Query 024112
Match_columns 272
No_of_seqs 238 out of 462
Neff 4.4
Searched_HMMs 46136
Date Fri Mar 29 09:03:46 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/024112.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/024112hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF03479 DUF296: Domain of unk 99.9 1.3E-27 2.8E-32 195.3 9.7 113 154-270 1-116 (120)
2 COG1661 Predicted DNA-binding 99.9 2E-21 4.4E-26 165.0 13.1 109 153-268 8-119 (141)
3 PF02178 AT_hook: AT hook moti 96.4 0.0011 2.4E-08 35.8 0.6 12 89-100 1-12 (13)
4 smart00384 AT_hook DNA binding 96.4 0.0018 3.8E-08 41.1 1.4 15 89-103 1-15 (26)
5 PF14621 RFX5_DNA_bdg: RFX5 DN 84.1 0.37 8E-06 43.6 0.4 12 87-98 66-77 (219)
6 PF13546 DDE_5: DDE superfamil 75.9 1.6 3.5E-05 39.5 1.8 16 86-101 228-243 (273)
7 COG1710 Uncharacterized protei 75.9 1.2 2.7E-05 38.0 0.9 16 86-101 81-97 (139)
8 cd01817 RGS12_RBD Ubiquitin do 49.6 48 0.001 25.9 5.2 45 156-200 11-57 (73)
9 COG1777 Predicted transcriptio 49.5 7.1 0.00015 36.1 0.7 25 87-111 62-89 (217)
10 PF14869 DUF4488: Domain of un 47.4 25 0.00053 30.4 3.6 36 181-218 28-63 (133)
11 PF15333 TAF1D: TATA box-bindi 44.1 9.9 0.00022 35.1 0.8 12 91-102 64-75 (217)
12 PF02196 RBD: Raf-like Ras-bin 42.4 1.1E+02 0.0024 23.0 6.1 36 154-189 10-47 (71)
13 PF13737 DDE_Tnp_1_5: Transpos 28.0 30 0.00065 28.7 1.1 19 86-105 21-39 (112)
14 PF03306 AAL_decarboxy: Alpha- 28.0 2.5E+02 0.0054 25.8 7.1 104 159-266 84-198 (220)
15 smart00455 RBD Raf-like Ras-bi 26.8 1.3E+02 0.0029 22.6 4.3 46 155-200 10-57 (70)
16 cd04618 CBS_pair_5 The CBS dom 25.7 1.9E+02 0.0041 21.7 5.1 35 158-192 52-87 (98)
17 PF00571 CBS: CBS domain CBS d 25.5 88 0.0019 20.9 2.9 38 154-191 5-42 (57)
18 KOG4565 E93 protein involved i 23.6 27 0.00058 31.8 -0.0 15 87-101 111-125 (206)
19 cd01760 RBD Ubiquitin-like dom 23.5 1.4E+02 0.0031 22.7 4.0 37 155-191 10-48 (72)
20 PF11906 DUF3426: Protein of u 23.3 1.5E+02 0.0033 24.4 4.5 42 210-253 65-106 (149)
21 cd04603 CBS_pair_KefB_assoc Th 22.7 1.3E+02 0.0029 22.5 3.7 37 153-189 61-97 (111)
22 PF10623 PilI: Plasmid conjuga 20.2 1.1E+02 0.0023 24.5 2.7 40 152-191 16-55 (83)
No 1
>PF03479 DUF296: Domain of unknown function (DUF296); InterPro: IPR005175 This putative conserved domain is found in proteins that contain AT-hook motifs IPR000637 from INTERPRO, suggesting a DNA-binding function for the proteins as a whole, however, the function of this domain is unknown. Overexpression of a protein containing this domain, Q9S7C9 from SWISSPROT, in Arabidopsis thaliana causes late flowering and modified leaf development []. ; PDB: 2DT4_A 2P6Y_A 3HWU_A 3HTN_A 2NMU_A 2H6L_A 2HX0_A.
Probab=99.95 E-value=1.3e-27 Score=195.29 Aligned_cols=113 Identities=31% Similarity=0.388 Sum_probs=98.9
Q ss_pred ceEEEEEecCCCcHHHHHHHHHHhCCceEEEEeeeceeeeEEEecCCC--CCCceeEeeceEEEEeeceeeeCCCCCCCC
Q 024112 154 FTPHVITVAVGEDIAMKLLSFSQQGPRAICVLSANGAISTATLRQPSS--SGGSVTYEGRFEILCLSGSYLLSGNGGSRN 231 (272)
Q Consensus 154 ~~phVIrV~~GEDV~~kI~~faqq~~~aicILSa~GsVSnVTLRqp~s--~~~tvt~eG~FEILSLsGt~~~~~~~~~~~ 231 (272)
|++|++||++||||+++|++||+++++..|+++++|++++|+|++++. .....+|+|+|||+||+|||...++ .
