Query 032091
Match_columns 147
No_of_seqs 127 out of 1167
Neff 4.7
Searched_HMMs 46136
Date Fri Mar 29 09:28:17 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032091.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032091hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 CHL00160 rpl9 ribosomal protei 100.0 1.7E-29 3.8E-34 197.1 12.4 116 1-146 36-152 (153)
2 TIGR00158 L9 ribosomal protein 100.0 4.4E-29 9.4E-34 193.7 12.4 116 1-146 31-147 (148)
3 COG0359 RplI Ribosomal protein 100.0 8.9E-29 1.9E-33 192.7 11.7 116 1-146 31-146 (148)
4 PRK00137 rplI 50S ribosomal pr 100.0 5.9E-28 1.3E-32 186.8 12.5 116 1-146 31-146 (147)
5 PF03948 Ribosomal_L9_C: Ribos 99.9 2.4E-26 5.2E-31 164.0 10.2 86 43-146 1-86 (87)
6 PRK14538 putative bifunctional 99.9 5E-25 1.1E-29 207.4 12.8 117 1-146 718-834 (838)
7 KOG4607 Mitochondrial ribosoma 97.9 2.4E-05 5.3E-10 64.8 5.6 113 1-145 79-193 (222)
8 PF01281 Ribosomal_L9_N: Ribos 85.7 0.58 1.2E-05 30.3 1.8 18 1-18 31-48 (48)
9 PF10045 DUF2280: Uncharacteri 68.7 2.2 4.8E-05 32.0 0.7 32 86-117 21-52 (104)
10 PF00571 CBS: CBS domain CBS d 62.5 7.1 0.00015 23.8 2.1 17 79-95 40-56 (57)
11 PF08766 DEK_C: DEK C terminal 47.6 10 0.00022 24.3 1.0 25 82-106 18-42 (54)
12 PF13592 HTH_33: Winged helix- 35.6 22 0.00049 23.0 1.3 34 83-118 3-36 (60)
13 PF07523 Big_3: Bacterial Ig-l 34.9 61 0.0013 21.1 3.3 24 113-144 44-67 (67)
14 PF02082 Rrf2: Transcriptional 34.0 1.1E+02 0.0023 20.7 4.5 55 32-94 28-83 (83)
15 smart00116 CBS Domain in cysta 33.4 30 0.00065 18.7 1.4 16 79-94 33-48 (49)
16 PF14221 DUF4330: Domain of un 32.6 33 0.00072 27.0 2.0 19 77-95 6-24 (168)
17 PF08960 DUF1874: Domain of un 28.4 1.2E+02 0.0027 22.5 4.3 54 79-137 37-90 (105)
18 cd04608 CBS_pair_PALP_assoc Th 26.7 32 0.00069 24.2 0.9 18 77-94 107-124 (124)
19 cd01793 Fubi Fubi ubiquitin-li 24.6 53 0.0012 21.7 1.6 41 80-121 14-59 (74)
20 cd04624 CBS_pair_11 The CBS do 24.4 71 0.0015 21.2 2.3 18 79-96 34-51 (112)
21 cd04623 CBS_pair_10 The CBS do 23.9 70 0.0015 21.0 2.2 18 79-96 34-51 (113)
22 cd02980 TRX_Fd_family Thioredo 23.1 84 0.0018 20.3 2.4 17 79-95 59-75 (77)
23 cd04643 CBS_pair_30 The CBS do 22.9 75 0.0016 21.1 2.2 17 79-95 34-50 (116)
24 cd05718 Ig1_PVR_like First imm 22.7 1.9E+02 0.0041 19.1 4.2 27 113-144 71-97 (98)
25 cd04630 CBS_pair_17 The CBS do 22.7 69 0.0015 21.5 2.0 18 79-96 35-52 (114)
26 PF01282 Ribosomal_S24e: Ribos 22.6 55 0.0012 23.0 1.5 37 83-121 11-47 (84)
27 cd04619 CBS_pair_6 The CBS dom 22.4 77 0.0017 21.4 2.2 19 78-96 33-51 (114)
28 KOG2639 Sodium sulfate symport 22.3 71 0.0015 30.8 2.5 31 73-104 623-653 (685)
29 smart00557 IG_FLMN Filamin-typ 22.0 1.4E+02 0.003 20.5 3.4 27 113-140 64-90 (93)
30 PF05157 T2SE_Nter: Type II se 21.4 70 0.0015 21.6 1.8 26 83-108 5-31 (109)
31 cd04632 CBS_pair_19 The CBS do 21.4 76 0.0017 21.8 2.0 17 79-95 34-50 (128)
32 cd04590 CBS_pair_CorC_HlyC_ass 21.1 81 0.0018 20.8 2.0 18 79-96 35-52 (111)
33 cd04629 CBS_pair_16 The CBS do 20.9 93 0.002 20.6 2.3 18 79-96 34-51 (114)
34 COG2047 Uncharacterized protei 20.9 70 0.0015 27.4 2.0 25 79-104 135-159 (258)
35 cd04639 CBS_pair_26 The CBS do 20.7 98 0.0021 20.4 2.4 18 79-96 34-51 (111)
36 cd03081 TRX_Fd_NuoE_FDH_gamma 20.7 95 0.0021 21.1 2.3 18 79-96 62-79 (80)
37 cd04607 CBS_pair_NTP_transfera 20.6 76 0.0017 21.2 1.8 17 79-95 35-51 (113)
38 TIGR02010 IscR iron-sulfur clu 20.4 1.7E+02 0.0036 21.6 3.8 57 32-95 28-84 (135)
39 cd04582 CBS_pair_ABC_OpuCA_ass 20.3 81 0.0018 20.6 1.9 16 79-94 34-49 (106)
40 cd04593 CBS_pair_EriC_assoc_ba 20.2 85 0.0018 21.0 2.0 18 79-96 34-51 (115)
41 PF06570 DUF1129: Protein of u 20.2 3.6E+02 0.0078 21.4 5.9 16 80-97 50-65 (206)
42 cd04606 CBS_pair_Mg_transporte 20.1 54 0.0012 21.8 1.0 17 78-94 93-109 (109)
43 COG5556 Uncharacterized conser 20.0 58 0.0013 24.5 1.2 29 86-114 21-49 (110)
No 1
>CHL00160 rpl9 ribosomal protein L9; Provisional
Probab=99.96 E-value=1.7e-29 Score=197.10 Aligned_cols=116 Identities=16% Similarity=0.296 Sum_probs=107.4
Q ss_pred CCCcccccccHHHHHHHHHHHHhcCcchHHHHHHhhhhHHHHHHHHHHHHHHhccC-ceEEEEcccccccccccCCCCCC
Q 032091 1 MPKLLAVPNIEKFAHLIREQRRICQPVEEEEVKVIRKSEDNMSREFEKAARRLENA-RLVLRRFPNIEKLRSRASKDDPI 79 (147)
Q Consensus 1 ~p~~la~~a~~~~~~~~~~~~~~~~~~~~e~~k~i~k~~~~~~~eae~~a~~L~~~-~l~i~~~~g~~~~~~~~~~~~~g 79 (147)
||+++|++||..|++.++.+++..+. +.++.++++++++++|++. .+++.+++|++ |
T Consensus 36 iP~glA~~AT~~n~~~~e~~~~~~~~-----------~~~~~~~~a~~la~~l~~~~~~~i~~k~ge~-----------g 93 (153)
T CHL00160 36 IPNKMAKVATQGSLKQQKMYQKILDL-----------KLKEAKEKCLKVKQLLEEIQKFSVKKKVGEN-----------N 93 (153)
T ss_pred cccCchhhCCHHHHHHHHHHHHHHHH-----------HHHHHHHHHHHHHHHhhCCceEEEEEEeCCC-----------C
Confidence 79999999999999999988876655 7778889999999999998 59999999865 5
Q ss_pred ceeeccCHHHHHHHHHhhcCCccccccccCCCccccceeEEEEEEcCCCCCCCCCceEEEEEEEEEc
Q 032091 80 ELRSPVTKEELVAEVARQLSISIEPENLHLPSPLSAFGEYEVPMRLPKAIPLPEGKVQWTLNVKVRG 146 (147)
Q Consensus 80 kLfGSVT~~dI~~~l~~q~gi~Idk~~I~l~~pIk~lG~~~V~I~L~~~V~~~~~~~~a~l~V~V~~ 146 (147)
+||||||++||+++|++++|++|||++|+||+ |+++|+|+|.|+||++| +|+++|+|++
T Consensus 94 klfGSVt~~dIa~~l~~~~g~~idk~~I~l~~-Ik~~G~~~v~v~L~~~V-------~a~i~v~V~~ 152 (153)
T CHL00160 94 QIFGSVTEKEISQIIKNKTNIDLEKQNIELPE-IKTIGIYNIEIKLTSDV-------KANINLQILP 152 (153)
T ss_pred eEEcccCHHHHHHHHHHhhCCccccceeehhh-ccccEeEEEEEEecCCc-------EEEEEEEEEE
Confidence 99999999999999988889999999999988 99999999999999999 9999999986
No 2
>TIGR00158 L9 ribosomal protein L9. Ribosomal protein L9 appears to be universal in, but restricted to, eubacteria and chloroplast.
