Query 032297
Match_columns 143
No_of_seqs 126 out of 1166
Neff 4.0
Searched_HMMs 46136
Date Fri Mar 29 12:14:05 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032297.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032297hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1708 Mitochondrial/chloropl 100.0 1.8E-31 4E-36 218.7 7.0 134 1-134 1-137 (236)
2 PRK12281 rplX 50S ribosomal pr 99.9 8E-27 1.7E-31 164.1 7.8 73 65-137 2-74 (76)
3 CHL00141 rpl24 ribosomal prote 99.9 2.8E-25 6.1E-30 158.4 7.6 76 66-141 5-80 (83)
4 PRK00004 rplX 50S ribosomal pr 99.9 4.2E-25 9E-30 163.0 7.4 75 67-141 2-76 (105)
5 TIGR01079 rplX_bact ribosomal 99.9 1.1E-24 2.3E-29 161.0 7.5 74 67-140 1-75 (104)
6 COG0198 RplX Ribosomal protein 99.9 1.4E-24 3E-29 161.3 6.8 73 67-141 2-74 (104)
7 PRK01191 rpl24p 50S ribosomal 99.8 3.4E-19 7.3E-24 135.4 6.0 70 53-139 35-104 (120)
8 PTZ00194 60S ribosomal protein 99.8 2.7E-19 5.9E-24 139.3 5.4 71 53-140 36-106 (143)
9 TIGR01080 rplX_A_E ribosomal p 99.7 2.1E-18 4.6E-23 129.7 5.8 77 45-138 23-99 (114)
10 PF00467 KOW: KOW motif; Inte 98.8 6.3E-09 1.4E-13 61.8 4.7 32 72-103 1-32 (32)
11 KOG3401 60S ribosomal protein 98.1 2.8E-06 6.1E-11 66.8 3.3 70 54-140 39-109 (145)
12 smart00739 KOW KOW (Kyprides, 97.9 1.5E-05 3.3E-10 44.5 3.7 26 70-95 2-27 (28)
13 TIGR00405 L26e_arch ribosomal 97.2 0.00073 1.6E-08 51.0 5.3 37 70-106 87-123 (145)
14 PRK05609 nusG transcription an 97.2 0.0007 1.5E-08 52.2 4.9 36 68-103 125-160 (181)
15 TIGR00922 nusG transcription t 97.1 0.00089 1.9E-08 51.4 4.9 36 68-103 118-153 (172)
16 PRK08559 nusG transcription an 97.0 0.0012 2.7E-08 50.9 5.0 41 68-108 93-133 (153)
17 COG0250 NusG Transcription ant 96.8 0.0021 4.6E-08 51.5 4.7 38 66-103 120-157 (178)
18 TIGR01955 RfaH transcriptional 96.5 0.0043 9.3E-08 46.9 4.4 35 68-103 107-141 (159)
19 PRK09014 rfaH transcriptional 96.3 0.0059 1.3E-07 46.7 4.3 33 70-103 110-142 (162)
20 TIGR01956 NusG_myco NusG famil 95.9 0.014 3E-07 49.8 5.2 36 68-103 204-239 (258)
21 PRK04333 50S ribosomal protein 94.9 0.06 1.3E-06 38.7 4.7 36 69-105 3-38 (84)
22 PTZ00065 60S ribosomal protein 93.0 0.23 5E-06 38.6 5.1 35 70-105 8-42 (130)
23 KOG1999 RNA polymerase II tran 91.6 0.19 4.2E-06 49.7 3.8 29 68-96 458-486 (1024)
24 PTZ00471 60S ribosomal protein 88.4 0.84 1.8E-05 35.8 4.3 39 70-108 5-49 (134)
25 COG2163 RPL14A Ribosomal prote 87.4 0.99 2.1E-05 34.8 4.2 34 70-104 5-38 (125)
26 PRK04313 30S ribosomal protein 85.9 1.3 2.8E-05 37.5 4.4 41 66-106 168-212 (237)
27 PF09953 DUF2187: Uncharacteri 83.1 2.6 5.7E-05 28.7 4.1 27 71-103 5-31 (57)
28 COG5164 SPT5 Transcription elo 80.1 1.4 3.1E-05 41.2 2.6 29 69-97 139-167 (607)
29 KOG1999 RNA polymerase II tran 80.0 4.5 9.7E-05 40.5 6.1 27 70-96 408-434 (1024)
30 COG3700 AphA Acid phosphatase 79.3 0.53 1.2E-05 39.5 -0.3 67 66-134 123-192 (237)
31 PF01157 Ribosomal_L21e: Ribos 76.7 2.9 6.2E-05 31.1 3.0 29 69-97 32-70 (99)
32 PLN00036 40S ribosomal protein 76.2 4.9 0.00011 34.6 4.6 40 66-105 171-213 (261)
33 PTZ00223 40S ribosomal protein 74.9 4.9 0.00011 34.8 4.3 41 65-105 167-210 (273)
34 PF03144 GTP_EFTU_D2: Elongati 74.5 5.9 0.00013 25.7 3.8 31 68-99 11-44 (74)
35 PRK06531 yajC preprotein trans 73.7 8.9 0.00019 29.0 5.0 31 69-103 36-66 (113)
36 PTZ00118 40S ribosomal protein 73.5 6.3 0.00014 33.9 4.6 40 66-105 171-213 (262)
37 COG1532 Predicted RNA-binding 70.5 9.1 0.0002 26.1 3.9 35 70-104 21-57 (57)
38 PRK04306 50S ribosomal protein 69.8 8.3 0.00018 28.7 4.0 39 69-107 34-82 (98)
39 PF05641 Agenet: Agenet domain 69.3 10 0.00022 25.3 4.0 33 70-103 1-37 (68)
40 COG1471 RPS4A Ribosomal protei 68.2 9 0.0002 32.8 4.4 40 66-105 170-213 (241)
41 COG2139 RPL21A Ribosomal prote 66.4 13 0.00027 28.0 4.3 39 69-107 32-80 (98)
42 PRK05585 yajC preprotein trans 65.7 11 0.00023 28.1 3.9 30 68-103 51-80 (106)
43 PF00924 MS_channel: Mechanose 65.1 8.4 0.00018 29.5 3.3 61 69-134 60-128 (206)
44 COG1862 YajC Preprotein transl 64.6 15 0.00032 27.2 4.4 25 69-97 43-67 (97)
45 PF08206 OB_RNB: Ribonuclease 63.7 5.7 0.00012 25.9 1.9 25 69-93 31-58 (58)
46 PRK02749 photosystem I reactio 62.7 15 0.00033 26.1 4.0 29 69-97 2-32 (71)
47 PLN00045 photosystem I reactio 59.8 13 0.00028 28.0 3.3 39 69-107 39-84 (101)
48 PRK00409 recombination and DNA 59.1 12 0.00026 36.1 3.9 36 68-107 635-672 (782)
49 PF12701 LSM14: Scd6-like Sm d 58.9 27 0.00058 25.6 4.9 35 72-106 7-41 (96)
50 PF11623 DUF3252: Protein of u 58.4 23 0.0005 23.9 4.0 40 70-109 2-43 (53)
51 CHL00125 psaE photosystem I su 58.4 16 0.00034 25.6 3.4 28 70-97 2-31 (64)
52 PF02699 YajC: Preprotein tran 56.1 3.7 8.1E-05 28.8 0.0 30 68-103 35-64 (82)
53 PRK05886 yajC preprotein trans 55.7 21 0.00045 26.9 4.0 29 69-103 38-66 (109)
54 TIGR00739 yajC preprotein tran 55.4 21 0.00046 25.3 3.8 29 69-103 37-65 (84)
55 TIGR01069 mutS2 MutS2 family p 53.8 19 0.0004 34.8 4.2 33 71-107 626-660 (771)
56 cd05793 S1_IF1A S1_IF1A: Trans 53.7 15 0.00033 25.6 2.8 31 67-97 36-66 (77)
57 TIGR03170 flgA_cterm flagella 53.4 24 0.00051 25.4 3.8 35 66-100 62-109 (122)
58 KOG3418 60S ribosomal protein 53.0 23 0.0005 28.0 3.9 38 70-107 5-48 (136)
59 cd04717 BAH_polybromo BAH, or 52.2 47 0.001 24.1 5.3 36 69-104 3-41 (121)
60 COG0361 InfA Translation initi 51.4 25 0.00054 25.0 3.6 31 66-96 43-73 (75)
61 PF02427 PSI_PsaE: Photosystem 51.3 18 0.0004 25.0 2.8 28 70-97 1-30 (61)
62 cd03692 mtIF2_IVc mtIF2_IVc: t 51.0 29 0.00062 23.9 3.8 33 68-100 25-57 (84)
63 smart00652 eIF1a eukaryotic tr 50.8 20 0.00044 25.4 3.1 31 67-97 41-71 (83)
64 PLN00190 60S ribosomal protein 50.0 24 0.00051 28.4 3.6 47 69-115 33-99 (158)
65 PF01079 Hint: Hint module; I 49.7 25 0.00053 29.0 3.8 39 67-105 103-153 (217)
66 PF14505 DUF4438: Domain of un 49.6 37 0.00079 29.4 4.9 33 71-103 59-91 (258)
67 cd04456 S1_IF1A_like S1_IF1A_l 49.3 23 0.0005 24.9 3.1 30 68-97 37-67 (78)
68 cd05689 S1_RPS1_repeat_ec4 S1_ 49.3 46 0.001 21.4 4.4 24 68-101 47-70 (72)
69 smart00743 Agenet Tudor-like d 48.5 58 0.0013 20.6 4.8 33 69-102 2-35 (61)
70 PF01176 eIF-1a: Translation i 48.1 24 0.00052 23.5 3.0 27 66-92 38-64 (65)
71 PTZ00189 60S ribosomal protein 47.9 26 0.00055 28.3 3.5 47 69-115 33-99 (160)
72 PRK07018 flgA flagellar basal 47.5 28 0.0006 28.5 3.8 35 66-100 173-220 (235)
73 PRK12618 flgA flagellar basal 46.8 34 0.00073 26.4 4.0 33 67-99 79-124 (141)
74 PF04452 Methyltrans_RNA: RNA 46.5 26 0.00057 28.1 3.5 38 66-103 13-50 (225)
75 PF01426 BAH: BAH domain; Int 46.2 31 0.00066 24.0 3.4 29 69-97 2-32 (119)
76 PF05257 CHAP: CHAP domain; I 45.9 31 0.00068 24.7 3.5 37 69-106 62-100 (124)
77 PRK08515 flgA flagellar basal 44.7 33 0.00072 28.1 3.9 35 66-100 162-208 (222)
78 cd05792 S1_eIF1AD_like S1_eIF1 43.0 39 0.00083 24.0 3.5 31 67-97 36-67 (78)
79 PRK11281 hypothetical protein; 43.0 63 0.0014 32.9 6.1 61 67-132 936-1004(1113)
80 cd04715 BAH_Orc1p_like BAH, or 42.8 66 0.0014 25.4 5.1 30 68-97 28-57 (159)
81 cd04721 BAH_plant_1 BAH, or Br 42.8 57 0.0012 24.7 4.6 31 67-97 5-35 (130)
82 KOG4225 Sorbin and SH3 domain- 42.6 30 0.00064 32.3 3.5 47 36-90 223-277 (489)
83 TIGR00523 eIF-1A eukaryotic/ar 42.4 19 0.00042 26.4 2.0 32 66-97 54-86 (99)
84 cd05688 S1_RPS1_repeat_ec3 S1_ 41.9 56 0.0012 20.2 3.8 25 68-102 43-67 (68)
85 COG1193 Mismatch repair ATPase 41.5 29 0.00063 33.8 3.5 34 67-104 610-643 (753)
86 cd03698 eRF3_II_like eRF3_II_l 41.4 50 0.0011 22.3 3.8 26 68-96 25-50 (83)
87 cd04466 S1_YloQ_GTPase S1_YloQ 41.0 52 0.0011 20.9 3.7 29 70-100 38-66 (68)
88 PRK06005 flgA flagellar basal 41.0 43 0.00093 26.3 3.8 39 66-104 97-147 (160)
89 smart00439 BAH Bromo adjacent 40.9 55 0.0012 22.7 4.0 29 70-98 2-32 (120)
90 cd04471 S1_RNase_R S1_RNase_R: 40.5 99 0.0021 20.0 5.0 25 68-102 56-80 (83)
91 cd03695 CysN_NodQ_II CysN_NodQ 40.5 63 0.0014 22.0 4.2 29 68-99 25-53 (81)
92 KOG3421 60S ribosomal protein 40.4 32 0.0007 27.2 3.0 35 70-105 7-41 (136)
93 PF00018 SH3_1: SH3 domain; I 40.4 37 0.00081 20.6 2.8 18 66-83 12-29 (48)
94 cd05698 S1_Rrp5_repeat_hs6_sc5 39.3 58 0.0013 20.7 3.7 24 69-102 44-67 (70)
95 PF02211 NHase_beta: Nitrile h 39.2 26 0.00056 29.2 2.4 29 66-94 131-169 (222)
96 cd05695 S1_Rrp5_repeat_hs3 S1_ 39.2 51 0.0011 21.5 3.4 24 69-102 42-65 (66)
97 cd05708 S1_Rrp5_repeat_sc12 S1 39.0 73 0.0016 20.3 4.1 26 68-103 46-71 (77)
98 COG1162 Predicted GTPases [Gen 38.5 44 0.00096 29.2 3.8 30 68-100 43-72 (301)
99 PRK10929 putative mechanosensi 38.2 83 0.0018 32.2 6.1 36 67-107 933-976 (1109)
100 cd03696 selB_II selB_II: this 37.9 53 0.0011 22.1 3.5 27 68-97 25-51 (83)
101 cd05707 S1_Rrp5_repeat_sc11 S1 37.9 54 0.0012 20.9 3.3 24 69-102 44-67 (68)
102 cd05697 S1_Rrp5_repeat_hs5 S1_ 37.5 71 0.0015 20.4 3.9 24 69-102 44-67 (69)
103 KOG3482 Small nuclear ribonucl 37.2 22 0.00048 25.7 1.5 58 44-105 20-77 (79)
104 cd04714 BAH_BAHCC1 BAH, or Bro 36.9 77 0.0017 23.4 4.5 35 69-103 3-40 (121)
105 cd01854 YjeQ_engC YjeQ/EngC. 36.4 74 0.0016 26.5 4.8 30 69-100 34-63 (287)
106 PRK12617 flgA flagellar basal 36.2 51 0.0011 27.2 3.7 30 66-95 152-193 (214)
107 PRK04012 translation initiatio 36.1 43 0.00093 24.7 2.9 30 67-96 57-86 (100)
108 cd00174 SH3 Src homology 3 dom 36.0 35 0.00077 19.7 2.1 16 67-82 15-30 (54)
109 cd04461 S1_Rrp5_repeat_hs8_sc7 36.0 64 0.0014 21.5 3.6 26 67-102 56-81 (83)
110 TIGR00358 3_prime_RNase VacB a 35.9 64 0.0014 30.4 4.7 36 68-103 49-87 (654)
111 CHL00010 infA translation init 35.8 81 0.0018 21.9 4.2 28 68-95 45-72 (78)
112 PLN02661 Putative thiazole syn 35.3 26 0.00056 31.2 1.9 45 17-61 25-71 (357)
113 cd04451 S1_IF1 S1_IF1: Transla 34.9 55 0.0012 21.3 3.1 21 70-90 41-61 (64)
114 PRK10334 mechanosensitive chan 34.6 41 0.00089 28.5 3.0 60 68-133 128-195 (286)
115 cd03693 EF1_alpha_II EF1_alpha 34.4 59 0.0013 22.5 3.3 27 68-97 29-55 (91)
116 PRK11713 16S ribosomal RNA met 33.7 70 0.0015 25.9 4.1 31 66-96 26-56 (234)
117 PRK06804 flgA flagellar basal 33.3 66 0.0014 27.3 4.0 28 68-95 201-240 (261)
118 cd04089 eRF3_II eRF3_II: domai 33.2 75 0.0016 21.5 3.6 26 68-96 24-49 (82)
119 TIGR00046 RNA methyltransferas 33.2 73 0.0016 26.0 4.1 36 66-101 28-63 (240)
120 cd00164 S1_like S1_like: Ribos 33.0 85 0.0018 18.6 3.5 24 68-101 40-63 (65)
121 cd05690 S1_RPS1_repeat_ec5 S1_ 32.5 83 0.0018 19.8 3.6 23 69-101 45-67 (69)
122 PF00575 S1: S1 RNA binding do 32.3 1E+02 0.0022 19.7 4.1 25 68-102 47-71 (74)
123 PF07653 SH3_2: Variant SH3 do 32.0 33 0.00071 21.5 1.5 14 66-79 14-27 (55)
124 cd04452 S1_IF2_alpha S1_IF2_al 31.8 1.1E+02 0.0024 19.6 4.1 24 69-102 49-72 (76)
125 PF11717 Tudor-knot: RNA bindi 31.7 62 0.0014 20.7 2.9 29 70-98 1-29 (55)
126 PRK00276 infA translation init 31.7 94 0.002 21.0 3.9 24 68-91 45-68 (72)
127 cd03694 GTPBP_II Domain II of 31.1 91 0.002 21.4 3.8 31 67-97 24-55 (87)
128 cd05703 S1_Rrp5_repeat_hs12_sc 31.1 89 0.0019 20.8 3.7 25 69-103 46-70 (73)
129 PF09926 DUF2158: Uncharacteri 31.0 28 0.00061 23.0 1.1 15 70-84 1-15 (53)
130 cd01736 LSm14_N LSm14 (also kn 30.8 1.3E+02 0.0029 21.4 4.6 36 71-106 4-39 (74)
131 PRK12442 translation initiatio 30.8 96 0.0021 22.8 4.0 28 66-93 43-70 (87)
132 smart00326 SH3 Src homology 3 30.7 48 0.001 19.3 2.1 16 67-82 18-33 (58)
133 PF01191 RNA_pol_Rpb5_C: RNA p 30.5 29 0.00063 24.5 1.2 27 56-82 28-61 (74)
134 smart00316 S1 Ribosomal protei 30.2 1.3E+02 0.0028 18.1 4.2 24 69-102 46-69 (72)
135 cd05696 S1_Rrp5_repeat_hs4 S1_ 30.0 1E+02 0.0022 20.3 3.8 24 69-102 46-69 (71)
136 PRK11642 exoribonuclease R; Pr 29.9 83 0.0018 30.8 4.5 35 69-103 117-154 (813)
137 cd03697 EFTU_II EFTU_II: Elong 29.8 71 0.0015 21.8 3.1 29 68-97 25-53 (87)
138 TIGR02594 conserved hypothetic 29.7 1.1E+02 0.0025 23.0 4.4 35 71-106 75-109 (129)
139 cd05685 S1_Tex S1_Tex: The C-t 29.6 97 0.0021 18.9 3.5 22 70-101 45-66 (68)
140 cd04719 BAH_Orc1p_animal BAH, 29.6 86 0.0019 24.0 3.8 30 68-97 2-32 (128)
141 COG5164 SPT5 Transcription elo 29.5 58 0.0013 30.9 3.3 33 71-103 353-385 (607)
142 PF14001 YdfZ: YdfZ protein 29.3 1.3E+02 0.0028 21.1 4.2 42 56-106 2-52 (64)
143 cd05706 S1_Rrp5_repeat_sc10 S1 29.3 1.1E+02 0.0025 19.5 3.9 23 70-102 48-70 (73)
144 cd04709 BAH_MTA BAH, or Bromo 29.1 1.1E+02 0.0025 24.2 4.5 29 70-98 4-33 (164)
145 PF13144 SAF_2: SAF-like 29.0 82 0.0018 24.4 3.7 32 66-97 136-179 (196)
146 cd05687 S1_RPS1_repeat_ec1_hs1 28.3 1.1E+02 0.0025 19.3 3.7 23 70-102 45-67 (70)
147 KOG4315 G-patch nucleic acid b 28.0 29 0.00062 32.2 1.0 36 70-105 394-429 (455)
148 cd04370 BAH BAH, or Bromo Adja 27.9 1.4E+02 0.0031 20.4 4.4 30 69-98 3-36 (123)
149 PF11948 DUF3465: Protein of u 27.8 37 0.00081 26.6 1.5 18 62-79 77-95 (131)
150 cd04716 BAH_plantDCM_I BAH, or 27.5 1.3E+02 0.0028 22.6 4.4 32 70-101 4-37 (122)
151 COG2002 AbrB Regulators of sta 26.8 43 0.00093 23.5 1.6 22 65-86 23-44 (89)
152 PRK12786 flgA flagellar basal 26.8 88 0.0019 27.4 3.8 37 67-104 256-305 (338)
153 PRK12289 GTPase RsgA; Reviewed 26.5 1.2E+02 0.0027 26.5 4.7 32 70-101 52-83 (352)
154 smart00357 CSP Cold shock prot 26.3 98 0.0021 18.8 3.0 24 70-93 37-63 (64)
155 TIGR00008 infA translation ini 26.0 93 0.002 21.6 3.1 24 67-90 42-65 (68)
156 cd05691 S1_RPS1_repeat_ec6 S1_ 26.0 1.5E+02 0.0032 18.7 3.9 24 69-102 44-67 (73)
157 cd04091 mtEFG1_II_like mtEFG1_ 25.9 1.1E+02 0.0025 20.4 3.5 13 68-80 24-36 (81)
158 PF02887 PK_C: Pyruvate kinase 25.9 35 0.00076 24.5 1.0 20 69-88 89-108 (117)
159 cd04090 eEF2_II_snRNP Loc2 eEF 25.5 1.2E+02 0.0027 20.9 3.7 14 68-81 26-39 (94)
160 PRK00049 elongation factor Tu; 25.1 1.4E+02 0.003 26.1 4.7 33 66-99 235-267 (396)
161 PRK06437 hypothetical protein; 24.9 54 0.0012 21.9 1.7 15 66-80 48-62 (67)
162 PRK08577 hypothetical protein; 24.6 56 0.0012 24.3 1.9 24 65-88 22-45 (136)
163 cd03691 BipA_TypA_II BipA_TypA 24.5 1.2E+02 0.0026 20.2 3.4 17 67-83 24-40 (86)
164 TIGR02062 RNase_B exoribonucle 24.1 1.4E+02 0.003 28.3 4.8 35 69-103 50-85 (639)
165 PF07497 Rho_RNA_bind: Rho ter 23.2 76 0.0016 22.6 2.2 18 64-81 37-54 (78)
166 PRK08187 pyruvate kinase; Vali 22.9 2.9E+02 0.0064 25.7 6.6 98 39-140 189-308 (493)
167 PF06701 MIB_HERC2: Mib_herc2; 22.9 1.1E+02 0.0023 21.2 2.9 20 84-103 19-43 (68)
168 PRK07252 hypothetical protein; 22.9 1.5E+02 0.0032 22.1 3.9 25 69-103 47-71 (120)
169 PF02941 FeThRed_A: Ferredoxin 22.7 1.1E+02 0.0023 21.6 2.8 25 72-96 1-39 (67)
170 COG1385 Uncharacterized protei 22.7 1.3E+02 0.0029 25.1 4.0 37 67-103 31-67 (246)
171 PRK05054 exoribonuclease II; P 22.1 1.5E+02 0.0033 28.0 4.7 34 69-102 53-87 (644)
172 PF14604 SH3_9: Variant SH3 do 21.7 69 0.0015 19.9 1.6 16 66-81 11-26 (49)
173 COG1261 FlgA Flagellar basal b 21.5 1.7E+02 0.0036 24.5 4.3 40 66-105 158-209 (220)
174 PLN00208 translation initiatio 21.4 1.4E+02 0.0029 23.8 3.6 31 67-97 68-98 (145)
175 PF09356 Phage_BR0599: Phage c 21.0 74 0.0016 22.3 1.8 17 69-85 40-56 (80)
176 cd05686 S1_pNO40 S1_pNO40: pNO 21.0 1.5E+02 0.0033 19.3 3.3 19 69-97 48-66 (73)
177 TIGR02063 RNase_R ribonuclease 20.9 1.5E+02 0.0033 28.0 4.4 36 68-103 101-140 (709)
178 cd04713 BAH_plant_3 BAH, or Br 20.8 2.2E+02 0.0047 21.8 4.6 30 68-97 19-49 (146)
179 TIGR00157 ribosome small subun 20.8 1.5E+02 0.0033 24.1 3.9 34 71-106 2-38 (245)
180 PF04351 PilP: Pilus assembly 20.8 2.1E+02 0.0045 21.8 4.5 47 74-132 101-148 (149)
181 KOG4792 Crk family adapters [S 20.7 1.6E+02 0.0035 25.7 4.2 44 36-80 213-258 (293)
182 TIGR00219 mreC rod shape-deter 20.6 1.2E+02 0.0027 25.7 3.4 28 69-100 143-171 (283)
183 PF13550 Phage-tail_3: Putativ 20.6 1.5E+02 0.0032 21.5 3.5 28 66-94 136-163 (164)
184 cd06462 Peptidase_S24_S26 The 20.4 2.4E+02 0.0052 17.8 4.5 34 70-106 29-64 (84)
185 PTZ00329 eukaryotic translatio 20.2 1.4E+02 0.0031 23.9 3.5 31 67-97 68-98 (155)
186 PRK05352 Na(+)-translocating N 20.0 1.3E+02 0.0028 27.5 3.6 30 66-95 42-82 (448)
No 1
>KOG1708 consensus Mitochondrial/chloroplast ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=99.97 E-value=1.8e-31 Score=218.70 Aligned_cols=134 Identities=42% Similarity=0.568 Sum_probs=125.1
Q ss_pred Chhhhhhhhhcccccccc-ccccCccc-CCCCCCC-ccccCCCCceeeeeeeeeeeeeccCCCCCcccccceeeeCCEEE
Q 032297 1 MAAMAALQSSMTSLSISS-NSFFGQRL-SFPSLSP-ITVKPTDKPCLIVVRLKRWERKECKPNSLPVLHKMHVKAGDTVK 77 (143)
Q Consensus 1 ~~~~~~~~~~~~~l~~~~-~~f~g~~l-~~~~~~~-~~~~~~~~~~~~~~~~k~Werk~~kpn~lp~~~k~~IkkGD~V~ 77 (143)
|+.|+||||++++||++- .+|.+|.+ +|.++.+ .+.+..+|+|+.....++|+|+.|.++..+..++|+++.||+|+
T Consensus 1 M~ts~aL~s~l~s~s~lPs~y~er~y~isP~~~~~~~pr~~adk~~~~~qk~~~w~rrr~~~~e~i~d~dw~ff~GDtVe 80 (236)
T KOG1708|consen 1 MRTSSALASSLTSLSLLPSSYFERQYLISPISLSVTSPRKVADKRCLVLQKNKPWERRRCVPVEPIIDEDWHFFFGDTVE 80 (236)
T ss_pred CchHHHHHHHhhhhhcCCHHHhhceeeeccccccccCCCChhhhhhhHHhhcCccccccCCCCCCccccceeEecCCEEE
Confidence 889999999999999865 66778888 5667774 34788899999999999999999999999999999999999999
Q ss_pred EEecCCCCeEeEEEEEEccCCEEEEeceeeeeeeecCCcccCCceEEEEeeceeecc
Q 032297 78 VIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQIIKLKCDALLKR 134 (143)
Q Consensus 78 VIsG~dKGK~G~V~~V~~k~n~ViVegvN~~kkhvKp~~~~~~GgIi~~E~PIhiSn 134 (143)
||.|+||||+|+|++|++++|+|+|+|+|.+.+|++...++.+|.|++.|+|||+||
T Consensus 81 VlvGkDkGkqG~Vtqv~r~~s~VvV~gln~k~r~~gsekeg~pgtivk~EaPlhvsk 137 (236)
T KOG1708|consen 81 VLVGKDKGKQGEVTQVIRHRSWVVVKGLNTKYRHMGSEKEGEPGTIVKSEAPLHVSK 137 (236)
T ss_pred EEecccCCccceEEEEeecCceEEEcccchhhhhhcccccCCCceEEeecCCceecc
Confidence 999999999999999999999999999999999999998899999999999999999
No 2
>PRK12281 rplX 50S ribosomal protein L24; Reviewed
Probab=99.94 E-value=8e-27 Score=164.10 Aligned_cols=73 Identities=32% Similarity=0.492 Sum_probs=69.6
Q ss_pred cccceeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEeceeeeeeeecCCcccCCceEEEEeeceeeccccc
Q 032297 65 LHKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQIIKLKCDALLKRNGS 137 (143)
Q Consensus 65 ~~k~~IkkGD~V~VIsG~dKGK~G~V~~V~~k~n~ViVegvN~~kkhvKp~~~~~~GgIi~~E~PIhiSnv~~ 137 (143)
+.+|+|++||+|+||+|+||||+|+|++|++++++|+|||+|+.++|+||+++++.|+|+++|+|||+|||..
