Query 047565
Match_columns 106
No_of_seqs 104 out of 348
Neff 4.0
Searched_HMMs 46136
Date Fri Mar 29 12:17:08 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/047565.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/047565hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN00190 60S ribosomal protein 100.0 4.6E-46 9.9E-51 279.2 9.5 88 1-88 1-88 (158)
2 PTZ00189 60S ribosomal protein 100.0 4.4E-46 9.5E-51 279.7 9.4 88 1-88 1-88 (160)
3 PRK04306 50S ribosomal protein 100.0 2.8E-44 6E-49 252.1 9.1 81 1-83 2-82 (98)
4 PF01157 Ribosomal_L21e: Ribos 100.0 8.2E-44 1.8E-48 249.7 5.9 87 2-88 1-87 (99)
5 COG2139 RPL21A Ribosomal prote 100.0 3.7E-39 8.1E-44 226.2 8.4 83 2-86 1-83 (98)
6 KOG1732 60S ribosomal protein 100.0 1.5E-32 3.2E-37 206.4 3.8 91 1-91 1-91 (160)
7 PRK01191 rpl24p 50S ribosomal 84.4 1.7 3.7E-05 31.7 3.9 58 33-100 45-107 (120)
8 PF09629 YorP: YorP protein; 82.3 1.6 3.4E-05 29.3 2.8 31 33-67 6-36 (71)
9 TIGR01080 rplX_A_E ribosomal p 76.8 6 0.00013 28.5 4.5 54 34-97 42-100 (114)
10 PTZ00194 60S ribosomal protein 74.4 3 6.4E-05 31.4 2.5 56 33-98 46-106 (143)
11 smart00739 KOW KOW (Kyprides, 73.4 7.5 0.00016 19.8 3.3 26 34-69 2-27 (28)
12 CHL00141 rpl24 ribosomal prote 73.0 6.3 0.00014 26.7 3.6 36 33-78 8-43 (83)
13 PF02211 NHase_beta: Nitrile h 70.7 3.3 7.2E-05 32.7 2.1 36 32-68 133-169 (222)
14 PRK12281 rplX 50S ribosomal pr 70.1 7.9 0.00017 25.8 3.6 36 33-78 6-41 (76)
15 PRK00004 rplX 50S ribosomal pr 67.1 9.6 0.00021 26.7 3.7 36 33-78 4-39 (105)
16 TIGR01079 rplX_bact ribosomal 65.1 11 0.00024 26.5 3.7 34 33-76 3-36 (104)
17 PF00924 MS_channel: Mechanose 63.3 5.9 0.00013 28.7 2.1 29 32-75 59-87 (206)
18 PF09953 DUF2187: Uncharacteri 57.5 19 0.0004 23.4 3.4 32 33-78 3-34 (57)
19 KOG3141 Mitochondrial/chloropl 56.1 6.2 0.00014 33.1 1.3 39 6-44 113-173 (310)
20 COG0797 RlpA Lipoproteins [Cel 55.2 17 0.00038 29.3 3.6 47 37-87 102-152 (233)
21 PRK14980 DNA-directed RNA poly 54.6 52 0.0011 24.5 5.8 56 29-95 44-99 (127)
22 PF00970 FAD_binding_6: Oxidor 51.7 16 0.00035 23.5 2.5 19 26-44 74-92 (99)
23 PHA02763 hypothetical protein; 49.0 18 0.00039 25.8 2.5 24 33-64 27-50 (102)
24 PF11261 IRF-2BP1_2: Interfero 46.9 8.8 0.00019 24.7 0.6 8 94-101 6-13 (54)
25 PRK10672 rare lipoprotein A; P 46.6 27 0.00059 29.8 3.7 48 36-87 97-148 (361)
26 TIGR01955 RfaH transcriptional 45.9 51 0.0011 23.3 4.6 49 33-102 108-156 (159)
27 TIGR01843 type_I_hlyD type I s 44.3 35 0.00076 27.1 3.8 39 28-71 318-356 (423)
28 KOG3391 Transcriptional co-rep 42.5 16 0.00034 27.9 1.5 17 31-47 122-138 (151)
29 KOG1384 tRNA delta(2)-isopente 42.4 5.5 0.00012 33.9 -1.1 30 27-56 37-66 (348)
30 TIGR00413 rlpA rare lipoprotei 41.2 36 0.00078 27.1 3.4 48 36-87 17-68 (208)
31 PF14031 D-ser_dehydrat: Putat 39.6 11 0.00023 25.6 0.2 31 15-45 48-78 (94)
32 PF06940 DUF1287: Domain of un 33.9 23 0.00051 27.3 1.3 41 19-69 91-132 (164)
33 cd04370 BAH BAH, or Bromo Adja 33.6 74 0.0016 20.6 3.5 32 32-66 2-33 (123)
34 smart00538 POP4 A domain found 33.2 1.2E+02 0.0026 20.7 4.6 46 53-102 22-67 (92)
35 PF02513 Spin-Ssty: Spin/Ssty 32.1 43 0.00093 21.1 2.0 17 83-99 33-49 (50)
36 COG1588 POP4 RNase P/RNase MRP 31.2 53 0.0011 23.3 2.6 54 36-101 16-69 (95)
37 PRK10334 mechanosensitive chan 30.9 57 0.0012 26.2 3.1 30 31-75 127-156 (286)
38 COG1862 YajC Preprotein transl 30.7 1E+02 0.0022 21.6 4.0 38 27-78 37-74 (97)
39 TIGR00739 yajC preprotein tran 30.7 1.2E+02 0.0026 20.3 4.2 38 27-78 31-68 (84)
40 smart00743 Agenet Tudor-like d 30.6 44 0.00095 20.1 1.9 12 33-44 2-13 (61)
41 PLN02249 indole-3-acetic acid- 30.5 33 0.00072 30.7 1.8 39 31-72 407-445 (597)
42 KOG0544 FKBP-type peptidyl-pro 30.0 53 0.0011 23.8 2.5 44 35-78 18-71 (108)
43 cd04714 BAH_BAHCC1 BAH, or Bro 30.0 90 0.0019 21.8 3.7 30 32-66 2-31 (121)
44 TIGR02768 TraA_Ti Ti-type conj 29.7 1E+02 0.0022 28.1 4.7 41 32-77 606-646 (744)
45 PF10377 ATG11: Autophagy-rela 29.6 33 0.00071 24.7 1.4 32 31-62 40-81 (129)
46 PF03321 GH3: GH3 auxin-respon 29.4 18 0.00039 31.3 0.0 39 31-72 368-406 (528)
47 PF09926 DUF2158: Uncharacteri 28.5 38 0.00083 21.2 1.4 11 34-44 1-11 (53)
48 PRK05609 nusG transcription an 28.5 1.5E+02 0.0033 21.3 4.7 26 33-68 126-151 (181)
49 COG0668 MscS Small-conductance 28.2 52 0.0011 25.0 2.3 30 31-74 145-174 (316)
50 cd04709 BAH_MTA BAH, or Bromo 26.4 1E+02 0.0022 23.2 3.7 27 32-64 2-28 (164)
51 PLN02247 indole-3-acetic acid- 26.3 44 0.00096 30.2 1.9 36 31-69 414-449 (606)
52 PF14468 DUF4427: Protein of u 25.8 38 0.00082 25.4 1.2 18 73-92 58-75 (132)
53 PF01835 A2M_N: MG2 domain; I 25.5 55 0.0012 21.2 1.8 19 33-51 10-28 (99)
54 PRK13712 conjugal transfer pro 25.5 17 0.00037 26.3 -0.7 15 85-99 82-96 (115)
55 KOG1999 RNA polymerase II tran 25.2 1.1E+02 0.0025 29.6 4.4 39 26-74 452-490 (1024)
56 PRK03879 ribonuclease P protei 25.1 1.7E+02 0.0038 20.2 4.3 23 53-75 24-46 (96)
57 cd04455 S1_NusA S1_NusA: N-uti 23.9 44 0.00094 20.6 1.0 23 24-46 29-53 (67)
58 PF10134 RPA: Replication init 23.8 46 0.00099 26.0 1.3 24 31-55 22-45 (229)
59 PF02107 FlgH: Flagellar L-rin 23.7 59 0.0013 24.5 1.9 23 25-47 16-38 (179)
60 PF08755 YccV-like: Hemimethyl 23.2 49 0.0011 22.6 1.3 25 33-70 3-27 (100)
61 PRK02749 photosystem I reactio 23.2 1.8E+02 0.0039 19.7 3.9 30 34-71 3-32 (71)
62 KOG0534 NADH-cytochrome b-5 re 22.8 60 0.0013 26.7 1.9 20 26-45 126-145 (286)
63 COG3061 OapA Cell envelope opa 22.5 61 0.0013 26.5 1.8 41 7-47 162-213 (242)
64 cd04473 S1_RecJ_like S1_RecJ_l 22.5 36 0.00077 21.6 0.4 11 31-41 11-21 (77)
65 PF01197 Ribosomal_L31: Riboso 22.3 29 0.00063 22.6 -0.0 29 36-70 30-58 (69)
66 COG0198 RplX Ribosomal protein 22.2 1.6E+02 0.0035 20.9 3.8 31 33-73 4-34 (104)
67 KOG4225 Sorbin and SH3 domain- 21.9 71 0.0015 28.5 2.3 28 33-64 248-277 (489)
68 TIGR00443 hisZ_biosyn_reg ATP 21.7 77 0.0017 25.2 2.3 54 29-91 239-292 (314)
69 PF01272 GreA_GreB: Transcript 21.6 1.3E+02 0.0027 19.2 2.9 23 25-47 44-66 (77)
70 PRK13889 conjugal transfer rel 21.4 2.2E+02 0.0047 27.4 5.4 41 32-77 599-639 (988)
71 TIGR00405 L26e_arch ribosomal 21.3 1.8E+02 0.004 20.4 4.0 36 32-77 85-122 (145)
72 PF06487 SAP18: Sin3 associate 21.1 67 0.0014 23.2 1.7 13 32-44 108-120 (120)
73 COG3738 Uncharacterized protei 21.1 58 0.0013 25.8 1.4 44 24-77 131-175 (200)
74 PLN02620 indole-3-acetic acid- 21.0 64 0.0014 29.3 1.8 36 31-69 420-455 (612)
75 smart00316 S1 Ribosomal protei 20.9 93 0.002 17.7 2.0 23 61-83 7-29 (72)
76 TIGR00717 rpsA ribosomal prote 20.9 1.4E+02 0.0031 25.1 3.8 22 61-82 364-385 (516)
77 PRK06299 rpsA 30S ribosomal pr 20.6 1.3E+02 0.0029 25.8 3.6 40 26-85 363-402 (565)
78 PRK09812 toxin ChpB; Provision 20.5 83 0.0018 22.0 2.0 16 33-48 6-21 (116)
79 PF15591 Imm17: Immunity prote 20.3 1.8E+02 0.004 19.8 3.5 36 56-97 22-57 (74)
80 cd05699 S1_Rrp5_repeat_hs7 S1_ 20.3 1E+02 0.0022 20.6 2.3 25 61-85 5-30 (72)
No 1
>PLN00190 60S ribosomal protein L21; Provisional
Probab=100.00 E-value=4.6e-46 Score=279.18 Aligned_cols=88 Identities=82% Similarity=1.332 Sum_probs=86.4
Q ss_pred CCCCCCCCcccccccCCcccCCCCCchHHHHHhccCCCEEEEEEcCceecCCCCCcccCcceEEEcccCCEEEEEEecee
Q 047565 1 MPAGHGLRSRTRDLFARPFRKKGYIPLSTYLRTYKIGDYVDVKVNGAVHKGMPHKFYHGRTGRVWNVTKRAIGVEINKQV 80 (106)
Q Consensus 1 M~~S~G~R~~TR~~fsk~fR~~G~~~ls~~l~~yk~GD~VdIkid~svqKGMPHk~YHGkTG~V~~v~~~AvgV~VnK~V 80 (106)
|++|+|+|++||+||||+||+||++|||+||++|++||+|||++|||+||||||++|||+||+|||++++||||+|||+|
