Query 032182
Match_columns 146
No_of_seqs 153 out of 1103
Neff 4.8
Searched_HMMs 46136
Date Fri Mar 29 10:42:08 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032182.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032182hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00194 60S ribosomal protein 100.0 5.7E-51 1.2E-55 314.7 9.9 138 3-142 1-138 (143)
2 PRK01191 rpl24p 50S ribosomal 100.0 2.3E-47 5.1E-52 287.5 9.2 116 6-121 3-119 (120)
3 TIGR01080 rplX_A_E ribosomal p 100.0 5.6E-44 1.2E-48 267.1 9.5 113 8-120 1-114 (114)
4 KOG3401 60S ribosomal protein 100.0 4E-43 8.7E-48 270.7 5.8 142 1-144 1-143 (145)
5 PRK00004 rplX 50S ribosomal pr 99.9 2.7E-24 5.8E-29 158.5 6.7 81 46-126 2-96 (105)
6 TIGR01079 rplX_bact ribosomal 99.9 1.6E-23 3.4E-28 154.4 7.0 80 47-126 2-96 (104)
7 COG0198 RplX Ribosomal protein 99.9 1.3E-23 2.8E-28 155.2 5.6 80 45-126 1-95 (104)
8 CHL00141 rpl24 ribosomal prote 99.9 3.1E-22 6.8E-27 142.3 7.5 66 46-111 6-82 (83)
9 PRK12281 rplX 50S ribosomal pr 99.8 5.4E-21 1.2E-25 134.0 6.4 61 46-106 4-75 (76)
10 KOG1708 Mitochondrial/chloropl 99.7 3.6E-17 7.7E-22 133.6 5.9 100 19-126 51-165 (236)
11 PF00467 KOW: KOW motif; Inte 98.8 1.1E-08 2.4E-13 60.4 4.4 32 51-82 1-32 (32)
12 smart00739 KOW KOW (Kyprides, 97.8 3.4E-05 7.4E-10 42.9 3.6 26 49-74 2-27 (28)
13 PRK08559 nusG transcription an 97.7 0.00024 5.2E-09 54.9 7.9 73 29-107 72-149 (153)
14 TIGR00405 L26e_arch ribosomal 97.7 0.00019 4.1E-09 54.4 7.1 74 30-107 65-141 (145)
15 PRK05609 nusG transcription an 97.2 0.0011 2.3E-08 51.5 6.5 54 46-103 124-177 (181)
16 COG0250 NusG Transcription ant 97.2 0.00096 2.1E-08 53.3 6.3 54 47-104 122-175 (178)
17 TIGR00922 nusG transcription t 97.1 0.00078 1.7E-08 52.0 4.9 36 47-82 118-153 (172)
18 TIGR01956 NusG_myco NusG famil 96.6 0.0062 1.4E-07 51.6 6.2 54 46-103 203-256 (258)
19 TIGR01955 RfaH transcriptional 96.6 0.0039 8.4E-08 47.4 4.5 35 47-82 107-141 (159)
20 PRK09014 rfaH transcriptional 96.3 0.0059 1.3E-07 46.9 4.4 51 48-103 109-159 (162)
21 PRK04333 50S ribosomal protein 92.8 0.22 4.8E-06 35.5 4.4 59 47-110 2-60 (84)
22 KOG1999 RNA polymerase II tran 92.4 0.14 3.1E-06 50.3 3.9 27 49-75 460-486 (1024)
23 PTZ00471 60S ribosomal protein 89.6 0.62 1.3E-05 36.2 4.3 39 49-87 5-49 (134)
24 COG2163 RPL14A Ribosomal prote 85.8 0.95 2.1E-05 34.7 3.3 35 49-84 5-39 (125)
25 COG5164 SPT5 Transcription elo 85.7 1.7 3.6E-05 40.4 5.3 69 32-110 337-405 (607)
26 PTZ00065 60S ribosomal protein 85.4 1.8 3.9E-05 33.4 4.6 57 49-110 8-64 (130)
27 PRK04306 50S ribosomal protein 82.0 3 6.4E-05 30.8 4.4 49 24-81 19-77 (98)
28 PF12701 LSM14: Scd6-like Sm d 79.4 4.2 9.2E-05 29.6 4.5 52 51-102 7-58 (96)
29 PF05641 Agenet: Agenet domain 77.8 6.9 0.00015 26.1 4.8 37 49-86 1-41 (68)
30 KOG1999 RNA polymerase II tran 77.4 1.9 4.1E-05 42.8 2.7 29 47-75 406-434 (1024)
31 PRK06531 yajC preprotein trans 75.9 5.1 0.00011 30.2 4.1 31 48-82 36-66 (113)
32 COG5164 SPT5 Transcription elo 74.0 2.7 5.8E-05 39.1 2.6 30 49-78 140-169 (607)
33 CHL00084 rpl19 ribosomal prote 72.3 14 0.00031 27.9 5.8 71 36-108 9-89 (117)
34 PRK04313 30S ribosomal protein 72.2 7.3 0.00016 32.9 4.6 55 46-107 169-227 (237)
35 PF09953 DUF2187: Uncharacteri 71.1 9.5 0.00021 25.7 4.1 27 50-82 5-31 (57)
36 PF04452 Methyltrans_RNA: RNA 70.6 13 0.00028 29.9 5.6 43 40-82 8-50 (225)
37 PTZ00189 60S ribosomal protein 69.8 9.7 0.00021 30.4 4.6 44 31-82 24-77 (160)
38 COG1862 YajC Preprotein transl 69.8 7.5 0.00016 28.5 3.7 29 48-82 43-71 (97)
39 PLN00190 60S ribosomal protein 69.7 10 0.00023 30.2 4.8 44 31-82 24-77 (158)
40 PRK05585 yajC preprotein trans 68.1 9.4 0.0002 28.2 4.0 29 48-82 52-80 (106)
41 COG1532 Predicted RNA-binding 68.0 10 0.00022 25.5 3.7 34 50-83 22-57 (57)
42 COG2002 AbrB Regulators of sta 65.4 8 0.00017 27.2 3.1 28 33-65 17-44 (89)
43 TIGR01024 rplS_bact ribosomal 64.5 40 0.00087 25.4 6.8 70 38-109 7-86 (113)
44 cd01736 LSm14_N LSm14 (also kn 64.1 24 0.00052 24.9 5.2 53 51-103 5-58 (74)
45 TIGR00739 yajC preprotein tran 63.9 14 0.0003 26.1 4.0 29 48-82 37-65 (84)
46 PRK05886 yajC preprotein trans 63.8 13 0.00029 27.8 4.1 29 48-82 38-66 (109)
47 COG0361 InfA Translation initi 62.4 9.4 0.0002 26.9 2.9 41 30-74 32-72 (75)
48 PF01157 Ribosomal_L21e: Ribos 61.9 11 0.00023 27.9 3.2 36 33-76 25-70 (99)
49 PRK02749 photosystem I reactio 60.0 20 0.00042 25.1 4.1 30 47-76 1-32 (71)
50 PF08206 OB_RNB: Ribonuclease 60.0 11 0.00025 24.3 2.8 24 49-72 32-58 (58)
51 PF03144 GTP_EFTU_D2: Elongati 59.8 20 0.00042 23.2 4.0 31 48-79 12-45 (74)
52 KOG3418 60S ribosomal protein 58.7 17 0.00036 28.4 3.9 39 49-87 5-49 (136)
53 PTZ00223 40S ribosomal protein 58.4 19 0.00042 31.0 4.7 56 46-108 169-227 (273)
54 PLN00036 40S ribosomal protein 58.0 21 0.00045 30.6 4.7 56 46-108 172-230 (261)
55 PF14505 DUF4438: Domain of un 57.4 20 0.00044 30.7 4.6 33 50-82 59-91 (258)
56 COG1471 RPS4A Ribosomal protei 57.1 21 0.00046 30.3 4.6 38 46-83 171-212 (241)
57 PF04014 Antitoxin-MazE: Antid 57.1 10 0.00023 23.3 2.2 24 32-60 9-32 (47)
58 PF02699 YajC: Preprotein tran 56.8 3.6 7.8E-05 28.8 0.0 29 48-82 36-64 (82)
59 cd05793 S1_IF1A S1_IF1A: Trans 56.5 11 0.00025 26.2 2.5 42 30-76 25-66 (77)
60 KOG4315 G-patch nucleic acid b 55.3 5 0.00011 36.6 0.7 38 47-84 392-429 (455)
61 smart00743 Agenet Tudor-like d 55.2 39 0.00083 21.4 4.7 34 48-82 2-36 (61)
62 PTZ00118 40S ribosomal protein 54.6 23 0.0005 30.3 4.5 55 46-107 172-229 (262)
63 PRK00409 recombination and DNA 52.2 21 0.00045 34.5 4.3 38 47-87 635-673 (782)
64 smart00652 eIF1a eukaryotic tr 52.0 16 0.00034 25.8 2.7 41 31-76 31-71 (83)
65 CHL00125 psaE photosystem I su 48.5 34 0.00073 23.5 3.7 28 49-76 2-31 (64)
66 cd04456 S1_IF1A_like S1_IF1A_l 47.3 23 0.00049 24.7 2.8 42 30-76 25-67 (78)
67 TIGR00523 eIF-1A eukaryotic/ar 46.8 14 0.0003 27.1 1.7 43 29-76 43-86 (99)
68 TIGR00008 infA translation ini 46.4 23 0.0005 24.4 2.7 39 28-70 28-66 (68)
69 PLN00045 photosystem I reactio 45.9 30 0.00066 25.7 3.4 31 45-75 36-68 (101)
70 PF11623 DUF3252: Protein of u 45.4 55 0.0012 21.7 4.2 38 49-86 2-41 (53)
71 PRK05338 rplS 50S ribosomal pr 45.3 98 0.0021 23.4 6.2 61 48-110 18-87 (116)
72 PF15276 PP1_bind: Protein pho 44.9 17 0.00037 25.0 1.8 39 26-64 4-42 (64)
73 COG3700 AphA Acid phosphatase 44.9 10 0.00022 31.7 0.9 40 46-87 124-163 (237)
74 COG1193 Mismatch repair ATPase 43.4 25 0.00054 34.1 3.4 33 46-82 610-642 (753)
75 PF01176 eIF-1a: Translation i 43.0 36 0.00078 22.5 3.2 36 31-71 29-64 (65)
76 PRK04012 translation initiatio 42.9 24 0.00052 25.9 2.5 41 30-75 46-86 (100)
77 TIGR01069 mutS2 MutS2 family p 42.9 36 0.00079 32.9 4.4 35 50-87 626-661 (771)
78 PF01245 Ribosomal_L19: Riboso 40.5 1E+02 0.0023 22.9 5.7 59 48-108 18-85 (113)
79 PRK12442 translation initiatio 40.3 22 0.00047 25.8 1.9 43 28-74 30-72 (87)
80 COG1385 Uncharacterized protei 40.2 67 0.0014 26.8 5.1 50 34-84 20-69 (246)
81 PRK08577 hypothetical protein; 39.8 38 0.00082 25.2 3.2 28 33-65 16-43 (136)
82 cd05696 S1_Rrp5_repeat_hs4 S1_ 39.6 56 0.0012 21.5 3.8 24 48-81 46-69 (71)
83 cd03692 mtIF2_IVc mtIF2_IVc: t 39.4 61 0.0013 22.1 4.0 30 48-77 26-55 (84)
84 cd05707 S1_Rrp5_repeat_sc11 S1 39.3 46 0.00099 21.2 3.2 24 48-81 44-67 (68)
85 cd05703 S1_Rrp5_repeat_hs12_sc 39.3 55 0.0012 21.7 3.7 25 48-82 46-70 (73)
86 KOG1728 40S ribosomal protein 38.6 20 0.00043 28.5 1.5 26 24-57 101-126 (156)
87 COG2139 RPL21A Ribosomal prote 38.5 50 0.0011 24.5 3.6 44 31-82 23-76 (98)
