Query 033270
Match_columns 123
No_of_seqs 257 out of 1170
Neff 5.0
Searched_HMMs 46136
Date Fri Mar 29 11:52:45 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033270.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033270hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3436 60S ribosomal protein 100.0 4.3E-51 9.3E-56 296.9 10.8 123 1-123 1-123 (123)
2 PRK14549 50S ribosomal protein 99.9 5.4E-24 1.2E-28 142.2 8.7 67 1-67 1-67 (69)
3 CHL00154 rpl29 ribosomal prote 99.9 1.8E-23 3.8E-28 139.3 8.5 64 1-65 1-64 (67)
4 COG0255 RpmC Ribosomal protein 99.9 1.3E-22 2.7E-27 136.1 8.1 62 7-69 6-67 (69)
5 PRK00306 50S ribosomal protein 99.9 1.3E-21 2.8E-26 129.2 8.5 64 4-68 1-64 (66)
6 PF00831 Ribosomal_L29: Riboso 99.8 4.1E-21 9E-26 124.0 7.3 58 6-64 1-58 (58)
7 PRK00461 rpmC 50S ribosomal pr 99.8 7.5E-21 1.6E-25 132.4 8.7 66 5-71 1-66 (87)
8 cd00427 Ribosomal_L29_HIP Ribo 99.8 3.5E-20 7.6E-25 119.3 6.5 57 7-64 1-57 (57)
9 TIGR00012 L29 ribosomal protei 99.8 4.6E-20 1E-24 118.1 6.5 55 8-63 1-55 (55)
10 PF06984 MRP-L47: Mitochondria 96.8 0.0072 1.6E-07 42.2 7.0 60 5-64 24-87 (87)
11 KOG3331 Mitochondrial/chloropl 95.0 0.16 3.4E-06 40.6 7.6 63 5-68 67-134 (213)
12 PF06698 DUF1192: Protein of u 77.3 3.2 6.9E-05 27.1 3.0 30 7-36 16-45 (59)
13 PF10666 Phage_Gp14: Phage pro 70.8 32 0.0007 26.0 7.3 66 8-75 58-133 (140)
14 PF10044 Ret_tiss: Retinal tis 54.3 20 0.00043 25.4 3.4 30 5-34 51-80 (95)
15 PRK11546 zraP zinc resistance 51.9 70 0.0015 24.2 6.3 46 15-65 64-109 (143)
16 smart00540 LEM in nuclear memb 44.0 17 0.00037 22.2 1.6 17 8-24 2-18 (44)
17 PF04999 FtsL: Cell division p 43.3 48 0.001 22.3 4.0 33 14-49 44-76 (97)
18 PF11656 DUF3811: YjbD family 43.3 1.2E+02 0.0025 21.4 7.7 68 8-82 5-72 (87)
19 PF03962 Mnd1: Mnd1 family; I 41.2 91 0.002 24.1 5.6 61 14-75 105-167 (188)
20 PLN00210 40S ribosomal protein 40.5 45 0.00098 25.0 3.7 43 43-85 72-121 (141)
21 PHA03155 hypothetical protein; 40.3 88 0.0019 23.0 5.1 30 11-40 7-36 (115)
22 COG5493 Uncharacterized conser 35.6 60 0.0013 26.4 3.9 52 12-63 46-106 (231)
23 PF07106 TBPIP: Tat binding pr 33.7 2E+02 0.0043 21.3 7.8 47 14-63 81-127 (169)
24 PF08700 Vps51: Vps51/Vps67; 33.1 1.2E+02 0.0026 19.6 4.5 57 6-64 21-77 (87)
25 PF11593 Med3: Mediator comple 33.0 1.5E+02 0.0032 26.0 6.1 80 3-82 7-114 (379)
26 PF10655 DUF2482: Hypothetical 32.7 50 0.0011 23.7 2.7 28 7-34 3-30 (100)
27 PHA03162 hypothetical protein; 32.4 1.1E+02 0.0024 23.1 4.6 29 10-38 11-39 (135)
28 PRK10515 hypothetical protein; 31.0 1.9E+02 0.0042 20.4 7.8 70 4-80 3-72 (90)
29 TIGR01639 P_fal_TIGR01639 Plas 29.5 60 0.0013 20.7 2.5 22 5-26 2-24 (61)
30 PF08188 Protamine_3: Spermato 27.5 1.6E+02 0.0034 18.2 4.3 41 45-85 5-48 (48)
31 PF07989 Microtub_assoc: Micro 26.5 94 0.002 20.8 3.1 22 13-34 1-22 (75)
32 PRK11546 zraP zinc resistance 26.2 1.2E+02 0.0026 22.9 4.0 23 14-36 91-113 (143)
33 PF08621 RPAP1_N: RPAP1-like, 25.9 73 0.0016 19.8 2.3 21 8-28 11-31 (49)
34 COG0103 RpsI Ribosomal protein 25.6 1E+02 0.0022 23.1 3.5 38 44-85 73-110 (130)
35 PF10200 Ndufs5: NADH:ubiquino 25.5 1.3E+02 0.0027 21.4 3.7 30 47-81 66-95 (96)
36 PF05812 Herpes_BLRF2: Herpesv 25.5 1.5E+02 0.0033 21.9 4.2 29 11-39 2-30 (118)
37 PRK09413 IS2 repressor TnpA; R 25.4 1E+02 0.0022 21.7 3.3 21 16-36 75-95 (121)
38 PF08312 cwf21: cwf21 domain; 25.1 1.1E+02 0.0024 18.7 3.0 21 10-30 23-43 (46)
39 PF08285 DPM3: Dolichol-phosph 25.1 81 0.0017 21.9 2.7 17 14-30 70-86 (91)
40 PF10498 IFT57: Intra-flagella 24.6 3.6E+02 0.0078 23.1 7.0 53 13-65 295-348 (359)
41 PF11652 DUF3259: Protein of u 24.6 1.5E+02 0.0032 20.7 3.8 26 13-38 4-29 (84)
42 TIGR02209 ftsL_broad cell divi 24.2 1.6E+02 0.0034 19.0 3.9 34 13-49 32-65 (85)
43 PF13591 MerR_2: MerR HTH fami 23.0 97 0.0021 20.6 2.7 18 15-32 66-83 (84)
44 PHA03041 virion core protein; 22.9 1.1E+02 0.0024 23.5 3.2 29 6-34 87-115 (153)
45 PF11629 Mst1_SARAH: C termina 22.8 1.5E+02 0.0033 18.7 3.3 27 8-34 4-34 (49)
46 PF08627 CRT-like: CRT-like; 22.6 33 0.00072 25.8 0.3 10 112-121 121-130 (130)
47 COG1137 YhbG ABC-type (unclass 22.3 1.7E+02 0.0037 24.1 4.3 50 8-60 105-156 (243)
48 COG4741 Predicted secreted end 22.1 1.3E+02 0.0028 23.6 3.5 41 45-85 70-111 (175)
49 COG4942 Membrane-bound metallo 21.1 4.4E+02 0.0095 23.4 7.0 48 13-65 60-107 (420)
50 PRK15178 Vi polysaccharide exp 21.1 3.6E+02 0.0078 23.9 6.5 45 14-63 288-332 (434)
51 PF07106 TBPIP: Tat binding pr 20.4 3.6E+02 0.0078 19.9 6.2 52 11-62 108-162 (169)
52 PRK10265 chaperone-modulator p 20.3 1.2E+02 0.0027 20.9 2.9 20 15-34 74-93 (101)
No 1
>KOG3436 consensus 60S ribosomal protein L35 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=4.3e-51 Score=296.90 Aligned_cols=123 Identities=73% Similarity=0.999 Sum_probs=121.9
Q ss_pred CCCCChHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCC
Q 033270 1 MARVKVHELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTVISQKQKAALREAYKNKKFLP 80 (123)
Q Consensus 1 M~~mKa~ELR~~s~eEL~~qL~eLK~EL~~LR~qk~tgg~~~k~~kIr~vRK~IARvlTVl~ekq~~~lr~~y~~kk~~p 80 (123)
|+++++.|||+.|.+||.+||+||+.||++||+++++||..+++++|+++|++|||||||+||++.+++++||+|++|+|
T Consensus 1 M~kik~~eLr~~~ke~L~~ql~dLK~ELa~LRv~K~tgg~~~klskik~vrKsiArvLTVine~~k~~lr~~yk~~k~~p 80 (123)
T KOG3436|consen 1 MAKIKARELRGKSKEQLLKQLDDLKVELAQLRVAKVTGGAASKLSKIKVVRKSIARVLTVINEKQKEELREAYKGKKYLP 80 (123)
T ss_pred CcchhHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHhhccchhhhHHHHHHHHHHHHHHHHhhhhhHHHHHHHhhcccccc
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCchhhHHHHhhcChHHhhhhhHHHHHHHhhCCcchhhhcC
Q 033270 81 LDLRPKKTRAIRRRLTKHQASLKTEREKKREMYFPMRKYAIKV 123 (123)
Q Consensus 81 ~dlr~kktra~rr~Lt~~~~~~kt~k~~~k~~~~p~r~~a~ka 123 (123)
+|||||+||||||+||+||.|++|.+|++++++||.|+|||||
T Consensus 81 ~dLr~KktRa~rr~ltk~~~slkt~kq~~k~~~~p~rk~A~ka 123 (123)
T KOG3436|consen 81 KDLRPKKTRAIRRRLTKHQLSLKTEKQQAKERLFPLRKYAVKA 123 (123)
T ss_pred hhhhHHHHHHHHHhccccchhHhHHHHHHHHHhchHHHhhccC
Confidence 9999999999999999999999999999999999999999997
No 2
>PRK14549 50S ribosomal protein L29P; Provisional
Probab=99.91 E-value=5.4e-24 Score=142.23 Aligned_cols=67 Identities=33% Similarity=0.519 Sum_probs=64.3
Q ss_pred CCCCChHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCccchhHHHHHHHHHHHHHHHHHHHH
Q 033270 1 MARVKVHELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTVISQKQKA 67 (123)
Q Consensus 1 M~~mKa~ELR~~s~eEL~~qL~eLK~EL~~LR~qk~tgg~~~k~~kIr~vRK~IARvlTVl~ekq~~ 67 (123)
|+.|+++||+++|.+||.++|.+++.|||+|||++++|++++|||.|+.+||+||||+||++|++++
T Consensus 1 M~~mk~~elr~ls~~eL~~~l~elk~eLf~LR~q~~~~~~l~n~~~ir~~Rk~IARi~Tvl~ek~~~ 67 (69)
T PRK14549 1 MAILRASEIREMSPEEREEKLEELKLELLKERAQAAMGGAPENPGRIREIRRTIARILTIQREKKRE 67 (69)
T ss_pred CCcCcHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHhCcCccccHHHHHHHHHHHHHHHHHHHHHhc
Confidence 8899999999999999999999999999999999999955999999999999999999999998865
No 3
>CHL00154 rpl29 ribosomal protein L29; Validated
Probab=99.90 E-value=1.8e-23 Score=139.30 Aligned_cols=64 Identities=25% Similarity=0.296 Sum_probs=62.4
Q ss_pred CCCCChHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCccchhHHHHHHHHHHHHHHHHHH
Q 033270 1 MARVKVHELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTVISQKQ 65 (123)
Q Consensus 1 M~~mKa~ELR~~s~eEL~~qL~eLK~EL~~LR~qk~tgg~~~k~~kIr~vRK~IARvlTVl~ekq 65 (123)
|+.|+++|||++|.+||.++|.+++.|||+||||+++| +++|||.|+.+|++||||+||++|+.
