Query gi|254780786|ref|YP_003065199.1| ribosome-binding factor A [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 128
No_of_seqs 102 out of 1288
Neff 6.6
Searched_HMMs 39220
Date Sun May 29 20:32:13 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254780786.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK13816 ribosome-binding fact 100.0 1.9E-33 4.7E-38 209.2 15.2 111 8-121 1-119 (131)
2 PRK13817 ribosome-binding fact 100.0 1.5E-33 3.9E-38 209.7 14.0 115 8-126 1-115 (119)
3 PRK13815 ribosome-binding fact 100.0 1E-32 2.5E-37 205.1 13.0 115 9-127 2-117 (122)
4 PRK13818 ribosome-binding fact 100.0 3.8E-32 9.7E-37 201.8 13.6 111 9-123 2-114 (121)
5 PRK00521 rbfA ribosome-binding 100.0 4.5E-32 1.2E-36 201.4 13.2 111 5-119 1-113 (114)
6 COG0858 RbfA Ribosome-binding 100.0 1.5E-30 3.8E-35 192.8 13.0 112 9-124 4-117 (118)
7 pfam02033 RBFA Ribosome-bindin 100.0 3.3E-29 8.4E-34 185.2 13.0 103 11-117 1-104 (104)
8 TIGR00082 rbfA ribosome-bindin 100.0 2.4E-28 6.1E-33 180.4 12.0 114 6-121 2-119 (121)
9 KOG4700 consensus 99.4 2.5E-12 6.5E-17 89.9 11.2 115 6-122 26-140 (207)
10 TIGR01011 rpsB_bact ribosomal 87.5 0.66 1.7E-05 25.5 3.4 39 72-111 134-172 (227)
11 COG0052 RpsB Ribosomal protein 72.4 5.2 0.00013 20.4 3.6 37 74-111 135-171 (252)
12 cd04927 ACT_ACR-like_2 Second 65.9 11 0.00029 18.5 5.6 22 41-62 25-48 (76)
13 PRK12311 rpsB 30S ribosomal pr 64.3 11 0.00028 18.6 3.9 35 75-110 139-173 (332)
14 pfam11454 DUF3016 Protein of u 43.9 27 0.00069 16.4 5.3 47 6-55 22-68 (141)
15 PRK05299 rpsB 30S ribosomal pr 41.6 30 0.00075 16.2 3.8 34 76-110 138-171 (255)
16 COG1438 ArgR Arginine represso 34.6 20 0.00052 17.1 1.3 99 6-123 2-117 (150)
17 cd04894 ACT_ACR-like_1 ACT dom 34.6 38 0.00098 15.5 3.3 26 42-67 26-51 (69)
18 TIGR02065 ECX1 exosome complex 32.3 23 0.0006 16.7 1.4 30 4-33 83-112 (231)
19 PRK00441 argR arginine repress 32.0 43 0.0011 15.3 3.2 95 8-121 2-113 (149)
20 pfam05872 DUF853 Bacterial pro 26.8 53 0.0013 14.7 2.4 27 96-122 256-293 (504)
21 pfam08371 PLD_envelope Phospho 25.7 36 0.00092 15.7 1.4 71 46-124 51-129 (163)
22 pfam03027 consensus 22.7 63 0.0016 14.3 7.0 52 39-90 47-101 (126)
23 PRK09437 bcp thioredoxin-depen 21.2 68 0.0017 14.1 3.9 34 46-79 123-156 (156)
No 1
>PRK13816 ribosome-binding factor A; Provisional
Probab=100.00 E-value=1.9e-33 Score=209.23 Aligned_cols=111 Identities=26% Similarity=0.363 Sum_probs=100.7
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEEEEEEEECCCCCEEEEEEEECCCC--------CHHHHHHHHHHHH
Q ss_conf 77389999999999999999514134201265168988889858756559999827986--------4778999999856
Q gi|254780786|r 8 NSRRALRVGEEVRSALMWVILNNEFQDRLISRDVISISEVCMSVDLRVATVYISLPLDV--------SPDRVISALNCNI 79 (128)
Q Consensus 8 ~s~R~~rv~~~i~~~is~il~~~~~~d~~~~~~~vtIt~V~vS~Dl~~AkVyvs~~~~~--------~~~~~~~~L~~~~ 79 (128)
.|+|+.||+++||++||++|.+ +++||++.+ +||||+|+|||||++|+||||++|.. ..++++++||+++
T Consensus 1 gs~R~~Rv~~~I~~els~ii~~-evkDprl~~-~VTIT~V~vS~DL~~AkVyvSvlg~~~~~~~~~~~~~~~l~~L~~a~ 78 (131)
T PRK13816 1 GGQRLKRMADSVQRELSELIRQ-ELKDPRLGG-LVTISGVKVSPDLGYADVYVTVMGRELSDDQNEVAHRETLDVLNKAS 78 (131)
T ss_pred CCHHHHHHHHHHHHHHHHHHHH-HCCCCCCCC-CEEEEEEEECCCCCEEEEEEEECCCCCCCCHHHHHHHHHHHHHHHHH
T ss_conf 9727799999999999999997-565976478-46897999779977479999976674552023666999999999989
Q ss_pred HHHHHHHHHHHHHCCCCCEEEEEECCCHHHHHHHHHHHCCHH
Q ss_conf 899999999875214578589997386888999999855767
Q gi|254780786|r 80 KFIRGRIGRSLRNLRYVPELRFRYDTSLQSYWKLNALMCLPK 121 (128)
Q Consensus 80 ~~ir~~l~~~l~~lr~~P~L~F~~D~s~e~~~~I~~LL~~~~ 121 (128)
||||+.||++| +||+||+|+|++|+|++++.+|++||+...
