Query 043141
Match_columns 135
No_of_seqs 119 out of 1081
Neff 4.8
Searched_HMMs 46136
Date Fri Mar 29 13:16:56 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/043141.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/043141hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0216 PrfA Protein chain rel 100.0 5.3E-39 1.2E-43 272.4 6.6 116 2-130 198-314 (363)
2 TIGR00019 prfA peptide chain r 100.0 2.4E-33 5.2E-38 239.7 7.1 115 3-130 198-312 (360)
3 TIGR03072 release_prfH putativ 100.0 3.5E-33 7.6E-38 222.8 6.8 112 4-133 88-200 (200)
4 KOG2726 Mitochondrial polypept 100.0 4.2E-33 9E-38 239.2 7.5 115 3-130 223-339 (386)
5 PRK00591 prfA peptide chain re 100.0 5.4E-33 1.2E-37 237.4 7.1 115 3-130 198-312 (359)
6 PF00472 RF-1: RF-1 domain; I 100.0 2.1E-32 4.6E-37 200.1 6.9 101 18-131 4-104 (113)
7 PRK08179 prfH peptide chain re 100.0 8.6E-32 1.9E-36 214.8 6.7 109 4-130 89-197 (200)
8 PRK05589 peptide chain release 100.0 1E-31 2.2E-36 227.1 7.3 115 3-131 172-287 (325)
9 PRK06746 peptide chain release 100.0 2.9E-31 6.4E-36 224.4 7.2 115 3-131 173-288 (326)
10 PRK08787 peptide chain release 100.0 4.5E-31 9.7E-36 222.3 7.8 114 3-130 152-266 (313)
11 PRK07342 peptide chain release 100.0 6.9E-31 1.5E-35 223.1 7.4 115 3-131 175-290 (339)
12 PRK00578 prfB peptide chain re 100.0 8.8E-31 1.9E-35 224.3 7.4 114 3-130 211-325 (367)
13 TIGR00020 prfB peptide chain r 100.0 1.3E-30 2.8E-35 223.2 6.1 115 3-131 211-326 (364)
14 PRK09256 hypothetical protein; 99.9 1.1E-25 2.3E-30 170.8 9.9 83 17-103 4-110 (138)
15 COG1186 PrfB Protein chain rel 99.9 1.3E-25 2.7E-30 183.4 4.5 115 4-132 87-202 (239)
16 KOG3429 Predicted peptidyl-tRN 99.8 3.4E-20 7.4E-25 144.6 6.8 70 22-95 36-130 (172)
17 PF10213 MRP-S28: Mitochondria 92.9 0.74 1.6E-05 34.6 7.5 34 61-94 60-94 (127)
18 cd02394 vigilin_like_KH K homo 62.7 9 0.00019 24.0 2.6 39 41-84 16-61 (62)
19 KOG3933 Mitochondrial ribosoma 60.1 39 0.00085 29.1 6.8 31 61-91 202-233 (296)
20 COG1186 PrfB Protein chain rel 54.4 2 4.3E-05 35.8 -1.9 33 63-95 168-200 (239)
21 PF02815 MIR: MIR domain; Int 42.7 53 0.0012 25.0 4.6 39 34-72 121-159 (190)
22 smart00322 KH K homology RNA-b 40.7 44 0.00095 19.8 3.1 45 41-88 19-68 (69)
23 cd00105 KH-I K homology RNA-bi 35.6 33 0.00073 20.9 2.0 40 40-84 15-63 (64)
24 cd00552 RaiA RaiA ("ribosome-a 33.7 1.4E+02 0.0031 19.7 7.3 53 32-90 36-89 (93)
25 cd02395 SF1_like-KH Splicing f 29.8 66 0.0014 23.7 3.1 25 63-89 70-94 (120)
26 PF14048 MBD_C: C-terminal dom 28.9 29 0.00064 24.9 1.0 27 62-88 70-96 (96)
27 cd02393 PNPase_KH Polynucleoti 27.8 55 0.0012 20.9 2.1 29 40-68 17-48 (61)
28 COG3514 Uncharacterized protei 27.7 9 0.0002 27.8 -1.8 13 34-46 67-79 (93)
29 KOG3259 Peptidyl-prolyl cis-tr 25.4 1.2E+02 0.0026 24.0 3.9 49 36-91 40-96 (163)
30 PF04149 DUF397: Domain of unk 25.1 1.4E+02 0.003 19.1 3.6 19 52-70 16-34 (56)
31 smart00472 MIR Domain in ryano 23.8 87 0.0019 19.0 2.4 21 51-71 7-27 (57)
32 PF13014 KH_3: KH domain 22.9 25 0.00055 20.7 -0.2 20 41-60 7-28 (43)
No 1
>COG0216 PrfA Protein chain release factor A [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=5.3e-39 Score=272.45 Aligned_cols=116 Identities=34% Similarity=0.520 Sum_probs=104.6
Q ss_pred ccccCcceeccCCCCCcC-CcccChhhhhccceEEEEeccCCCccCCCccCceEEEEEcCCeeEEEeccccCHHHHHHHH
Q 043141 2 CYHTNDNCSSSSSSSKKN-YLELTDDELFRECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRVSA 80 (135)
Q Consensus 2 ~~ht~~~~~~~~~~~~~~-~~~i~~~~L~~~~~~~~~RsSGPGGQ~VNK~~t~V~l~h~ptGi~v~~~e~RSq~~Nk~~A 80 (135)
-+|||||+|.++|..... -+.|+++|| +|+++||||+||||||+|+|+||||||||||+|+||++|||++||+.|
T Consensus 198 RIHTStaTVaVlPE~ee~~ei~I~~~Dl----rIDt~RsSGaGGQhVNtTdSAVRiTHlPTGIvV~cQderSQ~kNk~kA 273 (363)
T COG0216 198 RIHTSAATVAVLPEVEEVEEIEINPKDL----RIDTFRSSGAGGQHVNTTDSAVRITHLPTGIVVECQDERSQHKNKAKA 273 (363)
T ss_pred ceeecceeEEeccCCCcccccccChHHc----eeeeeecCCCCCCCcCccchhheeeecCCceEEEecchhhhhhhHHHH
Confidence 389999999999987543 589999999 999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHhHhcccccCCCCCCccccccCCCCcccccCCCCCCCCCCC
Q 043141 81 LSRLRTLLALNVRSSVKLDAYSPPPQLLQILPPKSTIRSSEVGPQIGPNN 130 (135)
Q Consensus 81 ~~rL~~~l~~~~~~~~~~~~~~~~~~~~~~~~~k~q~~~g~~~~kIr~~n 130 (135)
|+.|++.|....+..-.. ++...||+|+++|||||+|||||
T Consensus 274 mkvL~ARl~~~~~~~~~~---------~~~~~RksqVGSGDRSErIRTYN 314 (363)
T COG0216 274 MKVLRARLYDAERQKAQA---------EEASERKSQVGSGDRSERIRTYN 314 (363)
T ss_pred HHHHHHHHHHHHHHHHHH---------HHHHHHHHhcCCCchhhhhhccC
Confidence 999999988766554222 33468999999999999999999
No 2
>TIGR00019 prfA peptide chain release factor 1. This model describes peptide chain release factor 1 (PrfA, RF-1), and excludes the related peptide chain release factor 2 (PrfB, RF-2). RF-1 helps recognize and terminate translation at UAA and UAG stop codons. The mitochondrial release factors are prfA-like, although not included above the trusted cutoff for this model. RF-1 does not have a translational frameshift.
