Query 043842
Match_columns 129
No_of_seqs 109 out of 1057
Neff 5.2
Searched_HMMs 46136
Date Fri Mar 29 08:49:52 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/043842.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/043842hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR01171 rplB_bact ribosomal 100.0 1.4E-60 3.1E-65 389.4 12.3 122 4-128 132-254 (273)
2 PRK09374 rplB 50S ribosomal pr 100.0 1.1E-60 2.4E-65 390.4 11.7 122 4-128 134-256 (276)
3 PF03947 Ribosomal_L2_C: Ribos 100.0 4.8E-61 1E-65 356.0 5.7 118 4-124 11-130 (130)
4 PTZ00031 ribosomal protein L2; 100.0 6.3E-60 1.4E-64 391.0 11.9 122 4-128 165-287 (317)
5 CHL00052 rpl2 ribosomal protei 100.0 9.3E-60 2E-64 384.5 12.3 122 4-128 132-255 (273)
6 COG0090 RplB Ribosomal protein 100.0 1.6E-58 3.4E-63 374.8 12.2 122 4-128 134-256 (275)
7 PRK09612 rpl2p 50S ribosomal p 100.0 3.8E-52 8.2E-57 334.3 11.9 114 4-121 99-219 (238)
8 PTZ00180 60S ribosomal protein 100.0 5.7E-50 1.2E-54 325.0 12.1 115 4-121 106-228 (260)
9 KOG0438 Mitochondrial/chloropl 100.0 5.8E-43 1.3E-47 287.6 2.6 122 5-129 167-289 (312)
10 KOG2309 60s ribosomal protein 100.0 2.1E-33 4.5E-38 224.3 6.1 112 4-117 100-217 (248)
11 PF02736 Myosin_N: Myosin N-te 78.6 3.7 8.1E-05 24.4 3.4 26 32-58 16-41 (42)
12 TIGR00739 yajC preprotein tran 62.5 19 0.00041 24.7 4.4 40 21-61 41-80 (84)
13 PRK05585 yajC preprotein trans 62.2 16 0.00035 26.1 4.2 42 20-62 55-96 (106)
14 PF02699 YajC: Preprotein tran 55.0 4 8.7E-05 27.7 0.0 41 21-62 40-80 (82)
15 PRK05886 yajC preprotein trans 47.5 62 0.0014 23.4 5.2 42 20-62 41-82 (109)
16 PF06592 DUF1138: Protein of u 34.3 18 0.00038 24.7 0.6 25 76-101 41-67 (73)
17 PF13953 PapC_C: PapC C-termin 33.0 80 0.0017 20.2 3.6 51 3-63 9-61 (68)
18 PF09962 DUF2196: Uncharacteri 31.9 24 0.00052 23.3 0.9 17 88-104 30-46 (62)
19 cd01770 p47_UBX p47-like ubiqu 30.8 25 0.00054 23.5 0.9 27 40-66 4-30 (79)
20 PF01176 eIF-1a: Translation i 30.5 1E+02 0.0022 19.7 3.8 24 31-54 6-29 (65)
21 PF12791 RsgI_N: Anti-sigma fa 30.2 66 0.0014 19.7 2.7 28 39-66 4-31 (56)
22 smart00166 UBX Domain present 28.4 30 0.00065 22.7 0.9 26 40-65 4-29 (80)
23 PF06822 DUF1235: Protein of u 28.2 1.4E+02 0.0031 24.9 5.1 45 26-70 81-127 (266)
24 KOG0265 U5 snRNP-specific prot 26.6 1.5E+02 0.0032 25.6 5.0 46 9-55 48-96 (338)
25 cd01771 Faf1_UBX Faf1 UBX doma 25.8 75 0.0016 21.3 2.6 19 41-59 5-25 (80)
26 PHA02985 hypothetical protein; 25.2 1.6E+02 0.0034 24.8 4.8 45 26-70 86-132 (271)
27 PF08661 Rep_fac-A_3: Replicat 23.0 2.1E+02 0.0046 19.8 4.6 47 22-70 25-73 (109)
28 cd01767 UBX UBX (ubiquitin reg 22.3 42 0.00092 21.7 0.8 21 42-64 4-26 (77)
29 cd04456 S1_IF1A_like S1_IF1A_l 22.0 1.9E+02 0.0041 19.4 4.0 24 31-54 3-26 (78)
30 cd01773 Faf1_like1_UBX Faf1 ik 21.8 66 0.0014 22.1 1.7 15 40-54 5-19 (82)
31 PF09923 DUF2155: Uncharacteri 21.6 35 0.00075 23.8 0.3 8 95-102 74-81 (90)
32 cd05792 S1_eIF1AD_like S1_eIF1 21.4 1.7E+02 0.0038 19.8 3.7 16 39-54 11-26 (78)
33 smart00652 eIF1a eukaryotic tr 20.7 1.9E+02 0.0041 19.6 3.8 24 31-54 8-31 (83)
No 1
>TIGR01171 rplB_bact ribosomal protein L2, bacterial/organellar. This model distinguishes bacterial and organellar ribosomal protein L2 from its counterparts in the archaea nad in the eukaryotic cytosol. Plant mitochondrial examples tend to have long, variable inserts.
Probab=100.00 E-value=1.4e-60 Score=389.39 Aligned_cols=122 Identities=36% Similarity=0.640 Sum_probs=117.0
Q ss_pred CccccceEEEeeEeCCCCeeEEecCCCceEEEEecCCCeEEEEecCCceEEecCCCceeEEeeeCCCccceeeccccccc
Q 043842 4 PGRITHMWNDLRVQPSRWEASSSCRDVNQDFEKEPTSRYCLVRLRCGNEKVIDPRCRATIGTVSNPSHGAKKLSKAGQRS 83 (129)
Q Consensus 4 ~~p~Gt~I~nIE~~pg~gg~l~RsAGt~a~ii~~~~~~~~~ikLPSGe~r~v~~~c~AtiG~vsn~~~~~~~~gKAG~~R 83 (129)
-||+||.|||||++||+|+||||||||||+|+.+ ++++++|||||||+++|+++|+||||+|||.+|.+++|+|||++|
T Consensus 132 ~IP~Gt~I~NIE~~pg~Ggkl~RsAGt~A~ii~k-~~~~~~vkLPSGe~r~i~~~c~AtiG~Vsn~~~~~~~~gKAG~~r 210 (273)
T TIGR01171 132 NIPVGTTVHNIELKPGKGGQLARSAGTSAQILAK-EGGYVTLRLPSGEMRMVLKECRATIGEVGNEDHNNIVLGKAGRSR 210 (273)
T ss_pred cCCCCCEEEEEEecCCCCceEEEecCCeEEEEEe-cCCEEEEECCCCCeEEECCcCeEEEEEccCCchhccEeccchhhe
Confidence 3799999999999999999999999999999988 689999999999999999999999999999999999999999999
Q ss_pred ccCCCceeeEEEeeceeCCCC-CCCCCCCCCCCCCCCCCCcccCCC
Q 043842 84 WLGRRAVVRGVAMIPVDHPHV-ERSKSSGNNGRCSFTPWGKPCKSG 128 (129)
Q Consensus 84 ~~G~RP~VRGvamNpvdHPhG-G~~k~~g~~gr~~~spwG~~~kg~ 128 (129)
|+|+||+|||||||||||||| |++++++ ||+|+||||++|||.
