Query 033131
Match_columns 126
No_of_seqs 145 out of 1267
Neff 5.3
Searched_HMMs 46136
Date Fri Mar 29 10:11:45 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033131.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033131hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR01079 rplX_bact ribosomal 100.0 8.9E-40 1.9E-44 233.2 12.5 102 1-102 2-104 (104)
2 PRK00004 rplX 50S ribosomal pr 100.0 3.1E-39 6.8E-44 230.5 12.7 103 1-103 3-105 (105)
3 COG0198 RplX Ribosomal protein 100.0 1.5E-36 3.3E-41 216.7 10.9 101 1-103 3-104 (104)
4 KOG1708 Mitochondrial/chloropl 100.0 7E-32 1.5E-36 212.0 9.0 108 1-108 71-179 (236)
5 CHL00141 rpl24 ribosomal prote 100.0 3.9E-29 8.4E-34 172.2 8.8 76 1-76 7-82 (83)
6 PRK12281 rplX 50S ribosomal pr 100.0 2.9E-28 6.4E-33 165.4 7.9 71 1-71 5-75 (76)
7 PTZ00194 60S ribosomal protein 99.9 4.6E-22 1E-26 149.0 6.6 67 1-78 45-111 (143)
8 PRK01191 rpl24p 50S ribosomal 99.9 7.4E-22 1.6E-26 144.3 7.4 70 1-81 44-113 (120)
9 TIGR01080 rplX_A_E ribosomal p 99.8 1.7E-20 3.8E-25 136.0 6.6 69 1-80 40-108 (114)
10 PF00467 KOW: KOW motif; Inte 98.9 4.7E-09 1E-13 60.0 4.9 32 5-36 1-32 (32)
11 KOG3401 60S ribosomal protein 98.7 1.2E-08 2.7E-13 76.7 3.9 65 1-76 47-112 (145)
12 smart00739 KOW KOW (Kyprides, 98.0 1.5E-05 3.2E-10 43.0 4.1 27 2-28 1-27 (28)
13 PRK08559 nusG transcription an 97.6 0.00026 5.6E-09 53.1 6.5 57 2-73 94-150 (153)
14 TIGR00405 L26e_arch ribosomal 97.5 0.0003 6.4E-09 51.7 6.5 37 3-39 87-123 (145)
15 PRK05609 nusG transcription an 97.1 0.001 2.2E-08 50.1 5.4 35 2-36 126-160 (181)
16 TIGR00922 nusG transcription t 97.1 0.0012 2.6E-08 49.5 5.3 34 3-36 120-153 (172)
17 COG0250 NusG Transcription ant 97.0 0.0014 3E-08 50.7 4.8 35 2-36 123-157 (178)
18 TIGR01955 RfaH transcriptional 96.5 0.005 1.1E-07 45.4 4.9 33 3-36 109-141 (159)
19 PRK09014 rfaH transcriptional 96.3 0.0078 1.7E-07 44.8 4.7 33 3-36 110-142 (162)
20 TIGR01956 NusG_myco NusG famil 96.3 0.0096 2.1E-07 48.9 5.5 35 2-36 205-239 (258)
21 PRK04333 50S ribosomal protein 95.2 0.052 1.1E-06 37.5 5.0 37 1-38 2-38 (84)
22 PTZ00065 60S ribosomal protein 91.4 0.43 9.3E-06 35.6 4.7 34 4-38 9-42 (130)
23 PTZ00471 60S ribosomal protein 90.5 0.52 1.1E-05 35.4 4.4 40 3-42 5-50 (134)
24 KOG1999 RNA polymerase II tran 90.5 0.32 6.9E-06 46.4 3.9 28 2-29 459-486 (1024)
25 COG2163 RPL14A Ribosomal prote 84.7 2.1 4.5E-05 31.7 4.5 36 2-38 4-39 (125)
26 PRK04313 30S ribosomal protein 82.7 2.3 4.9E-05 34.7 4.4 36 2-37 171-210 (237)
27 PRK06531 yajC preprotein trans 80.1 3.9 8.4E-05 29.7 4.4 31 2-36 36-66 (113)
28 PF09953 DUF2187: Uncharacteri 78.0 5.8 0.00013 25.7 4.3 27 4-36 5-31 (57)
29 COG5164 SPT5 Transcription elo 78.0 2 4.3E-05 38.6 2.8 28 3-30 140-167 (607)
30 COG1862 YajC Preprotein transl 75.8 5.2 0.00011 28.3 4.0 29 2-36 43-71 (97)
31 KOG1999 RNA polymerase II tran 75.6 1.8 4E-05 41.5 2.0 28 2-29 581-608 (1024)
32 PRK05585 yajC preprotein trans 73.8 7.2 0.00016 27.8 4.3 29 2-36 52-80 (106)
33 COG1471 RPS4A Ribosomal protei 71.6 8.3 0.00018 31.6 4.6 36 2-37 173-212 (241)
34 PTZ00223 40S ribosomal protein 71.4 6.9 0.00015 32.5 4.2 27 2-28 171-197 (273)
35 PLN00036 40S ribosomal protein 70.8 8.7 0.00019 31.7 4.7 28 2-29 174-201 (261)
36 TIGR00739 yajC preprotein tran 69.1 10 0.00023 25.8 4.1 29 2-36 37-65 (84)
37 PRK05886 yajC preprotein trans 69.0 11 0.00023 27.3 4.3 29 2-36 38-66 (109)
38 COG3700 AphA Acid phosphatase 66.6 1.9 4E-05 34.7 -0.0 33 1-33 125-157 (237)
39 PF05641 Agenet: Agenet domain 66.0 23 0.0005 22.7 5.1 33 3-36 1-37 (68)
40 PTZ00118 40S ribosomal protein 64.8 13 0.00029 30.7 4.6 28 2-29 174-201 (262)
41 PF02699 YajC: Preprotein tran 63.5 2.3 5.1E-05 28.7 0.0 29 2-36 36-64 (82)
42 PF03144 GTP_EFTU_D2: Elongati 63.3 12 0.00025 23.6 3.3 29 2-31 12-43 (74)
43 KOG3418 60S ribosomal protein 61.5 16 0.00035 27.5 4.1 40 2-41 4-49 (136)
44 PRK00409 recombination and DNA 60.9 17 0.00037 34.0 5.1 37 2-41 636-673 (782)
45 PRK02749 photosystem I reactio 60.0 11 0.00025 25.3 2.8 30 1-30 1-32 (71)
46 PF08206 OB_RNB: Ribonuclease 55.6 15 0.00033 22.9 2.8 23 4-26 33-58 (58)
47 COG1532 Predicted RNA-binding 52.2 19 0.0004 23.3 2.7 33 5-37 23-57 (57)
48 COG5164 SPT5 Transcription elo 51.8 16 0.00034 33.1 3.2 33 4-36 353-385 (607)
49 KOG4315 G-patch nucleic acid b 51.2 7 0.00015 34.5 0.9 33 4-36 395-427 (455)
50 TIGR01069 mutS2 MutS2 family p 48.9 31 0.00066 32.3 4.7 34 4-41 626-661 (771)
51 smart00743 Agenet Tudor-like d 46.2 67 0.0015 19.6 5.2 34 1-35 1-35 (61)
52 CHL00125 psaE photosystem I su 46.1 24 0.00053 23.3 2.6 28 3-30 2-31 (64)
53 PF04452 Methyltrans_RNA: RNA 45.4 33 0.00072 26.7 3.8 36 1-36 15-50 (225)
54 PF14505 DUF4438: Domain of un 44.9 51 0.0011 27.3 4.9 32 5-36 60-91 (258)
55 PF02427 PSI_PsaE: Photosystem 44.8 35 0.00076 22.4 3.2 28 3-30 1-30 (61)
56 PF12353 eIF3g: Eukaryotic tra 44.6 52 0.0011 24.1 4.5 28 72-99 8-35 (128)
57 cd04466 S1_YloQ_GTPase S1_YloQ 42.5 64 0.0014 19.8 4.2 28 3-32 38-65 (68)
58 cd03692 mtIF2_IVc mtIF2_IVc: t 41.4 49 0.0011 21.9 3.7 28 3-30 27-54 (84)
59 PF12701 LSM14: Scd6-like Sm d 41.1 80 0.0017 22.1 4.8 34 5-38 7-40 (96)
60 PLN00045 photosystem I reactio 40.6 44 0.00096 23.9 3.4 27 3-29 40-68 (101)
61 PF01079 Hint: Hint module; I 38.5 52 0.0011 26.1 4.0 37 2-38 105-153 (217)
62 cd05707 S1_Rrp5_repeat_sc11 S1 38.3 63 0.0014 19.9 3.7 23 3-35 45-67 (68)
63 KOG3421 60S ribosomal protein 37.4 43 0.00094 25.2 3.2 34 4-38 8-41 (136)
64 cd00174 SH3 Src homology 3 dom 36.2 45 0.00097 18.6 2.5 13 2-14 17-29 (54)
65 cd05698 S1_Rrp5_repeat_hs6_sc5 35.9 82 0.0018 19.3 3.9 23 3-35 45-67 (70)
66 cd05697 S1_Rrp5_repeat_hs5 S1_ 35.7 1E+02 0.0022 19.0 4.3 23 3-35 45-67 (69)
67 COG1193 Mismatch repair ATPase 35.2 42 0.00092 31.5 3.4 37 2-42 612-650 (753)
68 cd05695 S1_Rrp5_repeat_hs3 S1_ 35.0 79 0.0017 19.8 3.8 15 21-35 51-65 (66)
69 cd05708 S1_Rrp5_repeat_sc12 S1 34.1 1E+02 0.0022 18.9 4.2 24 3-36 48-71 (77)
70 PRK00750 lysK lysyl-tRNA synth 34.0 79 0.0017 28.1 4.8 41 60-100 166-207 (510)
71 cd05793 S1_IF1A S1_IF1A: Trans 33.5 41 0.00089 22.5 2.3 26 2-28 38-64 (77)
72 cd04717 BAH_polybromo BAH, or 33.2 1.2E+02 0.0026 21.1 4.9 36 2-37 3-41 (121)
73 PF11623 DUF3252: Protein of u 32.0 1.3E+02 0.0027 19.3 4.2 39 3-41 2-42 (53)
74 cd05688 S1_RPS1_repeat_ec3 S1_ 32.0 96 0.0021 18.4 3.7 13 22-34 54-66 (68)
75 smart00326 SH3 Src homology 3 31.2 59 0.0013 18.3 2.5 14 2-15 20-33 (58)
76 PF00924 MS_channel: Mechanose 31.2 40 0.00086 25.1 2.2 37 2-45 60-96 (206)
77 PF02211 NHase_beta: Nitrile h 30.7 59 0.0013 26.1 3.1 25 2-26 134-168 (222)
78 PF03983 SHD1: SLA1 homology d 30.6 1.1E+02 0.0024 20.4 4.0 41 64-105 8-49 (70)
79 PF07653 SH3_2: Variant SH3 do 30.5 35 0.00077 20.5 1.5 12 1-12 16-27 (55)
80 PRK11713 16S ribosomal RNA met 30.2 99 0.0021 24.2 4.3 29 1-29 28-56 (234)
81 PF00018 SH3_1: SH3 domain; I 29.8 65 0.0014 18.7 2.6 15 1-15 14-28 (48)
82 cd05685 S1_Tex S1_Tex: The C-t 29.6 1.1E+02 0.0025 18.0 3.7 22 3-34 45-66 (68)
83 TIGR00523 eIF-1A eukaryotic/ar 29.6 34 0.00075 24.1 1.5 10 2-11 57-66 (99)
84 PF09526 DUF2387: Probable met 29.3 1.3E+02 0.0028 20.0 4.1 35 71-106 10-44 (71)
85 PF09926 DUF2158: Uncharacteri 29.2 39 0.00085 21.3 1.5 22 3-27 1-22 (53)
86 TIGR00046 RNA methyltransferas 29.1 1.1E+02 0.0025 24.0 4.5 30 1-30 30-59 (240)
87 PRK10334 mechanosensitive chan 28.5 75 0.0016 26.0 3.5 23 2-29 129-151 (286)
88 cd05706 S1_Rrp5_repeat_sc10 S1 28.1 1.5E+02 0.0033 18.3 4.2 14 22-35 57-70 (73)
89 PF11717 Tudor-knot: RNA bindi 27.8 90 0.0019 19.1 3.0 30 3-32 1-30 (55)
90 PRK09510 tolA cell envelope in 27.5 94 0.002 27.1 4.0 26 75-100 324-349 (387)
91 cd04456 S1_IF1A_like S1_IF1A_l 27.3 70 0.0015 21.5 2.6 28 2-29 38-66 (78)
92 PF01176 eIF-1a: Translation i 27.3 1.1E+02 0.0023 19.5 3.4 23 2-24 41-63 (65)
93 cd05690 S1_RPS1_repeat_ec5 S1_ 26.6 1.2E+02 0.0027 18.3 3.5 11 23-33 56-66 (69)
94 PF15057 DUF4537: Domain of un 26.3 1.3E+02 0.0029 21.6 4.1 42 2-44 55-103 (124)
95 smart00439 BAH Bromo adjacent 26.3 1.5E+02 0.0033 19.8 4.3 30 2-31 1-32 (120)
96 smart00652 eIF1a eukaryotic tr 26.2 72 0.0016 21.6 2.5 27 2-28 43-69 (83)
97 cd00164 S1_like S1_like: Ribos 26.2 1.3E+02 0.0028 17.2 3.5 9 22-30 51-59 (65)
98 cd04715 BAH_Orc1p_like BAH, or 25.8 1.7E+02 0.0037 22.1 4.8 28 3-30 30-57 (159)
99 cd04452 S1_IF2_alpha S1_IF2_al 25.6 1.7E+02 0.0037 18.0 4.2 13 22-34 59-71 (76)
100 cd05689 S1_RPS1_repeat_ec4 S1_ 25.3 1.2E+02 0.0027 18.6 3.4 6 6-11 52-57 (72)
101 cd04721 BAH_plant_1 BAH, or Br 24.9 1.8E+02 0.004 21.0 4.7 29 2-30 7-35 (130)
102 PF01426 BAH: BAH domain; Int 24.6 93 0.002 20.9 2.9 29 2-30 2-32 (119)
103 PRK02935 hypothetical protein; 24.3 35 0.00076 24.8 0.7 36 63-105 64-99 (110)
104 PLN00190 60S ribosomal protein 24.0 1.2E+02 0.0027 23.3 3.7 32 3-34 34-75 (158)
105 cd03696 selB_II selB_II: this 23.5 1.2E+02 0.0026 19.5 3.2 11 3-13 27-37 (83)
106 PF01157 Ribosomal_L21e: Ribos 23.4 2E+02 0.0043 20.3 4.5 29 2-30 32-70 (99)
107 cd01854 YjeQ_engC YjeQ/EngC. 23.2 1.6E+02 0.0035 23.7 4.5 30 2-33 34-63 (287)
108 PF11910 NdhO: Cyanobacterial 23.1 44 0.00096 22.3 1.0 16 3-18 1-16 (67)
109 cd05687 S1_RPS1_repeat_ec1_hs1 23.1 1.9E+02 0.0041 17.6 4.0 12 23-34 55-66 (70)
110 cd00674 LysRS_core_class_I cat 23.0 1.8E+02 0.0038 24.8 4.8 42 60-101 160-201 (353)
111 cd05696 S1_Rrp5_repeat_hs4 S1_ 22.8 2.1E+02 0.0045 18.0 4.1 15 21-35 55-69 (71)
112 PF06519 TolA: TolA C-terminal 22.7 1.3E+02 0.0029 20.8 3.4 42 74-115 34-93 (96)
113 cd05792 S1_eIF1AD_like S1_eIF1 22.6 1E+02 0.0022 20.8 2.8 29 2-30 38-67 (78)
114 KOG0122 Translation initiation 22.5 1.6E+02 0.0034 24.6 4.2 49 62-113 17-72 (270)
115 cd03698 eRF3_II_like eRF3_II_l 22.4 1.3E+02 0.0029 19.4 3.3 16 24-39 33-48 (83)
116 TIGR03170 flgA_cterm flagella 22.4 1.4E+02 0.0031 20.6 3.6 11 3-13 66-76 (122)
117 cd04090 eEF2_II_snRNP Loc2 eEF 22.1 2.5E+02 0.0054 18.6 4.9 13 2-14 27-39 (94)
118 cd04709 BAH_MTA BAH, or Bromo 22.0 2.7E+02 0.0058 21.2 5.2 33 3-35 4-38 (164)
119 cd03693 EF1_alpha_II EF1_alpha 21.9 1.3E+02 0.0029 19.9 3.2 15 25-39 38-52 (91)
120 COG1162 Predicted GTPases [Gen 21.8 1.3E+02 0.0028 25.3 3.8 27 3-32 45-71 (301)
121 PF06701 MIB_HERC2: Mib_herc2; 21.3 1.2E+02 0.0027 19.9 2.9 10 17-26 19-28 (68)
122 PRK07252 hypothetical protein; 21.3 2E+02 0.0043 20.6 4.2 24 3-36 48-71 (120)
123 cd05691 S1_RPS1_repeat_ec6 S1_ 20.9 2.1E+02 0.0045 17.3 4.2 14 22-35 54-67 (73)
124 PF05257 CHAP: CHAP domain; I 20.8 1.8E+02 0.0038 20.0 3.8 36 3-39 63-100 (124)
125 PF08813 Phage_tail_3: Phage t 20.8 3.1E+02 0.0068 20.6 5.4 71 22-93 9-80 (165)
126 COG1385 Uncharacterized protei 20.7 1.7E+02 0.0037 23.6 4.1 34 1-34 32-65 (246)
127 COG2053 RPS28A Ribosomal prote 20.6 84 0.0018 21.0 1.9 12 8-19 27-38 (69)
128 PF09356 Phage_BR0599: Phage c 20.5 92 0.002 20.9 2.2 17 2-18 40-56 (80)
129 PRK04306 50S ribosomal protein 20.3 2E+02 0.0043 20.4 3.9 33 3-35 35-77 (98)
130 smart00357 CSP Cold shock prot 20.2 1.9E+02 0.0041 16.9 3.4 24 3-26 37-63 (64)
131 cd04714 BAH_BAHCC1 BAH, or Bro 20.2 2E+02 0.0044 20.3 4.0 34 3-36 4-40 (121)
132 PF07076 DUF1344: Protein of u 20.2 1.1E+02 0.0025 19.9 2.4 19 19-37 5-23 (61)
No 1
>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=100.00 E-value=8.9e-40 Score=233.25 Aligned_cols=102 Identities=51% Similarity=0.779 Sum_probs=98.6
Q ss_pred CCcccCCEEEEeecCCCCeEeEEEEEEccCCeEEEeceeeeEEEecCCcccC-CceEEEEeecCcCCCeeeeecCCCCee
Q 033131 1 MHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEE-QGQIIKIEAPIHSSNVMLYSKEMEVAS 79 (126)
Q Consensus 1 ~~I~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~VeGvN~~kkh~k~~~~~~-~ggi~~~e~pI~~SNV~Lv~p~~~~~~ 79 (126)
|+|++||+|+||+|+|||++|+|++|++++++|+|||+|+.++|++|++.++ +|+|+++|+|||+|||+|+||.+++|+
T Consensus 2 ~~ikkGD~V~Vi~G~dKGK~G~V~~V~~~~~~V~VegvN~~kkh~k~~~~~~~~g~i~~~e~pI~~SnV~lv~p~~~k~~ 81 (104)
T TIGR01079 2 MKIKKGDTVKVISGKDKGKRGKVLKVLPKTNKVIVEGVNMVKKHVKPKPTQRSQGGIIEKEAPIHISNVMLFDPKTGKAT 81 (104)
T ss_pred CcccCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEECCcEEEEEecCcccCCCCCCceEEEEccCCHHHeEEEcCcCCCCe
Confidence 6899999999999999999999999999999999999999999999988776 899999999999999999999999999
Q ss_pred eEEEEEccCCcEEEEEcccCccc
Q 033131 80 RVGHKVLDDGTRVRYLIKTGEII 102 (126)
Q Consensus 80 rv~~~~~~dG~kvRv~k~sg~~i 102 (126)
|++|++++||+++|+|++||+.|
T Consensus 82 rv~~~~~~~g~kvRv~k~~g~~i 104 (104)
T TIGR01079 82 RVGIRFEEDGKKVRVFKKTGEII 104 (104)
T ss_pred EEEEEEccCCcEEEEEeccCCcC
Confidence 99999999999999999999875
No 2
>PRK00004 rplX 50S ribosomal protein L24; Reviewed
Probab=100.00 E-value=3.1e-39 Score=230.54 Aligned_cols=103 Identities=50% Similarity=0.742 Sum_probs=99.7
Q ss_pred CCcccCCEEEEeecCCCCeEeEEEEEEccCCeEEEeceeeeEEEecCCcccCCceEEEEeecCcCCCeeeeecCCCCeee
Q 033131 1 MHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQIIKIEAPIHSSNVMLYSKEMEVASR 80 (126)
Q Consensus 1 ~~I~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~VeGvN~~kkh~k~~~~~~~ggi~~~e~pI~~SNV~Lv~p~~~~~~r 80 (126)
|+|++||+|+||+|+|||++|+|++|++++++|+|||+|+.++|+|+++++.+|+++++|+|||+|||+|++|.+++|+|
T Consensus 3 ~~i~kGD~V~Vi~G~dKGk~G~V~~V~~~~~~V~Vegvn~~k~h~k~~~~~~~G~i~~~e~pI~~SnV~lv~p~~~~~~r 82 (105)
T PRK00004 3 MKIKKGDTVIVIAGKDKGKRGKVLKVLPKKNKVIVEGVNIVKKHQKPNQENPQGGIIEKEAPIHISNVALVDPKTGKATR 82 (105)
T ss_pred CcccCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEEcCcEEEEEecCCCCCCCCCceEEEECCcCHHHEEEEeCcCCCCeE
Confidence 58999999999999999999999999999999999999999999999887888999999999999999999999999999
Q ss_pred EEEEEccCCcEEEEEcccCcccc
Q 033131 81 VGHKVLDDGTRVRYLIKTGEIID 103 (126)
Q Consensus 81 v~~~~~~dG~kvRv~k~sg~~i~ 103 (126)
++|++++||+++|+|++||+.|+
T Consensus 83 v~~~~~~~g~kvRv~k~~g~~i~ 105 (105)
T PRK00004 83 VGFKFLEDGKKVRVAKKSGEVID 105 (105)
T ss_pred EEEEEccCCcEEEEEecCCCCcC
Confidence 99999999999999999999874
No 3
>COG0198 RplX Ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.5e-36 Score=216.71 Aligned_cols=101 Identities=50% Similarity=0.746 Sum_probs=96.2
Q ss_pred CCcccCCEEEEeecCCCCeEeEEEEEEccCCeEEEeceeeeEEEecCCcccCCceEEEEeecCcCCCeeeeec-CCCCee
Q 033131 1 MHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQIIKIEAPIHSSNVMLYSK-EMEVAS 79 (126)
Q Consensus 1 ~~I~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~VeGvN~~kkh~k~~~~~~~ggi~~~e~pI~~SNV~Lv~p-~~~~~~ 79 (126)
|+|++||+|.||+|+|||++|+|++|+++. |+|||+|++++|.+|++++++|||+++|+|||+|||||++| .+++++
T Consensus 3 ~~IrkGD~V~Vi~GkdKGk~GkVl~v~~k~--V~VEGvnv~kkh~k~~~~~~~ggii~~EapIh~SnV~i~~~~~~~~~~ 80 (104)
T COG0198 3 MKVKKGDTVKVIAGKDKGKEGKVLKVLPKK--VVVEGVNVVKKHIKPSQENPEGGIINKEAPIHISNVAIIDPNKTGKPT 80 (104)
T ss_pred cceecCCEEEEEecCCCCcceEEEEEecCe--EEEECcEEEEecCCCCCcCCCCceeeeeecccHHHeEEeccccCCCcc
Confidence 589999999999999999999999999998 99999999999999877778899999999999999999999 799999
Q ss_pred eEEEEEccCCcEEEEEcccCcccc
Q 033131 80 RVGHKVLDDGTRVRYLIKTGEIID 103 (126)
Q Consensus 80 rv~~~~~~dG~kvRv~k~sg~~i~ 103 (126)
|++|++.+||+++|++++||+.|+
T Consensus 81 Rv~~~~~~~~kkvr~~Kk~g~~i~ 104 (104)
T COG0198 81 RVGYKVEEDGKKVRVAKKSGEVID 104 (104)
T ss_pred eEEEEEecCCcEEEEEeccCcccC
Confidence 999998779999999999999874
No 4
>KOG1708 consensus Mitochondrial/chloroplast ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=99.97 E-value=7e-32 Score=211.96 Aligned_cols=108 Identities=44% Similarity=0.693 Sum_probs=103.8
Q ss_pred CCcccCCEEEEeecCCCCeEeEEEEEEccCCeEEEeceeeeEEEecCCcccCCceEEEEeecCcCCC-eeeeecCCCCee
Q 033131 1 MHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQIIKIEAPIHSSN-VMLYSKEMEVAS 79 (126)
Q Consensus 1 ~~I~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~VeGvN~~kkh~k~~~~~~~ggi~~~e~pI~~SN-V~Lv~p~~~~~~ 79 (126)
++++.||+|+||.|+||||+|.|++|.+.+++|+|+|+|...+|+....+|..|.|+..|+|||.|| ||||||++.+||
T Consensus 71 w~ff~GDtVeVlvGkDkGkqG~Vtqv~r~~s~VvV~gln~k~r~~gsekeg~pgtivk~EaPlhvsk~VmLvdp~d~q~t 150 (236)
T KOG1708|consen 71 WHFFFGDTVEVLVGKDKGKQGEVTQVIRHRSWVVVKGLNTKYRHMGSEKEGEPGTIVKSEAPLHVSKQVMLVDPEDDQPT 150 (236)
T ss_pred eeEecCCEEEEEecccCCccceEEEEeecCceEEEcccchhhhhhcccccCCCceEEeecCCceecceeEEECccccCCc
Confidence 4789999999999999999999999999999999999999999998877788999999999999999 999999999999
Q ss_pred eEEEEEccCCcEEEEEcccCcccccchhh
Q 033131 80 RVGHKVLDDGTRVRYLIKTGEIIDSAENW 108 (126)
Q Consensus 80 rv~~~~~~dG~kvRv~k~sg~~i~~p~~~ 108 (126)
+++|+++++|++|||+.+||++||.||.|
T Consensus 151 e~~wr~~e~GekVRvstrSG~iIpipe~~ 179 (236)
T KOG1708|consen 151 EVEWRFTEDGEKVRVSTRSGRIIPIPEKW 179 (236)
T ss_pred eeeEEEcCCCcEEEEEecccccccCcccc
Confidence 99999999999999999999999998766
No 5
>CHL00141 rpl24 ribosomal protein L24; Validated
Probab=99.96 E-value=3.9e-29 Score=172.16 Aligned_cols=76 Identities=59% Similarity=0.938 Sum_probs=73.0
Q ss_pred CCcccCCEEEEeecCCCCeEeEEEEEEccCCeEEEeceeeeEEEecCCcccCCceEEEEeecCcCCCeeeeecCCC
Q 033131 1 MHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQIIKIEAPIHSSNVMLYSKEME 76 (126)
Q Consensus 1 ~~I~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~VeGvN~~kkh~k~~~~~~~ggi~~~e~pI~~SNV~Lv~p~~~ 76 (126)
|+|++||+|+||+|+|||++|+|++|++++++|+|||+|+.++|++|+..+.+|+++++|+|||+|||+|+||++.