Probab=99.98 E-value=2.4e-33 Score=239.65 Aligned_cols=115 Identities=33% Similarity=0.512 Sum_probs=100.6
Q ss_pred cccCcceeccCCCCCcCCcccChhhhhccceEEEEeccCCCccCCCccCceEEEEEcCCeeEEEeccccCHHHHHHHHHH
Q 043141 3 YHTNDNCSSSSSSSKKNYLELTDDELFRECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRVSALS 82 (135)
Q Consensus 3 ~ht~~~~~~~~~~~~~~~~~i~~~~L~~~~~~~~~RsSGPGGQ~VNK~~t~V~l~h~ptGi~v~~~e~RSq~~Nk~~A~~ 82 (135)
.|||++.|.+.|......+.|++.|| +|+|+|||||||||||||+|+|+|+|+||||+|.|+++|||++||+.||+
T Consensus 198 ~hTsfa~V~v~P~~~~~~~~i~~~dl----~~~~~RssG~GGQ~VNkt~SaVrl~h~ptgi~V~~~~eRSQ~~Nk~~A~~ 273 (360)
T TIGR00019 198 IHTSAATVAVMPELEEVEVDINPADL----RIDTFRSSGAGGQHVNTTDSAVRITHLPTGIVVECQDERSQHKNKDKAMK 273 (360)
T ss_pred eecceeEEEEEcCCCccccccCcccE----EEEEEECCCCCCCCcCceeeeEEEEECCCcEEEEECCccCHHHHHHHHHH
Confidence 69999999998866555577888888 99999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhHhcccccCCCCCCccccccCCCCcccccCCCCCCCCCCC
Q 043141 83 RLRTLLALNVRSSVKLDAYSPPPQLLQILPPKSTIRSSEVGPQIGPNN 130 (135)
Q Consensus 83 rL~~~l~~~~~~~~~~~~~~~~~~~~~~~~~k~q~~~g~~~~kIr~~n 130 (135)
+|+++|.....+.... ++...+|+++++|+||++||+||
T Consensus 274 ~L~~~L~~~~~~~~~~---------~~~~~r~~~~~~~~Rs~~IRtY~ 312 (360)
T TIGR00019 274 VLRARLYEAEQEKQQA---------AQASTRKSQVGSGDRSERIRTYN 312 (360)
T ss_pred HHHHHHHHHHHHHHHH---------HHHHHHhhhcceecccCCeEEEE
Confidence 9999988776542221 12346799999999999999999
No 3
>TIGR03072 release_prfH putative peptide chain release factor H. Members of this protein family are bacterial proteins homologous to peptide chain release factors 1 (RF-1, product of the prfA gene), and 2 (RF-2, product of the prfB gene). The member from Escherichia coli K-12, designated prfH, appears to be a pseudogene. This class I release factor is always found as the downstream gene of a two-gene operon.
Probab=99.98 E-value=3.5e-33 Score=222.77 Aligned_cols=112 Identities=31% Similarity=0.348 Sum_probs=97.0
Q ss_pred ccCcceeccCCCCCcCCcccChhhhhccceEEEEeccCCCccCCCccCceEEEEEcCCeeEEEeccccCHHHHHHHHHHH
Q 043141 4 HTNDNCSSSSSSSKKNYLELTDDELFRECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRVSALSR 83 (135)
Q Consensus 4 ht~~~~~~~~~~~~~~~~~i~~~~L~~~~~~~~~RsSGPGGQ~VNK~~t~V~l~h~ptGi~v~~~e~RSq~~Nk~~A~~r 83 (135)
|||+++|.+.+ ..++|+++|| +|+|+|||||||||||||+|+|+|+|+||||+|+|+++|||++||+.|+++
T Consensus 88 ~ts~~~V~v~~----~~~~i~~~dl----~~~~~RssGpGGQ~vNkt~saVrl~h~ptgi~v~~~~~RSQ~~Nk~~A~~~ 159 (200)
T TIGR03072 88 KNWFIGVQRFS----ASEEATEDEI----RFETLRSSGPGGQHVNKTESAVRATHLASGISVKVQSERSQHANKRLATLL 159 (200)
T ss_pred eEEEEEEEEec----CccccChhhe----EEEEEECCCCCcccccccceeEEEEECCCcEEEEECCccCHHHHHHHHHHH
Confidence 67888888865 3466888888 999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhHhcccccCCCCCCccccccCCCCcccccCCCCCCCCCCC-CCC
Q 043141 84 LRTLLALNVRSSVKLDAYSPPPQLLQILPPKSTIRSSEVGPQIGPNN-PKF 133 (135)
Q Consensus 84 L~~~l~~~~~~~~~~~~~~~~~~~~~~~~~k~q~~~g~~~~kIr~~n-~~~ 133 (135)
|+++|.....+... ++...++++...++||++||+|| ++|
T Consensus 160 L~~~l~~~~~~~~~----------~~~~~~r~~~~~~~Rg~~iRty~~~~f 200 (200)
T TIGR03072 160 LAVRLADLQQEQAA----------ALRAERRTAHHQIERGNPVRVFKGELF 200 (200)
T ss_pred HHHHHHHHHHHHHH----------HHHHHHHhccccccccCceEeeeCCcC
Confidence 99998876555432 23456788888889999999999 766
No 4
>KOG2726 consensus Mitochondrial polypeptide chain release factor [Translation, ribosomal structure and biogenesis]
Probab=99.98 E-value=4.2e-33 Score=239.19 Aligned_cols=115 Identities=37% Similarity=0.593 Sum_probs=103.3
Q ss_pred cccCcceeccCCCC--CcCCcccChhhhhccceEEEEeccCCCccCCCccCceEEEEEcCCeeEEEeccccCHHHHHHHH
Q 043141 3 YHTNDNCSSSSSSS--KKNYLELTDDELFRECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRVSA 80 (135)
Q Consensus 3 ~ht~~~~~~~~~~~--~~~~~~i~~~~L~~~~~~~~~RsSGPGGQ~VNK~~t~V~l~h~ptGi~v~~~e~RSq~~Nk~~A 80 (135)
.|||+..|++.|.. ....+.+++.|| +++|+|+||||||||||++|+|+|+|+||||+|+|+++|||++||+.|
T Consensus 223 ~htstasV~ViP~~~~~~~~~~~~~~dl----~i~~~R~~G~GGQhvNktdsaVrl~HiPTGIvv~cq~eRSq~~Nr~~A 298 (386)
T KOG2726|consen 223 RHTSTASVAVIPQPGRDEVDVEIDEKDL----RIETFRASGPGGQHVNKTDSAVRLTHIPTGIVVECQEERSQHKNRALA 298 (386)
T ss_pred cccccceEEEeccCCCCccceecCchhe----eEEecccCCCCcccccccccceEEEeecCceEEEeecHHhHHhhHHHH
Confidence 79999999999887 555566887777 999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHhHhcccccCCCCCCccccccCCCCcccccCCCCCCCCCCC
Q 043141 81 LSRLRTLLALNVRSSVKLDAYSPPPQLLQILPPKSTIRSSEVGPQIGPNN 130 (135)
Q Consensus 81 ~~rL~~~l~~~~~~~~~~~~~~~~~~~~~~~~~k~q~~~g~~~~kIr~~n 130 (135)
+.+|+++|..........+ ..+.++.|+++++++++||+||
T Consensus 299 ~~~L~akL~~~~~~~~~~~---------~~~~r~~qv~s~~rsekiRTy~ 339 (386)
T KOG2726|consen 299 LKRLRAKLAVIYREEKSEE---------EKKKRKAQVGSLKRSEKIRTYN 339 (386)
T ss_pred HHHHHHHHHHHHHhhhhHH---------hhhhhHHhhcccCchhceeecc
Confidence 9999999998877764433 2367999999999999999998
No 5
>PRK00591 prfA peptide chain release factor 1; Validated
Probab=99.98 E-value=5.4e-33 Score=237.38 Aligned_cols=115 Identities=34% Similarity=0.554 Sum_probs=101.5
Q ss_pred cccCcceeccCCCCCcCCcccChhhhhccceEEEEeccCCCccCCCccCceEEEEEcCCeeEEEeccccCHHHHHHHHHH
Q 043141 3 YHTNDNCSSSSSSSKKNYLELTDDELFRECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRVSALS 82 (135)
Q Consensus 3 ~ht~~~~~~~~~~~~~~~~~i~~~~L~~~~~~~~~RsSGPGGQ~VNK~~t~V~l~h~ptGi~v~~~e~RSq~~Nk~~A~~ 82 (135)
