Query psy4242
Match_columns 74
No_of_seqs 118 out of 849
Neff 5.3
Searched_HMMs 46136
Date Fri Aug 16 20:27:07 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy4242.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/4242hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0049 RpsG Ribosomal protein 99.9 7.7E-26 1.7E-30 154.0 5.1 58 1-74 29-86 (148)
2 TIGR01029 rpsG_bact ribosomal 99.9 2.9E-23 6.3E-28 141.2 5.8 58 1-74 28-85 (154)
3 TIGR01028 S7_S5_E_A ribosomal 99.9 7.4E-23 1.6E-27 143.5 6.7 58 1-74 58-119 (186)
4 PRK04027 30S ribosomal protein 99.9 8.6E-23 1.9E-27 144.1 6.7 58 1-74 67-128 (195)
5 PRK05302 30S ribosomal protein 99.9 7.9E-23 1.7E-27 139.3 5.7 58 1-74 30-87 (156)
6 CHL00053 rps7 ribosomal protei 99.9 3.6E-22 7.8E-27 135.8 6.1 58 1-74 30-87 (155)
7 PTZ00091 40S ribosomal protein 99.9 1.3E-21 2.9E-26 137.9 6.5 58 1-74 65-126 (193)
8 PF00177 Ribosomal_S7: Ribosom 99.8 2.1E-20 4.5E-25 125.7 5.6 58 1-74 29-86 (148)
9 KOG3291|consensus 99.8 8.5E-20 1.8E-24 129.9 5.1 58 1-74 86-143 (208)
10 KOG3960|consensus 73.4 4.5 9.8E-05 30.4 3.2 34 12-55 131-164 (284)
11 PF14202 TnpW: Transposon-enco 57.1 6.3 0.00014 21.0 1.0 13 62-74 2-14 (37)
12 PF09336 Vps4_C: Vps4 C termin 56.7 6.2 0.00013 22.9 1.0 16 46-61 32-47 (62)
13 COG5012 Predicted cobalamin bi 44.5 28 0.0006 25.6 3.0 38 3-61 27-64 (227)
14 cd06403 PB1_Par6 The PB1 domai 32.7 37 0.0008 21.2 1.8 17 47-63 60-76 (80)
15 cd08036 LARP_5 La RNA-binding 32.0 53 0.0011 20.2 2.4 19 44-63 49-67 (75)
16 PF03855 M-factor: M-factor; 31.7 25 0.00054 19.5 0.8 20 42-61 18-38 (44)
17 cd03338 TCP1_delta TCP-1 (CTT 31.2 1.3E+02 0.0029 23.4 5.1 39 4-54 421-459 (515)
18 cd03341 TCP1_theta TCP-1 (CTT 30.4 1.4E+02 0.0031 23.1 5.1 38 3-52 374-411 (472)
19 TIGR03065 srtB_sig_QVPTGV sort 29.0 49 0.0011 17.2 1.6 19 55-73 9-27 (32)
20 PF09453 HIRA_B: HIRA B motif; 28.6 14 0.0003 18.2 -0.5 9 1-9 6-14 (24)
21 COG0053 MMT1 Predicted Co/Zn/C 28.3 1.1E+02 0.0024 22.6 4.1 56 9-69 188-243 (304)
22 cd03340 TCP1_eta TCP-1 (CTT or 28.3 1.6E+02 0.0035 23.1 5.1 39 4-54 424-462 (522)
23 cd03337 TCP1_gamma TCP-1 (CTT 28.0 1.7E+02 0.0036 22.8 5.1 38 4-53 385-422 (480)
24 PF04231 Endonuclease_1: Endon 27.8 1.5E+02 0.0032 21.2 4.5 27 6-32 156-189 (218)
25 cd03343 cpn60 cpn60 chaperonin 27.7 1.7E+02 0.0036 22.9 5.1 38 4-53 422-459 (517)
26 TIGR02342 chap_CCT_delta T-com 27.7 1.6E+02 0.0035 23.2 5.0 39 4-54 422-460 (517)
27 cd00309 chaperonin_type_I_II c 27.6 1.6E+02 0.0035 22.5 4.9 41 3-55 370-410 (464)
28 TIGR02344 chap_CCT_gamma T-com 26.4 1.8E+02 0.004 22.8 5.1 39 4-54 426-464 (525)
29 TIGR02346 chap_CCT_theta T-com 26.1 1.8E+02 0.004 23.0 5.1 38 4-53 423-460 (531)
30 PF03120 DNA_ligase_OB: NAD-de 26.0 32 0.0007 21.2 0.7 19 55-73 17-35 (82)
31 PTZ00212 T-complex protein 1 s 25.4 1.9E+02 0.0042 22.8 5.1 37 4-52 431-467 (533)
32 TIGR02339 thermosome_arch ther 25.3 2E+02 0.0042 22.6 5.1 38 4-53 425-462 (519)
33 cd03336 TCP1_beta TCP-1 (CTT o 25.2 1.9E+02 0.0042 22.7 5.0 37 4-52 419-455 (517)
34 TIGR02341 chap_CCT_beta T-comp 24.9 2E+02 0.0043 22.7 5.1 39 4-54 420-458 (519)
35 TIGR02347 chap_CCT_zeta T-comp 24.4 2E+02 0.0044 22.8 5.0 36 4-51 431-466 (531)
36 PF13656 RNA_pol_L_2: RNA poly 24.1 45 0.00097 20.0 1.1 15 42-56 52-66 (77)
37 cd01223 PH_Vav Vav pleckstrin 24.0 60 0.0013 21.4 1.7 15 44-58 102-116 (116)
38 TIGR02345 chap_CCT_eta T-compl 23.8 2.2E+02 0.0047 22.5 5.1 40 3-54 424-463 (522)
39 PF07719 TPR_2: Tetratricopept 23.2 81 0.0018 14.4 1.8 17 3-19 13-29 (34)
40 cd03342 TCP1_zeta TCP-1 (CTT o 22.9 2.3E+02 0.0051 22.1 5.1 38 4-53 388-425 (484)
41 TIGR00264 alpha-NAC-related pr 22.8 43 0.00093 22.2 0.9 17 57-74 46-62 (116)
42 TIGR02340 chap_CCT_alpha T-com 20.6 2.7E+02 0.0058 22.0 5.0 38 4-53 427-464 (536)
43 cd03339 TCP1_epsilon TCP-1 (CT 20.5 2.8E+02 0.006 21.8 5.1 39 3-53 431-469 (526)
44 TIGR03188 histidine_hisI phosp 20.4 2.2E+02 0.0048 17.4 4.3 23 2-24 25-47 (84)
45 TIGR02343 chap_CCT_epsi T-comp 20.3 2.7E+02 0.0058 22.1 5.0 37 4-52 436-472 (532)
46 cd03335 TCP1_alpha TCP-1 (CTT 20.2 2.8E+02 0.006 21.8 5.0 38 4-53 423-460 (527)
47 CHL00093 groEL chaperonin GroE 20.2 3.9E+02 0.0084 21.2 5.8 47 3-62 433-479 (529)
48 PF01193 RNA_pol_L: RNA polyme 20.1 61 0.0013 18.4 1.1 15 42-56 47-61 (66)
49 PF12651 RHH_3: Ribbon-helix-h 20.1 1.6E+02 0.0035 15.7 3.8 14 42-55 25-38 (44)
No 1
>COG0049 RpsG Ribosomal protein S7 [Translation, ribosomal structure and biogenesis]
Probab=99.92 E-value=7.7e-26 Score=154.02 Aligned_cols=58 Identities=31% Similarity=0.484 Sum_probs=56.8
Q ss_pred CCCcChHHHHHHHHHHHHHHHHHHHHHHHhhhCChHHHhhhcCCHHHHHHHHHHcCCCceeEEEEeeCcccccC
Q psy4242 1 MMKKGNKELAREVFEYTVKSIKRIQIEKYNKATSDEERESIILDPYVIIDKAIENTKPILKLRSIKRAAVTYQM 74 (74)
Q Consensus 1 iMk~GkK~~A~~Iv~~al~~Ik~~~~~k~~~~~~~~~~~~i~~nP~~i~~~Ai~N~~P~vev~~~r~GG~tYqV 74 (74)
||+||||++|++|||.||++|.+++ ++||++||++||+|++|.+||+++|+||++|||
T Consensus 29 iM~~GKK~~A~~Ivy~Af~ii~~kT----------------g~~Piqvf~~Ai~N~~P~~Ev~srrvGGa~yqv 86 (148)
T COG0049 29 IMRDGKKSLAEKIVYGAFDIIEKKT----------------GQNPLQVFEKAIENVKPREEVKSRRVGGATYQV 86 (148)
T ss_pred HHHhccHHHHHHHHHHHHHHHHHHH----------------CCChHHHHHHHHHhcCchhheeeeeeCCeeeEe
Confidence 6999999999999999999999999 999999999999999999999999999999997
No 2
>TIGR01029 rpsG_bact ribosomal protein S7, bacterial/organelle. This model describes the bacterial and organellar branch of the ribosomal protein S7 family (includes prokaroytic S7 and eukaryotic S5). The eukaryotic and archaeal branch is described by model TIGR01028.
