Query 031473
Match_columns 159
No_of_seqs 152 out of 1246
Neff 6.1
Searched_HMMs 46136
Date Fri Mar 29 14:36:42 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031473.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031473hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK00004 rplX 50S ribosomal pr 100.0 1.5E-33 3.3E-38 206.1 11.5 99 12-110 2-101 (105)
2 TIGR01079 rplX_bact ribosomal 100.0 2.5E-33 5.5E-38 204.6 11.4 98 13-110 2-101 (104)
3 KOG1708 Mitochondrial/chloropl 100.0 1.4E-33 3.1E-38 224.9 9.7 139 11-152 69-211 (236)
4 COG0198 RplX Ribosomal protein 100.0 1.8E-30 3.8E-35 189.0 10.1 98 11-110 1-100 (104)
5 CHL00141 rpl24 ribosomal prote 99.9 2.5E-26 5.3E-31 161.6 7.8 76 12-87 6-82 (83)
6 PRK12281 rplX 50S ribosomal pr 99.9 2.5E-25 5.5E-30 154.1 7.5 71 12-82 4-75 (76)
7 PRK01191 rpl24p 50S ribosomal 99.9 4.2E-22 9.1E-27 148.4 6.7 77 5-91 36-112 (120)
8 PTZ00194 60S ribosomal protein 99.9 8.3E-22 1.8E-26 150.5 6.0 75 5-89 37-111 (143)
9 TIGR01080 rplX_A_E ribosomal p 99.8 5.8E-20 1.3E-24 136.1 6.1 76 4-89 31-106 (114)
10 KOG3401 60S ribosomal protein 98.9 1.2E-09 2.5E-14 83.6 3.5 74 5-88 39-113 (145)
11 PF00467 KOW: KOW motif; Inte 98.8 6.3E-09 1.4E-13 60.6 4.8 32 17-48 1-32 (32)
12 smart00739 KOW KOW (Kyprides, 98.0 1.4E-05 3.1E-10 44.1 3.9 26 15-40 2-27 (28)
13 PRK08559 nusG transcription an 97.6 0.00019 4.2E-09 55.4 5.9 57 13-83 93-149 (153)
14 TIGR00405 L26e_arch ribosomal 97.4 0.00042 9.2E-09 52.6 5.6 37 15-51 87-123 (145)
15 COG0250 NusG Transcription ant 97.2 0.00074 1.6E-08 53.7 5.4 36 13-48 122-157 (178)
16 PRK05609 nusG transcription an 97.0 0.0015 3.3E-08 50.9 5.3 36 13-48 125-160 (181)
17 TIGR00922 nusG transcription t 97.0 0.0016 3.4E-08 50.5 5.2 36 13-48 118-153 (172)
18 TIGR01955 RfaH transcriptional 96.3 0.0077 1.7E-07 46.0 4.7 35 13-48 107-141 (159)
19 PRK09014 rfaH transcriptional 96.1 0.0096 2.1E-07 45.8 4.5 34 14-48 109-142 (162)
20 TIGR01956 NusG_myco NusG famil 96.1 0.012 2.7E-07 49.4 5.3 37 12-48 203-239 (258)
21 PRK04333 50S ribosomal protein 93.5 0.19 4.2E-06 35.3 4.9 37 13-50 2-38 (84)
22 PTZ00065 60S ribosomal protein 89.0 0.92 2E-05 34.5 4.8 35 15-50 8-42 (130)
23 PRK04313 30S ribosomal protein 87.3 0.91 2E-05 37.8 4.2 42 8-49 165-210 (237)
24 PTZ00471 60S ribosomal protein 87.3 1.1 2.4E-05 34.2 4.3 40 15-54 5-50 (134)
25 COG2163 RPL14A Ribosomal prote 84.7 1.8 3.8E-05 32.7 4.3 35 15-50 5-39 (125)
26 KOG1999 RNA polymerase II tran 84.6 0.99 2.1E-05 44.2 3.5 28 14-41 459-486 (1024)
27 PRK06531 yajC preprotein trans 82.8 2.7 5.9E-05 31.1 4.5 32 13-48 35-66 (113)
28 COG1471 RPS4A Ribosomal protei 81.5 2.7 6E-05 35.0 4.5 42 8-49 167-212 (241)
29 PRK05585 yajC preprotein trans 79.5 4.1 8.8E-05 29.7 4.4 31 12-48 50-80 (106)
30 PLN00036 40S ribosomal protein 78.8 3.2 6.9E-05 35.1 4.2 42 8-49 168-212 (261)
31 COG5164 SPT5 Transcription elo 78.7 1.8 3.8E-05 39.6 2.7 28 15-42 140-167 (607)
32 PTZ00223 40S ribosomal protein 78.2 3.1 6.8E-05 35.4 3.9 42 8-49 165-209 (273)
33 COG1862 YajC Preprotein transl 76.8 4.7 0.0001 29.1 4.0 30 13-48 42-71 (97)
34 KOG1999 RNA polymerase II tran 76.7 2.1 4.5E-05 42.0 2.8 30 12-41 405-434 (1024)
35 TIGR00739 yajC preprotein tran 76.1 6.5 0.00014 27.4 4.5 31 12-48 35-65 (84)
36 PF09953 DUF2187: Uncharacteri 74.6 7.7 0.00017 25.4 4.2 27 16-48 5-31 (57)
37 PTZ00118 40S ribosomal protein 74.5 4.7 0.0001 34.1 4.0 42 8-49 168-212 (262)
38 PRK05886 yajC preprotein trans 73.6 7.1 0.00015 28.8 4.3 30 13-48 37-66 (109)
39 PF02699 YajC: Preprotein tran 72.9 1.7 3.7E-05 30.1 0.9 31 12-48 34-64 (82)
40 COG1532 Predicted RNA-binding 68.1 11 0.00023 24.6 3.7 34 16-49 22-57 (57)
41 COG5164 SPT5 Transcription elo 62.0 8.8 0.00019 35.3 3.3 34 16-49 353-386 (607)
42 PF11623 DUF3252: Protein of u 61.8 27 0.00058 22.5 4.6 40 15-54 2-43 (53)
43 PF03144 GTP_EFTU_D2: Elongati 58.1 14 0.00031 23.8 3.1 35 9-44 7-44 (74)
44 PF04452 Methyltrans_RNA: RNA 55.2 20 0.00042 28.9 4.1 45 4-48 6-50 (225)
45 PF05641 Agenet: Agenet domain 53.0 42 0.00092 21.9 4.8 33 15-48 1-37 (68)
46 PRK00409 recombination and DNA 51.7 23 0.00051 34.1 4.6 37 13-52 635-672 (782)
47 PF14505 DUF4438: Domain of un 51.0 35 0.00077 28.7 4.9 33 16-48 59-91 (258)
48 KOG4315 G-patch nucleic acid b 50.7 7.1 0.00015 35.2 0.9 33 16-48 395-427 (455)
49 KOG3418 60S ribosomal protein 48.7 34 0.00073 26.2 4.1 39 15-53 5-49 (136)
50 PF02211 NHase_beta: Nitrile h 47.8 22 0.00049 29.2 3.3 27 12-38 132-168 (222)
51 PF12701 LSM14: Scd6-like Sm d 44.8 50 0.0011 23.7 4.4 34 17-50 7-40 (96)
52 cd04466 S1_YloQ_GTPase S1_YloQ 43.4 51 0.0011 20.9 3.9 30 14-45 37-66 (68)
53 cd05703 S1_Rrp5_repeat_hs12_sc 43.3 47 0.001 21.9 3.9 25 14-48 46-70 (73)
54 TIGR01069 mutS2 MutS2 family p 42.3 38 0.00082 32.7 4.4 33 16-52 626-660 (771)
55 PRK04306 50S ribosomal protein 41.9 55 0.0012 23.7 4.2 34 15-48 35-78 (98)
56 PF14001 YdfZ: YdfZ protein 41.7 59 0.0013 21.8 4.0 35 14-51 9-52 (64)
57 CHL00125 psaE photosystem I su 41.5 32 0.0007 23.0 2.7 28 15-42 2-31 (64)
58 cd05695 S1_Rrp5_repeat_hs3 S1_ 41.2 49 0.0011 21.3 3.6 24 14-47 42-65 (66)
59 cd03692 mtIF2_IVc mtIF2_IVc: t 41.1 43 0.00093 22.7 3.5 35 10-44 22-56 (84)
60 COG3700 AphA Acid phosphatase 40.3 11 0.00023 30.8 0.4 33 12-44 124-156 (237)
61 PF08206 OB_RNB: Ribonuclease 40.0 33 0.00071 21.8 2.6 24 15-38 32-58 (58)
62 cd05707 S1_Rrp5_repeat_sc11 S1 39.0 53 0.0011 20.8 3.5 23 15-47 45-67 (68)
63 PF01157 Ribosomal_L21e: Ribos 38.9 57 0.0012 23.6 3.9 33 14-46 32-74 (99)
64 COG2139 RPL21A Ribosomal prote 38.0 72 0.0016 23.1 4.2 39 15-53 33-81 (98)
65 PRK02749 photosystem I reactio 37.6 44 0.00094 22.8 2.9 29 14-42 2-32 (71)
66 PF02427 PSI_PsaE: Photosystem 37.0 49 0.0011 22.0 3.0 28 15-42 1-30 (61)
67 PRK11713 16S ribosomal RNA met 36.3 63 0.0014 26.1 4.3 44 4-47 19-62 (234)
68 PF07497 Rho_RNA_bind: Rho ter 36.2 27 0.00059 24.2 1.8 18 8-25 36-53 (78)
69 PF01176 eIF-1a: Translation i 36.0 61 0.0013 21.1 3.5 29 9-37 36-64 (65)
70 PF07076 DUF1344: Protein of u 35.9 1.3E+02 0.0028 19.9 5.8 20 31-50 5-24 (61)
71 PRK10334 mechanosensitive chan 35.6 1.3E+02 0.0029 25.3 6.3 24 13-41 128-151 (286)
72 cd05698 S1_Rrp5_repeat_hs6_sc5 35.5 74 0.0016 20.1 3.8 24 14-47 44-67 (70)
73 cd05697 S1_Rrp5_repeat_hs5 S1_ 35.2 90 0.002 19.8 4.2 24 14-47 44-67 (69)
74 TIGR00046 RNA methyltransferas 34.8 69 0.0015 26.1 4.3 42 4-47 21-64 (240)
75 PF02887 PK_C: Pyruvate kinase 34.1 32 0.00069 24.6 2.0 24 10-33 85-108 (117)
76 PF06701 MIB_HERC2: Mib_herc2; 33.2 53 0.0011 22.1 2.8 27 22-48 3-43 (68)
77 COG1162 Predicted GTPases [Gen 32.8 48 0.001 28.6 3.2 32 11-45 41-72 (301)
78 PLN00045 photosystem I reactio 32.8 71 0.0015 23.2 3.5 31 11-41 36-68 (101)
79 KOG3421 60S ribosomal protein 32.7 53 0.0011 25.2 3.0 34 16-50 8-41 (136)
80 PF03120 DNA_ligase_OB: NAD-de 32.4 32 0.00069 24.0 1.7 31 8-40 43-73 (82)
81 cd05708 S1_Rrp5_repeat_sc12 S1 32.3 1E+02 0.0022 19.6 4.1 25 14-48 47-71 (77)
82 cd05793 S1_IF1A S1_IF1A: Trans 32.2 47 0.001 22.7 2.5 30 12-41 36-65 (77)
83 PF09926 DUF2158: Uncharacteri 31.9 31 0.00066 22.1 1.4 15 15-29 1-15 (53)
84 cd05688 S1_RPS1_repeat_ec3 S1_ 31.9 88 0.0019 19.2 3.7 23 15-47 45-67 (68)
85 PF11604 CusF_Ec: Copper bindi 31.6 1.6E+02 0.0034 19.5 6.0 17 33-49 1-17 (70)
86 cd04461 S1_Rrp5_repeat_hs8_sc7 31.3 93 0.002 20.6 3.8 24 14-47 58-81 (83)
87 PF02941 FeThRed_A: Ferredoxin 31.1 55 0.0012 22.2 2.6 25 17-41 1-39 (67)
88 cd04717 BAH_polybromo BAH, or 30.8 1.1E+02 0.0025 21.9 4.5 35 14-48 3-40 (121)
89 PF12353 eIF3g: Eukaryotic tra 30.6 1E+02 0.0022 23.0 4.3 70 84-154 9-85 (128)
90 PF01079 Hint: Hint module; I 30.4 76 0.0016 25.9 3.8 31 10-40 101-132 (217)
91 PRK12618 flgA flagellar basal 29.9 88 0.0019 23.7 3.9 37 9-45 76-125 (141)
92 cd04709 BAH_MTA BAH, or Bromo 28.9 1.2E+02 0.0026 23.7 4.6 29 15-43 4-33 (164)
93 cd04459 Rho_CSD Rho_CSD: Rho p 28.8 78 0.0017 21.2 3.0 20 8-27 34-53 (68)
94 TIGR03170 flgA_cterm flagella 28.7 99 0.0021 22.1 3.9 38 8-45 59-109 (122)
95 PF08772 NOB1_Zn_bind: Nin one 28.3 34 0.00075 23.4 1.2 41 80-120 24-71 (73)
96 cd05792 S1_eIF1AD_like S1_eIF1 28.2 73 0.0016 22.0 2.9 29 14-42 38-67 (78)
97 cd05706 S1_Rrp5_repeat_sc10 S1 28.0 1.3E+02 0.0029 19.1 4.1 23 15-47 48-70 (73)
98 PF11717 Tudor-knot: RNA bindi 27.9 77 0.0017 19.9 2.8 29 15-43 1-29 (55)
99 PRK07018 flgA flagellar basal 27.6 94 0.002 25.3 4.0 38 8-45 170-220 (235)
100 CHL00010 infA translation init 27.3 1.3E+02 0.0027 20.5 4.0 13 12-24 44-56 (78)
101 cd05690 S1_RPS1_repeat_ec5 S1_ 27.3 1.1E+02 0.0023 19.2 3.5 22 15-46 46-67 (69)
102 cd00164 S1_like S1_like: Ribos 26.9 1.1E+02 0.0024 18.1 3.4 21 15-45 42-62 (65)
103 cd04456 S1_IF1A_like S1_IF1A_l 26.6 81 0.0018 21.6 2.9 30 13-42 37-67 (78)
104 cd03693 EF1_alpha_II EF1_alpha 26.3 94 0.002 21.2 3.2 25 12-39 28-52 (91)
105 PF01426 BAH: BAH domain; Int 26.3 79 0.0017 22.0 2.9 28 15-42 3-32 (119)
106 PRK10708 hypothetical protein; 26.1 1.4E+02 0.0031 19.6 3.8 29 16-44 2-30 (62)
107 cd05689 S1_RPS1_repeat_ec4 S1_ 26.0 1.1E+02 0.0023 19.5 3.3 22 15-46 49-70 (72)
108 smart00743 Agenet Tudor-like d 25.9 1.7E+02 0.0037 18.1 4.8 34 14-48 2-36 (61)
109 cd05685 S1_Tex S1_Tex: The C-t 25.9 1.3E+02 0.0028 18.3 3.6 22 15-46 45-66 (68)
110 smart00652 eIF1a eukaryotic tr 25.9 79 0.0017 21.9 2.8 31 11-41 40-70 (83)
111 cd05696 S1_Rrp5_repeat_hs4 S1_ 25.8 1.4E+02 0.0031 19.3 3.9 24 14-47 46-69 (71)
112 cd03698 eRF3_II_like eRF3_II_l 25.7 98 0.0021 20.6 3.2 26 12-40 24-49 (83)
113 cd05691 S1_RPS1_repeat_ec6 S1_ 25.6 1.6E+02 0.0034 18.4 4.1 24 15-48 45-68 (73)
114 cd03696 selB_II selB_II: this 25.6 1E+02 0.0022 20.5 3.2 29 10-41 22-50 (83)
115 cd03695 CysN_NodQ_II CysN_NodQ 25.6 1.4E+02 0.003 20.0 3.9 26 11-39 23-48 (81)
116 PF00018 SH3_1: SH3 domain; I 25.6 81 0.0017 18.7 2.5 17 10-26 11-27 (48)
117 cd01854 YjeQ_engC YjeQ/EngC. 25.5 1.2E+02 0.0026 25.2 4.4 31 13-45 33-63 (287)
118 COG0361 InfA Translation initi 25.5 91 0.002 21.5 2.9 26 12-37 44-69 (75)
119 PF14801 GCD14_N: tRNA methylt 25.4 47 0.001 21.5 1.4 21 11-33 2-22 (54)
120 COG2411 Uncharacterized conser 25.4 78 0.0017 25.5 2.9 32 8-39 26-59 (188)
121 cd00174 SH3 Src homology 3 dom 25.2 77 0.0017 18.2 2.3 16 11-26 14-29 (54)
122 TIGR02594 conserved hypothetic 24.7 1.6E+02 0.0035 21.9 4.4 34 15-49 74-107 (129)
123 PF05257 CHAP: CHAP domain; I 24.6 1.3E+02 0.0027 21.5 3.8 40 11-51 59-100 (124)
124 TIGR00523 eIF-1A eukaryotic/ar 24.6 53 0.0012 23.6 1.7 29 11-41 54-85 (99)
125 PF00924 MS_channel: Mechanose 24.4 56 0.0012 25.2 2.0 23 14-41 60-82 (206)
126 cd04452 S1_IF2_alpha S1_IF2_al 24.4 1.7E+02 0.0038 18.5 4.1 23 15-47 50-72 (76)
127 COG1193 Mismatch repair ATPase 24.4 83 0.0018 30.5 3.5 33 12-48 610-642 (753)
128 cd05705 S1_Rrp5_repeat_hs14 S1 24.3 1.3E+02 0.0029 19.8 3.6 24 14-47 50-73 (74)
129 PF10781 DSRB: Dextransucrase 24.0 1.6E+02 0.0034 19.4 3.7 29 16-44 2-30 (62)
130 cd04715 BAH_Orc1p_like BAH, or 23.8 1.8E+02 0.0039 22.5 4.7 32 11-42 26-57 (159)
131 cd05687 S1_RPS1_repeat_ec1_hs1 23.0 1.7E+02 0.0038 18.3 3.9 23 15-47 45-67 (70)
132 COG2053 RPS28A Ribosomal prote 22.9 69 0.0015 21.7 1.9 13 20-32 27-39 (69)
133 PRK12289 GTPase RsgA; Reviewed 22.8 1.3E+02 0.0027 26.3 4.1 32 15-46 52-83 (352)
134 PF15232 DUF4585: Domain of un 22.7 1E+02 0.0022 21.3 2.7 30 65-94 17-46 (75)
135 COG2002 AbrB Regulators of sta 22.7 76 0.0017 21.9 2.2 23 9-31 22-44 (89)
136 TIGR00219 mreC rod shape-deter 22.7 1.1E+02 0.0024 25.8 3.5 30 14-47 143-173 (283)
137 COG1385 Uncharacterized protei 22.6 1.3E+02 0.0028 25.0 3.9 44 5-48 24-67 (246)
138 smart00326 SH3 Src homology 3 22.4 91 0.002 18.0 2.3 17 11-27 17-33 (58)
139 TIGR00008 infA translation ini 22.4 67 0.0014 21.7 1.8 19 9-27 39-57 (68)
140 smart00439 BAH Bromo adjacent 22.2 1.7E+02 0.0036 20.3 4.0 29 15-43 2-32 (120)
141 cd01736 LSm14_N LSm14 (also kn 21.7 2.1E+02 0.0046 19.6 4.2 35 17-51 5-39 (74)
142 cd04471 S1_RNase_R S1_RNase_R: 21.7 1.7E+02 0.0036 18.9 3.7 23 14-46 57-79 (83)
143 PRK08515 flgA flagellar basal 21.4 1.4E+02 0.003 24.3 3.8 38 8-45 159-208 (222)
144 PF11910 NdhO: Cyanobacterial 21.2 49 0.0011 22.3 0.9 14 15-28 1-14 (67)
145 KOG0171 Mitochondrial inner me 20.7 1.3E+02 0.0027 24.1 3.2 39 16-54 91-132 (176)
146 KOG4225 Sorbin and SH3 domain- 20.7 76 0.0016 29.0 2.3 28 8-35 242-277 (489)
147 PRK12442 translation initiatio 20.7 1.1E+02 0.0023 21.7 2.6 30 8-37 40-69 (87)
148 PRK07252 hypothetical protein; 20.5 1.9E+02 0.0041 21.2 4.1 25 14-48 47-71 (120)
149 smart00357 CSP Cold shock prot 20.3 1.7E+02 0.0036 17.6 3.3 26 13-38 35-63 (64)
150 PF07653 SH3_2: Variant SH3 do 20.3 71 0.0015 19.6 1.5 15 10-24 13-27 (55)
151 cd04721 BAH_plant_1 BAH, or Br 20.1 1.9E+02 0.004 21.5 4.0 30 13-42 6-35 (130)
No 1
>PRK00004 rplX 50S ribosomal protein L24; Reviewed
Probab=100.00 E-value=1.5e-33 Score=206.09 Aligned_cols=99 Identities=55% Similarity=0.871 Sum_probs=94.2
Q ss_pred hcccccCCEEEEeecCCCCcEeeEEEEEccCCEEEEeccceeeeeeCCCC-CCCCceEEEeeeccCCCccccCCCCCCce
Q 031473 12 HWKILRGDNVMIIRGKDKGETGAIKRVIRSQNRVIVEGKNLVKKHIKGGE-GHEGGIFTVEAPIHASNVQVLDPVTGKPC 90 (159)
Q Consensus 12 ~~~i~kGD~V~Vi~G~dKGk~G~V~~V~~~~~~V~Vegvn~~~~~~k~~~-~~~g~i~~~e~pI~~SnV~Lvdp~~g~~~ 90 (159)
.|+|++||+|+||+|+|||++|+|++|++++++|+|||+|+.++|+++++ +.+|+++++|+|||+|||+|+||.+++++
T Consensus 2 ~~~i~kGD~V~Vi~G~dKGk~G~V~~V~~~~~~V~Vegvn~~k~h~k~~~~~~~G~i~~~e~pI~~SnV~lv~p~~~~~~ 81 (105)
T PRK00004 2 MMKIKKGDTVIVIAGKDKGKRGKVLKVLPKKNKVIVEGVNIVKKHQKPNQENPQGGIIEKEAPIHISNVALVDPKTGKAT 81 (105)
T ss_pred CCcccCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEEcCcEEEEEecCCCCCCCCCceEEEECCcCHHHEEEEeCcCCCCe
Confidence 57999999999999999999999999999999999999999999999875 66899999999999999999999999999
Q ss_pred eEEEEEccCCcEEEEEEecC
Q 031473 91 KVGTKYLEDGTKVRVARGIG 110 (159)
Q Consensus 91 rV~~~~~~~g~k~R~~k~~~ 110 (159)
||+|+++++|+++|+|++|+
T Consensus 82 rv~~~~~~~g~kvRv~k~~g 101 (105)
T PRK00004 82 RVGFKFLEDGKKVRVAKKSG 101 (105)
T ss_pred EEEEEEccCCcEEEEEecCC
Confidence 99999999999999999654
No 2
>TIGR01079 rplX_bact ribosomal protein L24, bacterial/organelle. This model recognizes bacterial and organellar forms of ribosomal protein L24. It excludes eukaryotic and archaeal forms, designated L26 in eukaryotes.