T Consensus 211 ~lg~rP~VRGvAMNpvDHPHGGGegk~~~--g~~~~spwG~~~kg~ 254 (273)
T TIGR01171 211 WLGIRPTVRGVAMNPVDHPHGGGEGRTPG--GRHPVTPWGKPTKGY 254 (273)
T ss_pred eCCCCCccccEecCcccCCCCCCCCcCCC--CCCCCCCCeeecccc
Confidence 999999999999999999999 6787764 699999999999985
No 2
>PRK09374 rplB 50S ribosomal protein L2; Validated
Probab=100.00 E-value=1.1e-60 Score=390.40 Aligned_cols=122 Identities=37% Similarity=0.659 Sum_probs=117.3
Q ss_pred CccccceEEEeeEeCCCCeeEEecCCCceEEEEecCCCeEEEEecCCceEEecCCCceeEEeeeCCCccceeeccccccc
Q 043842 4 PGRITHMWNDLRVQPSRWEASSSCRDVNQDFEKEPTSRYCLVRLRCGNEKVIDPRCRATIGTVSNPSHGAKKLSKAGQRS 83 (129)
Q Consensus 4 ~~p~Gt~I~nIE~~pg~gg~l~RsAGt~a~ii~~~~~~~~~ikLPSGe~r~v~~~c~AtiG~vsn~~~~~~~~gKAG~~R 83 (129)
-||+||.|||||++||+|+||||||||||+|+.+ ++++++|||||||+|+|+++|+||||+|||.+|.+++|+|||++|
T Consensus 134 ~IP~Gt~I~NIE~~pG~Ggkl~RsAGt~A~ii~k-~~~~~~vkLPSGe~r~i~~~c~AtIG~Vsn~~~~~~~lgKAG~~r 212 (276)
T PRK09374 134 NIPVGTTVHNIELKPGKGGQLARSAGTSAQLVAK-EGKYATLRLPSGEVRKVLAECRATIGEVGNEEHSNISLGKAGRSR 212 (276)
T ss_pred cCCCCCEEEEEEecCCCCceeEeecCCeEEEEEe-cCCEEEEECCCCCeEEEcccccEEEEeecCcchhhcchhhhhhhe
Confidence 3799999999999999999999999999999988 689999999999999999999999999999999999999999999
Q ss_pred ccCCCceeeEEEeeceeCCCC-CCCCCCCCCCCCCCCCCCcccCCC
Q 043842 84 WLGRRAVVRGVAMIPVDHPHV-ERSKSSGNNGRCSFTPWGKPCKSG 128 (129)
Q Consensus 84 ~~G~RP~VRGvamNpvdHPhG-G~~k~~g~~gr~~~spwG~~~kg~ 128 (129)
|+|+||+|||||||||||||| |++++++ ||+|+||||++|||+
T Consensus 213 ~lg~rP~VRGVAMNpvDHPHGGGegkt~~--g~~~~spwG~~~kg~ 256 (276)
T PRK09374 213 WLGIRPTVRGVAMNPVDHPHGGGEGRTSG--GRHPVTPWGKPTKGY 256 (276)
T ss_pred eCCCCCccccEecCcccCCCCCCCCcCCC--CCCCCCCCeeecccc
Confidence 999999999999999999999 6888875 699999999999986
No 3
>PF03947 Ribosomal_L2_C: Ribosomal Proteins L2, C-terminal domain; InterPro: IPR022669 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 L2 is one of the proteins from the large ribosomal subunit. This entry represents the best conserved region located in the C-terminal section of these proteins.In Escherichia coli, L2 is known to bind to the 23S rRNA and to have peptidyltransferase activity. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities [, ], groups: Eubacterial L2. Algal and plant chloroplast L2. Cyanelle L2. Archaebacterial L2. Plant L2. Slime mold L2. Marchantia polymorpha mitochondrial L2. Paramecium tetraurelia mitochondrial L2. Fission yeast K5, K37 and KD4. Yeast YL6. Vertebrate L8. ; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3MRZ_C 3F1H_D 3PYO_C 3F1F_D 3PYV_C 3PYR_C 1VSA_B 3D5B_D 3PYT_C 3MS1_C ....
Probab=100.00 E-value=4.8e-61 Score=356.03 Aligned_cols=118 Identities=41% Similarity=0.727 Sum_probs=110.6
Q ss_pred CccccceEEEeeEeCCCCeeEEecCCCceEEEEecCCCeEEEEecCCceEEecCCCceeEEeeeCCCccceeeccccccc
Q 043842 4 PGRITHMWNDLRVQPSRWEASSSCRDVNQDFEKEPTSRYCLVRLRCGNEKVIDPRCRATIGTVSNPSHGAKKLSKAGQRS 83 (129)
Q Consensus 4 ~~p~Gt~I~nIE~~pg~gg~l~RsAGt~a~ii~~~~~~~~~ikLPSGe~r~v~~~c~AtiG~vsn~~~~~~~~gKAG~~R 83 (129)
-||+||+|||||++||+|++|+|||||||+|+++ ++++++|||||||+|+|+.+|+||||+|||.+|++++++|||++|
T Consensus 11 ~ip~Gt~I~nIE~~pg~g~~~~RaAGt~a~ii~k-~~~~~~ikLPSG~~k~v~~~c~AtiG~vsn~~~~~~~~~KAG~~r 89 (130)
T PF03947_consen 11 NIPIGTIIHNIELKPGDGGKLARAAGTYAQIISK-EGNYVVIKLPSGEIKLVSSNCRATIGRVSNGGHKEKKLGKAGRNR 89 (130)
T ss_dssp GSSTTEEEESBESSTTSSEEBSSSTTBBEEEEEE-ESSEEEEEETTSEEEEEETTSEEEESCBSSTTGGGSB-SSHHHHH
T ss_pred hCCCCCEEEEEecCCCCCceEEeeCCCEEEEEEe-ccceeEEEecCCCeEeecccceEEEEEecCccccchhhhhhhhcc
Confidence 4899999999999999999999999999999988 579999999999999999999999999999999999999999999
Q ss_pred ccCCCceeeEEEeeceeCCCCC-CCCCCCCCCC-CCCCCCCcc
Q 043842 84 WLGRRAVVRGVAMIPVDHPHVE-RSKSSGNNGR-CSFTPWGKP 124 (129)
Q Consensus 84 ~~G~RP~VRGvamNpvdHPhGG-~~k~~g~~gr-~~~spwG~~ 124 (129)
|+|+||+||||||||||||||| ++|+++ || +|+||||++
T Consensus 90 ~~g~rP~VRGvamNpvdHPhGGG~g~~~~--gr~~~~s~wg~p 130 (130)
T PF03947_consen 90 WLGKRPKVRGVAMNPVDHPHGGGEGKTSG--GRPPPVSPWGKP 130 (130)
T ss_dssp HTCCSSS-SGTCSTTTTSSTCTSSSSSST--SSSSEBTTTSSS
T ss_pred ccccCccccceeeccccCcCCCCCCcCCC--CCCCCCCCCCCC
Confidence 9999999999999999999994 778874 68 899999986
No 4
>PTZ00031 ribosomal protein L2; Provisional
Probab=100.00 E-value=6.3e-60 Score=391.00 Aligned_cols=122 Identities=29% Similarity=0.439 Sum_probs=117.1
Q ss_pred CccccceEEEeeEeCCCCeeEEecCCCceEEEEecCCCeEEEEecCCceEEecCCCceeEEeeeCCCccceeeccccccc
Q 043842 4 PGRITHMWNDLRVQPSRWEASSSCRDVNQDFEKEPTSRYCLVRLRCGNEKVIDPRCRATIGTVSNPSHGAKKLSKAGQRS 83 (129)
Q Consensus 4 ~~p~Gt~I~nIE~~pg~gg~l~RsAGt~a~ii~~~~~~~~~ikLPSGe~r~v~~~c~AtiG~vsn~~~~~~~~gKAG~~R 83 (129)
-||+||.|||||++||+|+||||||||||+|+.+ +++|++|||||||+|+|+++|+||||+|||.+|.+++++|||++|
T Consensus 165 ~IP~GT~IhNIE~~pG~Ggkl~RSAGt~A~Ii~k-~~~~~~VkLPSGe~r~i~~~C~ATIG~Vsn~~~~~k~lgKAG~~R 243 (317)
T PTZ00031 165 NIPVGSIVHNVEMRPGAGGQIIRAGGTYATVVSK-DEQFATLKLKSTEIRKFPLDCWATIGQVSNLEHHMRILGKAGVNR 243 (317)
T ss_pred cCCCCCEEEEEEecCCCCceEEEecCCeEEEEEc-cCCEEEEECCCCCEEEECccCeEEEEEccCCccccceeccchhhh
Confidence 3799999999999999999999999999999988 689999999999999999999999999999999999999999999
Q ss_pred ccCCCceeeEEEeeceeCCCC-CCCCCCCCCCCCCCCCCCcccCCC
Q 043842 84 WLGRRAVVRGVAMIPVDHPHV-ERSKSSGNNGRCSFTPWGKPCKSG 128 (129)
Q Consensus 84 ~~G~RP~VRGvamNpvdHPhG-G~~k~~g~~gr~~~spwG~~~kg~ 128 (129)
|+|+||+|||||||||||||| |++|+++ ||+|+||||++|||.