Probab=99.88 E-value=2.9e-23 Score=141.18 Aligned_cols=58 Identities=31% Similarity=0.535 Sum_probs=56.3
Q ss_pred CCCcChHHHHHHHHHHHHHHHHHHHHHHHhhhCChHHHhhhcCCHHHHHHHHHHcCCCceeEEEEeeCcccccC
Q psy4242 1 MMKKGNKELAREVFEYTVKSIKRIQIEKYNKATSDEERESIILDPYVIIDKAIENTKPILKLRSIKRAAVTYQM 74 (74)
Q Consensus 1 iMk~GkK~~A~~Iv~~al~~Ik~~~~~k~~~~~~~~~~~~i~~nP~~i~~~Ai~N~~P~vev~~~r~GG~tYqV 74 (74)
||++|||++|++|||+||++|+..+ +.||++||++||+||+|++||+++|+||++|||
T Consensus 28 lM~~GKK~~A~kI~~~al~~i~~~~----------------~~nPi~vl~~Ai~nv~P~~evk~~r~gG~~yqv 85 (154)
T TIGR01029 28 VMKDGKKSLAESIVYKAFERIAKKT----------------GEDPLEVFEQALENVKPLVEVKSRRVGGATYQV 85 (154)
T ss_pred HHhcccHHHHHHHHHHHHHHHHHHc----------------CCCHHHHHHHHHHhCCCCeeeEEeecCCEEEEE
Confidence 6999999999999999999999887 889999999999999999999999999999997
No 3
>TIGR01028 S7_S5_E_A ribosomal protein S7(archaeal)/S5(eukaryotic). This model describes the members from the eukaryotic cytosol and the Archaea of the family that includes ribosomal protein S7 of bacteria and S5 of eukaryotes. A separate model describes bacterial and organellar S7.
Probab=99.88 E-value=7.4e-23 Score=143.55 Aligned_cols=58 Identities=22% Similarity=0.315 Sum_probs=55.9
Q ss_pred CCCc----ChHHHHHHHHHHHHHHHHHHHHHHHhhhCChHHHhhhcCCHHHHHHHHHHcCCCceeEEEEeeCcccccC
Q psy4242 1 MMKK----GNKELAREVFEYTVKSIKRIQIEKYNKATSDEERESIILDPYVIIDKAIENTKPILKLRSIKRAAVTYQM 74 (74)
Q Consensus 1 iMk~----GkK~~A~~Iv~~al~~Ik~~~~~k~~~~~~~~~~~~i~~nP~~i~~~Ai~N~~P~vev~~~r~GG~tYqV 74 (74)
||++ |||++|++|||+||++|+.++ +.||++||++||+||+|++||+++|+||++|||
T Consensus 58 lM~~g~n~GKK~~A~kIv~~A~~iI~~~t----------------~~nPi~vl~~AI~N~~P~~ev~~~r~GG~~yqV 119 (186)
T TIGR01028 58 VMRSGRNNGKKLKAYRIVKEAFEIIEKRT----------------GENPIQVLVDAIENAGPREDTTRIGYGGIVYRQ 119 (186)
T ss_pred HhccCcCCCcHHHHHHHHHHHHHHHHHHh----------------CCChHHHHHHHHHcCCCCeEEEEEecCCEEEEe
Confidence 5786 999999999999999999998 899999999999999999999999999999997
No 4
>PRK04027 30S ribosomal protein S7P; Reviewed
Probab=99.88 E-value=8.6e-23 Score=144.11 Aligned_cols=58 Identities=24% Similarity=0.400 Sum_probs=56.2
Q ss_pred CCCc----ChHHHHHHHHHHHHHHHHHHHHHHHhhhCChHHHhhhcCCHHHHHHHHHHcCCCceeEEEEeeCcccccC
Q psy4242 1 MMKK----GNKELAREVFEYTVKSIKRIQIEKYNKATSDEERESIILDPYVIIDKAIENTKPILKLRSIKRAAVTYQM 74 (74)
Q Consensus 1 iMk~----GkK~~A~~Iv~~al~~Ik~~~~~k~~~~~~~~~~~~i~~nP~~i~~~Ai~N~~P~vev~~~r~GG~tYqV 74 (74)
||++ |||++|++|||+||++|+.++ +.||++||++||+|++|.+||+++|+||++|||
T Consensus 67 lM~~~~n~GKK~~A~~Iv~~AfeiI~~kT----------------~~nPiqVl~~AI~N~~P~~Ev~~~r~GG~tyqv 128 (195)
T PRK04027 67 LMRTERNTGKKQKAYNIVKEAFEIIEKRT----------------KQNPIQVLVDAIENAAPREETTRIKYGGISYPK 128 (195)
T ss_pred HhccCccCCcHHHHHHHHHHHHHHHHHHH----------------CCCHHHHHHHHHHcCCCCeEEEEEecCCEEEEe
Confidence 5888 999999999999999999998 899999999999999999999999999999997
No 5
>PRK05302 30S ribosomal protein S7; Validated
Probab=99.87 E-value=7.9e-23 Score=139.28 Aligned_cols=58 Identities=29% Similarity=0.502 Sum_probs=56.2
Q ss_pred CCCcChHHHHHHHHHHHHHHHHHHHHHHHhhhCChHHHhhhcCCHHHHHHHHHHcCCCceeEEEEeeCcccccC
Q psy4242 1 MMKKGNKELAREVFEYTVKSIKRIQIEKYNKATSDEERESIILDPYVIIDKAIENTKPILKLRSIKRAAVTYQM 74 (74)
Q Consensus 1 iMk~GkK~~A~~Iv~~al~~Ik~~~~~k~~~~~~~~~~~~i~~nP~~i~~~Ai~N~~P~vev~~~r~GG~tYqV 74 (74)
||++|||++|++||++||++|+..+ +.||+.||++||+||+|++||+++|+||++|||
T Consensus 30 lmk~GKK~~A~kI~~~al~~I~~~~----------------~~npl~il~~Ai~nv~P~~evk~~r~gG~~~~v 87 (156)
T PRK05302 30 LMLDGKKSVAEKIVYGALDIIEEKT----------------GKDPLEVFEKALENVKPVVEVKSRRVGGATYQV 87 (156)
T ss_pred HhhcccHHHHHHHHHHHHHHHHHHc----------------CCChHHHHHHHHHhCCCCeEEeeeccCCEEEEE
Confidence 6999999999999999999999887 899999999999999999999999999999997
No 6
>CHL00053 rps7 ribosomal protein S7
Probab=99.86 E-value=3.6e-22 Score=135.84 Aligned_cols=58 Identities=26% Similarity=0.465 Sum_probs=56.2
Q ss_pred CCCcChHHHHHHHHHHHHHHHHHHHHHHHhhhCChHHHhhhcCCHHHHHHHHHHcCCCceeEEEEeeCcccccC
Q psy4242 1 MMKKGNKELAREVFEYTVKSIKRIQIEKYNKATSDEERESIILDPYVIIDKAIENTKPILKLRSIKRAAVTYQM 74 (74)
Q Consensus 1 iMk~GkK~~A~~Iv~~al~~Ik~~~~~k~~~~~~~~~~~~i~~nP~~i~~~Ai~N~~P~vev~~~r~GG~tYqV 74 (74)
+|++|||++|++||++||++|+..+ +.||+++|++||+||+|++||+++|+||++|||
T Consensus 30 lm~~GKK~~A~kIv~~al~~i~~~~----------------~~npi~vl~~Ai~N~~P~~evk~~r~gG~~~qv 87 (155)
T CHL00053 30 ILKSGKKSLAYRIVYRALKKIQQKT----------------EKNPLSVLRQAIRNVTPDVEVKARRVGGSTYQV 87 (155)
T ss_pred HHhcccHHHHHHHHHHHHHHHHHHc----------------CCCHHHHHHHHHHhCCCcEEEEEEeeCCEEEEE
Confidence 6999999999999999999999887 899999999999999999999999999999997
No 7
>PTZ00091 40S ribosomal protein S5; Provisional
Probab=99.85 E-value=1.3e-21 Score=137.92 Aligned_cols=58 Identities=19% Similarity=0.257 Sum_probs=56.0
Q ss_pred CCCc----ChHHHHHHHHHHHHHHHHHHHHHHHhhhCChHHHhhhcCCHHHHHHHHHHcCCCceeEEEEeeCcccccC
Q psy4242 1 MMKK----GNKELAREVFEYTVKSIKRIQIEKYNKATSDEERESIILDPYVIIDKAIENTKPILKLRSIKRAAVTYQM 74 (74)
Q Consensus 1 iMk~----GkK~~A~~Iv~~al~~Ik~~~~~k~~~~~~~~~~~~i~~nP~~i~~~Ai~N~~P~vev~~~r~GG~tYqV 74 (74)
||++ |||++|++|||+||++|..++ ++||++||++||+||+|.+|++++++||++|||
T Consensus 65 lM~~grn~GKK~~A~~IV~~AfeiI~~~t----------------~~nPiqVl~~AI~N~~P~~e~~ri~~GG~~yqv 126 (193)
T PTZ00091 65 LMFHGRNNGKKLLAVRIVKHAFEIIHLLT----------------DKNPLQVLVDAVQNGGPREDSTRVGSGGVVRRQ 126 (193)
T ss_pred HhccCccCCcHHHHHHHHHHHHHHHHHHH----------------CCChHHHHHHHHHhCCCCeeeEEeecCCeEEEE
Confidence 5888 999999999999999999988 899999999999999999999999999999996
No 8
>PF00177 Ribosomal_S7: Ribosomal protein S7p/S5e; InterPro: IPR023798 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 S7 is one of the proteins from the small ribosomal subunit. In Escherichia coli, S7 is known to bind directly to part of the 3'end of 16S ribosomal RNA. It belongs to a family of ribosomal proteins which have been grouped on the basis of sequence similarities [, , ]. This entry represents the S7 structural domain, which consists of a bundle of six helices and an extended beta hairpin between helices 3 and 4, with two or more RNA-binding sites on its surface [].; PDB: 3IZ6_F 3V28_G 2WRN_G 2HHH_G 2V46_G 3KNL_G 2UUC_G 2Y16_G 2Y0W_G 2J02_G ....
