Query 028677
Match_columns 205
No_of_seqs 116 out of 486
Neff 5.0
Searched_HMMs 46136
Date Fri Mar 29 15:15:43 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028677.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028677hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN00051 RNA-binding S4 domain 100.0 1E-36 2.2E-41 269.1 14.3 127 66-193 12-138 (267)
2 TIGR03069 PS_II_S4 photosystem 100.0 1.8E-36 3.9E-41 265.9 13.3 128 64-194 2-130 (257)
3 COG2302 Uncharacterized conser 100.0 8.3E-34 1.8E-38 247.6 12.5 126 67-195 3-130 (257)
4 KOG4837 Uncharacterized conser 99.4 4.3E-14 9.3E-19 121.5 2.0 127 59-197 7-133 (248)
5 PF03880 DbpA: DbpA RNA bindin 93.8 0.057 1.2E-06 38.8 2.7 31 164-194 11-42 (74)
6 cd02644 R3H_jag R3H domain fou 87.3 5.4 0.00012 28.5 7.7 58 78-137 6-63 (67)
7 COG1847 Jag Predicted RNA-bind 66.6 28 0.0006 30.5 7.2 56 80-136 149-204 (208)
8 PF05566 Pox_vIL-18BP: Orthopo 64.3 4.5 9.8E-05 32.4 1.7 17 187-203 29-45 (126)
9 COG0529 CysC Adenylylsulfate k 62.0 17 0.00036 31.6 4.9 85 50-134 32-136 (197)
10 cd02640 R3H_NRF R3H domain of 46.8 65 0.0014 22.5 5.1 41 94-137 17-57 (60)
11 cd02638 R3H_unknown_1 R3H doma 45.1 1.1E+02 0.0025 21.9 6.2 48 88-137 11-58 (62)
12 PF02495 7kD_coat: 7kD viral c 42.1 20 0.00043 24.8 1.9 17 185-201 26-42 (59)
13 cd06007 R3H_DEXH_helicase R3H 39.7 1.1E+02 0.0024 21.3 5.4 41 94-137 16-56 (59)
14 cd02639 R3H_RRM R3H domain of 39.2 73 0.0016 22.4 4.4 36 94-130 17-52 (60)
15 cd02645 R3H_AAA R3H domain of 36.3 1.5E+02 0.0032 20.7 7.0 51 84-137 6-57 (60)
16 smart00393 R3H Putative single 34.6 1.7E+02 0.0037 20.8 7.5 56 78-137 18-75 (79)
17 cd02641 R3H_Smubp-2_like R3H d 30.2 1.9E+02 0.0041 20.0 5.4 41 94-137 17-57 (60)
18 PF01424 R3H: R3H domain; Int 27.4 2E+02 0.0042 19.3 7.5 46 88-137 13-59 (63)
19 KOG3143 Imidazoleglycerol-phos 24.8 28 0.0006 30.1 0.3 21 166-188 134-154 (219)
20 PRK11634 ATP-dependent RNA hel 22.7 74 0.0016 31.7 2.9 42 152-194 486-528 (629)
21 TIGR00824 EIIA-man PTS system, 21.9 2.5E+02 0.0054 21.5 5.2 71 50-122 12-87 (116)
22 PF03610 EIIA-man: PTS system 21.6 2.1E+02 0.0046 21.5 4.7 71 50-120 10-84 (116)
23 PF04502 DUF572: Family of unk 20.3 80 0.0017 28.8 2.4 66 132-203 2-86 (324)
24 PF07788 DUF1626: Protein of u 20.2 3E+02 0.0066 20.0 5.0 44 70-113 20-66 (70)
No 1
>PLN00051 RNA-binding S4 domain-containing protein; Provisional
Probab=100.00 E-value=1e-36 Score=269.09 Aligned_cols=127 Identities=70% Similarity=1.062 Sum_probs=114.7
Q ss_pred HHHhccCCCcchHHHHHHHHHHHHHHhcCCceEEecCCCHHHHHHHHHHhhccCCceEEEeCCCcccceeEEEeeCCCCC
Q 028677 66 DDLLKGVGDKNAIEEVKHILEMARRASSRREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRLSVGHPEAL 145 (205)
Q Consensus 66 ~~ll~~~~~~e~~e~v~rilD~~~~a~k~~~~~~TdFLdP~e~~i~~~il~~~~di~~~~~GGY~~AERkri~i~~pe~~ 145 (205)
..+++|+. ++++.++++++|++++|.+++.+++|+||||+||.+++++++++.++++.++|||++|||+|++|.|+++.
T Consensus 12 ~~i~~h~~-~ee~~~~~~~~d~~~~a~~~~~~~~T~FL~p~e~~i~~~~~~~~~~i~~~~~GGy~~AER~r~~~~p~~~~ 90 (267)
T PLN00051 12 SALLGVVD-PAHREEVKRILEMAERASDRWEVEHTDFLTPPIVKDSMAALEKLADVKAVAWGGYAQAERCRLSIGRPEVL 90 (267)
T ss_pred hHHHhhcC-hhhHHHHHHHHHHHHHHHhcCCEEECccCCHHHHHHHHHHhcccCCeEEEEecCCchHeEEEEEEechHhc
Confidence 46889977 56699999999999999999999999999999999999999888899999999999999999998666554
Q ss_pred CCCcCceEEEEeecCCCCCCCChhhHHHHHHcCCCCCCCcccEEEeCC
Q 028677 146 TSDPDIVAALSITGNFGFQPCSHGDFLGSILGTGIAREKIGDIILQNK 193 (205)
Q Consensus 146 ~~~~~~I~~L~I~~n~kF~~lsHRDfLGALmgLGIkREkIGDIlv~~~ 193 (205)
+.++.+|++++|++++||.+++|||||||||||||+||+||||++.++
T Consensus 91 ~~~~f~i~~l~i~~~~kF~~l~HrD~LGaLm~LGIkRe~iGDIlv~~~ 138 (267)
T PLN00051 91 TSQPDIVAALSVSGNFMFDPASHGDFLGAILGTGITRDKVGDILVQGE 138 (267)
T ss_pred cccCCcEEEEEEEcccCCCCCCHHHHHHHHHHcCCcHhhcCCEEEcCC
Confidence 222357999999999999999999999999999999999999999654
No 2
>TIGR03069 PS_II_S4 photosystem II S4 domain protein. Members of this protein family are about 265 residues long and each contains an S4 RNA-binding domain of about 48 residues. The member from the Cyanobacterium, Synechocystis sp. PCC 6803, was detected as a novel polypeptide in a highly purified preparation of active photosystem II (Kashino, et al., 2002). The phylogenetic distribution, including Cyanobacteria and Arabidopsis, supports a role in photosystem II, although the high bit score cutoffs for this model reflect similar sequences in non-photosynthetic organisms such as Carboxydothermus hydrogenoformans, a Gram-positive bacterium.