.|||+++|.+.|......+.|++.|| +|+|+|||||||||||||+|+|+|+|+||||+|.|+++|||++||+.|++
T Consensus 198 ~~tsfa~V~v~P~~~~~~~~i~~~dl----~~~~~RssG~GGQ~VNkt~saVrl~H~ptGi~v~~~~eRSQ~~Nk~~Al~ 273 (359)
T PRK00591 198 IHTSAATVAVLPEAEEVEVEINPKDL----RIDTFRSSGAGGQHVNTTDSAVRITHLPTGIVVECQDERSQHKNKAKAMK 273 (359)
T ss_pred eecceEEEEEEcCCCccccccCcccE----EEEEEECCCCCCCCccceeeeEEEEECCCcEEEEECCcCCHHHHHHHHHH
Confidence 69999999998876665677888887 99999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhHhcccccCCCCCCccccccCCCCcccccCCCCCCCCCCC
Q 043141 83 RLRTLLALNVRSSVKLDAYSPPPQLLQILPPKSTIRSSEVGPQIGPNN 130 (135)
Q Consensus 83 rL~~~l~~~~~~~~~~~~~~~~~~~~~~~~~k~q~~~g~~~~kIr~~n 130 (135)
+|+.+|.....+....+ ..+.+|+++.+|+||++||+||
T Consensus 274 ~L~~~L~~~~~~~~~~~---------~~~~r~~~~~~~~Rse~IRtY~ 312 (359)
T PRK00591 274 VLRARLYDAERQKAQAE---------EAATRKSQVGSGDRSERIRTYN 312 (359)
T ss_pred HHHHHHHHHHHHHHHHH---------HHHHHHhhcccccccCCeeeEE
Confidence 99999887665543322 2236699999999999999998
No 6
>PF00472 RF-1: RF-1 domain; InterPro: IPR000352 Peptide chain release factors (RFs) are required for the termination of protein biosynthesis []. At present two classes of RFs can be distinguished. Class I RFs bind to ribosomes that have encountered a stop codon at their decoding site and induce release of the nascent polypeptide. Class II RFs are GTP-binding proteins that interact with class I RFs and enhance class I RF activity. In prokaryotes there are two class I RFs that act in a codon specific manner []: RF-1 (gene prfA) mediates UAA and UAG-dependent termination while RF-2 (gene prfB) mediates UAA and UGA-dependent termination. RF-1 and RF-2 are structurally and evolutionary related proteins which have been shown to be part of a larger family [].; GO: 0003747 translation release factor activity, 0006415 translational termination; PDB: 2JY9_A 1ZBT_A 1GQE_A 3F1G_X 3F1E_X 1RQ0_C 4DH9_Y 2JVA_A 1J26_A 3D5A_X ....
Probab=99.97 E-value=2.1e-32 Score=200.10 Aligned_cols=101 Identities=36% Similarity=0.558 Sum_probs=87.6
Q ss_pred cCCcccChhhhhccceEEEEeccCCCccCCCccCceEEEEEcCCeeEEEeccccCHHHHHHHHHHHHHHHHHHhHhcccc
Q 043141 18 KNYLELTDDELFRECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRVSALSRLRTLLALNVRSSVK 97 (135)
Q Consensus 18 ~~~~~i~~~~L~~~~~~~~~RsSGPGGQ~VNK~~t~V~l~h~ptGi~v~~~e~RSq~~Nk~~A~~rL~~~l~~~~~~~~~ 97 (135)
...+.|+++|| +|+|+|||||||||||||+|+|+|+|+|+||+|+|+++|||.+|++.|+++|+++|..+..+...
T Consensus 4 ~~~~~i~~~dl----~~~~~RssGpGGQ~VNk~~s~V~l~h~ptgi~v~~~~~Rsq~~Nr~~A~~~L~~~l~~~~~~~~~ 79 (113)
T PF00472_consen 4 EKEIDIPEKDL----EISFSRSSGPGGQNVNKTNSKVRLRHIPTGIVVKCQESRSQHQNREDALEKLREKLDEAYREKRR 79 (113)
T ss_dssp SSSSCC-GGGE----EEEEEESSSSSSCHHHSSSEEEEEEETTTTEEEEEESSSSHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred ccccccCHHHe----EEEEEecCCCCCCcccccCCEEEEEEecccEEEEEcccCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34578888888 99999999999999999999999999999999999999999999999999999999988744333
Q ss_pred cCCCCCCccccccCCCCcccccCCCCCCCCCCCC
Q 043141 98 LDAYSPPPQLLQILPPKSTIRSSEVGPQIGPNNP 131 (135)
Q Consensus 98 ~~~~~~~~~~~~~~~~k~q~~~g~~~~kIr~~n~ 131 (135)
.. ....++++.+.++++++||+||-
T Consensus 80 ~~---------~~~~~~~~~~~~~~~~~iR~y~~ 104 (113)
T PF00472_consen 80 EK---------TREIRKSQVKRLERKKKIRTYNF 104 (113)
T ss_dssp HH---------TTTTTTTSCCCSSTTSEEEEEET
T ss_pred HH---------HHHHHHHHHhHHhhhcceecccC
Confidence 22 23568888888999999999984
No 7
>PRK08179 prfH peptide chain release factor-like protein; Reviewed
Probab=99.97 E-value=8.6e-32 Score=214.79 Aligned_cols=109 Identities=28% Similarity=0.275 Sum_probs=93.6
Q ss_pred ccCcceeccCCCCCcCCcccChhhhhccceEEEEeccCCCccCCCccCceEEEEEcCCeeEEEeccccCHHHHHHHHHHH
Q 043141 4 HTNDNCSSSSSSSKKNYLELTDDELFRECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRVSALSR 83 (135)
Q Consensus 4 ht~~~~~~~~~~~~~~~~~i~~~~L~~~~~~~~~RsSGPGGQ~VNK~~t~V~l~h~ptGi~v~~~e~RSq~~Nk~~A~~r 83 (135)
|||+++|.+.+ ..+.|+++|| +|+|+|||||||||||||+|+|+|+|+||||+|+|+++|||++||+.|+++
T Consensus 89 ~~s~~~V~v~~----~~~~i~~~dl----~~~~~RssGpGGQ~VNkt~saVrl~h~ptgi~v~~~~~RSQ~~Nk~~A~~~ 160 (200)
T PRK08179 89 KNWFVGIGRFS----ADEEEQSDEI----RFETLRSSGPGGQHVNKTDSAVRATHLASGISVKVQSERSQHANKRLARLL 160 (200)
T ss_pred eEEEEEEEEeC----CcCccCHHHe----EEEEEEccCCcccccccccceEEEEEcCCcEEEEECCCCCHHHHHHHHHHH
Confidence 67788888764 3467888888 999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhHhcccccCCCCCCccccccCCCCcccccCCCCCCCCCCC
Q 043141 84 LRTLLALNVRSSVKLDAYSPPPQLLQILPPKSTIRSSEVGPQIGPNN 130 (135)
Q Consensus 84 L~~~l~~~~~~~~~~~~~~~~~~~~~~~~~k~q~~~g~~~~kIr~~n 130 (135)
|+++|.....++... +...++++...++||++||+|-
T Consensus 161 L~~~L~~~~~~~~~~----------~~~~~~~~~~~~~Rg~~IRt~~ 197 (200)
T PRK08179 161 IAWKLEQQQQEQSAA----------LKSQRRMFHHQIERGNPRRVFT 197 (200)
T ss_pred HHHHHHHHHHHHHHH----------HHHHHHhccccccccCceEeee
Confidence 999988765554332 2356777778888999999984
No 8
>PRK05589 peptide chain release factor 2; Provisional
Probab=99.97 E-value=1e-31 Score=227.15 Aligned_cols=115 Identities=32% Similarity=0.481 Sum_probs=94.5
Q ss_pred cccCcceeccCCCCCc-CCcccChhhhhccceEEEEeccCCCccCCCccCceEEEEEcCCeeEEEeccccCHHHHHHHHH
Q 043141 3 YHTNDNCSSSSSSSKK-NYLELTDDELFRECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRVSAL 81 (135)
Q Consensus 3 ~ht~~~~~~~~~~~~~-~~~~i~~~~L~~~~~~~~~RsSGPGGQ~VNK~~t~V~l~h~ptGi~v~~~e~RSq~~Nk~~A~ 81 (135)