Probab=99.82 E-value=2.1e-20 Score=125.70 Aligned_cols=58 Identities=38% Similarity=0.609 Sum_probs=55.1
Q ss_pred CCCcChHHHHHHHHHHHHHHHHHHHHHHHhhhCChHHHhhhcCCHHHHHHHHHHcCCCceeEEEEeeCcccccC
Q psy4242 1 MMKKGNKELAREVFEYTVKSIKRIQIEKYNKATSDEERESIILDPYVIIDKAIENTKPILKLRSIKRAAVTYQM 74 (74)
Q Consensus 1 iMk~GkK~~A~~Iv~~al~~Ik~~~~~k~~~~~~~~~~~~i~~nP~~i~~~Ai~N~~P~vev~~~r~GG~tYqV 74 (74)
+|++|||++|++||++||+.|+.++ +.||+.||++||+||+|+++|+++++||.+|||
T Consensus 29 lmk~GkK~~A~~i~~~al~~i~~~~----------------~~npi~il~~Ai~n~~P~~~v~~~k~gg~~~~v 86 (148)
T PF00177_consen 29 LMKDGKKSKAEKIVYKALEIIKKKT----------------NKNPIQILKQAIENVKPLVEVRSIKKGGKTYQV 86 (148)
T ss_dssp HHSTTBHHHHHHHHHHHHHHHHHHH----------------SSSHHHHHHHHHHHHS-SEEEEEEEETTEEEEE
T ss_pred HHHHhHHHHHHHHHHHHHHHhhccc----------------CCCHHHHHHHHHHHhccceeeeeeccCceeEEE
Confidence 5999999999999999999999887 889999999999999999999999999999996
No 9
>KOG3291|consensus
Probab=99.79 E-value=8.5e-20 Score=129.92 Aligned_cols=58 Identities=38% Similarity=0.591 Sum_probs=56.6
Q ss_pred CCCcChHHHHHHHHHHHHHHHHHHHHHHHhhhCChHHHhhhcCCHHHHHHHHHHcCCCceeEEEEeeCcccccC
Q psy4242 1 MMKKGNKELAREVFEYTVKSIKRIQIEKYNKATSDEERESIILDPYVIIDKAIENTKPILKLRSIKRAAVTYQM 74 (74)
Q Consensus 1 iMk~GkK~~A~~Iv~~al~~Ik~~~~~k~~~~~~~~~~~~i~~nP~~i~~~Ai~N~~P~vev~~~r~GG~tYqV 74 (74)
+|++|||.+|++||+.||++|++.| +.||++||++||+||.|++.++++.+||++|||
T Consensus 86 ~~~~GKK~~a~~Iv~~aleiI~~~t----------------~~NPiqvl~~AI~n~~P~~~~~~i~r~g~~~~v 143 (208)
T KOG3291|consen 86 IMKNGKKLLARRIVKHALEIIKRLT----------------ERNPIQVLVQAIENCGPLEDVTRIGRAGTTYQV 143 (208)
T ss_pred HHhcccHHHHHHHHHHHHHHHHHHh----------------cCCHHHHHHHHHHhcCchhhceeecccceEEEe
Confidence 5899999999999999999999999 999999999999999999999999999999997
No 10
>KOG3960|consensus
Probab=73.39 E-value=4.5 Score=30.44 Aligned_cols=34 Identities=18% Similarity=0.178 Sum_probs=22.7
Q ss_pred HHHHHHHHHHHHHHHHHHhhhCChHHHhhhcCCHHHHHHHHHHc
Q psy4242 12 EVFEYTVKSIKRIQIEKYNKATSDEERESIILDPYVIIDKAIEN 55 (74)
Q Consensus 12 ~Iv~~al~~Ik~~~~~k~~~~~~~~~~~~i~~nP~~i~~~Ai~N 55 (74)
+=|++|||.+|+.+. .++ +-..-=++||+.||+=
T Consensus 131 kKVNEAFE~LKRrT~-----~NP-----NQRLPKVEILRsAI~Y 164 (284)
T KOG3960|consen 131 KKVNEAFETLKRRTS-----SNP-----NQRLPKVEILRSAIRY 164 (284)
T ss_pred HHHHHHHHHHHhhcC-----CCc-----cccccHHHHHHHHHHH
Confidence 458999999999981 111 0123347899999864
No 11
>PF14202 TnpW: Transposon-encoded protein TnpW
Probab=57.15 E-value=6.3 Score=20.96 Aligned_cols=13 Identities=23% Similarity=0.204 Sum_probs=10.4
Q ss_pred EEEEeeCcccccC
Q psy4242 62 LRSIKRAAVTYQM 74 (74)
Q Consensus 62 v~~~r~GG~tYqV 74 (74)
+...++||.+|-|
T Consensus 2 ~~~~kIG~Tty~V 14 (37)
T PF14202_consen 2 TTEKKIGKTTYVV 14 (37)
T ss_pred eEEEEECCEEEEE
Confidence 4568999999965
No 12
>PF09336 Vps4_C: Vps4 C terminal oligomerisation domain; InterPro: IPR015415 This domain is found at the C-terminal of ATPase proteins involved in vacuolar sorting. It forms an alpha helix structure and is required for oligomerisation []. ; PDB: 1XWI_A 3EIH_C 2QPA_C 3EIE_A 2RKO_A 2QP9_X 3MHV_C 3CF3_C 3CF1_A 3CF2_A ....
Probab=56.65 E-value=6.2 Score=22.95 Aligned_cols=16 Identities=19% Similarity=0.358 Sum_probs=13.0
Q ss_pred HHHHHHHHHcCCCcee
Q psy4242 46 YVIIDKAIENTKPILK 61 (74)
Q Consensus 46 ~~i~~~Ai~N~~P~ve 61 (74)
+.=|..||.+++|.|.
T Consensus 32 ~~DF~~Al~~~kpSVs 47 (62)
T PF09336_consen 32 MEDFEEALKKVKPSVS 47 (62)
T ss_dssp HHHHHHHHHTCGGSS-
T ss_pred HHHHHHHHHHcCCCCC
Confidence 4559999999999874
No 13
>COG5012 Predicted cobalamin binding protein [General function prediction only]
Probab=44.50 E-value=28 Score=25.57 Aligned_cols=38 Identities=26% Similarity=0.477 Sum_probs=25.6
Q ss_pred CcChHHHHHHHHHHHHHHHHHHHHHHHhhhCChHHHhhhcCCHHHHHHHHHHcCCCcee
Q psy4242 3 KKGNKELAREVFEYTVKSIKRIQIEKYNKATSDEERESIILDPYVIIDKAIENTKPILK 61 (74)
Q Consensus 3 k~GkK~~A~~Iv~~al~~Ik~~~~~k~~~~~~~~~~~~i~~nP~~i~~~Ai~N~~P~ve 61 (74)
.+|+++.++.....+++. +.+|+.++.+++.-.++.+.
T Consensus 27 ~dg~~~~~~e~~~~al~~---------------------Gidp~~ii~~~l~~gm~~Vg 64 (227)
T COG5012 27 VDGEEEMAVELTQKALEA---------------------GIDPYDIIEDGLSAGMSIVG 64 (227)
T ss_pred hcchHHHHHHHHHHHHHc---------------------CCCHHHHHHHHHHhHHHHHh
Confidence 456666666665555541 67899999888877666553
No 14
>cd06403 PB1_Par6 The PB1 domain is an essential part of Par6 protein which in complex with Par3 and aPKC proteins is crucial for establishment of apical-basal polarity of animal cells. The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants. The
Probab=32.74 E-value=37 Score=21.22 Aligned_cols=17 Identities=24% Similarity=0.372 Sum_probs=14.3
Q ss_pred HHHHHHHHcCCCceeEE
Q psy4242 47 VIIDKAIENTKPILKLR 63 (74)
Q Consensus 47 ~i~~~Ai~N~~P~vev~ 63 (74)
.=|++|+.++.|++-|-
T Consensus 60 dNf~kAlssa~plLRl~ 76 (80)
T cd06403 60 DNFLKALSSANPLLRIF 76 (80)
T ss_pred HHHHHHHHcCCCceEEE
Confidence 45899999999998764
No 15
>cd08036 LARP_5 La RNA-binding domain of La-related protein 5. This domain is found in vertebrate La-related protein 5 (LARP5). A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes.
Probab=32.01 E-value=53 Score=20.19 Aligned_cols=19 Identities=11% Similarity=0.314 Sum_probs=15.9
Q ss_pred CHHHHHHHHHHcCCCceeEE
Q psy4242 44 DPYVIIDKAIENTKPILKLR 63 (74)
Q Consensus 44 nP~~i~~~Ai~N~~P~vev~ 63 (74)
+.+.++..|+.+. |+++|.
T Consensus 49 ~D~~lI~~aL~~S-~~vevs 67 (75)
T cd08036 49 TDVDLIVDVLRSL-PLVQVD 67 (75)
T ss_pred CCHHHHHHHHhhC-CeEEEC
Confidence 5688999999995 799884
No 16
>PF03855 M-factor: M-factor; InterPro: IPR005555 The M-factor is a pheromone produced upon nitrogen starvation. The production of M-factor is increased by the pheromone signal. The protein undergoes post-translational modification to remove the C-terminal signal peptide, the carboxy-terminal cysteine residue is carboxy-methylated and S-alkylated with a farnesyl residue [].
Probab=31.65 E-value=25 Score=19.47 Aligned_cols=20 Identities=20% Similarity=0.351 Sum_probs=17.1
Q ss_pred cCCHHHHHH-HHHHcCCCcee
Q psy4242 42 ILDPYVIID-KAIENTKPILK 61 (74)
Q Consensus 42 ~~nP~~i~~-~Ai~N~~P~ve 61 (74)
+.||-.++. +-|+|.+|-+-
T Consensus 18 n~np~~~~~t~~iknytpkvp 38 (44)
T PF03855_consen 18 NNNPTDVVKTQNIKNYTPKVP 38 (44)
T ss_pred CCChhHhhcccccccCCCCCc
Confidence 678999998 99999999653
No 17
>cd03338 TCP1_delta TCP-1 (CTT or eukaryotic type II) chaperonin family, delta subunit. Chaperonins are involved in productive folding of proteins. They share a common general morphology, a double toroid of 2 stacked rings. In contrast to bacterial group I chaperonins (GroEL), each ring of the eukaryotic cytosolic chaperonin (CTT) consists of eight different, but homologous subunits. Their common function is to sequester nonnative proteins inside their central cavity and promote folding by using energy derived from ATP hydrolysis. The best studied in vivo substrates of CTT are actin and tubulin.