T Consensus 2 ~~~~~I~kGD~V~Vi~G~dKGK~G~V~~V~~~~~~V~Vegvn~~kkh~kp~~~~~~G~i~~~e~pI~~SnV~l 74 (76)
T PRK12281 2 KVKLKVKKGDMVKVIAGDDKGKTGKVLAVLPKKNRVIVEGVKIAKKAIKPSQKNPNGGFIEKEMPIHISNVKK 74 (76)
T ss_pred CccccccCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEEcCcEEEEEEcCCCccCCCCCEEEEEcCcCHHHcee
Confidence 3578999999999999999999999999999999999999999999999998888999999999999999974
No 3
>CHL00141 rpl24 ribosomal protein L24; Validated
Probab=99.92 E-value=2.8e-25 Score=158.38 Aligned_cols=76 Identities=43% Similarity=0.653 Sum_probs=72.0
Q ss_pred ccceeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEeceeeeeeeecCCcccCCceEEEEeeceeecccccCCCC
Q 032297 66 HKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQIIKLKCDALLKRNGSSKPG 141 (143)
Q Consensus 66 ~k~~IkkGD~V~VIsG~dKGK~G~V~~V~~k~n~ViVegvN~~kkhvKp~~~~~~GgIi~~E~PIhiSnv~~~~~~ 141 (143)
.+++|++||+|+||+|+||||+|+|++|++++++|+|||+|+.++|+|++++++.|+++++|+|||+|||..-.|.
T Consensus 5 ~~~~I~~GD~V~Vi~G~dKGK~G~V~~V~~~~~~V~Vegvn~~~k~~k~~~~~~~g~i~~~e~pI~~SnV~lvdp~ 80 (83)
T CHL00141 5 KKMHVKIGDTVKIISGSDKGKIGEVLKIIKKSNKVIVKGINIKFKHIKPNKENEVGEIKQFEAPIHSSNVMLYNEE 80 (83)
T ss_pred eeCcccCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEEcCcEEEEEEcCCccCCCCCCEEEEECCCCHHHEEEeCcc
Confidence 4678999999999999999999999999999999999999999999999988899999999999999999987664
No 4
>PRK00004 rplX 50S ribosomal protein L24; Reviewed
Probab=99.92 E-value=4.2e-25 Score=162.96 Aligned_cols=75 Identities=39% Similarity=0.566 Sum_probs=71.6
Q ss_pred cceeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEeceeeeeeeecCCcccCCceEEEEeeceeecccccCCCC
Q 032297 67 KMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQIIKLKCDALLKRNGSSKPG 141 (143)
Q Consensus 67 k~~IkkGD~V~VIsG~dKGK~G~V~~V~~k~n~ViVegvN~~kkhvKp~~~~~~GgIi~~E~PIhiSnv~~~~~~ 141 (143)
+|+|++||+|+||+|+|||++|+|++|++++++|+|||+|+.++|+|+++++++|+|+++|+|||+|||..-.|.
T Consensus 2 ~~~i~kGD~V~Vi~G~dKGk~G~V~~V~~~~~~V~Vegvn~~k~h~k~~~~~~~G~i~~~e~pI~~SnV~lv~p~ 76 (105)
T PRK00004 2 MMKIKKGDTVIVIAGKDKGKRGKVLKVLPKKNKVIVEGVNIVKKHQKPNQENPQGGIIEKEAPIHISNVALVDPK 76 (105)
T ss_pred CCcccCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEEcCcEEEEEecCCCCCCCCCceEEEECCcCHHHEEEEeCc
Confidence 689999999999999999999999999999999999999999999999988899999999999999999887653
No 5
>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=99.91 E-value=1.1e-24 Score=160.98 Aligned_cols=74 Identities=41% Similarity=0.604 Sum_probs=69.6
Q ss_pred cceeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEeceeeeeeeecCCcccC-CceEEEEeeceeecccccCCC
Q 032297 67 KMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEE-QGQIIKLKCDALLKRNGSSKP 140 (143)
Q Consensus 67 k~~IkkGD~V~VIsG~dKGK~G~V~~V~~k~n~ViVegvN~~kkhvKp~~~~~-~GgIi~~E~PIhiSnv~~~~~ 140 (143)
+++|++||+|+||+|+||||+|+|++|++++++|+|||+|+.++|+||++.++ +|+|+++|+|||+|||..-.|
T Consensus 1 ~~~ikkGD~V~Vi~G~dKGK~G~V~~V~~~~~~V~VegvN~~kkh~k~~~~~~~~g~i~~~e~pI~~SnV~lv~p 75 (104)
T TIGR01079 1 KMKIKKGDTVKVISGKDKGKRGKVLKVLPKTNKVIVEGVNMVKKHVKPKPTQRSQGGIIEKEAPIHISNVMLFDP 75 (104)
T ss_pred CCcccCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEECCcEEEEEecCcccCCCCCCceEEEEccCCHHHeEEEcC
Confidence 35899999999999999999999999999999999999999999999998777 899999999999999987655
No 6
>COG0198 RplX Ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=99.91 E-value=1.4e-24 Score=161.25 Aligned_cols=73 Identities=42% Similarity=0.630 Sum_probs=69.4
Q ss_pred cceeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEeceeeeeeeecCCcccCCceEEEEeeceeecccccCCCC
Q 032297 67 KMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQIIKLKCDALLKRNGSSKPG 141 (143)
Q Consensus 67 k~~IkkGD~V~VIsG~dKGK~G~V~~V~~k~n~ViVegvN~~kkhvKp~~~~~~GgIi~~E~PIhiSnv~~~~~~ 141 (143)
.++|++||+|+||+|+|||++|+|++|++++ |+|||||+.++|.||.++++.|+|+++|+|||+|||....|.
T Consensus 2 ~~~IrkGD~V~Vi~GkdKGk~GkVl~v~~k~--V~VEGvnv~kkh~k~~~~~~~ggii~~EapIh~SnV~i~~~~ 74 (104)
T COG0198 2 KMKVKKGDTVKVIAGKDKGKEGKVLKVLPKK--VVVEGVNVVKKHIKPSQENPEGGIINKEAPIHISNVAIIDPN 74 (104)
T ss_pred CcceecCCEEEEEecCCCCcceEEEEEecCe--EEEECcEEEEecCCCCCcCCCCceeeeeecccHHHeEEeccc
Confidence 5789999999999999999999999999998 999999999999998888888999999999999999988773
No 7
>PRK01191 rpl24p 50S ribosomal protein L24P; Validated
Probab=99.77 E-value=3.4e-19 Score=135.37 Aligned_cols=70 Identities=26% Similarity=0.324 Sum_probs=60.9
Q ss_pred eeeccCCCCCcccccceeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEeceeeeeeeecCCcccCCceEEEEeeceee
Q 032297 53 ERKECKPNSLPVLHKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQIIKLKCDALL 132 (143)
Q Consensus 53 erk~~kpn~lp~~~k~~IkkGD~V~VIsG~dKGK~G~V~~V~~k~n~ViVegvN~~kkhvKp~~~~~~GgIi~~E~PIhi 132 (143)
.|++|+.++ |+|++||+|+||+|+|||++|+|++|++++++|+|||||+.++ +| +++|+|||+
T Consensus 35 Lr~~y~ir~------~~IkkGD~V~VisG~~KGk~GkV~~V~~~~~~V~VeGvn~~k~---------~G--~~~e~pIh~ 97 (120)
T PRK01191 35 LREKYGIRS------LPVRKGDTVKVMRGDFKGEEGKVVEVDLKRGRIYVEGVTVKKA---------DG--TEVPRPIHP 97 (120)
T ss_pred HHHHhCCcc------ceEeCCCEEEEeecCCCCceEEEEEEEcCCCEEEEeCcEEECC---------CC--eEEEcccch
Confidence 467777554 4599999999999999999999999999999999999999772 34 689999999
Q ss_pred cccccCC
Q 032297 133 KRNGSSK 139 (143)
Q Consensus 133 Snv~~~~ 139 (143)
|||.+-.
T Consensus 98 SNV~l~~ 104 (120)
T PRK01191 98 SNVMITK 104 (120)
T ss_pred hHeEEEe
Confidence 9998654
No 8
>PTZ00194 60S ribosomal protein L26; Provisional
Probab=99.77 E-value=2.7e-19 Score=139.35 Aligned_cols=71 Identities=23% Similarity=0.340 Sum_probs=64.7
Q ss_pred eeeccCCCCCcccccceeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEeceeeeeeeecCCcccCCceEEEEeeceee
Q 032297 53 ERKECKPNSLPVLHKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQIIKLKCDALL 132 (143)
Q Consensus 53 erk~~kpn~lp~~~k~~IkkGD~V~VIsG~dKGK~G~V~~V~~k~n~ViVegvN~~kkhvKp~~~~~~GgIi~~E~PIhi 132 (143)
.|.+|+.++++ |++||+|+||+|+|||++|+|++|++++++|+|||||+.++|.++ .|+|||+
T Consensus 36 Lr~k~~~Rs~~------IkkGD~V~Vi~Gk~KGk~GkV~~V~~k~~~ViVEgvn~~Kk~gk~-----------~e~PIh~ 98 (143)
T PTZ00194 36 LRAKYNVRSMP------VRKDDEVMVVRGHHKGREGKVTAVYRKKWVIHIEKITREKANGEP-----------VQIGIHP 98 (143)
T ss_pred HHHHhCCccce------eecCCEEEEecCCCCCCceEEEEEEcCCCEEEEeCeEEEecCCCE-----------eecCcCc
Confidence 47788877765 899999999999999999999999999999999999999999776 7999999
Q ss_pred cccccCCC
Q 032297 133 KRNGSSKP 140 (143)
Q Consensus 133 Snv~~~~~ 140 (143)
|||.+-++
T Consensus 99 SNV~iv~l 106 (143)
T PTZ00194 99 SNVIITKL 106 (143)
T ss_pred hheEEEcc
Confidence 99988665
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=99.74 E-value=2.1e-18 Score=129.73 Aligned_cols=77 Identities=19% Similarity=0.268 Sum_probs=66.7
Q ss_pred eeeeeeeeeeeccCCCCCcccccceeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEeceeeeeeeecCCcccCCceEE
Q 032297 45 IVVRLKRWERKECKPNSLPVLHKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQII 124 (143)
Q Consensus 45 ~~~~~k~Werk~~kpn~lp~~~k~~IkkGD~V~VIsG~dKGK~G~V~~V~~k~n~ViVegvN~~kkhvKp~~~~~~GgIi 124 (143)
....+-+|.|++|++++. +|++||+|+||+|+|||++|+|++|++++++|+|||+|+.+ ++ | +
T Consensus 23 ~~a~ls~elr~~y~~r~~------~IkkGD~V~Vi~Gk~KGk~GkV~~V~~~~~~V~Vegvn~~k----~~-----G--~ 85 (114)
T TIGR01080 23 MSAPLSKELREKYGKRAL------PVRKGDKVRIMRGDFKGHEGKVSKVDLKRYRIYVEGVTKEK----VN-----G--T 85 (114)
T ss_pred eecccCHHHHHHcCcccc------eeecCCEEEEecCCCCCCEEEEEEEEcCCCEEEEcCeEEEC----CC-----C--e
Confidence 334566789999986665 48999999999999999999999999999999999999976 21 4 6
Q ss_pred EEeeceeecccccC
Q 032297 125 KLKCDALLKRNGSS 138 (143)
Q Consensus 125 ~~E~PIhiSnv~~~ 138 (143)
+.|+|||+|||+.-
T Consensus 86 ~~e~pIh~SnV~l~ 99 (114)
T TIGR01080 86 EVPVPIHPSNVMIT 99 (114)
T ss_pred EEEeeechHHeEEE
Confidence 89999999999864
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=98.84 E-value=6.3e-09 Score=61.81 Aligned_cols=32 Identities=53% Similarity=0.709 Sum_probs=30.8
Q ss_pred eCCEEEEEecCCCCeEeEEEEEEccCCEEEEe
Q 032297 72 AGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 103 (143)
Q Consensus 72 kGD~V~VIsG~dKGK~G~V~~V~~k~n~ViVe 103 (143)
+||.|+|++|+++|++|+|++|++++++|+||
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 59999999999999999999999999999986
No 11
>KOG3401 consensus 60S ribosomal protein L26 [Translation, ribosomal structure and biogenesis]
Probab=98.08 E-value=2.8e-06 Score=66.84 Aligned_cols=70 Identities=21% Similarity=0.409 Sum_probs=56.5
Q ss_pred eeccCCCCCcccccceeeeCCEEEEEecCCCC-eEeEEEEEEccCCEEEEeceeeeeeeecCCcccCCceEEEEeeceee
Q 032297 54 RKECKPNSLPVLHKMHVKAGDTVKVIAGCDKG-KIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQIIKLKCDALL 132 (143)
Q Consensus 54 rk~~kpn~lp~~~k~~IkkGD~V~VIsG~dKG-K~G~V~~V~~k~n~ViVegvN~~kkhvKp~~~~~~GgIi~~E~PIhi 132 (143)
|.+++..++| |+.+|+|.|..|.++| ++|+|++|++++..+++|.|... |.... ....|||.
T Consensus 39 R~~y~vrs~p------ir~ddev~v~rg~~kG~q~G~v~~vyrKk~~iyie~v~~e-K~nGt----------~v~vgihP 101 (145)
T KOG3401|consen 39 RQKYNVRSMP------IRKDDEVQVVRGHFKGFQIGKVSQVYRKKYVIYIERVQRE-KANGT----------TVPVGIHP 101 (145)
T ss_pred HHHhCccccc------eeeccEEEEEeccccccccceehhhhhhhheeeeEeEEEe-eccCc----------ccccccCc
Confidence 6677766666 8999999999999999 99999999999999999998643 22222 25678888
Q ss_pred cccccCCC
Q 032297 133 KRNGSSKP 140 (143)
Q Consensus 133 Snv~~~~~ 140 (143)
|.+-+++|
T Consensus 102 sK~~iTkl 109 (145)
T KOG3401|consen 102 SKVVITKL 109 (145)
T ss_pred cceeeccc
Confidence 88877665
No 12
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=97.94 E-value=1.5e-05 Score=44.45 Aligned_cols=26 Identities=50% Similarity=0.704 Sum_probs=24.3
Q ss_pred eeeCCEEEEEecCCCCeEeEEEEEEc
Q 032297 70 VKAGDTVKVIAGCDKGKIGEITKVFR 95 (143)
Q Consensus 70 IkkGD~V~VIsG~dKGK~G~V~~V~~ 95 (143)
+.+||.|+|+.|+++|++|+|++++.
T Consensus 2 ~~~G~~V~I~~G~~~g~~g~i~~i~~ 27 (28)
T smart00739 2 FEVGDTVRVIAGPFKGKVGKVLEVDG 27 (28)
T ss_pred CCCCCEEEEeECCCCCcEEEEEEEcC
Confidence 57999999999999999999999975
No 13
>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=97.21 E-value=0.00073 Score=50.99 Aligned_cols=37 Identities=30% Similarity=0.457 Sum_probs=34.3
Q ss_pred eeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEecee
Q 032297 70 VKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDIN 106 (143)
Q Consensus 70 IkkGD~V~VIsG~dKGK~G~V~~V~~k~n~ViVegvN 106 (143)
++.||.|.|+.|+++|-.|+|.+++.++..|.|+-.+
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 7899999999999999999999999888899888665
No 14
>PRK05609 nusG transcription antitermination protein NusG; Validated
Probab=97.17 E-value=0.0007 Score=52.18 Aligned_cols=36 Identities=25% Similarity=0.288 Sum_probs=32.5
Q ss_pred ceeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEe
Q 032297 68 MHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 103 (143)
Q Consensus 68 ~~IkkGD~V~VIsG~dKGK~G~V~~V~~k~n~ViVe 103 (143)
..+++||+|.|+.|+++|.+|+|.+++++++++.|.
T Consensus 125 ~~~~~Gd~VrI~~GPf~G~~g~v~~i~~~~~r~~v~ 160 (181)
T PRK05609 125 VDFEVGEMVRVIDGPFADFNGTVEEVDYEKSKLKVL 160 (181)
T ss_pred cCCCCCCEEEEeccCCCCCEEEEEEEeCCCCEEEEE
Confidence 447899999999999999999999999888888775
No 15
>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=97.10 E-value=0.00089 Score=51.45 Aligned_cols=36 Identities=22% Similarity=0.282 Sum_probs=32.2
Q ss_pred ceeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEe
Q 032297 68 MHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 103 (143)
Q Consensus 68 ~~IkkGD~V~VIsG~dKGK~G~V~~V~~k~n~ViVe 103 (143)
..+++||+|.|+.|+++|-+|+|.+++++++++.|.
T Consensus 118 ~~~~~G~~V~I~~Gpf~G~~g~v~~~~~~~~r~~V~ 153 (172)
T TIGR00922 118 IDFEVGEQVRVNDGPFANFTGTVEEVDYEKSKLKVS 153 (172)
T ss_pred cCCCCCCEEEEeecCCCCcEEEEEEEcCCCCEEEEE
Confidence 347899999999999999999999999888888775
No 16
>PRK08559 nusG transcription antitermination protein NusG; Validated
Probab=97.02 E-value=0.0012 Score=50.92 Aligned_cols=41 Identities=29% Similarity=0.379 Sum_probs=36.7
Q ss_pred ceeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEeceeee
Q 032297 68 MHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLK 108 (143)
Q Consensus 68 ~~IkkGD~V~VIsG~dKGK~G~V~~V~~k~n~ViVegvN~~ 108 (143)
..+.+||.|.|+.|+++|..|.|.+++.++.++.|+-++..
T Consensus 93 ~~~~~G~~V~I~~Gpf~g~~g~V~~vd~~k~~v~v~ll~~~ 133 (153)
T PRK08559 93 EGIKEGDIVELIAGPFKGEKARVVRVDESKEEVTVELLEAA 133 (153)
T ss_pred cCCCCCCEEEEeccCCCCceEEEEEEcCCCCEEEEEEECCc
Confidence 34799999999999999999999999999999999877643
No 17
>COG0250 NusG Transcription antiterminator [Transcription]
Probab=96.79 E-value=0.0021 Score=51.47 Aligned_cols=38 Identities=24% Similarity=0.366 Sum_probs=34.9
Q ss_pred ccceeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEe
Q 032297 66 HKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 103 (143)
Q Consensus 66 ~k~~IkkGD~V~VIsG~dKGK~G~V~~V~~k~n~ViVe 103 (143)
.+..+.+||.|.|++|+++|-.|+|.+|+.+++++.|+
T Consensus 120 ~~~~~e~Gd~VrI~~GpFa~f~g~V~evd~ek~~~~v~ 157 (178)
T COG0250 120 PKVDFEPGDVVRIIDGPFAGFKAKVEEVDEEKGKLKVE 157 (178)
T ss_pred ccccCCCCCEEEEeccCCCCccEEEEEEcCcCcEEEEE
Confidence 45668999999999999999999999999999888776
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=96.50 E-value=0.0043 Score=46.88 Aligned_cols=35 Identities=17% Similarity=0.102 Sum_probs=29.6
Q ss_pred ceeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEe
Q 032297 68 MHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 103 (143)
Q Consensus 68 ~~IkkGD~V~VIsG~dKGK~G~V~~V~~k~n~ViVe 103 (143)
..+.+||+|.|+.|+++|-.|.|.+++ .++++.|.
T Consensus 107 ~~~~~G~~V~V~~GPf~g~~g~v~~~~-~~~r~~v~ 141 (159)
T TIGR01955 107 TLPYKGDKVRITDGAFAGFEAIFLEPD-GEKRSMLL 141 (159)
T ss_pred cCCCCCCEEEEeccCCCCcEEEEEEEC-CCceEEEE
Confidence 447899999999999999999999997 44576554
No 19
>PRK09014 rfaH transcriptional activator RfaH; Provisional
Probab=96.33 E-value=0.0059 Score=46.67 Aligned_cols=33 Identities=21% Similarity=0.198 Sum_probs=28.5
Q ss_pred eeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEe
Q 032297 70 VKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 103 (143)
Q Consensus 70 IkkGD~V~VIsG~dKGK~G~V~~V~~k~n~ViVe 103 (143)
+++||+|.|+.|+++|-+|+|.+++ .+++++|.
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 6899999999999999999999998 55665543
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=95.95 E-value=0.014 Score=49.79 Aligned_cols=36 Identities=28% Similarity=0.508 Sum_probs=32.5
Q ss_pred ceeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEe
Q 032297 68 MHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 103 (143)
Q Consensus 68 ~~IkkGD~V~VIsG~dKGK~G~V~~V~~k~n~ViVe 103 (143)
..+..||.|.|+.|+++|-.|+|.+++.++.++.|.
T Consensus 204 ~~f~vGd~VrI~dGPF~GfeG~I~eid~~k~Rv~Vl 239 (258)
T TIGR01956 204 SKFRVGNFVKIVDGPFKGIVGKIKKIDQEKKKAIVE 239 (258)
T ss_pred cCCCCCCEEEEEecCCCCcEEEEEEEeCCCCEEEEE
Confidence 447899999999999999999999999888888776
No 21
>PRK04333 50S ribosomal protein L14e; Validated
Probab=94.87 E-value=0.06 Score=38.70 Aligned_cols=36 Identities=19% Similarity=0.310 Sum_probs=32.2
Q ss_pred eeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEece
Q 032297 69 HVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDI 105 (143)
Q Consensus 69 ~IkkGD~V~VIsG~dKGK~G~V~~V~~k~n~ViVegv 105 (143)
.+..|-.|.+..|+|+|+...|+++.. +++|+|+|-
T Consensus 3 ~v~~GrvV~~~~Grd~gk~~vIv~i~d-~~~vlVdg~ 38 (84)
T PRK04333 3 AIEVGRVCVKTAGREAGRKCVIVDIID-KNFVLVTGP 38 (84)
T ss_pred cccccEEEEEeccCCCCCEEEEEEEec-CCEEEEECC
Confidence 478899999999999999999999876 489999886
No 22
>PTZ00065 60S ribosomal protein L14; Provisional
Probab=93.03 E-value=0.23 Score=38.65 Aligned_cols=35 Identities=26% Similarity=0.367 Sum_probs=32.0
Q ss_pred eeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEece
Q 032297 70 VKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDI 105 (143)
Q Consensus 70 IkkGD~V~VIsG~dKGK~G~V~~V~~k~n~ViVegv 105 (143)
+..|=.|.|..|+++||.+.|+.|..+ |+|+|+|=
T Consensus 8 VEiGRVvli~~Gp~~GKL~vIVDIID~-nRvLVDGP 42 (130)
T PTZ00065 8 VEPGRLCLIQYGPDAGKLCFIVDIVTP-TRVLVDGA 42 (130)
T ss_pred eeeceEEEEecCCCCCCEEEEEEEEcC-CeEEEeCC
Confidence 678889999999999999999999975 79999986
No 23
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=91.64 E-value=0.19 Score=49.70 Aligned_cols=29 Identities=38% Similarity=0.505 Sum_probs=26.7
Q ss_pred ceeeeCCEEEEEecCCCCeEeEEEEEEcc
Q 032297 68 MHVKAGDTVKVIAGCDKGKIGEITKVFRH 96 (143)
Q Consensus 68 ~~IkkGD~V~VIsG~dKGK~G~V~~V~~k 96 (143)
-.|+.||-|+||+|+++|.+|.|++|...
T Consensus 458 KyF~~GDhVKVi~G~~eG~tGlVvrVe~~ 486 (1024)
T KOG1999|consen 458 KYFEPGDHVKVIAGRYEGDTGLVVRVEQG 486 (1024)
T ss_pred hhccCCCeEEEEeccccCCcceEEEEeCC
Confidence 46899999999999999999999999874
No 24
>PTZ00471 60S ribosomal protein L27; Provisional
Probab=88.39 E-value=0.84 Score=35.81 Aligned_cols=39 Identities=26% Similarity=0.349 Sum_probs=34.3
Q ss_pred eeeCCEEEEEecCCCCeEeEEEEEEccC------CEEEEeceeee
Q 032297 70 VKAGDTVKVIAGCDKGKIGEITKVFRHN------STVMVKDINLK 108 (143)
Q Consensus 70 IkkGD~V~VIsG~dKGK~G~V~~V~~k~------n~ViVegvN~~ 108 (143)
+++|-.|.|++|++.|+...|++.+.+. +.++|-|+...
T Consensus 5 ~kpgkVVivL~GR~AGkKaVivk~~ddgt~drpy~halVaGIdry 49 (134)
T PTZ00471 5 LKPGKVVIVTSGRYAGRKAVIVQNFDTASKERPYGHALVAGIKKY 49 (134)
T ss_pred ccCCEEEEEEccccCCcEEEEEeecCCCCccCcCceEEEEeeccc
Confidence 6789999999999999999999988776 78999997643
No 25
>COG2163 RPL14A Ribosomal protein L14E/L6E/L27E [Translation, ribosomal structure and biogenesis]
Probab=87.44 E-value=0.99 Score=34.83 Aligned_cols=34 Identities=32% Similarity=0.401 Sum_probs=31.3
Q ss_pred eeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEec
Q 032297 70 VKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKD 104 (143)
Q Consensus 70 IkkGD~V~VIsG~dKGK~G~V~~V~~k~n~ViVeg 104 (143)
+.+|=.|.|++|++.||...|+++..++ .+++.|
T Consensus 5 l~~GrVvvv~~GR~aGkk~VIv~~iDd~-~v~i~g 38 (125)
T COG2163 5 LEVGRVVVVTAGRFAGKKVVIVKIIDDN-FVLITG 38 (125)
T ss_pred ccCCeEEEEecceeCCceEEEEEEccCC-EEEEeC
Confidence 6789999999999999999999999887 888887
No 26
>PRK04313 30S ribosomal protein S4e; Validated
Probab=85.94 E-value=1.3 Score=37.53 Aligned_cols=41 Identities=20% Similarity=0.393 Sum_probs=34.9
Q ss_pred ccceeeeCCEEEEEecCCCCeEeEEEEEEccC----CEEEEecee
Q 032297 66 HKMHVKAGDTVKVIAGCDKGKIGEITKVFRHN----STVMVKDIN 106 (143)
Q Consensus 66 ~k~~IkkGD~V~VIsG~dKGK~G~V~~V~~k~----n~ViVegvN 106 (143)
.-+++..|-.|.|+.|++-|.+|+|.++.+.. |.|.||+-+
T Consensus 168 ~~i~fe~G~l~~itgG~n~GriG~I~~i~~~~~~~~~~V~i~d~~ 212 (237)
T PRK04313 168 DHIPFEEGNLAIITGGKHVGEIGKIKEIEVTKSSKPNIVTLEDKD 212 (237)
T ss_pred EEEecCCCCEEEEECCeeeeeEEEEEEEEEccCCCCcEEEEEcCC
Confidence 45778999999999999999999999998655 778888654
No 27
>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=83.10 E-value=2.6 Score=28.70 Aligned_cols=27 Identities=33% Similarity=0.665 Sum_probs=22.8
Q ss_pred eeCCEEEEEecCCCCeEeEEEEEEccCCEEEEe
Q 032297 71 KAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 103 (143)
Q Consensus 71 kkGD~V~VIsG~dKGK~G~V~~V~~k~n~ViVe 103 (143)
..||.+.. .+|-+|+|.+|+ .|+|+|+
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 57999986 358999999997 6899997
No 28
>COG5164 SPT5 Transcription elongation factor [Transcription]
Probab=80.05 E-value=1.4 Score=41.24 Aligned_cols=29 Identities=31% Similarity=0.444 Sum_probs=26.2
Q ss_pred eeeeCCEEEEEecCCCCeEeEEEEEEccC
Q 032297 69 HVKAGDTVKVIAGCDKGKIGEITKVFRHN 97 (143)
Q Consensus 69 ~IkkGD~V~VIsG~dKGK~G~V~~V~~k~ 97 (143)
.+.+||.|+||.|.+++.+|.|..|..++
T Consensus 139 ~f~~gD~vkVI~g~~~~d~g~V~rI~~~~ 167 (607)
T COG5164 139 GFYKGDLVKVIEGGEMVDIGTVPRIDGEK 167 (607)
T ss_pred ccccCCeEEEeccccccccceEEEecCce
Confidence 37899999999999999999999997663
No 29
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=80.04 E-value=4.5 Score=40.55 Aligned_cols=27 Identities=37% Similarity=0.473 Sum_probs=25.1
Q ss_pred eeeCCEEEEEecCCCCeEeEEEEEEcc
Q 032297 70 VKAGDTVKVIAGCDKGKIGEITKVFRH 96 (143)
Q Consensus 70 IkkGD~V~VIsG~dKGK~G~V~~V~~k 96 (143)
|.+||.|.|+.|..+|-.|+|..|+-.