.|||+++|.+.|.... ..+.|+++|| +|+|+|||||||||||||+|+|+|+|+||||+|+|+++|||++||+.|+
T Consensus 172 r~ts~a~V~VlP~~~~~~~~~i~~~dl----~~~~~rssG~GGQ~VNkt~saVrl~H~ptgi~v~~q~eRSQ~~Nk~~A~ 247 (325)
T PRK05589 172 RQTSFASVEVLPELTDDQDIEIRSEDL----KIDTYRAGGAGGQHVNKTESAVRITHIPTGIVVQCQNERSQHSNKETAM 247 (325)
T ss_pred eEeeeEEEEEecCcCccccccCCchhe----EEEEeeCCCCCCCcccceeeEEEEEECCCCEEEEECCccCHHHHHHHHH
Confidence 6999999999987643 2578888888 9999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHhHhcccccCCCCCCccccccCCCCcccccCCCCCCCCCCCC
Q 043141 82 SRLRTLLALNVRSSVKLDAYSPPPQLLQILPPKSTIRSSEVGPQIGPNNP 131 (135)
Q Consensus 82 ~rL~~~l~~~~~~~~~~~~~~~~~~~~~~~~~k~q~~~g~~~~kIr~~n~ 131 (135)
++|+++|.......... +...++.+.....||++||+||=
T Consensus 248 ~~L~~kL~~~~~~~~~~----------~~~~~r~~~~~~~~g~~IRtY~~ 287 (325)
T PRK05589 248 KMLKSKLVELKERAHKE----------KIEDLTGELKDMGWGSQIRSYVF 287 (325)
T ss_pred HHHHHHHHHHHHHHHHH----------HHHHHhcccccccccCCceeeEC
Confidence 99999888654332221 11223344445567789999984
No 9
>PRK06746 peptide chain release factor 2; Provisional
Probab=99.97 E-value=2.9e-31 Score=224.42 Aligned_cols=115 Identities=30% Similarity=0.368 Sum_probs=97.1
Q ss_pred cccCcceeccCCCCC-cCCcccChhhhhccceEEEEeccCCCccCCCccCceEEEEEcCCeeEEEeccccCHHHHHHHHH
Q 043141 3 YHTNDNCSSSSSSSK-KNYLELTDDELFRECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRVSAL 81 (135)
Q Consensus 3 ~ht~~~~~~~~~~~~-~~~~~i~~~~L~~~~~~~~~RsSGPGGQ~VNK~~t~V~l~h~ptGi~v~~~e~RSq~~Nk~~A~ 81 (135)
.|||++.|.+.|... ...+.|+++|| +|+|+|||||||||||||+|+|+|+|+||||+|+|+++|||++||+.|+
T Consensus 173 rhTsfa~V~v~P~~~~~~~i~i~~~dl----~~~~~rssG~GGQ~vNkt~saVrl~h~ptgi~v~~q~~RSQ~~Nk~~A~ 248 (326)
T PRK06746 173 RHTSFVSCEVVPEFNDEVEIEVRTEDL----KIDTYRASGAGGQHVNTTDSAVRITHTPTNTVVTCQSERSQIKNREHAM 248 (326)
T ss_pred eEeeEEEEEEecCcCCccccccChHHe----EEEEEeCCCCCCCCccceeeEEEEEEeCCeEEEEECCCCCHHHHHHHHH
Confidence 699999999987652 45677888888 9999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHhHhcccccCCCCCCccccccCCCCcccccCCCCCCCCCCCC
Q 043141 82 SRLRTLLALNVRSSVKLDAYSPPPQLLQILPPKSTIRSSEVGPQIGPNNP 131 (135)
Q Consensus 82 ~rL~~~l~~~~~~~~~~~~~~~~~~~~~~~~~k~q~~~g~~~~kIr~~n~ 131 (135)
++|+++|.....+....+ ....|++++..+ ||++||+||=
T Consensus 249 ~~L~akL~~~~~~~~~~~---------~~~~r~~~~~~~-rg~~IRtYnf 288 (326)
T PRK06746 249 KMLKAKLYQKKLEEQQAE---------LDEIRGEQKEIG-WGSQIRSYVF 288 (326)
T ss_pred HHHHHHHHHHHHHHHHHH---------HHHHHhhhccCc-cCCCeEEEEC
Confidence 999998886655543322 235677777664 6789999984
No 10
>PRK08787 peptide chain release factor 2; Provisional
Probab=99.97 E-value=4.5e-31 Score=222.25 Aligned_cols=114 Identities=33% Similarity=0.405 Sum_probs=92.5
Q ss_pred cccCcceeccCCCCCc-CCcccChhhhhccceEEEEeccCCCccCCCccCceEEEEEcCCeeEEEeccccCHHHHHHHHH
Q 043141 3 YHTNDNCSSSSSSSKK-NYLELTDDELFRECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRVSAL 81 (135)
Q Consensus 3 ~ht~~~~~~~~~~~~~-~~~~i~~~~L~~~~~~~~~RsSGPGGQ~VNK~~t~V~l~h~ptGi~v~~~e~RSq~~Nk~~A~ 81 (135)
.|||++.|.+.|.... ..+.|++.|| +|+|+|||||||||||||+|+|+|+|+||||+|+|+++|||++||+.|+
T Consensus 152 rhTsfasV~V~P~~~~~~~i~i~~~dl----~~~~~RssG~GGQ~VNkt~saVri~H~Ptgi~v~~q~eRSQ~~Nk~~A~ 227 (313)
T PRK08787 152 RHTSFTSVFVSPEVDDNIEIDINPADL----RTDVYRSSGAGGQHVNKTESAVRITHIPTNTVVACQTGRSQHQNRDNAM 227 (313)
T ss_pred EEeeeEEEEEecCcCcccccccChhHe----EEEEEECCCCCCCCcCCEeeEEEEEECCCcEEEEECCcccHHHHHHHHH
Confidence 6999999999876643 3577888888 9999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHhHhcccccCCCCCCccccccCCCCcccccCCCCCCCCCCC
Q 043141 82 SRLRTLLALNVRSSVKLDAYSPPPQLLQILPPKSTIRSSEVGPQIGPNN 130 (135)
Q Consensus 82 ~rL~~~l~~~~~~~~~~~~~~~~~~~~~~~~~k~q~~~g~~~~kIr~~n 130 (135)
++|+++|.....+....+.. .....|+++++| +|||+||
T Consensus 228 ~~L~~~L~~~~~e~~~~~~~-------~~~~~k~~i~~g---~qIRtY~ 266 (313)
T PRK08787 228 KMLAAKLYELEVQKRNAEKD-------ALEATKSDIGWG---SQIRNYV 266 (313)
T ss_pred HHHHHHHHHHHHHHHHHHHH-------HHhhhhhhCccc---cccccee
Confidence 99999888654443222100 011236666544 5899998
No 11
>PRK07342 peptide chain release factor 2; Provisional
Probab=99.97 E-value=6.9e-31 Score=223.09 Aligned_cols=115 Identities=34% Similarity=0.448 Sum_probs=93.2
Q ss_pred cccCcceeccCCCCCc-CCcccChhhhhccceEEEEeccCCCccCCCccCceEEEEEcCCeeEEEeccccCHHHHHHHHH
Q 043141 3 YHTNDNCSSSSSSSKK-NYLELTDDELFRECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRVSAL 81 (135)
Q Consensus 3 ~ht~~~~~~~~~~~~~-~~~~i~~~~L~~~~~~~~~RsSGPGGQ~VNK~~t~V~l~h~ptGi~v~~~e~RSq~~Nk~~A~ 81 (135)
.|||+++|.+.|.... ..+.|++.|| +|+|+|||||||||||||+|+|+|+|+||||+|+|+++|||++||+.|+
T Consensus 175 rhTs~a~V~VlP~~~~~~~~~i~~~dl----~~~~~RssG~GGQ~VNkt~saVrl~H~ptgi~v~~~~eRSQ~~Nk~~A~ 250 (339)
T PRK07342 175 RHTSFASIWVYPVIDDNIEVDVNESDV----RIDTYRSSGAGGQHVNTTDSAVRITHIPTGIVVQCQQERSQHKNRAKAW 250 (339)
T ss_pred eEeEEEEEEEEcCCCcccccccCcccE----EEEEEECCCCCCCCccceeeeEEEEEcCCcEEEEECCcccHHHHHHHHH
Confidence 6999999999886643 2467777777 9999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHhHhcccccCCCCCCccccccCCCCcccccCCCCCCCCCCCC
Q 043141 82 SRLRTLLALNVRSSVKLDAYSPPPQLLQILPPKSTIRSSEVGPQIGPNNP 131 (135)
Q Consensus 82 ~rL~~~l~~~~~~~~~~~~~~~~~~~~~~~~~k~q~~~g~~~~kIr~~n~ 131 (135)
++|+++|.....+....+.. ....+++++++|+ +||+||=
T Consensus 251 ~~L~~~L~~~~~~~~~~~~~-------~~~~~~~~i~~g~---~IRtY~~ 290 (339)
T PRK07342 251 SMLRARLYEEELKKREEATN-------AAAASKTDIGWGH---QIRSYVL 290 (339)