T Consensus 7 ~~I~~GD~V~Vi~G~dKGK~G~V~~V~~~~~~V~Vegvn~~~k~~k~~~~~~~g~i~~~e~pI~~SnV~lvdp~~~ 82 (83)
T CHL00141 7 MHVKIGDTVKIISGSDKGKIGEVLKIIKKSNKVIVKGINIKFKHIKPNKENEVGEIKQFEAPIHSSNVMLYNEESN 82 (83)
T ss_pred CcccCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEEcCcEEEEEEcCCccCCCCCCEEEEECCCCHHHEEEeCcccC
Confidence 5899999999999999999999999999999999999999999999988788899999999999999999999874
No 6
>PRK12281 rplX 50S ribosomal protein L24; Reviewed
Probab=99.95 E-value=2.9e-28 Score=165.43 Aligned_cols=71 Identities=41% Similarity=0.635 Sum_probs=68.7
Q ss_pred CCcccCCEEEEeecCCCCeEeEEEEEEccCCeEEEeceeeeEEEecCCcccCCceEEEEeecCcCCCeeee
Q 033131 1 MHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQIIKIEAPIHSSNVMLY 71 (126)
Q Consensus 1 ~~I~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~VeGvN~~kkh~k~~~~~~~ggi~~~e~pI~~SNV~Lv 71 (126)
|+|++||+|+||+|+|||++|+|++|++++++|+|||+|+.++|+||++++.+|+++++|+|||+|||+|+
T Consensus 5 ~~I~kGD~V~Vi~G~dKGK~G~V~~V~~~~~~V~Vegvn~~kkh~kp~~~~~~G~i~~~e~pI~~SnV~l~ 75 (76)
T PRK12281 5 LKVKKGDMVKVIAGDDKGKTGKVLAVLPKKNRVIVEGVKIAKKAIKPSQKNPNGGFIEKEMPIHISNVKKV 75 (76)
T ss_pred ccccCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEEcCcEEEEEEcCCCccCCCCCEEEEEcCcCHHHceec
Confidence 68999999999999999999999999999999999999999999999988878999999999999999996
No 7
>PTZ00194 60S ribosomal protein L26; Provisional
Probab=99.86 E-value=4.6e-22 Score=149.01 Aligned_cols=67 Identities=27% Similarity=0.479 Sum_probs=62.6
Q ss_pred CCcccCCEEEEeecCCCCeEeEEEEEEccCCeEEEeceeeeEEEecCCcccCCceEEEEeecCcCCCeeeeecCCCCe
Q 033131 1 MHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQIIKIEAPIHSSNVMLYSKEMEVA 78 (126)
Q Consensus 1 ~~I~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~VeGvN~~kkh~k~~~~~~~ggi~~~e~pI~~SNV~Lv~p~~~~~ 78 (126)
|+|++||+|+||+|+|||++|+|++|+++.++|+|||||+.++|.+| +|+|||+|||+|+++..+..
T Consensus 45 ~~IkkGD~V~Vi~Gk~KGk~GkV~~V~~k~~~ViVEgvn~~Kk~gk~-----------~e~PIh~SNV~iv~l~l~~~ 111 (143)
T PTZ00194 45 MPVRKDDEVMVVRGHHKGREGKVTAVYRKKWVIHIEKITREKANGEP-----------VQIGIHPSNVIITKLKLNKD 111 (143)
T ss_pred ceeecCCEEEEecCCCCCCceEEEEEEcCCCEEEEeCeEEEecCCCE-----------eecCcCchheEEEccccCch
Confidence 58999999999999999999999999999999999999999987643 69999999999999998776
No 8
>PRK01191 rpl24p 50S ribosomal protein L24P; Validated
Probab=99.86 E-value=7.4e-22 Score=144.25 Aligned_cols=70 Identities=33% Similarity=0.535 Sum_probs=62.8
Q ss_pred CCcccCCEEEEeecCCCCeEeEEEEEEccCCeEEEeceeeeEEEecCCcccCCceEEEEeecCcCCCeeeeecCCCCeee
Q 033131 1 MHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQIIKIEAPIHSSNVMLYSKEMEVASR 80 (126)
Q Consensus 1 ~~I~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~VeGvN~~kkh~k~~~~~~~ggi~~~e~pI~~SNV~Lv~p~~~~~~r 80 (126)
|+|++||.|+||+|+|||++|+|++|++++++|+|||||+.+ + +| .++|+|||+|||+|+|+..+...|
T Consensus 44 ~~IkkGD~V~VisG~~KGk~GkV~~V~~~~~~V~VeGvn~~k----~-----~G--~~~e~pIh~SNV~l~~l~l~~~~R 112 (120)
T PRK01191 44 LPVRKGDTVKVMRGDFKGEEGKVVEVDLKRGRIYVEGVTVKK----A-----DG--TEVPRPIHPSNVMITKLDLSDERR 112 (120)
T ss_pred ceEeCCCEEEEeecCCCCceEEEEEEEcCCCEEEEeCcEEEC----C-----CC--eEEEcccchhHeEEEeCccCCHHH
Confidence 589999999999999999999999999999999999999987 2 24 599999999999999998865554
Q ss_pred E
Q 033131 81 V 81 (126)
Q Consensus 81 v 81 (126)
.
T Consensus 113 ~ 113 (120)
T PRK01191 113 E 113 (120)
T ss_pred H
Confidence 3
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=99.82 E-value=1.7e-20 Score=136.01 Aligned_cols=69 Identities=29% Similarity=0.510 Sum_probs=62.3
Q ss_pred CCcccCCEEEEeecCCCCeEeEEEEEEccCCeEEEeceeeeEEEecCCcccCCceEEEEeecCcCCCeeeeecCCCCeee
Q 033131 1 MHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQIIKIEAPIHSSNVMLYSKEMEVASR 80 (126)
Q Consensus 1 ~~I~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~VeGvN~~kkh~k~~~~~~~ggi~~~e~pI~~SNV~Lv~p~~~~~~r 80 (126)
|+|++||+|+||+|+|||++|+|++|++++++|+|||+|+.+ ++ | .++|+|||+|||+|+|+..+...|
T Consensus 40 ~~IkkGD~V~Vi~Gk~KGk~GkV~~V~~~~~~V~Vegvn~~k----~~-----G--~~~e~pIh~SnV~l~~l~l~~~~R 108 (114)
T TIGR01080 40 LPVRKGDKVRIMRGDFKGHEGKVSKVDLKRYRIYVEGVTKEK----VN-----G--TEVPVPIHPSNVMITKLNLDDEKR 108 (114)
T ss_pred ceeecCCEEEEecCCCCCCEEEEEEEEcCCCEEEEcCeEEEC----CC-----C--eEEEeeechHHeEEEeccCChHHH
Confidence 589999999999999999999999999999999999999997 32 3 699999999999999998776533
No 10
>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=98.88 E-value=4.7e-09 Score=60.03 Aligned_cols=32 Identities=53% Similarity=0.709 Sum_probs=30.7
Q ss_pred cCCEEEEeecCCCCeEeEEEEEEccCCeEEEe
Q 033131 5 AGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 36 (126)
Q Consensus 5 kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~Ve 36 (126)
+||.|.|++|+++|++|+|+++++++++|+||
T Consensus 1 ~Gd~V~V~~G~~~G~~G~I~~i~~~~~~V~ve 32 (32)
T PF00467_consen 1 VGDTVKVISGPFKGKIGKIVEIDRSKVRVTVE 32 (32)
T ss_dssp TTSEEEESSSTTTTEEEEEEEEETTTTEEEES
T ss_pred CCCEEEEeEcCCCCceEEEEEEECCCCEEEEC
Confidence 69999999999999999999999999999986
No 11
>KOG3401 consensus 60S ribosomal protein L26 [Translation, ribosomal structure and biogenesis]
Probab=98.71 E-value=1.2e-08 Score=76.69 Aligned_cols=65 Identities=23% Similarity=0.518 Sum_probs=56.1
Q ss_pred CCcccCCEEEEeecCCCC-eEeEEEEEEccCCeEEEeceeeeEEEecCCcccCCceEEEEeecCcCCCeeeeecCCC
Q 033131 1 MHVKAGDTVKVIAGCDKG-KIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQIIKIEAPIHSSNVMLYSKEME 76 (126)
Q Consensus 1 ~~I~kGD~V~Vi~GkdKG-K~G~V~~V~~~~~~V~VeGvN~~kkh~k~~~~~~~ggi~~~e~pI~~SNV~Lv~p~~~ 76 (126)
|+|+.+|.|.|..|.++| ++|+|++|++++..+++|.|...+ .+ +. ..+.|||+|++.+..|...
T Consensus 47 ~pir~ddev~v~rg~~kG~q~G~v~~vyrKk~~iyie~v~~eK----~n--Gt-----~v~vgihPsK~~iTkl~lD 112 (145)
T KOG3401|consen 47 MPIRKDDEVQVVRGHFKGFQIGKVSQVYRKKYVIYIERVQREK----AN--GT-----TVPVGIHPSKVVITKLKLD 112 (145)
T ss_pred cceeeccEEEEEeccccccccceehhhhhhhheeeeEeEEEee----cc--Cc-----ccccccCccceeecccchh
Confidence 689999999999999999 889999999999999999976554 22 22 7889999999999987654
No 12
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=97.98 E-value=1.5e-05 Score=43.00 Aligned_cols=27 Identities=48% Similarity=0.685 Sum_probs=24.7
Q ss_pred CcccCCEEEEeecCCCCeEeEEEEEEc
Q 033131 2 HVKAGDTVKVIAGCDKGKIGEITKVFR 28 (126)
Q Consensus 2 ~I~kGD~V~Vi~GkdKGK~G~V~~V~~ 28 (126)
.+.+||.|+|+.|+++|+.|.|++++.
T Consensus 1 ~~~~G~~V~I~~G~~~g~~g~i~~i~~ 27 (28)
T smart00739 1 KFEVGDTVRVIAGPFKGKVGKVLEVDG 27 (28)
T ss_pred CCCCCCEEEEeECCCCCcEEEEEEEcC
Confidence 367999999999999999999999875
No 13
>PRK08559 nusG transcription antitermination protein NusG; Validated
Probab=97.57 E-value=0.00026 Score=53.08 Aligned_cols=57 Identities=26% Similarity=0.367 Sum_probs=44.8
Q ss_pred CcccCCEEEEeecCCCCeEeEEEEEEccCCeEEEeceeeeEEEecCCcccCCceEEEEeecCcCCCeeeeec
Q 033131 2 HVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQIIKIEAPIHSSNVMLYSK 73 (126)
Q Consensus 2 ~I~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~VeGvN~~kkh~k~~~~~~~ggi~~~e~pI~~SNV~Lv~p 73 (126)
.+.+||.|.|++|+++|..|.|.+++.+++++.|+-++... ..+.-++.+.|.++.+
T Consensus 94 ~~~~G~~V~I~~Gpf~g~~g~V~~vd~~k~~v~v~ll~~~~---------------~~pv~v~~~~~~~~~~ 150 (153)
T PRK08559 94 GIKEGDIVELIAGPFKGEKARVVRVDESKEEVTVELLEAAV---------------PIPVTVRGDQVRVVKK 150 (153)
T ss_pred CCCCCCEEEEeccCCCCceEEEEEEcCCCCEEEEEEECCcc---------------eeeEEEeccEEEEecc
Confidence 47899999999999999999999999999999988665332 2345566666766653
No 14
>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=97.55 E-value=0.0003 Score=51.74 Aligned_cols=37 Identities=30% Similarity=0.457 Sum_probs=33.3
Q ss_pred cccCCEEEEeecCCCCeEeEEEEEEccCCeEEEecee
Q 033131 3 VKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDIN 39 (126)
Q Consensus 3 I~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~VeGvN 39 (126)
+..||.|.|++|+++|-.|.|.+++..+..|.|+-.+
T Consensus 87 ~~~Gd~V~I~~GPf~G~~g~v~~~d~~k~~v~v~l~~ 123 (145)
T TIGR00405 87 IKKGDIVEIISGPFKGERAKVIRVDESKEEVTLELIE 123 (145)
T ss_pred cCCCCEEEEeecCCCCCeEEEEEEcCCCCEEEEEEEE
Confidence 6799999999999999999999999888888887554
No 15
>PRK05609 nusG transcription antitermination protein NusG; Validated
Probab=97.13 E-value=0.001 Score=50.07 Aligned_cols=35 Identities=26% Similarity=0.281 Sum_probs=31.4
Q ss_pred CcccCCEEEEeecCCCCeEeEEEEEEccCCeEEEe
Q 033131 2 HVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 36 (126)
Q Consensus 2 ~I~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~Ve 36 (126)
.+.+||+|.|++|+++|-.|.|.++++.++++.|+
T Consensus 126 ~~~~Gd~VrI~~GPf~G~~g~v~~i~~~~~r~~v~ 160 (181)
T PRK05609 126 DFEVGEMVRVIDGPFADFNGTVEEVDYEKSKLKVL 160 (181)
T ss_pred CCCCCCEEEEeccCCCCCEEEEEEEeCCCCEEEEE
Confidence 36799999999999999999999999877787766
No 16
>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=97.09 E-value=0.0012 Score=49.50 Aligned_cols=34 Identities=24% Similarity=0.270 Sum_probs=31.0
Q ss_pred cccCCEEEEeecCCCCeEeEEEEEEccCCeEEEe
Q 033131 3 VKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 36 (126)
Q Consensus 3 I~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~Ve 36 (126)
+.+||+|.|++|+++|-.|.|.+++..++++.|.
T Consensus 120 ~~~G~~V~I~~Gpf~G~~g~v~~~~~~~~r~~V~ 153 (172)
T TIGR00922 120 FEVGEQVRVNDGPFANFTGTVEEVDYEKSKLKVS 153 (172)
T ss_pred CCCCCEEEEeecCCCCcEEEEEEEcCCCCEEEEE
Confidence 6799999999999999999999999877787776
No 17
>COG0250 NusG Transcription antiterminator [Transcription]
Probab=96.95 E-value=0.0014 Score=50.73 Aligned_cols=35 Identities=23% Similarity=0.362 Sum_probs=32.5
Q ss_pred CcccCCEEEEeecCCCCeEeEEEEEEccCCeEEEe
Q 033131 2 HVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 36 (126)
Q Consensus 2 ~I~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~Ve 36 (126)
.+.+||.|.|++|+++|-.|+|.+|+.+++++.|+
T Consensus 123 ~~e~Gd~VrI~~GpFa~f~g~V~evd~ek~~~~v~ 157 (178)
T COG0250 123 DFEPGDVVRIIDGPFAGFKAKVEEVDEEKGKLKVE 157 (178)
T ss_pred cCCCCCEEEEeccCCCCccEEEEEEcCcCcEEEEE
Confidence 36799999999999999999999999999988877
No 18
>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=96.54 E-value=0.005 Score=45.39 Aligned_cols=33 Identities=18% Similarity=0.137 Sum_probs=28.2
Q ss_pred cccCCEEEEeecCCCCeEeEEEEEEccCCeEEEe
Q 033131 3 VKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 36 (126)
Q Consensus 3 I~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~Ve 36 (126)
+.+||+|.|+.|+++|-.|.|.+++. ++++.|.
