V~~~nr~l~ 56 (83)
T PF10623_consen 17 HCERKLFDTKPDNDPDKIARRFCTPDNCLVCVLQDNRFLF 56 (83)
T ss_pred CcceeEeecCCCCCHHHHHhhccCcCCeEEEEEeCCceEE
Confidence 3445688899999999999999999999999998775543
No 28
>cd04606 CBS_pair_Mg_transporter This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domain in the magnesium transporter, MgtE. MgtE and its homologs are found in eubacteria, archaebacteria, and eukaryota. Members of this family transport Mg2+ or other divalent cations into the cell via two highly conserved aspartates. 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=25.85 E-value=1.4e+02 Score=20.99 Aligned_cols=41 Identities=20% Similarity=0.194 Sum_probs=32.3
Q ss_pred CCceeEEEEeCCCchHHHHHHhhhhcCCceEEEecCCCcee
Q 028357 152 MGFTPHVITVAVGEDIAMKLLSFSQQGPRAICVLSANGAIS 192 (210)
Q Consensus 152 ~~ftPHVItV~~GEDV~~kI~sFaqqg~raICILSA~GaVS 192 (210)
..++++++.|...+.+.+.+-.|.+.....+.|+..+|.+.
T Consensus 57 ~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~Vv~~~~~~~ 97 (109)
T cd04606 57 DIMDTDVISVSADDDQEEVARLFEKYDLLALPVVDEEGRLV 97 (109)
T ss_pred HHhCCCCeEEcCCCCHHHHHHHHHHcCCceeeeECCCCcEE
Confidence 34577899999999988777778777777889998777643
No 29
>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=25.57 E-value=1.6e+02 Score=20.63 Aligned_cols=39 Identities=23% Similarity=0.290 Sum_probs=30.5
Q ss_pred CceeEEEEeCCCchHHHHHHhhhhcCCceEEEecCCCce
Q 028357 153 GFTPHVITVAVGEDIAMKLLSFSQQGPRAICVLSANGAI 191 (210)
Q Consensus 153 ~ftPHVItV~~GEDV~~kI~sFaqqg~raICILSA~GaV 191 (210)
.++.++++|...+.+.+-+-.|.+.....++|+..+|.+
T Consensus 63 ~~~~~~~~v~~~~~l~~~~~~~~~~~~~~~~Vvd~~g~~ 101 (113)
T cd04615 63 VMNSPVITIDANDSIAKARWLMSNNNISRLPVLDDKGKV 101 (113)
T ss_pred hccCCceEECCCCcHHHHHHHHHHcCCCeeeEECCCCeE
Confidence 356789999999888877777877777789999877653
No 30
>cd04588 CBS_pair_CAP-ED_DUF294_assoc_arch This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the archaeal CAP_ED (cAMP receptor protein effector domain) family of transcription factors and the DUF294 domain. Members of CAP_ED, include CAP which binds cAMP, FNR (fumarate and nitrate reductase) which uses an iron-sulfur cluster to sense oxygen, and CooA a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. DUF294 is a putative nucleotidyltransferase with a conserved DxD motif. 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.
Probab=25.30 E-value=1.7e+02 Score=20.42 Aligned_cols=40 Identities=18% Similarity=0.179 Sum_probs=32.2
Q ss_pred CceeEEEEeCCCchHHHHHHhhhhcCCceEEEecCCCcee
Q 028357 153 GFTPHVITVAVGEDIAMKLLSFSQQGPRAICVLSANGAIS 192 (210)
Q Consensus 153 ~ftPHVItV~~GEDV~~kI~sFaqqg~raICILSA~GaVS 192 (210)
.+..+++.|...+.+.+-+-.|.+.....++|+...|.+-
T Consensus 60 ~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~V~~~~~~~~ 99 (110)
T cd04588 60 VMTKDVITIDEDEQLYDAIRLMNKHNVGRLIVTDDEGRPV 99 (110)
T ss_pred HhcCCceEECCCCCHHHHHHHHHhcCCCEEEEECCCCCEE
Confidence 3457889999999998877778888878999998877543
No 31
>cd04600 CBS_pair_HPP_assoc This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the HPP motif domain. These proteins are integral membrane proteins with four transmembrane spanning helices. The function of these proteins is uncertain, but they are thought to be transporters. 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=25.08 E-value=1.5e+02 Score=21.18 Aligned_cols=43 Identities=19% Similarity=0.200 Sum_probs=34.5
Q ss_pred CCceeEEEEeCCCchHHHHHHhhhhcCCceEEEecCCCceeeE
Q 028357 152 MGFTPHVITVAVGEDIAMKLLSFSQQGPRAICVLSANGAISTA 194 (210)
Q Consensus 152 ~~ftPHVItV~~GEDV~~kI~sFaqqg~raICILSA~GaVSnV 194 (210)
..++.+++.+...+.+.+.+--|.+.+...++|+..+|.+-.+
T Consensus 73 ~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~Vv~~~g~~~Gv 115 (124)
