Query 035907
Match_columns 105
No_of_seqs 104 out of 341
Neff 4.4
Searched_HMMs 46136
Date Fri Mar 29 07:32:27 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/035907.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/035907hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00471 60S ribosomal protein 100.0 5.7E-55 1.2E-59 318.1 10.3 103 1-104 1-131 (134)
2 KOG3418 60S ribosomal protein 100.0 6.6E-48 1.4E-52 281.1 8.3 104 1-104 1-133 (136)
3 PF01777 Ribosomal_L27e: Ribos 99.9 2.4E-26 5.2E-31 156.6 -6.7 57 48-104 25-82 (85)
4 COG2163 RPL14A Ribosomal prote 99.8 1.6E-18 3.4E-23 125.5 6.4 97 1-98 1-124 (125)
5 PRK04333 50S ribosomal protein 99.4 5.4E-13 1.2E-17 90.7 5.9 52 4-62 3-63 (84)
6 PTZ00065 60S ribosomal protein 99.2 3.9E-11 8.5E-16 87.6 5.9 54 3-63 6-68 (130)
7 KOG3421 60S ribosomal protein 97.7 0.00012 2.6E-09 54.1 6.5 55 2-63 4-66 (136)
8 PF00467 KOW: KOW motif; Inte 96.7 0.0032 6.9E-08 35.1 3.9 26 7-32 1-26 (32)
9 smart00739 KOW KOW (Kyprides, 96.3 0.0075 1.6E-07 31.5 3.4 26 5-30 2-27 (28)
10 PRK12281 rplX 50S ribosomal pr 95.2 0.034 7.3E-07 37.1 3.9 47 4-56 6-53 (76)
11 CHL00141 rpl24 ribosomal prote 94.9 0.053 1.2E-06 36.6 4.3 38 4-47 8-45 (83)
12 PRK01191 rpl24p 50S ribosomal 94.1 0.1 2.2E-06 37.9 4.4 37 5-47 46-82 (120)
13 PRK00004 rplX 50S ribosomal pr 93.9 0.13 2.9E-06 35.9 4.6 40 2-47 2-41 (105)
14 TIGR01079 rplX_bact ribosomal 93.5 0.15 3.3E-06 35.7 4.3 38 4-47 3-40 (104)
15 PF01159 Ribosomal_L6e: Riboso 93.3 0.027 5.9E-07 40.0 0.4 29 48-76 10-41 (108)
16 PTZ00194 60S ribosomal protein 93.0 0.18 3.8E-06 37.7 4.2 45 5-55 47-92 (143)
17 TIGR01080 rplX_A_E ribosomal p 92.5 0.24 5.3E-06 35.5 4.3 37 5-47 42-78 (114)
18 COG0198 RplX Ribosomal protein 89.0 0.8 1.7E-05 32.5 4.1 38 2-47 2-39 (104)
19 PTZ00328 eukaryotic initiation 73.5 7.5 0.00016 29.7 4.5 56 3-63 26-86 (166)
20 PF13234 rRNA_proc-arch: rRNA- 60.6 8 0.00017 30.0 2.5 29 3-31 71-99 (268)
21 COG1471 RPS4A Ribosomal protei 60.4 10 0.00022 30.7 3.0 24 5-28 174-197 (241)
22 KOG1708 Mitochondrial/chloropl 59.3 12 0.00025 30.1 3.2 37 5-47 73-109 (236)
23 PRK05609 nusG transcription an 54.7 28 0.00061 25.1 4.4 28 4-31 126-153 (181)
24 PLN00036 40S ribosomal protein 53.8 24 0.00052 28.7 4.2 25 5-29 175-199 (261)
25 PRK04313 30S ribosomal protein 52.6 14 0.00031 29.5 2.8 24 5-28 172-195 (237)
26 TIGR00405 L26e_arch ribosomal 51.8 35 0.00075 24.1 4.4 27 4-30 86-112 (145)
27 PTZ00118 40S ribosomal protein 51.2 15 0.00033 29.9 2.7 23 5-27 175-197 (262)
28 PTZ00223 40S ribosomal protein 48.9 19 0.00041 29.5 3.0 24 5-28 172-195 (273)
29 KOG1694 60s ribosomal protein 48.6 14 0.00031 27.7 2.1 12 4-15 33-44 (152)
30 TIGR00922 nusG transcription t 48.1 42 0.00091 24.1 4.5 25 5-29 120-144 (172)
31 cd07933 RHD-n_c-Rel N-terminal 46.2 48 0.001 25.5 4.6 74 18-98 48-121 (172)
32 KOG1999 RNA polymerase II tran 44.7 19 0.00042 34.3 2.7 29 2-30 457-485 (1024)
33 PF15591 Imm17: Immunity prote 42.2 47 0.001 22.4 3.6 26 16-43 21-46 (74)
34 PRK09014 rfaH transcriptional 38.2 72 0.0016 22.8 4.3 26 4-29 109-134 (162)
35 cd04822 PA_M28_1_3 PA_M28_1_3: 34.3 50 0.0011 24.4 3.1 10 7-16 47-56 (151)
36 PF02491 SHS2_FTSA: SHS2 domai 33.4 26 0.00056 22.4 1.3 15 48-62 43-57 (80)
37 TIGR01955 RfaH transcriptional 32.4 98 0.0021 21.8 4.2 24 5-28 109-132 (159)
38 PF08584 Ribonuc_P_40: Ribonuc 31.7 1.7E+02 0.0037 23.2 5.9 86 3-103 12-108 (284)
39 COG5137 Histone chaperone invo 28.9 52 0.0011 26.9 2.5 20 8-27 91-110 (279)
40 PF01929 Ribosomal_L14e: Ribos 28.2 24 0.00053 23.5 0.5 16 48-63 6-21 (77)
41 cd04814 PA_M28_1 PA_M28_1: Pro 26.3 87 0.0019 22.9 3.1 10 7-16 47-56 (142)
42 PF11061 DUF2862: Protein of u 26.2 28 0.00062 22.8 0.5 11 93-103 49-59 (64)
43 PRK08559 nusG transcription an 25.8 2.5E+02 0.0054 20.2 5.5 27 5-31 95-121 (153)
44 PF06102 DUF947: Domain of unk 25.6 66 0.0014 24.0 2.4 25 81-105 107-131 (168)
45 KOG2544 Dihydropteroate syntha 25.3 1.3E+02 0.0027 27.5 4.4 33 22-63 6-38 (711)
46 PF05257 CHAP: CHAP domain; I 25.2 1.9E+02 0.004 19.4 4.5 29 4-32 62-92 (124)
47 PF10307 DUF2410: Hypothetical 23.5 53 0.0011 25.5 1.6 13 6-18 69-81 (197)
48 COG2876 AroA 3-deoxy-D-arabino 23.0 56 0.0012 27.1 1.8 22 39-62 181-204 (286)
49 KOG2037 Guanylate-binding prot 22.2 78 0.0017 28.3 2.6 51 4-54 27-90 (552)
50 cd07886 RHD-n_RelB N-terminal 20.4 2.4E+02 0.0052 21.7 4.6 74 18-97 48-123 (172)
No 1
>PTZ00471 60S ribosomal protein L27; Provisional
Probab=100.00 E-value=5.7e-55 Score=318.14 Aligned_cols=103 Identities=40% Similarity=0.640 Sum_probs=101.7
Q ss_pred CcccccCcEEEEEeccccCCceEEEeeecCCCCCCCCCceEEEeccc----------------------------CCcee
Q 035907 1 MVTFLKPNKAVILLQGRNASRKAVIMKSFDDGTRERPNGHCLVARIK----------------------------NYQHL 52 (105)
Q Consensus 1 m~k~~kpgkVvivL~Gr~aGkKaVivk~~d~gt~~~~y~~~lVaGi~----------------------------N~nHl 52 (105)
|+|||+||+|||||+|||||||||||+++||||+||||+|||||||+ |||||
T Consensus 1 M~K~~kpgkVVivL~GR~AGkKaVivk~~ddgt~drpy~halVaGIdryP~kVtk~M~kkki~KRskiK~FvK~vNynHl 80 (134)
T PTZ00471 1 MTKFLKPGKVVIVTSGRYAGRKAVIVQNFDTASKERPYGHALVAGIKKYPKKVVRGMSKRTIARRSQVGVFLRVVNHKHF 80 (134)
T ss_pred CCccccCCEEEEEEccccCCcEEEEEeecCCCCccCcCceEEEEeecccchhhhhhccHHHHHHHhccccceEEEeecee
Confidence 99999999999999999999999999999999999999999999998 99999
Q ss_pred eeeceEeecCCccccCcccccChhhHHHHHHHHHHHHHHHHhcCCceeeeeC
Q 035907 53 MPTCYTLDVDLKEVVTTNSLQSKDKKVTACEETKKHLEEKFKTGKNLGSLLS 104 (105)
Q Consensus 53 ~pTry~vdi~~k~~v~~~~~~d~~~k~~akk~~k~~feer~k~gknkwfF~k 104 (105)
|||||+||++ +++++.++|+||++|++|+++++..|||+|++|||+|||++
T Consensus 81 mPTRY~vdi~-~~~v~~~~~~d~~~k~~ar~~~k~~feer~k~gKn~wFF~k 131 (134)
T PTZ00471 81 LPTRYNMDMS-KELRGRINVSDASKKARSKQLVKKLFQARYNAGSSRWFFQR 131 (134)
T ss_pred cccceeeecc-ccccCHHHhhChHHHHHHHHHHHHHHHHHHhcCccceeeee
Confidence 9999999999 89999999999999999999999999999999999999997
No 2
>KOG3418 consensus 60S ribosomal protein L27 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=6.6e-48 Score=281.12 Aligned_cols=104 Identities=51% Similarity=0.777 Sum_probs=102.4