T Consensus 1 M~~mk~~elr~ls~~eL~~~l~elk~elf~LRfq~atg-ql~n~~~ir~~RrdIARikTil~ek~ 64 (67)
T CHL00154 1 MSLPKITDIIDLTDSEISEEIIKTKKELFDLRLKKATR-QNFKPHLFKHKKHRLAQLLTLLSSRL 64 (67)
T ss_pred CCCCCHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHhC-cccChHHHHHHHHHHHHHHHHHHHHh
Confidence 78899999999999999999999999999999999999 99999999999999999999999975
No 4
>COG0255 RpmC Ribosomal protein L29 [Translation, ribosomal structure and biogenesis]
Probab=99.88 E-value=1.3e-22 Score=136.08 Aligned_cols=62 Identities=40% Similarity=0.522 Sum_probs=59.0
Q ss_pred HHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCccchhHHHHHHHHHHHHHHHHHHHHHH
Q 033270 7 HELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTVISQKQKAAL 69 (123)
Q Consensus 7 ~ELR~~s~eEL~~qL~eLK~EL~~LR~qk~tgg~~~k~~kIr~vRK~IARvlTVl~ekq~~~l 69 (123)
+|||++|.+||.++|.+|+.|||+||||.++| +++|||+|+.|||+||||+||++|++....
T Consensus 6 ~elR~~s~eeL~~~l~eLK~ELf~LR~q~a~g-~l~n~~~ir~vRr~IARi~Tv~~E~~~~~~ 67 (69)
T COG0255 6 KELREKSVEELEEELRELKKELFNLRFQLATG-QLENPHRIREVRRDIARILTVLREKELEAA 67 (69)
T ss_pred HHHHhCCHHHHHHHHHHHHHHHHHHHHHHHhC-CCCCcHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence 59999999999999999999999999999999 789999999999999999999999987653
No 5
>PRK00306 50S ribosomal protein L29; Reviewed
Probab=99.86 E-value=1.3e-21 Score=129.23 Aligned_cols=64 Identities=36% Similarity=0.477 Sum_probs=61.2
Q ss_pred CChHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCccchhHHHHHHHHHHHHHHHHHHHHH
Q 033270 4 VKVHELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTVISQKQKAA 68 (123)
Q Consensus 4 mKa~ELR~~s~eEL~~qL~eLK~EL~~LR~qk~tgg~~~k~~kIr~vRK~IARvlTVl~ekq~~~ 68 (123)
|+++||+++|.+||.++|.+++.|||+|||++++| +++|||.|+.+||+||||+||++|++.+.
T Consensus 1 Mk~~elr~ls~~eL~~~l~~lkkeL~~lR~~~~~~-~~~n~~~i~~~rk~IARi~Tvl~er~~~~ 64 (66)
T PRK00306 1 MKAKELRELSVEELNEKLLELKKELFNLRFQKATG-QLENTHRLREVRRDIARIKTVLRERELGA 64 (66)
T ss_pred CCHHHHhhCCHHHHHHHHHHHHHHHHHHHHHHHhC-CCcCcHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 68999999999999999999999999999999999 79999999999999999999999998753
No 6
>PF00831 Ribosomal_L29: Ribosomal L29 protein; InterPro: IPR001854 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 L29 is one of the proteins from the large ribosomal subunit. L29 belongs to a family of ribosomal proteins of 63 to 138 amino-acid residues which, on the basis of sequence similarities [], groups: Red algal L29. Bacterial L29. Mammalian L35 Caenorhabditis elegans L35 (ZK652.4). Yeast L35. ; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1VSP_W 3MS1_Y 3MRZ_Y 3F1H_2 3PYT_Y 3PYO_Y 3D5D_2 3D5B_2 3PYR_Y 1VSA_W ....
Probab=99.85 E-value=4.1e-21 Score=124.05 Aligned_cols=58 Identities=38% Similarity=0.559 Sum_probs=56.1
Q ss_pred hHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCccchhHHHHHHHHHHHHHHHHH
Q 033270 6 VHELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTVISQK 64 (123)
Q Consensus 6 a~ELR~~s~eEL~~qL~eLK~EL~~LR~qk~tgg~~~k~~kIr~vRK~IARvlTVl~ek 64 (123)
++||++||.+||.++|.+++.|||+|||++++| +++|||.|+.+||+||||+||++|+
T Consensus 1 ~~elr~ls~~eL~~~l~elk~eL~~Lr~q~~~~-~l~n~~~ir~~Rr~IARi~Tvl~er 58 (58)
T PF00831_consen 1 AKELRELSDEELQEKLEELKKELFNLRFQKATG-QLENPHRIREIRRDIARILTVLRER 58 (58)
T ss_dssp CHHHCHSHHHHHHHHHHHHHHHHHHHHHHHHHS-SSSCCHHHHHHHHHHHHHHHHHHHH
T ss_pred CHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHhc-ccccccHHHHHHHHHHHHHHHHhcC
Confidence 579999999999999999999999999999998 7899999999999999999999986
No 7
>PRK00461 rpmC 50S ribosomal protein L29; Reviewed
Probab=99.84 E-value=7.5e-21 Score=132.43 Aligned_cols=66 Identities=35% Similarity=0.482 Sum_probs=62.1
Q ss_pred ChHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCccchhHHHHHHHHHHHHHHHHHHHHHHHH
Q 033270 5 KVHELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTVISQKQKAALRE 71 (123)
Q Consensus 5 Ka~ELR~~s~eEL~~qL~eLK~EL~~LR~qk~tgg~~~k~~kIr~vRK~IARvlTVl~ekq~~~lr~ 71 (123)
+++|||++|.+||.++|.+++.|||+|||++++| +++|||.|+.+||+||||+||++|++.++..+
T Consensus 1 ~~~elR~lS~eEL~e~L~elkkELf~LR~q~atg-ql~n~~~ir~iRR~IARilTvl~Ek~~~~~~~ 66 (87)
T PRK00461 1 LFKELRKKSVEELEKLVIELKAELFTLRFKNATG-SLDQTHKIKEIRKDIARILTILNERELEEKEN 66 (87)
T ss_pred ChHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHhC-cccccHHHHHHHHHHHHHHHHHHHHHHHhhhc
Confidence 4689999999999999999999999999999999 89999999999999999999999999876643
No 8
>cd00427 Ribosomal_L29_HIP Ribosomal L29 protein/HIP. L29 is a protein of the large ribosomal Subunit. A homolog, called heparin/heparan sulfate interacting protein (HIP), has also been identified in mammals. L29 is located on the surface of the large ribosomal subunit, where it participates in forming a protein ring that surrounds the polypeptide exit channel, providing structural support for the ribosome. L29 is involved in forming the translocon binding site, along with L19, L22, L23, L24, and L31e. In addition, L29 and L23 form the interaction site for trigger factor (TF) on the ribosomal surface, adjacent to the exit tunnel. L29 forms numerous interactions with L23 and with the 23S rRNA. In some eukaryotes, L29 is referred to as L35, which is distinct from L35 found in bacteria and some eukaryotes (primarily plastids and mitochondria). The mammalian homolog, HIP, is found on the surface of many tissues and cell lines. It is believed to play a role in cell adhesion and modulat
Probab=99.82 E-value=3.5e-20 Score=119.25 Aligned_cols=57 Identities=42% Similarity=0.572 Sum_probs=54.8
Q ss_pred HHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCccchhHHHHHHHHHHHHHHHHH
Q 033270 7 HELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTVISQK 64 (123)
Q Consensus 7 ~ELR~~s~eEL~~qL~eLK~EL~~LR~qk~tgg~~~k~~kIr~vRK~IARvlTVl~ek 64 (123)
+||+++|.+||.++|.+++.|||+|||++++| +++|||.|+.+|++||||+||++|+
T Consensus 1 ~eir~ls~~eL~~~l~~l~~elf~Lr~q~~~~-~~~~~~~~~~~Rr~IARi~Til~er 57 (57)
T cd00427 1 KELREKSDEELQEKLDELKKELFNLRFQKATG-QLENPHRIRKVRKDIARIKTVLNEK 57 (57)
T ss_pred ChHHHCCHHHHHHHHHHHHHHHHHHHHHHHHC-CCcCcHHHHHHHHHHHHHHHHHHcC
Confidence 48999999999999999999999999999999 7999999999999999999999974
No 9
>TIGR00012 L29 ribosomal protein L29. called L29 in prokaryotic (50S) large subunits and L35 in eukaryotic (60S) large subunits.
