Query 036919
Match_columns 132
No_of_seqs 110 out of 746
Neff 4.4
Searched_HMMs 46136
Date Fri Mar 29 06:41:43 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/036919.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/036919hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0093 RplN Ribosomal protein 100.0 3.3E-42 7.3E-47 256.6 11.1 97 35-131 1-99 (122)
2 CHL00057 rpl14 ribosomal prote 100.0 3.5E-41 7.6E-46 251.5 11.6 97 35-131 1-99 (122)
3 PRK05483 rplN 50S ribosomal pr 100.0 3.5E-41 7.7E-46 251.4 11.5 97 35-131 1-99 (122)
4 TIGR01067 rplN_bact ribosomal 100.0 5.7E-41 1.2E-45 250.1 11.4 97 35-131 1-99 (122)
5 PTZ00054 60S ribosomal protein 100.0 1.8E-39 4E-44 247.1 11.2 94 35-131 18-117 (139)
6 PRK08571 rpl14p 50S ribosomal 100.0 2.9E-39 6.3E-44 244.2 11.2 94 35-131 11-110 (132)
7 TIGR03673 rpl14p_arch 50S ribo 100.0 3.8E-39 8.2E-44 243.3 11.2 95 34-131 9-109 (131)
8 PF00238 Ribosomal_L14: Riboso 100.0 8.9E-39 1.9E-43 237.6 10.9 97 35-131 1-99 (122)
9 PTZ00320 ribosomal protein L14 100.0 8.8E-37 1.9E-41 241.0 11.3 95 37-131 61-165 (188)
10 KOG0901 60S ribosomal protein 100.0 2.3E-28 5E-33 187.3 9.6 99 33-131 17-123 (145)
11 KOG3441 Mitochondrial ribosoma 99.7 5.9E-18 1.3E-22 128.6 6.8 84 36-132 32-123 (149)
12 cd03696 selB_II selB_II: this 65.7 19 0.00041 23.9 4.8 55 35-90 26-81 (83)
13 cd03695 CysN_NodQ_II CysN_NodQ 65.1 30 0.00064 23.3 5.7 52 36-90 27-79 (81)
14 PF08447 PAS_3: PAS fold; Int 60.0 10 0.00022 24.1 2.6 30 98-127 57-86 (91)
15 cd03698 eRF3_II_like eRF3_II_l 58.4 25 0.00055 23.4 4.4 54 36-90 27-81 (83)
16 cd03693 EF1_alpha_II EF1_alpha 56.9 28 0.00062 23.7 4.6 55 35-90 30-85 (91)
17 cd04089 eRF3_II eRF3_II: domai 49.5 42 0.00091 22.3 4.4 54 36-90 26-80 (82)
18 COG1465 Predicted alternative 47.6 1.2E+02 0.0026 26.9 7.8 71 47-127 260-344 (376)
19 cd03694 GTPBP_II Domain II of 44.4 59 0.0013 22.0 4.5 53 36-89 27-84 (87)
20 PF14578 GTP_EFTU_D4: Elongati 41.2 88 0.0019 22.0 5.0 51 35-91 29-80 (81)
21 PF00575 S1: S1 RNA binding do 35.1 80 0.0017 19.9 3.8 25 85-114 3-27 (74)
22 TIGR01024 rplS_bact ribosomal 35.1 72 0.0016 23.8 4.0 35 64-100 18-52 (113)
23 PF01245 Ribosomal_L19: Riboso 34.6 75 0.0016 23.5 4.0 34 64-100 18-52 (113)
24 PF10382 DUF2439: Protein of u 33.6 55 0.0012 22.6 3.0 26 104-130 20-47 (83)
25 cd03697 EFTU_II EFTU_II: Elong 30.2 1.7E+02 0.0036 19.6 5.0 54 36-90 27-83 (87)
26 PRK05338 rplS 50S ribosomal pr 28.3 1.1E+02 0.0023 22.9 4.0 35 64-100 18-52 (116)
27 CHL00084 rpl19 ribosomal prote 27.9 1.1E+02 0.0024 22.9 4.0 34 64-99 22-55 (117)
28 TIGR01644 phage_P2_V phage bas 26.7 2.7E+02 0.0058 21.4 6.2 82 33-123 6-107 (191)
29 KOG2449 Methylmalonate semiald 26.5 1E+02 0.0023 24.4 3.8 54 66-124 66-122 (157)
30 PRK06299 rpsA 30S ribosomal pr 25.9 2.4E+02 0.0052 25.3 6.4 50 66-120 420-489 (565)
31 cd04454 S1_Rrp4_like S1_Rrp4_l 25.1 1.8E+02 0.0038 19.0 4.3 15 84-98 51-65 (82)
32 cd04497 hPOT1_OB1_like hPOT1_O 23.6 1.4E+02 0.003 22.0 3.9 33 40-73 39-77 (138)
33 PF08206 OB_RNB: Ribonuclease 22.5 96 0.0021 19.6 2.5 15 63-77 30-44 (58)
34 KOG0149 Predicted RNA-binding 21.3 97 0.0021 26.2 2.8 30 86-115 36-65 (247)
35 cd04492 YhaM_OBF_like YhaM_OBF 21.1 1.3E+02 0.0028 18.9 2.9 37 40-76 21-58 (83)
36 COG0335 RplS Ribosomal protein 21.1 1.6E+02 0.0034 22.3 3.7 31 66-99 22-53 (115)
37 PF04170 NlpE: NlpE N-terminal 20.9 1.3E+02 0.0028 20.6 3.0 24 106-129 63-86 (87)
38 cd06555 ASCH_PF0470_like ASC-1 20.3 1.3E+02 0.0028 22.1 3.0 29 48-76 15-43 (109)
No 1
>COG0093 RplN Ribosomal protein L14 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=3.3e-42 Score=256.55 Aligned_cols=97 Identities=53% Similarity=0.722 Sum_probs=94.2
Q ss_pred ccccCCeEEEeeccCcceEEEEEeeCC--eeeeecCcEEEEEEeeecCCCcccccceEEEEEEecccccccCCCcEEEec
Q 036919 35 FIQMRTVLKVADNSGVKTVMCIQPLKG--KKVARLGDTIVVSVKEVMPNAKVKKGEVVKAVVVRAAMDHGRCDGSFVKFD 112 (132)
Q Consensus 35 MIq~~T~L~VaDNSGak~v~CI~vl~g--rk~a~vGD~IivsVKk~~p~~kikKg~V~kAVIVRtKk~~~R~dG~~IkFd 112 (132)
|||.+|+|+||||||||+++||+++++ |++|.+||+|++|||++.|...+||||+++|||||||++++|+||++|+||
T Consensus 1 miq~~t~l~vADNSGAk~v~~I~V~gg~~r~~A~vGD~ivvsVKka~P~~~vKkg~V~~AViVRtkk~~rR~DGs~i~Fd 80 (122)
T COG0093 1 MIQVQTRLNVADNSGAKEVMCIKVLGGSRRRYAGVGDIIVVSVKKAIPRGMVKKGDVVKAVVVRTKKEVRRPDGSYIKFD 80 (122)
T ss_pred CcccccEEEEccCCCCcEEEEEEEeccccccccCCCCEEEEEEeeccCCcceeccceEEEEEEEeCCceEcCCCCEEEeC
Confidence 899999999999999999999999986 669999999999999999999999999999999999999999999999999
Q ss_pred cceEEEEcCCCCcceeecc
Q 036919 113 DNAVVLIDNLCVLAFAEHT 131 (132)
Q Consensus 113 dNAvVLIn~kg~p~~~~~~ 131 (132)
|||+||+|++|+|+|+|+.
T Consensus 81 dNA~Viin~~g~P~GtrI~ 99 (122)
T COG0093 81 DNAAVIINPDGEPRGTRIF 99 (122)
T ss_pred CceEEEECCCCCcccceEe
Confidence 9999999999999999974
No 2
>CHL00057 rpl14 ribosomal protein L14
Probab=100.00 E-value=3.5e-41 Score=251.49 Aligned_cols=97 Identities=43% Similarity=0.643 Sum_probs=94.2
Q ss_pred ccccCCeEEEeeccCcceEEEEEeeCC--eeeeecCcEEEEEEeeecCCCcccccceEEEEEEecccccccCCCcEEEec
Q 036919 35 FIQMRTVLKVADNSGVKTVMCIQPLKG--KKVARLGDTIVVSVKEVMPNAKVKKGEVVKAVVVRAAMDHGRCDGSFVKFD 112 (132)
Q Consensus 35 MIq~~T~L~VaDNSGak~v~CI~vl~g--rk~a~vGD~IivsVKk~~p~~kikKg~V~kAVIVRtKk~~~R~dG~~IkFd 112 (132)
|||.+|+|+|+|||||++++||++|++ +++|++||+|+||||+++|+++++|||+++|||||||++++|+||++++||
T Consensus 1 MIq~~t~l~v~DNSGak~v~cI~v~~~~~~~~a~vGD~IvvsVk~~~~~~k~kkg~v~kAvIVrtk~~~~r~dG~~i~F~ 80 (122)
T CHL00057 1 MIQPQTYLNVADNSGARKLMCIRVLGASNRKYAHIGDVIIAVVKEAVPNMPLKRSEVVRAVIVRTCKELKRDNGMIIRFD 80 (122)
T ss_pred CCCcCCEEEEeECCCCcEEEEEEEeCCCCCccccCCCEEEEEEEeccCCCceecCCEEEEEEEEeccccCcCCCcEEEcC
Confidence 999999999999999999999999975 678999999999999999999999999999999999999999999999999
Q ss_pred cceEEEEcCCCCcceeecc
Q 036919 113 DNAVVLIDNLCVLAFAEHT 131 (132)
Q Consensus 113 dNAvVLIn~kg~p~~~~~~ 131 (132)
|||+||+|++++|+|+|+.