T Consensus 109 ~~~G~~V~V~~GPf~g~~g~v~~~~~-~~r~~v~ 141 (159)
T TIGR01955 109 PYKGDKVRITDGAFAGFEAIFLEPDG-EKRSMLL 141 (159)
T ss_pred CCCCCEEEEeccCCCCcEEEEEEECC-CceEEEE
Confidence 67999999999999999999999974 4566654
No 19
>PRK09014 rfaH transcriptional activator RfaH; Provisional
Probab=96.29 E-value=0.0078 Score=44.79 Aligned_cols=33 Identities=21% Similarity=0.198 Sum_probs=27.9
Q ss_pred cccCCEEEEeecCCCCeEeEEEEEEccCCeEEEe
Q 033131 3 VKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 36 (126)
Q Consensus 3 I~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~Ve 36 (126)
+.+||+|.|+.|+++|-.|.|.+++ .+.++.|.
T Consensus 110 ~~~G~~V~I~~Gp~~g~eg~v~~~~-~~~r~~v~ 142 (162)
T PRK09014 110 PKPGDKVIITEGAFEGLQAIYTEPD-GEARSILL 142 (162)
T ss_pred CCCCCEEEEecCCCCCcEEEEEEeC-CCeEEEEe
Confidence 5689999999999999999999998 44565544
No 20
>TIGR01956 NusG_myco NusG family protein. This model represents a family of Mycoplasma proteins orthologous to the bacterial transcription termination/antitermination factor NusG. These sequences from Mycoplasma are notably diverged (long branches in a Neighbor-joining phylogenetic tree) from the bacterial species. And although NusA and ribosomal protein S10 (NusE) appear to be present, NusB may be absent in Mycoplasmas calling into question whether these species have a functional Nus system including this family as a member.
Probab=96.27 E-value=0.0096 Score=48.86 Aligned_cols=35 Identities=29% Similarity=0.536 Sum_probs=31.7
Q ss_pred CcccCCEEEEeecCCCCeEeEEEEEEccCCeEEEe
Q 033131 2 HVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 36 (126)
Q Consensus 2 ~I~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~Ve 36 (126)
.+..||.|.|++|+++|..|.|.+++..+.++.|.
T Consensus 205 ~f~vGd~VrI~dGPF~GfeG~I~eid~~k~Rv~Vl 239 (258)
T TIGR01956 205 KFRVGNFVKIVDGPFKGIVGKIKKIDQEKKKAIVE 239 (258)
T ss_pred CCCCCCEEEEEecCCCCcEEEEEEEeCCCCEEEEE
Confidence 36799999999999999999999999878888776
No 21
>PRK04333 50S ribosomal protein L14e; Validated
Probab=95.21 E-value=0.052 Score=37.49 Aligned_cols=37 Identities=19% Similarity=0.280 Sum_probs=32.5
Q ss_pred CCcccCCEEEEeecCCCCeEeEEEEEEccCCeEEEece
Q 033131 1 MHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDI 38 (126)
Q Consensus 1 ~~I~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~VeGv 38 (126)
|.+..|-.|.+.+|+|+|+...|+.+.. .++|+|+|-
T Consensus 2 ~~v~~GrvV~~~~Grd~gk~~vIv~i~d-~~~vlVdg~ 38 (84)
T PRK04333 2 PAIEVGRVCVKTAGREAGRKCVIVDIID-KNFVLVTGP 38 (84)
T ss_pred CcccccEEEEEeccCCCCCEEEEEEEec-CCEEEEECC
Confidence 4678999999999999999999999864 579999875
No 22
>PTZ00065 60S ribosomal protein L14; Provisional
Probab=91.42 E-value=0.43 Score=35.61 Aligned_cols=34 Identities=24% Similarity=0.345 Sum_probs=29.5
Q ss_pred ccCCEEEEeecCCCCeEeEEEEEEccCCeEEEece
Q 033131 4 KAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDI 38 (126)
Q Consensus 4 ~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~VeGv 38 (126)
-.|=.|.|..|+++||...|..|. +.|+|+|+|=
T Consensus 9 EiGRVvli~~Gp~~GKL~vIVDII-D~nRvLVDGP 42 (130)
T PTZ00065 9 EPGRLCLIQYGPDAGKLCFIVDIV-TPTRVLVDGA 42 (130)
T ss_pred eeceEEEEecCCCCCCEEEEEEEE-cCCeEEEeCC
Confidence 467788899999999999999997 5589999975
No 23
>PTZ00471 60S ribosomal protein L27; Provisional
Probab=90.54 E-value=0.52 Score=35.35 Aligned_cols=40 Identities=25% Similarity=0.341 Sum_probs=34.5
Q ss_pred cccCCEEEEeecCCCCeEeEEEEEEccC------CeEEEeceeeeE
Q 033131 3 VKAGDTVKVIAGCDKGKIGEITKVFRHN------STVMVKDINLKT 42 (126)
Q Consensus 3 I~kGD~V~Vi~GkdKGK~G~V~~V~~~~------~~V~VeGvN~~k 42 (126)
+++|-.|.|++|++.|+...|++.+.+. +..+|-|+...-
T Consensus 5 ~kpgkVVivL~GR~AGkKaVivk~~ddgt~drpy~halVaGIdryP 50 (134)
T PTZ00471 5 LKPGKVVIVTSGRYAGRKAVIVQNFDTASKERPYGHALVAGIKKYP 50 (134)
T ss_pred ccCCEEEEEEccccCCcEEEEEeecCCCCccCcCceEEEEeecccc
Confidence 6789999999999999999999987665 689999987543
No 24
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=90.47 E-value=0.32 Score=46.37 Aligned_cols=28 Identities=39% Similarity=0.540 Sum_probs=25.6
Q ss_pred CcccCCEEEEeecCCCCeEeEEEEEEcc
Q 033131 2 HVKAGDTVKVIAGCDKGKIGEITKVFRH 29 (126)
Q Consensus 2 ~I~kGD~V~Vi~GkdKGK~G~V~~V~~~ 29 (126)
.|..||-|.||+|++.|.+|-|++|...
T Consensus 459 yF~~GDhVKVi~G~~eG~tGlVvrVe~~ 486 (1024)
T KOG1999|consen 459 YFEPGDHVKVIAGRYEGDTGLVVRVEQG 486 (1024)
T ss_pred hccCCCeEEEEeccccCCcceEEEEeCC
Confidence 4789999999999999999999999764
No 25
>COG2163 RPL14A Ribosomal protein L14E/L6E/L27E [Translation, ribosomal structure and biogenesis]
Probab=84.70 E-value=2.1 Score=31.73 Aligned_cols=36 Identities=31% Similarity=0.353 Sum_probs=31.1
Q ss_pred CcccCCEEEEeecCCCCeEeEEEEEEccCCeEEEece
Q 033131 2 HVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDI 38 (126)
Q Consensus 2 ~I~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~VeGv 38 (126)
-+.+|=-|++++|+++|+...|+++.-++ .+++.|-
T Consensus 4 ~l~~GrVvvv~~GR~aGkk~VIv~~iDd~-~v~i~gp 39 (125)
T COG2163 4 SLEVGRVVVVTAGRFAGKKVVIVKIIDDN-FVLITGP 39 (125)
T ss_pred cccCCeEEEEecceeCCceEEEEEEccCC-EEEEeCC
Confidence 36789999999999999999999998665 8888874
No 26
>PRK04313 30S ribosomal protein S4e; Validated
Probab=82.73 E-value=2.3 Score=34.66 Aligned_cols=36 Identities=22% Similarity=0.414 Sum_probs=28.8
Q ss_pred CcccCCEEEEeecCCCCeEeEEEEEEccC----CeEEEec
Q 033131 2 HVKAGDTVKVIAGCDKGKIGEITKVFRHN----STVMVKD 37 (126)
Q Consensus 2 ~I~kGD~V~Vi~GkdKGK~G~V~~V~~~~----~~V~VeG 37 (126)
++..|-.+.|+.|++-|.+|+|.++.... +.|.+++
T Consensus 171 ~fe~G~l~~itgG~n~GriG~I~~i~~~~~~~~~~V~i~d 210 (237)
T PRK04313 171 PFEEGNLAIITGGKHVGEIGKIKEIEVTKSSKPNIVTLED 210 (237)
T ss_pred ecCCCCEEEEECCeeeeeEEEEEEEEEccCCCCcEEEEEc
Confidence 56789999999999999999999886443 4566663
No 27
>PRK06531 yajC preprotein translocase subunit YajC; Validated
Probab=80.10 E-value=3.9 Score=29.70 Aligned_cols=31 Identities=26% Similarity=0.472 Sum_probs=26.1
Q ss_pred CcccCCEEEEeecCCCCeEeEEEEEEccCCeEEEe
Q 033131 2 HVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 36 (126)
Q Consensus 2 ~I~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~Ve 36 (126)
.|++||+|+-+.| -.|+|.+|..+.+.|.+|
T Consensus 36 sLk~GD~VvT~GG----i~G~V~~I~~~~~~v~le 66 (113)
T PRK06531 36 AIQKGDEVVTIGG----LYGTVDEVDTEAKTIVLD 66 (113)
T ss_pred hcCCCCEEEECCC----cEEEEEEEecCCCEEEEE
Confidence 5789999988876 589999998777788886
No 28
>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=78.04 E-value=5.8 Score=25.71 Aligned_cols=27 Identities=33% Similarity=0.665 Sum_probs=22.2
Q ss_pred ccCCEEEEeecCCCCeEeEEEEEEccCCeEEEe
Q 033131 4 KAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 36 (126)
Q Consensus 4 ~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~Ve 36 (126)
..||.+.. ..|-+|+|.+|+ .|+|+|+
T Consensus 5 ~vGdiIef----k~g~~G~V~kv~--eNSVIVd 31 (57)
T PF09953_consen 5 KVGDIIEF----KDGFTGIVEKVY--ENSVIVD 31 (57)
T ss_pred ccCcEEEE----cCCcEEEEEEEe--cCcEEEE
Confidence 47999986 357899999997 5899987
No 29
>COG5164 SPT5 Transcription elongation factor [Transcription]
Probab=77.99 E-value=2 Score=38.58 Aligned_cols=28 Identities=32% Similarity=0.476 Sum_probs=25.1
Q ss_pred cccCCEEEEeecCCCCeEeEEEEEEccC
Q 033131 3 VKAGDTVKVIAGCDKGKIGEITKVFRHN 30 (126)
Q Consensus 3 I~kGD~V~Vi~GkdKGK~G~V~~V~~~~ 30 (126)
+.+||.|.||.|.+++-+|.|..|+.++
T Consensus 140 f~~gD~vkVI~g~~~~d~g~V~rI~~~~ 167 (607)
T COG5164 140 FYKGDLVKVIEGGEMVDIGTVPRIDGEK 167 (607)
T ss_pred cccCCeEEEeccccccccceEEEecCce
Confidence 5689999999999999999999997653
No 30
>COG1862 YajC Preprotein translocase subunit YajC [Intracellular trafficking and secretion]
Probab=75.85 E-value=5.2 Score=28.31 Aligned_cols=29 Identities=38% Similarity=0.566 Sum_probs=22.9
Q ss_pred CcccCCEEEEeecCCCCeEeEEEEEEccCCeEEEe
Q 033131 2 HVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 36 (126)
Q Consensus 2 ~I~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~Ve 36 (126)
.+++||+|.-+.| -.|+|.+|..+. +.|+
T Consensus 43 sL~kGD~VvT~gG----i~G~V~~v~d~~--v~I~ 71 (97)
T COG1862 43 SLKKGDEVVTIGG----IVGTVTKVGDDT--VEIE 71 (97)
T ss_pred hccCCCEEEEcCC----eEEEEEEEecCc--EEEE
Confidence 5789999998886 589999997655 5444
No 31
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=75.59 E-value=1.8 Score=41.45 Aligned_cols=28 Identities=43% Similarity=0.775 Sum_probs=25.7
Q ss_pred CcccCCEEEEeecCCCCeEeEEEEEEcc
Q 033131 2 HVKAGDTVKVIAGCDKGKIGEITKVFRH 29 (126)
Q Consensus 2 ~I~kGD~V~Vi~GkdKGK~G~V~~V~~~ 29 (126)
.|+.+|+|.||.|+.+|++|.|+.+++.
T Consensus 581 ~I~~kD~Vkvi~Gp~~g~~G~v~~i~r~ 608 (1024)
T KOG1999|consen 581 EIRVKDTVKVIGGPSKGREGEVLHIYRP 608 (1024)
T ss_pred eecccceEEEecCCCCCccCccceeecc
Confidence 4789999999999999999999999874
No 32
>PRK05585 yajC preprotein translocase subunit YajC; Validated
Probab=73.75 E-value=7.2 Score=27.79 Aligned_cols=29 Identities=34% Similarity=0.529 Sum_probs=23.9
Q ss_pred CcccCCEEEEeecCCCCeEeEEEEEEccCCeEEEe
Q 033131 2 HVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 36 (126)
Q Consensus 2 ~I~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~Ve 36 (126)
.+++||+|+-++| -.|+|.+++. +.|.||
T Consensus 52 ~Lk~Gd~VvT~gG----i~G~Vv~i~~--~~v~le 80 (106)
T PRK05585 52 SLAKGDEVVTNGG----IIGKVTKVSE--DFVIIE 80 (106)
T ss_pred hcCCCCEEEECCC----eEEEEEEEeC--CEEEEE
Confidence 5789999999887 5899999964 677776
No 33
>COG1471 RPS4A Ribosomal protein S4E [Translation, ribosomal structure and biogenesis]
Probab=71.56 E-value=8.3 Score=31.57 Aligned_cols=36 Identities=28% Similarity=0.458 Sum_probs=29.1
Q ss_pred CcccCCEEEEeecCCCCeEeEEEEEEccC----CeEEEec
Q 033131 2 HVKAGDTVKVIAGCDKGKIGEITKVFRHN----STVMVKD 37 (126)
Q Consensus 2 ~I~kGD~V~Vi~GkdKGK~G~V~~V~~~~----~~V~VeG 37 (126)
++..|-.|.|+.|++-|..|+|.+|.... +.|.+|+
T Consensus 173 ~fe~g~~~~vtgG~h~G~~G~I~~I~~~~~~~~~~v~~e~ 212 (241)
T COG1471 173 KFEEGALVYVTGGRHVGRVGTIVEIEIQESSKPNLVTVED 212 (241)
T ss_pred ccCCCcEEEEECCccccceEEEEEEEEecCCCccEEEEec
Confidence 56788999999999999999999998653 4566654
No 34
>PTZ00223 40S ribosomal protein S4; Provisional
Probab=71.43 E-value=6.9 Score=32.55 Aligned_cols=27 Identities=37% Similarity=0.700 Sum_probs=23.3
Q ss_pred CcccCCEEEEeecCCCCeEeEEEEEEc
Q 033131 2 HVKAGDTVKVIAGCDKGKIGEITKVFR 28 (126)
Q Consensus 2 ~I~kGD~V~Vi~GkdKGK~G~V~~V~~ 28 (126)
++..|-.|.|+.|++-|.+|+|.++..
T Consensus 171 kfe~G~l~~vtgG~n~GriG~I~~i~~ 197 (273)
T PTZ00223 171 KNRNGKVVMVTGGANRGRIGEIVSIER 197 (273)
T ss_pred ecCCCCEEEEECCeeceeEEEEEEEEe
Confidence 567899999999999999999988843
No 35
>PLN00036 40S ribosomal protein S4; Provisional
Probab=70.79 E-value=8.7 Score=31.74 Aligned_cols=28 Identities=29% Similarity=0.574 Sum_probs=23.8
Q ss_pred CcccCCEEEEeecCCCCeEeEEEEEEcc
Q 033131 2 HVKAGDTVKVIAGCDKGKIGEITKVFRH 29 (126)
Q Consensus 2 ~I~kGD~V~Vi~GkdKGK~G~V~~V~~~ 29 (126)
++..|-.+.|+.|++-|.+|+|.++...
T Consensus 174 kfe~G~l~~vtgG~n~GrvG~I~~i~~~ 201 (261)
T PLN00036 174 KFDVGNLVMVTGGRNRGRVGVIKNREKH 201 (261)
T ss_pred ecCCCCEEEEECCeeceeEEEEEEEEec
Confidence 5678999999999999999999888743
No 36
>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=69.06 E-value=10 Score=25.80 Aligned_cols=29 Identities=38% Similarity=0.678 Sum_probs=23.2
Q ss_pred CcccCCEEEEeecCCCCeEeEEEEEEccCCeEEEe
Q 033131 2 HVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 36 (126)
Q Consensus 2 ~I~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~Ve 36 (126)
.+++||+|+-.+| -.|+|.+++. +.+.||
T Consensus 37 ~L~~Gd~VvT~gG----i~G~V~~i~d--~~v~ve 65 (84)
T TIGR00739 37 SLKKGDKVLTIGG----IIGTVTKIAE--NTIVIE 65 (84)
T ss_pred hCCCCCEEEECCC----eEEEEEEEeC--CEEEEE
Confidence 5789999998886 5899999974 466665
No 37
>PRK05886 yajC preprotein translocase subunit YajC; Validated
Probab=69.01 E-value=11 Score=27.29 Aligned_cols=29 Identities=24% Similarity=0.368 Sum_probs=23.7
Q ss_pred CcccCCEEEEeecCCCCeEeEEEEEEccCCeEEEe
Q 033131 2 HVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 36 (126)
Q Consensus 2 ~I~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~Ve 36 (126)
.|++||+|+-++| -.|+|.+|.. +.|.||
T Consensus 38 ~Lk~GD~VvT~gG----i~G~V~~I~d--~~v~le 66 (109)
T PRK05886 38 SLQPGDRVHTTSG----LQATIVGITD--DTVDLE 66 (109)
T ss_pred hcCCCCEEEECCC----eEEEEEEEeC--CEEEEE
Confidence 5789999998876 5899999963 577777
No 38
>COG3700 AphA Acid phosphatase (class B) [General function prediction only]
Probab=66.63 E-value=1.9 Score=34.66 Aligned_cols=33 Identities=27% Similarity=0.548 Sum_probs=29.0
Q ss_pred CCcccCCEEEEeecCCCCeEeEEEEEEccCCeE
Q 033131 1 MHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTV 33 (126)
Q Consensus 1 ~~I~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V 33 (126)
||.++||.+.-++|+-.||+-+|.+.+.+.-.+
T Consensus 125 MHq~RGD~i~FvTGRt~gk~d~vsk~Lak~F~i 157 (237)
T COG3700 125 MHQRRGDAIYFVTGRTPGKTDTVSKTLAKNFHI 157 (237)
T ss_pred HHHhcCCeEEEEecCCCCcccccchhHHhhccc
Confidence 688999999999999999999999888776544
No 39
>PF05641 Agenet: Agenet domain; InterPro: IPR008395 This domain is related to the TUDOR domain IPR008191 from INTERPRO []. The function of the agenet domain is unknown. This signature matches one of the two Agenet domains in the FMR proteins [].; GO: 0003723 RNA binding; PDB: 2BKD_N 3O8V_A 3KUF_A 3H8Z_A.
Probab=66.02 E-value=23 Score=22.68 Aligned_cols=33 Identities=24% Similarity=0.292 Sum_probs=19.9
Q ss_pred cccCCEEEEeecC--CCCe--EeEEEEEEccCCeEEEe
Q 033131 3 VKAGDTVKVIAGC--DKGK--IGEITKVFRHNSTVMVK 36 (126)
Q Consensus 3 I~kGD~V~Vi~Gk--dKGK--~G~V~~V~~~~~~V~Ve 36 (126)
|++||.|.|.+-. +.|- .++|++...+. ++.|+
T Consensus 1 F~~G~~VEV~s~e~g~~gaWf~a~V~~~~~~~-~~~V~ 37 (68)
T PF05641_consen 1 FKKGDEVEVSSDEDGFRGAWFPATVLKENGDD-KYLVE 37 (68)
T ss_dssp --TT-EEEEEE-SBTT--EEEEEEEEEEETT--EEEEE
T ss_pred CCCCCEEEEEEcCCCCCcEEEEEEEEEeCCCc-EEEEE
Confidence 5799999999843 2443 38999998765 66665
No 40
>PTZ00118 40S ribosomal protein S4; Provisional
Probab=64.79 E-value=13 Score=30.71 Aligned_cols=28 Identities=25% Similarity=0.553 Sum_probs=23.1
Q ss_pred CcccCCEEEEeecCCCCeEeEEEEEEcc
Q 033131 2 HVKAGDTVKVIAGCDKGKIGEITKVFRH 29 (126)
Q Consensus 2 ~I~kGD~V~Vi~GkdKGK~G~V~~V~~~ 29 (126)
++..|-.|.|+.|++-|.+|+|.++...