T Consensus 408 F~~GD~VeV~~Gel~glkG~ve~vdg~ 434 (1024)
T KOG1999|consen 408 FSPGDAVEVIVGELKGLKGKVESVDGT 434 (1024)
T ss_pred cCCCCeEEEeeeeeccceeEEEeccCc
Confidence 899999999999999999999999654
No 30
>COG3700 AphA Acid phosphatase (class B) [General function prediction only]
Probab=79.33 E-value=0.53 Score=39.51 Aligned_cols=67 Identities=18% Similarity=0.252 Sum_probs=44.6
Q ss_pred ccceeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEeceee---eeeeecCCcccCCceEEEEeeceeecc
Q 032297 66 HKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINL---KTKHVKKREEEEQGQIIKLKCDALLKR 134 (143)
Q Consensus 66 ~k~~IkkGD~V~VIsG~dKGK~G~V~~V~~k~n~ViVegvN~---~kkhvKp~~~~~~GgIi~~E~PIhiSn 134 (143)
-.||.++||.|..++|+-.||+-.|.+...++-.+ ++.|- .--.-||.+.+..--|.+.-.-|||-+
T Consensus 123 I~MHq~RGD~i~FvTGRt~gk~d~vsk~Lak~F~i--~~m~pv~f~Gdk~k~~qy~Kt~~i~~~~~~IhYGD 192 (237)
T COG3700 123 IDMHQRRGDAIYFVTGRTPGKTDTVSKTLAKNFHI--TNMNPVIFAGDKPKPGQYTKTQWIQDKNIRIHYGD 192 (237)
T ss_pred HHHHHhcCCeEEEEecCCCCcccccchhHHhhccc--CCCcceeeccCCCCcccccccHHHHhcCceEEecC
Confidence 35899999999999999999999999998886555 32221 100113333333345666667777743
No 31
>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=76.75 E-value=2.9 Score=31.07 Aligned_cols=29 Identities=28% Similarity=0.381 Sum_probs=17.9
Q ss_pred eeeeCCEEEEEecC----------CCCeEeEEEEEEccC
Q 032297 69 HVKAGDTVKVIAGC----------DKGKIGEITKVFRHN 97 (143)
Q Consensus 69 ~IkkGD~V~VIsG~----------dKGK~G~V~~V~~k~ 97 (143)
.++.||.|-|.--+ +-|++|+|..|.+..
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 46899999987543 789999999888754
No 32
>PLN00036 40S ribosomal protein S4; Provisional
Probab=76.22 E-value=4.9 Score=34.57 Aligned_cols=40 Identities=28% Similarity=0.505 Sum_probs=33.4
Q ss_pred ccceeeeCCEEEEEecCCCCeEeEEEEEEccC---CEEEEece
Q 032297 66 HKMHVKAGDTVKVIAGCDKGKIGEITKVFRHN---STVMVKDI 105 (143)
Q Consensus 66 ~k~~IkkGD~V~VIsG~dKGK~G~V~~V~~k~---n~ViVegv 105 (143)
.-+++..|-.|.|+.|++-|.+|+|.++..+. +.|.|++-
T Consensus 171 ~~ikfe~G~l~~vtgG~n~GrvG~I~~i~~~~~~~~iV~i~d~ 213 (261)
T PLN00036 171 DFIKFDVGNLVMVTGGRNRGRVGVIKNREKHKGSFEIIHVKDA 213 (261)
T ss_pred eEEecCCCCEEEEECCeeceeEEEEEEEEecCCCCCEEEEEeC
Confidence 45678999999999999999999999998543 56888863
No 33
>PTZ00223 40S ribosomal protein S4; Provisional
Probab=74.88 E-value=4.9 Score=34.79 Aligned_cols=41 Identities=32% Similarity=0.583 Sum_probs=33.6
Q ss_pred cccceeeeCCEEEEEecCCCCeEeEEEEEEccC---CEEEEece
Q 032297 65 LHKMHVKAGDTVKVIAGCDKGKIGEITKVFRHN---STVMVKDI 105 (143)
Q Consensus 65 ~~k~~IkkGD~V~VIsG~dKGK~G~V~~V~~k~---n~ViVegv 105 (143)
..-+++..|-.|.|+.|++-|++|+|.++..+. +.|.+++-
T Consensus 167 ~~~ikfe~G~l~~vtgG~n~GriG~I~~i~~~~~~~~iv~i~d~ 210 (273)
T PTZ00223 167 VDLIKNRNGKVVMVTGGANRGRIGEIVSIERHPGAFDIARLKDA 210 (273)
T ss_pred eEEEecCCCCEEEEECCeeceeEEEEEEEEecCCCCCEEEEEeC
Confidence 345778999999999999999999999996553 56788863
No 34
>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=74.48 E-value=5.9 Score=25.74 Aligned_cols=31 Identities=32% Similarity=0.490 Sum_probs=24.9
Q ss_pred ceeeeCCEEEEEecCCCCeE---eEEEEEEccCCE
Q 032297 68 MHVKAGDTVKVIAGCDKGKI---GEITKVFRHNST 99 (143)
Q Consensus 68 ~~IkkGD~V~VIsG~dKGK~---G~V~~V~~k~n~ 99 (143)
=.|++||+|.++. .+.++. .+|.+++...+.
T Consensus 11 G~l~~gd~v~~~~-~~~~~~~~~~~I~~i~~~~~~ 44 (74)
T PF03144_consen 11 GTLKKGDKVRVLP-NGTGKKGQVVKIKSIFMFNGD 44 (74)
T ss_dssp SEEETTEEEEEES-TTTTEECEEEEEEEEEETTEE
T ss_pred eEEcCCCEEEECc-cCCcceeeeeecccccccccC
Confidence 3589999999988 666555 999999988654
No 35
>PRK06531 yajC preprotein translocase subunit YajC; Validated
Probab=73.69 E-value=8.9 Score=29.04 Aligned_cols=31 Identities=26% Similarity=0.472 Sum_probs=26.0
Q ss_pred eeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEe
Q 032297 69 HVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 103 (143)
Q Consensus 69 ~IkkGD~V~VIsG~dKGK~G~V~~V~~k~n~ViVe 103 (143)
.+++||+|.-+. |-.|+|.+|..+++.|.++
T Consensus 36 sLk~GD~VvT~G----Gi~G~V~~I~~~~~~v~le 66 (113)
T PRK06531 36 AIQKGDEVVTIG----GLYGTVDEVDTEAKTIVLD 66 (113)
T ss_pred hcCCCCEEEECC----CcEEEEEEEecCCCEEEEE
Confidence 579999998765 5689999999888888886
No 36
>PTZ00118 40S ribosomal protein S4; Provisional
Probab=73.49 E-value=6.3 Score=33.93 Aligned_cols=40 Identities=25% Similarity=0.467 Sum_probs=32.7
Q ss_pred ccceeeeCCEEEEEecCCCCeEeEEEEEEccC---CEEEEece
Q 032297 66 HKMHVKAGDTVKVIAGCDKGKIGEITKVFRHN---STVMVKDI 105 (143)
Q Consensus 66 ~k~~IkkGD~V~VIsG~dKGK~G~V~~V~~k~---n~ViVegv 105 (143)
.-+++..|-.|.|+.|++-|.+|+|.++..+. +.|.||+-
T Consensus 171 ~~ikfe~G~l~~vtgG~n~GriG~I~~~~~~~~~~~~V~i~d~ 213 (262)
T PTZ00118 171 EFLKFEVGNLVMITGGHNVGRVGTIVSKEKHPGSFDLIHVKDS 213 (262)
T ss_pred eEEecCCCCEEEEECCeeceeEEEEEEEEecCCCCcEEEEEeC
Confidence 45678899999999999999999999876553 56777763
No 37
>COG1532 Predicted RNA-binding protein [General function prediction only]
Probab=70.49 E-value=9.1 Score=26.15 Aligned_cols=35 Identities=14% Similarity=0.201 Sum_probs=29.6
Q ss_pred eeeCCEEEE--EecCCCCeEeEEEEEEccCCEEEEec
Q 032297 70 VKAGDTVKV--IAGCDKGKIGEITKVFRHNSTVMVKD 104 (143)
Q Consensus 70 IkkGD~V~V--IsG~dKGK~G~V~~V~~k~n~ViVeg 104 (143)
...||.|+. |-|..|--.|+|++|+...++|++|+
T Consensus 21 ev~~e~V~a~Dilgd~ke~~G~vkriDldehkI~lE~ 57 (57)
T COG1532 21 EVTEEGVVARDILGDEKEFEGQVKRIDLDEHKIELEG 57 (57)
T ss_pred EEecCcEEEEeccCCceEecceEEEEEccccEEEecC
Confidence 456777776 46889999999999999999999985
No 38
>PRK04306 50S ribosomal protein L21e; Reviewed
Probab=69.78 E-value=8.3 Score=28.68 Aligned_cols=39 Identities=26% Similarity=0.273 Sum_probs=29.8
Q ss_pred eeeeCCEEEEEecC----------CCCeEeEEEEEEccCCEEEEeceee
Q 032297 69 HVKAGDTVKVIAGC----------DKGKIGEITKVFRHNSTVMVKDINL 107 (143)
Q Consensus 69 ~IkkGD~V~VIsG~----------dKGK~G~V~~V~~k~n~ViVegvN~ 107 (143)
.++.||.|-|.--. +-|++|+|..+..+-.-|+|..-|.
T Consensus 34 ~y~~Gd~V~I~~d~sv~kGmPh~~yhGkTG~V~~v~~~A~~V~v~vg~k 82 (98)
T PRK04306 34 EFEEGDKVHIVIDPSVHKGMPHPRFHGKTGTVVGKRGRAYIVEVKDGGK 82 (98)
T ss_pred hccCCCEEEEEecCceecCCccccccCCCEEEEeecCeEEEEEEEECCc
Confidence 46789999887543 7899999999988877777754443
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=69.27 E-value=10 Score=25.34 Aligned_cols=33 Identities=27% Similarity=0.355 Sum_probs=19.8
Q ss_pred eeeCCEEEEEecCC--CC--eEeEEEEEEccCCEEEEe
Q 032297 70 VKAGDTVKVIAGCD--KG--KIGEITKVFRHNSTVMVK 103 (143)
Q Consensus 70 IkkGD~V~VIsG~d--KG--K~G~V~~V~~k~n~ViVe 103 (143)
|++||.|+|.+-.+ .| -.++|++...++ ++.|+
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 58999999998542 22 246899988875 66665
No 40
>COG1471 RPS4A Ribosomal protein S4E [Translation, ribosomal structure and biogenesis]
Probab=68.20 E-value=9 Score=32.75 Aligned_cols=40 Identities=25% Similarity=0.419 Sum_probs=33.2
Q ss_pred ccceeeeCCEEEEEecCCCCeEeEEEEEEccC----CEEEEece
Q 032297 66 HKMHVKAGDTVKVIAGCDKGKIGEITKVFRHN----STVMVKDI 105 (143)
Q Consensus 66 ~k~~IkkGD~V~VIsG~dKGK~G~V~~V~~k~----n~ViVegv 105 (143)
.-+++..|-.|.|..|++-|.+|+|.+|.... |.|.+|+-
T Consensus 170 ~~i~fe~g~~~~vtgG~h~G~~G~I~~I~~~~~~~~~~v~~e~~ 213 (241)
T COG1471 170 EHIKFEEGALVYVTGGRHVGRVGTIVEIEIQESSKPNLVTVEDE 213 (241)
T ss_pred eEeccCCCcEEEEECCccccceEEEEEEEEecCCCccEEEEecC
Confidence 34567788889999999999999999998764 67888874
No 41
>COG2139 RPL21A Ribosomal protein L21E [Translation, ribosomal structure and biogenesis]
Probab=66.43 E-value=13 Score=27.96 Aligned_cols=39 Identities=31% Similarity=0.262 Sum_probs=30.9
Q ss_pred eeeeCCEEEEEecC----------CCCeEeEEEEEEccCCEEEEeceee
Q 032297 69 HVKAGDTVKVIAGC----------DKGKIGEITKVFRHNSTVMVKDINL 107 (143)
Q Consensus 69 ~IkkGD~V~VIsG~----------dKGK~G~V~~V~~k~n~ViVegvN~ 107 (143)
.++.||.|-|.--+ +-|++|+|.-+--+...|.|.+-|.
T Consensus 32 ey~~Gd~V~I~IdpSv~kGmPh~rf~G~TG~Vvg~~g~ay~V~v~~G~k 80 (98)
T COG2139 32 EYKVGDKVHIDIDPSVHKGMPHPRFQGKTGTVVGVRGRAYKVEVYDGNK 80 (98)
T ss_pred hccCCCEEEEEeCcccccCCCCccccCcceEEEeccCCEEEEEEecCCc
Confidence 46899999987653 8899999988877777777776554
No 42
>PRK05585 yajC preprotein translocase subunit YajC; Validated
Probab=65.73 E-value=11 Score=28.05 Aligned_cols=30 Identities=33% Similarity=0.496 Sum_probs=23.8
Q ss_pred ceeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEe
Q 032297 68 MHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 103 (143)
Q Consensus 68 ~~IkkGD~V~VIsG~dKGK~G~V~~V~~k~n~ViVe 103 (143)
-.+++||+|.-+.| -.|+|.+|+. +.|.+|
T Consensus 51 ~~Lk~Gd~VvT~gG----i~G~Vv~i~~--~~v~le 80 (106)
T PRK05585 51 SSLAKGDEVVTNGG----IIGKVTKVSE--DFVIIE 80 (106)
T ss_pred HhcCCCCEEEECCC----eEEEEEEEeC--CEEEEE
Confidence 35899999988775 6899999965 577776
No 43
>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=65.10 E-value=8.4 Score=29.54 Aligned_cols=61 Identities=11% Similarity=0.184 Sum_probs=31.1
Q ss_pred eeeeCCEEEEEecCCCCeEeEEEEEEcc--------CCEEEEeceeeeeeeecCCcccCCceEEEEeeceeecc
Q 032297 69 HVKAGDTVKVIAGCDKGKIGEITKVFRH--------NSTVMVKDINLKTKHVKKREEEEQGQIIKLKCDALLKR 134 (143)
Q Consensus 69 ~IkkGD~V~VIsG~dKGK~G~V~~V~~k--------~n~ViVegvN~~kkhvKp~~~~~~GgIi~~E~PIhiSn 134 (143)
+++.||.|+|= |..|+|.+|... +..+++-+-.+.+.-+.-...+..+..+..+.+++++.
T Consensus 60 pf~vGD~I~i~-----~~~G~V~~I~l~~t~l~~~~g~~v~IPNs~l~~~~i~N~s~~~~~~~~~v~~~v~~~~ 128 (206)
T PF00924_consen 60 PFKVGDRIEIG-----GVEGRVEEIGLRSTRLRTWDGEIVIIPNSKLISSPIVNYSRSSPYRRVVVEIPVDYDT 128 (206)
T ss_dssp SS-TT-EEESS-----S-EEEEEEE-SSEEEEEETTS-EEEEEHHHHHCS-EEETTT-SSEEEEEEEEEE-TTS
T ss_pred CccCCCEEEEE-----EeehHHHhcCcceeeeecCCCCEEEEEchheeeEEEEEeeccCCceeeeeeeeEecCC
Confidence 47999998875 888999888643 33455555444332222211123456666777766643
No 44
>COG1862 YajC Preprotein translocase subunit YajC [Intracellular trafficking and secretion]
Probab=64.58 E-value=15 Score=27.18 Aligned_cols=25 Identities=40% Similarity=0.581 Sum_probs=20.9
Q ss_pred eeeeCCEEEEEecCCCCeEeEEEEEEccC
Q 032297 69 HVKAGDTVKVIAGCDKGKIGEITKVFRHN 97 (143)
Q Consensus 69 ~IkkGD~V~VIsG~dKGK~G~V~~V~~k~ 97 (143)
.+++||+|.-+. |-.|+|++|..+.
T Consensus 43 sL~kGD~VvT~g----Gi~G~V~~v~d~~ 67 (97)
T COG1862 43 SLKKGDEVVTIG----GIVGTVTKVGDDT 67 (97)
T ss_pred hccCCCEEEEcC----CeEEEEEEEecCc
Confidence 479999998776 4689999998876
No 45
>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=63.71 E-value=5.7 Score=25.89 Aligned_cols=25 Identities=36% Similarity=0.412 Sum_probs=15.7
Q ss_pred eeeeCCEEEE-Eec--CCCCeEeEEEEE
Q 032297 69 HVKAGDTVKV-IAG--CDKGKIGEITKV 93 (143)
Q Consensus 69 ~IkkGD~V~V-IsG--~dKGK~G~V~~V 93 (143)
.-.-||+|.| +.. +.+..+|+|++|
T Consensus 31 ~A~~gD~V~v~i~~~~~~~~~eg~vv~V 58 (58)
T PF08206_consen 31 GAMDGDKVLVRITPPSRGKRPEGEVVEV 58 (58)
T ss_dssp TS-TT-EEEEEEEESSSEEEEEEEEEE-
T ss_pred CCCCCCEEEEEEecCCCCCCCCEEEEeC
Confidence 3567999987 444 456778888876
No 46
>PRK02749 photosystem I reaction center subunit IV; Provisional
Probab=62.70 E-value=15 Score=26.08 Aligned_cols=29 Identities=17% Similarity=0.341 Sum_probs=25.1
Q ss_pred eeeeCCEEEEEecC--CCCeEeEEEEEEccC
Q 032297 69 HVKAGDTVKVIAGC--DKGKIGEITKVFRHN 97 (143)
Q Consensus 69 ~IkkGD~V~VIsG~--dKGK~G~V~~V~~k~ 97 (143)
-|++||+|.|++=. +-..+|+|.+|+...
T Consensus 2 ~i~rGskVrIlR~ESYWyn~vGtV~svD~sg 32 (71)
T PRK02749 2 AISRGDKVRILRPESYWYNEVGTVASVDKSG 32 (71)
T ss_pred ccccCCEEEEccccceeecCcceEEEEccCC
Confidence 47899999999986 678899999999874
No 47
>PLN00045 photosystem I reaction center subunit IV; Provisional
Probab=59.83 E-value=13 Score=28.02 Aligned_cols=39 Identities=23% Similarity=0.311 Sum_probs=29.3
Q ss_pred eeeeCCEEEEEecC--CCCeEeEEEEEEcc---CCEEEE--eceee
Q 032297 69 HVKAGDTVKVIAGC--DKGKIGEITKVFRH---NSTVMV--KDINL 107 (143)
Q Consensus 69 ~IkkGD~V~VIsG~--dKGK~G~V~~V~~k---~n~ViV--egvN~ 107 (143)
-+++||.|+|++=. +-..+|+|..|+.. ++-|+| +.+|-
T Consensus 39 g~~RGskVrIlR~ESYWyn~vGtVvsVDq~~girYPVvVRF~kvNY 84 (101)
T PLN00045 39 GPKRGSKVKILRPESYWFNDVGKVVAVDQDPGVRYPVVVRFEKVNY 84 (101)
T ss_pred ccCCCCEEEEccccceeecCcceEEEEeCCCCcccceEEEeeeeec
Confidence 37999999999986 67889999999987 333444 44543
No 48
>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed
Probab=59.08 E-value=12 Score=36.13 Aligned_cols=36 Identities=22% Similarity=0.371 Sum_probs=25.8
Q ss_pred ceeeeCCEEEEEecCCCCeEeEEEEEEccCCEE--EEeceee
Q 032297 68 MHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTV--MVKDINL 107 (143)
Q Consensus 68 ~~IkkGD~V~VIsG~dKGK~G~V~~V~~k~n~V--iVegvN~ 107 (143)
..++.||+|.|.+ -|+.|+|++|..+ +.+ -+.++.+
T Consensus 635 ~~~~~Gd~V~v~~---~~~~g~v~~i~~~-~~~~V~~g~~k~ 672 (782)
T PRK00409 635 EELKVGDEVKYLS---LGQKGEVLSIPDD-KEAIVQAGIMKM 672 (782)
T ss_pred cCCCCCCEEEEcc---CCceEEEEEEcCC-CeEEEEECCEEE
Confidence 4589999999965 6789999999753 344 4445443
No 49
>PF12701 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC8_A 2VXF_A 2VXE_A.
Probab=58.90 E-value=27 Score=25.63 Aligned_cols=35 Identities=20% Similarity=0.344 Sum_probs=32.4
Q ss_pred eCCEEEEEecCCCCeEeEEEEEEccCCEEEEecee
Q 032297 72 AGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDIN 106 (143)
Q Consensus 72 kGD~V~VIsG~dKGK~G~V~~V~~k~n~ViVegvN 106 (143)
-|-+|-+|+..+..-+|.+..|+..+++|.++++-
T Consensus 7 IGs~ISlisk~~iRYeG~L~~Id~~~sTItL~nVr 41 (96)
T PF12701_consen 7 IGSKISLISKSDIRYEGILYSIDTEDSTITLKNVR 41 (96)
T ss_dssp TTCEEEEEETTTEEEEEEEEEEETTTTEEEEEEEE
T ss_pred cCCEEEEEECCCcEEEEEEEEEcCCCCEEEeeeee
Confidence 58899999999999999999999999999999863
No 50
>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=58.43 E-value=23 Score=23.92 Aligned_cols=40 Identities=23% Similarity=0.237 Sum_probs=29.8
Q ss_pred eeeCCEEEEEecC--CCCeEeEEEEEEccCCEEEEeceeeee
Q 032297 70 VKAGDTVKVIAGC--DKGKIGEITKVFRHNSTVMVKDINLKT 109 (143)
Q Consensus 70 IkkGD~V~VIsG~--dKGK~G~V~~V~~k~n~ViVegvN~~k 109 (143)
|.+|-+|.|+.-+ +-|-+|.|.+|...+--|+.||-|-.|
T Consensus 2 ilPG~~V~V~n~~~~Y~~y~G~VQRvsdgkaaVLFEGGnWdK 43 (53)
T PF11623_consen 2 ILPGSTVRVKNPNDIYYGYEGFVQRVSDGKAAVLFEGGNWDK 43 (53)
T ss_dssp --TT-EEEE--TTSTTTT-EEEEEEEETTEEEEEEEETTEEE
T ss_pred ccCCCEEEEeCCCCccchheEEEEEeeCCeEEEEecCCCceE
Confidence 6789999999885 789999999999999999999988543
No 51
>CHL00125 psaE photosystem I subunit IV; Reviewed
Probab=58.42 E-value=16 Score=25.56 Aligned_cols=28 Identities=25% Similarity=0.355 Sum_probs=24.0
Q ss_pred eeeCCEEEEEecC--CCCeEeEEEEEEccC
Q 032297 70 VKAGDTVKVIAGC--DKGKIGEITKVFRHN 97 (143)
Q Consensus 70 IkkGD~V~VIsG~--dKGK~G~V~~V~~k~ 97 (143)
|++||.|.|++=. +-..+|+|..|+...