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 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred Cceeceee
Q 047565 81 KFFMPFLF 88 (106)
Q Consensus 81 ~gk~~~~~ 88 (106)
+|||+++-
T Consensus 81 ggr~~~Kr 88 (158)
T PLN00190 81 GNRIIRKR 88 (158)
T ss_pred CCeEeeEE
Confidence 99998873
No 2
>PTZ00189 60S ribosomal protein L21; Provisional
Probab=100.00 E-value=4.4e-46 Score=279.74 Aligned_cols=88 Identities=59% Similarity=0.935 Sum_probs=86.6
Q ss_pred CCCCCCCCcccccccCCcccCCCCCchHHHHHhccCCCEEEEEEcCceecCCCCCcccCcceEEEcccCCEEEEEEecee
Q 047565 1 MPAGHGLRSRTRDLFARPFRKKGYIPLSTYLRTYKIGDYVDVKVNGAVHKGMPHKFYHGRTGRVWNVTKRAIGVEINKQV 80 (106)
Q Consensus 1 M~~S~G~R~~TR~~fsk~fR~~G~~~ls~~l~~yk~GD~VdIkid~svqKGMPHk~YHGkTG~V~~v~~~AvgV~VnK~V 80 (106)
|++|+|+|++||+||||+||+||++|||+||++|++||+|||++|||+||||||++|||+||+|||++++||||+|||+|
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 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred Cceeceee
Q 047565 81 KFFMPFLF 88 (106)
Q Consensus 81 ~gk~~~~~ 88 (106)
+||||++-
T Consensus 81 g~ki~~Kr 88 (160)
T PTZ00189 81 RGRIVRKR 88 (160)
T ss_pred CCEEeeeE
Confidence 99999873
No 3
>PRK04306 50S ribosomal protein L21e; Reviewed
Probab=100.00 E-value=2.8e-44 Score=252.06 Aligned_cols=81 Identities=40% Similarity=0.621 Sum_probs=79.7
Q ss_pred CCCCCCCCcccccccCCcccCCCCCchHHHHHhccCCCEEEEEEcCceecCCCCCcccCcceEEEcccCCEEEEEEecee
Q 047565 1 MPAGHGLRSRTRDLFARPFRKKGYIPLSTYLRTYKIGDYVDVKVNGAVHKGMPHKFYHGRTGRVWNVTKRAIGVEINKQV 80 (106)
Q Consensus 1 M~~S~G~R~~TR~~fsk~fR~~G~~~ls~~l~~yk~GD~VdIkid~svqKGMPHk~YHGkTG~V~~v~~~AvgV~VnK~V 80 (106)
|++|+|+|++||++|||+||++|++|||+||++|++||+|||++|||+||||||++|||+||+|+|++++||+|+| +|
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 7899999999999999999999999999999999999999999999999999999999999999999999999999 78
Q ss_pred Cce
Q 047565 81 KFF 83 (106)
Q Consensus 81 ~gk 83 (106)
+||
T Consensus 80 g~k 82 (98)
T PRK04306 80 GGK 82 (98)
T ss_pred CCc
Confidence 898
No 4
>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=8.2e-44 Score=249.74 Aligned_cols=87 Identities=59% Similarity=0.891 Sum_probs=68.4
Q ss_pred CCCCCCCcccccccCCcccCCCCCchHHHHHhccCCCEEEEEEcCceecCCCCCcccCcceEEEcccCCEEEEEEeceeC
Q 047565 2 PAGHGLRSRTRDLFARPFRKKGYIPLSTYLRTYKIGDYVDVKVNGAVHKGMPHKFYHGRTGRVWNVTKRAIGVEINKQVK 81 (106)
Q Consensus 2 ~~S~G~R~~TR~~fsk~fR~~G~~~ls~~l~~yk~GD~VdIkid~svqKGMPHk~YHGkTG~V~~v~~~AvgV~VnK~V~ 81 (106)
++|+|+|++||++|||+||++|++||++||++|++||+|||++|||+||||||++|||+||+|+||+++|+|++++++|+
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 ceeceee
Q 047565 82 FFMPFLF 88 (106)
Q Consensus 82 gk~~~~~ 88 (106)
++++++-
T Consensus 81 ~~~~~K~ 87 (99)
T PF01157_consen 81 DRIKEKR 87 (99)
T ss_dssp SSCEEEE
T ss_pred CCcccEE
Confidence 9998873
No 5
>COG2139 RPL21A Ribosomal protein L21E [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=3.7e-39 Score=226.24 Aligned_cols=83 Identities=42% Similarity=0.648 Sum_probs=79.1
Q ss_pred CCCCCCCcccccccCCcccCCCCCchHHHHHhccCCCEEEEEEcCceecCCCCCcccCcceEEEcccCCEEEEEEeceeC
Q 047565 2 PAGHGLRSRTRDLFARPFRKKGYIPLSTYLRTYKIGDYVDVKVNGAVHKGMPHKFYHGRTGRVWNVTKRAIGVEINKQVK 81 (106)
Q Consensus 2 ~~S~G~R~~TR~~fsk~fR~~G~~~ls~~l~~yk~GD~VdIkid~svqKGMPHk~YHGkTG~V~~v~~~AvgV~VnK~V~ 81 (106)
++|+|||++||++|+|++||+|.+|+++||++|++||+|+|+||||+||||||++|||+||+|+|++|+||.|+|+ ++
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 4799999999999999999999999999999999999999999999999999999999999999999999999999 66
Q ss_pred ceece
Q 047565 82 FFMPF 86 (106)
Q Consensus 82 gk~~~ 86 (106)
|+.=.
T Consensus 79 ~k~K~ 83 (98)
T COG2139 79 NKEKT 83 (98)
T ss_pred CceEE
Confidence 77433
No 6
>KOG1732 consensus 60S ribosomal protein L21 [Translation, ribosomal structure and biogenesis]
Probab=99.97 E-value=1.5e-32 Score=206.45 Aligned_cols=91 Identities=56% Similarity=0.879 Sum_probs=88.5
Q ss_pred CCCCCCCCcccccccCCcccCCCCCchHHHHHhccCCCEEEEEEcCceecCCCCCcccCcceEEEcccCCEEEEEEecee
Q 047565 1 MPAGHGLRSRTRDLFARPFRKKGYIPLSTYLRTYKIGDYVDVKVNGAVHKGMPHKFYHGRTGRVWNVTKRAIGVEINKQV 80 (106)
Q Consensus 1 M~~S~G~R~~TR~~fsk~fR~~G~~~ls~~l~~yk~GD~VdIkid~svqKGMPHk~YHGkTG~V~~v~~~AvgV~VnK~V 80 (106)
|++++|+|++||++|+++||+||..|+++||+.|++||+|||+++++.||||||++|||+||+|++++++|+||++||||
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 Cceeceeecce
Q 047565 81 KFFMPFLFDSF 91 (106)
Q Consensus 81 ~gk~~~~~~~~ 91 (106)
+||||++-+.-
T Consensus 81 kgKil~KRinV 91 (160)
T KOG1732|consen 81 KGKILAKRINV 91 (160)
T ss_pred ccceeeeeeee
Confidence 99999986543
No 7
>PRK01191 rpl24p 50S ribosomal protein L24P; Validated
Probab=84.39 E-value=1.7 Score=31.74 Aligned_cols=58 Identities=16% Similarity=0.114 Sum_probs=37.8
Q ss_pred hccCCCEEEEEEcCceecCCCCCcccCcceEEEcccCCEEEEEEec-----eeCceeceeecceeeEEeeecC
Q 047565 33 TYKIGDYVDVKVNGAVHKGMPHKFYHGRTGRVWNVTKRAIGVEINK-----QVKFFMPFLFDSFRCIYLCELP 100 (106)
Q Consensus 33 ~yk~GD~VdIkid~svqKGMPHk~YHGkTG~V~~v~~~AvgV~VnK-----~V~gk~~~~~~~~~~~~~~~~~ 100 (106)
..+.||.|-|.--+ |-|++|+|..|...--.|.|.. .-+....+-|+.-.+.+.|-.-
T Consensus 45 ~IkkGD~V~VisG~----------~KGk~GkV~~V~~~~~~V~VeGvn~~k~~G~~~e~pIh~SNV~l~~l~l 107 (120)
T PRK01191 45 PVRKGDTVKVMRGD----------FKGEEGKVVEVDLKRGRIYVEGVTVKKADGTEVPRPIHPSNVMITKLDL 107 (120)
T ss_pred eEeCCCEEEEeecC----------CCCceEEEEEEEcCCCEEEEeCcEEECCCCeEEEcccchhHeEEEeCcc
Confidence 36789999987654 6699999999976654444432 2234555666666666665433
No 8
>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=82.33 E-value=1.6 Score=29.29 Aligned_cols=31 Identities=32% Similarity=0.639 Sum_probs=19.4
Q ss_pred hccCCCEEEEEEcCceecCCCCCcccCcceEEEcc
Q 047565 33 TYKIGDYVDVKVNGAVHKGMPHKFYHGRTGRVWNV 67 (106)
Q Consensus 33 ~yk~GD~VdIkid~svqKGMPHk~YHGkTG~V~~v 67 (106)
.|..||.|.| |....-|||| +-|+-|+|...
T Consensus 6 sY~~~~~VeI--N~NAkyg~P~--~VG~kG~IIe~ 36 (71)
T PF09629_consen 6 SYPLGLEVEI--NSNAKYGCPH--HVGRKGKIIEK 36 (71)
T ss_dssp -S-TT-EEEE---TT-TTTSTT----SSEEEEEEE
T ss_pred ccCCCCEEEE--cCcccccCcc--ccccccchhhh
Confidence 5889999988 7888899999 45877766543
No 9
>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=76.78 E-value=6 Score=28.51 Aligned_cols=54 Identities=15% Similarity=0.220 Sum_probs=34.4
Q ss_pred ccCCCEEEEEEcCceecCCCCCcccCcceEEEcccCCEEEEEEecee-----CceeceeecceeeEEee
Q 047565 34 YKIGDYVDVKVNGAVHKGMPHKFYHGRTGRVWNVTKRAIGVEINKQV-----KFFMPFLFDSFRCIYLC 97 (106)
Q Consensus 34 yk~GD~VdIkid~svqKGMPHk~YHGkTG~V~~v~~~AvgV~VnK~V-----~gk~~~~~~~~~~~~~~ 97 (106)
.+.||.|-|..-. |.|++|.|..|...-..|.|...- +.-..+-|+.-.....|
T Consensus 42 IkkGD~V~Vi~Gk----------~KGk~GkV~~V~~~~~~V~Vegvn~~k~~G~~~e~pIh~SnV~l~~ 100 (114)
T TIGR01080 42 VRKGDKVRIMRGD----------FKGHEGKVSKVDLKRYRIYVEGVTKEKVNGTEVPVPIHPSNVMITK 100 (114)
T ss_pred eecCCEEEEecCC----------CCCCEEEEEEEEcCCCEEEEcCeEEECCCCeEEEeeechHHeEEEe
Confidence 3579999885443 679999999998776666665531 11344456554444444
No 10
>PTZ00194 60S ribosomal protein L26; Provisional
Probab=74.40 E-value=3 Score=31.40 Aligned_cols=56 Identities=20% Similarity=0.090 Sum_probs=38.0
Q ss_pred hccCCCEEEEEEcCceecCCCCCcccCcceEEEcccCCEEEEEEe-----ceeCceeceeecceeeEEeee
Q 047565 33 TYKIGDYVDVKVNGAVHKGMPHKFYHGRTGRVWNVTKRAIGVEIN-----KQVKFFMPFLFDSFRCIYLCE 98 (106)
Q Consensus 33 ~yk~GD~VdIkid~svqKGMPHk~YHGkTG~V~~v~~~AvgV~Vn-----K~V~gk~~~~~~~~~~~~~~~ 98 (106)
..+.||.|-|.--. |-|++|.|..|.....-|.|. |.-+--..+-|+.-.+...|.