T cd04600 73 DIMSPPVVTVRPDTPIAELVPLLADGGHHHVPVVDEDRRLVGI 115 (124)
T ss_pred HhccCCCeeeCCCCcHHHHHHHHHhcCCCceeEEcCCCCEEEE
Confidence 3456789999999999988888888888899999877765443
No 32
>cd04612 CBS_pair_SpoIVFB_EriC_assoc This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in association with either the SpoIVFB domain (sporulation protein, stage IV cell wall formation, F locus, promoter-distal B) or the chloride channel protein EriC. SpoIVFB is one of 4 proteins involved in endospore formation; the others are SpoIVFA (sporulation protein, stage IV cell wall formation, F locus, promoter-proximal A), BofA (bypass-of-forespore A ), and SpoIVB (sporulation protein, stage IV cell wall formation, B locus). SpoIVFB is negatively regulated by SpoIVFA and BofA and activated by SpoIVB. It is thought that SpoIVFB, SpoIVFA, and BofA are located in the mother-cell membrane that surrounds the forespore and that SpoIVB is secreted from the forespore into the space between the two where it activates SpoIVFB. EriC is involved in inorganic ion transport and metabolism. CBS is a small domain originally identified in cystathionine beta-synthase an
Probab=24.41 E-value=1.6e+02 Score=20.38 Aligned_cols=40 Identities=15% Similarity=0.179 Sum_probs=32.2
Q ss_pred CCceeEEEEeCCCchHHHHHHhhhhcCCceEEEecCCCce
Q 028357 152 MGFTPHVITVAVGEDIAMKLLSFSQQGPRAICVLSANGAI 191 (210)
Q Consensus 152 ~~ftPHVItV~~GEDV~~kI~sFaqqg~raICILSA~GaV 191 (210)
..+...++.|...+++.+.+-.|.+.+...+.|+...|.+
T Consensus 60 ~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~V~~~~~~~ 99 (111)
T cd04612 60 DVMTRDPVTASPDETLRDALKRMAERDIGRLPVVDDSGRL 99 (111)
T ss_pred HhccCCCeEECCCCCHHHHHHHHHhCCCCeeeEEcCCCCE
Confidence 3456778999999999988888988888889898765544
No 33
>cd04583 CBS_pair_ABC_OpuCA_assoc2 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in association with the ABC transporter OpuCA. OpuCA is the ATP binding component of a bacterial solute transporter that serves a protective role to cells growing in a hyperosmolar environment but the function of the CBS domains in OpuCA remains unknown. In the related ABC transporter, OpuA, the tandem CBS domains have been shown to function as sensors for ionic strength, whereby they control the transport activity through an electronic switching mechanism. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. They are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyz
Probab=23.84 E-value=1.8e+02 Score=20.03 Aligned_cols=40 Identities=20% Similarity=0.262 Sum_probs=31.1
Q ss_pred CceeEEEEeCCCchHHHHHHhhhhcCCceEEEecCCCcee
Q 028357 153 GFTPHVITVAVGEDIAMKLLSFSQQGPRAICVLSANGAIS 192 (210)
Q Consensus 153 ~ftPHVItV~~GEDV~~kI~sFaqqg~raICILSA~GaVS 192 (210)
.++.+++.|...+++.+-+-.|.+.....++|+..+|.+-
T Consensus 59 ~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~vv~~~g~~~ 98 (109)
T cd04583 59 IMLEDVFTVQPDASLRDVLGLVLKRGPKYVPVVDEDGKLV 98 (109)
T ss_pred hhcCCceEECCCCcHHHHHHHHHHcCCceeeEECCCCeEE
Confidence 3567788899999887767677776778899999887543
No 34
>cd04611 CBS_pair_PAS_GGDEF_DUF1_assoc This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in association with a PAS domain, a GGDEF (DiGuanylate-Cyclase (DGC) domain, and a DUF1 domain downstream. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction. The GGDEF domain has been suggested to be homologous to the adenylyl cyclase catalytic domain and is thought to be involved in regulating cell surface adhesiveness in bacteria. 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 CB
Probab=22.59 E-value=2e+02 Score=19.86 Aligned_cols=39 Identities=15% Similarity=0.291 Sum_probs=29.5