T Consensus 2 i~rGskVrIlR~ESYWyn~vGtV~svd~~g 31 (64)
T CHL00125 2 VKRGSKVRILRKESYWYNEIGTVATVDQSG 31 (64)
T ss_pred cccCCEEEEccccceeecCcceEEEEcCCC
Confidence 6899999999986 667889999999864
No 52
>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=56.13 E-value=3.7 Score=28.84 Aligned_cols=30 Identities=30% Similarity=0.591 Sum_probs=0.4
Q ss_pred ceeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEe
Q 032297 68 MHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 103 (143)
Q Consensus 68 ~~IkkGD~V~VIsG~dKGK~G~V~~V~~k~n~ViVe 103 (143)
-.+++||+|.-++| -.|+|.++ +++.+.+|
T Consensus 35 ~~Lk~Gd~VvT~gG----i~G~V~~i--~~~~v~le 64 (82)
T PF02699_consen 35 ASLKPGDEVVTIGG----IYGTVVEI--DDDTVVLE 64 (82)
T ss_dssp G-----------------------------------
T ss_pred HcCCCCCEEEECCc----EEEEEEEE--eCCEEEEE
Confidence 35799999988875 57889888 55666666
No 53
>PRK05886 yajC preprotein translocase subunit YajC; Validated
Probab=55.72 E-value=21 Score=26.90 Aligned_cols=29 Identities=24% Similarity=0.368 Sum_probs=23.0
Q ss_pred eeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEe
Q 032297 69 HVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 103 (143)
Q Consensus 69 ~IkkGD~V~VIsG~dKGK~G~V~~V~~k~n~ViVe 103 (143)
.+++||+|.-+. |-.|+|.+|.. +.|.||
T Consensus 38 ~Lk~GD~VvT~g----Gi~G~V~~I~d--~~v~le 66 (109)
T PRK05886 38 SLQPGDRVHTTS----GLQATIVGITD--DTVDLE 66 (109)
T ss_pred hcCCCCEEEECC----CeEEEEEEEeC--CEEEEE
Confidence 479999998776 46899999964 578776
No 54
>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=55.41 E-value=21 Score=25.29 Aligned_cols=29 Identities=38% Similarity=0.678 Sum_probs=22.5
Q ss_pred eeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEe
Q 032297 69 HVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 103 (143)
Q Consensus 69 ~IkkGD~V~VIsG~dKGK~G~V~~V~~k~n~ViVe 103 (143)
.+++||+|.-+.| -.|+|.+|+. +.+.||
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 5799999987764 6899999975 466665
No 55
>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=53.84 E-value=19 Score=34.84 Aligned_cols=33 Identities=24% Similarity=0.442 Sum_probs=24.4
Q ss_pred eeCCEEEEEecCCCCeEeEEEEEEccCCEEEEe--ceee
Q 032297 71 KAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK--DINL 107 (143)
Q Consensus 71 kkGD~V~VIsG~dKGK~G~V~~V~~k~n~ViVe--gvN~ 107 (143)
+.||+|.|. .-|+.|+|++|.. ++.+.|+ ++.+
T Consensus 626 ~~Gd~V~v~---~~~~~g~v~~i~~-~~~~~V~~g~~k~ 660 (771)
T TIGR01069 626 KIGDKVRIR---YFGQKGKIVQILG-GNKWNVTVGGMRM 660 (771)
T ss_pred CCCCEEEEc---cCCceEEEEEEcC-CCeEEEEECCEEE
Confidence 899999994 5788999999975 4555444 5544
No 56
>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=53.73 E-value=15 Score=25.65 Aligned_cols=31 Identities=16% Similarity=0.210 Sum_probs=22.5
Q ss_pred cceeeeCCEEEEEecCCCCeEeEEEEEEccC
Q 032297 67 KMHVKAGDTVKVIAGCDKGKIGEITKVFRHN 97 (143)
Q Consensus 67 k~~IkkGD~V~VIsG~dKGK~G~V~~V~~k~ 97 (143)
+..|+.||.|.|=-=++--..|.|+..+.++
T Consensus 36 ~iwI~~GD~V~Ve~~~~d~~kg~Iv~r~~~~ 66 (77)
T cd05793 36 RVWINEGDIVLVAPWDFQDDKADIIYKYTPD 66 (77)
T ss_pred cEEEcCCCEEEEEeccccCCEEEEEEEcCHH
Confidence 4569999999994444456788888777653
No 57
>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=53.38 E-value=24 Score=25.42 Aligned_cols=35 Identities=34% Similarity=0.499 Sum_probs=24.9
Q ss_pred ccceeeeCCEEEEEecC------------CCCeEeEEEEEEc-cCCEE
Q 032297 66 HKMHVKAGDTVKVIAGC------------DKGKIGEITKVFR-HNSTV 100 (143)
Q Consensus 66 ~k~~IkkGD~V~VIsG~------------dKGK~G~V~~V~~-k~n~V 100 (143)
..+-|++||.|.|+.-. .-|..|++++|.. .++++
T Consensus 62 ~~~~V~~G~~V~i~~~~~~~~i~~~g~Al~~g~~G~~I~V~N~~s~k~ 109 (122)
T TIGR03170 62 PPWLVKRGDTVTVIARGGGLSVTTEGKALEDGAVGDQIRVRNLSSGKI 109 (122)
T ss_pred CccEEcCCCEEEEEEecCCEEEEEEEEEccccCCCCEEEEEECCCCCE
Confidence 44669999999998654 5677787777773 44443
No 58
>KOG3418 consensus 60S ribosomal protein L27 [Translation, ribosomal structure and biogenesis]
Probab=52.98 E-value=23 Score=27.98 Aligned_cols=38 Identities=26% Similarity=0.389 Sum_probs=32.8
Q ss_pred eeeCCEEEEEecCCCCeEeEEEEEEccC------CEEEEeceee
Q 032297 70 VKAGDTVKVIAGCDKGKIGEITKVFRHN------STVMVKDINL 107 (143)
Q Consensus 70 IkkGD~V~VIsG~dKGK~G~V~~V~~k~------n~ViVegvN~ 107 (143)
+++|-.|.|++|.+.|+-..|++-+.+. ..++|+|+..
T Consensus 5 lkPgkvv~v~sG~yAg~KaVivk~~Ddg~~d~p~~h~LvAgi~r 48 (136)
T KOG3418|consen 5 LKPGKVVLVLSGRYAGKKAVIVKNIDDGTEDKPYGHALVAGVDR 48 (136)
T ss_pred ccCCcEEEeecccccCccEEEEeecccCCccCCCceeeeeehhh
Confidence 6889999999999999999998887765 4789999864
No 59
>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=52.22 E-value=47 Score=24.10 Aligned_cols=36 Identities=19% Similarity=0.233 Sum_probs=27.9
Q ss_pred eeeeCCEEEEEecC--CCCeEeEEEEEEccC-CEEEEec
Q 032297 69 HVKAGDTVKVIAGC--DKGKIGEITKVFRHN-STVMVKD 104 (143)
Q Consensus 69 ~IkkGD~V~VIsG~--dKGK~G~V~~V~~k~-n~ViVeg 104 (143)
.++.||-|.|.+.. .+--+|.|.++.... +...+.+
T Consensus 3 ~~~vGD~V~v~~~~~~~~~~i~~I~~i~~~~~g~~~~~~ 41 (121)
T cd04717 3 QYRVGDCVYVANPEDPSKPIIFRIERLWKDEDGEKFFFG 41 (121)
T ss_pred EEECCCEEEEeCCCCCCCCEEEEEeEEEECCCCCEEEEE
Confidence 47899999999865 667799999999875 4445443
No 60
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=51.43 E-value=25 Score=25.02 Aligned_cols=31 Identities=19% Similarity=0.263 Sum_probs=23.9
Q ss_pred ccceeeeCCEEEEEecCCCCeEeEEEEEEcc
Q 032297 66 HKMHVKAGDTVKVIAGCDKGKIGEITKVFRH 96 (143)
Q Consensus 66 ~k~~IkkGD~V~VIsG~dKGK~G~V~~V~~k 96 (143)
++..|.+||.|.|--=++--..|.|+--+++
T Consensus 43 ~~i~I~~GD~V~Ve~~~~d~~kg~I~~Ry~~ 73 (75)
T COG0361 43 NRIRILPGDVVLVELSPYDLTKGRIVYRYKK 73 (75)
T ss_pred eeEEeCCCCEEEEEecccccccccEEEEecC
Confidence 4677999999999888877777777655444
No 61
>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=51.34 E-value=18 Score=25.01 Aligned_cols=28 Identities=18% Similarity=0.341 Sum_probs=22.7
Q ss_pred eeeCCEEEEEecC--CCCeEeEEEEEEccC
Q 032297 70 VKAGDTVKVIAGC--DKGKIGEITKVFRHN 97 (143)
Q Consensus 70 IkkGD~V~VIsG~--dKGK~G~V~~V~~k~ 97 (143)
|.+||.|+|++=. +-..+|+|..|+...
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 4789999999986 778999999999875
No 62
>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=51.02 E-value=29 Score=23.89 Aligned_cols=33 Identities=21% Similarity=0.264 Sum_probs=23.5
Q ss_pred ceeeeCCEEEEEecCCCCeEeEEEEEEccCCEE
Q 032297 68 MHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTV 100 (143)
Q Consensus 68 ~~IkkGD~V~VIsG~dKGK~G~V~~V~~k~n~V 100 (143)
=.+++||.|.|+.+..-=..|+|.++.+.++.|
T Consensus 25 G~l~~g~~v~vlr~~~~~~~g~i~sl~~~~~~v 57 (84)
T cd03692 25 GKIKRNAKVRVLRNGEVIYEGKISSLKRFKDDV 57 (84)
T ss_pred CEEeCCCEEEEEcCCCEEEEEEEEEEEEcCccc
Confidence 358899999999985222567788887765544
No 63
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=50.75 E-value=20 Score=25.37 Aligned_cols=31 Identities=19% Similarity=0.192 Sum_probs=22.7
Q ss_pred cceeeeCCEEEEEecCCCCeEeEEEEEEccC
Q 032297 67 KMHVKAGDTVKVIAGCDKGKIGEITKVFRHN 97 (143)
Q Consensus 67 k~~IkkGD~V~VIsG~dKGK~G~V~~V~~k~ 97 (143)
..-|+.||.|.|=--++--..|.|+.++.++
T Consensus 41 ~iwI~~GD~VlVe~~~~~~~kg~Iv~r~~~~ 71 (83)
T smart00652 41 KVWIRRGDIVLVDPWDFQDVKADIIYKYTKD 71 (83)
T ss_pred cEEEcCCCEEEEEecCCCCCEEEEEEEeCHH
Confidence 4559999999996555545778887777653
No 64
>PLN00190 60S ribosomal protein L21; Provisional
Probab=49.98 E-value=24 Score=28.44 Aligned_cols=47 Identities=26% Similarity=0.411 Sum_probs=32.0
Q ss_pred eeeeCCEEEEEec----------CCCCeEeEEEEEEccCCEE----------EEeceeeeeeeecCC
Q 032297 69 HVKAGDTVKVIAG----------CDKGKIGEITKVFRHNSTV----------MVKDINLKTKHVKKR 115 (143)
Q Consensus 69 ~IkkGD~V~VIsG----------~dKGK~G~V~~V~~k~n~V----------iVegvN~~kkhvKp~ 115 (143)
.++.||.|-|..- .+-|++|+|..+..+-.-| +.+-+|+.--|++++
T Consensus 33 ~yk~GD~VdIk~~~svqKGMPhk~YHGkTG~V~nv~~~A~gV~V~K~vggr~~~Kri~vriEHlk~s 99 (158)
T PLN00190 33 TFKVGDYVDIKVNGAIHKGMPHKFYHGRTGIVWNVTKRAVGVEVNKQVGNRIIRKRIHVRVEHVQPS 99 (158)
T ss_pred HhcCCCEEEEEecCCeecCCCcccccCCCeEEEeecCcEEEEEEEEeeCCeEeeEEEEeCHHHccCc
Confidence 4678999988743 2789999998876554444 444556666666664
No 65
>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=49.71 E-value=25 Score=29.03 Aligned_cols=39 Identities=26% Similarity=0.367 Sum_probs=24.4
Q ss_pred cceeeeCCEEEE-EecCCCCeEeEEEEEEc-----------cCCEEEEece
Q 032297 67 KMHVKAGDTVKV-IAGCDKGKIGEITKVFR-----------HNSTVMVKDI 105 (143)
Q Consensus 67 k~~IkkGD~V~V-IsG~dKGK~G~V~~V~~-----------k~n~ViVegv 105 (143)
--.++.||.|.+ -.+..+-+.-+|++|.. ..+.++|+|+
T Consensus 103 A~~V~~Gd~v~~~~~~~~~~~~~~V~~v~~~~~~G~yAPLT~~GtivVdgV 153 (217)
T PF01079_consen 103 ASDVRVGDCVLVSDEGGGKLRPSRVVRVSTVEKRGVYAPLTSHGTIVVDGV 153 (217)
T ss_dssp GGG--TT-EEEEE-TTT--EEEEEEEEEEEEEEEEEEEEEESSSEEEETTE
T ss_pred hhhCCCCCEEEEEEcCCCcEEEEEEEEEEEEEEeeEEcCccCcceEEECCE
Confidence 346899999999 55566777778877763 4567888887
No 66
>PF14505 DUF4438: Domain of unknown function (DUF4438); PDB: 3N99_N 3DCL_A.
Probab=49.58 E-value=37 Score=29.40 Aligned_cols=33 Identities=30% Similarity=0.391 Sum_probs=24.5
Q ss_pred eeCCEEEEEecCCCCeEeEEEEEEccCCEEEEe
Q 032297 71 KAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 103 (143)
Q Consensus 71 kkGD~V~VIsG~dKGK~G~V~~V~~k~n~ViVe 103 (143)
-.|.+..|++|+-||..|.|+-=.---++|+|+
T Consensus 59 CiGN~A~VvSG~AKG~~G~VtGkHGGieHVlV~ 91 (258)
T PF14505_consen 59 CIGNEAKVVSGDAKGAKGVVTGKHGGIEHVLVD 91 (258)
T ss_dssp -BT-EEEE-SSTTTT-EEEEEEEETTTTEEEEE
T ss_pred ecCceeEEeecccCCCcCeEecccCCeeeEEEE
Confidence 579999999999999999998776666677774
No 67
>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=49.34 E-value=23 Score=24.86 Aligned_cols=30 Identities=20% Similarity=0.237 Sum_probs=22.9
Q ss_pred ceeeeCCEEEEEecCC-CCeEeEEEEEEccC
Q 032297 68 MHVKAGDTVKVIAGCD-KGKIGEITKVFRHN 97 (143)
Q Consensus 68 ~~IkkGD~V~VIsG~d-KGK~G~V~~V~~k~ 97 (143)
.-|+.||.|.|-.=++ .-..|.|+.++.++
T Consensus 37 iwI~~GD~VlV~~~~~~~~~kg~Iv~r~~~~ 67 (78)
T cd04456 37 IWIKRGDFLIVDPIEEGEDVKADIIFVYCKD 67 (78)
T ss_pred EEEcCCCEEEEEecccCCCceEEEEEEeCHH
Confidence 5599999999977665 45778888777654
No 68
>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=49.34 E-value=46 Score=21.37 Aligned_cols=24 Identities=21% Similarity=0.333 Sum_probs=17.9
Q ss_pred ceeeeCCEEEEEecCCCCeEeEEEEEEccCCEEE
Q 032297 68 MHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVM 101 (143)
Q Consensus 68 ~~IkkGD~V~VIsG~dKGK~G~V~~V~~k~n~Vi 101 (143)
..++.||+|.|. |.+++.++.++.
T Consensus 47 ~~~~~Gd~v~v~----------v~~id~~~~~i~ 70 (72)
T cd05689 47 KVVSLGDEVEVM----------VLDIDEERRRIS 70 (72)
T ss_pred cEeCCCCEEEEE----------EEEeeCCcCEEe
Confidence 448999999994 777777766653
No 69
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=48.49 E-value=58 Score=20.62 Aligned_cols=33 Identities=27% Similarity=0.379 Sum_probs=22.7
Q ss_pred eeeeCCEEEEEecCCCC-eEeEEEEEEccCCEEEE
Q 032297 69 HVKAGDTVKVIAGCDKG-KIGEITKVFRHNSTVMV 102 (143)
Q Consensus 69 ~IkkGD~V~VIsG~dKG-K~G~V~~V~~k~n~ViV 102 (143)
.+++||.|.+..=.+.+ -.|+|+++.. +++..|
T Consensus 2 ~~~~G~~Ve~~~~~~~~W~~a~V~~~~~-~~~~~V 35 (61)
T smart00743 2 DFKKGDRVEVFSKEEDSWWEAVVTKVLG-DGKYLV 35 (61)
T ss_pred CcCCCCEEEEEECCCCEEEEEEEEEECC-CCEEEE
Confidence 47899999999743222 4588999987 334443
No 70
>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=48.05 E-value=24 Score=23.50 Aligned_cols=27 Identities=26% Similarity=0.255 Sum_probs=18.2
Q ss_pred ccceeeeCCEEEEEecCCCCeEeEEEE
Q 032297 66 HKMHVKAGDTVKVIAGCDKGKIGEITK 92 (143)
Q Consensus 66 ~k~~IkkGD~V~VIsG~dKGK~G~V~~ 92 (143)
++..|+.||.|.|---++--..|+|+.
T Consensus 38 ~~iwI~~GD~V~V~~~~~d~~kG~Ii~ 64 (65)
T PF01176_consen 38 KRIWIKRGDFVLVEPSPYDKVKGRIIY 64 (65)
T ss_dssp TCC---TTEEEEEEESTTCTTEEEEEE
T ss_pred eeEecCCCCEEEEEecccCCCeEEEEE
Confidence 456699999999987666577787753
No 71
>PTZ00189 60S ribosomal protein L21; Provisional
Probab=47.88 E-value=26 Score=28.31 Aligned_cols=47 Identities=26% Similarity=0.497 Sum_probs=32.7
Q ss_pred eeeeCCEEEEEecC----------CCCeEeEEEEEEccC----------CEEEEeceeeeeeeecCC
Q 032297 69 HVKAGDTVKVIAGC----------DKGKIGEITKVFRHN----------STVMVKDINLKTKHVKKR 115 (143)
Q Consensus 69 ~IkkGD~V~VIsG~----------dKGK~G~V~~V~~k~----------n~ViVegvN~~kkhvKp~ 115 (143)
.++.||.|-|..-. +-|++|+|..+..+- |+++.+-+|+.--|++++
T Consensus 33 ~yk~GD~VdIk~d~svqkGMPhk~YHGkTG~V~nv~~~A~gViV~k~vg~ki~~Kri~vr~EHlk~s 99 (160)
T PTZ00189 33 TFKVGDYVDIVVDSAVHKGMPYKYYHGRTGRVFNVTPRAVGVIVNKRVRGRIVRKRIHVRIEHVRKS 99 (160)
T ss_pred HccCCCEEEEEecCCeecCCCcccccCCCeEEEeecCeEEEEEEEEEECCEEeeeEEecCHhHcCCc
Confidence 46789999876532 779999998765443 444555667766777775
No 72
>PRK07018 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=47.50 E-value=28 Score=28.51 Aligned_cols=35 Identities=29% Similarity=0.391 Sum_probs=25.8
Q ss_pred ccceeeeCCEEEEEecC------------CCCeEeEEEEEE-ccCCEE
Q 032297 66 HKMHVKAGDTVKVIAGC------------DKGKIGEITKVF-RHNSTV 100 (143)
Q Consensus 66 ~k~~IkkGD~V~VIsG~------------dKGK~G~V~~V~-~k~n~V 100 (143)
..+-|++||.|.|+... .-|..|+.++|. ..++++
T Consensus 173 ~~~~V~~G~~V~i~~~~g~~~i~~~G~Al~~G~~Gd~IrVrN~~Sgk~ 220 (235)
T PRK07018 173 QAWVVCKGQTVSIIARGDGFSVKTEGEALNDGAVGQQIRVRNMASGQV 220 (235)
T ss_pred CccEeCCCCEEEEEEecCCEEEEEEEEEcCCCCCCCeEEEEECCCCCE
Confidence 34679999999998764 567788888887 444444
No 73
>PRK12618 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=46.83 E-value=34 Score=26.36 Aligned_cols=33 Identities=18% Similarity=0.281 Sum_probs=24.9
Q ss_pred cceeeeCCEEEEEecC------------CCCeEeEEEEEEc-cCCE
Q 032297 67 KMHVKAGDTVKVIAGC------------DKGKIGEITKVFR-HNST 99 (143)
Q Consensus 67 k~~IkkGD~V~VIsG~------------dKGK~G~V~~V~~-k~n~ 99 (143)
.+-|.+||.|.|+... .-|..|+.+.|.. .+++
T Consensus 79 p~lV~rG~~V~i~~~~ggl~i~~~G~AL~~G~~Gd~IrV~N~~S~r 124 (141)
T PRK12618 79 PAIVDRNQLVPLAYRLGGLEIRTEGRALSRGGVGDEIRVMNLSSRT 124 (141)
T ss_pred ccEEeCCCEEEEEEecCCEEEEEEEEEcccCCCCCEEEEEECCCCC
Confidence 4679999999998764 6788888888844 4444
No 74
>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=46.52 E-value=26 Score=28.10 Aligned_cols=38 Identities=24% Similarity=0.410 Sum_probs=27.7
Q ss_pred ccceeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEe
Q 032297 66 HKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 103 (143)
Q Consensus 66 ~k~~IkkGD~V~VIsG~dKGK~G~V~~V~~k~n~ViVe 103 (143)
+-+.++.||.|.|..|...--.++|.++.++.-.+.+.
T Consensus 13 ~VlR~k~Gd~i~v~dg~g~~~~a~i~~i~~~~~~~~i~ 50 (225)
T PF04452_consen 13 KVLRLKEGDSIEVFDGDGGEYRAEITEISKKSATLRIL 50 (225)
T ss_dssp TTST--TT-EEEEEESSSEEEEEEEEEEESSEEEEEEE
T ss_pred HhcCCCCCCEEEEEECCCCEEEEEEEECcCcEEEEEEe
Confidence 34678999999999999888889999998875544444
No 75
>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=46.20 E-value=31 Score=24.02 Aligned_cols=29 Identities=21% Similarity=0.307 Sum_probs=24.6
Q ss_pred eeeeCCEEEEEecC--CCCeEeEEEEEEccC
Q 032297 69 HVKAGDTVKVIAGC--DKGKIGEITKVFRHN 97 (143)
Q Consensus 69 ~IkkGD~V~VIsG~--dKGK~G~V~~V~~k~ 97 (143)
.++.||-|.|..+. ..--+|.|.+|....
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 47899999999998 667899999998654
No 76
>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=45.91 E-value=31 Score=24.70 Aligned_cols=37 Identities=24% Similarity=0.286 Sum_probs=25.3
Q ss_pred eeeeCCEEEE--EecCCCCeEeEEEEEEccCCEEEEecee
Q 032297 69 HVKAGDTVKV--IAGCDKGKIGEITKVFRHNSTVMVKDIN 106 (143)
Q Consensus 69 ~IkkGD~V~V--IsG~dKGK~G~V~~V~~k~n~ViVegvN 106 (143)
..++||.|.. -.+..-|.+|.|.+|.. ++.|.+-+-|
T Consensus 62 ~P~~Gdivv~~~~~~~~~GHVaIV~~v~~-~~~i~v~e~N 100 (124)
T PF05257_consen 62 TPQPGDIVVWDSGSGGGYGHVAIVESVND-GGTITVIEQN 100 (124)
T ss_dssp ---TTEEEEEEECTTTTT-EEEEEEEE-T-TSEEEEEECS
T ss_pred ccccceEEEeccCCCCCCCeEEEEEEECC-CCEEEEEECC
Confidence 3489999887 45578899999999954 4677766666
No 77
>PRK08515 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=44.65 E-value=33 Score=28.07 Aligned_cols=35 Identities=14% Similarity=0.333 Sum_probs=26.0
Q ss_pred ccceeeeCCEEEEEecC------------CCCeEeEEEEEEccCCEE
Q 032297 66 HKMHVKAGDTVKVIAGC------------DKGKIGEITKVFRHNSTV 100 (143)
Q Consensus 66 ~k~~IkkGD~V~VIsG~------------dKGK~G~V~~V~~k~n~V 100 (143)
..+-|++||.|.|+.-. .-|..|++++|...++++
T Consensus 162 ~~~lV~rGd~V~i~~~~gg~~I~~~G~Al~~G~~Gd~IrVrN~Sgki 208 (222)
T PRK08515 162 ALILVRKNDIINGVLKEGGVSIEISLKALQDGNLGDIIQAKNKSNKI 208 (222)
T ss_pred CcceEecCCEEEEEEECCCEEEEEEEEEcccCCCCCEEEEEeCCCCE
Confidence 44679999999998754 667888888887744444
No 78
>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=42.98 E-value=39 Score=24.02 Aligned_cols=31 Identities=29% Similarity=0.366 Sum_probs=23.2
Q ss_pred cceeeeCCEEEEEecCCCCe-EeEEEEEEccC
Q 032297 67 KMHVKAGDTVKVIAGCDKGK-IGEITKVFRHN 97 (143)
Q Consensus 67 k~~IkkGD~V~VIsG~dKGK-~G~V~~V~~k~ 97 (143)
.+=|+.||.|.|-.-++-.| .|+|..++.+.
T Consensus 36 ~iWIkrGd~VlV~p~~~~~kvkgeIv~i~~~~ 67 (78)
T cd05792 36 NIWIKRGDFVLVEPIEEGDKVKAEIVKILTRD 67 (78)
T ss_pred cEEEEeCCEEEEEecccCCceEEEEEEEECHH
Confidence 34499999999977665443 88898888764
No 79
>PRK11281 hypothetical protein; Provisional
Probab=42.98 E-value=63 Score=32.92 Aligned_cols=61 Identities=20% Similarity=0.275 Sum_probs=33.8
Q ss_pred cceeeeCCEEEEEecCCCCeEeEEEEEEc--------cCCEEEEeceeeeeeeecCCcccCCceEEEEeeceee
Q 032297 67 KMHVKAGDTVKVIAGCDKGKIGEITKVFR--------HNSTVMVKDINLKTKHVKKREEEEQGQIIKLKCDALL 132 (143)
Q Consensus 67 k~~IkkGD~V~VIsG~dKGK~G~V~~V~~--------k~n~ViVegvN~~kkhvKp~~~~~~GgIi~~E~PIhi 132 (143)
.-+++.||.|.| | |..|+|.+|.- ++..|+|-+-.+.+..+.-......-..+..+..|.|
T Consensus 936 eRPfrIGD~I~I--~---~~~G~V~~I~lRsT~Irt~D~~~ViIPNs~~~t~~IiN~S~~~~~~Rv~i~vgV~Y 1004 (1113)
T PRK11281 936 ERPVRIGDTVTI--G---TFSGTVSKIRIRATTITDFDRKEVIVPNKAFVTERLINWSLSDTVTRVVIKVGVAY 1004 (1113)
T ss_pred cCCcCCCCEEEE--C---CEEEEEEEEEeEEEEEEcCCCCEEEEechhhhcCceEeCCCCCcceEEEEEEEeCC
Confidence 345899999998 3 57888888753 3445666654443332222111111123555566655
No 80
>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=42.78 E-value=66 Score=25.37 Aligned_cols=30 Identities=27% Similarity=0.369 Sum_probs=26.7
Q ss_pred ceeeeCCEEEEEecCCCCeEeEEEEEEccC
Q 032297 68 MHVKAGDTVKVIAGCDKGKIGEITKVFRHN 97 (143)
Q Consensus 68 ~~IkkGD~V~VIsG~dKGK~G~V~~V~~k~ 97 (143)
..++.||-|.|-++..+--+|+|.++....
T Consensus 28 ~~y~lGD~Vlv~s~~~~~yIgkI~~iwe~~ 57 (159)
T cd04715 28 VEYRLYDDVYVHNGDSEPYIGKIIKIYETA 57 (159)
T ss_pred EEEeCCCEEEEeCCCCCCEEEEEEEEEEcC
Confidence 348999999999999888999999999864
No 81
>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=42.76 E-value=57 Score=24.69 Aligned_cols=31 Identities=13% Similarity=0.252 Sum_probs=25.0
Q ss_pred cceeeeCCEEEEEecCCCCeEeEEEEEEccC
Q 032297 67 KMHVKAGDTVKVIAGCDKGKIGEITKVFRHN 97 (143)
Q Consensus 67 k~~IkkGD~V~VIsG~dKGK~G~V~~V~~k~ 97 (143)
...|+.||.|.|.+-..+=-+|.|.++....