Probab=100.00 E-value=2.5e-33 Score=204.59 Aligned_cols=98 Identities=52% Similarity=0.840 Sum_probs=92.5
Q ss_pred cccccCCEEEEeecCCCCcEeeEEEEEccCCEEEEeccceeeeeeCCCC-CC-CCceEEEeeeccCCCccccCCCCCCce
Q 031473 13 WKILRGDNVMIIRGKDKGETGAIKRVIRSQNRVIVEGKNLVKKHIKGGE-GH-EGGIFTVEAPIHASNVQVLDPVTGKPC 90 (159)
Q Consensus 13 ~~i~kGD~V~Vi~G~dKGk~G~V~~V~~~~~~V~Vegvn~~~~~~k~~~-~~-~g~i~~~e~pI~~SnV~Lvdp~~g~~~ 90 (159)
++|++||+|+||+|+|||++|+|++|++++++|+|||+|+.++|.++++ ++ +|+++++|+|||+|||+|+||++++++
T Consensus 2 ~~ikkGD~V~Vi~G~dKGK~G~V~~V~~~~~~V~VegvN~~kkh~k~~~~~~~~g~i~~~e~pI~~SnV~lv~p~~~k~~ 81 (104)
T TIGR01079 2 MKIKKGDTVKVISGKDKGKRGKVLKVLPKTNKVIVEGVNMVKKHVKPKPTQRSQGGIIEKEAPIHISNVMLFDPKTGKAT 81 (104)
T ss_pred CcccCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEECCcEEEEEecCcccCCCCCCceEEEEccCCHHHeEEEcCcCCCCe
Confidence 4899999999999999999999999999999999999999999999875 33 799999999999999999999999999
Q ss_pred eEEEEEccCCcEEEEEEecC
Q 031473 91 KVGTKYLEDGTKVRVARGIG 110 (159)
Q Consensus 91 rV~~~~~~~g~k~R~~k~~~ 110 (159)
+|+|+++++|+++|+|++|+
T Consensus 82 rv~~~~~~~g~kvRv~k~~g 101 (104)
T TIGR01079 82 RVGIRFEEDGKKVRVFKKTG 101 (104)
T ss_pred EEEEEEccCCcEEEEEeccC
Confidence 99999999999999999654
No 3
>KOG1708 consensus Mitochondrial/chloroplast ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.4e-33 Score=224.86 Aligned_cols=139 Identities=40% Similarity=0.658 Sum_probs=127.4
Q ss_pred hhcccccCCEEEEeecCCCCcEeeEEEEEccCCEEEEeccceeeeeeCCC-CCCCCceEEEeeeccCCC-ccccCCCCCC
Q 031473 11 RHWKILRGDNVMIIRGKDKGETGAIKRVIRSQNRVIVEGKNLVKKHIKGG-EGHEGGIFTVEAPIHASN-VQVLDPVTGK 88 (159)
Q Consensus 11 r~~~i~kGD~V~Vi~G~dKGk~G~V~~V~~~~~~V~Vegvn~~~~~~k~~-~~~~g~i~~~e~pI~~Sn-V~Lvdp~~g~ 88 (159)
..|.++.||+|+||.|+||||||.|++|.+.+|+|+|+|+|...+|+... .|..|.++..|+|||.|| |+||||++.+
T Consensus 69 ~dw~ff~GDtVeVlvGkDkGkqG~Vtqv~r~~s~VvV~gln~k~r~~gsekeg~pgtivk~EaPlhvsk~VmLvdp~d~q 148 (236)
T KOG1708|consen 69 EDWHFFFGDTVEVLVGKDKGKQGEVTQVIRHRSWVVVKGLNTKYRHMGSEKEGEPGTIVKSEAPLHVSKQVMLVDPEDDQ 148 (236)
T ss_pred cceeEecCCEEEEEecccCCccceEEEEeecCceEEEcccchhhhhhcccccCCCceEEeecCCceecceeEEECccccC
Confidence 57999999999999999999999999999999999999999999998876 467899999999999999 9999999999
Q ss_pred ceeEEEEEccCCcEEEEEEecCCCCeeecCCCccc-ccCCCCCCCCCC-CCCChhhhccceeeeCC
Q 031473 89 PCKVGTKYLEDGTKVRVARGIGASGSIIPRPEILK-IRTTPRPTVAGP-KDTPVDLVMKKTYDAKS 152 (159)
Q Consensus 89 ~~rV~~~~~~~g~k~R~~k~~~~~~~~IPwP~~~~-~~~~~~~~~d~~-~DT~~~~v~e~Ty~p~~ 152 (159)
++++.|+++++|+++|++. +||.+||.|+... ....|..+.+.+ +||+..+|+|+||.|.+
T Consensus 149 ~te~~wr~~e~GekVRvst---rSG~iIpipe~~t~dy~~pe~yiE~e~KdTp~~av~erTy~pkl 211 (236)
T KOG1708|consen 149 PTEVEWRFTEDGEKVRVST---RSGRIIPIPEKWTADYIKPELYIEAEDKDTPQVAVLERTYVPKL 211 (236)
T ss_pred CceeeEEEcCCCcEEEEEe---cccccccCcccccccccCchheeecccCCCcHhhhhhhhcchhH
Confidence 9999999999999999998 7999999998762 234566677766 99999999999999987
No 4
>COG0198 RplX Ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=99.97 E-value=1.8e-30 Score=188.95 Aligned_cols=98 Identities=55% Similarity=0.861 Sum_probs=90.8
Q ss_pred hhcccccCCEEEEeecCCCCcEeeEEEEEccCCEEEEeccceeeeeeCCC-CCCCCceEEEeeeccCCCccccCC-CCCC
Q 031473 11 RHWKILRGDNVMIIRGKDKGETGAIKRVIRSQNRVIVEGKNLVKKHIKGG-EGHEGGIFTVEAPIHASNVQVLDP-VTGK 88 (159)
Q Consensus 11 r~~~i~kGD~V~Vi~G~dKGk~G~V~~V~~~~~~V~Vegvn~~~~~~k~~-~~~~g~i~~~e~pI~~SnV~Lvdp-~~g~ 88 (159)
+.|+|++||+|+||+|+|||++|+|++|+++. |+|||+|+.++|.++. +..+|+++++|+|||+|||||+++ .+++
T Consensus 1 ~~~~IrkGD~V~Vi~GkdKGk~GkVl~v~~k~--V~VEGvnv~kkh~k~~~~~~~ggii~~EapIh~SnV~i~~~~~~~~ 78 (104)
T COG0198 1 MKMKVKKGDTVKVIAGKDKGKEGKVLKVLPKK--VVVEGVNVVKKHIKPSQENPEGGIINKEAPIHISNVAIIDPNKTGK 78 (104)
T ss_pred CCcceecCCEEEEEecCCCCcceEEEEEecCe--EEEECcEEEEecCCCCCcCCCCceeeeeecccHHHeEEeccccCCC
Confidence 46899999999999999999999999999998 9999999999999955 455799999999999999999999 7899
Q ss_pred ceeEEEEEccCCcEEEEEEecC
Q 031473 89 PCKVGTKYLEDGTKVRVARGIG 110 (159)
Q Consensus 89 ~~rV~~~~~~~g~k~R~~k~~~ 110 (159)
++|++|++..+|+++|++++++
T Consensus 79 ~~Rv~~~~~~~~kkvr~~Kk~g 100 (104)
T COG0198 79 PTRVGYKVEEDGKKVRVAKKSG 100 (104)
T ss_pred cceEEEEEecCCcEEEEEeccC
Confidence 9999999877899999999643
No 5
>CHL00141 rpl24 ribosomal protein L24; Validated
Probab=99.93 E-value=2.5e-26 Score=161.64 Aligned_cols=76 Identities=41% Similarity=0.639 Sum_probs=71.5
Q ss_pred hcccccCCEEEEeecCCCCcEeeEEEEEccCCEEEEeccceeeeeeCCCC-CCCCceEEEeeeccCCCccccCCCCC
Q 031473 12 HWKILRGDNVMIIRGKDKGETGAIKRVIRSQNRVIVEGKNLVKKHIKGGE-GHEGGIFTVEAPIHASNVQVLDPVTG 87 (159)
Q Consensus 12 ~~~i~kGD~V~Vi~G~dKGk~G~V~~V~~~~~~V~Vegvn~~~~~~k~~~-~~~g~i~~~e~pI~~SnV~Lvdp~~g 87 (159)
+++|++||+|+||+|+||||+|+|++|++++++|+|||+|+.++|++++. +.+|+++++|+|||+|||+|+||++.
T Consensus 6 ~~~I~~GD~V~Vi~G~dKGK~G~V~~V~~~~~~V~Vegvn~~~k~~k~~~~~~~g~i~~~e~pI~~SnV~lvdp~~~ 82 (83)
T CHL00141 6 KMHVKIGDTVKIISGSDKGKIGEVLKIIKKSNKVIVKGINIKFKHIKPNKENEVGEIKQFEAPIHSSNVMLYNEESN 82 (83)
T ss_pred eCcccCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEEcCcEEEEEEcCCccCCCCCCEEEEECCCCHHHEEEeCcccC
Confidence 46999999999999999999999999999999999999999999999875 55799999999999999999999874
No 6
>PRK12281 rplX 50S ribosomal protein L24; Reviewed
Probab=99.92 E-value=2.5e-25 Score=154.11 Aligned_cols=71 Identities=45% Similarity=0.715 Sum_probs=67.0
Q ss_pred hcccccCCEEEEeecCCCCcEeeEEEEEccCCEEEEeccceeeeeeCCCC-CCCCceEEEeeeccCCCcccc
Q 031473 12 HWKILRGDNVMIIRGKDKGETGAIKRVIRSQNRVIVEGKNLVKKHIKGGE-GHEGGIFTVEAPIHASNVQVL 82 (159)
Q Consensus 12 ~~~i~kGD~V~Vi~G~dKGk~G~V~~V~~~~~~V~Vegvn~~~~~~k~~~-~~~g~i~~~e~pI~~SnV~Lv 82 (159)
+++|++||+|+|++|+|||++|+|++|++++++|+|||+|+.++|+++++ +.+|+++++|+|||+|||+|+
T Consensus 4 ~~~I~kGD~V~Vi~G~dKGK~G~V~~V~~~~~~V~Vegvn~~kkh~kp~~~~~~G~i~~~e~pI~~SnV~l~ 75 (76)
T PRK12281 4 KLKVKKGDMVKVIAGDDKGKTGKVLAVLPKKNRVIVEGVKIAKKAIKPSQKNPNGGFIEKEMPIHISNVKKV 75 (76)
T ss_pred cccccCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEEcCcEEEEEEcCCCccCCCCCEEEEEcCcCHHHceec
Confidence 37999999999999999999999999999999999999999999999875 446999999999999999996
No 7
>PRK01191 rpl24p 50S ribosomal protein L24P; Validated
Probab=99.86 E-value=4.2e-22 Score=148.36 Aligned_cols=77 Identities=32% Similarity=0.464 Sum_probs=69.4
Q ss_pred hHhhcchhcccccCCEEEEeecCCCCcEeeEEEEEccCCEEEEeccceeeeeeCCCCCCCCceEEEeeeccCCCccccCC
Q 031473 5 AAEKLIRHWKILRGDNVMIIRGKDKGETGAIKRVIRSQNRVIVEGKNLVKKHIKGGEGHEGGIFTVEAPIHASNVQVLDP 84 (159)
Q Consensus 5 ~~~~~ir~~~i~kGD~V~Vi~G~dKGk~G~V~~V~~~~~~V~Vegvn~~~~~~k~~~~~~g~i~~~e~pI~~SnV~Lvdp 84 (159)
..+|.++.|+|++||.|+|++|+|||++|+|++|++++++|+|||+|+.+. + | .++|+|||+|||+|+|+
T Consensus 36 r~~y~ir~~~IkkGD~V~VisG~~KGk~GkV~~V~~~~~~V~VeGvn~~k~-----~---G--~~~e~pIh~SNV~l~~l 105 (120)
T PRK01191 36 REKYGIRSLPVRKGDTVKVMRGDFKGEEGKVVEVDLKRGRIYVEGVTVKKA-----D---G--TEVPRPIHPSNVMITKL 105 (120)
T ss_pred HHHhCCccceEeCCCEEEEeecCCCCceEEEEEEEcCCCEEEEeCcEEECC-----C---C--eEEEcccchhHeEEEeC
Confidence 468999999999999999999999999999999999999999999999873 2 3 58999999999999999
Q ss_pred CCCCcee
Q 031473 85 VTGKPCK 91 (159)
Q Consensus 85 ~~g~~~r 91 (159)
..+...|
T Consensus 106 ~l~~~~R 112 (120)
T PRK01191 106 DLSDERR 112 (120)
T ss_pred ccCCHHH
Confidence 8855443
No 8
>PTZ00194 60S ribosomal protein L26; Provisional
Probab=99.85 E-value=8.3e-22 Score=150.54 Aligned_cols=75 Identities=28% Similarity=0.373 Sum_probs=69.9
Q ss_pred hHhhcchhcccccCCEEEEeecCCCCcEeeEEEEEccCCEEEEeccceeeeeeCCCCCCCCceEEEeeeccCCCccccCC
Q 031473 5 AAEKLIRHWKILRGDNVMIIRGKDKGETGAIKRVIRSQNRVIVEGKNLVKKHIKGGEGHEGGIFTVEAPIHASNVQVLDP 84 (159)
Q Consensus 5 ~~~~~ir~~~i~kGD~V~Vi~G~dKGk~G~V~~V~~~~~~V~Vegvn~~~~~~k~~~~~~g~i~~~e~pI~~SnV~Lvdp 84 (159)
..+|.+|.|+|++||.|+||+|+|||++|+|++|++++++|+|||+|+.++|.+ .+|+|||+|||+|+++
T Consensus 37 r~k~~~Rs~~IkkGD~V~Vi~Gk~KGk~GkV~~V~~k~~~ViVEgvn~~Kk~gk----------~~e~PIh~SNV~iv~l 106 (143)
T PTZ00194 37 RAKYNVRSMPVRKDDEVMVVRGHHKGREGKVTAVYRKKWVIHIEKITREKANGE----------PVQIGIHPSNVIITKL 106 (143)
T ss_pred HHHhCCccceeecCCEEEEecCCCCCCceEEEEEEcCCCEEEEeCeEEEecCCC----------EeecCcCchheEEEcc
Confidence 468999999999999999999999999999999999999999999999998744 3799999999999999
Q ss_pred CCCCc
Q 031473 85 VTGKP 89 (159)
Q Consensus 85 ~~g~~ 89 (159)
..+..
T Consensus 107 ~l~~~ 111 (143)
T PTZ00194 107 KLNKD 111 (143)
T ss_pred ccCch
Confidence 98776
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=99.80 E-value=5.8e-20 Score=136.09 Aligned_cols=76 Identities=32% Similarity=0.403 Sum_probs=68.7
Q ss_pred HhHhhcchhcccccCCEEEEeecCCCCcEeeEEEEEccCCEEEEeccceeeeeeCCCCCCCCceEEEeeeccCCCccccC
Q 031473 4 KAAEKLIRHWKILRGDNVMIIRGKDKGETGAIKRVIRSQNRVIVEGKNLVKKHIKGGEGHEGGIFTVEAPIHASNVQVLD 83 (159)
Q Consensus 4 ~~~~~~ir~~~i~kGD~V~Vi~G~dKGk~G~V~~V~~~~~~V~Vegvn~~~~~~k~~~~~~g~i~~~e~pI~~SnV~Lvd 83 (159)
-..+|.++.++|++||+|+|++|+|||++|+|++|++++++|+|||+|+.+. . | .++|+|||+|||+|+|
T Consensus 31 lr~~y~~r~~~IkkGD~V~Vi~Gk~KGk~GkV~~V~~~~~~V~Vegvn~~k~-----~---G--~~~e~pIh~SnV~l~~ 100 (114)
T TIGR01080 31 LREKYGKRALPVRKGDKVRIMRGDFKGHEGKVSKVDLKRYRIYVEGVTKEKV-----N---G--TEVPVPIHPSNVMITK 100 (114)
T ss_pred HHHHcCcccceeecCCEEEEecCCCCCCEEEEEEEEcCCCEEEEcCeEEECC-----C---C--eEEEeeechHHeEEEe
Confidence 4567889999999999999999999999999999999999999999999872 1 3 5899999999999999
Q ss_pred CCCCCc
Q 031473 84 PVTGKP 89 (159)
Q Consensus 84 p~~g~~ 89 (159)
+..+..
T Consensus 101 l~l~~~ 106 (114)
T TIGR01080 101 LNLDDE 106 (114)
T ss_pred ccCChH
Confidence 988665
No 10
>KOG3401 consensus 60S ribosomal protein L26 [Translation, ribosomal structure and biogenesis]
Probab=98.89 E-value=1.2e-09 Score=83.59 Aligned_cols=74 Identities=28% Similarity=0.394 Sum_probs=63.8
Q ss_pred hHhhcchhcccccCCEEEEeecCCCC-cEeeEEEEEccCCEEEEeccceeeeeeCCCCCCCCceEEEeeeccCCCccccC
Q 031473 5 AAEKLIRHWKILRGDNVMIIRGKDKG-ETGAIKRVIRSQNRVIVEGKNLVKKHIKGGEGHEGGIFTVEAPIHASNVQVLD 83 (159)
Q Consensus 5 ~~~~~ir~~~i~kGD~V~Vi~G~dKG-k~G~V~~V~~~~~~V~Vegvn~~~~~~k~~~~~~g~i~~~e~pI~~SnV~Lvd 83 (159)
..+|.+++++|+.+|.|+|.+|.++| ++|+|++|++++..+++|.|...+. .|. +++.|||+|++.+..
T Consensus 39 R~~y~vrs~pir~ddev~v~rg~~kG~q~G~v~~vyrKk~~iyie~v~~eK~-----nGt-----~v~vgihPsK~~iTk 108 (145)
T KOG3401|consen 39 RQKYNVRSMPIRKDDEVQVVRGHFKGFQIGKVSQVYRKKYVIYIERVQREKA-----NGT-----TVPVGIHPSKVVITK 108 (145)
T ss_pred HHHhCccccceeeccEEEEEeccccccccceehhhhhhhheeeeEeEEEeec-----cCc-----ccccccCccceeecc
Confidence 45789999999999999999999999 9999999999999999998765443 233 789999999999987
Q ss_pred CCCCC
Q 031473 84 PVTGK 88 (159)
Q Consensus 84 p~~g~ 88 (159)
|...+
T Consensus 109 l~lDk 113 (145)
T KOG3401|consen 109 LKLDK 113 (145)
T ss_pred cchhh
Confidence 66543
No 11
>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=98.85 E-value=6.3e-09 Score=60.56 Aligned_cols=32 Identities=47% Similarity=0.620 Sum_probs=30.7
Q ss_pred cCCEEEEeecCCCCcEeeEEEEEccCCEEEEe
Q 031473 17 RGDNVMIIRGKDKGETGAIKRVIRSQNRVIVE 48 (159)
Q Consensus 17 kGD~V~Vi~G~dKGk~G~V~~V~~~~~~V~Ve 48 (159)
+||.|+|++|+++|++|+|.++++++++|+||
T Consensus 1 ~Gd~V~V~~G~~~G~~G~I~~i~~~~~~V~ve 32 (32)
T PF00467_consen 1 VGDTVKVISGPFKGKIGKIVEIDRSKVRVTVE 32 (32)
T ss_dssp TTSEEEESSSTTTTEEEEEEEEETTTTEEEES
T ss_pred CCCEEEEeEcCCCCceEEEEEEECCCCEEEEC
Confidence 69999999999999999999999999999986
No 12
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=97.96 E-value=1.4e-05 Score=44.07 Aligned_cols=26 Identities=35% Similarity=0.449 Sum_probs=24.4
Q ss_pred cccCCEEEEeecCCCCcEeeEEEEEc
Q 031473 15 ILRGDNVMIIRGKDKGETGAIKRVIR 40 (159)
Q Consensus 15 i~kGD~V~Vi~G~dKGk~G~V~~V~~ 40 (159)
+.+||.|+|+.|+++|++|.|++++.
T Consensus 2 ~~~G~~V~I~~G~~~g~~g~i~~i~~ 27 (28)
T smart00739 2 FEVGDTVRVIAGPFKGKVGKVLEVDG 27 (28)
T ss_pred CCCCCEEEEeECCCCCcEEEEEEEcC
Confidence 67999999999999999999999875
No 13
>PRK08559 nusG transcription antitermination protein NusG; Validated
Probab=97.56 E-value=0.00019 Score=55.38 Aligned_cols=57 Identities=30% Similarity=0.359 Sum_probs=46.2
Q ss_pred cccccCCEEEEeecCCCCcEeeEEEEEccCCEEEEeccceeeeeeCCCCCCCCceEEEeeeccCCCccccC
Q 031473 13 WKILRGDNVMIIRGKDKGETGAIKRVIRSQNRVIVEGKNLVKKHIKGGEGHEGGIFTVEAPIHASNVQVLD 83 (159)
Q Consensus 13 ~~i~kGD~V~Vi~G~dKGk~G~V~~V~~~~~~V~Vegvn~~~~~~k~~~~~~g~i~~~e~pI~~SnV~Lvd 83 (159)
..+.+||.|.|++|+++|..|.|.+++.+++.+.|+-++.. +..+.-|+.+.|+++.