T Consensus 244 wlg~RP~VRGVAMNPVDHPHGGGeGkt~~--gr~p~spWG~~tkG~ 287 (317)
T PTZ00031 244 WLGKRPVVRGVAMNPSKHPHGGGTSKKGT--KRPKCSLWGICRDGY 287 (317)
T ss_pred cCCCCCCcccCccCCccCCCCCCCCCCCC--CCCCCCCCccccCCc
Confidence 999999999999999999999 6788774 699999999999985
No 5
>CHL00052 rpl2 ribosomal protein L2
Probab=100.00 E-value=9.3e-60 Score=384.52 Aligned_cols=122 Identities=32% Similarity=0.580 Sum_probs=115.9
Q ss_pred CccccceEEEeeEeCCCCeeEEecCCCceEEEEecCCCeEEEEecCCceEEecCCCceeEEeeeCCCccceeeccccccc
Q 043842 4 PGRITHMWNDLRVQPSRWEASSSCRDVNQDFEKEPTSRYCLVRLRCGNEKVIDPRCRATIGTVSNPSHGAKKLSKAGQRS 83 (129)
Q Consensus 4 ~~p~Gt~I~nIE~~pg~gg~l~RsAGt~a~ii~~~~~~~~~ikLPSGe~r~v~~~c~AtiG~vsn~~~~~~~~gKAG~~R 83 (129)
-||+||.|||||+.||+|+||||||||||+|+.+ +++|++|||||||+++|+++|+||||+|||.+|.+++++|||++|
T Consensus 132 ~IP~Gt~I~NIE~~pg~Ggk~~RsAGt~A~ii~k-~~~~~~vkLPSGe~r~v~~~c~AtIG~Vsn~~~~~~~lgKAG~~r 210 (273)
T CHL00052 132 NIPLGTAIHNIEITPGKGGQLARAAGAVAKLIAK-EGKSATLKLPSGEVRLISKNCSATIGQVGNVDVNNKSLGKAGSKR 210 (273)
T ss_pred cCCCCCEEEEEEecCCCCceEEEecCCeEEEEEe-cCCEEEEECCCCCeEEECCcCeEEEEEccCCchhhcEecchhhhh
Confidence 3799999999999999999999999999999988 689999999999999999999999999999999999999999999
Q ss_pred ccCCCceeeEEEeeceeCCCC-CCCCCCCCCCC-CCCCCCCcccCCC
Q 043842 84 WLGRRAVVRGVAMIPVDHPHV-ERSKSSGNNGR-CSFTPWGKPCKSG 128 (129)
Q Consensus 84 ~~G~RP~VRGvamNpvdHPhG-G~~k~~g~~gr-~~~spwG~~~kg~ 128 (129)
|+|+||+|||||||||||||| |++++++ || +|+||||++|||+
T Consensus 211 ~lg~rP~VRGvAMNpvDHPHGGGegkt~~--Gr~~~vspwG~~~kg~ 255 (273)
T CHL00052 211 WLGKRPKVRGVVMNPVDHPHGGGEGRAPI--GRKKPVTPWGKPALGR 255 (273)
T ss_pred cCCCCCcCCeEecCCccCCCCCCCccCCC--CCcCCCCcCccccccc
Confidence 999999999999999999999 6777764 65 5999999999985
No 6
>COG0090 RplB Ribosomal protein L2 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.6e-58 Score=374.79 Aligned_cols=122 Identities=34% Similarity=0.549 Sum_probs=116.2
Q ss_pred CccccceEEEeeEeCCCCeeEEecCCCceEEEEecCCCeEEEEecCCceEEecCCCceeEEeeeCCCccceeeccccccc
Q 043842 4 PGRITHMWNDLRVQPSRWEASSSCRDVNQDFEKEPTSRYCLVRLRCGNEKVIDPRCRATIGTVSNPSHGAKKLSKAGQRS 83 (129)
Q Consensus 4 ~~p~Gt~I~nIE~~pg~gg~l~RsAGt~a~ii~~~~~~~~~ikLPSGe~r~v~~~c~AtiG~vsn~~~~~~~~gKAG~~R 83 (129)
-||+||.|||||++||+|+||||||||||+|+.+ +.+|++|+|||||+|.|+++|+||||+|+|.+|.+++|+|||++|
T Consensus 134 ~IP~Gt~VhNVE~~pG~GGq~aRSaGtyA~vv~~-~~~y~~vrLpSGe~r~v~~~CrATIGvV~n~~~~~~~lgKAGr~r 212 (275)
T COG0090 134 NIPEGTIVHNVELKPGDGGQLARSAGTYAQVVGK-EGNYVIVRLPSGEMRKVLSECRATIGVVANGGHILKPLGKAGRAR 212 (275)
T ss_pred cCCCCceEEeeeeccCCCceEEEeCCceEEEEEc-cCCEEEEECCCCCeEeecccccEEEEEecCCccccceecccchhc
Confidence 4899999999999999999999999999999988 699999999999999999999999999999999999999999999
Q ss_pred ccCCCceeeEEEeeceeCCCC-CCCCCCCCCCCCCCCCCCcccCCC
Q 043842 84 WLGRRAVVRGVAMIPVDHPHV-ERSKSSGNNGRCSFTPWGKPCKSG 128 (129)
Q Consensus 84 ~~G~RP~VRGvamNpvdHPhG-G~~k~~g~~gr~~~spwG~~~kg~ 128 (129)
|+|+||+|||||||||||||| |++++.| |++|+||||++++|+
T Consensus 213 ~~g~rPtVRGvAMNpvDHPHGGGeg~~~g--gk~p~~pwg~~~~Gk 256 (275)
T COG0090 213 HKGKRPTVRGVAMNPVDHPHGGGEGQHPG--GKPPTVPWGKPTPGK 256 (275)
T ss_pred CCccCCccceeecCCCcCCCCCCCCCCCC--CCCCCCCCCCCCCcc
Confidence 999999999999999999999 5776663 689999999999984
No 7
>PRK09612 rpl2p 50S ribosomal protein L2P; Validated
Probab=100.00 E-value=3.8e-52 Score=334.32 Aligned_cols=114 Identities=27% Similarity=0.335 Sum_probs=105.2
Q ss_pred CccccceEEEeeEeCCCCeeEEecCCCceEEEEecCCCeEEEEecCCceEEecCCCceeEEeeeCCCccceeeccccccc
Q 043842 4 PGRITHMWNDLRVQPSRWEASSSCRDVNQDFEKEPTSRYCLVRLRCGNEKVIDPRCRATIGTVSNPSHGAKKLSKAGQRS 83 (129)
Q Consensus 4 ~~p~Gt~I~nIE~~pg~gg~l~RsAGt~a~ii~~~~~~~~~ikLPSGe~r~v~~~c~AtiG~vsn~~~~~~~~gKAG~~R 83 (129)
-||+||.|||||++||+|++|||||||||+|+.+ +++|++|||||||+|+|+++|+||||+|||.+|.+++|+|||++|
T Consensus 99 ~IP~Gt~I~NIE~~pG~Ggkl~RSAGt~A~Ii~k-~~~~~~vkLPSGe~r~i~~~c~AtiG~Vsn~~~~~~~lgKAG~~r 177 (238)
T PRK09612 99 EIPEGTPVCNIESRPGDGGKFARSSGTYALVVGH-EGDKVIVQLPSGKIKELNPRCRATIGVVAGGGRKEKPFLKAGKKY 177 (238)
T ss_pred hCCCCCEEEEEEecCCCCcceEEcCCCeEEEEEe-cCCEEEEECCCCCeEEECCcCeEEEEEccCCccccceeeechhhh
Confidence 3799999999999999999999999999999988 689999999999999999999999999999999999999999999