Probab=99.96 E-value=4.4e-29 Score=193.66 Aligned_cols=116 Identities=21% Similarity=0.287 Sum_probs=107.4
Q ss_pred CCCcccccccHHHHHHHHHHHHhcCcchHHHHHHhhhhHHHHHHHHHHHHHHhccCceEEEEcccccccccccCCCCCCc
Q 032091 1 MPKLLAVPNIEKFAHLIREQRRICQPVEEEEVKVIRKSEDNMSREFEKAARRLENARLVLRRFPNIEKLRSRASKDDPIE 80 (147)
Q Consensus 1 ~p~~la~~a~~~~~~~~~~~~~~~~~~~~e~~k~i~k~~~~~~~eae~~a~~L~~~~l~i~~~~g~~~~~~~~~~~~~gk 80 (147)
+|++||++||..|++.++.+++..+. +.++.++++++++++|++..+++.+++|++ |+
T Consensus 31 iP~g~A~~aT~~nl~~~e~~~~~~~~-----------~~~~~~~~a~~l~~~l~~~~~~i~~k~ge~-----------gk 88 (148)
T TIGR00158 31 IPKGLAVPATKKNIEFFEARRKKLEE-----------KLAANKAAAARLKEVLELGTLTISKKVGDE-----------GK 88 (148)
T ss_pred cccCchhhCCHHHHHHHHHHHHHHHH-----------HHHHHHHHHHHHHHHhcCcEEEEEEEeCCC-----------Ce
Confidence 79999999999999999888877666 667888999999999999999999999866 59
Q ss_pred eeeccCHHHHHHHHHhhcCCccccccccCCCc-cccceeEEEEEEcCCCCCCCCCceEEEEEEEEEc
Q 032091 81 LRSPVTKEELVAEVARQLSISIEPENLHLPSP-LSAFGEYEVPMRLPKAIPLPEGKVQWTLNVKVRG 146 (147)
Q Consensus 81 LfGSVT~~dI~~~l~~q~gi~Idk~~I~l~~p-Ik~lG~~~V~I~L~~~V~~~~~~~~a~l~V~V~~ 146 (147)
||||||++||+++|+++ |++|||+.|.||+| ||++|+|.|.|+||++| +++++|+|.+
T Consensus 89 lfGSVt~~~I~~~l~~~-g~~idk~~I~l~~~~Ik~~G~y~v~i~L~~~V-------~a~i~v~V~~ 147 (148)
T TIGR00158 89 LFGSITTKQIADALKAA-GLDLDKKKIELPDGVIRTTGEHEVTIKLHEEV-------FAVLKVIVVP 147 (148)
T ss_pred EEEeECHHHHHHHHHHc-CCcccHhhEECCCCceeceEEEEEEEEEcCCc-------EEEEEEEEEE
Confidence 99999999999999876 99999999999986 99999999999999999 9999999975
No 3
>COG0359 RplI Ribosomal protein L9 [Translation, ribosomal structure and biogenesis]
Probab=99.96 E-value=8.9e-29 Score=192.66 Aligned_cols=116 Identities=22% Similarity=0.322 Sum_probs=108.4
Q ss_pred CCCcccccccHHHHHHHHHHHHhcCcchHHHHHHhhhhHHHHHHHHHHHHHHhccCceEEEEcccccccccccCCCCCCc
Q 032091 1 MPKLLAVPNIEKFAHLIREQRRICQPVEEEEVKVIRKSEDNMSREFEKAARRLENARLVLRRFPNIEKLRSRASKDDPIE 80 (147)
Q Consensus 1 ~p~~la~~a~~~~~~~~~~~~~~~~~~~~e~~k~i~k~~~~~~~eae~~a~~L~~~~l~i~~~~g~~~~~~~~~~~~~gk 80 (147)
+||+||++||+.|+..++.+++..+. +....+++++++++.|++..+.+..++|++ |+
T Consensus 31 iPkglAv~At~~n~~~~e~~r~~~e~-----------~~~~~~~~a~~lk~~Le~~~~~i~~kag~~-----------Gk 88 (148)
T COG0359 31 IPKGLAVPATKGNLKLLEARRAKLEK-----------KAAEELAEAEALKEKLEGKTVEIAVKAGED-----------GK 88 (148)
T ss_pred ccccchhhCCHHHHHHHHHHHHHHHH-----------HHHHHHHHHHHHHHHhhCceEEEEEEcCCC-----------Cc
Confidence 69999999999999999997776666 777888999999999999889999999966 59
Q ss_pred eeeccCHHHHHHHHHhhcCCccccccccCCCccccceeEEEEEEcCCCCCCCCCceEEEEEEEEEc
Q 032091 81 LRSPVTKEELVAEVARQLSISIEPENLHLPSPLSAFGEYEVPMRLPKAIPLPEGKVQWTLNVKVRG 146 (147)
Q Consensus 81 LfGSVT~~dI~~~l~~q~gi~Idk~~I~l~~pIk~lG~~~V~I~L~~~V~~~~~~~~a~l~V~V~~ 146 (147)
||||||++||++++.++ |++|||++|.||++|+++|+|+|+|+||++| +++++|.|.+
T Consensus 89 lfGSVt~~dIa~~l~~~-g~~idk~~i~l~~~ik~~G~~~V~vkLh~eV-------~a~v~v~V~~ 146 (148)
T COG0359 89 LFGSVTSKDIAEALKAA-GFKLDKRKIRLPNGIKTLGEHEVEVKLHEEV-------TATVKVNVVA 146 (148)
T ss_pred eeccccHHHHHHHHHHc-CCCcchheeEcCchhhhcceeEEEEEecCce-------EEEEEEEEEe
Confidence 99999999999999998 9999999999999999999999999999999 9999999976
No 4
>PRK00137 rplI 50S ribosomal protein L9; Reviewed
Probab=99.95 E-value=5.9e-28 Score=186.79 Aligned_cols=116 Identities=24% Similarity=0.389 Sum_probs=107.9
Q ss_pred CCCcccccccHHHHHHHHHHHHhcCcchHHHHHHhhhhHHHHHHHHHHHHHHhccCceEEEEcccccccccccCCCCCCc
Q 032091 1 MPKLLAVPNIEKFAHLIREQRRICQPVEEEEVKVIRKSEDNMSREFEKAARRLENARLVLRRFPNIEKLRSRASKDDPIE 80 (147)
Q Consensus 1 ~p~~la~~a~~~~~~~~~~~~~~~~~~~~e~~k~i~k~~~~~~~eae~~a~~L~~~~l~i~~~~g~~~~~~~~~~~~~gk 80 (147)
+|++||++||..|+..++..++..+. +.++.++++++++..|++..+++.+++|++ |+
T Consensus 31 iP~~lA~~aT~~~~~~~~~~~~~~~~-----------~~~~~~~~a~~l~~~l~~~~l~i~~k~g~~-----------gk 88 (147)
T PRK00137 31 IPQGKAVRATKGNLKQLEARRAELEA-----------KAAEELAEAEALAEKLEGLTVTIKAKAGED-----------GK 88 (147)
T ss_pred ccCCceeeCCHHHHHHHHHHHHHHHH-----------HHHHHHHHHHHHHHHhhCCEEEEEEEcCCC-----------Ce
Confidence 79999999999999999988777655 677889999999999999999999999855 59
Q ss_pred eeeccCHHHHHHHHHhhcCCccccccccCCCccccceeEEEEEEcCCCCCCCCCceEEEEEEEEEc
Q 032091 81 LRSPVTKEELVAEVARQLSISIEPENLHLPSPLSAFGEYEVPMRLPKAIPLPEGKVQWTLNVKVRG 146 (147)
Q Consensus 81 LfGSVT~~dI~~~l~~q~gi~Idk~~I~l~~pIk~lG~~~V~I~L~~~V~~~~~~~~a~l~V~V~~ 146 (147)
||||||++||+++|.++ |++||++.|.||+||+++|+|.|+|+||++| +|+++|+|.+
T Consensus 89 lfGsVt~~~I~~~l~~~-g~~idk~~I~l~~~Ik~~G~y~v~i~L~~~v-------~a~l~v~V~~ 146 (147)
T PRK00137 89 LFGSVTTKDIAEALKKQ-GIEIDKRKIELPGPIKTLGEYEVPVKLHPEV-------TATIKVNVVA 146 (147)
T ss_pred EEeeeCHHHHHHHHHHc-CCccCHHHeECCCcccccEEEEEEEEECCCc-------EEEEEEEEEE