T Consensus 93 ~~~~~G~~V~I~~Gpf~g~~g~V~~vd~~k~~v~v~ll~~~--------------~~~pv~v~~~~~~~~~ 149 (153)
T PRK08559 93 EGIKEGDIVELIAGPFKGEKARVVRVDESKEEVTVELLEAA--------------VPIPVTVRGDQVRVVK 149 (153)
T ss_pred cCCCCCCEEEEeccCCCCceEEEEEEcCCCCEEEEEEECCc--------------ceeeEEEeccEEEEec
Confidence 45889999999999999999999999999999998865432 1345667777777775
No 14
>TIGR00405 L26e_arch ribosomal protein L24p/L26e, archaeal. This protein contains a KOW domain, shared by bacterial NusG and the L24p/L26e family of ribosomal proteins. Although called archaeal NusG in several publications, it is the only close homolog of eukaryotic L26e in archaeal genomes, shares an operon with L11 in many genomes, and has been sequenced from purified ribosomes. It is here designated as a ribosomal protein for these reasons.
Probab=97.37 E-value=0.00042 Score=52.58 Aligned_cols=37 Identities=41% Similarity=0.455 Sum_probs=33.7
Q ss_pred cccCCEEEEeecCCCCcEeeEEEEEccCCEEEEeccc
Q 031473 15 ILRGDNVMIIRGKDKGETGAIKRVIRSQNRVIVEGKN 51 (159)
Q Consensus 15 i~kGD~V~Vi~G~dKGk~G~V~~V~~~~~~V~Vegvn 51 (159)
+.+||.|.|++|+++|-.|.|.+++..+..|.|+-.+
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 7899999999999999999999999888888888544
No 15
>COG0250 NusG Transcription antiterminator [Transcription]
Probab=97.19 E-value=0.00074 Score=53.67 Aligned_cols=36 Identities=28% Similarity=0.315 Sum_probs=33.6
Q ss_pred cccccCCEEEEeecCCCCcEeeEEEEEccCCEEEEe
Q 031473 13 WKILRGDNVMIIRGKDKGETGAIKRVIRSQNRVIVE 48 (159)
Q Consensus 13 ~~i~kGD~V~Vi~G~dKGk~G~V~~V~~~~~~V~Ve 48 (159)
..|.+||.|.|++|+++|-.|+|.+|+.+++++.|+
T Consensus 122 ~~~e~Gd~VrI~~GpFa~f~g~V~evd~ek~~~~v~ 157 (178)
T COG0250 122 VDFEPGDVVRIIDGPFAGFKAKVEEVDEEKGKLKVE 157 (178)
T ss_pred ccCCCCCEEEEeccCCCCccEEEEEEcCcCcEEEEE
Confidence 568899999999999999999999999999988887
No 16
>PRK05609 nusG transcription antitermination protein NusG; Validated
Probab=96.98 E-value=0.0015 Score=50.91 Aligned_cols=36 Identities=19% Similarity=0.213 Sum_probs=32.5
Q ss_pred cccccCCEEEEeecCCCCcEeeEEEEEccCCEEEEe
Q 031473 13 WKILRGDNVMIIRGKDKGETGAIKRVIRSQNRVIVE 48 (159)
Q Consensus 13 ~~i~kGD~V~Vi~G~dKGk~G~V~~V~~~~~~V~Ve 48 (159)
..+.+||+|.|++|+++|-.|.|.++++.++++.|.
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 557899999999999999999999999888787776
No 17
>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=96.96 E-value=0.0016 Score=50.52 Aligned_cols=36 Identities=19% Similarity=0.233 Sum_probs=32.3
Q ss_pred cccccCCEEEEeecCCCCcEeeEEEEEccCCEEEEe
Q 031473 13 WKILRGDNVMIIRGKDKGETGAIKRVIRSQNRVIVE 48 (159)
Q Consensus 13 ~~i~kGD~V~Vi~G~dKGk~G~V~~V~~~~~~V~Ve 48 (159)
-.+.+||+|.|++|+++|-.|.|.++++.++++.|.
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 347899999999999999999999999888788776
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=96.27 E-value=0.0077 Score=45.95 Aligned_cols=35 Identities=20% Similarity=0.149 Sum_probs=29.5
Q ss_pred cccccCCEEEEeecCCCCcEeeEEEEEccCCEEEEe
Q 031473 13 WKILRGDNVMIIRGKDKGETGAIKRVIRSQNRVIVE 48 (159)
Q Consensus 13 ~~i~kGD~V~Vi~G~dKGk~G~V~~V~~~~~~V~Ve 48 (159)
-.+.+||+|.|+.|+++|-.|.|.+++. ++++.|.
T Consensus 107 ~~~~~G~~V~V~~GPf~g~~g~v~~~~~-~~r~~v~ 141 (159)
T TIGR01955 107 TLPYKGDKVRITDGAFAGFEAIFLEPDG-EKRSMLL 141 (159)
T ss_pred cCCCCCCEEEEeccCCCCcEEEEEEECC-CceEEEE
Confidence 3478999999999999999999999984 4566654
No 19
>PRK09014 rfaH transcriptional activator RfaH; Provisional
Probab=96.10 E-value=0.0096 Score=45.79 Aligned_cols=34 Identities=24% Similarity=0.251 Sum_probs=28.9
Q ss_pred ccccCCEEEEeecCCCCcEeeEEEEEccCCEEEEe
Q 031473 14 KILRGDNVMIIRGKDKGETGAIKRVIRSQNRVIVE 48 (159)
Q Consensus 14 ~i~kGD~V~Vi~G~dKGk~G~V~~V~~~~~~V~Ve 48 (159)
.+.+||+|.|+.|+++|-.|.|.+++ ..+++.|.
T Consensus 109 ~~~~G~~V~I~~Gp~~g~eg~v~~~~-~~~r~~v~ 142 (162)
T PRK09014 109 TPKPGDKVIITEGAFEGLQAIYTEPD-GEARSILL 142 (162)
T ss_pred CCCCCCEEEEecCCCCCcEEEEEEeC-CCeEEEEe
Confidence 37799999999999999999999998 45565554
No 20
>TIGR01956 NusG_myco NusG family protein. This model represents a family of Mycoplasma proteins orthologous to the bacterial transcription termination/antitermination factor NusG. These sequences from Mycoplasma are notably diverged (long branches in a Neighbor-joining phylogenetic tree) from the bacterial species. And although NusA and ribosomal protein S10 (NusE) appear to be present, NusB may be absent in Mycoplasmas calling into question whether these species have a functional Nus system including this family as a member.
Probab=96.07 E-value=0.012 Score=49.36 Aligned_cols=37 Identities=35% Similarity=0.461 Sum_probs=33.1
Q ss_pred hcccccCCEEEEeecCCCCcEeeEEEEEccCCEEEEe
Q 031473 12 HWKILRGDNVMIIRGKDKGETGAIKRVIRSQNRVIVE 48 (159)
Q Consensus 12 ~~~i~kGD~V~Vi~G~dKGk~G~V~~V~~~~~~V~Ve 48 (159)
...+.+||.|.|++|+++|-.|.|.+++..++++.|.
T Consensus 203 ~~~f~vGd~VrI~dGPF~GfeG~I~eid~~k~Rv~Vl 239 (258)
T TIGR01956 203 LSKFRVGNFVKIVDGPFKGIVGKIKKIDQEKKKAIVE 239 (258)
T ss_pred ccCCCCCCEEEEEecCCCCcEEEEEEEeCCCCEEEEE
Confidence 3557899999999999999999999999878888776
No 21
>PRK04333 50S ribosomal protein L14e; Validated
Probab=93.50 E-value=0.19 Score=35.34 Aligned_cols=37 Identities=27% Similarity=0.356 Sum_probs=31.9
Q ss_pred cccccCCEEEEeecCCCCcEeeEEEEEccCCEEEEecc
Q 031473 13 WKILRGDNVMIIRGKDKGETGAIKRVIRSQNRVIVEGK 50 (159)
Q Consensus 13 ~~i~kGD~V~Vi~G~dKGk~G~V~~V~~~~~~V~Vegv 50 (159)
..+..|-.|.+..|+|+|+...|..+.- .++|+|+|-
T Consensus 2 ~~v~~GrvV~~~~Grd~gk~~vIv~i~d-~~~vlVdg~ 38 (84)
T PRK04333 2 PAIEVGRVCVKTAGREAGRKCVIVDIID-KNFVLVTGP 38 (84)
T ss_pred CcccccEEEEEeccCCCCCEEEEEEEec-CCEEEEECC
Confidence 3567899999999999999999999864 589999884
No 22
>PTZ00065 60S ribosomal protein L14; Provisional
Probab=88.99 E-value=0.92 Score=34.51 Aligned_cols=35 Identities=29% Similarity=0.491 Sum_probs=30.1
Q ss_pred cccCCEEEEeecCCCCcEeeEEEEEccCCEEEEecc
Q 031473 15 ILRGDNVMIIRGKDKGETGAIKRVIRSQNRVIVEGK 50 (159)
Q Consensus 15 i~kGD~V~Vi~G~dKGk~G~V~~V~~~~~~V~Vegv 50 (159)
+-.|=.|.|..|+++||.+.|..|. +.|+|+|+|-
T Consensus 8 VEiGRVvli~~Gp~~GKL~vIVDII-D~nRvLVDGP 42 (130)
T PTZ00065 8 VEPGRLCLIQYGPDAGKLCFIVDIV-TPTRVLVDGA 42 (130)
T ss_pred eeeceEEEEecCCCCCCEEEEEEEE-cCCeEEEeCC
Confidence 4568788888999999999999997 5589999984
No 23
>PRK04313 30S ribosomal protein S4e; Validated
Probab=87.32 E-value=0.91 Score=37.80 Aligned_cols=42 Identities=31% Similarity=0.499 Sum_probs=34.7
Q ss_pred hcchhcccccCCEEEEeecCCCCcEeeEEEEEccC----CEEEEec
Q 031473 8 KLIRHWKILRGDNVMIIRGKDKGETGAIKRVIRSQ----NRVIVEG 49 (159)
Q Consensus 8 ~~ir~~~i~kGD~V~Vi~G~dKGk~G~V~~V~~~~----~~V~Veg 49 (159)
+-....++..|-.|+|+.|++.|.+|+|.++.+.. |.|.+++
T Consensus 165 kI~~~i~fe~G~l~~itgG~n~GriG~I~~i~~~~~~~~~~V~i~d 210 (237)
T PRK04313 165 EIVDHIPFEEGNLAIITGGKHVGEIGKIKEIEVTKSSKPNIVTLED 210 (237)
T ss_pred ceeEEEecCCCCEEEEECCeeeeeEEEEEEEEEccCCCCcEEEEEc
Confidence 34567889999999999999999999999987443 6777774
No 24
>PTZ00471 60S ribosomal protein L27; Provisional
Probab=87.30 E-value=1.1 Score=34.23 Aligned_cols=40 Identities=18% Similarity=0.327 Sum_probs=33.4
Q ss_pred cccCCEEEEeecCCCCcEeeEEEEEccC------CEEEEeccceee
Q 031473 15 ILRGDNVMIIRGKDKGETGAIKRVIRSQ------NRVIVEGKNLVK 54 (159)
Q Consensus 15 i~kGD~V~Vi~G~dKGk~G~V~~V~~~~------~~V~Vegvn~~~ 54 (159)
+++|=.|.|++|++.|+...|++.+-+. +..+|.|+....
T Consensus 5 ~kpgkVVivL~GR~AGkKaVivk~~ddgt~drpy~halVaGIdryP 50 (134)
T PTZ00471 5 LKPGKVVIVTSGRYAGRKAVIVQNFDTASKERPYGHALVAGIKKYP 50 (134)
T ss_pred ccCCEEEEEEccccCCcEEEEEeecCCCCccCcCceEEEEeecccc
Confidence 5688899999999999999999977664 689999976543
No 25
>COG2163 RPL14A Ribosomal protein L14E/L6E/L27E [Translation, ribosomal structure and biogenesis]
Probab=84.74 E-value=1.8 Score=32.73 Aligned_cols=35 Identities=23% Similarity=0.412 Sum_probs=30.5
Q ss_pred cccCCEEEEeecCCCCcEeeEEEEEccCCEEEEecc
Q 031473 15 ILRGDNVMIIRGKDKGETGAIKRVIRSQNRVIVEGK 50 (159)
Q Consensus 15 i~kGD~V~Vi~G~dKGk~G~V~~V~~~~~~V~Vegv 50 (159)
+.+|=-|+|++|.++|+...|+++.-++ .+++.|-
T Consensus 5 l~~GrVvvv~~GR~aGkk~VIv~~iDd~-~v~i~gp 39 (125)
T COG2163 5 LEVGRVVVVTAGRFAGKKVVIVKIIDDN-FVLITGP 39 (125)
T ss_pred ccCCeEEEEecceeCCceEEEEEEccCC-EEEEeCC
Confidence 5789999999999999999999987654 8888873
No 26
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=84.61 E-value=0.99 Score=44.19 Aligned_cols=28 Identities=36% Similarity=0.593 Sum_probs=25.5
Q ss_pred ccccCCEEEEeecCCCCcEeeEEEEEcc
Q 031473 14 KILRGDNVMIIRGKDKGETGAIKRVIRS 41 (159)
Q Consensus 14 ~i~kGD~V~Vi~G~dKGk~G~V~~V~~~ 41 (159)
.|.+||-|.|++|++.|..|.|.+|...
T Consensus 459 yF~~GDhVKVi~G~~eG~tGlVvrVe~~ 486 (1024)
T KOG1999|consen 459 YFEPGDHVKVIAGRYEGDTGLVVRVEQG 486 (1024)
T ss_pred hccCCCeEEEEeccccCCcceEEEEeCC
Confidence 3689999999999999999999999764
No 27
>PRK06531 yajC preprotein translocase subunit YajC; Validated
Probab=82.82 E-value=2.7 Score=31.14 Aligned_cols=32 Identities=25% Similarity=0.465 Sum_probs=26.3
Q ss_pred cccccCCEEEEeecCCCCcEeeEEEEEccCCEEEEe
Q 031473 13 WKILRGDNVMIIRGKDKGETGAIKRVIRSQNRVIVE 48 (159)
Q Consensus 13 ~~i~kGD~V~Vi~G~dKGk~G~V~~V~~~~~~V~Ve 48 (159)
-.+++||+|+-+. |-.|+|.+|+-+.+.|.|+
T Consensus 35 ~sLk~GD~VvT~G----Gi~G~V~~I~~~~~~v~le 66 (113)
T PRK06531 35 NAIQKGDEVVTIG----GLYGTVDEVDTEAKTIVLD 66 (113)
T ss_pred HhcCCCCEEEECC----CcEEEEEEEecCCCEEEEE
Confidence 3678999998554 7889999998877888886
No 28
>COG1471 RPS4A Ribosomal protein S4E [Translation, ribosomal structure and biogenesis]
Probab=81.54 E-value=2.7 Score=34.97 Aligned_cols=42 Identities=31% Similarity=0.476 Sum_probs=34.6
Q ss_pred hcchhcccccCCEEEEeecCCCCcEeeEEEEEccC----CEEEEec
Q 031473 8 KLIRHWKILRGDNVMIIRGKDKGETGAIKRVIRSQ----NRVIVEG 49 (159)
Q Consensus 8 ~~ir~~~i~kGD~V~Vi~G~dKGk~G~V~~V~~~~----~~V~Veg 49 (159)
+-....++-+|-.|.|+.|++.|.+|+|.+|.... |.|.+++
T Consensus 167 ~I~~~i~fe~g~~~~vtgG~h~G~~G~I~~I~~~~~~~~~~v~~e~ 212 (241)
T COG1471 167 KIVEHIKFEEGALVYVTGGRHVGRVGTIVEIEIQESSKPNLVTVED 212 (241)
T ss_pred hheeEeccCCCcEEEEECCccccceEEEEEEEEecCCCccEEEEec
Confidence 34556788999999999999999999999998653 5677765
No 29
>PRK05585 yajC preprotein translocase subunit YajC; Validated
Probab=79.53 E-value=4.1 Score=29.74 Aligned_cols=31 Identities=29% Similarity=0.458 Sum_probs=24.8
Q ss_pred hcccccCCEEEEeecCCCCcEeeEEEEEccCCEEEEe
Q 031473 12 HWKILRGDNVMIIRGKDKGETGAIKRVIRSQNRVIVE 48 (159)
Q Consensus 12 ~~~i~kGD~V~Vi~G~dKGk~G~V~~V~~~~~~V~Ve 48 (159)
.-.+++||+|+-++ |-.|+|.+++. +.|.||
T Consensus 50 ~~~Lk~Gd~VvT~g----Gi~G~Vv~i~~--~~v~le 80 (106)
T PRK05585 50 LSSLAKGDEVVTNG----GIIGKVTKVSE--DFVIIE 80 (106)
T ss_pred HHhcCCCCEEEECC----CeEEEEEEEeC--CEEEEE
Confidence 35689999999766 67899999965 677776
No 30
>PLN00036 40S ribosomal protein S4; Provisional
Probab=78.80 E-value=3.2 Score=35.07 Aligned_cols=42 Identities=26% Similarity=0.468 Sum_probs=32.6
Q ss_pred hcchhcccccCCEEEEeecCCCCcEeeEEEEEccC---CEEEEec
Q 031473 8 KLIRHWKILRGDNVMIIRGKDKGETGAIKRVIRSQ---NRVIVEG 49 (159)
Q Consensus 8 ~~ir~~~i~kGD~V~Vi~G~dKGk~G~V~~V~~~~---~~V~Veg 49 (159)
+-....++..|-.|+|+.|++-|.+|+|.++.... +.|.|++
T Consensus 168 kI~~~ikfe~G~l~~vtgG~n~GrvG~I~~i~~~~~~~~iV~i~d 212 (261)
T PLN00036 168 KIVDFIKFDVGNLVMVTGGRNRGRVGVIKNREKHKGSFEIIHVKD 212 (261)
T ss_pred ceeeEEecCCCCEEEEECCeeceeEEEEEEEEecCCCCCEEEEEe
Confidence 34557888999999999999999999999887432 3455553
No 31
>COG5164 SPT5 Transcription elongation factor [Transcription]
Probab=78.67 E-value=1.8 Score=39.63 Aligned_cols=28 Identities=25% Similarity=0.495 Sum_probs=25.7
Q ss_pred cccCCEEEEeecCCCCcEeeEEEEEccC
Q 031473 15 ILRGDNVMIIRGKDKGETGAIKRVIRSQ 42 (159)
Q Consensus 15 i~kGD~V~Vi~G~dKGk~G~V~~V~~~~ 42 (159)
+.+||.|.||.|.+++-+|.|.+|+.++
T Consensus 140 f~~gD~vkVI~g~~~~d~g~V~rI~~~~ 167 (607)
T COG5164 140 FYKGDLVKVIEGGEMVDIGTVPRIDGEK 167 (607)
T ss_pred cccCCeEEEeccccccccceEEEecCce
Confidence 6799999999999999999999998654
No 32
>PTZ00223 40S ribosomal protein S4; Provisional
Probab=78.19 E-value=3.1 Score=35.35 Aligned_cols=42 Identities=24% Similarity=0.384 Sum_probs=32.6
Q ss_pred hcchhcccccCCEEEEeecCCCCcEeeEEEEEccC---CEEEEec
Q 031473 8 KLIRHWKILRGDNVMIIRGKDKGETGAIKRVIRSQ---NRVIVEG 49 (159)
Q Consensus 8 ~~ir~~~i~kGD~V~Vi~G~dKGk~G~V~~V~~~~---~~V~Veg 49 (159)
+-..+.++..|-.|+|+.|++.|.+|+|.++.... +.|.+++
T Consensus 165 kI~~~ikfe~G~l~~vtgG~n~GriG~I~~i~~~~~~~~iv~i~d 209 (273)
T PTZ00223 165 KVVDLIKNRNGKVVMVTGGANRGRIGEIVSIERHPGAFDIARLKD 209 (273)
T ss_pred eeeEEEecCCCCEEEEECCeeceeEEEEEEEEecCCCCCEEEEEe
Confidence 34567889999999999999999999999885432 4556653
No 33
>COG1862 YajC Preprotein translocase subunit YajC [Intracellular trafficking and secretion]
Probab=76.77 E-value=4.7 Score=29.15 Aligned_cols=30 Identities=30% Similarity=0.479 Sum_probs=23.1
Q ss_pred cccccCCEEEEeecCCCCcEeeEEEEEccCCEEEEe
Q 031473 13 WKILRGDNVMIIRGKDKGETGAIKRVIRSQNRVIVE 48 (159)
Q Consensus 13 ~~i~kGD~V~Vi~G~dKGk~G~V~~V~~~~~~V~Ve 48 (159)
-.+++||+|.-+. |-.|+|.+|.... +.|+
T Consensus 42 ~sL~kGD~VvT~g----Gi~G~V~~v~d~~--v~I~ 71 (97)
T COG1862 42 NSLKKGDEVVTIG----GIVGTVTKVGDDT--VEIE 71 (97)
T ss_pred HhccCCCEEEEcC----CeEEEEEEEecCc--EEEE
Confidence 4579999999665 6789999997665 5554
No 34
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=76.68 E-value=2.1 Score=42.05 Aligned_cols=30 Identities=30% Similarity=0.385 Sum_probs=26.4
Q ss_pred hcccccCCEEEEeecCCCCcEeeEEEEEcc
Q 031473 12 HWKILRGDNVMIIRGKDKGETGAIKRVIRS 41 (159)
Q Consensus 12 ~~~i~kGD~V~Vi~G~dKGk~G~V~~V~~~ 41 (159)
.-.|.+||.|.|+.|.++|-.|+|..|+-.