Q ss_pred CceeEEEEeCCCchHHHHHHhhhhcCCceEEEecCCCce
Q 028357 153 GFTPHVITVAVGEDIAMKLLSFSQQGPRAICVLSANGAI 191 (210)
Q Consensus 153 ~ftPHVItV~~GEDV~~kI~sFaqqg~raICILSA~GaV 191 (210)
.+...++.+...+++.+.+-.|.+.+.+.++|+..+|.+
T Consensus 61 ~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~Vv~~~~~~ 99 (111)
T cd04611 61 VMSSPLLTVPADTSLYDARQLMREHGIRHLVVVDDDGEL 99 (111)
T ss_pred hcCCCceEECCCCCHHHHHHHHHHcCCeEEEEECCCCcE
Confidence 345678889999988766666666777789999887763
No 35
>cd04614 CBS_pair_1 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=22.13 E-value=2.1e+02 Score=20.16 Aligned_cols=34 Identities=12% Similarity=0.184 Sum_probs=29.9
Q ss_pred EEEeCCCchHHHHHHhhhhcCCceEEEecCCCce
Q 028357 158 VITVAVGEDIAMKLLSFSQQGPRAICVLSANGAI 191 (210)
Q Consensus 158 VItV~~GEDV~~kI~sFaqqg~raICILSA~GaV 191 (210)
++++.+.+.+.+.+-.|.+++-+.++|+...|.+
T Consensus 51 ~~~v~~~~~l~~a~~~m~~~~~~~lpVv~~~~~~ 84 (96)
T cd04614 51 VVTATKRTTVSECAQKMKRNRIEQIPIINGNDKL 84 (96)
T ss_pred cEEecCCCCHHHHHHHHHHhCCCeeeEECCCCcE
Confidence 8899999999988888999999999999886654
No 36
>cd04631 CBS_pair_18 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=21.58 E-value=2e+02 Score=20.48 Aligned_cols=39 Identities=18% Similarity=0.244 Sum_probs=30.2
Q ss_pred ceeEEEEeCCCchHHHHHHhhhhcCCceEEEecCCCcee
Q 028357 154 FTPHVITVAVGEDIAMKLLSFSQQGPRAICVLSANGAIS 192 (210)
Q Consensus 154 ftPHVItV~~GEDV~~kI~sFaqqg~raICILSA~GaVS 192 (210)
+++.++.|...+.+.+-+-.|.+.+...++|+-.+|.+.
T Consensus 76 ~~~~~~~v~~~~~l~~~~~~~~~~~~~~~~V~~~~~~~~ 114 (125)
T cd04631 76 MTRNVITITPDDSIKDAAELMLEKRVGGLPVVDDDGKLV 114 (125)
T ss_pred hcCCceEeCCCCcHHHHHHHHHHcCCceEEEEcCCCcEE
Confidence 456789999999997766667777777899998766543
No 37
>cd04630 CBS_pair_17 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=20.86 E-value=2e+02 Score=20.41 Aligned_cols=41 Identities=20% Similarity=0.281 Sum_probs=29.8
Q ss_pred eEEEEeCCCchHHHHHHhhhhcCCceEEEecCC-Cc-eeeEEe
Q 028357 156 PHVITVAVGEDIAMKLLSFSQQGPRAICVLSAN-GA-ISTATL 196 (210)
Q Consensus 156 PHVItV~~GEDV~~kI~sFaqqg~raICILSA~-Ga-VSnVTL 196 (210)
|+++.|.....+.+.+-.+..++...+.|+..+ |. +.-||+
T Consensus 1 ~~~~~v~~~~~~~~~~~~~~~~~~~~~~V~~~~~~~~~G~v~~ 43 (114)
T cd04630 1 PNVVTIDGLATVAEALQLMKEHGVSSLVVEKRRESDAYGIVTM 43 (114)
T ss_pred CCcEEECCCCcHHHHHHHHHHcCCCEEEEEECCCCcEEEEEeh
Confidence 467889999988888877766676778888765 43 555554
No 38
>cd04582 CBS_pair_ABC_OpuCA_assoc This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in association with the ABC transporter OpuCA. OpuCA is the ATP binding component of a bacterial solute transporter that serves a protective role to cells growing in a hyperosmolar environment but the function of the CBS domains in OpuCA remains unknown. In the related ABC transporter, OpuA, the tandem CBS domains have been shown to function as sensors for ionic strength, whereby they control the transport activity through an electronic switching mechanism. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. They are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzi
Probab=20.67 E-value=2.5e+02 Score=19.36 Aligned_cols=41 Identities=17% Similarity=0.220 Sum_probs=32.1
Q ss_pred CCceeEEEEeCCCchHHHHHHhhhhcCCceEEEecCCCcee
Q 028357 152 MGFTPHVITVAVGEDIAMKLLSFSQQGPRAICVLSANGAIS 192 (210)
Q Consensus 152 ~~ftPHVItV~~GEDV~~kI~sFaqqg~raICILSA~GaVS 192 (210)
..+++++..+...+.+.+.+-.|.++....++|+..+|.+-
T Consensus 55 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Vv~~~~~~~ 95 (106)
T cd04582 55 DHAEPFKVTVSVDDDLRIVLSRMFAHDMSWLPCVDEDGRYV 95 (106)
T ss_pred hhcccCCEEECCCCCHHHHHHHHHHCCCCeeeEECCCCcEE
Confidence 44677778899988888777778888878899998876543
Done!