T Consensus 79 gfiR~~Lak~l-~lR~~P~L~F~~D~s~e~~~~i~~Li~~~~ 119 (131)
T PRK13816 79 GFLRQELSRRI-KTRITPRLRFHYDKTNAYGNYMFGLIEKAV 119 (131)
T ss_pred HHHHHHHHHHC-CCCCCCEEEEEECCCHHHHHHHHHHHHHHH
T ss_conf 99999999666-682498789995797889999999999999
No 2
>PRK13817 ribosome-binding factor A; Provisional
Probab=100.00 E-value=1.5e-33 Score=209.72 Aligned_cols=115 Identities=30% Similarity=0.417 Sum_probs=105.3
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEEEEEEEECCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 77389999999999999999514134201265168988889858756559999827986477899999985689999999
Q gi|254780786|r 8 NSRRALRVGEEVRSALMWVILNNEFQDRLISRDVISISEVCMSVDLRVATVYISLPLDVSPDRVISALNCNIKFIRGRIG 87 (128)
Q Consensus 8 ~s~R~~rv~~~i~~~is~il~~~~~~d~~~~~~~vtIt~V~vS~Dl~~AkVyvs~~~~~~~~~~~~~L~~~~~~ir~~l~ 87 (128)
-|+|+.||+++|+++||++|. ++++||++.+ ||||+|+|||||++|+||||++++.+.++++++||+++|+||+.||
T Consensus 1 mS~R~~Rv~~~i~~eis~il~-~ei~dp~l~~--vtIt~V~vS~DL~~AkVy~s~l~~~~~~~~~~~L~~~~g~iR~~l~ 77 (119)
T PRK13817 1 MSQRQQRVADLIHQQLAELLK-KEVRDSRLSK--ISLTAVSISPDLKQAKVFYSLLENQNEKEVQKALNKATGYLRHLLA 77 (119)
T ss_pred CCHHHHHHHHHHHHHHHHHHH-HHCCCCCCCC--EEEEEEEECCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHH
T ss_conf 982779999999999999999-7577877786--3886999889987689999978996889999999996999999998
Q ss_pred HHHHHCCCCCEEEEEECCCHHHHHHHHHHHCCHHHHHHH
Q ss_conf 987521457858999738688899999985576777764
Q gi|254780786|r 88 RSLRNLRYVPELRFRYDTSLQSYWKLNALMCLPKIPVAL 126 (128)
Q Consensus 88 ~~l~~lr~~P~L~F~~D~s~e~~~~I~~LL~~~~v~~d~ 126 (128)
+++ +|||+|+|+|++|++++++.+|++||+......+-
T Consensus 78 k~l-~lR~~P~L~F~~D~s~e~~~~I~~LL~~~~~~d~~ 115 (119)
T PRK13817 78 QAT-VLRYVPKLEFVYDESIERAHRISLLIERALKKDDS 115 (119)
T ss_pred HHC-CCEECCEEEEEECCCHHHHHHHHHHHHHHHHCCCC
T ss_conf 456-88579878999579778999999999999862113
No 3
>PRK13815 ribosome-binding factor A; Provisional
Probab=100.00 E-value=1e-32 Score=205.11 Aligned_cols=115 Identities=27% Similarity=0.441 Sum_probs=105.7
Q ss_pred CHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEEEEEEEECCCCCEEEEEEEECCCCCH-HHHHHHHHHHHHHHHHHHH
Q ss_conf 738999999999999999951413420126516898888985875655999982798647-7899999985689999999
Q gi|254780786|r 9 SRRALRVGEEVRSALMWVILNNEFQDRLISRDVISISEVCMSVDLRVATVYISLPLDVSP-DRVISALNCNIKFIRGRIG 87 (128)
Q Consensus 9 s~R~~rv~~~i~~~is~il~~~~~~d~~~~~~~vtIt~V~vS~Dl~~AkVyvs~~~~~~~-~~~~~~L~~~~~~ir~~l~ 87 (128)
++|+.||+++||++||++|++ ++.||+++ +||||+|+|||||++|+||||++|+... +.++++||+++|+||++||
T Consensus 2 ~~R~~Rv~~~I~~eis~il~~-~i~dp~~~--~vtIt~V~vS~DL~~AkVy~s~~~~~~~~~~~~~~L~~~~g~ir~~l~ 78 (122)
T PRK13815 2 FKRSEKVAEAIHELISGLLVK-GLKDPRIG--FVTITGVKVTDDLHLATIYFTVIGDDAAKKSTEAGLNSAKGFIRRELG 78 (122)
T ss_pred CCHHHHHHHHHHHHHHHHHHH-HCCCCCCC--CEEEEEEEECCCHHHEEEEEEECCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 857699999999999999997-37897668--258859998977033599999768704499999999984899999998
Q ss_pred HHHHHCCCCCEEEEEECCCHHHHHHHHHHHCCHHHHHHHC
Q ss_conf 9875214578589997386888999999855767777640
Q gi|254780786|r 88 RSLRNLRYVPELRFRYDTSLQSYWKLNALMCLPKIPVALE 127 (128)
Q Consensus 88 ~~l~~lr~~P~L~F~~D~s~e~~~~I~~LL~~~~v~~d~e 127 (128)
++|+ ||++|+|+|++|++++++.+|++||++.+.+++.+
T Consensus 79 k~l~-lR~~P~L~F~~D~s~e~~~~I~~lL~~i~~~~~~~ 117 (122)
T PRK13815 79 KVLR-MRYAPELIFKYDESQEYGNRIDSLLKEIGTEEDSD 117 (122)
T ss_pred HHCE-EEECCEEEEEECCCHHHHHHHHHHHHHHHHCCCCC
T ss_conf 5180-37798689996797778999999999877512135
No 4
>PRK13818 ribosome-binding factor A; Provisional
Probab=100.00 E-value=3.8e-32 Score=201.83 Aligned_cols=111 Identities=29% Similarity=0.337 Sum_probs=101.0
Q ss_pred CHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEEEEEEEECCCCCEEEEEEEECCCC--CHHHHHHHHHHHHHHHHHHH
Q ss_conf 7389999999999999999514134201265168988889858756559999827986--47789999998568999999
Q gi|254780786|r 9 SRRALRVGEEVRSALMWVILNNEFQDRLISRDVISISEVCMSVDLRVATVYISLPLDV--SPDRVISALNCNIKFIRGRI 86 (128)
Q Consensus 9 s~R~~rv~~~i~~~is~il~~~~~~d~~~~~~~vtIt~V~vS~Dl~~AkVyvs~~~~~--~~~~~~~~L~~~~~~ir~~l 86 (128)