88 cd05698 S1_Rrp5_repeat_hs6_sc5 38.4 59 0.0013 20.6 3.6 25 48-82 44-68 (70)
89 cd05697 S1_Rrp5_repeat_hs5 S1_ 37.2 72 0.0016 20.4 3.9 25 48-82 44-68 (69)
90 KOG0171 Mitochondrial inner me 36.5 50 0.0011 26.9 3.6 69 18-89 62-133 (176)
91 cd05708 S1_Rrp5_repeat_sc12 S1 36.2 80 0.0017 20.1 4.0 25 48-82 47-71 (77)
92 cd05695 S1_Rrp5_repeat_hs3 S1_ 36.0 59 0.0013 21.1 3.4 24 48-81 42-65 (66)
93 PF01079 Hint: Hint module; I 36.0 54 0.0012 26.9 3.9 28 47-74 104-132 (217)
94 PF00924 MS_channel: Mechanose 34.9 26 0.00057 26.9 1.8 24 48-76 60-83 (206)
95 TIGR01448 recD_rel helicase, p 34.6 1.1E+02 0.0023 29.4 6.0 37 46-82 584-629 (720)
96 PF02427 PSI_PsaE: Photosystem 34.1 49 0.0011 22.6 2.7 33 49-81 1-37 (61)
97 cd04461 S1_Rrp5_repeat_hs8_sc7 34.1 73 0.0016 21.2 3.7 25 48-82 58-82 (83)
98 cd03450 NodN NodN (nodulation 32.9 1.7E+02 0.0036 22.2 5.9 45 48-100 97-142 (149)
99 PRK11713 16S ribosomal RNA met 32.5 71 0.0015 25.9 4.0 48 33-81 15-62 (234)
100 TIGR03170 flgA_cterm flagella 32.4 76 0.0016 22.7 3.7 35 45-79 62-109 (122)
101 cd05688 S1_RPS1_repeat_ec3 S1_ 32.1 81 0.0018 19.4 3.5 24 48-81 44-67 (68)
102 cd05792 S1_eIF1AD_like S1_eIF1 31.9 89 0.0019 21.9 3.9 40 32-76 27-67 (78)
103 COG1153 FwdD Formylmethanofura 31.8 1.3E+02 0.0029 23.2 5.1 56 32-111 33-92 (128)
104 cd04452 S1_IF2_alpha S1_IF2_al 31.7 1E+02 0.0022 19.7 4.0 24 49-82 50-73 (76)
105 PF11717 Tudor-knot: RNA bindi 31.3 69 0.0015 20.4 3.0 29 49-77 1-29 (55)
106 cd05791 S1_CSL4 S1_CSL4: CSL4, 31.3 63 0.0014 22.7 3.1 44 50-104 5-48 (92)
107 cd04717 BAH_polybromo BAH, or 30.9 1.7E+02 0.0036 21.2 5.4 43 47-89 2-47 (121)
108 PRK00276 infA translation init 30.9 45 0.00097 22.5 2.2 39 28-70 30-68 (72)
109 cd05706 S1_Rrp5_repeat_sc10 S1 30.7 1E+02 0.0022 19.7 3.9 24 49-82 48-71 (73)
110 PRK10334 mechanosensitive chan 30.5 60 0.0013 27.5 3.4 24 48-76 129-152 (286)
111 cd01737 LSm16_N LSm16 belongs 30.4 89 0.0019 21.4 3.5 31 52-82 6-37 (62)
112 PF05257 CHAP: CHAP domain; I 30.3 81 0.0018 22.5 3.6 39 46-85 60-100 (124)
113 cd05685 S1_Tex S1_Tex: The C-t 29.9 87 0.0019 19.1 3.3 23 49-81 45-67 (68)
114 PF02887 PK_C: Pyruvate kinase 29.9 32 0.0007 24.7 1.4 19 49-67 90-108 (117)
115 PF00575 S1: S1 RNA binding do 29.9 1.1E+02 0.0024 19.5 3.9 26 47-82 47-72 (74)
116 cd04451 S1_IF1 S1_IF1: Transla 29.5 53 0.0012 21.3 2.3 37 29-69 25-61 (64)
117 PRK07018 flgA flagellar basal 29.4 76 0.0016 25.9 3.7 34 46-79 174-220 (235)
118 cd05705 S1_Rrp5_repeat_hs14 S1 29.3 88 0.0019 20.9 3.4 23 49-81 51-73 (74)
119 PF00018 SH3_1: SH3 domain; I 28.8 71 0.0015 19.2 2.7 17 46-62 13-29 (48)
120 TIGR01439 lp_hng_hel_AbrB loop 28.8 71 0.0015 18.5 2.6 26 31-61 8-33 (43)
121 PF07653 SH3_2: Variant SH3 do 28.3 44 0.00095 20.8 1.7 13 46-58 15-27 (55)
122 PRK08515 flgA flagellar basal 28.1 87 0.0019 25.6 3.8 34 46-79 163-208 (222)
123 cd00164 S1_like S1_like: Ribos 27.4 99 0.0021 18.3 3.2 23 48-80 41-63 (65)
124 cd01854 YjeQ_engC YjeQ/EngC. 27.2 90 0.002 26.0 3.8 32 46-79 32-63 (287)
125 cd00174 SH3 Src homology 3 dom 27.2 64 0.0014 18.6 2.2 16 46-61 15-30 (54)
126 CHL00010 infA translation init 26.6 97 0.0021 21.3 3.3 43 28-74 30-72 (78)
127 cd05690 S1_RPS1_repeat_ec5 S1_ 26.5 1.1E+02 0.0024 19.1 3.4 23 48-80 45-67 (69)
128 PRK11509 hydrogenase-1 operon 26.4 71 0.0015 24.5 2.8 29 33-61 78-110 (132)
129 cd04721 BAH_plant_1 BAH, or Br 26.2 2.4E+02 0.0052 21.2 5.7 43 46-88 5-48 (130)
130 cd04471 S1_RNase_R S1_RNase_R: 26.2 1.3E+02 0.0027 19.5 3.7 25 48-82 57-81 (83)
131 PF02941 FeThRed_A: Ferredoxin 26.1 73 0.0016 22.1 2.5 24 51-74 1-38 (67)
132 cd05691 S1_RPS1_repeat_ec6 S1_ 25.8 1.5E+02 0.0032 18.7 3.9 24 49-82 45-68 (73)
133 cd04715 BAH_Orc1p_like BAH, or 25.7 1.8E+02 0.0039 22.8 5.1 33 44-76 25-57 (159)
134 TIGR00046 RNA methyltransferas 25.6 1.1E+02 0.0024 24.9 4.0 48 33-81 17-64 (240)
135 cd05689 S1_RPS1_repeat_ec4 S1_ 25.5 1.1E+02 0.0023 19.6 3.2 23 48-80 48-70 (72)
136 cd05687 S1_RPS1_repeat_ec1_hs1 25.3 1.5E+02 0.0033 18.7 3.9 23 49-81 45-67 (70)
137 PF07497 Rho_RNA_bind: Rho ter 25.2 74 0.0016 22.4 2.5 26 25-59 28-53 (78)
138 smart00326 SH3 Src homology 3 25.0 73 0.0016 18.5 2.2 16 46-61 18-33 (58)
139 TIGR02594 conserved hypothetic 24.3 1.4E+02 0.0031 22.3 4.1 40 42-82 67-106 (129)
140 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 24.3 83 0.0018 21.0 2.6 38 48-104 3-40 (86)
141 PF11910 NdhO: Cyanobacterial 24.2 38 0.00083 23.5 0.9 16 49-64 1-16 (67)
142 PRK07252 hypothetical protein; 24.1 1.3E+02 0.0029 22.2 3.9 25 48-82 47-71 (120)
143 PRK12617 flgA flagellar basal 23.6 1.3E+02 0.0029 24.6 4.1 32 47-78 154-198 (214)
144 COG1792 MreC Cell shape-determ 23.6 1.1E+02 0.0025 25.9 3.8 40 37-77 201-245 (284)
145 cd04466 S1_YloQ_GTPase S1_YloQ 23.5 1.8E+02 0.0039 18.3 4.0 31 47-79 36-66 (68)
146 PF07076 DUF1344: Protein of u 23.2 1.2E+02 0.0025 20.7 3.1 18 65-82 5-22 (61)
147 smart00316 S1 Ribosomal protei 23.0 1.8E+02 0.0039 17.4 4.0 25 48-82 46-70 (72)
148 PF09926 DUF2158: Uncharacteri 22.7 53 0.0012 21.4 1.3 13 49-61 1-13 (53)
149 cd04714 BAH_BAHCC1 BAH, or Bro 22.6 2.8E+02 0.006 20.3 5.3 37 48-84 3-42 (121)
150 cd04459 Rho_CSD Rho_CSD: Rho p 22.4 92 0.002 21.2 2.5 20 44-63 36-55 (68)
151 PF01426 BAH: BAH domain; Int 22.4 1.4E+02 0.003 20.7 3.5 29 48-76 2-32 (119)
152 COG0668 MscS Small-conductance 22.3 1.6E+02 0.0034 23.8 4.3 29 47-79 146-174 (316)
153 KOG3421 60S ribosomal protein 21.8 96 0.0021 24.3 2.7 35 49-84 7-41 (136)
154 PLN00208 translation initiatio 21.5 1.2E+02 0.0026 23.8 3.3 30 47-76 69-98 (145)
155 cd03698 eRF3_II_like eRF3_II_l 21.5 1.6E+02 0.0035 19.7 3.6 13 48-60 26-38 (83)
156 cd05686 S1_pNO40 S1_pNO40: pNO 21.4 1.4E+02 0.0031 19.4 3.3 22 49-81 49-70 (73)
157 PRK12618 flgA flagellar basal 21.4 1.7E+02 0.0037 22.3 4.1 28 47-74 80-119 (141)
158 PF06701 MIB_HERC2: Mib_herc2; 21.4 1.1E+02 0.0025 20.8 2.8 27 56-82 3-43 (68)
159 cd04472 S1_PNPase S1_PNPase: P 21.2 1.4E+02 0.003 18.4 3.1 23 48-81 44-66 (68)
160 TIGR02609 doc_partner putative 21.0 1.2E+02 0.0025 20.6 2.8 26 30-60 10-35 (74)
161 COG0335 RplS Ribosomal protein 20.7 3E+02 0.0065 21.0 5.1 63 48-114 20-94 (115)
162 PHA00653 mtd major tropism det 20.5 2.1E+02 0.0045 25.8 4.9 56 48-108 6-70 (381)
163 PRK13922 rod shape-determining 20.3 2E+02 0.0044 23.6 4.6 40 38-78 204-248 (276)
No 1
>PTZ00194 60S ribosomal protein L26; Provisional
Probab=100.00 E-value=5.7e-51 Score=314.70 Aligned_cols=138 Identities=70% Similarity=1.054 Sum_probs=130.4
Q ss_pred CCCCCCCCcccccccccCCCCcccceeeeccCCHHHHhhhCCcccceecCCEEEEeecCCCCeEeeEEEEEecCCEEEEe
Q 032182 3 YNPRVSSSRRKNRKAHFTAPSSVRRILMSAPLSTDLRQKYNVRSMPVRKDDEVQVVRGTYKGREGKVVQVYRRKWVIHIE 82 (146)
Q Consensus 3 ~~~~~s~~~rKqRk~~~~Ap~h~r~k~msa~Ls~eLr~ky~~rs~~IkkGD~V~Vi~G~~KGk~GkV~~V~~k~~~V~VE 82 (146)
+||++|+|||||||++|+||.|+|+++|+|+||+|||++||+|+|+|++||+|+||+|+|||++|+|++|++++++|+||
T Consensus 1 ~n~~~S~~prKqRKa~~~Ap~h~r~k~msa~LSkeLr~k~~~Rs~~IkkGD~V~Vi~Gk~KGk~GkV~~V~~k~~~ViVE 80 (143)
T PTZ00194 1 FNSIVSSSRRKARKAHFTAPSHLRRKLMSAPLSKELRAKYNVRSMPVRKDDEVMVVRGHHKGREGKVTAVYRKKWVIHIE 80 (143)
T ss_pred CCccccCCchHHHHHhhcCcHHHHHHHhcCccCHHHHHHhCCccceeecCCEEEEecCCCCCCceEEEEEEcCCCEEEEe
Confidence 69999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeeEEeeCCcEEEeeccccceEEEcCCCcchhhhhhccccccchhhhhccCCccchhccc
Q 032182 83 RITREKVNGSTVNVGINPSKVVITKLRLDKDRKSLLDRKAKGRAAADKEKGTKFTPEDIM 142 (146)
Q Consensus 83 gin~~K~~G~~~e~pIh~SNv~i~~~~~~~~R~~~le~~~k~~~~~~~~~~~~~~~~~~~ 142 (146)
|||+.+.+|..+|+|||||||+|+|++++.+|.++||+++..+++. ..+| ++++|+..