Confidence 99999999999999887 9999999999999999999999999999999 9999999986
No 5
>PF03948 Ribosomal_L9_C: Ribosomal protein L9, C-terminal domain; InterPro: IPR020069 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L9 is one of the proteins from the large ribosomal subunit. In Escherichia coli, L9 is known to bind directly to the 23S rRNA. It belongs to a family of ribosomal proteins grouped on the basis of sequence similarities [, ]. The crystal structure of Bacillus stearothermophilus L9 shows the 149-residue protein comprises two globular domains connected by a rigid linker []. Each domain contains an rRNA binding site, and the protein functions as a structural protein in the large subunit of the ribosome. The C-terminal domain consists of two loops, an alpha-helix and a three-stranded mixed parallel, anti-parallel beta-sheet packed against the central alpha-helix. The long central alpha-helix is exposed to solvent in the middle and participates in the hydrophobic cores of the two domains at both ends. ; PDB: 3D5B_I 3PYV_H 3F1H_I 3PYR_H 3MRZ_H 1VSP_G 3MS1_H 1VSA_G 3PYT_H 2WH4_I ....
Probab=99.94 E-value=2.4e-26 Score=164.01 Aligned_cols=86 Identities=27% Similarity=0.462 Sum_probs=81.7
Q ss_pred HHHHHHHHHHhccCceEEEEcccccccccccCCCCCCceeeccCHHHHHHHHHhhcCCccccccccCCCccccceeEEEE
Q 032091 43 SREFEKAARRLENARLVLRRFPNIEKLRSRASKDDPIELRSPVTKEELVAEVARQLSISIEPENLHLPSPLSAFGEYEVP 122 (147)
Q Consensus 43 ~~eae~~a~~L~~~~l~i~~~~g~~~~~~~~~~~~~gkLfGSVT~~dI~~~l~~q~gi~Idk~~I~l~~pIk~lG~~~V~ 122 (147)
+++|++++++|++..+++.+++|++ |+||||||++||+++|++++|++|||++|.||+|||++|+|+|+
T Consensus 1 k~~A~~l~~~l~~~~l~i~~k~g~~-----------gklfGSVt~~dIa~~l~~~~g~~Idk~~I~l~~~IK~~G~~~v~ 69 (87)
T PF03948_consen 1 KAEAQALAEKLEGITLTIKRKAGEN-----------GKLFGSVTSKDIAKALKEQTGIEIDKKKIELPEPIKSLGEYEVK 69 (87)
T ss_dssp HHHHHHHHHHHCSSEEEEEECBSSC-----------SSBSSEBSHHHHHHHHHHCCSSSSSSSSBCSSSTBESSEEEEEE
T ss_pred CHHHHHHHHHhcCCEEEEEEEecCC-----------cceecCcCHHHHHHHHHHhhCCeEeccEEECCCchhccEEEEEE
Confidence 4688999999999999999999865 59999999999999999988999999999999999999999999
Q ss_pred EEcCCCCCCCCCceEEEEEEEEEc
Q 032091 123 MRLPKAIPLPEGKVQWTLNVKVRG 146 (147)
Q Consensus 123 I~L~~~V~~~~~~~~a~l~V~V~~ 146 (147)
|+||++| +|+++|+|.+
T Consensus 70 v~L~~~V-------~a~i~v~V~~ 86 (87)
T PF03948_consen 70 VKLHPEV-------SAKIKVNVVA 86 (87)
T ss_dssp EEEETTE-------EEEEEEEEEE
T ss_pred EEeCCCe-------EEEEEEEEEe
Confidence 9999999 9999999975
No 6
>PRK14538 putative bifunctional signaling protein/50S ribosomal protein L9; Provisional
Probab=99.92 E-value=5e-25 Score=207.44 Aligned_cols=117 Identities=17% Similarity=0.214 Sum_probs=109.5
Q ss_pred CCCcccccccHHHHHHHHHHHHhcCcchHHHHHHhhhhHHHHHHHHHHHHHHhccCceEEEEcccccccccccCCCCCCc
Q 032091 1 MPKLLAVPNIEKFAHLIREQRRICQPVEEEEVKVIRKSEDNMSREFEKAARRLENARLVLRRFPNIEKLRSRASKDDPIE 80 (147)
Q Consensus 1 ~p~~la~~a~~~~~~~~~~~~~~~~~~~~e~~k~i~k~~~~~~~eae~~a~~L~~~~l~i~~~~g~~~~~~~~~~~~~gk 80 (147)
+|++||++||+.|++.++.+++..+. +.++.+++|++++++|++.++++.+++|++ |+
T Consensus 718 iP~~~A~~aT~~nlk~~e~~~~~~~~-----------~~~~~~~~a~~l~~~l~~~~~~i~~k~ge~-----------gk 775 (838)
T PRK14538 718 IQNKKALLADKENLAKIKKKKILEQE-----------KKRNHELLMKKLKSEIDNKKITLDIQLGPK-----------GK 775 (838)
T ss_pred ccCCchhhcCHHHHHHHHHHHHHHHH-----------HHHHHHHHHHHHHHHhhCcEEEEEEEeCCC-----------Ce
Confidence 79999999999999999998877666 777888999999999999999999999966 49
Q ss_pred eeeccCHHHHHHHHHhhcCCccccccccCCCccccceeEEEEEEcCCCCCCCCCceEEEEEEEEEc
Q 032091 81 LRSPVTKEELVAEVARQLSISIEPENLHLPSPLSAFGEYEVPMRLPKAIPLPEGKVQWTLNVKVRG 146 (147)
Q Consensus 81 LfGSVT~~dI~~~l~~q~gi~Idk~~I~l~~pIk~lG~~~V~I~L~~~V~~~~~~~~a~l~V~V~~ 146 (147)
||||||++||+++|++++|++|||+.|.||+|||++|+|.|.|+||++| +|+++|+|+.
T Consensus 776 lfGSVt~~~I~~~l~~~~g~~idk~~I~l~~~Ik~~G~~~v~i~L~~~V-------~a~i~v~V~~ 834 (838)
T PRK14538 776 IYGKITLKQIVEEFHKIHNITIDRKKISLENEIISVGIYPVDVFLTDQI-------KATFFLNVIE 834 (838)
T ss_pred eeeccCHHHHHHHHHHhhCCccccceeeCCCcccccEEEEEEEEEcCCe-------EEEEEEEEEE
Confidence 9999999999999998889999999999999999999999999999999 9999999974
No 7
>KOG4607 consensus Mitochondrial ribosomal protein L9 [Translation, ribosomal structure and biogenesis]
Probab=97.88 E-value=2.4e-05 Score=64.78 Aligned_cols=113 Identities=19% Similarity=0.172 Sum_probs=76.8
Q ss_pred CCCcccccccHHHHHH--HHHHHHhcCcchHHHHHHhhhhHHHHHHHHHHHHHHhccCceEEEEcccccccccccCCCCC
Q 032091 1 MPKLLAVPNIEKFAHL--IREQRRICQPVEEEEVKVIRKSEDNMSREFEKAARRLENARLVLRRFPNIEKLRSRASKDDP 78 (147)
Q Consensus 1 ~p~~la~~a~~~~~~~--~~~~~~~~~~~~~e~~k~i~k~~~~~~~eae~~a~~L~~~~l~i~~~~g~~~~~~~~~~~~~ 78 (147)
||++||+.|+-.|... +.++++.+... .-..++..++ -|+...+.....-+...