Q ss_pred cc-----CCCceeeEEEeeceeCCCC-CCCCCCCCCCCC-CCCCC
Q 043842 84 WL-----GRRAVVRGVAMIPVDHPHV-ERSKSSGNNGRC-SFTPW 121 (129)
Q Consensus 84 ~~-----G~RP~VRGvamNpvdHPhG-G~~k~~g~~gr~-~~spw 121 (129)
|+ |+||+|||||||||||||| |++++ +|++ +++.+
T Consensus 178 ~~~k~~~g~rP~VRGvAMNpvDHPHGGGeg~~---~G~~stvsr~ 219 (238)
T PRK09612 178 HKMKAKAKKWPRVRGVAMNAVDHPHGGGNHQH---PGRPSTVSRN 219 (238)
T ss_pred hhhhccCCCCCccCeEeeCCccCCcCCCCCCC---CCCCCcccCC
Confidence 99 9999999999999999999 55554 3676 44443
No 8
>PTZ00180 60S ribosomal protein L8; Provisional
Probab=100.00 E-value=5.7e-50 Score=324.97 Aligned_cols=115 Identities=23% Similarity=0.255 Sum_probs=104.1
Q ss_pred CccccceEEEeeEeCCCCeeEEecCCCceEEEEe-cCCCeEEEEecCCceEEecCCCceeEEeeeCCCccceeecccccc
Q 043842 4 PGRITHMWNDLRVQPSRWEASSSCRDVNQDFEKE-PTSRYCLVRLRCGNEKVIDPRCRATIGTVSNPSHGAKKLSKAGQR 82 (129)
Q Consensus 4 ~~p~Gt~I~nIE~~pg~gg~l~RsAGt~a~ii~~-~~~~~~~ikLPSGe~r~v~~~c~AtiG~vsn~~~~~~~~gKAG~~ 82 (129)
-||+||.|||||+.||+|+||||||||||+|+.+ .++++++|||||||+|+|+++|+||||+|||.+|.+++|+|||++
T Consensus 106 ~IP~GT~IhNIE~~pG~GgklaRSAGt~A~ii~k~k~~~~~~vkLPSGe~r~v~~~c~ATIG~Vsn~~~~~k~l~KAG~~ 185 (260)
T PTZ00180 106 QIPEGTIVCNVEEKPGDRGTLARASGCYATIIGHSDDGGKTRIRLPSGQKKTVSSLSRAMIGIVAGGGRIDKPVLKAGNA 185 (260)
T ss_pred hCCCCCeEEEEeccCCCCceEEEecCCeEEEEEEcccCCEEEEECCCCCeEeECCCCeEEEEEccCCcchheeeccccch
Confidence 3799999999999999999999999999999975 368999999999999999999999999999999999999999999
Q ss_pred ccc-----CCCceeeEEEeeceeCCCC-CCCCCCCCCCCC-CCCCC
Q 043842 83 SWL-----GRRAVVRGVAMIPVDHPHV-ERSKSSGNNGRC-SFTPW 121 (129)
Q Consensus 83 R~~-----G~RP~VRGvamNpvdHPhG-G~~k~~g~~gr~-~~spw 121 (129)
||+ .+||+|||||||||||||| |+++ + +||+ ++|.+
T Consensus 186 ~~~~~a~~~rwP~VRGVAMNPvDHPHGGGegk-~--~Gr~~tvsr~ 228 (260)
T PTZ00180 186 FHKYRGKRNCWPKVRGVAMNPVEHPHGGGNHQ-H--IGHPSTVSRH 228 (260)
T ss_pred hhhhhCcCCCCCccccEeeCCccCCcCCCCCC-C--CCCCCCcCCC
Confidence 987 4679999999999999999 5665 3 3676 66554
No 9
>KOG0438 consensus Mitochondrial/chloroplast ribosomal protein L2 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=5.8e-43 Score=287.65 Aligned_cols=122 Identities=30% Similarity=0.569 Sum_probs=114.8
Q ss_pred ccccceEEEeeEeCCCCeeEEecCCCceEEEEecCCCeEEEEecCCceEEecCCCceeEEeeeCCCccceeecccccccc
Q 043842 5 GRITHMWNDLRVQPSRWEASSSCRDVNQDFEKEPTSRYCLVRLRCGNEKVIDPRCRATIGTVSNPSHGAKKLSKAGQRSW 84 (129)
Q Consensus 5 ~p~Gt~I~nIE~~pg~gg~l~RsAGt~a~ii~~~~~~~~~ikLPSGe~r~v~~~c~AtiG~vsn~~~~~~~~gKAG~~R~ 84 (129)
||+||+|||||+.|+.+++|||||||+|+|+.+ ++.+++|+|||++++.|+.+|+||||+|||.+|+.+.+||||++||
T Consensus 167 lp~GT~ih~~e~~p~~~~~f~raAGt~a~ilak-~~~~aiv~Lps~r~~~~~~tC~ATvGrvsni~~~~r~~GkAgr~rw 245 (312)
T KOG0438|consen 167 LPVGTLIHNVEITPGRSAQFARAAGTSATILAK-AGKFAIVQLPSKRERSVLRTCVATVGRVSNIDHNHRILGKAGRSRW 245 (312)
T ss_pred cchhhhhhhhccCCCcchhhhhhcCchhhhhhc-CCCceeEEccccchhhhhhhhheeeccccccccccceecccchhhh
Confidence 799999999999999999999999999999988 6899999999999999999999999999999999999999999999
Q ss_pred cCCCceeeEEEeeceeCCCC-CCCCCCCCCCCCCCCCCCcccCCCC
Q 043842 85 LGRRAVVRGVAMIPVDHPHV-ERSKSSGNNGRCSFTPWGKPCKSGN 129 (129)
Q Consensus 85 ~G~RP~VRGvamNpvdHPhG-G~~k~~g~~gr~~~spwG~~~kg~~ 129 (129)
+|+||.||||+||++||||| |.+++.+ -.+|++|||+++|+.+
T Consensus 246 lG~Rp~vrg~~~s~~~H~kgg~~gr~i~--~~~P~~~~~~~ak~~~ 289 (312)
T KOG0438|consen 246 LGKRPQVRGVLMSGLDHPKGGGKGRKIG--RKKPVTPWGKPAKGLR 289 (312)
T ss_pred cccCcccccccccCccCCCCCCcccccc--CCCCCCccccccccCC
Confidence 99999999999999999999 5666643 2579999999999853
No 10
>KOG2309 consensus 60s ribosomal protein L2/L8 [Translation, ribosomal structure and biogenesis]
Probab=99.98 E-value=2.1e-33 Score=224.33 Aligned_cols=112 Identities=28% Similarity=0.363 Sum_probs=103.3
Q ss_pred CccccceEEEeeEeCCCCeeEEecCCCceEEEE-ecCCCeEEEEecCCceEEecCCCceeEEeeeCCCccceeecccccc
Q 043842 4 PGRITHMWNDLRVQPSRWEASSSCRDVNQDFEK-EPTSRYCLVRLRCGNEKVIDPRCRATIGTVSNPSHGAKKLSKAGQR 82 (129)
Q Consensus 4 ~~p~Gt~I~nIE~~pg~gg~l~RsAGt~a~ii~-~~~~~~~~ikLPSGe~r~v~~~c~AtiG~vsn~~~~~~~~gKAG~~ 82 (129)
.+|+|+.|||+|..+||.+.|+|++|.||++|. ..+.+...|+||||..+.+++.|||+||+|++.+..++++.|||+.