T Consensus 46 ~IkkGD~V~Vi~Gk----------~KGk~GkV~~V~~k~~~ViVEgvn~~Kk~gk~~e~PIh~SNV~iv~l 106 (143)
T PTZ00194 46 PVRKDDEVMVVRGH----------HKGREGKVTAVYRKKWVIHIEKITREKANGEPVQIGIHPSNVIITKL 106 (143)
T ss_pred eeecCCEEEEecCC----------CCCCceEEEEEEcCCCEEEEeCeEEEecCCCEeecCcCchheEEEcc
Confidence 36789999885432 569999999997766555542 233334567777777777773
No 11
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=73.43 E-value=7.5 Score=19.83 Aligned_cols=26 Identities=31% Similarity=0.671 Sum_probs=18.4
Q ss_pred ccCCCEEEEEEcCceecCCCCCcccCcceEEEcccC
Q 047565 34 YKIGDYVDVKVNGAVHKGMPHKFYHGRTGRVWNVTK 69 (106)
Q Consensus 34 yk~GD~VdIkid~svqKGMPHk~YHGkTG~V~~v~~ 69 (106)
+++||.|-|.-.+ |.|++|.|..+.+
T Consensus 2 ~~~G~~V~I~~G~----------~~g~~g~i~~i~~ 27 (28)
T smart00739 2 FEVGDTVRVIAGP----------FKGKVGKVLEVDG 27 (28)
T ss_pred CCCCCEEEEeECC----------CCCcEEEEEEEcC
Confidence 6789999996532 5566887776654
No 12
>CHL00141 rpl24 ribosomal protein L24; Validated
Probab=73.00 E-value=6.3 Score=26.69 Aligned_cols=36 Identities=28% Similarity=0.427 Sum_probs=27.6
Q ss_pred hccCCCEEEEEEcCceecCCCCCcccCcceEEEcccCCEEEEEEec
Q 047565 33 TYKIGDYVDVKVNGAVHKGMPHKFYHGRTGRVWNVTKRAIGVEINK 78 (106)
Q Consensus 33 ~yk~GD~VdIkid~svqKGMPHk~YHGkTG~V~~v~~~AvgV~VnK 78 (106)
..+.||.|-|.--+ +.|++|+|..|......|.|..
T Consensus 8 ~I~~GD~V~Vi~G~----------dKGK~G~V~~V~~~~~~V~Veg 43 (83)
T CHL00141 8 HVKIGDTVKIISGS----------DKGKIGEVLKIIKKSNKVIVKG 43 (83)
T ss_pred cccCCCEEEEeEcC----------CCCcEEEEEEEEcCCCEEEEcC
Confidence 56889999986532 6799999999987766666543
No 13
>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=70.72 E-value=3.3 Score=32.72 Aligned_cols=36 Identities=28% Similarity=0.559 Sum_probs=17.6
Q ss_pred HhccCCCEEEEEEcCce-ecCCCCCcccCcceEEEccc
Q 047565 32 RTYKIGDYVDVKVNGAV-HKGMPHKFYHGRTGRVWNVT 68 (106)
Q Consensus 32 ~~yk~GD~VdIkid~sv-qKGMPHk~YHGkTG~V~~v~ 68 (106)
-.|++||.|.|+-.+.. |--+| .+=.||||+|.-+.
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 46999999999755443 33344 35579999988443
No 14
>PRK12281 rplX 50S ribosomal protein L24; Reviewed
Probab=70.14 E-value=7.9 Score=25.83 Aligned_cols=36 Identities=31% Similarity=0.389 Sum_probs=27.0
Q ss_pred hccCCCEEEEEEcCceecCCCCCcccCcceEEEcccCCEEEEEEec
Q 047565 33 TYKIGDYVDVKVNGAVHKGMPHKFYHGRTGRVWNVTKRAIGVEINK 78 (106)
Q Consensus 33 ~yk~GD~VdIkid~svqKGMPHk~YHGkTG~V~~v~~~AvgV~VnK 78 (106)
.++.||.|-|.--+ +-|++|+|..+....-.|.|..
T Consensus 6 ~I~kGD~V~Vi~G~----------dKGK~G~V~~V~~~~~~V~Veg 41 (76)
T PRK12281 6 KVKKGDMVKVIAGD----------DKGKTGKVLAVLPKKNRVIVEG 41 (76)
T ss_pred cccCCCEEEEeEcC----------CCCcEEEEEEEEcCCCEEEEcC
Confidence 57899999886432 6799999999976665555543
No 15
>PRK00004 rplX 50S ribosomal protein L24; Reviewed
Probab=67.14 E-value=9.6 Score=26.70 Aligned_cols=36 Identities=28% Similarity=0.311 Sum_probs=27.7
Q ss_pred hccCCCEEEEEEcCceecCCCCCcccCcceEEEcccCCEEEEEEec
Q 047565 33 TYKIGDYVDVKVNGAVHKGMPHKFYHGRTGRVWNVTKRAIGVEINK 78 (106)
Q Consensus 33 ~yk~GD~VdIkid~svqKGMPHk~YHGkTG~V~~v~~~AvgV~VnK 78 (106)
.++.||.|-|.--+ +-|++|+|..+......|.|..
T Consensus 4 ~i~kGD~V~Vi~G~----------dKGk~G~V~~V~~~~~~V~Veg 39 (105)
T PRK00004 4 KIKKGDTVIVIAGK----------DKGKRGKVLKVLPKKNKVIVEG 39 (105)
T ss_pred cccCCCEEEEeEcC----------CCCcEEEEEEEEcCCCEEEEcC
Confidence 46899999885432 5799999999987777776644
No 16
>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=65.06 E-value=11 Score=26.48 Aligned_cols=34 Identities=29% Similarity=0.372 Sum_probs=25.9
Q ss_pred hccCCCEEEEEEcCceecCCCCCcccCcceEEEcccCCEEEEEE
Q 047565 33 TYKIGDYVDVKVNGAVHKGMPHKFYHGRTGRVWNVTKRAIGVEI 76 (106)
Q Consensus 33 ~yk~GD~VdIkid~svqKGMPHk~YHGkTG~V~~v~~~AvgV~V 76 (106)
.++.||.|-|.--+ +-|++|+|..+....-.|.|
T Consensus 3 ~ikkGD~V~Vi~G~----------dKGK~G~V~~V~~~~~~V~V 36 (104)
T TIGR01079 3 KIKKGDTVKVISGK----------DKGKRGKVLKVLPKTNKVIV 36 (104)
T ss_pred cccCCCEEEEeEcC----------CCCcEEEEEEEEcCCCEEEE
Confidence 46889999886533 67999999999776555555
No 17
>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=63.32 E-value=5.9 Score=28.74 Aligned_cols=29 Identities=31% Similarity=0.640 Sum_probs=20.8
Q ss_pred HhccCCCEEEEEEcCceecCCCCCcccCcceEEEcccCCEEEEE
Q 047565 32 RTYKIGDYVDVKVNGAVHKGMPHKFYHGRTGRVWNVTKRAIGVE 75 (106)
Q Consensus 32 ~~yk~GD~VdIkid~svqKGMPHk~YHGkTG~V~~v~~~AvgV~ 75 (106)
+.|++||+|.|. |-+|+|..++=++..+.
T Consensus 59 ~pf~vGD~I~i~---------------~~~G~V~~I~l~~t~l~ 87 (206)
T PF00924_consen 59 RPFKVGDRIEIG---------------GVEGRVEEIGLRSTRLR 87 (206)
T ss_dssp -SS-TT-EEESS---------------S-EEEEEEE-SSEEEEE
T ss_pred CCccCCCEEEEE---------------EeehHHHhcCcceeeee
Confidence 579999998885 89999999999997764
No 18
>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=57.52 E-value=19 Score=23.39 Aligned_cols=32 Identities=31% Similarity=0.448 Sum_probs=25.5
Q ss_pred hccCCCEEEEEEcCceecCCCCCcccCcceEEEcccCCEEEEEEec
Q 047565 33 TYKIGDYVDVKVNGAVHKGMPHKFYHGRTGRVWNVTKRAIGVEINK 78 (106)
Q Consensus 33 ~yk~GD~VdIkid~svqKGMPHk~YHGkTG~V~~v~~~AvgV~VnK 78 (106)
.-++||.+.. + +|-||+|..+...++.|.+..
T Consensus 3 ~a~vGdiIef------k--------~g~~G~V~kv~eNSVIVdIT~ 34 (57)
T PF09953_consen 3 KAKVGDIIEF------K--------DGFTGIVEKVYENSVIVDITI 34 (57)
T ss_pred ccccCcEEEE------c--------CCcEEEEEEEecCcEEEEEEe
Confidence 4478998865 2 367999999999999999865
No 19
>KOG3141 consensus Mitochondrial/chloroplast ribosomal protein L3 [Translation, ribosomal structure and biogenesis]
Probab=56.14 E-value=6.2 Score=33.09 Aligned_cols=39 Identities=31% Similarity=0.549 Sum_probs=26.4
Q ss_pred CCCcccccccCCc----ccCCCCCchH------------------HHHHhccCCCEEEEEE
Q 047565 6 GLRSRTRDLFARP----FRKKGYIPLS------------------TYLRTYKIGDYVDVKV 44 (106)
Q Consensus 6 G~R~~TR~~fsk~----fR~~G~~~ls------------------~~l~~yk~GD~VdIki 44 (106)
|++...+.+++|. ||++|++|-. -+-.-|++|||||+.+
T Consensus 113 G~g~~~p~kltk~~~g~f~~~gv~pK~~l~eF~Vt~~al~~pGt~l~~~hFk~GqyVDV~g 173 (310)
T KOG3141|consen 113 GYGTVKPKKLTKAELGHFRSAGVPPKRHLREFRVTEEALLPPGTPLFARHFKPGQYVDVTG 173 (310)
T ss_pred ccccCChHHhhHHHHHHHHHcCCChhhhhheEeechhccCCCCcccchhhcCCCceEEEEe
Confidence 6666677777765 7777765421 1234578899999865
No 20
>COG0797 RlpA Lipoproteins [Cell envelope biogenesis, outer membrane]
Probab=55.18 E-value=17 Score=29.32 Aligned_cols=47 Identities=34% Similarity=0.381 Sum_probs=37.1
Q ss_pred CCEEEEEEcCceecCCCCCcccCcceEEEcc-cCCEEEEEEece---eCceecee
Q 047565 37 GDYVDVKVNGAVHKGMPHKFYHGRTGRVWNV-TKRAIGVEINKQ---VKFFMPFL 87 (106)
Q Consensus 37 GD~VdIkid~svqKGMPHk~YHGkTG~V~~v-~~~AvgV~VnK~---V~gk~~~~ 87 (106)
||.-|-.-..+-|+-+|...| =+|+|. +++++.|.||++ ++||||.+
T Consensus 102 Ge~~n~~~~tAAH~TLP~~t~----v~VtNl~NgrsvvVRINDRGPf~~gRiIDl 152 (233)
T COG0797 102 GERYDMNALTAAHKTLPLPTY----VRVTNLDNGRSVVVRINDRGPFVSGRIIDL 152 (233)
T ss_pred cccccccccccccccCCCCCE----EEEEEccCCcEEEEEEeCCCCCCCCcEeEc
Confidence 777777778888898988766 467776 578999999998 67777754
No 21
>PRK14980 DNA-directed RNA polymerase subunit G; Provisional
Probab=54.63 E-value=52 Score=24.49 Aligned_cols=56 Identities=5% Similarity=0.010 Sum_probs=37.0
Q ss_pred HHHHhccCCCEEEEEEcCceecCCCCCcccCcceEEEcccCCEEEEEEeceeCceeceeecceeeEE
Q 047565 29 TYLRTYKIGDYVDVKVNGAVHKGMPHKFYHGRTGRVWNVTKRAIGVEINKQVKFFMPFLFDSFRCIY 95 (106)
Q Consensus 29 ~~l~~yk~GD~VdIkid~svqKGMPHk~YHGkTG~V~~v~~~AvgV~VnK~V~gk~~~~~~~~~~~~ 95 (106)
.-|-.|++||.|.|.+--...+ --+..|.|+ .|.|...++-+|++...|--|--+.
T Consensus 44 ~~L~~fsege~v~iiIS~ekP~-~~~~dFCgh----------GyvV~~~k~~~~~y~~iISl~GlLv 99 (127)
T PRK14980 44 DSINIFSQKEKVKAIISKERPS-YTNDDFCAH----------GYIVTESSNNGNRYTTIISLFGLLV 99 (127)
T ss_pred hhhheecCCCcEEEEEeccCcc-cccceeecC----------cEEEEEEecCCCeEEEEEEeeeEEE
Confidence 4477899999999998777666 455777775 4444555556666665555444433
No 22
>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=51.70 E-value=16 Score=23.46 Aligned_cols=19 Identities=37% Similarity=0.581 Sum_probs=17.1
Q ss_pred chHHHHHhccCCCEEEEEE
Q 047565 26 PLSTYLRTYKIGDYVDVKV 44 (106)
Q Consensus 26 ~ls~~l~~yk~GD~VdIki 44 (106)
..|.+|...++||.|.|.+
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 5789999999999999975
No 23
>PHA02763 hypothetical protein; Provisional
Probab=48.96 E-value=18 Score=25.79 Aligned_cols=24 Identities=38% Similarity=0.439 Sum_probs=19.4
Q ss_pred hccCCCEEEEEEcCceecCCCCCcccCcceEE
Q 047565 33 TYKIGDYVDVKVNGAVHKGMPHKFYHGRTGRV 64 (106)
Q Consensus 33 ~yk~GD~VdIkid~svqKGMPHk~YHGkTG~V 64 (106)
.||+|++|.+++ -|++|+||.=.+
T Consensus 27 ~YK~gqkv~l~v--------~dr~f~gKvIa~ 50 (102)
T PHA02763 27 FYKIGQKVILKV--------GDKRFPGKVIAK 50 (102)
T ss_pred hhccCcEEEEEe--------cCccccceEEEe
Confidence 699999999998 478899885443
No 24
>PF11261 IRF-2BP1_2: Interferon regulatory factor 2-binding protein zinc finger; InterPro: IPR022750 IRF-2BP1 and IRF-2BP2 are nuclear transcriptional repressor proteins and can inhibit both enhancer-activated and basal transcription. They both contain N-terminal zinc finger and C-terminal RING finger domains []. This entry represents the N-terminal zinc finger domain of IRF-2BP1 and IRF-2BP2.