T Consensus 174 kfe~G~l~~vtgG~n~GriG~I~~~~~~ 201 (262)
T PTZ00118 174 KFEVGNLVMITGGHNVGRVGTIVSKEKH 201 (262)
T ss_pred ecCCCCEEEEECCeeceeEEEEEEEEec
Confidence 5678999999999999999999875443
No 41
>PF02699 YajC: Preprotein translocase subunit; InterPro: IPR003849 Secretion across the inner membrane in some Gram-negative bacteria occurs via the preprotein translocase pathway. Proteins are produced in the cytoplasm as precursors, and require a chaperone subunit to direct them to the translocase component []. From there, the mature proteins are either targeted to the outer membrane, or remain as periplasmic proteins []. The translocase protein subunits are encoded on the bacterial chromosome. The translocase itself comprises 7 proteins, including a chaperone (SecB), ATPase (SecA), an integral membrane complex (SecY, SecE and SecG), and two additional membrane proteins that promote the release of the mature peptide into the periplasm (SecD and SecF) []. Other cytoplasmic/periplasmic proteins play a part in preprotein translocase activity, namely YidC and YajC []. The latter is bound in a complex to SecD and SecF, and plays a part in stabilising and regulating secretion through the SecYEG integral membrane component via SecA []. Homologues of the YajC gene have been found in a range of pathogenic and commensal microbes. Brucella abortis YajC- and SecD-like proteins were shown to stimulate a Th1 cell-mediated immune response in mice, and conferred protection when challenged with B.abortis []. Therefore, these proteins may have an antigenic role as well as a secretory one in virulent bacteria []. A number of previously uncharacterised "hypothetical" proteins also show similarity to E.coli YajC, suggesting that this family is wider than first thought []. More recently, the precise interactions between the E.coli SecYEG complex, SecD, SecF, YajC and YidC have been studied []. Rather than acting individually, the four proteins form a heterotetrameric complex and associate with the SecYEG heterotrimeric complex []. The SecF and YajC subunits link the complex to the integral membrane translocase. ; PDB: 2RDD_B.
Probab=63.49 E-value=2.3 Score=28.74 Aligned_cols=29 Identities=31% Similarity=0.619 Sum_probs=0.0
Q ss_pred CcccCCEEEEeecCCCCeEeEEEEEEccCCeEEEe
Q 033131 2 HVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 36 (126)
Q Consensus 2 ~I~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~Ve 36 (126)
.+++||+|.-.+| -.|+|.++ +++.+.+|
T Consensus 36 ~Lk~Gd~VvT~gG----i~G~V~~i--~~~~v~le 64 (82)
T PF02699_consen 36 SLKPGDEVVTIGG----IYGTVVEI--DDDTVVLE 64 (82)
T ss_dssp -----------------------------------
T ss_pred cCCCCCEEEECCc----EEEEEEEE--eCCEEEEE
Confidence 5789999998887 47999998 55677766
No 42
>PF03144 GTP_EFTU_D2: Elongation factor Tu domain 2; InterPro: IPR004161 Translation elongation factors are responsible for two main processes during protein synthesis on the ribosome [, , ]. EF1A (or EF-Tu) is responsible for the selection and binding of the cognate aminoacyl-tRNA to the A-site (acceptor site) of the ribosome. EF2 (or EF-G) is responsible for the translocation of the peptidyl-tRNA from the A-site to the P-site (peptidyl-tRNA site) of the ribosome, thereby freeing the A-site for the next aminoacyl-tRNA to bind. Elongation factors are responsible for achieving accuracy of translation and both EF1A and EF2 are remarkably conserved throughout evolution. EF1A (also known as EF-1alpha or EF-Tu) is a G-protein. It forms a ternary complex of EF1A-GTP-aminoacyltRNA. The binding of aminoacyl-tRNA stimulates GTP hydrolysis by EF1A, causing a conformational change in EF1A that causes EF1A-GDP to detach from the ribosome, leaving the aminoacyl-tRNA attached at the A-site. Only the cognate aminoacyl-tRNA can induce the required conformational change in EF1A through its tight anticodon-codon binding [, ]. EF1A-GDP is returned to its active state, EF1A-GTP, through the action of another elongation factor, EF1B (also known as EF-Ts or EF-1beta/gamma/delta). EF1A consists of three structural domains. This entry represents domain 2 of EF2, which adopts a beta-barrel structure, and is involved in binding to both charged tRNA []. This domain is structurally related to the C-terminal domain of EF2 (IPR004160 from INTERPRO), to which it displays weak sequence matches. This domain is also found in other proteins such as translation initiation factor IF-2 and tetracycline-resistance proteins. More information about these proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005525 GTP binding; PDB: 3MCA_A 3AGJ_E 1SKQ_B 1JNY_A 1S0U_A 1ZUN_B 3SFS_W 3UOQ_W 2H5E_B 2XEX_A ....
Probab=63.35 E-value=12 Score=23.56 Aligned_cols=29 Identities=34% Similarity=0.564 Sum_probs=22.8
Q ss_pred CcccCCEEEEeecCCCCeE---eEEEEEEccCC
Q 033131 2 HVKAGDTVKVIAGCDKGKI---GEITKVFRHNS 31 (126)
Q Consensus 2 ~I~kGD~V~Vi~GkdKGK~---G~V~~V~~~~~ 31 (126)
.|++||+|.++. .+.++. .+|.+++...+
T Consensus 12 ~l~~gd~v~~~~-~~~~~~~~~~~I~~i~~~~~ 43 (74)
T PF03144_consen 12 TLKKGDKVRVLP-NGTGKKGQVVKIKSIFMFNG 43 (74)
T ss_dssp EEETTEEEEEES-TTTTEECEEEEEEEEEETTE
T ss_pred EEcCCCEEEECc-cCCcceeeeeeccccccccc
Confidence 478999999988 666555 88888887654
No 43
>KOG3418 consensus 60S ribosomal protein L27 [Translation, ribosomal structure and biogenesis]
Probab=61.53 E-value=16 Score=27.51 Aligned_cols=40 Identities=25% Similarity=0.351 Sum_probs=31.7
Q ss_pred CcccCCEEEEeecCCCCeEeEEEEEEccC------CeEEEeceeee
Q 033131 2 HVKAGDTVKVIAGCDKGKIGEITKVFRHN------STVMVKDINLK 41 (126)
Q Consensus 2 ~I~kGD~V~Vi~GkdKGK~G~V~~V~~~~------~~V~VeGvN~~ 41 (126)
-+++|--|.|++|.+.|+...|++-.-+. ..++|+|+-..
T Consensus 4 flkPgkvv~v~sG~yAg~KaVivk~~Ddg~~d~p~~h~LvAgi~ry 49 (136)
T KOG3418|consen 4 FLKPGKVVLVLSGRYAGKKAVIVKNIDDGTEDKPYGHALVAGVDRY 49 (136)
T ss_pred cccCCcEEEeecccccCccEEEEeecccCCccCCCceeeeeehhhc
Confidence 47899999999999999988887665443 37888987544
No 44
>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed
Probab=60.93 E-value=17 Score=33.95 Aligned_cols=37 Identities=27% Similarity=0.441 Sum_probs=26.7
Q ss_pred CcccCCEEEEeecCCCCeEeEEEEEEccCC-eEEEeceeee
Q 033131 2 HVKAGDTVKVIAGCDKGKIGEITKVFRHNS-TVMVKDINLK 41 (126)
Q Consensus 2 ~I~kGD~V~Vi~GkdKGK~G~V~~V~~~~~-~V~VeGvN~~ 41 (126)
.++.||.|.|.+ -|+.|+|+++..++. .|.+.++.+.
T Consensus 636 ~~~~Gd~V~v~~---~~~~g~v~~i~~~~~~~V~~g~~k~~ 673 (782)
T PRK00409 636 ELKVGDEVKYLS---LGQKGEVLSIPDDKEAIVQAGIMKMK 673 (782)
T ss_pred CCCCCCEEEEcc---CCceEEEEEEcCCCeEEEEECCEEEE
Confidence 488999999966 568899999974332 4555566555
No 45
>PRK02749 photosystem I reaction center subunit IV; Provisional
Probab=60.00 E-value=11 Score=25.31 Aligned_cols=30 Identities=20% Similarity=0.377 Sum_probs=25.1
Q ss_pred CCcccCCEEEEeecC--CCCeEeEEEEEEccC
Q 033131 1 MHVKAGDTVKVIAGC--DKGKIGEITKVFRHN 30 (126)
Q Consensus 1 ~~I~kGD~V~Vi~Gk--dKGK~G~V~~V~~~~ 30 (126)
|-|.+||+|.|++=. .-...|+|.+|+...
T Consensus 1 m~i~rGskVrIlR~ESYWyn~vGtV~svD~sg 32 (71)
T PRK02749 1 MAISRGDKVRILRPESYWYNEVGTVASVDKSG 32 (71)
T ss_pred CccccCCEEEEccccceeecCcceEEEEccCC
Confidence 568999999999863 457789999999875
No 46
>PF08206 OB_RNB: Ribonuclease B OB domain; InterPro: IPR013223 This domain includes the N-terminal OB domain found in ribonuclease B proteins in one or two copies.; PDB: 2ID0_D 2IX1_A 2IX0_A.
Probab=55.64 E-value=15 Score=22.86 Aligned_cols=23 Identities=39% Similarity=0.459 Sum_probs=13.2
Q ss_pred ccCCEEEE-eecCC--CCeEeEEEEE
Q 033131 4 KAGDTVKV-IAGCD--KGKIGEITKV 26 (126)
Q Consensus 4 ~kGD~V~V-i~Gkd--KGK~G~V~~V 26 (126)
.-||+|+| +..+. +...|+|.+|
T Consensus 33 ~~gD~V~v~i~~~~~~~~~eg~vv~V 58 (58)
T PF08206_consen 33 MDGDKVLVRITPPSRGKRPEGEVVEV 58 (58)
T ss_dssp -TT-EEEEEEEESSSEEEEEEEEEE-
T ss_pred CCCCEEEEEEecCCCCCCCCEEEEeC
Confidence 46899987 44433 4455888775
No 47
>COG1532 Predicted RNA-binding protein [General function prediction only]
Probab=52.20 E-value=19 Score=23.31 Aligned_cols=33 Identities=15% Similarity=0.249 Sum_probs=26.3
Q ss_pred cCCEEEE--eecCCCCeEeEEEEEEccCCeEEEec
Q 033131 5 AGDTVKV--IAGCDKGKIGEITKVFRHNSTVMVKD 37 (126)
Q Consensus 5 kGD~V~V--i~GkdKGK~G~V~~V~~~~~~V~VeG 37 (126)
.||.|.. |=|..|--.|+|.+++...+++++||
T Consensus 23 ~~e~V~a~Dilgd~ke~~G~vkriDldehkI~lE~ 57 (57)
T COG1532 23 TEEGVVARDILGDEKEFEGQVKRIDLDEHKIELEG 57 (57)
T ss_pred ecCcEEEEeccCCceEecceEEEEEccccEEEecC
Confidence 4565554 34777888899999999999999986
No 48
>COG5164 SPT5 Transcription elongation factor [Transcription]
Probab=51.82 E-value=16 Score=33.05 Aligned_cols=33 Identities=30% Similarity=0.454 Sum_probs=28.1
Q ss_pred ccCCEEEEeecCCCCeEeEEEEEEccCCeEEEe
Q 033131 4 KAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 36 (126)
Q Consensus 4 ~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~Ve 36 (126)
.-|-+|.|-+|.+||.-|.|..|++...+|.+-
T Consensus 353 aigktVrIr~g~yKG~lGVVKdv~~~~arVeLh 385 (607)
T COG5164 353 AIGKTVRIRCGEYKGHLGVVKDVDRNIARVELH 385 (607)
T ss_pred ccCceEEEeecccccccceeeeccCceEEEEEe
Confidence 357899999999999999999998877666554
No 49
>KOG4315 consensus G-patch nucleic acid binding protein [General function prediction only]
Probab=51.23 E-value=7 Score=34.53 Aligned_cols=33 Identities=27% Similarity=0.426 Sum_probs=28.1
Q ss_pred ccCCEEEEeecCCCCeEeEEEEEEccCCeEEEe
Q 033131 4 KAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 36 (126)
Q Consensus 4 ~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~Ve 36 (126)
+-|++|.|++|+++|+-|--++-++.+.+..|.
T Consensus 395 ~~Ge~vmvv~gkhkg~~g~llskd~~Ke~~~v~ 427 (455)
T KOG4315|consen 395 RGGEKVMVVSGKHKGVYGSLLSKDLDKETGVVR 427 (455)
T ss_pred ccCceeEEEecccccchhhhhhhhhhhhhccee
Confidence 469999999999999999998888777766654
No 50
>TIGR01069 mutS2 MutS2 family protein. Function of MutS2 is unknown. It should not be considered a DNA mismatch repair protein. It is likely a DNA mismatch binding protein of unknown cellular function.
Probab=48.86 E-value=31 Score=32.30 Aligned_cols=34 Identities=29% Similarity=0.523 Sum_probs=24.8
Q ss_pred ccCCEEEEeecCCCCeEeEEEEEEccCCe--EEEeceeee
Q 033131 4 KAGDTVKVIAGCDKGKIGEITKVFRHNST--VMVKDINLK 41 (126)
Q Consensus 4 ~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~--V~VeGvN~~ 41 (126)
+.||.|.|. .-|+.|+|+++.. ++. |.+.++.+.
T Consensus 626 ~~Gd~V~v~---~~~~~g~v~~i~~-~~~~~V~~g~~k~~ 661 (771)
T TIGR01069 626 KIGDKVRIR---YFGQKGKIVQILG-GNKWNVTVGGMRMK 661 (771)
T ss_pred CCCCEEEEc---cCCceEEEEEEcC-CCeEEEEECCEEEE
Confidence 789999995 4678899999974 344 555566555
No 51
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=46.25 E-value=67 Score=19.56 Aligned_cols=34 Identities=26% Similarity=0.354 Sum_probs=23.2
Q ss_pred CCcccCCEEEEeecCCCC-eEeEEEEEEccCCeEEE
Q 033131 1 MHVKAGDTVKVIAGCDKG-KIGEITKVFRHNSTVMV 35 (126)
Q Consensus 1 ~~I~kGD~V~Vi~GkdKG-K~G~V~~V~~~~~~V~V 35 (126)
+.+++||.|.+..=.+-+ -.|+|+++.. .++..|
T Consensus 1 ~~~~~G~~Ve~~~~~~~~W~~a~V~~~~~-~~~~~V 35 (61)
T smart00743 1 SDFKKGDRVEVFSKEEDSWWEAVVTKVLG-DGKYLV 35 (61)
T ss_pred CCcCCCCEEEEEECCCCEEEEEEEEEECC-CCEEEE
Confidence 568999999999733222 3489999987 334333
No 52
>CHL00125 psaE photosystem I subunit IV; Reviewed
Probab=46.07 E-value=24 Score=23.31 Aligned_cols=28 Identities=25% Similarity=0.355 Sum_probs=23.2
Q ss_pred cccCCEEEEeecC--CCCeEeEEEEEEccC
Q 033131 3 VKAGDTVKVIAGC--DKGKIGEITKVFRHN 30 (126)
Q Consensus 3 I~kGD~V~Vi~Gk--dKGK~G~V~~V~~~~ 30 (126)
|++||+|.|++=. .-..+|+|.+|+...
T Consensus 2 i~rGskVrIlR~ESYWyn~vGtV~svd~~g 31 (64)
T CHL00125 2 VKRGSKVRILRKESYWYNEIGTVATVDQSG 31 (64)
T ss_pred cccCCEEEEccccceeecCcceEEEEcCCC
Confidence 6899999999863 456789999999864
No 53
>PF04452 Methyltrans_RNA: RNA methyltransferase; InterPro: IPR006700 Methyltransferases (Mtases) are responsible for the transfer of methyl groups between two molecules. The transfer of the methyl group from the ubiquitous S-adenosyl-L-methionine (AdoMet) to either nitrogen, oxygen or carbon atoms is frequently employed in diverse organisms. The reaction is catalyzed by Mtases and modifies DNA, RNA, proteins or small molecules, such as catechol, for regulatory purposes. Proteins in this entry belong to the RsmE family of Mtases, this is supported by crystal structural studying, which show a close structural homology to other known methyltransferases []. This entry contains RsmE of Escherichia coli, which specifically methylates the uridine in position 1498 of 16S rRNA in the fully assembled 30S ribosomal subunit [, ].; GO: 0008168 methyltransferase activity, 0006364 rRNA processing; PDB: 1NXZ_B 1VHY_B 2EGW_A 2EGV_A 2Z0Y_A 2CX8_A 3KW2_A 1VHK_D 1Z85_B 1V6Z_A ....
Probab=45.36 E-value=33 Score=26.65 Aligned_cols=36 Identities=25% Similarity=0.443 Sum_probs=25.9
Q ss_pred CCcccCCEEEEeecCCCCeEeEEEEEEccCCeEEEe
Q 033131 1 MHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 36 (126)
Q Consensus 1 ~~I~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~Ve 36 (126)
++++.||.|.|.-|...--.++|.++.++.-.+.+.
T Consensus 15 lR~k~Gd~i~v~dg~g~~~~a~i~~i~~~~~~~~i~ 50 (225)
T PF04452_consen 15 LRLKEGDSIEVFDGDGGEYRAEITEISKKSATLRIL 50 (225)
T ss_dssp ST--TT-EEEEEESSSEEEEEEEEEEESSEEEEEEE
T ss_pred cCCCCCCEEEEEECCCCEEEEEEEECcCcEEEEEEe
Confidence 578999999999988777779999998765544444
No 54
>PF14505 DUF4438: Domain of unknown function (DUF4438); PDB: 3N99_N 3DCL_A.
Probab=44.95 E-value=51 Score=27.27 Aligned_cols=32 Identities=31% Similarity=0.432 Sum_probs=23.1
Q ss_pred cCCEEEEeecCCCCeEeEEEEEEccCCeEEEe
Q 033131 5 AGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 36 (126)
Q Consensus 5 kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~Ve 36 (126)
.|.+..|++|.-||..|.|+-=.---+.|+|+
T Consensus 60 iGN~A~VvSG~AKG~~G~VtGkHGGieHVlV~ 91 (258)
T PF14505_consen 60 IGNEAKVVSGDAKGAKGVVTGKHGGIEHVLVD 91 (258)
T ss_dssp BT-EEEE-SSTTTT-EEEEEEEETTTTEEEEE
T ss_pred cCceeEEeecccCCCcCeEecccCCeeeEEEE
Confidence 48899999999999999998655544577765
No 55
>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=44.76 E-value=35 Score=22.39 Aligned_cols=28 Identities=18% Similarity=0.341 Sum_probs=21.8
Q ss_pred cccCCEEEEeecC--CCCeEeEEEEEEccC
Q 033131 3 VKAGDTVKVIAGC--DKGKIGEITKVFRHN 30 (126)
Q Consensus 3 I~kGD~V~Vi~Gk--dKGK~G~V~~V~~~~ 30 (126)
|.+|+.|.|++=. .-..+|+|.+|+...
T Consensus 1 i~rgskVrIlR~ESYWyn~vGtV~svdqs~ 30 (61)
T PF02427_consen 1 IKRGSKVRILRKESYWYNEVGTVASVDQSG 30 (61)
T ss_dssp S-TTSEEEE-SSSSTTTTSEEEEEEETTSS
T ss_pred CCCCCEEEEccccceeecccceEEEEccCC
Confidence 5789999999863 567899999998775
No 56
>PF12353 eIF3g: Eukaryotic translation initiation factor 3 subunit G ; InterPro: IPR024675 At least eleven different protein factors are involved in initiation of protein synthesis in eukaryotes. Binding of initiator tRNA and mRNA to the 40S subunit requires the presence of the translation initiation factors eIF-2 and eIF-3, with eIF-3 being particularly important for 80S ribosome dissociation and mRNA binding []. eIF-3 is the most complex translation inititation factor, consisting of about 13 putative subunits and having a molecular weight of between 550 - 700 kDa in mammalian cells. Subunits are designated eIF-3a - eIF-3m; the large number of subunits means that the interactions between the individual subunits that make up the eIF-3 complex are complex and varied. Subunit G is required for eIF3 integrity. This entry represents a domain of approximately 130 amino acids in length found at the N terminus of eukaryotic translation initiation factor 3 subunit G. This domain is commonly found in association with the RNA recognition domain PF00076 from PFAM.
Probab=44.60 E-value=52 Score=24.06 Aligned_cols=28 Identities=25% Similarity=0.302 Sum_probs=21.3
Q ss_pred ecCCCCeeeEEEEEccCCcEEEEEcccC
Q 033131 72 SKEMEVASRVGHKVLDDGTRVRYLIKTG 99 (126)
Q Consensus 72 ~p~~~~~~rv~~~~~~dG~kvRv~k~sg 99 (126)
....|.-+=+.|++++||+++.+.++--
T Consensus 8 ~~~~G~KtViey~~n~dGkkvKvtk~~k 35 (128)
T PF12353_consen 8 PDEDGIKTVIEYKFNDDGKKVKVTKKIK 35 (128)
T ss_pred cCCCCcEEEEEEEECCCCCEEEEEEEEE
Confidence 3455777889999999998888775544
No 57
>cd04466 S1_YloQ_GTPase S1_YloQ_GTPase: YloQ GTase family (also known as YjeQ and CpgA), S1-like RNA-binding domain. Proteins in the YloQ GTase family bind the ribosome and have GTPase activity. The precise role of this family is unknown. The protein structure is composed of three domains: an N-terminal S1 domain, a central GTPase domain, and a C-terminal zinc finger domain. This N-terminal S1 domain binds ssRNA. The central GTPase domain contains nucleotide-binding signature motifs: G1 (walker A), G3 (walker B) and G4 motifs. Experiments show that the bacterial YloQ and YjeQ proteins have low intrinsic GTPase activity. The C-terminal zinc-finger domain has structural similarity to a portion of the DNA-repair protein Rad51. This suggests a possible role for this GTPase as a regulator of translation, perhaps as a translation initiation factor. This family is classified based on the N-terminal S1 domain.