Probab=100.00 E-value=1.8e-36 Score=265.87 Aligned_cols=128 Identities=40% Similarity=0.637 Sum_probs=114.6
Q ss_pred chHHHhccCCCcchHHHHHHHHHHHHHHhcCCceEEecCCCHHHHHHHHHHhhccCCceEEEeCCCcccceeEEEeeCCC
Q 028677 64 NFDDLLKGVGDKNAIEEVKHILEMARRASSRREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRLSVGHPE 143 (205)
Q Consensus 64 ~~~~ll~~~~~~e~~e~v~rilD~~~~a~k~~~~~~TdFLdP~e~~i~~~il~~~~di~~~~~GGY~~AERkri~i~~pe 143 (205)
+++++++++.++|+ +++++||+++|.++|++++|+||||+|+.++++++++.+++++.++|||++|||+|+++.|++
T Consensus 2 ~~~~~~~~~~~~ee---~~~~~d~~~~~~~~~~~~~T~FL~p~e~~i~~~~~~~~~~~~~~~~GG~~~AER~r~~~~p~~ 78 (257)
T TIGR03069 2 PREELLKGANYPEE---LERLLDLAEQALRTWEPVWSDFLSAPLQEEILKRFSNLTDLKWLAWGGYPQAERQRIACARSD 78 (257)
T ss_pred ChHHHHHhCCCHHH---HHHHHHHHHHHHhhCCEEECCCCCHHHHHHHHHHhcccCCcEEEEecCCcHHhEEEEEEeccc
Confidence 57889999886453 999999999999999999999999999999999998888999999999999999999986554
Q ss_pred CCCCCc-CceEEEEeecCCCCCCCChhhHHHHHHcCCCCCCCcccEEEeCCe
Q 028677 144 ALTSDP-DIVAALSITGNFGFQPCSHGDFLGSILGTGIAREKIGDIILQNKG 194 (205)
Q Consensus 144 ~~~~~~-~~I~~L~I~~n~kF~~lsHRDfLGALmgLGIkREkIGDIlv~~~~ 194 (205)
+.++.+ .+|++++|+++++|.+++|||||||||||||+||++|||++.+++
T Consensus 79 ~~~~~~df~i~~l~i~~~~kF~~l~Hrd~LGalm~lGi~R~~iGDI~v~~~~ 130 (257)
T TIGR03069 79 NPLDPDIIPIQGLLIEGNFLFDPASHEDFRGALLGTGIVREKIGDIWVLGDR 130 (257)
T ss_pred ccCCcccCceEEEEEEcccccCCCCHHHHHHHHHHcCCcHhhcCCEEEecCC
Confidence 443332 479999999999999999999999999999999999999887653
No 3
>COG2302 Uncharacterized conserved protein, contains S4-like domain [Function unknown]
Probab=100.00 E-value=8.3e-34 Score=247.61 Aligned_cols=126 Identities=32% Similarity=0.479 Sum_probs=114.8
Q ss_pred HHhccCCCcchHHHHHHHHHHHHHHhcCCceEEecCCCHHHHHHHHHHhhccCCceEEEeCCCcccceeEEEeeCCCCCC
Q 028677 67 DLLKGVGDKNAIEEVKHILEMARRASSRREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRLSVGHPEALT 146 (205)
Q Consensus 67 ~ll~~~~~~e~~e~v~rilD~~~~a~k~~~~~~TdFLdP~e~~i~~~il~~~~di~~~~~GGY~~AERkri~i~~pe~~~ 146 (205)
.+.+|+. .|++++++|++||+++|+++|.+++||||||+|+.+++.+++ +.|+++.++||||+|||+|+++ +|+|++
T Consensus 3 ~iyqhf~-~eer~fidr~l~~~~~ve~~y~v~~T~Fl~P~e~~i~~~l~~-~~~v~~~~~Gg~~~aEr~r~~l-~P~y~~ 79 (257)
T COG2302 3 GIYQHFR-AEERPFIDRVLEWIKQVEKTYTVVVTDFLDPREQAILKTLAG-LEDVKVSFSGGYPRAERKRLIL-YPAYYP 79 (257)
T ss_pred cHhhhcC-chhHHHHHHHHHHHHHHhcCceEEEccCcCcHHHHHHHHHhC-ccceeEEeecCCchhheeEEEE-cccccC
Confidence 4677766 789999999999999999999999999999999999988888 7899999999999999999988 565654
Q ss_pred -CCcC-ceEEEEeecCCCCCCCChhhHHHHHHcCCCCCCCcccEEEeCCeE
Q 028677 147 -SDPD-IVAALSITGNFGFQPCSHGDFLGSILGTGIAREKIGDIILQNKGF 195 (205)
Q Consensus 147 -~~~~-~I~~L~I~~n~kF~~lsHRDfLGALmgLGIkREkIGDIlv~~~~~ 195 (205)
++.| ++++++|.+++||.+++|+||||+||||||+||++|||++.++++
T Consensus 80 ~~~~df~l~l~eI~y~~kF~~l~H~~~LGtll~lGikRe~~GDIiv~~~~a 130 (257)
T COG2302 80 LEESDFELTLLEISYASKFVSLTHRDILGTLLSLGIKREKFGDIIVEGEGA 130 (257)
T ss_pred hhhcccceEEEEEEcccccccccHHHHHHHHHhccCcHHhhccEEEeCCee
Confidence 3334 599999999999999999999999999999999999999998874
No 4
>KOG4837 consensus Uncharacterized conserved protein [Function unknown]
Probab=99.42 E-value=4.3e-14 Score=121.51 Aligned_cols=127 Identities=62% Similarity=0.966 Sum_probs=114.1
Q ss_pred HhhccchHHHhccCCCcchHHHHHHHHHHHHHHhcCCceEEecCCCHHHHHHHHHHhhccCCceEEEeCCCcccceeEEE
Q 028677 59 QAVKGNFDDLLKGVGDKNAIEEVKHILEMARRASSRREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRLS 138 (205)
Q Consensus 59 ~~~~~~~~~ll~~~~~~e~~e~v~rilD~~~~a~k~~~~~~TdFLdP~e~~i~~~il~~~~di~~~~~GGY~~AERkri~ 138 (205)
.++|++.+.+++++.+.-.-..+.++++++..+.......+|+||.| +....++|+.....|||+.||++++-
T Consensus 7 ~~i~g~~~~~~~~vg~~~v~k~~~~~~~m~~~~~~~r~f~~t~~l~p-------sl~t~F~~v~s~~lpgl~~a~ec~~p 79 (248)
T KOG4837|consen 7 EAIKGDVDFLLKGVGDQAVAKEVKQILEMARRASSKREFLHTDFLTP-------SLLTKFADVKSVALPGLPEAEECRIP 79 (248)