Probab=31.22 E-value=1.3e+02 Score=23.45 Aligned_cols=39 Identities=18% Similarity=0.250 Sum_probs=30.8
Q ss_pred cChHHHHHHHHHHHHHHHHHHHHHHHhhhCChHHHhhhcCCHHHHHHHHHH
Q psy4242 4 KGNKELAREVFEYTVKSIKRIQIEKYNKATSDEERESIILDPYVIIDKAIE 54 (74)
Q Consensus 4 ~GkK~~A~~Iv~~al~~Ik~~~~~k~~~~~~~~~~~~i~~nP~~i~~~Ai~ 54 (74)
+|+..++.++|.+||+.|-+.-. .++ +.||..++.+-..
T Consensus 421 ~~~~~~~~~~~a~al~~ip~~L~---~Na---------G~d~~~~~~~l~~ 459 (515)
T cd03338 421 TGVEQYCVRAFADALEVIPYTLA---ENA---------GLNPISIVTELRN 459 (515)
T ss_pred CcHHHHHHHHHHHHHHHHHHHHH---HHC---------CCCHHHHHHHHHH
Confidence 68889999999999999987762 233 8899998887544
No 18
>cd03341 TCP1_theta TCP-1 (CTT or eukaryotic type II) chaperonin family, theta subunit. Chaperonins are involved in productive folding of proteins. They share a common general morphology, a double toroid of 2 stacked rings. In contrast to bacterial group I chaperonins (GroEL), each ring of the eukaryotic cytosolic chaperonin (CTT) consists of eight different, but homologous subunits. Their common function is to sequester nonnative proteins inside their central cavity and promote folding by using energy derived from ATP hydrolysis. The best studied in vivo substrates of CTT are actin and tubulin.
Probab=30.40 E-value=1.4e+02 Score=23.15 Aligned_cols=38 Identities=18% Similarity=0.231 Sum_probs=30.2
Q ss_pred CcChHHHHHHHHHHHHHHHHHHHHHHHhhhCChHHHhhhcCCHHHHHHHH
Q psy4242 3 KKGNKELAREVFEYTVKSIKRIQIEKYNKATSDEERESIILDPYVIIDKA 52 (74)
Q Consensus 3 k~GkK~~A~~Iv~~al~~Ik~~~~~k~~~~~~~~~~~~i~~nP~~i~~~A 52 (74)
.+|+..++.++|.+||+.|-+.-. .++ +.||..++.+-
T Consensus 374 ~~~~~~~~~~~~a~al~~ip~~L~---~Na---------G~d~~~~~~~l 411 (472)
T cd03341 374 TPGLEQYAIKKFAEAFEVVPRTLA---ENA---------GLDATEVLSEL 411 (472)
T ss_pred cCCHHHHHHHHHHHHHHHHHHHHH---HHC---------CCCHHHHHHHH
Confidence 368889999999999999987762 233 88999888774
No 19
>TIGR03065 srtB_sig_QVPTGV sortase B signal domain, QVPTGV class. This model represents a boutique (unusual) sorting signal, recognized by a member of the sortase SrtB family rather than by the housekeeping sortase, SrtA.
Probab=28.98 E-value=49 Score=17.20 Aligned_cols=19 Identities=16% Similarity=0.230 Sum_probs=15.9
Q ss_pred cCCCceeEEEEeeCccccc
Q psy4242 55 NTKPILKLRSIKRAAVTYQ 73 (74)
Q Consensus 55 N~~P~vev~~~r~GG~tYq 73 (74)
.+.|...+.-+-+||..|-
T Consensus 9 tlapf~al~iva~gg~~y~ 27 (32)
T TIGR03065 9 TLAPFAALGIVAIGGAIYF 27 (32)
T ss_pred eeccceeEEEEEeccEEEE
Confidence 3578899988999999884
No 20
>PF09453 HIRA_B: HIRA B motif; InterPro: IPR019015 The HirA B (Histone regulatory homologue A binding) motif is the essential binding interface between IPR011494 from INTERPRO and ASF1a, of approx. 40 residues. It forms an antiparallel beta-hairpin that binds perpendicular to the strands of the beta-sandwich of ASF1a N-terminal core domain, via beta-sheet, salt bridge and van der Waals interactions []. The two histone chaperone proteins, HIRA and ASF1a, form a heterodimer with histones H3 and H4. HIRA is the human orthologue of Hir proteins known to silence histone gene expression and create transcriptionally silent heterochromatin in yeast, flies, plants and humans. The HIR complex is composed of HIR1, HIR2, HIR3 and HPC2, and interacts with ASF1. The HIR complex cooperates with ASF1 to promote replication-independent chromatin assembly. The HIR complex is also required for the periodic repression of three of the four histone gene loci during cell cycle as well as for autogenous regulation of the HTA1-HTB1 locus by H2A and H2B. DNA-binding by the HIR complex may repress transcription by inhibiting nucleosome remodeling by the SWI/SNF complex. The HIR complex may also be required for transcriptional silencing of centromeric, telomeric and mating-type loci in the absence of CAF-1. ; GO: 0003682 chromatin binding, 0006355 regulation of transcription, DNA-dependent, 0016568 chromatin modification, 0005634 nucleus; PDB: 2I32_E.
Probab=28.65 E-value=14 Score=18.19 Aligned_cols=9 Identities=33% Similarity=0.719 Sum_probs=4.4
Q ss_pred CCCcChHHH
Q psy4242 1 MMKKGNKEL 9 (74)
Q Consensus 1 iMk~GkK~~ 9 (74)
+|++|||-+
T Consensus 6 ~~k~GKkRi 14 (24)
T PF09453_consen 6 ITKDGKKRI 14 (24)
T ss_dssp E-TTS-EEE
T ss_pred eccCCceEe
Confidence 367887744
No 21
>COG0053 MMT1 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]
Probab=28.32 E-value=1.1e+02 Score=22.58 Aligned_cols=56 Identities=20% Similarity=0.190 Sum_probs=33.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhhCChHHHhhhcCCHHHHHHHHHHcCCCceeEEEEeeCc
Q psy4242 9 LAREVFEYTVKSIKRIQIEKYNKATSDEERESIILDPYVIIDKAIENTKPILKLRSIKRAA 69 (74)
Q Consensus 9 ~A~~Iv~~al~~Ik~~~~~k~~~~~~~~~~~~i~~nP~~i~~~Ai~N~~P~vev~~~r~GG 69 (74)
.+--|++.+++.+++.-..--..+-++++.+.|.. .-.+.+++..+-.++.++.|.
T Consensus 188 I~~~Il~~~~~~~~~s~~~L~d~~~~~~~~~~i~~-----~i~~~~~V~~v~~lr~R~~G~ 243 (304)
T COG0053 188 ISLYILKTGFRLFKESVNELMDAALDPEDLEKIRA-----IILSVPGVKGVHDLRTRKSGS 243 (304)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCcCCCHHHHHHHHH-----HHhcCCcceeeecceeeeeCC
Confidence 45568888888888776555454444444443322 133344666777888874444
No 22
>cd03340 TCP1_eta TCP-1 (CTT or eukaryotic type II) chaperonin family, eta subunit. Chaperonins are involved in productive folding of proteins. They share a common general morphology, a double toroid of 2 stacked rings. In contrast to bacterial group I chaperonins (GroEL), each ring of the eukaryotic cytosolic chaperonin (CTT) consists of eight different, but homologous subunits. Their common function is to sequester nonnative proteins inside their central cavity and promote folding by using energy derived from ATP hydrolysis. The best studied in vivo substrates of CTT are actin and tubulin.
Probab=28.27 E-value=1.6e+02 Score=23.09 Aligned_cols=39 Identities=23% Similarity=0.313 Sum_probs=30.3
Q ss_pred cChHHHHHHHHHHHHHHHHHHHHHHHhhhCChHHHhhhcCCHHHHHHHHHH
Q psy4242 4 KGNKELAREVFEYTVKSIKRIQIEKYNKATSDEERESIILDPYVIIDKAIE 54 (74)
Q Consensus 4 ~GkK~~A~~Iv~~al~~Ik~~~~~k~~~~~~~~~~~~i~~nP~~i~~~Ai~ 54 (74)
+|+..++.+.|.+||+.|-+.-. .++ +.||..++.+-..
T Consensus 424 ~~~~~~~~~~fa~aL~~ip~~La---~Na---------G~d~~~~l~~l~~ 462 (522)
T cd03340 424 AGKQQLVINAFAKALEIIPRQLC---DNA---------GFDATDILNKLRQ 462 (522)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHH---HhC---------CCCHHHHHHHHHH
Confidence 68899999999999999987762 122 7888888776543
No 23
>cd03337 TCP1_gamma TCP-1 (CTT or eukaryotic type II) chaperonin family, gamma subunit. Chaperonins are involved in productive folding of proteins. They share a common general morphology, a double toroid of 2 stacked rings. In contrast to bacterial group I chaperonins (GroEL), each ring of the eukaryotic cytosolic chaperonin (CTT) consists of eight different, but homologous subunits. Their common function is to sequester nonnative proteins inside their central cavity and promote folding by using energy derived from ATP hydrolysis. The best studied in vivo substrates of CTT are actin and tubulin.