T Consensus 81 gvn~~Kk~gk~~e~PIh~SNV~iv~l~l~~~R~~~l~~k~~~~~~~-~~~g-~~~~~~~~ 138 (143)
T PTZ00194 81 KITREKANGEPVQIGIHPSNVIITKLKLNKDRKAILERKARSTKSD-KGKG-KYTAADKA 138 (143)
T ss_pred CeEEEecCCCEeecCcCchheEEEccccCchHHHHHhhhhhhhhhh-hhcC-ccchhHhh
Confidence 9999999999999999999999999999766999999999988865 4458 88877653
No 2
>PRK01191 rpl24p 50S ribosomal protein L24P; Validated
Probab=100.00 E-value=2.3e-47 Score=287.47 Aligned_cols=116 Identities=50% Similarity=0.789 Sum_probs=113.1
Q ss_pred CCCCCcccccccccCCCCcccceeeeccCCHHHHhhhCCcccceecCCEEEEeecCCCCeEeeEEEEEecCCEEEEeeee
Q 032182 6 RVSSSRRKNRKAHFTAPSSVRRILMSAPLSTDLRQKYNVRSMPVRKDDEVQVVRGTYKGREGKVVQVYRRKWVIHIERIT 85 (146)
Q Consensus 6 ~~s~~~rKqRk~~~~Ap~h~r~k~msa~Ls~eLr~ky~~rs~~IkkGD~V~Vi~G~~KGk~GkV~~V~~k~~~V~VEgin 85 (146)
.||+|||||||++|+||.|+|+++|||+||+|||++||+++|+|++||+|+||+|+|||++|+|++|++++++|+|||||
T Consensus 3 ~~s~~~rK~Rk~~f~a~~~~r~k~msa~LSkeLr~~y~ir~~~IkkGD~V~VisG~~KGk~GkV~~V~~~~~~V~VeGvn 82 (120)
T PRK01191 3 TMSKQPRKQRKALYNAPLHLRQKLMSAPLSKELREKYGIRSLPVRKGDTVKVMRGDFKGEEGKVVEVDLKRGRIYVEGVT 82 (120)
T ss_pred cccCCchHHHHHhhcCCHHHHHHHhcCccCHHHHHHhCCccceEeCCCEEEEeecCCCCceEEEEEEEcCCCEEEEeCcE
Confidence 58999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEeeCCcEEEeeccccceEEEcCCC-cchhhhhhccc
Q 032182 86 REKVNGSTVNVGINPSKVVITKLRL-DKDRKSLLDRK 121 (146)
Q Consensus 86 ~~K~~G~~~e~pIh~SNv~i~~~~~-~~~R~~~le~~ 121 (146)
+++++|.++|+|||+|||+|+|+++ |++|++.|+..
T Consensus 83 ~~k~~G~~~e~pIh~SNV~l~~l~l~~~~R~~~l~~~ 119 (120)
T PRK01191 83 VKKADGTEVPRPIHPSNVMITKLDLSDERREKILERR 119 (120)
T ss_pred EECCCCeEEEcccchhHeEEEeCccCCHHHHHHhhcc
Confidence 9999999999999999999999999 89999998864
No 3
>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=100.00 E-value=5.6e-44 Score=267.11 Aligned_cols=113 Identities=56% Similarity=0.877 Sum_probs=109.4
Q ss_pred CCCcccccccccCCCCcccceeeeccCCHHHHhhhCCcccceecCCEEEEeecCCCCeEeeEEEEEecCCEEEEeeeeEE
Q 032182 8 SSSRRKNRKAHFTAPSSVRRILMSAPLSTDLRQKYNVRSMPVRKDDEVQVVRGTYKGREGKVVQVYRRKWVIHIERITRE 87 (146)
Q Consensus 8 s~~~rKqRk~~~~Ap~h~r~k~msa~Ls~eLr~ky~~rs~~IkkGD~V~Vi~G~~KGk~GkV~~V~~k~~~V~VEgin~~ 87 (146)
|+|||||||++|+||.|+|+++|+|+||+|||++|++++|+|++||+|+||+|+|||++|+|++|++++++|+|||||++
T Consensus 1 s~~~rK~Rk~~~~a~~~~r~~~~~a~ls~elr~~y~~r~~~IkkGD~V~Vi~Gk~KGk~GkV~~V~~~~~~V~Vegvn~~ 80 (114)
T TIGR01080 1 SKQPRKQRKALFTAPLHVRRKLMSAPLSKELREKYGKRALPVRKGDKVRIMRGDFKGHEGKVSKVDLKRYRIYVEGVTKE 80 (114)
T ss_pred CCCchhhHHHhhcCcHhhhhheeecccCHHHHHHcCcccceeecCCEEEEecCCCCCCEEEEEEEEcCCCEEEEcCeEEE
Confidence 78999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeCCcEEEeeccccceEEEcCCCc-chhhhhhcc
Q 032182 88 KVNGSTVNVGINPSKVVITKLRLD-KDRKSLLDR 120 (146)
Q Consensus 88 K~~G~~~e~pIh~SNv~i~~~~~~-~~R~~~le~ 120 (146)
+++|.++|+|||+|||+|+|++++ +.|...||.
T Consensus 81 k~~G~~~e~pIh~SnV~l~~l~l~~~~R~~~l~~ 114 (114)
T TIGR01080 81 KVNGTEVPVPIHPSNVMITKLNLDDEKRKKIIER 114 (114)
T ss_pred CCCCeEEEeeechHHeEEEeccCChHHHHHHhcC
Confidence 999999999999999999999996 559988874
No 4
>KOG3401 consensus 60S ribosomal protein L26 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=4e-43 Score=270.68 Aligned_cols=142 Identities=71% Similarity=1.057 Sum_probs=133.5
Q ss_pred CCCCCCCCCCcccccccccCCCCcccceeeeccCCHHHHhhhCCcccceecCCEEEEeecCCCC-eEeeEEEEEecCCEE
Q 032182 1 MKYNPRVSSSRRKNRKAHFTAPSSVRRILMSAPLSTDLRQKYNVRSMPVRKDDEVQVVRGTYKG-REGKVVQVYRRKWVI 79 (146)
Q Consensus 1 mk~~~~~s~~~rKqRk~~~~Ap~h~r~k~msa~Ls~eLr~ky~~rs~~IkkGD~V~Vi~G~~KG-k~GkV~~V~~k~~~V 79 (146)
|||||||||+|+||||+||+||+|+|+++||||||+|||++|++++|+|+.+|+|.|.+|.++| ++|+|++|+++++.+
T Consensus 1 mk~np~vtS~r~k~rK~hF~aps~~rR~i~sa~ls~eLR~~y~vrs~pir~ddev~v~rg~~kG~q~G~v~~vyrKk~~i 80 (145)
T KOG3401|consen 1 MKFNPFVTSDRRKNRKAHFNAPSHIRRKIMSAPLSKELRQKYNVRSMPIRKDDEVQVVRGHFKGFQIGKVSQVYRKKYVI 80 (145)
T ss_pred CCCCcccccchhhhhHhhcCCcHHHHHHHhcchhhHHHHHHhCccccceeeccEEEEEeccccccccceehhhhhhhhee
Confidence 9999999999999999999999999999999999999999999999999999999999999999 889999999999999
Q ss_pred EEeeeeEEeeCCcEEEeeccccceEEEcCCCcchhhhhhccccccchhhhhccCCccchhccccc
Q 032182 80 HIERITREKVNGSTVNVGINPSKVVITKLRLDKDRKSLLDRKAKGRAAADKEKGTKFTPEDIMQS 144 (146)
Q Consensus 80 ~VEgin~~K~~G~~~e~pIh~SNv~i~~~~~~~~R~~~le~~~k~~~~~~~~~~~~~~~~~~~~~ 144 (146)
++|.|...|++|+.+++|||||+++|+.|.+|++|+++||.++++++ ++++.| .|..+++-+.