T Consensus 79 lp~glAvy~tp~~~~~~k~~~~e~~~~k~-------------~vk~e~k~V~-~lqt~v~~~~~~k~~kw---------- 134 (222)
T KOG4607|consen 79 LPKGLAVYNTPLNLKKYKLREQEEEAEKI-------------RVKEEAKVVA-VLQTVVLFKVMNKGGKW---------- 134 (222)
T ss_pred ccccccccCChhhHHHHHHHHHHHHhhhh-------------ccHHHHHHHH-HHHhhhhhheeccCCce----------
Confidence 7999999999999433 33344333331 1222232333 45544433333333221
Q ss_pred CceeeccCHHHHHHHHHhhcCCccccccccCCCccccceeEEEEEEcCCCCCCCCCceEEEEEEEEE
Q 032091 79 IELRSPVTKEELVAEVARQLSISIEPENLHLPSPLSAFGEYEVPMRLPKAIPLPEGKVQWTLNVKVR 145 (147)
Q Consensus 79 gkLfGSVT~~dI~~~l~~q~gi~Idk~~I~l~~pIk~lG~~~V~I~L~~~V~~~~~~~~a~l~V~V~ 145 (147)
-=-|++|+++.....+.+++-+.+|++-|+.|. ++.-|+|.+.|+++++. ++-+...|.
T Consensus 135 ~l~~~~V~~~l~~gv~~~~~t~~l~k~~vs~P~-~k~e~~~~~~V~in~~~-------~vr~~~~v~ 193 (222)
T KOG4607|consen 135 KLNPNLVKASLRKGVIVAELTIKLDKELVSGPI-TKEEGEYICEVKINPDV-------TVRVKIRVT 193 (222)
T ss_pred eecHHHHHHHHhcceEeccccccCcccccCCCc-ccccceEEEEEEECCcc-------eEEeeeeee
Confidence 135899999998888877788999999999986 78888999999999999 888777664
No 8
>PF01281 Ribosomal_L9_N: Ribosomal protein L9, N-terminal domain; InterPro: IPR020070 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L9 is one of the proteins from the large ribosomal subunit. In Escherichia coli, L9 is known to bind directly to the 23S rRNA. It belongs to a family of ribosomal proteins grouped on the basis of sequence similarities [, ]. The crystal structure of Bacillus stearothermophilus L9 shows the 149-residue protein comprises two globular domains connected by a rigid linker []. Each domain contains an rRNA binding site, and the protein functions as a structural protein in the large subunit of the ribosome. The C-terminal domain consists of two loops, an alpha-helix and a three-stranded mixed parallel, anti-parallel beta-sheet packed against the central alpha-helix. The long central alpha-helix is exposed to solvent in the middle and participates in the hydrophobic cores of the two domains at both ends. ; PDB: 3D5B_I 3PYV_H 3F1H_I 3PYR_H 3MRZ_H 1VSP_G 3MS1_H 1VSA_G 3PYT_H 2WH4_I ....
Probab=85.72 E-value=0.58 Score=30.26 Aligned_cols=18 Identities=22% Similarity=0.217 Sum_probs=16.3
Q ss_pred CCCcccccccHHHHHHHH
Q 032091 1 MPKLLAVPNIEKFAHLIR 18 (147)
Q Consensus 1 ~p~~la~~a~~~~~~~~~ 18 (147)
+|+++|+.||..+++.++
T Consensus 31 ~p~~~A~~at~~~~~~~e 48 (48)
T PF01281_consen 31 IPQGLAVYATPENLKQLE 48 (48)
T ss_dssp TTTTSEEECSHHHHHHHH
T ss_pred cCCCceeeCCHHHHHhcC
Confidence 699999999999998764
No 9
>PF10045 DUF2280: Uncharacterized conserved protein (DUF2280); InterPro: IPR018738 This entry is represented by Burkholderia phage Bups phi1, Orf2.36. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=68.67 E-value=2.2 Score=31.96 Aligned_cols=32 Identities=19% Similarity=0.335 Sum_probs=28.2
Q ss_pred CHHHHHHHHHhhcCCccccccccCCCccccce
Q 032091 86 TKEELVAEVARQLSISIEPENLHLPSPLSAFG 117 (147)
Q Consensus 86 T~~dI~~~l~~q~gi~Idk~~I~l~~pIk~lG 117 (147)
|+.++++++++.+|++|++..++.-+|=|.-|
T Consensus 21 TPs~v~~aVk~eFgi~vsrQqve~yDPTK~aG 52 (104)
T PF10045_consen 21 TPSEVAEAVKEEFGIDVSRQQVESYDPTKRAG 52 (104)
T ss_pred CHHHHHHHHHHHhCCccCHHHHHHcCchHHHH
Confidence 89999999999999999999998777776655
No 10
>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=62.52 E-value=7.1 Score=23.75 Aligned_cols=17 Identities=12% Similarity=0.251 Sum_probs=15.4
Q ss_pred CceeeccCHHHHHHHHH
Q 032091 79 IELRSPVTKEELVAEVA 95 (147)
Q Consensus 79 gkLfGSVT~~dI~~~l~ 95 (147)
|++-|.||..||..++.
T Consensus 40 ~~~~G~is~~dl~~~l~ 56 (57)
T PF00571_consen 40 GKLVGIISRSDLLKALL 56 (57)
T ss_dssp SBEEEEEEHHHHHHHHH
T ss_pred CEEEEEEEHHHHHhhhh
Confidence 59999999999999874
No 11
>PF08766 DEK_C: DEK C terminal domain; InterPro: IPR014876 DEK is a chromatin associated protein that is linked with cancers and autoimmune disease. This domain is found at the C-terminal of DEK and is of clinical importance since it can reverse the characteristic abnormal DNA-mutagen sensitivity in fibroblasts from ataxia-telangiectasia (A-T) patients []. The structure of this domain shows it to be homologous to the E2F/DP transcription factor family []. This domain is also found in chitin synthase proteins like Q8TF96 from SWISSPROT, and in protein phosphatases such as Q6NN85 from SWISSPROT. ; PDB: 1Q1V_A.
Probab=47.60 E-value=10 Score=24.28 Aligned_cols=25 Identities=12% Similarity=0.351 Sum_probs=16.5
Q ss_pred eeccCHHHHHHHHHhhcCCcccccc
Q 032091 82 RSPVTKEELVAEVARQLSISIEPEN 106 (147)
Q Consensus 82 fGSVT~~dI~~~l~~q~gi~Idk~~ 106 (147)
+.+||.++|-.+|.+.+|+++..++
T Consensus 18 l~~vT~k~vr~~Le~~~~~dL~~~K 42 (54)
T PF08766_consen 18 LDTVTKKQVREQLEERFGVDLSSRK 42 (54)
T ss_dssp GGG--HHHHHHHHHHH-SS--SHHH
T ss_pred HhHhhHHHHHHHHHHHHCCCcHHHH
Confidence 4569999999999999998887544
No 12
>PF13592 HTH_33: Winged helix-turn helix
Probab=35.60 E-value=22 Score=23.00 Aligned_cols=34 Identities=18% Similarity=0.281 Sum_probs=25.5
Q ss_pred eccCHHHHHHHHHhhcCCccccccccCCCcccccee
Q 032091 83 SPVTKEELVAEVARQLSISIEPENLHLPSPLSAFGE 118 (147)
Q Consensus 83 GSVT~~dI~~~l~~q~gi~Idk~~I~l~~pIk~lG~ 118 (147)
|--|..+|++.|.+.+|+.+....|. .-++.+|-
T Consensus 3 ~~wt~~~i~~~I~~~fgv~ys~~~v~--~lL~r~G~ 36 (60)
T PF13592_consen 3 GRWTLKEIAAYIEEEFGVKYSPSGVY--RLLKRLGF 36 (60)
T ss_pred CcccHHHHHHHHHHHHCCEEcHHHHH--HHHHHcCC
Confidence 45799999999999999998877663 13555553
No 13
>PF07523 Big_3: Bacterial Ig-like domain (group 3); InterPro: IPR011080 This entry represents bacterial domains with an Ig-like fold. These domains are found in a variety of bacterial surface proteins.; PDB: 2L7Y_A 2KPN_A.
