Query 031165
Match_columns 164
No_of_seqs 158 out of 395
Neff 4.3
Searched_HMMs 46136
Date Fri Mar 29 10:10:34 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031165.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031165hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00189 60S ribosomal protein 100.0 2.4E-80 5.1E-85 496.4 16.4 158 1-158 1-160 (160)
2 PLN00190 60S ribosomal protein 100.0 1E-79 2.2E-84 491.9 16.4 158 1-158 1-158 (158)
3 KOG1732 60S ribosomal protein 100.0 2.4E-66 5.2E-71 415.9 8.6 158 1-158 1-160 (160)
4 PRK04306 50S ribosomal protein 100.0 3.2E-50 7E-55 300.8 9.2 97 1-101 2-98 (98)
5 PF01157 Ribosomal_L21e: Ribos 100.0 8.1E-50 1.8E-54 299.0 7.7 99 2-100 1-99 (99)
6 COG2139 RPL21A Ribosomal prote 100.0 3.2E-45 7E-50 272.9 8.2 98 2-103 1-98 (98)
7 TIGR01079 rplX_bact ribosomal 82.5 3 6.4E-05 31.6 4.7 48 33-100 3-50 (104)
8 PRK12281 rplX 50S ribosomal pr 81.6 3.6 7.8E-05 29.5 4.7 48 33-100 6-53 (76)
9 PRK00004 rplX 50S ribosomal pr 80.8 3.7 8E-05 31.0 4.7 48 33-100 4-51 (105)
10 CHL00141 rpl24 ribosomal prote 80.4 4.1 8.9E-05 29.6 4.7 48 33-100 8-55 (83)
11 PTZ00194 60S ribosomal protein 76.0 9.5 0.00021 30.8 5.9 66 34-109 47-119 (143)
12 smart00739 KOW KOW (Kyprides, 69.4 9.8 0.00021 20.9 3.4 26 34-69 2-27 (28)
13 PF09629 YorP: YorP protein; 66.2 5.6 0.00012 28.3 2.3 32 33-68 6-37 (71)
14 KOG3141 Mitochondrial/chloropl 60.7 5.1 0.00011 35.9 1.6 40 6-45 113-174 (310)
15 TIGR01080 rplX_A_E ribosomal p 57.5 15 0.00032 28.4 3.5 33 35-77 43-75 (114)
16 PF02211 NHase_beta: Nitrile h 55.2 11 0.00024 32.0 2.7 36 32-68 133-169 (222)
17 PRK01191 rpl24p 50S ribosomal 51.1 24 0.00052 27.7 3.7 34 34-77 46-79 (120)
18 PF00924 MS_channel: Mechanose 49.3 14 0.0003 29.1 2.2 30 31-75 58-87 (206)
19 PF09953 DUF2187: Uncharacteri 48.6 30 0.00064 24.0 3.5 33 32-78 2-34 (57)
20 PF00970 FAD_binding_6: Oxidor 47.4 21 0.00045 24.8 2.7 19 26-44 74-92 (99)
21 COG0198 RplX Ribosomal protein 46.9 47 0.001 25.4 4.7 46 33-100 4-49 (104)
22 COG1588 POP4 RNase P/RNase MRP 45.5 29 0.00064 26.3 3.4 47 36-91 16-62 (95)
23 TIGR01843 type_I_hlyD type I s 35.0 53 0.0012 28.3 3.8 40 28-72 318-357 (423)
24 TIGR00922 nusG transcription t 34.3 1.1E+02 0.0025 23.7 5.3 50 34-97 120-171 (172)
25 PRK14980 DNA-directed RNA poly 32.6 98 0.0021 24.6 4.6 31 29-60 44-74 (127)
26 PF00467 KOW: KOW motif; Inte 32.2 48 0.001 19.4 2.2 29 36-74 1-29 (32)
27 KOG3391 Transcriptional co-rep 30.5 33 0.00072 27.9 1.7 15 32-46 123-137 (151)
28 PF03321 GH3: GH3 auxin-respon 30.4 22 0.00049 33.2 0.8 37 31-70 368-404 (528)
29 PLN02249 indole-3-acetic acid- 30.1 31 0.00068 33.2 1.7 37 31-70 407-443 (597)
30 PRK02749 photosystem I reactio 28.7 1.1E+02 0.0025 22.0 4.0 30 34-71 3-32 (71)
31 KOG1384 tRNA delta(2)-isopente 28.1 13 0.00028 34.0 -1.1 29 27-55 37-65 (348)
32 cd06080 MUM1_like Mutated mela 26.9 2.5E+02 0.0054 20.3 6.4 71 34-119 1-73 (80)
33 PRK05609 nusG transcription an 26.3 1.8E+02 0.004 22.6 5.3 50 33-96 126-177 (181)
34 PHA02763 hypothetical protein; 26.1 61 0.0013 24.6 2.3 21 33-61 27-47 (102)
35 PLN00045 photosystem I reactio 25.5 1E+02 0.0023 23.6 3.5 36 33-76 39-77 (101)
36 smart00316 S1 Ribosomal protei 25.5 29 0.00064 21.6 0.5 14 33-46 46-59 (72)
37 smart00743 Agenet Tudor-like d 25.2 68 0.0015 20.7 2.2 53 33-100 2-57 (61)
38 COG0668 MscS Small-conductance 25.1 74 0.0016 26.3 2.9 30 31-74 145-174 (316)
39 TIGR00405 L26e_arch ribosomal 24.8 1.7E+02 0.0038 22.2 4.8 55 32-100 85-141 (145)
40 PF06107 DUF951: Bacterial pro 24.7 50 0.0011 22.8 1.5 16 33-56 1-16 (57)
41 cd04370 BAH BAH, or Bromo Adja 24.6 1.1E+02 0.0024 21.5 3.4 53 33-99 3-55 (123)
42 cd00773 HisRS-like_core Class 24.3 99 0.0021 25.6 3.5 47 28-84 183-232 (261)
43 PF02290 SRP14: Signal recogni 24.1 42 0.00091 24.7 1.1 30 101-133 2-33 (93)
44 PF11132 SplA: Transcriptional 23.8 63 0.0014 23.6 2.0 30 31-72 3-32 (75)
45 COG1566 EmrA Multidrug resista 23.7 1E+02 0.0022 28.0 3.7 60 29-94 254-317 (352)
46 CHL00125 psaE photosystem I su 23.2 86 0.0019 22.2 2.5 29 34-70 2-30 (64)
47 PF14031 D-ser_dehydrat: Putat 22.4 28 0.00062 25.3 -0.0 31 15-45 48-78 (94)
48 PF09926 DUF2158: Uncharacteri 22.0 58 0.0013 21.9 1.4 11 34-44 1-11 (53)
49 PLN02247 indole-3-acetic acid- 21.6 62 0.0013 31.5 2.0 36 31-69 414-449 (606)
50 cd04473 S1_RecJ_like S1_RecJ_l 21.5 34 0.00074 23.4 0.2 12 31-42 11-22 (77)
51 cd04714 BAH_BAHCC1 BAH, or Bro 21.2 1.4E+02 0.003 22.5 3.5 52 32-99 2-53 (121)
52 cd04455 S1_NusA S1_NusA: N-uti 21.2 50 0.0011 21.9 1.0 23 23-45 28-52 (67)
53 PF02427 PSI_PsaE: Photosystem 21.1 1.5E+02 0.0032 20.9 3.3 29 35-71 2-30 (61)
54 cd05687 S1_RPS1_repeat_ec1_hs1 20.9 52 0.0011 21.5 1.0 25 22-46 25-57 (70)
55 PF01835 A2M_N: MG2 domain; I 20.8 61 0.0013 22.7 1.4 19 33-51 10-28 (99)
56 PRK10334 mechanosensitive chan 20.8 1.2E+02 0.0026 26.3 3.5 30 31-75 127-156 (286)
57 PF06940 DUF1287: Domain of un 20.6 59 0.0013 26.9 1.4 19 32-54 105-123 (164)
58 COG3061 OapA Cell envelope opa 20.2 67 0.0015 28.0 1.8 42 5-46 160-212 (242)
59 KOG0544 FKBP-type peptidyl-pro 20.1 96 0.0021 24.0 2.4 41 35-75 18-68 (108)
No 1
>PTZ00189 60S ribosomal protein L21; Provisional
Probab=100.00 E-value=2.4e-80 Score=496.42 Aligned_cols=158 Identities=57% Similarity=0.947 Sum_probs=156.4
Q ss_pred CCCCCCCCcccccccCCcccCCCCCChHHHHHhhCCCCEEEEEecCceeeCccCccccccceeEEeeeccEEEEEEEeee
Q 031165 1 MPAGHGLRSRTRDLFARPFRKKGYIPLSTYLRTYKIGDYVDVKVNGAVHKGMPHKFYHGRTGRVWNVTKRAIGVEINKQV 80 (164)
Q Consensus 1 m~~s~G~R~~TR~~fsk~fR~~G~~~ls~~l~~yk~GD~VdIk~~~svqKGmPhk~YHGkTG~V~~v~~~AvgV~Vnk~v 80 (164)
|++|+|||+|||+|||++||+||++|||+||++|++||+|||++||||||||||+||||+||+|||||++||||+||++|
T Consensus 1 M~~s~G~R~~TR~~fsk~~R~~G~~pls~~l~~yk~GD~VdIk~d~svqkGMPhk~YHGkTG~V~nv~~~A~gViV~k~v 80 (160)
T PTZ00189 1 MPHSYGYRAGTRHKFAKPFRKHGVPSLSTYLTTFKVGDYVDIVVDSAVHKGMPYKYYHGRTGRVFNVTPRAVGVIVNKRV 80 (160)
T ss_pred CCCCCCccccchhhhCccccccCCCcHHHHHHHccCCCEEEEEecCCeecCCCcccccCCCeEEEeecCeEEEEEEEEEE
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CcEeeeeEEeeeeceeecccChHHHHHHHhhcHHHHHHHHHcCCceecccCCCCCcceeee--cCCceeEeeeeceeEEe
Q 031165 81 GNRIIKKRIHVRVEHVQPSRCTEEFKLRKKKNDELKADAKARGEVISTKRQPKGPKPGFMV--EGATLETVTPIPYDVVN 158 (164)
Q Consensus 81 ~~k~i~KrI~VriEHik~sk~r~~fl~rvk~nd~~k~eak~~g~~v~~kr~p~~Pr~a~~v--~~~~p~~l~p~py~~~~ 158 (164)
||+||+|+||||||||++|+|+++||+|||+||++++|||++|+||+|||||++||+|||| ++++|++|+|+||+|++
T Consensus 81 g~ki~~Kri~vr~EHlk~sk~r~~fl~Rvk~n~~~~~~ak~~g~~v~~Kr~p~~Pr~a~~v~~~~~~p~~~~p~py~~~~ 160 (160)
T PTZ00189 81 RGRIVRKRIHVRIEHVRKSRCREDFLKRVAANDAIKAEAKKKGELPSTKRQPAQPRPAGFVKPKPTEVVTVRPLPFVEIY 160 (160)
T ss_pred CCEEeeeEEecCHhHcCCcCCHHHHHHHHHHhHHHHHHHHHcCCccccccCCCCCCCceEEecCCCceeEecccceEeeC
Confidence 9999999999999999999999999999999999999999999999999999999999999 78999999999999975
No 2
>PLN00190 60S ribosomal protein L21; Provisional
Probab=100.00 E-value=1e-79 Score=491.92 Aligned_cols=158 Identities=90% Similarity=1.433 Sum_probs=154.8
Q ss_pred CCCCCCCCcccccccCCcccCCCCCChHHHHHhhCCCCEEEEEecCceeeCccCccccccceeEEeeeccEEEEEEEeee
Q 031165 1 MPAGHGLRSRTRDLFARPFRKKGYIPLSTYLRTYKIGDYVDVKVNGAVHKGMPHKFYHGRTGRVWNVTKRAIGVEINKQV 80 (164)
Q Consensus 1 m~~s~G~R~~TR~~fsk~fR~~G~~~ls~~l~~yk~GD~VdIk~~~svqKGmPhk~YHGkTG~V~~v~~~AvgV~Vnk~v 80 (164)
|++|+|||++||||||++||+||++|||+||++|++||+|||++||||||||||+||||+||+|||||++||||+|||+|
T Consensus 1 M~~s~G~R~~TR~~fsk~~R~~G~~pls~~l~~yk~GD~VdIk~~~svqKGMPhk~YHGkTG~V~nv~~~A~gV~V~K~v 80 (158)
T PLN00190 1 MPAGHGLRSRTRDLFARPFRKKGYIPLTTYLRTFKVGDYVDIKVNGAIHKGMPHKFYHGRTGIVWNVTKRAVGVEVNKQV 80 (158)
T ss_pred CCCCCCccccchhhhCccccccCCCcHHHHHHHhcCCCEEEEEecCCeecCCCcccccCCCeEEEeecCcEEEEEEEEee
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CcEeeeeEEeeeeceeecccChHHHHHHHhhcHHHHHHHHHcCCceecccCCCCCcceeeecCCceeEeeeeceeEEe
Q 031165 81 GNRIIKKRIHVRVEHVQPSRCTEEFKLRKKKNDELKADAKARGEVISTKRQPKGPKPGFMVEGATLETVTPIPYDVVN 158 (164)
Q Consensus 81 ~~k~i~KrI~VriEHik~sk~r~~fl~rvk~nd~~k~eak~~g~~v~~kr~p~~Pr~a~~v~~~~p~~l~p~py~~~~ 158 (164)
||+|++|+||||||||++|+||+|||+|||+||++++|||++|+||+|||||++||+||||++++|++|+|+||+|+.