T ss_pred HHHHHHHHHHHHHHHHHHHH-------HHHhhhhhccccC---CcCCccC
Confidence 99999888665544332110 1123466666554 8999983
No 12
>PRK00578 prfB peptide chain release factor 2; Validated
Probab=99.97 E-value=8.8e-31 Score=224.31 Aligned_cols=114 Identities=33% Similarity=0.474 Sum_probs=95.4
Q ss_pred cccCcceeccCCCCCcC-CcccChhhhhccceEEEEeccCCCccCCCccCceEEEEEcCCeeEEEeccccCHHHHHHHHH
Q 043141 3 YHTNDNCSSSSSSSKKN-YLELTDDELFRECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRVSAL 81 (135)
Q Consensus 3 ~ht~~~~~~~~~~~~~~-~~~i~~~~L~~~~~~~~~RsSGPGGQ~VNK~~t~V~l~h~ptGi~v~~~e~RSq~~Nk~~A~ 81 (135)
.|||+++|.+.|..... .+.|+++|| +|+|+|||||||||||||+|+|+|+|+||||+|.|+++|||++||+.|+
T Consensus 211 ~hts~~~V~vlP~~~~~~~~~i~~~dl----~~~~~rssGpGGQ~vNkt~saVrl~h~ptgi~v~~~~~RSQ~~Nk~~A~ 286 (367)
T PRK00578 211 RHTSFASVEVYPEVDDTIEIEINPKDL----RIDTYRSSGAGGQHVNKTDSAVRITHIPTGIVVQCQNERSQHQNKASAM 286 (367)
T ss_pred eecceeeEEecCCCCCccccccChhhE----EEEEeeCCCCCCCcccceeeEEEEEECCCcEEEEECCCCCHHHHHHHHH
Confidence 69999999999876432 567888888 9999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHhHhcccccCCCCCCccccccCCCCcccccCCCCCCCCCCC
Q 043141 82 SRLRTLLALNVRSSVKLDAYSPPPQLLQILPPKSTIRSSEVGPQIGPNN 130 (135)
Q Consensus 82 ~rL~~~l~~~~~~~~~~~~~~~~~~~~~~~~~k~q~~~g~~~~kIr~~n 130 (135)
++|+++|..........+ ..+.|+.+ ...+||++||+||
T Consensus 287 ~~L~~kL~~~~~~~~~~~---------~~~~r~~~-~~~~rg~~IRtYn 325 (367)
T PRK00578 287 KMLKAKLYELELEKRAAE---------KDALKGEK-KEIGWGSQIRSYV 325 (367)
T ss_pred HHHHHHHHHHHHHHHHHH---------HHHHHhhh-ccccccCCeEEEE
Confidence 999998887665543322 12344444 4556778999999
No 13
>TIGR00020 prfB peptide chain release factor 2. In many but not all taxa, there is a conserved real translational frameshift at a TGA codon. RF-2 helps terminate translation at TGA codons and can therefore regulate its own production by readthrough when RF-2 is insufficient. There is a Pfam model called "RF-1" for the superfamily of RF-1, RF-2, mitochondrial, RF-H, etc.
Probab=99.96 E-value=1.3e-30 Score=223.16 Aligned_cols=115 Identities=34% Similarity=0.449 Sum_probs=94.2
Q ss_pred cccCcceeccCCCC-CcCCcccChhhhhccceEEEEeccCCCccCCCccCceEEEEEcCCeeEEEeccccCHHHHHHHHH
Q 043141 3 YHTNDNCSSSSSSS-KKNYLELTDDELFRECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRVSAL 81 (135)
Q Consensus 3 ~ht~~~~~~~~~~~-~~~~~~i~~~~L~~~~~~~~~RsSGPGGQ~VNK~~t~V~l~h~ptGi~v~~~e~RSq~~Nk~~A~ 81 (135)
.|||++.|.+.|.. ....+.|++.|| +|+|+||||||||||||++|+|+|+|+||||+|+|+++|||++||+.|+
T Consensus 211 rhts~a~V~vlP~~~~~~~~~i~~~d~----~~~~~rssG~GGQ~VNkt~saVri~H~ptgi~v~~q~~RSQ~~Nk~~A~ 286 (364)
T TIGR00020 211 RHTSFASVFVMPEVDDDIDIEIKPEDL----RIDTYRASGAGGQHVNKTDSAVRITHIPTGIVVQCQNDRSQHKNKDSAM 286 (364)
T ss_pred eEeeeEEEEEecCCCcccceecccccE----EEEEeeCCCCCCccccccceEEEEEECCCcEEEEECCccCHHHHHHHHH
Confidence 69999999998866 344567777777 9999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHhHhcccccCCCCCCccccccCCCCcccccCCCCCCCCCCCC
Q 043141 82 SRLRTLLALNVRSSVKLDAYSPPPQLLQILPPKSTIRSSEVGPQIGPNNP 131 (135)
Q Consensus 82 ~rL~~~l~~~~~~~~~~~~~~~~~~~~~~~~~k~q~~~g~~~~kIr~~n~ 131 (135)
++|+++|.....+....+ ....|+++... +||++||+||=
T Consensus 287 ~~L~~kL~~~~~~~~~~~---------~~~~r~~~~~~-~rg~~IRtY~~ 326 (364)
T TIGR00020 287 KVLKAKLYELEMEKEQAE---------KDAKEGEKSEI-GWGSQIRSYVL 326 (364)
T ss_pred HHHHHHHHHHHHHHHHHH---------HHHHHhhhhcc-CccCCeEEEEC
Confidence 999998886655443321 12345333333 57789999984
No 14
>PRK09256 hypothetical protein; Provisional
Probab=99.93 E-value=1.1e-25 Score=170.81 Aligned_cols=83 Identities=37% Similarity=0.585 Sum_probs=72.4
Q ss_pred CcCCcccChhhhhccceEEEEeccCCCccCCCccCceEEEEE------cC-----------------Ce-eEEEeccccC
Q 043141 17 KKNYLELTDDELFRECEMDTYKSSGPGGQHINKRESAVRIKH------VP-----------------TG-VIAQAAEDRS 72 (135)
Q Consensus 17 ~~~~~~i~~~~L~~~~~~~~~RsSGPGGQ~VNK~~t~V~l~h------~p-----------------tG-i~v~~~e~RS 72 (135)
.+..+.|+.++| +|+|+|||||||||||||+|+|+|+| +| +| |+|+|+++||
T Consensus 4 ~~~~~~i~~~~l----~~~~~RSSGPGGQ~VNKt~SkV~l~~~~~~~~lp~~~~~~l~~~~~~r~~~~g~l~i~~~~~RS 79 (138)
T PRK09256 4 ITRRLVIPENEL----EWRFIRASGPGGQNVNKVSTAVELRFDIAASSLPEFYKERLLALAGHRITKDGVIVIKAQEFRS 79 (138)
T ss_pred cCccCccCHHHe----EEEEEEcCCCCcccccccceeeEEEechhhccCCHHHHHHHHHHhcCcccCCCcEEEEECCcCC
Confidence 445688998888 99999999999999999999999996 66 46 9999999999
Q ss_pred HHHHHHHHHHHHHHHHHHhHhcccccCCCCC
Q 043141 73 QHKNRVSALSRLRTLLALNVRSSVKLDAYSP 103 (135)
Q Consensus 73 q~~Nk~~A~~rL~~~l~~~~~~~~~~~~~~~ 103 (135)
|.+|+++|+++|.++|..++..+....+..|
T Consensus 80 Q~~Nr~~al~kL~~~i~~~~~~p~~r~~tk~ 110 (138)
T PRK09256 80 QERNREDALERLVALIREALKPPKKRRATKP 110 (138)
T ss_pred HHHHHHHHHHHHHHHHHHHhhccccccCCcc
Confidence 9999999999999999998886555444443
No 15
>COG1186 PrfB Protein chain release factor B [Translation, ribosomal structure and biogenesis]
Probab=99.91 E-value=1.3e-25 Score=183.40 Aligned_cols=115 Identities=32% Similarity=0.426 Sum_probs=84.7
Q ss_pred ccCcceeccCCCC-CcCCcccChhhhhccceEEEEeccCCCccCCCccCceEEEEEcCCeeEEEeccccCHHHHHHHHHH
Q 043141 4 HTNDNCSSSSSSS-KKNYLELTDDELFRECEMDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRSQHKNRVSALS 82 (135)
Q Consensus 4 ht~~~~~~~~~~~-~~~~~~i~~~~L~~~~~~~~~RsSGPGGQ~VNK~~t~V~l~h~ptGi~v~~~e~RSq~~Nk~~A~~ 82 (135)
|||=.-+.+.|.- ....+.|+++|| +++|+|||||||||||||+|+|+|+|+|+||+|.|+.+|||+.|++.|+.
