Query 026821
Match_columns 232
No_of_seqs 165 out of 294
Neff 3.6
Searched_HMMs 46136
Date Fri Mar 29 13:11:47 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026821.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026821hhsearch_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 98.6 1.6E-08 3.5E-13 80.3 2.0 47 177-223 1-47 (120)
2 PF02178 AT_hook: AT hook moti 96.5 0.00087 1.9E-08 36.1 0.6 12 103-114 1-12 (13)
3 smart00384 AT_hook DNA binding 96.5 0.0013 2.8E-08 41.5 1.4 15 103-117 1-15 (26)
4 COG1661 Predicted DNA-binding 93.4 0.13 2.9E-06 43.4 4.6 45 179-223 11-55 (141)
5 PF14621 RFX5_DNA_bdg: RFX5 DN 88.2 0.16 3.6E-06 45.3 0.3 12 101-112 66-77 (219)
6 PF13546 DDE_5: DDE superfamil 77.6 1.3 2.7E-05 38.9 1.5 15 101-115 229-243 (273)
7 COG1710 Uncharacterized protei 70.5 1.9 4.1E-05 36.5 0.8 14 101-114 82-96 (139)
8 PF13737 DDE_Tnp_1_5: Transpos 59.7 3 6.5E-05 34.0 -0.0 21 100-121 21-41 (112)
9 cd04618 CBS_pair_5 The CBS dom 58.2 27 0.00058 25.6 4.9 36 181-216 52-88 (98)
10 COG1777 Predicted transcriptio 54.1 5.8 0.00013 36.1 0.9 23 102-124 63-86 (217)
11 KOG4565 E93 protein involved i 44.3 7.4 0.00016 34.8 -0.0 14 101-114 111-124 (206)
12 PF01582 TIR: TIR domain; Int 38.1 24 0.00053 27.8 2.1 28 184-211 38-65 (141)
13 PF00571 CBS: CBS domain CBS d 37.5 59 0.0013 21.1 3.6 40 177-216 5-44 (57)
14 cd04595 CBS_pair_DHH_polyA_Pol 36.5 72 0.0016 22.7 4.2 39 177-216 62-100 (110)
15 cd04603 CBS_pair_KefB_assoc Th 36.1 78 0.0017 23.0 4.4 39 176-214 61-99 (111)
16 cd04585 CBS_pair_ACT_assoc2 Th 34.4 78 0.0017 22.6 4.1 39 177-215 73-111 (122)
17 cd02955 SSP411 TRX domain, SSP 31.8 1.4E+02 0.003 24.1 5.5 50 175-224 49-103 (124)
18 cd04590 CBS_pair_CorC_HlyC_ass 31.0 92 0.002 22.1 4.0 36 180-215 65-100 (111)
19 cd04610 CBS_pair_ParBc_assoc T 30.0 1.2E+02 0.0026 21.3 4.4 39 177-215 58-96 (107)
20 cd04596 CBS_pair_DRTGG_assoc T 29.8 1.1E+02 0.0024 21.9 4.2 38 177-214 59-96 (108)
21 cd04606 CBS_pair_Mg_transporte 28.8 1.1E+02 0.0025 21.8 4.2 40 176-215 58-97 (109)
22 cd04600 CBS_pair_HPP_assoc Thi 28.1 1.2E+02 0.0025 22.0 4.2 42 176-217 74-115 (124)
23 cd04607 CBS_pair_NTP_transfera 28.1 1.3E+02 0.0027 21.6 4.3 41 176-216 63-103 (113)
24 cd04588 CBS_pair_CAP-ED_DUF294 28.0 1.4E+02 0.003 21.2 4.5 39 176-214 60-98 (110)
25 PF15333 TAF1D: TATA box-bindi 27.8 26 0.00057 31.9 0.8 12 105-116 64-75 (217)
26 cd04587 CBS_pair_CAP-ED_DUF294 27.8 1E+02 0.0022 21.9 3.7 39 177-215 64-102 (113)
27 cd04615 CBS_pair_2 The CBS dom 27.4 1.4E+02 0.0031 21.2 4.5 39 176-214 63-101 (113)
28 cd04624 CBS_pair_11 The CBS do 27.2 1.4E+02 0.003 21.2 4.3 40 176-215 62-101 (112)
29 cd04583 CBS_pair_ABC_OpuCA_ass 26.6 1.5E+02 0.0033 20.8 4.4 40 176-215 59-98 (109)
30 smart00116 CBS Domain in cysta 26.5 1.4E+02 0.0029 17.1 4.0 33 182-214 3-35 (49)
31 PF14869 DUF4488: Domain of un 26.2 64 0.0014 27.4 2.7 27 203-231 27-53 (133)
32 cd04612 CBS_pair_SpoIVFB_EriC_ 26.0 1.4E+02 0.0031 21.0 4.2 39 176-214 61-99 (111)
33 cd04611 CBS_pair_PAS_GGDEF_DUF 24.4 1.7E+02 0.0038 20.5 4.4 38 177-214 62-99 (111)
34 cd04614 CBS_pair_1 The CBS dom 24.3 1.8E+02 0.0039 20.9 4.6 34 181-214 51-84 (96)
35 PF10623 PilI: Plasmid conjuga 24.3 1.1E+02 0.0023 24.3 3.4 39 178-216 19-57 (83)
36 PF14601 TFX_C: DNA_binding pr 23.8 47 0.001 25.9 1.4 15 178-192 13-27 (84)
37 cd04597 CBS_pair_DRTGG_assoc2 23.5 1.4E+02 0.0031 22.3 4.0 41 174-214 61-101 (113)
38 cd04631 CBS_pair_18 The CBS do 23.2 1.7E+02 0.0038 21.1 4.3 39 177-215 76-114 (125)
39 cd04582 CBS_pair_ABC_OpuCA_ass 22.3 2.2E+02 0.0047 19.9 4.6 40 175-214 55-94 (106)
40 smart00412 Cu_FIST Copper-Fist 21.7 41 0.00088 23.2 0.6 8 102-109 31-38 (39)
41 cd04619 CBS_pair_6 The CBS dom 21.2 2E+02 0.0043 20.9 4.3 40 177-216 65-104 (114)
42 PRK13337 putative lipid kinase 20.7 1.3E+02 0.0027 27.1 3.7 44 175-218 31-74 (304)
43 cd04627 CBS_pair_14 The CBS do 20.6 2.3E+02 0.0051 20.7 4.6 43 177-219 74-117 (123)
44 cd04802 CBS_pair_3 The CBS dom 20.3 2.3E+02 0.005 20.1 4.4 35 177-211 64-98 (112)
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=98.61 E-value=1.6e-08 Score=80.34 Aligned_cols=47 Identities=28% Similarity=0.340 Sum_probs=44.2
Q ss_pred ceeEEEEeCCCCcHHHHHHHhhhcCCceEEEecCCCeeeeeEecCCC
Q 026821 177 FTPHVITVKAGEDISSKIFAFSQQGPRTVCILSASGAICNVTLRQPT 223 (232)
Q Consensus 177 ftPHVItV~~GEDV~~kI~sFaqqg~raICILSAnGaVSnVTLRQP~ 223 (232)
|++|+|.+.+||||.++|..||++.....|+||+.|++++|+|+.+.