Probab=46.91 E-value=8.8 Score=24.75 Aligned_cols=8 Identities=63% Similarity=1.506 Sum_probs=6.7
Q ss_pred EEeeecCc
Q 047565 94 IYLCELPD 101 (106)
Q Consensus 94 ~~~~~~~~ 101 (106)
-||||||.
T Consensus 6 CyLCdlPr 13 (54)
T PF11261_consen 6 CYLCDLPR 13 (54)
T ss_pred EEeccCCC
Confidence 39999995
No 25
>PRK10672 rare lipoprotein A; Provisional
Probab=46.58 E-value=27 Score=29.82 Aligned_cols=48 Identities=31% Similarity=0.259 Sum_probs=37.0
Q ss_pred CCCEEEEEEcCceecCCCCCcccCcceEEEcc-cCCEEEEEEece---eCceecee
Q 047565 36 IGDYVDVKVNGAVHKGMPHKFYHGRTGRVWNV-TKRAIGVEINKQ---VKFFMPFL 87 (106)
Q Consensus 36 ~GD~VdIkid~svqKGMPHk~YHGkTG~V~~v-~~~AvgV~VnK~---V~gk~~~~ 87 (106)
.|+..|-.-..+-|+-.|...|- +|.|. +|+.+.|.||++ +.||+|.+
T Consensus 97 ~Ge~~~~~~~tAAH~tLPlps~v----rVtNl~ngrsvvVrVnDRGP~~~gRiiDL 148 (361)
T PRK10672 97 SGERFDPNALTAAHPTLPIPSYV----RVTNLANGRMIVVRINDRGPYGPGRVIDL 148 (361)
T ss_pred CceeecCCcCeeeccCCCCCCEE----EEEECCCCcEEEEEEeCCCCCCCCCeeEc
Confidence 47888888888888888887663 56665 688999999998 45777654
No 26
>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=45.94 E-value=51 Score=23.31 Aligned_cols=49 Identities=12% Similarity=0.084 Sum_probs=31.9
Q ss_pred hccCCCEEEEEEcCceecCCCCCcccCcceEEEcccCCEEEEEEeceeCceeceeecceeeEEeeecCch
Q 047565 33 TYKIGDYVDVKVNGAVHKGMPHKFYHGRTGRVWNVTKRAIGVEINKQVKFFMPFLFDSFRCIYLCELPDD 102 (106)
Q Consensus 33 ~yk~GD~VdIkid~svqKGMPHk~YHGkTG~V~~v~~~AvgV~VnK~V~gk~~~~~~~~~~~~~~~~~~~ 102 (106)
.|++||.|.|.--| |.|-.|.|..+.+ ++|..-.+|.|-+.-..+++.+
T Consensus 108 ~~~~G~~V~V~~GP----------f~g~~g~v~~~~~-----------~~r~~v~l~~~gr~~~v~~~~~ 156 (159)
T TIGR01955 108 LPYKGDKVRITDGA----------FAGFEAIFLEPDG-----------EKRSMLLLNMIGKQIKVSVPNT 156 (159)
T ss_pred CCCCCCEEEEeccC----------CCCcEEEEEEECC-----------CceEEEEEhhhCCceEEEecHH
Confidence 47889998875433 5666666554332 2456667777877777777654
No 27
>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=44.26 E-value=35 Score=27.09 Aligned_cols=39 Identities=15% Similarity=0.309 Sum_probs=31.1
Q ss_pred HHHHHhccCCCEEEEEEcCceecCCCCCcccCcceEEEcccCCE
Q 047565 28 STYLRTYKIGDYVDVKVNGAVHKGMPHKFYHGRTGRVWNVTKRA 71 (106)
Q Consensus 28 s~~l~~yk~GD~VdIkid~svqKGMPHk~YHGkTG~V~~v~~~A 71 (106)
...+...++|+.|.|.+++ -|...|..-+|+|..+.+.+
T Consensus 318 ~~~~~~i~~G~~v~v~~~~-----~~~~~~~~~~g~V~~i~~~~ 356 (423)
T TIGR01843 318 PKDIGFVHVGQPAEIKFSA-----FPYRRYGILNGKVKSISPDT 356 (423)
T ss_pred hhhhhhhCCCCceEEEEec-----CCCcccCCccEEEEEECCCc
Confidence 4667788899999998874 57888877788899888765
No 28
>KOG3391 consensus Transcriptional co-repressor component [Transcription]
Probab=42.53 E-value=16 Score=27.91 Aligned_cols=17 Identities=35% Similarity=0.774 Sum_probs=14.1
Q ss_pred HHhccCCCEEEEEEcCc
Q 047565 31 LRTYKIGDYVDVKVNGA 47 (106)
Q Consensus 31 l~~yk~GD~VdIkid~s 47 (106)
=+.|++||++||-|-|-
T Consensus 122 ~~kf~iGD~lDVaI~~p 138 (151)
T KOG3391|consen 122 QTKFEIGDYLDVAITPP 138 (151)
T ss_pred hCCccccceEEEEecCc
Confidence 35799999999999764
No 29
>KOG1384 consensus tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]
Probab=42.38 E-value=5.5 Score=33.90 Aligned_cols=30 Identities=33% Similarity=0.414 Sum_probs=27.1
Q ss_pred hHHHHHhccCCCEEEEEEcCceecCCCCCc
Q 047565 27 LSTYLRTYKIGDYVDVKVNGAVHKGMPHKF 56 (106)
Q Consensus 27 ls~~l~~yk~GD~VdIkid~svqKGMPHk~ 56 (106)
-+.-||.|+-=|+|.-++-+..++||||+-
T Consensus 37 NsDkmQvYkGldivTnK~t~~e~~gVPHHL 66 (348)
T KOG1384|consen 37 NSDKMQVYKGLDIVTNKITLQERKGVPHHL 66 (348)
T ss_pred cccceeeecCcccccccCChhhcCCCChHH
Confidence 367799999999999999999999999973
No 30
>TIGR00413 rlpA rare lipoprotein A. This is a family of prokaryotic proteins with unknown function. Lipoprotein annotation based on the presence of consensus lipoprotein signal sequence. Included in this family is the E. coli putative lipoprotein rlpA.
Probab=41.25 E-value=36 Score=27.10 Aligned_cols=48 Identities=29% Similarity=0.349 Sum_probs=35.8
Q ss_pred CCCEEEEEEcCceecCCCCCcccCcceEEEcc-cCCEEEEEEece---eCceecee
Q 047565 36 IGDYVDVKVNGAVHKGMPHKFYHGRTGRVWNV-TKRAIGVEINKQ---VKFFMPFL 87 (106)
Q Consensus 36 ~GD~VdIkid~svqKGMPHk~YHGkTG~V~~v-~~~AvgV~VnK~---V~gk~~~~ 87 (106)
-|+..+...+.+-|+-.|-..+ =+|.|. +++.+.|.||++ +.||+|.+
T Consensus 17 nGe~y~~~~~tAAHktLPlgT~----V~VtNl~ngrsviVrVnDRGPf~~gRiIDL 68 (208)
T TIGR00413 17 NGEVYNMKALTAAHKTLPFNTY----VKVTNLHNNRSVIVRINDRGPFSDDRIIDL 68 (208)
T ss_pred CCeecCCCccccccccCCCCCE----EEEEECCCCCEEEEEEeCCCCCCCCCEEEC
Confidence 4788888888899999987544 356664 588999999998 45666543
No 31
>PF14031 D-ser_dehydrat: Putative serine dehydratase domain; PDB: 3LLX_A 3ANV_A 3AWO_A 3AWN_A 3ANU_A 3GWQ_A.
Probab=39.59 E-value=11 Score=25.60 Aligned_cols=31 Identities=26% Similarity=0.357 Sum_probs=18.6
Q ss_pred cCCcccCCCCCchHHHHHhccCCCEEEEEEc
Q 047565 15 FARPFRKKGYIPLSTYLRTYKIGDYVDVKVN 45 (106)
Q Consensus 15 fsk~fR~~G~~~ls~~l~~yk~GD~VdIkid 45 (106)
+.+---|||+..+..-...+++||+|.|..+
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 3444568887766555667999999999765
No 32
>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=33.89 E-value=23 Score=27.29 Aligned_cols=41 Identities=27% Similarity=0.512 Sum_probs=26.4
Q ss_pred ccCCCCC-chHHHHHhccCCCEEEEEEcCceecCCCCCcccCcceEEEcccC
Q 047565 19 FRKKGYI-PLSTYLRTYKIGDYVDVKVNGAVHKGMPHKFYHGRTGRVWNVTK 69 (106)
Q Consensus 19 fR~~G~~-~ls~~l~~yk~GD~VdIkid~svqKGMPHk~YHGkTG~V~~v~~ 69 (106)
|+.+|.. +++.--.+|+.||+|.-...+ |.|| .|.|...+.
T Consensus 91 F~R~g~~L~~~~~~~~~q~GDIVtw~l~~----~~~H------IgIVSd~r~ 132 (164)
T PF06940_consen 91 FKRHGQSLTTDINPEDWQPGDIVTWRLPG----GLPH------IGIVSDRRS 132 (164)
T ss_pred HHhcCeeccCCCChhhcCCCCEEEEeCCC----CCCe------EEEEeCCcC
Confidence 4455532 333333799999999987665 6777 566665543
No 33
>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=33.56 E-value=74 Score=20.62 Aligned_cols=32 Identities=28% Similarity=0.555 Sum_probs=20.4
Q ss_pred HhccCCCEEEEEEcCceecCCCCCcccCcceEEEc
Q 047565 32 RTYKIGDYVDVKVNGAVHKGMPHKFYHGRTGRVWN 66 (106)
Q Consensus 32 ~~yk~GD~VdIkid~svqKGMPHk~YHGkTG~V~~ 66 (106)
..|++||.|.|.-+... .|-+.|-|+.=.++.
T Consensus 2 ~~y~vgd~V~v~~~~~~---~~~~~~i~~I~~i~~ 33 (123)
T cd04370 2 ITYEVGDSVYVEPDDSI---KSDPPYIARIEELWE 33 (123)
T ss_pred CEEecCCEEEEecCCcC---CCCCCEEEEEeeeeE
Confidence 36899999999887664 344455444443333
No 34
>smart00538 POP4 A domain found in a protein subunit of human RNase MRP and RNase P ribonucleoprotein complexes and archaeal proteins.