T Consensus 81 ggr~~~Kri~vriEHlk~sk~r~~Fl~Rvk~n~~~~~eak~~g~~v~lKrqp~~Pr~~~~v~~~~p~~l~p~py~~~~ 158 (158)
T PLN00190 81 GNRIIRKRIHVRVEHVQPSRCREEFLLRKKSNDEAKAEAKAKGEKISTKRQPKGPKPGFMVEGATLETVTPIPYDVVN 158 (158)
T ss_pred CCeEeeEEEEeCHHHccCccCHHHHHHHHHHhHHHHHHHHHcCCccccCCCCCCCCcceEecCCCeeEecccceEecC
Confidence 999999999999999999999999999999999999999999999999999999999999943499999999999873
No 3
>KOG1732 consensus 60S ribosomal protein L21 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.4e-66 Score=415.88 Aligned_cols=158 Identities=52% Similarity=0.913 Sum_probs=155.1
Q ss_pred CCCCCCCCcccccccCCcccCCCCCChHHHHHhhCCCCEEEEEecCceeeCccCccccccceeEEeeeccEEEEEEEeee
Q 031165 1 MPAGHGLRSRTRDLFARPFRKKGYIPLSTYLRTYKIGDYVDVKVNGAVHKGMPHKFYHGRTGRVWNVTKRAIGVEINKQV 80 (164)
Q Consensus 1 m~~s~G~R~~TR~~fsk~fR~~G~~~ls~~l~~yk~GD~VdIk~~~svqKGmPhk~YHGkTG~V~~v~~~AvgV~Vnk~v 80 (164)
|++++|+|++|||+|+++||+||+.||++||++|++||+|||+++++.|+||||+||||+||+||+|+++|+||++||||
T Consensus 1 m~~~~g~~~~t~~~~~~~~~k~~~~~l~~y~~i~k~gdivdi~~~~~~~kg~p~k~y~gktgrvy~v~~~a~giv~nKqv 80 (160)
T KOG1732|consen 1 MTNTKGKRRGTRYMFSRPFRKHGVVPLATYMRIYKKGDIVDIKGNGTVQKGMPHKCYHGKTGRVYNVTQHAVGVVVNKQV 80 (160)
T ss_pred CCcccCcccccceeecchhhhcCeeeeeeeeeeecccceeecccccchhcCCccccccccccceeeccceeEEEEEEEee
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CcEeeeeEEeeeeceeecccChHHHHHHHhhcHHHHHHHHHcCCceecccCCCCCcceeee--cCCceeEeeeeceeEEe
Q 031165 81 GNRIIKKRIHVRVEHVQPSRCTEEFKLRKKKNDELKADAKARGEVISTKRQPKGPKPGFMV--EGATLETVTPIPYDVVN 158 (164)
Q Consensus 81 ~~k~i~KrI~VriEHik~sk~r~~fl~rvk~nd~~k~eak~~g~~v~~kr~p~~Pr~a~~v--~~~~p~~l~p~py~~~~ 158 (164)
+|||++|||||+|||+++|+|+++||+|++|||++++||||+|+|||++|+|++||+|||| ++++||+|+||||+|++
T Consensus 81 kgKil~KRinV~iEhik~sk~~~~fl~r~kendqkkkeAKekg~wvq~k~p~~~prea~~Vrt~gkepell~pip~~f~a 160 (160)
T KOG1732|consen 81 KGKILAKRINVRIEHIKHSKCRDEFLKRVKENDQKKKEAKEKGTWVQLKRQPAPPREAHFVRTNGKEPELLEPIPYEFMA 160 (160)
T ss_pred ccceeeeeeeeEeeccccccchhhhhhhhcccchhhhhHHhcCceeecccCCCCCcceeEEEcCCCCccccccccccccC
Confidence 9999999999999999999999999999999999999999999999977777789999999 99999999999999975
No 4
>PRK04306 50S ribosomal protein L21e; Reviewed
Probab=100.00 E-value=3.2e-50 Score=300.83 Aligned_cols=97 Identities=40% Similarity=0.696 Sum_probs=94.7
Q ss_pred CCCCCCCCcccccccCCcccCCCCCChHHHHHhhCCCCEEEEEecCceeeCccCccccccceeEEeeeccEEEEEEEeee
Q 031165 1 MPAGHGLRSRTRDLFARPFRKKGYIPLSTYLRTYKIGDYVDVKVNGAVHKGMPHKFYHGRTGRVWNVTKRAIGVEINKQV 80 (164)
Q Consensus 1 m~~s~G~R~~TR~~fsk~fR~~G~~~ls~~l~~yk~GD~VdIk~~~svqKGmPhk~YHGkTG~V~~v~~~AvgV~Vnk~v 80 (164)
|++|+|||++||++||++||+||++|||+||++|++||+|||++||||||||||+||||+||+|||++++||+|+| +|
T Consensus 2 M~~s~G~R~~TR~~fsk~~R~~G~~~ls~~l~~y~~Gd~V~I~~d~sv~kGmPh~~yhGkTG~V~~v~~~A~~V~v--~v 79 (98)
T PRK04306 2 MKKSHGFRSKTRKKLSKSPRERGLSPLSRALQEFEEGDKVHIVIDPSVHKGMPHPRFHGKTGTVVGKRGRAYIVEV--KD 79 (98)
T ss_pred CCCCCCccccchhhhCcCccccCCCcHHHHHHhccCCCEEEEEecCceecCCccccccCCCEEEEeecCeEEEEEE--EE
Confidence 8899999999999999999999999999999999999999999999999999999999999999999999999999 58
Q ss_pred CcEeeeeEEeeeeceeecccC
Q 031165 81 GNRIIKKRIHVRVEHVQPSRC 101 (164)
Q Consensus 81 ~~k~i~KrI~VriEHik~sk~ 101 (164)
||+ +|+||||||||++|+.
T Consensus 80 g~k--~Kri~vr~eHlk~~~~ 98 (98)
T PRK04306 80 GGK--EKTLIVRPEHLRPQKG 98 (98)
T ss_pred CCc--eeEEEcCHHHcCccCC
Confidence 999 8999999999999974
No 5
>PF01157 Ribosomal_L21e: Ribosomal protein L21e; InterPro: IPR001147 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 [, ]. L21E family contains proteins from a number of eukaryotic and archaebacterial organisms which include; mammalian L2, Entamoeba histolytica L21, Caenorhabditis elegans L21 (C14B9.7), Saccharomyces cerevisiae (Baker's yeast) L21E (URP1) and Haloarcula marismortui HL31.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3IZR_U 1S1I_Q 3O58_T 3IZS_U 3O5H_T 1Q82_R 1KQS_P 3CCJ_Q 3CCQ_Q 1VQ5_Q ....
Probab=100.00 E-value=8.1e-50 Score=299.04 Aligned_cols=99 Identities=62% Similarity=0.992 Sum_probs=80.3
Q ss_pred CCCCCCCcccccccCCcccCCCCCChHHHHHhhCCCCEEEEEecCceeeCccCccccccceeEEeeeccEEEEEEEeeeC
Q 031165 2 PAGHGLRSRTRDLFARPFRKKGYIPLSTYLRTYKIGDYVDVKVNGAVHKGMPHKFYHGRTGRVWNVTKRAIGVEINKQVG 81 (164)
Q Consensus 2 ~~s~G~R~~TR~~fsk~fR~~G~~~ls~~l~~yk~GD~VdIk~~~svqKGmPhk~YHGkTG~V~~v~~~AvgV~Vnk~v~ 81 (164)
++|+|+|++||+|||++||+||++||++||++|++||+|||++|||+||||||+||||+||+||||+++|+|++++++|+
T Consensus 1 ~~S~G~R~~TR~~fsk~~R~~G~~~ls~~l~~yk~GD~V~I~id~sv~kGmPh~~yHGkTG~V~~v~~~~~G~~~~~~v~ 80 (99)
T PF01157_consen 1 TRSKGYRRGTRYKFSKPFRKHGMIPLSTYLQEYKVGDKVDIKIDPSVHKGMPHKRYHGKTGRVFNVTKGARGVAYNKQVK 80 (99)
T ss_dssp -SS-STTTTTHHHHS--CCCTSS--CHHHH----TT-EEEE---TTSSSSS--GGGTTEEEEEEEE-SSCEEEEEEEECS
T ss_pred CCCCCccCCCchhhcCCCccCCCCcHHHHHHHccCCCEEEEEecCccccCCCcceECCCceeEEEeCCCceEEEEEEEec
Confidence 58999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cEeeeeEEeeeeceeeccc
Q 031165 82 NRIIKKRIHVRVEHVQPSR 100 (164)
Q Consensus 82 ~k~i~KrI~VriEHik~sk 100 (164)
+++++|+|||++|||++||
T Consensus 81 ~~~~~K~i~vr~eHlk~sK 99 (99)
T PF01157_consen 81 DRIKEKRIIVRPEHLKPSK 99 (99)
T ss_dssp SSCEEEEEEEEGGGEEE-S
T ss_pred CCcccEEEEECHHHcccCC
Confidence 9999999999999999996
No 6
>COG2139 RPL21A Ribosomal protein L21E [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=3.2e-45 Score=272.94 Aligned_cols=98 Identities=46% Similarity=0.803 Sum_probs=95.4
Q ss_pred CCCCCCCcccccccCCcccCCCCCChHHHHHhhCCCCEEEEEecCceeeCccCccccccceeEEeeeccEEEEEEEeeeC
Q 031165 2 PAGHGLRSRTRDLFARPFRKKGYIPLSTYLRTYKIGDYVDVKVNGAVHKGMPHKFYHGRTGRVWNVTKRAIGVEINKQVG 81 (164)
Q Consensus 2 ~~s~G~R~~TR~~fsk~fR~~G~~~ls~~l~~yk~GD~VdIk~~~svqKGmPhk~YHGkTG~V~~v~~~AvgV~Vnk~v~ 81 (164)
++|+|||++||++|++++|++|.+|||+||++|++||+|||+||||||+||||++|||+||+|+|++++||.|+|+ +|
T Consensus 1 ~~S~G~R~~TR~kl~k~~RerG~~plsr~l~ey~~Gd~V~I~IdpSv~kGmPh~rf~G~TG~Vvg~~g~ay~V~v~--~G 78 (98)
T COG2139 1 KRSHGYRSRTRYKLQKDPRERGLSPLSRYLQEYKVGDKVHIDIDPSVHKGMPHPRFQGKTGTVVGVRGRAYKVEVY--DG 78 (98)
T ss_pred CCCccccccchhhhccCccccCCcchhhHHhhccCCCEEEEEeCcccccCCCCccccCcceEEEeccCCEEEEEEe--cC
Confidence 4799999999999999999999999999999999999999999999999999999999999999999999999998 89
Q ss_pred cEeeeeEEeeeeceeecccChH
Q 031165 82 NRIIKKRIHVRVEHVQPSRCTE 103 (164)
Q Consensus 82 ~k~i~KrI~VriEHik~sk~r~ 103 (164)
|+ .|+|||+||||++++|++
T Consensus 79 ~k--~K~liv~peHLk~~~~~~ 98 (98)
T COG2139 79 NK--EKTLIVRPEHLKPQKCRE 98 (98)
T ss_pred Cc--eEEEEeCHHHccccccCC
Confidence 99 799999999999999974
No 7
>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=82.45 E-value=3 Score=31.57 Aligned_cols=48 Identities=27% Similarity=0.412 Sum_probs=35.2
Q ss_pred hhCCCCEEEEEecCceeeCccCccccccceeEEeeeccEEEEEEEeeeCcEeeeeEEeeeeceeeccc
Q 031165 33 TYKIGDYVDVKVNGAVHKGMPHKFYHGRTGRVWNVTKRAIGVEINKQVGNRIIKKRIHVRVEHVQPSR 100 (164)
Q Consensus 33 ~yk~GD~VdIk~~~svqKGmPhk~YHGkTG~V~~v~~~AvgV~Vnk~v~~k~i~KrI~VriEHik~sk 100 (164)
.++.||.|-|.--. +-|++|.|..|....-.|.| .-+|++..|++++.