T Consensus 5 ~~~i~vGD~V~v~~~~~~~~va~Ie~i~ed~ 35 (130)
T cd04721 5 GVTISVHDFVYVLSEEEDRYVAYIEDLYEDK 35 (130)
T ss_pred CEEEECCCEEEEeCCCCCcEEEEEEEEEEcC
Confidence 3559999999999765555699999998865
No 82
>KOG4225 consensus Sorbin and SH3 domain-containing protein [Signal transduction mechanisms]
Probab=42.55 E-value=30 Score=32.33 Aligned_cols=47 Identities=23% Similarity=0.400 Sum_probs=31.1
Q ss_pred ccCCCCceeeeeeeeeeeeeccCCCCCcccccceeeeCCEEEEEe--------cCCCCeEeEE
Q 032297 36 VKPTDKPCLIVVRLKRWERKECKPNSLPVLHKMHVKAGDTVKVIA--------GCDKGKIGEI 90 (143)
Q Consensus 36 ~~~~~~~~~~~~~~k~Werk~~kpn~lp~~~k~~IkkGD~V~VIs--------G~dKGK~G~V 90 (143)
-..++++|....++=..+-++. ..+.+.+||+|.|+. |.+-|.+|.+
T Consensus 223 r~~~~~~~~~aralf~F~~qt~--------kEL~~~kGDIVyI~rkvD~nWyeGEhhGr~Gif 277 (489)
T KOG4225|consen 223 RRKTEKPKRAARALFDFEAQTP--------KELPFNKGDIVYILRKVDQNWYEGEHHGRVGIF 277 (489)
T ss_pred CCCCccccchhhheeccccCCc--------cccccCCCCEEEEEeeccCceeeeeecceecce
Confidence 5566777776444433333322 355689999999974 7788998854
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=42.39 E-value=19 Score=26.45 Aligned_cols=32 Identities=16% Similarity=0.197 Sum_probs=19.1
Q ss_pred ccceeeeCCEEEEEecCCC-CeEeEEEEEEccC
Q 032297 66 HKMHVKAGDTVKVIAGCDK-GKIGEITKVFRHN 97 (143)
Q Consensus 66 ~k~~IkkGD~V~VIsG~dK-GK~G~V~~V~~k~ 97 (143)
.++.|+.||.|.|--=+.- ...|.|+.++..+
T Consensus 54 k~iwI~~GD~VlVsp~d~~~~~kg~Iv~r~~~~ 86 (99)
T TIGR00523 54 KRIWIREGDVVIVKPWEFQGDDKCDIVWRYTKT 86 (99)
T ss_pred ccEEecCCCEEEEEEccCCCCccEEEEEEcCHH
Confidence 3566999999999210111 1247787776543
No 84
>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=41.92 E-value=56 Score=20.16 Aligned_cols=25 Identities=24% Similarity=0.372 Sum_probs=18.6
Q ss_pred ceeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEE
Q 032297 68 MHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMV 102 (143)
Q Consensus 68 ~~IkkGD~V~VIsG~dKGK~G~V~~V~~k~n~ViV 102 (143)
-.++.||+|++. |.+++..++++.+
T Consensus 43 ~~~~~Gd~v~v~----------i~~vd~~~~~i~l 67 (68)
T cd05688 43 EVVNVGDEVEVK----------VLKIDKERKRISL 67 (68)
T ss_pred HEECCCCEEEEE----------EEEEECCCCEEec
Confidence 458999999984 7777777766643
No 85
>COG1193 Mismatch repair ATPase (MutS family) [DNA replication, recombination, and repair]
Probab=41.51 E-value=29 Score=33.81 Aligned_cols=34 Identities=32% Similarity=0.522 Sum_probs=28.1
Q ss_pred cceeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEec
Q 032297 67 KMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKD 104 (143)
Q Consensus 67 k~~IkkGD~V~VIsG~dKGK~G~V~~V~~k~n~ViVeg 104 (143)
.-.++.||.|.+++ |..|.|++|......++|+-
T Consensus 610 ~~~l~~gDev~~~t----~e~G~~~~i~a~~~e~~v~~ 643 (753)
T COG1193 610 KRKLKLGDEVEVIT----GEPGAVVKIIAGILEALVQS 643 (753)
T ss_pred ccCceecceeEeec----CCccceeeeeccCceeEEec
Confidence 56689999999999 66788888887777877774
No 86
>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=41.39 E-value=50 Score=22.33 Aligned_cols=26 Identities=19% Similarity=0.353 Sum_probs=18.0
Q ss_pred ceeeeCCEEEEEecCCCCeEeEEEEEEcc
Q 032297 68 MHVKAGDTVKVIAGCDKGKIGEITKVFRH 96 (143)
Q Consensus 68 ~~IkkGD~V~VIsG~dKGK~G~V~~V~~k 96 (143)
=.|++||+|.+.-.. ...+|.+|..+
T Consensus 25 G~i~~Gd~v~i~P~~---~~~~V~si~~~ 50 (83)
T cd03698 25 GSIQKGDTLLVMPSK---ESVEVKSIYVD 50 (83)
T ss_pred eEEeCCCEEEEeCCC---cEEEEEEEEEC
Confidence 357889999887653 55667766654
No 87
>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=41.03 E-value=52 Score=20.93 Aligned_cols=29 Identities=21% Similarity=0.302 Sum_probs=19.6
Q ss_pred eeeCCEEEEEecCCCCeEeEEEEEEccCCEE
Q 032297 70 VKAGDTVKVIAGCDKGKIGEITKVFRHNSTV 100 (143)
Q Consensus 70 IkkGD~V~VIsG~dKGK~G~V~~V~~k~n~V 100 (143)
+..||.|.+-. .+ +..+.|.+|.+.++.+
T Consensus 38 ~~VGD~V~~~~-~~-~~~~~I~~vl~R~s~l 66 (68)
T cd04466 38 PAVGDRVEFEP-ED-DGEGVIEEILPRKNLL 66 (68)
T ss_pred CCCCcEEEEEE-CC-CCcEEEEEEeccceEE
Confidence 58999998732 22 2347788888877654
No 88
>PRK06005 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=40.98 E-value=43 Score=26.27 Aligned_cols=39 Identities=26% Similarity=0.417 Sum_probs=27.7
Q ss_pred ccceeeeCCEEEEEecC------------CCCeEeEEEEEEccCCEEEEec
Q 032297 66 HKMHVKAGDTVKVIAGC------------DKGKIGEITKVFRHNSTVMVKD 104 (143)
Q Consensus 66 ~k~~IkkGD~V~VIsG~------------dKGK~G~V~~V~~k~n~ViVeg 104 (143)
..+-|++||.|.|+... +-|..|++++|..-...-+|.+
T Consensus 97 ~p~~V~rG~~V~i~~~~~g~~i~~~G~Al~~G~~Gd~IrVrN~~Sgkiv~g 147 (160)
T PRK06005 97 EPSLVTRGSPVKLVFSAGGLTITAAGTPLQSGAAGDLIRVRNVDSGVIVSG 147 (160)
T ss_pred CCcEEeCCCEEEEEEecCCEEEEEEEEEcccCCCCCEEEEEECCCCCEEEE
Confidence 45679999999998764 6788888888874444444444
No 89
>smart00439 BAH Bromo adjacent homology domain.
Probab=40.92 E-value=55 Score=22.67 Aligned_cols=29 Identities=28% Similarity=0.431 Sum_probs=23.7
Q ss_pred eeeCCEEEEEecC--CCCeEeEEEEEEccCC
Q 032297 70 VKAGDTVKVIAGC--DKGKIGEITKVFRHNS 98 (143)
Q Consensus 70 IkkGD~V~VIsG~--dKGK~G~V~~V~~k~n 98 (143)
++.||.|.|.... ..=-+|.|.++....+
T Consensus 2 ~~vgd~V~v~~~~~~~~~~i~~I~~i~~~~~ 32 (120)
T smart00439 2 IRVGDFVLVEPDDADEPYYIGRIEEIFETKK 32 (120)
T ss_pred cccCCEEEEeCCCCCCCCEEEEEEEEEECCC
Confidence 6889999999886 3467999999988654
No 90
>cd04471 S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase play an important role in the degradation of RNA with extensive secondary structure, such as rRNA, tRNA, and certain mRNA which contains repetitive extragenic palindromic sequences. The C-terminal S1 domain binds ssRNA.
Probab=40.51 E-value=99 Score=20.01 Aligned_cols=25 Identities=24% Similarity=0.275 Sum_probs=17.3
Q ss_pred ceeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEE
Q 032297 68 MHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMV 102 (143)
Q Consensus 68 ~~IkkGD~V~VIsG~dKGK~G~V~~V~~k~n~ViV 102 (143)
-.++.||+|.|. |..++..+.++.+
T Consensus 56 ~~~~~gd~v~v~----------v~~vd~~~~~i~~ 80 (83)
T cd04471 56 KVFRLGDKVKVR----------VVRVDLDRRKIDF 80 (83)
T ss_pred CEEcCCCEEEEE----------EEEeccccCEEEE
Confidence 457889999984 6667665555544
No 91
>cd03695 CysN_NodQ_II CysN_NodQ_II: This subfamily represents the domain II of the large subunit of ATP sulfurylase (ATPS): CysN or the N-terminal portion of NodQ, found mainly in proteobacteria and homologous to the domain II of EF-Tu. Escherichia coli ATPS consists of CysN and a smaller subunit CysD and CysN. ATPS produces adenosine-5'-phosphosulfate (APS) from ATP and sulfate, coupled with GTP hydrolysis. In the subsequent reaction APS is phosphorylated by an APS kinase (CysC), to produce 3'-phosphoadenosine-5'-phosphosulfate (PAPS) for use in amino acid (aa) biosynthesis. The Rhizobiaceae group (alpha-proteobacteria) appears to carry out the same chemistry for the sufation of a nodulation factor. In Rhizobium meliloti, a the hererodimeric complex comprised of NodP and NodQ appears to possess both ATPS and APS kinase activities. The N and C termini of NodQ correspond to CysN and CysC, respectively. Other eubacteria, Archaea, and eukaryotes use a different ATP sulfurylase, which sho
Probab=40.51 E-value=63 Score=22.01 Aligned_cols=29 Identities=21% Similarity=0.423 Sum_probs=20.3
Q ss_pred ceeeeCCEEEEEecCCCCeEeEEEEEEccCCE
Q 032297 68 MHVKAGDTVKVIAGCDKGKIGEITKVFRHNST 99 (143)
Q Consensus 68 ~~IkkGD~V~VIsG~dKGK~G~V~~V~~k~n~ 99 (143)
=.+++||+|.+.-. +...+|..|..++..
T Consensus 25 G~v~~Gd~v~~~P~---~~~~~V~si~~~~~~ 53 (81)
T cd03695 25 GSIRVGDEVVVLPS---GKTSRVKSIETFDGE 53 (81)
T ss_pred ceEECCCEEEEcCC---CCeEEEEEEEECCcE
Confidence 35789999988865 466777777665433
No 92
>KOG3421 consensus 60S ribosomal protein L14 [Translation, ribosomal structure and biogenesis]
Probab=40.42 E-value=32 Score=27.15 Aligned_cols=35 Identities=29% Similarity=0.384 Sum_probs=30.7
Q ss_pred eeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEece
Q 032297 70 VKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDI 105 (143)
Q Consensus 70 IkkGD~V~VIsG~dKGK~G~V~~V~~k~n~ViVegv 105 (143)
+-.|-.+.|-.|+|.||.--|..|+.+ |++.|+|-
T Consensus 7 veVGrva~v~~G~~~GkL~AIVdviDq-nr~lvDGp 41 (136)
T KOG3421|consen 7 VEVGRVALVSFGPDAGKLVAIVDVIDQ-NRALVDGP 41 (136)
T ss_pred hhcceEEEEEecCCCceEEEEEEeecc-hhhhccCc
Confidence 467889999999999999999999864 79999984
No 93
>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=40.41 E-value=37 Score=20.62 Aligned_cols=18 Identities=28% Similarity=0.593 Sum_probs=13.0
Q ss_pred ccceeeeCCEEEEEecCC
Q 032297 66 HKMHVKAGDTVKVIAGCD 83 (143)
Q Consensus 66 ~k~~IkkGD~V~VIsG~d 83 (143)
..+.+++||.+.|+.=.+
T Consensus 12 ~eLs~~~Gd~i~v~~~~~ 29 (48)
T PF00018_consen 12 DELSFKKGDIIEVLEKSD 29 (48)
T ss_dssp TBSEB-TTEEEEEEEESS
T ss_pred CEEeEECCCEEEEEEecC
Confidence 456689999999987543
No 94
>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=39.35 E-value=58 Score=20.71 Aligned_cols=24 Identities=21% Similarity=0.440 Sum_probs=18.8
Q ss_pred eeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEE
Q 032297 69 HVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMV 102 (143)
Q Consensus 69 ~IkkGD~V~VIsG~dKGK~G~V~~V~~k~n~ViV 102 (143)
.++.||+|.+ +|++++.+++++.+
T Consensus 44 ~~~~G~~i~v----------~v~~~d~~~~~i~l 67 (70)
T cd05698 44 HFRVGQVVKV----------KVLSCDPEQQRLLL 67 (70)
T ss_pred cccCCCEEEE----------EEEEEcCCCCEEEE
Confidence 4789999998 57788887777765
No 95
>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=39.20 E-value=26 Score=29.20 Aligned_cols=29 Identities=31% Similarity=0.374 Sum_probs=16.8
Q ss_pred ccceeeeCCEEEEEecC----------CCCeEeEEEEEE
Q 032297 66 HKMHVKAGDTVKVIAGC----------DKGKIGEITKVF 94 (143)
Q Consensus 66 ~k~~IkkGD~V~VIsG~----------dKGK~G~V~~V~ 94 (143)
..-.++.||+|.|..-. -+||+|+|..+.
T Consensus 131 ~~~~F~vGd~Vrv~~~~~~~HtR~P~Y~rg~~G~I~~~~ 169 (222)
T PF02211_consen 131 APPRFAVGDRVRVRNLPPPGHTRLPRYVRGKTGTIERVH 169 (222)
T ss_dssp SS-SS-TT-EEEE-----SS--SS-GGGTT-EEEEEEEE
T ss_pred CCCCCCCCCEEEECCCCCCCcccccHhhCCCeeEEEEEe
Confidence 34568999999998754 689999998553
No 96
>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=39.16 E-value=51 Score=21.49 Aligned_cols=24 Identities=25% Similarity=0.234 Sum_probs=19.3
Q ss_pred eeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEE
Q 032297 69 HVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMV 102 (143)
Q Consensus 69 ~IkkGD~V~VIsG~dKGK~G~V~~V~~k~n~ViV 102 (143)
.++.||+|++ +|+.+++++.+|.+
T Consensus 42 ~~~~G~~i~~----------kVi~id~~~~~i~L 65 (66)
T cd05695 42 TYKEGQKVRA----------RILYVDPSTKVVGL 65 (66)
T ss_pred CcCCCCEEEE----------EEEEEeCCCCEEec
Confidence 3789999987 68999998877654
No 97
>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=39.00 E-value=73 Score=20.29 Aligned_cols=26 Identities=15% Similarity=0.278 Sum_probs=20.2
Q ss_pred ceeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEe
Q 032297 68 MHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 103 (143)
Q Consensus 68 ~~IkkGD~V~VIsG~dKGK~G~V~~V~~k~n~ViVe 103 (143)
-.++.||+|.+. |.+++.++.++.++
T Consensus 46 ~~~~~Gd~v~v~----------i~~vd~~~~~i~ls 71 (77)
T cd05708 46 KLFRVGDKVRAK----------VLKIDAEKKRISLG 71 (77)
T ss_pred HeecCCCEEEEE----------EEEEeCCCCEEEEE
Confidence 457999999984 78888877777654
No 98
>COG1162 Predicted GTPases [General function prediction only]
Probab=38.46 E-value=44 Score=29.25 Aligned_cols=30 Identities=20% Similarity=0.339 Sum_probs=25.6
Q ss_pred ceeeeCCEEEEEecCCCCeEeEEEEEEccCCEE
Q 032297 68 MHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTV 100 (143)
Q Consensus 68 ~~IkkGD~V~VIsG~dKGK~G~V~~V~~k~n~V 100 (143)
....+||+|.+-.+... |.|.+|...+|.+
T Consensus 43 ~~~vVGD~V~~~~~~~~---g~I~~i~~Rkn~L 72 (301)
T COG1162 43 LKPVVGDRVVFEDENNN---GVIEKILPRKNVL 72 (301)
T ss_pred ccccccCeEEEecCCCc---ceEEEEecccCce
Confidence 44689999999999877 9999999988765
No 99
>PRK10929 putative mechanosensitive channel protein; Provisional
Probab=38.20 E-value=83 Score=32.16 Aligned_cols=36 Identities=22% Similarity=0.469 Sum_probs=25.3
Q ss_pred cceeeeCCEEEEEecCCCCeEeEEEEEEc--------cCCEEEEeceee
Q 032297 67 KMHVKAGDTVKVIAGCDKGKIGEITKVFR--------HNSTVMVKDINL 107 (143)
Q Consensus 67 k~~IkkGD~V~VIsG~dKGK~G~V~~V~~--------k~n~ViVegvN~ 107 (143)
.-+++.||.|.| .|..|+|.+|.- ++..|+|-+-.+
T Consensus 933 erPfrVGD~I~I-----~~~~GtV~~I~lRsT~Irt~Dg~~IiIPNs~~ 976 (1109)
T PRK10929 933 EKPIRIGDTVTI-----RDLTGSVTKINTRATTISDWDRKEIIVPNKAF 976 (1109)
T ss_pred hCCCCCCCEEEE-----CCEEEEEEEEeeeEEEEEeCCCCEEEEEChhh
Confidence 345899999998 368899988864 445566665443
No 100
>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=37.89 E-value=53 Score=22.07 Aligned_cols=27 Identities=22% Similarity=0.304 Sum_probs=19.6
Q ss_pred ceeeeCCEEEEEecCCCCeEeEEEEEEccC
Q 032297 68 MHVKAGDTVKVIAGCDKGKIGEITKVFRHN 97 (143)
Q Consensus 68 ~~IkkGD~V~VIsG~dKGK~G~V~~V~~k~ 97 (143)
=.+++||+|.+.-+. ..++|.+|..++
T Consensus 25 G~i~~g~~v~~~p~~---~~~~V~sI~~~~ 51 (83)
T cd03696 25 GSVKVGDKVEILPLG---EETRVRSIQVHG 51 (83)
T ss_pred cEEeCCCEEEECCCC---ceEEEEEEEECC
Confidence 347899998888754 577888776553
No 101
>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=37.87 E-value=54 Score=20.94 Aligned_cols=24 Identities=25% Similarity=0.329 Sum_probs=18.7
Q ss_pred eeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEE
Q 032297 69 HVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMV 102 (143)
Q Consensus 69 ~IkkGD~V~VIsG~dKGK~G~V~~V~~k~n~ViV 102 (143)
.++.||.|++ +|+++++++.++.+
T Consensus 44 ~~~~Gd~v~~----------~v~~~d~~~~~i~l 67 (68)
T cd05707 44 RFKVGQLVKG----------KIVSIDPDNGRIEM 67 (68)
T ss_pred ccCCCCEEEE----------EEEEEeCCCCEEec
Confidence 3789999988 57888887777754
No 102
>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=37.55 E-value=71 Score=20.42 Aligned_cols=24 Identities=21% Similarity=0.282 Sum_probs=19.8
Q ss_pred eeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEE
Q 032297 69 HVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMV 102 (143)
Q Consensus 69 ~IkkGD~V~VIsG~dKGK~G~V~~V~~k~n~ViV 102 (143)
.++.||++.+ +|++++.+++++.+
T Consensus 44 ~~~~Gd~i~~----------~V~~id~~~~~i~l 67 (69)
T cd05697 44 KFKPGLKVKC----------RVLSVEPERKRLVL 67 (69)
T ss_pred cCCCCCEEEE----------EEEEEECCCCEEEE
Confidence 4789999988 58889988888765
No 103
>KOG3482 consensus Small nuclear ribonucleoprotein (snRNP) SMF [RNA processing and modification]
Probab=37.24 E-value=22 Score=25.66 Aligned_cols=58 Identities=28% Similarity=0.578 Sum_probs=42.2
Q ss_pred eeeeeeeeeeeeccCCCCCcccccceeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEece
Q 032297 44 LIVVRLKRWERKECKPNSLPVLHKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDI 105 (143)
Q Consensus 44 ~~~~~~k~Werk~~kpn~lp~~~k~~IkkGD~V~VIsG~dKGK~G~V~~V~~k~n~ViVegv 105 (143)
++..++| |- .|+|---...-..+++.-+..=+.|.|..-|+.|+| .+|=+|-.+|.|+
T Consensus 20 ~V~vkLK-wg-~eYkG~LvsvD~YmNlqL~~~eE~idG~~~g~lGEi--lIRCNNvlyi~gv 77 (79)
T KOG3482|consen 20 PVLVKLK-WG-QEYKGTLVSVDNYMNLQLANAEEYIDGVSTGNLGEI--LIRCNNVLYIRGV 77 (79)
T ss_pred eEEEEEe-cC-cEEEEEEEEecchhheehhhhhhhhcccccccceeE--EEEeccEEEEecC
Confidence 3556776 84 777743333335678888888889999999999999 4566777777665
No 104
>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=36.94 E-value=77 Score=23.37 Aligned_cols=35 Identities=14% Similarity=0.283 Sum_probs=26.2
Q ss_pred eeeeCCEEEEEecC--CCCeEeEEEEEEccC-CEEEEe
Q 032297 69 HVKAGDTVKVIAGC--DKGKIGEITKVFRHN-STVMVK 103 (143)
Q Consensus 69 ~IkkGD~V~VIsG~--dKGK~G~V~~V~~k~-n~ViVe 103 (143)
.++.||-|.|.+.. ++=-+|+|.++.... +...+.
T Consensus 3 ~~~vGD~V~v~~~~~~~~pyIgrI~~i~e~~~g~~~~~ 40 (121)
T cd04714 3 IIRVGDCVLFKSPGRPSLPYVARIESLWEDPEGNMVVR 40 (121)
T ss_pred EEEcCCEEEEeCCCCCCCCEEEEEEEEEEcCCCCEEEE
Confidence 47899999999865 456799999998754 344443
No 105
>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=36.37 E-value=74 Score=26.53 Aligned_cols=30 Identities=23% Similarity=0.252 Sum_probs=22.6
Q ss_pred eeeeCCEEEEEecCCCCeEeEEEEEEccCCEE
Q 032297 69 HVKAGDTVKVIAGCDKGKIGEITKVFRHNSTV 100 (143)
Q Consensus 69 ~IkkGD~V~VIsG~dKGK~G~V~~V~~k~n~V 100 (143)
.+.+||.|.+-.-. +..|.|.+|.+.+|.+
T Consensus 34 ~~~vGD~V~~~~~~--~~~~~i~~i~~R~~~l 63 (287)
T cd01854 34 KPVVGDWVEVEPDD--DGEGVIVRVLPRKNLL 63 (287)
T ss_pred CccCCCEEEEEecC--CCcEEEEEEECCCceE
Confidence 36899999885422 4578999999887754
No 106
>PRK12617 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=36.21 E-value=51 Score=27.17 Aligned_cols=30 Identities=23% Similarity=0.248 Sum_probs=23.2
Q ss_pred ccceeeeCCEEEEEecC------------CCCeEeEEEEEEc
Q 032297 66 HKMHVKAGDTVKVIAGC------------DKGKIGEITKVFR 95 (143)
Q Consensus 66 ~k~~IkkGD~V~VIsG~------------dKGK~G~V~~V~~ 95 (143)
..+-|++||.|.|+... ..|..|+.++|..
T Consensus 152 ~p~lV~rG~~V~I~a~~~g~~Vs~~G~AL~~G~~Ge~IrVrN 193 (214)
T PRK12617 152 SQRLVRRGDTVPLVSRNGGLEVRMSGRALSDAGENERVSVEN 193 (214)
T ss_pred CcceEcCCCEEEEEEecCCEEEEEEEEEccCCCCCCEEEEEE
Confidence 34679999999999865 5677777777774
No 107
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=36.12 E-value=43 Score=24.72 Aligned_cols=30 Identities=20% Similarity=0.258 Sum_probs=21.2
Q ss_pred cceeeeCCEEEEEecCCCCeEeEEEEEEcc
Q 032297 67 KMHVKAGDTVKVIAGCDKGKIGEITKVFRH 96 (143)
Q Consensus 67 k~~IkkGD~V~VIsG~dKGK~G~V~~V~~k 96 (143)
+..|+.||.|.|--=++--..|.|+..+..
T Consensus 57 ~IwI~~GD~VlVe~~~~~~~kg~Iv~r~~~ 86 (100)
T PRK04012 57 RMWIREGDVVIVAPWDFQDEKADIIWRYTK 86 (100)
T ss_pred cEEecCCCEEEEEecccCCCEEEEEEEcCH
Confidence 456899999998654443556888777654
No 108
>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=36.04 E-value=35 Score=19.71 Aligned_cols=16 Identities=25% Similarity=0.561 Sum_probs=13.0
Q ss_pred cceeeeCCEEEEEecC
Q 032297 67 KMHVKAGDTVKVIAGC 82 (143)
Q Consensus 67 k~~IkkGD~V~VIsG~ 82 (143)
.+.+.+||.|.|+...
T Consensus 15 ~l~~~~Gd~v~v~~~~ 30 (54)
T cd00174 15 ELSFKKGDIIEVLEKS 30 (54)
T ss_pred CCCCCCCCEEEEEEcC
Confidence 4568999999999873
No 109
>cd04461 S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains. 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 S. cerevisiae Rrp5 and 14 S1 repeats in H. 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 8 and S. cerevisiae S1 repeat 7. Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=36.02 E-value=64 Score=21.54 Aligned_cols=26 Identities=19% Similarity=0.359 Sum_probs=19.7
Q ss_pred cceeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEE
Q 032297 67 KMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMV 102 (143)
Q Consensus 67 k~~IkkGD~V~VIsG~dKGK~G~V~~V~~k~n~ViV 102 (143)
.-.++.||+|.+ +|.+++.+++++.+
T Consensus 56 ~~~~~~Gd~v~v----------kV~~id~~~~~i~l 81 (83)
T cd04461 56 SFGFKKGQSVTA----------KVTSVDEEKQRFLL 81 (83)
T ss_pred HHhcCCCCEEEE----------EEEEEcCCCCEEEE
Confidence 355899999998 57778777777765
No 110
>TIGR00358 3_prime_RNase VacB and RNase II family 3'-5' exoribonucleases. This model is defined to identify a pair of paralogous 3-prime exoribonucleases in E. coli, plus the set of proteins apparently orthologous to one or the other in other eubacteria. VacB was characterized originally as required for the expression of virulence genes, but is now recognized as the exoribonuclease RNase R (Rnr). Its paralog in E. coli and H. influenzae is designated exoribonuclease II (Rnb). Both are involved in the degradation of mRNA, and consequently have strong pleiotropic effects that may be difficult to disentangle. Both these proteins share domain-level similarity (RNB, S1) with a considerable number of other proteins, and full-length similarity scoring below the trusted cutoff to proteins associated with various phenotypes but uncertain biochemistry; it may be that these latter proteins are also 3-prime exoribonucleases.
Probab=35.89 E-value=64 Score=30.45 Aligned_cols=36 Identities=22% Similarity=0.346 Sum_probs=24.9
Q ss_pred ceeeeCCEEEEE-ecC-CCCe-EeEEEEEEccCCEEEEe
Q 032297 68 MHVKAGDTVKVI-AGC-DKGK-IGEITKVFRHNSTVMVK 103 (143)
Q Consensus 68 ~~IkkGD~V~VI-sG~-dKGK-~G~V~~V~~k~n~ViVe 103 (143)
-....||+|.|. ... .+|+ .|+|.+|......-+|-
T Consensus 49 ~~a~~GD~V~v~i~~~~~~~~~~g~v~~il~r~~~~~vG 87 (654)
T TIGR00358 49 KKVMHGDLVEACPLSQPQRGRFEAEVERILEPALTRFVG 87 (654)
T ss_pred CcCCCCCEEEEEEeecCCCCCceEEEEEEeccCCCEEEE
Confidence 345679999764 333 3444 89999999887665554
No 111
>CHL00010 infA translation initiation factor 1
Probab=35.85 E-value=81 Score=21.86 Aligned_cols=28 Identities=29% Similarity=0.278 Sum_probs=17.2
Q ss_pred ceeeeCCEEEEEecCCCCeEeEEEEEEc
Q 032297 68 MHVKAGDTVKVIAGCDKGKIGEITKVFR 95 (143)
Q Consensus 68 ~~IkkGD~V~VIsG~dKGK~G~V~~V~~ 95 (143)
..+..||.|.|--=.+-...|.|+.-++
T Consensus 45 i~~~vGD~V~ve~~~~~~~~g~Ii~r~~ 72 (78)
T CHL00010 45 IRILPGDRVKVELSPYDLTKGRIIYRLR 72 (78)
T ss_pred cccCCCCEEEEEEcccCCCeEEEEEEec
Confidence 4468999999874333344566754443
No 112
>PLN02661 Putative thiazole synthesis
Probab=35.27 E-value=26 Score=31.24 Aligned_cols=45 Identities=20% Similarity=0.149 Sum_probs=23.2
Q ss_pred ccccccCcccCCCCCCCccccCCCCc--eeeeeeeeeeeeeccCCCC
Q 032297 17 SSNSFFGQRLSFPSLSPITVKPTDKP--CLIVVRLKRWERKECKPNS 61 (143)
Q Consensus 17 ~~~~f~g~~l~~~~~~~~~~~~~~~~--~~~~~~~k~Werk~~kpn~ 61 (143)
|++||.|.||.+...+|....++-.. .+-...--.|..+++.+-.