T Consensus 1 ~r~~~~rl~~Gedl~~~l~~~~~~~~i~~~~is~iGsl~~~~l~~~~ 47 (120)
T PF03479_consen 1 GRVFVIRLDPGEDLLESLEAFAREHGIRSGVISGIGSLSNVTLGYYD 47 (120)
T ss_dssp EEEEEEEEETTSBHHHHHHHHHHHHT-SSEEEEEEEEEEEEEEEEEE
T ss_pred CcEEEEEECCCCHHHHHHHHHHHHCCCcEEEEEEEeEEeEEEEEEec
Confidence 68999999999999999999999999999999999999999999974
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=96.53 E-value=0.00087 Score=36.14 Aligned_cols=12 Identities=67% Similarity=1.088 Sum_probs=4.6
Q ss_pred cccCCCCCCCCC
Q 026821 103 KKKRGRPRKYTP 114 (232)
Q Consensus 103 KKKRGRPRKY~p 114 (232)
+||||||+|+..
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 689999999854
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=96.51 E-value=0.0013 Score=41.49 Aligned_cols=15 Identities=60% Similarity=0.922 Sum_probs=12.7
Q ss_pred cccCCCCCCCCCCCc
Q 026821 103 KKKRGRPRKYTPDGN 117 (232)
Q Consensus 103 KKKRGRPRKY~pDg~ 117 (232)
|||||||||+..+..
T Consensus 1 kRkRGRPrK~~~~~~ 15 (26)
T smart00384 1 KRKRGRPRKAPKDXX 15 (26)
T ss_pred CCCCCCCCCCCCccc
Confidence 699999999977654
No 4
>COG1661 Predicted DNA-binding protein with PD1-like DNA-binding motif [General function prediction only]
Probab=93.35 E-value=0.13 Score=43.45 Aligned_cols=45 Identities=27% Similarity=0.386 Sum_probs=40.9
Q ss_pred eEEEEeCCCCcHHHHHHHhhhcCCceEEEecCCCeeeeeEecCCC
Q 026821 179 PHVITVKAGEDISSKIFAFSQQGPRTVCILSASGAICNVTLRQPT 223 (232)
Q Consensus 179 PHVItV~~GEDV~~kI~sFaqqg~raICILSAnGaVSnVTLRQP~ 223 (232)
-.++-+..|||+.+.|.+||++..-...|.++-|++++++|+--+
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 457788999999999999999999888999999999999998644
No 5
>PF14621 RFX5_DNA_bdg: RFX5 DNA-binding domain
Probab=88.22 E-value=0.16 Score=45.27 Aligned_cols=12 Identities=75% Similarity=1.115 Sum_probs=10.6
Q ss_pred cCcccCCCCCCC
Q 026821 101 PAKKKRGRPRKY 112 (232)
Q Consensus 101 ~~KKKRGRPRKY 112 (232)
.+|||||||||-
T Consensus 66 dAKRKRGRPRKK 77 (219)
T PF14621_consen 66 DAKRKRGRPRKK 77 (219)
T ss_pred hhhhhcCCCccC
Confidence 579999999976
No 6
>PF13546 DDE_5: DDE superfamily endonuclease
Probab=77.62 E-value=1.3 Score=38.89 Aligned_cols=15 Identities=60% Similarity=1.041 Sum_probs=11.5
Q ss_pred cCcccCCCCCCCCCC
Q 026821 101 PAKKKRGRPRKYTPD 115 (232)
Q Consensus 101 ~~KKKRGRPRKY~pD 115 (232)
...+||||||||+.-
T Consensus 229 ~~~~~rGRPr~~g~~ 243 (273)
T PF13546_consen 229 PPPPKRGRPRKYGRR 243 (273)
T ss_pred ccCCCCCCCCCCCCc
Confidence 445669999999854
No 7
>COG1710 Uncharacterized protein conserved in archaea [Function unknown]
Probab=70.45 E-value=1.9 Score=36.48 Aligned_cols=14 Identities=71% Similarity=1.222 Sum_probs=11.5
Q ss_pred cCc-ccCCCCCCCCC
Q 026821 101 PAK-KKRGRPRKYTP 114 (232)
Q Consensus 101 ~~K-KKRGRPRKY~p 114 (232)
+.| |-|||||||+-
T Consensus 82 Pvk~KgrGrprkyd~ 96 (139)
T COG1710 82 PVKLKGRGRPRKYDR 96 (139)
T ss_pred eeeecCCCCCcccch
Confidence 567 88999999964
No 8
>PF13737 DDE_Tnp_1_5: Transposase DDE domain
Probab=59.69 E-value=3 Score=33.95 Aligned_cols=21 Identities=43% Similarity=0.813 Sum_probs=15.8
Q ss_pred CcCcccCCCCCCCCCCCccccc
Q 026821 100 DPAKKKRGRPRKYTPDGNIALR 121 (232)
Q Consensus 100 ~~~KKKRGRPRKY~pDg~i~l~ 121 (232)
+....|||||++| +|-.|...