Probab=33.24 E-value=1.2e+02 Score=20.70 Aligned_cols=46 Identities=17% Similarity=0.148 Sum_probs=33.2
Q ss_pred CCCcccCcceEEEcccCCEEEEEEeceeCceeceeecceeeEEeeecCch
Q 047565 53 PHKFYHGRTGRVWNVTKRAIGVEINKQVKFFMPFLFDSFRCIYLCELPDD 102 (106)
Q Consensus 53 PHk~YHGkTG~V~~v~~~AvgV~VnK~V~gk~~~~~~~~~~~~~~~~~~~ 102 (106)
+.+.|-|..|.|+.=|.+++.|+... |+ +..+----|+|.-+||++
T Consensus 22 ~~ps~vGi~GiVv~ET~nt~~I~t~~---~~-~~~IpK~~~vF~f~l~~~ 67 (92)
T smart00538 22 KNPSLVGIEGIVVDETRNTLKIETKE---GR-VKTVPKDGAVFEFELPGG 67 (92)
T ss_pred CCCCccCcEEEEEEeeeeEEEEEeCC---Cc-EEEEECCCeEEEEEECCC
Confidence 67899999999999999999988654 22 222333356677777763
No 35
>PF02513 Spin-Ssty: Spin/Ssty Family; InterPro: IPR003671 Spindlin (Spin) and Ssty were first identified for their involvement in gametogenesis. Spindlin was identified as a maternal transcript present in the unfertilised egg and early embryo, and was subsequently shown to interact with the spindle apparatus during oogenesis, and may therefore be important for mitosis []. In addition, spindlin appears to be a target for cell cycle-dependent phosphorylation, and as such may play a role in cell cycle regulation during the transition from gamete to embryo []. Ssty is a multi-copy, Y-linked spermatogenesis-specific transcript that appears to be required for normal spermatogenesis []. Ssty may play an analogous role to spindlin in sperm cells, namely during the transition from sperm cells to early embryo, and in mitosis.; GO: 0007276 gamete generation; PDB: 2NS2_A.
Probab=32.08 E-value=43 Score=21.13 Aligned_cols=17 Identities=29% Similarity=0.440 Sum_probs=14.3
Q ss_pred eeceeecceeeEEeeec
Q 047565 83 FMPFLFDSFRCIYLCEL 99 (106)
Q Consensus 83 k~~~~~~~~~~~~~~~~ 99 (106)
=++-++|-+-|||..||
T Consensus 33 ~y~Ikyd~d~~iY~y~L 49 (50)
T PF02513_consen 33 LYYIKYDGDDHIYVYEL 49 (50)
T ss_dssp EEEEEETTESBEEEEEC
T ss_pred EEEEEECCCcEEEEEEe
Confidence 35668999999999987
No 36
>COG1588 POP4 RNase P/RNase MRP subunit p29 [Translation, ribosomal structure and biogenesis]
Probab=31.22 E-value=53 Score=23.32 Aligned_cols=54 Identities=26% Similarity=0.235 Sum_probs=36.4
Q ss_pred CCCEEEEEEcCceecCCCCCcccCcceEEEcccCCEEEEEEeceeCceeceeecceeeEEeeecCc
Q 047565 36 IGDYVDVKVNGAVHKGMPHKFYHGRTGRVWNVTKRAIGVEINKQVKFFMPFLFDSFRCIYLCELPD 101 (106)
Q Consensus 36 ~GD~VdIkid~svqKGMPHk~YHGkTG~V~~v~~~AvgV~VnK~V~gk~~~~~~~~~~~~~~~~~~ 101 (106)
+|=.|-|.- -+|+.|-|-.|+|++-|.+.+.|.--. +-+++.| --|++.-|+||
T Consensus 16 iGl~vrVv~-------s~~~s~vGI~G~VVdETkNtLvi~t~~--~~~~VpK---~~~vfef~~~~ 69 (95)
T COG1588 16 IGLEVRVVR-------STNPSYVGIEGRVVDETKNTLVIDTGS--REKVVPK---DGAVFEFEGPD 69 (95)
T ss_pred cCcEEEEEe-------cCCCCccceeEEEEeeeccEEEEECCC--ceEEEec---CcEEEEEEcCC
Confidence 466666643 379999999999999999999876432 2222222 23666666664
No 37
>PRK10334 mechanosensitive channel MscS; Provisional
Probab=30.92 E-value=57 Score=26.22 Aligned_cols=30 Identities=30% Similarity=0.602 Sum_probs=23.8
Q ss_pred HHhccCCCEEEEEEcCceecCCCCCcccCcceEEEcccCCEEEEE
Q 047565 31 LRTYKIGDYVDVKVNGAVHKGMPHKFYHGRTGRVWNVTKRAIGVE 75 (106)
Q Consensus 31 l~~yk~GD~VdIkid~svqKGMPHk~YHGkTG~V~~v~~~AvgV~ 75 (106)
-+.|++||.|.+ .|.+|+|..++=++..+.
T Consensus 127 ~rpf~vGD~I~i---------------~~~~G~V~~I~~r~T~i~ 156 (286)
T PRK10334 127 FRPFRAGEYVDL---------------GGVAGTVLSVQIFSTTMR 156 (286)
T ss_pred cCCCCCCCEEEE---------------CCEEEEEEEEEeEEEEEE
Confidence 467999999997 267899999887776654
No 38
>COG1862 YajC Preprotein translocase subunit YajC [Intracellular trafficking and secretion]
Probab=30.75 E-value=1e+02 Score=21.55 Aligned_cols=38 Identities=26% Similarity=0.316 Sum_probs=31.5
Q ss_pred hHHHHHhccCCCEEEEEEcCceecCCCCCcccCcceEEEcccCCEEEEEEec
Q 047565 27 LSTYLRTYKIGDYVDVKVNGAVHKGMPHKFYHGRTGRVWNVTKRAIGVEINK 78 (106)
Q Consensus 27 ls~~l~~yk~GD~VdIkid~svqKGMPHk~YHGkTG~V~~v~~~AvgV~VnK 78 (106)
-..+|...++||.|...+ |--|+|..+....+.|++++
T Consensus 37 ~~~ml~sL~kGD~VvT~g--------------Gi~G~V~~v~d~~v~I~l~~ 74 (97)
T COG1862 37 HQELLNSLKKGDEVVTIG--------------GIVGTVTKVGDDTVEIELGD 74 (97)
T ss_pred HHHHHHhccCCCEEEEcC--------------CeEEEEEEEecCcEEEEECC
Confidence 457889999999998732 56789999999999999884
No 39
>TIGR00739 yajC preprotein translocase, YajC subunit. While this protein is part of the preprotein translocase in Escherichia coli, it is not essential for viability or protein secretion. The N-terminus region contains a predicted membrane-spanning region followed by a region consisting almost entirely of residues with charged (acidic, basic, or zwitterionic) side chains. This small protein is about 100 residues in length, and is restricted to bacteria; however, this protein is absent from some lineages, including spirochetes and Mycoplasmas.
Probab=30.68 E-value=1.2e+02 Score=20.30 Aligned_cols=38 Identities=26% Similarity=0.354 Sum_probs=31.4
Q ss_pred hHHHHHhccCCCEEEEEEcCceecCCCCCcccCcceEEEcccCCEEEEEEec
Q 047565 27 LSTYLRTYKIGDYVDVKVNGAVHKGMPHKFYHGRTGRVWNVTKRAIGVEINK 78 (106)
Q Consensus 27 ls~~l~~yk~GD~VdIkid~svqKGMPHk~YHGkTG~V~~v~~~AvgV~VnK 78 (106)
....+.+.++||.|... -|--|+|.++....+.|++++
T Consensus 31 ~~~m~~~L~~Gd~VvT~--------------gGi~G~V~~i~d~~v~vei~~ 68 (84)
T TIGR00739 31 HKKLIESLKKGDKVLTI--------------GGIIGTVTKIAENTIVIELND 68 (84)
T ss_pred HHHHHHhCCCCCEEEEC--------------CCeEEEEEEEeCCEEEEEECC
Confidence 45788999999999873 266788999999999988875
No 40
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=30.61 E-value=44 Score=20.10 Aligned_cols=12 Identities=42% Similarity=0.581 Sum_probs=10.7
Q ss_pred hccCCCEEEEEE
Q 047565 33 TYKIGDYVDVKV 44 (106)
Q Consensus 33 ~yk~GD~VdIki 44 (106)
.|++||.|++.-
T Consensus 2 ~~~~G~~Ve~~~ 13 (61)
T smart00743 2 DFKKGDRVEVFS 13 (61)
T ss_pred CcCCCCEEEEEE
Confidence 489999999988
No 41
>PLN02249 indole-3-acetic acid-amido synthetase
Probab=30.50 E-value=33 Score=30.66 Aligned_cols=39 Identities=21% Similarity=0.391 Sum_probs=31.5
Q ss_pred HHhccCCCEEEEEEcCceecCCCCCcccCcceEEEcccCCEE
Q 047565 31 LRTYKIGDYVDVKVNGAVHKGMPHKFYHGRTGRVWNVTKRAI 72 (106)
Q Consensus 31 l~~yk~GD~VdIkid~svqKGMPHk~YHGkTG~V~~v~~~Av 72 (106)
|--|.+||.|-+.+ .+.+-|.=.|-||++.+.|+.|--+
T Consensus 407 LyRY~iGDvVrvtg---f~~~~P~i~F~gR~~~~ls~~GEKl 445 (597)
T PLN02249 407 LYRYRVGDILRVTG---FHNSAPQFKFIRRKNVLLSIESDKT 445 (597)
T ss_pred eeEeecCCEEEEee---ccCCCcEEEEEccCCcceecccccC
Confidence 44578899998854 5778999999999999999887544
No 42
>KOG0544 consensus FKBP-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]
Probab=30.02 E-value=53 Score=23.81 Aligned_cols=44 Identities=23% Similarity=0.365 Sum_probs=33.7
Q ss_pred cCCCEEEE----------EEcCceecCCCCCcccCcceEEEcccCCEEEEEEec
Q 047565 35 KIGDYVDV----------KVNGAVHKGMPHKFYHGRTGRVWNVTKRAIGVEINK 78 (106)
Q Consensus 35 k~GD~VdI----------kid~svqKGMPHk~YHGkTG~V~~v~~~AvgV~VnK 78 (106)
|.||.|.+ +.|+|.+.+-|+++--|+--+|-+...-.....|-.
T Consensus 18 K~Gqtvt~hYtg~L~dG~kfDSs~dr~kPfkf~IGkgeVIkGwdegv~qmsvGe 71 (108)
T KOG0544|consen 18 KKGQTVTVHYTGTLQDGKKFDSSRDRGKPFKFKIGKGEVIKGWDEGVAQMSVGE 71 (108)
T ss_pred CCCCEEEEEEEeEecCCcEeecccccCCCeeEEecCcceeechhhcchhccccc
Confidence 56777776 678999999999999999888877776655554433
No 43
>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=30.01 E-value=90 Score=21.80 Aligned_cols=30 Identities=30% Similarity=0.560 Sum_probs=20.8
Q ss_pred HhccCCCEEEEEEcCceecCCCCCcccCcceEEEc
Q 047565 32 RTYKIGDYVDVKVNGAVHKGMPHKFYHGRTGRVWN 66 (106)
Q Consensus 32 ~~yk~GD~VdIkid~svqKGMPHk~YHGkTG~V~~ 66 (106)
+.|++||.|.|+..++ |-+-|-|+.=.++.
T Consensus 2 ~~~~vGD~V~v~~~~~-----~~~pyIgrI~~i~e 31 (121)
T cd04714 2 EIIRVGDCVLFKSPGR-----PSLPYVARIESLWE 31 (121)
T ss_pred CEEEcCCEEEEeCCCC-----CCCCEEEEEEEEEE
Confidence 3689999999987654 34566666555554
No 44
>TIGR02768 TraA_Ti Ti-type conjugative transfer relaxase TraA. This protein contains domains distinctive of a single strand exonuclease (N-terminus, MobA/MobL, pfam03389) as well as a helicase domain (central region, homologous to the corresponding region of the F-type relaxase TraI, TIGR02760). This protein likely fills the same role as TraI(F), nicking (at the oriT site) and unwinding the coiled plasmid prior to conjugative transfer.
Probab=29.69 E-value=1e+02 Score=28.13 Aligned_cols=41 Identities=20% Similarity=0.294 Sum_probs=32.3
Q ss_pred HhccCCCEEEEEEcCceecCCCCCcccCcceEEEcccCCEEEEEEe
Q 047565 32 RTYKIGDYVDVKVNGAVHKGMPHKFYHGRTGRVWNVTKRAIGVEIN 77 (106)
Q Consensus 32 ~~yk~GD~VdIkid~svqKGMPHk~YHGkTG~V~~v~~~AvgV~Vn 77 (106)
..|.+||.|-..-|-. .. .-|.|-+|+|.++.+..+.|...
T Consensus 606 ~~~~~GDrV~~~~N~~-~~----gv~NGd~g~V~~i~~~~i~v~~~ 646 (744)
T TIGR02768 606 RKFAAGDRIVFLENNR-DL----GVKNGMLGTVEEIEDGRLVVQLD 646 (744)
T ss_pred ceecCCCEEEEEeccc-cc----CCcCCCEEEEEEecCCeEEEEEC
Confidence 3689999999987743 23 37999999999999887776654
No 45
>PF10377 ATG11: Autophagy-related protein 11; InterPro: IPR019460 This family consists of proteins involved in telomere maintenance. In Schizosaccharomyces pombe (fission yeast) this protein is called Taf1 (taz1 interacting factor) and is part of the telomere cap complex. In Saccharomyces cerevisiae (baker's yeast) this protein is called ATG11 and is known to be involved in vacuolar targeting and peroxisome degradation [, ].