T Consensus 405 ~~~F~~GD~VeV~~Gel~glkG~ve~vdg~ 434 (1024)
T KOG1999|consen 405 KHLFSPGDAVEVIVGELKGLKGKVESVDGT 434 (1024)
T ss_pred ccccCCCCeEEEeeeeeccceeEEEeccCc
Confidence 345899999999999999999999999743
No 35
>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=76.11 E-value=6.5 Score=27.44 Aligned_cols=31 Identities=26% Similarity=0.574 Sum_probs=24.0
Q ss_pred hcccccCCEEEEeecCCCCcEeeEEEEEccCCEEEEe
Q 031473 12 HWKILRGDNVMIIRGKDKGETGAIKRVIRSQNRVIVE 48 (159)
Q Consensus 12 ~~~i~kGD~V~Vi~G~dKGk~G~V~~V~~~~~~V~Ve 48 (159)
.-++++||+|+-.. |-.|+|.+++- +.+.|+
T Consensus 35 ~~~L~~Gd~VvT~g----Gi~G~V~~i~d--~~v~ve 65 (84)
T TIGR00739 35 IESLKKGDKVLTIG----GIIGTVTKIAE--NTIVIE 65 (84)
T ss_pred HHhCCCCCEEEECC----CeEEEEEEEeC--CEEEEE
Confidence 35689999999665 67899999975 466665
No 36
>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=74.64 E-value=7.7 Score=25.45 Aligned_cols=27 Identities=37% Similarity=0.581 Sum_probs=22.4
Q ss_pred ccCCEEEEeecCCCCcEeeEEEEEccCCEEEEe
Q 031473 16 LRGDNVMIIRGKDKGETGAIKRVIRSQNRVIVE 48 (159)
Q Consensus 16 ~kGD~V~Vi~G~dKGk~G~V~~V~~~~~~V~Ve 48 (159)
..||.+.. .+|-+|+|.+|+ .|+|+|+
T Consensus 5 ~vGdiIef----k~g~~G~V~kv~--eNSVIVd 31 (57)
T PF09953_consen 5 KVGDIIEF----KDGFTGIVEKVY--ENSVIVD 31 (57)
T ss_pred ccCcEEEE----cCCcEEEEEEEe--cCcEEEE
Confidence 47999986 357899999997 6899998
No 37
>PTZ00118 40S ribosomal protein S4; Provisional
Probab=74.50 E-value=4.7 Score=34.07 Aligned_cols=42 Identities=26% Similarity=0.400 Sum_probs=31.9
Q ss_pred hcchhcccccCCEEEEeecCCCCcEeeEEEEEccC---CEEEEec
Q 031473 8 KLIRHWKILRGDNVMIIRGKDKGETGAIKRVIRSQ---NRVIVEG 49 (159)
Q Consensus 8 ~~ir~~~i~kGD~V~Vi~G~dKGk~G~V~~V~~~~---~~V~Veg 49 (159)
+-..+.+|..|-.|+|+.|++-|.+|+|.++.... +.|.|++
T Consensus 168 kI~~~ikfe~G~l~~vtgG~n~GriG~I~~~~~~~~~~~~V~i~d 212 (262)
T PTZ00118 168 KVLEFLKFEVGNLVMITGGHNVGRVGTIVSKEKHPGSFDLIHVKD 212 (262)
T ss_pred ceeeEEecCCCCEEEEECCeeceeEEEEEEEEecCCCCcEEEEEe
Confidence 34567888999999999999999999998855432 4455553
No 38
>PRK05886 yajC preprotein translocase subunit YajC; Validated
Probab=73.57 E-value=7.1 Score=28.78 Aligned_cols=30 Identities=23% Similarity=0.266 Sum_probs=23.7
Q ss_pred cccccCCEEEEeecCCCCcEeeEEEEEccCCEEEEe
Q 031473 13 WKILRGDNVMIIRGKDKGETGAIKRVIRSQNRVIVE 48 (159)
Q Consensus 13 ~~i~kGD~V~Vi~G~dKGk~G~V~~V~~~~~~V~Ve 48 (159)
-.+++||+|+-+. |-.|+|.+|+- +.|.||
T Consensus 37 ~~Lk~GD~VvT~g----Gi~G~V~~I~d--~~v~le 66 (109)
T PRK05886 37 ESLQPGDRVHTTS----GLQATIVGITD--DTVDLE 66 (109)
T ss_pred HhcCCCCEEEECC----CeEEEEEEEeC--CEEEEE
Confidence 4689999999655 67899999973 577776
No 39
>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=72.92 E-value=1.7 Score=30.14 Aligned_cols=31 Identities=26% Similarity=0.468 Sum_probs=1.0
Q ss_pred hcccccCCEEEEeecCCCCcEeeEEEEEccCCEEEEe
Q 031473 12 HWKILRGDNVMIIRGKDKGETGAIKRVIRSQNRVIVE 48 (159)
Q Consensus 12 ~~~i~kGD~V~Vi~G~dKGk~G~V~~V~~~~~~V~Ve 48 (159)
.-.+++||+|.-.+ |-.|+|.++ +++.|.||
T Consensus 34 ~~~Lk~Gd~VvT~g----Gi~G~V~~i--~~~~v~le 64 (82)
T PF02699_consen 34 LASLKPGDEVVTIG----GIYGTVVEI--DDDTVVLE 64 (82)
T ss_dssp GG-----------------------------------
T ss_pred HHcCCCCCEEEECC----cEEEEEEEE--eCCEEEEE
Confidence 45689999999766 678999998 55667666
No 40
>COG1532 Predicted RNA-binding protein [General function prediction only]
Probab=68.14 E-value=11 Score=24.63 Aligned_cols=34 Identities=24% Similarity=0.439 Sum_probs=27.5
Q ss_pred ccCCEEEEe--ecCCCCcEeeEEEEEccCCEEEEec
Q 031473 16 LRGDNVMII--RGKDKGETGAIKRVIRSQNRVIVEG 49 (159)
Q Consensus 16 ~kGD~V~Vi--~G~dKGk~G~V~~V~~~~~~V~Veg 49 (159)
..||.|+.. -|..|--.|+|.+++-..+++++||
T Consensus 22 v~~e~V~a~Dilgd~ke~~G~vkriDldehkI~lE~ 57 (57)
T COG1532 22 VTEEGVVARDILGDEKEFEGQVKRIDLDEHKIELEG 57 (57)
T ss_pred EecCcEEEEeccCCceEecceEEEEEccccEEEecC
Confidence 356666653 5788888899999999999999985
No 41
>COG5164 SPT5 Transcription elongation factor [Transcription]
Probab=62.00 E-value=8.8 Score=35.25 Aligned_cols=34 Identities=35% Similarity=0.420 Sum_probs=30.1
Q ss_pred ccCCEEEEeecCCCCcEeeEEEEEccCCEEEEec
Q 031473 16 LRGDNVMIIRGKDKGETGAIKRVIRSQNRVIVEG 49 (159)
Q Consensus 16 ~kGD~V~Vi~G~dKGk~G~V~~V~~~~~~V~Veg 49 (159)
.-|-+|+|-+|.+||.-|.|+.|++...+|-+.-
T Consensus 353 aigktVrIr~g~yKG~lGVVKdv~~~~arVeLhs 386 (607)
T COG5164 353 AIGKTVRIRCGEYKGHLGVVKDVDRNIARVELHS 386 (607)
T ss_pred ccCceEEEeecccccccceeeeccCceEEEEEec
Confidence 4588999999999999999999999888877753
No 42
>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=61.84 E-value=27 Score=22.53 Aligned_cols=40 Identities=33% Similarity=0.422 Sum_probs=29.7
Q ss_pred cccCCEEEEeecC--CCCcEeeEEEEEccCCEEEEeccceee
Q 031473 15 ILRGDNVMIIRGK--DKGETGAIKRVIRSQNRVIVEGKNLVK 54 (159)
Q Consensus 15 i~kGD~V~Vi~G~--dKGk~G~V~~V~~~~~~V~Vegvn~~~ 54 (159)
|.+|-.|.|+.-. +-|-+|.|.+|-..+-.|+.||-|--|
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 6799999999774 689999999999988899999987654
No 43
>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=58.10 E-value=14 Score=23.84 Aligned_cols=35 Identities=17% Similarity=0.285 Sum_probs=26.1
Q ss_pred cchhcccccCCEEEEeecCCCCcE---eeEEEEEccCCE
Q 031473 9 LIRHWKILRGDNVMIIRGKDKGET---GAIKRVIRSQNR 44 (159)
Q Consensus 9 ~ir~~~i~kGD~V~Vi~G~dKGk~---G~V~~V~~~~~~ 44 (159)
++.+=.|++||+|.++. ...++. ++|.++....+.
T Consensus 7 rV~sG~l~~gd~v~~~~-~~~~~~~~~~~I~~i~~~~~~ 44 (74)
T PF03144_consen 7 RVYSGTLKKGDKVRVLP-NGTGKKGQVVKIKSIFMFNGD 44 (74)
T ss_dssp EEEESEEETTEEEEEES-TTTTEECEEEEEEEEEETTEE
T ss_pred EEEEeEEcCCCEEEECc-cCCcceeeeeecccccccccC
Confidence 34556789999999988 655555 888888877654
No 44
>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=55.19 E-value=20 Score=28.90 Aligned_cols=45 Identities=13% Similarity=0.324 Sum_probs=33.8
Q ss_pred HhHhhcchhcccccCCEEEEeecCCCCcEeeEEEEEccCCEEEEe
Q 031473 4 KAAEKLIRHWKILRGDNVMIIRGKDKGETGAIKRVIRSQNRVIVE 48 (159)
Q Consensus 4 ~~~~~~ir~~~i~kGD~V~Vi~G~dKGk~G~V~~V~~~~~~V~Ve 48 (159)
..++|..+-.+++.||.|.|.-|...--.++|.++.++.-.+.+.
T Consensus 6 ~~~~Hl~~VlR~k~Gd~i~v~dg~g~~~~a~i~~i~~~~~~~~i~ 50 (225)
T PF04452_consen 6 EEAHHLVKVLRLKEGDSIEVFDGDGGEYRAEITEISKKSATLRIL 50 (225)
T ss_dssp HHHHHHHTTST--TT-EEEEEESSSEEEEEEEEEEESSEEEEEEE
T ss_pred HHHHHHHHhcCCCCCCEEEEEECCCCEEEEEEEECcCcEEEEEEe
Confidence 467788899999999999999988666678999998776655554
No 45
>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=53.00 E-value=42 Score=21.94 Aligned_cols=33 Identities=18% Similarity=0.349 Sum_probs=19.8
Q ss_pred cccCCEEEEeecC--CCCc--EeeEEEEEccCCEEEEe
Q 031473 15 ILRGDNVMIIRGK--DKGE--TGAIKRVIRSQNRVIVE 48 (159)
Q Consensus 15 i~kGD~V~Vi~G~--dKGk--~G~V~~V~~~~~~V~Ve 48 (159)
|++||.|.|.+-. +.|- .++|++...+. ++.|+
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 6799999998732 2443 47999987764 66666
No 46
>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed
Probab=51.65 E-value=23 Score=34.12 Aligned_cols=37 Identities=16% Similarity=0.223 Sum_probs=26.0
Q ss_pred cccccCCEEEEeecCCCCcEeeEEEEEccCC-EEEEeccce
Q 031473 13 WKILRGDNVMIIRGKDKGETGAIKRVIRSQN-RVIVEGKNL 52 (159)
Q Consensus 13 ~~i~kGD~V~Vi~G~dKGk~G~V~~V~~~~~-~V~Vegvn~ 52 (159)
..|++||+|.|.+ -|+.|+|+++..+++ .|.+.++.+
T Consensus 635 ~~~~~Gd~V~v~~---~~~~g~v~~i~~~~~~~V~~g~~k~ 672 (782)
T PRK00409 635 EELKVGDEVKYLS---LGQKGEVLSIPDDKEAIVQAGIMKM 672 (782)
T ss_pred cCCCCCCEEEEcc---CCceEEEEEEcCCCeEEEEECCEEE
Confidence 5689999999965 578999999974332 244445544
No 47
>PF14505 DUF4438: Domain of unknown function (DUF4438); PDB: 3N99_N 3DCL_A.
Probab=51.00 E-value=35 Score=28.73 Aligned_cols=33 Identities=21% Similarity=0.441 Sum_probs=25.6
Q ss_pred ccCCEEEEeecCCCCcEeeEEEEEccCCEEEEe
Q 031473 16 LRGDNVMIIRGKDKGETGAIKRVIRSQNRVIVE 48 (159)
Q Consensus 16 ~kGD~V~Vi~G~dKGk~G~V~~V~~~~~~V~Ve 48 (159)
..|.+..|++|.-||..|.|+------+.|+|+
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 369999999999999999999877666788886
No 48
>KOG4315 consensus G-patch nucleic acid binding protein [General function prediction only]
Probab=50.73 E-value=7.1 Score=35.19 Aligned_cols=33 Identities=27% Similarity=0.442 Sum_probs=28.2
Q ss_pred ccCCEEEEeecCCCCcEeeEEEEEccCCEEEEe
Q 031473 16 LRGDNVMIIRGKDKGETGAIKRVIRSQNRVIVE 48 (159)
Q Consensus 16 ~kGD~V~Vi~G~dKGk~G~V~~V~~~~~~V~Ve 48 (159)
.-|++|.|++|+++|+.|.-++-++.+.+..+.
T Consensus 395 ~~Ge~vmvv~gkhkg~~g~llskd~~Ke~~~v~ 427 (455)
T KOG4315|consen 395 RGGEKVMVVSGKHKGVYGSLLSKDLDKETGVVR 427 (455)
T ss_pred ccCceeEEEecccccchhhhhhhhhhhhhccee
Confidence 569999999999999999998888777766655
No 49
>KOG3418 consensus 60S ribosomal protein L27 [Translation, ribosomal structure and biogenesis]
Probab=48.67 E-value=34 Score=26.24 Aligned_cols=39 Identities=21% Similarity=0.414 Sum_probs=30.0
Q ss_pred cccCCEEEEeecCCCCcEeeEEEEEccC------CEEEEecccee
Q 031473 15 ILRGDNVMIIRGKDKGETGAIKRVIRSQ------NRVIVEGKNLV 53 (159)
Q Consensus 15 i~kGD~V~Vi~G~dKGk~G~V~~V~~~~------~~V~Vegvn~~ 53 (159)
+.+|--|.|++|.+.|+...|.+-.-+. ..++|+|+...
T Consensus 5 lkPgkvv~v~sG~yAg~KaVivk~~Ddg~~d~p~~h~LvAgi~ry 49 (136)
T KOG3418|consen 5 LKPGKVVLVLSGRYAGKKAVIVKNIDDGTEDKPYGHALVAGVDRY 49 (136)
T ss_pred ccCCcEEEeecccccCccEEEEeecccCCccCCCceeeeeehhhc
Confidence 6789999999999999988877654333 36788887543
No 50
>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=47.80 E-value=22 Score=29.20 Aligned_cols=27 Identities=33% Similarity=0.425 Sum_probs=15.9
Q ss_pred hcccccCCEEEEeecC----------CCCcEeeEEEE
Q 031473 12 HWKILRGDNVMIIRGK----------DKGETGAIKRV 38 (159)
Q Consensus 12 ~~~i~kGD~V~Vi~G~----------dKGk~G~V~~V 38 (159)
.-+|.+||+|.|..-. -+||+|+|..+
T Consensus 132 ~~~F~vGd~Vrv~~~~~~~HtR~P~Y~rg~~G~I~~~ 168 (222)
T PF02211_consen 132 PPRFAVGDRVRVRNLPPPGHTRLPRYVRGKTGTIERV 168 (222)
T ss_dssp S-SS-TT-EEEE-----SS--SS-GGGTT-EEEEEEE
T ss_pred CCCCCCCCEEEECCCCCCCcccccHhhCCCeeEEEEE
Confidence 4578899999997643 48999999865
No 51
>PF12701 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC8_A 2VXF_A 2VXE_A.
Probab=44.84 E-value=50 Score=23.66 Aligned_cols=34 Identities=12% Similarity=0.227 Sum_probs=31.5
Q ss_pred cCCEEEEeecCCCCcEeeEEEEEccCCEEEEecc
Q 031473 17 RGDNVMIIRGKDKGETGAIKRVIRSQNRVIVEGK 50 (159)
Q Consensus 17 kGD~V~Vi~G~dKGk~G~V~~V~~~~~~V~Vegv 50 (159)
-|-+|-+++..+-.-+|.+..||...+.|.+.++
T Consensus 7 IGs~ISlisk~~iRYeG~L~~Id~~~sTItL~nV 40 (96)
T PF12701_consen 7 IGSKISLISKSDIRYEGILYSIDTEDSTITLKNV 40 (96)
T ss_dssp TTCEEEEEETTTEEEEEEEEEEETTTTEEEEEEE
T ss_pred cCCEEEEEECCCcEEEEEEEEEcCCCCEEEeeee
Confidence 4889999999998899999999999999999975
No 52
>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=43.39 E-value=51 Score=20.85 Aligned_cols=30 Identities=23% Similarity=0.339 Sum_probs=19.6
Q ss_pred ccccCCEEEEeecCCCCcEeeEEEEEccCCEE
Q 031473 14 KILRGDNVMIIRGKDKGETGAIKRVIRSQNRV 45 (159)
Q Consensus 14 ~i~kGD~V~Vi~G~dKGk~G~V~~V~~~~~~V 45 (159)
.+..||.|.+- ..+ +-.+.|.++.+.+|.+
T Consensus 37 ~~~VGD~V~~~-~~~-~~~~~I~~vl~R~s~l 66 (68)
T cd04466 37 PPAVGDRVEFE-PED-DGEGVIEEILPRKNLL 66 (68)
T ss_pred CCCCCcEEEEE-ECC-CCcEEEEEEeccceEE
Confidence 36899999863 222 2346777888777643
No 53
>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=43.26 E-value=47 Score=21.85 Aligned_cols=25 Identities=12% Similarity=0.153 Sum_probs=20.0
Q ss_pred ccccCCEEEEeecCCCCcEeeEEEEEccCCEEEEe
Q 031473 14 KILRGDNVMIIRGKDKGETGAIKRVIRSQNRVIVE 48 (159)
Q Consensus 14 ~i~kGD~V~Vi~G~dKGk~G~V~~V~~~~~~V~Ve 48 (159)
.+..||.|. ++|+++++++.++.+.
T Consensus 46 ~~~vG~~v~----------~kV~~id~~~~~i~Ls 70 (73)
T cd05703 46 KFPIGQALK----------AKVVGVDKEHKLLRLS 70 (73)
T ss_pred hCCCCCEEE----------EEEEEEeCCCCEEEEE
Confidence 367788887 5789999999888764
No 54
>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=42.25 E-value=38 Score=32.68 Aligned_cols=33 Identities=30% Similarity=0.413 Sum_probs=23.9
Q ss_pred ccCCEEEEeecCCCCcEeeEEEEEccCCEEEEe--ccce
Q 031473 16 LRGDNVMIIRGKDKGETGAIKRVIRSQNRVIVE--GKNL 52 (159)
Q Consensus 16 ~kGD~V~Vi~G~dKGk~G~V~~V~~~~~~V~Ve--gvn~ 52 (159)
++||+|.|.+ -|+.|+|+++.. ++.+.|+ ++.+
T Consensus 626 ~~Gd~V~v~~---~~~~g~v~~i~~-~~~~~V~~g~~k~ 660 (771)
T TIGR01069 626 KIGDKVRIRY---FGQKGKIVQILG-GNKWNVTVGGMRM 660 (771)
T ss_pred CCCCEEEEcc---CCceEEEEEEcC-CCeEEEEECCEEE
Confidence 7899999944 688899999974 4454444 5444
No 55
>PRK04306 50S ribosomal protein L21e; Reviewed
Probab=41.91 E-value=55 Score=23.69 Aligned_cols=34 Identities=26% Similarity=0.282 Sum_probs=25.7
Q ss_pred cccCCEEEEee-c---------CCCCcEeeEEEEEccCCEEEEe
Q 031473 15 ILRGDNVMIIR-G---------KDKGETGAIKRVIRSQNRVIVE 48 (159)
Q Consensus 15 i~kGD~V~Vi~-G---------~dKGk~G~V~~V~~~~~~V~Ve 48 (159)
+..||.|-|.- | .+-|+.|.|..+....-.|.|.
T Consensus 35 y~~Gd~V~I~~d~sv~kGmPh~~yhGkTG~V~~v~~~A~~V~v~ 78 (98)
T PRK04306 35 FEEGDKVHIVIDPSVHKGMPHPRFHGKTGTVVGKRGRAYIVEVK 78 (98)
T ss_pred ccCCCEEEEEecCceecCCccccccCCCEEEEeecCeEEEEEEE
Confidence 56799998763 2 2678999999998776666664
No 56
>PF14001 YdfZ: YdfZ protein
Probab=41.66 E-value=59 Score=21.80 Aligned_cols=35 Identities=40% Similarity=0.562 Sum_probs=25.0
Q ss_pred ccccCCEEEEeecCCCCcEeeEEEEEccC---------CEEEEeccc
Q 031473 14 KILRGDNVMIIRGKDKGETGAIKRVIRSQ---------NRVIVEGKN 51 (159)
Q Consensus 14 ~i~kGD~V~Vi~G~dKGk~G~V~~V~~~~---------~~V~Vegvn 51 (159)
.|..|-+|+| +|. |.+|.|.+|.-+. ..|.|+|++
T Consensus 9 ~i~~G~rVMi-agt--G~~gvikAih~~gl~~eq~rR~kcVel~g~~ 52 (64)
T PF14001_consen 9 AITTGSRVMI-AGT--GATGVIKAIHADGLTAEQIRRAKCVELEGCE 52 (64)
T ss_pred cCCCCCEEEE-cCC--CcccEEeeeecCCCCHHHhhhccEEEEeCCC
Confidence 4789999984 554 9999999987443 345666654
No 57
>CHL00125 psaE photosystem I subunit IV; Reviewed
Probab=41.52 E-value=32 Score=22.96 Aligned_cols=28 Identities=32% Similarity=0.418 Sum_probs=22.6
Q ss_pred cccCCEEEEeecC--CCCcEeeEEEEEccC
Q 031473 15 ILRGDNVMIIRGK--DKGETGAIKRVIRSQ 42 (159)
Q Consensus 15 i~kGD~V~Vi~G~--dKGk~G~V~~V~~~~ 42 (159)
|.+||.|.|++=. .-..+|+|.+|+...