Probab=34.89 E-value=61 Score=21.05 Aligned_cols=24 Identities=29% Similarity=0.351 Sum_probs=19.7
Q ss_pred cccceeEEEEEEcCCCCCCCCCceEEEEEEEE
Q 032091 113 LSAFGEYEVPMRLPKAIPLPEGKVQWTLNVKV 144 (147)
Q Consensus 113 Ik~lG~~~V~I~L~~~V~~~~~~~~a~l~V~V 144 (147)
-...|.|.|.+.... . +++++|.|
T Consensus 44 ~~~~G~y~Vt~~y~~-~-------t~t~~VtV 67 (67)
T PF07523_consen 44 TSKAGTYTVTYTYKG-V-------TATFTVTV 67 (67)
T ss_dssp TTS-CCEEEEEEECT-E-------EEEEEEEE
T ss_pred cCCCceEEEEEEECC-E-------EEEEEEEC
Confidence 567899999999887 6 88988876
No 14
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp. (strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.
Probab=33.97 E-value=1.1e+02 Score=20.68 Aligned_cols=55 Identities=18% Similarity=0.149 Sum_probs=37.9
Q ss_pred HHHhhhhHHHHHHHHHHHHHHhccCceEEEEccc-ccccccccCCCCCCceeeccCHHHHHHHH
Q 032091 32 VKVIRKSEDNMSREFEKAARRLENARLVLRRFPN-IEKLRSRASKDDPIELRSPVTKEELVAEV 94 (147)
Q Consensus 32 ~k~i~k~~~~~~~eae~~a~~L~~~~l~i~~~~g-~~~~~~~~~~~~~gkLfGSVT~~dI~~~l 94 (147)
+++|.++..--..-++++...|....++-..+ | .+|+.+.....+ ||-.||+.++
T Consensus 28 ~~eiA~~~~i~~~~l~kil~~L~~~Gli~s~~-G~~GGy~L~~~~~~-------Itl~dI~~av 83 (83)
T PF02082_consen 28 SKEIAERLGISPSYLRKILQKLKKAGLIESSR-GRGGGYRLARPPEE-------ITLLDIVRAV 83 (83)
T ss_dssp HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET-STTSEEEESS-CCG-------SBHHHHHHHH
T ss_pred HHHHHHHHCcCHHHHHHHHHHHhhCCeeEecC-CCCCceeecCCHHH-------CCHHHHHHhC
Confidence 45666666667777888888999888854444 5 577777666554 8888888764
No 15
>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=33.40 E-value=30 Score=18.66 Aligned_cols=16 Identities=19% Similarity=0.308 Sum_probs=13.6
Q ss_pred CceeeccCHHHHHHHH
Q 032091 79 IELRSPVTKEELVAEV 94 (147)
Q Consensus 79 gkLfGSVT~~dI~~~l 94 (147)
+++.|.++..++...+
T Consensus 33 ~~~~g~i~~~~l~~~~ 48 (49)
T smart00116 33 GRLVGIVTRRDIIKAL 48 (49)
T ss_pred CeEEEEEEHHHHHHhh
Confidence 4899999999997765
No 16
>PF14221 DUF4330: Domain of unknown function (DUF4330)
Probab=32.58 E-value=33 Score=27.02 Aligned_cols=19 Identities=16% Similarity=0.095 Sum_probs=15.1
Q ss_pred CCCceeeccCHHHHHHHHH
Q 032091 77 DPIELRSPVTKEELVAEVA 95 (147)
Q Consensus 77 ~~gkLfGSVT~~dI~~~l~ 95 (147)
+.|+|||.|+.=|+...|.
T Consensus 6 ~kGrlFgkiniiDl~~~lv 24 (168)
T PF14221_consen 6 SKGRLFGKINIIDLLAILV 24 (168)
T ss_pred cCCcEeeeEeHHHHHHHHH
Confidence 4579999999999776543
No 17
>PF08960 DUF1874: Domain of unknown function (DUF1874); InterPro: IPR015055 This entry is represented by Acidianus two-tailed virus, Orf117. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.; PDB: 2J85_A 2X4I_C.
Probab=28.36 E-value=1.2e+02 Score=22.54 Aligned_cols=54 Identities=20% Similarity=0.324 Sum_probs=24.6
Q ss_pred CceeeccCHHHHHHHHHhhcCCccccccccCCCccccceeEEEEEEcCCCCCCCCCceE
Q 032091 79 IELRSPVTKEELVAEVARQLSISIEPENLHLPSPLSAFGEYEVPMRLPKAIPLPEGKVQ 137 (147)
Q Consensus 79 gkLfGSVT~~dI~~~l~~q~gi~Idk~~I~l~~pIk~lG~~~V~I~L~~~V~~~~~~~~ 137 (147)
+.+-.+|.=++-++.+...+|..|....+.+ --.-|.--+.++|.. |+|||++.
T Consensus 37 ~~~vSaIGH~sTa~lls~llg~~ip~NR~~i---~~~~Gd~alv~~L~~--Rl~EG~Vl 90 (105)
T PF08960_consen 37 EGFVSAIGHDSTAQLLSELLGVNIPMNRIQI---KLDPGDKALVFQLKQ--RLPEGKVL 90 (105)
T ss_dssp TTEEE----HHHHHHHHHHHT--------------B-TT-EEEEEEESS-----TT---
T ss_pred CceEEeeCcHHHHHHHHHHhCCccccccEEE---EecCCCEEEEEEecc--cCCCCcCC
Confidence 4678888888889999888887666555544 224577777888877 66999875
No 18
>cd04608 CBS_pair_PALP_assoc This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the pyridoxal-phosphate (PALP) dependent enzyme domain upstream. The vitamin B6 complex comprises pyridoxine, pyridoxal, and pyridoxamine, as well as the 5'-phosphate esters of pyridoxal (PALP) and pyridoxamine, the last two being the biologically active coenzyme derivatives. The members of the PALP family are principally involved in the biosynthesis of amino acids and amino acid-derived metabolites, but they are also found in the biosynthetic pathways of amino sugars and other amine-containing compounds. 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 poten
Probab=26.72 E-value=32 Score=24.23 Aligned_cols=18 Identities=22% Similarity=0.156 Sum_probs=15.2
Q ss_pred CCCceeeccCHHHHHHHH
Q 032091 77 DPIELRSPVTKEELVAEV 94 (147)
Q Consensus 77 ~~gkLfGSVT~~dI~~~l 94 (147)
++|++-|.||..||..++
T Consensus 107 ~~~~~~Givt~~Dl~~~~ 124 (124)
T cd04608 107 KQEKPIGIVTKIDLLSYI 124 (124)
T ss_pred cccceEEEEehhHhhhhC
Confidence 457999999999998753
No 19
>cd01793 Fubi Fubi ubiquitin-like protein. Fubi is a ubiquitin-like protein encoded by the fau gene which has an N-terminal ubiquitin-like domain (also referred to as FUBI) fused to the ribosomal protein S30. Fubi is thought to be a tumor suppressor protein and the FUBI domain may act as a substitute or an inhibitor of ubiquitin or one of ubiquitin's close relatives UCRP, FAT10, and Nedd8.