Probab=42.47 E-value=64 Score=19.79 Aligned_cols=28 Identities=21% Similarity=0.268 Sum_probs=16.4
Q ss_pred cccCCEEEEeecCCCCeEeEEEEEEccCCe
Q 033131 3 VKAGDTVKVIAGCDKGKIGEITKVFRHNST 32 (126)
Q Consensus 3 I~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~ 32 (126)
+..||.|.+- ..+ +-.+.|.++++.++.
T Consensus 38 ~~VGD~V~~~-~~~-~~~~~I~~vl~R~s~ 65 (68)
T cd04466 38 PAVGDRVEFE-PED-DGEGVIEEILPRKNL 65 (68)
T ss_pred CCCCcEEEEE-ECC-CCcEEEEEEeccceE
Confidence 4678888763 122 224667777776654
No 58
>cd03692 mtIF2_IVc mtIF2_IVc: this family represents the C2 subdomain of domain IV of mitochondrial translation initiation factor 2 (mtIF2) which adopts a beta-barrel fold displaying a high degree of structural similarity with domain II of the translation elongation factor EF-Tu. The C-terminal part of mtIF2 contains the entire fMet-tRNAfmet binding site of IF-2 and is resistant to proteolysis. This C-terminal portion consists of two domains, IF2 C1 and IF2 C2. IF2 C2 been shown to contain all molecular determinants necessary and sufficient for the recognition and binding of fMet-tRNAfMet. Like IF2 from certain prokaryotes such as Thermus thermophilus, mtIF2lacks domain II which is thought to be involved in binding of E.coli IF-2 to 30S subunits.
Probab=41.42 E-value=49 Score=21.87 Aligned_cols=28 Identities=21% Similarity=0.299 Sum_probs=15.0
Q ss_pred cccCCEEEEeecCCCCeEeEEEEEEccC
Q 033131 3 VKAGDTVKVIAGCDKGKIGEITKVFRHN 30 (126)
Q Consensus 3 I~kGD~V~Vi~GkdKGK~G~V~~V~~~~ 30 (126)
|++|+.|.|+.+..-=..|+|.++.+.+
T Consensus 27 l~~g~~v~vlr~~~~~~~g~i~sl~~~~ 54 (84)
T cd03692 27 IKRNAKVRVLRNGEVIYEGKISSLKRFK 54 (84)
T ss_pred EeCCCEEEEEcCCCEEEEEEEEEEEEcC
Confidence 5667777777763111335555555443
No 59
>PF12701 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC8_A 2VXF_A 2VXE_A.
Probab=41.12 E-value=80 Score=22.13 Aligned_cols=34 Identities=21% Similarity=0.351 Sum_probs=31.0
Q ss_pred cCCEEEEeecCCCCeEeEEEEEEccCCeEEEece
Q 033131 5 AGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDI 38 (126)
Q Consensus 5 kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~VeGv 38 (126)
-|-+|-+++..+-.-+|.+..|+...++|.+.++
T Consensus 7 IGs~ISlisk~~iRYeG~L~~Id~~~sTItL~nV 40 (96)
T PF12701_consen 7 IGSKISLISKSDIRYEGILYSIDTEDSTITLKNV 40 (96)
T ss_dssp TTCEEEEEETTTEEEEEEEEEEETTTTEEEEEEE
T ss_pred cCCEEEEEECCCcEEEEEEEEEcCCCCEEEeeee
Confidence 5889999999999999999999999999998865
No 60
>PLN00045 photosystem I reaction center subunit IV; Provisional
Probab=40.59 E-value=44 Score=23.89 Aligned_cols=27 Identities=22% Similarity=0.274 Sum_probs=22.9
Q ss_pred cccCCEEEEeecC--CCCeEeEEEEEEcc
Q 033131 3 VKAGDTVKVIAGC--DKGKIGEITKVFRH 29 (126)
Q Consensus 3 I~kGD~V~Vi~Gk--dKGK~G~V~~V~~~ 29 (126)
+.+||.|.|++=. .-..+|+|.+|+..
T Consensus 40 ~~RGskVrIlR~ESYWyn~vGtVvsVDq~ 68 (101)
T PLN00045 40 PKRGSKVKILRPESYWFNDVGKVVAVDQD 68 (101)
T ss_pred cCCCCEEEEccccceeecCcceEEEEeCC
Confidence 6799999999863 45678999999987
No 61
>PF01079 Hint: Hint module; InterPro: IPR001767 This domain identifies a group of cysteine peptidases correspond to MEROPS peptidase family C46 (clan CH). The type example is the Hedgehog protein from Drosophila melanogaster (Fruit fly). These are involved in intracellular signalling required for a variety of patterning events during development. The hedgehog family of proteins self process by a cysteine-dependent mechanism, which is a one-time autolytic cleavage. It is differentiated from a typical peptidase reaction by the fact that the newly-formed carboxyl group is esterified with cholesterol, rather than being left free. The three-dimensional structure of the autolytic domain of the hedgehog protein of D. melanogaster shows that it is formed from two divergent copies of a module that also occurs in inteins, called a Hint domain [,].; GO: 0008233 peptidase activity, 0006508 proteolysis; PDB: 3K7H_B 3K7I_B 3K7G_B 1AT0_A 3MXW_A 3M1N_B 3HO5_H 2WFR_A 2WFQ_A 2WG3_B ....
Probab=38.53 E-value=52 Score=26.11 Aligned_cols=37 Identities=27% Similarity=0.403 Sum_probs=20.4
Q ss_pred CcccCCEEEE-eecCCCCeEeEEEEEEc-----------cCCeEEEece
Q 033131 2 HVKAGDTVKV-IAGCDKGKIGEITKVFR-----------HNSTVMVKDI 38 (126)
Q Consensus 2 ~I~kGD~V~V-i~GkdKGK~G~V~~V~~-----------~~~~V~VeGv 38 (126)
.++.||.|.+ -.+...-+.-+|.+|.. ..++++|+|+
T Consensus 105 ~V~~Gd~v~~~~~~~~~~~~~~V~~v~~~~~~G~yAPLT~~GtivVdgV 153 (217)
T PF01079_consen 105 DVRVGDCVLVSDEGGGKLRPSRVVRVSTVEKRGVYAPLTSHGTIVVDGV 153 (217)
T ss_dssp G--TT-EEEEE-TTT--EEEEEEEEEEEEEEEEEEEEEESSSEEEETTE
T ss_pred hCCCCCEEEEEEcCCCcEEEEEEEEEEEEEEeeEEcCccCcceEEECCE
Confidence 4789999999 44455556677777653 3445666665
No 62
>cd05707 S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: 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 S. cerevisiae S1 repeat 11 (sc11). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=38.30 E-value=63 Score=19.88 Aligned_cols=23 Identities=26% Similarity=0.335 Sum_probs=14.5
Q ss_pred cccCCEEEEeecCCCCeEeEEEEEEccCCeEEE
Q 033131 3 VKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMV 35 (126)
Q Consensus 3 I~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~V 35 (126)
++.||.|.+ +|++++++++++.+
T Consensus 45 ~~~Gd~v~~----------~v~~~d~~~~~i~l 67 (68)
T cd05707 45 FKVGQLVKG----------KIVSIDPDNGRIEM 67 (68)
T ss_pred cCCCCEEEE----------EEEEEeCCCCEEec
Confidence 456666655 66777776666653
No 63
>KOG3421 consensus 60S ribosomal protein L14 [Translation, ribosomal structure and biogenesis]
Probab=37.38 E-value=43 Score=25.22 Aligned_cols=34 Identities=26% Similarity=0.364 Sum_probs=28.4
Q ss_pred ccCCEEEEeecCCCCeEeEEEEEEccCCeEEEece
Q 033131 4 KAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDI 38 (126)
Q Consensus 4 ~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~VeGv 38 (126)
-.|--+.|..|++.|+--.|..|+ +.|++.++|-
T Consensus 8 eVGrva~v~~G~~~GkL~AIVdvi-Dqnr~lvDGp 41 (136)
T KOG3421|consen 8 EVGRVALVSFGPDAGKLVAIVDVI-DQNRALVDGP 41 (136)
T ss_pred hcceEEEEEecCCCceEEEEEEee-cchhhhccCc
Confidence 457788999999999999998886 5579998874
No 64
>cd00174 SH3 Src homology 3 domains; SH3 domains bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs; they play a role in the regulation of enzymes by intramolecular interactions, changing the subcellular localization of signal pathway components and mediate multiprotein complex assemblies.
Probab=36.16 E-value=45 Score=18.65 Aligned_cols=13 Identities=31% Similarity=0.585 Sum_probs=10.8
Q ss_pred CcccCCEEEEeec
Q 033131 2 HVKAGDTVKVIAG 14 (126)
Q Consensus 2 ~I~kGD~V~Vi~G 14 (126)
.+.+||.|.|+..
T Consensus 17 ~~~~Gd~v~v~~~ 29 (54)
T cd00174 17 SFKKGDIIEVLEK 29 (54)
T ss_pred CCCCCCEEEEEEc
Confidence 5788999999876
No 65
>cd05698 S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: 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 6 (hs6) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=35.94 E-value=82 Score=19.29 Aligned_cols=23 Identities=17% Similarity=0.372 Sum_probs=14.1
Q ss_pred cccCCEEEEeecCCCCeEeEEEEEEccCCeEEE
Q 033131 3 VKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMV 35 (126)
Q Consensus 3 I~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~V 35 (126)
++.||.+.+ +|++++++.+++.+
T Consensus 45 ~~~G~~i~v----------~v~~~d~~~~~i~l 67 (70)
T cd05698 45 FRVGQVVKV----------KVLSCDPEQQRLLL 67 (70)
T ss_pred ccCCCEEEE----------EEEEEcCCCCEEEE
Confidence 455666655 56667766666554
No 66
>cd05697 S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: 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 5 (hs5) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=35.75 E-value=1e+02 Score=18.99 Aligned_cols=23 Identities=22% Similarity=0.286 Sum_probs=14.7
Q ss_pred cccCCEEEEeecCCCCeEeEEEEEEccCCeEEE
Q 033131 3 VKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMV 35 (126)
Q Consensus 3 I~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~V 35 (126)
+..||.+.+ +|++++++++++.+
T Consensus 45 ~~~Gd~i~~----------~V~~id~~~~~i~l 67 (69)
T cd05697 45 FKPGLKVKC----------RVLSVEPERKRLVL 67 (69)
T ss_pred CCCCCEEEE----------EEEEEECCCCEEEE
Confidence 445666554 67777777776654
No 67
>COG1193 Mismatch repair ATPase (MutS family) [DNA replication, recombination, and repair]
Probab=35.17 E-value=42 Score=31.54 Aligned_cols=37 Identities=27% Similarity=0.458 Sum_probs=27.8
Q ss_pred CcccCCEEEEeecCCCCeEeEEEEEEccCCeEEEe--ceeeeE
Q 033131 2 HVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK--DINLKT 42 (126)
Q Consensus 2 ~I~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~Ve--GvN~~k 42 (126)
.++.||.|.+++ |..|.|++|.-....+.|+ .+.|.-
T Consensus 612 ~l~~gDev~~~t----~e~G~~~~i~a~~~e~~v~~g~~kv~V 650 (753)
T COG1193 612 KLKLGDEVEVIT----GEPGAVVKIIAGILEALVQSGILKVIV 650 (753)
T ss_pred CceecceeEeec----CCccceeeeeccCceeEEecceeEEEE
Confidence 578999999999 6778899998666776666 344443
No 68
>cd05695 S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: 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 3 (hs3). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=34.97 E-value=79 Score=19.75 Aligned_cols=15 Identities=20% Similarity=0.038 Sum_probs=10.0
Q ss_pred eEEEEEEccCCeEEE
Q 033131 21 GEITKVFRHNSTVMV 35 (126)
Q Consensus 21 G~V~~V~~~~~~V~V 35 (126)
.+|+.+++++.++.+
T Consensus 51 ~kVi~id~~~~~i~L 65 (66)
T cd05695 51 ARILYVDPSTKVVGL 65 (66)
T ss_pred EEEEEEeCCCCEEec
Confidence 377778777766543
No 69
>cd05708 S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: 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 S. cerevisiae S1 repeat 12 (sc12). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=34.09 E-value=1e+02 Score=18.95 Aligned_cols=24 Identities=17% Similarity=0.393 Sum_probs=14.5
Q ss_pred cccCCEEEEeecCCCCeEeEEEEEEccCCeEEEe
Q 033131 3 VKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 36 (126)
Q Consensus 3 I~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~Ve 36 (126)
++.||.|.+ +|++++.+.+++.+.
T Consensus 48 ~~~Gd~v~v----------~i~~vd~~~~~i~ls 71 (77)
T cd05708 48 FRVGDKVRA----------KVLKIDAEKKRISLG 71 (77)
T ss_pred ecCCCEEEE----------EEEEEeCCCCEEEEE
Confidence 356666655 466777666666544
No 70
>PRK00750 lysK lysyl-tRNA synthetase; Reviewed
Probab=33.99 E-value=79 Score=28.08 Aligned_cols=41 Identities=12% Similarity=0.024 Sum_probs=27.7
Q ss_pred eecCcCCCeeeeecCCCCeeeEEE-EEccCCcEEEEEcccCc
Q 033131 60 EAPIHSSNVMLYSKEMEVASRVGH-KVLDDGTRVRYLIKTGE 100 (126)
Q Consensus 60 e~pI~~SNV~Lv~p~~~~~~rv~~-~~~~dG~kvRv~k~sg~ 100 (126)
+.+=.+|=...+|++||+-+.+.. .++.+...|++.-.||.
T Consensus 166 ~~~~~~~P~~pic~~cg~~~~~~~~~~d~~~~~v~y~~~cG~ 207 (510)
T PRK00750 166 ERQATYSPFLPICPKCGKVLTTPVISYDAEAGTVTYDCECGH 207 (510)
T ss_pred ccCCCeeeeeeeCCCCCccceEEEEEEeCCCCEEEEEcCCCC
Confidence 455566778889999998654333 44555556888766776
No 71
>cd05793 S1_IF1A S1_IF1A: Translation initiation factor IF1A, also referred to as eIF1A in eukaryotes and aIF1A in archaea, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea.
Probab=33.48 E-value=41 Score=22.50 Aligned_cols=26 Identities=19% Similarity=0.242 Sum_probs=13.6
Q ss_pred CcccCCEEEE-eecCCCCeEeEEEEEEc
Q 033131 2 HVKAGDTVKV-IAGCDKGKIGEITKVFR 28 (126)
Q Consensus 2 ~I~kGD~V~V-i~GkdKGK~G~V~~V~~ 28 (126)
.|++||.|.| ++.-| -..|.|...+.
T Consensus 38 wI~~GD~V~Ve~~~~d-~~kg~Iv~r~~ 64 (77)
T cd05793 38 WINEGDIVLVAPWDFQ-DDKADIIYKYT 64 (77)
T ss_pred EEcCCCEEEEEecccc-CCEEEEEEEcC
Confidence 3566666666 44332 33455655543
No 72
>cd04717 BAH_polybromo BAH, or Bromo Adjacent Homology domain, as present in polybromo and yeast RSC1/2. The human polybromo protein (BAF180) is a component of the SWI/SNF chromatin-remodeling complex PBAF. It is thought that polybromo participates in transcriptional regulation. Saccharomyces cerevisiae RSC1 and RSC2 are part of the 15-subunit nucleosome remodeling RSC complex. 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=33.16 E-value=1.2e+02 Score=21.14 Aligned_cols=36 Identities=19% Similarity=0.233 Sum_probs=26.8
Q ss_pred CcccCCEEEEeecC--CCCeEeEEEEEEccC-CeEEEec
Q 033131 2 HVKAGDTVKVIAGC--DKGKIGEITKVFRHN-STVMVKD 37 (126)
Q Consensus 2 ~I~kGD~V~Vi~Gk--dKGK~G~V~~V~~~~-~~V~VeG 37 (126)
.++.||-|.|.+.. .+--+|.|.++.... +...+.+
T Consensus 3 ~~~vGD~V~v~~~~~~~~~~i~~I~~i~~~~~g~~~~~~ 41 (121)
T cd04717 3 QYRVGDCVYVANPEDPSKPIIFRIERLWKDEDGEKFFFG 41 (121)
T ss_pred EEECCCEEEEeCCCCCCCCEEEEEeEEEECCCCCEEEEE
Confidence 46899999999765 556689999998765 4445543
No 73
>PF11623 DUF3252: Protein of unknown function (DUF3252); InterPro: IPR021659 This family of proteins has no known function. Some members are annotated as Ssl0352 however this cannot be confirmed. Currently there is no known function. ; PDB: 3C4S_B 2JZ2_A.
Probab=32.04 E-value=1.3e+02 Score=19.28 Aligned_cols=39 Identities=23% Similarity=0.242 Sum_probs=27.9
Q ss_pred cccCCEEEEeecC--CCCeEeEEEEEEccCCeEEEeceeee
Q 033131 3 VKAGDTVKVIAGC--DKGKIGEITKVFRHNSTVMVKDINLK 41 (126)
Q Consensus 3 I~kGD~V~Vi~Gk--dKGK~G~V~~V~~~~~~V~VeGvN~~ 41 (126)
|.+|-.|.|+.-. +-|-+|.|.+|...+--|+.||=|--
T Consensus 2 ilPG~~V~V~n~~~~Y~~y~G~VQRvsdgkaaVLFEGGnWd 42 (53)
T PF11623_consen 2 ILPGSTVRVKNPNDIYYGYEGFVQRVSDGKAAVLFEGGNWD 42 (53)
T ss_dssp --TT-EEEE--TTSTTTT-EEEEEEEETTEEEEEEEETTEE
T ss_pred ccCCCEEEEeCCCCccchheEEEEEeeCCeEEEEecCCCce
Confidence 6789999999885 67999999999887778999986644
No 74
>cd05688 S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: 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 3 (ec3) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=31.99 E-value=96 Score=18.43 Aligned_cols=13 Identities=8% Similarity=0.253 Sum_probs=6.5
Q ss_pred EEEEEEccCCeEE
Q 033131 22 EITKVFRHNSTVM 34 (126)
Q Consensus 22 ~V~~V~~~~~~V~ 34 (126)
+|+++++.++++.
T Consensus 54 ~i~~vd~~~~~i~ 66 (68)
T cd05688 54 KVLKIDKERKRIS 66 (68)
T ss_pred EEEEEECCCCEEe
Confidence 3555555554443
No 75
>smart00326 SH3 Src homology 3 domains. Src homology 3 (SH3) domains bind to target proteins through sequences containing proline and hydrophobic amino acids. Pro-containing polypeptides may bind to SH3 domains in 2 different binding orientations.
Probab=31.24 E-value=59 Score=18.29 Aligned_cols=14 Identities=29% Similarity=0.520 Sum_probs=10.9
Q ss_pred CcccCCEEEEeecC
Q 033131 2 HVKAGDTVKVIAGC 15 (126)
Q Consensus 2 ~I~kGD~V~Vi~Gk 15 (126)
.+.+||.|.|+...
T Consensus 20 ~~~~Gd~v~v~~~~ 33 (58)
T smart00326 20 SFKKGDIITVLEKS 33 (58)
T ss_pred CCCCCCEEEEEEcC
Confidence 57788988888764
No 76
>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=31.23 E-value=40 Score=25.08 Aligned_cols=37 Identities=14% Similarity=0.237 Sum_probs=21.1
Q ss_pred CcccCCEEEEeecCCCCeEeEEEEEEccCCeEEEeceeeeEEEe
Q 033131 2 HVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHV 45 (126)
Q Consensus 2 ~I~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~VeGvN~~kkh~ 45 (126)
+++.||.|.|= |..|.|.++... ...+...+-....+
T Consensus 60 pf~vGD~I~i~-----~~~G~V~~I~l~--~t~l~~~~g~~v~I 96 (206)
T PF00924_consen 60 PFKVGDRIEIG-----GVEGRVEEIGLR--STRLRTWDGEIVII 96 (206)
T ss_dssp SS-TT-EEESS-----S-EEEEEEE-SS--EEEEEETTS-EEEE
T ss_pred CccCCCEEEEE-----EeehHHHhcCcc--eeeeecCCCCEEEE
Confidence 68899998875 889999998654 34444444333333
No 77
>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=30.74 E-value=59 Score=26.07 Aligned_cols=25 Identities=36% Similarity=0.565 Sum_probs=15.4
Q ss_pred CcccCCEEEEee----------cCCCCeEeEEEEE
Q 033131 2 HVKAGDTVKVIA----------GCDKGKIGEITKV 26 (126)
Q Consensus 2 ~I~kGD~V~Vi~----------GkdKGK~G~V~~V 26 (126)
.++.||+|.|.. |.-+|++|+|..+
T Consensus 134 ~F~vGd~Vrv~~~~~~~HtR~P~Y~rg~~G~I~~~ 168 (222)
T PF02211_consen 134 RFAVGDRVRVRNLPPPGHTRLPRYVRGKTGTIERV 168 (222)
T ss_dssp SS-TT-EEEE-----SS--SS-GGGTT-EEEEEEE
T ss_pred CCCCCCEEEECCCCCCCcccccHhhCCCeeEEEEE
Confidence 467899999975 4457899999754
No 78
>PF03983 SHD1: SLA1 homology domain 1, SHD1 ; InterPro: IPR007131 The SLA1 homology domain is found in the cytoskeleton assembly control protein SLA1, which is responsible for the correct formation of the actin cytoskeleton.; GO: 0008092 cytoskeletal protein binding, 0030674 protein binding, bridging, 0042802 identical protein binding, 0043130 ubiquitin binding; PDB: 2HBP_A.