Probab=28.05 E-value=1.7e+02 Score=22.83 Aligned_cols=38 Identities=8% Similarity=0.066 Sum_probs=29.7
Q ss_pred cChHHHHHHHHHHHHHHHHHHHHHHHhhhCChHHHhhhcCCHHHHHHHHH
Q psy4242 4 KGNKELAREVFEYTVKSIKRIQIEKYNKATSDEERESIILDPYVIIDKAI 53 (74)
Q Consensus 4 ~GkK~~A~~Iv~~al~~Ik~~~~~k~~~~~~~~~~~~i~~nP~~i~~~Ai 53 (74)
+|+..+|.+.|.+||+.|-+.-. .++ +.||.+++.+-.
T Consensus 385 ~~~~~~~~~~~a~al~~ip~~La---~Na---------G~d~~~~l~~l~ 422 (480)
T cd03337 385 EGVEQWPYKAVASALEVIPRTLA---QNC---------GANVIRTLTELR 422 (480)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHH---HHc---------CCCHHHHHHHHH
Confidence 68899999999999999987762 222 788888877554
No 24
>PF04231 Endonuclease_1: Endonuclease I; InterPro: IPR007346 Bacterial periplasmic or secreted (3.1.21.1 from EC) Escherichia coli endonuclease I (EndoI) is a sequence independent endonuclease located in the periplasm. It is inhibited by different RNA species. It is thought to normally generate double strand breaks in DNA, except in the presence of high salt concentrations and RNA, when it generates single strand breaks in DNA. Its biological role is unknown []. Other family members are known to be extracellular []. This family also includes a non-specific, Mg2+-activated ribonuclease precursor (Q03091 from SWISSPROT) [].; GO: 0004518 nuclease activity; PDB: 1OUO_A 1OUP_B 2IVK_C 2VND_A 2PU3_A 2G7F_A 2G7E_A.
Probab=27.84 E-value=1.5e+02 Score=21.20 Aligned_cols=27 Identities=19% Similarity=0.375 Sum_probs=20.9
Q ss_pred hHHHHHHHHHHHHHH--H-----HHHHHHHHhhh
Q psy4242 6 NKELAREVFEYTVKS--I-----KRIQIEKYNKA 32 (74)
Q Consensus 6 kK~~A~~Iv~~al~~--I-----k~~~~~k~~~~ 32 (74)
|-.+||.+||-+... + ...++.+||+.
T Consensus 156 KGdIARa~fYm~~rY~~~~~~~~~~~~l~~W~~~ 189 (218)
T PF04231_consen 156 KGDIARAYFYMATRYEGLPLSDQQRQLLLAWHKE 189 (218)
T ss_dssp HHHHHHHHHHHHHHC-T----HHHHHHHHHHHHH
T ss_pred hHHHHHHHHHHHHHHcCCCCCchhHHHHHHHHhh
Confidence 567999999988766 1 24678999988
No 25
>cd03343 cpn60 cpn60 chaperonin family. Chaperonins are involved in productive folding of proteins. They share a common general morphology, a double toroid of 2 stacked rings. Archaeal cpn60 (thermosome), together with TF55 from thermophilic bacteria and the eukaryotic cytosol chaperonin (CTT), belong to the type II group of chaperonins. Cpn60 consists of two stacked octameric rings, which are composed of one or two different subunits. Their common function is to sequester nonnative proteins inside their central cavity and promote folding by using energy derived from ATP hydrolysis.
Probab=27.74 E-value=1.7e+02 Score=22.88 Aligned_cols=38 Identities=29% Similarity=0.344 Sum_probs=30.2
Q ss_pred cChHHHHHHHHHHHHHHHHHHHHHHHhhhCChHHHhhhcCCHHHHHHHHH
Q psy4242 4 KGNKELAREVFEYTVKSIKRIQIEKYNKATSDEERESIILDPYVIIDKAI 53 (74)
Q Consensus 4 ~GkK~~A~~Iv~~al~~Ik~~~~~k~~~~~~~~~~~~i~~nP~~i~~~Ai 53 (74)
+|+..++.++|.+||+.|-+.-. .++ +.||..++.+-.
T Consensus 422 ~~~~~~~~~~~~~aL~~ip~~L~---~Na---------G~d~~~~~~~l~ 459 (517)
T cd03343 422 GGREQLAVEAFADALEEIPRTLA---ENA---------GLDPIDTLVELR 459 (517)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHH---HHc---------CCCHHHHHHHHH
Confidence 68889999999999999987762 333 888988887754
No 26
>TIGR02342 chap_CCT_delta T-complex protein 1, delta subunit. Members of this family, all eukaryotic, are part of the group II chaperonin complex called CCT (chaperonin containing TCP-1) or TRiC. The archaeal equivalent group II chaperonin is often called the thermosome. Both are somewhat related to the group I chaperonin of bacterial, GroEL/GroES. This family consists exclusively of the CCT delta chain (part of a paralogous family) from animals, plants, fungi, and other eukaryotes.
Probab=27.69 E-value=1.6e+02 Score=23.15 Aligned_cols=39 Identities=18% Similarity=0.240 Sum_probs=30.6
Q ss_pred cChHHHHHHHHHHHHHHHHHHHHHHHhhhCChHHHhhhcCCHHHHHHHHHH
Q psy4242 4 KGNKELAREVFEYTVKSIKRIQIEKYNKATSDEERESIILDPYVIIDKAIE 54 (74)
Q Consensus 4 ~GkK~~A~~Iv~~al~~Ik~~~~~k~~~~~~~~~~~~i~~nP~~i~~~Ai~ 54 (74)
+|+..+|-+.+.+||+.|-+.-. .++ +.||..++.+-..
T Consensus 422 ~~~~~~~i~~~a~al~~ip~~La---~Na---------G~d~~~~l~~l~~ 460 (517)
T TIGR02342 422 KGVESYCVRAFADALEVIPYTLA---ENA---------GLNPIDVVTELRN 460 (517)
T ss_pred CcHHHHHHHHHHHHHHHHHHHHH---HHc---------CCCHHHHHHHHHH
Confidence 68889999999999999987762 223 8899888876544
No 27
>cd00309 chaperonin_type_I_II chaperonin families, type I and type II. Chaperonins are involved in productive folding of proteins. They share a common general morphology, a double toroid of 2 stacked rings, each composed of 7-9 subunits. There are 2 main chaperonin groups. The symmetry of type I is seven-fold and they are found in eubacteria (GroEL) and in organelles of eubacterial descent (hsp60 and RBP). The symmetry of type II is eight- or nine-fold and they are found in archea (thermosome), thermophilic bacteria (TF55) and in the eukaryotic cytosol (CTT). Their common function is to sequester nonnative proteins inside their central cavity and promote folding by using energy derived from ATP hydrolysis.
Probab=27.56 E-value=1.6e+02 Score=22.51 Aligned_cols=41 Identities=27% Similarity=0.369 Sum_probs=31.5
Q ss_pred CcChHHHHHHHHHHHHHHHHHHHHHHHhhhCChHHHhhhcCCHHHHHHHHHHc
Q psy4242 3 KKGNKELAREVFEYTVKSIKRIQIEKYNKATSDEERESIILDPYVIIDKAIEN 55 (74)
Q Consensus 3 k~GkK~~A~~Iv~~al~~Ik~~~~~k~~~~~~~~~~~~i~~nP~~i~~~Ai~N 55 (74)
.+|+...+.++|.+||+.|-+.-. .++ +.||..++.+-...
T Consensus 370 ~~~~~~~~~~~~a~aL~~ip~~L~---~Na---------G~d~~~~~~~l~~~ 410 (464)
T cd00309 370 LPGKEQLGIEAFADALEVIPRTLA---ENA---------GLDPIEVVTKLRAK 410 (464)
T ss_pred cchHHHHHHHHHHHHHHHHHHHHH---HHc---------CCCHHHHHHHHHHH
Confidence 368889999999999999987762 222 78888888776543
No 28
>TIGR02344 chap_CCT_gamma T-complex protein 1, gamma subunit. Members of this family, all eukaryotic, are part of the group II chaperonin complex called CCT (chaperonin containing TCP-1) or TRiC. The archaeal equivalent group II chaperonin is often called the thermosome. Both are somewhat related to the group I chaperonin of bacterial, GroEL/GroES. This family consists exclusively of the CCT gamma chain (part of a paralogous family) from animals, plants, fungi, and other eukaryotes.
Probab=26.36 E-value=1.8e+02 Score=22.79 Aligned_cols=39 Identities=8% Similarity=0.072 Sum_probs=30.3
Q ss_pred cChHHHHHHHHHHHHHHHHHHHHHHHhhhCChHHHhhhcCCHHHHHHHHHH
Q psy4242 4 KGNKELAREVFEYTVKSIKRIQIEKYNKATSDEERESIILDPYVIIDKAIE 54 (74)
Q Consensus 4 ~GkK~~A~~Iv~~al~~Ik~~~~~k~~~~~~~~~~~~i~~nP~~i~~~Ai~ 54 (74)
+|+..++.++|.+||+.|-+.-. .++ +.||..++.+-..
T Consensus 426 ~~~~~~~~~~~a~al~~ip~~La---~Na---------G~d~~~~l~~l~~ 464 (525)
T TIGR02344 426 EGVQQWPYRAVADALEIIPRTLA---QNC---------GVNVIRTLTELRA 464 (525)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHH---HHC---------CCCHHHHHHHHHH
Confidence 68889999999999999987762 223 8889888776543
No 29
>TIGR02346 chap_CCT_theta T-complex protein 1, theta subunit. Members of this family, all eukaryotic, are part of the group II chaperonin complex called CCT (chaperonin containing TCP-1) or TRiC. The archaeal equivalent group II chaperonin is often called the thermosome. Both are somewhat related to the group I chaperonin of bacterial, GroEL/GroES. This family consists exclusively of the CCT alpha chain (part of a paralogous family) from animals, plants, fungi, and other eukaryotes.