Probab=24.57 E-value=53 Score=21.67 Aligned_cols=41 Identities=27% Similarity=0.311 Sum_probs=28.1
Q ss_pred ceeeccCHHHHHHHHHhhcCCcccccccc-----CCCccccceeEEE
Q 032091 80 ELRSPVTKEELVAEVARQLSISIEPENLH-----LPSPLSAFGEYEV 121 (147)
Q Consensus 80 kLfGSVT~~dI~~~l~~q~gi~Idk~~I~-----l~~pIk~lG~~~V 121 (147)
.+..+-|..++-..+....|+..+.-.+. |.+ =++|+.|.+
T Consensus 14 ~v~~~~tV~~lK~~i~~~~gip~~~q~Li~~Gk~L~D-~~tL~~~~i 59 (74)
T cd01793 14 EVTGQETVSDIKAHVAGLEGIDVEDQVLLLAGVPLED-DATLGQCGV 59 (74)
T ss_pred EECCcCcHHHHHHHHHhhhCCCHHHEEEEECCeECCC-CCCHHHcCC
Confidence 34567899999999988888877765542 332 256777665
No 20
>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=24.41 E-value=71 Score=21.15 Aligned_cols=18 Identities=28% Similarity=0.220 Sum_probs=15.5
Q ss_pred CceeeccCHHHHHHHHHh
Q 032091 79 IELRSPVTKEELVAEVAR 96 (147)
Q Consensus 79 gkLfGSVT~~dI~~~l~~ 96 (147)
|++.|.||..|+...+..
T Consensus 34 ~~~~G~v~~~~l~~~~~~ 51 (112)
T cd04624 34 ERPIGIVTERDIVRAVAA 51 (112)
T ss_pred CCEEEEeeHHHHHHHHhc
Confidence 599999999999887654
No 21
>cd04623 CBS_pair_10 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=23.92 E-value=70 Score=20.99 Aligned_cols=18 Identities=22% Similarity=0.224 Sum_probs=15.8
Q ss_pred CceeeccCHHHHHHHHHh
Q 032091 79 IELRSPVTKEELVAEVAR 96 (147)
Q Consensus 79 gkLfGSVT~~dI~~~l~~ 96 (147)
|++.|.||..|+...+..
T Consensus 34 ~~~~Giv~~~~l~~~~~~ 51 (113)
T cd04623 34 GRLVGIFSERDIVRKVAL 51 (113)
T ss_pred CCEEEEEehHHHHHHHhh
Confidence 599999999999988764
No 22
>cd02980 TRX_Fd_family Thioredoxin (TRX)-like [2Fe-2S] Ferredoxin (Fd) family; composed of [2Fe-2S] Fds with a TRX fold (TRX-like Fds) and proteins containing domains similar to TRX-like Fd including formate dehydrogenases, NAD-reducing hydrogenases and the subunit E of NADH:ubiquinone oxidoreductase (NuoE). TRX-like Fds are soluble low-potential electron carriers containing a single [2Fe-2S] cluster. The exact role of TRX-like Fd is still unclear. It has been suggested that it may be involved in nitrogen fixation. Its homologous domains in large redox enzymes (such as Nuo and hydrogenases) function as electron carriers.
Probab=23.14 E-value=84 Score=20.34 Aligned_cols=17 Identities=24% Similarity=0.057 Sum_probs=15.0
Q ss_pred CceeeccCHHHHHHHHH
Q 032091 79 IELRSPVTKEELVAEVA 95 (147)
Q Consensus 79 gkLfGSVT~~dI~~~l~ 95 (147)
+.+||-||+.++.+.|.
T Consensus 59 ~~~y~~v~~~~~~~il~ 75 (77)
T cd02980 59 GVWYGRVTPEDVEEIVE 75 (77)
T ss_pred CeEEccCCHHHHHHHHH
Confidence 58999999999988775
No 23
>cd04643 CBS_pair_30 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=22.93 E-value=75 Score=21.09 Aligned_cols=17 Identities=0% Similarity=0.079 Sum_probs=15.1
Q ss_pred CceeeccCHHHHHHHHH
Q 032091 79 IELRSPVTKEELVAEVA 95 (147)
Q Consensus 79 gkLfGSVT~~dI~~~l~ 95 (147)
|++.|.||..||...+.
T Consensus 34 ~~~~Giv~~~dl~~~~~ 50 (116)
T cd04643 34 GKYVGTISLTDILWKLK 50 (116)
T ss_pred CcEEEEEeHHHHHHHhh
Confidence 59999999999988775
No 24
>cd05718 Ig1_PVR_like First immunoglobulin (Ig) domain of poliovirus receptor (PVR, also known as CD155) and similar proteins. Ig1_PVR_like: domain similar to the first immunoglobulin (Ig) domain of poliovirus receptor (PVR, also known as CD155). Poliovirus (PV) binds to its cellular receptor (PVR/CD155) to initiate infection. CD155 is a membrane-anchored, single-span glycoprotein; its extracellular region has three Ig-like domains. There are four different isotypes of CD155 (referred to as alpha, beta, gamma, and delta), that result from alternate splicing of the CD155 mRNA, and have identical extracellular domains. CD155-beta and - gamma, are secreted, CD155-alpha and delta are membrane-bound and function as PV receptors. The virus recognition site is contained in the amino-terminal domain, D1. Having the virus attachment site on the receptor distal from the plasma membrane, may be important for successful initiation of infection of cells by the virus. CD155 binds in the poliovirus "c
Probab=22.75 E-value=1.9e+02 Score=19.12 Aligned_cols=27 Identities=26% Similarity=0.327 Sum_probs=20.9
Q ss_pred cccceeEEEEEEcCCCCCCCCCceEEEEEEEE
Q 032091 113 LSAFGEYEVPMRLPKAIPLPEGKVQWTLNVKV 144 (147)
Q Consensus 113 Ik~lG~~~V~I~L~~~V~~~~~~~~a~l~V~V 144 (147)
..-=|.|.+.+..+ |.|..++.+.+.|
T Consensus 71 ~~D~G~Y~C~v~~~-----~~g~~~~~~~l~V 97 (98)
T cd05718 71 LEDEGNYICEFATF-----PQGNRQKVTTLTV 97 (98)
T ss_pred cccCEEEEEEEEeC-----CCCcEEEEEEEEe
Confidence 44569999999844 5677799998887
No 25
>cd04630 CBS_pair_17 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic gener
Probab=22.65 E-value=69 Score=21.50 Aligned_cols=18 Identities=17% Similarity=0.217 Sum_probs=15.5
Q ss_pred CceeeccCHHHHHHHHHh
Q 032091 79 IELRSPVTKEELVAEVAR 96 (147)
Q Consensus 79 gkLfGSVT~~dI~~~l~~ 96 (147)
|++.|.||..|+...+..
T Consensus 35 ~~~~G~v~~~dl~~~~~~ 52 (114)
T cd04630 35 SDAYGIVTMRDILKKVVA 52 (114)
T ss_pred CcEEEEEehHHHHHHHHh
Confidence 599999999999987654
No 26
>PF01282 Ribosomal_S24e: Ribosomal protein S24e; InterPro: IPR001976 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family contains the S24e ribosomal proteins from eukaryotes and archaebacteria. These proteins have 101 to 148 amino acids.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2V94_B 1YWX_A 2G1D_A 3IZ6_U 1XN9_A 2XZM_P 2XZN_P 3U5G_Y 3J16_D 3IZB_U ....
Probab=22.65 E-value=55 Score=23.04 Aligned_cols=37 Identities=16% Similarity=0.319 Sum_probs=26.9
Q ss_pred eccCHHHHHHHHHhhcCCccccccccCCCccccceeEEE
Q 032091 83 SPVTKEELVAEVARQLSISIEPENLHLPSPLSAFGEYEV 121 (147)
Q Consensus 83 GSVT~~dI~~~l~~q~gi~Idk~~I~l~~pIk~lG~~~V 121 (147)
+..+-.||.+.|++.+| +|+..|.+-.--..+|.+..