T Consensus 87 ~tsf~~v~v~p~~~~~i~i~I~~~dl----~idt~RASGaGGQhVNKt~SAVrlth~ptgivv~cq~eRSq~~n~~~a~~ 162 (239)
T COG1186 87 HTSFASVEVFPELDISIEIEIPDDDL----RIDTYRASGAGGQHVNKTDSAVRLTHLPTGIVVLCQNERSQHLNKALARK 162 (239)
T ss_pred ccceeeeeecCCCCcccceecCccce----EEEEEEcCCCCCCccccccccEEEEEcCCCCEecCHHHHHHHHHHHHHHH
Confidence 5665444444322 455677888888 99999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhHhcccccCCCCCCccccccCCCCcccccCCCCCCCCCCCCC
Q 043141 83 RLRTLLALNVRSSVKLDAYSPPPQLLQILPPKSTIRSSEVGPQIGPNNPK 132 (135)
Q Consensus 83 rL~~~l~~~~~~~~~~~~~~~~~~~~~~~~~k~q~~~g~~~~kIr~~n~~ 132 (135)
.|+..|.....+....+ ..++...+..+.+|. +||.|-.+
T Consensus 163 ~l~~kL~~~~~~~Rsqe-------~n~~~a~~k~i~wg~---qirsyv~~ 202 (239)
T COG1186 163 MLKGKLYILAQEKRSQE-------KNRERALKKLIGWGN---QIRSYVLD 202 (239)
T ss_pred HHHHHHHHHHHHHHHHH-------HHHHHHHhhhHHHHH---hccccCCC
Confidence 99997664443322211 011223344454443 78877654
No 16
>KOG3429 consensus Predicted peptidyl-tRNA hydrolase [Translation, ribosomal structure and biogenesis]
Probab=99.81 E-value=3.4e-20 Score=144.59 Aligned_cols=70 Identities=34% Similarity=0.643 Sum_probs=62.7
Q ss_pred ccChhhhhccceEEEEeccCCCccCCCccCceEEEEE-------cC-----------------Ce-eEEEeccccCHHHH
Q 043141 22 ELTDDELFRECEMDTYKSSGPGGQHINKRESAVRIKH-------VP-----------------TG-VIAQAAEDRSQHKN 76 (135)
Q Consensus 22 ~i~~~~L~~~~~~~~~RsSGPGGQ~VNK~~t~V~l~h-------~p-----------------tG-i~v~~~e~RSq~~N 76 (135)
.|+.+.| ++.|+||||||||||||++|+|.|++ || .| |+|.++.+|||+.|
T Consensus 36 ~ipld~~----~i~y~RSSGPGGQNVNKvNTKv~vrf~vs~a~Wipe~~R~~~~~~~~~rink~gelvI~Sd~TRsq~~N 111 (172)
T KOG3429|consen 36 KIPLDQL----EISYSRSSGPGGQNVNKVNTKVEVRFKVSNAEWIPEFLRNKLLTTEKNRINKDGELVIYSDKTRSQHKN 111 (172)
T ss_pred CCchhhe----EEEEeecCCCCCcccccccceEEEEEecchhhhccHHHHHHHHHHHHHhhccCccEEEecchhHHhhcc
Confidence 3666777 99999999999999999999999996 44 45 99999999999999
Q ss_pred HHHHHHHHHHHHHHhHhcc
Q 043141 77 RVSALSRLRTLLALNVRSS 95 (135)
Q Consensus 77 k~~A~~rL~~~l~~~~~~~ 95 (135)
.++||++|+++|..+...+
T Consensus 112 iaDcleKlr~~I~~~~~~~ 130 (172)
T KOG3429|consen 112 IADCLEKLRDIIRAAEQTP 130 (172)
T ss_pred HHHHHHHHHHHHHHHhcCC
Confidence 9999999999999877654
No 17
>PF10213 MRP-S28: Mitochondrial ribosomal subunit protein ; InterPro: IPR019349 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 a conserved region of approx. 125 residues of one of the proteins that makes up the small subunit of the mitochondrial ribosome. In Saccharomyces cerevisiae (Baker's yeast) it is mitochondrial ribosomal protein S24 whereas in humans it is S35.
Probab=92.87 E-value=0.74 Score=34.58 Aligned_cols=34 Identities=12% Similarity=0.017 Sum_probs=31.5
Q ss_pred Ce-eEEEeccccCHHHHHHHHHHHHHHHHHHhHhc
Q 043141 61 TG-VIAQAAEDRSQHKNRVSALSRLRTLLALNVRS 94 (135)
Q Consensus 61 tG-i~v~~~e~RSq~~Nk~~A~~rL~~~l~~~~~~ 94 (135)
+| |.+.|+..-++.+|+.-|...|..+|.++.+.
T Consensus 60 ~d~l~i~sdr~~~~~qN~~~l~~~l~~L~~EA~~~ 94 (127)
T PF10213_consen 60 TDILKISSDRFPTRAQNKKYLSDLLTRLIHEAKDL 94 (127)
T ss_pred CCEEEEecccCCCHHHHHHHHHHHHHHHHHHHhhc
Confidence 67 99999999999999999999999999988774
No 18
>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like. The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=62.68 E-value=9 Score=23.98 Aligned_cols=39 Identities=23% Similarity=0.396 Sum_probs=25.0
Q ss_pred CCCccCCCc--cCceEEEEEcC----Ce-eEEEeccccCHHHHHHHHHHHH
Q 043141 41 GPGGQHINK--RESAVRIKHVP----TG-VIAQAAEDRSQHKNRVSALSRL 84 (135)
Q Consensus 41 GPGGQ~VNK--~~t~V~l~h~p----tG-i~v~~~e~RSq~~Nk~~A~~rL 84 (135)
|+||.++++ ..+.|.|..-+ .+ ++|... ..+-..|..+|
T Consensus 16 G~~G~~i~~i~~~~g~~I~i~~~~~~~~~v~I~G~-----~~~v~~A~~~i 61 (62)
T cd02394 16 GKKGSNIRKIMEETGVKIRFPDPGSKSDTITITGP-----KENVEKAKEEI 61 (62)
T ss_pred CCCCCcHHHHHHHhCCEEEcCCCCCCCCEEEEEcC-----HHHHHHHHHHh
Confidence 789999995 34777777655 45 555555 34555665543
No 19
>KOG3933 consensus Mitochondrial ribosomal protein S28 [Translation, ribosomal structure and biogenesis]
Probab=60.13 E-value=39 Score=29.09 Aligned_cols=31 Identities=19% Similarity=0.103 Sum_probs=28.3
Q ss_pred Ce-eEEEeccccCHHHHHHHHHHHHHHHHHHh
Q 043141 61 TG-VIAQAAEDRSQHKNRVSALSRLRTLLALN 91 (135)
Q Consensus 61 tG-i~v~~~e~RSq~~Nk~~A~~rL~~~l~~~ 91 (135)
++ ++|.|+..-+..+|+..|+..|..++.+.