T Consensus 81 ~Na~VLin~~~~p~GTrI~ 99 (122)
T CHL00057 81 DNAAVVIDQEGNPKGTRVF 99 (122)
T ss_pred CceEEEECCCCCEeEeEEE
Confidence 9999999999999999975
No 3
>PRK05483 rplN 50S ribosomal protein L14; Validated
Probab=100.00 E-value=3.5e-41 Score=251.35 Aligned_cols=97 Identities=55% Similarity=0.747 Sum_probs=94.1
Q ss_pred ccccCCeEEEeeccCcceEEEEEeeCC--eeeeecCcEEEEEEeeecCCCcccccceEEEEEEecccccccCCCcEEEec
Q 036919 35 FIQMRTVLKVADNSGVKTVMCIQPLKG--KKVARLGDTIVVSVKEVMPNAKVKKGEVVKAVVVRAAMDHGRCDGSFVKFD 112 (132)
Q Consensus 35 MIq~~T~L~VaDNSGak~v~CI~vl~g--rk~a~vGD~IivsVKk~~p~~kikKg~V~kAVIVRtKk~~~R~dG~~IkFd 112 (132)
|||.+|+|+|+|||||++++||+++++ +++|++||+|+||||++.|+++++|||+++|||||||++++|+||++++||
T Consensus 1 MIq~~t~l~v~DNSGak~v~cI~v~g~~~~~~a~iGD~I~vsVkk~~~~~~~kkg~v~~AvIVrtkk~~~r~dG~~i~F~ 80 (122)
T PRK05483 1 MIQQETRLNVADNSGAKEVMCIKVLGGSKRRYASIGDVIVVSVKEAIPRGKVKKGDVVKAVVVRTKKGVRRPDGSYIRFD 80 (122)
T ss_pred CCCCCCEEEEeECCCCCEEEEEEEeCCCCCCccccCCEEEEEEEEcCCCCcccCCCEeeEEEEEeccceecCCCCEEEcC
Confidence 999999999999999999999999975 568999999999999999999999999999999999999999999999999
Q ss_pred cceEEEEcCCCCcceeecc
Q 036919 113 DNAVVLIDNLCVLAFAEHT 131 (132)
Q Consensus 113 dNAvVLIn~kg~p~~~~~~ 131 (132)
|||+||||++++|+|+|+.
T Consensus 81 dNavVLin~~~~p~GTrI~ 99 (122)
T PRK05483 81 DNAAVLLNNDGEPRGTRIF 99 (122)
T ss_pred CCEEEEECCCCCEeEeEEe
Confidence 9999999999999999974
No 4
>TIGR01067 rplN_bact ribosomal protein L14, bacterial/organelle. This model distinguishes bacterial and most organellar examples of ribosomal protein L14 from all archaeal and eukaryotic forms.
Probab=100.00 E-value=5.7e-41 Score=250.12 Aligned_cols=97 Identities=51% Similarity=0.719 Sum_probs=94.1
Q ss_pred ccccCCeEEEeeccCcceEEEEEeeCC--eeeeecCcEEEEEEeeecCCCcccccceEEEEEEecccccccCCCcEEEec
Q 036919 35 FIQMRTVLKVADNSGVKTVMCIQPLKG--KKVARLGDTIVVSVKEVMPNAKVKKGEVVKAVVVRAAMDHGRCDGSFVKFD 112 (132)
Q Consensus 35 MIq~~T~L~VaDNSGak~v~CI~vl~g--rk~a~vGD~IivsVKk~~p~~kikKg~V~kAVIVRtKk~~~R~dG~~IkFd 112 (132)
|||.+|+|+|+|||||++++||++|++ +++|++||+|+||||++.|+++++|||+++|||||||++++|+||++++||
T Consensus 1 MIq~~t~l~v~DNSGak~v~cI~v~~~~~~~~a~iGD~I~vsVk~~~~~~~~kkg~v~~AvIVrtkk~~~r~dG~~i~F~ 80 (122)
T TIGR01067 1 MIQQQSRLNVADNSGAKKVQCIKVLGGSRRRYATVGDVIVVVVKDAIPNGKVKKGDVVKAVIVRTKKGVRRKDGSYIRFD 80 (122)
T ss_pred CCCcCCEEEEeECCCCcEEEEEEEeCCCCCCccccCCEEEEEEEEcCCCCccccccEEEEEEEEeecceEeCCCCEEECC
Confidence 999999999999999999999999975 568999999999999999999999999999999999999999999999999
Q ss_pred cceEEEEcCCCCcceeecc
Q 036919 113 DNAVVLIDNLCVLAFAEHT 131 (132)
Q Consensus 113 dNAvVLIn~kg~p~~~~~~ 131 (132)
|||+||+|++++|+|+|+.
T Consensus 81 ~Na~VLin~~~~p~GTrI~ 99 (122)
T TIGR01067 81 DNACVLINKNKEPRGTRIF 99 (122)
T ss_pred CceEEEECCCCCEeeeEEE
Confidence 9999999999999999975
No 5
>PTZ00054 60S ribosomal protein L23; Provisional
Probab=100.00 E-value=1.8e-39 Score=247.13 Aligned_cols=94 Identities=31% Similarity=0.425 Sum_probs=89.3
Q ss_pred ccccCCeEEEeeccCcceEEEEEeeC---C--e-eeeecCcEEEEEEeeecCCCcccccceEEEEEEecccccccCCCcE
Q 036919 35 FIQMRTVLKVADNSGVKTVMCIQPLK---G--K-KVARLGDTIVVSVKEVMPNAKVKKGEVVKAVVVRAAMDHGRCDGSF 108 (132)
Q Consensus 35 MIq~~T~L~VaDNSGak~v~CI~vl~---g--r-k~a~vGD~IivsVKk~~p~~kikKg~V~kAVIVRtKk~~~R~dG~~ 108 (132)
|||.+|+|+|+|||||++++||++++ + + ++|++||+|+||||++.| ++|||+++|||||||++++|+||++
T Consensus 18 mIq~~t~L~vaDNSGAk~v~cI~vlg~~g~~~r~~~a~iGD~IvvsVKk~~p---~~kg~V~kAVIVRtKk~~rR~dGs~ 94 (139)
T PTZ00054 18 GLPVGAVVNCADNSGAKNLYIIAVKGIHGRLNRLPSASLGDMVLATVKKGKP---ELRKKVLNAVIIRQRKAWRRKDGVF 94 (139)
T ss_pred eecCCCEEEEeeCCCccEEEEEEEeccCcCCccCcccccCCEEEEEEEECCC---cccCCEeeEEEEEECcceEcCCCcE
Confidence 99999999999999999999999996 3 3 579999999999999999 6789999999999999999999999
Q ss_pred EEeccceEEEEcCCCCcceeecc
Q 036919 109 VKFDDNAVVLIDNLCVLAFAEHT 131 (132)
Q Consensus 109 IkFddNAvVLIn~kg~p~~~~~~ 131 (132)
|+|||||+||||++++|+|+|+.
T Consensus 95 i~F~dNA~VLin~~~~p~GTRI~ 117 (139)
T PTZ00054 95 IYFEDNAGVIVNPKGEMKGSAIT 117 (139)
T ss_pred EEeCCcEEEEECCCCCEeeeEEe
Confidence 99999999999999999999974
No 6
>PRK08571 rpl14p 50S ribosomal protein L14P; Reviewed
Probab=100.00 E-value=2.9e-39 Score=244.21 Aligned_cols=94 Identities=36% Similarity=0.405 Sum_probs=88.8
Q ss_pred ccccCCeEEEeeccCcceEEEEEeeC---C--e-eeeecCcEEEEEEeeecCCCcccccceEEEEEEecccccccCCCcE
Q 036919 35 FIQMRTVLKVADNSGVKTVMCIQPLK---G--K-KVARLGDTIVVSVKEVMPNAKVKKGEVVKAVVVRAAMDHGRCDGSF 108 (132)
Q Consensus 35 MIq~~T~L~VaDNSGak~v~CI~vl~---g--r-k~a~vGD~IivsVKk~~p~~kikKg~V~kAVIVRtKk~~~R~dG~~ 108 (132)
|||.+|+|+|+|||||++++||++++ + + ++|++||+|+||||++.| ++|||+++|||||||++++|+||++
T Consensus 11 mIq~~T~L~VaDNSGAk~v~cI~vlg~~g~~~r~~~a~iGD~IvvsVK~~~p---~~kg~v~kAVIVRtkk~~~R~dGs~ 87 (132)
T PRK08571 11 GLPVGARLVCADNTGAKEVEIISVKGYKGVKRRLPKAGVGDMVVVSVKKGTP---EMRKQVLRAVVVRQRKEYRRPDGTR 87 (132)
T ss_pred eecCCCEEEEeeCCCCCeEEEEEEeccCCCCccCCccccCCEEEEEEEECCC---cccCCEeEEEEEEeccceEcCCCcE
Confidence 99999999999999999999999986 2 2 469999999999999999 5689999999999999999999999
Q ss_pred EEeccceEEEEcCCCCcceeecc
Q 036919 109 VKFDDNAVVLIDNLCVLAFAEHT 131 (132)
Q Consensus 109 IkFddNAvVLIn~kg~p~~~~~~ 131 (132)
++|||||+||||++++|+|+|+.