T Consensus 1 ~r~~~~rl~~Gedl~~~l~~~~~~~~i~~~~is~iGsl~~~~l~~~~~~~~~~~~~~~g~~Ei~sl~G~i~~~~g----~ 76 (120)
T PF03479_consen 1 GRVFVIRLDPGEDLLESLEAFAREHGIRSGVISGIGSLSNVTLGYYDPPSYYEPLEFEGPFEIISLSGTISPEDG----K 76 (120)
T ss_dssp EEEEEEEEETTSBHHHHHHHHHHHHT-SSEEEEEEEEEEEEEEEEEETTTEEEEEEEESEEEEEEEEEEEEEETT----E
T ss_pred CcEEEEEECCCCHHHHHHHHHHHHCCCcEEEEEEEeEEeEEEEEEecccCCcceEEecccEEEEEeEEEEECCCC----C
Confidence 789999999999999999999999999888999999999999999843 3457899999999999999998433 2
Q ss_pred CCCceEEEEeCCCCeEEeeecC-cceEeecceEEEEEEcc
Q 024112 232 RSGGLSVSLASPDGRVIGGGVG-GMLIAANNVQVTFRLCL 270 (272)
Q Consensus 232 ~~~hLhISLAg~dGqViGGhV~-G~LIAAtpVqVvv~sF~ 270 (272)
++.||||+|+|.||+|+||||. |.++++..|+|+..++.
T Consensus 77 ~~~HlHisl~~~~g~v~gGHl~~g~v~~t~Ev~i~~~~~~ 116 (120)
T PF03479_consen 77 PFVHLHISLADPDGQVFGGHLLEGTVFATAEVVITELSGI 116 (120)
T ss_dssp EEEEEEEEEE-TTSEEEEEEEEEEEEEEEEEEEEEEETTE
T ss_pred CcceEEEEEECCCCeEEeeEeCCCEEeEEEEEEEEEecCc
Confidence 6679999999999999999999 88878888888877664
No 2
>COG1661 Predicted DNA-binding protein with PD1-like DNA-binding motif [General function prediction only]
Probab=99.87 E-value=2e-21 Score=165.02 Aligned_cols=109 Identities=23% Similarity=0.274 Sum_probs=98.9
Q ss_pred CceEEEEEecCCCcHHHHHHHHHHhCCceEEEEeeeceeeeEEEecCCCCC---CceeEeeceEEEEeeceeeeCCCCCC
Q 024112 153 GFTPHVITVAVGEDIAMKLLSFSQQGPRAICVLSANGAISTATLRQPSSSG---GSVTYEGRFEILCLSGSYLLSGNGGS 229 (272)
Q Consensus 153 ~~~phVIrV~~GEDV~~kI~~faqq~~~aicILSa~GsVSnVTLRqp~s~~---~tvt~eG~FEILSLsGt~~~~~~~~~ 229 (272)
.=+-+++||++|||+.+.|.+||+++++..++++|+|++++++||+++..+ .++++.++||||||.|||..++
T Consensus 8 ~gr~~~~Rld~G~d~~~~l~~~a~~~~i~aa~v~~iGal~~~~l~~~~~~~~~y~~~~~~e~~EvlSL~G~i~~~~---- 83 (141)
T COG1661 8 SGRVIALRLDPGEDLFSELEAFAEQEDIHAAVVTAIGALRDAKLRYFDPEEKEYETIPVNEPLEVLSLLGNIALDD---- 83 (141)
T ss_pred cceEEEEEeCCCccHHHHHHHHHHhcCceEEEEEEeeeeeeeEEEEecCCCCceEEEecCCcEEEEEecceeecCC----
Confidence 346899999999999999999999999988999999999999999998433 4788999999999999999987
Q ss_pred CCCCCceEEEEeCCCCeEEeeecCcceEeecceEEEEEE
Q 024112 230 RNRSGGLSVSLASPDGRVIGGGVGGMLIAANNVQVTFRL 268 (272)
Q Consensus 230 ~~~~~hLhISLAg~dGqViGGhV~G~LIAAtpVqVvv~s 268 (272)
+..|||++|++++|+++||||.+..+-. ++||++.-
T Consensus 84 --p~~HlHa~l~~~~G~~~GGHL~~~~V~~-t~Ev~I~e 119 (141)
T COG1661 84 --PFVHLHAALGDENGITLGGHLLEGEVFP-TAEVFIRE 119 (141)
T ss_pred --CcEEEEEEEecCCCcEEeeeecccEEeE-EEEEEEEE
Confidence 4569999999999999999999888777 99998864
No 3