T ss_pred hHhhhhhhhhhhcccHHHHHhhcHHHHHHHHHHHhhHHHHhhhhhCc-------hhhhccccchhhhcCCCCCChheEee
Confidence 78899999999999998888889999999999999999999999999 44457789999999999999999999
Q ss_pred eeCCCCCCCCcCceEEEEeecCCCCCCCChhhHHHHHHcCCCCCCCcccEEEeCCeEEe
Q 028677 139 VGHPEALTSDPDIVAALSITGNFGFQPCSHGDFLGSILGTGIAREKIGDIILQNKGFLC 197 (205)
Q Consensus 139 i~~pe~~~~~~~~I~~L~I~~n~kF~~lsHRDfLGALmgLGIkREkIGDIlv~~~~~~~ 197 (205)
|.+|+-.....+..+.++++.|+.|++.+|.||+|+++ ||+.|||.+..+.+.+
T Consensus 80 i~~~~~~ts~k~~kksl~~td~~dsd~esh~Df~~e~~-----~e~~~D~~Vvk~~~~i 133 (248)
T KOG4837|consen 80 IGHPDVLTSDKDIKKSLSITDNFDSDPESHGDFLGEIL-----REKLGDILVVKEKVLI 133 (248)
T ss_pred ccCccccccchhHHHHhhhccccCCCcccchhHHHHHH-----HHhcCCceeeehhhhh
Confidence 99997776666668899999999999999999999998 9999999998876544
No 5
>PF03880 DbpA: DbpA RNA binding domain ; InterPro: IPR005580 This RNA binding domain is found at the C terminus of a number of DEAD helicase proteins [].; PDB: 2G0C_A 3MOJ_B.
Probab=93.82 E-value=0.057 Score=38.81 Aligned_cols=31 Identities=26% Similarity=0.372 Sum_probs=24.0
Q ss_pred CCCChhhHHHHHHcC-CCCCCCcccEEEeCCe
Q 028677 164 QPCSHGDFLGSILGT-GIAREKIGDIILQNKG 194 (205)
Q Consensus 164 ~~lsHRDfLGALmgL-GIkREkIGDIlv~~~~ 194 (205)
+.++++|++|+|.+. ||+++.||+|-+.++.
T Consensus 11 dg~~~~~iv~~i~~~~gi~~~~IG~I~I~~~~ 42 (74)
T PF03880_consen 11 DGLTPRDIVGAICNEAGIPGRDIGRIDIFDNF 42 (74)
T ss_dssp GT--HHHHHHHHHTCTTB-GGGEEEEEE-SS-
T ss_pred cCCCHHHHHHHHHhccCCCHHhEEEEEEeeeE
Confidence 568999999999985 9999999999988875
No 6
>cd02644 R3H_jag R3H domain found in proteins homologous to Bacillus subtilus Jag, which is associated with SpoIIIJ. SpoIIIJ is necessary for the third stage of sporulation. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
Probab=87.27 E-value=5.4 Score=28.47 Aligned_cols=58 Identities=12% Similarity=0.039 Sum_probs=47.3
Q ss_pred HHHHHHHHHHHHHHhcCCceEEecCCCHHHHHHHHHHhhccCCceEEEeCCCcccceeEE
Q 028677 78 IEEVKHILEMARRASSRREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRL 137 (205)
Q Consensus 78 ~e~v~rilD~~~~a~k~~~~~~TdFLdP~e~~i~~~il~~~~di~~~~~GGY~~AERkri 137 (205)
..+.....++++++.+++.++.-+=+++.|..++-.++++++++.-...| ++..|..+
T Consensus 6 ~~L~~~A~~~a~~v~~tg~~~~l~PM~~~eRrivH~~~~~~~~l~T~S~G--~~~~R~vv 63 (67)
T cd02644 6 ETLIRLAERAAEKVRRTGKPVKLEPMNAYERRIIHDALANDEDVETESEG--EGPYRRVV 63 (67)
T ss_pred HHHHHHHHHHHHHHHHHCCeeEeCCCCHHHHHHHHHHHHhCCCceEEeec--CCCCeEEE
Confidence 34566777888889999999999999999999999999988889888887 33355554
No 7
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=66.56 E-value=28 Score=30.49 Aligned_cols=56 Identities=18% Similarity=0.105 Sum_probs=43.7
Q ss_pred HHHHHHHHHHHHhcCCceEEecCCCHHHHHHHHHHhhccCCceEEEeCCCcccceeE
Q 028677 80 EVKHILEMARRASSRREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCR 136 (205)
Q Consensus 80 ~v~rilD~~~~a~k~~~~~~TdFLdP~e~~i~~~il~~~~di~~~~~GGY~~AERkr 136 (205)
+++=....+++|.++++++..+=++|.|++++-..++..+|+.-..-| .+..-|.+
T Consensus 149 L~~LA~~~A~rV~~tg~~v~L~pM~~~ERkIVH~~l~~~~~V~T~SeG-~ep~R~vV 204 (208)
T COG1847 149 LIKLAERAAERVLETGRSVELEPMPPFERKIVHTALSANPGVETYSEG-EEPNRRVV 204 (208)
T ss_pred HHHHHHHHHHHHHhhCCeeecCCCCHHHHHHHHHHHHhcCCcceeecC-CCCceEEE
Confidence 344455667889999999999999999999999999999999776655 44443333
No 8
>PF05566 Pox_vIL-18BP: Orthopoxvirus interleukin 18 binding protein; InterPro: IPR008791 Interleukin-18 (IL-18) is a proinflammatory cytokine that plays a key role in the activation of natural killer and T helper 1 cell responses principally by inducing interferon-gamma (IFN-gamma). Several poxvirus genes encode proteins with sequence similarity to IL-18BPs. It has been shown that vaccinia, ectromelia and cowpox viruses secrete from infected cells a soluble IL-18BP (vIL-18BP) that may modulate the host antiviral response. The expression of vIL-18BPs by distinct poxvirus genera that cause local or general viral dissemination, or persistent or acute infections in the host, emphasises the importance of IL-18 in response to viral infections [].; PDB: 3F62_A.