T Consensus 88 i~F~dNa~VLin~~~~p~GTRI~ 110 (132)
T PRK08571 88 VKFEDNAAVIVTPEGTPKGTEIK 110 (132)
T ss_pred EEeCCcEEEEECCCCCEeeeEEe
Confidence 99999999999999999999974
No 7
>TIGR03673 rpl14p_arch 50S ribosomal protein L14P. Part of the 50S ribosomal subunit. Forms a cluster with proteins L3 and L24e, part of which may contact the 16S rRNA in 2 intersubunit bridges.
Probab=100.00 E-value=3.8e-39 Score=243.31 Aligned_cols=95 Identities=38% Similarity=0.433 Sum_probs=89.1
Q ss_pred cccccCCeEEEeeccCcceEEEEEeeC---C--e-eeeecCcEEEEEEeeecCCCcccccceEEEEEEecccccccCCCc
Q 036919 34 TFIQMRTVLKVADNSGVKTVMCIQPLK---G--K-KVARLGDTIVVSVKEVMPNAKVKKGEVVKAVVVRAAMDHGRCDGS 107 (132)
Q Consensus 34 ~MIq~~T~L~VaDNSGak~v~CI~vl~---g--r-k~a~vGD~IivsVKk~~p~~kikKg~V~kAVIVRtKk~~~R~dG~ 107 (132)
.|||.+|+|+|+|||||++++||++++ + + ++|.+||+|+||||++.| ++|||+++|||||||++++|+||+
T Consensus 9 ~mIq~~t~L~VaDNSGak~v~cI~vl~~~g~~~r~~~a~iGD~IvvsVK~~~p---~~kg~v~kAVIVRtkk~~~R~dGs 85 (131)
T TIGR03673 9 RALPVGSLLVCADNTGAKEVEVISVKGYKGVKRRLPCAGVGDMVVVSVKKGTP---EMRKQVFKAVVVRQRKEYRRPDGT 85 (131)
T ss_pred eeeccCCEEEEeeCCCCceEEEEEEeeeCCCcccCCccccCCEEEEEEEECCc---cccCCEeEEEEEEeCcceecCCCc
Confidence 399999999999999999999999993 2 3 569999999999999999 568999999999999999999999
Q ss_pred EEEeccceEEEEcCCCCcceeecc
Q 036919 108 FVKFDDNAVVLIDNLCVLAFAEHT 131 (132)
Q Consensus 108 ~IkFddNAvVLIn~kg~p~~~~~~ 131 (132)
+++|||||+||||++++|+|+|+.
T Consensus 86 ~i~FddNa~VLin~~~~P~GTRI~ 109 (131)
T TIGR03673 86 RVKFEDNAVVIVTPDGEPKGTEIK 109 (131)
T ss_pred EEEeCCcEEEEECCCCCEeeeEEE
Confidence 999999999999999999999974
No 8
>PF00238 Ribosomal_L14: Ribosomal protein L14p/L23e; InterPro: IPR000218 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 L14 is one of the proteins from the large ribosomal subunit. In eubacteria, L14 is known to bind directly to the 23S rRNA. It belongs to a family of ribosomal proteins, which have been grouped on the basis of sequence similarities []. Based on amino-acid sequence homology, it is predicted that ribosomal protein L14 is a member of a recently identified family of structurally related RNA-binding proteins []. L14 is a protein of 119 to 137 amino-acid residues.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome; PDB: 3IZR_M 4A1C_J 4A1E_J 4A1A_J 4A17_J 1VSP_I 3D5D_O 1VSA_I 3MRZ_K 3F1F_O ....
Probab=100.00 E-value=8.9e-39 Score=237.60 Aligned_cols=97 Identities=55% Similarity=0.704 Sum_probs=91.3
Q ss_pred ccccCCeEEEeeccCcceEEEEEeeCC--eeeeecCcEEEEEEeeecCCCcccccceEEEEEEecccccccCCCcEEEec
Q 036919 35 FIQMRTVLKVADNSGVKTVMCIQPLKG--KKVARLGDTIVVSVKEVMPNAKVKKGEVVKAVVVRAAMDHGRCDGSFVKFD 112 (132)
Q Consensus 35 MIq~~T~L~VaDNSGak~v~CI~vl~g--rk~a~vGD~IivsVKk~~p~~kikKg~V~kAVIVRtKk~~~R~dG~~IkFd 112 (132)
|||.+|+|+|+|||||++++||+++++ +++|++||+|++|||+.+|+.+++|||+++|||||||++++|.||++++||
T Consensus 1 MIq~~t~L~v~DNSGak~v~cI~v~~~~~~~~a~vGD~I~vsVkk~~~~~~vkkg~v~~avIVrtk~~~~r~dg~~i~F~ 80 (122)
T PF00238_consen 1 MIQKGTILKVADNSGAKKVKCIKVLGGKRRKYASVGDIIVVSVKKGRPKSKVKKGQVYKAVIVRTKKPIRRKDGSFIKFD 80 (122)
T ss_dssp -BETTEEEEESBSSSEEEEEEEEETSSTTTSEE-TTSEEEEEEEEE-SSSSSTTTEEEEEEEEECSSEEETTTSEEEEES
T ss_pred CCCCCCEEEEeeCCCCcEEEEEEEeCCcCccccccceEEEEEEeecccCccccccceEEEEEEEEeEEEEEeCCcEEEeC
Confidence 999999999999999999999999974 679999999999999999999999999999999999999999999999999
Q ss_pred cceEEEEcCCCCcceeecc
Q 036919 113 DNAVVLIDNLCVLAFAEHT 131 (132)
Q Consensus 113 dNAvVLIn~kg~p~~~~~~ 131 (132)
|||+||+|++++|+|+|+.
T Consensus 81 ~Na~VLln~~~~p~GtrI~ 99 (122)
T PF00238_consen 81 DNAVVLLNKKGNPLGTRIF 99 (122)
T ss_dssp SEEEEEEETTSSBSSSSBC
T ss_pred CccEEEEcCCCCEeeeEEE
Confidence 9999999999999999874
No 9
>PTZ00320 ribosomal protein L14; Provisional
Probab=100.00 E-value=8.8e-37 Score=241.01 Aligned_cols=95 Identities=21% Similarity=0.230 Sum_probs=91.2
Q ss_pred ccCCeEEEeeccCcceEEEEEeeCCeeeeecCcE----EEEEEeeecC------CCcccccceEEEEEEecccccccCCC
Q 036919 37 QMRTVLKVADNSGVKTVMCIQPLKGKKVARLGDT----IVVSVKEVMP------NAKVKKGEVVKAVVVRAAMDHGRCDG 106 (132)
Q Consensus 37 q~~T~L~VaDNSGak~v~CI~vl~grk~a~vGD~----IivsVKk~~p------~~kikKg~V~kAVIVRtKk~~~R~dG 106 (132)
.-||+|+|+||||||+++||+++.++++|.+||+ |+||||++.| ++++|||||++|||||||++++|+||
T Consensus 61 ~~qT~L~VaDNSGAK~V~CIkVl~~rr~A~IGDi~~~~IvVsVKka~P~~~~~~~~kVKKG~V~kAVIVRTKK~irR~DG 140 (188)
T PTZ00320 61 SDQVKLHCVDNTNCKHVRLISKATAERFAHCRVFPAVAHRVSVQRFKSGRGEVSRHRVKPGNIYWVCLLSRRQTNTRMSG 140 (188)
T ss_pred CCCcEEEEEeCCCCcEEEEEEEecCCCceeeccccCceEEEEEeecccCccccccCceecCCEEEEEEEEECcccCCCCC
Confidence 4589999999999999999999977899999999 9999999999 78999999999999999999999999
Q ss_pred cEEEeccceEEEEcCCCCcceeecc
Q 036919 107 SFVKFDDNAVVLIDNLCVLAFAEHT 131 (132)
Q Consensus 107 ~~IkFddNAvVLIn~kg~p~~~~~~ 131 (132)
++|+|||||+||||++++|+|+|+.
T Consensus 141 s~IrFDdNAaVLIN~qgePlGTRIf 165 (188)
T PTZ00320 141 LQTNFDRNTCILMNDQRVPLGTRVM 165 (188)
T ss_pred CEEEeCCcEEEEECCCCCEeeeEEe
Confidence 9999999999999999999999974
No 10
>KOG0901 consensus 60S ribosomal protein L14/L17/L23 [Translation, ribosomal structure and biogenesis]
Probab=99.95 E-value=2.3e-28 Score=187.31 Aligned_cols=99 Identities=37% Similarity=0.484 Sum_probs=94.0
Q ss_pred hcccccCCeEEEeeccCcceEEEEEeeC--C----eeeeecCcEEEEEEee--ecCCCcccccceEEEEEEecccccccC
Q 036919 33 RTFIQMRTVLKVADNSGVKTVMCIQPLK--G----KKVARLGDTIVVSVKE--VMPNAKVKKGEVVKAVVVRAAMDHGRC 104 (132)
Q Consensus 33 ~~MIq~~T~L~VaDNSGak~v~CI~vl~--g----rk~a~vGD~IivsVKk--~~p~~kikKg~V~kAVIVRtKk~~~R~ 104 (132)
..|||++|.++|+||||||.++||++.+ | .+.|.+||+|+++||+ ..|+.++|+|+++.|+|||+++++.|.