Probab=99.81 E-value=4.6e-20 Score=118.11 Aligned_cols=55 Identities=47% Similarity=0.619 Sum_probs=53.1
Q ss_pred HHhcCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCccchhHHHHHHHHHHHHHHHH
Q 033270 8 ELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTVISQ 63 (123)
Q Consensus 8 ELR~~s~eEL~~qL~eLK~EL~~LR~qk~tgg~~~k~~kIr~vRK~IARvlTVl~e 63 (123)
||+++|.+||.++|.+++.|||+|||++++| +++|||.|+.+||+||||+||++|
T Consensus 1 elr~~s~~EL~~~l~~lr~eLf~Lr~~~~~~-~~~~~~~i~~~Rk~IARi~Tvl~e 55 (55)
T TIGR00012 1 ELREKSKEELAKKLDELKKELFELRFQKATG-QLAKPHRIRQVRRDIARLLTVLRE 55 (55)
T ss_pred CHhhCCHHHHHHHHHHHHHHHHHHHHHHHhC-CcccchHHHHHHHHHHHHHHHHhC
Confidence 6899999999999999999999999999999 789999999999999999999985
No 10
>PF06984 MRP-L47: Mitochondrial 39-S ribosomal protein L47 (MRP-L47); InterPro: IPR010729 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 entry represents the N-terminal region (approximately 8 residues) of the eukaryotic mitochondrial 39-S ribosomal protein L47 (MRP-L47). Mitochondrial ribosomal proteins (MRPs) are the counterparts of the cytoplasmic ribosomal proteins, in that they fulfil similar functions in protein biosynthesis. However, they are distinct in number, features and primary structure [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005761 mitochondrial ribosome
Probab=96.82 E-value=0.0072 Score=42.22 Aligned_cols=60 Identities=25% Similarity=0.266 Sum_probs=40.1
Q ss_pred ChHHHhcCCHHHHHHHHHHH---HHHHHHHH-HHHHHCCCCCccchhHHHHHHHHHHHHHHHHH
Q 033270 5 KVHELRTKSKTDLLNQLKDL---KAELALLR-VAKVTGGAPNKLSKIKVVRLSIAQVLTVISQK 64 (123)
Q Consensus 5 Ka~ELR~~s~eEL~~qL~eL---K~EL~~LR-~qk~tgg~~~k~~kIr~vRK~IARvlTVl~ek 64 (123)
.+.|||.+|-+||.+-==-+ +.-|...+ .....+...+++.++..|+++-++|++|++|+
T Consensus 24 t~~ELR~KS~eDLHkLWyv~lKERN~L~T~~~e~~r~~~~~~~~~r~~kV~~sM~~Ik~Vl~ER 87 (87)
T PF06984_consen 24 TAEELRRKSFEDLHKLWYVCLKERNMLLTEEYEARRQGEGMPSPERLEKVRKSMARIKHVLTER 87 (87)
T ss_pred cHHHHHccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccchHHHHHHHHHHHHHHHHHhcC
Confidence 47899999999998832222 22221111 11122223578899999999999999999984
No 11
>KOG3331 consensus Mitochondrial/chloroplast ribosomal protein L4/L29 [Translation, ribosomal structure and biogenesis]
Probab=94.95 E-value=0.16 Score=40.60 Aligned_cols=63 Identities=27% Similarity=0.289 Sum_probs=48.0
Q ss_pred ChHHHhcCCHHHHHHHHHHHHHH---HHHHHH--HHHHCCCCCccchhHHHHHHHHHHHHHHHHHHHHH
Q 033270 5 KVHELRTKSKTDLLNQLKDLKAE---LALLRV--AKVTGGAPNKLSKIKVVRLSIAQVLTVISQKQKAA 68 (123)
Q Consensus 5 Ka~ELR~~s~eEL~~qL~eLK~E---L~~LR~--qk~tgg~~~k~~kIr~vRK~IARvlTVl~ekq~~~ 68 (123)
.+.|||-+|-.||.+.--.+-+| |+..+- +...| +..||-+|-.||.+.+||.+|++|++++-
T Consensus 67 ~aeELR~KS~nDLH~LWYvcLkErNmL~T~~~~~k~~~~-~~PnpERi~kV~~TM~~I~~Vl~ER~~Ay 134 (213)
T KOG3331|consen 67 SAEELRLKSFNDLHKLWYVCLKERNMLATMRHELKNIVG-SFPNPERIDKVRTTMWRIEHVLNERNLAY 134 (213)
T ss_pred chHHHhcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHh-cCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 57899999999998865444443 333332 23334 78899999999999999999999998753
No 12
>PF06698 DUF1192: Protein of unknown function (DUF1192); InterPro: IPR009579 This family consists of several short, hypothetical, bacterial proteins of around 60 residues in length. The function of this family is unknown.
Probab=77.32 E-value=3.2 Score=27.08 Aligned_cols=30 Identities=30% Similarity=0.309 Sum_probs=25.4
Q ss_pred HHHhcCCHHHHHHHHHHHHHHHHHHHHHHH
Q 033270 7 HELRTKSKTDLLNQLKDLKAELALLRVAKV 36 (123)
Q Consensus 7 ~ELR~~s~eEL~~qL~eLK~EL~~LR~qk~ 36 (123)
.||-.+|.+||.+.|.-|+.|...++-.-.
T Consensus 16 ~dLs~lSv~EL~~RIa~L~aEI~R~~~~~~ 45 (59)
T PF06698_consen 16 EDLSLLSVEELEERIALLEAEIARLEAAIA 45 (59)
T ss_pred CCchhcCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 578899999999999999999888776543
No 13
>PF10666 Phage_Gp14: Phage protein Gp14; InterPro: IPR018923 This Listeria phage Gp14 protein family is of unknown function but is expressed from within a cluster of tail- and base plate genes [].
Probab=70.78 E-value=32 Score=25.96 Aligned_cols=66 Identities=17% Similarity=0.148 Sum_probs=51.0
Q ss_pred HHhcCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCccchhHHHHHHHHHHHHHHHHH----------HHHHHHHHHhC
Q 033270 8 ELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTVISQK----------QKAALREAYKN 75 (123)
Q Consensus 8 ELR~~s~eEL~~qL~eLK~EL~~LR~qk~tgg~~~k~~kIr~vRK~IARvlTVl~ek----------q~~~lr~~y~~ 75 (123)
++++||.+|+.. |.+-..|+...-+.--.| .-+-..++-..-|+|-++.||.++- +....++.|+.
T Consensus 58 ~~~EmS~e~~~a-Le~~~re~L~ea~~~~l~-de~tfee~Ye~~k~~~~M~~v~~~v~e~~~~~m~v~Q~e~qk~Y~~ 133 (140)
T PF10666_consen 58 FDREMSSEEYRA-LEEQQREALKEAIEIFLG-DENTFEECYEKCKDLVNMTKVYMQVSEWLVGKMEVQQNEIQKKYKA 133 (140)
T ss_pred chhhcCHHHHHH-HHHHHHHHHHHHHHHHhC-cHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 458899999866 466667888888888888 4566789999999999999999863 33556777764
No 14
>PF10044 Ret_tiss: Retinal tissue protein; InterPro: IPR018737 Rtp is a family of proteins of approximately 112 amino acids in length which is conserved from nematodes to humans. The proposed tertiary structure is of almost entirely alpha helix interrupted only by loops located at proline residues. Three sites in the protein sequence reveal two types of possible post-translation modification. A serine residue, at position 41, is a candidate for protein kinase C phosphorylation. Glycine residues at position 69 and 91 are probable sites for acetylation by covalent amide linkage of myristate via N-myristoyl transferase. Rtp is differentially expressed in the trout retina between parr and smolt developmental stages (smoltification). It is likely to be a house-keeping protein [].