Probab=30.60 E-value=1.1e+02 Score=20.44 Aligned_cols=41 Identities=15% Similarity=0.178 Sum_probs=25.6
Q ss_pred cCCCeeeeecCCCC-eeeEEEEEccCCcEEEEEcccCcccccc
Q 033131 64 HSSNVMLYSKEMEV-ASRVGHKVLDDGTRVRYLIKTGEIIDSA 105 (126)
Q Consensus 64 ~~SNV~Lv~p~~~~-~~rv~~~~~~dG~kvRv~k~sg~~i~~p 105 (126)
+++.++.+.-.+|. ...-.|--..|| ++++-+..|..|..|
T Consensus 8 ~~~~~RtWtD~tG~f~VeA~fv~~~dg-kV~L~k~nG~~i~VP 49 (70)
T PF03983_consen 8 DPSKTRTWTDRTGKFKVEAEFVGVNDG-KVHLHKTNGVKIAVP 49 (70)
T ss_dssp ----SEEEEBSSS--EEEEEEEEEETT-EEEEE-TTS-EEEEE
T ss_pred CCCcceEEEeCCCCEEEEEEEEEeeCC-EEEEEecCCeEEEeE
Confidence 45788998888887 445555444555 699999999999887
No 79
>PF07653 SH3_2: Variant SH3 domain; InterPro: IPR011511 SH3 (src Homology-3) domains are small protein modules containing approximately 50 amino acid residues [, ]. They are found in a great variety of intracellular or membrane-associated proteins [, , ] for example, in a variety of proteins with enzymatic activity, in adaptor proteins that lack catalytic sequences and in cytoskeletal proteins, such as fodrin and yeast actin binding protein ABP-1. The SH3 domain has a characteristic fold which consists of five or six beta-strands arranged as two tightly packed anti-parallel beta sheets. The linker regions may contain short helices []. The surface of the SH3-domain bears a flat, hydrophobic ligand-binding pocket which consists of three shallow grooves defined by conservative aromatic residues in which the ligand adopts an extended left-handed helical arrangement. The ligand binds with low affinity but this may be enhanced by multiple interactions. The region bound by the SH3 domain is in all cases proline-rich and contains PXXP as a core-conserved binding motif. The function of the SH3 domain is not well understood but they may mediate many diverse processes such as increasing local concentration of proteins, altering their subcellular location and mediating the assembly of large multiprotein complexes []. This entry represents a variant of the SH3 domain.; PDB: 1I1J_B 1K0X_A 1HJD_A 2KEA_A 1KJW_A 1JXM_A 1JXO_B 2EBP_A 2DL3_A 2EYX_A ....
Probab=30.52 E-value=35 Score=20.50 Aligned_cols=12 Identities=33% Similarity=0.758 Sum_probs=8.7
Q ss_pred CCcccCCEEEEe
Q 033131 1 MHVKAGDTVKVI 12 (126)
Q Consensus 1 ~~I~kGD~V~Vi 12 (126)
+.+.+||.|.|+
T Consensus 16 Ls~~~Gd~i~v~ 27 (55)
T PF07653_consen 16 LSFKKGDVIEVL 27 (55)
T ss_dssp -EB-TTEEEEEE
T ss_pred eEEecCCEEEEE
Confidence 357899999998
No 80
>PRK11713 16S ribosomal RNA methyltransferase RsmE; Provisional
Probab=30.18 E-value=99 Score=24.22 Aligned_cols=29 Identities=24% Similarity=0.483 Sum_probs=21.6
Q ss_pred CCcccCCEEEEeecCCCCeEeEEEEEEcc
Q 033131 1 MHVKAGDTVKVIAGCDKGKIGEITKVFRH 29 (126)
Q Consensus 1 ~~I~kGD~V~Vi~GkdKGK~G~V~~V~~~ 29 (126)
|+++.||.+.|..|...=-.++|..+.++
T Consensus 28 lR~~~Gd~i~v~~g~g~~~~~~i~~i~~~ 56 (234)
T PRK11713 28 LRLKEGDELRLFDGDGGEYLAEITEIGKK 56 (234)
T ss_pred ccCCCCCEEEEEeCCCCEEEEEEEEecCc
Confidence 47899999999998652234788877654
No 81
>PF00018 SH3_1: SH3 domain; InterPro: IPR001452 SH3 (src Homology-3) domains are small protein modules containing approximately 50 amino acid residues [, ]. They are found in a great variety of intracellular or membrane-associated proteins [, , ] for example, in a variety of proteins with enzymatic activity, in adaptor proteins that lack catalytic sequences and in cytoskeletal proteins, such as fodrin and yeast actin binding protein ABP-1. The SH3 domain has a characteristic fold which consists of five or six beta-strands arranged as two tightly packed anti-parallel beta sheets. The linker regions may contain short helices []. The surface of the SH3-domain bears a flat, hydrophobic ligand-binding pocket which consists of three shallow grooves defined by conservative aromatic residues in which the ligand adopts an extended left-handed helical arrangement. The ligand binds with low affinity but this may be enhanced by multiple interactions. The region bound by the SH3 domain is in all cases proline-rich and contains PXXP as a core-conserved binding motif. The function of the SH3 domain is not well understood but they may mediate many diverse processes such as increasing local concentration of proteins, altering their subcellular location and mediating the assembly of large multiprotein complexes []. The crystal structure of the SH3 domain of the cytoskeletal protein spectrin, and the solution structures of SH3 domains of phospholipase C (PLC-y) and phosphatidylinositol 3-kinase p85 alpha-subunit, have been determined [, , ]. In spite of relatively limited sequence similarity, their overall structures are similar. The domains belong to the alpha+beta structural class, with 5 to 8 beta-strands forming 2 tightly-packed, anti-parallel beta-sheets arranged in a barrel-like structure, and intervening loops sometimes forming helices. Conserved aliphatic and aromatic residues form a hydrophobic core (A11, L23, A29, V34, W42, L52 and V59 in PLC-y []) and a hydrophobic pocket on the molecular surface (L12, F13, W53 and P55 in PLC-y). The conserved core is believed to stabilise the fold, while the pocket is thought to serve as a binding site for target proteins. Conserved carboxylic amino acids located in the loops, on the periphery of the pocket (D14 and E22), may be involved in protein-protein interactions via proline-rich regions. The N- and C-termini are packed in close proximity, indicating that they are independent structural modules.; GO: 0005515 protein binding; PDB: 1UHF_A 1W1F_A 1WA7_A 1SEM_A 1KFZ_A 2SEM_B 1K76_A 3SEM_B 1X2Q_A 2J06_B ....
Probab=29.81 E-value=65 Score=18.71 Aligned_cols=15 Identities=27% Similarity=0.572 Sum_probs=9.8
Q ss_pred CCcccCCEEEEeecC
Q 033131 1 MHVKAGDTVKVIAGC 15 (126)
Q Consensus 1 ~~I~kGD~V~Vi~Gk 15 (126)
+.+.+||.+.|+.=.
T Consensus 14 Ls~~~Gd~i~v~~~~ 28 (48)
T PF00018_consen 14 LSFKKGDIIEVLEKS 28 (48)
T ss_dssp SEB-TTEEEEEEEES
T ss_pred EeEECCCEEEEEEec
Confidence 357788888888633
No 82
>cd05685 S1_Tex S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin expression. Tex has two functional domains, an N-terminal domain homologous to the Escherichia coli maltose repression protein, which is a poorly defined transcriptional factor, and a C-terminal S1 RNA-binding domain. Tex is found in prokaryotes, eukaryotes, and archaea.
Probab=29.61 E-value=1.1e+02 Score=17.96 Aligned_cols=22 Identities=23% Similarity=0.421 Sum_probs=12.3
Q ss_pred cccCCEEEEeecCCCCeEeEEEEEEccCCeEE
Q 033131 3 VKAGDTVKVIAGCDKGKIGEITKVFRHNSTVM 34 (126)
Q Consensus 3 I~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~ 34 (126)
++.||.|.+ +|+++++...++.
T Consensus 45 ~~~Gd~v~v----------~i~~vd~~~~~i~ 66 (68)
T cd05685 45 VSVGDIVEV----------KVISIDEERGRIS 66 (68)
T ss_pred cCCCCEEEE----------EEEEEECCCCEEe
Confidence 355666655 4566665555543
No 83
>TIGR00523 eIF-1A eukaryotic/archaeal initiation factor 1A. Recommended nomenclature: eIF-1A for eukaryotes, aIF-1A for Archaea. Also called eIF-4C
Probab=29.58 E-value=34 Score=24.08 Aligned_cols=10 Identities=40% Similarity=0.700 Sum_probs=6.8
Q ss_pred CcccCCEEEE
Q 033131 2 HVKAGDTVKV 11 (126)
Q Consensus 2 ~I~kGD~V~V 11 (126)
.|+.||.|.|
T Consensus 57 wI~~GD~VlV 66 (99)
T TIGR00523 57 WIREGDVVIV 66 (99)
T ss_pred EecCCCEEEE
Confidence 4667777777
No 84
>PF09526 DUF2387: Probable metal-binding protein (DUF2387); InterPro: IPR012658 Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various proteobacteria.
Probab=29.28 E-value=1.3e+02 Score=19.96 Aligned_cols=35 Identities=6% Similarity=0.046 Sum_probs=27.6
Q ss_pred eecCCCCeeeEEEEEccCCcEEEEEcccCcccccch
Q 033131 71 YSKEMEVASRVGHKVLDDGTRVRYLIKTGEIIDSAE 106 (126)
Q Consensus 71 v~p~~~~~~rv~~~~~~dG~kvRv~k~sg~~i~~p~ 106 (126)
++|.++.-.++.+- .+++...|-|.+||..=..|.
T Consensus 10 ~CP~C~~~D~i~~~-~e~~ve~vECV~CGy~e~~~~ 44 (71)
T PF09526_consen 10 VCPKCQAMDTIMMW-RENGVEYVECVECGYTERQPD 44 (71)
T ss_pred cCCCCcCccEEEEE-EeCCceEEEecCCCCeeccCC
Confidence 57899888888764 478899999999998755543
No 85
>PF09926 DUF2158: Uncharacterized small protein (DUF2158); InterPro: IPR019226 This entry represents a family of predominantly prokaryotic proteins with no known function.
Probab=29.17 E-value=39 Score=21.26 Aligned_cols=22 Identities=32% Similarity=0.341 Sum_probs=14.8
Q ss_pred cccCCEEEEeecCCCCeEeEEEEEE
Q 033131 3 VKAGDTVKVIAGCDKGKIGEITKVF 27 (126)
Q Consensus 3 I~kGD~V~Vi~GkdKGK~G~V~~V~ 27 (126)
++.||.|+..+|-- .=+|..|.
T Consensus 1 f~~GDvV~LKSGGp---~MTV~~v~ 22 (53)
T PF09926_consen 1 FKIGDVVQLKSGGP---RMTVTEVG 22 (53)
T ss_pred CCCCCEEEEccCCC---CeEEEEcc
Confidence 46899999999843 33455443
No 86
>TIGR00046 RNA methyltransferase, RsmE family. Members of this protein family, previously called conserved hypothetical protein TIGR00046, include the YggJ protein of E. coli, which has now been shown to methylate U1498 in 16S rRNA.
Probab=29.09 E-value=1.1e+02 Score=24.04 Aligned_cols=30 Identities=27% Similarity=0.329 Sum_probs=20.6
Q ss_pred CCcccCCEEEEeecCCCCeEeEEEEEEccC
Q 033131 1 MHVKAGDTVKVIAGCDKGKIGEITKVFRHN 30 (126)
Q Consensus 1 ~~I~kGD~V~Vi~GkdKGK~G~V~~V~~~~ 30 (126)
|+++.||.|.|..|...=-.++|.++..+.
T Consensus 30 lR~~~Gd~v~v~~g~g~~~~a~i~~~~~~~ 59 (240)
T TIGR00046 30 LRLKKGDKLKLLDGDGFIYHCEIKKISKKF 59 (240)
T ss_pred ccCCCCCEEEEEeCCCCEEEEEEEEEcCCe
Confidence 578999999999984221235777776543
No 87
>PRK10334 mechanosensitive channel MscS; Provisional
Probab=28.46 E-value=75 Score=26.02 Aligned_cols=23 Identities=26% Similarity=0.391 Sum_probs=19.1
Q ss_pred CcccCCEEEEeecCCCCeEeEEEEEEcc
Q 033131 2 HVKAGDTVKVIAGCDKGKIGEITKVFRH 29 (126)
Q Consensus 2 ~I~kGD~V~Vi~GkdKGK~G~V~~V~~~ 29 (126)
+++.||.|.+ .|..|+|.++.-.
T Consensus 129 pf~vGD~I~i-----~~~~G~V~~I~~r 151 (286)
T PRK10334 129 PFRAGEYVDL-----GGVAGTVLSVQIF 151 (286)
T ss_pred CCCCCCEEEE-----CCEEEEEEEEEeE
Confidence 6899999998 3788999988643
No 88
>cd05706 S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: 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 S. cerevisiae S1 repeat 10 (sc10). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=28.07 E-value=1.5e+02 Score=18.25 Aligned_cols=14 Identities=14% Similarity=0.071 Sum_probs=7.7
Q ss_pred EEEEEEccCCeEEE
Q 033131 22 EITKVFRHNSTVMV 35 (126)
Q Consensus 22 ~V~~V~~~~~~V~V 35 (126)
+|+++++++.++.+
T Consensus 57 ~V~~~d~~~~~i~l 70 (73)
T cd05706 57 CVLSVDVPNKKIAL 70 (73)
T ss_pred EEEEEeCCCCEEEE
Confidence 56666665555443
No 89
>PF11717 Tudor-knot: RNA binding activity-knot of a chromodomain ; PDB: 2EKO_A 2RO0_A 2RNZ_A 1WGS_A 3E9G_A 3E9F_A 2K3X_A 2K3Y_A 2EFI_A 2F5K_F ....
Probab=27.79 E-value=90 Score=19.12 Aligned_cols=30 Identities=13% Similarity=0.071 Sum_probs=22.5
Q ss_pred cccCCEEEEeecCCCCeEeEEEEEEccCCe
Q 033131 3 VKAGDTVKVIAGCDKGKIGEITKVFRHNST 32 (126)
Q Consensus 3 I~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~ 32 (126)
|..|++|.+..+...--.++|+++..+.+.
T Consensus 1 ~~vG~~v~~~~~~~~~y~A~I~~~r~~~~~ 30 (55)
T PF11717_consen 1 FEVGEKVLCKYKDGQWYEAKILDIREKNGE 30 (55)
T ss_dssp --TTEEEEEEETTTEEEEEEEEEEEECTTC
T ss_pred CCcCCEEEEEECCCcEEEEEEEEEEecCCC
Confidence 468999999996666677999999886643
No 90
>PRK09510 tolA cell envelope integrity inner membrane protein TolA; Provisional
Probab=27.50 E-value=94 Score=27.08 Aligned_cols=26 Identities=19% Similarity=0.215 Sum_probs=22.0
Q ss_pred CCCeeeEEEEEccCCcEEEEEcccCc
Q 033131 75 MEVASRVGHKVLDDGTRVRYLIKTGE 100 (126)
Q Consensus 75 ~~~~~rv~~~~~~dG~kvRv~k~sg~ 100 (126)
.|..|+|.+++..||.-+.|...||.
T Consensus 324 ~gktc~VrI~LapDG~V~sV~~sSGd 349 (387)
T PRK09510 324 AGKTCTLRIKLAPDGTLLDIKKEGGD 349 (387)
T ss_pred cCceEEEEEEEcCCCcEEeeeeCCCC
Confidence 47789999999999988888777876
No 91
>cd04456 S1_IF1A_like S1_IF1A_like: Translation initiation factor IF1A-like, S1-like RNA-binding domain. IF1A is also referred to as eIF1A in eukaryotes and aIF1A in archaea. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea.
Probab=27.30 E-value=70 Score=21.46 Aligned_cols=28 Identities=21% Similarity=0.198 Sum_probs=15.1
Q ss_pred CcccCCEEEEeecCC-CCeEeEEEEEEcc
Q 033131 2 HVKAGDTVKVIAGCD-KGKIGEITKVFRH 29 (126)
Q Consensus 2 ~I~kGD~V~Vi~Gkd-KGK~G~V~~V~~~ 29 (126)
.|+.||.|.|--=++ .-..|.|..++..
T Consensus 38 wI~~GD~VlV~~~~~~~~~kg~Iv~r~~~ 66 (78)
T cd04456 38 WIKRGDFLIVDPIEEGEDVKADIIFVYCK 66 (78)
T ss_pred EEcCCCEEEEEecccCCCceEEEEEEeCH
Confidence 366777777754333 2234566555543
No 92
>PF01176 eIF-1a: Translation initiation factor 1A / IF-1; InterPro: IPR006196 The S1 domain of around 70 amino acids, originally identified in ribosomal protein S1, is found in a large number of RNA-associated proteins. It has been shown that S1 proteins bind RNA through their S1 domains with some degree of sequence specificity. This type of S1 domain is found in translation initiation factor 1. The solution structure of one S1 RNA-binding domain from Escherichia coli polynucleotide phosphorylase has been determined []. It displays some similarity with the cold shock domain (CSD) (IPR002059 from INTERPRO). Both the S1 and the CSD domain consist of an antiparallel beta barrel of the same topology with 5 beta strands. This fold is also shared by many other proteins of unrelated function and is known as the OB fold. However, the S1 and CSD fold can be distinguished from the other OB folds by the presence of a short 3(10) helix at the end of strand 3. This unique feature is likely to form a part of the DNA/RNA-binding site. This entry is specific for bacterial, chloroplastic and eukaryotic IF-1 type S1 domains.; GO: 0003723 RNA binding, 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1JT8_A 3I4O_A 1AH9_A 1ZO1_W 1D7Q_A 2OQK_A 2DGY_A 1HR0_W.
Probab=27.27 E-value=1.1e+02 Score=19.46 Aligned_cols=23 Identities=30% Similarity=0.245 Sum_probs=13.5
Q ss_pred CcccCCEEEEeecCCCCeEeEEE
Q 033131 2 HVKAGDTVKVIAGCDKGKIGEIT 24 (126)
Q Consensus 2 ~I~kGD~V~Vi~GkdKGK~G~V~ 24 (126)
.|+.||.|.|---++--..|.|.
T Consensus 41 wI~~GD~V~V~~~~~d~~kG~Ii 63 (65)
T PF01176_consen 41 WIKRGDFVLVEPSPYDKVKGRII 63 (65)
T ss_dssp ---TTEEEEEEESTTCTTEEEEE
T ss_pred ecCCCCEEEEEecccCCCeEEEE
Confidence 57889999887554445556664
No 93
>cd05690 S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: 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 5 (ec5) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=26.56 E-value=1.2e+02 Score=18.28 Aligned_cols=11 Identities=0% Similarity=0.093 Sum_probs=5.8
Q ss_pred EEEEEccCCeE
Q 033131 23 ITKVFRHNSTV 33 (126)
Q Consensus 23 V~~V~~~~~~V 33 (126)
|+++++++.++
T Consensus 56 v~~id~~~~~i 66 (69)
T cd05690 56 VLNIDVERERI 66 (69)
T ss_pred EEEEECCcCEE
Confidence 55555555444
No 94
>PF15057 DUF4537: Domain of unknown function (DUF4537)
Probab=26.34 E-value=1.3e+02 Score=21.60 Aligned_cols=42 Identities=19% Similarity=0.093 Sum_probs=26.3
Q ss_pred CcccCCEEEEeecCCCCeE---eEEEEE----EccCCeEEEeceeeeEEE
Q 033131 2 HVKAGDTVKVIAGCDKGKI---GEITKV----FRHNSTVMVKDINLKTKH 44 (126)
Q Consensus 2 ~I~kGD~V~Vi~GkdKGK~---G~V~~V----~~~~~~V~VeGvN~~kkh 44 (126)
+|+.||.|.... ...+.. |+|+.. ..+...++|.=.|-.+.+
T Consensus 55 ~L~~GD~VLA~~-~~~~~~Y~Pg~V~~~~~~~~~~~~~~~V~f~ng~~~~ 103 (124)
T PF15057_consen 55 SLQVGDKVLAPW-EPDDCRYGPGTVIAGPERRASEDKEYTVRFYNGKTAK 103 (124)
T ss_pred cCCCCCEEEEec-CcCCCEEeCEEEEECccccccCCceEEEEEECCCCCc
Confidence 688999999983 323322 888864 334456676665544433
No 95
>smart00439 BAH Bromo adjacent homology domain.
Probab=26.30 E-value=1.5e+02 Score=19.78 Aligned_cols=30 Identities=27% Similarity=0.413 Sum_probs=23.4
Q ss_pred CcccCCEEEEeecC--CCCeEeEEEEEEccCC
Q 033131 2 HVKAGDTVKVIAGC--DKGKIGEITKVFRHNS 31 (126)
Q Consensus 2 ~I~kGD~V~Vi~Gk--dKGK~G~V~~V~~~~~ 31 (126)
.++.||.|.|.+.. ..=-+|.|.++....+
T Consensus 1 ~~~vgd~V~v~~~~~~~~~~i~~I~~i~~~~~ 32 (120)
T smart00439 1 TIRVGDFVLVEPDDADEPYYIGRIEEIFETKK 32 (120)
T ss_pred CcccCCEEEEeCCCCCCCCEEEEEEEEEECCC
Confidence 36889999999876 2346899999987653
No 96
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=26.24 E-value=72 Score=21.61 Aligned_cols=27 Identities=19% Similarity=0.127 Sum_probs=12.7
Q ss_pred CcccCCEEEEeecCCCCeEeEEEEEEc
Q 033131 2 HVKAGDTVKVIAGCDKGKIGEITKVFR 28 (126)
Q Consensus 2 ~I~kGD~V~Vi~GkdKGK~G~V~~V~~ 28 (126)
.|+.||.|.|=--++--..|.|..++.