|+|..||+++|+++||++|.+ +++||++++ ||||+|+||+||++|+||||++++. ..++++++|++++|+||+.|
T Consensus 2 ~~R~~Rv~~~I~reis~il~~-~i~Dprl~~--vtIt~V~vS~DL~~AkVy~sv~~~~~~~~~~~~~~L~~a~g~iR~~L 78 (121)
T PRK13818 2 KHRIGRVEGEILRELTKILRK-NIRDPRLSN--VTITAVECTNDLSYATVYYSLLTEDEQKEKEVEEGLEKAKGMMRHLL 78 (121)
T ss_pred CCHHHHHHHHHHHHHHHHHHH-HCCCCCCCC--EEEEEEEECCCCCEEEEEEEECCCCHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 827799999999999999997-587865585--37879997499775799999759967679999999999599999999
Q ss_pred HHHHHHCCCCCEEEEEECCCHHHHHHHHHHHCCHHHH
Q ss_conf 9987521457858999738688899999985576777
Q gi|254780786|r 87 GRSLRNLRYVPELRFRYDTSLQSYWKLNALMCLPKIP 123 (128)
Q Consensus 87 ~~~l~~lr~~P~L~F~~D~s~e~~~~I~~LL~~~~v~ 123 (128)
|+++ +||++|+|+|++|+|++++.+|++||++.+-+
T Consensus 79 a~~l-~lR~~P~L~F~~D~s~e~~~~I~~Ll~~l~~~ 114 (121)
T PRK13818 79 GQTL-TVYKVPELIFKRDQSVIYGSKIDRLIADVKKQ 114 (121)
T ss_pred HHHC-CCEECCEEEEEECCCHHHHHHHHHHHHHHHHH
T ss_conf 8357-89589858999689778899999999999998
No 5
>PRK00521 rbfA ribosome-binding factor A; Validated
Probab=100.00 E-value=4.5e-32 Score=201.39 Aligned_cols=111 Identities=35% Similarity=0.559 Sum_probs=101.7
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEEEEEEEECCCCCEEEEEEEECCCC--CHHHHHHHHHHHHHHH
Q ss_conf 87777389999999999999999514134201265168988889858756559999827986--4778999999856899
Q gi|254780786|r 5 NPKNSRRALRVGEEVRSALMWVILNNEFQDRLISRDVISISEVCMSVDLRVATVYISLPLDV--SPDRVISALNCNIKFI 82 (128)
Q Consensus 5 ~~~~s~R~~rv~~~i~~~is~il~~~~~~d~~~~~~~vtIt~V~vS~Dl~~AkVyvs~~~~~--~~~~~~~~L~~~~~~i 82 (128)
|.++|+|+.||+++||++||++|.+ +++||+++ +||||+|++|+||++|+||||++|+. +.++++++||+++|+|
T Consensus 1 mm~~s~R~~Rv~~~i~~~is~il~~-~~~d~~~~--~vtIt~V~vS~DL~~AkVy~s~~~~~~~~~~~~~~~L~~~~~~i 77 (114)
T PRK00521 1 MMKESQRALRVAEQIRRELAEILQR-EIKDPRLG--MVTVTDVEVSPDLAHAKVYVTVLGDDEEDVEEALAALKKAAGFL 77 (114)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHH-HCCCCCCC--EEEEEEEEECCCHHHHEEEEEECCCCHHHHHHHHHHHHHHHHHH
T ss_conf 9862467899999999999999998-67586668--06886999885735515667866897544999999999979999
Q ss_pred HHHHHHHHHHCCCCCEEEEEECCCHHHHHHHHHHHCC
Q ss_conf 9999998752145785899973868889999998557
Q gi|254780786|r 83 RGRIGRSLRNLRYVPELRFRYDTSLQSYWKLNALMCL 119 (128)
Q Consensus 83 r~~l~~~l~~lr~~P~L~F~~D~s~e~~~~I~~LL~~ 119 (128)
|+.||+++ .+||+|+|+|++|++++++.+|++||++
T Consensus 78 r~~l~~~l-~lr~~P~L~F~~D~s~e~~~~I~~lL~e 113 (114)
T PRK00521 78 RSELGKRL-RLRKVPELRFVYDESLEYGMRIDELLRQ 113 (114)
T ss_pred HHHHHHHC-CCCCCCEEEEEECCCHHHHHHHHHHHHH
T ss_conf 99998654-6662772799816977899999999960
No 6
>COG0858 RbfA Ribosome-binding factor A [Translation, ribosomal structure and biogenesis]
Probab=99.97 E-value=1.5e-30 Score=192.80 Aligned_cols=112 Identities=35% Similarity=0.508 Sum_probs=102.3
Q ss_pred CHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEEEEEEEECCCCCEEEEEEEECC-CC-CHHHHHHHHHHHHHHHHHHH
Q ss_conf 73899999999999999995141342012651689888898587565599998279-86-47789999998568999999
Q gi|254780786|r 9 SRRALRVGEEVRSALMWVILNNEFQDRLISRDVISISEVCMSVDLRVATVYISLPL-DV-SPDRVISALNCNIKFIRGRI 86 (128)
Q Consensus 9 s~R~~rv~~~i~~~is~il~~~~~~d~~~~~~~vtIt~V~vS~Dl~~AkVyvs~~~-~~-~~~~~~~~L~~~~~~ir~~l 86 (128)
+.|+.|++++|+++|++++++ +++||++++ ++||+|+||+||++|+||||++| .. ..++++++|++++|+||+++
T Consensus 4 ~~R~~rv~e~i~~~l~~il~~-eikDprl~~--~~Vt~V~vS~Dl~~A~Vyvt~l~~~~~~~~~~~~~L~~A~g~ir~~l 80 (118)
T COG0858 4 STRAKRVAEQIQKELAEILQR-EIKDPRLGL--VTVTDVEVSKDLSHAKVYVTVLGDEESSKAEILAALNKAKGFIRSEL 80 (118)
T ss_pred CHHHHHHHHHHHHHHHHHHHH-HCCCCCCCC--EEEEEEEECCCCCEEEEEEEECCCCHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 278899999999999999998-754977686--68889998799755899996267742228999999999699999999
Q ss_pred HHHHHHCCCCCEEEEEECCCHHHHHHHHHHHCCHHHHH
Q ss_conf 99875214578589997386888999999855767777
Q gi|254780786|r 87 GRSLRNLRYVPELRFRYDTSLQSYWKLNALMCLPKIPV 124 (128)
Q Consensus 87 ~~~l~~lr~~P~L~F~~D~s~e~~~~I~~LL~~~~v~~ 124 (128)
|++++ ||++|+|+|++|++++++.+|++||++++...