T Consensus 81 yie~v~~eK~nGt~v~vgihPsK~~iTkl~lDkdrkkl~erk~k~~q-vg~~~g-~~K~~qi~~~ 143 (145)
T KOG3401|consen 81 YIERVQREKANGTTVPVGIHPSKVVITKLKLDKDRKKLLERKAKSRQ-VGKEQG-KYKFEQIEKM 143 (145)
T ss_pred eeEeEEEeeccCcccccccCccceeecccchhhHHHHHHHHHHhhhh-hhhhcC-ccchhhhhhc
Confidence 99999999999999999999999999999999999999999999999 555666 5555555443
No 5
>PRK00004 rplX 50S ribosomal protein L24; Reviewed
Probab=99.90 E-value=2.7e-24 Score=158.47 Aligned_cols=81 Identities=28% Similarity=0.401 Sum_probs=72.5
Q ss_pred ccceecCCEEEEeecCCCCeEeeEEEEEecCCEEEEeeeeEEee---------CCc--EEEeeccccceEEEcCCC-cch
Q 032182 46 SMPVRKDDEVQVVRGTYKGREGKVVQVYRRKWVIHIERITREKV---------NGS--TVNVGINPSKVVITKLRL-DKD 113 (146)
Q Consensus 46 s~~IkkGD~V~Vi~G~~KGk~GkV~~V~~k~~~V~VEgin~~K~---------~G~--~~e~pIh~SNv~i~~~~~-~~~ 113 (146)
.|+|++||+|+||+|+|||++|+|++|++++++|+|||||+.+. .|+ +.|+|||+|||+|+|+.+ +++
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 47999999999999999999999999999999999999999853 243 579999999999999999 688
Q ss_pred h--hhhhccccccch
Q 032182 114 R--KSLLDRKAKGRA 126 (146)
Q Consensus 114 R--~~~le~~~k~~~ 126 (146)
| ++++|++.++|-
T Consensus 82 rv~~~~~~~g~kvRv 96 (105)
T PRK00004 82 RVGFKFLEDGKKVRV 96 (105)
T ss_pred EEEEEEccCCcEEEE
Confidence 9 777778888765
No 6
>TIGR01079 rplX_bact ribosomal protein L24, bacterial/organelle. This model recognizes bacterial and organellar forms of ribosomal protein L24. It excludes eukaryotic and archaeal forms, designated L26 in eukaryotes.
Probab=99.89 E-value=1.6e-23 Score=154.42 Aligned_cols=80 Identities=26% Similarity=0.390 Sum_probs=71.8
Q ss_pred cceecCCEEEEeecCCCCeEeeEEEEEecCCEEEEeeeeEEee----------CCc--EEEeeccccceEEEcCCC-cch
Q 032182 47 MPVRKDDEVQVVRGTYKGREGKVVQVYRRKWVIHIERITREKV----------NGS--TVNVGINPSKVVITKLRL-DKD 113 (146)
Q Consensus 47 ~~IkkGD~V~Vi~G~~KGk~GkV~~V~~k~~~V~VEgin~~K~----------~G~--~~e~pIh~SNv~i~~~~~-~~~ 113 (146)
++|++||+|+||+|+|||++|+|++|++++++|+|||+|+.+. .|+ +.|+|||+|||+|+|+.+ .++
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 5899999999999999999999999999999999999999853 243 579999999999999999 588
Q ss_pred h--hhhhccccccch
Q 032182 114 R--KSLLDRKAKGRA 126 (146)
Q Consensus 114 R--~~~le~~~k~~~ 126 (146)
| ++++|++.++|-
T Consensus 82 rv~~~~~~~g~kvRv 96 (104)
T TIGR01079 82 RVGIRFEEDGKKVRV 96 (104)
T ss_pred EEEEEEccCCcEEEE
Confidence 8 777888888776
No 7
>COG0198 RplX Ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=99.89 E-value=1.3e-23 Score=155.24 Aligned_cols=80 Identities=30% Similarity=0.360 Sum_probs=68.2
Q ss_pred cccceecCCEEEEeecCCCCeEeeEEEEEecCCEEEEeeeeEEeeCC---------c--EEEeeccccceEEEcCC-C-c
Q 032182 45 RSMPVRKDDEVQVVRGTYKGREGKVVQVYRRKWVIHIERITREKVNG---------S--TVNVGINPSKVVITKLR-L-D 111 (146)
Q Consensus 45 rs~~IkkGD~V~Vi~G~~KGk~GkV~~V~~k~~~V~VEgin~~K~~G---------~--~~e~pIh~SNv~i~~~~-~-~ 111 (146)
++|+|++||+|.||+|+|||++|+|++|+++. |+|||||+++.++ + +.|+|||+|||||++++ + +
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 9999999997543 3 46899999999999994 5 7
Q ss_pred chhhhhhc--cccccch
Q 032182 112 KDRKSLLD--RKAKGRA 126 (146)
Q Consensus 112 ~~R~~~le--~~~k~~~ 126 (146)
++|..+.. ++.++|.
T Consensus 79 ~~Rv~~~~~~~~kkvr~ 95 (104)
T COG0198 79 PTRVGYKVEEDGKKVRV 95 (104)
T ss_pred cceEEEEEecCCcEEEE
Confidence 99954444 5676665
No 8
>CHL00141 rpl24 ribosomal protein L24; Validated
Probab=99.87 E-value=3.1e-22 Score=142.29 Aligned_cols=66 Identities=21% Similarity=0.379 Sum_probs=59.9
Q ss_pred ccceecCCEEEEeecCCCCeEeeEEEEEecCCEEEEeeeeEEee---------CCc--EEEeeccccceEEEcCCCc
Q 032182 46 SMPVRKDDEVQVVRGTYKGREGKVVQVYRRKWVIHIERITREKV---------NGS--TVNVGINPSKVVITKLRLD 111 (146)
Q Consensus 46 s~~IkkGD~V~Vi~G~~KGk~GkV~~V~~k~~~V~VEgin~~K~---------~G~--~~e~pIh~SNv~i~~~~~~ 111 (146)
+++|++||+|+||+|+|||++|+|++|++++++|+|||||+.+. .|+ +.|+|||+|||+|+|++++
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 57999999999999999999999999999999999999999752 244 4699999999999999874
No 9
>PRK12281 rplX 50S ribosomal protein L24; Reviewed
Probab=99.83 E-value=5.4e-21 Score=134.02 Aligned_cols=61 Identities=33% Similarity=0.443 Sum_probs=55.2
Q ss_pred ccceecCCEEEEeecCCCCeEeeEEEEEecCCEEEEeeeeEEe---------eCCcE--EEeeccccceEEE
Q 032182 46 SMPVRKDDEVQVVRGTYKGREGKVVQVYRRKWVIHIERITREK---------VNGST--VNVGINPSKVVIT 106 (146)
Q Consensus 46 s~~IkkGD~V~Vi~G~~KGk~GkV~~V~~k~~~V~VEgin~~K---------~~G~~--~e~pIh~SNv~i~ 106 (146)
+|+|++||+|+||+|+|||++|+|++|++++++|+|||||+.+ ++|+. .|+|||+|||+++
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 4799999999999999999999999999999999999999974 23654 4999999999986
No 10
>KOG1708 consensus Mitochondrial/chloroplast ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=99.68 E-value=3.6e-17 Score=133.55 Aligned_cols=100 Identities=22% Similarity=0.289 Sum_probs=86.1
Q ss_pred cCCCCcccceeeeccCCHHHHhhhCCcccceecCCEEEEeecCCCCeEeeEEEEEecCCEEEEeeeeEEee---------
Q 032182 19 FTAPSSVRRILMSAPLSTDLRQKYNVRSMPVRKDDEVQVVRGTYKGREGKVVQVYRRKWVIHIERITREKV--------- 89 (146)
Q Consensus 19 ~~Ap~h~r~k~msa~Ls~eLr~ky~~rs~~IkkGD~V~Vi~G~~KGk~GkV~~V~~k~~~V~VEgin~~K~--------- 89 (146)
-|-|...|+...+++++.+ .|.+..||+|+||.|+|||++|+|++|++.+++|+|+|+|....
T Consensus 51 k~~~w~rrr~~~~e~i~d~--------dw~ff~GDtVeVlvGkDkGkqG~Vtqv~r~~s~VvV~gln~k~r~~gsekeg~ 122 (236)
T KOG1708|consen 51 KNKPWERRRCVPVEPIIDE--------DWHFFFGDTVEVLVGKDKGKQGEVTQVIRHRSWVVVKGLNTKYRHMGSEKEGE 122 (236)
T ss_pred hcCccccccCCCCCCcccc--------ceeEecCCEEEEEecccCCccceEEEEeecCceEEEcccchhhhhhcccccCC
Confidence 4667788888888888765 69999999999999999999999999999999999999998732
Q ss_pred CCcE--EEeeccccc-eEEEcCCCc-chh--hhhhccccccch
Q 032182 90 NGST--VNVGINPSK-VVITKLRLD-KDR--KSLLDRKAKGRA 126 (146)
Q Consensus 90 ~G~~--~e~pIh~SN-v~i~~~~~~-~~R--~~~le~~~k~~~ 126 (146)
.|+. .|+|||.|| |||+|+.-+ +++ -+++|+|.++|-
T Consensus 123 pgtivk~EaPlhvsk~VmLvdp~d~q~te~~wr~~e~GekVRv 165 (236)
T KOG1708|consen 123 PGTIVKSEAPLHVSKQVMLVDPEDDQPTEVEWRFTEDGEKVRV 165 (236)
T ss_pred CceEEeecCCceecceeEEECccccCCceeeEEEcCCCcEEEE
Confidence 2443 499999999 999999884 766 688999987765
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=98.78 E-value=1.1e-08 Score=60.38 Aligned_cols=32 Identities=38% Similarity=0.695 Sum_probs=30.7
Q ss_pred cCCEEEEeecCCCCeEeeEEEEEecCCEEEEe
Q 032182 51 KDDEVQVVRGTYKGREGKVVQVYRRKWVIHIE 82 (146)
Q Consensus 51 kGD~V~Vi~G~~KGk~GkV~~V~~k~~~V~VE 82 (146)
+||.|.|++|+|+|..|+|++|++++.+|+||
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=97.80 E-value=3.4e-05 Score=42.88 Aligned_cols=26 Identities=38% Similarity=0.680 Sum_probs=24.3
Q ss_pred eecCCEEEEeecCCCCeEeeEEEEEe
Q 032182 49 VRKDDEVQVVRGTYKGREGKVVQVYR 74 (146)
Q Consensus 49 IkkGD~V~Vi~G~~KGk~GkV~~V~~ 74 (146)
+..||.|.|+.|+++|..|.|++++.