>PF02178 AT_hook: AT hook motif; InterPro: IPR017956 AT hooks are DNA-binding motifs with a preference for A/T rich regions. These motifs are found in a variety of proteins, including the high mobility group (HMG) proteins [], in DNA-binding proteins from plants [] and in hBRG1 protein, a central ATPase of the human switching/sucrose non-fermenting (SWI/SNF) remodeling complex []. High mobility group (HMG) proteins are a family of relatively low molecular weight non-histone components in chromatin []. HMG-I and HMG-Y (HMGA) are proteins of about 100 amino acid residues which are produced by the alternative splicing of a single gene. HMG-I/Y proteins bind preferentially to the minor groove of AT-rich regions in double-stranded DNA in a non-sequence specific manner [, ]. It is suggested that these proteins could function in nucleosome phasing and in the 3' end processing of mRNA transcripts. They are also involved in the transcription regulation of genes containing, or in close proximity to, AT-rich regions. ; GO: 0003677 DNA binding; PDB: 2EZE_A 2EZD_A 2EZF_A 2EZG_A.
Probab=96.42 E-value=0.0011 Score=35.81 Aligned_cols=12 Identities=75% Similarity=1.140 Sum_probs=4.3
Q ss_pred cccCCCCCCCCC
Q 024112 89 KRKRGRPRKYGP 100 (272)
Q Consensus 89 KkKRGRPRKY~p 100 (272)
+|+||||+|+..
T Consensus 1 ~r~RGRP~k~~~ 12 (13)
T PF02178_consen 1 KRKRGRPRKNAK 12 (13)
T ss_dssp S--SS--TT---
T ss_pred CCcCCCCccccC
Confidence 589999999764
No 4
>smart00384 AT_hook DNA binding domain with preference for A/T rich regions. Small DNA-binding motif first described in the high mobility group non-histone chromosomal protein HMG-I(Y).
Probab=96.37 E-value=0.0018 Score=41.08 Aligned_cols=15 Identities=67% Similarity=0.948 Sum_probs=13.0
Q ss_pred cccCCCCCCCCCCCC
Q 024112 89 KRKRGRPRKYGPDGS 103 (272)
Q Consensus 89 KkKRGRPRKY~pdg~ 103 (272)
|||||||||+..+..
T Consensus 1 kRkRGRPrK~~~~~~ 15 (26)
T smart00384 1 KRKRGRPRKAPKDXX 15 (26)
T ss_pred CCCCCCCCCCCCccc
Confidence 699999999998764
No 5
>PF14621 RFX5_DNA_bdg: RFX5 DNA-binding domain
Probab=84.09 E-value=0.37 Score=43.60 Aligned_cols=12 Identities=75% Similarity=1.107 Sum_probs=10.4
Q ss_pred cccccCCCCCCC
Q 024112 87 PVKRKRGRPRKY 98 (272)
Q Consensus 87 ~~KkKRGRPRKY 98 (272)
-.|||||||||-
T Consensus 66 dAKRKRGRPRKK 77 (219)
T PF14621_consen 66 DAKRKRGRPRKK 77 (219)
T ss_pred hhhhhcCCCccC
Confidence 489999999965
No 6
>PF13546 DDE_5: DDE superfamily endonuclease
Probab=75.93 E-value=1.6 Score=39.50 Aligned_cols=16 Identities=63% Similarity=1.076 Sum_probs=12.2
Q ss_pred ccccccCCCCCCCCCC
Q 024112 86 EPVKRKRGRPRKYGPD 101 (272)
Q Consensus 86 ~~~KkKRGRPRKY~pd 101 (272)
.+..+|||||||||.-
T Consensus 228 ~~~~~~rGRPr~~g~~ 243 (273)
T PF13546_consen 228 PPPPPKRGRPRKYGRR 243 (273)
T ss_pred cccCCCCCCCCCCCCc
Confidence 3455559999999965
No 7
>COG1710 Uncharacterized protein conserved in archaea [Function unknown]
Probab=75.85 E-value=1.2 Score=38.00 Aligned_cols=16 Identities=63% Similarity=1.120 Sum_probs=13.3
Q ss_pred cccc-ccCCCCCCCCCC
Q 024112 86 EPVK-RKRGRPRKYGPD 101 (272)
Q Consensus 86 ~~~K-kKRGRPRKY~pd 101 (272)
-|+| |.|||||||+-.