T Consensus 11 ~Tpsr~ei~~klA~~~~--~~~~~ivv~~~~t~fG~~~s 47 (84)
T PF01282_consen 11 PTPSRKEIREKLAAMLN--VDPDLIVVFGIKTEFGGGKS 47 (84)
T ss_dssp SS--HHHHHHHHHHHHT--STGCCEEEEEEEESSSSSEE
T ss_pred CCCCHHHHHHHHHHHhC--CCCCeEEEeccEecCCCceE
Confidence 56899999999999876 58888888665557766643
No 27
>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=22.37 E-value=77 Score=21.40 Aligned_cols=19 Identities=26% Similarity=0.366 Sum_probs=15.7
Q ss_pred CCceeeccCHHHHHHHHHh
Q 032091 78 PIELRSPVTKEELVAEVAR 96 (147)
Q Consensus 78 ~gkLfGSVT~~dI~~~l~~ 96 (147)
+|++.|.||..|+...+..
T Consensus 33 ~g~~~G~vt~~dl~~~~~~ 51 (114)
T cd04619 33 HGKLAGVLTKTDVVRQMGR 51 (114)
T ss_pred CCCEEEEEehHHHHHHHhh
Confidence 3599999999999887643
No 28
>KOG2639 consensus Sodium sulfate symporter and related arsenite permeases [Inorganic ion transport and metabolism]
Probab=22.27 E-value=71 Score=30.76 Aligned_cols=31 Identities=16% Similarity=0.071 Sum_probs=24.4
Q ss_pred cCCCCCCceeeccCHHHHHHHHHhhcCCcccc
Q 032091 73 ASKDDPIELRSPVTKEELVAEVARQLSISIEP 104 (147)
Q Consensus 73 ~~~~~~gkLfGSVT~~dI~~~l~~q~gi~Idk 104 (147)
+.-|++|.|.|| ++.-|+..+++|||+.+.=
T Consensus 623 a~~gGNgTLiGa-sANvv~A~iAeqHGYkltF 653 (685)
T KOG2639|consen 623 ACLGGNGTLIGA-SANVVAAGIAEQHGYKLTF 653 (685)
T ss_pred hhhcCCceeech-hhHHHHHHHHHHcCceEEe
Confidence 345677899998 6777888899999988753
No 29
>smart00557 IG_FLMN Filamin-type immunoglobulin domains. These form a rod-like structure in the actin-binding cytoskeleton protein, filamin. The C-terminal repeats of filamin bind beta1-integrin (CD29).
Probab=21.97 E-value=1.4e+02 Score=20.50 Aligned_cols=27 Identities=15% Similarity=0.324 Sum_probs=20.8
Q ss_pred cccceeEEEEEEcCCCCCCCCCceEEEE
Q 032091 113 LSAFGEYEVPMRLPKAIPLPEGKVQWTL 140 (147)
Q Consensus 113 Ik~lG~~~V~I~L~~~V~~~~~~~~a~l 140 (147)
-+.-|.|.|.|.+. +.++|+.|-.+.+
T Consensus 64 P~~~G~~~i~V~~~-g~~I~gSPF~v~V 90 (93)
T smart00557 64 PTEPGDYTVTVKFG-GEHIPGSPFTVKV 90 (93)
T ss_pred eCCCEeEEEEEEEC-CEECCCCCEEEEE
Confidence 45669999999976 5778888877654
No 30
>PF05157 T2SE_Nter: Type II secretion system (T2SS), protein E, N-terminal domain; InterPro: IPR007831 This domain is found at the N terminus of members of the general secretory system II protein E. Proteins in this subfamily are typically involved in Type IV pilus biogenesis (e.g. Q9X4G8 from SWISSPROT), though some are involved in other processes; for instance aggregation in Myxococcus xanthus (e.g. Q9RF11 from SWISSPROT) [].; GO: 0005524 ATP binding, 0006810 transport; PDB: 2D27_A 2D28_C.
Probab=21.42 E-value=70 Score=21.61 Aligned_cols=26 Identities=19% Similarity=0.501 Sum_probs=15.9
Q ss_pred eccCHHHHHHHHHhhcCCc-ccccccc
Q 032091 83 SPVTKEELVAEVARQLSIS-IEPENLH 108 (147)
Q Consensus 83 GSVT~~dI~~~l~~q~gi~-Idk~~I~ 108 (147)
|-||..++..+|++++|+. +|...+.
T Consensus 5 g~ise~~l~~~la~~~~l~~~~~~~~~ 31 (109)
T PF05157_consen 5 GLISEDQLLEALAEQLGLPFVDLDELP 31 (109)
T ss_dssp T-S-HHHHHHHHHHHHT--B--GGGS-
T ss_pred CCCCHHHHHHHHHHHhCCCeechhhcC
Confidence 6799999999999999986 4444443
No 31
>cd04632 CBS_pair_19 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic gener
Probab=21.40 E-value=76 Score=21.75 Aligned_cols=17 Identities=29% Similarity=0.305 Sum_probs=14.6
Q ss_pred CceeeccCHHHHHHHHH
Q 032091 79 IELRSPVTKEELVAEVA 95 (147)
Q Consensus 79 gkLfGSVT~~dI~~~l~ 95 (147)
|++.|.||..|+...+.
T Consensus 34 ~~~~G~it~~dl~~~~~ 50 (128)
T cd04632 34 GKLTGIVTRHDIVDFVV 50 (128)
T ss_pred CcEEEEEEHHHHHHHHh
Confidence 59999999999987753
No 32
>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=21.08 E-value=81 Score=20.82 Aligned_cols=18 Identities=17% Similarity=0.209 Sum_probs=15.6
Q ss_pred CceeeccCHHHHHHHHHh
Q 032091 79 IELRSPVTKEELVAEVAR 96 (147)
Q Consensus 79 gkLfGSVT~~dI~~~l~~ 96 (147)
|++.|.||..|+...+..
T Consensus 35 ~~~~G~v~~~~l~~~~~~ 52 (111)
T cd04590 35 DNIIGVVHVKDLLRALAE 52 (111)
T ss_pred ceEEEEEEHHHHHHHHHc
Confidence 599999999999988753
No 33
>cd04629 CBS_pair_16 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=20.94 E-value=93 Score=20.56 Aligned_cols=18 Identities=6% Similarity=0.123 Sum_probs=15.5
Q ss_pred CceeeccCHHHHHHHHHh
Q 032091 79 IELRSPVTKEELVAEVAR 96 (147)
Q Consensus 79 gkLfGSVT~~dI~~~l~~ 96 (147)
|++.|.||..+|..++..
T Consensus 34 ~~~~G~v~~~~l~~~~~~ 51 (114)
T cd04629 34 GNLVGFLSEQDCLKQLLE 51 (114)
T ss_pred CeEEEEeehHHHHHHhhh
Confidence 599999999999987754
No 34
>COG2047 Uncharacterized protein (ATP-grasp superfamily) [General function prediction only]
Probab=20.90 E-value=70 Score=27.43 Aligned_cols=25 Identities=20% Similarity=0.335 Sum_probs=21.0
Q ss_pred CceeeccCHHHHHHHHHhhcCCcccc
Q 032091 79 IELRSPVTKEELVAEVARQLSISIEP 104 (147)
Q Consensus 79 gkLfGSVT~~dI~~~l~~q~gi~Idk 104 (147)
-+++|.||..++++.|++ +|+..-.
T Consensus 135 p~VlGA~ts~eLi~~lke-~gV~fr~ 159 (258)
T COG2047 135 PRVLGAVTSKELIEELKE-HGVEFRS 159 (258)
T ss_pred ceeEEecCCHHHHHHHHH-cCeEecc
Confidence 489999999999999987 5876543
No 35
>cd04639 CBS_pair_26 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=20.71 E-value=98 Score=20.41 Aligned_cols=18 Identities=22% Similarity=0.362 Sum_probs=15.5
Q ss_pred CceeeccCHHHHHHHHHh
Q 032091 79 IELRSPVTKEELVAEVAR 96 (147)
Q Consensus 79 gkLfGSVT~~dI~~~l~~ 96 (147)
|++.|.||..++...+..