T Consensus 2 ~~~G~~V~I~~G~~~g~~g~i~~i~~ 27 (28)
T smart00739 2 FEVGDTVRVIAGPFKGKVGKVLEVDG 27 (28)
T ss_pred CCCCCEEEEeECCCCCcEEEEEEEcC
Confidence 67899999999999999999999875
No 13
>PRK08559 nusG transcription antitermination protein NusG; Validated
Probab=97.68 E-value=0.00024 Score=54.92 Aligned_cols=73 Identities=21% Similarity=0.360 Sum_probs=52.6
Q ss_pred eeeccCCHHHHhhhCC---cccceecCCEEEEeecCCCCeEeeEEEEEecCCEEEEeeeeEEeeCCcEEE--eeccccce
Q 032182 29 LMSAPLSTDLRQKYNV---RSMPVRKDDEVQVVRGTYKGREGKVVQVYRRKWVIHIERITREKVNGSTVN--VGINPSKV 103 (146)
Q Consensus 29 ~msa~Ls~eLr~ky~~---rs~~IkkGD~V~Vi~G~~KGk~GkV~~V~~k~~~V~VEgin~~K~~G~~~e--~pIh~SNv 103 (146)
++..+|+++--....- ....+..||.|.|++|+++|..|.|.+++..+..+.|+.+ |..+. +-|+.+-|
T Consensus 72 ~lg~~l~~~Ei~~il~~~~~~~~~~~G~~V~I~~Gpf~g~~g~V~~vd~~k~~v~v~ll------~~~~~~pv~v~~~~~ 145 (153)
T PRK08559 72 VVPGEISFEEVEHFLKPKPIVEGIKEGDIVELIAGPFKGEKARVVRVDESKEEVTVELL------EAAVPIPVTVRGDQV 145 (153)
T ss_pred eCCCCCCHHHHHHHHhccCcccCCCCCCEEEEeccCCCCceEEEEEEcCCCCEEEEEEE------CCcceeeEEEeccEE
Confidence 3445677765443321 2356899999999999999999999999999999999988 44433 44555555
Q ss_pred EEEc
Q 032182 104 VITK 107 (146)
Q Consensus 104 ~i~~ 107 (146)
.+++
T Consensus 146 ~~~~ 149 (153)
T PRK08559 146 RVVK 149 (153)
T ss_pred EEec
Confidence 5544
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=97.67 E-value=0.00019 Score=54.39 Aligned_cols=74 Identities=20% Similarity=0.378 Sum_probs=51.3
Q ss_pred eeccCCHHHHhhhCCc-c--cceecCCEEEEeecCCCCeEeeEEEEEecCCEEEEeeeeEEeeCCcEEEeeccccceEEE
Q 032182 30 MSAPLSTDLRQKYNVR-S--MPVRKDDEVQVVRGTYKGREGKVVQVYRRKWVIHIERITREKVNGSTVNVGINPSKVVIT 106 (146)
Q Consensus 30 msa~Ls~eLr~ky~~r-s--~~IkkGD~V~Vi~G~~KGk~GkV~~V~~k~~~V~VEgin~~K~~G~~~e~pIh~SNv~i~ 106 (146)
+.++||.+.-+..... . -.+..||.|.|++|+++|-.|.|.+++..+..|.|+-++. +...++-+..+.|..+
T Consensus 65 v~~~i~~~ei~~l~~~~~~~~~~~~Gd~V~I~~GPf~G~~g~v~~~d~~k~~v~v~l~~~----~~~~~v~v~~~~l~~~ 140 (145)
T TIGR00405 65 VEGEIDFEEIERFLTPKKIIESIKKGDIVEIISGPFKGERAKVIRVDESKEEVTLELIEA----AVPIPVTVKGDQVRII 140 (145)
T ss_pred cCCCCCHHHHHHHhcccccccccCCCCEEEEeecCCCCCeEEEEEEcCCCCEEEEEEEEc----CccceEEEeeeEEEEe
Confidence 3456777654433211 1 2378999999999999999999999998888999987743 3343344445666554
Q ss_pred c
Q 032182 107 K 107 (146)
Q Consensus 107 ~ 107 (146)
+
T Consensus 141 ~ 141 (145)
T TIGR00405 141 Q 141 (145)
T ss_pred c
Confidence 4
No 15
>PRK05609 nusG transcription antitermination protein NusG; Validated
Probab=97.23 E-value=0.0011 Score=51.47 Aligned_cols=54 Identities=20% Similarity=0.311 Sum_probs=39.9
Q ss_pred ccceecCCEEEEeecCCCCeEeeEEEEEecCCEEEEeeeeEEeeCCcEEEeeccccce
Q 032182 46 SMPVRKDDEVQVVRGTYKGREGKVVQVYRRKWVIHIERITREKVNGSTVNVGINPSKV 103 (146)
Q Consensus 46 s~~IkkGD~V~Vi~G~~KGk~GkV~~V~~k~~~V~VEgin~~K~~G~~~e~pIh~SNv 103 (146)
+..+..||.|.|++|+++|.+|.|.+++..+.++.|+ + .-=|..+.+.|..+.+
T Consensus 124 ~~~~~~Gd~VrI~~GPf~G~~g~v~~i~~~~~r~~v~-l---~~~G~~~~v~l~~~~l 177 (181)
T PRK05609 124 KVDFEVGEMVRVIDGPFADFNGTVEEVDYEKSKLKVL-V---SIFGRETPVELEFSQV 177 (181)
T ss_pred ccCCCCCCEEEEeccCCCCCEEEEEEEeCCCCEEEEE-E---EECCCceEEEEchHHE
Confidence 3558899999999999999999999999877777775 1 1125555554444443
No 16
>COG0250 NusG Transcription antiterminator [Transcription]
Probab=97.22 E-value=0.00096 Score=53.35 Aligned_cols=54 Identities=22% Similarity=0.336 Sum_probs=41.6
Q ss_pred cceecCCEEEEeecCCCCeEeeEEEEEecCCEEEEeeeeEEeeCCcEEEeeccccceE
Q 032182 47 MPVRKDDEVQVVRGTYKGREGKVVQVYRRKWVIHIERITREKVNGSTVNVGINPSKVV 104 (146)
Q Consensus 47 ~~IkkGD~V~Vi~G~~KGk~GkV~~V~~k~~~V~VEgin~~K~~G~~~e~pIh~SNv~ 104 (146)
..+..||.|.|++|+|+|-.|+|.+||.+++++.|+=- .=|...++-+..+.|.
T Consensus 122 ~~~e~Gd~VrI~~GpFa~f~g~V~evd~ek~~~~v~v~----ifgr~tPVel~~~qVe 175 (178)
T COG0250 122 VDFEPGDVVRIIDGPFAGFKAKVEEVDEEKGKLKVEVS----IFGRPTPVELEFDQVE 175 (178)
T ss_pred ccCCCCCEEEEeccCCCCccEEEEEEcCcCcEEEEEEE----EeCCceEEEEehhhEE
Confidence 56899999999999999999999999999998888722 2254444444444443
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=97.14 E-value=0.00078 Score=52.02 Aligned_cols=36 Identities=19% Similarity=0.311 Sum_probs=32.3
Q ss_pred cceecCCEEEEeecCCCCeEeeEEEEEecCCEEEEe
Q 032182 47 MPVRKDDEVQVVRGTYKGREGKVVQVYRRKWVIHIE 82 (146)
Q Consensus 47 ~~IkkGD~V~Vi~G~~KGk~GkV~~V~~k~~~V~VE 82 (146)
..++.||.|.|++|+++|.+|.|.+++..++++.|.
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 458899999999999999999999999877777775
No 18
>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=96.56 E-value=0.0062 Score=51.65 Aligned_cols=54 Identities=26% Similarity=0.430 Sum_probs=40.3
Q ss_pred ccceecCCEEEEeecCCCCeEeeEEEEEecCCEEEEeeeeEEeeCCcEEEeeccccce
Q 032182 46 SMPVRKDDEVQVVRGTYKGREGKVVQVYRRKWVIHIERITREKVNGSTVNVGINPSKV 103 (146)
Q Consensus 46 s~~IkkGD~V~Vi~G~~KGk~GkV~~V~~k~~~V~VEgin~~K~~G~~~e~pIh~SNv 103 (146)
.+.+..||.|.|+.|+|+|..|.|.+++..+.++.|. | .-=|...++-+..+.|
T Consensus 203 ~~~f~vGd~VrI~dGPF~GfeG~I~eid~~k~Rv~Vl-V---~IfGR~TpVeL~~~qV 256 (258)
T TIGR01956 203 LSKFRVGNFVKIVDGPFKGIVGKIKKIDQEKKKAIVE-V---EILGKSVDVDLNFKHL 256 (258)
T ss_pred ccCCCCCCEEEEEecCCCCcEEEEEEEeCCCCEEEEE-E---EecCCcEEEEEchHHE
Confidence 3568899999999999999999999999877887775 1 1225554444444444
No 19
>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=96.55 E-value=0.0039 Score=47.35 Aligned_cols=35 Identities=17% Similarity=0.176 Sum_probs=29.6
Q ss_pred cceecCCEEEEeecCCCCeEeeEEEEEecCCEEEEe
Q 032182 47 MPVRKDDEVQVVRGTYKGREGKVVQVYRRKWVIHIE 82 (146)
Q Consensus 47 ~~IkkGD~V~Vi~G~~KGk~GkV~~V~~k~~~V~VE 82 (146)
..+..||.|.|+.|+++|.+|.|.+++. +.++.|.
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 4566664
No 20
>PRK09014 rfaH transcriptional activator RfaH; Provisional
Probab=96.33 E-value=0.0059 Score=46.86 Aligned_cols=51 Identities=10% Similarity=0.155 Sum_probs=35.8
Q ss_pred ceecCCEEEEeecCCCCeEeeEEEEEecCCEEEEeeeeEEeeCCcEEEeeccccce
Q 032182 48 PVRKDDEVQVVRGTYKGREGKVVQVYRRKWVIHIERITREKVNGSTVNVGINPSKV 103 (146)
Q Consensus 48 ~IkkGD~V~Vi~G~~KGk~GkV~~V~~k~~~V~VEgin~~K~~G~~~e~pIh~SNv 103 (146)
.+..||.|.|+.|+++|.+|.|.+++. +.++.|. ..-=|..+++-++.++|
T Consensus 109 ~~~~G~~V~I~~Gp~~g~eg~v~~~~~-~~r~~v~----v~~~gr~~~v~v~~~~~ 159 (162)
T PRK09014 109 TPKPGDKVIITEGAFEGLQAIYTEPDG-EARSILL----LNLLNKQVKHSVDNTQF 159 (162)
T ss_pred CCCCCCEEEEecCCCCCcEEEEEEeCC-CeEEEEe----ehhhCCcEEEEECHHHe
Confidence 378999999999999999999999984 5565553 11114444444445444
No 21
>PRK04333 50S ribosomal protein L14e; Validated
Probab=92.81 E-value=0.22 Score=35.52 Aligned_cols=59 Identities=12% Similarity=0.087 Sum_probs=44.5
Q ss_pred cceecCCEEEEeecCCCCeEeeEEEEEecCCEEEEeeeeEEeeCCcEEEeeccccceEEEcCCC
Q 032182 47 MPVRKDDEVQVVRGTYKGREGKVVQVYRRKWVIHIERITREKVNGSTVNVGINPSKVVITKLRL 110 (146)
Q Consensus 47 ~~IkkGD~V~Vi~G~~KGk~GkV~~V~~k~~~V~VEgin~~K~~G~~~e~pIh~SNv~i~~~~~ 110 (146)
+.+..|-.|.+.+|.|+|+...|+.+.- .++|+|+|-.. . ...+-.+++..|.+++..+
T Consensus 2 ~~v~~GrvV~~~~Grd~gk~~vIv~i~d-~~~vlVdg~~~---~-~~~rk~kn~khl~lt~~ki 60 (84)
T PRK04333 2 PAIEVGRVCVKTAGREAGRKCVIVDIID-KNFVLVTGPSL---T-GVKRRRCNIKHLEPTDKKV 60 (84)
T ss_pred CcccccEEEEEeccCCCCCEEEEEEEec-CCEEEEECCCc---C-CCCCeeechHHEEEeeEEE
Confidence 3578999999999999999999999865 47899986521 1 1345567777777776554
No 22
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=92.41 E-value=0.14 Score=50.28 Aligned_cols=27 Identities=37% Similarity=0.636 Sum_probs=25.6
Q ss_pred eecCCEEEEeecCCCCeEeeEEEEEec
Q 032182 49 VRKDDEVQVVRGTYKGREGKVVQVYRR 75 (146)
Q Consensus 49 IkkGD~V~Vi~G~~KGk~GkV~~V~~k 75 (146)
++.||-|.||+|.|.|.+|-|++|...