Probab=64.31 E-value=4.5 Score=32.37 Aligned_cols=17 Identities=47% Similarity=1.175 Sum_probs=14.1
Q ss_pred cEEEeCCeEEecccccc
Q 028677 187 DIILQNKGFLCSGCLQY 203 (205)
Q Consensus 187 DIlv~~~~~~~~~~~~~ 203 (205)
||....+.++||||..|
T Consensus 29 ~ivTSs~~fhCsGcv~~ 45 (126)
T PF05566_consen 29 DIVTSSEEFHCSGCVKY 45 (126)
T ss_dssp EEEEETTEEEEEEEE-S
T ss_pred eEEeccceEEEechhhh
Confidence 67888899999999776
No 9
>COG0529 CysC Adenylylsulfate kinase and related kinases [Inorganic ion transport and metabolism]
Probab=62.04 E-value=17 Score=31.58 Aligned_cols=85 Identities=20% Similarity=0.270 Sum_probs=56.1
Q ss_pred cccchhhHHHhh------ccchHHHhcc------------CCCcchHHHHHHHHHHHHHHhcCCceEEecCCCHH--HHH
Q 028677 50 TASGIRHLIQAV------KGNFDDLLKG------------VGDKNAIEEVKHILEMARRASSRREVLHSDFLTPP--VLK 109 (205)
Q Consensus 50 ~~~~~~~~~~~~------~~~~~~ll~~------------~~~~e~~e~v~rilD~~~~a~k~~~~~~TdFLdP~--e~~ 109 (205)
-.||....|.++ ++-..++|++ +.+.+-.+.+.|+.+.++...+.+-++.+.|.+|. +..
T Consensus 32 SGsGKSTiA~ale~~L~~~G~~~y~LDGDnvR~gL~~dLgFs~edR~eniRRvaevAkll~daG~iviva~ISP~r~~R~ 111 (197)
T COG0529 32 SGSGKSTIANALEEKLFAKGYHVYLLDGDNVRHGLNRDLGFSREDRIENIRRVAEVAKLLADAGLIVIVAFISPYREDRQ 111 (197)
T ss_pred CCCCHHHHHHHHHHHHHHcCCeEEEecChhHhhcccCCCCCChHHHHHHHHHHHHHHHHHHHCCeEEEEEeeCccHHHHH
Confidence 478888888887 3333333332 23344456699999999999999999999999997 355
Q ss_pred HHHHHhhccCCceEEEeCCCcccce
Q 028677 110 ESMMALEKLADVKAVAQGGYPQAER 134 (205)
Q Consensus 110 i~~~il~~~~di~~~~~GGY~~AER 134 (205)
.+..+++.-.-+.+...--.+-+|+
T Consensus 112 ~aR~~~~~~~FiEVyV~~pl~vce~ 136 (197)
T COG0529 112 MARELLGEGEFIEVYVDTPLEVCER 136 (197)
T ss_pred HHHHHhCcCceEEEEeCCCHHHHHh
Confidence 6677776533355554444444443
No 10
>cd02640 R3H_NRF R3H domain of the NF-kappaB-repression factor (NRF). NRF is a nuclear inhibitor of NF-kappaB proteins that can silence the IFNbeta promoter via binding to a negative regulatory element (NRE). Beside R3H NRF also contains a G-patch domain. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
Probab=46.77 E-value=65 Score=22.53 Aligned_cols=41 Identities=15% Similarity=0.111 Sum_probs=31.6
Q ss_pred CCceEEecCCCHHHHHHHHHHhhccCCceEEEeCCCcccceeEE
Q 028677 94 RREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRL 137 (205)
Q Consensus 94 ~~~~~~TdFLdP~e~~i~~~il~~~~di~~~~~GGY~~AERkri 137 (205)
.....+.+=||+.|+.++-.+..+ -+++....|- +.+|..+
T Consensus 17 ~~~l~f~p~lt~~eR~~vH~~a~~-~gL~s~S~G~--g~~R~v~ 57 (60)
T cd02640 17 IRDMVFSPEFSKEERALIHQIAQK-YGLKSRSYGS--GNDRYLV 57 (60)
T ss_pred cceEEcCCCCCHHHHHHHHHHHHH-cCCceeeEeC--CCCeEEE
Confidence 567788888999999999888777 4888888774 4466544
No 11
>cd02638 R3H_unknown_1 R3H domain of a group of eukaryotic proteins with unknown function. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
Probab=45.07 E-value=1.1e+02 Score=21.87 Aligned_cols=48 Identities=15% Similarity=-0.065 Sum_probs=35.9
Q ss_pred HHHHhcCCceEEecCCCHHHHHHHHHHhhccCCceEEEeCCCcccceeEE
Q 028677 88 ARRASSRREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRL 137 (205)
Q Consensus 88 ~~~a~k~~~~~~TdFLdP~e~~i~~~il~~~~di~~~~~GGY~~AERkri 137 (205)
.-...+.++++.-+=++|.|++++-+.+.+.+++.-...| ++.-|+.+
T Consensus 11 f~~~~~~~r~v~LePM~~~ERkIIH~~Lq~~~~v~T~S~G--~ep~RrVV 58 (62)
T cd02638 11 FLLSFQRYRVLLFPPLNSRRRYLIHQTVENRFLLSTFSVG--EGWARRTV 58 (62)
T ss_pred HHHhcccCCeEecCCCChHHHHHHHHHHhcCCCceEEEcc--CCCCcEEE
Confidence 3344556789999999999999999999988888766665 34444444
No 12
>PF02495 7kD_coat: 7kD viral coat protein; InterPro: IPR003411 This family consists of a 7 kDa coat protein from Carlavirus and Potexvirus [].