T Consensus 100 s~peg~~v~~ve~~~gdrg~lar~sGnya~vIaHn~dt~kTrIkLPsgaKKvV~S~~RamIG~vAggG~~dKp~lKag~a 179 (248)
T KOG2309|consen 100 SMPEGTIVCNVEEKPGDRGALARASGNYAIVIAHNPDTKKTRIKLPSGAKKVVQSACRAMIGVVAGGGRTDKPLLKAGRA 179 (248)
T ss_pred ccccceEEEEeeccCchhhhHHhhcCceeEEEecCccccceEEecCCCccceeccccceEEEEecCCccccchhhhhhhH
Confidence 479999999999999999999999999999995 4688999999999999999999999999999999999999999999
Q ss_pred ccc-----CCCceeeEEEeeceeCCCCCCCCCCCCCCCCC
Q 043842 83 SWL-----GRRAVVRGVAMIPVDHPHVERSKSSGNNGRCS 117 (129)
Q Consensus 83 R~~-----G~RP~VRGvamNpvdHPhGG~~k~~g~~gr~~ 117 (129)
+++ ..||+|||||||||||||||++..- +|.++
T Consensus 180 ~~K~~~Krn~wPrvRGVAMnPVeHphGGgnhqh--ig~~s 217 (248)
T KOG2309|consen 180 YHKYKAKRNCWPRVRGVAMNPVEHPHGGGNHQH--IGKPS 217 (248)
T ss_pred HHHhhhhcCCchhhcceecccccCCCCCCcccc--cCCcc
Confidence 863 4699999999999999999988773 55654
No 11
>PF02736 Myosin_N: Myosin N-terminal SH3-like domain; InterPro: IPR004009 This domain has an SH3-like fold. It is found at the N terminus of many but not all myosins. The function of this domain is unknown.; GO: 0003774 motor activity, 0005524 ATP binding, 0016459 myosin complex; PDB: 2EC6_A 2W4H_M 1O1E_P 1O1D_D 1O18_A 1O1C_P 1O1B_D 1O1F_A 2W4A_M 2W4G_M ....
Probab=78.55 E-value=3.7 Score=24.45 Aligned_cols=26 Identities=15% Similarity=0.199 Sum_probs=20.8
Q ss_pred eEEEEecCCCeEEEEecCCceEEecCC
Q 043842 32 QDFEKEPTSRYCLVRLRCGNEKVIDPR 58 (129)
Q Consensus 32 a~ii~~~~~~~~~ikLPSGe~r~v~~~ 58 (129)
|.|+.. +++.++|++.+|+.+.++.+
T Consensus 16 g~I~~~-~g~~vtV~~~~G~~~tv~~d 41 (42)
T PF02736_consen 16 GEIIEE-EGDKVTVKTEDGKEVTVKKD 41 (42)
T ss_dssp EEEEEE-ESSEEEEEETTTEEEEEEGG
T ss_pred EEEEEE-cCCEEEEEECCCCEEEeCCC
Confidence 566765 68899999999999988753
No 12
>TIGR00739 yajC preprotein translocase, YajC subunit. While this protein is part of the preprotein translocase in Escherichia coli, it is not essential for viability or protein secretion. The N-terminus region contains a predicted membrane-spanning region followed by a region consisting almost entirely of residues with charged (acidic, basic, or zwitterionic) side chains. This small protein is about 100 residues in length, and is restricted to bacteria; however, this protein is absent from some lineages, including spirochetes and Mycoplasmas.
Probab=62.54 E-value=19 Score=24.65 Aligned_cols=40 Identities=8% Similarity=0.009 Sum_probs=32.2
Q ss_pred CeeEEecCCCceEEEEecCCCeEEEEecCCceEEecCCCce
Q 043842 21 WEASSSCRDVNQDFEKEPTSRYCLVRLRCGNEKVIDPRCRA 61 (129)
Q Consensus 21 gg~l~RsAGt~a~ii~~~~~~~~~ikLPSGe~r~v~~~c~A 61 (129)
|.+..-++|-|++|++- +++++.|++..|-...++....+
T Consensus 41 Gd~VvT~gGi~G~V~~i-~d~~v~vei~~g~~i~~~r~aI~ 80 (84)
T TIGR00739 41 GDKVLTIGGIIGTVTKI-AENTIVIELNDNTEITFSKNAIV 80 (84)
T ss_pred CCEEEECCCeEEEEEEE-eCCEEEEEECCCeEEEEEhHHhh
Confidence 46689999999999986 56799999988877777766543
No 13
>PRK05585 yajC preprotein translocase subunit YajC; Validated
Probab=62.25 E-value=16 Score=26.09 Aligned_cols=42 Identities=12% Similarity=0.151 Sum_probs=33.9
Q ss_pred CCeeEEecCCCceEEEEecCCCeEEEEecCCceEEecCCCcee
Q 043842 20 RWEASSSCRDVNQDFEKEPTSRYCLVRLRCGNEKVIDPRCRAT 62 (129)
Q Consensus 20 ~gg~l~RsAGt~a~ii~~~~~~~~~ikLPSGe~r~v~~~c~At 62 (129)
.|.+..-++|-|++|++- +++.+.|++..|-...|+....+.
T Consensus 55 ~Gd~VvT~gGi~G~Vv~i-~~~~v~lei~~g~~i~~~r~aI~~ 96 (106)
T PRK05585 55 KGDEVVTNGGIIGKVTKV-SEDFVIIELNDDTEIKIQKSAIAA 96 (106)
T ss_pred CCCEEEECCCeEEEEEEE-eCCEEEEEECCCeEEEEEhHHhhh
Confidence 356799999999999986 568999999988777787775543
No 14
>PF02699 YajC: Preprotein translocase subunit; InterPro: IPR003849 Secretion across the inner membrane in some Gram-negative bacteria occurs via the preprotein translocase pathway. Proteins are produced in the cytoplasm as precursors, and require a chaperone subunit to direct them to the translocase component []. From there, the mature proteins are either targeted to the outer membrane, or remain as periplasmic proteins []. The translocase protein subunits are encoded on the bacterial chromosome. The translocase itself comprises 7 proteins, including a chaperone (SecB), ATPase (SecA), an integral membrane complex (SecY, SecE and SecG), and two additional membrane proteins that promote the release of the mature peptide into the periplasm (SecD and SecF) []. Other cytoplasmic/periplasmic proteins play a part in preprotein translocase activity, namely YidC and YajC []. The latter is bound in a complex to SecD and SecF, and plays a part in stabilising and regulating secretion through the SecYEG integral membrane component via SecA []. Homologues of the YajC gene have been found in a range of pathogenic and commensal microbes. Brucella abortis YajC- and SecD-like proteins were shown to stimulate a Th1 cell-mediated immune response in mice, and conferred protection when challenged with B.abortis []. Therefore, these proteins may have an antigenic role as well as a secretory one in virulent bacteria []. A number of previously uncharacterised "hypothetical" proteins also show similarity to E.coli YajC, suggesting that this family is wider than first thought []. More recently, the precise interactions between the E.coli SecYEG complex, SecD, SecF, YajC and YidC have been studied []. Rather than acting individually, the four proteins form a heterotetrameric complex and associate with the SecYEG heterotrimeric complex []. The SecF and YajC subunits link the complex to the integral membrane translocase. ; PDB: 2RDD_B.
Probab=54.97 E-value=4 Score=27.73 Aligned_cols=41 Identities=7% Similarity=0.053 Sum_probs=0.0
Q ss_pred CeeEEecCCCceEEEEecCCCeEEEEecCCceEEecCCCcee
Q 043842 21 WEASSSCRDVNQDFEKEPTSRYCLVRLRCGNEKVIDPRCRAT 62 (129)
Q Consensus 21 gg~l~RsAGt~a~ii~~~~~~~~~ikLPSGe~r~v~~~c~At 62 (129)
|.+..-++|-|++|++- +++.+.|++.+|-...++.+..+.