T Consensus 460 F~~GDhVKVi~G~~eG~tGlVvrVe~~ 486 (1024)
T KOG1999|consen 460 FEPGDHVKVIAGRYEGDTGLVVRVEQG 486 (1024)
T ss_pred ccCCCeEEEEeccccCCcceEEEEeCC
Confidence 599999999999999999999999984
No 23
>PTZ00471 60S ribosomal protein L27; Provisional
Probab=89.59 E-value=0.62 Score=36.22 Aligned_cols=39 Identities=23% Similarity=0.353 Sum_probs=34.3
Q ss_pred eecCCEEEEeecCCCCeEeeEEEEEecC------CEEEEeeeeEE
Q 032182 49 VRKDDEVQVVRGTYKGREGKVVQVYRRK------WVIHIERITRE 87 (146)
Q Consensus 49 IkkGD~V~Vi~G~~KGk~GkV~~V~~k~------~~V~VEgin~~ 87 (146)
+++|-.|+|++|.+.|+...|++.+.+. +.++|-||..-
T Consensus 5 ~kpgkVVivL~GR~AGkKaVivk~~ddgt~drpy~halVaGIdry 49 (134)
T PTZ00471 5 LKPGKVVIVTSGRYAGRKAVIVQNFDTASKERPYGHALVAGIKKY 49 (134)
T ss_pred ccCCEEEEEEccccCCcEEEEEeecCCCCccCcCceEEEEeeccc
Confidence 6789999999999999999999987765 68999998654
No 24
>COG2163 RPL14A Ribosomal protein L14E/L6E/L27E [Translation, ribosomal structure and biogenesis]
Probab=85.83 E-value=0.95 Score=34.70 Aligned_cols=35 Identities=17% Similarity=0.305 Sum_probs=31.4
Q ss_pred eecCCEEEEeecCCCCeEeeEEEEEecCCEEEEeee
Q 032182 49 VRKDDEVQVVRGTYKGREGKVVQVYRRKWVIHIERI 84 (146)
Q Consensus 49 IkkGD~V~Vi~G~~KGk~GkV~~V~~k~~~V~VEgi 84 (146)
+..|=.|.|++|.|.|+...|+++.-++ .+++.|-
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 6889999999999999999999998876 8888854
No 25
>COG5164 SPT5 Transcription elongation factor [Transcription]
Probab=85.73 E-value=1.7 Score=40.41 Aligned_cols=69 Identities=23% Similarity=0.254 Sum_probs=48.8
Q ss_pred ccCCHHHHhhhCCcccceecCCEEEEeecCCCCeEeeEEEEEecCCEEEEeeeeEEeeCCcEEEeeccccceEEEcCCC
Q 032182 32 APLSTDLRQKYNVRSMPVRKDDEVQVVRGTYKGREGKVVQVYRRKWVIHIERITREKVNGSTVNVGINPSKVVITKLRL 110 (146)
Q Consensus 32 a~Ls~eLr~ky~~rs~~IkkGD~V~Vi~G~~KGk~GkV~~V~~k~~~V~VEgin~~K~~G~~~e~pIh~SNv~i~~~~~ 110 (146)
-|-+.+|.++-+-|.. --|-+|.|-+|.+||.-|.|..|+....+|-+- ...+.+-|.-||++++...-
T Consensus 337 ~p~~~~l~r~i~gRd~--aigktVrIr~g~yKG~lGVVKdv~~~~arVeLh--------s~nK~VTI~K~~l~y~~reG 405 (607)
T COG5164 337 NPKTNELERKIVGRDP--AIGKTVRIRCGEYKGHLGVVKDVDRNIARVELH--------SNNKFVTIEKSRLAYLGREG 405 (607)
T ss_pred CCcchhhhcccccccc--ccCceEEEeecccccccceeeeccCceEEEEEe--------cCCceEEeehhheEEecccc
Confidence 3445666666544444 458899999999999999999999876665443 34556667777777766543
No 26
>PTZ00065 60S ribosomal protein L14; Provisional
Probab=85.35 E-value=1.8 Score=33.44 Aligned_cols=57 Identities=12% Similarity=0.170 Sum_probs=42.9
Q ss_pred eecCCEEEEeecCCCCeEeeEEEEEecCCEEEEeeeeEEeeCCcEEEeeccccceEEEcCCC
Q 032182 49 VRKDDEVQVVRGTYKGREGKVVQVYRRKWVIHIERITREKVNGSTVNVGINPSKVVITKLRL 110 (146)
Q Consensus 49 IkkGD~V~Vi~G~~KGk~GkV~~V~~k~~~V~VEgin~~K~~G~~~e~pIh~SNv~i~~~~~ 110 (146)
+..|=.|.|..|++.|+...|+.|.-. ++|.|+|=. ..| -.--.|...++.|+++.+
T Consensus 8 VEiGRVvli~~Gp~~GKL~vIVDIID~-nRvLVDGP~---~tg-V~Rq~i~~k~l~LT~~~v 64 (130)
T PTZ00065 8 VEPGRLCLIQYGPDAGKLCFIVDIVTP-TRVLVDGAF---ITG-VKRQSIPLKRLKLTDEKI 64 (130)
T ss_pred eeeceEEEEecCCCCCCEEEEEEEEcC-CeEEEeCCC---cCC-cceeEEeccceEEccEEE
Confidence 678999999999999999999999875 799999640 012 122346677788877765
No 27
>PRK04306 50S ribosomal protein L21e; Reviewed
Probab=81.97 E-value=3 Score=30.79 Aligned_cols=49 Identities=29% Similarity=0.548 Sum_probs=34.3
Q ss_pred cccceeeeccCCHHHHhhhCCcccceecCCEEEEee-cC---------CCCeEeeEEEEEecCCEEEE
Q 032182 24 SVRRILMSAPLSTDLRQKYNVRSMPVRKDDEVQVVR-GT---------YKGREGKVVQVYRRKWVIHI 81 (146)
Q Consensus 24 h~r~k~msa~Ls~eLr~ky~~rs~~IkkGD~V~Vi~-G~---------~KGk~GkV~~V~~k~~~V~V 81 (146)
+.|.+-+ .+||.-|+. .+.||.|-|.- |. |-|++|.|..+...-.-|.|
T Consensus 19 ~~R~~G~-~~ls~~l~~--------y~~Gd~V~I~~d~sv~kGmPh~~yhGkTG~V~~v~~~A~~V~v 77 (98)
T PRK04306 19 SPRERGL-SPLSRALQE--------FEEGDKVHIVIDPSVHKGMPHPRFHGKTGTVVGKRGRAYIVEV 77 (98)
T ss_pred CccccCC-CcHHHHHHh--------ccCCCEEEEEecCceecCCccccccCCCEEEEeecCeEEEEEE
Confidence 3344443 557776654 48899998763 32 67999999999887666666
No 28
>PF12701 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC8_A 2VXF_A 2VXE_A.
Probab=79.38 E-value=4.2 Score=29.64 Aligned_cols=52 Identities=13% Similarity=0.213 Sum_probs=36.3
Q ss_pred cCCEEEEeecCCCCeEeeEEEEEecCCEEEEeeeeEEeeCCcEEEeeccccc
Q 032182 51 KDDEVQVVRGTYKGREGKVVQVYRRKWVIHIERITREKVNGSTVNVGINPSK 102 (146)
Q Consensus 51 kGD~V~Vi~G~~KGk~GkV~~V~~k~~~V~VEgin~~K~~G~~~e~pIh~SN 102 (146)
-|-.|-+++..+-..+|.+..|+...++|.+.+|-.--..|.....+|+|++
T Consensus 7 IGs~ISlisk~~iRYeG~L~~Id~~~sTItL~nVr~~GtE~R~~~~~ipp~~ 58 (96)
T PF12701_consen 7 IGSKISLISKSDIRYEGILYSIDTEDSTITLKNVRSFGTEGRPTDREIPPSD 58 (96)
T ss_dssp TTCEEEEEETTTEEEEEEEEEEETTTTEEEEEEEEETTETTSS-SS---C-C
T ss_pred cCCEEEEEECCCcEEEEEEEEEcCCCCEEEeeeeeecCcCCCCcCcccCCCC
Confidence 4889999999998899999999999999999987433222322333555543
No 29
>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=77.79 E-value=6.9 Score=26.05 Aligned_cols=37 Identities=22% Similarity=0.297 Sum_probs=22.2
Q ss_pred eecCCEEEEeecC--CCCe--EeeEEEEEecCCEEEEeeeeE
Q 032182 49 VRKDDEVQVVRGT--YKGR--EGKVVQVYRRKWVIHIERITR 86 (146)
Q Consensus 49 IkkGD~V~Vi~G~--~KGk--~GkV~~V~~k~~~V~VEgin~ 86 (146)
|++||.|+|.+-. +.|. .|+|++...+. ++.|+=.++
T Consensus 1 F~~G~~VEV~s~e~g~~gaWf~a~V~~~~~~~-~~~V~Y~~~ 41 (68)
T PF05641_consen 1 FKKGDEVEVSSDEDGFRGAWFPATVLKENGDD-KYLVEYDDL 41 (68)
T ss_dssp --TT-EEEEEE-SBTT--EEEEEEEEEEETT--EEEEEETT-
T ss_pred CCCCCEEEEEEcCCCCCcEEEEEEEEEeCCCc-EEEEEECCc
Confidence 5799999999843 4554 58999999875 666664333
No 30
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=77.36 E-value=1.9 Score=42.77 Aligned_cols=29 Identities=34% Similarity=0.418 Sum_probs=26.4
Q ss_pred cceecCCEEEEeecCCCCeEeeEEEEEec
Q 032182 47 MPVRKDDEVQVVRGTYKGREGKVVQVYRR 75 (146)
Q Consensus 47 ~~IkkGD~V~Vi~G~~KGk~GkV~~V~~k 75 (146)
..+.+||.|+|+.|..+|-.|+|..|+-.