T Consensus 17 s~~~~~g~~incaDNSgAknL~~isv~g~~Grlnrl~~A~~GD~vva~vKka~~~Pe~r~k~g~~~~avvVr~~k~~~r~ 96 (145)
T KOG0901|consen 17 SLGLPVGAVINCADNSGAKNLYCISVKGIKGRLNRLPAAGVGDMVVATVKKAHGKPELRKKVGEVLPAVVVRQKKSKRRK 96 (145)
T ss_pred hhccccceEEEecCCCCcceEEEEEEeccccccccccCCCcCCEEEEEEecccCCCccCcEecccceeeEEeeccccccC
Confidence 4589999999999999999999999987 5 3589999999999999 799999999999999999999999999
Q ss_pred CCcEEEeccceEEEEcCCCCcceeecc
Q 036919 105 DGSFVKFDDNAVVLIDNLCVLAFAEHT 131 (132)
Q Consensus 105 dG~~IkFddNAvVLIn~kg~p~~~~~~ 131 (132)
||++++|+|||+|++|+.++|+|++.+
T Consensus 97 dgs~~~f~dnA~v~~~~~~e~~gs~i~ 123 (145)
T KOG0901|consen 97 DGSIAYFEDNAGVIVNNKGEPKGSAIT 123 (145)
T ss_pred CCcEEEEcCceEEEEcccCccccceec
Confidence 999999999999999999999999876
No 11
>KOG3441 consensus Mitochondrial ribosomal protein L14 [Translation, ribosomal structure and biogenesis]
Probab=99.73 E-value=5.9e-18 Score=128.56 Aligned_cols=84 Identities=38% Similarity=0.460 Sum_probs=75.0
Q ss_pred cccCCeEEEeeccC--------cceEEEEEeeCCeeeeecCcEEEEEEeeecCCCcccccceEEEEEEecccccccCCCc
Q 036919 36 IQMRTVLKVADNSG--------VKTVMCIQPLKGKKVARLGDTIVVSVKEVMPNAKVKKGEVVKAVVVRAAMDHGRCDGS 107 (132)
Q Consensus 36 Iq~~T~L~VaDNSG--------ak~v~CI~vl~grk~a~vGD~IivsVKk~~p~~kikKg~V~kAVIVRtKk~~~R~dG~ 107 (132)
|++.|+|+|+|||. .+..+||++|+++..+.+||.|+|+|| ||..+|+||....+.++ .
T Consensus 32 I~k~tRlrVVDNSaLGk~a~~~gr~PrCIHVYkkrgvg~~GDkiLvAIk----------GQmkKa~vVGh~~~~k~---~ 98 (149)
T KOG3441|consen 32 IHKRTRLRVVDNSALGKEADTTGRLPRCIHVYKKRGVGELGDKILVAIK----------GQMKKAYVVGHVHYRKH---G 98 (149)
T ss_pred hhhhheEEEecchhhcccccccCCCCceEEEEecccccccccEEEEEEe----------cceeeeEEEEeeccCCC---C
Confidence 55589999999995 378899999998889999999999999 99999999997766554 4
Q ss_pred EEEeccceEEEEcCCCCcceeeccC
Q 036919 108 FVKFDDNAVVLIDNLCVLAFAEHTA 132 (132)
Q Consensus 108 ~IkFddNAvVLIn~kg~p~~~~~~~ 132 (132)
..+||+|.+||||++|+|+|+|.|+
T Consensus 99 ~P~fDsNniVLiddnGnPlGtRI~~ 123 (149)
T KOG3441|consen 99 VPVFDSNNIVLIDDNGNPLGTRITA 123 (149)
T ss_pred CcccCCCcEEEECCCCCcccceEec
Confidence 6899999999999999999999875
No 12
>cd03696 selB_II selB_II: this subfamily represents the domain of elongation factor SelB, homologous to domain II of EF-Tu. SelB may function by replacing EF-Tu. In prokaryotes, the incorporation of selenocysteine as the 21st amino acid, encoded by TGA, requires several elements: SelC is the tRNA itself, SelD acts as a donor of reduced selenium, SelA modifies a serine residue on SelC into selenocysteine, and SelB is a selenocysteine-specific translation elongation factor. 3' or 5' non-coding elements of mRNA have been found as probable structures for directing selenocysteine incorporation.
Probab=65.68 E-value=19 Score=23.93 Aligned_cols=55 Identities=16% Similarity=0.260 Sum_probs=33.9
Q ss_pred ccccCCeEEEeeccCcceEEEEEeeCC-eeeeecCcEEEEEEeeecCCCcccccceE
Q 036919 35 FIQMRTVLKVADNSGVKTVMCIQPLKG-KKVARLGDTIVVSVKEVMPNAKVKKGEVV 90 (132)
Q Consensus 35 MIq~~T~L~VaDNSGak~v~CI~vl~g-rk~a~vGD~IivsVKk~~p~~kikKg~V~ 90 (132)
.|+++..+.+..+--.-.++=|+.... ...|..||.|-+.++...+ ..+++|++.
T Consensus 26 ~i~~g~~v~~~p~~~~~~V~sI~~~~~~~~~a~aGd~v~i~l~~~~~-~~i~~G~vl 81 (83)
T cd03696 26 SVKVGDKVEILPLGEETRVRSIQVHGKDVEEAKAGDRVALNLTGVDA-KDLERGDVL 81 (83)
T ss_pred EEeCCCEEEECCCCceEEEEEEEECCcCcCEEcCCCEEEEEEcCCCH-HHcCCccEE
Confidence 356677777777432233333433222 4578999999999986554 346667653
No 13
>cd03695 CysN_NodQ_II CysN_NodQ_II: This subfamily represents the domain II of the large subunit of ATP sulfurylase (ATPS): CysN or the N-terminal portion of NodQ, found mainly in proteobacteria and homologous to the domain II of EF-Tu. Escherichia coli ATPS consists of CysN and a smaller subunit CysD and CysN. ATPS produces adenosine-5'-phosphosulfate (APS) from ATP and sulfate, coupled with GTP hydrolysis. In the subsequent reaction APS is phosphorylated by an APS kinase (CysC), to produce 3'-phosphoadenosine-5'-phosphosulfate (PAPS) for use in amino acid (aa) biosynthesis. The Rhizobiaceae group (alpha-proteobacteria) appears to carry out the same chemistry for the sufation of a nodulation factor. In Rhizobium meliloti, a the hererodimeric complex comprised of NodP and NodQ appears to possess both ATPS and APS kinase activities. The N and C termini of NodQ correspond to CysN and CysC, respectively. Other eubacteria, Archaea, and eukaryotes use a different ATP sulfurylase, which sho
Probab=65.07 E-value=30 Score=23.26 Aligned_cols=52 Identities=19% Similarity=0.418 Sum_probs=34.0
Q ss_pred cccCCeEEEeeccCcceEEEEEeeCC-eeeeecCcEEEEEEeeecCCCcccccceE
Q 036919 36 IQMRTVLKVADNSGVKTVMCIQPLKG-KKVARLGDTIVVSVKEVMPNAKVKKGEVV 90 (132)
Q Consensus 36 Iq~~T~L~VaDNSGak~v~CI~vl~g-rk~a~vGD~IivsVKk~~p~~kikKg~V~ 90 (132)
++++..+.+.+.-=.-.++-|+.... ...|..||.|-+.+++ ...+++|++.
T Consensus 27 v~~Gd~v~~~P~~~~~~V~si~~~~~~~~~a~aGd~v~l~l~~---~~~i~~G~vl 79 (81)
T cd03695 27 IRVGDEVVVLPSGKTSRVKSIETFDGELDEAGAGESVTLTLED---EIDVSRGDVI 79 (81)
T ss_pred EECCCEEEEcCCCCeEEEEEEEECCcEeCEEcCCCEEEEEECC---ccccCCCCEE
Confidence 45566677766422345666766554 4678999999999973 3446677764
No 14
>PF08447 PAS_3: PAS fold; InterPro: IPR013655 The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs []. The PAS fold appears in archaea, eubacteria and eukarya. The PAS domain contains a sensory box, or S-box domain that occupies the central portion of the PAS domain but is more widely distributed. It is often tandemly repeated. Known prosthetic groups bound in the S-box domain include haem in the oxygen sensor FixL [], FAD in the redox potential sensor NifL [], and a 4-hydroxycinnamyl chromophore in photoactive yellow protein []. Proteins containing the domain often contain other regulatory domains such as response regulator or sensor histidine kinase domains. Other S-box proteins include phytochromes and the aryl hydrocarbon receptor nuclear translocator. This domain has been found in the gene product of the madA gene of the filamentous zygomycete fungus Phycomyces blakesleeanus. It has been shown that MadA encodes a blue-light photoreceptor for phototropism and other light responses. The gene is involved in the phototropic responses associated with sporangiophore growth; they exhibit phototropism by bending toward near-UV and blue wavelengths and away from far-UV wavelengths in a manner that is physiologically similar to plant phototropic responses [].; GO: 0005515 protein binding; PDB: 3NJA_D 3H9W_A 3GDI_B 3ICY_A 3EEH_A 3MR0_B.
Probab=60.04 E-value=10 Score=24.11 Aligned_cols=30 Identities=13% Similarity=0.041 Sum_probs=25.3
Q ss_pred ccccccCCCcEEEeccceEEEEcCCCCcce
Q 036919 98 AMDHGRCDGSFVKFDDNAVVLIDNLCVLAF 127 (132)
Q Consensus 98 Kk~~~R~dG~~IkFddNAvVLIn~kg~p~~ 127 (132)
....+++||.++-+...+.++-|++|+|..