Probab=42.11 E-value=20 Score=24.77 Aligned_cols=17 Identities=24% Similarity=0.401 Sum_probs=13.9
Q ss_pred cccEEEeCCeEEecccc
Q 028677 185 IGDIILQNKGFLCSGCL 201 (205)
Q Consensus 185 IGDIlv~~~~~~~~~~~ 201 (205)
-==|.++|+.++++||.
T Consensus 26 ~C~I~ItGeSv~I~gC~ 42 (59)
T PF02495_consen 26 SCVIVITGESVTISGCE 42 (59)
T ss_pred CcEEEEeCcEEEEECCC
Confidence 33478999999999993
No 13
>cd06007 R3H_DEXH_helicase R3H domain of a group of proteins which also contain a DEXH-box helicase domain, and may function as ATP-dependent DNA or RNA helicases. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
Probab=39.71 E-value=1.1e+02 Score=21.34 Aligned_cols=41 Identities=17% Similarity=0.028 Sum_probs=31.3
Q ss_pred CCceEEecCCCHHHHHHHHHHhhccCCceEEEeCCCcccceeEE
Q 028677 94 RREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRL 137 (205)
Q Consensus 94 ~~~~~~TdFLdP~e~~i~~~il~~~~di~~~~~GGY~~AERkri 137 (205)
.....+.+=||+.|+..+-.+..+ -++.....|- +.+|...
T Consensus 16 ~~~l~Fpp~ls~~eR~~vH~~a~~-~gL~s~S~G~--g~~R~v~ 56 (59)
T cd06007 16 NEEYEFPSSLTNHERAVIHRLCRK-LGLKSKSKGK--GSNRRLS 56 (59)
T ss_pred ccEEEcCCCCCHHHHHHHHHHHHH-cCCCceeecC--CCCeEEE
Confidence 567788888999999999888777 4888887774 4466544
No 14
>cd02639 R3H_RRM R3H domain of mainly fungal proteins which are associated with a RNA recognition motif (RRM) domain. Present in this group is the RNA-binding post-transcriptional regulator Cip2 (Csx1-interacting protein 2) involved in counteracting Csx1 function. Csx1 plays a central role in controlling gene expression during oxidative stress. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
Probab=39.22 E-value=73 Score=22.37 Aligned_cols=36 Identities=19% Similarity=0.272 Sum_probs=29.0
Q ss_pred CCceEEecCCCHHHHHHHHHHhhccCCceEEEeCCCc
Q 028677 94 RREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYP 130 (205)
Q Consensus 94 ~~~~~~TdFLdP~e~~i~~~il~~~~di~~~~~GGY~ 130 (205)
.+..++..-|+|.|..++-.+..++ ++.....|+.+
T Consensus 17 ~~eL~Fp~~ls~~eRriih~la~~l-GL~~~s~G~g~ 52 (60)
T cd02639 17 RDELAFPSSLSPAERRIVHLLASRL-GLNHVSDGTGE 52 (60)
T ss_pred ceEEEcCCCCCHHHHHHHHHHHHHc-CCceEEeCCCc
Confidence 4577788889999999997777776 78888888853
No 15
>cd02645 R3H_AAA R3H domain of a group of proteins with unknown function, who also contain a AAA-ATPase (AAA) domain. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to be binding ssDNA or ssRNA in a sequence-specific manner.
Probab=36.32 E-value=1.5e+02 Score=20.72 Aligned_cols=51 Identities=8% Similarity=-0.004 Sum_probs=39.2
Q ss_pred HHHHHHHHhcCC-ceEEecCCCHHHHHHHHHHhhccCCceEEEeCCCcccceeEE
Q 028677 84 ILEMARRASSRR-EVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRL 137 (205)
Q Consensus 84 ilD~~~~a~k~~-~~~~TdFLdP~e~~i~~~il~~~~di~~~~~GGY~~AERkri 137 (205)
....++++...+ +++--.=+++.++++.-.+++++ ++.....| ++..|+.+
T Consensus 6 a~~aa~~V~~~~~~~veL~Pm~~~eRri~H~~v~~~-~l~s~S~G--~ep~Rrvv 57 (60)
T cd02645 6 ARLAIEQVVIPKGEPVELLPRSAYIRRLQHDLVERY-QLRSESFG--SEPNRRLR 57 (60)
T ss_pred HHHHHHHHHhcCCceEEcCCCCHHHHHHHHHHHHHC-CCeEEEec--CCCCcEEE
Confidence 445566677777 88888889999999998888875 89888888 55556555
No 16
>smart00393 R3H Putative single-stranded nucleic acids-binding domain.