Probab=29.62 E-value=33 Score=24.74 Aligned_cols=32 Identities=28% Similarity=0.486 Sum_probs=25.9
Q ss_pred HHhccCCCEEEEEEcCcee----------cCCCCCcccCcce
Q 047565 31 LRTYKIGDYVDVKVNGAVH----------KGMPHKFYHGRTG 62 (106)
Q Consensus 31 l~~yk~GD~VdIkid~svq----------KGMPHk~YHGkTG 62 (106)
++.|++||.|.+.-++.-+ -|-||-+-|---.
T Consensus 40 ~~~f~~GDlvLflpt~~~~~~~~~~~af~~~~~~YFL~~~s~ 81 (129)
T PF10377_consen 40 FRNFQVGDLVLFLPTRNHNNKKQPWAAFNVGCPHYFLHEDSI 81 (129)
T ss_pred EecCCCCCEEEEEecCCCCccccceEEeeCCCceEEEecccc
Confidence 7899999999999887754 4888888776654
No 46
>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=29.39 E-value=18 Score=31.28 Aligned_cols=39 Identities=31% Similarity=0.516 Sum_probs=29.9
Q ss_pred HHhccCCCEEEEEEcCceecCCCCCcccCcceEEEcccCCEE
Q 047565 31 LRTYKIGDYVDVKVNGAVHKGMPHKFYHGRTGRVWNVTKRAI 72 (106)
Q Consensus 31 l~~yk~GD~VdIkid~svqKGMPHk~YHGkTG~V~~v~~~Av 72 (106)
|--|..||.|-+. ..+.+.|-=.|.||+|.+.|+.|--+
T Consensus 368 LyRY~iGDvVrv~---gf~~~~P~i~F~~R~~~~l~l~gEkl 406 (528)
T PF03321_consen 368 LYRYRIGDVVRVT---GFYNQTPRIEFVGRRGQVLSLFGEKL 406 (528)
T ss_dssp -SSEEECEEEEEE---EEETTEEEEEEEEETTEEE-SSS--E
T ss_pred eeeeecCCEEEEe---eccCCCcEEEEeccCCceeecceeec
Confidence 5568899999985 46677899999999999999988543
No 47
>PF09926 DUF2158: Uncharacterized small protein (DUF2158); InterPro: IPR019226 This entry represents a family of predominantly prokaryotic proteins with no known function.
Probab=28.55 E-value=38 Score=21.22 Aligned_cols=11 Identities=55% Similarity=0.933 Sum_probs=8.5
Q ss_pred ccCCCEEEEEE
Q 047565 34 YKIGDYVDVKV 44 (106)
Q Consensus 34 yk~GD~VdIki 44 (106)
|++||+|-+|-
T Consensus 1 f~~GDvV~LKS 11 (53)
T PF09926_consen 1 FKIGDVVQLKS 11 (53)
T ss_pred CCCCCEEEEcc
Confidence 67888888763
No 48
>PRK05609 nusG transcription antitermination protein NusG; Validated
Probab=28.48 E-value=1.5e+02 Score=21.34 Aligned_cols=26 Identities=23% Similarity=0.390 Sum_probs=18.3
Q ss_pred hccCCCEEEEEEcCceecCCCCCcccCcceEEEccc
Q 047565 33 TYKIGDYVDVKVNGAVHKGMPHKFYHGRTGRVWNVT 68 (106)
Q Consensus 33 ~yk~GD~VdIkid~svqKGMPHk~YHGkTG~V~~v~ 68 (106)
.|++||.|.|.--| |.|-.|+|..+.
T Consensus 126 ~~~~Gd~VrI~~GP----------f~G~~g~v~~i~ 151 (181)
T PRK05609 126 DFEVGEMVRVIDGP----------FADFNGTVEEVD 151 (181)
T ss_pred CCCCCCEEEEeccC----------CCCCEEEEEEEe
Confidence 47789999986433 667777776664
No 49
>COG0668 MscS Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]
Probab=28.17 E-value=52 Score=25.00 Aligned_cols=30 Identities=27% Similarity=0.611 Sum_probs=23.0
Q ss_pred HHhccCCCEEEEEEcCceecCCCCCcccCcceEEEcccCCEEEE
Q 047565 31 LRTYKIGDYVDVKVNGAVHKGMPHKFYHGRTGRVWNVTKRAIGV 74 (106)
Q Consensus 31 l~~yk~GD~VdIkid~svqKGMPHk~YHGkTG~V~~v~~~AvgV 74 (106)
-+.|++||.|.+-. |-.|+|.+++=+.-.+
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 46789999999943 7788888877776544
No 50
>cd04709 BAH_MTA BAH, or Bromo Adjacent Homology domain, as present in MTA1 and similar proteins. The Metastasis-associated protein MTA1 is part of the NURD (nucleosome remodeling and deacetylating) complex and plays a role in cellular transformation and metastasis. 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=26.44 E-value=1e+02 Score=23.20 Aligned_cols=27 Identities=26% Similarity=0.578 Sum_probs=17.7
Q ss_pred HhccCCCEEEEEEcCceecCCCCCcccCcceEE
Q 047565 32 RTYKIGDYVDVKVNGAVHKGMPHKFYHGRTGRV 64 (106)
Q Consensus 32 ~~yk~GD~VdIkid~svqKGMPHk~YHGkTG~V 64 (106)
..|++||.|.|... .+.| .|-|+.=++
T Consensus 2 ~~yrvGD~Vy~~~~----~~~P--y~I~rI~e~ 28 (164)
T cd04709 2 NMYRVGDYVYFESS----PNNP--YLIRRIEEL 28 (164)
T ss_pred cEEecCCEEEEECC----CCCC--CEEEEEEEE
Confidence 36899999999765 3556 444554443
No 51
>PLN02247 indole-3-acetic acid-amido synthetase
Probab=26.26 E-value=44 Score=30.16 Aligned_cols=36 Identities=22% Similarity=0.350 Sum_probs=30.2
Q ss_pred HHhccCCCEEEEEEcCceecCCCCCcccCcceEEEcccC
Q 047565 31 LRTYKIGDYVDVKVNGAVHKGMPHKFYHGRTGRVWNVTK 69 (106)
Q Consensus 31 l~~yk~GD~VdIkid~svqKGMPHk~YHGkTG~V~~v~~ 69 (106)
|--|+.||+|-+.+ .+.+.|.=+|-||.+.|.++.+
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 45578899998865 5889999999999999988765
No 52
>PF14468 DUF4427: Protein of unknown function (DUF4427)
Probab=25.75 E-value=38 Score=25.35 Aligned_cols=18 Identities=28% Similarity=0.257 Sum_probs=15.1
Q ss_pred EEEEeceeCceeceeeccee
Q 047565 73 GVEINKQVKFFMPFLFDSFR 92 (106)
Q Consensus 73 gV~VnK~V~gk~~~~~~~~~ 92 (106)
-|+|||- ||+|+++|.|-
T Consensus 58 rV~v~~e--GRYLl~l~~~~ 75 (132)
T PF14468_consen 58 RVKVNKE--GRYLLDLDLFD 75 (132)
T ss_pred ceeeccC--ceeeeeccccc
Confidence 3788998 99999998774
No 53
>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=25.54 E-value=55 Score=21.15 Aligned_cols=19 Identities=16% Similarity=0.191 Sum_probs=14.4
Q ss_pred hccCCCEEEEEEcCceecC
Q 047565 33 TYKIGDYVDVKVNGAVHKG 51 (106)
Q Consensus 33 ~yk~GD~VdIkid~svqKG 51 (106)
.|++||.|.+++--.-+.+
T Consensus 10 iYrPGetV~~~~~~~~~~~ 28 (99)
T PF01835_consen 10 IYRPGETVHFRAIVRDLDN 28 (99)
T ss_dssp EE-TTSEEEEEEEEEEECT
T ss_pred CcCCCCEEEEEEEEecccc
Confidence 5999999999988665554
No 54
>PRK13712 conjugal transfer protein TrbA; Provisional
Probab=25.48 E-value=17 Score=26.28 Aligned_cols=15 Identities=47% Similarity=0.906 Sum_probs=12.3
Q ss_pred ceeecceeeEEeeec
Q 047565 85 PFLFDSFRCIYLCEL 99 (106)
Q Consensus 85 ~~~~~~~~~~~~~~~ 99 (106)
+.+|||||-|+.|-.
T Consensus 82 vtsfd~frrificim 96 (115)
T PRK13712 82 VTSFDSFRRIFICIM 96 (115)
T ss_pred cchhhhhhhhhheee
Confidence 458999999999864
No 55
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=25.21 E-value=1.1e+02 Score=29.58 Aligned_cols=39 Identities=31% Similarity=0.405 Sum_probs=30.3
Q ss_pred chHHHHHhccCCCEEEEEEcCceecCCCCCcccCcceEEEcccCCEEEE
Q 047565 26 PLSTYLRTYKIGDYVDVKVNGAVHKGMPHKFYHGRTGRVWNVTKRAIGV 74 (106)
Q Consensus 26 ~ls~~l~~yk~GD~VdIkid~svqKGMPHk~YHGkTG~V~~v~~~AvgV 74 (106)
|.+.+-..|+.||.|-|.- -+|.|.||.|+-|.+.-+.|
T Consensus 452 ~~~eLrKyF~~GDhVKVi~----------G~~eG~tGlVvrVe~~~vi~ 490 (1024)
T KOG1999|consen 452 PASELRKYFEPGDHVKVIA----------GRYEGDTGLVVRVEQGDVIL 490 (1024)
T ss_pred chHhhhhhccCCCeEEEEe----------ccccCCcceEEEEeCCeEEE
Confidence 5667778899999998743 26899999998888765543
No 56
>PRK03879 ribonuclease P protein component 1; Validated
Probab=25.14 E-value=1.7e+02 Score=20.16 Aligned_cols=23 Identities=26% Similarity=0.362 Sum_probs=21.6
Q ss_pred CCCcccCcceEEEcccCCEEEEE
Q 047565 53 PHKFYHGRTGRVWNVTKRAIGVE 75 (106)
Q Consensus 53 PHk~YHGkTG~V~~v~~~AvgV~ 75 (106)
+.+.+-|..|.|..=|++.+.|+
T Consensus 24 ~npslvGi~GiVv~ETknt~~I~ 46 (96)
T PRK03879 24 TNPSLVGIKGRVVDETRNTLVIE 46 (96)
T ss_pred CCCCcccceEEEEEeceeEEEEE
Confidence 67889999999999999999988
No 57
>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=23.93 E-value=44 Score=20.61 Aligned_cols=23 Identities=22% Similarity=0.424 Sum_probs=15.2
Q ss_pred CCchHHHH--HhccCCCEEEEEEcC
Q 047565 24 YIPLSTYL--RTYKIGDYVDVKVNG 46 (106)
Q Consensus 24 ~~~ls~~l--~~yk~GD~VdIkid~ 46 (106)
..|.+... ..|++||.|...+..
T Consensus 29 ~lp~~e~~~~~~~~~Gd~v~v~v~~ 53 (67)
T cd04455 29 ILPKKEQIPGESYRPGDRIKAYVLE 53 (67)
T ss_pred EeeHHHCCCCCcCCCCCEEEEEEEE
Confidence 44554443 468999999887743
No 58
>PF10134 RPA: Replication initiator protein A; InterPro: IPR018777 Members of this family of bacterial proteins are single-stranded DNA binding proteins that are involved in DNA replication, repair and recombination.