T Consensus 406 ~~F~~GD~VeV~~Gel~glkG~ve~vdg~ 434 (1024)
T KOG1999|consen 406 HLFSPGDAVEVIVGELKGLKGKVESVDGT 434 (1024)
T ss_pred cccCCCCeEEEeeeeeccceeEEEeccCc
Confidence 45899999999999999999999999764
No 31
>PRK06531 yajC preprotein translocase subunit YajC; Validated
Probab=75.93 E-value=5.1 Score=30.15 Aligned_cols=31 Identities=29% Similarity=0.383 Sum_probs=26.1
Q ss_pred ceecCCEEEEeecCCCCeEeeEEEEEecCCEEEEe
Q 032182 48 PVRKDDEVQVVRGTYKGREGKVVQVYRRKWVIHIE 82 (146)
Q Consensus 48 ~IkkGD~V~Vi~G~~KGk~GkV~~V~~k~~~V~VE 82 (146)
.+++||+|.-+.| -.|+|..|+...+.|.||
T Consensus 36 sLk~GD~VvT~GG----i~G~V~~I~~~~~~v~le 66 (113)
T PRK06531 36 AIQKGDEVVTIGG----LYGTVDEVDTEAKTIVLD 66 (113)
T ss_pred hcCCCCEEEECCC----cEEEEEEEecCCCEEEEE
Confidence 4799999987765 589999999877888887
No 32
>COG5164 SPT5 Transcription elongation factor [Transcription]
Probab=73.96 E-value=2.7 Score=39.14 Aligned_cols=30 Identities=27% Similarity=0.230 Sum_probs=26.8
Q ss_pred eecCCEEEEeecCCCCeEeeEEEEEecCCE
Q 032182 49 VRKDDEVQVVRGTYKGREGKVVQVYRRKWV 78 (146)
Q Consensus 49 IkkGD~V~Vi~G~~KGk~GkV~~V~~k~~~ 78 (146)
+.+||-|.||.|.+++-.|.|+.|+.++-.
T Consensus 140 f~~gD~vkVI~g~~~~d~g~V~rI~~~~vt 169 (607)
T COG5164 140 FYKGDLVKVIEGGEMVDIGTVPRIDGEKVT 169 (607)
T ss_pred cccCCeEEEeccccccccceEEEecCceeE
Confidence 589999999999999999999999876533
No 33
>CHL00084 rpl19 ribosomal protein L19
Probab=72.27 E-value=14 Score=27.93 Aligned_cols=71 Identities=15% Similarity=0.193 Sum_probs=42.8
Q ss_pred HHHHhhhCCccc-ceecCCEEEEee---cCCC----CeEeeEEEEEecC--CEEEEeeeeEEeeCCcEEEeeccccceEE
Q 032182 36 TDLRQKYNVRSM-PVRKDDEVQVVR---GTYK----GREGKVVQVYRRK--WVIHIERITREKVNGSTVNVGINPSKVVI 105 (146)
Q Consensus 36 ~eLr~ky~~rs~-~IkkGD~V~Vi~---G~~K----Gk~GkV~~V~~k~--~~V~VEgin~~K~~G~~~e~pIh~SNv~i 105 (146)
.++-+.+--..+ .++.||+|.|-. ..+| --+|.|+.+.... .+++|..+ ...-|-+.-.|+|..++.=
T Consensus 9 ~~~~~~~~~~~~p~f~~GDtV~V~~~i~eg~k~R~q~F~GvvI~~r~~G~~~tftvRki--~~gvGVEr~fpl~SP~I~~ 86 (117)
T CHL00084 9 KEIESEFLKKNLPKIRVGDTVKVGVLIQEGNKERVQFYEGTVIAKKNSGLNTTITVRKV--FQGIGVERVFLLHSPKLAS 86 (117)
T ss_pred HHHHHHHhhcCCCccCCCCEEEEEEEEecCCeeEeceEEEEEEEEeCCCCCeeEEEEEe--ccCccEEEEEecCCCccce
Confidence 344444433334 489999999854 2223 2468999886432 34666654 1222457779999988865
Q ss_pred EcC
Q 032182 106 TKL 108 (146)
Q Consensus 106 ~~~ 108 (146)
++.
T Consensus 87 IeV 89 (117)
T CHL00084 87 IEV 89 (117)
T ss_pred EEE
Confidence 554
No 34
>PRK04313 30S ribosomal protein S4e; Validated
Probab=72.17 E-value=7.3 Score=32.85 Aligned_cols=55 Identities=16% Similarity=0.285 Sum_probs=41.7
Q ss_pred ccceecCCEEEEeecCCCCeEeeEEEEEecC----CEEEEeeeeEEeeCCcEEEeeccccceEEEc
Q 032182 46 SMPVRKDDEVQVVRGTYKGREGKVVQVYRRK----WVIHIERITREKVNGSTVNVGINPSKVVITK 107 (146)
Q Consensus 46 s~~IkkGD~V~Vi~G~~KGk~GkV~~V~~k~----~~V~VEgin~~K~~G~~~e~pIh~SNv~i~~ 107 (146)
-+++..|..|.|+.|..-|..|+|..+.... +.|.||+. +|.+++ ...+||+++.
T Consensus 169 ~i~fe~G~l~~itgG~n~GriG~I~~i~~~~~~~~~~V~i~d~-----~G~~F~--T~~~~vfvIG 227 (237)
T PRK04313 169 HIPFEEGNLAIITGGKHVGEIGKIKEIEVTKSSKPNIVTLEDK-----DGEKFE--TILDYVFVIG 227 (237)
T ss_pred EEecCCCCEEEEECCeeeeeEEEEEEEEEccCCCCcEEEEEcC-----CCCEEE--EEeeeEEEEc
Confidence 3789999999999999999999999997544 56777733 454433 3457777775
No 35
>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=71.06 E-value=9.5 Score=25.65 Aligned_cols=27 Identities=22% Similarity=0.393 Sum_probs=22.2
Q ss_pred ecCCEEEEeecCCCCeEeeEEEEEecCCEEEEe
Q 032182 50 RKDDEVQVVRGTYKGREGKVVQVYRRKWVIHIE 82 (146)
Q Consensus 50 kkGD~V~Vi~G~~KGk~GkV~~V~~k~~~V~VE 82 (146)
..||.++. -.|-+|+|.+|. .++|+|+
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 57999987 347899999998 5789987
No 36
>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=70.64 E-value=13 Score=29.95 Aligned_cols=43 Identities=12% Similarity=0.268 Sum_probs=31.3
Q ss_pred hhhCCcccceecCCEEEEeecCCCCeEeeEEEEEecCCEEEEe
Q 032182 40 QKYNVRSMPVRKDDEVQVVRGTYKGREGKVVQVYRRKWVIHIE 82 (146)
Q Consensus 40 ~ky~~rs~~IkkGD~V~Vi~G~~KGk~GkV~~V~~k~~~V~VE 82 (146)
..|=.+-++++.||.|.|.-|.-.--.++|..++.+.-.+.+.
T Consensus 8 ~~Hl~~VlR~k~Gd~i~v~dg~g~~~~a~i~~i~~~~~~~~i~ 50 (225)
T PF04452_consen 8 AHHLVKVLRLKEGDSIEVFDGDGGEYRAEITEISKKSATLRIL 50 (225)
T ss_dssp HHHHHTTST--TT-EEEEEESSSEEEEEEEEEEESSEEEEEEE
T ss_pred HHHHHHhcCCCCCCEEEEEECCCCEEEEEEEECcCcEEEEEEe
Confidence 3444577899999999999988766789999999877666655
No 37
>PTZ00189 60S ribosomal protein L21; Provisional
Probab=69.84 E-value=9.7 Score=30.44 Aligned_cols=44 Identities=32% Similarity=0.432 Sum_probs=32.7
Q ss_pred eccCCHHHHhhhCCcccceecCCEEEEee-c---------CCCCeEeeEEEEEecCCEEEEe
Q 032182 31 SAPLSTDLRQKYNVRSMPVRKDDEVQVVR-G---------TYKGREGKVVQVYRRKWVIHIE 82 (146)
Q Consensus 31 sa~Ls~eLr~ky~~rs~~IkkGD~V~Vi~-G---------~~KGk~GkV~~V~~k~~~V~VE 82 (146)
..+||.-|+. .+.||.|-|.. | .|-|++|.|..|...-.-|+|+
T Consensus 24 ~~pls~~l~~--------yk~GD~VdIk~d~svqkGMPhk~YHGkTG~V~nv~~~A~gViV~ 77 (160)
T PTZ00189 24 VPSLSTYLTT--------FKVGDYVDIVVDSAVHKGMPYKYYHGRTGRVFNVTPRAVGVIVN 77 (160)
T ss_pred CCcHHHHHHH--------ccCCCEEEEEecCCeecCCCcccccCCCeEEEeecCeEEEEEEE
Confidence 4778877654 38899998764 3 2779999999998876656664
No 38
>COG1862 YajC Preprotein translocase subunit YajC [Intracellular trafficking and secretion]
Probab=69.78 E-value=7.5 Score=28.52 Aligned_cols=29 Identities=34% Similarity=0.511 Sum_probs=23.0
Q ss_pred ceecCCEEEEeecCCCCeEeeEEEEEecCCEEEEe
Q 032182 48 PVRKDDEVQVVRGTYKGREGKVVQVYRRKWVIHIE 82 (146)
Q Consensus 48 ~IkkGD~V~Vi~G~~KGk~GkV~~V~~k~~~V~VE 82 (146)
.+++||+|.-+.| -.|+|++|.... +.|+
T Consensus 43 sL~kGD~VvT~gG----i~G~V~~v~d~~--v~I~ 71 (97)
T COG1862 43 SLKKGDEVVTIGG----IVGTVTKVGDDT--VEIE 71 (97)
T ss_pred hccCCCEEEEcCC----eEEEEEEEecCc--EEEE
Confidence 4799999988775 589999998865 5554
No 39
>PLN00190 60S ribosomal protein L21; Provisional
Probab=69.69 E-value=10 Score=30.20 Aligned_cols=44 Identities=34% Similarity=0.537 Sum_probs=32.8
Q ss_pred eccCCHHHHhhhCCcccceecCCEEEEee-c---------CCCCeEeeEEEEEecCCEEEEe
Q 032182 31 SAPLSTDLRQKYNVRSMPVRKDDEVQVVR-G---------TYKGREGKVVQVYRRKWVIHIE 82 (146)
Q Consensus 31 sa~Ls~eLr~ky~~rs~~IkkGD~V~Vi~-G---------~~KGk~GkV~~V~~k~~~V~VE 82 (146)
..+||.-|+. | +.||.|-|.. | .|-|++|.|..|.....-|+|.