Probab=26.08 E-value=1.8e+02 Score=22.98 Aligned_cols=38 Identities=26% Similarity=0.282 Sum_probs=30.1
Q ss_pred cChHHHHHHHHHHHHHHHHHHHHHHHhhhCChHHHhhhcCCHHHHHHHHH
Q psy4242 4 KGNKELAREVFEYTVKSIKRIQIEKYNKATSDEERESIILDPYVIIDKAI 53 (74)
Q Consensus 4 ~GkK~~A~~Iv~~al~~Ik~~~~~k~~~~~~~~~~~~i~~nP~~i~~~Ai 53 (74)
+|+-.++.++|.+||+.|-+.-. .++ +.||..++.+-.
T Consensus 423 ~~~~~~~~~~~a~aL~~ip~~L~---~Na---------G~d~~~~~~~l~ 460 (531)
T TIGR02346 423 PGLDQYAIKKFAEAFEIIPRTLA---ENA---------GLNPNEVIPKLY 460 (531)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHH---HhC---------CCCHHHHHHHHH
Confidence 67888999999999999987762 233 889998887753
No 30
>PF03120 DNA_ligase_OB: NAD-dependent DNA ligase OB-fold domain; InterPro: IPR004150 DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This family is a small domain found after the adenylation domain DNA_ligase_N in NAD+-dependent ligases (IPR001679 from INTERPRO). OB-fold domains generally are involved in nucleic acid binding.; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 2OWO_A 1TAE_A 3UQ8_A 1DGS_A 1V9P_B 3SGI_A.
Probab=25.99 E-value=32 Score=21.24 Aligned_cols=19 Identities=16% Similarity=0.296 Sum_probs=16.1
Q ss_pred cCCCceeEEEEeeCccccc
Q psy4242 55 NTKPILKLRSIKRAAVTYQ 73 (74)
Q Consensus 55 N~~P~vev~~~r~GG~tYq 73 (74)
.++|+..+.|+..+|++.+
T Consensus 17 ~itPva~lePV~l~G~~Vs 35 (82)
T PF03120_consen 17 KITPVAVLEPVELDGTTVS 35 (82)
T ss_dssp BEEEEEEEEEEECTTCEEE
T ss_pred EEEEEEEEEEEEECCeEEE
Confidence 3689999999999998753
No 31
>PTZ00212 T-complex protein 1 subunit beta; Provisional
Probab=25.42 E-value=1.9e+02 Score=22.84 Aligned_cols=37 Identities=27% Similarity=0.387 Sum_probs=28.9
Q ss_pred cChHHHHHHHHHHHHHHHHHHHHHHHhhhCChHHHhhhcCCHHHHHHHH
Q psy4242 4 KGNKELAREVFEYTVKSIKRIQIEKYNKATSDEERESIILDPYVIIDKA 52 (74)
Q Consensus 4 ~GkK~~A~~Iv~~al~~Ik~~~~~k~~~~~~~~~~~~i~~nP~~i~~~A 52 (74)
+|+..++.++|.+||+.|-+.-. .++ +.||..++.+-
T Consensus 431 ~~~~~~~i~~~a~aL~~ip~~La---~Na---------G~d~~~vl~~l 467 (533)
T PTZ00212 431 EGKKSLAIEAFAKALRQIPTIIA---DNG---------GYDSAELVSKL 467 (533)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHH---HhC---------CCCHHHHHHHH
Confidence 68899999999999999987762 222 77888877654
No 32
>TIGR02339 thermosome_arch thermosome, various subunits, archaeal. Thermosome is the name given to the archaeal rather than eukaryotic form of the group II chaperonin (counterpart to the group I chaperonin, GroEL/GroES, in bacterial), a torroidal, ATP-dependent molecular chaperone that assists in the folding or refolding of nascent or denatured proteins. Various homologous subunits, one to five per archaeal genome, may be designated alpha, beta, etc., but phylogenetic analysis does not show distinct alpha subunit and beta subunit lineages traceable to ancient paralogs.
Probab=25.26 E-value=2e+02 Score=22.59 Aligned_cols=38 Identities=32% Similarity=0.379 Sum_probs=30.1
Q ss_pred cChHHHHHHHHHHHHHHHHHHHHHHHhhhCChHHHhhhcCCHHHHHHHHH
Q psy4242 4 KGNKELAREVFEYTVKSIKRIQIEKYNKATSDEERESIILDPYVIIDKAI 53 (74)
Q Consensus 4 ~GkK~~A~~Iv~~al~~Ik~~~~~k~~~~~~~~~~~~i~~nP~~i~~~Ai 53 (74)
+|+...+-++|.+||+.|-+.-. .++ +.||..++.+-.
T Consensus 425 ~~~~~~~~~~~a~aL~~ip~~L~---~Na---------G~d~~~~l~~l~ 462 (519)
T TIGR02339 425 GGREQLAIEAFADALEEIPRILA---ENA---------GLDPIDALVELR 462 (519)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHH---Hhc---------CCCHHHHHHHHH
Confidence 67888999999999999987762 233 889988887654
No 33
>cd03336 TCP1_beta TCP-1 (CTT or eukaryotic type II) chaperonin family, beta subunit. Chaperonins are involved in productive folding of proteins. They share a common general morphology, a double toroid of 2 stacked rings. In contrast to bacterial group I chaperonins (GroEL), each ring of the eukaryotic cytosolic chaperonin (CTT) consists of eight different, but homologous subunits. Their common function is to sequester nonnative proteins inside their central cavity and promote folding by using energy derived from ATP hydrolysis. The best studied in vivo substrates of CTT are actin and tubulin.
Probab=25.21 E-value=1.9e+02 Score=22.70 Aligned_cols=37 Identities=24% Similarity=0.359 Sum_probs=28.8
Q ss_pred cChHHHHHHHHHHHHHHHHHHHHHHHhhhCChHHHhhhcCCHHHHHHHH
Q psy4242 4 KGNKELAREVFEYTVKSIKRIQIEKYNKATSDEERESIILDPYVIIDKA 52 (74)
Q Consensus 4 ~GkK~~A~~Iv~~al~~Ik~~~~~k~~~~~~~~~~~~i~~nP~~i~~~A 52 (74)
+|+..++-++|.+||+.|-+.-.+ ++ +.||..++.+-
T Consensus 419 ~~~~~~~i~~~a~ALe~ip~~La~---Na---------G~d~~~~l~~l 455 (517)
T cd03336 419 PGKKSLAIEAFAKALRQLPTIIAD---NA---------GYDSAELVAQL 455 (517)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHH---hC---------CCCHHHHHHHH
Confidence 688999999999999999877632 22 77888777653
No 34
>TIGR02341 chap_CCT_beta T-complex protein 1, beta subunit. Members of this family, all eukaryotic, are part of the group II chaperonin complex called CCT (chaperonin containing TCP-1) or TRiC. The archaeal equivalent group II chaperonin is often called the thermosome. Both are somewhat related to the group I chaperonin of bacterial, GroEL/GroES. This family consists exclusively of the CCT beta chain (part of a paralogous family) from animals, plants, fungi, and other eukaryotes.
Probab=24.90 E-value=2e+02 Score=22.71 Aligned_cols=39 Identities=21% Similarity=0.324 Sum_probs=30.2
Q ss_pred cChHHHHHHHHHHHHHHHHHHHHHHHhhhCChHHHhhhcCCHHHHHHHHHH
Q psy4242 4 KGNKELAREVFEYTVKSIKRIQIEKYNKATSDEERESIILDPYVIIDKAIE 54 (74)
Q Consensus 4 ~GkK~~A~~Iv~~al~~Ik~~~~~k~~~~~~~~~~~~i~~nP~~i~~~Ai~ 54 (74)
+|+..++-+.|.+||+.|-+.-.+ ++ +.||..++.+-..
T Consensus 420 ~~~~~~~i~~~a~Ale~ip~~La~---Na---------G~d~~~~l~~l~~ 458 (519)
T TIGR02341 420 PGKEALAVEAFARALRQLPTIIAD---NA---------GFDSAELVAQLRA 458 (519)
T ss_pred CChHHHHHHHHHHHHHHHHHHHHH---HC---------CCCHHHHHHHHHH
Confidence 688899999999999999877632 22 8888888765543
No 35
>TIGR02347 chap_CCT_zeta T-complex protein 1, zeta subunit. Members of this family, all eukaryotic, are part of the group II chaperonin complex called CCT (chaperonin containing TCP-1) or TRiC. The archaeal equivalent group II chaperonin is often called the thermosome. Both are somewhat related to the group I chaperonin of bacterial, GroEL/GroES. This family consists exclusively of the CCT zeta chain (part of a paralogous family) from animals, plants, fungi, and other eukaryotes.
Probab=24.41 E-value=2e+02 Score=22.83 Aligned_cols=36 Identities=25% Similarity=0.287 Sum_probs=28.5
Q ss_pred cChHHHHHHHHHHHHHHHHHHHHHHHhhhCChHHHhhhcCCHHHHHHH
Q psy4242 4 KGNKELAREVFEYTVKSIKRIQIEKYNKATSDEERESIILDPYVIIDK 51 (74)
Q Consensus 4 ~GkK~~A~~Iv~~al~~Ik~~~~~k~~~~~~~~~~~~i~~nP~~i~~~ 51 (74)
+|+..++-++|.+||+.|-+.-. .++ +.||..++.+
T Consensus 431 ~~~~~~~i~~fa~ALe~ip~~La---~Na---------G~d~~~vl~~ 466 (531)
T TIGR02347 431 KGKAKLGVEAFANALLVIPKTLA---ENS---------GLDAQDTLVK 466 (531)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHH---Hhc---------CCCHHHHHHH
Confidence 68899999999999999987762 222 7788888765
No 36
>PF13656 RNA_pol_L_2: RNA polymerase Rpb3/Rpb11 dimerisation domain; PDB: 2Y0S_L 1I3Q_K 4A3D_K 2JA8_K 3GTP_K 1R9T_K 3PO2_K 4A3J_K 3HOX_K 2JA7_K ....