T Consensus 81 IPvk~KgrGrprkyd~~ 97 (139)
T COG1710 81 IPVKLKGRGRPRKYDRN 97 (139)
T ss_pred eeeeecCCCCCcccchh
Confidence 3777 889999999864
No 8
>cd01817 RGS12_RBD Ubiquitin domain of RGS12 and RGS14. RGS12 (regulator of G signalling 12), and RGS14, are members of a family of GTPase-activating proteins (GAP's) specific for the G-alpha subunit, which act as key inhibitors of G-protein-mediated cell responses in eukaryotes. Their domain architecture includes tandem RBD domains as well as PDZ , PTB, and RGS, and GoLoco domains.
Probab=49.59 E-value=48 Score=25.86 Aligned_cols=45 Identities=24% Similarity=0.167 Sum_probs=34.1
Q ss_pred EEEEEecCCCcHHHHHHHHHHhCCc--eEEEEeeeceeeeEEEecCC
Q 024112 156 PHVITVAVGEDIAMKLLSFSQQGPR--AICVLSANGAISTATLRQPS 200 (272)
Q Consensus 156 phVIrV~~GEDV~~kI~~faqq~~~--aicILSa~GsVSnVTLRqp~ 200 (272)
--++.+.+|+-|.+.|+..+++++. +.|.+--.|.=.-+.+.|..
T Consensus 11 ~T~V~vrpG~ti~d~L~kllekRgl~~~~~~vf~~g~~k~l~~~qD~ 57 (73)
T cd01817 11 TTVVPTRPGESIRDLLSGLCEKRGINYAAVDLFLVGGDKPLVLDQDS 57 (73)
T ss_pred eEEEEecCCCCHHHHHHHHHHHcCCChhHEEEEEecCCcccccCCcc
Confidence 4578999999999999999999984 56666655655555555543
No 9
>COG1777 Predicted transcriptional regulators [Transcription]
Probab=49.49 E-value=7.1 Score=36.11 Aligned_cols=25 Identities=48% Similarity=0.663 Sum_probs=16.9
Q ss_pred cccccCCCCCCCC-CCCCcce--ecCCC
Q 024112 87 PVKRKRGRPRKYG-PDGSVSL--ALSPS 111 (272)
Q Consensus 87 ~~KkKRGRPRKY~-pdg~~~l--~~~p~ 111 (272)
-.|.+|||||||- ..++++| .++|.
T Consensus 62 ie~~~Rg~~rKYY~Is~~~rleV~lsp~ 89 (217)
T COG1777 62 IEKIPRGRPRKYYMISRNLRLEVTLSPN 89 (217)
T ss_pred ccccccCCCcceeeccCCeEEEEEecCc
Confidence 3677789999997 4555554 45553
No 10
>PF14869 DUF4488: Domain of unknown function (DUF4488)
Probab=47.43 E-value=25 Score=30.39 Aligned_cols=36 Identities=28% Similarity=0.400 Sum_probs=29.7
Q ss_pred eEEEEeeeceeeeEEEecCCCCCCceeEeeceEEEEee
Q 024112 181 AICVLSANGAISTATLRQPSSSGGSVTYEGRFEILCLS 218 (272)
Q Consensus 181 aicILSa~GsVSnVTLRqp~s~~~tvt~eG~FEILSLs 218 (272)
.+=|||.-|+..|+++. +. ++..+|++|.||+.|=+
T Consensus 28 ~lKilS~Dgtf~Ni~~~-~~-~~aiIt~~GtY~~~sD~ 63 (133)
T PF14869_consen 28 VLKILSDDGTFVNITMI-PK-SGAIITGYGTYEQPSDN 63 (133)
T ss_pred cEEEEcCCCcEEEEEEe-CC-CCcEEEEeEEEEEcCCc
Confidence 47799999999999994 33 35799999999999743
No 11
>PF15333 TAF1D: TATA box-binding protein-associated factor 1D
Probab=44.07 E-value=9.9 Score=35.07 Aligned_cols=12 Identities=50% Similarity=0.994 Sum_probs=9.4
Q ss_pred cCCCCCCCCCCC
Q 024112 91 KRGRPRKYGPDG 102 (272)
Q Consensus 91 KRGRPRKY~pdg 102 (272)
|+-+.|||-+-|
T Consensus 64 KkrkkrKYk~tg 75 (217)
T PF15333_consen 64 KKRKKRKYKPTG 75 (217)
T ss_pred HHhhhhccCccC
Confidence 566779999877
No 12
>PF02196 RBD: Raf-like Ras-binding domain; InterPro: IPR003116 This is the Ras-binding domain found in proteins related to Ras. It is found in association with the PE-bind and pkinase domains.; GO: 0005057 receptor signaling protein activity, 0007165 signal transduction; PDB: 1RFA_A 1C1Y_B 3KUD_B 1GUA_B 3KUC_B 2L05_A 3NY5_D 1RRB_A 1WFY_A 1WXM_A.