T Consensus 202 tD~~tissDR~~~r~QN~~y~~~lLt~L~~ES 233 (296)
T KOG3933|consen 202 TDLLTISSDRCEHREQNYDYALYLLTVLYHES 233 (296)
T ss_pred CCeEEEeccccchhhHhHHHHHHHHHHHHHHh
Confidence 56 89999999999999999999999998876
No 20
>COG1186 PrfB Protein chain release factor B [Translation, ribosomal structure and biogenesis]
Probab=54.39 E-value=2 Score=35.84 Aligned_cols=33 Identities=33% Similarity=0.198 Sum_probs=28.8
Q ss_pred eEEEeccccCHHHHHHHHHHHHHHHHHHhHhcc
Q 043141 63 VIAQAAEDRSQHKNRVSALSRLRTLLALNVRSS 95 (135)
Q Consensus 63 i~v~~~e~RSq~~Nk~~A~~rL~~~l~~~~~~~ 95 (135)
|.+..+++|+|..|++.|++++.+.+.....-+
T Consensus 168 L~~~~~~~Rsqe~n~~~a~~k~i~wg~qirsyv 200 (239)
T COG1186 168 LYILAQEKRSQEKNRERALKKLIGWGNQIRSYV 200 (239)
T ss_pred HHHHHHHHHHHHHHHHHHHhhhHHHHHhccccC
Confidence 888999999999999999999999887665543
No 21
>PF02815 MIR: MIR domain; InterPro: IPR003608 The MIR domain is named after three of the proteins in which it occurs: protein Mannosyltransferase (2.4.1.109 from EC), Inositol 1,4,5-trisphosphate receptor (IP3R) and Ryanodine receptor (RyR). MIR domains have also been found in eukaryotic stromal cell-derived factor 2 (SDF-2) and in Chlamydia trachomatis protein CT153. The MIR domain may have a ligand transferase function. This domain has a closed beta-barrel structure with a hairpin triplet, and has an internal pseudo-threefold symmetry. The MIR motifs that make up the MIR domain consist of ~50 residues and are often found in multiple copies. Inositol 1,4,5-trisphosphate (InsP3) is an intracellular second messenger that transduces growth factor and neurotransmitter signals. InsP3 mediates the release of Ca2+ from intracellular stores by binding to specific Ca2+ channel-coupled receptors. Ryanodine receptors are involved in communication between transverse-tubules and the sarcoplamic reticulum of cardiac and skeletal muscle. The proteins function as a Ca2+-release channels following depolarisation of transverse-tubules []. The function is modulated by Ca2+, Mg2+, ATP and calmodulin. Deficiency in the ryanodine receptor may be the cause of malignant hyperthermia (MH) and of central core disease of muscle (CCD) []. protein O-mannosyltransferases transfer mannose from DOL-P-mannose to ser or thr residues on proteins.; GO: 0016020 membrane; PDB: 1T9F_A 3UJ4_B 3UJ0_B 3T8S_B 3MAL_B 2XOA_A 1N4K_A.
Probab=42.71 E-value=53 Score=25.05 Aligned_cols=39 Identities=26% Similarity=0.434 Sum_probs=30.4
Q ss_pred EEEEeccCCCccCCCccCceEEEEEcCCeeEEEeccccC
Q 043141 34 MDTYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRS 72 (135)
Q Consensus 34 ~~~~RsSGPGGQ~VNK~~t~V~l~h~ptGi~v~~~e~RS 72 (135)
++..-..|-++..+-..++.|+|+|..+|..+.++..+.
T Consensus 121 ~~~~~~~~~~~~~~~~~~s~frL~H~~t~~~L~~~~~~l 159 (190)
T PF02815_consen 121 FEEKSSTGMGEDEIKTLDSYFRLRHVATGCWLHSHDVKL 159 (190)
T ss_dssp EEEEESSSCSSSSBBBTTSEEEEEETTTTEEEEEEEEES
T ss_pred EEecccCCccCCcEEecccEEEEEECCcCEEEecCCccc
Confidence 445556677788888889999999999997777766543
No 22
>smart00322 KH K homology RNA-binding domain.
Probab=40.67 E-value=44 Score=19.81 Aligned_cols=45 Identities=27% Similarity=0.398 Sum_probs=26.3
Q ss_pred CCCccCCCc--cCceEEEEEcCCe---eEEEeccccCHHHHHHHHHHHHHHHH
Q 043141 41 GPGGQHINK--RESAVRIKHVPTG---VIAQAAEDRSQHKNRVSALSRLRTLL 88 (135)
Q Consensus 41 GPGGQ~VNK--~~t~V~l~h~ptG---i~v~~~e~RSq~~Nk~~A~~rL~~~l 88 (135)
|++|.++.. -.+.+.+...+.+ -++..... ..+.+.|...|.+.+
T Consensus 19 G~~G~~i~~i~~~~~~~i~~~~~~~~~~~v~i~g~---~~~v~~a~~~i~~~~ 68 (69)
T smart00322 19 GKGGSTIKKIEEETGVKIDIPEDGSEERVVEITGP---PENVEKAAELILEIL 68 (69)
T ss_pred CCCchHHHHHHHHHCCEEEECCCCCCccEEEEEcC---HHHHHHHHHHHHHHh
Confidence 788988874 3355555544421 22333222 578888887777654
No 23
>cd00105 KH-I K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension.
Probab=35.55 E-value=33 Score=20.93 Aligned_cols=40 Identities=20% Similarity=0.246 Sum_probs=24.4
Q ss_pred cCCCccCCCccC--ceEEEEEcCC------e-eEEEeccccCHHHHHHHHHHHH
Q 043141 40 SGPGGQHINKRE--SAVRIKHVPT------G-VIAQAAEDRSQHKNRVSALSRL 84 (135)
Q Consensus 40 SGPGGQ~VNK~~--t~V~l~h~pt------G-i~v~~~e~RSq~~Nk~~A~~rL 84 (135)
=||||.+++... +.|.|...+. . +.+... ..|.+.|...|
T Consensus 15 IG~~G~~i~~I~~~s~~~I~i~~~~~~~~~~~v~i~G~-----~~~v~~a~~~i 63 (64)
T cd00105 15 IGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGT-----PEAVEKAKELI 63 (64)
T ss_pred ECCCCHHHHHHHHHHCCEEEEcCCCCCCCceEEEEEcC-----HHHHHHHHHHh
Confidence 378999999544 5577776552 2 344333 45666666544
No 24
>cd00552 RaiA RaiA ("ribosome-associated inhibitor A", also known as Protein Y (PY), YfiA, and SpotY, is a stress-response protein that binds the ribosomal subunit interface and arrests translation by interfering with aminoacyl-tRNA binding to the ribosomal A site. RaiA is also thought to counteract miscoding at the A site thus reducing translation errors. The RaiA fold structurally resembles the double-stranded RNA-binding domain (dsRBD).
Probab=33.70 E-value=1.4e+02 Score=19.73 Aligned_cols=53 Identities=21% Similarity=0.233 Sum_probs=28.2
Q ss_pred ceEEEEeccCCCccCCCccCceEEEE-EcCCeeEEEeccccCHHHHHHHHHHHHHHHHHH
Q 043141 32 CEMDTYKSSGPGGQHINKRESAVRIK-HVPTGVIAQAAEDRSQHKNRVSALSRLRTLLAL 90 (135)
Q Consensus 32 ~~~~~~RsSGPGGQ~VNK~~t~V~l~-h~ptGi~v~~~e~RSq~~Nk~~A~~rL~~~l~~ 90 (135)
+++.+..-.+||++ -.|+++ ++|.+.++...+.-..+.=-..|+++|...|..