T Consensus 81 ~~~~~-lr~~PeL~F~~D~s~~~~~ki~~Ll~~l~~~~ 117 (118)
T COG0858 81 GKRLR-LRKTPELHFVYDDSIENGNKIDALLNDLKKAD 117 (118)
T ss_pred HHHCC-EEECCEEEEEECCCCCHHHHHHHHHHHHHHCC
T ss_conf 98577-57687689996764204788999998755248
No 7
>pfam02033 RBFA Ribosome-binding factor A.
Probab=99.96 E-value=3.3e-29 Score=185.24 Aligned_cols=103 Identities=36% Similarity=0.578 Sum_probs=95.7
Q ss_pred HHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEEEEEEEECCCCCEEEEEEEECCC-CCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 8999999999999999951413420126516898888985875655999982798-647789999998568999999998
Q gi|254780786|r 11 RALRVGEEVRSALMWVILNNEFQDRLISRDVISISEVCMSVDLRVATVYISLPLD-VSPDRVISALNCNIKFIRGRIGRS 89 (128)
Q Consensus 11 R~~rv~~~i~~~is~il~~~~~~d~~~~~~~vtIt~V~vS~Dl~~AkVyvs~~~~-~~~~~~~~~L~~~~~~ir~~l~~~ 89 (128)
|+.||+++|+++||++|.+ ++.||++. +||||+|++|+||++|+||||++|+ .+.++++++||+++|+||+.||++
T Consensus 1 R~~rv~~~I~~~is~il~~-~i~d~~~~--~vtIt~V~~S~Dl~~AkVy~s~~~~~~~~~~~~~~L~~~~~~ir~~l~~~ 77 (104)
T pfam02033 1 RTERVAELIQRELAEILQR-ELKDPRLG--LVTVTEVEVSPDLSHAKVYVSVLGDEEEKEETLKALNKAAGFIRSELAKR 77 (104)
T ss_pred CCHHHHHHHHHHHHHHHHH-HCCCCCCC--EEEEEEEEECCCCCEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 9389999999999999997-57586778--37998999657800189999965762049999999999899999998756
Q ss_pred HHHCCCCCEEEEEECCCHHHHHHHHHHH
Q ss_conf 7521457858999738688899999985
Q gi|254780786|r 90 LRNLRYVPELRFRYDTSLQSYWKLNALM 117 (128)
Q Consensus 90 l~~lr~~P~L~F~~D~s~e~~~~I~~LL 117 (128)
+. +||+|+|+|++|++++++.+|++||
T Consensus 78 l~-lr~~P~L~F~~D~s~e~~~~I~~lL 104 (104)
T pfam02033 78 LR-LRYTPELRFVYDDSIEYGARIEELL 104 (104)
T ss_pred CC-CCCCCEEEEEECCCHHHHHHHHHHC
T ss_conf 47-6607727998269777899999739
No 8
>TIGR00082 rbfA ribosome-binding factor A; InterPro: IPR000238 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 of 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 , . Ribosome-binding factor A (gene rbfA) is a bacterial protein that associates with free 30S ribosomal subunits. It does not associate with 30S subunits that are part of 70S ribosomes or polysomes. It is essential for efficient processing of 16S rRNA. Ribosome-binding factor A is a protein of from 13 to 15 Kd which is found in most prokaryotic organisms. A putative chloroplastic form seems to exist in plants.; GO: 0006364 rRNA processing.
Probab=99.96 E-value=2.4e-28 Score=180.37 Aligned_cols=114 Identities=29% Similarity=0.454 Sum_probs=103.6
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCC-EEEEEEEEECCCCCEEEEEEEECCC--CC-HHHHHHHHHHHHHH
Q ss_conf 77773899999999999999995141342012651-6898888985875655999982798--64-77899999985689
Q gi|254780786|r 6 PKNSRRALRVGEEVRSALMWVILNNEFQDRLISRD-VISISEVCMSVDLRVATVYISLPLD--VS-PDRVISALNCNIKF 81 (128)
Q Consensus 6 ~~~s~R~~rv~~~i~~~is~il~~~~~~d~~~~~~-~vtIt~V~vS~Dl~~AkVyvs~~~~--~~-~~~~~~~L~~~~~~ 81 (128)
...+.|..||++.|+++|+.+|++ +++||++..+ ++|||+|++|.||.+|+||++++++ .. .+.++++|++|+|+
T Consensus 2 A~~~~r~~Rv~~~i~~ei~~~l~~-e~~d~~~~~~~~~~Vt~Ve~S~DL~~A~Vfv~~~~d~D~~~~~~~~~~L~~A~Gf 80 (121)
T TIGR00082 2 ASEFRRKERVESEIKREIGRILIR-EIKDPRVIHGMMLTVTKVEVSKDLQHAKVFVSVLGDKDEEAIEKAVKALKKAKGF 80 (121)
T ss_pred CCCCCCHHHHHHHHHHHHHHHHHH-CCCCCCCCCCEEEEEEEEEECCCEEEEEEEEEEECCCCHHHHHHHHHHHHHCCCH
T ss_conf 644410445899999999999871-2667631056047766788738805788888741377767899999989827845
Q ss_pred HHHHHHHHHHHCCCCCEEEEEECCCHHHHHHHHHHHCCHH
Q ss_conf 9999999875214578589997386888999999855767
Q gi|254780786|r 82 IRGRIGRSLRNLRYVPELRFRYDTSLQSYWKLNALMCLPK 121 (128)
Q Consensus 82 ir~~l~~~l~~lr~~P~L~F~~D~s~e~~~~I~~LL~~~~ 121 (128)
||..|+++++ ||.||+|.|..|+|++++.+|++|++++.