Probab=42.43 E-value=1.1e+02 Score=22.99 Aligned_cols=36 Identities=19% Similarity=0.150 Sum_probs=29.7
Q ss_pred ceEEEEEecCCCcHHHHHHHHHHhCCc--eEEEEeeec
Q 024112 154 FTPHVITVAVGEDIAMKLLSFSQQGPR--AICVLSANG 189 (272)
Q Consensus 154 ~~phVIrV~~GEDV~~kI~~faqq~~~--aicILSa~G 189 (272)
-++-++.+.+|+-|.+.|...|++++. ..|.+--.|
T Consensus 10 ~q~t~V~vrpg~ti~d~L~~~~~kr~L~~~~~~V~~~~ 47 (71)
T PF02196_consen 10 GQRTVVQVRPGMTIRDALSKACKKRGLNPECCDVRLVG 47 (71)
T ss_dssp TEEEEEEE-TTSBHHHHHHHHHHTTT--CCCEEEEEEE
T ss_pred CCEEEEEEcCCCCHHHHHHHHHHHcCCCHHHEEEEEcC
Confidence 357789999999999999999999984 677777777
No 13
>PF13737 DDE_Tnp_1_5: Transposase DDE domain
Probab=28.04 E-value=30 Score=28.73 Aligned_cols=19 Identities=42% Similarity=0.945 Sum_probs=13.8
Q ss_pred ccccccCCCCCCCCCCCCcc
Q 024112 86 EPVKRKRGRPRKYGPDGSVS 105 (272)
Q Consensus 86 ~~~KkKRGRPRKY~pdg~~~ 105 (272)
++...|||||++|- |-.|.
T Consensus 21 ~~~~~kRGr~~~yS-D~aI~ 39 (112)
T PF13737_consen 21 APPRGKRGRPPRYS-DAAIQ 39 (112)
T ss_pred cCCCCCCCCCcccc-hHHHH
Confidence 35668999999996 44443
No 14
>PF03306 AAL_decarboxy: Alpha-acetolactate decarboxylase; InterPro: IPR005128 Alpha-acetolactate decarboxylase plays a dual role in the cell: (i) it catalyzes the second step of the acetoin pathway, (S)-2-hydroxy-2-methyl-3-oxobutanoate = (R)-2-acetoin + CO2 and thus potentially the internal pH of cells and (ii) it controls the pool of alpha-acetolactate during leucine and valine synthesis.; GO: 0047605 acetolactate decarboxylase activity, 0019751 polyol metabolic process, 0005789 endoplasmic reticulum membrane; PDB: 1XV2_B.
Probab=28.02 E-value=2.5e+02 Score=25.79 Aligned_cols=104 Identities=16% Similarity=0.228 Sum_probs=59.5
Q ss_pred EEecCCCcHHHHHHHHHHhCCceEEEEeeeceeeeEEEecCCCCCC-------ceeEeeceEEEEeecee----eeCCCC
Q 024112 159 ITVAVGEDIAMKLLSFSQQGPRAICVLSANGAISTATLRQPSSSGG-------SVTYEGRFEILCLSGSY----LLSGNG 227 (272)
Q Consensus 159 IrV~~GEDV~~kI~~faqq~~~aicILSa~GsVSnVTLRqp~s~~~-------tvt~eG~FEILSLsGt~----~~~~~~ 227 (272)
.....-+++.+.|.+..... .....+-..|..+.|++|-.....+ .+.-+-.||.--++||+ +|.--.