Probab=24.05 E-value=45 Score=19.96 Aligned_cols=15 Identities=27% Similarity=0.417 Sum_probs=12.0
Q ss_pred cCCHHHHHHHHHHcC
Q psy4242 42 ILDPYVIIDKAIENT 56 (74)
Q Consensus 42 ~~nP~~i~~~Ai~N~ 56 (74)
+.+|.++|.+|++++
T Consensus 52 ~~~p~~~l~~a~~~l 66 (77)
T PF13656_consen 52 GITPIEALKKALEDL 66 (77)
T ss_dssp TS-HHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHH
Confidence 448999999999875
No 37
>cd01223 PH_Vav Vav pleckstrin homology (PH) domain. Vav pleckstrin homology (PH) domain. Vav acts as a guanosine nucleotide exchange factor(GEF) for Rho/Rac proteins. Mammalian Vav proteins consist of a calponin homology (CH) domain, an acidic region, a rho-GEF (DH)domain, a PH domain, a Zinc finger region and an SH2 domain, flanked by two SH3 domains. In invertebrates such as Drosophila and C.elegans, Vav is missing the N-terminal SH3 domain . PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains.
Probab=23.98 E-value=60 Score=21.40 Aligned_cols=15 Identities=20% Similarity=0.350 Sum_probs=12.9
Q ss_pred CHHHHHHHHHHcCCC
Q psy4242 44 DPYVIIDKAIENTKP 58 (74)
Q Consensus 44 nP~~i~~~Ai~N~~P 58 (74)
+=+.-|..|++|+.|
T Consensus 102 kWm~al~~a~sni~P 116 (116)
T cd01223 102 KWLKALEMAMSNIRP 116 (116)
T ss_pred HHHHHHHHHHhcCCC
Confidence 347889999999998
No 38
>TIGR02345 chap_CCT_eta T-complex protein 1, eta subunit. Members of this family, all eukaryotic, are part of the group II chaperonin complex called CCT (chaperonin containing TCP-1) or TRiC. The archaeal equivalent group II chaperonin is often called the thermosome. Both are somewhat related to the group I chaperonin of bacterial, GroEL/GroES. This family consists exclusively of the CCT eta chain (part of a paralogous family) from animals, plants, fungi, and other eukaryotes.
Probab=23.85 E-value=2.2e+02 Score=22.46 Aligned_cols=40 Identities=25% Similarity=0.307 Sum_probs=30.9
Q ss_pred CcChHHHHHHHHHHHHHHHHHHHHHHHhhhCChHHHhhhcCCHHHHHHHHHH
Q psy4242 3 KKGNKELAREVFEYTVKSIKRIQIEKYNKATSDEERESIILDPYVIIDKAIE 54 (74)
Q Consensus 3 k~GkK~~A~~Iv~~al~~Ik~~~~~k~~~~~~~~~~~~i~~nP~~i~~~Ai~ 54 (74)
.+|+..++-++|.+||+.|-+.-. .++ +.||..++.+-..
T Consensus 424 ~~~~~~~~i~~~a~aL~~ip~~La---~Na---------G~d~~~vl~~l~~ 463 (522)
T TIGR02345 424 IDGKQQLIIEAFAKALEIIPRSLC---ENA---------GFDSIEILNKLRS 463 (522)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHH---HHC---------CCCHHHHHHHHHH
Confidence 368889999999999999987762 223 7888888877543
No 39
>PF07719 TPR_2: Tetratricopeptide repeat; InterPro: IPR013105 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]. It mediates protein-protein interactions and the assembly of multiprotein complexes []. The TPR motif consists of 3-16 tandem-repeats of 34 amino acids residues, although individual TPR motifs can be dispersed in the protein sequence. Sequence alignment of the TPR domains reveals a consensus sequence defined by a pattern of small and large amino acids. TPR motifs have been identified in various different organisms, ranging from bacteria to humans. Proteins containing TPRs are involved in a variety of biological processes, such as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding. This repeat includes outlying Tetratricopeptide-like repeats (TPR) that are not matched by IPR001440 from INTERPRO.; PDB: 1XNF_B 3Q15_A 4ABN_A 1OUV_A 3U4T_A 3MA5_C 2KCV_A 2KCL_A 2XEV_A 3NF1_A ....
Probab=23.19 E-value=81 Score=14.41 Aligned_cols=17 Identities=41% Similarity=0.454 Sum_probs=9.1
Q ss_pred CcChHHHHHHHHHHHHH
Q psy4242 3 KKGNKELAREVFEYTVK 19 (74)
Q Consensus 3 k~GkK~~A~~Iv~~al~ 19 (74)
..|+...|.+.+.+++.
T Consensus 13 ~~~~~~~A~~~~~~al~ 29 (34)
T PF07719_consen 13 QLGNYEEAIEYFEKALE 29 (34)
T ss_dssp HTT-HHHHHHHHHHHHH
T ss_pred HhCCHHHHHHHHHHHHH
Confidence 34555666666665554
No 40
>cd03342 TCP1_zeta TCP-1 (CTT or eukaryotic type II) chaperonin family, zeta subunit. Chaperonins are involved in productive folding of proteins. They share a common general morphology, a double toroid of 2 stacked rings. In contrast to bacterial group I chaperonins (GroEL), each ring of the eukaryotic cytosolic chaperonin (CTT) consists of eight different, but homologous subunits. Their common function is to sequester nonnative proteins inside their central cavity and promote folding by using energy derived from ATP hydrolysis. The best studied in vivo substrates of CTT are actin and tubulin.
Probab=22.92 E-value=2.3e+02 Score=22.07 Aligned_cols=38 Identities=24% Similarity=0.230 Sum_probs=29.6
Q ss_pred cChHHHHHHHHHHHHHHHHHHHHHHHhhhCChHHHhhhcCCHHHHHHHHH
Q psy4242 4 KGNKELAREVFEYTVKSIKRIQIEKYNKATSDEERESIILDPYVIIDKAI 53 (74)
Q Consensus 4 ~GkK~~A~~Iv~~al~~Ik~~~~~k~~~~~~~~~~~~i~~nP~~i~~~Ai 53 (74)
+|+..++-++|.+||+.|-+.-.+ ++ +.||..++.+-.
T Consensus 388 ~~~~~~~i~~~a~Al~~ip~~La~---Na---------G~d~~~~l~~l~ 425 (484)
T cd03342 388 KGKAKLGVQAFADALLVIPKTLAE---NS---------GLDVQETLVKLQ 425 (484)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHH---Hc---------CCCHHHHHHHHH
Confidence 688899999999999999877621 22 788888877643
No 41
>TIGR00264 alpha-NAC-related protein. This hypothetical protein is found so far only in the Archaea. Its C-terminal domain of about 40 amino acids is homologous to the C-termini of the nascent polypeptide-associated complex alpha chain (alpha-NAC) and its yeast ortholog Egd2p and to the huntingtin-interacting protein HYPK. It shows weaker similarity, possibly through shared structural constraints rather than through homology, with the amino-terminal domain of elongation factor Ts. Alpha-NAC plays a role in preventing nascent polypeptides from binding inappropriately to membrane-targeting apparatus during translation, but is also active as a transcription regulator.
Probab=22.83 E-value=43 Score=22.20 Aligned_cols=17 Identities=29% Similarity=0.520 Sum_probs=12.8
Q ss_pred CCceeEEEEeeCcccccC
Q psy4242 57 KPILKLRSIKRAAVTYQM 74 (74)
Q Consensus 57 ~P~vev~~~r~GG~tYqV 74 (74)
.|.+.+-... |+.||||
T Consensus 46 ~p~V~~m~~~-G~~tYqI 62 (116)
T TIGR00264 46 NPKVQVMDIL-GVKTYQI 62 (116)
T ss_pred cCeeEEEecC-CcEEEEE
Confidence 4667776666 8899996
No 42
>TIGR02340 chap_CCT_alpha T-complex protein 1, alpha subunit. Members of this family, all eukaryotic, are part of the group II chaperonin complex called CCT (chaperonin containing TCP-1) or TRiC. The archaeal equivalent group II chaperonin is often called the thermosome. Both are somewhat related to the group I chaperonin of bacterial, GroEL/GroES. This family consists exclusively of the CCT alpha chain (part of a paralogous family) from animals, plants, fungi, and other eukaryotes.
Probab=20.64 E-value=2.7e+02 Score=22.03 Aligned_cols=38 Identities=21% Similarity=0.220 Sum_probs=29.5
Q ss_pred cChHHHHHHHHHHHHHHHHHHHHHHHhhhCChHHHhhhcCCHHHHHHHHH
Q psy4242 4 KGNKELAREVFEYTVKSIKRIQIEKYNKATSDEERESIILDPYVIIDKAI 53 (74)
Q Consensus 4 ~GkK~~A~~Iv~~al~~Ik~~~~~k~~~~~~~~~~~~i~~nP~~i~~~Ai 53 (74)
+|+-..+-++|.+||+.|-+.-. .++ +.||..++.+-.
T Consensus 427 ~~~~~~~~~~fa~AL~~ip~~La---~Na---------G~d~~~~l~~l~ 464 (536)
T TIGR02340 427 GSREQLAIAEFAEALLIIPKVLA---VNA---------ALDSTELVAKLR 464 (536)
T ss_pred CChhHHHHHHHHHHHHHHHHHHH---HHC---------CCCHHHHHHHHH
Confidence 68888999999999999986652 222 889998877643
No 43
>cd03339 TCP1_epsilon TCP-1 (CTT or eukaryotic type II) chaperonin family, epsilon subunit. Chaperonins are involved in productive folding of proteins. They share a common general morphology, a double toroid of 2 stacked rings. In contrast to bacterial group I chaperonins (GroEL), each ring of the eukaryotic cytosolic chaperonin (CTT) consists of eight different, but homologous subunits. Their common function is to sequester nonnative proteins inside their central cavity and promote folding by using energy derived from ATP hydrolysis. The best studied in vivo substrates of CTT are actin and tubulin.