T Consensus 3 ~ikkGD~V~Vi~G~----------dKGK~G~V~~V~~~~~~V~V----------egvN~~kkh~k~~~ 50 (104)
T TIGR01079 3 KIKKGDTVKVISGK----------DKGKRGKVLKVLPKTNKVIV----------EGVNMVKKHVKPKP 50 (104)
T ss_pred cccCCCEEEEeEcC----------CCCcEEEEEEEEcCCCEEEE----------CCcEEEEEecCccc
Confidence 46899999886422 66999999887665544444 55788888998864
No 8
>PRK12281 rplX 50S ribosomal protein L24; Reviewed
Probab=81.65 E-value=3.6 Score=29.48 Aligned_cols=48 Identities=29% Similarity=0.450 Sum_probs=34.3
Q ss_pred hhCCCCEEEEEecCceeeCccCccccccceeEEeeeccEEEEEEEeeeCcEeeeeEEeeeeceeeccc
Q 031165 33 TYKIGDYVDVKVNGAVHKGMPHKFYHGRTGRVWNVTKRAIGVEINKQVGNRIIKKRIHVRVEHVQPSR 100 (164)
Q Consensus 33 ~yk~GD~VdIk~~~svqKGmPhk~YHGkTG~V~~v~~~AvgV~Vnk~v~~k~i~KrI~VriEHik~sk 100 (164)
..+.||.|-|.- | .+-|++|+|..+....-.|.| .-+|+.--|++++.
T Consensus 6 ~I~kGD~V~Vi~-G---------~dKGK~G~V~~V~~~~~~V~V----------egvn~~kkh~kp~~ 53 (76)
T PRK12281 6 KVKKGDMVKVIA-G---------DDKGKTGKVLAVLPKKNRVIV----------EGVKIAKKAIKPSQ 53 (76)
T ss_pred cccCCCEEEEeE-c---------CCCCcEEEEEEEEcCCCEEEE----------cCcEEEEEEcCCCc
Confidence 578999998863 2 266999999887665544444 55677778888753
No 9
>PRK00004 rplX 50S ribosomal protein L24; Reviewed
Probab=80.80 E-value=3.7 Score=30.97 Aligned_cols=48 Identities=27% Similarity=0.409 Sum_probs=35.2
Q ss_pred hhCCCCEEEEEecCceeeCccCccccccceeEEeeeccEEEEEEEeeeCcEeeeeEEeeeeceeeccc
Q 031165 33 TYKIGDYVDVKVNGAVHKGMPHKFYHGRTGRVWNVTKRAIGVEINKQVGNRIIKKRIHVRVEHVQPSR 100 (164)
Q Consensus 33 ~yk~GD~VdIk~~~svqKGmPhk~YHGkTG~V~~v~~~AvgV~Vnk~v~~k~i~KrI~VriEHik~sk 100 (164)
.+++||.|-|.- | .+-|++|+|..|......|.| .-||++--|++++.
T Consensus 4 ~i~kGD~V~Vi~-G---------~dKGk~G~V~~V~~~~~~V~V----------egvn~~k~h~k~~~ 51 (105)
T PRK00004 4 KIKKGDTVIVIA-G---------KDKGKRGKVLKVLPKKNKVIV----------EGVNIVKKHQKPNQ 51 (105)
T ss_pred cccCCCEEEEeE-c---------CCCCcEEEEEEEEcCCCEEEE----------cCcEEEEEecCCCC
Confidence 468999998863 2 256999999988776666655 44677788888763
No 10
>CHL00141 rpl24 ribosomal protein L24; Validated
Probab=80.37 E-value=4.1 Score=29.61 Aligned_cols=48 Identities=31% Similarity=0.595 Sum_probs=34.3
Q ss_pred hhCCCCEEEEEecCceeeCccCccccccceeEEeeeccEEEEEEEeeeCcEeeeeEEeeeeceeeccc
Q 031165 33 TYKIGDYVDVKVNGAVHKGMPHKFYHGRTGRVWNVTKRAIGVEINKQVGNRIIKKRIHVRVEHVQPSR 100 (164)
Q Consensus 33 ~yk~GD~VdIk~~~svqKGmPhk~YHGkTG~V~~v~~~AvgV~Vnk~v~~k~i~KrI~VriEHik~sk 100 (164)
..++||.|-|.- | .+.|++|+|..|....-.|.| .-+|+.--|++++.
T Consensus 8 ~I~~GD~V~Vi~-G---------~dKGK~G~V~~V~~~~~~V~V----------egvn~~~k~~k~~~ 55 (83)
T CHL00141 8 HVKIGDTVKIIS-G---------SDKGKIGEVLKIIKKSNKVIV----------KGINIKFKHIKPNK 55 (83)
T ss_pred cccCCCEEEEeE-c---------CCCCcEEEEEEEEcCCCEEEE----------cCcEEEEEEcCCcc
Confidence 567899999864 2 266999999888766555554 44667777887753
No 11
>PTZ00194 60S ribosomal protein L26; Provisional
Probab=76.00 E-value=9.5 Score=30.76 Aligned_cols=66 Identities=21% Similarity=0.238 Sum_probs=43.3
Q ss_pred hCCCCEEEEEecCceeeCccCccccccceeEEeeeccEEEEEEEee----eCcEeeeeEE---eeeeceeecccChHHHH
Q 031165 34 YKIGDYVDVKVNGAVHKGMPHKFYHGRTGRVWNVTKRAIGVEINKQ----VGNRIIKKRI---HVRVEHVQPSRCTEEFK 106 (164)
Q Consensus 34 yk~GD~VdIk~~~svqKGmPhk~YHGkTG~V~~v~~~AvgV~Vnk~----v~~k~i~KrI---~VriEHik~sk~r~~fl 106 (164)
.+.||.|-|.--. |-|++|.|..|.....-|+|... -.|+..+--| ||.+-.+.-++.|..+|
T Consensus 47 IkkGD~V~Vi~Gk----------~KGk~GkV~~V~~k~~~ViVEgvn~~Kk~gk~~e~PIh~SNV~iv~l~l~~~R~~~l 116 (143)
T PTZ00194 47 VRKDDEVMVVRGH----------HKGREGKVTAVYRKKWVIHIEKITREKANGEPVQIGIHPSNVIITKLKLNKDRKAIL 116 (143)
T ss_pred eecCCEEEEecCC----------CCCCceEEEEEEcCCCEEEEeCeEEEecCCCEeecCcCchheEEEccccCchHHHHH
Confidence 5789999886322 56999999999777666665310 0111111112 67777778888899999
Q ss_pred HHH
Q 031165 107 LRK 109 (164)
Q Consensus 107 ~rv 109 (164)
++-
T Consensus 117 ~~k 119 (143)
T PTZ00194 117 ERK 119 (143)
T ss_pred hhh
Confidence 883
No 12
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=69.39 E-value=9.8 Score=20.85 Aligned_cols=26 Identities=35% Similarity=0.788 Sum_probs=18.6
Q ss_pred hCCCCEEEEEecCceeeCccCccccccceeEEeeec
Q 031165 34 YKIGDYVDVKVNGAVHKGMPHKFYHGRTGRVWNVTK 69 (164)
Q Consensus 34 yk~GD~VdIk~~~svqKGmPhk~YHGkTG~V~~v~~ 69 (164)
+++||.|-|... | |.|.+|.|..+.+
T Consensus 2 ~~~G~~V~I~~G-------~---~~g~~g~i~~i~~ 27 (28)
T smart00739 2 FEVGDTVRVIAG-------P---FKGKVGKVLEVDG 27 (28)
T ss_pred CCCCCEEEEeEC-------C---CCCcEEEEEEEcC
Confidence 678999999742 2 5577888877654
No 13
>PF09629 YorP: YorP protein; InterPro: IPR018591 This entry is represented by Bacteriophage SP-beta, YorP. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. YorP is a 71 residue protein. The structure is of an alpha helix between two of five beta strands. The function is unknown. ; PDB: 2HEQ_A.
Probab=66.18 E-value=5.6 Score=28.34 Aligned_cols=32 Identities=31% Similarity=0.635 Sum_probs=20.0
Q ss_pred hhCCCCEEEEEecCceeeCccCccccccceeEEeee
Q 031165 33 TYKIGDYVDVKVNGAVHKGMPHKFYHGRTGRVWNVT 68 (164)
Q Consensus 33 ~yk~GD~VdIk~~~svqKGmPhk~YHGkTG~V~~v~ 68 (164)
.|..||.|.| |....-||||. -|+-|.|...-
T Consensus 6 sY~~~~~VeI--N~NAkyg~P~~--VG~kG~IIe~l 37 (71)
T PF09629_consen 6 SYPLGLEVEI--NSNAKYGCPHH--VGRKGKIIEKL 37 (71)
T ss_dssp -S-TT-EEEE---TT-TTTSTT----SSEEEEEEE-
T ss_pred ccCCCCEEEE--cCcccccCccc--cccccchhhhh
Confidence 5889999988 67778899984 68888876543
No 14
>KOG3141 consensus Mitochondrial/chloroplast ribosomal protein L3 [Translation, ribosomal structure and biogenesis]
Probab=60.69 E-value=5.1 Score=35.90 Aligned_cols=40 Identities=30% Similarity=0.542 Sum_probs=27.4
Q ss_pred CCCcccccccCCc----ccCCCCCChH------------------HHHHhhCCCCEEEEEec
Q 031165 6 GLRSRTRDLFARP----FRKKGYIPLS------------------TYLRTYKIGDYVDVKVN 45 (164)
Q Consensus 6 G~R~~TR~~fsk~----fR~~G~~~ls------------------~~l~~yk~GD~VdIk~~ 45 (164)
|++...+.++++. ||++|++|-. -+-+.|++|||||+.+-
T Consensus 113 G~g~~~p~kltk~~~g~f~~~gv~pK~~l~eF~Vt~~al~~pGt~l~~~hFk~GqyVDV~g~ 174 (310)
T KOG3141|consen 113 GYGTVKPKKLTKAELGHFRSAGVPPKRHLREFRVTEEALLPPGTPLFARHFKPGQYVDVTGK 174 (310)
T ss_pred ccccCChHHhhHHHHHHHHHcCCChhhhhheEeechhccCCCCcccchhhcCCCceEEEEee
Confidence 6666666777765 7777776521 23456889999998753
No 15
>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=57.53 E-value=15 Score=28.40 Aligned_cols=33 Identities=21% Similarity=0.427 Sum_probs=24.4
Q ss_pred CCCCEEEEEecCceeeCccCccccccceeEEeeeccEEEEEEE
Q 031165 35 KIGDYVDVKVNGAVHKGMPHKFYHGRTGRVWNVTKRAIGVEIN 77 (164)
Q Consensus 35 k~GD~VdIk~~~svqKGmPhk~YHGkTG~V~~v~~~AvgV~Vn 77 (164)
+.||.|-|..-. |.|++|.|..|...-..|+|.