T Consensus 40 Gd~VvT~gGi~G~V~~i-~~~~v~lei~~g~~i~v~k~aI~~ 80 (82)
T PF02699_consen 40 GDEVVTIGGIYGTVVEI-DDDTVVLEIAPGVEITVEKSAIAR 80 (82)
T ss_dssp ------------------------------------------
T ss_pred CCEEEECCcEEEEEEEE-eCCEEEEEECCCeEEEEEHHHhHh
Confidence 45688899999999987 788999999999777777766543
No 15
>PRK05886 yajC preprotein translocase subunit YajC; Validated
Probab=47.55 E-value=62 Score=23.43 Aligned_cols=42 Identities=5% Similarity=-0.112 Sum_probs=33.2
Q ss_pred CCeeEEecCCCceEEEEecCCCeEEEEecCCceEEecCCCcee
Q 043842 20 RWEASSSCRDVNQDFEKEPTSRYCLVRLRCGNEKVIDPRCRAT 62 (129)
Q Consensus 20 ~gg~l~RsAGt~a~ii~~~~~~~~~ikLPSGe~r~v~~~c~At 62 (129)
.|.+.+-++|=|++|++- ++++++|++..|-...|+....+.
T Consensus 41 ~GD~VvT~gGi~G~V~~I-~d~~v~leia~gv~i~~~r~AI~~ 82 (109)
T PRK05886 41 PGDRVHTTSGLQATIVGI-TDDTVDLEIAPGVVTTWMKLAVRD 82 (109)
T ss_pred CCCEEEECCCeEEEEEEE-eCCEEEEEECCCeEEEEEhhheee
Confidence 346799999999999986 567999999888777777765543
No 16
>PF06592 DUF1138: Protein of unknown function (DUF1138); InterPro: IPR009515 This family consists of several hypothetical short plant proteins from Arabidopsis thaliana and Oryza sativa. The function of this family is unknown.
Probab=34.29 E-value=18 Score=24.72 Aligned_cols=25 Identities=24% Similarity=0.311 Sum_probs=15.3
Q ss_pred ecccccccccCCCceeeE--EEeeceeC
Q 043842 76 LSKAGQRSWLGRRAVVRG--VAMIPVDH 101 (129)
Q Consensus 76 ~gKAG~~R~~G~RP~VRG--vamNpvdH 101 (129)
+.+|=..++. -||+.-| |+|||++|
T Consensus 41 W~~aT~~K~q-aWPR~agpPVvmNPisr 67 (73)
T PF06592_consen 41 WWKATDKKFQ-AWPREAGPPVVMNPISR 67 (73)
T ss_pred HHHHHHHHHh-hCcccCCCCeeeccccc
Confidence 3444444444 3666654 89999987
No 17
>PF13953 PapC_C: PapC C-terminal domain; PDB: 3L48_E 2XET_A 3RFZ_E 2KT6_A.
Probab=33.00 E-value=80 Score=20.15 Aligned_cols=51 Identities=12% Similarity=0.088 Sum_probs=23.5
Q ss_pred cCccccceEEEeeEeCCCCeeEEecCCCceEEE-E-ecCCCeEEEEecCCceEEecCCCceeE
Q 043842 3 IPGRITHMWNDLRVQPSRWEASSSCRDVNQDFE-K-EPTSRYCLVRLRCGNEKVIDPRCRATI 63 (129)
Q Consensus 3 ~~~p~Gt~I~nIE~~pg~gg~l~RsAGt~a~ii-~-~~~~~~~~ikLPSGe~r~v~~~c~Ati 63 (129)
-|+|.|+.|.+-+ ++.+=-.|--.++. + ..+.+...|+...+. ...|.+.+
T Consensus 9 ~~lPfGA~v~~~~------g~~~g~Vg~~G~vyl~~~~~~~~L~V~w~~~~----~~~C~~~~ 61 (68)
T PF13953_consen 9 KPLPFGASVSDED------GNNIGIVGQDGQVYLSGLPPKGTLTVKWGDGA----NQQCQIDY 61 (68)
T ss_dssp EE--TT-EEEETT------SSEEEEB-GCGEEEEEEE-TCEEEEEESTSCT----TSEEEEEE
T ss_pred CcCCCCcEEEcCC------CCEEEEEcCCCEEEEECCCCCcEEEEEECCCC----CCeEEEEe
Confidence 3789999999632 22333333333332 1 224566666665553 44565544
No 18
>PF09962 DUF2196: Uncharacterized conserved protein (DUF2196); InterPro: IPR019240 A pair of adjacent genes, ablAB (acetyl-beta-lysine biosynthesis) encodes lysine 2,3-aminomutase and beta-lysine acetyltransferase in methanogenic archaea. Homologous pairs, possibly with identical function, occur in a wide range of species, including Bacillus subtilis. This model describes a conserved hypothetical protein, small in size, with a phylogenetic distribution moderately well correlated to that of the acetyltransferase family. This protein family is also described as DUF2196 and COG4895 from COG. The function is unknown.
Probab=31.87 E-value=24 Score=23.34 Aligned_cols=17 Identities=24% Similarity=0.464 Sum_probs=14.1
Q ss_pred CceeeEEEeeceeCCCC
Q 043842 88 RAVVRGVAMIPVDHPHV 104 (129)
Q Consensus 88 RP~VRGvamNpvdHPhG 104 (129)
+..|.=+--|..+||||
T Consensus 30 ~GiV~~iLT~s~~HP~G 46 (62)
T PF09962_consen 30 EGIVKDILTNSPTHPHG 46 (62)
T ss_pred cEEhheeecCCCCCCCC
Confidence 56677777899999999
No 19
>cd01770 p47_UBX p47-like ubiquitin domain. p47_UBX p47 is an adaptor molecule of the cytosolic AAA ATPase p97. The principal role of the p97-p47 complex is to regulate membrane fusion events. Mono-ubiquitin recognition by p47 is crucial for p97-p47-mediated Golgi membrane fusion events. p47 has carboxy-terminal SEP and UBX domains. The UBX domain has a beta-grasp fold similar to that of ubiquitin however, UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins.
Probab=30.76 E-value=25 Score=23.53 Aligned_cols=27 Identities=19% Similarity=0.183 Sum_probs=18.0
Q ss_pred CCeEEEEecCCceEEecCCCceeEEee
Q 043842 40 SRYCLVRLRCGNEKVIDPRCRATIGTV 66 (129)
Q Consensus 40 ~~~~~ikLPSGe~r~v~~~c~AtiG~v 66 (129)
...+.||||+|+.....-+.-.||+.|
T Consensus 4 ~t~iqiRlpdG~r~~~rF~~~~tv~~l 30 (79)
T cd01770 4 TTSIQIRLADGKRLVQKFNSSHRVSDV 30 (79)
T ss_pred eeEEEEECCCCCEEEEEeCCCCcHHHH
Confidence 357889999998775444455666544
No 20
>PF01176 eIF-1a: Translation initiation factor 1A / IF-1; InterPro: IPR006196 The S1 domain of around 70 amino acids, originally identified in ribosomal protein S1, is found in a large number of RNA-associated proteins. It has been shown that S1 proteins bind RNA through their S1 domains with some degree of sequence specificity. This type of S1 domain is found in translation initiation factor 1. The solution structure of one S1 RNA-binding domain from Escherichia coli polynucleotide phosphorylase has been determined []. It displays some similarity with the cold shock domain (CSD) (IPR002059 from INTERPRO). Both the S1 and the CSD domain consist of an antiparallel beta barrel of the same topology with 5 beta strands. This fold is also shared by many other proteins of unrelated function and is known as the OB fold. However, the S1 and CSD fold can be distinguished from the other OB folds by the presence of a short 3(10) helix at the end of strand 3. This unique feature is likely to form a part of the DNA/RNA-binding site. This entry is specific for bacterial, chloroplastic and eukaryotic IF-1 type S1 domains.; GO: 0003723 RNA binding, 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1JT8_A 3I4O_A 1AH9_A 1ZO1_W 1D7Q_A 2OQK_A 2DGY_A 1HR0_W.