T Consensus 2 i~rGskVrIlR~ESYWyn~vGtV~svd~~g 31 (64)
T CHL00125 2 VKRGSKVRILRKESYWYNEIGTVATVDQSG 31 (64)
T ss_pred cccCCEEEEccccceeecCcceEEEEcCCC
Confidence 6799999999853 456789999998764
No 58
>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=41.19 E-value=49 Score=21.28 Aligned_cols=24 Identities=25% Similarity=0.097 Sum_probs=17.9
Q ss_pred ccccCCEEEEeecCCCCcEeeEEEEEccCCEEEE
Q 031473 14 KILRGDNVMIIRGKDKGETGAIKRVIRSQNRVIV 47 (159)
Q Consensus 14 ~i~kGD~V~Vi~G~dKGk~G~V~~V~~~~~~V~V 47 (159)
.++.||.|.+ +|+.+++++.++.+
T Consensus 42 ~~~~G~~i~~----------kVi~id~~~~~i~L 65 (66)
T cd05695 42 TYKEGQKVRA----------RILYVDPSTKVVGL 65 (66)
T ss_pred CcCCCCEEEE----------EEEEEeCCCCEEec
Confidence 4677777764 78899988877654
No 59
>cd03692 mtIF2_IVc mtIF2_IVc: this family represents the C2 subdomain of domain IV of mitochondrial translation initiation factor 2 (mtIF2) which adopts a beta-barrel fold displaying a high degree of structural similarity with domain II of the translation elongation factor EF-Tu. The C-terminal part of mtIF2 contains the entire fMet-tRNAfmet binding site of IF-2 and is resistant to proteolysis. This C-terminal portion consists of two domains, IF2 C1 and IF2 C2. IF2 C2 been shown to contain all molecular determinants necessary and sufficient for the recognition and binding of fMet-tRNAfMet. Like IF2 from certain prokaryotes such as Thermus thermophilus, mtIF2lacks domain II which is thought to be involved in binding of E.coli IF-2 to 30S subunits.
Probab=41.07 E-value=43 Score=22.74 Aligned_cols=35 Identities=23% Similarity=0.291 Sum_probs=21.8
Q ss_pred chhcccccCCEEEEeecCCCCcEeeEEEEEccCCE
Q 031473 10 IRHWKILRGDNVMIIRGKDKGETGAIKRVIRSQNR 44 (159)
Q Consensus 10 ir~~~i~kGD~V~Vi~G~dKGk~G~V~~V~~~~~~ 44 (159)
+.+=.|.+|+.|.|+++..-=..|+|.++.+.++.
T Consensus 22 V~~G~l~~g~~v~vlr~~~~~~~g~i~sl~~~~~~ 56 (84)
T cd03692 22 VTDGKIKRNAKVRVLRNGEVIYEGKISSLKRFKDD 56 (84)
T ss_pred EEECEEeCCCEEEEEcCCCEEEEEEEEEEEEcCcc
Confidence 44556788999999987411134666666655443
No 60
>COG3700 AphA Acid phosphatase (class B) [General function prediction only]
Probab=40.27 E-value=11 Score=30.80 Aligned_cols=33 Identities=18% Similarity=0.451 Sum_probs=28.4
Q ss_pred hcccccCCEEEEeecCCCCcEeeEEEEEccCCE
Q 031473 12 HWKILRGDNVMIIRGKDKGETGAIKRVIRSQNR 44 (159)
Q Consensus 12 ~~~i~kGD~V~Vi~G~dKGk~G~V~~V~~~~~~ 44 (159)
.++.++||.++.+.|+-.||+-.|.....+.-.
T Consensus 124 ~MHq~RGD~i~FvTGRt~gk~d~vsk~Lak~F~ 156 (237)
T COG3700 124 DMHQRRGDAIYFVTGRTPGKTDTVSKTLAKNFH 156 (237)
T ss_pred HHHHhcCCeEEEEecCCCCcccccchhHHhhcc
Confidence 478899999999999999999999988766543
No 61
>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=40.01 E-value=33 Score=21.82 Aligned_cols=24 Identities=29% Similarity=0.537 Sum_probs=13.6
Q ss_pred cccCCEEEE-eecCC--CCcEeeEEEE
Q 031473 15 ILRGDNVMI-IRGKD--KGETGAIKRV 38 (159)
Q Consensus 15 i~kGD~V~V-i~G~d--KGk~G~V~~V 38 (159)
-.-||+|.| +..+. +...|+|.+|
T Consensus 32 A~~gD~V~v~i~~~~~~~~~eg~vv~V 58 (58)
T PF08206_consen 32 AMDGDKVLVRITPPSRGKRPEGEVVEV 58 (58)
T ss_dssp S-TT-EEEEEEEESSSEEEEEEEEEE-
T ss_pred CCCCCEEEEEEecCCCCCCCCEEEEeC
Confidence 357999988 34333 4456888775
No 62
>cd05707 S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 11 (sc11). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=38.98 E-value=53 Score=20.82 Aligned_cols=23 Identities=17% Similarity=0.108 Sum_probs=17.5
Q ss_pred cccCCEEEEeecCCCCcEeeEEEEEccCCEEEE
Q 031473 15 ILRGDNVMIIRGKDKGETGAIKRVIRSQNRVIV 47 (159)
Q Consensus 15 i~kGD~V~Vi~G~dKGk~G~V~~V~~~~~~V~V 47 (159)
+..||.|.+ +|++++++++++.+
T Consensus 45 ~~~Gd~v~~----------~v~~~d~~~~~i~l 67 (68)
T cd05707 45 FKVGQLVKG----------KIVSIDPDNGRIEM 67 (68)
T ss_pred cCCCCEEEE----------EEEEEeCCCCEEec
Confidence 678888886 67888887777654
No 63
>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=38.88 E-value=57 Score=23.58 Aligned_cols=33 Identities=27% Similarity=0.318 Sum_probs=19.8
Q ss_pred ccccCCEEEEee-c---------CCCCcEeeEEEEEccCCEEE
Q 031473 14 KILRGDNVMIIR-G---------KDKGETGAIKRVIRSQNRVI 46 (159)
Q Consensus 14 ~i~kGD~V~Vi~-G---------~dKGk~G~V~~V~~~~~~V~ 46 (159)
.+..||.|-|.- | .+-|+.|.|..|.+..-.+.
T Consensus 32 ~yk~GD~V~I~id~sv~kGmPh~~yHGkTG~V~~v~~~~~G~~ 74 (99)
T PF01157_consen 32 EYKVGDKVDIKIDPSVHKGMPHKRYHGKTGRVFNVTKGARGVA 74 (99)
T ss_dssp ---TT-EEEE---TTSSSSS--GGGTTEEEEEEEE-SSCEEEE
T ss_pred HccCCCEEEEEecCccccCCCcceECCCceeEEEeCCCceEEE
Confidence 357899999763 2 15789999999988764443
No 64
>COG2139 RPL21A Ribosomal protein L21E [Translation, ribosomal structure and biogenesis]
Probab=38.00 E-value=72 Score=23.14 Aligned_cols=39 Identities=28% Similarity=0.224 Sum_probs=28.0
Q ss_pred cccCCEEEEeec----------CCCCcEeeEEEEEccCCEEEEecccee
Q 031473 15 ILRGDNVMIIRG----------KDKGETGAIKRVIRSQNRVIVEGKNLV 53 (159)
Q Consensus 15 i~kGD~V~Vi~G----------~dKGk~G~V~~V~~~~~~V~Vegvn~~ 53 (159)
+..||.|-|.-- .+-|+.|+|.-+.-....|.|..-|..
T Consensus 33 y~~Gd~V~I~IdpSv~kGmPh~rf~G~TG~Vvg~~g~ay~V~v~~G~k~ 81 (98)
T COG2139 33 YKVGDKVHIDIDPSVHKGMPHPRFQGKTGTVVGVRGRAYKVEVYDGNKE 81 (98)
T ss_pred ccCCCEEEEEeCcccccCCCCccccCcceEEEeccCCEEEEEEecCCce
Confidence 578999987643 378999999888766666666544443
No 65
>PRK02749 photosystem I reaction center subunit IV; Provisional
Probab=37.59 E-value=44 Score=22.78 Aligned_cols=29 Identities=38% Similarity=0.472 Sum_probs=23.7
Q ss_pred ccccCCEEEEeecC--CCCcEeeEEEEEccC
Q 031473 14 KILRGDNVMIIRGK--DKGETGAIKRVIRSQ 42 (159)
Q Consensus 14 ~i~kGD~V~Vi~G~--dKGk~G~V~~V~~~~ 42 (159)
-|.+||.|.|++=. .-..+|+|.+|+...
T Consensus 2 ~i~rGskVrIlR~ESYWyn~vGtV~svD~sg 32 (71)
T PRK02749 2 AISRGDKVRILRPESYWYNEVGTVASVDKSG 32 (71)
T ss_pred ccccCCEEEEccccceeecCcceEEEEccCC
Confidence 37899999999853 467889999999874
No 66
>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=36.96 E-value=49 Score=21.96 Aligned_cols=28 Identities=36% Similarity=0.436 Sum_probs=21.4
Q ss_pred cccCCEEEEeecC--CCCcEeeEEEEEccC
Q 031473 15 ILRGDNVMIIRGK--DKGETGAIKRVIRSQ 42 (159)
Q Consensus 15 i~kGD~V~Vi~G~--dKGk~G~V~~V~~~~ 42 (159)
|.+|+.|.|++=. .-..+|+|.+|+...
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 5689999999853 467899999998764
No 67
>PRK11713 16S ribosomal RNA methyltransferase RsmE; Provisional
Probab=36.30 E-value=63 Score=26.15 Aligned_cols=44 Identities=16% Similarity=0.328 Sum_probs=30.6
Q ss_pred HhHhhcchhcccccCCEEEEeecCCCCcEeeEEEEEccCCEEEE
Q 031473 4 KAAEKLIRHWKILRGDNVMIIRGKDKGETGAIKRVIRSQNRVIV 47 (159)
Q Consensus 4 ~~~~~~ir~~~i~kGD~V~Vi~G~dKGk~G~V~~V~~~~~~V~V 47 (159)
...+|..+-++++.||.+.|.-|...=-.|+|..+.++.-.+.+
T Consensus 19 ~~~~Hl~~VlR~~~Gd~i~v~~g~g~~~~~~i~~i~~~~~~~~i 62 (234)
T PRK11713 19 EEAHHLVRVLRLKEGDELRLFDGDGGEYLAEITEIGKKEVELEI 62 (234)
T ss_pred HHHhHHHhhccCCCCCEEEEEeCCCCEEEEEEEEecCcEEEEEE
Confidence 45667778899999999999988642223688888664433333
No 68
>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=36.18 E-value=27 Score=24.18 Aligned_cols=18 Identities=28% Similarity=0.224 Sum_probs=12.8
Q ss_pred hcchhcccccCCEEEEee
Q 031473 8 KLIRHWKILRGDNVMIIR 25 (159)
Q Consensus 8 ~~ir~~~i~kGD~V~Vi~ 25 (159)
-.||.+.++.||.|.-..
T Consensus 36 ~qIrrf~LR~GD~V~G~v 53 (78)
T PF07497_consen 36 SQIRRFGLRTGDLVEGQV 53 (78)
T ss_dssp CCCCCTT--TTEEEEEEE
T ss_pred HHHHHcCCCCCCEEEEEE
Confidence 468999999999998443
No 69
>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=36.02 E-value=61 Score=21.10 Aligned_cols=29 Identities=24% Similarity=0.218 Sum_probs=17.6
Q ss_pred cchhcccccCCEEEEeecCCCCcEeeEEE
Q 031473 9 LIRHWKILRGDNVMIIRGKDKGETGAIKR 37 (159)
Q Consensus 9 ~ir~~~i~kGD~V~Vi~G~dKGk~G~V~~ 37 (159)
..+...|+.||.|.|---++--..|.|..
T Consensus 36 ~r~~iwI~~GD~V~V~~~~~d~~kG~Ii~ 64 (65)
T PF01176_consen 36 FRKRIWIKRGDFVLVEPSPYDKVKGRIIY 64 (65)
T ss_dssp HHTCC---TTEEEEEEESTTCTTEEEEEE
T ss_pred eeeeEecCCCCEEEEEecccCCCeEEEEE
Confidence 45566799999999875554456676653
No 70
>PF07076 DUF1344: Protein of unknown function (DUF1344); InterPro: IPR009780 This family consists of several short, hypothetical bacterial proteins of around 80 residues in length. Members of this family are found in Rhizobium, Agrobacterium and Brucella species. The function of this family is unknown.
Probab=35.90 E-value=1.3e+02 Score=19.93 Aligned_cols=20 Identities=15% Similarity=0.242 Sum_probs=17.4
Q ss_pred cEeeEEEEEccCCEEEEecc
Q 031473 31 ETGAIKRVIRSQNRVIVEGK 50 (159)
Q Consensus 31 k~G~V~~V~~~~~~V~Vegv 50 (159)
-+|+|.+|++.+..+.+++-
T Consensus 5 veG~I~~id~~~~titLdDG 24 (61)
T PF07076_consen 5 VEGTIKSIDPETMTITLDDG 24 (61)
T ss_pred ceEEEEEEcCCceEEEecCC
Confidence 36999999999999999863
No 71
>PRK10334 mechanosensitive channel MscS; Provisional
Probab=35.58 E-value=1.3e+02 Score=25.31 Aligned_cols=24 Identities=21% Similarity=0.219 Sum_probs=19.2
Q ss_pred cccccCCEEEEeecCCCCcEeeEEEEEcc
Q 031473 13 WKILRGDNVMIIRGKDKGETGAIKRVIRS 41 (159)
Q Consensus 13 ~~i~kGD~V~Vi~G~dKGk~G~V~~V~~~ 41 (159)
-+++.||.|.+ .|..|+|.++.-.
T Consensus 128 rpf~vGD~I~i-----~~~~G~V~~I~~r 151 (286)
T PRK10334 128 RPFRAGEYVDL-----GGVAGTVLSVQIF 151 (286)
T ss_pred CCCCCCCEEEE-----CCEEEEEEEEEeE
Confidence 46899999997 2788999988643
No 72
>cd05698 S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 6 (hs6) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=35.47 E-value=74 Score=20.08 Aligned_cols=24 Identities=17% Similarity=0.254 Sum_probs=17.7
Q ss_pred ccccCCEEEEeecCCCCcEeeEEEEEccCCEEEE
Q 031473 14 KILRGDNVMIIRGKDKGETGAIKRVIRSQNRVIV 47 (159)
Q Consensus 14 ~i~kGD~V~Vi~G~dKGk~G~V~~V~~~~~~V~V 47 (159)
.+..||.+.+ +|++++++++++.+
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 3677888887 66778877777665
No 73
>cd05697 S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 5 (hs5) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=35.17 E-value=90 Score=19.76 Aligned_cols=24 Identities=21% Similarity=0.271 Sum_probs=18.8
Q ss_pred ccccCCEEEEeecCCCCcEeeEEEEEccCCEEEE
Q 031473 14 KILRGDNVMIIRGKDKGETGAIKRVIRSQNRVIV 47 (159)
Q Consensus 14 ~i~kGD~V~Vi~G~dKGk~G~V~~V~~~~~~V~V 47 (159)
.+..||.+.+ +|++++++++++.+
T Consensus 44 ~~~~Gd~i~~----------~V~~id~~~~~i~l 67 (69)
T cd05697 44 KFKPGLKVKC----------RVLSVEPERKRLVL 67 (69)
T ss_pred cCCCCCEEEE----------EEEEEECCCCEEEE
Confidence 4778888886 77888888887765
No 74
>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=34.77 E-value=69 Score=26.07 Aligned_cols=42 Identities=21% Similarity=0.444 Sum_probs=30.1
Q ss_pred HhHhhcchhcccccCCEEEEeecCCCCcE--eeEEEEEccCCEEEE
Q 031473 4 KAAEKLIRHWKILRGDNVMIIRGKDKGET--GAIKRVIRSQNRVIV 47 (159)
Q Consensus 4 ~~~~~~ir~~~i~kGD~V~Vi~G~dKGk~--G~V~~V~~~~~~V~V 47 (159)
..+.|..+-++++.||.|.|.-|. |.. ++|..+.++.-.+.+
T Consensus 21 ~~~~Hl~~VlR~~~Gd~v~v~~g~--g~~~~a~i~~~~~~~~~~~i 64 (240)
T TIGR00046 21 EEAHHLVRVLRLKKGDKLKLLDGD--GFIYHCEIKKISKKFVKCEL 64 (240)
T ss_pred HHHhHHHHcccCCCCCEEEEEeCC--CCEEEEEEEEEcCCeEEEEE
Confidence 456677778899999999999884 554 567777665444433
No 75
>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=34.12 E-value=32 Score=24.61 Aligned_cols=24 Identities=25% Similarity=0.414 Sum_probs=16.6
Q ss_pred chhcccccCCEEEEeecCCCCcEe
Q 031473 10 IRHWKILRGDNVMIIRGKDKGETG 33 (159)
Q Consensus 10 ir~~~i~kGD~V~Vi~G~dKGk~G 33 (159)
.+.--+.+||.|+++.|..-|..|
T Consensus 85 ~~~g~~~~gd~vVv~~g~~~~~~g 108 (117)
T PF02887_consen 85 KERGLLKPGDKVVVVAGMPFGTPG 108 (117)
T ss_dssp HHTTSS-TTSEEEEEEESSTTTTS
T ss_pred HHcCCCCCCCEEEEEeCCCCCCCC
Confidence 344447899999999996555554
No 76
>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=33.20 E-value=53 Score=22.09 Aligned_cols=27 Identities=26% Similarity=0.598 Sum_probs=13.4
Q ss_pred EEeecCC---------CCcEeeEEEE-----EccCCEEEEe
Q 031473 22 MIIRGKD---------KGETGAIKRV-----IRSQNRVIVE 48 (159)
Q Consensus 22 ~Vi~G~d---------KGk~G~V~~V-----~~~~~~V~Ve 48 (159)
.|++|+| .|..|+|.+| ......|.|.
T Consensus 3 rVvRGpDW~WgdQDGG~g~~GtV~~i~~~~~~~~~~~v~V~ 43 (68)
T PF06701_consen 3 RVVRGPDWKWGDQDGGEGHVGTVVSIRDWSSESPDGWVVVQ 43 (68)
T ss_dssp EEEE-TT--STTTTSSTT--EEE-S--------BTTEEEEE
T ss_pred eeeeCcCCCccCcCCCCCcceEEEecccccccCCCCeEEEE
Confidence 3568875 6789999997 3445566664
No 77
>COG1162 Predicted GTPases [General function prediction only]
Probab=32.84 E-value=48 Score=28.59 Aligned_cols=32 Identities=22% Similarity=0.469 Sum_probs=26.4
Q ss_pred hhcccccCCEEEEeecCCCCcEeeEEEEEccCCEE
Q 031473 11 RHWKILRGDNVMIIRGKDKGETGAIKRVIRSQNRV 45 (159)
Q Consensus 11 r~~~i~kGD~V~Vi~G~dKGk~G~V~~V~~~~~~V 45 (159)
.......||+|++-.+... |.|.+|.+.+|.+
T Consensus 41 ~~~~~vVGD~V~~~~~~~~---g~I~~i~~Rkn~L 72 (301)
T COG1162 41 KDLKPVVGDRVVFEDENNN---GVIEKILPRKNVL 72 (301)
T ss_pred cCccccccCeEEEecCCCc---ceEEEEecccCce
Confidence 3567789999999988766 9999999888754
No 78
>PLN00045 photosystem I reaction center subunit IV; Provisional
Probab=32.78 E-value=71 Score=23.15 Aligned_cols=31 Identities=23% Similarity=0.210 Sum_probs=24.7
Q ss_pred hhcccccCCEEEEeecC--CCCcEeeEEEEEcc
Q 031473 11 RHWKILRGDNVMIIRGK--DKGETGAIKRVIRS 41 (159)
Q Consensus 11 r~~~i~kGD~V~Vi~G~--dKGk~G~V~~V~~~ 41 (159)
.-.-+.+||.|.|++=. .-..+|+|.+|+..
T Consensus 36 p~ig~~RGskVrIlR~ESYWyn~vGtVvsVDq~ 68 (101)
T PLN00045 36 PPIGPKRGSKVKILRPESYWFNDVGKVVAVDQD 68 (101)
T ss_pred CCcccCCCCEEEEccccceeecCcceEEEEeCC
Confidence 34557899999999864 46778999999987
No 79
>KOG3421 consensus 60S ribosomal protein L14 [Translation, ribosomal structure and biogenesis]
Probab=32.69 E-value=53 Score=25.18 Aligned_cols=34 Identities=38% Similarity=0.514 Sum_probs=29.0
Q ss_pred ccCCEEEEeecCCCCcEeeEEEEEccCCEEEEecc
Q 031473 16 LRGDNVMIIRGKDKGETGAIKRVIRSQNRVIVEGK 50 (159)
Q Consensus 16 ~kGD~V~Vi~G~dKGk~G~V~~V~~~~~~V~Vegv 50 (159)
-.|--+.|..|++.|+.-.|..|+ +.|++.++|-
T Consensus 8 eVGrva~v~~G~~~GkL~AIVdvi-Dqnr~lvDGp 41 (136)
T KOG3421|consen 8 EVGRVALVSFGPDAGKLVAIVDVI-DQNRALVDGP 41 (136)
T ss_pred hcceEEEEEecCCCceEEEEEEee-cchhhhccCc
Confidence 468888999999999999999886 4589999984
No 80
>PF03120 DNA_ligase_OB: NAD-dependent DNA ligase OB-fold domain; InterPro: IPR004150 DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This family is a small domain found after the adenylation domain DNA_ligase_N in NAD+-dependent ligases (IPR001679 from INTERPRO). OB-fold domains generally are involved in nucleic acid binding.; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 2OWO_A 1TAE_A 3UQ8_A 1DGS_A 1V9P_B 3SGI_A.
Probab=32.40 E-value=32 Score=24.01 Aligned_cols=31 Identities=26% Similarity=0.404 Sum_probs=19.4
Q ss_pred hcchhcccccCCEEEEeecCCCCcEeeEEEEEc
Q 031473 8 KLIRHWKILRGDNVMIIRGKDKGETGAIKRVIR 40 (159)
Q Consensus 8 ~~ir~~~i~kGD~V~Vi~G~dKGk~G~V~~V~~ 40 (159)
..++.+.|+.||.|.|.+.- .-+-+|.++..