Probab=23.82 E-value=46 Score=26.02 Aligned_cols=24 Identities=29% Similarity=0.538 Sum_probs=20.6
Q ss_pred HHhccCCCEEEEEEcCceecCCCCC
Q 047565 31 LRTYKIGDYVDVKVNGAVHKGMPHK 55 (106)
Q Consensus 31 l~~yk~GD~VdIkid~svqKGMPHk 55 (106)
...|+.|| +.|.|.|+..-||||=
T Consensus 22 ~~~y~~~~-~~i~v~~~~~~G~pti 45 (229)
T PF10134_consen 22 PIRYEHGD-VTIEVEPSPKHGLPTI 45 (229)
T ss_pred ceEEEeCC-EEEEEEccCCCCCCcc
Confidence 56799999 9999999987799983
No 59
>PF02107 FlgH: Flagellar L-ring protein; InterPro: IPR000527 The flgH, flgI and fliF genes of Salmonella typhimurium encode the major proteins for the L, P and M rings of the flagellar basal body []. In fact, the basal body consists of four rings (L,P,S and M) surrounding the flagellar rod, which is believed to transmit motor rotation to the filament []. The M ring is integral to the inner membrane of the cell, and may be connected to the rod via the S (supramembrane) ring, which lies just distal to it. The L and P rings reside in the outer membrane and periplasmic space, respectively. FlgH and FlgI, which are exported across the cell membrane to their destinations in the outer membrane and periplasmic space, have typical N-terminal cleaved signal-peptide sequences. FlgH is predicted to have an extensive beta-sheet structure, in keeping with other outer membrane proteins [].; GO: 0003774 motor activity, 0001539 ciliary or flagellar motility, 0009427 bacterial-type flagellum basal body, distal rod, L ring
Probab=23.72 E-value=59 Score=24.49 Aligned_cols=23 Identities=26% Similarity=0.343 Sum_probs=18.8
Q ss_pred CchHHHHHhccCCCEEEEEEcCc
Q 047565 25 IPLSTYLRTYKIGDYVDVKVNGA 47 (106)
Q Consensus 25 ~~ls~~l~~yk~GD~VdIkid~s 47 (106)
.+|....+.+++||+|.|.++-+
T Consensus 16 ~~l~~D~rA~~VGDiiTV~v~E~ 38 (179)
T PF02107_consen 16 RSLFSDRRARRVGDIITVVVSEN 38 (179)
T ss_pred cchhccccccCCCCEEEEEEEEc
Confidence 46677788899999999998754
No 60
>PF08755 YccV-like: Hemimethylated DNA-binding protein YccV like; InterPro: IPR011722 This entry describes the small protein from Escherichia coli YccV and its homologs in other Proteobacteria. YccV is now described as a hemimethylated DNA binding protein []. The model entry describes a domain in longer eukaryotic proteins.; PDB: 1VBV_A.
Probab=23.24 E-value=49 Score=22.57 Aligned_cols=25 Identities=24% Similarity=0.541 Sum_probs=14.2
Q ss_pred hccCCCEEEEEEcCceecCCCCCcccCcceEEEcccCC
Q 047565 33 TYKIGDYVDVKVNGAVHKGMPHKFYHGRTGRVWNVTKR 70 (106)
Q Consensus 33 ~yk~GD~VdIkid~svqKGMPHk~YHGkTG~V~~v~~~ 70 (106)
.|.+|++| =|+.| |-+|+|+++...
T Consensus 3 ~f~vGqvv------------~Hr~~-~y~GVIvgwD~~ 27 (100)
T PF08755_consen 3 KFRVGQVV------------RHRRY-GYRGVIVGWDPE 27 (100)
T ss_dssp SS-TT-EE------------EETTT---EEEEEEEE--
T ss_pred ccccCCEE------------EEeee-CccEEEECcccc
Confidence 47888887 25665 788999987765
No 61
>PRK02749 photosystem I reaction center subunit IV; Provisional
Probab=23.24 E-value=1.8e+02 Score=19.69 Aligned_cols=30 Identities=27% Similarity=0.429 Sum_probs=25.2
Q ss_pred ccCCCEEEEEEcCceecCCCCCcccCcceEEEcccCCE
Q 047565 34 YKIGDYVDVKVNGAVHKGMPHKFYHGRTGRVWNVTKRA 71 (106)
Q Consensus 34 yk~GD~VdIkid~svqKGMPHk~YHGkTG~V~~v~~~A 71 (106)
.+.||+|-|. .|-.++...+|.|.+|.+..
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 4689999986 57778899999999998874
No 62
>KOG0534 consensus NADH-cytochrome b-5 reductase [Coenzyme transport and metabolism; Energy production and conversion]
Probab=22.80 E-value=60 Score=26.70 Aligned_cols=20 Identities=35% Similarity=0.479 Sum_probs=18.4
Q ss_pred chHHHHHhccCCCEEEEEEc
Q 047565 26 PLSTYLRTYKIGDYVDVKVN 45 (106)
Q Consensus 26 ~ls~~l~~yk~GD~VdIkid 45 (106)
+.|.+|+..++||.|.|++-
T Consensus 126 ~mS~~l~~LkiGd~ve~rGP 145 (286)
T KOG0534|consen 126 KMSQHLDSLKIGDTVEFRGP 145 (286)
T ss_pred cccHHHhcCCCCCEEEEecC
Confidence 67999999999999999876
No 63
>COG3061 OapA Cell envelope opacity-associated protein A [Cell envelope biogenesis, outer membrane]
Probab=22.55 E-value=61 Score=26.48 Aligned_cols=41 Identities=20% Similarity=0.239 Sum_probs=30.2
Q ss_pred CCcccccccCCcccCCCCCchH-----------HHHHhccCCCEEEEEEcCc
Q 047565 7 LRSRTRDLFARPFRKKGYIPLS-----------TYLRTYKIGDYVDVKVNGA 47 (106)
Q Consensus 7 ~R~~TR~~fsk~fR~~G~~~ls-----------~~l~~yk~GD~VdIkid~s 47 (106)
|+=.+-+.|+.=||.|+++... .-|-+||-||.|-|..|.+
T Consensus 162 y~V~~G~TLaQlFRdn~LpitDVnAMakveGagkpLSnlkaGq~Vki~~naq 213 (242)
T COG3061 162 YTVPQGKTLAQLFRDNNLPITDVNAMAKVEGAGKPLSNLKAGQKVKISLNAQ 213 (242)
T ss_pred EEecCCccHHHHHhccCCChHHhHHHHhhccCCCchhhccCCCEEEEEEcCc
Confidence 4445556788889999975322 2366899999999999874
No 64
>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=22.51 E-value=36 Score=21.59 Aligned_cols=11 Identities=9% Similarity=0.425 Sum_probs=5.0
Q ss_pred HHhccCCCEEE
Q 047565 31 LRTYKIGDYVD 41 (106)
Q Consensus 31 l~~yk~GD~Vd 41 (106)
++.++.|+.+.
T Consensus 11 ~~~~~~G~~~~ 21 (77)
T cd04473 11 MEDLEVGKLYK 21 (77)
T ss_pred hhhCCCCCEEE
Confidence 34445554443
No 65
>PF01197 Ribosomal_L31: Ribosomal protein L31; InterPro: IPR002150 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 L31 is one of the proteins from the large ribosomal subunit. L31 is a protein of 66 to 97 amino-acid residues which has only been found so far in bacteria and in some plant and algal chloroplasts.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3D5D_4 3PYO_1 3D5B_4 3PYV_1 3PYT_1 3MRZ_1 3MS1_1 3PYR_1 3F1F_4 3F1H_4 ....
Probab=22.34 E-value=29 Score=22.61 Aligned_cols=29 Identities=24% Similarity=0.444 Sum_probs=19.8
Q ss_pred CCCEEEEEEcCceecCCCCCcccCcceEEEcccCC
Q 047565 36 IGDYVDVKVNGAVHKGMPHKFYHGRTGRVWNVTKR 70 (106)
Q Consensus 36 ~GD~VdIkid~svqKGMPHk~YHGkTG~V~~v~~~ 70 (106)
.++.+.|+|++.- |+.|.|+ ..+...+|+
T Consensus 30 ~~~~~~vdi~s~~-----HPfytG~-~~~~~~~Gr 58 (69)
T PF01197_consen 30 EYPVIKVDICSNC-----HPFYTGK-QKVVDTAGR 58 (69)
T ss_dssp SES-EEECSCSSS-----SCTTCSC-SSCSCCCCC
T ss_pred cceEEEEeecCCC-----CEEEcCc-EEEEccccC
Confidence 4566888888875 9999995 445555554
No 66
>COG0198 RplX Ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=22.17 E-value=1.6e+02 Score=20.95 Aligned_cols=31 Identities=29% Similarity=0.381 Sum_probs=24.0
Q ss_pred hccCCCEEEEEEcCceecCCCCCcccCcceEEEcccCCEEE
Q 047565 33 TYKIGDYVDVKVNGAVHKGMPHKFYHGRTGRVWNVTKRAIG 73 (106)
Q Consensus 33 ~yk~GD~VdIkid~svqKGMPHk~YHGkTG~V~~v~~~Avg 73 (106)
..+.||.|.+.-- -+-|++|+|..+.+.-+.
T Consensus 4 ~IrkGD~V~Vi~G----------kdKGk~GkVl~v~~k~V~ 34 (104)
T COG0198 4 KVKKGDTVKVIAG----------KDKGKEGKVLKVLPKKVV 34 (104)
T ss_pred ceecCCEEEEEec----------CCCCcceEEEEEecCeEE
Confidence 4578999987532 367999999999999733
No 67
>KOG4225 consensus Sorbin and SH3 domain-containing protein [Signal transduction mechanisms]
Probab=21.93 E-value=71 Score=28.47 Aligned_cols=28 Identities=36% Similarity=0.549 Sum_probs=21.7
Q ss_pred hccCCCEEEE--EEcCceecCCCCCcccCcceEE
Q 047565 33 TYKIGDYVDV--KVNGAVHKGMPHKFYHGRTGRV 64 (106)
Q Consensus 33 ~yk~GD~VdI--kid~svqKGMPHk~YHGkTG~V 64 (106)
.|.+||+|.| +||.-.-.|| +||+.|.+
T Consensus 248 ~~~kGDIVyI~rkvD~nWyeGE----hhGr~Gif 277 (489)
T KOG4225|consen 248 PFNKGDIVYILRKVDQNWYEGE----HHGRVGIF 277 (489)
T ss_pred ccCCCCEEEEEeeccCceeeee----ecceecce
Confidence 3678999998 6888888887 57887743
No 68
>TIGR00443 hisZ_biosyn_reg ATP phosphoribosyltransferase, regulatory subunit. Apparant second copies of histidyl-tRNA synthetase, found in Bacillus subtilis, Synechocystis sp., Aquifex aeolicus, and others, are in fact a regulatory subunit of ATP phosphoribosyltransferase, and usually encoded by a gene adjacent to that encoding the catalytic subunit.
Probab=21.67 E-value=77 Score=25.19 Aligned_cols=54 Identities=15% Similarity=0.151 Sum_probs=33.6
Q ss_pred HHHHhccCCCEEEEEEcCceecCCCCCcccCcceEEEcccCCEEEEEEeceeCceeceeecce
Q 047565 29 TYLRTYKIGDYVDVKVNGAVHKGMPHKFYHGRTGRVWNVTKRAIGVEINKQVKFFMPFLFDSF 91 (106)
Q Consensus 29 ~~l~~yk~GD~VdIkid~svqKGMPHk~YHGkTG~V~~v~~~AvgV~VnK~V~gk~~~~~~~~ 91 (106)
.+|+.+... ..|.+|++...|+.+ .||.||.+.-...+-.| -.+|||=.++.+|
T Consensus 239 ~~l~~~~~~--~~i~~D~~~~r~~~Y-----YtGivFe~~~~~~~~~i--~~GGRYD~L~~~f 292 (314)
T TIGR00443 239 ELLEARGVE--EYISLDLGLVRGYHY-----YTGLIFEGYAPGLGAPI--AGGGRYDNLLGRF 292 (314)
T ss_pred HHHHHhCCC--CeEEEecccccCCCC-----ccceEEEEEECCCCCcc--cCCccHHHHHHHc
Confidence 456655544 468889999998876 46777766321111111 1578887777776
No 69
>PF01272 GreA_GreB: Transcription elongation factor, GreA/GreB, C-term; InterPro: IPR001437 Bacterial proteins greA and greB are necessary for efficient RNA polymerase transcription elongation past template-encoded arresting sites. Arresting sites in DNA have the property of trapping a certain fraction of elongating RNA polymerases that pass through, resulting in locked DNA/RNA/ polymerase ternary complexes. Cleavage of the nascent transcript by cleavage factors, such as greA or greB, allows the resumption of elongation from the new 3' terminus [, ]. Escherichia coli GreA and GreB are sequence homologues and have homologues in every known bacterial genome []. GreA induces cleavage two or three nucleotides behind the terminus and can only prevent the formation of arrested complexes while greB releases longer sequences up to eighteen nucleotides in length and can rescue preexisting arrested complexes. These functional differences correlate with a distinctive structural feature, the distribution of positively charged residues on one face of the N-terminal coiled coil. Remarkably, despite close functional similarity, the prokaryotic Gre factors have no sequence or structural similarity with eukaryotic TFIIS. ; GO: 0003677 DNA binding, 0032784 regulation of transcription elongation, DNA-dependent; PDB: 2P4V_E 2ETN_B 3BMB_B 2PN0_D 1GRJ_A 2EUL_C 3AOH_Y 3AOI_X 2F23_A.