T Consensus 21 ~~~~~kRGr~~~y-SD~aI~~~ 41 (112)
T PF13737_consen 21 APPRGKRGRPPRY-SDAAIQTC 41 (112)
T ss_pred cCCCCCCCCCccc-chHHHHHH
Confidence 3457899999999 68765543
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=58.16 E-value=27 Score=25.62 Aligned_cols=36 Identities=6% Similarity=0.157 Sum_probs=32.2
Q ss_pred EEEeCCCCcHHHHHHHhhhcCCceEEEecCC-Ceeee
Q 026821 181 VITVKAGEDISSKIFAFSQQGPRTVCILSAS-GAICN 216 (232)
Q Consensus 181 VItV~~GEDV~~kI~sFaqqg~raICILSAn-GaVSn 216 (232)
+++|.+.+++.+.+-.|.+++-+.++|+..+ |.+..
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 10
>COG1777 Predicted transcriptional regulators [Transcription]
Probab=54.06 E-value=5.8 Score=36.05 Aligned_cols=23 Identities=43% Similarity=0.671 Sum_probs=16.9
Q ss_pred CcccCCCCCCCC-CCCcccccccc
Q 026821 102 AKKKRGRPRKYT-PDGNIALRLAT 124 (232)
Q Consensus 102 ~KKKRGRPRKY~-pDg~i~l~l~p 124 (232)
.|.+|||||||. .-+++++-..-
T Consensus 63 e~~~Rg~~rKYY~Is~~~rleV~l 86 (217)
T COG1777 63 EKIPRGRPRKYYMISRNLRLEVTL 86 (217)
T ss_pred cccccCCCcceeeccCCeEEEEEe
Confidence 478889999995 67777665443
No 11
>KOG4565 consensus E93 protein involved in programmed cell death, putative transcription regulator [Transcription]
Probab=44.26 E-value=7.4 Score=34.81 Aligned_cols=14 Identities=50% Similarity=0.845 Sum_probs=11.8
Q ss_pred cCcccCCCCCCCCC
Q 026821 101 PAKKKRGRPRKYTP 114 (232)
Q Consensus 101 ~~KKKRGRPRKY~p 114 (232)
.-+|||||=|+|+-
T Consensus 111 qpRkKRGrYRqYd~ 124 (206)
T KOG4565|consen 111 QPRKKRGRYRQYDK 124 (206)
T ss_pred CccccccchhhhhH
Confidence 35899999999964
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=38.11 E-value=24 Score=27.83 Aligned_cols=28 Identities=29% Similarity=0.383 Sum_probs=25.3
Q ss_pred eCCCCcHHHHHHHhhhcCCceEEEecCC
Q 026821 184 VKAGEDISSKIFAFSQQGPRTVCILSAS 211 (232)
Q Consensus 184 V~~GEDV~~kI~sFaqqg~raICILSAn 211 (232)
...|+.+.+.|....++..+.|+|||.+
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 5689999999999999999999999954
No 13
>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=37.53 E-value=59 Score=21.11 Aligned_cols=40 Identities=18% Similarity=0.372 Sum_probs=33.7
Q ss_pred ceeEEEEeCCCCcHHHHHHHhhhcCCceEEEecCCCeeee
Q 026821 177 FTPHVITVKAGEDISSKIFAFSQQGPRTVCILSASGAICN 216 (232)
Q Consensus 177 ftPHVItV~~GEDV~~kI~sFaqqg~raICILSAnGaVSn 216 (232)
+++-++.|...+.+.+.+-.|.+.+-+.+.|+..+|.+--
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 4566788999999999999999999999999977776643
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=36.54 E-value=72 Score=22.73 Aligned_cols=39 Identities=15% Similarity=0.227 Sum_probs=32.3
Q ss_pred ceeEEEEeCCCCcHHHHHHHhhhcCCceEEEecCCCeeee
Q 026821 177 FTPHVITVKAGEDISSKIFAFSQQGPRTVCILSASGAICN 216 (232)
Q Consensus 177 ftPHVItV~~GEDV~~kI~sFaqqg~raICILSAnGaVSn 216 (232)
+..+++.|...+.+.+.+..|.+.+-..++|+. +|.+.-
T Consensus 62 ~~~~~~~v~~~~~l~~~~~~~~~~~~~~~~V~~-~~~~~G 100 (110)
T cd04595 62 MSTDVVTVPPDTPLSEVQELMVEHDIGRVPVVE-DGRLVG 100 (110)
T ss_pred hcCCCEEECCCCcHHHHHHHHHHcCCCeeEEEe-CCEEEE
Confidence 456889999999999988889888888899988 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=36.08 E-value=78 Score=22.98 Aligned_cols=39 Identities=15% Similarity=0.304 Sum_probs=33.1
Q ss_pred CceeEEEEeCCCCcHHHHHHHhhhcCCceEEEecCCCee
Q 026821 176 GFTPHVITVKAGEDISSKIFAFSQQGPRTVCILSASGAI 214 (232)
Q Consensus 176 ~ftPHVItV~~GEDV~~kI~sFaqqg~raICILSAnGaV 214 (232)
.+...++.|...+++.+.+..|.+++...++|+..+|.+
T Consensus 61 ~~~~~~~~v~~~~~l~~al~~m~~~~~~~lpVvd~~~~~ 99 (111)
T cd04603 61 VYIVPVPIVYCDSKVTDLLRIFRETEPPVVAVVDKEGKL 99 (111)
T ss_pred eeecCCcEECCCCcHHHHHHHHHHcCCCeEEEEcCCCeE