T Consensus 43 ~~i~~~~i~~Gd~V~V~raG--dVIP~I~~vv~ 73 (82)
T PF03120_consen 43 DYIKELDIRIGDTVLVTRAG--DVIPKIVGVVK 73 (82)
T ss_dssp HHHHHTT-BBT-EEEEEEET--TTEEEEEEE-G
T ss_pred HHHHHcCCCCCCEEEEEECC--CccceEeEeeh
Confidence 45778999999999998543 24556666554
No 81
>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=32.33 E-value=1e+02 Score=19.55 Aligned_cols=25 Identities=16% Similarity=0.258 Sum_probs=17.9
Q ss_pred ccccCCEEEEeecCCCCcEeeEEEEEccCCEEEEe
Q 031473 14 KILRGDNVMIIRGKDKGETGAIKRVIRSQNRVIVE 48 (159)
Q Consensus 14 ~i~kGD~V~Vi~G~dKGk~G~V~~V~~~~~~V~Ve 48 (159)
.++.||.|.+ +|.+++.+..++.+.
T Consensus 47 ~~~~Gd~v~v----------~i~~vd~~~~~i~ls 71 (77)
T cd05708 47 LFRVGDKVRA----------KVLKIDAEKKRISLG 71 (77)
T ss_pred eecCCCEEEE----------EEEEEeCCCCEEEEE
Confidence 3578888886 467788777777654
No 82
>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=32.19 E-value=47 Score=22.67 Aligned_cols=30 Identities=17% Similarity=0.075 Sum_probs=19.5
Q ss_pred hcccccCCEEEEeecCCCCcEeeEEEEEcc
Q 031473 12 HWKILRGDNVMIIRGKDKGETGAIKRVIRS 41 (159)
Q Consensus 12 ~~~i~kGD~V~Vi~G~dKGk~G~V~~V~~~ 41 (159)
...|++||.|.|--=++--..|.|...+..
T Consensus 36 ~iwI~~GD~V~Ve~~~~d~~kg~Iv~r~~~ 65 (77)
T cd05793 36 RVWINEGDIVLVAPWDFQDDKADIIYKYTP 65 (77)
T ss_pred cEEEcCCCEEEEEeccccCCEEEEEEEcCH
Confidence 566889999988433333456777766544
No 83
>PF09926 DUF2158: Uncharacterized small protein (DUF2158); InterPro: IPR019226 This entry represents a family of predominantly prokaryotic proteins with no known function.
Probab=31.95 E-value=31 Score=22.12 Aligned_cols=15 Identities=27% Similarity=0.357 Sum_probs=11.8
Q ss_pred cccCCEEEEeecCCC
Q 031473 15 ILRGDNVMIIRGKDK 29 (159)
Q Consensus 15 i~kGD~V~Vi~G~dK 29 (159)
|+.||.|+..+|--+
T Consensus 1 f~~GDvV~LKSGGp~ 15 (53)
T PF09926_consen 1 FKIGDVVQLKSGGPR 15 (53)
T ss_pred CCCCCEEEEccCCCC
Confidence 468999999998433
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=31.91 E-value=88 Score=19.21 Aligned_cols=23 Identities=17% Similarity=0.442 Sum_probs=15.9
Q ss_pred cccCCEEEEeecCCCCcEeeEEEEEccCCEEEE
Q 031473 15 ILRGDNVMIIRGKDKGETGAIKRVIRSQNRVIV 47 (159)
Q Consensus 15 i~kGD~V~Vi~G~dKGk~G~V~~V~~~~~~V~V 47 (159)
+..||+|.+ +|.+++.+++++.+
T Consensus 45 ~~~Gd~v~v----------~i~~vd~~~~~i~l 67 (68)
T cd05688 45 VNVGDEVEV----------KVLKIDKERKRISL 67 (68)
T ss_pred ECCCCEEEE----------EEEEEECCCCEEec
Confidence 678888887 46777776666543
No 85
>PF11604 CusF_Ec: Copper binding periplasmic protein CusF; InterPro: IPR021647 CusF is a periplasmic protein involved in copper and silver resistance in Escherichia coil. CusF forms a five-stranded beta-barrel OB fold. Cu(I) binds to H36, M47 and M49 which are conserved residues in the protein []. ; PDB: 2L55_A 2VB3_X 1ZEQ_X 2QCP_X 3E6Z_X 2VB2_X.
Probab=31.57 E-value=1.6e+02 Score=19.47 Aligned_cols=17 Identities=18% Similarity=0.317 Sum_probs=15.5
Q ss_pred eeEEEEEccCCEEEEec
Q 031473 33 GAIKRVIRSQNRVIVEG 49 (159)
Q Consensus 33 G~V~~V~~~~~~V~Veg 49 (159)
|.|.+|+++.+.|.|..
T Consensus 1 G~V~~vd~~~~~iti~H 17 (70)
T PF11604_consen 1 GVVKSVDPEAGTITISH 17 (70)
T ss_dssp EEEEEEETTTTEEEEEE
T ss_pred CEEEEEecCCCEEEEec
Confidence 78999999999999984
No 86
>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=31.28 E-value=93 Score=20.59 Aligned_cols=24 Identities=17% Similarity=0.353 Sum_probs=17.2
Q ss_pred ccccCCEEEEeecCCCCcEeeEEEEEccCCEEEE
Q 031473 14 KILRGDNVMIIRGKDKGETGAIKRVIRSQNRVIV 47 (159)
Q Consensus 14 ~i~kGD~V~Vi~G~dKGk~G~V~~V~~~~~~V~V 47 (159)
.+..||.|.| +|.+++.+++++.+
T Consensus 58 ~~~~Gd~v~v----------kV~~id~~~~~i~l 81 (83)
T cd04461 58 GFKKGQSVTA----------KVTSVDEEKQRFLL 81 (83)
T ss_pred hcCCCCEEEE----------EEEEEcCCCCEEEE
Confidence 3677888886 66777777776654
No 87
>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=31.13 E-value=55 Score=22.15 Aligned_cols=25 Identities=28% Similarity=0.497 Sum_probs=13.9
Q ss_pred cCCEEEEeec--------------CCCCcEeeEEEEEcc
Q 031473 17 RGDNVMIIRG--------------KDKGETGAIKRVIRS 41 (159)
Q Consensus 17 kGD~V~Vi~G--------------~dKGk~G~V~~V~~~ 41 (159)
.||+|.|.+- ..+|.+|.|.++...
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 4889888753 147888888887644
No 88
>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=30.84 E-value=1.1e+02 Score=21.94 Aligned_cols=35 Identities=17% Similarity=0.151 Sum_probs=25.4
Q ss_pred ccccCCEEEEeecC--CCCcEeeEEEEEccC-CEEEEe
Q 031473 14 KILRGDNVMIIRGK--DKGETGAIKRVIRSQ-NRVIVE 48 (159)
Q Consensus 14 ~i~kGD~V~Vi~G~--dKGk~G~V~~V~~~~-~~V~Ve 48 (159)
.++.||-|.|.+.. .+--+|.|.++.... +...+.
T Consensus 3 ~~~vGD~V~v~~~~~~~~~~i~~I~~i~~~~~g~~~~~ 40 (121)
T cd04717 3 QYRVGDCVYVANPEDPSKPIIFRIERLWKDEDGEKFFF 40 (121)
T ss_pred EEECCCEEEEeCCCCCCCCEEEEEeEEEECCCCCEEEE
Confidence 36889999998754 555689999988765 334444
No 89
>PF12353 eIF3g: Eukaryotic translation initiation factor 3 subunit G ; InterPro: IPR024675 At least eleven different protein factors are involved in initiation of protein synthesis in eukaryotes. Binding of initiator tRNA and mRNA to the 40S subunit requires the presence of the translation initiation factors eIF-2 and eIF-3, with eIF-3 being particularly important for 80S ribosome dissociation and mRNA binding []. eIF-3 is the most complex translation inititation factor, consisting of about 13 putative subunits and having a molecular weight of between 550 - 700 kDa in mammalian cells. Subunits are designated eIF-3a - eIF-3m; the large number of subunits means that the interactions between the individual subunits that make up the eIF-3 complex are complex and varied. Subunit G is required for eIF3 integrity. This entry represents a domain of approximately 130 amino acids in length found at the N terminus of eukaryotic translation initiation factor 3 subunit G. This domain is commonly found in association with the RNA recognition domain PF00076 from PFAM.
Probab=30.63 E-value=1e+02 Score=23.03 Aligned_cols=70 Identities=14% Similarity=0.197 Sum_probs=37.7
Q ss_pred CCCCCceeEEEEEccCCcEEEEEEecC--CCCeeecCCCcccccCCC---CC--CCCCCCCCChhhhccceeeeCCCC
Q 031473 84 PVTGKPCKVGTKYLEDGTKVRVARGIG--ASGSIIPRPEILKIRTTP---RP--TVAGPKDTPVDLVMKKTYDAKSGK 154 (159)
Q Consensus 84 p~~g~~~rV~~~~~~~g~k~R~~k~~~--~~~~~IPwP~~~~~~~~~---~~--~~d~~~DT~~~~v~e~Ty~p~~~~ 154 (159)
.+.|.-+=+.|+++++|+++.+.+.+- ..-..++.-..++ +.+. .. ...|+.-..-..++|..+.+....
T Consensus 9 ~~~G~KtViey~~n~dGkkvKvtk~~k~~~~~~~V~k~VaeR-k~W~KFG~~~~~~pGp~~~Tt~~~EeI~l~~~~~~ 85 (128)
T PF12353_consen 9 DEDGIKTVIEYKFNDDGKKVKVTKKIKVTVVKEKVNKAVAER-KKWKKFGDEKNDPPGPDSSTTQVGEEIFLELSRNW 85 (128)
T ss_pred CCCCcEEEEEEEECCCCCEEEEEEEEEEEEEEEEeCHHHHHh-hCccccCccccCCCCCCcccccccceEEEEecCCc
Confidence 345767778899999999877776442 1122333222222 2221 11 112333333356888888877643
No 90
>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=30.41 E-value=76 Score=25.87 Aligned_cols=31 Identities=23% Similarity=0.247 Sum_probs=16.8
Q ss_pred chhcccccCCEEEE-eecCCCCcEeeEEEEEc
Q 031473 10 IRHWKILRGDNVMI-IRGKDKGETGAIKRVIR 40 (159)
Q Consensus 10 ir~~~i~kGD~V~V-i~G~dKGk~G~V~~V~~ 40 (159)
+..-.+++||.|.+ -.+..+-+.-+|.+|..
T Consensus 101 vfA~~V~~Gd~v~~~~~~~~~~~~~~V~~v~~ 132 (217)
T PF01079_consen 101 VFASDVRVGDCVLVSDEGGGKLRPSRVVRVST 132 (217)
T ss_dssp EEGGG--TT-EEEEE-TTT--EEEEEEEEEEE
T ss_pred eehhhCCCCCEEEEEEcCCCcEEEEEEEEEEE
Confidence 44567899999999 34445555667776653
No 91
>PRK12618 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=29.86 E-value=88 Score=23.73 Aligned_cols=37 Identities=22% Similarity=0.075 Sum_probs=25.8
Q ss_pred cchhcccccCCEEEEeecC------------CCCcEeeEEEE-EccCCEE
Q 031473 9 LIRHWKILRGDNVMIIRGK------------DKGETGAIKRV-IRSQNRV 45 (159)
Q Consensus 9 ~ir~~~i~kGD~V~Vi~G~------------dKGk~G~V~~V-~~~~~~V 45 (159)
.-..|-|.+||.|.|+... .-|..|...+| |..++++
T Consensus 76 L~~p~lV~rG~~V~i~~~~ggl~i~~~G~AL~~G~~Gd~IrV~N~~S~ri 125 (141)
T PRK12618 76 LGPPAIVDRNQLVPLAYRLGGLEIRTEGRALSRGGVGDEIRVMNLSSRTT 125 (141)
T ss_pred cCCccEEeCCCEEEEEEecCCEEEEEEEEEcccCCCCCEEEEEECCCCCE
Confidence 3345778999999998643 46778888887 4455543
No 92
>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=28.94 E-value=1.2e+02 Score=23.74 Aligned_cols=29 Identities=14% Similarity=0.090 Sum_probs=23.1
Q ss_pred cccCCEEEEeecCC-CCcEeeEEEEEccCC
Q 031473 15 ILRGDNVMIIRGKD-KGETGAIKRVIRSQN 43 (159)
Q Consensus 15 i~kGD~V~Vi~G~d-KGk~G~V~~V~~~~~ 43 (159)
+++||-|.|..++. -..+|.|.++....+
T Consensus 4 yrvGD~Vy~~~~~~~Py~I~rI~e~~~~~~ 33 (164)
T cd04709 4 YRVGDYVYFESSPNNPYLIRRIEELNKTAR 33 (164)
T ss_pred EecCCEEEEECCCCCCCEEEEEEEEEeCCC
Confidence 68999999998854 367999999876554
No 93
>cd04459 Rho_CSD Rho_CSD: Rho protein cold-shock domain (CSD). Rho protein is a transcription termination factor in most bacteria. In bacteria, there are two distinct mechanisms for mRNA transcription termination. In intrinsic termination, RNA polymerase and nascent mRNA are released from DNA template by an mRNA stem loop structure, which resembles the transcription termination mechanism used by eukaryotic pol III. The second mechanism is mediated by Rho factor. Rho factor terminates transcription by using energy from ATP hydrolysis to forcibly dissociate the transcripts from RNA polymerase. Rho protein contains an N-terminal S1-like domain, which binds single-stranded RNA. Rho has a C-terminal ATPase domain which hydrolyzes ATP to provide energy to strip RNA polymerase and mRNA from the DNA template. Rho functions as a homohexamer.
Probab=28.79 E-value=78 Score=21.23 Aligned_cols=20 Identities=25% Similarity=0.318 Sum_probs=16.0
Q ss_pred hcchhcccccCCEEEEeecC
Q 031473 8 KLIRHWKILRGDNVMIIRGK 27 (159)
Q Consensus 8 ~~ir~~~i~kGD~V~Vi~G~ 27 (159)
..||.+.++.||.|.-..-+
T Consensus 34 ~~Irr~~LR~GD~V~G~vr~ 53 (68)
T cd04459 34 SQIRRFNLRTGDTVVGQIRP 53 (68)
T ss_pred HHHHHhCCCCCCEEEEEEeC
Confidence 46899999999999865443
No 94
>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=28.67 E-value=99 Score=22.08 Aligned_cols=38 Identities=32% Similarity=0.520 Sum_probs=25.1
Q ss_pred hcchhcccccCCEEEEeecC------------CCCcEeeEEEEE-ccCCEE
Q 031473 8 KLIRHWKILRGDNVMIIRGK------------DKGETGAIKRVI-RSQNRV 45 (159)
Q Consensus 8 ~~ir~~~i~kGD~V~Vi~G~------------dKGk~G~V~~V~-~~~~~V 45 (159)
+....+-+++||.|.|+.-. .-|..|...+|. ..++++
T Consensus 59 ~l~~~~~V~~G~~V~i~~~~~~~~i~~~g~Al~~g~~G~~I~V~N~~s~k~ 109 (122)
T TIGR03170 59 MLRPPWLVKRGDTVTVIARGGGLSVTTEGKALEDGAVGDQIRVRNLSSGKI 109 (122)
T ss_pred hcCCccEEcCCCEEEEEEecCCEEEEEEEEEccccCCCCEEEEEECCCCCE
Confidence 34455778999999988532 456677777766 344443
No 95
>PF08772 NOB1_Zn_bind: Nin one binding (NOB1) Zn-ribbon like; InterPro: IPR014881 This entry corresponds to a zinc ribbon and is found on the RNA binding protein NOB1. ; PDB: 2CON_A.
Probab=28.33 E-value=34 Score=23.37 Aligned_cols=41 Identities=20% Similarity=0.340 Sum_probs=9.5
Q ss_pred cccCCCCCCc--eeEEEEEccCCcE-----EEEEEecCCCCeeecCCC
Q 031473 80 QVLDPVTGKP--CKVGTKYLEDGTK-----VRVARGIGASGSIIPRPE 120 (159)
Q Consensus 80 ~Lvdp~~g~~--~rV~~~~~~~g~k-----~R~~k~~~~~~~~IPwP~ 120 (159)
++++|.+|.. .||.+.++++|+. .++--..-++-+.||.|+
T Consensus 24 k~FCp~CGn~TL~rvsvsv~~~G~~~~~~~~~~~~n~RG~~ySlPkPk 71 (73)
T PF08772_consen 24 KQFCPKCGNATLKRVSVSVDEDGKIKLHLKKNFQWNLRGTKYSLPKPK 71 (73)
T ss_dssp --S-SSS--S--EEEE-B--SS---B----------------------
T ss_pred ceeCcccCCCcceEEEEEECCCCCEEEEecCCceeccCCCCccCCCCC
Confidence 4678999765 6788878888853 111111124556777775
No 96
>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=28.20 E-value=73 Score=21.99 Aligned_cols=29 Identities=21% Similarity=0.330 Sum_probs=19.5
Q ss_pred ccccCCEEEEeecCCCCc-EeeEEEEEccC
Q 031473 14 KILRGDNVMIIRGKDKGE-TGAIKRVIRSQ 42 (159)
Q Consensus 14 ~i~kGD~V~Vi~G~dKGk-~G~V~~V~~~~ 42 (159)
-|+.||-|.|-.-.+-.| .|.|..++.+.
T Consensus 38 WIkrGd~VlV~p~~~~~kvkgeIv~i~~~~ 67 (78)
T cd05792 38 WIKRGDFVLVEPIEEGDKVKAEIVKILTRD 67 (78)
T ss_pred EEEeCCEEEEEecccCCceEEEEEEEECHH
Confidence 389999999866443333 57777776554
No 97
>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=27.99 E-value=1.3e+02 Score=19.07 Aligned_cols=23 Identities=13% Similarity=0.182 Sum_probs=15.9
Q ss_pred cccCCEEEEeecCCCCcEeeEEEEEccCCEEEE
Q 031473 15 ILRGDNVMIIRGKDKGETGAIKRVIRSQNRVIV 47 (159)
Q Consensus 15 i~kGD~V~Vi~G~dKGk~G~V~~V~~~~~~V~V 47 (159)
+..||.|.+ +|+++++++..+.+
T Consensus 48 ~~~Gd~v~~----------~V~~~d~~~~~i~l 70 (73)
T cd05706 48 FKKNDIVRA----------CVLSVDVPNKKIAL 70 (73)
T ss_pred cCCCCEEEE----------EEEEEeCCCCEEEE
Confidence 567888775 66777777666654
No 98
>PF11717 Tudor-knot: RNA binding activity-knot of a chromodomain ; PDB: 2EKO_A 2RO0_A 2RNZ_A 1WGS_A 3E9G_A 3E9F_A 2K3X_A 2K3Y_A 2EFI_A 2F5K_F ....
Probab=27.87 E-value=77 Score=19.85 Aligned_cols=29 Identities=10% Similarity=0.068 Sum_probs=21.9
Q ss_pred cccCCEEEEeecCCCCcEeeEEEEEccCC
Q 031473 15 ILRGDNVMIIRGKDKGETGAIKRVIRSQN 43 (159)
Q Consensus 15 i~kGD~V~Vi~G~dKGk~G~V~~V~~~~~ 43 (159)
|..|++|.+..+...--.++|+++..+.+
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 46799999999666666799999987653
No 99
>PRK07018 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=27.59 E-value=94 Score=25.29 Aligned_cols=38 Identities=29% Similarity=0.486 Sum_probs=26.6
Q ss_pred hcchhcccccCCEEEEeecC------------CCCcEeeEEEEE-ccCCEE
Q 031473 8 KLIRHWKILRGDNVMIIRGK------------DKGETGAIKRVI-RSQNRV 45 (159)
Q Consensus 8 ~~ir~~~i~kGD~V~Vi~G~------------dKGk~G~V~~V~-~~~~~V 45 (159)
+....|-|++||.|.|+... .-|..|...+|. ..++++
T Consensus 170 ~L~~~~~V~~G~~V~i~~~~g~~~i~~~G~Al~~G~~Gd~IrVrN~~Sgk~ 220 (235)
T PRK07018 170 MLRQAWVVCKGQTVSIIARGDGFSVKTEGEALNDGAVGQQIRVRNMASGQV 220 (235)
T ss_pred HccCccEeCCCCEEEEEEecCCEEEEEEEEEcCCCCCCCeEEEEECCCCCE
Confidence 44456789999999998643 466777777776 455554
No 100
>CHL00010 infA translation initiation factor 1
Probab=27.29 E-value=1.3e+02 Score=20.46 Aligned_cols=13 Identities=38% Similarity=0.560 Sum_probs=8.2
Q ss_pred hcccccCCEEEEe
Q 031473 12 HWKILRGDNVMII 24 (159)
Q Consensus 12 ~~~i~kGD~V~Vi 24 (159)
...+..||.|.|-
T Consensus 44 ~i~~~vGD~V~ve 56 (78)
T CHL00010 44 SIRILPGDRVKVE 56 (78)
T ss_pred CcccCCCCEEEEE
Confidence 3445677777765
No 101
>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=27.27 E-value=1.1e+02 Score=19.16 Aligned_cols=22 Identities=14% Similarity=0.293 Sum_probs=16.2
Q ss_pred cccCCEEEEeecCCCCcEeeEEEEEccCCEEE
Q 031473 15 ILRGDNVMIIRGKDKGETGAIKRVIRSQNRVI 46 (159)
Q Consensus 15 i~kGD~V~Vi~G~dKGk~G~V~~V~~~~~~V~ 46 (159)
++.||+|.|. |++++.++.++.
T Consensus 46 ~~~G~~v~v~----------v~~id~~~~~i~ 67 (69)
T cd05690 46 YKKGQEVEAV----------VLNIDVERERIS 67 (69)
T ss_pred ECCCCEEEEE----------EEEEECCcCEEe
Confidence 6788888873 777887777654
No 102
>cd00164 S1_like S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.