Probab=54.30 E-value=20 Score=25.45 Aligned_cols=30 Identities=27% Similarity=0.433 Sum_probs=26.0
Q ss_pred ChHHHhcCCHHHHHHHHHHHHHHHHHHHHH
Q 033270 5 KVHELRTKSKTDLLNQLKDLKAELALLRVA 34 (123)
Q Consensus 5 Ka~ELR~~s~eEL~~qL~eLK~EL~~LR~q 34 (123)
+..||..+|.++|.+.+.+|..+..+|=+.
T Consensus 51 ~~~eLs~Lt~~~L~~~Ik~L~~~aYqLGl~ 80 (95)
T PF10044_consen 51 KMNELSSLTPDQLIEKIKKLQDEAYQLGLE 80 (95)
T ss_pred HHHHHHcCCHHHHHHHHHHHHHHHHHHhHH
Confidence 467899999999999999999999887544
No 15
>PRK11546 zraP zinc resistance protein; Provisional
Probab=51.92 E-value=70 Score=24.19 Aligned_cols=46 Identities=24% Similarity=0.296 Sum_probs=30.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCCCCccchhHHHHHHHHHHHHHHHHHH
Q 033270 15 TDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTVISQKQ 65 (123)
Q Consensus 15 eEL~~qL~eLK~EL~~LR~qk~tgg~~~k~~kIr~vRK~IARvlTVl~ekq 65 (123)
++|.++|-.-+.||..| ..+ ..+.+.+|+.+.++|+.+.+-|-+..
T Consensus 64 ~~LRqqL~aKr~ELnAL----l~~-~~pD~~kI~aL~kEI~~Lr~kL~e~r 109 (143)
T PRK11546 64 SALRQQLVSKRYEYNAL----LTA-NPPDSSKINAVAKEMENLRQSLDELR 109 (143)
T ss_pred HHHHHHHHHHHHHHHHH----HcC-CCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 44444444444444444 223 45677899999999999999887654
No 16
>smart00540 LEM in nuclear membrane-associated proteins. LEM, domain in nuclear membrane-associated proteins, including lamino-associated polypeptide 2 and emerin.
Probab=44.01 E-value=17 Score=22.25 Aligned_cols=17 Identities=24% Similarity=0.378 Sum_probs=13.8
Q ss_pred HHhcCCHHHHHHHHHHH
Q 033270 8 ELRTKSKTDLLNQLKDL 24 (123)
Q Consensus 8 ELR~~s~eEL~~qL~eL 24 (123)
|+..+|++||..+|.++
T Consensus 2 d~~~LSd~eL~~~L~~~ 18 (44)
T smart00540 2 DVDRLSDAELRAELKQY 18 (44)
T ss_pred chhHcCHHHHHHHHHHc
Confidence 67889999998887654
No 17
>PF04999 FtsL: Cell division protein FtsL; InterPro: IPR007082 In Escherichia coli, nine gene products are known to be essential for assembly of the division septum. One of these, FtsL, is a bitopic membrane protein whose precise function is not understood. It has been proposed that FtsL interacts with the DivIC protein IPR007060 from INTERPRO [], however this interaction may be indirect [].; GO: 0007049 cell cycle, 0016021 integral to membrane
Probab=43.31 E-value=48 Score=22.30 Aligned_cols=33 Identities=24% Similarity=0.265 Sum_probs=27.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHCCCCCccchhHH
Q 033270 14 KTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKV 49 (123)
Q Consensus 14 ~eEL~~qL~eLK~EL~~LR~qk~tgg~~~k~~kIr~ 49 (123)
.+++..+.+.+..|-.+|++..++ +++|.+|..
T Consensus 44 l~~l~~~~~~l~~e~~~L~lE~~~---l~~~~rIe~ 76 (97)
T PF04999_consen 44 LQQLEKEIDQLQEENERLRLEIAT---LSSPSRIER 76 (97)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH---hhCHHHHHH
Confidence 678899999999999999999984 567777754
No 18
>PF11656 DUF3811: YjbD family (DUF3811); InterPro: IPR020317 This entry contains proteins with no known function.
Probab=43.26 E-value=1.2e+02 Score=21.40 Aligned_cols=68 Identities=16% Similarity=0.222 Sum_probs=44.0
Q ss_pred HHhcCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCC
Q 033270 8 ELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTVISQKQKAALREAYKNKKFLPLD 82 (123)
Q Consensus 8 ELR~~s~eEL~~qL~eLK~EL~~LR~qk~tgg~~~k~~kIr~vRK~IARvlTVl~ekq~~~lr~~y~~kk~~p~d 82 (123)
.+.+|+..|- .+++..|.+-|... |..+.| +.-..|+.+|--=+..-.+.....+|.--+..+|.|.|
T Consensus 5 T~keMTeseq----~evkt~L~~aRk~~--gR~LTN-aE~NkiKde~i~ki~~ere~~aKkar~ekkk~k~~ps~ 72 (87)
T PF11656_consen 5 TLKEMTESEQ----REVKTLLDQARKNL--GRELTN-AEQNKIKDEIIDKIMAEREKAAKKARAEKKKNKVKPSS 72 (87)
T ss_pred hHHHhhHHHH----HHHHHHHHHHHHHc--CCccch-hhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCc
Confidence 4555565553 56777777776554 657777 77778888875444455555556667666777777743
No 19
>PF03962 Mnd1: Mnd1 family; InterPro: IPR005647 This family of proteins includes meiotic nuclear division protein 1 (MND1) from Saccharomyces cerevisiae (Baker's yeast). The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair [].
Probab=41.23 E-value=91 Score=24.09 Aligned_cols=61 Identities=23% Similarity=0.282 Sum_probs=40.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHCCCCCccchhHHHHHHHHHHHHHHHH--HHHHHHHHHHhC
Q 033270 14 KTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTVISQ--KQKAALREAYKN 75 (123)
Q Consensus 14 ~eEL~~qL~eLK~EL~~LR~qk~tgg~~~k~~kIr~vRK~IARvlTVl~e--kq~~~lr~~y~~ 75 (123)
..++.+++.+|+.++..|.-+...- ...+|..|..++.++....--+|. -....+..+..+
T Consensus 105 R~~~l~~l~~l~~~~~~l~~el~~~-~~~Dp~~i~~~~~~~~~~~~~anrwTDNI~~l~~~~~~ 167 (188)
T PF03962_consen 105 REELLEELEELKKELKELKKELEKY-SENDPEKIEKLKEEIKIAKEAANRWTDNIFSLKSYLKK 167 (188)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH-HhcCHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHH
Confidence 3456677777777777777666543 346788999999988888877765 233444444333
No 20
>PLN00210 40S ribosomal protein S16; Provisional
Probab=40.52 E-value=45 Score=25.04 Aligned_cols=43 Identities=26% Similarity=0.363 Sum_probs=34.0
Q ss_pred ccchhHHHHHHHHHHHHHHH-----HHHHHHHHHHHhC--CCCCCCCCCc
Q 033270 43 KLSKIKVVRLSIAQVLTVIS-----QKQKAALREAYKN--KKFLPLDLRP 85 (123)
Q Consensus 43 k~~kIr~vRK~IARvlTVl~-----ekq~~~lr~~y~~--kk~~p~dlr~ 85 (123)
-.++...+|-.|||.|..++ +..++.|+..|.. ..++--|-|-
T Consensus 72 ~sgQa~Air~aiaraL~~~~~~~~~~~~r~~Lk~~l~~yd~glLtrD~R~ 121 (141)
T PLN00210 72 HTSQIYAIRQSIAKALVAYYQKYVDEQSKKEIKDILLRYDRTLLVADPRR 121 (141)
T ss_pred HhHHHHHHHHHHHHHHHHhcccccChhHHHHHHHHHHhccCCCccCCchh
Confidence 45888999999999999994 4667788887776 6777767664
No 21
>PHA03155 hypothetical protein; Provisional
Probab=40.34 E-value=88 Score=23.04 Aligned_cols=30 Identities=23% Similarity=0.277 Sum_probs=26.5
Q ss_pred cCCHHHHHHHHHHHHHHHHHHHHHHHHCCC
Q 033270 11 TKSKTDLLNQLKDLKAELALLRVAKVTGGA 40 (123)
Q Consensus 11 ~~s~eEL~~qL~eLK~EL~~LR~qk~tgg~ 40 (123)
++|.|||.++|..|+-|=..|+-+-..||.