T Consensus 43 kkGD~V~Vi~Gk----------~KGk~GkV~~V~~~~~~V~Ve 75 (114)
T TIGR01080 43 RKGDKVRIMRGD----------FKGHEGKVSKVDLKRYRIYVE 75 (114)
T ss_pred ecCCEEEEecCC----------CCCCEEEEEEEEcCCCEEEEc
Confidence 579999886332 679999999997666656553
No 16
>PF02211 NHase_beta: Nitrile hydratase beta subunit; InterPro: IPR024690 Nitrile hydratases (EC:4.2.1.84) are unusual metalloenzymes that catalyse the hydration of nitriles to their corresponding amides. They are used as biocatalysts in acrylamide production, one of the few commercial scale bioprocesses, as well as in environmental remediation for the removal of nitriles from waste streams. Nitrile hydratases are composed of two subunits, alpha and beta, and they contain one iron atom per alpha beta unit []. This entry represents the structural domain of nitrile hydratase beta subunit which contains irregular array of helices in the N-terminal extension.; GO: 0018822 nitrile hydratase activity; PDB: 2DXB_H 2DD5_K 2DD4_H 2ZZD_B 2DXC_H 1AHJ_F 2ZPE_B 2ZCF_B 2D0Q_B 2CZ7_B ....
Probab=55.21 E-value=11 Score=32.04 Aligned_cols=36 Identities=28% Similarity=0.545 Sum_probs=18.2
Q ss_pred HhhCCCCEEEEEecC-ceeeCccCccccccceeEEeee
Q 031165 32 RTYKIGDYVDVKVNG-AVHKGMPHKFYHGRTGRVWNVT 68 (164)
Q Consensus 32 ~~yk~GD~VdIk~~~-svqKGmPhk~YHGkTG~V~~v~ 68 (164)
..|++||.|-|+-.+ .-|--+| .+=.|+||+|.-+.
T Consensus 133 ~~F~vGd~Vrv~~~~~~~HtR~P-~Y~rg~~G~I~~~~ 169 (222)
T PF02211_consen 133 PRFAVGDRVRVRNLPPPGHTRLP-RYVRGKTGTIERVH 169 (222)
T ss_dssp -SS-TT-EEEE-----SS--SS--GGGTT-EEEEEEEE
T ss_pred CCCCCCCEEEECCCCCCCccccc-HhhCCCeeEEEEEe
Confidence 359999999997544 4455555 45679999887443
No 17
>PRK01191 rpl24p 50S ribosomal protein L24P; Validated
Probab=51.08 E-value=24 Score=27.66 Aligned_cols=34 Identities=24% Similarity=0.386 Sum_probs=25.4
Q ss_pred hCCCCEEEEEecCceeeCccCccccccceeEEeeeccEEEEEEE
Q 031165 34 YKIGDYVDVKVNGAVHKGMPHKFYHGRTGRVWNVTKRAIGVEIN 77 (164)
Q Consensus 34 yk~GD~VdIk~~~svqKGmPhk~YHGkTG~V~~v~~~AvgV~Vn 77 (164)
.++||.|-|..-. |-|++|+|..|...--.|.|.
T Consensus 46 IkkGD~V~VisG~----------~KGk~GkV~~V~~~~~~V~Ve 79 (120)
T PRK01191 46 VRKGDTVKVMRGD----------FKGEEGKVVEVDLKRGRIYVE 79 (120)
T ss_pred EeCCCEEEEeecC----------CCCceEEEEEEEcCCCEEEEe
Confidence 5789999987443 569999999997665555553
No 18
>PF00924 MS_channel: Mechanosensitive ion channel; InterPro: IPR006685 Mechanosensitive (MS) channels provide protection against hypo-osmotic shock, responding both to stretching of the cell membrane and to membrane depolarisation. They are present in the membranes of organisms from the three domains of life: bacteria, archaea, and eukarya []. There are two families of MS channels: large-conductance MS channels (MscL) and small-conductance MS channels (MscS or YGGB). The pressure threshold for MscS opening is 50% that of MscL []. The MscS family is much larger and more variable in size and sequence than the MscL family. Much of the diversity in MscS proteins occurs in the size of the transmembrane regions, which ranges from three to eleven transmembrane helices, although the three C-terminal helices are conserved. This family contains sequences form the MscS family of proteins. MscS folds as a homo-heptamer with a cylindrical shape, and can be divided into transmembrane and extramembrane regions: an N-terminal periplasmic region, a transmembrane region, and a C-terminal cytoplasmic region (middle and C-terminal domains). The transmembrane region forms a channel through the membrane that opens into a chamber enclosed by the extramembrane portion, the latter connecting to the cytoplasm through distinct portals [].; GO: 0055085 transmembrane transport, 0016020 membrane; PDB: 2OAU_E 2VV5_F.
Probab=49.34 E-value=14 Score=29.08 Aligned_cols=30 Identities=30% Similarity=0.587 Sum_probs=20.8
Q ss_pred HHhhCCCCEEEEEecCceeeCccCccccccceeEEeeeccEEEEE
Q 031165 31 LRTYKIGDYVDVKVNGAVHKGMPHKFYHGRTGRVWNVTKRAIGVE 75 (164)
Q Consensus 31 l~~yk~GD~VdIk~~~svqKGmPhk~YHGkTG~V~~v~~~AvgV~ 75 (164)
-+.|++||+|.|. |-+|+|..++=++..+.
T Consensus 58 ~~pf~vGD~I~i~---------------~~~G~V~~I~l~~t~l~ 87 (206)
T PF00924_consen 58 ERPFKVGDRIEIG---------------GVEGRVEEIGLRSTRLR 87 (206)
T ss_dssp C-SS-TT-EEESS---------------S-EEEEEEE-SSEEEEE
T ss_pred cCCccCCCEEEEE---------------EeehHHHhcCcceeeee
Confidence 3579999998885 88999999999987664
No 19
>PF09953 DUF2187: Uncharacterized protein conserved in bacteria (DUF2187); InterPro: IPR018690 This family consists of various hypothetical bacterial proteins with known function. It includes the uncharacterised YkvS protein from Bacillus subtilis.
Probab=48.55 E-value=30 Score=23.98 Aligned_cols=33 Identities=33% Similarity=0.488 Sum_probs=26.0
Q ss_pred HhhCCCCEEEEEecCceeeCccCccccccceeEEeeeccEEEEEEEe
Q 031165 32 RTYKIGDYVDVKVNGAVHKGMPHKFYHGRTGRVWNVTKRAIGVEINK 78 (164)
Q Consensus 32 ~~yk~GD~VdIk~~~svqKGmPhk~YHGkTG~V~~v~~~AvgV~Vnk 78 (164)
..-++||++..+ +|-||+|..+...++.|.+..
T Consensus 2 ~~a~vGdiIefk--------------~g~~G~V~kv~eNSVIVdIT~ 34 (57)
T PF09953_consen 2 KKAKVGDIIEFK--------------DGFTGIVEKVYENSVIVDITI 34 (57)
T ss_pred cccccCcEEEEc--------------CCcEEEEEEEecCcEEEEEEe
Confidence 445789998652 356999999999999998853
No 20
>PF00970 FAD_binding_6: Oxidoreductase FAD-binding domain; InterPro: IPR008333 These sequences contain an oxidoreductase FAD-binding domain. To date, the 3D-structures of the flavoprotein domain of Zea mays (Maize) nitrate reductase [] and of pig NADH:cytochrome b5 reductase [] have been solved. The overall fold is similar to that of ferredoxin:NADP+ reductase []: the FAD-binding domain (N-terminal) has the topology of an anti-parallel beta-barrel, while the NAD(P)-binding domain (C-terminal) has the topology of a classical pyridine dinucleotide-binding fold (i.e. a central parallel beta-sheet flanked by 2 helices on each side).; PDB: 1JB9_A 3LVB_A 3LO8_A 1FRN_A 1FND_A 1BX1_A 1FNC_A 1FNB_A 1BX0_A 1FRQ_A ....
Probab=47.41 E-value=21 Score=24.79 Aligned_cols=19 Identities=37% Similarity=0.581 Sum_probs=17.1
Q ss_pred ChHHHHHhhCCCCEEEEEe
Q 031165 26 PLSTYLRTYKIGDYVDVKV 44 (164)
Q Consensus 26 ~ls~~l~~yk~GD~VdIk~ 44 (164)
.+|.||...+.||.|.|.+
T Consensus 74 ~~S~~L~~l~~Gd~v~i~g 92 (99)
T PF00970_consen 74 RVSRYLHQLKPGDEVEIRG 92 (99)
T ss_dssp HHHHHHHTSCTTSEEEEEE
T ss_pred HHHHHHHhCCCCCEEEEEE
Confidence 3789999999999999975
No 21
>COG0198 RplX Ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=46.86 E-value=47 Score=25.42 Aligned_cols=46 Identities=30% Similarity=0.489 Sum_probs=33.2
Q ss_pred hhCCCCEEEEEecCceeeCccCccccccceeEEeeeccEEEEEEEeeeCcEeeeeEEeeeeceeeccc
Q 031165 33 TYKIGDYVDVKVNGAVHKGMPHKFYHGRTGRVWNVTKRAIGVEINKQVGNRIIKKRIHVRVEHVQPSR 100 (164)
Q Consensus 33 ~yk~GD~VdIk~~~svqKGmPhk~YHGkTG~V~~v~~~AvgV~Vnk~v~~k~i~KrI~VriEHik~sk 100 (164)
-.++||.|-+.-- -+-|++|.|..|...- |+| .-+|+.--|.+++.
T Consensus 4 ~IrkGD~V~Vi~G----------kdKGk~GkVl~v~~k~--V~V----------EGvnv~kkh~k~~~ 49 (104)
T COG0198 4 KVKKGDTVKVIAG----------KDKGKEGKVLKVLPKK--VVV----------EGVNVVKKHIKPSQ 49 (104)
T ss_pred ceecCCEEEEEec----------CCCCcceEEEEEecCe--EEE----------ECcEEEEecCCCCC
Confidence 3578999988532 3679999999999888 444 33667777887553
No 22
>COG1588 POP4 RNase P/RNase MRP subunit p29 [Translation, ribosomal structure and biogenesis]
Probab=45.49 E-value=29 Score=26.30 Aligned_cols=47 Identities=28% Similarity=0.331 Sum_probs=33.3
Q ss_pred CCCEEEEEecCceeeCccCccccccceeEEeeeccEEEEEEEeeeCcEeeeeEEee
Q 031165 36 IGDYVDVKVNGAVHKGMPHKFYHGRTGRVWNVTKRAIGVEINKQVGNRIIKKRIHV 91 (164)
Q Consensus 36 ~GD~VdIk~~~svqKGmPhk~YHGkTG~V~~v~~~AvgV~Vnk~v~~k~i~KrI~V 91 (164)
.|=.|-|.- -+|+.|-|-.|+|++-|++++.+.--. +-+++.|.+.+
T Consensus 16 iGl~vrVv~-------s~~~s~vGI~G~VVdETkNtLvi~t~~--~~~~VpK~~~v 62 (95)
T COG1588 16 IGLEVRVVR-------STNPSYVGIEGRVVDETKNTLVIDTGS--REKVVPKDGAV 62 (95)
T ss_pred cCcEEEEEe-------cCCCCccceeEEEEeeeccEEEEECCC--ceEEEecCcEE
Confidence 455555542 489999999999999999999876431 44556665543
No 23
>TIGR01843 type_I_hlyD type I secretion membrane fusion protein, HlyD family. Type I secretion is an ABC transport process that exports proteins, without cleavage of any signal sequence, from the cytosol to extracellular medium across both inner and outer membranes. The secretion signal is found in the C-terminus of the transported protein. This model represents the adaptor protein between the ATP-binding cassette (ABC) protein of the inner membrane and the outer membrane protein, and is called the membrane fusion protein. This model selects a subfamily closely related to HlyD; it is defined narrowly and excludes, for example, colicin V secretion protein CvaA and multidrug efflux proteins.