Probab=26.85 E-value=1.1e+02 Score=18.09 Aligned_cols=21 Identities=24% Similarity=0.370 Sum_probs=13.1
Q ss_pred cccCCEEEEeecCCCCcEeeEEEEEccCCEE
Q 031473 15 ILRGDNVMIIRGKDKGETGAIKRVIRSQNRV 45 (159)
Q Consensus 15 i~kGD~V~Vi~G~dKGk~G~V~~V~~~~~~V 45 (159)
++.||+|.+ +|++++++++.+
T Consensus 42 ~~~G~~v~~----------~v~~~d~~~~~i 62 (65)
T cd00164 42 FKVGDEVEV----------KVLEVDPEKGRI 62 (65)
T ss_pred eCCCCEEEE----------EEEEEcCCcCEE
Confidence 677777775 556666555544
No 103
>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=26.60 E-value=81 Score=21.58 Aligned_cols=30 Identities=20% Similarity=0.130 Sum_probs=19.7
Q ss_pred cccccCCEEEEeecCC-CCcEeeEEEEEccC
Q 031473 13 WKILRGDNVMIIRGKD-KGETGAIKRVIRSQ 42 (159)
Q Consensus 13 ~~i~kGD~V~Vi~G~d-KGk~G~V~~V~~~~ 42 (159)
..|++||.|.|--=++ .-..|.|..++...
T Consensus 37 iwI~~GD~VlV~~~~~~~~~kg~Iv~r~~~~ 67 (78)
T cd04456 37 IWIKRGDFLIVDPIEEGEDVKADIIFVYCKD 67 (78)
T ss_pred EEEcCCCEEEEEecccCCCceEEEEEEeCHH
Confidence 6688999998865444 23457777665543
No 104
>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=26.32 E-value=94 Score=21.22 Aligned_cols=25 Identities=28% Similarity=0.247 Sum_probs=13.5
Q ss_pred hcccccCCEEEEeecCCCCcEeeEEEEE
Q 031473 12 HWKILRGDNVMIIRGKDKGETGAIKRVI 39 (159)
Q Consensus 12 ~~~i~kGD~V~Vi~G~dKGk~G~V~~V~ 39 (159)
+-.|++||+|.++-. +...+|.++.
T Consensus 28 ~G~i~~gd~v~i~P~---~~~~~V~sI~ 52 (91)
T cd03693 28 TGVLKPGMVVTFAPA---GVTGEVKSVE 52 (91)
T ss_pred cceeecCCEEEECCC---CcEEEEEEEE
Confidence 344566666666643 2445555554
No 105
>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=26.28 E-value=79 Score=21.98 Aligned_cols=28 Identities=14% Similarity=0.172 Sum_probs=21.4
Q ss_pred cccCCEEEEeecC--CCCcEeeEEEEEccC
Q 031473 15 ILRGDNVMIIRGK--DKGETGAIKRVIRSQ 42 (159)
Q Consensus 15 i~kGD~V~Vi~G~--dKGk~G~V~~V~~~~ 42 (159)
++.||-|.|..+. .---+|.|.++....
T Consensus 3 ~~vGD~V~v~~~~~~~~~~v~~I~~i~~~~ 32 (119)
T PF01426_consen 3 YKVGDFVYVKPDDPPEPPYVARIEEIWEDK 32 (119)
T ss_dssp EETTSEEEEECTSTTSEEEEEEEEEEEEET
T ss_pred EeCCCEEEEeCCCCCCCCEEEEEEEEEcCC
Confidence 6789999999988 344678888886443
No 106
>PRK10708 hypothetical protein; Provisional
Probab=26.09 E-value=1.4e+02 Score=19.63 Aligned_cols=29 Identities=14% Similarity=0.099 Sum_probs=20.9
Q ss_pred ccCCEEEEeecCCCCcEeeEEEEEccCCE
Q 031473 16 LRGDNVMIIRGKDKGETGAIKRVIRSQNR 44 (159)
Q Consensus 16 ~kGD~V~Vi~G~dKGk~G~V~~V~~~~~~ 44 (159)
+.+|+|.|-.--.--..|.|+.|.+.+..
T Consensus 2 kvnD~VtVKTDG~~rR~G~iLavE~F~EG 30 (62)
T PRK10708 2 KVNDRVTVKTDGGPRRPGVVLAVEEFSEG 30 (62)
T ss_pred ccccEEEEecCCCccccceEEEEeeccCc
Confidence 46899998764444567999998876643
No 107
>cd05689 S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (ec4) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=25.95 E-value=1.1e+02 Score=19.46 Aligned_cols=22 Identities=18% Similarity=0.353 Sum_probs=14.1
Q ss_pred cccCCEEEEeecCCCCcEeeEEEEEccCCEEE
Q 031473 15 ILRGDNVMIIRGKDKGETGAIKRVIRSQNRVI 46 (159)
Q Consensus 15 i~kGD~V~Vi~G~dKGk~G~V~~V~~~~~~V~ 46 (159)
++.||+|.| +|.+++.++.++.
T Consensus 49 ~~~Gd~v~v----------~v~~id~~~~~i~ 70 (72)
T cd05689 49 VSLGDEVEV----------MVLDIDEERRRIS 70 (72)
T ss_pred eCCCCEEEE----------EEEEeeCCcCEEe
Confidence 567787776 3566666665543
No 108
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=25.90 E-value=1.7e+02 Score=18.13 Aligned_cols=34 Identities=15% Similarity=0.389 Sum_probs=22.7
Q ss_pred ccccCCEEEEeecCCCC-cEeeEEEEEccCCEEEEe
Q 031473 14 KILRGDNVMIIRGKDKG-ETGAIKRVIRSQNRVIVE 48 (159)
Q Consensus 14 ~i~kGD~V~Vi~G~dKG-k~G~V~~V~~~~~~V~Ve 48 (159)
.+.+||.|.+..=.+.+ -.|+|+++.. .++..|.
T Consensus 2 ~~~~G~~Ve~~~~~~~~W~~a~V~~~~~-~~~~~V~ 36 (61)
T smart00743 2 DFKKGDRVEVFSKEEDSWWEAVVTKVLG-DGKYLVR 36 (61)
T ss_pred CcCCCCEEEEEECCCCEEEEEEEEEECC-CCEEEEE
Confidence 57899999998633222 3589999987 3444443
No 109
>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=25.89 E-value=1.3e+02 Score=18.30 Aligned_cols=22 Identities=18% Similarity=0.308 Sum_probs=15.2
Q ss_pred cccCCEEEEeecCCCCcEeeEEEEEccCCEEE
Q 031473 15 ILRGDNVMIIRGKDKGETGAIKRVIRSQNRVI 46 (159)
Q Consensus 15 i~kGD~V~Vi~G~dKGk~G~V~~V~~~~~~V~ 46 (159)
++.||.|.+ +|++++.++.++.
T Consensus 45 ~~~Gd~v~v----------~i~~vd~~~~~i~ 66 (68)
T cd05685 45 VSVGDIVEV----------KVISIDEERGRIS 66 (68)
T ss_pred cCCCCEEEE----------EEEEEECCCCEEe
Confidence 678888887 4677776665554
No 110
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=25.86 E-value=79 Score=21.87 Aligned_cols=31 Identities=19% Similarity=0.071 Sum_probs=19.1
Q ss_pred hhcccccCCEEEEeecCCCCcEeeEEEEEcc
Q 031473 11 RHWKILRGDNVMIIRGKDKGETGAIKRVIRS 41 (159)
Q Consensus 11 r~~~i~kGD~V~Vi~G~dKGk~G~V~~V~~~ 41 (159)
+...|+.||.|.|---++-=..|.|..++.+
T Consensus 40 k~iwI~~GD~VlVe~~~~~~~kg~Iv~r~~~ 70 (83)
T smart00652 40 KKVWIRRGDIVLVDPWDFQDVKADIIYKYTK 70 (83)
T ss_pred ccEEEcCCCEEEEEecCCCCCEEEEEEEeCH
Confidence 3566888999888533332344666666544
No 111
>cd05696 S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 4 (hs4). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=25.77 E-value=1.4e+02 Score=19.28 Aligned_cols=24 Identities=8% Similarity=-0.028 Sum_probs=16.9
Q ss_pred ccccCCEEEEeecCCCCcEeeEEEEEccCCEEEE
Q 031473 14 KILRGDNVMIIRGKDKGETGAIKRVIRSQNRVIV 47 (159)
Q Consensus 14 ~i~kGD~V~Vi~G~dKGk~G~V~~V~~~~~~V~V 47 (159)
+++.||.|. .+|+.+++++.++.+
T Consensus 46 ~~~vG~~v~----------~kV~~id~~~~~i~l 69 (71)
T cd05696 46 PFKAGTTHK----------ARIIGYSPMDGLLQL 69 (71)
T ss_pred ccCCCCEEE----------EEEEEEeCCCCEEEE
Confidence 366677765 467888888877765
No 112
>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=25.68 E-value=98 Score=20.65 Aligned_cols=26 Identities=19% Similarity=0.382 Sum_probs=15.1
Q ss_pred hcccccCCEEEEeecCCCCcEeeEEEEEc
Q 031473 12 HWKILRGDNVMIIRGKDKGETGAIKRVIR 40 (159)
Q Consensus 12 ~~~i~kGD~V~Vi~G~dKGk~G~V~~V~~ 40 (159)
+-.|++||.|.++-. +...+|.++..
T Consensus 24 ~G~i~~Gd~v~i~P~---~~~~~V~si~~ 49 (83)
T cd03698 24 SGSIQKGDTLLVMPS---KESVEVKSIYV 49 (83)
T ss_pred eeEEeCCCEEEEeCC---CcEEEEEEEEE
Confidence 445677777776643 34455555543
No 113
>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=25.59 E-value=1.6e+02 Score=18.44 Aligned_cols=24 Identities=25% Similarity=0.350 Sum_probs=17.0
Q ss_pred cccCCEEEEeecCCCCcEeeEEEEEccCCEEEEe
Q 031473 15 ILRGDNVMIIRGKDKGETGAIKRVIRSQNRVIVE 48 (159)
Q Consensus 15 i~kGD~V~Vi~G~dKGk~G~V~~V~~~~~~V~Ve 48 (159)
+..||.|.+ +|++++++++.+.+.
T Consensus 45 ~~~Gd~v~~----------~v~~~d~~~~~i~ls 68 (73)
T cd05691 45 FKVGDEVEA----------KITNVDRKNRKISLS 68 (73)
T ss_pred cCCCCEEEE----------EEEEEeCCCCEEEEE
Confidence 577888875 578888777666543
No 114
>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=25.58 E-value=1e+02 Score=20.51 Aligned_cols=29 Identities=17% Similarity=0.187 Sum_probs=18.3
Q ss_pred chhcccccCCEEEEeecCCCCcEeeEEEEEcc
Q 031473 10 IRHWKILRGDNVMIIRGKDKGETGAIKRVIRS 41 (159)
Q Consensus 10 ir~~~i~kGD~V~Vi~G~dKGk~G~V~~V~~~ 41 (159)
+..-.|++||+|.++-+. ..++|.++...
T Consensus 22 v~sG~i~~g~~v~~~p~~---~~~~V~sI~~~ 50 (83)
T cd03696 22 VLSGSVKVGDKVEILPLG---EETRVRSIQVH 50 (83)
T ss_pred EeecEEeCCCEEEECCCC---ceEEEEEEEEC
Confidence 344557788888777643 46777766543
No 115
>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=25.56 E-value=1.4e+02 Score=20.00 Aligned_cols=26 Identities=27% Similarity=0.441 Sum_probs=14.3
Q ss_pred hhcccccCCEEEEeecCCCCcEeeEEEEE
Q 031473 11 RHWKILRGDNVMIIRGKDKGETGAIKRVI 39 (159)
Q Consensus 11 r~~~i~kGD~V~Vi~G~dKGk~G~V~~V~ 39 (159)
..-.+++||+|.++-. +...+|.++.
T Consensus 23 ~~G~v~~Gd~v~~~P~---~~~~~V~si~ 48 (81)
T cd03695 23 ASGSIRVGDEVVVLPS---GKTSRVKSIE 48 (81)
T ss_pred ccceEECCCEEEEcCC---CCeEEEEEEE
Confidence 3445666777766643 3445555554
No 116
>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=25.55 E-value=81 Score=18.75 Aligned_cols=17 Identities=12% Similarity=0.263 Sum_probs=12.6
Q ss_pred chhcccccCCEEEEeec
Q 031473 10 IRHWKILRGDNVMIIRG 26 (159)
Q Consensus 10 ir~~~i~kGD~V~Vi~G 26 (159)
-....|.+||.+.|+.=
T Consensus 11 ~~eLs~~~Gd~i~v~~~ 27 (48)
T PF00018_consen 11 PDELSFKKGDIIEVLEK 27 (48)
T ss_dssp TTBSEB-TTEEEEEEEE
T ss_pred CCEEeEECCCEEEEEEe
Confidence 45678899999999863
No 117
>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=25.54 E-value=1.2e+02 Score=25.23 Aligned_cols=31 Identities=29% Similarity=0.332 Sum_probs=23.1
Q ss_pred cccccCCEEEEeecCCCCcEeeEEEEEccCCEE
Q 031473 13 WKILRGDNVMIIRGKDKGETGAIKRVIRSQNRV 45 (159)
Q Consensus 13 ~~i~kGD~V~Vi~G~dKGk~G~V~~V~~~~~~V 45 (159)
-.+..||.|.+-.-. +..|.|.+|.+.+|.+
T Consensus 33 ~~~~vGD~V~~~~~~--~~~~~i~~i~~R~~~l 63 (287)
T cd01854 33 IKPVVGDWVEVEPDD--DGEGVIVRVLPRKNLL 63 (287)
T ss_pred CCccCCCEEEEEecC--CCcEEEEEEECCCceE
Confidence 358899999975322 5678999999887754
No 118
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=25.51 E-value=91 Score=21.47 Aligned_cols=26 Identities=27% Similarity=0.280 Sum_probs=16.5
Q ss_pred hcccccCCEEEEeecCCCCcEeeEEE
Q 031473 12 HWKILRGDNVMIIRGKDKGETGAIKR 37 (159)
Q Consensus 12 ~~~i~kGD~V~Vi~G~dKGk~G~V~~ 37 (159)
+..|.+||.|.|--=++-=+.|.|.-
T Consensus 44 ~i~I~~GD~V~Ve~~~~d~~kg~I~~ 69 (75)
T COG0361 44 RIRILPGDVVLVELSPYDLTKGRIVY 69 (75)
T ss_pred eEEeCCCCEEEEEecccccccccEEE
Confidence 56688888888765555444454443
No 119
>PF14801 GCD14_N: tRNA methyltransferase complex GCD14 subunit N-term; PDB: 1I9G_A.
Probab=25.44 E-value=47 Score=21.54 Aligned_cols=21 Identities=29% Similarity=0.366 Sum_probs=9.1
Q ss_pred hhcccccCCEEEEeecCCCCcEe
Q 031473 11 RHWKILRGDNVMIIRGKDKGETG 33 (159)
Q Consensus 11 r~~~i~kGD~V~Vi~G~dKGk~G 33 (159)
|.-+|+.||+|++.- -||+.-
T Consensus 2 R~Gpf~~GdrVQlTD--~Kgr~~ 22 (54)
T PF14801_consen 2 RRGPFRAGDRVQLTD--PKGRKH 22 (54)
T ss_dssp ---S--TT-EEEEEE--TT--EE
T ss_pred CcCCCCCCCEEEEcc--CCCCee
Confidence 345789999999764 345543
No 120
>COG2411 Uncharacterized conserved protein [Function unknown]
Probab=25.43 E-value=78 Score=25.47 Aligned_cols=32 Identities=28% Similarity=0.202 Sum_probs=21.6
Q ss_pred hcchhc--ccccCCEEEEeecCCCCcEeeEEEEE
Q 031473 8 KLIRHW--KILRGDNVMIIRGKDKGETGAIKRVI 39 (159)
Q Consensus 8 ~~ir~~--~i~kGD~V~Vi~G~dKGk~G~V~~V~ 39 (159)
-+||.| ...+|+.|.|.+|..-=-..+|.+|.
T Consensus 26 ~TIR~G~~~~k~g~eVyIh~~g~i~gkAkIk~V~ 59 (188)
T COG2411 26 TTIRLGKIVLKPGSEVYIHSGGYIIGKAKIKKVK 59 (188)
T ss_pred EEEecCcccCCCCCEEEEEECCEEEEEEEEEEEE
Confidence 357777 77899999999986332234444443
No 121
>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=25.18 E-value=77 Score=18.19 Aligned_cols=16 Identities=13% Similarity=0.333 Sum_probs=13.2
Q ss_pred hhcccccCCEEEEeec
Q 031473 11 RHWKILRGDNVMIIRG 26 (159)
Q Consensus 11 r~~~i~kGD~V~Vi~G 26 (159)
..+.+.+||.|.|+..
T Consensus 14 ~~l~~~~Gd~v~v~~~ 29 (54)
T cd00174 14 DELSFKKGDIIEVLEK 29 (54)
T ss_pred CCCCCCCCCEEEEEEc
Confidence 3567899999999976
No 122
>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=24.71 E-value=1.6e+02 Score=21.89 Aligned_cols=34 Identities=24% Similarity=0.246 Sum_probs=25.9
Q ss_pred cccCCEEEEeecCCCCcEeeEEEEEccCCEEEEec
Q 031473 15 ILRGDNVMIIRGKDKGETGAIKRVIRSQNRVIVEG 49 (159)
Q Consensus 15 i~kGD~V~Vi~G~dKGk~G~V~~V~~~~~~V~Veg 49 (159)
-++||.|..-.|. .|..|.+...+...+.|++=|
T Consensus 74 p~~GDiv~f~~~~-~~HVGi~~g~~~~~g~i~~lg 107 (129)
T TIGR02594 74 PAYGCIAVKRRGG-GGHVGFVVGKDKQTGTIIVLG 107 (129)
T ss_pred CCccEEEEEECCC-CCEEEEEEeEcCCCCEEEEee
Confidence 4799999876554 788999999887766765533
No 123
>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=24.57 E-value=1.3e+02 Score=21.48 Aligned_cols=40 Identities=20% Similarity=0.157 Sum_probs=25.2
Q ss_pred hhcccccCCEEEE--eecCCCCcEeeEEEEEccCCEEEEeccc
Q 031473 11 RHWKILRGDNVMI--IRGKDKGETGAIKRVIRSQNRVIVEGKN 51 (159)
Q Consensus 11 r~~~i~kGD~V~V--i~G~dKGk~G~V~~V~~~~~~V~Vegvn 51 (159)
..-..++||.|+. -.+..-|-+|.|.+|.. .+.|.+-+-|
T Consensus 59 ~~~~P~~Gdivv~~~~~~~~~GHVaIV~~v~~-~~~i~v~e~N 100 (124)
T PF05257_consen 59 TGSTPQPGDIVVWDSGSGGGYGHVAIVESVND-GGTITVIEQN 100 (124)
T ss_dssp ECS---TTEEEEEEECTTTTT-EEEEEEEE-T-TSEEEEEECS
T ss_pred cCcccccceEEEeccCCCCCCCeEEEEEEECC-CCEEEEEECC
Confidence 3445689999987 35567899999999954 4566655444
No 124
>TIGR00523 eIF-1A eukaryotic/archaeal initiation factor 1A. Recommended nomenclature: eIF-1A for eukaryotes, aIF-1A for Archaea. Also called eIF-4C
Probab=24.57 E-value=53 Score=23.63 Aligned_cols=29 Identities=17% Similarity=0.113 Sum_probs=17.1
Q ss_pred hhcccccCCEEEEeecCCCC---cEeeEEEEEcc
Q 031473 11 RHWKILRGDNVMIIRGKDKG---ETGAIKRVIRS 41 (159)
Q Consensus 11 r~~~i~kGD~V~Vi~G~dKG---k~G~V~~V~~~ 41 (159)
++..|++||.|.| + +.-- ..|.|...+..
T Consensus 54 k~iwI~~GD~VlV-s-p~d~~~~~kg~Iv~r~~~ 85 (99)
T TIGR00523 54 KRIWIREGDVVIV-K-PWEFQGDDKCDIVWRYTK 85 (99)
T ss_pred ccEEecCCCEEEE-E-EccCCCCccEEEEEEcCH
Confidence 3566889999988 2 2111 13666666543
No 125
>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=24.42 E-value=56 Score=25.15 Aligned_cols=23 Identities=22% Similarity=0.291 Sum_probs=15.3
Q ss_pred ccccCCEEEEeecCCCCcEeeEEEEEcc
Q 031473 14 KILRGDNVMIIRGKDKGETGAIKRVIRS 41 (159)
Q Consensus 14 ~i~kGD~V~Vi~G~dKGk~G~V~~V~~~ 41 (159)
+++.||.|+|= |..|.|.++.-.
T Consensus 60 pf~vGD~I~i~-----~~~G~V~~I~l~ 82 (206)
T PF00924_consen 60 PFKVGDRIEIG-----GVEGRVEEIGLR 82 (206)
T ss_dssp SS-TT-EEESS-----S-EEEEEEE-SS
T ss_pred CccCCCEEEEE-----EeehHHHhcCcc
Confidence 78999999854 888999988643
No 126
>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=24.36 E-value=1.7e+02 Score=18.51 Aligned_cols=23 Identities=13% Similarity=0.261 Sum_probs=15.3
Q ss_pred cccCCEEEEeecCCCCcEeeEEEEEccCCEEEE
Q 031473 15 ILRGDNVMIIRGKDKGETGAIKRVIRSQNRVIV 47 (159)
Q Consensus 15 i~kGD~V~Vi~G~dKGk~G~V~~V~~~~~~V~V 47 (159)
+..||.|.+ +|.+++..++.+.+
T Consensus 50 ~~~Gd~v~v----------kv~~~d~~~~~i~l 72 (76)
T cd04452 50 VKVGRKEVV----------KVIRVDKEKGYIDL 72 (76)
T ss_pred eCCCCEEEE----------EEEEEECCCCEEEE
Confidence 578888886 46667766665544
No 127
>COG1193 Mismatch repair ATPase (MutS family) [DNA replication, recombination, and repair]
Probab=24.36 E-value=83 Score=30.50 Aligned_cols=33 Identities=33% Similarity=0.556 Sum_probs=26.0
Q ss_pred hcccccCCEEEEeecCCCCcEeeEEEEEccCCEEEEe
Q 031473 12 HWKILRGDNVMIIRGKDKGETGAIKRVIRSQNRVIVE 48 (159)
Q Consensus 12 ~~~i~kGD~V~Vi~G~dKGk~G~V~~V~~~~~~V~Ve 48 (159)
.-+++.||.|.+++ |..|.|.+|......+.|+
T Consensus 610 ~~~l~~gDev~~~t----~e~G~~~~i~a~~~e~~v~ 642 (753)
T COG1193 610 KRKLKLGDEVEVIT----GEPGAVVKIIAGILEALVQ 642 (753)
T ss_pred ccCceecceeEeec----CCccceeeeeccCceeEEe
Confidence 56789999999998 6677777777666777665
No 128
>cd05705 S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: 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 14 (hs14). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=24.28 E-value=1.3e+02 Score=19.77 Aligned_cols=24 Identities=17% Similarity=0.158 Sum_probs=17.9
Q ss_pred ccccCCEEEEeecCCCCcEeeEEEEEccCCEEEE
Q 031473 14 KILRGDNVMIIRGKDKGETGAIKRVIRSQNRVIV 47 (159)
Q Consensus 14 ~i~kGD~V~Vi~G~dKGk~G~V~~V~~~~~~V~V 47 (159)
.+..||.|. ++|++++++++++.+
T Consensus 50 ~~~~G~~v~----------~kVl~id~~~~~i~L 73 (74)
T cd05705 50 YLPEGKLLT----------AKVLSVNSEKNLVEL 73 (74)
T ss_pred ccCCCCEEE----------EEEEEEECCCCEEec
Confidence 457788876 478999988887654
No 129
>PF10781 DSRB: Dextransucrase DSRB; InterPro: IPR019717 DSRB is a novel dextransucrase which produces a dextran different from the typical dextran, as it contains (1-6) and (1-2) linkages, when this strain is grown in the presence of sucrose [].