T Consensus 25 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~ 71 (357)
T PLN02661 25 SSSSFAGVRLVTSVRAPLADASAPARSSSSSSTAPYDLNNFKFAPIK 71 (357)
T ss_pred ccccccCccccccccCCccccccccccccCCCCCCCccccccceech
Confidence 56999999997655444311111111 1111223457777666544
No 113
>cd04451 S1_IF1 S1_IF1: Translation Initiation Factor IF1, S1-like RNA-binding domain. IF1 contains an S1-like RNA-binding domain, which is found in a wide variety of RNA-associated proteins. Translation initiation includes a number of interrelated steps preceding the formation of the first peptide bond. In Escherichia coli, the initiation mechanism requires, in addition to mRNA, fMet-tRNA, and ribosomal subunits, the presence of three additional proteins (initiation factors IF1, IF2, and IF3) and at least one GTP molecule. The three initiation factors influence both the kinetics and the stability of ternary complex formation. IF1 is the smallest of the three factors. IF1 enhances the rate of 70S ribosome subunit association and dissociation and the interaction of 30S ribosomal subunit with IF2 and IF3. It stimulates 30S complex formation. In addition, by binding to the A-site of the 30S ribosomal subunit, IF1 may contribute to the fidelity of the selection of the initiation site of th
Probab=34.94 E-value=55 Score=21.31 Aligned_cols=21 Identities=33% Similarity=0.289 Sum_probs=13.3
Q ss_pred eeeCCEEEEEecCCCCeEeEE
Q 032297 70 VKAGDTVKVIAGCDKGKIGEI 90 (143)
Q Consensus 70 IkkGD~V~VIsG~dKGK~G~V 90 (143)
+..||.|.+---.+.+..|.|
T Consensus 41 ~~vGD~V~~~~~~~~~~~g~I 61 (64)
T cd04451 41 ILPGDRVKVELSPYDLTKGRI 61 (64)
T ss_pred cCCCCEEEEEEeecCCCEEEE
Confidence 689999988744322334544
No 114
>PRK10334 mechanosensitive channel MscS; Provisional
Probab=34.64 E-value=41 Score=28.54 Aligned_cols=60 Identities=12% Similarity=0.157 Sum_probs=33.9
Q ss_pred ceeeeCCEEEEEecCCCCeEeEEEEEEc--------cCCEEEEeceeeeeeeecCCcccCCceEEEEeeceeec
Q 032297 68 MHVKAGDTVKVIAGCDKGKIGEITKVFR--------HNSTVMVKDINLKTKHVKKREEEEQGQIIKLKCDALLK 133 (143)
Q Consensus 68 ~~IkkGD~V~VIsG~dKGK~G~V~~V~~--------k~n~ViVegvN~~kkhvKp~~~~~~GgIi~~E~PIhiS 133 (143)
-+++.||.|++ .|..|+|.+|.- ++..|+|-+-.+.+..+.-... ..-..++.+..+.|.
T Consensus 128 rpf~vGD~I~i-----~~~~G~V~~I~~r~T~i~t~d~~~v~IPNs~~~~~~i~N~s~-~~~rr~~~~v~V~y~ 195 (286)
T PRK10334 128 RPFRAGEYVDL-----GGVAGTVLSVQIFSTTMRTADGKIIVIPNGKIIAGNIINFSR-EPVRRNEFIIGVAYD 195 (286)
T ss_pred CCCCCCCEEEE-----CCEEEEEEEEEeEEEEEEcCCCCEEEEcchHhcCCeeEEcCC-CCeEEEEEEEEecCC
Confidence 34799999998 378999988863 4445566654443332222111 111234555555554
No 115
>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=34.40 E-value=59 Score=22.46 Aligned_cols=27 Identities=30% Similarity=0.369 Sum_probs=18.0
Q ss_pred ceeeeCCEEEEEecCCCCeEeEEEEEEccC
Q 032297 68 MHVKAGDTVKVIAGCDKGKIGEITKVFRHN 97 (143)
Q Consensus 68 ~~IkkGD~V~VIsG~dKGK~G~V~~V~~k~ 97 (143)
=.|++||+|.++-. +...+|.+|..++
T Consensus 29 G~i~~gd~v~i~P~---~~~~~V~sI~~~~ 55 (91)
T cd03693 29 GVLKPGMVVTFAPA---GVTGEVKSVEMHH 55 (91)
T ss_pred ceeecCCEEEECCC---CcEEEEEEEEECC
Confidence 45788888887754 3567777776553
No 116
>PRK11713 16S ribosomal RNA methyltransferase RsmE; Provisional
Probab=33.72 E-value=70 Score=25.92 Aligned_cols=31 Identities=23% Similarity=0.440 Sum_probs=23.5
Q ss_pred ccceeeeCCEEEEEecCCCCeEeEEEEEEcc
Q 032297 66 HKMHVKAGDTVKVIAGCDKGKIGEITKVFRH 96 (143)
Q Consensus 66 ~k~~IkkGD~V~VIsG~dKGK~G~V~~V~~k 96 (143)
.-+.++.||+|.|..|...=-.|+|..+.++
T Consensus 26 ~VlR~~~Gd~i~v~~g~g~~~~~~i~~i~~~ 56 (234)
T PRK11713 26 RVLRLKEGDELRLFDGDGGEYLAEITEIGKK 56 (234)
T ss_pred hhccCCCCCEEEEEeCCCCEEEEEEEEecCc
Confidence 4467899999999999753344788888654
No 117
>PRK06804 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=33.26 E-value=66 Score=27.32 Aligned_cols=28 Identities=36% Similarity=0.510 Sum_probs=22.7
Q ss_pred ceeeeCCEEEEEecC------------CCCeEeEEEEEEc
Q 032297 68 MHVKAGDTVKVIAGC------------DKGKIGEITKVFR 95 (143)
Q Consensus 68 ~~IkkGD~V~VIsG~------------dKGK~G~V~~V~~ 95 (143)
+-|++||.|.|+... +-|..|+.++|..
T Consensus 201 ~lV~rG~~V~Iva~~gg~~i~~~G~AL~~G~~Gd~IrVrN 240 (261)
T PRK06804 201 VLVERGQHVLMIAAQDGIEAQTLGIAQKNGRKGELIKVKN 240 (261)
T ss_pred cEEecCCEEEEEEecCCEEEEEEEEEccCCCCCCEEEEEE
Confidence 579999999998765 6678888888874
No 118
>cd04089 eRF3_II eRF3_II: domain II of the eukaryotic class II release factor (eRF3). In eukaryotes, translation termination is mediated by two interacting release factors, eRF1 and eRF3, which act as class I and II factors, respectively. eRF1 functions as an omnipotent release factor, decoding all three stop codons and triggering the release of the nascent peptide catalyzed by the ribsome. eRF3 is a GTPase, which enhances the termination efficiency by stimulating the eRF1 activity in a GTP-dependent manner. Sequence comparison of class II release factors with elongation factors shows that eRF3 is more similar to eEF1alpha whereas prokaryote RF3 is more similar to EF-G, implying that their precise function may differ. Only eukaryote RF3s are found in this group. Saccharomyces cerevisiae eRF3 (Sup35p) is a translation termination factor which is divided into three regions N, M and a C-terminal eEF1a-like region essential for translation termination. Sup35NM is a non-pathogenic prion-li
Probab=33.21 E-value=75 Score=21.46 Aligned_cols=26 Identities=19% Similarity=0.360 Sum_probs=16.2
Q ss_pred ceeeeCCEEEEEecCCCCeEeEEEEEEcc
Q 032297 68 MHVKAGDTVKVIAGCDKGKIGEITKVFRH 96 (143)
Q Consensus 68 ~~IkkGD~V~VIsG~dKGK~G~V~~V~~k 96 (143)
=.+++||+|.+.-. |+..+|.+|..+
T Consensus 24 G~i~~G~~v~i~P~---~~~~~V~si~~~ 49 (82)
T cd04089 24 GTIKKGDKLLVMPN---KTQVEVLSIYNE 49 (82)
T ss_pred eEEecCCEEEEeCC---CcEEEEEEEEEC
Confidence 34788888887654 345566665443
No 119
>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=33.17 E-value=73 Score=25.98 Aligned_cols=36 Identities=22% Similarity=0.238 Sum_probs=24.3
Q ss_pred ccceeeeCCEEEEEecCCCCeEeEEEEEEccCCEEE
Q 032297 66 HKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVM 101 (143)
Q Consensus 66 ~k~~IkkGD~V~VIsG~dKGK~G~V~~V~~k~n~Vi 101 (143)
+-+.++.||.|.|..|...=-.++|..+.++.-.+.
T Consensus 28 ~VlR~~~Gd~v~v~~g~g~~~~a~i~~~~~~~~~~~ 63 (240)
T TIGR00046 28 RVLRLKKGDKLKLLDGDGFIYHCEIKKISKKFVKCE 63 (240)
T ss_pred HcccCCCCCEEEEEeCCCCEEEEEEEEEcCCeEEEE
Confidence 346789999999999953223457877766543333
No 120
>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=32.97 E-value=85 Score=18.55 Aligned_cols=24 Identities=25% Similarity=0.333 Sum_probs=16.8
Q ss_pred ceeeeCCEEEEEecCCCCeEeEEEEEEccCCEEE
Q 032297 68 MHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVM 101 (143)
Q Consensus 68 ~~IkkGD~V~VIsG~dKGK~G~V~~V~~k~n~Vi 101 (143)
-.++.||+|.+ +|++++.+++.+.
T Consensus 40 ~~~~~G~~v~~----------~v~~~d~~~~~i~ 63 (65)
T cd00164 40 EVFKVGDEVEV----------KVLEVDPEKGRIS 63 (65)
T ss_pred hEeCCCCEEEE----------EEEEEcCCcCEEe
Confidence 34899999987 4666766665554
No 121
>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=32.48 E-value=83 Score=19.77 Aligned_cols=23 Identities=13% Similarity=0.238 Sum_probs=18.1
Q ss_pred eeeeCCEEEEEecCCCCeEeEEEEEEccCCEEE
Q 032297 69 HVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVM 101 (143)
Q Consensus 69 ~IkkGD~V~VIsG~dKGK~G~V~~V~~k~n~Vi 101 (143)
.++.||+|.|. |++|+.++.++.
T Consensus 45 ~~~~G~~v~v~----------v~~id~~~~~i~ 67 (69)
T cd05690 45 IYKKGQEVEAV----------VLNIDVERERIS 67 (69)
T ss_pred EECCCCEEEEE----------EEEEECCcCEEe
Confidence 47999999984 788888777664
No 122
>PF00575 S1: S1 RNA binding domain; InterPro: IPR003029 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The S1 domain was originally identified in ribosomal protein S1 but is found in a large number of RNA-associated proteins. The structure of the S1 RNA-binding domain from the Escherichia coli polynucleotide phosphorylase has been determined using NMR methods and consists of a five-stranded antiparallel beta barrel. Conserved residues on one face of the barrel and adjacent loops form the putative RNA-binding site []. The structure of the S1 domain is very similar to that of cold shock proteins. This suggests that they may both be derived from an ancient nucleic acid-binding protein []. More information about these proteins can be found at Protein of the Month: RNA Exosomes []. This entry does not include translation initiation factor IF-1 S1 domains.; GO: 0003723 RNA binding; PDB: 3L7Z_F 2JE6_I 2JEA_I 2JEB_I 1E3P_A 2Y0S_E 1WI5_A 2BH8_A 2CQO_A 2EQS_A ....
Probab=32.35 E-value=1e+02 Score=19.66 Aligned_cols=25 Identities=28% Similarity=0.356 Sum_probs=20.9
Q ss_pred ceeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEE
Q 032297 68 MHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMV 102 (143)
Q Consensus 68 ~~IkkGD~V~VIsG~dKGK~G~V~~V~~k~n~ViV 102 (143)
-.++.||+|.+. |++++.+++++.+
T Consensus 47 ~~~~~G~~v~v~----------v~~vd~~~~~i~l 71 (74)
T PF00575_consen 47 EVYKIGQTVRVK----------VIKVDKEKGRIRL 71 (74)
T ss_dssp GTCETTCEEEEE----------EEEEETTTTEEEE
T ss_pred cccCCCCEEEEE----------EEEEECCCCeEEE
Confidence 357999999875 8999999988876
No 123
>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=32.04 E-value=33 Score=21.49 Aligned_cols=14 Identities=29% Similarity=0.688 Sum_probs=10.3
Q ss_pred ccceeeeCCEEEEE
Q 032297 66 HKMHVKAGDTVKVI 79 (143)
Q Consensus 66 ~k~~IkkGD~V~VI 79 (143)
..+.+++||.|.|+
T Consensus 14 ~~Ls~~~Gd~i~v~ 27 (55)
T PF07653_consen 14 DELSFKKGDVIEVL 27 (55)
T ss_dssp TB-EB-TTEEEEEE
T ss_pred CceEEecCCEEEEE
Confidence 34678999999999
No 124
>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=31.85 E-value=1.1e+02 Score=19.58 Aligned_cols=24 Identities=21% Similarity=0.288 Sum_probs=17.3
Q ss_pred eeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEE
Q 032297 69 HVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMV 102 (143)
Q Consensus 69 ~IkkGD~V~VIsG~dKGK~G~V~~V~~k~n~ViV 102 (143)
.++.||.|.+ +|.+++..++++.+
T Consensus 49 ~~~~Gd~v~v----------kv~~~d~~~~~i~l 72 (76)
T cd04452 49 LVKVGRKEVV----------KVIRVDKEKGYIDL 72 (76)
T ss_pred eeCCCCEEEE----------EEEEEECCCCEEEE
Confidence 3799999998 36677776665544
No 125
>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=31.70 E-value=62 Score=20.72 Aligned_cols=29 Identities=14% Similarity=0.075 Sum_probs=23.1
Q ss_pred eeeCCEEEEEecCCCCeEeEEEEEEccCC
Q 032297 70 VKAGDTVKVIAGCDKGKIGEITKVFRHNS 98 (143)
Q Consensus 70 IkkGD~V~VIsG~dKGK~G~V~~V~~k~n 98 (143)
|..|++|.+.-+...-..++|+++..+++
T Consensus 1 ~~vG~~v~~~~~~~~~y~A~I~~~r~~~~ 29 (55)
T PF11717_consen 1 FEVGEKVLCKYKDGQWYEAKILDIREKNG 29 (55)
T ss_dssp --TTEEEEEEETTTEEEEEEEEEEEECTT
T ss_pred CCcCCEEEEEECCCcEEEEEEEEEEecCC
Confidence 46799999999777888999999988663
No 126
>PRK00276 infA translation initiation factor IF-1; Validated
Probab=31.69 E-value=94 Score=21.01 Aligned_cols=24 Identities=29% Similarity=0.292 Sum_probs=15.4
Q ss_pred ceeeeCCEEEEEecCCCCeEeEEE
Q 032297 68 MHVKAGDTVKVIAGCDKGKIGEIT 91 (143)
Q Consensus 68 ~~IkkGD~V~VIsG~dKGK~G~V~ 91 (143)
..+..||.|.+---.+-...|.|+
T Consensus 45 i~i~vGD~V~ve~~~~~~~~g~Iv 68 (72)
T PRK00276 45 IRILPGDKVTVELSPYDLTKGRIT 68 (72)
T ss_pred cccCCCCEEEEEEcccCCCeEEEE
Confidence 336899999987544334446664
No 127
>cd03694 GTPBP_II Domain II of the GP-1 family of GTPase. This group includes proteins similar to GTPBP1 and GTPBP2. GTPB1 is structurally, related to elongation factor 1 alpha, a key component of protein biosynthesis machinery. Immunohistochemical analyses on mouse tissues revealed that GTPBP1 is expressed in some neurons and smooth muscle cells of various organs as well as macrophages. Immunofluorescence analyses revealed that GTPBP1 is localized exclusively in cytoplasm and shows a diffuse granular network forming a gradient from the nucleus to the periphery of the cells in smooth muscle cell lines and macrophages. No significant difference was observed in the immune response to protein antigen between mutant mice and wild-type mice, suggesting normal function of antigen-presenting cells of the mutant mice. The absence of an eminent phenotype in GTPBP1-deficient mice may be due to functional compensation by GTPBP2, which is similar to GTPBP1 in structure and tissue distribution.
Probab=31.06 E-value=91 Score=21.37 Aligned_cols=31 Identities=19% Similarity=0.216 Sum_probs=20.1
Q ss_pred cceeeeCCEEEEEecCC-CCeEeEEEEEEccC
Q 032297 67 KMHVKAGDTVKVIAGCD-KGKIGEITKVFRHN 97 (143)
Q Consensus 67 k~~IkkGD~V~VIsG~d-KGK~G~V~~V~~k~ 97 (143)
.=.+++||.|.+.-..+ +.+..+|.+|..++
T Consensus 24 ~G~v~~g~~v~~~P~~~g~~~~~~V~sI~~~~ 55 (87)
T cd03694 24 KGVIRLGDTLLLGPDQDGSFRPVTVKSIHRNR 55 (87)
T ss_pred cCEEeCCCEEEECCCCCCCEeEEEEEEEEECC
Confidence 34578999888755432 12677888776553
No 128
>cd05703 S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: 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 12 (hs12) and S. cerevisiae S1 repeat 9 (sc9). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=31.06 E-value=89 Score=20.78 Aligned_cols=25 Identities=12% Similarity=0.264 Sum_probs=20.2
Q ss_pred eeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEe
Q 032297 69 HVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 103 (143)
Q Consensus 69 ~IkkGD~V~VIsG~dKGK~G~V~~V~~k~n~ViVe 103 (143)
.++.||.|++ +|+.|++++.+|.+.
T Consensus 46 ~~~vG~~v~~----------kV~~id~~~~~i~Ls 70 (73)
T cd05703 46 KFPIGQALKA----------KVVGVDKEHKLLRLS 70 (73)
T ss_pred hCCCCCEEEE----------EEEEEeCCCCEEEEE
Confidence 3789999975 599999998888653
No 129
>PF09926 DUF2158: Uncharacterized small protein (DUF2158); InterPro: IPR019226 This entry represents a family of predominantly prokaryotic proteins with no known function.
Probab=30.97 E-value=28 Score=23.01 Aligned_cols=15 Identities=33% Similarity=0.581 Sum_probs=12.0
Q ss_pred eeeCCEEEEEecCCC
Q 032297 70 VKAGDTVKVIAGCDK 84 (143)
Q Consensus 70 IkkGD~V~VIsG~dK 84 (143)
++.||.|+..+|--+
T Consensus 1 f~~GDvV~LKSGGp~ 15 (53)
T PF09926_consen 1 FKIGDVVQLKSGGPR 15 (53)
T ss_pred CCCCCEEEEccCCCC
Confidence 468999999999533
No 130
>cd01736 LSm14_N LSm14 (also known as RAP55) belongs to a family of Sm-like proteins that associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold, containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet, that associates with other Sm proteins to form hexameric and heptameric ring structures. In addition to the N-terminal Sm-like domain, LSm14 has an uncharacterized C-terminal domain containing a conserved DFDF box. In Xenopus laevis, LSm14 is an oocyte-specific constituent of ribonucleoprotein particles.
Probab=30.84 E-value=1.3e+02 Score=21.35 Aligned_cols=36 Identities=19% Similarity=0.327 Sum_probs=33.0
Q ss_pred eeCCEEEEEecCCCCeEeEEEEEEccCCEEEEecee
Q 032297 71 KAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDIN 106 (143)
Q Consensus 71 kkGD~V~VIsG~dKGK~G~V~~V~~k~n~ViVegvN 106 (143)
.-|.++.+|+=.|.--+|..-.|+.++++|.+++|-
T Consensus 4 ~IG~~isLISk~~iRYeGiL~~In~~~sTi~L~nVr 39 (74)
T cd01736 4 YIGSKISLISKSDIRYEGILYTINTEDSTIALKNVR 39 (74)
T ss_pred ccCceEEEEecCCcEEEEEEEeeccccCEEEeeeeE
Confidence 468999999999999999999999999999999863
No 131
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=30.77 E-value=96 Score=22.75 Aligned_cols=28 Identities=25% Similarity=0.269 Sum_probs=20.4
Q ss_pred ccceeeeCCEEEEEecCCCCeEeEEEEE
Q 032297 66 HKMHVKAGDTVKVIAGCDKGKIGEITKV 93 (143)
Q Consensus 66 ~k~~IkkGD~V~VIsG~dKGK~G~V~~V 93 (143)
+...|..||+|.|---++-=..|.|+--
T Consensus 43 ~rIrIl~GD~V~VE~spYDltkGRIiyR 70 (87)
T PRK12442 43 HRIRILAGDRVTLELSPYDLTKGRINFR 70 (87)
T ss_pred eeEEecCCCEEEEEECcccCCceeEEEE
Confidence 3566899999999877766666777433
No 132
>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=30.67 E-value=48 Score=19.27 Aligned_cols=16 Identities=25% Similarity=0.538 Sum_probs=12.8
Q ss_pred cceeeeCCEEEEEecC
Q 032297 67 KMHVKAGDTVKVIAGC 82 (143)
Q Consensus 67 k~~IkkGD~V~VIsG~ 82 (143)
.+.+.+||.|.|+...
T Consensus 18 ~l~~~~Gd~v~v~~~~ 33 (58)
T smart00326 18 ELSFKKGDIITVLEKS 33 (58)
T ss_pred CCCCCCCCEEEEEEcC
Confidence 3457999999999775
No 133
>PF01191 RNA_pol_Rpb5_C: RNA polymerase Rpb5, C-terminal domain; InterPro: IPR000783 Prokaryotes contain a single DNA-dependent RNA polymerase (RNAP; 2.7.7.6 from EC) that is responsible for the transcription of all genes, while eukaryotes have three classes of RNAPs (I-III) that transcribe different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. Certain subunits of RNAPs, including RPB5 (POLR2E in mammals), are common to all three eukaryotic polymerases. RPB5 plays a role in the transcription activation process. Eukaryotic RPB5 has a bipartite structure consisting of a unique N-terminal region (IPR005571 from INTERPRO), plus a C-terminal region that is structurally homologous to the prokaryotic RPB5 homologue, subunit H (gene rpoH) [, , , ]. This entry represents prokaryotic subunit H and the C-terminal domain of eukaryotic RPB5, which share a two-layer alpha/beta fold, with a core structure of beta/alpha/beta/alpha/beta(2). ; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 1EIK_A 2Y0S_Z 1DZF_A 3GTG_E 2VUM_E 3GTP_E 3GTO_E 3S17_E 3S1R_E 1I3Q_E ....
Probab=30.46 E-value=29 Score=24.47 Aligned_cols=27 Identities=37% Similarity=0.603 Sum_probs=15.1
Q ss_pred ccCCCCCcccc-------cceeeeCCEEEEEecC
Q 032297 56 ECKPNSLPVLH-------KMHVKAGDTVKVIAGC 82 (143)
Q Consensus 56 ~~kpn~lp~~~-------k~~IkkGD~V~VIsG~ 82 (143)
.+++..||.+. .+-+++||.|+|++-.
T Consensus 28 ~i~~~qLP~I~~~DPv~r~~g~k~GdVvkI~R~S 61 (74)
T PF01191_consen 28 NIKPEQLPKILSSDPVARYLGAKPGDVVKIIRKS 61 (74)
T ss_dssp T--TTCSSEEETTSHHHHHTT--TTSEEEEEEEE
T ss_pred CCChhhCCcccccChhhhhcCCCCCCEEEEEecC
Confidence 45666666543 3578888888887653
No 134
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=30.18 E-value=1.3e+02 Score=18.07 Aligned_cols=24 Identities=29% Similarity=0.494 Sum_probs=18.3
Q ss_pred eeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEE
Q 032297 69 HVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMV 102 (143)
Q Consensus 69 ~IkkGD~V~VIsG~dKGK~G~V~~V~~k~n~ViV 102 (143)
.++.||+|.+ .|.+++.+++++.+
T Consensus 46 ~~~~G~~v~~----------~V~~~~~~~~~i~l 69 (72)
T smart00316 46 VLKVGDEVKV----------KVLSVDEEKGRIIL 69 (72)
T ss_pred eecCCCEEEE----------EEEEEeCCCCEEEE
Confidence 4899999987 47778777666655
No 135
>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=30.00 E-value=1e+02 Score=20.25 Aligned_cols=24 Identities=25% Similarity=0.217 Sum_probs=19.0
Q ss_pred eeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEE
Q 032297 69 HVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMV 102 (143)
Q Consensus 69 ~IkkGD~V~VIsG~dKGK~G~V~~V~~k~n~ViV 102 (143)
.++.||.|.+ +|+.+++++.++.+
T Consensus 46 ~~~vG~~v~~----------kV~~id~~~~~i~l 69 (71)
T cd05696 46 PFKAGTTHKA----------RIIGYSPMDGLLQL 69 (71)
T ss_pred ccCCCCEEEE----------EEEEEeCCCCEEEE
Confidence 3789999976 48888888877765
No 136
>PRK11642 exoribonuclease R; Provisional
Probab=29.89 E-value=83 Score=30.81 Aligned_cols=35 Identities=23% Similarity=0.317 Sum_probs=24.8
Q ss_pred eeeeCCEEEEE-ecCC--CCeEeEEEEEEccCCEEEEe
Q 032297 69 HVKAGDTVKVI-AGCD--KGKIGEITKVFRHNSTVMVK 103 (143)
Q Consensus 69 ~IkkGD~V~VI-sG~d--KGK~G~V~~V~~k~n~ViVe 103 (143)
+..-||+|.|. .+.+ +..+|+|++|....+.-+|-
T Consensus 117 ~A~~GD~V~v~i~~~~~~~r~eg~Vv~IleR~~~~~vG 154 (813)
T PRK11642 117 TCIHGDQVLAQPLGADRKGRREARIVRVLVPKTSQIVG 154 (813)
T ss_pred cCCCCCEEEEEEccCCCCCCcEEEEEEEEecCCCEEEE
Confidence 45569999775 4422 33599999999888776654
No 137
>cd03697 EFTU_II EFTU_II: Elongation factor Tu domain II. Elongation factors Tu (EF-Tu) are three-domain GTPases with an essential function in the elongation phase of mRNA translation. The GTPase center of EF-Tu is in the N-terminal domain (domain I), also known as the catalytic or G-domain. The G-domain is composed of about 200 amino acid residues, arranged into a predominantly parallel six-stranded beta-sheet core surrounded by seven a-helices. Non-catalytic domains II and III are beta-barrels of seven and six, respectively, antiparallel beta-strands that share an extended interface. Either non-catalytic domain is composed of about 100 amino acid residues. EF-Tu proteins exist in two principal conformations: in a compact one, EF-Tu*GTP, with tight interfaces between all three domains and a high affinity for aminoacyl-tRNA, and in an open one, EF-Tu*GDP, with essentially no G-domain-domain II interactions and a low affinity for aminoacyl-tRNA. EF-Tu has approximately a 100-fold higher
Probab=29.78 E-value=71 Score=21.80 Aligned_cols=29 Identities=17% Similarity=0.172 Sum_probs=19.2
Q ss_pred ceeeeCCEEEEEecCCCCeEeEEEEEEccC
Q 032297 68 MHVKAGDTVKVIAGCDKGKIGEITKVFRHN 97 (143)
Q Consensus 68 ~~IkkGD~V~VIsG~dKGK~G~V~~V~~k~ 97 (143)
=.+++||+|.++-.. .+...+|.+|..+.