Confidence 356678899999999999999999998999999887653
No 16
>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=34.44 E-value=78 Score=22.58 Aligned_cols=39 Identities=13% Similarity=0.176 Sum_probs=31.9
Q ss_pred ceeEEEEeCCCCcHHHHHHHhhhcCCceEEEecCCCeee
Q 026821 177 FTPHVITVKAGEDISSKIFAFSQQGPRTVCILSASGAIC 215 (232)
Q Consensus 177 ftPHVItV~~GEDV~~kI~sFaqqg~raICILSAnGaVS 215 (232)
++.+++.|...+.+.+-+..|.+.+...+.|+..+|.+-
T Consensus 73 ~~~~~~~v~~~~~l~~~~~~~~~~~~~~~~Vv~~~~~~~ 111 (122)
T cd04585 73 MTRDPITVSPDASVEEAAELMLERKISGLPVVDDQGRLV 111 (122)
T ss_pred ccCCCeEeCCCCcHHHHHHHHHHcCCCceeEECCCCcEE
Confidence 455788899999998888889989888899998877543
No 17
>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=31.75 E-value=1.4e+02 Score=24.13 Aligned_cols=50 Identities=14% Similarity=0.039 Sum_probs=40.4
Q ss_pred CCceeEEEEeCCCCcHHHHHHHh-----hhcCCceEEEecCCCeeeeeEecCCCC
Q 026821 175 VGFTPHVITVKAGEDISSKIFAF-----SQQGPRTVCILSASGAICNVTLRQPTM 224 (232)
Q Consensus 175 ~~ftPHVItV~~GEDV~~kI~sF-----aqqg~raICILSAnGaVSnVTLRQP~s 224 (232)
..|.+..+.+....|+..+++.+ -..|..++.+|..+|.+-+.+-..|..
T Consensus 49 ~~fv~VkvD~~~~~~~~~~~~~~~~~~~~~~G~Pt~vfl~~~G~~~~~~~~~~~~ 103 (124)
T cd02955 49 ENFVPIKVDREERPDVDKIYMNAAQAMTGQGGWPLNVFLTPDLKPFFGGTYFPPE 103 (124)
T ss_pred CCEEEEEEeCCcCcHHHHHHHHHHHHhcCCCCCCEEEEECCCCCEEeeeeecCCC
Confidence 46888888888888998888774 456788999999999999888776554
No 18
>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=30.97 E-value=92 Score=22.13 Aligned_cols=36 Identities=6% Similarity=0.134 Sum_probs=30.0
Q ss_pred EEEEeCCCCcHHHHHHHhhhcCCceEEEecCCCeee
Q 026821 180 HVITVKAGEDISSKIFAFSQQGPRTVCILSASGAIC 215 (232)
Q Consensus 180 HVItV~~GEDV~~kI~sFaqqg~raICILSAnGaVS 215 (232)
++..|...+++.+.+-.|.+.+...++|+..+|.+-
T Consensus 65 ~~~~v~~~~~l~~~~~~~~~~~~~~~~Vv~~~~~~~ 100 (111)
T cd04590 65 PPLFVPESTPLDDLLEEMRKERSHMAIVVDEYGGTA 100 (111)
T ss_pred CCeecCCCCcHHHHHHHHHhcCCcEEEEEECCCCEE
Confidence 578889999998888888888888999999887643
No 19
>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=30.01 E-value=1.2e+02 Score=21.30 Aligned_cols=39 Identities=8% Similarity=0.167 Sum_probs=30.9
Q ss_pred ceeEEEEeCCCCcHHHHHHHhhhcCCceEEEecCCCeee
Q 026821 177 FTPHVITVKAGEDISSKIFAFSQQGPRTVCILSASGAIC 215 (232)
Q Consensus 177 ftPHVItV~~GEDV~~kI~sFaqqg~raICILSAnGaVS 215 (232)
+...++.|...+.+.+.+-.|.+.....++|+..+|.+-
T Consensus 58 ~~~~~~~v~~~~~l~~~~~~~~~~~~~~~~Vv~~~g~~~ 96 (107)
T cd04610 58 MSKDLVVAVPEMDIMDAARVMFRTGISKLPVVDENNNLV 96 (107)
T ss_pred CCCCCeEECCCCCHHHHHHHHHHhCCCeEeEECCCCeEE
Confidence 456688899999988877777777777899999888643
No 20
>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=29.85 E-value=1.1e+02 Score=21.86 Aligned_cols=38 Identities=16% Similarity=0.220 Sum_probs=31.7
Q ss_pred ceeEEEEeCCCCcHHHHHHHhhhcCCceEEEecCCCee
Q 026821 177 FTPHVITVKAGEDISSKIFAFSQQGPRTVCILSASGAI 214 (232)
Q Consensus 177 ftPHVItV~~GEDV~~kI~sFaqqg~raICILSAnGaV 214 (232)
+..+++.|...+.+.+.+-.|...+.+.++|+..+|-+
T Consensus 59 ~~~~~~~v~~~~~l~~~~~~~~~~~~~~~~Vv~~~~~~ 96 (108)
T cd04596 59 MTKNPITVNPKTSVASVAHMMIWEGIEMLPVVDDNKKL 96 (108)
T ss_pred hcCCCeEECCCCCHHHHHHHHHHcCCCeeeEEcCCCCE
Confidence 45678899999999888888888888999999877654
No 21
>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=28.84 E-value=1.1e+02 Score=21.80 Aligned_cols=40 Identities=18% Similarity=0.233 Sum_probs=32.2
Q ss_pred CceeEEEEeCCCCcHHHHHHHhhhcCCceEEEecCCCeee
Q 026821 176 GFTPHVITVKAGEDISSKIFAFSQQGPRTVCILSASGAIC 215 (232)
Q Consensus 176 ~ftPHVItV~~GEDV~~kI~sFaqqg~raICILSAnGaVS 215 (232)
.++++++.|..++.+.+.+-.|...+...+.|+..+|.+.