T Consensus 84 ~~~~~~~~l~~~l~~~~~~~-N~f~airi~G~F~~v~~Rsv~~qe~Py~~l~e~~~~Q~~f~~~ni~GTlVGf~sP~~~~ 162 (220)
T PF03306_consen 84 DSPMSKEELEAKLDELLPSK-NLFYAIRIDGTFSSVKTRSVPKQEKPYPPLAEVAKNQPEFTFENIEGTLVGFYSPEYMG 162 (220)
T ss_dssp EEEEEHHHHHHHHHHHSS-T-TS-EEEEEEEEEEEEEEE------SS---THHHHTT--EEEEEEEEEEEEEEEE-GGGB
T ss_pred CCCCCHHHHHHHHHHhcCCC-ceEEEEEEEEEECeEEEEeccCccCCCCChhHHhccCceEEecCcEEEEEEEEcchhcc
Confidence 34445577888888877643 3467777899999999997654322 11123455666566665 454322
Q ss_pred CCCCCCCceEEEEeCCCCeEEeeecCcceEeecceEEEE
Q 024112 228 GSRNRSGGLSVSLASPDGRVIGGGVGGMLIAANNVQVTF 266 (272)
Q Consensus 228 ~~~~~~~hLhISLAg~dGqViGGhV~G~LIAAtpVqVvv 266 (272)
+- --.++|+.+-+. -+-+||||.+.-+....|+|-.
T Consensus 163 gi--~v~G~HlHFls~-Dr~~GGHvld~~~~~~~v~~~~ 198 (220)
T PF03306_consen 163 GI--NVPGFHLHFLSD-DRTFGGHVLDFELDNGTVEIDV 198 (220)
T ss_dssp TT--B-CEEEEEEEET-TSS-EEEEEEEEEEEEEEEEEE
T ss_pred cc--CCceEEEEEecC-CCCCCCCeEEEEeceEEEEEEe
Confidence 21 112577777654 4789999999888777777643
No 15
>smart00455 RBD Raf-like Ras-binding domain.
Probab=26.84 E-value=1.3e+02 Score=22.57 Aligned_cols=46 Identities=22% Similarity=0.297 Sum_probs=34.7
Q ss_pred eEEEEEecCCCcHHHHHHHHHHhCCc--eEEEEeeeceeeeEEEecCC
Q 024112 155 TPHVITVAVGEDIAMKLLSFSQQGPR--AICVLSANGAISTATLRQPS 200 (272)
Q Consensus 155 ~phVIrV~~GEDV~~kI~~faqq~~~--aicILSa~GsVSnVTLRqp~ 200 (272)
+...+.+.||+-|.+.|...|++++. ..|.|.-.|.=..+.+.++.
T Consensus 10 ~~~~V~vrpg~tl~e~L~~~~~kr~l~~~~~~v~~~g~~k~ldl~~~~ 57 (70)
T smart00455 10 QRTVVKVRPGKTVRDALAKALKKRGLNPECCVVRLRGEKKPLDLNQPI 57 (70)
T ss_pred CEEEEEECCCCCHHHHHHHHHHHcCCCHHHEEEEEcCCCcceecCCcc
Confidence 46789999999999999999999984 56666666643444555543
No 16
>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=25.74 E-value=1.9e+02 Score=21.70 Aligned_cols=35 Identities=9% Similarity=0.111 Sum_probs=30.7
Q ss_pred EEEecCCCcHHHHHHHHHHhCCceEEEEeee-ceee
Q 024112 158 VITVAVGEDIAMKLLSFSQQGPRAICVLSAN-GAIS 192 (272)
Q Consensus 158 VIrV~~GEDV~~kI~~faqq~~~aicILSa~-GsVS 192 (272)
++.+.+.+++.+.+..|.+++-..++|+... |.+.