T Consensus 81 ir~~l~~~~~-lr~~P~l~Fv~D~Sl~~~~ri~~li~~l~ 119 (121)
T TIGR00082 81 IRSLLGQRMR-LRKTPELSFVKDDSLDKGLRIENLINSLK 119 (121)
T ss_pred HHHHHHHHHC-CCCCCEEEEEECHHHHHHHHHHHHHHHHC
T ss_conf 8899987610-01166577754356777788999986420
No 9
>KOG4700 consensus
Probab=99.42 E-value=2.5e-12 Score=89.92 Aligned_cols=115 Identities=18% Similarity=0.272 Sum_probs=99.6
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEEEEEEEECCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 77773899999999999999995141342012651689888898587565599998279864778999999856899999
Q gi|254780786|r 6 PKNSRRALRVGEEVRSALMWVILNNEFQDRLISRDVISISEVCMSVDLRVATVYISLPLDVSPDRVISALNCNIKFIRGR 85 (128)
Q Consensus 6 ~~~s~R~~rv~~~i~~~is~il~~~~~~d~~~~~~~vtIt~V~vS~Dl~~AkVyvs~~~~~~~~~~~~~L~~~~~~ir~~ 85 (128)
+-...|.-.++.++-+.|++++..+++.+ .+.+..|-|+.|++++|++-+.|||..-++.+-.++.+.|++.++.||+.
T Consensus 26 ~~d~~r~~~Ln~Ll~~~itdvlaTgava~-~l~~l~vqiS~V~vt~dFS~~~vYWm~~~~geN~e~e~~L~rs~~~~rh~ 104 (207)
T KOG4700 26 RLDDKKVVQLNRLLEERITDVLATGAVAE-MLGRLQVQISRVRVTRDFSQVSVYWMCRGDGENSEIEDFLERSKHQIRHR 104 (207)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHCHHHHH-HHHHCCEEEEEEEECCCHHHHEEEEEECCCCCHHHHHHHHHHHHHHHHHH
T ss_conf 23307899999999999999971667899-98641506899985345014235777358853789999999979999999
Q ss_pred HHHHHHHCCCCCEEEEEECCCHHHHHHHHHHHCCHHH
Q ss_conf 9998752145785899973868889999998557677
Q gi|254780786|r 86 IGRSLRNLRYVPELRFRYDTSLQSYWKLNALMCLPKI 122 (128)
Q Consensus 86 l~~~l~~lr~~P~L~F~~D~s~e~~~~I~~LL~~~~v 122 (128)
|.... .|+.+|+|+|+-|.+.---..+++||+..+.
T Consensus 105 l~~~~-~~g~vP~IkFV~DK~~~~l~e~d~ll~~aD~ 140 (207)
T KOG4700 105 LEESI-GIGTVPEIKFVGDKALLMLQEMDKLLREADY 140 (207)
T ss_pred HHHHH-CCCCCCCEEEECCHHHHHHHHHHHHHHHHCC
T ss_conf 99872-1256896478523377789999999998413
No 10
>TIGR01011 rpsB_bact ribosomal protein S2; InterPro: IPR005706 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 of ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome , . This family describes the bacterial, mitochondrial and chloroplast forms of ribosomal protein S2.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015935 small ribosomal subunit.
Probab=87.54 E-value=0.66 Score=25.49 Aligned_cols=39 Identities=18% Similarity=0.349 Sum_probs=33.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEECCCHHHHH
Q ss_conf 9999985689999999987521457858999738688899
Q gi|254780786|r 72 ISALNCNIKFIRGRIGRSLRNLRYVPELRFRYDTSLQSYW 111 (128)
Q Consensus 72 ~~~L~~~~~~ir~~l~~~l~~lr~~P~L~F~~D~s~e~~~ 111 (128)
.-.|.+-...|.+.||. +++|+..|.+-|+.|...|+-+
T Consensus 134 ~~~L~Re~~KL~k~LgG-Ik~M~~lPd~l~viD~~~E~IA 172 (227)
T TIGR01011 134 ILMLSREKEKLEKNLGG-IKDMKKLPDLLFVIDPRKEKIA 172 (227)
T ss_pred HHHHHHHHHHHHHHHHH-HHHHHCCCCEEEEECCCCCHHH
T ss_conf 77678999998655300-2545316970899748210689
No 11
>COG0052 RpsB Ribosomal protein S2 [Translation, ribosomal structure and biogenesis]
Probab=72.36 E-value=5.2 Score=20.42 Aligned_cols=37 Identities=14% Similarity=0.350 Sum_probs=30.2
Q ss_pred HHHHHHHHHHHHHHHHHHHCCCCCEEEEEECCCHHHHH
Q ss_conf 99985689999999987521457858999738688899
Q gi|254780786|r 74 ALNCNIKFIRGRIGRSLRNLRYVPELRFRYDTSLQSYW 111 (128)
Q Consensus 74 ~L~~~~~~ir~~l~~~l~~lr~~P~L~F~~D~s~e~~~ 111 (128)
.|++-...+.+.||. +++|+..|++-|..|...|...
T Consensus 135 ~l~re~~kL~k~lgG-Ik~m~~~Pd~l~ViDp~~e~iA 171 (252)
T COG0052 135 MLTRELEKLEKSLGG-IKDMKGLPDVLFVIDPRKEKIA 171 (252)
T ss_pred HHHHHHHHHHHHHCC-HHHCCCCCCEEEEECCCHHHHH
T ss_conf 777789999874014-1112679998999688176899
No 12
>cd04927 ACT_ACR-like_2 Second ACT domain, of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). This CD includes the second ACT domain, of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). ACR proteins, found only in Arabidopsis and Oryza, as yet, are proposed to function as novel regulatory or sensor proteins in plants. Nine ACR gene products (ACR1-8 in Arabidopsis and OsARC1-9 in Oryza) have been described, however, the ACR-like sequences in this CD are distinct from those characterized. This CD includes the Oryza sativa ACR-like protein (Os05g0113000) encoded on chromosome 5 and the Arabidopsis thaliana predicted gene product, At2g39570. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=65.86 E-value=11 Score=18.50 Aligned_cols=22 Identities=27% Similarity=0.329 Sum_probs=17.8
Q ss_pred EEEEEEEEEC--CCCCEEEEEEEE
Q ss_conf 6898888985--875655999982
Q gi|254780786|r 41 VISISEVCMS--VDLRVATVYISL 62 (128)
Q Consensus 41 ~vtIt~V~vS--~Dl~~AkVyvs~ 62 (128)
-+||..|+|| ||.+.+.+||-.