T Consensus 7 ~~tvEeLaaeL~kL~~ENK~LKkkl~~~~~ 36 (115)
T PHA03155 7 CADVEELEKELQKLKIENKALKKKLLQHGN 36 (115)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHccCC
Confidence 789999999999999999999988766644
No 22
>COG5493 Uncharacterized conserved protein containing a coiled-coil domain [Function unknown]
Probab=35.64 E-value=60 Score=26.37 Aligned_cols=52 Identities=19% Similarity=0.246 Sum_probs=37.6
Q ss_pred CCHHHHHHHHHHHHHHHHH----HHHHHHHCCCCC-----ccchhHHHHHHHHHHHHHHHH
Q 033270 12 KSKTDLLNQLKDLKAELAL----LRVAKVTGGAPN-----KLSKIKVVRLSIAQVLTVISQ 63 (123)
Q Consensus 12 ~s~eEL~~qL~eLK~EL~~----LR~qk~tgg~~~-----k~~kIr~vRK~IARvlTVl~e 63 (123)
-+.+||.++++..+.+|.. -|++++|...+. -...++.+..+|-|+-|+|+-
T Consensus 46 ~dve~l~~e~E~~~k~l~de~~E~r~~~~tke~lk~l~~~~~~~f~a~~edi~rlE~~i~~ 106 (231)
T COG5493 46 QDVEELRKETEQRQKELADEKLEVRKQKATKEDLKLLQRFQEEEFRATKEDIKRLETIITG 106 (231)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4678888888888888875 677777652211 123478888999999998875
No 23
>PF07106 TBPIP: Tat binding protein 1(TBP-1)-interacting protein (TBPIP); InterPro: IPR010776 This family consists of several eukaryotic TBP-1 interacting protein (TBPIP) sequences. TBP-1 has been demonstrated to interact with the human immunodeficiency virus type 1 (HIV-1) viral protein Tat, then modulate the essential replication process of HIV. In addition, TBP-1 has been shown to be a component of the 26S proteasome, a basic multiprotein complex that degrades ubiquitinated proteins in an ATP-dependent fashion. Human TBPIP interacts with human TBP-1 then modulates the inhibitory action of human TBP-1 on HIV-Tat-mediated transactivation [].
Probab=33.68 E-value=2e+02 Score=21.29 Aligned_cols=47 Identities=19% Similarity=0.218 Sum_probs=26.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHCCCCCccchhHHHHHHHHHHHHHHHH
Q 033270 14 KTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTVISQ 63 (123)
Q Consensus 14 ~eEL~~qL~eLK~EL~~LR~qk~tgg~~~k~~kIr~vRK~IARvlTVl~e 63 (123)
..+|.+++.+++.+...|+-.... +.+....-.++..|+.+...+.+
T Consensus 81 i~~L~~el~~l~~~~k~l~~eL~~---L~~~~t~~el~~~i~~l~~e~~~ 127 (169)
T PF07106_consen 81 IKELREELAELKKEVKSLEAELAS---LSSEPTNEELREEIEELEEEIEE 127 (169)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH---HhcCCCHHHHHHHHHHHHHHHHH
Confidence 556677777777777777655442 23333344455566655555444
No 24
>PF08700 Vps51: Vps51/Vps67; InterPro: IPR014812 The VFT tethering complex (also known as GARP complex, Golgi associated retrograde protein complex, Vps53 tethering complex) is a conserved eukaryotic docking complex which is involved in recycling of proteins from endosomes to the late Golgi. Vps51 (also known as Vps67) is a subunit of VFT and interacts with the SNARE Tlg1 [].
Probab=33.11 E-value=1.2e+02 Score=19.58 Aligned_cols=57 Identities=14% Similarity=0.233 Sum_probs=34.6
Q ss_pred hHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCccchhHHHHHHHHHHHHHHHHH
Q 033270 6 VHELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTVISQK 64 (123)
Q Consensus 6 a~ELR~~s~eEL~~qL~eLK~EL~~LR~qk~tgg~~~k~~kIr~vRK~IARvlTVl~ek 64 (123)
..+|+.. ...|..++.+...||-.+-+.+-.. -+.-...|..++.++-.+.+.+.+-
T Consensus 21 ~~~i~~~-~~~L~~~i~~~~~eLr~~V~~nY~~-fI~as~~I~~m~~~~~~l~~~l~~l 77 (87)
T PF08700_consen 21 IKEIRQL-ENKLRQEIEEKDEELRKLVYENYRD-FIEASDEISSMENDLSELRNLLSEL 77 (87)
T ss_pred HHHHHHH-HHHHHHHHHHHHHHHHHHHHhhHHH-HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4444443 3556666666666776666655543 3444566777777777777766654
No 25
>PF11593 Med3: Mediator complex subunit 3 fungal; InterPro: IPR020998 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. This entry represents the subunit Med3, which is a physical target for Cyc8-Tup1, a yeast transcriptional co-repressor []. ; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex
Probab=32.96 E-value=1.5e+02 Score=25.98 Aligned_cols=80 Identities=21% Similarity=0.397 Sum_probs=55.5
Q ss_pred CCChHHHhcC------CHHHHHHHHHHHHHHHHHHHHHHH--------HC--CCCCccchhHHHHHHHHHHHHHHHHHHH
Q 033270 3 RVKVHELRTK------SKTDLLNQLKDLKAELALLRVAKV--------TG--GAPNKLSKIKVVRLSIAQVLTVISQKQK 66 (123)
Q Consensus 3 ~mKa~ELR~~------s~eEL~~qL~eLK~EL~~LR~qk~--------tg--g~~~k~~kIr~vRK~IARvlTVl~ekq~ 66 (123)
.|+..||.++ +++.+.++|.|.+.++.=||++-- +. +..+.-.+|-.||-.|=.+..-|.+-..
T Consensus 7 ~~~LeeLe~kLa~~d~~Kd~V~~~I~ea~~sILPlRL~FNeFi~tma~Ie~~~~~s~qeKFl~IR~KlleL~~~lQ~lS~ 86 (379)
T PF11593_consen 7 NLKLEELEEKLASNDNSKDSVMDKISEAQDSILPLRLQFNEFIQTMANIEEMNNKSPQEKFLLIRSKLLELYNKLQELSS 86 (379)
T ss_pred CCcHHHHHHHHhcCCchHHHHHHHHHHHHhccccHHHHHHHHHHHHHHhhcccccCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4667777644 788999999999999988887621 11 1234456778888888877766665322
Q ss_pred ------------HHHHHHHhCCCCCCCC
Q 033270 67 ------------AALREAYKNKKFLPLD 82 (123)
Q Consensus 67 ------------~~lr~~y~~kk~~p~d 82 (123)
.+-.+.|..++|.||+
T Consensus 87 df~~LqPLF~Ti~eyse~~~~kkF~pLE 114 (379)
T PF11593_consen 87 DFQKLQPLFDTIPEYSEKYNSKKFQPLE 114 (379)
T ss_pred HHHHhchHHhhhHHHhcccCCccceech
Confidence 3335667889999975
No 26
>PF10655 DUF2482: Hypothetical protein of unknown function (DUF2482); InterPro: IPR018917 This entry is represented by Bacteriophage 80, Orf10. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. All the members of this very small, very short family are derived from bacteriophages, of the SA bacteriophages 11, Mu50B, system, and from the Staphylococcal_phi-Mu50B-like_prophages subsystem. All members are hypothetical proteins.
Probab=32.69 E-value=50 Score=23.70 Aligned_cols=28 Identities=18% Similarity=0.233 Sum_probs=24.4
Q ss_pred HHHhcCCHHHHHHHHHHHHHHHHHHHHH
Q 033270 7 HELRTKSKTDLLNQLKDLKAELALLRVA 34 (123)
Q Consensus 7 ~ELR~~s~eEL~~qL~eLK~EL~~LR~q 34 (123)
+...+|+.+||..-|.+--.||+.|-..
T Consensus 3 knyKdMTqeelr~llseK~~ELydL~~e 30 (100)
T PF10655_consen 3 KNYKDMTQEELRDLLSEKNGELYDLANE 30 (100)
T ss_pred chhhhhhHHHHHHHHHHhhHHHHHHHHH
Confidence 3577899999999999999999998754
No 27
>PHA03162 hypothetical protein; Provisional
Probab=32.39 E-value=1.1e+02 Score=23.09 Aligned_cols=29 Identities=21% Similarity=0.245 Sum_probs=24.9
Q ss_pred hcCCHHHHHHHHHHHHHHHHHHHHHHHHC
Q 033270 10 RTKSKTDLLNQLKDLKAELALLRVAKVTG 38 (123)
Q Consensus 10 R~~s~eEL~~qL~eLK~EL~~LR~qk~tg 38 (123)
.++|.|||.++|..|+-|=..|+-+-..|
T Consensus 11 ~~~tmEeLaaeL~kLqmENK~LKkkl~~~ 39 (135)
T PHA03162 11 AQPTMEDLAAEIAKLQLENKALKKKIKEG 39 (135)
T ss_pred cCCCHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 36899999999999999999998776444
No 28
>PRK10515 hypothetical protein; Provisional
Probab=31.03 E-value=1.9e+02 Score=20.39 Aligned_cols=70 Identities=16% Similarity=0.243 Sum_probs=45.3
Q ss_pred CChHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCC
Q 033270 4 VKVHELRTKSKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTVISQKQKAALREAYKNKKFLP 80 (123)
Q Consensus 4 mKa~ELR~~s~eEL~~qL~eLK~EL~~LR~qk~tgg~~~k~~kIr~vRK~IARvlTVl~ekq~~~lr~~y~~kk~~p 80 (123)
|+.=.+.+|+..|- -+++..|.+.|... |..+.| +.-..|++.|--=++.-++.....+|..-+..+|+|
T Consensus 3 m~~Lt~keMTEseq----revkt~L~~aR~~~--gR~LTN-aE~NkvK~e~i~ki~aere~~aK~~R~~kK~~~~kp 72 (90)
T PRK10515 3 LPRITQKEMTEREQ----RELKTLLDRARIAH--GRPLTN-SETNSIKKEYIDKLMAEREAEAKKARQLKKKQAYKP 72 (90)
T ss_pred chhHHHHHhhHHHH----HHHHHHHHHHHHHc--CCccch-hhHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCC
Confidence 34445666666553 56777777777654 657777 777778887755555556665556666666666666
No 29
>TIGR01639 P_fal_TIGR01639 Plasmodium falciparum uncharacterized domain TIGR01639. This model represents a conserved sequence region of about 60 amino acids found in over 40 predicted proteins of Plasmodium falciparum. It is not found elsewhere, including closely related species such as Plasmodium yoelii. No member of this family is characterized.