T Consensus 43 wI~~GD~VlVe~~~~~~~kg~Iv~r~~ 69 (83)
T smart00652 43 WIRRGDIVLVDPWDFQDVKADIIYKYT 69 (83)
T ss_pred EEcCCCEEEEEecCCCCCEEEEEEEeC
Confidence 356666666633222223355554443
No 97
>cd00164 S1_like S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.
Probab=26.24 E-value=1.3e+02 Score=17.19 Aligned_cols=9 Identities=11% Similarity=0.128 Sum_probs=3.6
Q ss_pred EEEEEEccC
Q 033131 22 EITKVFRHN 30 (126)
Q Consensus 22 ~V~~V~~~~ 30 (126)
+|+++++.+
T Consensus 51 ~v~~~d~~~ 59 (65)
T cd00164 51 KVLEVDPEK 59 (65)
T ss_pred EEEEEcCCc
Confidence 344444333
No 98
>cd04715 BAH_Orc1p_like BAH, or Bromo Adjacent Homology domain, as present in the Schizosaccharomyces pombe homolog of Saccharomyces cerevisiae Orc1p and similar proteins. Orc1 is part of the Yeast Sir1-origin recognition complex, the Orc1p BAH doman functions in epigenetic silencing. 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=25.79 E-value=1.7e+02 Score=22.11 Aligned_cols=28 Identities=29% Similarity=0.371 Sum_probs=24.5
Q ss_pred cccCCEEEEeecCCCCeEeEEEEEEccC
Q 033131 3 VKAGDTVKVIAGCDKGKIGEITKVFRHN 30 (126)
Q Consensus 3 I~kGD~V~Vi~GkdKGK~G~V~~V~~~~ 30 (126)
++.||-|.|-++..+--+|+|.++....
T Consensus 30 y~lGD~Vlv~s~~~~~yIgkI~~iwe~~ 57 (159)
T cd04715 30 YRLYDDVYVHNGDSEPYIGKIIKIYETA 57 (159)
T ss_pred EeCCCEEEEeCCCCCCEEEEEEEEEEcC
Confidence 6789999999998778899999998754
No 99
>cd04452 S1_IF2_alpha S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Eukaryotic and archaeal Initiation Factor 2 (e- and aIF2, respectively) are heterotrimeric proteins with three subunits (alpha, beta, and gamma). IF2 plays a crucial role in the process of translation initiation. The IF2 gamma subunit contains a GTP-binding site. The IF2 beta and gamma subunits together are thought to be responsible for binding methionyl-initiator tRNA. The ternary complex consisting of IF2, GTP, and the methionyl-initiator tRNA binds to the small subunit of the ribosome, as part of a pre-initiation complex that scans the mRNA to find the AUG start codon. The IF2-bound GTP is hydrolyzed to GDP when the methionyl-initiator tRNA binds the AUG start codon, at which time the IF2 is released with its bound GDP. The large ribosomal subunit then joins with the small subunit to c
Probab=25.58 E-value=1.7e+02 Score=17.99 Aligned_cols=13 Identities=8% Similarity=0.202 Sum_probs=6.3
Q ss_pred EEEEEEccCCeEE
Q 033131 22 EITKVFRHNSTVM 34 (126)
Q Consensus 22 ~V~~V~~~~~~V~ 34 (126)
+|++++..++++.
T Consensus 59 kv~~~d~~~~~i~ 71 (76)
T cd04452 59 KVIRVDKEKGYID 71 (76)
T ss_pred EEEEEECCCCEEE
Confidence 3555555544443
No 100
>cd05689 S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: 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 4 (ec4) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=25.28 E-value=1.2e+02 Score=18.61 Aligned_cols=6 Identities=67% Similarity=1.066 Sum_probs=2.3
Q ss_pred CCEEEE
Q 033131 6 GDTVKV 11 (126)
Q Consensus 6 GD~V~V 11 (126)
||+|.|
T Consensus 52 Gd~v~v 57 (72)
T cd05689 52 GDEVEV 57 (72)
T ss_pred CCEEEE
Confidence 333333
No 101
>cd04721 BAH_plant_1 BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. 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=24.86 E-value=1.8e+02 Score=21.04 Aligned_cols=29 Identities=14% Similarity=0.264 Sum_probs=22.3
Q ss_pred CcccCCEEEEeecCCCCeEeEEEEEEccC
Q 033131 2 HVKAGDTVKVIAGCDKGKIGEITKVFRHN 30 (126)
Q Consensus 2 ~I~kGD~V~Vi~GkdKGK~G~V~~V~~~~ 30 (126)
.|+.||.|.|.+-..+=-.|.|.++....
T Consensus 7 ~i~vGD~V~v~~~~~~~~va~Ie~i~ed~ 35 (130)
T cd04721 7 TISVHDFVYVLSEEEDRYVAYIEDLYEDK 35 (130)
T ss_pred EEECCCEEEEeCCCCCcEEEEEEEEEEcC
Confidence 58899999999744333579999988764
No 102
>PF01426 BAH: BAH domain; InterPro: IPR001025 The BAH (bromo-adjacent homology) family contains proteins such as eukaryotic DNA (cytosine-5) methyltransferases IPR001525 from INTERPRO, the origin recognition complex 1 (Orc1) proteins, as well as several proteins involved in transcriptional regulation. The BAH domain appears to act as a protein-protein interaction module specialised in gene silencing, as suggested for example by its interaction within yeast Orc1p with the silent information regulator Sir1p. The BAH module might therefore play an important role by linking DNA methylation, replication and transcriptional regulation [].; GO: 0003677 DNA binding; PDB: 4DA4_A 3PT6_B 3AV6_A 3AV5_A 3AV4_A 3PT9_A 3SWR_A 3PTA_A 1M4Z_A 1ZBX_A ....
Probab=24.64 E-value=93 Score=20.88 Aligned_cols=29 Identities=21% Similarity=0.307 Sum_probs=22.9
Q ss_pred CcccCCEEEEeecC--CCCeEeEEEEEEccC
Q 033131 2 HVKAGDTVKVIAGC--DKGKIGEITKVFRHN 30 (126)
Q Consensus 2 ~I~kGD~V~Vi~Gk--dKGK~G~V~~V~~~~ 30 (126)
.++.||-|.|..+. ..--+|.|.++....
T Consensus 2 ~~~vGD~V~v~~~~~~~~~~v~~I~~i~~~~ 32 (119)
T PF01426_consen 2 TYKVGDFVYVKPDDPPEPPYVARIEEIWEDK 32 (119)
T ss_dssp EEETTSEEEEECTSTTSEEEEEEEEEEEEET
T ss_pred EEeCCCEEEEeCCCCCCCCEEEEEEEEEcCC
Confidence 36789999999998 444669999887554
No 103
>PRK02935 hypothetical protein; Provisional
Probab=24.34 E-value=35 Score=24.83 Aligned_cols=36 Identities=8% Similarity=0.122 Sum_probs=27.6
Q ss_pred CcCCCeeeeecCCCCeeeEEEEEccCCcEEEEEcccCcccccc
Q 033131 63 IHSSNVMLYSKEMEVASRVGHKVLDDGTRVRYLIKTGEIIDSA 105 (126)
Q Consensus 63 I~~SNV~Lv~p~~~~~~rv~~~~~~dG~kvRv~k~sg~~i~~p 105 (126)
++.+.|++.||+|+++|++-=| +=.|--|++.+-.+
T Consensus 64 lStkavqV~CP~C~K~TKmLGr-------vD~CM~C~~PLTLd 99 (110)
T PRK02935 64 LSTKAVQVICPSCEKPTKMLGR-------VDACMHCNQPLTLD 99 (110)
T ss_pred hcccceeeECCCCCchhhhccc-------eeecCcCCCcCCcC
Confidence 4568899999999999987443 34788888887653
No 104
>PLN00190 60S ribosomal protein L21; Provisional
Probab=23.96 E-value=1.2e+02 Score=23.30 Aligned_cols=32 Identities=28% Similarity=0.396 Sum_probs=22.0
Q ss_pred cccCCEEEEee------c----CCCCeEeEEEEEEccCCeEE
Q 033131 3 VKAGDTVKVIA------G----CDKGKIGEITKVFRHNSTVM 34 (126)
Q Consensus 3 I~kGD~V~Vi~------G----kdKGK~G~V~~V~~~~~~V~ 34 (126)
++.||.|-|.. | .+-|++|.|..|....--|+
T Consensus 34 yk~GD~VdIk~~~svqKGMPhk~YHGkTG~V~nv~~~A~gV~ 75 (158)
T PLN00190 34 FKVGDYVDIKVNGAIHKGMPHKFYHGRTGIVWNVTKRAVGVE 75 (158)
T ss_pred hcCCCEEEEEecCCeecCCCcccccCCCeEEEeecCcEEEEE
Confidence 56899998763 2 35689999988765433333
No 105
>cd03696 selB_II selB_II: this subfamily represents the domain of elongation factor SelB, homologous to domain II of EF-Tu. SelB may function by replacing EF-Tu. In prokaryotes, the incorporation of selenocysteine as the 21st amino acid, encoded by TGA, requires several elements: SelC is the tRNA itself, SelD acts as a donor of reduced selenium, SelA modifies a serine residue on SelC into selenocysteine, and SelB is a selenocysteine-specific translation elongation factor. 3' or 5' non-coding elements of mRNA have been found as probable structures for directing selenocysteine incorporation.
Probab=23.46 E-value=1.2e+02 Score=19.52 Aligned_cols=11 Identities=45% Similarity=0.875 Sum_probs=5.5
Q ss_pred cccCCEEEEee
Q 033131 3 VKAGDTVKVIA 13 (126)
Q Consensus 3 I~kGD~V~Vi~ 13 (126)
|++||+|.+.-
T Consensus 27 i~~g~~v~~~p 37 (83)
T cd03696 27 VKVGDKVEILP 37 (83)
T ss_pred EeCCCEEEECC
Confidence 44555555544
No 106
>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=23.42 E-value=2e+02 Score=20.34 Aligned_cols=29 Identities=28% Similarity=0.391 Sum_probs=17.1
Q ss_pred CcccCCEEEEeec----------CCCCeEeEEEEEEccC
Q 033131 2 HVKAGDTVKVIAG----------CDKGKIGEITKVFRHN 30 (126)
Q Consensus 2 ~I~kGD~V~Vi~G----------kdKGK~G~V~~V~~~~ 30 (126)
.++.||.|-|.-= .+-|++|.|..|.+..
T Consensus 32 ~yk~GD~V~I~id~sv~kGmPh~~yHGkTG~V~~v~~~~ 70 (99)
T PF01157_consen 32 EYKVGDKVDIKIDPSVHKGMPHKRYHGKTGRVFNVTKGA 70 (99)
T ss_dssp ---TT-EEEE---TTSSSSS--GGGTTEEEEEEEE-SSC
T ss_pred HccCCCEEEEEecCccccCCCcceECCCceeEEEeCCCc
Confidence 3578999988642 2458999999888765
No 107
>cd01854 YjeQ_engC YjeQ/EngC. YjeQ (YloQ in Bacillus subtilis) represents a protein family whose members are broadly conserved in bacteria and have been shown to be essential to the growth of E. coli and B. subtilis. Proteins of the YjeQ family contain all sequence motifs typical of the vast class of P-loop-containing GTPases, but show a circular permutation, with a G4-G1-G3 pattern of motifs as opposed to the regular G1-G3-G4 pattern seen in most GTPases. All YjeQ family proteins display a unique domain architecture, which includes an N-terminal OB-fold RNA-binding domain, the central permuted GTPase domain, and a zinc knuckle-like C-terminal cysteine domain. This domain architecture suggests a role for YjeQ as a regulator of translation.
Probab=23.20 E-value=1.6e+02 Score=23.73 Aligned_cols=30 Identities=23% Similarity=0.252 Sum_probs=22.1
Q ss_pred CcccCCEEEEeecCCCCeEeEEEEEEccCCeE
Q 033131 2 HVKAGDTVKVIAGCDKGKIGEITKVFRHNSTV 33 (126)
Q Consensus 2 ~I~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V 33 (126)
.+..||.|.+-.-. +..|.|.+|.+.+|.+
T Consensus 34 ~~~vGD~V~~~~~~--~~~~~i~~i~~R~~~l 63 (287)
T cd01854 34 KPVVGDWVEVEPDD--DGEGVIVRVLPRKNLL 63 (287)
T ss_pred CccCCCEEEEEecC--CCcEEEEEEECCCceE
Confidence 35789999885322 4578999999888754
No 108
>PF11910 NdhO: Cyanobacterial and plant NDH-1 subunit O; InterPro: IPR020905 NAD(P)H-quinone oxidoreductase (NDH-1) shuttles electrons from an unknown electron donor, via FMN and iron-sulphur (Fe-S) centres, to quinones in the respiratory and/or the photosynthetic chain. The immediate electron acceptor for the enzyme in this species is believed to be plastoquinone. It couples the redox reaction to proton translocation, and thus conserves the redox energy in a proton gradient. Cyanobacterial NDH-1 also plays a role in inorganic carbon-concentration. NDH-1 can be composed of about 15 different subunits, although different subcomplexes with different compositions have been identified which probably have different functions. This entry represents subunit O. ; GO: 0016655 oxidoreductase activity, acting on NADH or NADPH, quinone or similar compound as acceptor, 0055114 oxidation-reduction process, 0005886 plasma membrane
Probab=23.11 E-value=44 Score=22.29 Aligned_cols=16 Identities=25% Similarity=0.246 Sum_probs=10.8
Q ss_pred cccCCEEEEeecCCCC
Q 033131 3 VKAGDTVKVIAGCDKG 18 (126)
Q Consensus 3 I~kGD~V~Vi~GkdKG 18 (126)
|+||+.|.|++.++-+
T Consensus 1 lKKG~lVrv~re~~~n 16 (67)
T PF11910_consen 1 LKKGSLVRVNREKYEN 16 (67)
T ss_pred CCcceEEEeehHhhcC
Confidence 5677777777766544
No 109
>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=23.09 E-value=1.9e+02 Score=17.63 Aligned_cols=12 Identities=17% Similarity=0.304 Sum_probs=5.7
Q ss_pred EEEEEccCCeEE
Q 033131 23 ITKVFRHNSTVM 34 (126)
Q Consensus 23 V~~V~~~~~~V~ 34 (126)
|++++++..++.
T Consensus 55 i~~~~~~~~~i~ 66 (70)
T cd05687 55 VLRVEDEEGNVV 66 (70)
T ss_pred EEEEECCCCeEE
Confidence 555554444443
No 110
>cd00674 LysRS_core_class_I catalytic core domain of class I lysyl tRNA synthetase. Class I lysyl tRNA synthetase (LysRS) catalytic core domain. This class I enzyme is a monomer which aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. The class I LysRS is found only in archaea and some bacteria and has evolved separately from class II LysRS, as the two do not share structural or sequence similarity.
Probab=23.03 E-value=1.8e+02 Score=24.85 Aligned_cols=42 Identities=14% Similarity=0.057 Sum_probs=25.1
Q ss_pred eecCcCCCeeeeecCCCCeeeEEEEEccCCcEEEEEcccCcc
Q 033131 60 EAPIHSSNVMLYSKEMEVASRVGHKVLDDGTRVRYLIKTGEI 101 (126)
Q Consensus 60 e~pI~~SNV~Lv~p~~~~~~rv~~~~~~dG~kvRv~k~sg~~ 101 (126)
+.+=.+|=...+|++||+-+-.-..++.+...|++.-.||..
T Consensus 160 ~~~~~~~P~~p~c~~cg~~~~~v~~~d~~~~~v~y~c~cG~~ 201 (353)
T cd00674 160 ELQETWYPFMPYCEKCGKDTTTVEAYDAKAGTVTYKCECGHE 201 (353)
T ss_pred ccCCCceeeeeecCCcCcceeEEEEEeCCCCeEEEEcCCCCE
Confidence 444555667888999986432112345555567776666663
No 111
>cd05696 S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: 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 4 (hs4). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=22.80 E-value=2.1e+02 Score=18.01 Aligned_cols=15 Identities=7% Similarity=0.025 Sum_probs=9.7
Q ss_pred eEEEEEEccCCeEEE
Q 033131 21 GEITKVFRHNSTVMV 35 (126)
Q Consensus 21 G~V~~V~~~~~~V~V 35 (126)
.+|+.+++++.++.+
T Consensus 55 ~kV~~id~~~~~i~l 69 (71)
T cd05696 55 ARIIGYSPMDGLLQL 69 (71)
T ss_pred EEEEEEeCCCCEEEE
Confidence 466777777666654
No 112
>PF06519 TolA: TolA C-terminal; InterPro: IPR014161 TolA couples the inner membrane complex of itself with TolQ and TolR to the outer membrane complex of TolB and OprL (also called Pal). Most of the length of the protein consists of low-complexity sequence that may differ in both length and composition from one species to another, complicating efforts to discriminate TolA (the most divergent gene in the tol-pal system) from paralogs such as TonB. Selection of members of the seed alignment and criteria for setting scoring cut-offs are based largely on conserved operon structure. The Tol-Pal complex is required for maintaining outer membrane integrity, and is also involved in transport (uptake) of colicins and filamentous DNA, and implicated in pathogenesis. Transport is energized by the proton motive force. TolA is an inner membrane protein that interacts with periplasmic TolB and with outer membrane porins OmpC, PhoE and LamB.; GO: 0005215 transporter activity, 0006810 transport, 0016020 membrane; PDB: 2X9A_D 3QDP_A 3QDR_A 1TOL_A 1S62_A.
Probab=22.74 E-value=1.3e+02 Score=20.81 Aligned_cols=42 Identities=19% Similarity=0.321 Sum_probs=25.4
Q ss_pred CCCCeeeEEEEEccCCcEEEEEcccCc---------------cccc---chhhhhhhhcc
Q 033131 74 EMEVASRVGHKVLDDGTRVRYLIKTGE---------------IIDS---AENWKKLKEAN 115 (126)
Q Consensus 74 ~~~~~~rv~~~~~~dG~kvRv~k~sg~---------------~i~~---p~~~~~~~k~~ 115 (126)
-.|+.|++.+++..||.-..+-..+|. .+|. |++|+.+++-+
T Consensus 34 y~GK~C~v~i~l~~dG~v~~v~~~~GD~~lC~aa~~Ai~k~~~~P~ppd~~vy~~~k~~~ 93 (96)
T PF06519_consen 34 YKGKECRVRIRLAPDGLVLSVTVESGDPALCRAAKSAIAKAAKFPPPPDPDVYEKFKNIN 93 (96)
T ss_dssp GTT--EEEEEEEETTSEEEEEEEEEE-HHHHHHHHHH-HCCS-----SSHHHHHHHTTEE
T ss_pred cCCCEEEEEEEECCCCcEEEeeecCCCHHHHHHHHHHHHHhcCCCCCcCHHHHHHHhcCC
Confidence 348999999999999976565444432 2332 47888887654
No 113
>cd05792 S1_eIF1AD_like S1_eIF1AD_like: eukaryotic translation initiation factor 1A domain containing protein (eIF1AD)-like, S1-like RNA-binding domain. eIF1AD is also known as MGC11102 protein. Little is known about the function of eIF1AD. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins, including translation initiation factor IF1A (also referred to as eIF1A in eukaryotes). eIF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors.
Probab=22.62 E-value=1e+02 Score=20.83 Aligned_cols=29 Identities=31% Similarity=0.353 Sum_probs=18.8
Q ss_pred CcccCCEEEEeecCCCCe-EeEEEEEEccC
Q 033131 2 HVKAGDTVKVIAGCDKGK-IGEITKVFRHN 30 (126)
Q Consensus 2 ~I~kGD~V~Vi~GkdKGK-~G~V~~V~~~~ 30 (126)
-|+.||-|.|-.-.+-.| .|.|..++.+.
T Consensus 38 WIkrGd~VlV~p~~~~~kvkgeIv~i~~~~ 67 (78)
T cd05792 38 WIKRGDFVLVEPIEEGDKVKAEIVKILTRD 67 (78)
T ss_pred EEEeCCEEEEEecccCCceEEEEEEEECHH
Confidence 378899888866443333 47777776554
No 114
>KOG0122 consensus Translation initiation factor 3, subunit g (eIF-3g) [Translation, ribosomal structure and biogenesis]
Probab=22.49 E-value=1.6e+02 Score=24.61 Aligned_cols=49 Identities=16% Similarity=0.287 Sum_probs=30.5
Q ss_pred cCcCCCeeeeecCCCCeeeEEEEEccCCcEEEEE---cccCcccccc----hhhhhhhh
Q 033131 62 PIHSSNVMLYSKEMEVASRVGHKVLDDGTRVRYL---IKTGEIIDSA----ENWKKLKE 113 (126)
Q Consensus 62 pI~~SNV~Lv~p~~~~~~rv~~~~~~dG~kvRv~---k~sg~~i~~p----~~~~~~~k 113 (126)
++.+++-.+- .|..+-+.|++++||+|+-|. +.....++.. ..|+++-.