T Consensus 57 e~R~~~~~G~~~wi~~~~~~~~d~~g~~~~ 86 (91)
T PF08447_consen 57 EYRIRRKDGEYRWIEVRGRPIFDENGKPIR 86 (91)
T ss_dssp EEEEEGTTSTEEEEEEEEEEEETTTS-EEE
T ss_pred EEEEECCCCCEEEEEEEEEEEECCCCCEEE
Confidence 455778999999999999999999999864
No 15
>cd03698 eRF3_II_like eRF3_II_like: domain similar to domain II of the eukaryotic class II release factor (eRF3). In eukaryotes, translation termination is mediated by two interacting release factors, eRF1 and eRF3, which act as class I and II factors, respectively. eRF1 functions as an omnipotent release factor, decoding all three stop codons and triggering the release of the nascent peptide catalyzed by the ribsome. eRF3 is a GTPase, which enhances the termination efficiency by stimulating the eRF1 activity in a GTP-dependent manner. Sequence comparison of class II release factors with elongation factors shows that eRF3 is more similar to eEF1alpha whereas prokaryote RF3 is more similar to EF-G, implying that their precise function may differ. Only eukaryote RF3s are found in this group. Saccharomyces cerevisiae eRF3 (Sup35p) is a translation termination factor which is divided into three regions N, M and a C-terminal eEF1a-like region essential for translation termination. Sup35NM
Probab=58.44 E-value=25 Score=23.41 Aligned_cols=54 Identities=20% Similarity=0.218 Sum_probs=32.7
Q ss_pred cccCCeEEEeeccCcceEEEEEeeCC-eeeeecCcEEEEEEeeecCCCcccccceE
Q 036919 36 IQMRTVLKVADNSGVKTVMCIQPLKG-KKVARLGDTIVVSVKEVMPNAKVKKGEVV 90 (132)
Q Consensus 36 Iq~~T~L~VaDNSGak~v~CI~vl~g-rk~a~vGD~IivsVKk~~p~~kikKg~V~ 90 (132)
|+++..+.+.-.--.-.++-|+.... ...|..||.|-+.++...+ ..+++|++.
T Consensus 27 i~~Gd~v~i~P~~~~~~V~si~~~~~~~~~a~aGd~v~~~l~~~~~-~~v~~G~vl 81 (83)
T cd03698 27 IQKGDTLLVMPSKESVEVKSIYVDDEEVDYAVAGENVRLKLKGIDE-EDISPGDVL 81 (83)
T ss_pred EeCCCEEEEeCCCcEEEEEEEEECCeECCEECCCCEEEEEECCCCH-HHCCCCCEE
Confidence 45566666655432234555655443 4578999999999975433 245667664
No 16
>cd03693 EF1_alpha_II EF1_alpha_II: this family represents the domain II of elongation factor 1-alpha (EF-1a) that is found in archaea and all eukaryotic lineages. EF-1A is very abundant in the cytosol, where it is involved in the GTP-dependent binding of aminoacyl-tRNAs to the A site of the ribosomes in the second step of translation from mRNAs to proteins. Both domain II of EF1A and domain IV of IF2/eIF5B have been implicated in recognition of the 3'-ends of tRNA. More than 61% of eukaryotic elongation factor 1A (eEF-1A) in cells is estimated to be associated with actin cytoskeleton. The binding of eEF1A to actin is a noncanonical function that may link two distinct cellular processes, cytoskeleton organization and gene expression.
Probab=56.90 E-value=28 Score=23.69 Aligned_cols=55 Identities=22% Similarity=0.268 Sum_probs=33.9
Q ss_pred ccccCCeEEEeeccCcceEEEEEeeCC-eeeeecCcEEEEEEeeecCCCcccccceE
Q 036919 35 FIQMRTVLKVADNSGVKTVMCIQPLKG-KKVARLGDTIVVSVKEVMPNAKVKKGEVV 90 (132)
Q Consensus 35 MIq~~T~L~VaDNSGak~v~CI~vl~g-rk~a~vGD~IivsVKk~~p~~kikKg~V~ 90 (132)
+|+.+..+.+.-+-=.-.++-|+..+. ...|..||.+-+.++...+ ..+++|++.
T Consensus 30 ~i~~gd~v~i~P~~~~~~V~sI~~~~~~~~~a~aG~~v~i~l~~i~~-~~v~~G~vl 85 (91)
T cd03693 30 VLKPGMVVTFAPAGVTGEVKSVEMHHEPLEEALPGDNVGFNVKNVSK-KDIKRGDVA 85 (91)
T ss_pred eeecCCEEEECCCCcEEEEEEEEECCcCcCEECCCCEEEEEECCCCH-HHcCCcCEE
Confidence 355566666665422234555655443 5678899999999975433 446677764
No 17
>cd04089 eRF3_II eRF3_II: domain II of the eukaryotic class II release factor (eRF3). In eukaryotes, translation termination is mediated by two interacting release factors, eRF1 and eRF3, which act as class I and II factors, respectively. eRF1 functions as an omnipotent release factor, decoding all three stop codons and triggering the release of the nascent peptide catalyzed by the ribsome. eRF3 is a GTPase, which enhances the termination efficiency by stimulating the eRF1 activity in a GTP-dependent manner. Sequence comparison of class II release factors with elongation factors shows that eRF3 is more similar to eEF1alpha whereas prokaryote RF3 is more similar to EF-G, implying that their precise function may differ. Only eukaryote RF3s are found in this group. Saccharomyces cerevisiae eRF3 (Sup35p) is a translation termination factor which is divided into three regions N, M and a C-terminal eEF1a-like region essential for translation termination. Sup35NM is a non-pathogenic prion-li
Probab=49.47 E-value=42 Score=22.33 Aligned_cols=54 Identities=22% Similarity=0.254 Sum_probs=31.0
Q ss_pred cccCCeEEEeeccCcceEEEEEeeCC-eeeeecCcEEEEEEeeecCCCcccccceE
Q 036919 36 IQMRTVLKVADNSGVKTVMCIQPLKG-KKVARLGDTIVVSVKEVMPNAKVKKGEVV 90 (132)
Q Consensus 36 Iq~~T~L~VaDNSGak~v~CI~vl~g-rk~a~vGD~IivsVKk~~p~~kikKg~V~ 90 (132)
|+++-.+.+...--.-.++-|+..+. ...|..||.+-+.++...+. .+++|++.
T Consensus 26 i~~G~~v~i~P~~~~~~V~si~~~~~~~~~a~aGd~v~l~l~~i~~~-~v~~G~vl 80 (82)
T cd04089 26 IKKGDKLLVMPNKTQVEVLSIYNEDVEVRYARPGENVRLRLKGIEEE-DISPGFVL 80 (82)
T ss_pred EecCCEEEEeCCCcEEEEEEEEECCEECCEECCCCEEEEEecCCCHH-HCCCCCEE
Confidence 34455555554322233455554433 45688999999999855442 46667664
No 18
>COG1465 Predicted alternative 3-dehydroquinate synthase [Amino acid transport and metabolism]
Probab=47.65 E-value=1.2e+02 Score=26.89 Aligned_cols=71 Identities=18% Similarity=0.262 Sum_probs=46.4
Q ss_pred ccCcceEEEEEeeCC-eee---eecCcEEEEEEeeecCCCcccccceEEEEEEecccccc-------cCCCcEEE---ec
Q 036919 47 NSGVKTVMCIQPLKG-KKV---ARLGDTIVVSVKEVMPNAKVKKGEVVKAVVVRAAMDHG-------RCDGSFVK---FD 112 (132)
Q Consensus 47 NSGak~v~CI~vl~g-rk~---a~vGD~IivsVKk~~p~~kikKg~V~kAVIVRtKk~~~-------R~dG~~Ik---Fd 112 (132)
|-|+-. ..|++.++ .+| -+.||.|.++=. +|....|+|=|.|.+.| ..+|..++ =+
T Consensus 260 NAG~Vh-aYi~vPg~kTkYLaEL~aGDeV~iVD~---------dGr~R~aiVGRvKIErRPl~lIeAey~g~~i~tiLQN 329 (376)
T COG1465 260 NAGAVH-AYIRVPGGKTKYLAELKAGDEVLIVDF---------DGRTRSAIVGRVKIERRPLMLIEAEYEGVEISTILQN 329 (376)
T ss_pred ccccee-EEEEcCCCceEEhhhhcCCCeEEEEec---------CCceeEEEEEEEEeecCceEEEEEEecCcEEEEEecc
Confidence 667766 45667665 344 379999999876 45666677777666544 33454443 34
Q ss_pred cceEEEEcCCCCcce
Q 036919 113 DNAVVLIDNLCVLAF 127 (132)
Q Consensus 113 dNAvVLIn~kg~p~~ 127 (132)
-..+=|++++|+|..
T Consensus 330 AETIkLv~~dG~pvS 344 (376)
T COG1465 330 AETIKLVNPDGEPVS 344 (376)
T ss_pred ceeEEEEcCCCcEee
Confidence 445678999999875
No 19
>cd03694 GTPBP_II Domain II of the GP-1 family of GTPase. This group includes proteins similar to GTPBP1 and GTPBP2. GTPB1 is structurally, related to elongation factor 1 alpha, a key component of protein biosynthesis machinery. Immunohistochemical analyses on mouse tissues revealed that GTPBP1 is expressed in some neurons and smooth muscle cells of various organs as well as macrophages. Immunofluorescence analyses revealed that GTPBP1 is localized exclusively in cytoplasm and shows a diffuse granular network forming a gradient from the nucleus to the periphery of the cells in smooth muscle cell lines and macrophages. No significant difference was observed in the immune response to protein antigen between mutant mice and wild-type mice, suggesting normal function of antigen-presenting cells of the mutant mice. The absence of an eminent phenotype in GTPBP1-deficient mice may be due to functional compensation by GTPBP2, which is similar to GTPBP1 in structure and tissue distribution.