Q ss_pred CcccccCcEEEEEeccccCCceEEEeeecCCCCCCCCCceEEEeccc----------------------------CCcee
Q 035907 1 MVTFLKPNKAVILLQGRNASRKAVIMKSFDDGTRERPNGHCLVARIK----------------------------NYQHL 52 (105)
Q Consensus 1 m~k~~kpgkVvivL~Gr~aGkKaVivk~~d~gt~~~~y~~~lVaGi~----------------------------N~nHl 52 (105)
|+|||+||+||++|+||||||||||||++|||++|+||+|||||||+ |||||
T Consensus 1 m~kflkPgkvv~v~sG~yAg~KaVivk~~Ddg~~d~p~~h~LvAgi~ryP~kvt~~~gkkk~~krsk~k~flKv~ny~hl 80 (136)
T KOG3418|consen 1 MAKFLKPGKVVLVLSGRYAGKKAVIVKNIDDGTEDKPYGHALVAGVDRYPRKVTKSMGKKKLAKRSKVKPFLKVINYNHL 80 (136)
T ss_pred CcccccCCcEEEeecccccCccEEEEeecccCCccCCCceeeeeehhhccccccccccchhhhhcccceeEEEEeecccc
Confidence 89999999999999999999999999999999999999999999999 99999
Q ss_pred eeeceEeecC-CccccCcccccChhhHHHHHHHHHHHHHHHHhcCCceeeeeC
Q 035907 53 MPTCYTLDVD-LKEVVTTNSLQSKDKKVTACEETKKHLEEKFKTGKNLGSLLS 104 (105)
Q Consensus 53 ~pTry~vdi~-~k~~v~~~~~~d~~~k~~akk~~k~~feer~k~gknkwfF~k 104 (105)
|||||++|++ ++++++.|+|++|++|..++++++..|||+|++|+|+|||++
T Consensus 81 MptRy~vdv~~~k~v~~kdv~~~p~~K~~a~~~~k~kfeer~k~gkn~wff~~ 133 (136)
T KOG3418|consen 81 MPTRYTVDVLALKTVINKDVFRDPVKKGTAIKEAKVKFEERYKTGKNKWFFTK 133 (136)
T ss_pred cCcceEEeehhhhccccHHhhhChhhhhhhhhHHHHHHHHHHHhCcccccccc
Confidence 9999999999 689999999999999999999999999999999999999987
No 3
>PF01777 Ribosomal_L27e: Ribosomal L27e protein family; InterPro: IPR001141 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, L27 is found in fungi, plants, algae and vertebrates [, ]. The family has a specific signature at the C terminus.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3IZS_a 4A1B_N 4A19_N 4A18_N 4A1D_N 3IZR_a.
Probab=99.89 E-value=2.4e-26 Score=156.56 Aligned_cols=57 Identities=46% Similarity=0.655 Sum_probs=51.6
Q ss_pred CCceeeeeceEeecC-CccccCcccccChhhHHHHHHHHHHHHHHHHhcCCceeeeeC
Q 035907 48 NYQHLMPTCYTLDVD-LKEVVTTNSLQSKDKKVTACEETKKHLEEKFKTGKNLGSLLS 104 (105)
Q Consensus 48 N~nHl~pTry~vdi~-~k~~v~~~~~~d~~~k~~akk~~k~~feer~k~gknkwfF~k 104 (105)
||||||||||+||++ ++++|++|+|+||+.|++|+++++..|||+|++|||+|||++
T Consensus 25 NynHlmPTRY~vd~~~~k~~v~~~~l~~~~~kk~a~k~~k~~feer~k~gKnkwFF~K 82 (85)
T PF01777_consen 25 NYNHLMPTRYSVDIPDDKTVVNKDALKDPSKKKKAKKEIKKKFEERYKTGKNKWFFQK 82 (85)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHCHHHHHTT--HHHHHHHHHHHHHHHHHHHHHHHHH--
T ss_pred eccceEeeeeeeechhhhcccCHHHHhChHHHHHHHHHHHHHHHHHhccCCCcEEeee
Confidence 999999999999995 689999999999999999999999999999999999999987
No 4
>COG2163 RPL14A Ribosomal protein L14E/L6E/L27E [Translation, ribosomal structure and biogenesis]
Probab=99.75 E-value=1.6e-18 Score=125.50 Aligned_cols=97 Identities=28% Similarity=0.322 Sum_probs=72.0
Q ss_pred CcccccCcEEEEEeccccCCceEEEeeecCCCCCCCCCceEEEeccc----CCceeeeeceEeecCC---ccc-------
Q 035907 1 MVTFLKPNKAVILLQGRNASRKAVIMKSFDDGTRERPNGHCLVARIK----NYQHLMPTCYTLDVDL---KEV------- 66 (105)
Q Consensus 1 m~k~~kpgkVvivL~Gr~aGkKaVivk~~d~gt~~~~y~~~lVaGi~----N~nHl~pTry~vdi~~---k~~------- 66 (105)
|.+++.||+||++++|||||+++|||+++||+ .-.+.++.+|+|+. |++|++||...++++= ...
T Consensus 1 ~~~~l~~GrVvvv~~GR~aGkk~VIv~~iDd~-~v~i~gp~~v~gv~r~r~n~~~l~~t~~~~~~~rg~~~~~v~~~~~a 79 (125)
T COG2163 1 MRASLEVGRVVVVTAGRFAGKKVVIVKIIDDN-FVLITGPKKVKGVPRRRINIKHLEPTDKVIDLVRGASDEKVKKANEA 79 (125)
T ss_pred CCccccCCeEEEEecceeCCceEEEEEEccCC-EEEEeCCccccCCccccccceeeeccceeeeecccccHHHHHHHHHh
Confidence 78899999999999999999999999999995 22333344444444 9999999999887651 111
Q ss_pred -------------cCcccccChhhHHHHHHHHHHHHHHHHhcCCc
Q 035907 67 -------------VTTNSLQSKDKKVTACEETKKHLEEKFKTGKN 98 (105)
Q Consensus 67 -------------v~~~~~~d~~~k~~akk~~k~~feer~k~gkn 98 (105)
+..+.+..+..+-+..+..+..++|+|..|++
T Consensus 80 ~~~~~~~~~~~~~~~~k~~~~~~~~~~r~~~~k~~~~~~~~~~k~ 124 (125)
T COG2163 80 AGVLAKLDKSAKNLETKKVREPLTDAERFKVMKLVKEERLQVGKA 124 (125)
T ss_pred hhhhccccccchhhhhhhhhcccchHHHHHHHHHHHHHHhhhhcc
Confidence 22233444556666667789999999999986
No 5
>PRK04333 50S ribosomal protein L14e; Validated
Probab=99.40 E-value=5.4e-13 Score=90.68 Aligned_cols=52 Identities=31% Similarity=0.478 Sum_probs=48.6
Q ss_pred cccCcEEEEEeccccCCceEEEeeecCCCCCCCCCceEEEeccc---------CCceeeeeceEeecC
Q 035907 4 FLKPNKAVILLQGRNASRKAVIMKSFDDGTRERPNGHCLVARIK---------NYQHLMPTCYTLDVD 62 (105)
Q Consensus 4 ~~kpgkVvivL~Gr~aGkKaVivk~~d~gt~~~~y~~~lVaGi~---------N~nHl~pTry~vdi~ 62 (105)
-+++|+||++++||++|+.+||++.+|+ +++||+|+. |.+||.+|...++++
T Consensus 3 ~v~~GrvV~~~~Grd~gk~~vIv~i~d~-------~~vlVdg~~~~~~~rk~kn~khl~lt~~ki~~~ 63 (84)
T PRK04333 3 AIEVGRVCVKTAGREAGRKCVIVDIIDK-------NFVLVTGPSLTGVKRRRCNIKHLEPTDKKVDIE 63 (84)
T ss_pred cccccEEEEEeccCCCCCEEEEEEEecC-------CEEEEECCCcCCCCCeeechHHEEEeeEEEECC
Confidence 4689999999999999999999999999 899999994 999999999999875
No 6
>PTZ00065 60S ribosomal protein L14; Provisional
Probab=99.19 E-value=3.9e-11 Score=87.62 Aligned_cols=54 Identities=17% Similarity=0.269 Sum_probs=51.2
Q ss_pred ccccCcEEEEEeccccCCceEEEeeecCCCCCCCCCceEEEeccc---------CCceeeeeceEeecCC
Q 035907 3 TFLKPNKAVILLQGRNASRKAVIMKSFDDGTRERPNGHCLVARIK---------NYQHLMPTCYTLDVDL 63 (105)
Q Consensus 3 k~~kpgkVvivL~Gr~aGkKaVivk~~d~gt~~~~y~~~lVaGi~---------N~nHl~pTry~vdi~~ 63 (105)
+|+++||||++..|.|+|+-||||..+|. +.+||.|++ |++||.||.+.++|+-
T Consensus 6 rfVEiGRVvli~~Gp~~GKL~vIVDIID~-------nRvLVDGP~~tgV~Rq~i~~k~l~LT~~~v~i~r 68 (130)
T PTZ00065 6 RFVEPGRLCLIQYGPDAGKLCFIVDIVTP-------TRVLVDGAFITGVKRQSIPLKRLKLTDEKIKINR 68 (130)
T ss_pred cceeeceEEEEecCCCCCCEEEEEEEEcC-------CeEEEeCCCcCCcceeEEeccceEEccEEEecCC
Confidence 58999999999999999999999999999 899999992 9999999999999983
No 7
>KOG3421 consensus 60S ribosomal protein L14 [Translation, ribosomal structure and biogenesis]
Probab=97.72 E-value=0.00012 Score=54.13 Aligned_cols=55 Identities=20% Similarity=0.279 Sum_probs=51.2
Q ss_pred cccccCcEEEEEeccccCCceEEEeeecCCCCCCCCCceEEEeccc--------CCceeeeeceEeecCC
Q 035907 2 VTFLKPNKAVILLQGRNASRKAVIMKSFDDGTRERPNGHCLVARIK--------NYQHLMPTCYTLDVDL 63 (105)
Q Consensus 2 ~k~~kpgkVvivL~Gr~aGkKaVivk~~d~gt~~~~y~~~lVaGi~--------N~nHl~pTry~vdi~~ 63 (105)
..+...|+|+++..|-|+||=++||..+|+ +.+||-|+. |++-+.-|-|.++++.