T Consensus 58 ~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~Vv~~~~~~~ 97 (109)
T cd04606 58 IMDTDVISVSADDDQEEVARLFEKYDLLALPVVDEEGRLV 97 (109)
T ss_pred HhCCCCeEEcCCCCHHHHHHHHHHcCCceeeeECCCCcEE
Confidence 4577899999999998888778878777889998777643
No 22
>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=28.12 E-value=1.2e+02 Score=22.04 Aligned_cols=42 Identities=17% Similarity=0.325 Sum_probs=34.0
Q ss_pred CceeEEEEeCCCCcHHHHHHHhhhcCCceEEEecCCCeeeee
Q 026821 176 GFTPHVITVKAGEDISSKIFAFSQQGPRTVCILSASGAICNV 217 (232)
Q Consensus 176 ~ftPHVItV~~GEDV~~kI~sFaqqg~raICILSAnGaVSnV 217 (232)
.++.+++.|...+.+.+.+--|.+.+...++|+...|.+-.+
T Consensus 74 ~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~Vv~~~g~~~Gv 115 (124)
T cd04600 74 IMSPPVVTVRPDTPIAELVPLLADGGHHHVPVVDEDRRLVGI 115 (124)
T ss_pred hccCCCeeeCCCCcHHHHHHHHHhcCCCceeEEcCCCCEEEE
Confidence 456789999999999988888888888889999877765443
No 23
>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=28.09 E-value=1.3e+02 Score=21.63 Aligned_cols=41 Identities=20% Similarity=0.273 Sum_probs=33.8
Q ss_pred CceeEEEEeCCCCcHHHHHHHhhhcCCceEEEecCCCeeee
Q 026821 176 GFTPHVITVKAGEDISSKIFAFSQQGPRTVCILSASGAICN 216 (232)
Q Consensus 176 ~ftPHVItV~~GEDV~~kI~sFaqqg~raICILSAnGaVSn 216 (232)
.+...++.|...+++.+.+-.|...+.+.++|+..+|.+-.
T Consensus 63 ~~~~~~~~v~~~~~l~~~~~~~~~~~~~~~~Vv~~~~~~~G 103 (113)
T cd04607 63 VMNRNPITAKVGSSREEILALMRERSIRHLPILDEEGRVVG 103 (113)
T ss_pred hhcCCCEEEcCCCCHHHHHHHHHHCCCCEEEEECCCCCEEE
Confidence 35677889999999999888899988888999988776543
No 24
>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=28.03 E-value=1.4e+02 Score=21.17 Aligned_cols=39 Identities=18% Similarity=0.243 Sum_probs=32.1
Q ss_pred CceeEEEEeCCCCcHHHHHHHhhhcCCceEEEecCCCee
Q 026821 176 GFTPHVITVKAGEDISSKIFAFSQQGPRTVCILSASGAI 214 (232)
Q Consensus 176 ~ftPHVItV~~GEDV~~kI~sFaqqg~raICILSAnGaV 214 (232)
.+..+++.|...+.+.+-+-.|.+.+-..++|+...|.+
T Consensus 60 ~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~V~~~~~~~ 98 (110)
T cd04588 60 VMTKDVITIDEDEQLYDAIRLMNKHNVGRLIVTDDEGRP 98 (110)
T ss_pred HhcCCceEECCCCCHHHHHHHHHhcCCCEEEEECCCCCE
Confidence 345788999999999887777888888899999987754
No 25
>PF15333 TAF1D: TATA box-binding protein-associated factor 1D
Probab=27.82 E-value=26 Score=31.89 Aligned_cols=12 Identities=50% Similarity=1.027 Sum_probs=8.8
Q ss_pred cCCCCCCCCCCC
Q 026821 105 KRGRPRKYTPDG 116 (232)
Q Consensus 105 KRGRPRKY~pDg 116 (232)
|+-+-|||-+-|
T Consensus 64 KkrkkrKYk~tg 75 (217)
T PF15333_consen 64 KKRKKRKYKPTG 75 (217)
T ss_pred HHhhhhccCccC
Confidence 556679998766
No 26
>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=27.80 E-value=1e+02 Score=21.91 Aligned_cols=39 Identities=15% Similarity=0.290 Sum_probs=32.0
Q ss_pred ceeEEEEeCCCCcHHHHHHHhhhcCCceEEEecCCCeee
Q 026821 177 FTPHVITVKAGEDISSKIFAFSQQGPRTVCILSASGAIC 215 (232)
Q Consensus 177 ftPHVItV~~GEDV~~kI~sFaqqg~raICILSAnGaVS 215 (232)
+..+++.|...+.+.+.+-.|.+.+...+.|+..+|.+.