Probab=30.53 E-value=1e+02 Score=19.66 Aligned_cols=24 Identities=13% Similarity=0.063 Sum_probs=18.0
Q ss_pred ceEEEEecCCCeEEEEecCCceEE
Q 043842 31 NQDFEKEPTSRYCLVRLRCGNEKV 54 (129)
Q Consensus 31 ~a~ii~~~~~~~~~ikLPSGe~r~ 54 (129)
+++|++-..+++..|+|++|+.++
T Consensus 6 ~~~V~~~lG~~~~~V~~~dg~~~l 29 (65)
T PF01176_consen 6 IGRVTEMLGNNLFEVECEDGEERL 29 (65)
T ss_dssp EEEEEEEESSSEEEEEETTSEEEE
T ss_pred EEEEEEECCCCEEEEEeCCCCEEE
Confidence 566775436788899999998776
No 21
>PF12791 RsgI_N: Anti-sigma factor N-terminus; InterPro: IPR024449 The heat shock genes in Bacillus subtilis can be classified into several groups according to their regulation [], and the sigma gene, sigI, of Bacillus subtilis belongs to the group IV heat-shock response genes and has many orthologues in the bacterial phylum Firmicutes []. Regulation of sigma factor I is carried out by RsgI from the same operon. This entry represents the N-terminal cytoplasmic portion of RsgI ('upstream' of the single transmembrane helix) which has been shown to interact directly with Sigma-I [].
Probab=30.23 E-value=66 Score=19.66 Aligned_cols=28 Identities=18% Similarity=0.226 Sum_probs=22.7
Q ss_pred CCCeEEEEecCCceEEecCCCceeEEee
Q 043842 39 TSRYCLVRLRCGNEKVIDPRCRATIGTV 66 (129)
Q Consensus 39 ~~~~~~ikLPSGe~r~v~~~c~AtiG~v 66 (129)
++++++|--|+|+...|....-.-||+.
T Consensus 4 ~~~~aiVlT~dGeF~~ik~~~~~~vG~e 31 (56)
T PF12791_consen 4 KKKYAIVLTPDGEFIKIKRKPGMEVGQE 31 (56)
T ss_pred cCCEEEEEcCCCcEEEEeCCCCCcccCE
Confidence 4678888888888888888888888863
No 22
>smart00166 UBX Domain present in ubiquitin-regulatory proteins. Present in FAF1 and Shp1p.
Probab=28.44 E-value=30 Score=22.68 Aligned_cols=26 Identities=23% Similarity=0.117 Sum_probs=15.2
Q ss_pred CCeEEEEecCCceEEecCCCceeEEe
Q 043842 40 SRYCLVRLRCGNEKVIDPRCRATIGT 65 (129)
Q Consensus 40 ~~~~~ikLPSGe~r~v~~~c~AtiG~ 65 (129)
.-.+.||||+|+.....-..-.+|..
T Consensus 4 ~~~I~iRlPdG~ri~~~F~~~~tl~~ 29 (80)
T smart00166 4 QCRLQIRLPDGSRLVRRFPSSDTLRT 29 (80)
T ss_pred eEEEEEEcCCCCEEEEEeCCCCcHHH
Confidence 34678899999855333333344443
No 23
>PF06822 DUF1235: Protein of unknown function (DUF1235); InterPro: IPR009641 This family contains a number of poxviral proteins, which include Vaccinia virus, A37, the function of which is unknown.
Probab=28.17 E-value=1.4e+02 Score=24.90 Aligned_cols=45 Identities=7% Similarity=0.020 Sum_probs=34.9
Q ss_pred ecC--CCceEEEEecCCCeEEEEecCCceEEecCCCceeEEeeeCCC
Q 043842 26 SCR--DVNQDFEKEPTSRYCLVRLRCGNEKVIDPRCRATIGTVSNPS 70 (129)
Q Consensus 26 RsA--Gt~a~ii~~~~~~~~~ikLPSGe~r~v~~~c~AtiG~vsn~~ 70 (129)
||| |-.-.|......+..+++|+.+....+|+.|.-+|-.|..+.
T Consensus 81 ~sakkGG~iii~~~~~~~kkii~~~~~~aVlLspl~~y~Vs~V~~G~ 127 (266)
T PF06822_consen 81 QSAKKGGCIIIRNTISNDKKIITPNQNMAVLLSPLADYDVSNVTKGS 127 (266)
T ss_pred eccccCCeEEEeecccCCceEEecCCCeEEEecchhheEEEEecCCc
Confidence 667 666555544346788999999999999999999997776654
No 24
>KOG0265 consensus U5 snRNP-specific protein-like factor and related proteins [RNA processing and modification]
Probab=26.61 E-value=1.5e+02 Score=25.62 Aligned_cols=46 Identities=7% Similarity=0.023 Sum_probs=32.7
Q ss_pred ceEEEeeEeCCCCeeEEecCCCceEEE-E--ecCCCeEEEEecCCceEEe
Q 043842 9 HMWNDLRVQPSRWEASSSCRDVNQDFE-K--EPTSRYCLVRLRCGNEKVI 55 (129)
Q Consensus 9 t~I~nIE~~pg~gg~l~RsAGt~a~ii-~--~~~~~~~~ikLPSGe~r~v 55 (129)
..|++++..| +|.-|+-+.=.-++++ . ..++|+.++|+-||.+.-+
T Consensus 48 geI~~~~F~P-~gs~~aSgG~Dr~I~LWnv~gdceN~~~lkgHsgAVM~l 96 (338)
T KOG0265|consen 48 GEIYTIKFHP-DGSCFASGGSDRAIVLWNVYGDCENFWVLKGHSGAVMEL 96 (338)
T ss_pred ceEEEEEECC-CCCeEeecCCcceEEEEeccccccceeeeccccceeEee
Confidence 4799999999 7766664443444445 3 2468999999999977643
No 25
>cd01771 Faf1_UBX Faf1 UBX domain. Faf1 (fas-associated factor1) is a nucleolar protein that was first identified as an interaction partner of the death receptor Fas. Faf1 contains N-terminal UAS (ubiquitin-associated) and C-terminal UBX (ubiquitin-like) domains and is closely related to other UBA/UBX-containing proteins like p47, Rep8 and SAKS1. Faf1 is thought to be involved in 18S rRNA synthesis and/or 40S ribosomal subunit assembly. The UBX domain has a beta-grasp fold similar to that of ubiquitin however, UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins.
Probab=25.82 E-value=75 Score=21.31 Aligned_cols=19 Identities=16% Similarity=-0.078 Sum_probs=14.0
Q ss_pred CeEEEEecCCceE--EecCCC
Q 043842 41 RYCLVRLRCGNEK--VIDPRC 59 (129)
Q Consensus 41 ~~~~ikLPSGe~r--~v~~~c 59 (129)
-.+.||||+|+.. .|+.++
T Consensus 5 ~~i~iRlP~G~r~~rrF~~t~ 25 (80)
T cd01771 5 SKLRVRTPSGDFLERRFLGDT 25 (80)
T ss_pred EEEEEECCCCCEEEEEeCCCC
Confidence 4678999999863 666655
No 26
>PHA02985 hypothetical protein; Provisional
Probab=25.21 E-value=1.6e+02 Score=24.82 Aligned_cols=45 Identities=16% Similarity=0.124 Sum_probs=33.8
Q ss_pred ecC--CCceEEEEecCCCeEEEEecCCceEEecCCCceeEEeeeCCC
Q 043842 26 SCR--DVNQDFEKEPTSRYCLVRLRCGNEKVIDPRCRATIGTVSNPS 70 (129)
Q Consensus 26 RsA--Gt~a~ii~~~~~~~~~ikLPSGe~r~v~~~c~AtiG~vsn~~ 70 (129)
||| |-.-.|..+...+..++.++.+....+|+.|.-+|-.|.-+.