T Consensus 4 ~r~veVGrva~v~~G~~~GkL~AIVdviDq-------nr~lvDGp~t~v~rq~~~~~~~~LT~~~~kfp~ 66 (136)
T KOG3421|consen 4 KRFVEVGRVALVSFGPDAGKLVAIVDVIDQ-------NRALVDGPCTGVPRQAMNLKCLQLTDFVLKFPR 66 (136)
T ss_pred hhhhhcceEEEEEecCCCceEEEEEEeecc-------hhhhccCcccccchhhcchhheeeeeeeEeccc
Confidence 457899999999999999999999999999 889999996 9999999999999986
No 8
>PF00467 KOW: KOW motif; InterPro: IPR005824 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 KOW (Kyprides, Ouzounis, Woese) motif is found in a variety of ribosomal proteins and the bacterial transcription antitermination proteins NusG []. ; PDB: 3BBO_W 2HGJ_X 2HGQ_X 2HGU_X 1NPP_B 1M1G_D 1NPR_A 2XHC_A 2KVQ_G 2JVV_A ....
Probab=96.75 E-value=0.0032 Score=35.15 Aligned_cols=26 Identities=12% Similarity=0.097 Sum_probs=24.0
Q ss_pred CcEEEEEeccccCCceEEEeeecCCC
Q 035907 7 PNKAVILLQGRNASRKAVIMKSFDDG 32 (105)
Q Consensus 7 pgkVvivL~Gr~aGkKaVivk~~d~g 32 (105)
||..|.|++|+|+|+.+.|++..++.
T Consensus 1 ~Gd~V~V~~G~~~G~~G~I~~i~~~~ 26 (32)
T PF00467_consen 1 VGDTVKVISGPFKGKIGKIVEIDRSK 26 (32)
T ss_dssp TTSEEEESSSTTTTEEEEEEEEETTT
T ss_pred CCCEEEEeEcCCCCceEEEEEEECCC
Confidence 68899999999999999999988874
No 9
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=96.29 E-value=0.0075 Score=31.54 Aligned_cols=26 Identities=8% Similarity=0.161 Sum_probs=23.2
Q ss_pred ccCcEEEEEeccccCCceEEEeeecC
Q 035907 5 LKPNKAVILLQGRNASRKAVIMKSFD 30 (105)
Q Consensus 5 ~kpgkVvivL~Gr~aGkKaVivk~~d 30 (105)
+++|..|.|+.|.|+|..++|++..+
T Consensus 2 ~~~G~~V~I~~G~~~g~~g~i~~i~~ 27 (28)
T smart00739 2 FEVGDTVRVIAGPFKGKVGKVLEVDG 27 (28)
T ss_pred CCCCCEEEEeECCCCCcEEEEEEEcC
Confidence 57999999999999999999997643
No 10
>PRK12281 rplX 50S ribosomal protein L24; Reviewed
Probab=95.22 E-value=0.034 Score=37.07 Aligned_cols=47 Identities=13% Similarity=0.294 Sum_probs=38.7
Q ss_pred cccCcEEEEEeccccCCceEEEeeecCCCCCCCCCceEEEeccc-CCceeeeec
Q 035907 4 FLKPNKAVILLQGRNASRKAVIMKSFDDGTRERPNGHCLVARIK-NYQHLMPTC 56 (105)
Q Consensus 4 ~~kpgkVvivL~Gr~aGkKaVivk~~d~gt~~~~y~~~lVaGi~-N~nHl~pTr 56 (105)
-+++|--|+|++|++.|+.+.|++...+. +.++|-|+. --.|+=|+.
T Consensus 6 ~I~kGD~V~Vi~G~dKGK~G~V~~V~~~~------~~V~Vegvn~~kkh~kp~~ 53 (76)
T PRK12281 6 KVKKGDMVKVIAGDDKGKTGKVLAVLPKK------NRVIVEGVKIAKKAIKPSQ 53 (76)
T ss_pred cccCCCEEEEeEcCCCCcEEEEEEEEcCC------CEEEEcCcEEEEEEcCCCc
Confidence 47889999999999999999999987664 579999997 445665665
No 11
>CHL00141 rpl24 ribosomal protein L24; Validated
Probab=94.93 E-value=0.053 Score=36.63 Aligned_cols=38 Identities=16% Similarity=0.343 Sum_probs=33.6
Q ss_pred cccCcEEEEEeccccCCceEEEeeecCCCCCCCCCceEEEeccc
Q 035907 4 FLKPNKAVILLQGRNASRKAVIMKSFDDGTRERPNGHCLVARIK 47 (105)
Q Consensus 4 ~~kpgkVvivL~Gr~aGkKaVivk~~d~gt~~~~y~~~lVaGi~ 47 (105)
-+++|--|.|++|++.|+.+.|++...+. +.++|-|+.
T Consensus 8 ~I~~GD~V~Vi~G~dKGK~G~V~~V~~~~------~~V~Vegvn 45 (83)
T CHL00141 8 HVKIGDTVKIISGSDKGKIGEVLKIIKKS------NKVIVKGIN 45 (83)
T ss_pred cccCCCEEEEeEcCCCCcEEEEEEEEcCC------CEEEEcCcE
Confidence 57899999999999999999999987764 579999986
No 12
>PRK01191 rpl24p 50S ribosomal protein L24P; Validated
Probab=94.12 E-value=0.1 Score=37.90 Aligned_cols=37 Identities=11% Similarity=0.218 Sum_probs=32.9
Q ss_pred ccCcEEEEEeccccCCceEEEeeecCCCCCCCCCceEEEeccc
Q 035907 5 LKPNKAVILLQGRNASRKAVIMKSFDDGTRERPNGHCLVARIK 47 (105)
Q Consensus 5 ~kpgkVvivL~Gr~aGkKaVivk~~d~gt~~~~y~~~lVaGi~ 47 (105)
++.|-.|.|++|.+.|+.+-|++...+. +.++|-||.
T Consensus 46 IkkGD~V~VisG~~KGk~GkV~~V~~~~------~~V~VeGvn 82 (120)
T PRK01191 46 VRKGDTVKVMRGDFKGEEGKVVEVDLKR------GRIYVEGVT 82 (120)
T ss_pred EeCCCEEEEeecCCCCceEEEEEEEcCC------CEEEEeCcE
Confidence 6789999999999999999999997664 579999987
No 13
>PRK00004 rplX 50S ribosomal protein L24; Reviewed
Probab=93.91 E-value=0.13 Score=35.93 Aligned_cols=40 Identities=15% Similarity=0.426 Sum_probs=34.9
Q ss_pred cccccCcEEEEEeccccCCceEEEeeecCCCCCCCCCceEEEeccc
Q 035907 2 VTFLKPNKAVILLQGRNASRKAVIMKSFDDGTRERPNGHCLVARIK 47 (105)
Q Consensus 2 ~k~~kpgkVvivL~Gr~aGkKaVivk~~d~gt~~~~y~~~lVaGi~ 47 (105)
..-+++|--|.|++|++.|+.+.|++.+.+. +.++|-|+.