Probab=35.02 E-value=53 Score=28.34 Aligned_cols=40 Identities=15% Similarity=0.310 Sum_probs=32.8
Q ss_pred HHHHHhhCCCCEEEEEecCceeeCccCccccccceeEEeeeccEE
Q 031165 28 STYLRTYKIGDYVDVKVNGAVHKGMPHKFYHGRTGRVWNVTKRAI 72 (164)
Q Consensus 28 s~~l~~yk~GD~VdIk~~~svqKGmPhk~YHGkTG~V~~v~~~Av 72 (164)
.+++...+.||.|.|.+++ .|...|..-+|+|..+...+.
T Consensus 318 ~~~~~~i~~G~~v~v~~~~-----~~~~~~~~~~g~V~~i~~~~~ 357 (423)
T TIGR01843 318 PKDIGFVHVGQPAEIKFSA-----FPYRRYGILNGKVKSISPDTF 357 (423)
T ss_pred hhhhhhhCCCCceEEEEec-----CCCcccCCccEEEEEECCCcc
Confidence 4678888999999998875 688888788899999987663
No 24
>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=34.26 E-value=1.1e+02 Score=23.70 Aligned_cols=50 Identities=26% Similarity=0.548 Sum_probs=34.9
Q ss_pred hCCCCEEEEEecCceeeCccCccccccceeEEeee--ccEEEEEEEeeeCcEeeeeEEeeeeceee
Q 031165 34 YKIGDYVDVKVNGAVHKGMPHKFYHGRTGRVWNVT--KRAIGVEINKQVGNRIIKKRIHVRVEHVQ 97 (164)
Q Consensus 34 yk~GD~VdIk~~~svqKGmPhk~YHGkTG~V~~v~--~~AvgV~Vnk~v~~k~i~KrI~VriEHik 97 (164)
|+.||.|.|. +| | |.|-.|.|..+. .+-+.|.|+ +-|+ ...+.+..++|.
T Consensus 120 ~~~G~~V~I~-~G------p---f~G~~g~v~~~~~~~~r~~V~v~--~~g~--~~~v~v~~~~l~ 171 (172)
T TIGR00922 120 FEVGEQVRVN-DG------P---FANFTGTVEEVDYEKSKLKVSVS--IFGR--ETPVELEFSQVE 171 (172)
T ss_pred CCCCCEEEEe-ec------C---CCCcEEEEEEEcCCCCEEEEEEE--ECCC--ceEEEEcHHHee
Confidence 7789999987 33 3 567789888885 335666664 5666 477777777664
No 25
>PRK14980 DNA-directed RNA polymerase subunit G; Provisional
Probab=32.62 E-value=98 Score=24.65 Aligned_cols=31 Identities=3% Similarity=0.080 Sum_probs=24.0
Q ss_pred HHHHhhCCCCEEEEEecCceeeCccCcccccc
Q 031165 29 TYLRTYKIGDYVDVKVNGAVHKGMPHKFYHGR 60 (164)
Q Consensus 29 ~~l~~yk~GD~VdIk~~~svqKGmPhk~YHGk 60 (164)
.-|-.|+.||.|.|.+--...+ --+..|.|+
T Consensus 44 ~~L~~fsege~v~iiIS~ekP~-~~~~dFCgh 74 (127)
T PRK14980 44 DSINIFSQKEKVKAIISKERPS-YTNDDFCAH 74 (127)
T ss_pred hhhheecCCCcEEEEEeccCcc-cccceeecC
Confidence 3477899999999998777666 555777776
No 26
>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=32.18 E-value=48 Score=19.43 Aligned_cols=29 Identities=31% Similarity=0.788 Sum_probs=19.2
Q ss_pred CCCEEEEEecCceeeCccCccccccceeEEeeeccEEEE
Q 031165 36 IGDYVDVKVNGAVHKGMPHKFYHGRTGRVWNVTKRAIGV 74 (164)
Q Consensus 36 ~GD~VdIk~~~svqKGmPhk~YHGkTG~V~~v~~~AvgV 74 (164)
+||.|-|. .| | |-|++|.|..+..+...|
T Consensus 1 ~Gd~V~V~-~G------~---~~G~~G~I~~i~~~~~~V 29 (32)
T PF00467_consen 1 VGDTVKVI-SG------P---FKGKIGKIVEIDRSKVRV 29 (32)
T ss_dssp TTSEEEES-SS------T---TTTEEEEEEEEETTTTEE
T ss_pred CCCEEEEe-Ec------C---CCCceEEEEEEECCCCEE
Confidence 47777774 22 3 558889888887765433
No 27
>KOG3391 consensus Transcriptional co-repressor component [Transcription]
Probab=30.52 E-value=33 Score=27.90 Aligned_cols=15 Identities=40% Similarity=0.906 Sum_probs=13.2
Q ss_pred HhhCCCCEEEEEecC
Q 031165 32 RTYKIGDYVDVKVNG 46 (164)
Q Consensus 32 ~~yk~GD~VdIk~~~ 46 (164)
+.|++||++||-|-+
T Consensus 123 ~kf~iGD~lDVaI~~ 137 (151)
T KOG3391|consen 123 TKFEIGDYLDVAITP 137 (151)
T ss_pred CCccccceEEEEecC
Confidence 469999999999876
No 28
>PF03321 GH3: GH3 auxin-responsive promoter; InterPro: IPR004993 Transcription of the gene family, GH3, has been shown to be specifically induced by the plant hormone auxin. The auxin-responsive GH3 gene promoter is composed of multiple auxin response elements (AuxREs), and each AuxRE contributes incrementally to the strong auxin inducibility to the promoter.; PDB: 4EPL_A 4EQ4_B 4EWV_B 4EQL_B 4EPM_A.
Probab=30.39 E-value=22 Score=33.20 Aligned_cols=37 Identities=32% Similarity=0.522 Sum_probs=28.3
Q ss_pred HHhhCCCCEEEEEecCceeeCccCccccccceeEEeeecc
Q 031165 31 LRTYKIGDYVDVKVNGAVHKGMPHKFYHGRTGRVWNVTKR 70 (164)
Q Consensus 31 l~~yk~GD~VdIk~~~svqKGmPhk~YHGkTG~V~~v~~~ 70 (164)
|--|..||+|-+. .++.+.|-=.|.||+|.+.|+.+-
T Consensus 368 LyRY~iGDvVrv~---gf~~~~P~i~F~~R~~~~l~l~gE 404 (528)
T PF03321_consen 368 LYRYRIGDVVRVT---GFYNQTPRIEFVGRRGQVLSLFGE 404 (528)
T ss_dssp -SSEEECEEEEEE---EEETTEEEEEEEEETTEEE-SSS-
T ss_pred eeeeecCCEEEEe---eccCCCcEEEEeccCCceeeccee
Confidence 5568899999885 466778999999999988887764
No 29
>PLN02249 indole-3-acetic acid-amido synthetase
Probab=30.09 E-value=31 Score=33.22 Aligned_cols=37 Identities=22% Similarity=0.455 Sum_probs=29.8
Q ss_pred HHhhCCCCEEEEEecCceeeCccCccccccceeEEeeecc
Q 031165 31 LRTYKIGDYVDVKVNGAVHKGMPHKFYHGRTGRVWNVTKR 70 (164)
Q Consensus 31 l~~yk~GD~VdIk~~~svqKGmPhk~YHGkTG~V~~v~~~ 70 (164)
|--|.+||+|-+. +++.+-|.=.|-||++.+.|+.+-
T Consensus 407 LyRY~iGDvVrvt---gf~~~~P~i~F~gR~~~~ls~~GE 443 (597)
T PLN02249 407 LYRYRVGDILRVT---GFHNSAPQFKFIRRKNVLLSIESD 443 (597)
T ss_pred eeEeecCCEEEEe---eccCCCcEEEEEccCCcceecccc
Confidence 4568899999886 457889999999999988887654
No 30
>PRK02749 photosystem I reaction center subunit IV; Provisional
Probab=28.67 E-value=1.1e+02 Score=22.02 Aligned_cols=30 Identities=27% Similarity=0.429 Sum_probs=26.1
Q ss_pred hCCCCEEEEEecCceeeCccCccccccceeEEeeeccE
Q 031165 34 YKIGDYVDVKVNGAVHKGMPHKFYHGRTGRVWNVTKRA 71 (164)
Q Consensus 34 yk~GD~VdIk~~~svqKGmPhk~YHGkTG~V~~v~~~A 71 (164)
.+.||+|-|+ .|-.++...+|+|.+|.+..
T Consensus 3 i~rGskVrIl--------R~ESYWyn~vGtV~svD~sg 32 (71)
T PRK02749 3 ISRGDKVRIL--------RPESYWYNEVGTVASVDKSG 32 (71)
T ss_pred cccCCEEEEc--------cccceeecCcceEEEEccCC
Confidence 4789999998 78899999999999998873
No 31
>KOG1384 consensus tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]
Probab=28.07 E-value=13 Score=33.95 Aligned_cols=29 Identities=34% Similarity=0.406 Sum_probs=26.9
Q ss_pred hHHHHHhhCCCCEEEEEecCceeeCccCc
Q 031165 27 LSTYLRTYKIGDYVDVKVNGAVHKGMPHK 55 (164)
Q Consensus 27 ls~~l~~yk~GD~VdIk~~~svqKGmPhk 55 (164)
-|.-||.|+-=|+|.-|+....++||||+
T Consensus 37 NsDkmQvYkGldivTnK~t~~e~~gVPHH 65 (348)
T KOG1384|consen 37 NSDKMQVYKGLDIVTNKITLQERKGVPHH 65 (348)
T ss_pred cccceeeecCcccccccCChhhcCCCChH
Confidence 36789999999999999999999999997
No 32
>cd06080 MUM1_like Mutated melanoma-associated antigen 1 (MUM-1) is a melanoma-associated antigen (MAA). MUM-1 belongs to the mutated or aberrantly expressed type of MAAs, along with antigens such as CDK4, beta-catenin, gp100-in4, p15, and N-acetylglucosaminyltransferase V. It is highly expressed in several types of human cancers. The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes.