Probab=34.57 E-value=1.7e+02 Score=20.81 Aligned_cols=56 Identities=16% Similarity=0.022 Sum_probs=36.1
Q ss_pred HHHHHHHHHHHH-HHhcC-CceEEecCCCHHHHHHHHHHhhccCCceEEEeCCCcccceeEE
Q 028677 78 IEEVKHILEMAR-RASSR-REVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRL 137 (205)
Q Consensus 78 ~e~v~rilD~~~-~a~k~-~~~~~TdFLdP~e~~i~~~il~~~~di~~~~~GGY~~AERkri 137 (205)
++.+.++...+. .+... ....+.+ +++.+..++-.++..+ ++.....|- +..|..+
T Consensus 18 ~~~l~~~~~~~~~~v~~~~~~~~~~p-m~~~~R~~iH~~a~~~-~l~s~S~g~--g~~R~vv 75 (79)
T smart00393 18 REELIELELEIARFVKSTKESVELPP-MNSYERKIVHELAEKY-GLESESFGE--GPKRRVV 75 (79)
T ss_pred HHHHHHHHHHHHHHHhccCCeEEcCC-CCHHHHHHHHHHHHHc-CCEEEEEcC--CCCcEEE
Confidence 334444433333 34333 4556666 9999999998888887 898888774 3446555
No 17
>cd02641 R3H_Smubp-2_like R3H domain of Smubp-2_like proteins. Smubp-2_like proteins also contain a helicase_like and an AN1-like Zinc finger domain and have been shown to bind single-stranded DNA. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA.
Probab=30.20 E-value=1.9e+02 Score=20.00 Aligned_cols=41 Identities=15% Similarity=0.073 Sum_probs=30.6
Q ss_pred CCceEEecCCCHHHHHHHHHHhhccCCceEEEeCCCcccceeEE
Q 028677 94 RREVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRL 137 (205)
Q Consensus 94 ~~~~~~TdFLdP~e~~i~~~il~~~~di~~~~~GGY~~AERkri 137 (205)
.....+.+=||+.|+..+-.+..++ ++.....|- +.+|..+
T Consensus 17 ~~~l~F~p~ls~~eR~~vH~lA~~~-gL~s~S~G~--g~~R~v~ 57 (60)
T cd02641 17 ATELEFPPTLSSHDRLLVHELAEEL-GLRHESTGE--GSDRVIT 57 (60)
T ss_pred cCcEECCCCCCHHHHHHHHHHHHHc-CCceEeeCC--CCceEEE
Confidence 3667888889999999998888774 788887763 4466544
No 18
>PF01424 R3H: R3H domain; InterPro: IPR001374 The R3H motif: a domain that binds single-stranded nucleic acids. The most prominent feature of the R3H motif is the presence of an invariant arginine residue and a highly conserved histidine residue that are separated by three residues. The motif also displays a conserved pattern of hydrophobic residues, prolines and glycines. The R3H motif is present in proteins from a diverse range of organisms that includes Eubacteria, green plants, fungi and various groups of metazoans. Intriguingly, it has not yet been identified in Archaea and Escherichia coli. The sequences that contain the R3H domain, many of which are hypothetical proteins predicted from genome sequencing projects, can be grouped into eight families on the basis of similarities outside the R3H region. Three of the families contain ATPase domains either upstream (families II and VII) or downstream of the R3H domain (family VIII). The N-terminal part of members of family VII contains an SF1 helicase domain5. The C-terminal part of family VIII contains an SF2 DEAH helicase domain5. The ATPase domain in the members of family II is similar to the stage-III sporulation protein AA (S3AA_BACSU), the proteasome ATPase, bacterial transcription-termination factor r and the mitochondrial F1-ATPase b subunit (the F5 helicase family5). Family VI contains Cys-rich repeats6, as well as a ring-type zinc finger upstream of the R3H domain. JAG bacterial proteins (family I) contain a KH domain N-terminal to the R3H domain. The functions of other domains in R3H proteins support the notion that the R3H domain might be involved in interactions with single-stranded nucleic acids [].; GO: 0003676 nucleic acid binding; PDB: 1WHR_A 1MSZ_A 1UG8_A 3GKU_B 2CPM_A.
Probab=27.41 E-value=2e+02 Score=19.30 Aligned_cols=46 Identities=13% Similarity=-0.013 Sum_probs=29.3
Q ss_pred HHHHhcCC-ceEEecCCCHHHHHHHHHHhhccCCceEEEeCCCcccceeEE
Q 028677 88 ARRASSRR-EVLHSDFLTPPVLKESMMALEKLADVKAVAQGGYPQAERCRL 137 (205)
Q Consensus 88 ~~~a~k~~-~~~~TdFLdP~e~~i~~~il~~~~di~~~~~GGY~~AERkri 137 (205)
++.+.+.. ...+-+ +|+.+..++-.++. ..++.....| ++..|..+
T Consensus 13 ~~~~~~~~~~~~f~p-m~~~~R~~iH~~a~-~~gL~s~S~g--~~~~R~vv 59 (63)
T PF01424_consen 13 IEFFLSSGESLEFPP-MNSFERKLIHELAE-YYGLKSKSEG--EGPNRRVV 59 (63)
T ss_dssp HHHHHHCSSEEEEEC---SHHHHHHHHHHH-HCTEEEEEES--SSSSSEEE
T ss_pred HHHHHcCCCEEEECC-CCHHHHHHHHHHHH-HCCCEEEEec--CCCCeEEE
Confidence 33333333 455555 99999999988877 5689888887 55556554
No 19
>KOG3143 consensus Imidazoleglycerol-phosphate dehydratase [Amino acid transport and metabolism]
Probab=24.83 E-value=28 Score=30.14 Aligned_cols=21 Identities=29% Similarity=0.493 Sum_probs=15.7
Q ss_pred CChhhHHHHHHcCCCCCCCcccE
Q 028677 166 CSHGDFLGSILGTGIAREKIGDI 188 (205)
Q Consensus 166 lsHRDfLGALmgLGIkREkIGDI 188 (205)
++-|-|++ .+|||+|||+||+
T Consensus 134 LSgRPYav--~~Lgl~rekVG~l 154 (219)
T KOG3143|consen 134 LSGRPYAV--YNLGLPREKVGTL 154 (219)
T ss_pred cCCCeeEE--EecCCchhhcccc
Confidence 34455543 6899999999997
No 20
>PRK11634 ATP-dependent RNA helicase DeaD; Provisional
Probab=22.69 E-value=74 Score=31.72 Aligned_cols=42 Identities=19% Similarity=0.183 Sum_probs=32.1
Q ss_pred eEEEEeecCCCCCCCChhhHHHHHHc-CCCCCCCcccEEEeCCe
Q 028677 152 VAALSITGNFGFQPCSHGDFLGSILG-TGIAREKIGDIILQNKG 194 (205)
Q Consensus 152 I~~L~I~~n~kF~~lsHRDfLGALmg-LGIkREkIGDIlv~~~~ 194 (205)
.+-+.|.-- +-+.++.+|++|+|-+ .||++..||+|-+.++.