T Consensus 36 ~~V~l~~~~~~~~~------~~v~i~v~~~g~~~~a~~~~~d~~~Aid~a~~kl~rqL~k 89 (93)
T cd00552 36 VDVVLSVEKNHGKR------FKVEITIHLPGGVLRAEASAEDLYAAIDLAVDKLERQLRK 89 (93)
T ss_pred EEEEEEEecCCCCc------eEEEEEEEeCCCEEEEEEccCCHHHHHHHHHHHHHHHHHH
Confidence 46666665555222 355555 567333333344456666666666666655544
No 25
>cd02395 SF1_like-KH Splicing factor 1 (SF1) K homology RNA-binding domain (KH). Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 defines an enlarged KH (hnRNP K) fold which is necessary and sufficient for BPS binding. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=29.81 E-value=66 Score=23.71 Aligned_cols=25 Identities=20% Similarity=0.276 Sum_probs=12.6
Q ss_pred eEEEeccccCHHHHHHHHHHHHHHHHH
Q 043141 63 VIAQAAEDRSQHKNRVSALSRLRTLLA 89 (135)
Q Consensus 63 i~v~~~e~RSq~~Nk~~A~~rL~~~l~ 89 (135)
+.|.+... .....+.|.+.+..+|.
T Consensus 70 V~I~a~~~--~~e~~~~A~~~I~~ll~ 94 (120)
T cd02395 70 VLITAETP--PEEALAKAVEAIEELLK 94 (120)
T ss_pred EEEEeCCc--HHHHHHHHHHHHHHHhc
Confidence 56666552 23444555555554444
No 26
>PF14048 MBD_C: C-terminal domain of methyl-CpG binding protein 2 and 3; PDB: 2L2L_B.
Probab=28.90 E-value=29 Score=24.90 Aligned_cols=27 Identities=22% Similarity=0.240 Sum_probs=19.9
Q ss_pred eeEEEeccccCHHHHHHHHHHHHHHHH
Q 043141 62 GVIAQAAEDRSQHKNRVSALSRLRTLL 88 (135)
Q Consensus 62 Gi~v~~~e~RSq~~Nk~~A~~rL~~~l 88 (135)
.++|+..+=|.|..--..|.+||++.|
T Consensus 70 ~~~VT~eDIr~QE~rVk~aR~RLaeAL 96 (96)
T PF14048_consen 70 QFVVTEEDIRRQERRVKKARKRLAEAL 96 (96)
T ss_dssp -----HHHHHHHHHHHHHHHHHHHHHH
T ss_pred CCccCHHHHHHHHHHHHHHHHHHHHHC
Confidence 467888889999999999999998864
No 27
>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH). PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=27.80 E-value=55 Score=20.88 Aligned_cols=29 Identities=41% Similarity=0.672 Sum_probs=20.1
Q ss_pred cCCCccCCCc--cCceEEEEEcCCe-eEEEec
Q 043141 40 SGPGGQHINK--RESAVRIKHVPTG-VIAQAA 68 (135)
Q Consensus 40 SGPGGQ~VNK--~~t~V~l~h~ptG-i~v~~~ 68 (135)
=|+||.+++. ..|.|.|.--..| +.|...
T Consensus 17 IGkgG~~ik~I~~~tg~~I~i~~~g~v~I~G~ 48 (61)
T cd02393 17 IGPGGKTIKKIIEETGVKIDIEDDGTVYIAAS 48 (61)
T ss_pred ECCCchHHHHHHHHHCCEEEeCCCCEEEEEeC
Confidence 4889999994 5577776654456 666664
No 28
>COG3514 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=27.72 E-value=9 Score=27.77 Aligned_cols=13 Identities=23% Similarity=0.664 Sum_probs=11.1
Q ss_pred EEEEeccCCCccC
Q 043141 34 MDTYKSSGPGGQH 46 (135)
Q Consensus 34 ~~~~RsSGPGGQ~ 46 (135)
++++|.+|||.|-
T Consensus 67 le~fra~GkGwQt 79 (93)
T COG3514 67 LEKFRAGGKGWQT 79 (93)
T ss_pred HHHHHcCCccHHH
Confidence 4679999999995
No 29
>KOG3259 consensus Peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]
Probab=25.40 E-value=1.2e+02 Score=24.04 Aligned_cols=49 Identities=27% Similarity=0.266 Sum_probs=30.1
Q ss_pred EEeccCCCccCCCccCceEEEEEcCCeeEEEeccccC--------HHHHHHHHHHHHHHHHHHh
Q 043141 36 TYKSSGPGGQHINKRESAVRIKHVPTGVIAQAAEDRS--------QHKNRVSALSRLRTLLALN 91 (135)
Q Consensus 36 ~~RsSGPGGQ~VNK~~t~V~l~h~ptGi~v~~~e~RS--------q~~Nk~~A~~rL~~~l~~~ 91 (135)
+..++|++||.-+ -.|+..|| .|+-+.+|- ...-|++|++.|+......
T Consensus 40 t~~~~~~~~~~~p---~~Vr~sHl----LVKH~~SRrpsSwr~~~it~skeeA~~llk~~~~~l 96 (163)
T KOG3259|consen 40 TSKSGGKIGQGEP---ARVRCSHL----LVKHKGSRRPSSWRSENITRSKEEALDLLKGYHEDL 96 (163)
T ss_pred cccccccccCCCc---cceeEEEE----EEccccCCCCcccccccchhhHHHHHHHHHHhHHHh
Confidence 4556667777655 57887785 344433333 3456889988887654433
No 30
>PF04149 DUF397: Domain of unknown function (DUF397); InterPro: IPR007278 The function of this family is unknown. It has been suggested that some members of this family are regulators of transcription.
Probab=25.05 E-value=1.4e+02 Score=19.14 Aligned_cols=19 Identities=26% Similarity=0.602 Sum_probs=13.1
Q ss_pred ceEEEEEcCCeeEEEeccc
Q 043141 52 SAVRIKHVPTGVIAQAAED 70 (135)
Q Consensus 52 t~V~l~h~ptGi~v~~~e~ 70 (135)
++|++...|.++.|..+..
T Consensus 16 ~CVEva~~~~~v~vRDSk~ 34 (56)
T PF04149_consen 16 NCVEVARLPGGVAVRDSKD 34 (56)
T ss_pred CcEEEEeecceEEEecCCC
Confidence 4888888877766655543
No 31
>smart00472 MIR Domain in ryanodine and inositol trisphosphate receptors and protein O-mannosyltransferases.
Probab=23.84 E-value=87 Score=18.97 Aligned_cols=21 Identities=33% Similarity=0.605 Sum_probs=16.5
Q ss_pred CceEEEEEcCCeeEEEecccc
Q 043141 51 ESAVRIKHVPTGVIAQAAEDR 71 (135)
Q Consensus 51 ~t~V~l~h~ptGi~v~~~e~R 71 (135)
.+.|||+|+-||--+.+++.+
T Consensus 7 g~~vrL~H~~tg~yL~s~~~~ 27 (57)
T smart00472 7 GDVVRLRHVTTGRYLHSHENK 27 (57)
T ss_pred CCEEEEEEhhhCcEeecCCCC
Confidence 479999999999666666655
No 32
>PF13014 KH_3: KH domain
Probab=22.87 E-value=25 Score=20.65 Aligned_cols=20 Identities=35% Similarity=0.742 Sum_probs=14.4
Q ss_pred CCCccCCC--ccCceEEEEEcC
Q 043141 41 GPGGQHIN--KRESAVRIKHVP 60 (135)
Q Consensus 41 GPGGQ~VN--K~~t~V~l~h~p 60 (135)
|+||+++| ..+|.|+|...+
T Consensus 7 G~~G~~I~~I~~~tg~~I~i~~ 28 (43)
T PF13014_consen 7 GKGGSTIKEIREETGAKIQIPP 28 (43)
T ss_pred CCCChHHHHHHHHhCcEEEECC
Confidence 78888888 456777777654
Done!