Probab=26.89 E-value=2.5e+02 Score=20.30 Aligned_cols=71 Identities=14% Similarity=0.215 Sum_probs=44.7
Q ss_pred hCCCCEEEEEecCceeeCccCccccccceeEEeeecc--EEEEEEEeeeCcEeeeeEEeeeeceeecccChHHHHHHHhh
Q 031165 34 YKIGDYVDVKVNGAVHKGMPHKFYHGRTGRVWNVTKR--AIGVEINKQVGNRIIKKRIHVRVEHVQPSRCTEEFKLRKKK 111 (164)
Q Consensus 34 yk~GD~VdIk~~~svqKGmPhk~YHGkTG~V~~v~~~--AvgV~Vnk~v~~k~i~KrI~VriEHik~sk~r~~fl~rvk~ 111 (164)
|++||.|--|+- |-|+= -|+|.++... -+-|.. .|+- .-.-.+.++-+++.....++.+..++
T Consensus 1 f~~gdlVWaK~~-----g~P~W-----Pa~I~~~~~~~~k~~V~F---fG~~--~~~a~~~~~~l~p~~~~~~~~ek~~~ 65 (80)
T cd06080 1 FEKNDLVWAKIQ-----GYPWW-----PAVIKSISRKKQKARVNF---IGDN--MQSEKKGIRVVKRWLKHFDCTEKQKL 65 (80)
T ss_pred CCCCCEEEEeCC-----CCCCC-----CEEEeeecCCCCEEEEEE---eCCC--CceeccchhhcccccccHHHHHHHHH
Confidence 688999988864 44443 4566666543 333333 3443 12223567888898888888877777
Q ss_pred cHHHHHHH
Q 031165 112 NDELKADA 119 (164)
Q Consensus 112 nd~~k~ea 119 (164)
++++|+.-
T Consensus 66 ~~k~ke~~ 73 (80)
T cd06080 66 TNKAKESY 73 (80)
T ss_pred HHHHHHHH
Confidence 77766543
No 33
>PRK05609 nusG transcription antitermination protein NusG; Validated
Probab=26.28 E-value=1.8e+02 Score=22.61 Aligned_cols=50 Identities=24% Similarity=0.458 Sum_probs=32.5
Q ss_pred hhCCCCEEEEEecCceeeCccCccccccceeEEeee--ccEEEEEEEeeeCcEeeeeEEeeeecee
Q 031165 33 TYKIGDYVDVKVNGAVHKGMPHKFYHGRTGRVWNVT--KRAIGVEINKQVGNRIIKKRIHVRVEHV 96 (164)
Q Consensus 33 ~yk~GD~VdIk~~~svqKGmPhk~YHGkTG~V~~v~--~~AvgV~Vnk~v~~k~i~KrI~VriEHi 96 (164)
.|++||.|.|.. | | |.|-.|+|..+. .+-+.|.++ .-|+ ...+.+..+-+
T Consensus 126 ~~~~Gd~VrI~~-G------P---f~G~~g~v~~i~~~~~r~~v~l~--~~G~--~~~v~l~~~~l 177 (181)
T PRK05609 126 DFEVGEMVRVID-G------P---FADFNGTVEEVDYEKSKLKVLVS--IFGR--ETPVELEFSQV 177 (181)
T ss_pred CCCCCCEEEEec-c------C---CCCCEEEEEEEeCCCCEEEEEEE--ECCC--ceEEEEchHHE
Confidence 377899999973 3 3 678889998886 335666665 4555 34555544444
No 34
>PHA02763 hypothetical protein; Provisional
Probab=26.09 E-value=61 Score=24.64 Aligned_cols=21 Identities=43% Similarity=0.608 Sum_probs=17.3
Q ss_pred hhCCCCEEEEEecCceeeCccCccccccc
Q 031165 33 TYKIGDYVDVKVNGAVHKGMPHKFYHGRT 61 (164)
Q Consensus 33 ~yk~GD~VdIk~~~svqKGmPhk~YHGkT 61 (164)
.|+.|++|.+++ -|++|+||.
T Consensus 27 ~YK~gqkv~l~v--------~dr~f~gKv 47 (102)
T PHA02763 27 FYKIGQKVILKV--------GDKRFPGKV 47 (102)
T ss_pred hhccCcEEEEEe--------cCccccceE
Confidence 699999999997 467788874
No 35
>PLN00045 photosystem I reaction center subunit IV; Provisional
Probab=25.50 E-value=1e+02 Score=23.56 Aligned_cols=36 Identities=22% Similarity=0.355 Sum_probs=29.2
Q ss_pred hhCCCCEEEEEecCceeeCccCccccccceeEEeeecc---EEEEEE
Q 031165 33 TYKIGDYVDVKVNGAVHKGMPHKFYHGRTGRVWNVTKR---AIGVEI 76 (164)
Q Consensus 33 ~yk~GD~VdIk~~~svqKGmPhk~YHGkTG~V~~v~~~---AvgV~V 76 (164)
-.+.||+|-|. .|-.++...+|+|.+|.+. -|-|+|
T Consensus 39 g~~RGskVrIl--------R~ESYWyn~vGtVvsVDq~~girYPVvV 77 (101)
T PLN00045 39 GPKRGSKVKIL--------RPESYWFNDVGKVVAVDQDPGVRYPVVV 77 (101)
T ss_pred ccCCCCEEEEc--------cccceeecCcceEEEEeCCCCcccceEE
Confidence 36789999998 6888999999999999887 344544
No 36
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=25.48 E-value=29 Score=21.59 Aligned_cols=14 Identities=50% Similarity=0.624 Sum_probs=10.8
Q ss_pred hhCCCCEEEEEecC
Q 031165 33 TYKIGDYVDVKVNG 46 (164)
Q Consensus 33 ~yk~GD~VdIk~~~ 46 (164)
.|+.||.|...+-.
T Consensus 46 ~~~~G~~v~~~V~~ 59 (72)
T smart00316 46 VLKVGDEVKVKVLS 59 (72)
T ss_pred eecCCCEEEEEEEE
Confidence 38999999887643
No 37
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=25.18 E-value=68 Score=20.74 Aligned_cols=53 Identities=19% Similarity=0.139 Sum_probs=33.2
Q ss_pred hhCCCCEEEEEe--cCceeeCccCccccccceeEEeeec-cEEEEEEEeeeCcEeeeeEEeeeeceeeccc
Q 031165 33 TYKIGDYVDVKV--NGAVHKGMPHKFYHGRTGRVWNVTK-RAIGVEINKQVGNRIIKKRIHVRVEHVQPSR 100 (164)
Q Consensus 33 ~yk~GD~VdIk~--~~svqKGmPhk~YHGkTG~V~~v~~-~AvgV~Vnk~v~~k~i~KrI~VriEHik~sk 100 (164)
.|++||.|++.- +++.- .|+|..+.+ ..+.|..-. .+- .....+...+||++.
T Consensus 2 ~~~~G~~Ve~~~~~~~~W~-----------~a~V~~~~~~~~~~V~~~~--~~~--~~~e~v~~~~LRp~~ 57 (61)
T smart00743 2 DFKKGDRVEVFSKEEDSWW-----------EAVVTKVLGDGKYLVRYLT--ESE--PLKETVDWSDLRPHP 57 (61)
T ss_pred CcCCCCEEEEEECCCCEEE-----------EEEEEEECCCCEEEEEECC--CCc--ccEEEEeHHHcccCC
Confidence 489999999987 44332 466777777 566665521 111 345566677777654
No 38
>COG0668 MscS Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]
Probab=25.10 E-value=74 Score=26.27 Aligned_cols=30 Identities=27% Similarity=0.611 Sum_probs=20.9
Q ss_pred HHhhCCCCEEEEEecCceeeCccCccccccceeEEeeeccEEEE
Q 031165 31 LRTYKIGDYVDVKVNGAVHKGMPHKFYHGRTGRVWNVTKRAIGV 74 (164)
Q Consensus 31 l~~yk~GD~VdIk~~~svqKGmPhk~YHGkTG~V~~v~~~AvgV 74 (164)
-+.|++||.|++-. |-.|+|.+++-+...+
T Consensus 145 ~~~f~vGD~I~i~~--------------~~~G~V~~i~~~~T~i 174 (316)
T COG0668 145 ERPFKVGDWIEIGS--------------GVEGTVEDIGLRSTTI 174 (316)
T ss_pred ecCcCcCCEEEECC--------------CceEEEEEEEEEEEEE
Confidence 56789999999953 5666666666555433
No 39
>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=24.82 E-value=1.7e+02 Score=22.25 Aligned_cols=55 Identities=22% Similarity=0.392 Sum_probs=33.2
Q ss_pred HhhCCCCEEEEEecCceeeCccCccccccceeEEeeeccEEEEEEEeeeCcEeeeeE--Eeeeeceeeccc
Q 031165 32 RTYKIGDYVDVKVNGAVHKGMPHKFYHGRTGRVWNVTKRAIGVEINKQVGNRIIKKR--IHVRVEHVQPSR 100 (164)
Q Consensus 32 ~~yk~GD~VdIk~~~svqKGmPhk~YHGkTG~V~~v~~~AvgV~Vnk~v~~k~i~Kr--I~VriEHik~sk 100 (164)
..|+.||.|.|.- | | |.|-.|.|..+.++-..|.|+ +-+. ... +.+..+.|+..+
T Consensus 85 ~~~~~Gd~V~I~~-G------P---f~G~~g~v~~~d~~k~~v~v~--l~~~--~~~~~v~v~~~~l~~~~ 141 (145)
T TIGR00405 85 ESIKKGDIVEIIS-G------P---FKGERAKVIRVDESKEEVTLE--LIEA--AVPIPVTVKGDQVRIIQ 141 (145)
T ss_pred cccCCCCEEEEee-c------C---CCCCeEEEEEEcCCCCEEEEE--EEEc--CccceEEEeeeEEEEec
Confidence 3489999999973 3 4 557778887775333333332 1223 234 677777776654
No 40
>PF06107 DUF951: Bacterial protein of unknown function (DUF951); InterPro: IPR009296 This family consists of several short hypothetical bacterial proteins of unknown function.
Probab=24.74 E-value=50 Score=22.85 Aligned_cols=16 Identities=44% Similarity=0.922 Sum_probs=13.6
Q ss_pred hhCCCCEEEEEecCceeeCccCcc
Q 031165 33 TYKIGDYVDVKVNGAVHKGMPHKF 56 (164)
Q Consensus 33 ~yk~GD~VdIk~~~svqKGmPhk~ 56 (164)
.|.+||+|..| =||+|
T Consensus 1 ~~~vgDiV~mK--------K~HPC 16 (57)
T PF06107_consen 1 EYEVGDIVEMK--------KPHPC 16 (57)
T ss_pred CccCCCEEEEc--------CCCCC
Confidence 48899999988 68886
No 41
>cd04370 BAH BAH, or Bromo Adjacent Homology domain (also called ELM1 and BAM for Bromo Adjacent Motif). BAH domains have first been described as domains found in the polybromo protein and Yeast Rsc1/Rsc2 (Remodeling of the Structure of Chromatin). They also occur in mammalian DNA methyltransferases and the MTA1 subunits of histone deacetylase complexes. A BAH domain is also found in Yeast Sir3p and in the origin receptor complex protein 1 (Orc1p), where it was found to interact with the N-terminal lobe of the silence information regulator 1 protein (Sir1p), confirming the initial hypothesis that BAH plays a role in protein-protein interactions.
Probab=24.61 E-value=1.1e+02 Score=21.51 Aligned_cols=53 Identities=25% Similarity=0.367 Sum_probs=30.0
Q ss_pred hhCCCCEEEEEecCceeeCccCccccccceeEEeeeccEEEEEEEeeeCcEeeeeEEeeeeceeecc
Q 031165 33 TYKIGDYVDVKVNGAVHKGMPHKFYHGRTGRVWNVTKRAIGVEINKQVGNRIIKKRIHVRVEHVQPS 99 (164)
Q Consensus 33 ~yk~GD~VdIk~~~svqKGmPhk~YHGkTG~V~~v~~~AvgV~Vnk~v~~k~i~KrI~VriEHik~s 99 (164)
.|++||.|.|.-+... .+-..|- |+|..+.... .+.+.+.=+-..|++.+.+.