T Consensus 64 ~~~~~~~v~~~~~l~~~~~~~~~~~~~~l~Vv~~~~~~~ 102 (113)
T cd04587 64 MTPNPVCATSDTPVLEALHLMVQGKFRHLPVVDKSGQVV 102 (113)
T ss_pred cCCCCeEEcCCCCHHHHHHHHHHcCCCcccEECCCCCEE
Confidence 567888999999998888888888877888998877643
No 27
>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=27.40 E-value=1.4e+02 Score=21.16 Aligned_cols=39 Identities=21% Similarity=0.347 Sum_probs=30.6
Q ss_pred CceeEEEEeCCCCcHHHHHHHhhhcCCceEEEecCCCee
Q 026821 176 GFTPHVITVKAGEDISSKIFAFSQQGPRTVCILSASGAI 214 (232)
Q Consensus 176 ~ftPHVItV~~GEDV~~kI~sFaqqg~raICILSAnGaV 214 (232)
.++.++++|...+.+.+-+-.|.+.+...++|+..+|-+
T Consensus 63 ~~~~~~~~v~~~~~l~~~~~~~~~~~~~~~~Vvd~~g~~ 101 (113)
T cd04615 63 VMNSPVITIDANDSIAKARWLMSNNNISRLPVLDDKGKV 101 (113)
T ss_pred hccCCceEECCCCcHHHHHHHHHHcCCCeeeEECCCCeE
Confidence 356789999999888877777877777789999877653
No 28
>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=27.22 E-value=1.4e+02 Score=21.24 Aligned_cols=40 Identities=15% Similarity=0.248 Sum_probs=30.5
Q ss_pred CceeEEEEeCCCCcHHHHHHHhhhcCCceEEEecCCCeee
Q 026821 176 GFTPHVITVKAGEDISSKIFAFSQQGPRTVCILSASGAIC 215 (232)
Q Consensus 176 ~ftPHVItV~~GEDV~~kI~sFaqqg~raICILSAnGaVS 215 (232)
.+..+++.|...+++...+-.|.+++...+.|+..+|.+.
T Consensus 62 ~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~Vv~~~g~~~ 101 (112)
T cd04624 62 IMTRDLVTVDPDEPVAEAAKLMRKNNIRHHLVVDKGGELV 101 (112)
T ss_pred hccCCCEEECCCCcHHHHHHHHHHcCccEEEEEcCCCcEE
Confidence 3456788899999887766667777777889999877643
No 29
>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=26.55 E-value=1.5e+02 Score=20.76 Aligned_cols=40 Identities=18% Similarity=0.313 Sum_probs=31.3
Q ss_pred CceeEEEEeCCCCcHHHHHHHhhhcCCceEEEecCCCeee
Q 026821 176 GFTPHVITVKAGEDISSKIFAFSQQGPRTVCILSASGAIC 215 (232)
Q Consensus 176 ~ftPHVItV~~GEDV~~kI~sFaqqg~raICILSAnGaVS 215 (232)
.+..+++.|...+++.+.+-.|...+...++|+..+|.+-
T Consensus 59 ~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~vv~~~g~~~ 98 (109)
T cd04583 59 IMLEDVFTVQPDASLRDVLGLVLKRGPKYVPVVDEDGKLV 98 (109)
T ss_pred hhcCCceEECCCCcHHHHHHHHHHcCCceeeEECCCCeEE
Confidence 3567888899999987777777776778899999888543
No 30
>smart00116 CBS Domain in cystathionine beta-synthase and other proteins. Domain present in all 3 forms of cellular life. Present in two copies in inosine monophosphate dehydrogenase, of which one is disordered in the crystal structure [3]. A number of disease states are associated with CBS-containing proteins including homocystinuria, Becker's and Thomsen disease.
Probab=26.49 E-value=1.4e+02 Score=17.14 Aligned_cols=33 Identities=15% Similarity=0.367 Sum_probs=22.9
Q ss_pred EEeCCCCcHHHHHHHhhhcCCceEEEecCCCee
Q 026821 182 ITVKAGEDISSKIFAFSQQGPRTVCILSASGAI 214 (232)
Q Consensus 182 ItV~~GEDV~~kI~sFaqqg~raICILSAnGaV 214 (232)
+.+..++++.+.+-.|...+-..++|+..+|-+
T Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~ 35 (49)
T smart00116 3 VTVSPDTTLEEALELLREHGIRRLPVVDEEGRL 35 (49)
T ss_pred eEecCCCcHHHHHHHHHHhCCCcccEECCCCeE
Confidence 556777777666666666666778888876543
No 31
>PF14869 DUF4488: Domain of unknown function (DUF4488)
Probab=26.16 E-value=64 Score=27.44 Aligned_cols=27 Identities=33% Similarity=0.469 Sum_probs=20.4
Q ss_pred ceEEEecCCCeeeeeEecCCCCCCCceee
Q 026821 203 RTVCILSASGAICNVTLRQPTMSGGTVTY 231 (232)
Q Consensus 203 raICILSAnGaVSnVTLRQP~ssGgtvTY 231 (232)
..+=|||.+|++.|+++.. . ++.++|+
T Consensus 27 ~~lKilS~Dgtf~Ni~~~~-~-~~aiIt~ 53 (133)
T PF14869_consen 27 NVLKILSDDGTFVNITMIP-K-SGAIITG 53 (133)
T ss_pred ccEEEEcCCCcEEEEEEeC-C-CCcEEEE
Confidence 3477999999999999943 2 3467765
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=26.00 E-value=1.4e+02 Score=20.97 Aligned_cols=39 Identities=13% Similarity=0.232 Sum_probs=31.8