T Consensus 486 ~~~~~~~~g-~~~~~~~~~~~~~i~~~~~~~~~~ig~i~i~~~~ 528 (629)
T PRK11634 486 MQLYRIEVG-RDDGVEVRHIVGAIANEGDISSRYIGNIKLFASH 528 (629)
T ss_pred CEEEEEecc-cccCCCHHHHHHHHHhhcCCChhhCCcEEEeCCc
Confidence 444566532 2256899999999997 79999999999877664
No 21
>TIGR00824 EIIA-man PTS system, mannose/fructose/sorbose family, IIA component. Bacterial PTS transporters transport and concomitantly phosphorylate their sugar substrates, and typically consist of multiple subunits or protein domains.The Man family is unique in several respects among PTS permease families It is the only PTS family in which members possess a IID protein. It is the only PTS family in which the IIB constituent is phosphorylated on a histidyl rather than a cysteyl residue. Its permease members exhibit broad specificity for a range of sugars, rather than being specific for just one or a few sugars. The mannose permease of E. coli, for example, can transport and phosphorylate glucose, mannose, fructose, glucosamine, N-acetylglucosamine, and other sugars. Other members of this can transport sorbose, fructose and N-acetylglucosamine. This family is specific for the IIA components.
Probab=21.88 E-value=2.5e+02 Score=21.51 Aligned_cols=71 Identities=10% Similarity=0.055 Sum_probs=41.7
Q ss_pred cccchhhHHHhhccchH--HHhccCCCcchHHHHHHHHHHHHHHhc-CCceEEecCC--CHHHHHHHHHHhhccCCce
Q 028677 50 TASGIRHLIQAVKGNFD--DLLKGVGDKNAIEEVKHILEMARRASS-RREVLHSDFL--TPPVLKESMMALEKLADVK 122 (205)
Q Consensus 50 ~~~~~~~~~~~~~~~~~--~ll~~~~~~e~~e~v~rilD~~~~a~k-~~~~~~TdFL--dP~e~~i~~~il~~~~di~ 122 (205)
.|.|.-.++..+-++.+ +.+....+.+..++.+++.+.++.... ....++||-+ ||... +.+.+.+.+++.
T Consensus 12 ~A~gl~~s~~~i~G~~~~i~~i~~~~~~~~~~~~~~l~~~i~~~~~~~~vivltDl~GGSp~n~--a~~~~~~~~~~~ 87 (116)
T TIGR00824 12 AAIALLKSAEMIFGEQNNVGAVPFVPGENAETLQEKYNAALADLDTEEEVLFLVDIFGGSPYNA--AARIIVDKPHMD 87 (116)
T ss_pred HHHHHHHHHHHHcCCcCCeEEEEcCCCcCHHHHHHHHHHHHHhcCCCCCEEEEEeCCCCCHHHH--HHHHHhhcCCEE
Confidence 46778888888865544 223333344455677777777766533 4568899985 46443 334443334443
No 22
>PF03610 EIIA-man: PTS system fructose IIA component; InterPro: IPR004701 The phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS) [, ] is a major carbohydrate transport system in bacteria. The PTS catalyses the phosphorylation of incoming sugar substrates and coupled with translocation across the cell membrane, makes the PTS a link between the uptake and metabolism of sugars. The general mechanism of the PTS is the following: a phosphoryl group from phosphoenolpyruvate (PEP) is transferred via a signal transduction pathway, to enzyme I (EI) which in turn transfers it to a phosphoryl carrier, the histidine protein (HPr). Phospho-HPr then transfers the phosphoryl group to a sugar-specific permease, a membrane-bound complex known as enzyme 2 (EII), which transports the sugar to the cell. EII consists of at least three structurally distinct domains IIA, IIB and IIC []. These can either be fused together in a single polypeptide chain or exist as two or three interactive chains, formerly called enzymes II (EII) and III (EIII). The first domain (IIA or EIIA) carries the first permease-specific phosphorylation site, a histidine which is phosphorylated by phospho-HPr. The second domain (IIB or EIIB) is phosphorylated by phospho-IIA on a cysteinyl or histidyl residue, depending on the sugar transported. Finally, the phosphoryl group is transferred from the IIB domain to the sugar substrate concomitantly with the sugar uptake processed by the IIC domain. This third domain (IIC or EIIC) forms the translocation channel and the specific substrate-binding site. An additional transmembrane domain IID, homologous to IIC, can be found in some PTSs, e.g. for mannose [, , , ]. The Man family is unique in several respects among PTS permease families. It is the only PTS family in which members possess a IID protein. It is the only PTS family in which the IIB constituent is phosphorylated on a histidyl rather than a cysteyl residue. Its permease members exhibit broad specificity for a range of sugars, rather than being specific for just one or a few sugars. The mannose permease of Escherichia coli, for example, can transport and phosphorylate glucose, mannose, fructose, glucosamine, N-acetylglucosamine, and other sugars. Other members of this can transport sorbose, fructose and N-acetylglucosamine. This family is specific for IIA and IIB components.; GO: 0009401 phosphoenolpyruvate-dependent sugar phosphotransferase system, 0016021 integral to membrane; PDB: 3GDW_B 2JZN_A 1VSQ_A 2JZO_B 1VRC_A 1PDO_A 3GX1_A 3B48_B 3BED_B 3IPR_C ....