T Consensus 2 ~~~i~kGD~V~Vi~G~dKGk~G~V~~V~~~~------~~V~Vegvn 41 (105)
T PRK00004 2 MMKIKKGDTVIVIAGKDKGKRGKVLKVLPKK------NKVIVEGVN 41 (105)
T ss_pred CCcccCCCEEEEeEcCCCCcEEEEEEEEcCC------CEEEEcCcE
Confidence 3457899999999999999999999998764 679999986
No 14
>TIGR01079 rplX_bact ribosomal protein L24, bacterial/organelle. This model recognizes bacterial and organellar forms of ribosomal protein L24. It excludes eukaryotic and archaeal forms, designated L26 in eukaryotes.
Probab=93.46 E-value=0.15 Score=35.69 Aligned_cols=38 Identities=13% Similarity=0.390 Sum_probs=33.6
Q ss_pred cccCcEEEEEeccccCCceEEEeeecCCCCCCCCCceEEEeccc
Q 035907 4 FLKPNKAVILLQGRNASRKAVIMKSFDDGTRERPNGHCLVARIK 47 (105)
Q Consensus 4 ~~kpgkVvivL~Gr~aGkKaVivk~~d~gt~~~~y~~~lVaGi~ 47 (105)
-+++|--|.|++|++.|+.+.|++.+.+. +.++|-|+.
T Consensus 3 ~ikkGD~V~Vi~G~dKGK~G~V~~V~~~~------~~V~VegvN 40 (104)
T TIGR01079 3 KIKKGDTVKVISGKDKGKRGKVLKVLPKT------NKVIVEGVN 40 (104)
T ss_pred cccCCCEEEEeEcCCCCcEEEEEEEEcCC------CEEEECCcE
Confidence 47889999999999999999999998764 679999996
No 15
>PF01159 Ribosomal_L6e: Ribosomal protein L6e ; InterPro: IPR000915 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 [, ]. A number of eukaryotic and archaeabacterial ribosomal proteins can be grouped on the basis of sequence similarities. One of these families includes mammalian ribosomal protein L6 (L6 was previously known as TAX-responsive enhancer element binding protein 107); Caenorhabditis elegans ribosomal protein L6 (R151.3); Saccharomyces cerevisiae (Baker's yeast) ribosomal protein YL16A/YL16B; and Mesembryanthemum crystallinum (Common ice plant) ribosomal protein YL16-like. These proteins have 175 (yeast) to 287 (mammalian) amino acids.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A18_E 4A1D_E 4A19_E 4A1B_E 3IZR_G 3O58_F 3O5H_F 3IZS_G.
Probab=93.35 E-value=0.027 Score=40.05 Aligned_cols=29 Identities=17% Similarity=0.303 Sum_probs=24.3
Q ss_pred CCceeeeeceEeecC-C--ccccCcccccChh
Q 035907 48 NYQHLMPTCYTLDVD-L--KEVVTTNSLQSKD 76 (105)
Q Consensus 48 N~nHl~pTry~vdi~-~--k~~v~~~~~~d~~ 76 (105)
|++|+++|+.+|||+ + .+.+|+++|+...
T Consensus 10 nQ~yVIATSTkvDis~v~ip~~~~D~YF~~~~ 41 (108)
T PF01159_consen 10 NQAYVIATSTKVDISGVKIPEKIDDAYFKRKK 41 (108)
T ss_dssp SSCCCEECSCESCHCCHHH-CCTTGSSSCHCC
T ss_pred ccceEEEEeeEEeccccchhhccchHHHHhhh
Confidence 999999999999998 3 5779999997555
No 16
>PTZ00194 60S ribosomal protein L26; Provisional
Probab=93.00 E-value=0.18 Score=37.66 Aligned_cols=45 Identities=11% Similarity=0.282 Sum_probs=36.8
Q ss_pred ccCcEEEEEeccccCCceEEEeeecCCCCCCCCCceEEEeccc-CCceeeee
Q 035907 5 LKPNKAVILLQGRNASRKAVIMKSFDDGTRERPNGHCLVARIK-NYQHLMPT 55 (105)
Q Consensus 5 ~kpgkVvivL~Gr~aGkKaVivk~~d~gt~~~~y~~~lVaGi~-N~nHl~pT 55 (105)
++-|-.|+|++|.+.|+.+-|++.+... +.++|-||. .-.|--|.
T Consensus 47 IkkGD~V~Vi~Gk~KGk~GkV~~V~~k~------~~ViVEgvn~~Kk~gk~~ 92 (143)
T PTZ00194 47 VRKDDEVMVVRGHHKGREGKVTAVYRKK------WVIHIEKITREKANGEPV 92 (143)
T ss_pred eecCCEEEEecCCCCCCceEEEEEEcCC------CEEEEeCeEEEecCCCEe
Confidence 6778999999999999999999987654 679999998 44555553
No 17
>TIGR01080 rplX_A_E ribosomal protein L24p/L26e, archaeal/eukaryotic. This model represents the archaeal and eukaryotic branch of the ribosomal protein L24p/L26e family. Bacterial and organellar forms are represented by the related TIGR01079.
Probab=92.51 E-value=0.24 Score=35.46 Aligned_cols=37 Identities=11% Similarity=0.113 Sum_probs=32.1
Q ss_pred ccCcEEEEEeccccCCceEEEeeecCCCCCCCCCceEEEeccc
Q 035907 5 LKPNKAVILLQGRNASRKAVIMKSFDDGTRERPNGHCLVARIK 47 (105)
Q Consensus 5 ~kpgkVvivL~Gr~aGkKaVivk~~d~gt~~~~y~~~lVaGi~ 47 (105)
++.|--|.|++|.+.|+.+.|++...+. +.++|-||.
T Consensus 42 IkkGD~V~Vi~Gk~KGk~GkV~~V~~~~------~~V~Vegvn 78 (114)
T TIGR01080 42 VRKGDKVRIMRGDFKGHEGKVSKVDLKR------YRIYVEGVT 78 (114)
T ss_pred eecCCEEEEecCCCCCCEEEEEEEEcCC------CEEEEcCeE
Confidence 6789999999999999999999987553 568999987
No 18
>COG0198 RplX Ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=88.96 E-value=0.8 Score=32.48 Aligned_cols=38 Identities=13% Similarity=0.327 Sum_probs=33.5
Q ss_pred cccccCcEEEEEeccccCCceEEEeeecCCCCCCCCCceEEEeccc
Q 035907 2 VTFLKPNKAVILLQGRNASRKAVIMKSFDDGTRERPNGHCLVARIK 47 (105)
Q Consensus 2 ~k~~kpgkVvivL~Gr~aGkKaVivk~~d~gt~~~~y~~~lVaGi~ 47 (105)
..-++-|-.|+|++|.+.|+.+.|++.+.. . ++|-|+.
T Consensus 2 ~~~IrkGD~V~Vi~GkdKGk~GkVl~v~~k-------~-V~VEGvn 39 (104)
T COG0198 2 KMKVKKGDTVKVIAGKDKGKEGKVLKVLPK-------K-VVVEGVN 39 (104)
T ss_pred CcceecCCEEEEEecCCCCcceEEEEEecC-------e-EEEECcE
Confidence 345678899999999999999999999987 4 9999988
No 19
>PTZ00328 eukaryotic initiation factor 5a; Provisional
Probab=73.46 E-value=7.5 Score=29.72 Aligned_cols=56 Identities=13% Similarity=0.161 Sum_probs=39.8
Q ss_pred ccccCcEEEEEeccccCCceEEEeeecCCCCCCCCCceEEEeccc-----CCceeeeeceEeecCC
Q 035907 3 TFLKPNKAVILLQGRNASRKAVIMKSFDDGTRERPNGHCLVARIK-----NYQHLMPTCYTLDVDL 63 (105)
Q Consensus 3 k~~kpgkVvivL~Gr~aGkKaVivk~~d~gt~~~~y~~~lVaGi~-----N~nHl~pTry~vdi~~ 63 (105)
..|+.|..|++ .|+-|=|+...-+.|..|=...|-++||+ -|.++.|+..++++|+
T Consensus 26 ~~LkkG~yvvI-----kGrPCKIveistSKtGKHGhAK~~ivaidIFTgkK~edi~Ps~hnv~VP~ 86 (166)
T PTZ00328 26 GALKKGGYVCI-----NGRPCKVIDLSVSKTGKHGHAKVSIVATDIFTGNRLEDQAPSTHNVEVPF 86 (166)
T ss_pred cceeECCEEEE-----CCeeeEEEEEecCCCCcCCceEEEEEEEecCCCCEEeeecCccceeEeee
Confidence 35778888776 45577777766555544544456778887 7888899988888874
No 20
>PF13234 rRNA_proc-arch: rRNA-processing arch domain; PDB: 4A4K_E 4A4Z_A 2XGJ_B 3L9O_A.
Probab=60.55 E-value=8 Score=29.99 Aligned_cols=29 Identities=21% Similarity=0.385 Sum_probs=23.5
Q ss_pred ccccCcEEEEEeccccCCceEEEeeecCC
Q 035907 3 TFLKPNKAVILLQGRNASRKAVIMKSFDD 31 (105)
Q Consensus 3 k~~kpgkVvivL~Gr~aGkKaVivk~~d~ 31 (105)
.||.|||+|.|-.|-+...=||||+....