Q ss_pred CceeEEEEeCCCCcHHHHHHHhhhcCCceEEEecCCCee
Q 026821 176 GFTPHVITVKAGEDISSKIFAFSQQGPRTVCILSASGAI 214 (232)
Q Consensus 176 ~ftPHVItV~~GEDV~~kI~sFaqqg~raICILSAnGaV 214 (232)
.+...++.|...+++.+.+-.|.+.+...+.|+...|.+
T Consensus 61 ~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~V~~~~~~~ 99 (111)
T cd04612 61 VMTRDPVTASPDETLRDALKRMAERDIGRLPVVDDSGRL 99 (111)
T ss_pred hccCCCeEECCCCCHHHHHHHHHhCCCCeeeEEcCCCCE
Confidence 356778999999999998888988888888888765544
No 33
>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=24.37 E-value=1.7e+02 Score=20.50 Aligned_cols=38 Identities=16% Similarity=0.348 Sum_probs=29.2
Q ss_pred ceeEEEEeCCCCcHHHHHHHhhhcCCceEEEecCCCee
Q 026821 177 FTPHVITVKAGEDISSKIFAFSQQGPRTVCILSASGAI 214 (232)
Q Consensus 177 ftPHVItV~~GEDV~~kI~sFaqqg~raICILSAnGaV 214 (232)
+...++.+...+++.+.+-.|...+.+.++|+..+|.+
T Consensus 62 ~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~Vv~~~~~~ 99 (111)
T cd04611 62 MSSPLLTVPADTSLYDARQLMREHGIRHLVVVDDDGEL 99 (111)
T ss_pred cCCCceEECCCCCHHHHHHHHHHcCCeEEEEECCCCcE
Confidence 45678889999998776666766777789999887763
No 34
>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=24.32 E-value=1.8e+02 Score=20.87 Aligned_cols=34 Identities=12% Similarity=0.187 Sum_probs=30.0
Q ss_pred EEEeCCCCcHHHHHHHhhhcCCceEEEecCCCee
Q 026821 181 VITVKAGEDISSKIFAFSQQGPRTVCILSASGAI 214 (232)
Q Consensus 181 VItV~~GEDV~~kI~sFaqqg~raICILSAnGaV 214 (232)
+++|...+.+.+.+-.|.+++-+.++|+...|.+
T Consensus 51 ~~~v~~~~~l~~a~~~m~~~~~~~lpVv~~~~~~ 84 (96)
T cd04614 51 VVTATKRTTVSECAQKMKRNRIEQIPIINGNDKL 84 (96)
T ss_pred cEEecCCCCHHHHHHHHHHhCCCeeeEECCCCcE
Confidence 8899999999988888999999999999886554
No 35
>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=24.27 E-value=1.1e+02 Score=24.32 Aligned_cols=39 Identities=15% Similarity=0.235 Sum_probs=32.6
Q ss_pred eeEEEEeCCCCcHHHHHHHhhhcCCceEEEecCCCeeee
Q 026821 178 TPHVITVKAGEDISSKIFAFSQQGPRTVCILSASGAICN 216 (232)
Q Consensus 178 tPHVItV~~GEDV~~kI~sFaqqg~raICILSAnGaVSn 216 (232)
.=-+|..++-+|+..-|+.|+--..+-||||--|--|-.
T Consensus 19 ~~kL~~~~~~~D~~~i~r~f~TpdN~lV~V~~~nr~l~r 57 (83)
T PF10623_consen 19 ERKLFDTKPDNDPDKIARRFCTPDNCLVCVLQDNRFLFR 57 (83)
T ss_pred ceeEeecCCCCCHHHHHhhccCcCCeEEEEEeCCceEEE
Confidence 345788899999999999999999999999987765543
No 36
>PF14601 TFX_C: DNA_binding protein, TFX, C-term; PDB: 1NR3_A.
Probab=23.80 E-value=47 Score=25.86 Aligned_cols=15 Identities=40% Similarity=0.607 Sum_probs=9.6
Q ss_pred eeEEEEeCCCCcHHH
Q 026821 178 TPHVITVKAGEDISS 192 (232)
Q Consensus 178 tPHVItV~~GEDV~~ 192 (232)
.|+.|+|.+|+|+.+
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 499999999998764
No 37
>cd04597 CBS_pair_DRTGG_assoc2 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=23.53 E-value=1.4e+02 Score=22.29 Aligned_cols=41 Identities=10% Similarity=0.184 Sum_probs=32.7
Q ss_pred CCCceeEEEEeCCCCcHHHHHHHhhhcCCceEEEecCCCee
Q 026821 174 GVGFTPHVITVKAGEDISSKIFAFSQQGPRTVCILSASGAI 214 (232)
Q Consensus 174 g~~ftPHVItV~~GEDV~~kI~sFaqqg~raICILSAnGaV 214 (232)
..-++..++.|..++.+.+.+-.|.+.+.+.+.|+..+|.+
T Consensus 61 ~dim~~~~~~v~~~~~l~~a~~~~~~~~~~~lpVvd~~~~l 101 (113)
T cd04597 61 RDVINRKPVTARPNDPLREALNLMHEHNIRTLPVVDDDGTP 101 (113)
T ss_pred HHhcCCCCCEECCcCcHHHHHHHHHHcCCCEEEEECCCCeE
Confidence 34455678889999999887777877888899999988763
No 38
>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=23.21 E-value=1.7e+02 Score=21.15 Aligned_cols=39 Identities=15% Similarity=0.262 Sum_probs=30.2
Q ss_pred ceeEEEEeCCCCcHHHHHHHhhhcCCceEEEecCCCeee
Q 026821 177 FTPHVITVKAGEDISSKIFAFSQQGPRTVCILSASGAIC 215 (232)
Q Consensus 177 ftPHVItV~~GEDV~~kI~sFaqqg~raICILSAnGaVS 215 (232)
+..+++.|..++.+.+-+-.|.+.+...++|+..+|.+.