Probab=23.99 E-value=1.6e+02 Score=19.43 Aligned_cols=29 Identities=17% Similarity=0.098 Sum_probs=20.8
Q ss_pred ccCCEEEEeecCCCCcEeeEEEEEccCCE
Q 031473 16 LRGDNVMIIRGKDKGETGAIKRVIRSQNR 44 (159)
Q Consensus 16 ~kGD~V~Vi~G~dKGk~G~V~~V~~~~~~ 44 (159)
+.+|+|.|-.--.--..|.|+.|.+.+..
T Consensus 2 kvnD~VtVKTDG~~rR~G~ilavE~F~EG 30 (62)
T PF10781_consen 2 KVNDRVTVKTDGGPRREGVILAVEPFNEG 30 (62)
T ss_pred ccccEEEEecCCcccccceEEEEeeccCc
Confidence 46899998764444567999998877643
No 130
>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=23.83 E-value=1.8e+02 Score=22.53 Aligned_cols=32 Identities=16% Similarity=0.188 Sum_probs=26.2
Q ss_pred hhcccccCCEEEEeecCCCCcEeeEEEEEccC
Q 031473 11 RHWKILRGDNVMIIRGKDKGETGAIKRVIRSQ 42 (159)
Q Consensus 11 r~~~i~kGD~V~Vi~G~dKGk~G~V~~V~~~~ 42 (159)
..-.++.||-|.|-+|..+--+|+|.++....
T Consensus 26 ~g~~y~lGD~Vlv~s~~~~~yIgkI~~iwe~~ 57 (159)
T cd04715 26 DGVEYRLYDDVYVHNGDSEPYIGKIIKIYETA 57 (159)
T ss_pred CCEEEeCCCEEEEeCCCCCCEEEEEEEEEEcC
Confidence 33457899999999988777899999998654
No 131
>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=22.98 E-value=1.7e+02 Score=18.32 Aligned_cols=23 Identities=26% Similarity=0.465 Sum_probs=14.7
Q ss_pred cccCCEEEEeecCCCCcEeeEEEEEccCCEEEE
Q 031473 15 ILRGDNVMIIRGKDKGETGAIKRVIRSQNRVIV 47 (159)
Q Consensus 15 i~kGD~V~Vi~G~dKGk~G~V~~V~~~~~~V~V 47 (159)
+++||.+.+. |++++++..++.+
T Consensus 45 ~~~Gd~i~~~----------i~~~~~~~~~i~l 67 (70)
T cd05687 45 VKVGDEVEVY----------VLRVEDEEGNVVL 67 (70)
T ss_pred CCCCCEEEEE----------EEEEECCCCeEEE
Confidence 6788888754 5666655555543
No 132
>COG2053 RPS28A Ribosomal protein S28E/S33 [Translation, ribosomal structure and biogenesis]
Probab=22.90 E-value=69 Score=21.65 Aligned_cols=13 Identities=46% Similarity=0.854 Sum_probs=10.0
Q ss_pred EEEEeecCCCCcE
Q 031473 20 NVMIIRGKDKGET 32 (159)
Q Consensus 20 ~V~Vi~G~dKGk~ 32 (159)
+|.++.|.|||.+
T Consensus 27 k~ril~grdkgRi 39 (69)
T COG2053 27 KVRILEGRDKGRI 39 (69)
T ss_pred EEEEeecCCcCcE
Confidence 5778899988853
No 133
>PRK12289 GTPase RsgA; Reviewed
Probab=22.80 E-value=1.3e+02 Score=26.29 Aligned_cols=32 Identities=25% Similarity=0.459 Sum_probs=23.9
Q ss_pred cccCCEEEEeecCCCCcEeeEEEEEccCCEEE
Q 031473 15 ILRGDNVMIIRGKDKGETGAIKRVIRSQNRVI 46 (159)
Q Consensus 15 i~kGD~V~Vi~G~dKGk~G~V~~V~~~~~~V~ 46 (159)
+.+||.|.+-.-.+.+..|.|.+|.+.+|.+.
T Consensus 52 ~~vGD~V~~~~~~~~~~~~~I~~vlpR~~~L~ 83 (352)
T PRK12289 52 VMVGDRVIVEEPDWQGQRGAIAEVLPRKTELD 83 (352)
T ss_pred cccCCEEEEeecCCCCCceEEEEEecccccee
Confidence 78899998753233456789999999888654
No 134
>PF15232 DUF4585: Domain of unknown function (DUF4585)
Probab=22.74 E-value=1e+02 Score=21.31 Aligned_cols=30 Identities=30% Similarity=0.566 Sum_probs=18.6
Q ss_pred CceEEEeeeccCCCccccCCCCCCceeEEE
Q 031473 65 GGIFTVEAPIHASNVQVLDPVTGKPCKVGT 94 (159)
Q Consensus 65 g~i~~~e~pI~~SnV~Lvdp~~g~~~rV~~ 94 (159)
|..+-+++|+..--=+|+||++|+-.+|-+
T Consensus 17 G~Yy~vd~P~Qp~~k~lfDPETGqYVeV~i 46 (75)
T PF15232_consen 17 GQYYVVDAPVQPKTKTLFDPETGQYVEVLI 46 (75)
T ss_pred CCEEEEecCCCcceeeeecCCCCcEEEEeC
Confidence 555566666665555667777776555543
No 135
>COG2002 AbrB Regulators of stationary/sporulation gene expression [Transcription]
Probab=22.68 E-value=76 Score=21.92 Aligned_cols=23 Identities=30% Similarity=0.364 Sum_probs=19.3
Q ss_pred cchhcccccCCEEEEeecCCCCc
Q 031473 9 LIRHWKILRGDNVMIIRGKDKGE 31 (159)
Q Consensus 9 ~ir~~~i~kGD~V~Vi~G~dKGk 31 (159)
.-+.+.|..||.|.+....+.|+
T Consensus 22 iR~~lgi~~Gd~lei~~~~~~~~ 44 (89)
T COG2002 22 IREALGIKEGDVLEIIVDGDGGR 44 (89)
T ss_pred HHHHhCCCCCCEEEEEEeCCCCE
Confidence 34568899999999999888877
No 136
>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=22.66 E-value=1.1e+02 Score=25.81 Aligned_cols=30 Identities=27% Similarity=0.427 Sum_probs=24.6
Q ss_pred ccccCCEEEEeecCC-CCcEeeEEEEEccCCEEEE
Q 031473 14 KILRGDNVMIIRGKD-KGETGAIKRVIRSQNRVIV 47 (159)
Q Consensus 14 ~i~kGD~V~Vi~G~d-KGk~G~V~~V~~~~~~V~V 47 (159)
-|++|+-|.- . .|-+|+|.+|.+.+.+|.+
T Consensus 143 GV~~g~~Vi~----~~~GLVG~V~~V~~~~S~V~l 173 (283)
T TIGR00219 143 GVYKDMPVIA----DGKGLVGKVVSVGSNTSRVLL 173 (283)
T ss_pred CCCCCCEEEc----CCCceEEEEEEECCCeEEEEE
Confidence 4678888773 5 8999999999999988754
No 137
>COG1385 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.58 E-value=1.3e+02 Score=25.00 Aligned_cols=44 Identities=16% Similarity=0.270 Sum_probs=34.1
Q ss_pred hHhhcchhcccccCCEEEEeecCCCCcEeeEEEEEccCCEEEEe
Q 031473 5 AAEKLIRHWKILRGDNVMIIRGKDKGETGAIKRVIRSQNRVIVE 48 (159)
Q Consensus 5 ~~~~~ir~~~i~kGD~V~Vi~G~dKGk~G~V~~V~~~~~~V~Ve 48 (159)
.++|..+=++++.||.+.+.-|.+.=-.+.|.++.++.-.+.+.
T Consensus 24 ~~~Hl~~VlRl~~gd~l~l~~g~g~~~~a~i~~~~kk~~~~~i~ 67 (246)
T COG1385 24 EAHHLKRVLRLKEGDELRLFDGSGGEFLAEITKIGKKEALLKIV 67 (246)
T ss_pred hhhhHHheeecCCCCEEEEEeCCCcEEEEEEeecCCCceEEEEE
Confidence 56777788999999999999998655556888887766555444
No 138
>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=22.44 E-value=91 Score=18.03 Aligned_cols=17 Identities=12% Similarity=0.343 Sum_probs=13.4
Q ss_pred hhcccccCCEEEEeecC
Q 031473 11 RHWKILRGDNVMIIRGK 27 (159)
Q Consensus 11 r~~~i~kGD~V~Vi~G~ 27 (159)
..+.+.+||.|.|+...
T Consensus 17 ~~l~~~~Gd~v~v~~~~ 33 (58)
T smart00326 17 DELSFKKGDIITVLEKS 33 (58)
T ss_pred CCCCCCCCCEEEEEEcC
Confidence 45678999999998764
No 139
>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=22.43 E-value=67 Score=21.67 Aligned_cols=19 Identities=26% Similarity=0.331 Sum_probs=11.6
Q ss_pred cchhcccccCCEEEEeecC
Q 031473 9 LIRHWKILRGDNVMIIRGK 27 (159)
Q Consensus 9 ~ir~~~i~kGD~V~Vi~G~ 27 (159)
+.++..|.+||+|.|--=+
T Consensus 39 r~~rI~I~~GD~V~Ve~sp 57 (68)
T TIGR00008 39 RMHYIRILPGDKVKVELSP 57 (68)
T ss_pred hhccEEECCCCEEEEEECc
Confidence 3445667777777765443
No 140
>smart00439 BAH Bromo adjacent homology domain.
Probab=22.23 E-value=1.7e+02 Score=20.27 Aligned_cols=29 Identities=21% Similarity=0.335 Sum_probs=22.2
Q ss_pred cccCCEEEEeecC--CCCcEeeEEEEEccCC
Q 031473 15 ILRGDNVMIIRGK--DKGETGAIKRVIRSQN 43 (159)
Q Consensus 15 i~kGD~V~Vi~G~--dKGk~G~V~~V~~~~~ 43 (159)
|+.||.|.|.... ..=-+|.|.++....+
T Consensus 2 ~~vgd~V~v~~~~~~~~~~i~~I~~i~~~~~ 32 (120)
T smart00439 2 IRVGDFVLVEPDDADEPYYIGRIEEIFETKK 32 (120)
T ss_pred cccCCEEEEeCCCCCCCCEEEEEEEEEECCC
Confidence 6789999988765 2345899999987654
No 141
>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=21.70 E-value=2.1e+02 Score=19.64 Aligned_cols=35 Identities=11% Similarity=0.231 Sum_probs=31.5
Q ss_pred cCCEEEEeecCCCCcEeeEEEEEccCCEEEEeccc
Q 031473 17 RGDNVMIIRGKDKGETGAIKRVIRSQNRVIVEGKN 51 (159)
Q Consensus 17 kGD~V~Vi~G~dKGk~G~V~~V~~~~~~V~Vegvn 51 (159)
-|.++.+|+=.+.--.|..-.|+.+...|.+++|-
T Consensus 5 IG~~isLISk~~iRYeGiL~~In~~~sTi~L~nVr 39 (74)
T cd01736 5 IGSKISLISKSDIRYEGILYTINTEDSTIALKNVR 39 (74)
T ss_pred cCceEEEEecCCcEEEEEEEeeccccCEEEeeeeE
Confidence 58899999988888999999999999999999854
No 142
>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=21.70 E-value=1.7e+02 Score=18.87 Aligned_cols=23 Identities=22% Similarity=0.281 Sum_probs=13.0
Q ss_pred ccccCCEEEEeecCCCCcEeeEEEEEccCCEEE
Q 031473 14 KILRGDNVMIIRGKDKGETGAIKRVIRSQNRVI 46 (159)
Q Consensus 14 ~i~kGD~V~Vi~G~dKGk~G~V~~V~~~~~~V~ 46 (159)
.++.||+|.| +|.+++.++.++.
T Consensus 57 ~~~~gd~v~v----------~v~~vd~~~~~i~ 79 (83)
T cd04471 57 VFRLGDKVKV----------RVVRVDLDRRKID 79 (83)
T ss_pred EEcCCCEEEE----------EEEEeccccCEEE
Confidence 3466777776 3555555444443
No 143
>PRK08515 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=21.36 E-value=1.4e+02 Score=24.25 Aligned_cols=38 Identities=16% Similarity=0.225 Sum_probs=25.8
Q ss_pred hcchhcccccCCEEEEeecC------------CCCcEeeEEEEEccCCEE
Q 031473 8 KLIRHWKILRGDNVMIIRGK------------DKGETGAIKRVIRSQNRV 45 (159)
Q Consensus 8 ~~ir~~~i~kGD~V~Vi~G~------------dKGk~G~V~~V~~~~~~V 45 (159)
+....|-+++||.|.|+.-. .-|..|.+.+|--.++++
T Consensus 159 ~l~~~~lV~rGd~V~i~~~~gg~~I~~~G~Al~~G~~Gd~IrVrN~Sgki 208 (222)
T PRK08515 159 KFKALILVRKNDIINGVLKEGGVSIEISLKALQDGNLGDIIQAKNKSNKI 208 (222)
T ss_pred HcCCcceEecCCEEEEEEECCCEEEEEEEEEcccCCCCCEEEEEeCCCCE
Confidence 33445778999999998543 467777777776544443
No 144
>PF11910 NdhO: Cyanobacterial and plant NDH-1 subunit O; InterPro: IPR020905 NAD(P)H-quinone oxidoreductase (NDH-1) shuttles electrons from an unknown electron donor, via FMN and iron-sulphur (Fe-S) centres, to quinones in the respiratory and/or the photosynthetic chain. The immediate electron acceptor for the enzyme in this species is believed to be plastoquinone. It couples the redox reaction to proton translocation, and thus conserves the redox energy in a proton gradient. Cyanobacterial NDH-1 also plays a role in inorganic carbon-concentration. NDH-1 can be composed of about 15 different subunits, although different subcomplexes with different compositions have been identified which probably have different functions. This entry represents subunit O. ; GO: 0016655 oxidoreductase activity, acting on NADH or NADPH, quinone or similar compound as acceptor, 0055114 oxidation-reduction process, 0005886 plasma membrane
Probab=21.17 E-value=49 Score=22.34 Aligned_cols=14 Identities=29% Similarity=0.330 Sum_probs=8.5
Q ss_pred cccCCEEEEeecCC
Q 031473 15 ILRGDNVMIIRGKD 28 (159)
Q Consensus 15 i~kGD~V~Vi~G~d 28 (159)
|+||+.|.|++.++
T Consensus 1 lKKG~lVrv~re~~ 14 (67)
T PF11910_consen 1 LKKGSLVRVNREKY 14 (67)
T ss_pred CCcceEEEeehHhh
Confidence 45666666666554
No 145
>KOG0171 consensus Mitochondrial inner membrane protease, subunit IMP1 [Posttranslational modification, protein turnover, chaperones]
Probab=20.74 E-value=1.3e+02 Score=24.12 Aligned_cols=39 Identities=23% Similarity=0.222 Sum_probs=23.3
Q ss_pred ccCCEEEEeecCCCCc---EeeEEEEEccCCEEEEeccceee
Q 031473 16 LRGDNVMIIRGKDKGE---TGAIKRVIRSQNRVIVEGKNLVK 54 (159)
Q Consensus 16 ~kGD~V~Vi~G~dKGk---~G~V~~V~~~~~~V~Vegvn~~~ 54 (159)
..||.|.|.-|+-.+. .+-+.-+.--.+.|.|+|-|...
T Consensus 91 ~eGD~v~v~~~~~~~n~~~e~~~~~i~VP~GhVfv~GDN~~n 132 (176)
T KOG0171|consen 91 MEGDLVEVHDGPLVVNDLVEKFSTPIRVPEGHVFVEGDNRNN 132 (176)
T ss_pred cCCceEEEecCCcccchhhhhccceeeccCceEEEecCCCCC
Confidence 5677777777766533 22223334445788888877643
No 146
>KOG4225 consensus Sorbin and SH3 domain-containing protein [Signal transduction mechanisms]
Probab=20.72 E-value=76 Score=29.04 Aligned_cols=28 Identities=29% Similarity=0.547 Sum_probs=21.8
Q ss_pred hcchhcccccCCEEEEee--------cCCCCcEeeE
Q 031473 8 KLIRHWKILRGDNVMIIR--------GKDKGETGAI 35 (159)
Q Consensus 8 ~~ir~~~i~kGD~V~Vi~--------G~dKGk~G~V 35 (159)
...+.+.+.+||.|+|++ |.+-|.+|.+
T Consensus 242 qt~kEL~~~kGDIVyI~rkvD~nWyeGEhhGr~Gif 277 (489)
T KOG4225|consen 242 QTPKELPFNKGDIVYILRKVDQNWYEGEHHGRVGIF 277 (489)
T ss_pred CCccccccCCCCEEEEEeeccCceeeeeecceecce
Confidence 345789999999999985 5677888844
No 147
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=20.69 E-value=1.1e+02 Score=21.75 Aligned_cols=30 Identities=23% Similarity=0.189 Sum_probs=17.9
Q ss_pred hcchhcccccCCEEEEeecCCCCcEeeEEE
Q 031473 8 KLIRHWKILRGDNVMIIRGKDKGETGAIKR 37 (159)
Q Consensus 8 ~~ir~~~i~kGD~V~Vi~G~dKGk~G~V~~ 37 (159)
-+..+.+|.+||+|.|---++-=..|.|..
T Consensus 40 mR~~rIrIl~GD~V~VE~spYDltkGRIiy 69 (87)
T PRK12442 40 MRKHRIRILAGDRVTLELSPYDLTKGRINF 69 (87)
T ss_pred eeeeeEEecCCCEEEEEECcccCCceeEEE
Confidence 344466778888888765554444455543
No 148
>PRK07252 hypothetical protein; Provisional
Probab=20.54 E-value=1.9e+02 Score=21.19 Aligned_cols=25 Identities=8% Similarity=0.205 Sum_probs=19.3
Q ss_pred ccccCCEEEEeecCCCCcEeeEEEEEccCCEEEEe
Q 031473 14 KILRGDNVMIIRGKDKGETGAIKRVIRSQNRVIVE 48 (159)
Q Consensus 14 ~i~kGD~V~Vi~G~dKGk~G~V~~V~~~~~~V~Ve 48 (159)
.++.||.|.| +|++++.+.+++.+.
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 3688999887 678888877777655
No 149
>smart00357 CSP Cold shock protein domain. RNA-binding domain that functions as a RNA-chaperone in bacteria and is involved in regulating translation in eukaryotes. Contains sub-family of RNA-binding domains in the Rho transcription termination factor.
Probab=20.32 E-value=1.7e+02 Score=17.61 Aligned_cols=26 Identities=12% Similarity=-0.083 Sum_probs=16.6
Q ss_pred cccccCCEEEEeec---CCCCcEeeEEEE
Q 031473 13 WKILRGDNVMIIRG---KDKGETGAIKRV 38 (159)
Q Consensus 13 ~~i~kGD~V~Vi~G---~dKGk~G~V~~V 38 (159)
..+..||+|.+--- ...+.++.+.+|
T Consensus 35 ~~~~~Gd~V~~~i~~~~~~~~~~a~~v~~ 63 (64)
T smart00357 35 KSLREGDEVEFKVVSPRGGGKPEAENVVK 63 (64)
T ss_pred CcCCCCCEEEEEEEEccCCCCcEEEEEEe
Confidence 44678999988632 234556776654
No 150
>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=20.30 E-value=71 Score=19.59 Aligned_cols=15 Identities=13% Similarity=0.326 Sum_probs=10.8
Q ss_pred chhcccccCCEEEEe
Q 031473 10 IRHWKILRGDNVMII 24 (159)
Q Consensus 10 ir~~~i~kGD~V~Vi 24 (159)
...+.|.+||.|.|+
T Consensus 13 ~~~Ls~~~Gd~i~v~ 27 (55)
T PF07653_consen 13 PDELSFKKGDVIEVL 27 (55)
T ss_dssp TTB-EB-TTEEEEEE
T ss_pred CCceEEecCCEEEEE
Confidence 345789999999999
No 151
>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=20.07 E-value=1.9e+02 Score=21.54 Aligned_cols=30 Identities=13% Similarity=0.148 Sum_probs=22.2
Q ss_pred cccccCCEEEEeecCCCCcEeeEEEEEccC
Q 031473 13 WKILRGDNVMIIRGKDKGETGAIKRVIRSQ 42 (159)
Q Consensus 13 ~~i~kGD~V~Vi~G~dKGk~G~V~~V~~~~ 42 (159)
..|+.||-|.|..-..+=-+|.|.++....
T Consensus 6 ~~i~vGD~V~v~~~~~~~~va~Ie~i~ed~ 35 (130)
T cd04721 6 VTISVHDFVYVLSEEEDRYVAYIEDLYEDK 35 (130)
T ss_pred EEEECCCEEEEeCCCCCcEEEEEEEEEEcC
Confidence 458999999998643333479999887764
Done!