T Consensus 71 ~fL~~GRlV~v~~~~~~~~wgvvv~~~~~ 99 (268)
T PF13234_consen 71 PFLQPGRLVVVRDGDRDFGWGVVVNFAKK 99 (268)
T ss_dssp HHS-TTEEEEEEETTCEEEEEEEEEEEE-
T ss_pred HhCCCCCEEEEecCCCccceeEEEecccc
Confidence 58999999999988888889999976443
No 21
>COG1471 RPS4A Ribosomal protein S4E [Translation, ribosomal structure and biogenesis]
Probab=60.39 E-value=10 Score=30.69 Aligned_cols=24 Identities=21% Similarity=0.351 Sum_probs=22.2
Q ss_pred ccCcEEEEEeccccCCceEEEeee
Q 035907 5 LKPNKAVILLQGRNASRKAVIMKS 28 (105)
Q Consensus 5 ~kpgkVvivL~Gr~aGkKaVivk~ 28 (105)
+.+|..+++..||++|+-+.|++.
T Consensus 174 fe~g~~~~vtgG~h~G~~G~I~~I 197 (241)
T COG1471 174 FEEGALVYVTGGRHVGRVGTIVEI 197 (241)
T ss_pred cCCCcEEEEECCccccceEEEEEE
Confidence 579999999999999999999965
No 22
>KOG1708 consensus Mitochondrial/chloroplast ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=59.35 E-value=12 Score=30.07 Aligned_cols=37 Identities=11% Similarity=0.234 Sum_probs=32.8
Q ss_pred ccCcEEEEEeccccCCceEEEeeecCCCCCCCCCceEEEeccc
Q 035907 5 LKPNKAVILLQGRNASRKAVIMKSFDDGTRERPNGHCLVARIK 47 (105)
Q Consensus 5 ~kpgkVvivL~Gr~aGkKaVivk~~d~gt~~~~y~~~lVaGi~ 47 (105)
+.+|--|=||.||-+||-+.+++.+.+. +-++|-|+.
T Consensus 73 ff~GDtVeVlvGkDkGkqG~Vtqv~r~~------s~VvV~gln 109 (236)
T KOG1708|consen 73 FFFGDTVEVLVGKDKGKQGEVTQVIRHR------SWVVVKGLN 109 (236)
T ss_pred EecCCEEEEEecccCCccceEEEEeecC------ceEEEcccc
Confidence 5789999999999999999999999875 568888877
No 23
>PRK05609 nusG transcription antitermination protein NusG; Validated
Probab=54.67 E-value=28 Score=25.09 Aligned_cols=28 Identities=11% Similarity=0.057 Sum_probs=24.3
Q ss_pred cccCcEEEEEeccccCCceEEEeeecCC
Q 035907 4 FLKPNKAVILLQGRNASRKAVIMKSFDD 31 (105)
Q Consensus 4 ~~kpgkVvivL~Gr~aGkKaVivk~~d~ 31 (105)
-+++|.-|.|+.|=++|..+.|++...+
T Consensus 126 ~~~~Gd~VrI~~GPf~G~~g~v~~i~~~ 153 (181)
T PRK05609 126 DFEVGEMVRVIDGPFADFNGTVEEVDYE 153 (181)
T ss_pred CCCCCCEEEEeccCCCCCEEEEEEEeCC
Confidence 3689999999999999999999986433
No 24
>PLN00036 40S ribosomal protein S4; Provisional
Probab=53.79 E-value=24 Score=28.71 Aligned_cols=25 Identities=28% Similarity=0.364 Sum_probs=22.3
Q ss_pred ccCcEEEEEeccccCCceEEEeeec
Q 035907 5 LKPNKAVILLQGRNASRKAVIMKSF 29 (105)
Q Consensus 5 ~kpgkVvivL~Gr~aGkKaVivk~~ 29 (105)
+.+|..|+|..|+++|+=++|....
T Consensus 175 fe~G~l~~vtgG~n~GrvG~I~~i~ 199 (261)
T PLN00036 175 FDVGNLVMVTGGRNRGRVGVIKNRE 199 (261)
T ss_pred cCCCCEEEEECCeeceeEEEEEEEE
Confidence 5789999999999999999997654
No 25
>PRK04313 30S ribosomal protein S4e; Validated
Probab=52.62 E-value=14 Score=29.51 Aligned_cols=24 Identities=13% Similarity=0.243 Sum_probs=22.1
Q ss_pred ccCcEEEEEeccccCCceEEEeee
Q 035907 5 LKPNKAVILLQGRNASRKAVIMKS 28 (105)
Q Consensus 5 ~kpgkVvivL~Gr~aGkKaVivk~ 28 (105)
+.+|.+|++..|+++|+=++|...
T Consensus 172 fe~G~l~~itgG~n~GriG~I~~i 195 (237)
T PRK04313 172 FEEGNLAIITGGKHVGEIGKIKEI 195 (237)
T ss_pred cCCCCEEEEECCeeeeeEEEEEEE
Confidence 578999999999999999999876
No 26
>TIGR00405 L26e_arch ribosomal protein L24p/L26e, archaeal. This protein contains a KOW domain, shared by bacterial NusG and the L24p/L26e family of ribosomal proteins. Although called archaeal NusG in several publications, it is the only close homolog of eukaryotic L26e in archaeal genomes, shares an operon with L11 in many genomes, and has been sequenced from purified ribosomes. It is here designated as a ribosomal protein for these reasons.
Probab=51.79 E-value=35 Score=24.10 Aligned_cols=27 Identities=15% Similarity=0.262 Sum_probs=24.1
Q ss_pred cccCcEEEEEeccccCCceEEEeeecC
Q 035907 4 FLKPNKAVILLQGRNASRKAVIMKSFD 30 (105)
Q Consensus 4 ~~kpgkVvivL~Gr~aGkKaVivk~~d 30 (105)
.+++|-.|.|..|=|+|-.|.|++.-.
T Consensus 86 ~~~~Gd~V~I~~GPf~G~~g~v~~~d~ 112 (145)
T TIGR00405 86 SIKKGDIVEIISGPFKGERAKVIRVDE 112 (145)
T ss_pred ccCCCCEEEEeecCCCCCeEEEEEEcC
Confidence 478999999999999999999998643
No 27
>PTZ00118 40S ribosomal protein S4; Provisional
Probab=51.22 E-value=15 Score=29.86 Aligned_cols=23 Identities=22% Similarity=0.414 Sum_probs=21.6
Q ss_pred ccCcEEEEEeccccCCceEEEee
Q 035907 5 LKPNKAVILLQGRNASRKAVIMK 27 (105)
Q Consensus 5 ~kpgkVvivL~Gr~aGkKaVivk 27 (105)
+.+|.+|+|..|+++|+=++|+.
T Consensus 175 fe~G~l~~vtgG~n~GriG~I~~ 197 (262)
T PTZ00118 175 FEVGNLVMITGGHNVGRVGTIVS 197 (262)
T ss_pred cCCCCEEEEECCeeceeEEEEEE
Confidence 57899999999999999999987
No 28
>PTZ00223 40S ribosomal protein S4; Provisional
Probab=48.91 E-value=19 Score=29.50 Aligned_cols=24 Identities=25% Similarity=0.315 Sum_probs=22.0
Q ss_pred ccCcEEEEEeccccCCceEEEeee
Q 035907 5 LKPNKAVILLQGRNASRKAVIMKS 28 (105)
Q Consensus 5 ~kpgkVvivL~Gr~aGkKaVivk~ 28 (105)
+.+|.+|+|..|+++|+=++|...
T Consensus 172 fe~G~l~~vtgG~n~GriG~I~~i 195 (273)
T PTZ00223 172 NRNGKVVMVTGGANRGRIGEIVSI 195 (273)
T ss_pred cCCCCEEEEECCeeceeEEEEEEE
Confidence 578999999999999999999776
No 29
>KOG1694 consensus 60s ribosomal protein L6 [Translation, ribosomal structure and biogenesis]
Probab=48.61 E-value=14 Score=27.68 Aligned_cols=12 Identities=33% Similarity=0.609 Sum_probs=10.6
Q ss_pred cccCcEEEEEec
Q 035907 4 FLKPNKAVILLQ 15 (105)
Q Consensus 4 ~~kpgkVvivL~ 15 (105)
-+.||+|+|+|+
T Consensus 33 ~l~~gtvliil~ 44 (152)
T KOG1694|consen 33 SLTPGTVLIILA 44 (152)
T ss_pred ccCCCeeEEEec
Confidence 578999999998
No 30
>TIGR00922 nusG transcription termination/antitermination factor NusG. Archaeal proteins once termed NusG share the KOW domain but are actually a ribosomal protein corresponding to L24p in bacterial and L26e in eukaryotes (TIGR00405).