T Consensus 76 ~~~~~~~v~~~~~l~~~~~~~~~~~~~~~~V~~~~~~~~ 114 (125)
T cd04631 76 MTRNVITITPDDSIKDAAELMLEKRVGGLPVVDDDGKLV 114 (125)
T ss_pred hcCCceEeCCCCcHHHHHHHHHHcCCceEEEEcCCCcEE
Confidence 456789999999998766667777777899998766543
No 39
>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=22.27 E-value=2.2e+02 Score=19.95 Aligned_cols=40 Identities=13% Similarity=0.117 Sum_probs=31.7
Q ss_pred CCceeEEEEeCCCCcHHHHHHHhhhcCCceEEEecCCCee
Q 026821 175 VGFTPHVITVKAGEDISSKIFAFSQQGPRTVCILSASGAI 214 (232)
Q Consensus 175 ~~ftPHVItV~~GEDV~~kI~sFaqqg~raICILSAnGaV 214 (232)
..+++++..+...+.+.+.+-.|.+.+-..++|+..+|-+
T Consensus 55 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Vv~~~~~~ 94 (106)
T cd04582 55 DHAEPFKVTVSVDDDLRIVLSRMFAHDMSWLPCVDEDGRY 94 (106)
T ss_pred hhcccCCEEECCCCCHHHHHHHHHHCCCCeeeEECCCCcE
Confidence 4467777889999888877778888887779999887654
No 40
>smart00412 Cu_FIST Copper-Fist. binds DNA only in present of copper or silver
Probab=21.74 E-value=41 Score=23.22 Aligned_cols=8 Identities=50% Similarity=1.012 Sum_probs=6.2
Q ss_pred CcccCCCC
Q 026821 102 AKKKRGRP 109 (232)
Q Consensus 102 ~KKKRGRP 109 (232)
.=||||||
T Consensus 31 ~i~kkGRP 38 (39)
T smart00412 31 PVRPRGRP 38 (39)
T ss_pred eecCCCCC
Confidence 35788998
No 41
>cd04619 CBS_pair_6 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=21.24 E-value=2e+02 Score=20.86 Aligned_cols=40 Identities=13% Similarity=0.266 Sum_probs=33.5
Q ss_pred ceeEEEEeCCCCcHHHHHHHhhhcCCceEEEecCCCeeee
Q 026821 177 FTPHVITVKAGEDISSKIFAFSQQGPRTVCILSASGAICN 216 (232)
Q Consensus 177 ftPHVItV~~GEDV~~kI~sFaqqg~raICILSAnGaVSn 216 (232)
++..++.|...+++.+.+-.|..++...+.|+..+|.+--
T Consensus 65 ~~~~~~~v~~~~~l~~a~~~m~~~~~~~lpVvd~~~~~~G 104 (114)
T cd04619 65 MTRAVVSCRPGDLLHDVWQVMKQRGLKNIPVVDENARPLG 104 (114)
T ss_pred hcCCCeeECCCCCHHHHHHHHHHcCCCeEEEECCCCcEEE
Confidence 4567889999999998888899999999999998876543
No 42
>PRK13337 putative lipid kinase; Reviewed
Probab=20.71 E-value=1.3e+02 Score=27.11 Aligned_cols=44 Identities=11% Similarity=0.105 Sum_probs=34.3
Q ss_pred CCceeEEEEeCCCCcHHHHHHHhhhcCCceEEEecCCCeeeeeE
Q 026821 175 VGFTPHVITVKAGEDISSKIFAFSQQGPRTVCILSASGAICNVT 218 (232)
Q Consensus 175 ~~ftPHVItV~~GEDV~~kI~sFaqqg~raICILSAnGaVSnVT 218 (232)
.++...++......|..+-+...+.++...|.|..+.|+|..|.
T Consensus 31 ~~~~~~~~~t~~~~~a~~~a~~~~~~~~d~vvv~GGDGTl~~vv 74 (304)
T PRK13337 31 AGYETSAHATTGPGDATLAAERAVERKFDLVIAAGGDGTLNEVV 74 (304)
T ss_pred cCCEEEEEEecCCCCHHHHHHHHHhcCCCEEEEEcCCCHHHHHH
Confidence 34667777777777777666677777888999999999998775
No 43
>cd04627 CBS_pair_14 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=20.63 E-value=2.3e+02 Score=20.70 Aligned_cols=43 Identities=19% Similarity=0.404 Sum_probs=33.9
Q ss_pred ceeEEEEeCCCCcHHHHHHHhhhcCCceEEEecCCCe-eeeeEe
Q 026821 177 FTPHVITVKAGEDISSKIFAFSQQGPRTVCILSASGA-ICNVTL 219 (232)
Q Consensus 177 ftPHVItV~~GEDV~~kI~sFaqqg~raICILSAnGa-VSnVTL 219 (232)
+...++.|+..+.+.+.+-.|.+++-..+-|+..+|. |--||+
T Consensus 74 ~~~~~~~v~~~~~l~~a~~~m~~~~~~~lpVvd~~~~~vGiit~ 117 (123)
T cd04627 74 GTSDVISINGDQPLIDALHLMHNEGISSVAVVDNQGNLIGNISV 117 (123)
T ss_pred CcCCceEeCCCCCHHHHHHHHHHcCCceEEEECCCCcEEEEEeH
Confidence 4577889999999988888889888888999987764 444443
No 44
>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=20.34 E-value=2.3e+02 Score=20.05 Aligned_cols=35 Identities=9% Similarity=0.283 Sum_probs=29.3
Q ss_pred ceeEEEEeCCCCcHHHHHHHhhhcCCceEEEecCC
Q 026821 177 FTPHVITVKAGEDISSKIFAFSQQGPRTVCILSAS 211 (232)
Q Consensus 177 ftPHVItV~~GEDV~~kI~sFaqqg~raICILSAn 211 (232)
++.+++.|..++.+.+.+-.|.+.....+||+..+
T Consensus 64 ~~~~~~~v~~~~~l~~~~~~~~~~~~~~~~Vv~~~ 98 (112)
T cd04802 64 MSTPLITIDPNASLNEAAKLMAKHGIKRLPVVDDD 98 (112)
T ss_pred cCCCcEEECCCCCHHHHHHHHHHcCCCeeEEeeCC
Confidence 46789999999999888888888888789998754
Done!