T Consensus 3 ~y~vgd~V~v~~~~~~---~~~~~~i---~~I~~i~~~~--------~~~~~~~v~wf~rp~e~~~~ 55 (123)
T cd04370 3 TYEVGDSVYVEPDDSI---KSDPPYI---ARIEELWEDT--------NGSKQVKVRWFYRPEETPKG 55 (123)
T ss_pred EEecCCEEEEecCCcC---CCCCCEE---EEEeeeeECC--------CCCEEEEEEEEEchhHhccc
Confidence 6899999999977654 2334443 3343333221 13333444556677777653
No 42
>cd00773 HisRS-like_core Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain. HisRS is a homodimer. It is responsible for the attachment of histidine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs. This domain is also found at the C-terminus of eukaryotic GCN2 protein kinase and at the N-terminus of the ATP phosphoribosyltransferase accessory subunit, HisZ. HisZ along with HisG catalyze the first reaction in histidine biosynthesis. HisZ is found only in a subset of bacteria and differs from HisRS in lacking a C-terminal anti-codon binding domain.
Probab=24.25 E-value=99 Score=25.64 Aligned_cols=47 Identities=19% Similarity=0.345 Sum_probs=31.1
Q ss_pred HHHHHhhCCCCEEEEEecCceeeCccCccccccceeEEeeeccEE---EEEEEeeeCcEe
Q 031165 28 STYLRTYKIGDYVDVKVNGAVHKGMPHKFYHGRTGRVWNVTKRAI---GVEINKQVGNRI 84 (164)
Q Consensus 28 s~~l~~yk~GD~VdIk~~~svqKGmPhk~YHGkTG~V~~v~~~Av---gV~Vnk~v~~k~ 84 (164)
-.+|+.+.. -.+|.+|++...||.+- ||.||.+.-... ..+. -|||+
T Consensus 183 ~~~l~~~~~--~~~i~~d~~~~r~~~YY-----tG~vF~~~~~~~~~~~~i~---~GGRY 232 (261)
T cd00773 183 LDYLEALGV--DIKYSIDLSLVRGLDYY-----TGIVFEAVADGLGAQGSIA---GGGRY 232 (261)
T ss_pred HHHHHHcCC--CceEEEcCccccCCccc-----CceEEEEEECCCCccCeEe---eccCH
Confidence 455665554 24688899999998543 888988864433 3333 48876
No 43
>PF02290 SRP14: Signal recognition particle 14kD protein; InterPro: IPR003210 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [, ]. SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. Eukaryotic SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor []. In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. In archaea, the SRP complex contains 7S RNA like its eukaryotic counterpart, yet only includes two of the six protein subunits found in the eukarytic complex: SRP19 and SRP54 []. This entry represents the 14 kDa SRP14 component. Both SRP9 and SRP14 have the same (beta)-alpha-beta(3)-alpha fold. The heterodimer has pseudo two-fold symmetry and is saddle-like, consisting of a curved six-stranded beta-sheet that has four helices packed on the convex side and an exposed concave surface lined with positively charged residues. The SRP9/SRP14 heterodimer is essential for SRP RNA binding, mediating the pausing of synthesis of ribosome associated nascent polypeptides that have been engaged by the targeting domain of SRP [].; GO: 0008312 7S RNA binding, 0030942 endoplasmic reticulum signal peptide binding, 0006614 SRP-dependent cotranslational protein targeting to membrane, 0005786 signal recognition particle, endoplasmic reticulum targeting; PDB: 1914_A 1RY1_D 1E8O_B 2W9J_B.
Probab=24.05 E-value=42 Score=24.66 Aligned_cols=30 Identities=27% Similarity=0.356 Sum_probs=21.5
Q ss_pred ChHHHHHHHhhcHHHHHHHHHcC--CceecccCCC
Q 031165 101 CTEEFKLRKKKNDELKADAKARG--EVISTKRQPK 133 (164)
Q Consensus 101 ~r~~fl~rvk~nd~~k~eak~~g--~~v~~kr~p~ 133 (164)
++++||..+.+ .=..++++| +|+.+||-+.
T Consensus 2 ~ndeFL~~L~~---lf~~~~~k~gSV~lT~KR~~~ 33 (93)
T PF02290_consen 2 SNDEFLSELTK---LFEKSKEKGGSVYLTQKRLDG 33 (93)
T ss_dssp -HHHHHHHHHH---HHHHCSSSSS-EEEEEEEEEE
T ss_pred CHHHHHHHHHH---HHHHcccCCceEEEEEeecCC
Confidence 47899999854 444566766 7888999873
No 44
>PF11132 SplA: Transcriptional regulator protein (SplA); InterPro: IPR022608 The SplA protein functions in trans as a negative regulator of the level of splB-lacZ expression in the developing forespore [].
Probab=23.81 E-value=63 Score=23.59 Aligned_cols=30 Identities=37% Similarity=0.572 Sum_probs=20.7
Q ss_pred HHhhCCCCEEEEEecCceeeCccCccccccceeEEeeeccEE
Q 031165 31 LRTYKIGDYVDVKVNGAVHKGMPHKFYHGRTGRVWNVTKRAI 72 (164)
Q Consensus 31 l~~yk~GD~VdIk~~~svqKGmPhk~YHGkTG~V~~v~~~Av 72 (164)
|+.|+.||+|-+..-- || |-.|.|++.-++
T Consensus 3 ~~~~~~GD~VyViYrN------PH------t~~VanIqeAei 32 (75)
T PF11132_consen 3 MKPYHAGDIVYVIYRN------PH------TQDVANIQEAEI 32 (75)
T ss_pred ccccCCCCEEEEEEcC------CC------Cccccccchhhe
Confidence 4789999999987643 55 455666665543
No 45
>COG1566 EmrA Multidrug resistance efflux pump [Defense mechanisms]
Probab=23.74 E-value=1e+02 Score=28.02 Aligned_cols=60 Identities=23% Similarity=0.343 Sum_probs=43.1
Q ss_pred HHHHhhCCCCEEEEEecCceeeCccC-ccccccceeEEeeeccEEEEE--EEeeeCcEe-eeeEEeeeec
Q 031165 29 TYLRTYKIGDYVDVKVNGAVHKGMPH-KFYHGRTGRVWNVTKRAIGVE--INKQVGNRI-IKKRIHVRVE 94 (164)
Q Consensus 29 ~~l~~yk~GD~VdIk~~~svqKGmPh-k~YHGkTG~V~~v~~~AvgV~--Vnk~v~~k~-i~KrI~VriE 94 (164)
|=|...++||.|.|.+|. -|. ..|+|+.-.|..-++.+..+. .|- -||=+ +.-|+-|||+
T Consensus 254 TqL~~~r~Gq~a~I~~da-----~~~~~~~~G~v~~i~~~tg~~fsllp~~na-tgN~tkvvQRvPVrI~ 317 (352)
T COG1566 254 TQLARVRPGQPAEITLDA-----YPGNGVVEGIVEGIAPATGSAFSLLPAQNA-TGNWTKVVQRVPVRIE 317 (352)
T ss_pred eecCcccCCCeEEEEEEc-----CCCceEEEEEEEEecCCcccccccCCCccC-CCCEEEEEEeeeEEEE
Confidence 346778999999999987 677 899999888888888877763 232 23322 4567777664
No 46
>CHL00125 psaE photosystem I subunit IV; Reviewed
Probab=23.24 E-value=86 Score=22.24 Aligned_cols=29 Identities=21% Similarity=0.296 Sum_probs=25.3
Q ss_pred hCCCCEEEEEecCceeeCccCccccccceeEEeeecc
Q 031165 34 YKIGDYVDVKVNGAVHKGMPHKFYHGRTGRVWNVTKR 70 (164)
Q Consensus 34 yk~GD~VdIk~~~svqKGmPhk~YHGkTG~V~~v~~~ 70 (164)
.+.||+|-|. .|-.++...+|+|.+|.+.
T Consensus 2 i~rGskVrIl--------R~ESYWyn~vGtV~svd~~ 30 (64)
T CHL00125 2 VKRGSKVRIL--------RKESYWYNEIGTVATVDQS 30 (64)
T ss_pred cccCCEEEEc--------cccceeecCcceEEEEcCC
Confidence 4689999997 6888999999999999886
No 47
>PF14031 D-ser_dehydrat: Putative serine dehydratase domain; PDB: 3LLX_A 3ANV_A 3AWO_A 3AWN_A 3ANU_A 3GWQ_A.
Probab=22.43 E-value=28 Score=25.32 Aligned_cols=31 Identities=26% Similarity=0.357 Sum_probs=18.7
Q ss_pred cCCcccCCCCCChHHHHHhhCCCCEEEEEec
Q 031165 15 FARPFRKKGYIPLSTYLRTYKIGDYVDVKVN 45 (164)
Q Consensus 15 fsk~fR~~G~~~ls~~l~~yk~GD~VdIk~~ 45 (164)
+.+---|||++.+..-...+++||+|.|..+
T Consensus 48 ~~~~seEHg~l~~~~~~~~~~vGd~v~iiP~ 78 (94)
T PF14031_consen 48 VVRLSEEHGILRLPDGADRLKVGDKVEIIPN 78 (94)
T ss_dssp EEEE-SS-EEEE-STTGCGT-TT-EEEEEES
T ss_pred EEeeecceeEEECCCCCCCCCCCCEEEEECC
Confidence 4445668998776655667999999999643
No 48
>PF09926 DUF2158: Uncharacterized small protein (DUF2158); InterPro: IPR019226 This entry represents a family of predominantly prokaryotic proteins with no known function.
Probab=22.02 E-value=58 Score=21.89 Aligned_cols=11 Identities=55% Similarity=0.933 Sum_probs=9.2
Q ss_pred hCCCCEEEEEe
Q 031165 34 YKIGDYVDVKV 44 (164)
Q Consensus 34 yk~GD~VdIk~ 44 (164)
|++||+|-+|-
T Consensus 1 f~~GDvV~LKS 11 (53)
T PF09926_consen 1 FKIGDVVQLKS 11 (53)
T ss_pred CCCCCEEEEcc
Confidence 78999999873
No 49
>PLN02247 indole-3-acetic acid-amido synthetase
Probab=21.56 E-value=62 Score=31.50 Aligned_cols=36 Identities=22% Similarity=0.350 Sum_probs=29.9
Q ss_pred HHhhCCCCEEEEEecCceeeCccCccccccceeEEeeec
Q 031165 31 LRTYKIGDYVDVKVNGAVHKGMPHKFYHGRTGRVWNVTK 69 (164)
Q Consensus 31 l~~yk~GD~VdIk~~~svqKGmPhk~YHGkTG~V~~v~~ 69 (164)
|--|+.||+|-+.+ ++.+.|.=.|-||.+.|.++++
T Consensus 414 LYRYrlGDvv~V~G---F~n~~P~~~Fv~R~~~vlsi~g 449 (606)
T PLN02247 414 LYRYRVGDILMVTG---FYNNAPQFRFVQRRNVVLSIDT 449 (606)
T ss_pred eEEEecCCEEEEee---ecCCCceEEEEecCCceeeccc
Confidence 55689999999864 5889999999999998877654
No 50
>cd04473 S1_RecJ_like S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease. The function of this family is not fully understood. In Escherichia coli, RecJ degrades single-stranded DNA in the 5'-3' direction and participates in homologous recombination and mismatch repair.