Probab=20.49 E-value=2.8e+02 Score=21.83 Aligned_cols=39 Identities=18% Similarity=0.212 Sum_probs=30.1
Q ss_pred CcChHHHHHHHHHHHHHHHHHHHHHHHhhhCChHHHhhhcCCHHHHHHHHH
Q psy4242 3 KKGNKELAREVFEYTVKSIKRIQIEKYNKATSDEERESIILDPYVIIDKAI 53 (74)
Q Consensus 3 k~GkK~~A~~Iv~~al~~Ik~~~~~k~~~~~~~~~~~~i~~nP~~i~~~Ai 53 (74)
.+|+-.++-++|.+||+.|-+.-. .++ +.||..++.+-.
T Consensus 431 ~~~~~~~~~~~~a~aL~~ip~~L~---~Na---------G~d~~~~l~~l~ 469 (526)
T cd03339 431 CSGIEQYAMRAFADALESIPLALA---ENS---------GLNPIETLSEVK 469 (526)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHH---HHC---------CCCHHHHHHHHH
Confidence 367888999999999999987762 233 889988877654
No 44
>TIGR03188 histidine_hisI phosphoribosyl-ATP pyrophosphohydrolase. This enzyme, phosphoribosyl-ATP pyrophosphohydrolase, catalyses the second step in the histidine biosynthesis pathway. It often occurs as a fusion protein. This model a somewhat narrower scope than Pfam model pfam01503, as some paralogs that appear to be functionally distinct are excluded from this model.
Probab=20.41 E-value=2.2e+02 Score=17.45 Aligned_cols=23 Identities=22% Similarity=0.264 Sum_probs=18.6
Q ss_pred CCcChHHHHHHHHHHHHHHHHHH
Q psy4242 2 MKKGNKELAREVFEYTVKSIKRI 24 (74)
Q Consensus 2 Mk~GkK~~A~~Iv~~al~~Ik~~ 24 (74)
+.+|.-.+++++..+|.|.|---
T Consensus 25 ~~~G~~ki~kKvgEEa~E~iiAa 47 (84)
T TIGR03188 25 FAKGLDKILKKVGEEAVEVVIAA 47 (84)
T ss_pred HhCcHHHHHHHHHHHHHHHHHHH
Confidence 46788889999999999888654
No 45
>TIGR02343 chap_CCT_epsi T-complex protein 1, epsilon subunit. Members of this family, all eukaryotic, are part of the group II chaperonin complex called CCT (chaperonin containing TCP-1) or TRiC. The archaeal equivalent group II chaperonin is often called the thermosome. Both are somewhat related to the group I chaperonin of bacterial, GroEL/GroES. This family consists exclusively of the CCT epsilon chain (part of a paralogous family) from animals, plants, fungi, and other eukaryotes.
Probab=20.26 E-value=2.7e+02 Score=22.09 Aligned_cols=37 Identities=19% Similarity=0.245 Sum_probs=28.9
Q ss_pred cChHHHHHHHHHHHHHHHHHHHHHHHhhhCChHHHhhhcCCHHHHHHHH
Q psy4242 4 KGNKELAREVFEYTVKSIKRIQIEKYNKATSDEERESIILDPYVIIDKA 52 (74)
Q Consensus 4 ~GkK~~A~~Iv~~al~~Ik~~~~~k~~~~~~~~~~~~i~~nP~~i~~~A 52 (74)
+|+..+|-+.|.+||+.|-+.-. .++ +.||..++.+-
T Consensus 436 ~~~~~~~i~~fa~ALe~ip~~La---~Na---------G~d~~~~l~~l 472 (532)
T TIGR02343 436 SGVEQYAIRAFADALEEIPMALA---ENS---------GLDPIGTLSDL 472 (532)
T ss_pred CcHHHHHHHHHHHHHHHHHHHHH---HHC---------CCCHHHHHHHH
Confidence 68889999999999999987762 222 78888887653
No 46
>cd03335 TCP1_alpha TCP-1 (CTT or eukaryotic type II) chaperonin family, alpha subunit. Chaperonins are involved in productive folding of proteins. They share a common general morphology, a double toroid of 2 stacked rings. In contrast to bacterial group I chaperonins (GroEL), each ring of the eukaryotic cytosolic chaperonin (CTT) consists of eight different, but homologous subunits. Their common function is to sequester nonnative proteins inside their central cavity and promote folding by using energy derived from ATP hydrolysis. The best studied in vivo substrates of CTT are actin and tubulin.
Probab=20.23 E-value=2.8e+02 Score=21.83 Aligned_cols=38 Identities=18% Similarity=0.141 Sum_probs=29.9
Q ss_pred cChHHHHHHHHHHHHHHHHHHHHHHHhhhCChHHHhhhcCCHHHHHHHHH
Q psy4242 4 KGNKELAREVFEYTVKSIKRIQIEKYNKATSDEERESIILDPYVIIDKAI 53 (74)
Q Consensus 4 ~GkK~~A~~Iv~~al~~Ik~~~~~k~~~~~~~~~~~~i~~nP~~i~~~Ai 53 (74)
+|+-.++-+.|.+||+.|-+.-. .++ +.||..++.+-.
T Consensus 423 ~~~~~~~i~~~a~aL~~ip~~La---~Na---------G~d~~~~~~~l~ 460 (527)
T cd03335 423 GSREQLAIAEFAEALLVIPKTLA---VNA---------AKDATELVAKLR 460 (527)
T ss_pred CcHHHHHHHHHHHHHHHHHHHHH---HHC---------CCCHHHHHHHHH
Confidence 67888999999999999987652 223 889999887643
No 47
>CHL00093 groEL chaperonin GroEL
Probab=20.16 E-value=3.9e+02 Score=21.24 Aligned_cols=47 Identities=17% Similarity=0.089 Sum_probs=34.8
Q ss_pred CcChHHHHHHHHHHHHHHHHHHHHHHHhhhCChHHHhhhcCCHHHHHHHHHHcCCCceeE
Q psy4242 3 KKGNKELAREVFEYTVKSIKRIQIEKYNKATSDEERESIILDPYVIIDKAIENTKPILKL 62 (74)
Q Consensus 3 k~GkK~~A~~Iv~~al~~Ik~~~~~k~~~~~~~~~~~~i~~nP~~i~~~Ai~N~~P~vev 62 (74)
.+|+...+.++|.+||+.+=+.-.+ ++ +.||..++.+-..+ .+.+++
T Consensus 433 ~~g~~~~~i~~~a~AL~~ip~~La~---Na---------G~d~~~v~~~l~~~-~~~~G~ 479 (529)
T CHL00093 433 LKEDELIGALIVARAILAPLKRIAE---NA---------GKNGSVIIEKVQEQ-DFEIGY 479 (529)
T ss_pred CChHHHHHHHHHHHHHHHHHHHHHH---hc---------CCCHHHHHHHHHcc-CCCEeE
Confidence 3788899999999999999877632 22 88999888877554 334444
No 48
>PF01193 RNA_pol_L: RNA polymerase Rpb3/Rpb11 dimerisation domain; InterPro: IPR011261 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. RNA polymerase (RNAP) II, which is responsible for all mRNA synthesis in eukaryotes, consists of 12 subunits. Subunits Rpb3 and Rpb11 form a heterodimer that is functionally analogous to the archaeal RNAP D/L heterodimer, and to the prokaryotic RNAP alpha subunit (RpoA) homodimer. In each case, they play a key role in RNAP assembly by forming a platform on which the catalytic subunits (eukaryotic Rpb1/Rpb2, and prokaryotic beta/beta') can interact []. These different subunits share regions of homology required for dimerisation. In eukaryotic Rpb11 and archaeal L subunits, the dimerisation domain consists of a contiguous Rpb11-like domain, whereas in eukaryotic Rpb3, archaeal D and bacterial RpoA subunits (IPR011263 from INTERPRO), the dimerisation domain consists of the Rpb11-like domain interrupted by an insert domain. In the prokaryotic alpha subunit, this dimerisation domain is the N-terminal domain [].; GO: 0003899 DNA-directed RNA polymerase activity, 0046983 protein dimerization activity, 0006351 transcription, DNA-dependent; PDB: 1HQM_B 1YNJ_A 1YNN_A 1I6V_A 2GHO_A 3HKZ_V 2PMZ_X 2PA8_L 3GTK_C 1TWH_C ....
Probab=20.14 E-value=61 Score=18.37 Aligned_cols=15 Identities=33% Similarity=0.235 Sum_probs=11.6
Q ss_pred cCCHHHHHHHHHHcC
Q psy4242 42 ILDPYVIIDKAIENT 56 (74)
Q Consensus 42 ~~nP~~i~~~Ai~N~ 56 (74)
..+|..+|.+|++.+
T Consensus 47 ~~~p~~~l~~A~~~l 61 (66)
T PF01193_consen 47 SLTPKEALLKAIKIL 61 (66)
T ss_dssp SS-HHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHH
Confidence 348999999999864
No 49
>PF12651 RHH_3: Ribbon-helix-helix domain
Probab=20.08 E-value=1.6e+02 Score=15.68 Aligned_cols=14 Identities=14% Similarity=0.261 Sum_probs=10.8
Q ss_pred cCCHHHHHHHHHHc
Q psy4242 42 ILDPYVIIDKAIEN 55 (74)
Q Consensus 42 ~~nP~~i~~~Ai~N 55 (74)
+..-=.++.+||+.
T Consensus 25 ~i~~S~Ll~eAle~ 38 (44)
T PF12651_consen 25 GIPKSKLLREALED 38 (44)
T ss_pred CCCHHHHHHHHHHH
Confidence 66677888999874
Done!