Probab=44.40 E-value=59 Score=21.98 Aligned_cols=53 Identities=25% Similarity=0.401 Sum_probs=33.9
Q ss_pred cccCCeEEEeecc-C---cceEEEEEeeCC-eeeeecCcEEEEEEeeecCCCcccccce
Q 036919 36 IQMRTVLKVADNS-G---VKTVMCIQPLKG-KKVARLGDTIVVSVKEVMPNAKVKKGEV 89 (132)
Q Consensus 36 Iq~~T~L~VaDNS-G---ak~v~CI~vl~g-rk~a~vGD~IivsVKk~~p~~kikKg~V 89 (132)
++++..+.+...- | .-.++-|+..+. ...|..||.+-+.++...+ ..+++|.+
T Consensus 27 v~~g~~v~~~P~~~g~~~~~~V~sI~~~~~~~~~a~aGd~v~l~l~~i~~-~~i~~G~v 84 (87)
T cd03694 27 IRLGDTLLLGPDQDGSFRPVTVKSIHRNRSPVRVVRAGQSASLALKKIDR-SLLRKGMV 84 (87)
T ss_pred EeCCCEEEECCCCCCCEeEEEEEEEEECCeECCEECCCCEEEEEEcCCCH-HHcCCccE
Confidence 4556667666542 3 335666665543 4578999999999976554 34556655
No 20
>PF14578 GTP_EFTU_D4: Elongation factor Tu domain 4; PDB: 1G7R_A 1G7S_A 1G7T_A 1XE1_A.
Probab=41.23 E-value=88 Score=21.96 Aligned_cols=51 Identities=20% Similarity=0.344 Sum_probs=29.9
Q ss_pred ccccCCeEEEeeccCcceEEEEEeeCC-eeeeecCcEEEEEEeeecCCCcccccceEE
Q 036919 35 FIQMRTVLKVADNSGVKTVMCIQPLKG-KKVARLGDTIVVSVKEVMPNAKVKKGEVVK 91 (132)
Q Consensus 35 MIq~~T~L~VaDNSGak~v~CI~vl~g-rk~a~vGD~IivsVKk~~p~~kikKg~V~k 91 (132)
.|.+++.| |..-+-.++=|+.-+. -..|..||.|-+++.... .++.||+++
T Consensus 29 ~ik~G~~l---~G~~iG~I~sIe~~~k~v~~A~~G~eVai~Ieg~~---~i~eGDiLy 80 (81)
T PF14578_consen 29 IIKPGYPL---DGRKIGRIKSIEDNGKNVDEAKKGDEVAISIEGPT---QIKEGDILY 80 (81)
T ss_dssp EEETT-EE---CSSCEEEEEEEEETTEEESEEETT-EEEEEEET-----TB-TT-EEE
T ss_pred EEeCCCcc---CCEEEEEEEEeEECCcCccccCCCCEEEEEEeCCc---cCCCCCEEe
Confidence 35678888 5554445555543221 247899999999998644 777888765
No 21
>PF00575 S1: S1 RNA binding domain; InterPro: IPR003029 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 [, ]. The S1 domain was originally identified in ribosomal protein S1 but is found in a large number of RNA-associated proteins. The structure of the S1 RNA-binding domain from the Escherichia coli polynucleotide phosphorylase has been determined using NMR methods and consists of a five-stranded antiparallel beta barrel. Conserved residues on one face of the barrel and adjacent loops form the putative RNA-binding site []. The structure of the S1 domain is very similar to that of cold shock proteins. This suggests that they may both be derived from an ancient nucleic acid-binding protein []. More information about these proteins can be found at Protein of the Month: RNA Exosomes []. This entry does not include translation initiation factor IF-1 S1 domains.; GO: 0003723 RNA binding; PDB: 3L7Z_F 2JE6_I 2JEA_I 2JEB_I 1E3P_A 2Y0S_E 1WI5_A 2BH8_A 2CQO_A 2EQS_A ....
Probab=35.11 E-value=80 Score=19.89 Aligned_cols=25 Identities=28% Similarity=0.497 Sum_probs=12.0
Q ss_pred cccceEEEEEEecccccccCCCcEEEeccc
Q 036919 85 KKGEVVKAVVVRAAMDHGRCDGSFVKFDDN 114 (132)
Q Consensus 85 kKg~V~kAVIVRtKk~~~R~dG~~IkFddN 114 (132)
+.|+++.|.|.+-.. +|.++.+.++
T Consensus 3 ~~G~iv~g~V~~v~~-----~g~~V~l~~~ 27 (74)
T PF00575_consen 3 KEGDIVEGKVTSVED-----FGVFVDLGNG 27 (74)
T ss_dssp STTSEEEEEEEEEET-----TEEEEEESTS
T ss_pred CCCCEEEEEEEEEEC-----CEEEEEECCc
Confidence 345555555554222 4555555533
No 22
>TIGR01024 rplS_bact ribosomal protein L19, bacterial type. This model describes bacterial ribosomoal protein L19 and its chloroplast equivalent. Putative mitochondrial L19 are found in several species (but not Saccharomyces cerevisiae) and score between trusted and noise cutoffs.
Probab=35.10 E-value=72 Score=23.77 Aligned_cols=35 Identities=34% Similarity=0.340 Sum_probs=24.8
Q ss_pred eeecCcEEEEEEeeecCCCcccccceEEEEEEecccc
Q 036919 64 VARLGDTIVVSVKEVMPNAKVKKGEVVKAVVVRAAMD 100 (132)
Q Consensus 64 ~a~vGD~IivsVKk~~p~~kikKg~V~kAVIVRtKk~ 100 (132)
.-.+||+|.|.++-... .-++-|.+.++|+..+..
T Consensus 18 ~f~~GD~v~V~~~i~eg--~k~R~q~f~GvvI~~~~~ 52 (113)
T TIGR01024 18 DFRVGDTVRVHVKIVEG--KKERIQVFEGVVIARRGG 52 (113)
T ss_pred ccCCCCEEEEEEEEccC--CceEcccEEEEEEEEeCC
Confidence 35799999999875332 222458899999987643
No 23
>PF01245 Ribosomal_L19: Ribosomal protein L19; InterPro: IPR001857 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 L19 is one of the proteins from the large ribosomal subunit [, ]. In Escherichia coli, L19 is known to be located at the 30S-50S ribosomal subunit interface [] and may play a role in the structure and function of the aminoacyl-tRNA binding site. It belongs to a family of ribosomal proteins, including L19 from bacteria and the chloroplasts of red algae. L19 is a protein of 120 to 130 amino-acid residues.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3HUZ_T 3V2D_T 3I8I_R 2XG2_T 2V49_T 2XUX_T 3HUX_T 3I9C_R 3V25_T 3UZ2_R ....
Probab=34.58 E-value=75 Score=23.45 Aligned_cols=34 Identities=26% Similarity=0.285 Sum_probs=25.9
Q ss_pred eeecCcEEEEEEeeecC-CCcccccceEEEEEEecccc
Q 036919 64 VARLGDTIVVSVKEVMP-NAKVKKGEVVKAVVVRAAMD 100 (132)
Q Consensus 64 ~a~vGD~IivsVKk~~p-~~kikKg~V~kAVIVRtKk~ 100 (132)
.-.+||+|.|.++.... +. +-|.+.++++.-+..
T Consensus 18 ~f~~GD~v~V~~~i~e~~k~---r~q~f~GvvIa~~~~ 52 (113)
T PF01245_consen 18 EFRVGDTVRVTYKISEGNKE---RIQVFEGVVIARRRR 52 (113)
T ss_dssp SSSSSSEEEEEEEEESSSSE---EEEEEEEEEEEEEBS
T ss_pred CcCCCCEEEEEEEEecCCCc---eeEEEEEEEEEEECC
Confidence 45799999999986633 33 348999999987664
No 24
>PF10382 DUF2439: Protein of unknown function (DUF2439); InterPro: IPR018838 This domain is found at the N-terminal of proteins implicated in telomere maintenance in Saccharomyces cerevisiae (Baker's yeast) [] and in meiotic chromosome segregation in Schizosaccharomyces pombe (Fission yeast) [].
Probab=33.60 E-value=55 Score=22.59 Aligned_cols=26 Identities=27% Similarity=0.356 Sum_probs=20.3
Q ss_pred CCCcEEEec--cceEEEEcCCCCcceeec
Q 036919 104 CDGSFVKFD--DNAVVLIDNLCVLAFAEH 130 (132)
Q Consensus 104 ~dG~~IkFd--dNAvVLIn~kg~p~~~~~ 130 (132)
.||. ++|. .|-+.|.|.++.++++.+
T Consensus 20 ~DG~-l~~~~~~~kv~Lyde~~~~i~~~~ 47 (83)
T PF10382_consen 20 HDGF-LKYHSFNKKVMLYDEDGNLIGSDF 47 (83)
T ss_pred ECCE-EEEEeCCCEEEEEcCCCCEEeEEE
Confidence 4885 5655 777999999999998765
No 25
>cd03697 EFTU_II EFTU_II: Elongation factor Tu domain II. Elongation factors Tu (EF-Tu) are three-domain GTPases with an essential function in the elongation phase of mRNA translation. The GTPase center of EF-Tu is in the N-terminal domain (domain I), also known as the catalytic or G-domain. The G-domain is composed of about 200 amino acid residues, arranged into a predominantly parallel six-stranded beta-sheet core surrounded by seven a-helices. Non-catalytic domains II and III are beta-barrels of seven and six, respectively, antiparallel beta-strands that share an extended interface. Either non-catalytic domain is composed of about 100 amino acid residues. EF-Tu proteins exist in two principal conformations: in a compact one, EF-Tu*GTP, with tight interfaces between all three domains and a high affinity for aminoacyl-tRNA, and in an open one, EF-Tu*GDP, with essentially no G-domain-domain II interactions and a low affinity for aminoacyl-tRNA. EF-Tu has approximately a 100-fold higher
Probab=30.16 E-value=1.7e+02 Score=19.58 Aligned_cols=54 Identities=22% Similarity=0.301 Sum_probs=30.7
Q ss_pred cccCCeEEEeec-cC-cceEEEEEeeCC-eeeeecCcEEEEEEeeecCCCcccccceE
Q 036919 36 IQMRTVLKVADN-SG-VKTVMCIQPLKG-KKVARLGDTIVVSVKEVMPNAKVKKGEVV 90 (132)
Q Consensus 36 Iq~~T~L~VaDN-SG-ak~v~CI~vl~g-rk~a~vGD~IivsVKk~~p~~kikKg~V~ 90 (132)
++.+..+.+... .+ .-.++=|+.... ...|..||.+-+.++...+ ..+.+|++.