T Consensus 25 eltI~rvKVsTtPdgrv~DlFfiT 48 (76)
T cd04927 25 ELTIERVKVSTTPDGRVLDLFFIT 48 (76)
T ss_pred EEEEEEEEEECCCCCCEEEEEEEE
T ss_conf 278899898718998289999992
No 13
>PRK12311 rpsB 30S ribosomal protein S2; Provisional
Probab=64.27 E-value=11 Score=18.61 Aligned_cols=35 Identities=20% Similarity=0.372 Sum_probs=26.5
Q ss_pred HHHHHHHHHHHHHHHHHHCCCCCEEEEEECCCHHHH
Q ss_conf 998568999999998752145785899973868889
Q gi|254780786|r 75 LNCNIKFIRGRIGRSLRNLRYVPELRFRYDTSLQSY 110 (128)
Q Consensus 75 L~~~~~~ir~~l~~~l~~lr~~P~L~F~~D~s~e~~ 110 (128)
|.+....+.+.++. +++|+..|++-|+.|..-|..
T Consensus 139 l~Re~~KL~k~lgG-Ik~M~~lPDlvfViD~~kE~i 173 (332)
T PRK12311 139 LQRERDKLDRSLGG-IKDMGGLPDLIFVIDTNKEDI 173 (332)
T ss_pred HHHHHHHHHHHHHH-HHHHCCCCCEEEEECCCCCHH
T ss_conf 98799999985462-542055999899968973389
No 14
>pfam11454 DUF3016 Protein of unknown function (DUF3016). This is a bacterial family of uncharacterized proteins.
Probab=43.85 E-value=27 Score=16.36 Aligned_cols=47 Identities=19% Similarity=0.050 Sum_probs=30.2
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEEEEEEEECCCCCE
Q ss_conf 77773899999999999999995141342012651689888898587565
Q gi|254780786|r 6 PKNSRRALRVGEEVRSALMWVILNNEFQDRLISRDVISISEVCMSVDLRV 55 (128)
Q Consensus 6 ~~~s~R~~rv~~~i~~~is~il~~~~~~d~~~~~~~vtIt~V~vS~Dl~~ 55 (128)
...+....++-..+.+.+.+.-.+. -|.-...-|+||+|++++|..-
T Consensus 22 ~~~~~~~~~~~~~l~~~~~~lA~~~---Lp~gq~L~i~VtDvDLAGd~~P 68 (141)
T pfam11454 22 GIQSRFRKRVFEALTEHLAKLAARY---LPPGQKLEIEVTDVDLAGDVEP 68 (141)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHC---CCCCCEEEEEEEECCCCCCCCC
T ss_conf 8510579999999999999998740---8999989999996023666530
No 15
>PRK05299 rpsB 30S ribosomal protein S2; Provisional
Probab=41.62 E-value=30 Score=16.16 Aligned_cols=34 Identities=12% Similarity=0.322 Sum_probs=23.7
Q ss_pred HHHHHHHHHHHHHHHHHCCCCCEEEEEECCCHHHH
Q ss_conf 98568999999998752145785899973868889
Q gi|254780786|r 76 NCNIKFIRGRIGRSLRNLRYVPELRFRYDTSLQSY 110 (128)
Q Consensus 76 ~~~~~~ir~~l~~~l~~lr~~P~L~F~~D~s~e~~ 110 (128)
.+....+.+.++. +++|+..|++.|..|...|..
T Consensus 138 ~r~~~kL~k~~~G-i~~m~~lPd~viv~d~~~e~~ 171 (255)
T PRK05299 138 TRELEKLEKSLGG-IKDMGGLPDALFVVDPNKEHI 171 (255)
T ss_pred HHHHHHHHHHHHH-HHHHCCCCCEEEEECCCCCHH
T ss_conf 7778889986540-532431998799847853379
No 16
>COG1438 ArgR Arginine repressor [Transcription]
Probab=34.60 E-value=20 Score=17.08 Aligned_cols=99 Identities=17% Similarity=0.110 Sum_probs=48.9
Q ss_pred CCCCHHHHHHHHHHH-------HHHHHHHHHCCCCCCCCCCCEEEEEEEEECCCCCEEEE---------E-EEECCCCCH
Q ss_conf 777738999999999-------99999995141342012651689888898587565599---------9-982798647
Q gi|254780786|r 6 PKNSRRALRVGEEVR-------SALMWVILNNEFQDRLISRDVISISEVCMSVDLRVATV---------Y-ISLPLDVSP 68 (128)
Q Consensus 6 ~~~s~R~~rv~~~i~-------~~is~il~~~~~~d~~~~~~~vtIt~V~vS~Dl~~AkV---------y-vs~~~~~~~ 68 (128)
.+...|+..+.++|. ++|.+.|.. . .+.||...||+|++--.. | |+++++ ..
T Consensus 2 ~kk~~R~~~Ik~iI~~~~i~TQ~Elv~~L~~---------~-Gi~vTQaTvSRDlkelglvKv~~~~g~~~Y~l~~~-~~ 70 (150)
T COG1438 2 MKKEERLELIKEIITEEKISTQEELVELLQE---------E-GIEVTQATVSRDLKELGLVKVRNEKGTYVYSLPAE-LG 70 (150)
T ss_pred CCHHHHHHHHHHHHHHCCCCCHHHHHHHHHH---------C-CCEEEHHHHHHHHHHCCCEEECCCCCCEEEEECCC-CC
T ss_conf 8478999999999986777789999999998---------2-97586398787799859889337897389984876-67
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEECCCHHHHHHHHHHHCCHHHH
Q ss_conf 7899999985689999999987521457858999738688899999985576777
Q gi|254780786|r 69 DRVISALNCNIKFIRGRIGRSLRNLRYVPELRFRYDTSLQSYWKLNALMCLPKIP 123 (128)
Q Consensus 69 ~~~~~~L~~~~~~ir~~l~~~l~~lr~~P~L~F~~D~s~e~~~~I~~LL~~~~v~ 123 (128)
......+. +.+...+.+.++.-.+.-..- ..-.+.-|..+|+....+
T Consensus 71 ~~~~~~~~-------~~~~~~v~~vd~~~~~ivlkT-~PG~A~~ia~~lD~~~~~ 117 (150)
T COG1438 71 VPPTSKLK-------RYLKDLVLSIDRNGNLIVLKT-SPGAAQLIARLLDSLAKD 117 (150)
T ss_pred CCCHHHHH-------HHHHHHHEEECCCCCEEEEEE-CCCHHHHHHHHHHHCCCH
T ss_conf 77046688-------899988101114786899980-896589999998743743
No 17
>cd04894 ACT_ACR-like_1 ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). This CD includes the N-terminal ACT domain of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). ACR proteins, found only in Arabidopsis and Oryza, as yet, are proposed to function as novel regulatory or sensor proteins in plants. Nine ACR gene products (ACR1-8 in Arabidopsis and OsARC1-9 in Oryza) have been described, however, the ACR-like sequences in this CD are distinct from those characterized. This CD includes the Oryza sativa ACR-like protein (Os05g0113000) encoded on chromosome 5 and the Arabidopsis thaliana predicted gene product, At2g39570. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=34.56 E-value=38 Score=15.51 Aligned_cols=26 Identities=15% Similarity=-0.010 Sum_probs=22.3
Q ss_pred EEEEEEEECCCCCEEEEEEEECCCCC
Q ss_conf 89888898587565599998279864
Q gi|254780786|r 42 ISISEVCMSVDLRVATVYISLPLDVS 67 (128)
Q Consensus 42 vtIt~V~vS~Dl~~AkVyvs~~~~~~ 67 (128)
++||+-++|-|.+.|.|-+++.+...