T Consensus 52 ~~~v~~~~~l~~a~~~m~~~~~~~lpVvd~~~~~~~ 87 (98)
T cd04618 52 LVSIHPERSLFDAALLLLKNKIHRLPVIDPSTGTGL 87 (98)
T ss_pred eEEeCCCCcHHHHHHHHHHCCCCEeeEEECCCCCce
Confidence 7889999999999999999988999999876 6543
No 17
>PF00571 CBS: CBS domain CBS domain web page. Mutations in the CBS domain of Swiss:P35520 lead to homocystinuria.; InterPro: IPR000644 CBS (cystathionine-beta-synthase) domains are small intracellular modules, mostly found in two or four copies within a protein, that occur in a variety of proteins in bacteria, archaea, and eukaryotes [, ]. Tandem pairs of CBS domains can act as binding domains for adenosine derivatives and may regulate the activity of attached enzymatic or other domains []. In some cases, CBS domains may act as sensors of cellular energy status by being activated by AMP and inhibited by ATP []. In chloride ion channels, the CBS domains have been implicated in intracellular targeting and trafficking, as well as in protein-protein interactions, but results vary with different channels: in the CLC-5 channel, the CBS domain was shown to be required for trafficking [], while in the CLC-1 channel, the CBS domain was shown to be critical for channel function, but not necessary for trafficking []. Recent experiments revealing that CBS domains can bind adenosine-containing ligands such ATP, AMP, or S-adenosylmethionine have led to the hypothesis that CBS domains function as sensors of intracellular metabolites [, ]. Crystallographic studies of CBS domains have shown that pairs of CBS sequences form a globular domain where each CBS unit adopts a beta-alpha-beta-beta-alpha pattern []. Crystal structure of the CBS domains of the AMP-activated protein kinase in complexes with AMP and ATP shows that the phosphate groups of AMP/ATP lie in a surface pocket at the interface of two CBS domains, which is lined with basic residues, many of which are associated with disease-causing mutations []. In humans, mutations in conserved residues within CBS domains cause a variety of human hereditary diseases, including (with the gene mutated in parentheses): homocystinuria (cystathionine beta-synthase); Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase); retinitis pigmentosa (IMP dehydrogenase-1); congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members).; GO: 0005515 protein binding; PDB: 3JTF_A 3TE5_C 3TDH_C 3T4N_C 2QLV_C 3OI8_A 3LV9_A 2QH1_B 1PVM_B 3LQN_A ....
Probab=25.55 E-value=88 Score=20.85 Aligned_cols=38 Identities=24% Similarity=0.392 Sum_probs=30.5
Q ss_pred ceEEEEEecCCCcHHHHHHHHHHhCCceEEEEeeecee
Q 024112 154 FTPHVITVAVGEDIAMKLLSFSQQGPRAICVLSANGAI 191 (272)
Q Consensus 154 ~~phVIrV~~GEDV~~kI~~faqq~~~aicILSa~GsV 191 (272)
|++-++.+.+.+.+.+.+..|.+.+-..+.|+...|.+
T Consensus 5 m~~~~~~v~~~~~l~~~~~~~~~~~~~~~~V~d~~~~~ 42 (57)
T PF00571_consen 5 MTPPPITVSPDDSLEEALEIMRKNGISRLPVVDEDGKL 42 (57)
T ss_dssp SBSSSEEEETTSBHHHHHHHHHHHTSSEEEEESTTSBE
T ss_pred CcCCCEEEcCcCcHHHHHHHHHHcCCcEEEEEecCCEE
Confidence 55567889999999999999999998888888544433
No 18
>KOG4565 consensus E93 protein involved in programmed cell death, putative transcription regulator [Transcription]
Probab=23.58 E-value=27 Score=31.76 Aligned_cols=15 Identities=40% Similarity=0.793 Sum_probs=12.9
Q ss_pred cccccCCCCCCCCCC
Q 024112 87 PVKRKRGRPRKYGPD 101 (272)
Q Consensus 87 ~~KkKRGRPRKY~pd 101 (272)
.-+|||||=|+|...
T Consensus 111 qpRkKRGrYRqYd~e 125 (206)
T KOG4565|consen 111 QPRKKRGRYRQYDKE 125 (206)
T ss_pred CccccccchhhhhHH
Confidence 578999999999864
No 19
>cd01760 RBD Ubiquitin-like domain of RBD-like S/T kinases. The ras-binding domain (RBD) of the serine/threonine kinase raf is structurally quite similar to the beta-grasp fold of ubiquitin. A raf-like RBD is also present in RGS12 and other members of a family of GTPase activating proteins and TIAM1, a guanine nucleotide exchange protein.