T Consensus 27 v~~gd~v~~~p~~~~~~~~V~si~~~~~~~~~a~~G~~v~l~l~~~~~-~~v~rG~vl 83 (87)
T cd03697 27 IKVGDEVEIVGFGETLKTTVTGIEMFRKTLDEAEAGDNVGVLLRGVKR-EDVERGMVL 83 (87)
T ss_pred CccCCEEEEeCCCCCceEEEEEEEECCcCCCEECCCCEEEEEECCCCH-HHcCCccEE
Confidence 344555555431 11 123444554443 4678899999999986543 345566653
No 26
>PRK05338 rplS 50S ribosomal protein L19; Provisional
Probab=28.33 E-value=1.1e+02 Score=22.95 Aligned_cols=35 Identities=31% Similarity=0.289 Sum_probs=23.7
Q ss_pred eeecCcEEEEEEeeecCCCcccccceEEEEEEecccc
Q 036919 64 VARLGDTIVVSVKEVMPNAKVKKGEVVKAVVVRAAMD 100 (132)
Q Consensus 64 ~a~vGD~IivsVKk~~p~~kikKg~V~kAVIVRtKk~ 100 (132)
.-.+||+|.|.++-...+ -++-|.+.++|+..+..
T Consensus 18 ~f~~GD~V~V~~~i~eg~--k~R~q~f~GvvI~~~~~ 52 (116)
T PRK05338 18 EFRPGDTVRVHVKVVEGN--KERIQAFEGVVIARRGR 52 (116)
T ss_pred CcCCCCEEEEEEEEccCC--ceEeccEEEEEEEEeCC
Confidence 347999999988743221 11348899999987643
No 27
>CHL00084 rpl19 ribosomal protein L19
Probab=27.92 E-value=1.1e+02 Score=22.89 Aligned_cols=34 Identities=24% Similarity=0.255 Sum_probs=23.5
Q ss_pred eeecCcEEEEEEeeecCCCcccccceEEEEEEeccc
Q 036919 64 VARLGDTIVVSVKEVMPNAKVKKGEVVKAVVVRAAM 99 (132)
Q Consensus 64 ~a~vGD~IivsVKk~~p~~kikKg~V~kAVIVRtKk 99 (132)
.-.+||+|.|.++-...+- ++-|.+.++|+..+.
T Consensus 22 ~f~~GDtV~V~~~i~eg~k--~R~q~F~GvvI~~r~ 55 (117)
T CHL00084 22 KIRVGDTVKVGVLIQEGNK--ERVQFYEGTVIAKKN 55 (117)
T ss_pred ccCCCCEEEEEEEEecCCe--eEeceEEEEEEEEeC
Confidence 4579999999996433211 134789999998654
No 28
>TIGR01644 phage_P2_V phage baseplate assembly protein V. This model describes a family of phage (and bacteriocin) proteins related to the phage P2 V gene product, which forms the small spike at the tip of the tail. Homologs in general are annotated as baseplate assembly protein V. At least one member is encoded within a region of Pectobacterium carotovorum (Erwinia carotovora) described as a bacteriocin, a phage tail-derived module able to kill bacteria closely related to the host strain.
Probab=26.73 E-value=2.7e+02 Score=21.39 Aligned_cols=82 Identities=22% Similarity=0.247 Sum_probs=47.0
Q ss_pred hcccccCCeEEEeeccCcceEEEEEeeCC--------------eeeeecCcEEEEEEeeecCCCcccccceEEEEEEec-
Q 036919 33 RTFIQMRTVLKVADNSGVKTVMCIQPLKG--------------KKVARLGDTIVVSVKEVMPNAKVKKGEVVKAVVVRA- 97 (132)
Q Consensus 33 ~~MIq~~T~L~VaDNSGak~v~CI~vl~g--------------rk~a~vGD~IivsVKk~~p~~kikKg~V~kAVIVRt- 97 (132)
++||+.++.-.|-|..+--.++.-..+.+ ...-.+|+.++|.-= -|+.-.|+|+..
T Consensus 6 ~~~ir~G~V~~vd~~~~~vrv~~~~~~t~wl~~~~~~ag~~~~~~~P~vGeqv~vl~~---------~G~l~~gvvl~gl 76 (191)
T TIGR01644 6 RNLIRRGVVAEVDDAAARVRVLQGELLTGWLPWDVERAGNYRHWSAPSPGEQVVVLSP---------GGQRAHGVVLPGV 76 (191)
T ss_pred hccEEEEEEEEEcCCCCcEEEecCCccccchhhhhHhhCCCceEcCCCCCCEEEEEcC---------CCCccccEEEeee
Confidence 56888888888777663222232222211 011258888776543 256667777772
Q ss_pred -----ccccccCCCcEEEeccceEEEEcCCC
Q 036919 98 -----AMDHGRCDGSFVKFDDNAVVLIDNLC 123 (132)
Q Consensus 98 -----Kk~~~R~dG~~IkFddNAvVLIn~kg 123 (132)
+.+-...|-..++|+|-+.|-+|++.
T Consensus 77 ~s~~~~~p~~~~~~~~~~~~DG~~i~yd~~~ 107 (191)
T TIGR01644 77 YSDAFRPPGLSAGDTVTYFADGARISYDKAA 107 (191)
T ss_pred cCCCCCCCCCCCCeEEEEeCCCCEEEEECCC
Confidence 22233445567777777777776654
No 29
>KOG2449 consensus Methylmalonate semialdehyde dehydrogenase [Amino acid transport and metabolism; Carbohydrate transport and metabolism]
Probab=26.47 E-value=1e+02 Score=24.36 Aligned_cols=54 Identities=26% Similarity=0.354 Sum_probs=38.9
Q ss_pred ecCcEEEEEEeeecCCCcccccceEEEEEEecccccccCCCcEEEecc---ceEEEEcCCCC
Q 036919 66 RLGDTIVVSVKEVMPNAKVKKGEVVKAVVVRAAMDHGRCDGSFVKFDD---NAVVLIDNLCV 124 (132)
Q Consensus 66 ~vGD~IivsVKk~~p~~kikKg~V~kAVIVRtKk~~~R~dG~~IkFdd---NAvVLIn~kg~ 124 (132)
-+|-.|++ ..|++..-|-|++..|.||...+. -.|+.+|.|++ |++-+++.+|.
T Consensus 66 f~~~tiLs----vtP~ms~ykeeI~gpVlv~l~~~t-ldd~I~Iin~nPygn~t~i~Tsn~a 122 (157)
T KOG2449|consen 66 FVGPTILS----VTPNMSCYKEEIFGPVLVRLETET-LDDAIFIINNNPYGNGTAIFTSNGA 122 (157)
T ss_pred cccceEEE----ecCCcceeHhhhhcceEEEEeecC-CCceeEEEecCCCCceeEEEecCcH
Confidence 35555555 569998888899999999965544 45788888875 66666666553
No 30
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=25.86 E-value=2.4e+02 Score=25.27 Aligned_cols=50 Identities=32% Similarity=0.454 Sum_probs=35.9
Q ss_pred ecCcEEEEEEeeecCC--------------------CcccccceEEEEEEecccccccCCCcEEEeccceEEEEc
Q 036919 66 RLGDTIVVSVKEVMPN--------------------AKVKKGEVVKAVVVRAAMDHGRCDGSFVKFDDNAVVLID 120 (132)
Q Consensus 66 ~vGD~IivsVKk~~p~--------------------~kikKg~V~kAVIVRtKk~~~R~dG~~IkFddNAvVLIn 120 (132)
++||.|.+.|....++ ...+.|+++.+.|++... .|.+++++++-.-++-
T Consensus 420 ~~Gd~v~v~Il~vd~~~~~i~ls~k~~~~~p~~~~~~~~~~G~vV~G~V~~v~~-----~G~fV~l~~gi~g~i~ 489 (565)
T PRK06299 420 KKGDEVEAVVLKVDVEKERISLGIKQLEEDPFEEFAKKHKKGSIVTGTVTEVKD-----KGAFVELEDGVEGLIR 489 (565)
T ss_pred CCCCEEEEEEEEEeCCCCEEEEEEehhhcCchhHHHhhcCCCCEEEEEEEEEec-----CceEEecCCCcEEEEE
Confidence 6899999988665431 125679999999988654 3889999876555544
No 31
>cd04454 S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein, and Rrp40 and Csl4 proteins, also represented in this group, are subunits of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=25.09 E-value=1.8e+02 Score=18.96 Aligned_cols=15 Identities=20% Similarity=0.470 Sum_probs=9.7
Q ss_pred ccccceEEEEEEecc
Q 036919 84 VKKGEVVKAVVVRAA 98 (132)
Q Consensus 84 ikKg~V~kAVIVRtK 98 (132)
++.|+.++|.|++.-
T Consensus 51 ~~~GD~i~~~V~~~~ 65 (82)
T cd04454 51 LQPGDLILAKVISLG 65 (82)
T ss_pred CCCCCEEEEEEEEeC
Confidence 556777777776643
No 32
>cd04497 hPOT1_OB1_like hPOT1_OB1_like: A subfamily of OB folds similar to the first OB fold (OB1) of human protection of telomeres 1 protein (hPOT1), the single OB fold of the N-terminal domain of Schizosaccharomyces pombe POT1 (SpPOT1), and the first OB fold of the N-terminal domain of the alpha subunit (OB1Nalpha) of Oxytricha nova telomere end binding protein (OnTEBP). POT1 proteins recognize single-stranded (ss) 3-prime ends of the telomere. A 3-prime ss overhang is conserved in ciliated protozoa, yeast, and mammals. SpPOT1 is essential for telomere maintenance. It binds specifically to the ss G-rich telomeric sequence (GGTTAC) of S. pombe. hPOT1 binds specifically to ss telomeric DNA repeats ending with the sequence GGTTAG. Deletion of the S. pombe pot1+ gene results in a rapid loss of telomere sequences, chromosome mis-segregation and chromosome circularization. hPOT1 is implicated in telomere length regulation. The hPOT1 monomer consists of two closely connected OB folds (OB1-OB
Probab=23.58 E-value=1.4e+02 Score=21.97 Aligned_cols=33 Identities=18% Similarity=0.418 Sum_probs=22.5
Q ss_pred CeEEEeeccCc--ceEEEEEeeCCe----eeeecCcEEEE
Q 036919 40 TVLKVADNSGV--KTVMCIQPLKGK----KVARLGDTIVV 73 (132)
Q Consensus 40 T~L~VaDNSGa--k~v~CI~vl~gr----k~a~vGD~Iiv 73 (132)
..|.++|-|++ ..+ .+++++.. +...+||+|.+
T Consensus 39 ~tl~i~D~S~~~~~~l-~v~~F~~~~~~LP~v~~GDVIll 77 (138)
T cd04497 39 CTLTITDPSLANSDGL-TVKLFRPNEESLPIVKVGDIILL 77 (138)
T ss_pred EEEEEECCCCCCCCcE-EEEEECCChhhCCCCCCCCEEEE
Confidence 56899999997 444 44466542 33489999875
No 33
>PF08206 OB_RNB: Ribonuclease B OB domain; InterPro: IPR013223 This domain includes the N-terminal OB domain found in ribonuclease B proteins in one or two copies.; PDB: 2ID0_D 2IX1_A 2IX0_A.