Probab=21.64 E-value=2.1e+02 Score=21.46 Aligned_cols=71 Identities=11% Similarity=0.073 Sum_probs=47.4
Q ss_pred cccchhhHHHhhccc---hHHHhccCCCcchHHHHHHHHHHHHHHh-cCCceEEecCCCHHHHHHHHHHhhccCC
Q 028677 50 TASGIRHLIQAVKGN---FDDLLKGVGDKNAIEEVKHILEMARRAS-SRREVLHSDFLTPPVLKESMMALEKLAD 120 (205)
Q Consensus 50 ~~~~~~~~~~~~~~~---~~~ll~~~~~~e~~e~v~rilD~~~~a~-k~~~~~~TdFLdP~e~~i~~~il~~~~d 120 (205)
.|+|...++..+.++ .-..+....+....++..++.+.++... .....++||...-.-...+.+.+.+.+.
T Consensus 10 ~A~g~~~~~~~i~G~~~~~i~~~~~~~~~~~~~~~~~l~~~i~~~~~~~~vlil~Dl~ggsp~n~a~~~~~~~~~ 84 (116)
T PF03610_consen 10 LAEGLLESAEMILGEDQDNIEAVDLYPDESIEDFEEKLEEAIEELDEGDGVLILTDLGGGSPFNEAARLLLDKPN 84 (116)
T ss_dssp HHHHHHHHHHHHHTSTCSSEEEEEETTTSCHHHHHHHHHHHHHHCCTTSEEEEEESSTTSHHHHHHHHHHCTSTT
T ss_pred HHHHHHHHHHHHcCCCcccEEEEECcCCCCHHHHHHHHHHHHHhccCCCcEEEEeeCCCCccchHHHHHhccCCC
Confidence 367777888887666 2334444555666677888888887764 4568899998886665555555544444
No 23
>PF04502 DUF572: Family of unknown function (DUF572) ; InterPro: IPR007590 This entry represents eukaryotic proteins with undetermined function belonging to the CWC16 family.
Probab=20.33 E-value=80 Score=28.84 Aligned_cols=66 Identities=20% Similarity=0.352 Sum_probs=39.8
Q ss_pred cceeEEEe-eCCCCCCCC-------cCceEEEEeecCCCC--CCCChhhHHHHHHcCCC----CCCCccc-----EEEeC
Q 028677 132 AERCRLSV-GHPEALTSD-------PDIVAALSITGNFGF--QPCSHGDFLGSILGTGI----AREKIGD-----IILQN 192 (205)
Q Consensus 132 AERkri~i-~~pe~~~~~-------~~~I~~L~I~~n~kF--~~lsHRDfLGALmgLGI----kREkIGD-----Ilv~~ 192 (205)
+|||.+.- +||||.... -..+-.+++.-+|.. ..+.. + ++-|. ++++||+ |-|-.
T Consensus 2 ~ERK~~nkYyPPD~d~~k~~~~kr~k~~~~~VRf~~Pf~i~C~~C~~--~----I~kG~rFNA~Ke~v~~E~Yls~~I~r 75 (324)
T PF04502_consen 2 SERKVLNKYYPPDFDPSKHPLRKRAKQGILTVRFMMPFNIWCNTCGE--Y----IYKGVRFNARKEKVGNEKYLSTPIYR 75 (324)
T ss_pred cccccCCCccCCCCCcccccccccCcCcceEEEEcCCccCcCCCCcc--c----cccceeeeeeeEecCCCccccceEEE
Confidence 79999984 356664311 023555566555433 33322 2 56665 6788999 55555
Q ss_pred CeEEecccccc
Q 028677 193 KGFLCSGCLQY 203 (205)
Q Consensus 193 ~~~~~~~~~~~ 203 (205)
=.++|..|..+
T Consensus 76 F~~kC~~C~~~ 86 (324)
T PF04502_consen 76 FYIKCPRCSNE 86 (324)
T ss_pred EEEEcCCCCCE
Confidence 56999999864
No 24
>PF07788 DUF1626: Protein of unknown function (DUF1626); InterPro: IPR012431 This is a family consisting of sequences from hypothetical proteins of unknown function expressed by certain species of archaea. One member (Q9YCN7 from SWISSPROT) is thought to be similar to tropomyosin [].
Probab=20.21 E-value=3e+02 Score=20.01 Aligned_cols=44 Identities=9% Similarity=0.134 Sum_probs=29.9
Q ss_pred ccCCCcchHHHHHHHHHHHHHHhcCC---ceEEecCCCHHHHHHHHH
Q 028677 70 KGVGDKNAIEEVKHILEMARRASSRR---EVLHSDFLTPPVLKESMM 113 (205)
Q Consensus 70 ~~~~~~e~~e~v~rilD~~~~a~k~~---~~~~TdFLdP~e~~i~~~ 113 (205)
+..-++.+-+.+.|-.++.+++..+. -...|+|.+++..+.+++
T Consensus 20 kSs~~~~Dv~~f~rk~~lYek~~grk~~r~ivVtp~id~~a~~~A~~ 66 (70)
T PF07788_consen 20 KSSVSRGDVYIFKRKAELYEKVHGRKVDRLIVVTPYIDDRAKEMAEE 66 (70)
T ss_pred EccCCHHHHHHHHHHHHHHHHHHCCCcceEEEEEeecCHHHHHHHHH
Confidence 33444566667777777777765544 567899999996665543
Done!