Probab=48.07 E-value=42 Score=24.10 Aligned_cols=25 Identities=12% Similarity=0.050 Sum_probs=23.1
Q ss_pred ccCcEEEEEeccccCCceEEEeeec
Q 035907 5 LKPNKAVILLQGRNASRKAVIMKSF 29 (105)
Q Consensus 5 ~kpgkVvivL~Gr~aGkKaVivk~~ 29 (105)
+++|--|.|..|=++|-.++|++.-
T Consensus 120 ~~~G~~V~I~~Gpf~G~~g~v~~~~ 144 (172)
T TIGR00922 120 FEVGEQVRVNDGPFANFTGTVEEVD 144 (172)
T ss_pred CCCCCEEEEeecCCCCcEEEEEEEc
Confidence 6899999999999999999999864
No 31
>cd07933 RHD-n_c-Rel N-terminal sub-domain of the Rel homology domain (RHD) of c-Rel. Proteins containing the Rel homology domain (RHD) are metazoan transcription factors. The RHD is composed of two structural sub-domains; this model characterizes the N-terminal RHD sub-domain of the c-Rel family of transcription factors, categorized as a class II member of the NF-kappa B family. In class II NF-kappa Bs, the RHD domain co-occurs with a C-terminal transactivation domain (TAD). NF-kappa B proteins are part of a protein complex that acts as a transcription factor, which is responsible for regulating a host of cellular responses to a variety of stimuli. This complex tightly regulates the expression of a large number of genes, and is involved in processes such as adaptive and innate immunity, stress response, inflammation, cell adhesion, proliferation and apoptosis. The cytosolic NF-kappa B complex is activated via phosphorylation of the ankyrin-repeat containing inhibitory protein I-kappa B
Probab=46.17 E-value=48 Score=25.55 Aligned_cols=74 Identities=15% Similarity=0.174 Sum_probs=46.1
Q ss_pred cCCceEEEeeecCCCCCCCCCceEEEecccCCceeeeeceEeecCCccccCcccccChhhHHHHHHHHHHHHHHHHhcCC
Q 035907 18 NASRKAVIMKSFDDGTRERPNGHCLVARIKNYQHLMPTCYTLDVDLKEVVTTNSLQSKDKKVTACEETKKHLEEKFKTGK 97 (105)
Q Consensus 18 ~aGkKaVivk~~d~gt~~~~y~~~lVaGi~N~nHl~pTry~vdi~~k~~v~~~~~~d~~~k~~akk~~k~~feer~k~gk 97 (105)
|.|.=.|+|.-......-+|.+|-|| |= ..++=+ |.+++.-++. ...|.+.-.-+-+||++...+++|.+.+-
T Consensus 48 Y~G~a~I~VslVT~d~P~rpHpH~LV-GK-~C~~G~---c~~~v~p~~~--~~~F~nLGIqcV~KK~v~e~L~~R~~~~~ 120 (172)
T cd07933 48 YTGKGKVRITLVTKNEPYKPHPHDLV-GK-DCRDGY---YEAEFGPERR--VLAFQNLGIQCVRRREVKEAIMLRISRGI 120 (172)
T ss_pred CcCCEEEEEEEEeCCCCCCCCccccc-cc-cCCCce---EEEEECCCCc--EEEecccceEEEEhhhHHHHHHHHHHhcC
Confidence 66766666665554445688999999 53 344322 6676654322 23477776666677777777777766554
Q ss_pred c
Q 035907 98 N 98 (105)
Q Consensus 98 n 98 (105)
|
T Consensus 121 ~ 121 (172)
T cd07933 121 N 121 (172)
T ss_pred C
Confidence 4
No 32
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=44.67 E-value=19 Score=34.31 Aligned_cols=29 Identities=14% Similarity=0.410 Sum_probs=26.1
Q ss_pred cccccCcEEEEEeccccCCceEEEeeecC
Q 035907 2 VTFLKPNKAVILLQGRNASRKAVIMKSFD 30 (105)
Q Consensus 2 ~k~~kpgkVvivL~Gr~aGkKaVivk~~d 30 (105)
-|.++||-.|=|++|||.|.-.+||+.-+
T Consensus 457 rKyF~~GDhVKVi~G~~eG~tGlVvrVe~ 485 (1024)
T KOG1999|consen 457 RKYFEPGDHVKVIAGRYEGDTGLVVRVEQ 485 (1024)
T ss_pred hhhccCCCeEEEEeccccCCcceEEEEeC
Confidence 37899999999999999999999998654
No 33
>PF15591 Imm17: Immunity protein 17
Probab=42.16 E-value=47 Score=22.44 Aligned_cols=26 Identities=8% Similarity=0.155 Sum_probs=18.6
Q ss_pred cccCCceEEEeeecCCCCCCCCCceEEE
Q 035907 16 GRNASRKAVIMKSFDDGTRERPNGHCLV 43 (105)
Q Consensus 16 Gr~aGkKaVivk~~d~gt~~~~y~~~lV 43 (105)
-+++|++.|||-.++++. .-|++.++
T Consensus 21 ~ei~Gk~GVVlG~SeeD~--~~~gY~Vl 46 (74)
T PF15591_consen 21 AEIWGKRGVVLGISEEDG--GNFGYSVL 46 (74)
T ss_pred hhhcCceeEEEEEecCCC--cEEEEEEE
Confidence 489999999997766543 45666643
No 34
>PRK09014 rfaH transcriptional activator RfaH; Provisional
Probab=38.20 E-value=72 Score=22.78 Aligned_cols=26 Identities=23% Similarity=0.275 Sum_probs=23.1
Q ss_pred cccCcEEEEEeccccCCceEEEeeec
Q 035907 4 FLKPNKAVILLQGRNASRKAVIMKSF 29 (105)
Q Consensus 4 ~~kpgkVvivL~Gr~aGkKaVivk~~ 29 (105)
.+++|.-|.|..|-++|--++|.+.-
T Consensus 109 ~~~~G~~V~I~~Gp~~g~eg~v~~~~ 134 (162)
T PRK09014 109 TPKPGDKVIITEGAFEGLQAIYTEPD 134 (162)
T ss_pred CCCCCCEEEEecCCCCCcEEEEEEeC
Confidence 36799999999999999999998864
No 35
>cd04822 PA_M28_1_3 PA_M28_1_3: Protease-associated (PA) domain, peptidase family M28, subfamily-1, subgroup 3. A subgroup of PA-domain containing proteins belonging to the peptidase family M28. Family M28 contains aminopeptidases and carboxypeptidases, and has co-catalytic zinc ions. The PA domain is an insert domain in a diverse fraction of proteases. The significance of the PA domain to many of the proteins in which it is inserted is undetermined. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate. Proteins into which the PA domain is inserted include the following members of the peptidase family M28: i) prostate-specific membrane antigen (PSMA), ii) yeast aminopeptidase Y, and ii) human TfR (transferrin receptor)1 and human TfR2. The proteins listed above belong to other subgroups; relatively litt
Probab=34.30 E-value=50 Score=24.39 Aligned_cols=10 Identities=30% Similarity=0.477 Sum_probs=8.9
Q ss_pred CcEEEEEecc
Q 035907 7 PNKAVILLQG 16 (105)
Q Consensus 7 pgkVvivL~G 16 (105)
.|||||+++|
T Consensus 47 kGKIVlv~~g 56 (151)
T cd04822 47 KGKIVLVLRH 56 (151)
T ss_pred CCeEEEEEcC
Confidence 5999999987
No 36
>PF02491 SHS2_FTSA: SHS2 domain inserted in FTSA; InterPro: IPR003494 FtsA is essential for bacterial cell division, and co-localizes to the septal ring with FtsZ. It has been suggested that the interaction of FtsA-FtsZ has arisen through coevolution in different bacterial strains [].; GO: 0007049 cell cycle; PDB: 1E4F_T 4A2B_A 4A2A_A 1E4G_T.
Probab=33.41 E-value=26 Score=22.41 Aligned_cols=15 Identities=33% Similarity=0.594 Sum_probs=11.7
Q ss_pred CCceeeeeceEeecC
Q 035907 48 NYQHLMPTCYTLDVD 62 (105)
Q Consensus 48 N~nHl~pTry~vdi~ 62 (105)
..=|++|.+|.||=.
T Consensus 43 ~iih~ip~~y~lD~~ 57 (80)
T PF02491_consen 43 EIIHVIPQEYILDGQ 57 (80)
T ss_dssp EEEEEEEEEEEETTT
T ss_pred EEEEEEeEEEEECCC
Confidence 445999999999743
No 37
>TIGR01955 RfaH transcriptional activator RfaH. This model represents the transcriptional activator protein, RfaH. This protein is most closely related to the transcriptional termination/antitermination protein NusG (TIGR00922) and contains the KOW motif (pfam00467). This protein appears to be limited to the gamma proteobacteria. In E. coli, this gene appears to control the expression of haemolysin, sex factor and lipopolysaccharide genes.
Probab=32.37 E-value=98 Score=21.75 Aligned_cols=24 Identities=17% Similarity=0.189 Sum_probs=22.7
Q ss_pred ccCcEEEEEeccccCCceEEEeee
Q 035907 5 LKPNKAVILLQGRNASRKAVIMKS 28 (105)
Q Consensus 5 ~kpgkVvivL~Gr~aGkKaVivk~ 28 (105)
+++|--|.|..|=++|--++|++.