Probab=22.47 E-value=96 Score=19.64 Aligned_cols=15 Identities=27% Similarity=0.366 Sum_probs=10.9
Q ss_pred eeeecCcEEEEEEee
Q 036919 63 KVARLGDTIVVSVKE 77 (132)
Q Consensus 63 k~a~vGD~IivsVKk 77 (132)
+.|--||.|+|.+.+
T Consensus 30 ~~A~~gD~V~v~i~~ 44 (58)
T PF08206_consen 30 NGAMDGDKVLVRITP 44 (58)
T ss_dssp TTS-TT-EEEEEEEE
T ss_pred CCCCCCCEEEEEEec
Confidence 467889999999987
No 34
>KOG0149 consensus Predicted RNA-binding protein SEB4 (RRM superfamily) [General function prediction only]
Probab=21.27 E-value=97 Score=26.25 Aligned_cols=30 Identities=33% Similarity=0.407 Sum_probs=24.0
Q ss_pred ccceEEEEEEecccccccCCCcEEEeccce
Q 036919 86 KGEVVKAVVVRAAMDHGRCDGSFVKFDDNA 115 (132)
Q Consensus 86 Kg~V~kAVIVRtKk~~~R~dG~~IkFddNA 115 (132)
=|||+.||||-.|..-+-+---+|.|.|-.
T Consensus 36 fGeI~eavvitd~~t~rskGyGfVTf~d~~ 65 (247)
T KOG0149|consen 36 FGEIVEAVVITDKNTGRSKGYGFVTFRDAE 65 (247)
T ss_pred hCceEEEEEEeccCCccccceeeEEeecHH
Confidence 499999999998877766665789998743
No 35
>cd04492 YhaM_OBF_like YhaM_OBF_like: A subfamily of OB folds similar to that found in Bacillus subtilis YhaM and Staphylococcus aureus cmp-binding factor-1 (SaCBF1). Both these proteins are 3'-to-5'exoribonucleases. YhaM requires Mn2+ or Co2+ for activity and is inactive in the presence of Mg2+. YhaM also has a Mn2+ dependent 3'-to-5'single-stranded DNA exonuclease activity. SaCBF is also a double-stranded DNA binding protein, binding specifically to cmp, the replication enhancer found in S. aureus plasmid pT181. Proteins in this group combine an N-terminal OB fold with a C-terminal HD domain. The HD domain is found in metal-dependent phosphohydrolases.
Probab=21.11 E-value=1.3e+02 Score=18.90 Aligned_cols=37 Identities=16% Similarity=0.206 Sum_probs=23.8
Q ss_pred CeEEEeeccCcceEEEEE-eeCCeeeeecCcEEEEEEe
Q 036919 40 TVLKVADNSGVKTVMCIQ-PLKGKKVARLGDTIVVSVK 76 (132)
Q Consensus 40 T~L~VaDNSGak~v~CI~-vl~grk~a~vGD~IivsVK 76 (132)
..+.+.|.||.-.+.|.. .+........|..+.+.-+
T Consensus 21 ~~~~l~D~tg~i~~~~f~~~~~~~~~l~~g~~v~v~G~ 58 (83)
T cd04492 21 LALTLQDKTGEIEAKLWDASEEDEEKFKPGDIVHVKGR 58 (83)
T ss_pred EEEEEEcCCCeEEEEEcCCChhhHhhCCCCCEEEEEEE
Confidence 678999999987777764 2111233456777666654
No 36
>COG0335 RplS Ribosomal protein L19 [Translation, ribosomal structure and biogenesis]
Probab=21.07 E-value=1.6e+02 Score=22.27 Aligned_cols=31 Identities=32% Similarity=0.352 Sum_probs=22.8
Q ss_pred ecCcEEEEEEeeecC-CCcccccceEEEEEEeccc
Q 036919 66 RLGDTIVVSVKEVMP-NAKVKKGEVVKAVVVRAAM 99 (132)
Q Consensus 66 ~vGD~IivsVKk~~p-~~kikKg~V~kAVIVRtKk 99 (132)
.+||+|.|.||=... +.+ =|.+-++|++-+.
T Consensus 22 ~~GDtvrv~vki~Eg~keR---~Q~FeGvVia~r~ 53 (115)
T COG0335 22 RPGDTVRVHVKIVEGSKER---VQAFEGVVIARRG 53 (115)
T ss_pred CCCCEEEEEEEEEeCCeEE---EeeeeEEEEEECC
Confidence 589999999985553 223 3788999998655
No 37
>PF04170 NlpE: NlpE N-terminal domain; InterPro: IPR007298 This family represents a bacterial outer membrane lipoprotein that is necessary for signalling by the Cpx pathway []. This pathway responds to cell envelope disturbances and increases the expression of periplasmic protein folding and degradation factors. While the molecular function of the NlpE protein is unknown, it may be involved in detecting bacterial adhesion to abiotic surfaces. NlpE from Escherichia coli and Salmonella typhi is also known to confer copper tolerance in copper-sensitive strains of E. coli, and may be involved in copper efflux and delivery of copper to copper-dependent enzymes [].; PDB: 3LHN_A 2Z4I_B 2Z4H_A.
Probab=20.86 E-value=1.3e+02 Score=20.63 Aligned_cols=24 Identities=17% Similarity=0.206 Sum_probs=16.9
Q ss_pred CcEEEeccceEEEEcCCCCcceee
Q 036919 106 GSFVKFDDNAVVLIDNLCVLAFAE 129 (132)
Q Consensus 106 G~~IkFddNAvVLIn~kg~p~~~~ 129 (132)
..+.+-++|...++|.+|+|+-++
T Consensus 63 ~~~f~v~~~~L~~Ld~~G~~i~g~ 86 (87)
T PF04170_consen 63 KRYFKVGENSLEMLDQDGNPIEGE 86 (87)
T ss_dssp CEEEEEETTEEEEE-TTS-B-ECC
T ss_pred EEEEEECCCEEEEECCCCCcCCCC
Confidence 356677899999999999998654
No 38
>cd06555 ASCH_PF0470_like ASC-1 homology domain, subfamily similar to Pyrococcus furiosus Pf0470. The ASCH domain, a small beta-barrel domain found in all three kingdoms of life, resembles the RNA-binding PUA domain and may also interact with RNA. ASCH has been proposed to function as an RNA-binding domain during coactivation, RNA-processing and the regulation of prokaryotic translation.
Probab=20.31 E-value=1.3e+02 Score=22.13 Aligned_cols=29 Identities=24% Similarity=0.273 Sum_probs=19.2
Q ss_pred cCcceEEEEEeeCCeeeeecCcEEEEEEe
Q 036919 48 SGVKTVMCIQPLKGKKVARLGDTIVVSVK 76 (132)
Q Consensus 48 SGak~v~CI~vl~grk~a~vGD~IivsVK 76 (132)
||.|.+.+=..-..++.-++||.|+..--
T Consensus 15 ~G~KtiEiRlnD~kr~~ikvGD~I~f~~~ 43 (109)
T cd06555 15 SGKKTIEIRLNDEKRQQIKVGDKILFNDL 43 (109)
T ss_pred cCCCEEEEEecccchhcCCCCCEEEEEEc
Confidence 67777765432233567789999988553
Done!