T Consensus 25 G~v~~gd~v~~~p~~-~~~~~~V~si~~~~ 53 (87)
T cd03697 25 GTIKVGDEVEIVGFG-ETLKTTVTGIEMFR 53 (87)
T ss_pred CCCccCCEEEEeCCC-CCceEEEEEEEECC
Confidence 357889998887532 24667777776543
No 138
>TIGR02594 conserved hypothetical protein TIGR02594. Members of this protein family known so far are restricted to the bacteria, and for the most to the proteobacteria. The function is unknown.
Probab=29.71 E-value=1.1e+02 Score=22.99 Aligned_cols=35 Identities=20% Similarity=0.190 Sum_probs=26.9
Q ss_pred eeCCEEEEEecCCCCeEeEEEEEEccCCEEEEecee
Q 032297 71 KAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDIN 106 (143)
Q Consensus 71 kkGD~V~VIsG~dKGK~G~V~~V~~k~n~ViVegvN 106 (143)
++||.|..-.+. .|.+|.++....++++|++=|=|
T Consensus 75 ~~GDiv~f~~~~-~~HVGi~~g~~~~~g~i~~lgGN 109 (129)
T TIGR02594 75 AYGCIAVKRRGG-GGHVGFVVGKDKQTGTIIVLGGN 109 (129)
T ss_pred CccEEEEEECCC-CCEEEEEEeEcCCCCEEEEeeCC
Confidence 899999876554 78999999988877776654444
No 139
>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=29.62 E-value=97 Score=18.91 Aligned_cols=22 Identities=23% Similarity=0.371 Sum_probs=16.5
Q ss_pred eeeCCEEEEEecCCCCeEeEEEEEEccCCEEE
Q 032297 70 VKAGDTVKVIAGCDKGKIGEITKVFRHNSTVM 101 (143)
Q Consensus 70 IkkGD~V~VIsG~dKGK~G~V~~V~~k~n~Vi 101 (143)
++.||.|.+. |.+++..+.++.
T Consensus 45 ~~~Gd~v~v~----------i~~vd~~~~~i~ 66 (68)
T cd05685 45 VSVGDIVEVK----------VISIDEERGRIS 66 (68)
T ss_pred cCCCCEEEEE----------EEEEECCCCEEe
Confidence 7899999984 777777666654
No 140
>cd04719 BAH_Orc1p_animal BAH, or Bromo Adjacent Homology domain, as present in animal homologs of Saccharomyces cerevisiae Orc1p. Orc1 is part of the Yeast Sir1-origin recognition complex. The Orc1p BAH doman functions in epigenetic silencing. In vertebrates, a similar ORC protein complex exists, which has been shown essential for DNA replication in Xenopus laevis. 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=29.56 E-value=86 Score=23.98 Aligned_cols=30 Identities=17% Similarity=0.358 Sum_probs=24.8
Q ss_pred ceeeeCCEEEEEecC-CCCeEeEEEEEEccC
Q 032297 68 MHVKAGDTVKVIAGC-DKGKIGEITKVFRHN 97 (143)
Q Consensus 68 ~~IkkGD~V~VIsG~-dKGK~G~V~~V~~k~ 97 (143)
.+|+.||-|.|...+ +.=-+|+|.+++...
T Consensus 2 ~~i~vGd~VlI~~~d~~~~yVAkI~~i~e~~ 32 (128)
T cd04719 2 LTIEVGDFVLIEGEDADGPDVARILHLYEDG 32 (128)
T ss_pred eEEecCCEEEEECCCCCCCcEeeehhhhccc
Confidence 468999999999887 666789998888765
No 141
>COG5164 SPT5 Transcription elongation factor [Transcription]
Probab=29.55 E-value=58 Score=30.95 Aligned_cols=33 Identities=30% Similarity=0.454 Sum_probs=27.5
Q ss_pred eeCCEEEEEecCCCCeEeEEEEEEccCCEEEEe
Q 032297 71 KAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 103 (143)
Q Consensus 71 kkGD~V~VIsG~dKGK~G~V~~V~~k~n~ViVe 103 (143)
.-|-+|.|-.|.+||.-|.|..|++..-+|-+.
T Consensus 353 aigktVrIr~g~yKG~lGVVKdv~~~~arVeLh 385 (607)
T COG5164 353 AIGKTVRIRCGEYKGHLGVVKDVDRNIARVELH 385 (607)
T ss_pred ccCceEEEeecccccccceeeeccCceEEEEEe
Confidence 567899999999999999999998776555443
No 142
>PF14001 YdfZ: YdfZ protein
Probab=29.33 E-value=1.3e+02 Score=21.06 Aligned_cols=42 Identities=21% Similarity=0.366 Sum_probs=30.0
Q ss_pred ccCCCCCcccccceeeeCCEEEEEecCCCCeEeEEEEEEccC---------CEEEEecee
Q 032297 56 ECKPNSLPVLHKMHVKAGDTVKVIAGCDKGKIGEITKVFRHN---------STVMVKDIN 106 (143)
Q Consensus 56 ~~kpn~lp~~~k~~IkkGD~V~VIsG~dKGK~G~V~~V~~k~---------n~ViVegvN 106 (143)
.|..|+.| |..|-+|.| +| -|.+|.|..|..++ .-|.+||++
T Consensus 2 tYDRnRN~------i~~G~rVMi-ag--tG~~gvikAih~~gl~~eq~rR~kcVel~g~~ 52 (64)
T PF14001_consen 2 TYDRNRNA------ITTGSRVMI-AG--TGATGVIKAIHADGLTAEQIRRAKCVELEGCE 52 (64)
T ss_pred ccccccCc------CCCCCEEEE-cC--CCcccEEeeeecCCCCHHHhhhccEEEEeCCC
Confidence 35566666 688999876 44 49999999998653 446666665
No 143
>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=29.31 E-value=1.1e+02 Score=19.53 Aligned_cols=23 Identities=22% Similarity=0.241 Sum_probs=17.5
Q ss_pred eeeCCEEEEEecCCCCeEeEEEEEEccCCEEEE
Q 032297 70 VKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMV 102 (143)
Q Consensus 70 IkkGD~V~VIsG~dKGK~G~V~~V~~k~n~ViV 102 (143)
++.||+|.+ +|++++.++.++.+
T Consensus 48 ~~~Gd~v~~----------~V~~~d~~~~~i~l 70 (73)
T cd05706 48 FKKNDIVRA----------CVLSVDVPNKKIAL 70 (73)
T ss_pred cCCCCEEEE----------EEEEEeCCCCEEEE
Confidence 688999987 47778777766654
No 144
>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=29.09 E-value=1.1e+02 Score=24.24 Aligned_cols=29 Identities=17% Similarity=0.149 Sum_probs=23.7
Q ss_pred eeeCCEEEEEecCC-CCeEeEEEEEEccCC
Q 032297 70 VKAGDTVKVIAGCD-KGKIGEITKVFRHNS 98 (143)
Q Consensus 70 IkkGD~V~VIsG~d-KGK~G~V~~V~~k~n 98 (143)
++.||-|.|.+++. -..+|.|.++....+
T Consensus 4 yrvGD~Vy~~~~~~~Py~I~rI~e~~~~~~ 33 (164)
T cd04709 4 YRVGDYVYFESSPNNPYLIRRIEELNKTAR 33 (164)
T ss_pred EecCCEEEEECCCCCCCEEEEEEEEEeCCC
Confidence 78999999998864 378999999886543
No 145
>PF13144 SAF_2: SAF-like
Probab=28.97 E-value=82 Score=24.40 Aligned_cols=32 Identities=34% Similarity=0.475 Sum_probs=23.1
Q ss_pred ccceeeeCCEEEEEecC------------CCCeEeEEEEEEccC
Q 032297 66 HKMHVKAGDTVKVIAGC------------DKGKIGEITKVFRHN 97 (143)
Q Consensus 66 ~k~~IkkGD~V~VIsG~------------dKGK~G~V~~V~~k~ 97 (143)
..+-|++||.|.|+.-. .-|..|++++|...+
T Consensus 136 ~~~~V~~G~~V~v~~~~g~i~i~~~g~Al~~G~~G~~I~V~N~~ 179 (196)
T PF13144_consen 136 PPPLVKRGDIVTVIARSGGISISTEGKALEDGALGDTIRVKNLS 179 (196)
T ss_pred cceecCCCCEEEEEEEeCCEEEEEEEEEccCCCCCCEEEEEECC
Confidence 45679999999987543 567777777776644
No 146
>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=28.32 E-value=1.1e+02 Score=19.35 Aligned_cols=23 Identities=35% Similarity=0.550 Sum_probs=16.6
Q ss_pred eeeCCEEEEEecCCCCeEeEEEEEEccCCEEEE
Q 032297 70 VKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMV 102 (143)
Q Consensus 70 IkkGD~V~VIsG~dKGK~G~V~~V~~k~n~ViV 102 (143)
++.||+|++. |+++++++.++.+
T Consensus 45 ~~~Gd~i~~~----------i~~~~~~~~~i~l 67 (70)
T cd05687 45 VKVGDEVEVY----------VLRVEDEEGNVVL 67 (70)
T ss_pred CCCCCEEEEE----------EEEEECCCCeEEE
Confidence 7899999876 6677766555554
No 147
>KOG4315 consensus G-patch nucleic acid binding protein [General function prediction only]
Probab=27.97 E-value=29 Score=32.18 Aligned_cols=36 Identities=25% Similarity=0.364 Sum_probs=30.5
Q ss_pred eeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEece
Q 032297 70 VKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDI 105 (143)
Q Consensus 70 IkkGD~V~VIsG~dKGK~G~V~~V~~k~n~ViVegv 105 (143)
=.-||.|.|++|+.+|+.|--++-++.+.+..|..+
T Consensus 394 r~~Ge~vmvv~gkhkg~~g~llskd~~Ke~~~v~~~ 429 (455)
T KOG4315|consen 394 RRGGEKVMVVSGKHKGVYGSLLSKDLDKETGVVRLV 429 (455)
T ss_pred cccCceeEEEecccccchhhhhhhhhhhhhcceecc
Confidence 478999999999999999999888888777766543
No 148
>cd04370 BAH BAH, or Bromo Adjacent Homology domain (also called ELM1 and BAM for Bromo Adjacent Motif). BAH domains have first been described as domains found in the polybromo protein and Yeast Rsc1/Rsc2 (Remodeling of the Structure of Chromatin). They also occur in mammalian DNA methyltransferases and the MTA1 subunits of histone deacetylase complexes. A BAH domain is also found in Yeast Sir3p and in the origin receptor complex protein 1 (Orc1p), where it was found to interact with the N-terminal lobe of the silence information regulator 1 protein (Sir1p), confirming the initial hypothesis that BAH plays a role in protein-protein interactions.
Probab=27.89 E-value=1.4e+02 Score=20.38 Aligned_cols=30 Identities=20% Similarity=0.287 Sum_probs=24.3
Q ss_pred eeeeCCEEEEEecCC----CCeEeEEEEEEccCC
Q 032297 69 HVKAGDTVKVIAGCD----KGKIGEITKVFRHNS 98 (143)
Q Consensus 69 ~IkkGD~V~VIsG~d----KGK~G~V~~V~~k~n 98 (143)
.++.||.|.|-...+ .=-+|.|.++....+
T Consensus 3 ~y~vgd~V~v~~~~~~~~~~~~i~~I~~i~~~~~ 36 (123)
T cd04370 3 TYEVGDSVYVEPDDSIKSDPPYIARIEELWEDTN 36 (123)
T ss_pred EEecCCEEEEecCCcCCCCCCEEEEEeeeeECCC
Confidence 478899999999874 456999999998754
No 149
>PF11948 DUF3465: Protein of unknown function (DUF3465); InterPro: IPR021856 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 131 to 151 amino acids in length. This protein has a conserved HWTH sequence motif.
Probab=27.85 E-value=37 Score=26.58 Aligned_cols=18 Identities=17% Similarity=0.444 Sum_probs=15.4
Q ss_pred Ccccccce-eeeCCEEEEE
Q 032297 62 LPVLHKMH-VKAGDTVKVI 79 (143)
Q Consensus 62 lp~~~k~~-IkkGD~V~VI 79 (143)
++++++++ +++||+|.+.
T Consensus 77 IDlaprip~l~~GD~V~f~ 95 (131)
T PF11948_consen 77 IDLAPRIPWLQKGDQVEFY 95 (131)
T ss_pred cCccccCcCcCCCCEEEEE
Confidence 67778888 9999999874
No 150
>cd04716 BAH_plantDCM_I BAH, or Bromo Adjacent Homology domain, first copy present in DNA (Cytosine-5)-methyltransferases (DCM) from plants. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the genome. These effects include transcriptional repression via inhibition of transcription factor binding, the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting, and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability. 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=27.54 E-value=1.3e+02 Score=22.63 Aligned_cols=32 Identities=25% Similarity=0.334 Sum_probs=24.7
Q ss_pred eeeCCEEEEEecC-CCCeEeEEEEEEcc-CCEEE
Q 032297 70 VKAGDTVKVIAGC-DKGKIGEITKVFRH-NSTVM 101 (143)
Q Consensus 70 IkkGD~V~VIsG~-dKGK~G~V~~V~~k-~n~Vi 101 (143)
++.||-|.|.++. ..--+|+|.++... ++...
T Consensus 4 ~~lgD~V~v~~~~~~~~yi~rI~~i~e~~~g~~~ 37 (122)
T cd04716 4 YNLGDDAYVQGGEGEEPFICKITEFFEGTDGKTY 37 (122)
T ss_pred EEcCCEEEEECCCCCCCEEEEEEEEEEcCCCceE
Confidence 6889999999986 45569999999875 34344
No 151
>COG2002 AbrB Regulators of stationary/sporulation gene expression [Transcription]
Probab=26.82 E-value=43 Score=23.53 Aligned_cols=22 Identities=27% Similarity=0.576 Sum_probs=18.8
Q ss_pred cccceeeeCCEEEEEecCCCCe
Q 032297 65 LHKMHVKAGDTVKVIAGCDKGK 86 (143)
Q Consensus 65 ~~k~~IkkGD~V~VIsG~dKGK 86 (143)
...+-|+.||.|.++...|.|+
T Consensus 23 R~~lgi~~Gd~lei~~~~~~~~ 44 (89)
T COG2002 23 REALGIKEGDVLEIIVDGDGGR 44 (89)
T ss_pred HHHhCCCCCCEEEEEEeCCCCE
Confidence 3456699999999999998888
No 152
>PRK12786 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=26.79 E-value=88 Score=27.44 Aligned_cols=37 Identities=22% Similarity=0.372 Sum_probs=27.3
Q ss_pred cceeeeCCEEEEEecC------------CCCeEeEEEEEE-ccCCEEEEec
Q 032297 67 KMHVKAGDTVKVIAGC------------DKGKIGEITKVF-RHNSTVMVKD 104 (143)
Q Consensus 67 k~~IkkGD~V~VIsG~------------dKGK~G~V~~V~-~k~n~ViVeg 104 (143)
-+-|++||.|.|+.-. .-|..|+.++|. ..++++ |.+
T Consensus 256 p~lV~rGd~V~i~~~~ggl~v~~~G~ALe~G~~Gd~IrV~N~~S~ki-v~g 305 (338)
T PRK12786 256 PDLVQRGQLVTLIYQTPGIYLTARGKALEDGAEGDVVRVLNLQSKRT-VTG 305 (338)
T ss_pred ccEEcCCCEEEEEEEcCCEEEEEEEEEccccCCCCEEEEEECCCCCE-EEE
Confidence 4679999999998643 678899999994 555554 444
No 153
>PRK12289 GTPase RsgA; Reviewed
Probab=26.52 E-value=1.2e+02 Score=26.50 Aligned_cols=32 Identities=28% Similarity=0.323 Sum_probs=24.4
Q ss_pred eeeCCEEEEEecCCCCeEeEEEEEEccCCEEE
Q 032297 70 VKAGDTVKVIAGCDKGKIGEITKVFRHNSTVM 101 (143)
Q Consensus 70 IkkGD~V~VIsG~dKGK~G~V~~V~~k~n~Vi 101 (143)
+.+||.|.+-.-.+.+..|.|.+|.+.+|.+.
T Consensus 52 ~~vGD~V~~~~~~~~~~~~~I~~vlpR~~~L~ 83 (352)
T PRK12289 52 VMVGDRVIVEEPDWQGQRGAIAEVLPRKTELD 83 (352)
T ss_pred cccCCEEEEeecCCCCCceEEEEEecccccee
Confidence 58999998854333456799999999988664
No 154
>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=26.30 E-value=98 Score=18.78 Aligned_cols=24 Identities=17% Similarity=0.080 Sum_probs=16.7
Q ss_pred eeeCCEEEEEec---CCCCeEeEEEEE
Q 032297 70 VKAGDTVKVIAG---CDKGKIGEITKV 93 (143)
Q Consensus 70 IkkGD~V~VIsG---~dKGK~G~V~~V 93 (143)
+..||+|.+-.- ..++.++.|.+|
T Consensus 37 ~~~Gd~V~~~i~~~~~~~~~~a~~v~~ 63 (64)
T smart00357 37 LREGDEVEFKVVSPRGGGKPEAENVVK 63 (64)
T ss_pred CCCCCEEEEEEEEccCCCCcEEEEEEe
Confidence 678999988642 345667777765
No 155
>TIGR00008 infA translation initiation factor IF-1. This family consists of translation initiation factor IF-1 as found in bacteria and chloroplasts. This protein, about 70 residues in length, consists largely of an S1 RNA binding domain (pfam00575).
Probab=26.05 E-value=93 Score=21.62 Aligned_cols=24 Identities=29% Similarity=0.267 Sum_probs=17.2
Q ss_pred cceeeeCCEEEEEecCCCCeEeEE
Q 032297 67 KMHVKAGDTVKVIAGCDKGKIGEI 90 (143)
Q Consensus 67 k~~IkkGD~V~VIsG~dKGK~G~V 90 (143)
+..|..||+|.|--=++-=..|.|
T Consensus 42 rI~I~~GD~V~Ve~spyd~tkgrI 65 (68)
T TIGR00008 42 YIRILPGDKVKVELSPYDLTRGRI 65 (68)
T ss_pred cEEECCCCEEEEEECcccCCcEeE
Confidence 566899999999766655445555
No 156
>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=25.99 E-value=1.5e+02 Score=18.67 Aligned_cols=24 Identities=38% Similarity=0.554 Sum_probs=18.3
Q ss_pred eeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEE
Q 032297 69 HVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMV 102 (143)
Q Consensus 69 ~IkkGD~V~VIsG~dKGK~G~V~~V~~k~n~ViV 102 (143)
.++.||+|.+ +|++++.+++.+.+
T Consensus 44 ~~~~Gd~v~~----------~v~~~d~~~~~i~l 67 (73)
T cd05691 44 RFKVGDEVEA----------KITNVDRKNRKISL 67 (73)
T ss_pred ccCCCCEEEE----------EEEEEeCCCCEEEE
Confidence 3789999987 48888887766654
No 157
>cd04091 mtEFG1_II_like mtEFG1_C: C-terminus of mitochondrial Elongation factor G1 (mtEFG1)-like proteins found in eukaryotes. Eukaryotic cells harbor 2 protein synthesis systems: one localized in the cytoplasm, the other in the mitochondria. Most factors regulating mitochondrial protein synthesis are encoded by nuclear genes, translated in the cytoplasm, and then transported to the mitochondria. The eukaryotic system of elongation factor (EF) components is more complex than that in prokaryotes, with both cytoplasmic and mitochondrial elongation factors and multiple isoforms being expressed in certain species. Eukaryotic EF-2 operates in the cytosolic protein synthesis machinery of eukaryotes, EF-Gs in protein synthesis in bacteria. Eukaryotic mtEFG1 proteins show significant homology to bacterial EF-Gs. Mutants in yeast mtEFG1 have impaired mitochondrial protein synthesis, respiratory defects and a tendency to lose mitochondrial DNA. There are two forms of mtEFG present in mammals
Probab=25.94 E-value=1.1e+02 Score=20.37 Aligned_cols=13 Identities=31% Similarity=0.432 Sum_probs=10.5
Q ss_pred ceeeeCCEEEEEe
Q 032297 68 MHVKAGDTVKVIA 80 (143)
Q Consensus 68 ~~IkkGD~V~VIs 80 (143)
=.|++||+|....
T Consensus 24 G~lk~gd~v~~~~ 36 (81)
T cd04091 24 GKLKKGDTIYNVR 36 (81)
T ss_pred CEEcCCCEEEEcC
Confidence 3688999998876
No 158
>PF02887 PK_C: Pyruvate kinase, alpha/beta domain; InterPro: IPR015795 Pyruvate kinase (2.7.1.40 from EC) (PK) catalyses the final step in glycolysis [], the conversion of phosphoenolpyruvate to pyruvate with concomitant phosphorylation of ADP to ATP: ADP + phosphoenolpyruvate = ATP + pyruvate The enzyme, which is found in all living organisms, requires both magnesium and potassium ions for its activity. In vertebrates, there are four tissue-specific isozymes: L (liver), R (red cells), M1 (muscle, heart and brain), and M2 (early foetal tissue). In plants, PK exists as cytoplasmic and plastid isozymes, while most bacteria and lower eukaryotes have one form, except in certain bacteria, such as Escherichia coli, that have two isozymes. All isozymes appear to be tetramers of identical subunits of ~500 residues. PK helps control the rate of glycolysis, along with phosphofructokinase (IPR000023 from INTERPRO) and hexokinase (IPR001312 from INTERPRO). PK possesses allosteric sites for numerous effectors, yet the isozymes respond differently, in keeping with their different tissue distributions []. The activity of L-type (liver) PK is increased by fructose-1,6-bisphosphate (F1,6BP) and lowered by ATP and alanine (gluconeogenic precursor), therefore when glucose levels are high, glycolysis is promoted, and when levels are low, gluconeogenesis is promoted. L-type PK is also hormonally regulated, being activated by insulin and inhibited by glucagon, which covalently modifies the PK enzyme. M1-type (muscle, brain) PK is inhibited by ATP, but F1,6BP and alanine have no effect, which correlates with the function of muscle and brain, as opposed to the liver. The structure of several pyruvate kinases from various organisms have been determined [, ]. The protein comprises three-four domains: a small N-terminal helical domain (absent in bacterial PK), a beta/alpha-barrel domain, a beta-barrel domain (inserted within the beta/alpha-barrel domain), and a 3-layer alpha/beta/alpha sandwich domain. This entry represents the 3-layer alpha/beta/alpha sandwich domain. This domain has a similar topology to the archaeal hypothetical protein, MTH1675 from Methanobacterium thermoautotrophicum.; PDB: 3QTG_B 1VP8_A 1T57_C 3N25_A 1AQF_C 2G50_B 1F3X_G 1A5U_F 1A49_E 1F3W_C ....
Probab=25.88 E-value=35 Score=24.45 Aligned_cols=20 Identities=45% Similarity=0.630 Sum_probs=14.5
Q ss_pred eeeeCCEEEEEecCCCCeEe
Q 032297 69 HVKAGDTVKVIAGCDKGKIG 88 (143)
Q Consensus 69 ~IkkGD~V~VIsG~dKGK~G 88 (143)
.+.+||.|.++.|..-|+.|
T Consensus 89 ~~~~gd~vVv~~g~~~~~~g 108 (117)
T PF02887_consen 89 LLKPGDKVVVVAGMPFGTPG 108 (117)
T ss_dssp SS-TTSEEEEEEESSTTTTS
T ss_pred CCCCCCEEEEEeCCCCCCCC
Confidence 37999999999995545444
No 159
>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=25.53 E-value=1.2e+02 Score=20.89 Aligned_cols=14 Identities=36% Similarity=0.529 Sum_probs=11.0
Q ss_pred ceeeeCCEEEEEec
Q 032297 68 MHVKAGDTVKVIAG 81 (143)
Q Consensus 68 ~~IkkGD~V~VIsG 81 (143)
=.|++||+|.++.-
T Consensus 26 Gtl~~g~~v~~~~~ 39 (94)
T cd04090 26 GTIKKGQKVKVLGE 39 (94)
T ss_pred CeEcCCCEEEEECC
Confidence 45889999988754
No 160
>PRK00049 elongation factor Tu; Reviewed
Probab=25.12 E-value=1.4e+02 Score=26.09 Aligned_cols=33 Identities=18% Similarity=0.211 Sum_probs=24.7
Q ss_pred ccceeeeCCEEEEEecCCCCeEeEEEEEEccCCE
Q 032297 66 HKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNST 99 (143)
Q Consensus 66 ~k~~IkkGD~V~VIsG~dKGK~G~V~~V~~k~n~ 99 (143)
..=.|++||+|.++-.++ ++..+|.+|..++..
T Consensus 235 ~~G~i~~gd~v~i~p~~~-~~~~~VksI~~~~~~ 267 (396)
T PRK00049 235 ERGIIKVGEEVEIVGIRD-TQKTTVTGVEMFRKL 267 (396)
T ss_pred eeeEEecCCEEEEeecCC-CceEEEEEEEECCcE
Confidence 344689999998886544 788999999876543
No 161
>PRK06437 hypothetical protein; Provisional
Probab=24.90 E-value=54 Score=21.93 Aligned_cols=15 Identities=27% Similarity=0.403 Sum_probs=12.1
Q ss_pred ccceeeeCCEEEEEe
Q 032297 66 HKMHVKAGDTVKVIA 80 (143)
Q Consensus 66 ~k~~IkkGD~V~VIs 80 (143)
....++.||+|.|+.
T Consensus 48 ~~~~L~dgD~Veiv~ 62 (67)
T PRK06437 48 EDHNVKKEDDVLILE 62 (67)
T ss_pred CceEcCCCCEEEEEe
Confidence 666789999998874
No 162
>PRK08577 hypothetical protein; Provisional
Probab=24.65 E-value=56 Score=24.26 Aligned_cols=24 Identities=29% Similarity=0.368 Sum_probs=20.0
Q ss_pred cccceeeeCCEEEEEecCCCCeEe
Q 032297 65 LHKMHVKAGDTVKVIAGCDKGKIG 88 (143)
Q Consensus 65 ~~k~~IkkGD~V~VIsG~dKGK~G 88 (143)
..++.|++||.|.+..-.|+|++=
T Consensus 22 r~~l~~~~g~~~~~~~~~~~~~~~ 45 (136)
T PRK08577 22 REALGIREGMYVLLIADTDKKEIH 45 (136)
T ss_pred HHHcCcCCCCEEEEEEECCCCEEE
Confidence 457889999999999888887763
No 163
>cd03691 BipA_TypA_II BipA_TypA_II: domain II of BipA (also called TypA) having homology to domain II of the elongation factors (EFs) EF-G and EF-Tu. BipA is a highly conserved protein with global regulatory properties in Escherichia coli. BipA is phosphorylated on a tyrosine residue under some cellular conditions. Mutants show altered regulation of some pathways. BipA functions as a translation factor that is required specifically for the expression of the transcriptional modulator Fis. BipA binds to ribosomes at a site that coincides with that of EF-G and has a GTPase activity that is sensitive to high GDP:GTP ratios and, is stimulated by 70S ribosomes programmed with mRNA and aminoacylated tRNAs. The growth rate-dependent induction of BipA allows the efficient expression of Fis, thereby modulating a range of downstream processes, including DNA metabolism and type III secretion.