T Consensus 26 L~I~rgD~sTDG~Wcyiv~wVv~~~~ 51 (69)
T cd04894 26 LNITRGDDSTDGRWCYIVFWVVPRPP 51 (69)
T ss_pred EEEEECCCCCCCCEEEEEEEEECCCC
T ss_conf 38982331358818999999824787
No 18
>TIGR02065 ECX1 exosome complex exonuclease 1; InterPro: IPR011807 The PH (phosphorolytic) domain is responsible for 3'-5' exoribonuclease activity, although in some proteins this domain has lost its catalytic function. An active PH domain uses inorganic phosphate as a nucleophile, adding it across the phosphodiester bond between the end two nucleotides in order to release ribonucleoside 5'-diphosphate (rNDP) from the 3' end of the RNA substrate. PH domains can be found in bacterial/organelle RNases and PNPases (polynucleotide phosphorylases) , as well as in archaeal and eukaryotic RNA exosomes , , the later acting as nano-compartments for the degradation or processing of RNA (including mRNA, rRNA, snRNA and snoRNA). Bacterial/organelle PNPases share a common barrel structure with RNA exosomes, consisting of a hexameric ring of PH domains that act as a degradation chamber, and an S1-domain/KH-domain containing cap that binds the RNA substrate (and sometimes accessory proteins) in order to regulate and restrict entry into the degradation chamber . Unstructured RNA substrates feed in through the pore made by the S1 domains, are degraded by the PH domain ring, and exit as nucleotides via the PH pore at the opposite end of the barrel , . This entry represents a family of archaeal proteins that are orthologous to the eukaryotic exosome protein Rrp41. It is somewhat more distantly related to the bacterial protein ribonuclease PH. An exosome-like complex has been demonstrated experimentally for the Archaea in Sulfolobus solfataricus, so members of this family are designated exosome complex exonuclease 1, after usage in SwissProt .; GO: 0016896 exoribonuclease activity producing 5'-phosphomonoesters, 0000178 exosome (RNase complex).
Probab=32.31 E-value=23 Score=16.72 Aligned_cols=30 Identities=33% Similarity=0.522 Sum_probs=26.5
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf 887777389999999999999999514134
Q gi|254780786|r 4 KNPKNSRRALRVGEEVRSALMWVILNNEFQ 33 (128)
Q Consensus 4 ~~~~~s~R~~rv~~~i~~~is~il~~~~~~ 33 (128)
|+|+||+|.-=++..+++.|...++-+.++
T Consensus 83 K~PgPdRR~iEiSKv~~EALepai~~E~fP 112 (231)
T TIGR02065 83 KRPGPDRREIEISKVIREALEPAILLEQFP 112 (231)
T ss_pred CCCCCCCCEEHHHHHHHHHCCCEEEEECCC
T ss_conf 872229441215668888513101322388
No 19
>PRK00441 argR arginine repressor; Provisional
Probab=31.98 E-value=43 Score=15.27 Aligned_cols=95 Identities=11% Similarity=0.065 Sum_probs=48.1
Q ss_pred CCHHHHHHHHHHH-------HHHHHHHHHCCCCCCCCCCCEEEEEEEEECCCCC---EEEE------E-EEECCCCCHHH
Q ss_conf 7738999999999-------9999999514134201265168988889858756---5599------9-98279864778
Q gi|254780786|r 8 NSRRALRVGEEVR-------SALMWVILNNEFQDRLISRDVISISEVCMSVDLR---VATV------Y-ISLPLDVSPDR 70 (128)
Q Consensus 8 ~s~R~~rv~~~i~-------~~is~il~~~~~~d~~~~~~~vtIt~V~vS~Dl~---~AkV------y-vs~~~~~~~~~ 70 (128)
.+.|+..+-++|+ ++|.+.|.. ..+++|..-+|+|++ ..|| | |+++.. ....
T Consensus 2 K~~Rq~~I~~lI~~~~I~tQ~eL~~~L~~----------~Gi~vTQATlSRDl~eL~~vKv~~~~G~~~Y~~~~~-~~~~ 70 (149)
T PRK00441 2 KVSRHAKILEIINSKEIETQEELAEELKK----------MGFDVTQATVSRDIKELKLIKVLGNNGKYKYATINK-TENN 70 (149)
T ss_pred CHHHHHHHHHHHHHCCCCCHHHHHHHHHH----------CCCCEEHHHHHHHHHHCCCEEEECCCCCEEEEECCC-CCCC
T ss_conf 48999999999972896789999999998----------699766589888699819889656999789996476-6641
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEECCCHHHHHHHHHHHCCHH
Q ss_conf 999999856899999999875214578589997386888999999855767
Q gi|254780786|r 71 VISALNCNIKFIRGRIGRSLRNLRYVPELRFRYDTSLQSYWKLNALMCLPK 121 (128)
Q Consensus 71 ~~~~L~~~~~~ir~~l~~~l~~lr~~P~L~F~~D~s~e~~~~I~~LL~~~~ 121 (128)
..+ .++..+...+....+...+.... ...-.+.-+..+|++..