T Consensus 17 ~l~P~~q~i~---~g~ktvieyk~n~dgkK~Kvt~~~kv~k~~v~K~vaeRknW~KFG~ 72 (270)
T KOG0122|consen 17 GLLPPKQTIE---DGTKTVIEYKINEDGKKVKVTRTFKVEKRAVPKAVAERKNWVKFGD 72 (270)
T ss_pred cCCCcceeec---CCcEEEEEEEEcCCCcEEEEEEEEEEEEEeccHHHHhhccchhhcc
Confidence 4555554443 577899999999999886554 3444444432 26666543
No 115
>cd03698 eRF3_II_like eRF3_II_like: domain similar to domain II of the eukaryotic class II release factor (eRF3). In eukaryotes, translation termination is mediated by two interacting release factors, eRF1 and eRF3, which act as class I and II factors, respectively. eRF1 functions as an omnipotent release factor, decoding all three stop codons and triggering the release of the nascent peptide catalyzed by the ribsome. eRF3 is a GTPase, which enhances the termination efficiency by stimulating the eRF1 activity in a GTP-dependent manner. Sequence comparison of class II release factors with elongation factors shows that eRF3 is more similar to eEF1alpha whereas prokaryote RF3 is more similar to EF-G, implying that their precise function may differ. Only eukaryote RF3s are found in this group. Saccharomyces cerevisiae eRF3 (Sup35p) is a translation termination factor which is divided into three regions N, M and a C-terminal eEF1a-like region essential for translation termination. Sup35NM
Probab=22.44 E-value=1.3e+02 Score=19.43 Aligned_cols=16 Identities=31% Similarity=0.295 Sum_probs=6.8
Q ss_pred EEEEccCCeEEEecee
Q 033131 24 TKVFRHNSTVMVKDIN 39 (126)
Q Consensus 24 ~~V~~~~~~V~VeGvN 39 (126)
+.+.+....+.|.++.
T Consensus 33 v~i~P~~~~~~V~si~ 48 (83)
T cd03698 33 LLVMPSKESVEVKSIY 48 (83)
T ss_pred EEEeCCCcEEEEEEEE
Confidence 3333433344444444
No 116
>TIGR03170 flgA_cterm flagella basal body P-ring formation protein FlgA. This model describes a conserved C-terminal region of the flagellar basal body P-ring formation protein FlgA. This sequence region contains a SAF domain, now described by Pfam model pfam08666.
Probab=22.40 E-value=1.4e+02 Score=20.57 Aligned_cols=11 Identities=82% Similarity=1.002 Sum_probs=7.8
Q ss_pred cccCCEEEEee
Q 033131 3 VKAGDTVKVIA 13 (126)
Q Consensus 3 I~kGD~V~Vi~ 13 (126)
+++||.|.++.
T Consensus 66 V~~G~~V~i~~ 76 (122)
T TIGR03170 66 VKRGDTVTVIA 76 (122)
T ss_pred EcCCCEEEEEE
Confidence 56788877765
No 117
>cd04090 eEF2_II_snRNP Loc2 eEF2_C_snRNP, cd01514/C terminal domain:eEF2_C_snRNP: This family includes C-terminal portion of the spliceosomal human 116kD U5 small nuclear ribonucleoprotein (snRNP) protein (U5-116 kD) and, its yeast counterpart Snu114p. This domain is homologous to domain II of the eukaryotic translational elongation factor EF-2. Yeast Snu114p is essential for cell viability and for splicing in vivo. U5-116 kD binds GTP. Experiments suggest that GTP binding and probably GTP hydrolysis is important for the function of the U5-116 kD/Snu114p. In complex with GTP, EF-2 promotes the translocation step of translation. During translocation the peptidyl-tRNA is moved from the A site to the P site, the uncharged tRNA from the P site to the E-site and, the mRNA is shifted one codon relative to the ribosome.
Probab=22.05 E-value=2.5e+02 Score=18.61 Aligned_cols=13 Identities=38% Similarity=0.659 Sum_probs=9.5
Q ss_pred CcccCCEEEEeec
Q 033131 2 HVKAGDTVKVIAG 14 (126)
Q Consensus 2 ~I~kGD~V~Vi~G 14 (126)
.|++||.|.++.-
T Consensus 27 tl~~g~~v~~~~~ 39 (94)
T cd04090 27 TIKKGQKVKVLGE 39 (94)
T ss_pred eEcCCCEEEEECC
Confidence 4678888888753
No 118
>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=21.96 E-value=2.7e+02 Score=21.24 Aligned_cols=33 Identities=18% Similarity=0.143 Sum_probs=25.1
Q ss_pred cccCCEEEEeecCC-CCeEeEEEEEEccCC-eEEE
Q 033131 3 VKAGDTVKVIAGCD-KGKIGEITKVFRHNS-TVMV 35 (126)
Q Consensus 3 I~kGD~V~Vi~Gkd-KGK~G~V~~V~~~~~-~V~V 35 (126)
++.||-|.+.++.. -..+|.|.++....+ .+.|
T Consensus 4 yrvGD~Vy~~~~~~~Py~I~rI~e~~~~~~~~~~v 38 (164)
T cd04709 4 YRVGDYVYFESSPNNPYLIRRIEELNKTARGHVEA 38 (164)
T ss_pred EecCCEEEEECCCCCCCEEEEEEEEEeCCCCCEEE
Confidence 68999999998864 368999999876543 4444
No 119
>cd03693 EF1_alpha_II EF1_alpha_II: this family represents the domain II of elongation factor 1-alpha (EF-1a) that is found in archaea and all eukaryotic lineages. EF-1A is very abundant in the cytosol, where it is involved in the GTP-dependent binding of aminoacyl-tRNAs to the A site of the ribosomes in the second step of translation from mRNAs to proteins. Both domain II of EF1A and domain IV of IF2/eIF5B have been implicated in recognition of the 3'-ends of tRNA. More than 61% of eukaryotic elongation factor 1A (eEF-1A) in cells is estimated to be associated with actin cytoskeleton. The binding of eEF1A to actin is a noncanonical function that may link two distinct cellular processes, cytoskeleton organization and gene expression.
Probab=21.92 E-value=1.3e+02 Score=19.91 Aligned_cols=15 Identities=20% Similarity=0.089 Sum_probs=6.1
Q ss_pred EEEccCCeEEEecee
Q 033131 25 KVFRHNSTVMVKDIN 39 (126)
Q Consensus 25 ~V~~~~~~V~VeGvN 39 (126)
.+.+....+.|.++.
T Consensus 38 ~i~P~~~~~~V~sI~ 52 (91)
T cd03693 38 TFAPAGVTGEVKSVE 52 (91)
T ss_pred EECCCCcEEEEEEEE
Confidence 333433344444443
No 120
>COG1162 Predicted GTPases [General function prediction only]
Probab=21.78 E-value=1.3e+02 Score=25.33 Aligned_cols=27 Identities=22% Similarity=0.313 Sum_probs=23.1
Q ss_pred cccCCEEEEeecCCCCeEeEEEEEEccCCe
Q 033131 3 VKAGDTVKVIAGCDKGKIGEITKVFRHNST 32 (126)
Q Consensus 3 I~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~ 32 (126)
...||.|.+-.+... |.|.+|.+.+|.
T Consensus 45 ~vVGD~V~~~~~~~~---g~I~~i~~Rkn~ 71 (301)
T COG1162 45 PVVGDRVVFEDENNN---GVIEKILPRKNV 71 (301)
T ss_pred ccccCeEEEecCCCc---ceEEEEecccCc
Confidence 458999999999876 899999998874
No 121
>PF06701 MIB_HERC2: Mib_herc2; InterPro: IPR010606 Mib is a RING ubiquitin ligase in the Notch pathway. Mib interacts with the intracellular domain of Delta to promote its ubiquitylation and internalisation. Cell transplantation studies suggest that mib function is essential in the signalling cell for efficient activation of Notch in neighbouring cells. This domain has been named 'mib/herc2 domain' in []and usually the protein also contains an E3 ligase domain (either Ring or Hect).; GO: 0004842 ubiquitin-protein ligase activity, 0046872 metal ion binding, 0016567 protein ubiquitination; PDB: 2DK3_A 3DKM_A.
Probab=21.32 E-value=1.2e+02 Score=19.92 Aligned_cols=10 Identities=20% Similarity=0.810 Sum_probs=4.2
Q ss_pred CCeEeEEEEE
Q 033131 17 KGKIGEITKV 26 (126)
Q Consensus 17 KGK~G~V~~V 26 (126)
.|..|+|.++
T Consensus 19 ~g~~GtV~~i 28 (68)
T PF06701_consen 19 EGHVGTVVSI 28 (68)
T ss_dssp TT--EEE-S-
T ss_pred CCcceEEEec
Confidence 3677787776
No 122
>PRK07252 hypothetical protein; Provisional
Probab=21.29 E-value=2e+02 Score=20.58 Aligned_cols=24 Identities=17% Similarity=0.275 Sum_probs=17.3
Q ss_pred cccCCEEEEeecCCCCeEeEEEEEEccCCeEEEe
Q 033131 3 VKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 36 (126)
Q Consensus 3 I~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~Ve 36 (126)
++.||.|.| +|++++.+.+++.+.
T Consensus 48 ~~vGD~V~V----------kI~~iD~~~~ri~lS 71 (120)
T PRK07252 48 LKVGEEVLV----------QVVDFDEYTGKASLS 71 (120)
T ss_pred cCCCCEEEE----------EEEEEeCCCCEEEEE
Confidence 566777766 677888877777655
No 123
>cd05691 S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: 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 6 (ec6) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=20.92 E-value=2.1e+02 Score=17.31 Aligned_cols=14 Identities=36% Similarity=0.475 Sum_probs=8.0
Q ss_pred EEEEEEccCCeEEE
Q 033131 22 EITKVFRHNSTVMV 35 (126)
Q Consensus 22 ~V~~V~~~~~~V~V 35 (126)
+|+++++..+.+.+
T Consensus 54 ~v~~~d~~~~~i~l 67 (73)
T cd05691 54 KITNVDRKNRKISL 67 (73)
T ss_pred EEEEEeCCCCEEEE
Confidence 56666666555443
No 124
>PF05257 CHAP: CHAP domain; InterPro: IPR007921 The CHAP (cysteine, histidine-dependent amidohydrolases/peptidases) domain is a region between 110 and 140 amino acids that is found in proteins from bacteria, bacteriophages, archaea and eukaryotes of the Trypanosomidae family. Many of these proteins are uncharacterised, but it has been proposed that they may function mainly in peptidoglycan hydrolysis. The CHAP domain is found in a wide range of protein architectures; it is commonly associated with bacterial type SH3 domains and with several families of amidase domains. It has been suggested that CHAP domain containing proteins utilise a catalytic cysteine residue in a nucleophilic-attack mechanism [, ]. The CHAP domain contains two invariant residues, a cysteine and a histidine. These residues form part of the putative active site of CHAP domain containing proteins. Secondary structure predictions show that the CHAP domain belongs to the alpha + beta structural class, with the N-terminal half largely containing predicted alpha helices and the C-terminal half principally composed of predicted beta strands [, ]. Some proteins known to contain a CHAP domain are listed below: Bacterial and trypanosomal glutathionylspermidine amidases. A variety of bacterial autolysins. A Nocardia aerocolonigenes putative esterase. Streptococcus pneumoniae choline-binding protein D. Methanosarcina mazei protein MM2478, a putative chloride channel. Several phage-encoded peptidoglycan hydrolases. Cysteine peptidases belonging to MEROPS peptidase family C51 (D-alanyl-glycyl endopeptidase, clan CA). ; PDB: 2LRJ_A 2VPM_B 2VOB_B 2VPS_A 2K3A_A 2IO9_A 2IO8_A 2IOB_A 2IOA_B 2IO7_B ....
Probab=20.81 E-value=1.8e+02 Score=20.04 Aligned_cols=36 Identities=25% Similarity=0.297 Sum_probs=23.9
Q ss_pred cccCCEEEE--eecCCCCeEeEEEEEEccCCeEEEecee
Q 033131 3 VKAGDTVKV--IAGCDKGKIGEITKVFRHNSTVMVKDIN 39 (126)
Q Consensus 3 I~kGD~V~V--i~GkdKGK~G~V~~V~~~~~~V~VeGvN 39 (126)
.++||.|+. -.+..-|-+|.|.+|.. .+.|.+-.-|
T Consensus 63 P~~Gdivv~~~~~~~~~GHVaIV~~v~~-~~~i~v~e~N 100 (124)
T PF05257_consen 63 PQPGDIVVWDSGSGGGYGHVAIVESVND-GGTITVIEQN 100 (124)
T ss_dssp --TTEEEEEEECTTTTT-EEEEEEEE-T-TSEEEEEECS
T ss_pred cccceEEEeccCCCCCCCeEEEEEEECC-CCEEEEEECC
Confidence 468998887 35567899999999944 4577766555
No 125
>PF08813 Phage_tail_3: Phage tail protein; InterPro: IPR014918 This entry is represented by Bacteriophage T1, Orf41. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. Proteins of this entry include phage tail proteins. They probably include bacterial Ig-like domains related to IPR003343 from INTERPRO. Which also includes a number of phage tail invasin proteins.
Probab=20.80 E-value=3.1e+02 Score=20.62 Aligned_cols=71 Identities=14% Similarity=0.087 Sum_probs=47.5
Q ss_pred EEEEEEc-cCCeEEEeceeeeEEEecCCcccCCceEEEEeecCcCCCeeeeecCCCCeeeEEEEEccCCcEEE
Q 033131 22 EITKVFR-HNSTVMVKDINLKTKHVKKREEEEQGQIIKIEAPIHSSNVMLYSKEMEVASRVGHKVLDDGTRVR 93 (126)
Q Consensus 22 ~V~~V~~-~~~~V~VeGvN~~kkh~k~~~~~~~ggi~~~e~pI~~SNV~Lv~p~~~~~~rv~~~~~~dG~kvR 93 (126)
+|.+|.- ..+.+.+||++-...+.=|.. ...|.......-..++.|.=+...-|++-.+.+.+++|..+.-
T Consensus 9 r~~rv~~~~~~~~~l~gidTt~~~~fpaG-~g~gs~~kit~w~~i~~v~ev~~sGGeqq~~~~t~L~d~~~~~ 80 (165)
T PF08813_consen 9 RVFRVKAVTADTFTLEGIDTTDTNKFPAG-SGTGSARKITTWTEIPQVKEVSTSGGEQQFIDVTFLEDDRQQQ 80 (165)
T ss_pred eEEEEecccCCeEEEEeecccCCccccCC-cccEEEEEccccEEeccccccCCCCCcceEEEEEEcccchhee
Confidence 3444432 447999999997764432321 1335666667777778877676677899999999999964433
No 126
>COG1385 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.65 E-value=1.7e+02 Score=23.59 Aligned_cols=34 Identities=24% Similarity=0.463 Sum_probs=25.8
Q ss_pred CCcccCCEEEEeecCCCCeEeEEEEEEccCCeEE
Q 033131 1 MHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVM 34 (126)
Q Consensus 1 ~~I~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~ 34 (126)
|+++.||.+.+..|.+.=-.+.|.++..+.-.+.
T Consensus 32 lRl~~gd~l~l~~g~g~~~~a~i~~~~kk~~~~~ 65 (246)
T COG1385 32 LRLKEGDELRLFDGSGGEFLAEITKIGKKEALLK 65 (246)
T ss_pred eecCCCCEEEEEeCCCcEEEEEEeecCCCceEEE
Confidence 4788999999999987766678887766554443
No 127
>COG2053 RPS28A Ribosomal protein S28E/S33 [Translation, ribosomal structure and biogenesis]
Probab=20.63 E-value=84 Score=21.03 Aligned_cols=12 Identities=42% Similarity=0.936 Sum_probs=9.8
Q ss_pred EEEEeecCCCCe
Q 033131 8 TVKVIAGCDKGK 19 (126)
Q Consensus 8 ~V~Vi~GkdKGK 19 (126)
+|.++.|+|||.
T Consensus 27 k~ril~grdkgR 38 (69)
T COG2053 27 KVRILEGRDKGR 38 (69)
T ss_pred EEEEeecCCcCc
Confidence 578899999885
No 128
>PF09356 Phage_BR0599: Phage conserved hypothetical protein BR0599; InterPro: IPR018964 This entry describes the C-terminal region of a family of proteins found almost exclusively in phage or in prophage regions of bacterial genomes, including the phage-like Rhodobacter capsulatus (Rhodopseudomonas capsulata) gene transfer agent, which packages DNA. An apparent exception is Wolbachia pipientis wMel, a bacterial endosymbiont of the fruit fly, which has several candidate phage-related genes physically separate from obvious prophage regions.
Probab=20.45 E-value=92 Score=20.86 Aligned_cols=17 Identities=47% Similarity=0.856 Sum_probs=14.9
Q ss_pred CcccCCEEEEeecCCCC
Q 033131 2 HVKAGDTVKVIAGCDKG 18 (126)
Q Consensus 2 ~I~kGD~V~Vi~GkdKG 18 (126)
.+..||.|.|..|-||.
T Consensus 40 ~~~~G~~v~l~~GCDkt 56 (80)
T PF09356_consen 40 GLAVGDTVTLYPGCDKT 56 (80)
T ss_pred cCCCCCEEEEEeCCCCC
Confidence 37789999999999984
No 129
>PRK04306 50S ribosomal protein L21e; Reviewed
Probab=20.29 E-value=2e+02 Score=20.41 Aligned_cols=33 Identities=27% Similarity=0.375 Sum_probs=23.4
Q ss_pred cccCCEEEEee------c----CCCCeEeEEEEEEccCCeEEE
Q 033131 3 VKAGDTVKVIA------G----CDKGKIGEITKVFRHNSTVMV 35 (126)
Q Consensus 3 I~kGD~V~Vi~------G----kdKGK~G~V~~V~~~~~~V~V 35 (126)
++.||.|-|.- | .+-|++|.|..+...-.-|.|
T Consensus 35 y~~Gd~V~I~~d~sv~kGmPh~~yhGkTG~V~~v~~~A~~V~v 77 (98)
T PRK04306 35 FEEGDKVHIVIDPSVHKGMPHPRFHGKTGTVVGKRGRAYIVEV 77 (98)
T ss_pred ccCCCEEEEEecCceecCCccccccCCCEEEEeecCeEEEEEE
Confidence 56799998763 3 245899999888766555554
No 130
>smart00357 CSP Cold shock protein domain. RNA-binding domain that functions as a RNA-chaperone in bacteria and is involved in regulating translation in eukaryotes. Contains sub-family of RNA-binding domains in the Rho transcription termination factor.
Probab=20.25 E-value=1.9e+02 Score=16.85 Aligned_cols=24 Identities=17% Similarity=0.080 Sum_probs=13.9
Q ss_pred cccCCEEEEeec---CCCCeEeEEEEE
Q 033131 3 VKAGDTVKVIAG---CDKGKIGEITKV 26 (126)
Q Consensus 3 I~kGD~V~Vi~G---kdKGK~G~V~~V 26 (126)
+..||+|.+--- ...+.++.+.+|
T Consensus 37 ~~~Gd~V~~~i~~~~~~~~~~a~~v~~ 63 (64)
T smart00357 37 LREGDEVEFKVVSPRGGGKPEAENVVK 63 (64)
T ss_pred CCCCCEEEEEEEEccCCCCcEEEEEEe
Confidence 456888877532 234455666554
No 131
>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=20.23 E-value=2e+02 Score=20.32 Aligned_cols=34 Identities=15% Similarity=0.304 Sum_probs=24.9
Q ss_pred cccCCEEEEeecCC--CCeEeEEEEEEccC-CeEEEe
Q 033131 3 VKAGDTVKVIAGCD--KGKIGEITKVFRHN-STVMVK 36 (126)
Q Consensus 3 I~kGD~V~Vi~Gkd--KGK~G~V~~V~~~~-~~V~Ve 36 (126)
++.||-|.|.+..+ +=-+|+|.++.... +...+.
T Consensus 4 ~~vGD~V~v~~~~~~~~pyIgrI~~i~e~~~g~~~~~ 40 (121)
T cd04714 4 IRVGDCVLFKSPGRPSLPYVARIESLWEDPEGNMVVR 40 (121)
T ss_pred EEcCCEEEEeCCCCCCCCEEEEEEEEEEcCCCCEEEE
Confidence 68899999998653 45689999998754 344443
No 132
>PF07076 DUF1344: Protein of unknown function (DUF1344); InterPro: IPR009780 This family consists of several short, hypothetical bacterial proteins of around 80 residues in length. Members of this family are found in Rhizobium, Agrobacterium and Brucella species. The function of this family is unknown.
Probab=20.17 E-value=1.1e+02 Score=19.94 Aligned_cols=19 Identities=21% Similarity=0.274 Sum_probs=16.4
Q ss_pred eEeEEEEEEccCCeEEEec
Q 033131 19 KIGEITKVFRHNSTVMVKD 37 (126)
Q Consensus 19 K~G~V~~V~~~~~~V~VeG 37 (126)
-+|+|.+|++...++.+++
T Consensus 5 veG~I~~id~~~~titLdD 23 (61)
T PF07076_consen 5 VEGTIKSIDPETMTITLDD 23 (61)
T ss_pred ceEEEEEEcCCceEEEecC
Confidence 3699999999999998884
Done!