Probab=21.52 E-value=34 Score=23.40 Aligned_cols=12 Identities=8% Similarity=0.299 Sum_probs=6.6
Q ss_pred HHhhCCCCEEEE
Q 031165 31 LRTYKIGDYVDV 42 (164)
Q Consensus 31 l~~yk~GD~VdI 42 (164)
++.++.||.+.-
T Consensus 11 ~~~~~~G~~~~g 22 (77)
T cd04473 11 MEDLEVGKLYKG 22 (77)
T ss_pred hhhCCCCCEEEE
Confidence 455666665553
No 51
>cd04714 BAH_BAHCC1 BAH, or Bromo Adjacent Homology domain, as present in mammalian BAHCC1 and similar proteins. BAHCC1 stands for BAH domain and coiled-coil containing 1. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=21.23 E-value=1.4e+02 Score=22.50 Aligned_cols=52 Identities=25% Similarity=0.426 Sum_probs=29.4
Q ss_pred HhhCCCCEEEEEecCceeeCccCccccccceeEEeeeccEEEEEEEeeeCcEeeeeEEeeeeceeecc
Q 031165 32 RTYKIGDYVDVKVNGAVHKGMPHKFYHGRTGRVWNVTKRAIGVEINKQVGNRIIKKRIHVRVEHVQPS 99 (164)
Q Consensus 32 ~~yk~GD~VdIk~~~svqKGmPhk~YHGkTG~V~~v~~~AvgV~Vnk~v~~k~i~KrI~VriEHik~s 99 (164)
++|++||.|.|+..++ |-+-|-|+.-.++.-. .|...+.=+-..|+|.+.+.
T Consensus 2 ~~~~vGD~V~v~~~~~-----~~~pyIgrI~~i~e~~-----------~g~~~~~v~WfyrPeEt~~~ 53 (121)
T cd04714 2 EIIRVGDCVLFKSPGR-----PSLPYVARIESLWEDP-----------EGNMVVRVKWYYRPEETKGG 53 (121)
T ss_pred CEEEcCCEEEEeCCCC-----CCCCEEEEEEEEEEcC-----------CCCEEEEEEEEEcHHHccCc
Confidence 3689999999987653 3445655543333211 12333334556677766543
No 52
>cd04455 S1_NusA S1_NusA: N-utilizing substance A protein (NusA), S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. NusA is a transcription elongation factor containing an N-terminal catalytic domain and three RNA binding domains (RBD's). The RBD's include one S1 domain and two KH domains that form an RNA binding surface. DNA transcription by RNA polymerase (RNAP) includes three phases - initiation, elongation, and termination. During initiation, sigma factors bind RNAP and target RNAP to specific promoters. During elongation, N-utilization substances (NusA, B, E, and G) replace sigma factors and regulate pausing, termination, and antitermination. NusA is cold-shock-inducible.
Probab=21.16 E-value=50 Score=21.95 Aligned_cols=23 Identities=22% Similarity=0.443 Sum_probs=15.8
Q ss_pred CCCChHHHH--HhhCCCCEEEEEec
Q 031165 23 GYIPLSTYL--RTYKIGDYVDVKVN 45 (164)
Q Consensus 23 G~~~ls~~l--~~yk~GD~VdIk~~ 45 (164)
|.+|.+... ..|++||.|++.+.
T Consensus 28 g~lp~~e~~~~~~~~~Gd~v~v~v~ 52 (67)
T cd04455 28 AILPKKEQIPGESYRPGDRIKAYVL 52 (67)
T ss_pred EEeeHHHCCCCCcCCCCCEEEEEEE
Confidence 455655544 46899999888774
No 53
>PF02427 PSI_PsaE: Photosystem I reaction centre subunit IV / PsaE; InterPro: IPR003375 PsaE is a 69 amino acid polypeptide from photosystem I present on the stromal side of the thylakoid membrane. The structure is comprised of a well-defined five-stranded beta-sheet similar to SH3 domains []. This subunit may form complexes with ferredoxin and ferredoxin-oxidoreductase in the photosystem I reaction centre.; GO: 0015979 photosynthesis, 0009522 photosystem I, 0009538 photosystem I reaction center; PDB: 1PSF_A 1PSE_A 2WSF_E 2WSC_E 2O01_E 2WSE_E 1GXI_E 1JB0_E 3PCQ_E 1QP2_A ....
Probab=21.07 E-value=1.5e+02 Score=20.91 Aligned_cols=29 Identities=21% Similarity=0.326 Sum_probs=24.2
Q ss_pred CCCCEEEEEecCceeeCccCccccccceeEEeeeccE
Q 031165 35 KIGDYVDVKVNGAVHKGMPHKFYHGRTGRVWNVTKRA 71 (164)
Q Consensus 35 k~GD~VdIk~~~svqKGmPhk~YHGkTG~V~~v~~~A 71 (164)
+.|++|-|. .|-.++...+|+|.+|.+..
T Consensus 2 ~rgskVrIl--------R~ESYWyn~vGtV~svdqs~ 30 (61)
T PF02427_consen 2 KRGSKVRIL--------RKESYWYNEVGTVASVDQSG 30 (61)
T ss_dssp -TTSEEEE---------SSSSTTTTSEEEEEEETTSS
T ss_pred CCCCEEEEc--------cccceeecccceEEEEccCC
Confidence 578999997 78899999999999998875
No 54
>cd05687 S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 1 of the Escherichia coli and Homo sapiens RPS1 (ec1 and hs1, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=20.92 E-value=52 Score=21.51 Aligned_cols=25 Identities=40% Similarity=0.624 Sum_probs=16.7
Q ss_pred CCCCChHHHH--------HhhCCCCEEEEEecC
Q 031165 22 KGYIPLSTYL--------RTYKIGDYVDVKVNG 46 (164)
Q Consensus 22 ~G~~~ls~~l--------~~yk~GD~VdIk~~~ 46 (164)
.|++|.+... ..|++||.+..++-.
T Consensus 25 ~g~l~~~e~~~~~~~~~~~~~~~Gd~i~~~i~~ 57 (70)
T cd05687 25 EGIIPISEFSDDPIENGEDEVKVGDEVEVYVLR 57 (70)
T ss_pred eEEEEHHHhCccccCCHhHcCCCCCEEEEEEEE
Confidence 4555555443 348999999988644
No 55
>PF01835 A2M_N: MG2 domain; InterPro: IPR002890 The proteinase-binding alpha-macroglobulins (A2M) [] are large glycoproteins found in the plasma of vertebrates, in the hemolymph of some invertebrates and in reptilian and avian egg white. A2M-like proteins are able to inhibit all four classes of proteinases by a 'trapping' mechanism. They have a peptide stretch, called the 'bait region', which contains specific cleavage sites for different proteinases. When a proteinase cleaves the bait region, a conformational change is induced in the protein, thus trapping the proteinase. The entrapped enzyme remains active against low molecular weight substrates, whilst its activity toward larger substrates is greatly reduced, due to steric hindrance. Following cleavage in the bait region, a thiol ester bond, formed between the side chains of a cysteine and a glutamine, is cleaved and mediates the covalent binding of the A2M-like protein to the proteinase. This family includes the N-terminal region of the alpha-2-macroglobulin family. The inhibitor domains belong to MEROPS inhibitor family I39.; GO: 0004866 endopeptidase inhibitor activity; PDB: 2B39_B 3KLS_B 3PRX_C 3KM9_B 3PVM_C 3CU7_A 4E0S_A 4A5W_A 4ACQ_C 2P9R_B ....
Probab=20.76 E-value=61 Score=22.65 Aligned_cols=19 Identities=16% Similarity=0.191 Sum_probs=14.2
Q ss_pred hhCCCCEEEEEecCceeeC
Q 031165 33 TYKIGDYVDVKVNGAVHKG 51 (164)
Q Consensus 33 ~yk~GD~VdIk~~~svqKG 51 (164)
.|++||.|.+++--.-+.+
T Consensus 10 iYrPGetV~~~~~~~~~~~ 28 (99)
T PF01835_consen 10 IYRPGETVHFRAIVRDLDN 28 (99)
T ss_dssp EE-TTSEEEEEEEEEEECT
T ss_pred CcCCCCEEEEEEEEecccc
Confidence 5999999999987555553
No 56
>PRK10334 mechanosensitive channel MscS; Provisional
Probab=20.75 E-value=1.2e+02 Score=26.33 Aligned_cols=30 Identities=30% Similarity=0.605 Sum_probs=23.8
Q ss_pred HHhhCCCCEEEEEecCceeeCccCccccccceeEEeeeccEEEEE
Q 031165 31 LRTYKIGDYVDVKVNGAVHKGMPHKFYHGRTGRVWNVTKRAIGVE 75 (164)
Q Consensus 31 l~~yk~GD~VdIk~~~svqKGmPhk~YHGkTG~V~~v~~~AvgV~ 75 (164)
-+.|++||+|.+. |.+|+|..++=++..+.
T Consensus 127 ~rpf~vGD~I~i~---------------~~~G~V~~I~~r~T~i~ 156 (286)
T PRK10334 127 FRPFRAGEYVDLG---------------GVAGTVLSVQIFSTTMR 156 (286)
T ss_pred cCCCCCCCEEEEC---------------CEEEEEEEEEeEEEEEE
Confidence 4679999999972 56899999888877654
No 57
>PF06940 DUF1287: Domain of unknown function (DUF1287); InterPro: IPR009706 This family consists of several hypothetical bacterial proteins of around 200 residues in length. The function of this family is unknown.
Probab=20.56 E-value=59 Score=26.90 Aligned_cols=19 Identities=37% Similarity=0.842 Sum_probs=16.0
Q ss_pred HhhCCCCEEEEEecCceeeCccC
Q 031165 32 RTYKIGDYVDVKVNGAVHKGMPH 54 (164)
Q Consensus 32 ~~yk~GD~VdIk~~~svqKGmPh 54 (164)
..|..||+|.-...+ |.||
T Consensus 105 ~~~q~GDIVtw~l~~----~~~H 123 (164)
T PF06940_consen 105 EDWQPGDIVTWRLPG----GLPH 123 (164)
T ss_pred hhcCCCCEEEEeCCC----CCCe
Confidence 789999999987665 6887
No 58
>COG3061 OapA Cell envelope opacity-associated protein A [Cell envelope biogenesis, outer membrane]
Probab=20.24 E-value=67 Score=28.04 Aligned_cols=42 Identities=19% Similarity=0.248 Sum_probs=31.7
Q ss_pred CCCCcccccccCCcccCCCCCChH-----------HHHHhhCCCCEEEEEecC
Q 031165 5 HGLRSRTRDLFARPFRKKGYIPLS-----------TYLRTYKIGDYVDVKVNG 46 (164)
Q Consensus 5 ~G~R~~TR~~fsk~fR~~G~~~ls-----------~~l~~yk~GD~VdIk~~~ 46 (164)
+-|+=.+-..|+.-||.|+.+.-. .-|-+|+-||.|-|..|.
T Consensus 160 qsy~V~~G~TLaQlFRdn~LpitDVnAMakveGagkpLSnlkaGq~Vki~~na 212 (242)
T COG3061 160 QSYTVPQGKTLAQLFRDNNLPITDVNAMAKVEGAGKPLSNLKAGQKVKISLNA 212 (242)
T ss_pred eeEEecCCccHHHHHhccCCChHHhHHHHhhccCCCchhhccCCCEEEEEEcC
Confidence 345556667788889999975422 236789999999999987
No 59
>KOG0544 consensus FKBP-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]
Probab=20.07 E-value=96 Score=24.00 Aligned_cols=41 Identities=24% Similarity=0.353 Sum_probs=31.7
Q ss_pred CCCCEEEE----------EecCceeeCccCccccccceeEEeeeccEEEEE
Q 031165 35 KIGDYVDV----------KVNGAVHKGMPHKFYHGRTGRVWNVTKRAIGVE 75 (164)
Q Consensus 35 k~GD~VdI----------k~~~svqKGmPhk~YHGkTG~V~~v~~~AvgV~ 75 (164)
+.||.|.+ |.|+|.+.|-|++|--|+--.|-+...-.....
T Consensus 18 K~Gqtvt~hYtg~L~dG~kfDSs~dr~kPfkf~IGkgeVIkGwdegv~qms 68 (108)
T KOG0544|consen 18 KKGQTVTVHYTGTLQDGKKFDSSRDRGKPFKFKIGKGEVIKGWDEGVAQMS 68 (108)
T ss_pred CCCCEEEEEEEeEecCCcEeecccccCCCeeEEecCcceeechhhcchhcc
Confidence 56777765 678888899999999999888777776655554
Done!