T Consensus 71 ~~~-------~l~~~~~~~v~~v~~~~~lvvIk-T~pG~A~~va~~iD~~~ 113 (149)
T PRK00441 71 LSD-------RLVNIFANTVISVENVDNMVVIK-TISGSASAAAEAIDTLN 113 (149)
T ss_pred HHH-------HHHHHHHHHEEEEEECCCEEEEE-ECCCCHHHHHHHHHHCC
T ss_conf 778-------99999998706775037789999-38995899999998379
No 20
>pfam05872 DUF853 Bacterial protein of unknown function (DUF853). This family consists of several bacterial proteins of unknown function. One member from Brucella melitensis is thought to be an ATPase.
Probab=26.84 E-value=53 Score=14.75 Aligned_cols=27 Identities=22% Similarity=0.349 Sum_probs=18.8
Q ss_pred CCEEEEEECCC-----------HHHHHHHHHHHCCHHH
Q ss_conf 78589997386-----------8889999998557677
Q gi|254780786|r 96 VPELRFRYDTS-----------LQSYWKLNALMCLPKI 122 (128)
Q Consensus 96 ~P~L~F~~D~s-----------~e~~~~I~~LL~~~~v 122 (128)
-|+|.|++|+. .+..+.+-+|+++.-|
T Consensus 256 KPKLVFFFDEAHLLF~dApkall~kIEqvVRLIRSKGV 293 (504)
T pfam05872 256 KPKLVFFFDEAHLLFNDAPKVLLEKVEQVVRLIRSKGV 293 (504)
T ss_pred CCEEEEEECHHHHHHCCCCHHHHHHHHHHHHHHHCCCC
T ss_conf 85389994016665247859999999999987530673
No 21
>pfam08371 PLD_envelope Phospholipase D/viral envelope. This domain is found in phospholipases and viral envelope proteins between Phospholipase D (PLD) active site motifs (pfam00641). PLD is associated with Golgi membranes and alters their lipid content by the conversion of phospholipids into phosphatidic acid, which is thought to be involved in the regulation of lipid movement. This might explain the prevalence of this domain in viral envelope proteins.
Probab=25.72 E-value=36 Score=15.68 Aligned_cols=71 Identities=23% Similarity=0.354 Sum_probs=45.9
Q ss_pred EEEECCCCCEEEEEEEECCC--------CCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEECCCHHHHHHHHHHH
Q ss_conf 88985875655999982798--------6477899999985689999999987521457858999738688899999985
Q gi|254780786|r 46 EVCMSVDLRVATVYISLPLD--------VSPDRVISALNCNIKFIRGRIGRSLRNLRYVPELRFRYDTSLQSYWKLNALM 117 (128)
Q Consensus 46 ~V~vS~Dl~~AkVyvs~~~~--------~~~~~~~~~L~~~~~~ir~~l~~~l~~lr~~P~L~F~~D~s~e~~~~I~~LL 117 (128)
...++-+-..+.+|+|..|. .+.+.++..++.++.+|. |--|-|.|-.+| +....+--.|+.-|
T Consensus 51 pl~~~~~~~~~~~y~S~SPp~~~~~~Rt~Dldail~~I~~A~~~I~------IsvMdy~P~~~~--~~~~~YWp~Id~AL 122 (163)
T pfam08371 51 PLSLPVNGTPAQVYLSSSPPPLLPYGRTDDLDAILSVIDSAKKFIY------ISVMDYVPLIRY--DKPRRYWPVIDNAL 122 (163)
T ss_pred CCEEEECCEEEEEEEECCCHHHCCCCCCHHHHHHHHHHHHHHCEEE------EEECCCCCEEEE--CCCCCCCHHHHHHH
T ss_conf 7277338955457880698435889987279999999998751899------996132452441--78876665789999
Q ss_pred CCHHHHH
Q ss_conf 5767777
Q gi|254780786|r 118 CLPKIPV 124 (128)
Q Consensus 118 ~~~~v~~ 124 (128)
+..-+.|
T Consensus 123 r~AA~~R 129 (163)
T pfam08371 123 RRAAIER 129 (163)
T ss_pred HHHHHHC
T ss_conf 9999856
No 22
>pfam03027 consensus
Probab=22.72 E-value=63 Score=14.29 Aligned_cols=52 Identities=12% Similarity=0.126 Sum_probs=38.3
Q ss_pred CCEEEEEEEEECCCCCEEEEEEE-ECCCCC--HHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 51689888898587565599998-279864--77899999985689999999987
Q gi|254780786|r 39 RDVISISEVCMSVDLRVATVYIS-LPLDVS--PDRVISALNCNIKFIRGRIGRSL 90 (128)
Q Consensus 39 ~~~vtIt~V~vS~Dl~~AkVyvs-~~~~~~--~~~~~~~L~~~~~~ir~~l~~~l 90 (128)
...+-|+++++..+...++++++ .+++.. .+.+-+.+|.+...+-.++...+
T Consensus 47 ~~yl~i~~~~~~~~~~~~~~~~~NLfnGd~~L~~~~n~~lNenw~~v~~e~~p~i 101 (126)
T pfam03027 47 KTYLKITSLKVKFEVGKVKFDLENLFNGNKELGDAMNQFLNENWRELLNELKPAI 101 (126)
T ss_pred EEEEEEEEEEEEEEECEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 1899999779998602399994045899979999999999878999999988999
No 23
>PRK09437 bcp thioredoxin-dependent thiol peroxidase; Reviewed
Probab=21.25 E-value=68 Score=14.12 Aligned_cols=34 Identities=18% Similarity=0.187 Sum_probs=20.9
Q ss_pred EEEECCCCCEEEEEEEECCCCCHHHHHHHHHHHH
Q ss_conf 8898587565599998279864778999999856
Q gi|254780786|r 46 EVCMSVDLRVATVYISLPLDVSPDRVISALNCNI 79 (128)
Q Consensus 46 ~V~vS~Dl~~AkVyvs~~~~~~~~~~~~~L~~~~ 79 (128)
-.-+.+|.++++||..+-+....++++++|.+++
T Consensus 123 tfiID~~G~I~~v~~~v~~~~h~~~vL~~Lk~~~ 156 (156)
T PRK09437 123 SFLIDEDGKIEHVFDKFKTKDHHDVVLDYLKENA 156 (156)
T ss_pred EEEECCCCEEEEEECCCCCCCCHHHHHHHHHHHC
T ss_conf 9999999989999789998753999999998529
Done!