T Consensus 109 ~~~G~~V~V~~GPf~g~~g~v~~~ 132 (159)
T TIGR01955 109 PYKGDKVRITDGAFAGFEAIFLEP 132 (159)
T ss_pred CCCCCEEEEeccCCCCcEEEEEEE
Confidence 789999999999999999999996
No 38
>PF08584 Ribonuc_P_40: Ribonuclease P 40kDa (Rpp40) subunit; InterPro: IPR013893 The tRNA processing enzyme ribonuclease P (RNase P) consists of an RNA molecule and at least eight protein subunits. Subunits hpop1, Rpp21, Rpp29, Rpp30, Rpp38, and Rpp40 (this entry) are involved in extensive, but weak, protein-protein interactions in the holoenzyme complex [].
Probab=31.73 E-value=1.7e+02 Score=23.21 Aligned_cols=86 Identities=16% Similarity=0.183 Sum_probs=47.2
Q ss_pred ccccCcEEEEEeccccCCceEEEeee-------cCCCCCCCCCceEEEeccc----CCceeeeeceEeecCCccccCccc
Q 035907 3 TFLKPNKAVILLQGRNASRKAVIMKS-------FDDGTRERPNGHCLVARIK----NYQHLMPTCYTLDVDLKEVVTTNS 71 (105)
Q Consensus 3 k~~kpgkVvivL~Gr~aGkKaVivk~-------~d~gt~~~~y~~~lVaGi~----N~nHl~pTry~vdi~~k~~v~~~~ 71 (105)
.+++.|.+..+-.||-..--++.+.. +|..| |.. +|+. -+++--..||.|.|+|.+ ..
T Consensus 12 ~~vk~g~~~~ls~~~~~~d~~~~~~~~G~L~l~l~k~t----ye~---~Gl~G~~~~~~~~~~~r~vV~idL~~----~s 80 (284)
T PF08584_consen 12 SYVKKGSVYALSNTRIDSDNVFALTPSGILTLSLDKET----YER---LGLEGKPSRFGGRKHQRYVVEIDLRD----PS 80 (284)
T ss_pred HhEEcCeEEEEeCCCCCCCCEEEEecCCeEEEEECHHH----HHH---cCCCCcccCCCCccceEEEEEEeCCC----cc
Confidence 57899999999888876666665442 12111 111 2333 223333339999999852 11
Q ss_pred ccChhhHHHHHHHHHHHHHHHHhcCCceeeee
Q 035907 72 LQSKDKKVTACEETKKHLEEKFKTGKNLGSLL 103 (105)
Q Consensus 72 ~~d~~~k~~akk~~k~~feer~k~gknkwfF~ 103 (105)
|. |.+|. -..++-.|+++.. .+..|+|.
T Consensus 81 ~~-~g~k~--y~Rl~~alk~~l~-~~~~~l~~ 108 (284)
T PF08584_consen 81 FL-PGKKG--YERLRWALKNVLP-LSFDWLFC 108 (284)
T ss_pred cC-CCcch--hHHHHHHHHhcCC-CceeEEEE
Confidence 31 22221 1236666766633 66778874
No 39
>COG5137 Histone chaperone involved in gene silencing [Transcription / Chromatin structure and dynamics]
Probab=28.90 E-value=52 Score=26.89 Aligned_cols=20 Identities=30% Similarity=0.303 Sum_probs=17.2
Q ss_pred cEEEEEeccccCCceEEEee
Q 035907 8 NKAVILLQGRNASRKAVIMK 27 (105)
Q Consensus 8 gkVvivL~Gr~aGkKaVivk 27 (105)
|--||+|+|||.|+--|-|-
T Consensus 91 gvTvILlsc~Y~g~eFvRvG 110 (279)
T COG5137 91 GVTVILLSCRYKGQEFVRVG 110 (279)
T ss_pred ceeEEEEEEeecCceeEEEE
Confidence 66799999999999887764
No 40
>PF01929 Ribosomal_L14e: Ribosomal protein L14; InterPro: IPR002784 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry includes the eukaryotic ribosomal protein L14, which binds to the 60S ribosomal subunit, and archaebacterial ribosomal protein L14E, which binds to the 50S ribosomal subunit.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3IZS_N 3O5H_N 3O58_N 2KDS_A 2JOY_A 4A1B_F 4A19_F 4A18_F 4A1D_F 3IZR_N.
Probab=28.17 E-value=24 Score=23.50 Aligned_cols=16 Identities=19% Similarity=0.297 Sum_probs=14.5
Q ss_pred CCceeeeeceEeecCC
Q 035907 48 NYQHLMPTCYTLDVDL 63 (105)
Q Consensus 48 N~nHl~pTry~vdi~~ 63 (105)
|++||.+|.+.|+|+-
T Consensus 6 ~~k~l~LT~~~i~i~r 21 (77)
T PF01929_consen 6 NLKRLHLTDFVIKIPR 21 (77)
T ss_dssp ECTSSEEEEEETTTTT
T ss_pred eccceEeecEEEeccC
Confidence 7899999999999884
No 41
>cd04814 PA_M28_1 PA_M28_1: Protease-associated (PA) domain, peptidase family M28, subfamily-1. A subfamily of PA-domain containing proteins belonging to the peptidase family M28. Family M28 contains aminopeptidases and carboxypeptidases, and has co-catalytic zinc ions. The PA domain is an insert domain in a diverse fraction of proteases. The significance of the PA domain to many of the proteins in which it is inserted is undetermined. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate. Proteins into which the PA domain is inserted include the following members of the peptidase family M28: i) prostate-specific membrane antigen (PSMA), ii) yeast aminopeptidase Y, and ii) human TfR (transferrin receptor)1 and human TfR2. The proteins listed above belong to other subfamilies, relatively little is known a
Probab=26.26 E-value=87 Score=22.93 Aligned_cols=10 Identities=30% Similarity=0.577 Sum_probs=8.9
Q ss_pred CcEEEEEecc
Q 035907 7 PNKAVILLQG 16 (105)
Q Consensus 7 pgkVvivL~G 16 (105)
.|||||++.|
T Consensus 47 kGKIVlv~~g 56 (142)
T cd04814 47 KGKVVVVLRN 56 (142)
T ss_pred CCcEEEEEcC
Confidence 6999999987
No 42
>PF11061 DUF2862: Protein of unknown function (DUF2862); InterPro: IPR021291 This family of proteins has no known function.
Probab=26.15 E-value=28 Score=22.75 Aligned_cols=11 Identities=18% Similarity=0.175 Sum_probs=8.6
Q ss_pred HhcCCceeeee
Q 035907 93 FKTGKNLGSLL 103 (105)
Q Consensus 93 ~k~gknkwfF~ 103 (105)
+..|...|||.
T Consensus 49 ~~ng~~~WFFe 59 (64)
T PF11061_consen 49 FSNGSRTWFFE 59 (64)
T ss_pred ecCCceeEEch
Confidence 36788899995
No 43
>PRK08559 nusG transcription antitermination protein NusG; Validated
Probab=25.84 E-value=2.5e+02 Score=20.21 Aligned_cols=27 Identities=22% Similarity=0.305 Sum_probs=24.4
Q ss_pred ccCcEEEEEeccccCCceEEEeeecCC
Q 035907 5 LKPNKAVILLQGRNASRKAVIMKSFDD 31 (105)
Q Consensus 5 ~kpgkVvivL~Gr~aGkKaVivk~~d~ 31 (105)
++||-.|-|..|-|+|-.|.|++.-.+
T Consensus 95 ~~~G~~V~I~~Gpf~g~~g~V~~vd~~ 121 (153)
T PRK08559 95 IKEGDIVELIAGPFKGEKARVVRVDES 121 (153)
T ss_pred CCCCCEEEEeccCCCCceEEEEEEcCC
Confidence 789999999999999999999987654
No 44
>PF06102 DUF947: Domain of unknown function (DUF947); InterPro: IPR009292 This is a family of eukaryotic proteins with unknown function.
Probab=25.62 E-value=66 Score=24.05 Aligned_cols=25 Identities=40% Similarity=0.279 Sum_probs=18.1
Q ss_pred HHHHHHHHHHHHHhcCCceeeeeCC
Q 035907 81 ACEETKKHLEEKFKTGKNLGSLLSS 105 (105)
Q Consensus 81 akk~~k~~feer~k~gknkwfF~k~ 105 (105)
+..+.+..-.|.-++|+..||.++|
T Consensus 107 ~~~~~kk~E~e~v~~GKkP~flKks 131 (168)
T PF06102_consen 107 VKKEHKKEEREKVKQGKKPFFLKKS 131 (168)
T ss_pred HHHHHHHHHHHHHHcCCCCcccCHH
Confidence 3344556666778999999998764
No 45
>KOG2544 consensus Dihydropteroate synthase/7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase/Dihydroneopterin aldolase [Coenzyme transport and metabolism]
Probab=25.26 E-value=1.3e+02 Score=27.51 Aligned_cols=33 Identities=24% Similarity=0.355 Sum_probs=27.2
Q ss_pred eEEEeeecCCCCCCCCCceEEEecccCCceeeeeceEeecCC
Q 035907 22 KAVIMKSFDDGTRERPNGHCLVARIKNYQHLMPTCYTLDVDL 63 (105)
Q Consensus 22 KaVivk~~d~gt~~~~y~~~lVaGi~N~nHl~pTry~vdi~~ 63 (105)
--|.+++++- -.|.|+|..|.+||....++++.