Probab=23.47 E-value=1.4e+02 Score=22.72 Aligned_cols=37 Identities=16% Similarity=0.111 Sum_probs=29.1
Q ss_pred eEEEEEecCCCcHHHHHHHHHHhCCc--eEEEEeeecee
Q 024112 155 TPHVITVAVGEDIAMKLLSFSQQGPR--AICVLSANGAI 191 (272)
Q Consensus 155 ~phVIrV~~GEDV~~kI~~faqq~~~--aicILSa~GsV 191 (272)
+..++.|.||+-|.+.|...|++++. ..|.|--.|.-
T Consensus 10 ~~t~V~vrpg~ti~d~L~~~c~kr~l~~~~~~v~~~~~~ 48 (72)
T cd01760 10 QRTVVPVRPGMSVRDVLAKACKKRGLNPECCDVFLLGLD 48 (72)
T ss_pred CeEEEEECCCCCHHHHHHHHHHHcCCCHHHEEEEEecCC
Confidence 46789999999999999999999984 45555554443
No 20
>PF11906 DUF3426: Protein of unknown function (DUF3426); InterPro: IPR021834 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 262 to 463 amino acids in length.
Probab=23.31 E-value=1.5e+02 Score=24.40 Aligned_cols=42 Identities=19% Similarity=0.158 Sum_probs=31.5
Q ss_pred eceEEEEeeceeeeCCCCCCCCCCCceEEEEeCCCCeEEeeecC
Q 024112 210 GRFEILCLSGSYLLSGNGGSRNRSGGLSVSLASPDGRVIGGGVG 253 (272)
Q Consensus 210 G~FEILSLsGt~~~~~~~~~~~~~~hLhISLAg~dGqViGGhV~ 253 (272)
+.=+.+-++|++.+.... ...+-.|.++|.|.+|+++.=-+.
T Consensus 65 ~~~~~l~v~g~i~N~~~~--~~~~P~l~l~L~D~~g~~l~~r~~ 106 (149)
T PF11906_consen 65 DGPGVLVVSGTIRNRADF--PQALPALELSLLDAQGQPLARRVF 106 (149)
T ss_pred CCCCEEEEEEEEEeCCCC--cccCceEEEEEECCCCCEEEEEEE
Confidence 345788888999887652 336669999999999998865444
No 21
>cd04603 CBS_pair_KefB_assoc This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the KefB (Kef-type K+ transport systems) domain which is involved in inorganic ion transport and metabolism. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide range of different proteins. CBS domains usually come in tandem repeats, which associate to form a so-called Bateman domain or a CBS pair which is reflected in this model. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown.
Probab=22.66 E-value=1.3e+02 Score=22.48 Aligned_cols=37 Identities=19% Similarity=0.272 Sum_probs=30.3
Q ss_pred CceEEEEEecCCCcHHHHHHHHHHhCCceEEEEeeec
Q 024112 153 GFTPHVITVAVGEDIAMKLLSFSQQGPRAICVLSANG 189 (272)
Q Consensus 153 ~~~phVIrV~~GEDV~~kI~~faqq~~~aicILSa~G 189 (272)
.|...+..+.+.+.+.+.+..+.+.+...++|+...|
T Consensus 61 ~~~~~~~~v~~~~~l~~al~~m~~~~~~~lpVvd~~~ 97 (111)
T cd04603 61 VYIVPVPIVYCDSKVTDLLRIFRETEPPVVAVVDKEG 97 (111)
T ss_pred eeecCCcEECCCCcHHHHHHHHHHcCCCeEEEEcCCC
Confidence 3556678899999999999999998888889987644
No 22
>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=20.16 E-value=1.1e+02 Score=24.52 Aligned_cols=40 Identities=15% Similarity=0.164 Sum_probs=33.3
Q ss_pred CCceEEEEEecCCCcHHHHHHHHHHhCCceEEEEeeecee
Q 024112 152 MGFTPHVITVAVGEDIAMKLLSFSQQGPRAICVLSANGAI 191 (272)
Q Consensus 152 ~~~~phVIrV~~GEDV~~kI~~faqq~~~aicILSa~GsV 191 (272)
+.-+--++.+++-+|+.+-++.||.-.+.-+||+--+=-|
T Consensus 16 n~c~~kL~~~~~~~D~~~i~r~f~TpdN~lV~V~~~nr~l 55 (83)
T PF10623_consen 16 NHCERKLFDTKPDNDPDKIARRFCTPDNCLVCVLQDNRFL 55 (83)
T ss_pred CCcceeEeecCCCCCHHHHHhhccCcCCeEEEEEeCCceE
Confidence 3455678899999999999999999999999998765433
Done!