Probab=21.56 E-value=1.3e+02 Score=19.23 Aligned_cols=23 Identities=39% Similarity=0.585 Sum_probs=18.4
Q ss_pred CchHHHHHhccCCCEEEEEEcCc
Q 047565 25 IPLSTYLRTYKIGDYVDVKVNGA 47 (106)
Q Consensus 25 ~~ls~~l~~yk~GD~VdIkid~s 47 (106)
.||...|---++||.|.+.+...
T Consensus 44 SPLG~ALlG~~~Gd~v~~~~~~g 66 (77)
T PF01272_consen 44 SPLGKALLGKKVGDEVEVELPGG 66 (77)
T ss_dssp SHHHHHHTT-BTT-EEEEEETTB
T ss_pred CHHHHHhcCCCCCCEEEEEeCCc
Confidence 58899999999999999988664
No 70
>PRK13889 conjugal transfer relaxase TraA; Provisional
Probab=21.44 E-value=2.2e+02 Score=27.36 Aligned_cols=41 Identities=22% Similarity=0.347 Sum_probs=32.6
Q ss_pred HhccCCCEEEEEEcCceecCCCCCcccCcceEEEcccCCEEEEEEe
Q 047565 32 RTYKIGDYVDVKVNGAVHKGMPHKFYHGRTGRVWNVTKRAIGVEIN 77 (106)
Q Consensus 32 ~~yk~GD~VdIkid~svqKGMPHk~YHGkTG~V~~v~~~AvgV~Vn 77 (106)
..|.+||.|-..-|-. . ...|.|-+|+|.++.+..+.|...
T Consensus 599 r~~~vGDrVm~~rNd~-~----lgV~NGd~GtV~~I~~~~i~V~~d 639 (988)
T PRK13889 599 RSFASGDRVMFLQNER-G----LGVKNGTLGTIEQVSAQSMSVRLD 639 (988)
T ss_pred ccccCCCEEEEeecCC-c----CCEeCCCeEEEEEecCCeEEEEEC
Confidence 3689999999988753 1 236999999999999988777654
No 71
>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=21.33 E-value=1.8e+02 Score=20.45 Aligned_cols=36 Identities=25% Similarity=0.462 Sum_probs=22.5
Q ss_pred HhccCCCEEEEEEcCceecCCCCCcccCcceEEEccc--CCEEEEEEe
Q 047565 32 RTYKIGDYVDVKVNGAVHKGMPHKFYHGRTGRVWNVT--KRAIGVEIN 77 (106)
Q Consensus 32 ~~yk~GD~VdIkid~svqKGMPHk~YHGkTG~V~~v~--~~AvgV~Vn 77 (106)
..|++||.|.|.--| |.|-.|.|..+. ++-+.|.+-
T Consensus 85 ~~~~~Gd~V~I~~GP----------f~G~~g~v~~~d~~k~~v~v~l~ 122 (145)
T TIGR00405 85 ESIKKGDIVEIISGP----------FKGERAKVIRVDESKEEVTLELI 122 (145)
T ss_pred cccCCCCEEEEeecC----------CCCCeEEEEEEcCCCCEEEEEEE
Confidence 348999999996433 566777776653 334444433
No 72
>PF06487 SAP18: Sin3 associated polypeptide p18 (SAP18); InterPro: IPR010516 This family consists of several eukaryotic Sin3 associated polypeptide p18 (SAP18) sequences. SAP18 is known to be a component of the Sin3-containing complex, which is responsible for the repression of transcription via the modification of histone polypeptides []. SAP18 is also present in the ASAP complex which is thought to be involved in the regulation of splicing during the execution of programmed cell death [].; PDB: 2HDE_A 4A90_A 4A6Q_A 4A8X_C.
Probab=21.15 E-value=67 Score=23.20 Aligned_cols=13 Identities=46% Similarity=0.974 Sum_probs=8.1
Q ss_pred HhccCCCEEEEEE
Q 047565 32 RTYKIGDYVDVKV 44 (106)
Q Consensus 32 ~~yk~GD~VdIki 44 (106)
..|.+||++|+-|
T Consensus 108 ~~F~iGDyidvaI 120 (120)
T PF06487_consen 108 LRFVIGDYIDVAI 120 (120)
T ss_dssp GT--TT-EEEEEE
T ss_pred CCcccCCEEEEeC
Confidence 4699999999865
No 73
>COG3738 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.08 E-value=58 Score=25.77 Aligned_cols=44 Identities=30% Similarity=0.514 Sum_probs=29.5
Q ss_pred CCchHHHHHhccCCCEEEEEEcCceecCCCCCcccCcceEEEc-ccCCEEEEEEe
Q 047565 24 YIPLSTYLRTYKIGDYVDVKVNGAVHKGMPHKFYHGRTGRVWN-VTKRAIGVEIN 77 (106)
Q Consensus 24 ~~~ls~~l~~yk~GD~VdIkid~svqKGMPHk~YHGkTG~V~~-v~~~AvgV~Vn 77 (106)
..|++.-...|+.||+|.=..+ .|.|| .|.|.. +++...-+++.
T Consensus 131 ~lp~~~~~s~y~aGDIvsWRLd----ngl~H------iGv~sd~~~~~g~plViH 175 (200)
T COG3738 131 TLPLSKDPSDYQAGDIVSWRLD----NGLAH------IGVVSDGFTRDGTPLVIH 175 (200)
T ss_pred cCCCCCCccccCCCceEEEEcC----CCCce------eEEEecCCCCCCCeEEEe
Confidence 3467777889999999998877 57888 566654 24444333333
No 74
>PLN02620 indole-3-acetic acid-amido synthetase
Probab=20.97 E-value=64 Score=29.28 Aligned_cols=36 Identities=22% Similarity=0.374 Sum_probs=30.4
Q ss_pred HHhccCCCEEEEEEcCceecCCCCCcccCcceEEEcccC
Q 047565 31 LRTYKIGDYVDVKVNGAVHKGMPHKFYHGRTGRVWNVTK 69 (106)
Q Consensus 31 l~~yk~GD~VdIkid~svqKGMPHk~YHGkTG~V~~v~~ 69 (106)
|--|..||+|-+.+ .+.+-|.=+|-||-+.|.++.+
T Consensus 420 LyRYrlGDvv~V~G---f~n~~P~~~Fv~R~~~~lsi~g 455 (612)
T PLN02620 420 LYRYRVGDVLRVAG---FKNKAPQFSFICRKNVVLSIDS 455 (612)
T ss_pred eEEEecCCEEEEee---ecCCCceEEEEeecCceeeccc
Confidence 45688899998865 5788999999999999988876
No 75
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=20.88 E-value=93 Score=17.67 Aligned_cols=23 Identities=22% Similarity=0.203 Sum_probs=14.9
Q ss_pred ceEEEcccCCEEEEEEeceeCce
Q 047565 61 TGRVWNVTKRAIGVEINKQVKFF 83 (106)
Q Consensus 61 TG~V~~v~~~AvgV~VnK~V~gk 83 (106)
+|+|.+++...+-|.+...+.|-
T Consensus 7 ~g~V~~v~~~g~~v~i~~~~~g~ 29 (72)
T smart00316 7 EGTVTEITPFGAFVDLGNGVEGL 29 (72)
T ss_pred EEEEEEEEccEEEEEeCCCCEEE
Confidence 46777777777777766444443
No 76
>TIGR00717 rpsA ribosomal protein S1. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned.
Probab=20.87 E-value=1.4e+02 Score=25.15 Aligned_cols=22 Identities=23% Similarity=0.253 Sum_probs=12.7
Q ss_pred ceEEEcccCCEEEEEEeceeCc
Q 047565 61 TGRVWNVTKRAIGVEINKQVKF 82 (106)
Q Consensus 61 TG~V~~v~~~AvgV~VnK~V~g 82 (106)
+|+|.+++...+-|.+...+.|
T Consensus 364 ~g~V~~v~~~G~fV~l~~~v~g 385 (516)
T TIGR00717 364 TGKIKKITDFGAFVELEGGIDG 385 (516)
T ss_pred EEEEEEEecceEEEECCCCCEE
Confidence 3667777666666666533333
No 77
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=20.59 E-value=1.3e+02 Score=25.79 Aligned_cols=40 Identities=25% Similarity=0.424 Sum_probs=0.0
Q ss_pred chHHHHHhccCCCEEEEEEcCceecCCCCCcccCcceEEEcccCCEEEEEEeceeCceec
Q 047565 26 PLSTYLRTYKIGDYVDVKVNGAVHKGMPHKFYHGRTGRVWNVTKRAIGVEINKQVKFFMP 85 (106)
Q Consensus 26 ~ls~~l~~yk~GD~VdIkid~svqKGMPHk~YHGkTG~V~~v~~~AvgV~VnK~V~gk~~ 85 (106)
|+..+...|++||.| +|+|.+++...+-|.+...+.|.+.
T Consensus 363 p~~~~~~~~~~G~~v--------------------~g~V~~v~~~G~fV~l~~~v~g~i~ 402 (565)
T PRK06299 363 PWEEFAEKYPVGDVV--------------------EGKVKNITDFGAFVGLEGGIDGLVH 402 (565)
T ss_pred hhhhHHHhCCCCCEE--------------------EEEEEEEecceEEEECCCCCEEEEE
No 78
>PRK09812 toxin ChpB; Provisional
Probab=20.47 E-value=83 Score=21.96 Aligned_cols=16 Identities=31% Similarity=0.385 Sum_probs=14.1
Q ss_pred hccCCCEEEEEEcCce
Q 047565 33 TYKIGDYVDVKVNGAV 48 (106)
Q Consensus 33 ~yk~GD~VdIkid~sv 48 (106)
.++.||++.+..||+.
T Consensus 6 ~~~rGdI~~v~l~P~~ 21 (116)
T PRK09812 6 KFERGDIVLVGFDPAS 21 (116)
T ss_pred cCCCCcEEEEECCCCC
Confidence 4789999999999985
No 79
>PF15591 Imm17: Immunity protein 17
Probab=20.33 E-value=1.8e+02 Score=19.79 Aligned_cols=36 Identities=22% Similarity=0.344 Sum_probs=25.9
Q ss_pred cccCcceEEEcccCCEEEEEEeceeCceeceeecceeeEEee
Q 047565 56 FYHGRTGRVWNVTKRAIGVEINKQVKFFMPFLFDSFRCIYLC 97 (106)
Q Consensus 56 ~YHGkTG~V~~v~~~AvgV~VnK~V~gk~~~~~~~~~~~~~~ 97 (106)
.++|+.|+|.+....--++-- =-+..+|---|+|+-
T Consensus 22 ei~Gk~GVVlG~SeeD~~~~g------Y~Vli~d~e~~~~~e 57 (74)
T PF15591_consen 22 EIWGKRGVVLGISEEDGGNFG------YSVLIFDMECCWYIE 57 (74)
T ss_pred hhcCceeEEEEEecCCCcEEE------EEEEEeeeeeEEEec
Confidence 899999999999877554432 223455777888874
No 80
>cd05699 S1_Rrp5_repeat_hs7 S1_Rrp5_repeat_hs7: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 7 (hs7). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=20.29 E-value=1e+02 Score=20.58 Aligned_cols=25 Identities=28% Similarity=0.489 Sum_probs=19.9
Q ss_pred ceEEEcccCCEEEEEEec-eeCceec
Q 047565 61 TGRVWNVTKRAIGVEINK-QVKFFMP 85 (106)
Q Consensus 61 TG~V~~v~~~AvgV~VnK-~V~gk~~ 85 (106)
+|+|+.++..++.|++.. -++|.++
T Consensus 5 ~~~V~EKt~D~l~v~l~~~~l~a~l~ 30 (72)
T cd05699 5 DARVLKKTLNGLEVAILPEEIRAFLP 30 (72)
T ss_pred EEEEEEEcCCcEEEEecCCCcEEEEE
Confidence 588999999999999887 5555544
Done!