T Consensus 6 d~v~i~~l~~---------~tvlg~d~w~~~~pq~~~l~l~m 38 (711)
T KOG2544|consen 6 DYVHIKKLEM---------NTVLGPDSWNQLMPQKCLLSLDM 38 (711)
T ss_pred ceEEEeeeec---------ceeechhhhhhcCCcceEEEEec
Confidence 3467788776 36899999999999999998875
No 46
>PF05257 CHAP: CHAP domain; InterPro: IPR007921 The CHAP (cysteine, histidine-dependent amidohydrolases/peptidases) domain is a region between 110 and 140 amino acids that is found in proteins from bacteria, bacteriophages, archaea and eukaryotes of the Trypanosomidae family. Many of these proteins are uncharacterised, but it has been proposed that they may function mainly in peptidoglycan hydrolysis. The CHAP domain is found in a wide range of protein architectures; it is commonly associated with bacterial type SH3 domains and with several families of amidase domains. It has been suggested that CHAP domain containing proteins utilise a catalytic cysteine residue in a nucleophilic-attack mechanism [, ]. The CHAP domain contains two invariant residues, a cysteine and a histidine. These residues form part of the putative active site of CHAP domain containing proteins. Secondary structure predictions show that the CHAP domain belongs to the alpha + beta structural class, with the N-terminal half largely containing predicted alpha helices and the C-terminal half principally composed of predicted beta strands [, ]. Some proteins known to contain a CHAP domain are listed below: Bacterial and trypanosomal glutathionylspermidine amidases. A variety of bacterial autolysins. A Nocardia aerocolonigenes putative esterase. Streptococcus pneumoniae choline-binding protein D. Methanosarcina mazei protein MM2478, a putative chloride channel. Several phage-encoded peptidoglycan hydrolases. Cysteine peptidases belonging to MEROPS peptidase family C51 (D-alanyl-glycyl endopeptidase, clan CA). ; PDB: 2LRJ_A 2VPM_B 2VOB_B 2VPS_A 2K3A_A 2IO9_A 2IO8_A 2IOB_A 2IOA_B 2IO7_B ....
Probab=25.24 E-value=1.9e+02 Score=19.43 Aligned_cols=29 Identities=21% Similarity=0.271 Sum_probs=18.1
Q ss_pred cccCcEEEEE--eccccCCceEEEeeecCCC
Q 035907 4 FLKPNKAVIL--LQGRNASRKAVIMKSFDDG 32 (105)
Q Consensus 4 ~~kpgkVviv--L~Gr~aGkKaVivk~~d~g 32 (105)
..+||-|++. ..+...|+=|||.+..+++
T Consensus 62 ~P~~Gdivv~~~~~~~~~GHVaIV~~v~~~~ 92 (124)
T PF05257_consen 62 TPQPGDIVVWDSGSGGGYGHVAIVESVNDGG 92 (124)
T ss_dssp ---TTEEEEEEECTTTTT-EEEEEEEE-TTS
T ss_pred ccccceEEEeccCCCCCCCeEEEEEEECCCC
Confidence 4578888887 5666778888888876664
No 47
>PF10307 DUF2410: Hypothetical protein (DUF2410); InterPro: IPR018812 This entry represents a family of proteins conserved in fungi whose function is not known. There are two characteristic sequence motifs, GGWW and TGR.
Probab=23.49 E-value=53 Score=25.52 Aligned_cols=13 Identities=38% Similarity=0.818 Sum_probs=11.7
Q ss_pred cCcEEEEEecccc
Q 035907 6 KPNKAVILLQGRN 18 (105)
Q Consensus 6 kpgkVvivL~Gr~ 18 (105)
.|.+++|+|+||-
T Consensus 69 ~~dtltVLLTGR~ 81 (197)
T PF10307_consen 69 DPDTLTVLLTGRR 81 (197)
T ss_pred CCCeeEEEEeCCC
Confidence 5889999999996
No 48
>COG2876 AroA 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase [Amino acid transport and metabolism]
Probab=22.96 E-value=56 Score=27.05 Aligned_cols=22 Identities=27% Similarity=0.614 Sum_probs=18.0
Q ss_pred ceEEEe--cccCCceeeeeceEeecC
Q 035907 39 GHCLVA--RIKNYQHLMPTCYTLDVD 62 (105)
Q Consensus 39 ~~~lVa--Gi~N~nHl~pTry~vdi~ 62 (105)
++++.+ ||-++.+ .|||++||+
T Consensus 181 ~~vILCERGIRtfe~--~TRntLDi~ 204 (286)
T COG2876 181 GNVILCERGIRTFEK--ATRNTLDIS 204 (286)
T ss_pred CcEEEEecccccccc--cccceechH
Confidence 566666 7888887 899999997
No 49
>KOG2037 consensus Guanylate-binding protein [General function prediction only]
Probab=22.23 E-value=78 Score=28.31 Aligned_cols=51 Identities=16% Similarity=0.217 Sum_probs=41.5
Q ss_pred cccCcEEEEEeccccCCceEEEeee-------cCCCCCCCCCceEEEeccc------CCceeee
Q 035907 4 FLKPNKAVILLQGRNASRKAVIMKS-------FDDGTRERPNGHCLVARIK------NYQHLMP 54 (105)
Q Consensus 4 ~~kpgkVvivL~Gr~aGkKaVivk~-------~d~gt~~~~y~~~lVaGi~------N~nHl~p 54 (105)
.+++..+|+++-|||.--|..|+.. ++.++.++|-.-.+|+|.. ++||+.-
T Consensus 27 ~~~~p~~Vv~i~g~~~~gksfiln~la~~~~gf~~~s~~~~~~~~~w~w~~p~~k~~~~~l~Ll 90 (552)
T KOG2037|consen 27 AIKQPVAVVAIVGLYRTGKSFILNQLAGKRIGFSVASTDKPVTKGIWMWCVPHGKSFLLNLVLL 90 (552)
T ss_pred hccCCceEEEEEEEEcCCCceehhhhHhhhcCCCcccccccceeeEEEEEeecCCccchhhhhh
Confidence 3677888999999998888888864 6778889999999999977 7777743
No 50
>cd07886 RHD-n_RelB N-terminal sub-domain of the Rel homology domain (RHD) of the reticuloendotheliosis viral oncogene homolog B (RelB) protein. Proteins containing the Rel homology domain (RHD) are metazoan transcription factors. The RHD is composed of two structural sub-domains; this model characterizes the N-terminal RHD sub-domain of the RelB family of transcription factors, categorized as class II NF-kappa B family members. In class II NF-kappa Bs, the RHD domain co-occurs with a C-terminal transactivation domain (TAD). NF-kappa B proteins are part of a protein complex that acts as a transcription factor, which is responsible for regulating a host of cellular responses to a variety of stimuli. This complex tightly regulates the expression of a large number of genes, and is involved in processes such as adaptive and innate immunity, stress response, inflammation, cell adhesion, proliferation and apoptosis. The cytosolic NF-kappa B complex is activated via phosphorylation of the anky
Probab=20.37 E-value=2.4e+02 Score=21.73 Aligned_cols=74 Identities=11% Similarity=0.116 Sum_probs=44.4
Q ss_pred cCCc-eE-EEeeecCCCCCCCCCceEEEecccCCceeeeeceEeecCCccccCcccccChhhHHHHHHHHHHHHHHHHhc
Q 035907 18 NASR-KA-VIMKSFDDGTRERPNGHCLVARIKNYQHLMPTCYTLDVDLKEVVTTNSLQSKDKKVTACEETKKHLEEKFKT 95 (105)
Q Consensus 18 ~aGk-Ka-Vivk~~d~gt~~~~y~~~lVaGi~N~nHl~pTry~vdi~~k~~v~~~~~~d~~~k~~akk~~k~~feer~k~ 95 (105)
|.|. ++ |+|.-.-.....+|.+|-||.- ..++ --|.++++-+.. ....|.+.-.-+-+|+++...+.+|.+.
T Consensus 48 y~G~a~v~V~vslVT~d~p~rpHpH~LVGK--~C~~---Gvc~v~v~p~~~-~~~~F~nLGIqcv~KK~v~e~L~~R~~~ 121 (172)
T cd07886 48 CIGLKEVTVTVCLVWKDPPHRVHPHGLVGK--DCPN---GICQVTLNPHSS-PRHSFSNLGIQCVRKREIEAAIETRLQL 121 (172)
T ss_pred ccCCceEEEEEEEeeCCCCCCCCCcccccc--cCCC---ceEEEEeCCCCc-cEEEEcCceeEeeehhhhHHHHHHHHHc
Confidence 6776 33 4556555555678999999863 2333 345666554311 1234777766666777777777777654
Q ss_pred CC
Q 035907 96 GK 97 (105)
Q Consensus 96 gk 97 (105)
+-
T Consensus 122 ~~ 123 (172)
T cd07886 122 NI 123 (172)
T ss_pred cC
Confidence 43
Done!