Probab=29.54 E-value=60 Score=20.71 Aligned_cols=22 Identities=27% Similarity=0.419 Sum_probs=17.6
Q ss_pred ChHHH-hcCCHHHHHHHHHHHHH
Q 033270 5 KVHEL-RTKSKTDLLNQLKDLKA 26 (123)
Q Consensus 5 Ka~EL-R~~s~eEL~~qL~eLK~ 26 (123)
+..|| ..+|.+||.+.|..|..
T Consensus 2 ~~~Dls~~lTeEEl~~~i~~L~~ 24 (61)
T TIGR01639 2 KYNDLSKKLSKEELNELINSLDE 24 (61)
T ss_pred ChhHHhHHccHHHHHHHHHhhcC
Confidence 45676 68999999999998863
No 30
>PF08188 Protamine_3: Spermatozal protamine family; InterPro: IPR012601 This entry consists of the spermatozal protamines. Spermatozal protamines play an important role in remodelling of the sperm chromatin during mammalian spermiogenesis. Nuclear elongation and chromatin condensation are concomitant with modifications in the basic protein complement associated with DNA. Somatic histones are initially replaced by testis-specific histone variants, then by transitional proteins, and ultimately by protamines [].; GO: 0003677 DNA binding, 0035092 sperm chromatin condensation, 0000228 nuclear chromosome
Probab=27.48 E-value=1.6e+02 Score=18.17 Aligned_cols=41 Identities=27% Similarity=0.434 Sum_probs=29.4
Q ss_pred chhHHHHHHHHHHHHHHHHHHHH-HHHHHHhCCCC--CCCCCCc
Q 033270 45 SKIKVVRLSIAQVLTVISQKQKA-ALREAYKNKKF--LPLDLRP 85 (123)
Q Consensus 45 ~kIr~vRK~IARvlTVl~ekq~~-~lr~~y~~kk~--~p~dlr~ 85 (123)
|.++.-|+++-|-.|--||+.+. .+-..|+...| .|-..||
T Consensus 5 hsmkkkrksvrrrktrknqrkrknslgrsfkahgflkqpprfrp 48 (48)
T PF08188_consen 5 HSMKKKRKSVRRRKTRKNQRKRKNSLGRSFKAHGFLKQPPRFRP 48 (48)
T ss_pred hHHHHHHHHHHHHHHHhhHHHhhhhhhhHHHhcccccCCCCCCC
Confidence 56778899999999999997664 45556666665 4555554
No 31
>PF07989 Microtub_assoc: Microtubule associated; InterPro: IPR012943 Proteins with this domain associate with the spindle body during cell division [].
Probab=26.52 E-value=94 Score=20.77 Aligned_cols=22 Identities=23% Similarity=0.228 Sum_probs=18.3
Q ss_pred CHHHHHHHHHHHHHHHHHHHHH
Q 033270 13 SKTDLLNQLKDLKAELALLRVA 34 (123)
Q Consensus 13 s~eEL~~qL~eLK~EL~~LR~q 34 (123)
|.-|..++|++|++|=|+|++.
T Consensus 1 tlrEqe~~i~~L~KENF~LKLr 22 (75)
T PF07989_consen 1 TLREQEEQIDKLKKENFNLKLR 22 (75)
T ss_pred CHHHHHHHHHHHHHhhhhHHHH
Confidence 3457889999999999998875
No 32
>PRK11546 zraP zinc resistance protein; Provisional
Probab=26.21 E-value=1.2e+02 Score=22.92 Aligned_cols=23 Identities=22% Similarity=0.385 Sum_probs=18.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Q 033270 14 KTDLLNQLKDLKAELALLRVAKV 36 (123)
Q Consensus 14 ~eEL~~qL~eLK~EL~~LR~qk~ 36 (123)
...|.++|.+|+.+|+++|++.-
T Consensus 91 I~aL~kEI~~Lr~kL~e~r~~~~ 113 (143)
T PRK11546 91 INAVAKEMENLRQSLDELRVKRD 113 (143)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 45688899999999998888543
No 33
>PF08621 RPAP1_N: RPAP1-like, N-terminal; InterPro: IPR013930 Inhibition of RNA polymerase II-associated protein 1 (RPAP1) synthesis in Saccharomyces cerevisiae (Baker's yeast) results in changes in global gene expression that are similar to those caused by the loss of the RNAPII subunit Rpb11 []. This entry represents the N-terminal region of RPAP-1 that is conserved from yeast to humans.
Probab=25.95 E-value=73 Score=19.77 Aligned_cols=21 Identities=19% Similarity=0.295 Sum_probs=15.7
Q ss_pred HHhcCCHHHHHHHHHHHHHHH
Q 033270 8 ELRTKSKTDLLNQLKDLKAEL 28 (123)
Q Consensus 8 ELR~~s~eEL~~qL~eLK~EL 28 (123)
-|.+||.+|+.+.-.+|...|
T Consensus 11 rL~~MS~eEI~~er~eL~~~L 31 (49)
T PF08621_consen 11 RLASMSPEEIEEEREELLESL 31 (49)
T ss_pred HHHhCCHHHHHHHHHHHHHhC
Confidence 378999999988777766433
No 34
>COG0103 RpsI Ribosomal protein S9 [Translation, ribosomal structure and biogenesis]
Probab=25.58 E-value=1e+02 Score=23.08 Aligned_cols=38 Identities=29% Similarity=0.332 Sum_probs=30.0
Q ss_pred cchhHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCCCCc
Q 033270 44 LSKIKVVRLSIAQVLTVISQKQKAALREAYKNKKFLPLDLRP 85 (123)
Q Consensus 44 ~~kIr~vRK~IARvlTVl~ekq~~~lr~~y~~kk~~p~dlr~ 85 (123)
.++...+|--|||.|...+ .+++..++...++-=|-|-
T Consensus 73 ~GQA~AiR~gIaRAL~~~~----~~lr~~lk~~g~LtrD~R~ 110 (130)
T COG0103 73 SGQAGAIRHGIARALVEYD----PELRPALKKAGLLTRDPRR 110 (130)
T ss_pred hHHHHHHHHHHHHHHHHHC----HHHHHHHHHCCCcccCccc
Confidence 4788999999999999999 5666666666677766663
No 35
>PF10200 Ndufs5: NADH:ubiquinone oxidoreductase, NDUFS5-15kDa; InterPro: IPR019342 Proteins in this entry form part of the NADH:ubiquinone oxidoreductase complex I. Complex I is the first multisubunit inner membrane protein complex of the mitochondrial electron transport chain and it transfers two electrons from NADH to ubiquinone. The mammalian complex I is composed of 45 different subunits. The proteins in this entry represent a component of the iron-sulphur (IP) fragment of the enzyme, that is not involved in catalysis. These proteins carry four highly conserved cysteine residues, but these do not appear to be in a configuration which would favour metal binding, so the exact function of the protein is uncertain [].
Probab=25.50 E-value=1.3e+02 Score=21.40 Aligned_cols=30 Identities=13% Similarity=0.191 Sum_probs=22.5
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCC
Q 033270 47 IKVVRLSIAQVLTVISQKQKAALREAYKNKKFLPL 81 (123)
Q Consensus 47 Ir~vRK~IARvlTVl~ekq~~~lr~~y~~kk~~p~ 81 (123)
.-.-.|.++|+.++..|++ +.|+.-+|.|-
T Consensus 66 Clh~~Ke~~R~~aI~kqR~-----K~~keGk~tpp 95 (96)
T PF10200_consen 66 CLHHTKEMKRMRAIRKQRD-----KQIKEGKYTPP 95 (96)
T ss_pred HHhhHHHHHHHHHHHHHHH-----HHHHccCCCCC
Confidence 3355899999999998876 45677777763
No 36
>PF05812 Herpes_BLRF2: Herpesvirus BLRF2 protein; InterPro: IPR008642 This family consists of several herpes virus BLRF2 tegument proteins.; PDB: 2OA5_B 2H3R_D.