T Consensus 34 ~~~~G~v~~~~l~~~~~~ 51 (111)
T cd04639 34 GHLVGLLTRDDLIRALAE 51 (111)
T ss_pred CcEEEEeeHHHHHHHHHh
Confidence 599999999999987654
No 36
>cd03081 TRX_Fd_NuoE_FDH_gamma TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E subfamily, NAD-dependent formate dehydrogenase (FDH) gamma subunit; composed of proteins similar to the gamma subunit of NAD-linked FDH of Ralstonia eutropha, a soluble enzyme that catalyzes the irreversible oxidation of formate to carbon dioxide accompanied by the reduction of NAD+ to NADH. FDH is a heteromeric enzyme composed of four nonidentical subunits (alpha, beta, gamma and delta). The FDH gamma subunit is closely related to NuoE, which is part of a multisubunit complex (Nuo) catalyzing the electron transfer of NADH to quinone coupled with the transfer of protons across the membrane. Electrons are transferred from NADH to quinone through a chain of iron-sulfur clusters in Nuo, including the [2Fe-2S] cluster present in NuoE. Similarly, the FDH gamma subunit is hypothesized to be involved in an electron transport chain involving other FDH subunits, upon the oxidat
Probab=20.67 E-value=95 Score=21.06 Aligned_cols=18 Identities=28% Similarity=0.222 Sum_probs=15.5
Q ss_pred CceeeccCHHHHHHHHHh
Q 032091 79 IELRSPVTKEELVAEVAR 96 (147)
Q Consensus 79 gkLfGSVT~~dI~~~l~~ 96 (147)
|++|+-+|+.+|.+.+.+
T Consensus 62 ~~~~~~~~~e~i~~il~~ 79 (80)
T cd03081 62 GEVHGRVDPEKFDALLAE 79 (80)
T ss_pred CEEECCCCHHHHHHHHHc
Confidence 589999999999888753
No 37
>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=20.59 E-value=76 Score=21.17 Aligned_cols=17 Identities=18% Similarity=0.145 Sum_probs=14.7
Q ss_pred CceeeccCHHHHHHHHH
Q 032091 79 IELRSPVTKEELVAEVA 95 (147)
Q Consensus 79 gkLfGSVT~~dI~~~l~ 95 (147)
|++.|.||..|+...+.
T Consensus 35 ~~~~G~v~~~dl~~~~~ 51 (113)
T cd04607 35 GRLLGTVTDGDIRRALL 51 (113)
T ss_pred CCEEEEEEcHHHHHHHh
Confidence 59999999999987764
No 38
>TIGR02010 IscR iron-sulfur cluster assembly transcription factor IscR. This model describes IscR, an iron-sulfur binding transcription factor of the ISC iron-sulfur cluster assembly system.
Probab=20.41 E-value=1.7e+02 Score=21.61 Aligned_cols=57 Identities=14% Similarity=0.112 Sum_probs=40.5
Q ss_pred HHHhhhhHHHHHHHHHHHHHHhccCceEEEEcccccccccccCCCCCCceeeccCHHHHHHHHH
Q 032091 32 VKVIRKSEDNMSREFEKAARRLENARLVLRRFPNIEKLRSRASKDDPIELRSPVTKEELVAEVA 95 (147)
Q Consensus 32 ~k~i~k~~~~~~~eae~~a~~L~~~~l~i~~~~g~~~~~~~~~~~~~gkLfGSVT~~dI~~~l~ 95 (147)
.++|..+...-..-++++...|..+.++-..+-..+|+.......+ ||..||+.++.
T Consensus 28 ~~~ia~~~~ip~~~l~kil~~L~~~glv~s~~G~~Ggy~l~~~~~~-------Itl~dv~~a~e 84 (135)
T TIGR02010 28 LADISERQGISLSYLEQLFAKLRKAGLVKSVRGPGGGYQLGRPAED-------ISVADIIDAVD 84 (135)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHHHCCceEEEeCCCCCEeccCCHHH-------CcHHHHHHHhC
Confidence 4566666667777888888999998887664433455555554332 99999999995
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=20.25 E-value=81 Score=20.62 Aligned_cols=16 Identities=19% Similarity=-0.014 Sum_probs=13.7
Q ss_pred CceeeccCHHHHHHHH
Q 032091 79 IELRSPVTKEELVAEV 94 (147)
Q Consensus 79 gkLfGSVT~~dI~~~l 94 (147)
|++.|.||..||....
T Consensus 34 g~~~Giv~~~dl~~~~ 49 (106)
T cd04582 34 GQPLGFVTRREAARAS 49 (106)
T ss_pred CCEEEEEeHHHHHHhc
Confidence 5999999999998653
No 40
>cd04593 CBS_pair_EriC_assoc_bac_arch This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in the EriC CIC-type chloride channels in bacteria and archaea. These ion channels are proteins with a seemingly simple task of allowing the passive flow of chloride ions across biological membranes. CIC-type chloride channels come from all kingdoms of life, have several gene families, and can be gated by voltage. The members of the CIC-type chloride channel are double-barreled: two proteins forming homodimers at a broad interface formed by four helices from each protein. The two pores are not found at this interface, but are completely contained within each subunit, as deduced from the mutational analyses, unlike many other channels, in which four or five identical or structurally related subunits jointly form one pore. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide range of different proteins. CBS d
Probab=20.21 E-value=85 Score=21.00 Aligned_cols=18 Identities=11% Similarity=0.084 Sum_probs=15.6
Q ss_pred CceeeccCHHHHHHHHHh
Q 032091 79 IELRSPVTKEELVAEVAR 96 (147)
Q Consensus 79 gkLfGSVT~~dI~~~l~~ 96 (147)
|++.|.||.+|+...+..
T Consensus 34 ~~~~G~v~~~dl~~~~~~ 51 (115)
T cd04593 34 GGVVGIITLPDLLRALEA 51 (115)
T ss_pred CCEEEEEEHHHHHHHHhc
Confidence 599999999999987754
No 41
>PF06570 DUF1129: Protein of unknown function (DUF1129); InterPro: IPR009214 There are currently no experimental data for members of this group or their homologues. However, these proteins contain predicted integral membrane proteins (with several transmembrane segments).
Probab=20.16 E-value=3.6e+02 Score=21.40 Aligned_cols=16 Identities=19% Similarity=0.293 Sum_probs=14.0
Q ss_pred ceeeccCHHHHHHHHHhh
Q 032091 80 ELRSPVTKEELVAEVARQ 97 (147)
Q Consensus 80 kLfGSVT~~dI~~~l~~q 97 (147)
.+|| |+++-|+++.++
T Consensus 50 ~lfG--~P~~~a~eli~~ 65 (206)
T PF06570_consen 50 QLFG--DPKEYADELIKP 65 (206)
T ss_pred HHcC--CHHHHHHHHhcc
Confidence 7999 999999998765
No 42
>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=20.09 E-value=54 Score=21.85 Aligned_cols=17 Identities=12% Similarity=0.204 Sum_probs=14.1
Q ss_pred CCceeeccCHHHHHHHH
Q 032091 78 PIELRSPVTKEELVAEV 94 (147)
Q Consensus 78 ~gkLfGSVT~~dI~~~l 94 (147)
+|++.|.||..||..++
T Consensus 93 ~~~~~Gvit~~dll~~~ 109 (109)
T cd04606 93 EGRLVGIITVDDVIDVI 109 (109)
T ss_pred CCcEEEEEEhHHhhhhC
Confidence 36999999999998653
No 43
>COG5556 Uncharacterized conserved protein [Function unknown]
Probab=20.00 E-value=58 Score=24.46 Aligned_cols=29 Identities=14% Similarity=0.267 Sum_probs=23.1
Q ss_pred CHHHHHHHHHhhcCCccccccccCCCccc
Q 032091 86 TKEELVAEVARQLSISIEPENLHLPSPLS 114 (147)
Q Consensus 86 T~~dI~~~l~~q~gi~Idk~~I~l~~pIk 114 (147)
|+.-+++++++.+||+|.+..++--+|=|
T Consensus 21 s~S~Va~aVkkEfGi~VsrQlveshdP~K 49 (110)
T COG5556 21 SPSVVAAAVKKEFGIDVSRQLVESHDPNK 49 (110)
T ss_pred cHHHHHHHHHHHhcchHHHHHHHhcCcch
Confidence 46778899999999999998887655544
Done!