T Consensus 86 qsAkkGG~iIi~~~~~~~K~ii~~~~n~aVlLSPLs~Y~Vs~V~kGs 132 (271)
T PHA02985 86 QSAKKGGCIIIINNITNNKKIITLNINHIIILSPLSKYTVSKVSKGS 132 (271)
T ss_pred eecccCCEEEEecccccCceEEecCCCeEEEecchhhceEEEecCCc
Confidence 455 544445444467788999999999999999999997766543
No 27
>PF08661 Rep_fac-A_3: Replication factor A protein 3; InterPro: IPR013970 Replication factor A is involved in eukaryotic DNA replication, recombination and repair. ; PDB: 2PI2_H 1L1O_D 3KDF_A 2Z6K_D 1QUQ_D 2PQA_D.
Probab=22.97 E-value=2.1e+02 Score=19.78 Aligned_cols=47 Identities=13% Similarity=0.160 Sum_probs=27.0
Q ss_pred eeEEecC--CCceEEEEecCCCeEEEEecCCceEEecCCCceeEEeeeCCC
Q 043842 22 EASSSCR--DVNQDFEKEPTSRYCLVRLRCGNEKVIDPRCRATIGTVSNPS 70 (129)
Q Consensus 22 g~l~RsA--Gt~a~ii~~~~~~~~~ikLPSGe~r~v~~~c~AtiG~vsn~~ 70 (129)
|++.+.. |..+++..- ++..+.|+|++...-.+ ..+.=+||+|.+..
T Consensus 25 Gkv~~~~~~g~~~~l~~~-d~~~V~v~l~~~~~~~~-~~~vEviG~V~~~~ 73 (109)
T PF08661_consen 25 GKVESVDPDGGSATLSTS-DGGQVTVSLNPPSDEEL-SKYVEVIGKVNDDG 73 (109)
T ss_dssp EEEEEE-TTSSEEEEE-T-TS-EEEEEESS--SS----SEEEEEEEE-TTS
T ss_pred EEEeeEcCCCCEEEEEcC-CCCEEEEEeCCCCCCCC-CCEEEEEEEEcCCC
Confidence 4444444 788887764 67788999887643322 45667889888765
No 28
>cd01767 UBX UBX (ubiquitin regulatory X) domain. The UBX (ubiquitin regulatory X) domain has a beta-grasp fold that is structurally quite similar to ubiquitin although UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins. Most UBX-containing proteins including p47, FAF1, and SAKS1 (Y33K) also contain a UBA (ubiquitin-associated) domain and are thought to serve as adaptor molecules that shuttle proteins to the proteasome for degradation.
Probab=22.30 E-value=42 Score=21.72 Aligned_cols=21 Identities=14% Similarity=0.257 Sum_probs=13.9
Q ss_pred eEEEEecCCce--EEecCCCceeEE
Q 043842 42 YCLVRLRCGNE--KVIDPRCRATIG 64 (129)
Q Consensus 42 ~~~ikLPSGe~--r~v~~~c~AtiG 64 (129)
.+.||||+|+. +.|+.+ ++|.
T Consensus 4 ~i~iRlpdG~~~~~~F~~~--~tl~ 26 (77)
T cd01767 4 KIQIRLPDGKRLEQRFNST--HKLS 26 (77)
T ss_pred EEEEEcCCCCEEEEEeCCC--CCHH
Confidence 57889999985 455544 4444
No 29
>cd04456 S1_IF1A_like S1_IF1A_like: Translation initiation factor IF1A-like, S1-like RNA-binding domain. IF1A is also referred to as eIF1A in eukaryotes and aIF1A in archaea. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea.
Probab=21.96 E-value=1.9e+02 Score=19.41 Aligned_cols=24 Identities=8% Similarity=-0.053 Sum_probs=15.6
Q ss_pred ceEEEEecCCCeEEEEecCCceEE
Q 043842 31 NQDFEKEPTSRYCLVRLRCGNEKV 54 (129)
Q Consensus 31 ~a~ii~~~~~~~~~ikLPSGe~r~ 54 (129)
+++|++-..++...+++++|+.++
T Consensus 3 i~~V~~~lG~~~~~V~~~dg~~~l 26 (78)
T cd04456 3 IVRVLRMLGNNRHEVECADGQRRL 26 (78)
T ss_pred EEEEEEECCCCEEEEEECCCCEEE
Confidence 566664335667777777777665
No 30
>cd01773 Faf1_like1_UBX Faf1 ike-1 UBX domain. Faf1_like1 is a protein of unknown function with a domain architecture that includes the UAS (ubiquitin-associated) and UBX (ubiquitin-like) domains. This protein is related to other UBA/UBX-containing proteins like Faf1, p47, and SAKS1 and may serve as an adaptor molecule that shuttles proteins to the proteasome for degradation. The UBX domain has a beta-grasp fold similar to that of ubiquitin however, UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins.
Probab=21.78 E-value=66 Score=22.06 Aligned_cols=15 Identities=13% Similarity=0.200 Sum_probs=11.8
Q ss_pred CCeEEEEecCCceEE
Q 043842 40 SRYCLVRLRCGNEKV 54 (129)
Q Consensus 40 ~~~~~ikLPSGe~r~ 54 (129)
...+.||||+|+.+.
T Consensus 5 ~t~i~vRlP~G~r~~ 19 (82)
T cd01773 5 KARLMLRYPDGKREQ 19 (82)
T ss_pred eeEEEEECCCCCEEE
Confidence 346789999999764
No 31
>PF09923 DUF2155: Uncharacterized protein conserved in bacteria (DUF2155); InterPro: IPR019225 This entry contains various hypothetical prokaryotic proteins that have no known function.
Probab=21.61 E-value=35 Score=23.82 Aligned_cols=8 Identities=38% Similarity=0.866 Sum_probs=6.9
Q ss_pred EeeceeCC
Q 043842 95 AMIPVDHP 102 (129)
Q Consensus 95 amNpvdHP 102 (129)
|+|+.|||
T Consensus 74 al~~~eHP 81 (90)
T PF09923_consen 74 ALNALEHP 81 (90)
T ss_pred ccccccCc
Confidence 68899998
No 32
>cd05792 S1_eIF1AD_like S1_eIF1AD_like: eukaryotic translation initiation factor 1A domain containing protein (eIF1AD)-like, S1-like RNA-binding domain. eIF1AD is also known as MGC11102 protein. Little is known about the function of eIF1AD. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins, including translation initiation factor IF1A (also referred to as eIF1A in eukaryotes). eIF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors.
Probab=21.38 E-value=1.7e+02 Score=19.82 Aligned_cols=16 Identities=13% Similarity=0.073 Sum_probs=7.6
Q ss_pred CCCeEEEEecCCceEE
Q 043842 39 TSRYCLVRLRCGNEKV 54 (129)
Q Consensus 39 ~~~~~~ikLPSGe~r~ 54 (129)
.++...+..|+|+.++
T Consensus 11 G~n~~~V~~~dG~~~l 26 (78)
T cd05792 11 GNNLHEVETPNGSRYL 26 (78)
T ss_pred CCcEEEEEcCCCCEEE
Confidence 3444445555554443
No 33
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=20.72 E-value=1.9e+02 Score=19.61 Aligned_cols=24 Identities=17% Similarity=-0.003 Sum_probs=13.6
Q ss_pred ceEEEEecCCCeEEEEecCCceEE
Q 043842 31 NQDFEKEPTSRYCLVRLRCGNEKV 54 (129)
Q Consensus 31 ~a~ii~~~~~~~~~ikLPSGe~r~ 54 (129)
+++|++-..++...|+|++|+.++
T Consensus 8 ~g~V~~~lG~~~~~V~~~dG~~~l 31 (83)
T smart00652 8 IAQVVKMLGNGRLEVMCADGKERL 31 (83)
T ss_pred EEEEEEEcCCCEEEEEECCCCEEE
Confidence 345553324566666777776654
Done!