Probab=25.46 E-value=1.5e+02 Score=21.85 Aligned_cols=29 Identities=17% Similarity=0.150 Sum_probs=24.4
Q ss_pred cCCHHHHHHHHHHHHHHHHHHHHHHHHCC
Q 033270 11 TKSKTDLLNQLKDLKAELALLRVAKVTGG 39 (123)
Q Consensus 11 ~~s~eEL~~qL~eLK~EL~~LR~qk~tgg 39 (123)
++|.|||.++|..|+-|=..|+=+-..|+
T Consensus 2 ~~t~EeLaaeL~kLqmENk~LKkkl~~~~ 30 (118)
T PF05812_consen 2 DMTMEELAAELQKLQMENKALKKKLRQSV 30 (118)
T ss_dssp -HHHHHHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHccC
Confidence 46889999999999999999987766664
No 37
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=25.42 E-value=1e+02 Score=21.68 Aligned_cols=21 Identities=19% Similarity=0.259 Sum_probs=12.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHH
Q 033270 16 DLLNQLKDLKAELALLRVAKV 36 (123)
Q Consensus 16 EL~~qL~eLK~EL~~LR~qk~ 36 (123)
++.+++.+|+.++.+|++...
T Consensus 75 ~~~~ei~~L~~el~~L~~E~d 95 (121)
T PRK09413 75 AAMKQIKELQRLLGKKTMENE 95 (121)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 455556666666666665554
No 38
>PF08312 cwf21: cwf21 domain; InterPro: IPR013170 The cwf21 domain is found in proteins involved in mRNA splicing. Proteins containing this domain have been isolated as a subcomplex of the splicosome in Schizosaccharomyces pombe (Fission yeast) []. In yeast, this domain binds the protein Prp8p [], a large and highly conserved U5 snRNP protein which has been proposed as a protein cofactor at the spliceosomal catalytic centre []. The cwf21 domain is found in, amongst others, the small Cwc21p protein in yeast as well as in the much larger human ortholog SRm300 (serine/arginine repetitive matrix protein). ; PDB: 2E62_A.
Probab=25.15 E-value=1.1e+02 Score=18.71 Aligned_cols=21 Identities=14% Similarity=0.306 Sum_probs=16.2
Q ss_pred hcCCHHHHHHHHHHHHHHHHH
Q 033270 10 RTKSKTDLLNQLKDLKAELAL 30 (123)
Q Consensus 10 R~~s~eEL~~qL~eLK~EL~~ 30 (123)
.+.+.+++..+++.++..|.+
T Consensus 23 ~g~~~eeIe~kv~~~R~~L~~ 43 (46)
T PF08312_consen 23 QGYSEEEIEEKVDELRKKLLE 43 (46)
T ss_dssp HT--HHHHHHHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHHHHHh
Confidence 466899999999999998864
No 39
>PF08285 DPM3: Dolichol-phosphate mannosyltransferase subunit 3 (DPM3); InterPro: IPR013174 This family corresponds to subunit 3 of dolichol-phosphate mannosyltransferase, an enzyme which generates mannosyl donors for glycosylphosphatidylinositols, N-glycan and protein O- and C-mannosylation. DPM3 is an integral membrane protein and plays a role in stabilising the dolichol-phosphate mannosyl transferase complex [].
Probab=25.11 E-value=81 Score=21.94 Aligned_cols=17 Identities=29% Similarity=0.479 Sum_probs=14.6
Q ss_pred HHHHHHHHHHHHHHHHH
Q 033270 14 KTDLLNQLKDLKAELAL 30 (123)
Q Consensus 14 ~eEL~~qL~eLK~EL~~ 30 (123)
-+||.++|+|.|.+|.+
T Consensus 70 ~~eL~~eI~eAK~dLr~ 86 (91)
T PF08285_consen 70 AKELQKEIKEAKADLRK 86 (91)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 57999999999998864
No 40
>PF10498 IFT57: Intra-flagellar transport protein 57 ; InterPro: IPR019530 Eukaryotic cilia and flagella are specialised organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bi-directional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated []. This protein is known as Huntington-interacting protein-1 in humans.
Probab=24.61 E-value=3.6e+02 Score=23.08 Aligned_cols=53 Identities=13% Similarity=0.214 Sum_probs=40.5
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHH-CCCCCccchhHHHHHHHHHHHHHHHHHH
Q 033270 13 SKTDLLNQLKDLKAELALLRVAKVT-GGAPNKLSKIKVVRLSIAQVLTVISQKQ 65 (123)
Q Consensus 13 s~eEL~~qL~eLK~EL~~LR~qk~t-gg~~~k~~kIr~vRK~IARvlTVl~ekq 65 (123)
+..++..+|.++-.||-+...+-.- |...+..+-+-.+|..|.++.+.|.+-.
T Consensus 295 ~V~~~t~~L~~IseeLe~vK~emeerg~~mtD~sPlv~IKqAl~kLk~EI~qMd 348 (359)
T PF10498_consen 295 GVSERTRELAEISEELEQVKQEMEERGSSMTDGSPLVKIKQALTKLKQEIKQMD 348 (359)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHhh
Confidence 5677777777777777777666443 4456777888999999999999998854
No 41
>PF11652 DUF3259: Protein of unknown function (DUF3259); InterPro: IPR024280 This entry describes a eukaryotic protein family of unknown function designated FAM167.
Probab=24.60 E-value=1.5e+02 Score=20.75 Aligned_cols=26 Identities=27% Similarity=0.393 Sum_probs=22.4
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHC
Q 033270 13 SKTDLLNQLKDLKAELALLRVAKVTG 38 (123)
Q Consensus 13 s~eEL~~qL~eLK~EL~~LR~qk~tg 38 (123)
-+.+|..||-.|+.++..|+++++-.
T Consensus 4 qD~qLArqLmrlR~~i~~lkveq~C~ 29 (84)
T PF11652_consen 4 QDQQLARQLMRLRSEIHRLKVEQTCH 29 (84)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 36789999999999999999998754
No 42
>TIGR02209 ftsL_broad cell division protein FtsL. This model represents FtsL, both forms similar to that in E. coli and similar to that in B. subtilis. FtsL is one of the later proteins active in cell division septum formation. FtsL is small, low in complexity, and highly divergent. The scope of this model is broader than that of the Pfam model pfam04999.3 for FtsL, as this one includes FtsL from Bacillus subtilis and related species.
Probab=24.16 E-value=1.6e+02 Score=19.02 Aligned_cols=34 Identities=15% Similarity=0.181 Sum_probs=25.3
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHCCCCCccchhHH
Q 033270 13 SKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKV 49 (123)
Q Consensus 13 s~eEL~~qL~eLK~EL~~LR~qk~tgg~~~k~~kIr~ 49 (123)
..+++..++++++.|-.+|+..... +++|..|..
T Consensus 32 ~~~~~~~~~~~l~~en~~L~~ei~~---l~~~~rIe~ 65 (85)
T TIGR02209 32 ELQKLQLEIDKLQKEWRDLQLEVAE---LSRHERIEK 65 (85)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH---HcCHHHHHH
Confidence 3567888888889999999888873 455666653
No 43
>PF13591 MerR_2: MerR HTH family regulatory protein
Probab=23.03 E-value=97 Score=20.65 Aligned_cols=18 Identities=44% Similarity=0.722 Sum_probs=15.5
Q ss_pred HHHHHHHHHHHHHHHHHH
Q 033270 15 TDLLNQLKDLKAELALLR 32 (123)
Q Consensus 15 eEL~~qL~eLK~EL~~LR 32 (123)
-+|.++++.|+.|+..|+
T Consensus 66 l~LLd~i~~L~~el~~L~ 83 (84)
T PF13591_consen 66 LDLLDRIEQLRRELRELR 83 (84)
T ss_pred HHHHHHHHHHHHHHHHhh
Confidence 478999999999998875
No 44
>PHA03041 virion core protein; Provisional
Probab=22.91 E-value=1.1e+02 Score=23.55 Aligned_cols=29 Identities=21% Similarity=0.389 Sum_probs=24.8
Q ss_pred hHHHhcCCHHHHHHHHHHHHHHHHHHHHH
Q 033270 6 VHELRTKSKTDLLNQLKDLKAELALLRVA 34 (123)
Q Consensus 6 a~ELR~~s~eEL~~qL~eLK~EL~~LR~q 34 (123)
+.+++..|.+|+.+++++.+.|-..|.-+
T Consensus 87 ~~~~~~~s~~ei~kE~esIKdeT~sLQ~e 115 (153)
T PHA03041 87 PKKIRSISIEEIIKELESIKDETSSLQNE 115 (153)
T ss_pred hhhhhhccHHHHHHHHHHHhHHHHHHHHH
Confidence 35788999999999999999998888544
No 45
>PF11629 Mst1_SARAH: C terminal SARAH domain of Mst1; InterPro: IPR024205 The SARAH (Sav/Rassf/Hpo) domain is found at the C terminus in three classes of eukaryotic tumour suppressors that give the domain its name. In the Sav (Salvador) and Hpo (Hippo) families, the SARAH domain mediates signal transduction from Hpo via the Sav scaffolding protein to the downstream component Wts (Warts); the phosphorylation of Wts by Hpo triggers cell cycle arrest and apoptosis by down-regulating cyclin E, Diap 1 and other targets []. The SARAH domain is also involved in dimerisation, as in the human Hpo orthologue, Mst1, which homodimerises via its C-terminal SARAH domain. The SARAH domain is found associated with other domains, such as protein kinase domains, WW/rsp5/WWP domain (IPR001202 from INTERPRO), C1 domain (IPR002219 from INTERPRO), LIM domain (IPR001781 from INTERPRO), or the Ras-associating (RA) domain (IPR000159 from INTERPRO).; GO: 0004674 protein serine/threonine kinase activity; PDB: 2JO8_A.