Probab=24.52 E-value=1.2e+02 Score=20.22 Aligned_cols=17 Identities=29% Similarity=0.356 Sum_probs=12.7
Q ss_pred cceeeeCCEEEEEecCC
Q 032297 67 KMHVKAGDTVKVIAGCD 83 (143)
Q Consensus 67 k~~IkkGD~V~VIsG~d 83 (143)
.=.|++||+|.+..-++
T Consensus 24 sG~l~~g~~v~~~~~~~ 40 (86)
T cd03691 24 RGTVKVGQQVAVVKRDG 40 (86)
T ss_pred eCEEcCCCEEEEEcCCC
Confidence 45689999998876543
No 164
>TIGR02062 RNase_B exoribonuclease II. This family consists of exoribonuclease II, the product of the rnb gene, as found in a number of gamma proteobacteria. In Escherichia coli, it is one of eight different exoribonucleases. It is involved in mRNA degradation and tRNA precursor end processing.
Probab=24.07 E-value=1.4e+02 Score=28.35 Aligned_cols=35 Identities=17% Similarity=0.173 Sum_probs=25.2
Q ss_pred eeeeCCEEEEE-ecCCCCeEeEEEEEEccCCEEEEe
Q 032297 69 HVKAGDTVKVI-AGCDKGKIGEITKVFRHNSTVMVK 103 (143)
Q Consensus 69 ~IkkGD~V~VI-sG~dKGK~G~V~~V~~k~n~ViVe 103 (143)
...-||+|.|. ....+.+.|+|.+|....+.-+|-
T Consensus 50 ~A~~GD~V~v~i~~~~~r~~~~v~~iver~~~~~vG 85 (639)
T TIGR02062 50 KVMHGDKIIAVIHSEKERESAEPEELIEPFLTRFVG 85 (639)
T ss_pred cCCCCCEEEEEEecCCCCcEEEEEEEEccCCCEEEE
Confidence 45669999664 554556789999999777665554
No 165
>PF07497 Rho_RNA_bind: Rho termination factor, RNA-binding domain; InterPro: IPR011113 The Rho termination factor disengages newly transcribed RNA from its DNA template at certain, specific transcripts. It is thought that two copies of Rho bind to RNA and that Rho functions as a hexamer of protomers [].; GO: 0003723 RNA binding, 0006353 transcription termination, DNA-dependent; PDB: 1A8V_B 1PVO_A 1PV4_D 3ICE_A 1XPU_C 1XPO_D 1XPR_F 2A8V_B 2HT1_B 1A63_A ....
Probab=23.17 E-value=76 Score=22.56 Aligned_cols=18 Identities=17% Similarity=0.342 Sum_probs=11.8
Q ss_pred ccccceeeeCCEEEEEec
Q 032297 64 VLHKMHVKAGDTVKVIAG 81 (143)
Q Consensus 64 ~~~k~~IkkGD~V~VIsG 81 (143)
++.++.++.||.|.-..-
T Consensus 37 qIrrf~LR~GD~V~G~vr 54 (78)
T PF07497_consen 37 QIRRFGLRTGDLVEGQVR 54 (78)
T ss_dssp CCCCTT--TTEEEEEEEE
T ss_pred HHHHcCCCCCCEEEEEEe
Confidence 467889999999984433
No 166
>PRK08187 pyruvate kinase; Validated
Probab=22.92 E-value=2.9e+02 Score=25.67 Aligned_cols=98 Identities=14% Similarity=0.165 Sum_probs=48.0
Q ss_pred CCCceeeeeeee--eeeeeccCCCCCcccccceeeeCCEEEEEecCCCC----eEeEE-------EEEEccCCEEEEece
Q 032297 39 TDKPCLIVVRLK--RWERKECKPNSLPVLHKMHVKAGDTVKVIAGCDKG----KIGEI-------TKVFRHNSTVMVKDI 105 (143)
Q Consensus 39 ~~~~~~~~~~~k--~Werk~~kpn~lp~~~k~~IkkGD~V~VIsG~dKG----K~G~V-------~~V~~k~n~ViVegv 105 (143)
..++|.|.+-++ +.+.-++++.. .+..+++||+|.+......+ ....| .+..+..++|+++|=
T Consensus 189 ~g~~i~Il~DL~GPKIRtG~l~~~~----~~~~l~~Gd~i~l~~~~~~~~~~~~~~~i~~~~~~l~~~v~~Gd~IlidDG 264 (493)
T PRK08187 189 TGRRCKILMDLAGPKIRTGAVAGPL----GKTRLYTGDRLALVAQGPPRRIDEEHFQVTCTLPEILARLAVGARVWIDDG 264 (493)
T ss_pred cCCCeEEEEeCCCCceeecccCCCC----ccEEecCCCEEEEeccccccCCCCCccEEEechHHHHHhcCCCCEEEEeCC
Confidence 445677775443 33333332210 13668999999987764322 11111 111233455665543
Q ss_pred eeeeeeecCCcc---------cCCceEEEEeeceeecccccCCC
Q 032297 106 NLKTKHVKKREE---------EEQGQIIKLKCDALLKRNGSSKP 140 (143)
Q Consensus 106 N~~kkhvKp~~~---------~~~GgIi~~E~PIhiSnv~~~~~ 140 (143)
.+.-+-.....+ ...|+.+..+..|++-+..+.-|
T Consensus 265 ~I~l~V~~v~~~~v~~~V~~~~~~gg~L~~~KgiNlP~~~vrin 308 (493)
T PRK08187 265 KLGARVERVGPGGALLEVTHARPKGLKLKPEKGLNFPDTALDLP 308 (493)
T ss_pred eEEEEEEEEeCCEEEEEEEEecCCCeEecCCCcccccCceecCC
Confidence 322221111100 12578888888888777665544
No 167
>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=22.91 E-value=1.1e+02 Score=21.22 Aligned_cols=20 Identities=20% Similarity=0.469 Sum_probs=11.0
Q ss_pred CCeEeEEEEE-----EccCCEEEEe
Q 032297 84 KGKIGEITKV-----FRHNSTVMVK 103 (143)
Q Consensus 84 KGK~G~V~~V-----~~k~n~ViVe 103 (143)
.|..|+|++| ...++.|.|.
T Consensus 19 ~g~~GtV~~i~~~~~~~~~~~v~V~ 43 (68)
T PF06701_consen 19 EGHVGTVVSIRDWSSESPDGWVVVQ 43 (68)
T ss_dssp TT--EEE-S--------BTTEEEEE
T ss_pred CCcceEEEecccccccCCCCeEEEE
Confidence 4899999998 5666777776
No 168
>PRK07252 hypothetical protein; Provisional
Probab=22.86 E-value=1.5e+02 Score=22.07 Aligned_cols=25 Identities=16% Similarity=0.239 Sum_probs=19.8
Q ss_pred eeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEe
Q 032297 69 HVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 103 (143)
Q Consensus 69 ~IkkGD~V~VIsG~dKGK~G~V~~V~~k~n~ViVe 103 (143)
.++.||.|.| +|++++..+.++.+.
T Consensus 47 ~~~vGD~V~V----------kI~~iD~~~~ri~lS 71 (120)
T PRK07252 47 LLKVGEEVLV----------QVVDFDEYTGKASLS 71 (120)
T ss_pred ccCCCCEEEE----------EEEEEeCCCCEEEEE
Confidence 4799999998 477888877777654
No 169
>PF02941 FeThRed_A: Ferredoxin thioredoxin reductase variable alpha chain; InterPro: IPR004207 Ferredoxin thioredoxin reductase is a [4FE-4S] protein which plays an important role in the ferredoxin/thioredoxin regulatory chain. It converts an electron signal (photoreduced ferredoxin) to a thiol signal (reduced thioredoxin), regulating enzymes by reduction of specific disulphide groups. It catalyses the light-dependent activation of several photosynthetis enzymes. Ferredoxin thioredoxin reductase is a heterodimer of subunit a and subunit b. Subunit a is the variable subunit, and b is the catalytic chain. This family is the alpha chain.; GO: 0008937 ferredoxin-NAD(P) reductase activity, 0015979 photosynthesis, 0009536 plastid; PDB: 2PUK_B 2PVO_B 2PVG_B 1DJ7_B 2PVD_B 2PU9_B 2PUO_B.
Probab=22.73 E-value=1.1e+02 Score=21.63 Aligned_cols=25 Identities=36% Similarity=0.510 Sum_probs=13.8
Q ss_pred eCCEEEEEec--------------CCCCeEeEEEEEEcc
Q 032297 72 AGDTVKVIAG--------------CDKGKIGEITKVFRH 96 (143)
Q Consensus 72 kGD~V~VIsG--------------~dKGK~G~V~~V~~k 96 (143)
.||+|.|.+- +-+|.+|+|.++..+
T Consensus 1 vGdrVrV~~sv~Vyh~P~hr~~~fDl~G~EGev~~~v~~ 39 (67)
T PF02941_consen 1 VGDRVRVKASVVVYHHPEHRNPPFDLKGMEGEVKQIVTD 39 (67)
T ss_dssp TT-EEEE-S--EES--TTSTTS-EE-TT-EEEEEEE-SE
T ss_pred CCCeEEEeeeEEEEeCCcccCCCccccCCEEEEEEEEee
Confidence 3777777642 257999999888754
No 170
>COG1385 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.70 E-value=1.3e+02 Score=25.09 Aligned_cols=37 Identities=22% Similarity=0.423 Sum_probs=28.9
Q ss_pred cceeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEe
Q 032297 67 KMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 103 (143)
Q Consensus 67 k~~IkkGD~V~VIsG~dKGK~G~V~~V~~k~n~ViVe 103 (143)
-+.++.||++.+..|.+.=-.++|.++.++.-.+.+.
T Consensus 31 VlRl~~gd~l~l~~g~g~~~~a~i~~~~kk~~~~~i~ 67 (246)
T COG1385 31 VLRLKEGDELRLFDGSGGEFLAEITKIGKKEALLKIV 67 (246)
T ss_pred eeecCCCCEEEEEeCCCcEEEEEEeecCCCceEEEEE
Confidence 4678999999999999777777898887775444433
No 171
>PRK05054 exoribonuclease II; Provisional
Probab=22.15 E-value=1.5e+02 Score=28.02 Aligned_cols=34 Identities=21% Similarity=0.221 Sum_probs=23.8
Q ss_pred eeeeCCEEEEE-ecCCCCeEeEEEEEEccCCEEEE
Q 032297 69 HVKAGDTVKVI-AGCDKGKIGEITKVFRHNSTVMV 102 (143)
Q Consensus 69 ~IkkGD~V~VI-sG~dKGK~G~V~~V~~k~n~ViV 102 (143)
....||+|.|. ..+.+++.|+|.+|......-+|
T Consensus 53 ~a~~GD~V~v~i~~~~~r~~g~v~~il~r~~~~~v 87 (644)
T PRK05054 53 KVMHGDRIIAVIHTEKDREIAEPEELIEPFLTRFV 87 (644)
T ss_pred cCCCCCEEEEEEecCCCCcEEEEEEEEecCCCEEE
Confidence 35569999764 55455668999999877655444
No 172
>PF14604 SH3_9: Variant SH3 domain; PDB: 2CRE_A 2E5K_A 2CT3_A 2DE0_X 2D8H_A 2DA9_A 2X3X_E 2X3W_D 2KRN_A 2ED0_A ....
Probab=21.71 E-value=69 Score=19.93 Aligned_cols=16 Identities=25% Similarity=0.557 Sum_probs=11.4
Q ss_pred ccceeeeCCEEEEEec
Q 032297 66 HKMHVKAGDTVKVIAG 81 (143)
Q Consensus 66 ~k~~IkkGD~V~VIsG 81 (143)
.++.+++||.|.|+.-
T Consensus 11 dELs~~~Gd~i~v~~~ 26 (49)
T PF14604_consen 11 DELSFKKGDVITVLEK 26 (49)
T ss_dssp TB-EB-TTEEEEEEEE
T ss_pred CEeeEcCCCEEEEEEe
Confidence 4678999999999843
No 173
>COG1261 FlgA Flagellar basal body P-ring biosynthesis protein [Cell motility and secretion / Posttranslational modification, protein turnover, chaperones]
Probab=21.47 E-value=1.7e+02 Score=24.53 Aligned_cols=40 Identities=30% Similarity=0.442 Sum_probs=30.5
Q ss_pred ccceeeeCCEEEEEecC------------CCCeEeEEEEEEccCCEEEEece
Q 032297 66 HKMHVKAGDTVKVIAGC------------DKGKIGEITKVFRHNSTVMVKDI 105 (143)
Q Consensus 66 ~k~~IkkGD~V~VIsG~------------dKGK~G~V~~V~~k~n~ViVegv 105 (143)
..|-|++||.|.++... .-|-.|++.+|...+...||.|.
T Consensus 158 ~~~lV~rg~~V~~v~~~ggi~i~~~g~aL~nga~Ge~IrVrn~~SgkIvsg~ 209 (220)
T COG1261 158 QAWLVKRGQIVTVVAEGGGISITAEGKALENGAVGEVIRVRNVSSGKIVSGT 209 (220)
T ss_pred cceeEecCCEEEEEEeCCCEEEEEeeeEccCccccceEEEecCCCCceEEEE
Confidence 45889999999998765 45777888888777766666664
No 174
>PLN00208 translation initiation factor (eIF); Provisional
Probab=21.41 E-value=1.4e+02 Score=23.76 Aligned_cols=31 Identities=16% Similarity=0.194 Sum_probs=24.3
Q ss_pred cceeeeCCEEEEEecCCCCeEeEEEEEEccC
Q 032297 67 KMHVKAGDTVKVIAGCDKGKIGEITKVFRHN 97 (143)
Q Consensus 67 k~~IkkGD~V~VIsG~dKGK~G~V~~V~~k~ 97 (143)
+.-|+.||.|.|---++.-..|.|+.++...
T Consensus 68 rIWI~~GD~VlVel~~~d~~KgdIv~ry~~d 98 (145)
T PLN00208 68 KVWIAAGDIILVGLRDYQDDKADVILKYMPD 98 (145)
T ss_pred eEEecCCCEEEEEccCCCCCEEEEEEEcCHH
Confidence 4559999999997666667788898887654
No 175
>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=20.99 E-value=74 Score=22.27 Aligned_cols=17 Identities=47% Similarity=0.856 Sum_probs=15.1
Q ss_pred eeeeCCEEEEEecCCCC
Q 032297 69 HVKAGDTVKVIAGCDKG 85 (143)
Q Consensus 69 ~IkkGD~V~VIsG~dKG 85 (143)
.+..||+|.|+.|-||.
T Consensus 40 ~~~~G~~v~l~~GCDkt 56 (80)
T PF09356_consen 40 GLAVGDTVTLYPGCDKT 56 (80)
T ss_pred cCCCCCEEEEEeCCCCC
Confidence 37899999999999984
No 176
>cd05686 S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function with an N-terminal S1 RNA binding domain, a CCHC type zinc finger, and clusters of basic amino acids representing a potential nucleolar targeting signal. pNO40 was identified through a yeast two-hybrid interaction screen of a human kidney cDNA library using the pinin (pnn) protein as bait. pNO40 is thought to play a role in ribosome maturation and/or biogenesis.
Probab=20.98 E-value=1.5e+02 Score=19.31 Aligned_cols=19 Identities=21% Similarity=0.164 Sum_probs=13.7
Q ss_pred eeeeCCEEEEEecCCCCeEeEEEEEEccC
Q 032297 69 HVKAGDTVKVIAGCDKGKIGEITKVFRHN 97 (143)
Q Consensus 69 ~IkkGD~V~VIsG~dKGK~G~V~~V~~k~ 97 (143)
.++.||+|.|. |.+++..+
T Consensus 48 ~~~~Gd~v~vk----------v~~vd~~~ 66 (73)
T cd05686 48 VVDVGEKVWVK----------VIGREMKD 66 (73)
T ss_pred EECCCCEEEEE----------EEEECCCC
Confidence 37899999983 66666643
No 177
>TIGR02063 RNase_R ribonuclease R. This family consists of an exoribonuclease, ribonuclease R, also called VacB. It is one of the eight exoribonucleases reported in E. coli and is broadly distributed throughout the bacteria. In E. coli, double mutants of this protein and polynucleotide phosphorylase are not viable. Scoring between trusted and noise cutoffs to the model are shorter, divergent forms from the Chlamydiae, and divergent forms from the Campylobacterales (including Helicobacter pylori) and Leptospira interrogans.
Probab=20.92 E-value=1.5e+02 Score=28.05 Aligned_cols=36 Identities=19% Similarity=0.216 Sum_probs=25.9
Q ss_pred ceeeeCCEEEEE-ec---CCCCeEeEEEEEEccCCEEEEe
Q 032297 68 MHVKAGDTVKVI-AG---CDKGKIGEITKVFRHNSTVMVK 103 (143)
Q Consensus 68 ~~IkkGD~V~VI-sG---~dKGK~G~V~~V~~k~n~ViVe 103 (143)
.....||+|.|- .. +.+...|+|++|..+....+|-
T Consensus 101 ~~a~~GD~Vlv~I~~~~~~~~~~eg~Vv~Il~r~~~~~VG 140 (709)
T TIGR02063 101 NGAMHGDRVLVRITGKPDGGDRFEARVIKILERANDQIVG 140 (709)
T ss_pred CcCCCCCEEEEEEecccCCCCCceEEEEEEEeeCCCEEEE
Confidence 346779999775 32 2456699999999887665554
No 178
>cd04713 BAH_plant_3 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=20.84 E-value=2.2e+02 Score=21.78 Aligned_cols=30 Identities=17% Similarity=0.274 Sum_probs=23.5
Q ss_pred ceeeeCCEEEEEecC-CCCeEeEEEEEEccC
Q 032297 68 MHVKAGDTVKVIAGC-DKGKIGEITKVFRHN 97 (143)
Q Consensus 68 ~~IkkGD~V~VIsG~-dKGK~G~V~~V~~k~ 97 (143)
..++.||.|.|..+. .+--+|.|.+|....
T Consensus 19 ~~y~vgD~Vlv~~~~~~~pyI~~I~~i~~~~ 49 (146)
T cd04713 19 NKYRLEDCVLLVPEDDQKPYIAIIKDIYKQE 49 (146)
T ss_pred EEEECCCEEEEeCCCCCCCEEEEEEEEEEcC
Confidence 458999999999765 444599999998654
No 179
>TIGR00157 ribosome small subunit-dependent GTPase A. The Aquifex aeolicus ortholog is split into consecutive open reading frames. Consequently, this model was build in fragment mode (-f option).
Probab=20.83 E-value=1.5e+02 Score=24.13 Aligned_cols=34 Identities=18% Similarity=0.110 Sum_probs=22.8
Q ss_pred eeCCEEEEEecCCCCeEeEEEEEEccCCEE---EEecee
Q 032297 71 KAGDTVKVIAGCDKGKIGEITKVFRHNSTV---MVKDIN 106 (143)
Q Consensus 71 kkGD~V~VIsG~dKGK~G~V~~V~~k~n~V---iVegvN 106 (143)
.+||.|.+-... +..|.|.+|..+.+.+ ++.++.
T Consensus 2 ~vGD~V~~~~~~--~~~~~i~~i~eR~~~L~r~~~~n~D 38 (245)
T TIGR00157 2 VVGDRVVWEPGN--VVKVYGGAIAERKNELTRPIVANID 38 (245)
T ss_pred CCCcEEEEEecC--CCceEEEEEecccceEECcccccCC
Confidence 579999986432 2458888888877655 444443
No 180
>PF04351 PilP: Pilus assembly protein, PilP; InterPro: IPR007446 The PilP family are periplasmic proteins involved in the biogenesis of type IV pili [].; PDB: 2Y4Y_B 2Y4X_A 2IVW_A 2LC4_A.
Probab=20.81 E-value=2.1e+02 Score=21.85 Aligned_cols=47 Identities=23% Similarity=0.299 Sum_probs=30.0
Q ss_pred CEEEEEecCCCCe-EeEEEEEEccCCEEEEeceeeeeeeecCCcccCCceEEEEeeceee
Q 032297 74 DTVKVIAGCDKGK-IGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQIIKLKCDALL 132 (143)
Q Consensus 74 D~V~VIsG~dKGK-~G~V~~V~~k~n~ViVegvN~~kkhvKp~~~~~~GgIi~~E~PIhi 132 (143)
-...|-.|.+-|+ .|+|++|... .|.|.-. + .+..|+.++++.-|.+
T Consensus 101 ~v~~V~~G~yiG~n~G~I~~Is~~--~I~l~E~------v----~d~~G~w~~R~~~l~L 148 (149)
T PF04351_consen 101 KVYRVKVGDYIGQNYGRITSISED--SIELVEI------V----PDGQGCWQERPATLAL 148 (149)
T ss_dssp EEEEEETTEEETTTTEEEEEEETT--EEEEEEE------E----E-SSSSEEEEEEEEEB
T ss_pred CEEEecCCCEeccCCCEEEEEeCC--eEEEEEE------c----ccCCCCEEEEeEEEec
Confidence 3445556777777 7889888754 4444322 1 2456899988887764
No 181
>KOG4792 consensus Crk family adapters [Signal transduction mechanisms]
Probab=20.69 E-value=1.6e+02 Score=25.70 Aligned_cols=44 Identities=27% Similarity=0.394 Sum_probs=28.0
Q ss_pred ccCCCCceeeeeeeeeeeeeccC--CCCCcccccceeeeCCEEEEEe
Q 032297 36 VKPTDKPCLIVVRLKRWERKECK--PNSLPVLHKMHVKAGDTVKVIA 80 (143)
Q Consensus 36 ~~~~~~~~~~~~~~k~Werk~~k--pn~lp~~~k~~IkkGD~V~VIs 80 (143)
..++.+|++...++.-.-|-..+ ||.-+. ..+.+.+||+|+|..
T Consensus 213 ~~s~~~~l~l~~~lPa~Arv~q~RVPnAYDk-TaL~levGdiVkVTk 258 (293)
T KOG4792|consen 213 STSSDTPLPLQQNLPAYARVIQKRVPNAYDK-TALALEVGDIVKVTK 258 (293)
T ss_pred CcccCCcCccccCCChheeeehhcCCCccCh-hhhhhhcCcEEEEEe
Confidence 45667777766666555554444 344332 357789999999964
No 182
>TIGR00219 mreC rod shape-determining protein MreC. MreC (murein formation C) is involved in the rod shape determination in E. coli, and more generally in cell shape determination of bacteria whether or not they are rod-shaped. Cells defective in MreC are round. Species with MreC include many of the Proteobacteria, Gram-positives, and spirochetes.
Probab=20.57 E-value=1.2e+02 Score=25.65 Aligned_cols=28 Identities=32% Similarity=0.355 Sum_probs=23.6
Q ss_pred eeeeCCEEEEEecCC-CCeEeEEEEEEccCCEE
Q 032297 69 HVKAGDTVKVIAGCD-KGKIGEITKVFRHNSTV 100 (143)
Q Consensus 69 ~IkkGD~V~VIsG~d-KGK~G~V~~V~~k~n~V 100 (143)
-|++||-|.- + +|-+|.|++|.....+|
T Consensus 143 GV~~g~~Vi~----~~~GLVG~V~~V~~~~S~V 171 (283)
T TIGR00219 143 GVYKDMPVIA----DGKGLVGKVVSVGSNTSRV 171 (283)
T ss_pred CCCCCCEEEc----CCCceEEEEEEECCCeEEE
Confidence 4788888765 5 89999999999998887
No 183
>PF13550 Phage-tail_3: Putative phage tail protein
Probab=20.57 E-value=1.5e+02 Score=21.52 Aligned_cols=28 Identities=14% Similarity=0.235 Sum_probs=21.2
Q ss_pred ccceeeeCCEEEEEecCCCCeEeEEEEEE
Q 032297 66 HKMHVKAGDTVKVIAGCDKGKIGEITKVF 94 (143)
Q Consensus 66 ~k~~IkkGD~V~VIsG~dKGK~G~V~~V~ 94 (143)
.-+.+.+||.|.|-.. .+.....|.+|.
T Consensus 136 ~~~~l~pGDvi~l~~~-~~~~~~RI~~i~ 163 (164)
T PF13550_consen 136 DGLALEPGDVIALSDD-GRDMRFRITEIE 163 (164)
T ss_pred hhccCCCCCEEEEEeC-CCceEEEEEEEe
Confidence 3466899999997665 777777887763
No 184
>cd06462 Peptidase_S24_S26 The S24, S26 LexA/signal peptidase superfamily contains LexA-related and type I signal peptidase families. The S24 LexA protein domains include: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC 3.4.21.88), the repressor of genes in the cellular SOS response to DNA damage; MucA and the related UmuD proteins, which are lesion-bypass DNA polymerases, induced in response to mitogenic DNA damage; RulA, a component of the rulAB locus that confers resistance to UV, and RuvA, which is a component of the RuvABC resolvasome that catalyzes the resolution of Holliday junctions that arise during genetic recombination and DNA repair. The S26 type I signal peptidase (SPase) family also includes mitochondrial inner membrane protease (IMP)-like members. SPases are essential membrane-bound proteases which function to cleave away the amino-terminal signal peptide from the translocated pre-protein, thus playing a crucial role in the tr
Probab=20.37 E-value=2.4e+02 Score=17.84 Aligned_cols=34 Identities=18% Similarity=0.049 Sum_probs=18.8
Q ss_pred eeeCCEEEEEecCCCCeEeEEEEEEccC--CEEEEecee
Q 032297 70 VKAGDTVKVIAGCDKGKIGEITKVFRHN--STVMVKDIN 106 (143)
Q Consensus 70 IkkGD~V~VIsG~dKGK~G~V~~V~~k~--n~ViVegvN 106 (143)
+..||.|.+..+. -.-.|.++.... +.+.+.+.|
T Consensus 29 ~~~G~iv~~~~~~---~~~~ikrl~~~~~~~~~~l~~~N 64 (84)
T cd06462 29 PKRGDIVVFRLPG---GELTVKRVIGLPGEGHYFLLGDN 64 (84)
T ss_pred CcCCEEEEEEcCC---CcEEEEEEEEECCCCEEEEECCC
Confidence 4666666666543 223444455444 566666666
No 185
>PTZ00329 eukaryotic translation initiation factor 1A; Provisional
Probab=20.16 E-value=1.4e+02 Score=23.89 Aligned_cols=31 Identities=10% Similarity=0.190 Sum_probs=24.8
Q ss_pred cceeeeCCEEEEEecCCCCeEeEEEEEEccC
Q 032297 67 KMHVKAGDTVKVIAGCDKGKIGEITKVFRHN 97 (143)
Q Consensus 67 k~~IkkGD~V~VIsG~dKGK~G~V~~V~~k~ 97 (143)
+..|+.||.|.|=--++.-..|.|+..+...
T Consensus 68 ~IWI~~GD~VlVel~~yd~~KgdIi~Ry~~d 98 (155)
T PTZ00329 68 RVWINIGDIILVSLRDFQDSKADVILKYTPD 98 (155)
T ss_pred eEEecCCCEEEEeccCCCCCEEEEEEEcCHH
Confidence 4569999999997777777889998887654
No 186
>PRK05352 Na(+)-translocating NADH-quinone reductase subunit A; Provisional
Probab=20.00 E-value=1.3e+02 Score=27.46 Aligned_cols=30 Identities=40% Similarity=0.419 Sum_probs=22.5
Q ss_pred ccceeeeCCEEEE--EecCCCCe---------EeEEEEEEc
Q 032297 66 HKMHVKAGDTVKV--IAGCDKGK---------IGEITKVFR 95 (143)
Q Consensus 66 ~k~~IkkGD~V~V--IsG~dKGK---------~G~V~~V~~ 95 (143)
.+..+++||+|+. .-+.++|- -|+|.+|.+
T Consensus 42 ~~~~V~~GD~V~~Gq~I~~~~~~~s~~~hspvSGtV~~I~~ 82 (448)
T PRK05352 42 PKMKVKEGDKVKKGQPLFEDKKNPGVKFTSPASGTVVAINR 82 (448)
T ss_pred CceEeCcCCEEcCCCEeEecCCCceEEEEcCCCeEEEEEcc
Confidence 4566999999987 55566664 489999963
Done!