Probab=22.85 E-value=1.5e+02 Score=18.70 Aligned_cols=27 Identities=30% Similarity=0.303 Sum_probs=16.7
Q ss_pred HHhcCCHHHHHHHHHHHH----HHHHHHHHH
Q 033270 8 ELRTKSKTDLLNQLKDLK----AELALLRVA 34 (123)
Q Consensus 8 ELR~~s~eEL~~qL~eLK----~EL~~LR~q 34 (123)
=|..+|.+||...|..|- .|+-+||-.
T Consensus 4 fLk~ls~~eL~~rl~~LD~~ME~Eieelr~R 34 (49)
T PF11629_consen 4 FLKFLSYEELQQRLASLDPEMEQEIEELRQR 34 (49)
T ss_dssp GGGGS-HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHhhCCHHHHHHHHHhCCHHHHHHHHHHHHH
Confidence 367788888888877654 344555443
No 46
>PF08627 CRT-like: CRT-like; InterPro: IPR013936 This region is found in proteins related to Plasmodium falciparum chloroquine resistance transporter (CRT).
Probab=22.65 E-value=33 Score=25.75 Aligned_cols=10 Identities=50% Similarity=0.740 Sum_probs=8.0
Q ss_pred hhCCcchhhh
Q 033270 112 MYFPMRKYAI 121 (123)
Q Consensus 112 ~~~p~r~~a~ 121 (123)
+.||.++|||
T Consensus 121 r~FPkyKFaI 130 (130)
T PF08627_consen 121 RAFPKYKFAI 130 (130)
T ss_pred HhCccccccC
Confidence 4689998886
No 47
>COG1137 YhbG ABC-type (unclassified) transport system, ATPase component [General function prediction only]
Probab=22.26 E-value=1.7e+02 Score=24.12 Aligned_cols=50 Identities=20% Similarity=0.256 Sum_probs=29.6
Q ss_pred HHhcCCHH--HHHHHHHHHHHHHHHHHHHHHHCCCCCccchhHHHHHHHHHHHHH
Q 033270 8 ELRTKSKT--DLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTV 60 (123)
Q Consensus 8 ELR~~s~e--EL~~qL~eLK~EL~~LR~qk~tgg~~~k~~kIr~vRK~IARvlTV 60 (123)
|+++.+.+ |-..++++|-.|+.=..+.+.-|.++|---+- |=.|||.|+.
T Consensus 105 E~~~~d~~~~~~~~~l~~LL~ef~i~hlr~~~a~sLSGGERR---R~EIARaLa~ 156 (243)
T COG1137 105 EIREKDLKKAERKEELDALLEEFHITHLRDSKAYSLSGGERR---RVEIARALAA 156 (243)
T ss_pred hhhhcchhHHHHHHHHHHHHHHhchHHHhcCcccccccchHH---HHHHHHHHhc
Confidence 45554433 44445667776666666666666556653332 3489999874
No 48
>COG4741 Predicted secreted endonuclease distantly related to archaeal Holliday junction resolvase [Nucleotide transport and metabolism]
Probab=22.07 E-value=1.3e+02 Score=23.55 Aligned_cols=41 Identities=24% Similarity=0.276 Sum_probs=31.6
Q ss_pred chhHHHHHH-HHHHHHHHHHHHHHHHHHHHhCCCCCCCCCCc
Q 033270 45 SKIKVVRLS-IAQVLTVISQKQKAALREAYKNKKFLPLDLRP 85 (123)
Q Consensus 45 ~kIr~vRK~-IARvlTVl~ekq~~~lr~~y~~kk~~p~dlr~ 85 (123)
-+|..+|.+ |-+-.-|+.-+--+++-.||-+=+|-|.|-|.
T Consensus 70 kkieeaR~dav~kS~~Vi~GrVtEqlaPffp~f~ynPkD~Rf 111 (175)
T COG4741 70 KKIEEAREDAVRKSRAVILGRVTEQLAPFFPEFKYNPKDARF 111 (175)
T ss_pred HHHHHHHHHHHHHhHHHHhhhhHhhhcccccCCCcCCcccee
Confidence 456555543 55666677777788999999999999999985
No 49
>COG4942 Membrane-bound metallopeptidase [Cell division and chromosome partitioning]
Probab=21.14 E-value=4.4e+02 Score=23.38 Aligned_cols=48 Identities=27% Similarity=0.370 Sum_probs=34.2
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHCCCCCccchhHHHHHHHHHHHHHHHHHH
Q 033270 13 SKTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTVISQKQ 65 (123)
Q Consensus 13 s~eEL~~qL~eLK~EL~~LR~qk~tgg~~~k~~kIr~vRK~IARvlTVl~ekq 65 (123)
....|.++|.+++.++..+.-+-.-. + ..+..++++|+.+..-++.-+
T Consensus 60 ~~~kL~~~lk~~e~~i~~~~~ql~~s-~----~~l~~~~~~I~~~~~~l~~l~ 107 (420)
T COG4942 60 QRAKLEKQLKSLETEIASLEAQLIET-A----DDLKKLRKQIADLNARLNALE 107 (420)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH-H----hHHHHHHhhHHHHHHHHHHHH
Confidence 35667788888888888877666533 1 567788888988887776543
No 50
>PRK15178 Vi polysaccharide export inner membrane protein VexD; Provisional
Probab=21.09 E-value=3.6e+02 Score=23.88 Aligned_cols=45 Identities=24% Similarity=0.197 Sum_probs=28.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHCCCCCccchhHHHHHHHHHHHHHHHH
Q 033270 14 KTDLLNQLKDLKAELALLRVAKVTGGAPNKLSKIKVVRLSIAQVLTVISQ 63 (123)
Q Consensus 14 ~eEL~~qL~eLK~EL~~LR~qk~tgg~~~k~~kIr~vRK~IARvlTVl~e 63 (123)
...|..+|.+++.+|..|+.. ..++...|..++..|+-+-.-|.+
T Consensus 288 I~~Le~qLa~~~aeL~~L~~~-----~~p~sPqV~~l~~rI~aLe~QIa~ 332 (434)
T PRK15178 288 IAGFETQLAEAKAEYAQLMVN-----GLDQNPLIPRLSAKIKVLEKQIGE 332 (434)
T ss_pred HHHHHHHHHHHHHHHHHHHhh-----cCCCCCchhHHHHHHHHHHHHHHH
Confidence 344555555555555555332 235568899999999988766654
No 51
>PF07106 TBPIP: Tat binding protein 1(TBP-1)-interacting protein (TBPIP); InterPro: IPR010776 This family consists of several eukaryotic TBP-1 interacting protein (TBPIP) sequences. TBP-1 has been demonstrated to interact with the human immunodeficiency virus type 1 (HIV-1) viral protein Tat, then modulate the essential replication process of HIV. In addition, TBP-1 has been shown to be a component of the 26S proteasome, a basic multiprotein complex that degrades ubiquitinated proteins in an ATP-dependent fashion. Human TBPIP interacts with human TBP-1 then modulates the inhibitory action of human TBP-1 on HIV-Tat-mediated transactivation [].
Probab=20.43 E-value=3.6e+02 Score=19.85 Aligned_cols=52 Identities=12% Similarity=0.150 Sum_probs=26.1
Q ss_pred cCCHHHHHHHHHHHHHHHHHHHHHHH--H-CCCCCccchhHHHHHHHHHHHHHHH
Q 033270 11 TKSKTDLLNQLKDLKAELALLRVAKV--T-GGAPNKLSKIKVVRLSIAQVLTVIS 62 (123)
Q Consensus 11 ~~s~eEL~~qL~eLK~EL~~LR~qk~--t-gg~~~k~~kIr~vRK~IARvlTVl~ 62 (123)
..|.+||..++.+|..|+..+.-.-. - |+..-.+..+..+.+...+......
T Consensus 108 ~~t~~el~~~i~~l~~e~~~l~~kL~~l~~~~~~vs~ee~~~~~~~~~~~~k~w~ 162 (169)
T PF07106_consen 108 EPTNEELREEIEELEEEIEELEEKLEKLRSGSKPVSPEEKEKLEKEYKKWRKEWK 162 (169)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHH
Confidence 34667777777777776665543322 1 2222234445555544444444333
No 52
>PRK10265 chaperone-modulator protein CbpM; Provisional
Probab=20.34 E-value=1.2e+02 Score=20.93 Aligned_cols=20 Identities=40% Similarity=0.517 Sum_probs=16.3
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q 033270 15 TDLLNQLKDLKAELALLRVA 34 (123)
Q Consensus 15 eEL~~qL~eLK~EL~~LR~q 34 (123)
-+|.++++.|+.|+-.|+-+
T Consensus 74 l~LLd~i~~Lr~el~~L~~~ 93 (101)
T PRK10265 74 LTLLDEIAHLKQENRLLRQR 93 (101)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 47889999999998888653
Done!