T Consensus 24 ~~pls~~l~~-y-------k~GD~VdIk~~~svqKGMPhk~YHGkTG~V~nv~~~A~gV~V~ 77 (158)
T PLN00190 24 YIPLTTYLRT-F-------KVGDYVDIKVNGAIHKGMPHKFYHGRTGIVWNVTKRAVGVEVN 77 (158)
T ss_pred CCcHHHHHHH-h-------cCCCEEEEEecCCeecCCCcccccCCCeEEEeecCcEEEEEEE
Confidence 4788877765 3 8899998763 3 3779999999998876555554
No 40
>PRK05585 yajC preprotein translocase subunit YajC; Validated
Probab=68.14 E-value=9.4 Score=28.16 Aligned_cols=29 Identities=38% Similarity=0.385 Sum_probs=23.9
Q ss_pred ceecCCEEEEeecCCCCeEeeEEEEEecCCEEEEe
Q 032182 48 PVRKDDEVQVVRGTYKGREGKVVQVYRRKWVIHIE 82 (146)
Q Consensus 48 ~IkkGD~V~Vi~G~~KGk~GkV~~V~~k~~~V~VE 82 (146)
.+++||+|.-++| -.|+|++|+. +.|.||
T Consensus 52 ~Lk~Gd~VvT~gG----i~G~Vv~i~~--~~v~le 80 (106)
T PRK05585 52 SLAKGDEVVTNGG----IIGKVTKVSE--DFVIIE 80 (106)
T ss_pred hcCCCCEEEECCC----eEEEEEEEeC--CEEEEE
Confidence 5799999998876 4899999975 577776
No 41
>COG1532 Predicted RNA-binding protein [General function prediction only]
Probab=67.98 E-value=10 Score=25.47 Aligned_cols=34 Identities=24% Similarity=0.245 Sum_probs=28.4
Q ss_pred ecCCEEEEe--ecCCCCeEeeEEEEEecCCEEEEee
Q 032182 50 RKDDEVQVV--RGTYKGREGKVVQVYRRKWVIHIER 83 (146)
Q Consensus 50 kkGD~V~Vi--~G~~KGk~GkV~~V~~k~~~V~VEg 83 (146)
..||.|.-. =|+.|--.|+|.++|-...+|++||
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 467777654 5888888999999999999999985
No 42
>COG2002 AbrB Regulators of stationary/sporulation gene expression [Transcription]
Probab=65.39 E-value=8 Score=27.17 Aligned_cols=28 Identities=14% Similarity=0.446 Sum_probs=23.7
Q ss_pred cCCHHHHhhhCCcccceecCCEEEEeecCCCCe
Q 032182 33 PLSTDLRQKYNVRSMPVRKDDEVQVVRGTYKGR 65 (146)
Q Consensus 33 ~Ls~eLr~ky~~rs~~IkkGD~V~Vi~G~~KGk 65 (146)
-+|+++|+.+| |+.||.|+++...+.|.
T Consensus 17 vIPkeiR~~lg-----i~~Gd~lei~~~~~~~~ 44 (89)
T COG2002 17 VIPKEIREALG-----IKEGDVLEIIVDGDGGR 44 (89)
T ss_pred EecHHHHHHhC-----CCCCCEEEEEEeCCCCE
Confidence 47999999885 68899999998887775
No 43
>TIGR01024 rplS_bact ribosomal protein L19, bacterial type. This model describes bacterial ribosomoal protein L19 and its chloroplast equivalent. Putative mitochondrial L19 are found in several species (but not Saccharomyces cerevisiae) and score between trusted and noise cutoffs.
Probab=64.54 E-value=40 Score=25.35 Aligned_cols=70 Identities=16% Similarity=0.117 Sum_probs=42.2
Q ss_pred HHhhhCCccc-ceecCCEEEEee---cCCCC----eEeeEEEEEecC--CEEEEeeeeEEeeCCcEEEeeccccceEEEc
Q 032182 38 LRQKYNVRSM-PVRKDDEVQVVR---GTYKG----REGKVVQVYRRK--WVIHIERITREKVNGSTVNVGINPSKVVITK 107 (146)
Q Consensus 38 Lr~ky~~rs~-~IkkGD~V~Vi~---G~~KG----k~GkV~~V~~k~--~~V~VEgin~~K~~G~~~e~pIh~SNv~i~~ 107 (146)
+-+.+--+.+ .++.||.|.|-. ...|. -+|.|+.+.... .+++|..+ ...-|-+.-+|+|..++.=+.
T Consensus 7 ~e~~~~~~~ip~f~~GD~v~V~~~i~eg~k~R~q~f~GvvI~~~~~G~~~tftvR~i--~~gvGVEr~fpl~SP~I~~Ie 84 (113)
T TIGR01024 7 IEQEQLKKDLPDFRVGDTVRVHVKIVEGKKERIQVFEGVVIARRGGGIGETFTVRKI--SYGVGVERIFPLHSPNIDSIE 84 (113)
T ss_pred HHHHHhhcCCCccCCCCEEEEEEEEccCCceEcccEEEEEEEEeCCCCceEEEEEEe--ccCccEEEEEEcCCCccceEE
Confidence 3333333344 489999999953 21222 368888887543 34666654 112245777999998876555
Q ss_pred CC
Q 032182 108 LR 109 (146)
Q Consensus 108 ~~ 109 (146)
.-
T Consensus 85 Vl 86 (113)
T TIGR01024 85 VV 86 (113)
T ss_pred EE
Confidence 43
No 44
>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=64.09 E-value=24 Score=24.86 Aligned_cols=53 Identities=13% Similarity=0.189 Sum_probs=41.0
Q ss_pred cCCEEEEeecCCCCeEeeEEEEEecCCEEEEeeeeEEeeCCcEEEee-ccccce
Q 032182 51 KDDEVQVVRGTYKGREGKVVQVYRRKWVIHIERITREKVNGSTVNVG-INPSKV 103 (146)
Q Consensus 51 kGD~V~Vi~G~~KGk~GkV~~V~~k~~~V~VEgin~~K~~G~~~e~p-Ih~SNv 103 (146)
-|..+.+|+=.+-=.+|..-.|+....+|..++|----..|.....| |.||+=
T Consensus 5 IG~~isLISk~~iRYeGiL~~In~~~sTi~L~nVr~fGTEgR~~~~~~ipp~~~ 58 (74)
T cd01736 5 IGSKISLISKSDIRYEGILYTINTEDSTIALKNVRSFGTEGRPTDGPEIPPSDE 58 (74)
T ss_pred cCceEEEEecCCcEEEEEEEeeccccCEEEeeeeEeecccCCCCCCCccCCCCc
Confidence 48889999999999999999999999999999875444444433444 666653
No 45
>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=63.94 E-value=14 Score=26.08 Aligned_cols=29 Identities=31% Similarity=0.442 Sum_probs=23.2
Q ss_pred ceecCCEEEEeecCCCCeEeeEEEEEecCCEEEEe
Q 032182 48 PVRKDDEVQVVRGTYKGREGKVVQVYRRKWVIHIE 82 (146)
Q Consensus 48 ~IkkGD~V~Vi~G~~KGk~GkV~~V~~k~~~V~VE 82 (146)
.+++||+|.-++| -.|+|.+++. +.+.||
T Consensus 37 ~L~~Gd~VvT~gG----i~G~V~~i~d--~~v~ve 65 (84)
T TIGR00739 37 SLKKGDKVLTIGG----IIGTVTKIAE--NTIVIE 65 (84)
T ss_pred hCCCCCEEEECCC----eEEEEEEEeC--CEEEEE
Confidence 5799999998776 4899999985 466666
No 46
>PRK05886 yajC preprotein translocase subunit YajC; Validated
Probab=63.76 E-value=13 Score=27.76 Aligned_cols=29 Identities=17% Similarity=0.352 Sum_probs=23.7
Q ss_pred ceecCCEEEEeecCCCCeEeeEEEEEecCCEEEEe
Q 032182 48 PVRKDDEVQVVRGTYKGREGKVVQVYRRKWVIHIE 82 (146)
Q Consensus 48 ~IkkGD~V~Vi~G~~KGk~GkV~~V~~k~~~V~VE 82 (146)
.+++||+|.-++| -.|+|++|+- +.|.||
T Consensus 38 ~Lk~GD~VvT~gG----i~G~V~~I~d--~~v~le 66 (109)
T PRK05886 38 SLQPGDRVHTTSG----LQATIVGITD--DTVDLE 66 (109)
T ss_pred hcCCCCEEEECCC----eEEEEEEEeC--CEEEEE
Confidence 4799999988775 4899999974 578887
No 47
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=62.43 E-value=9.4 Score=26.90 Aligned_cols=41 Identities=24% Similarity=0.357 Sum_probs=31.2
Q ss_pred eeccCCHHHHhhhCCcccceecCCEEEEeecCCCCeEeeEEEEEe
Q 032182 30 MSAPLSTDLRQKYNVRSMPVRKDDEVQVVRGTYKGREGKVVQVYR 74 (146)
Q Consensus 30 msa~Ls~eLr~ky~~rs~~IkkGD~V~Vi~G~~KGk~GkV~~V~~ 74 (146)
.-|+||--+|.-| +.|..||.|.|--=+|--..|.|+.-..
T Consensus 32 ~~ahI~GKmr~~~----i~I~~GD~V~Ve~~~~d~~kg~I~~Ry~ 72 (75)
T COG0361 32 RLAHISGKMRKNR----IRILPGDVVLVELSPYDLTKGRIVYRYK 72 (75)
T ss_pred EEEEccCcchhee----EEeCCCCEEEEEecccccccccEEEEec
Confidence 3567777777666 8999999999988777777777765443
No 48
>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=61.94 E-value=11 Score=27.85 Aligned_cols=36 Identities=33% Similarity=0.589 Sum_probs=21.2
Q ss_pred cCCHHHHhhhCCcccceecCCEEEEeecC----------CCCeEeeEEEEEecC
Q 032182 33 PLSTDLRQKYNVRSMPVRKDDEVQVVRGT----------YKGREGKVVQVYRRK 76 (146)
Q Consensus 33 ~Ls~eLr~ky~~rs~~IkkGD~V~Vi~G~----------~KGk~GkV~~V~~k~ 76 (146)
+||.-|+ . .+.||.|-|.--+ |-|++|.|..|.+..
T Consensus 25 ~ls~~l~-~-------yk~GD~V~I~id~sv~kGmPh~~yHGkTG~V~~v~~~~ 70 (99)
T PF01157_consen 25 PLSTYLQ-E-------YKVGDKVDIKIDPSVHKGMPHKRYHGKTGRVFNVTKGA 70 (99)
T ss_dssp -CHHHH------------TT-EEEE---TTSSSSS--GGGTTEEEEEEEE-SSC
T ss_pred cHHHHHH-H-------ccCCCEEEEEecCccccCCCcceECCCceeEEEeCCCc
Confidence 5776552 3 4899999887332 779999999999865
No 49
>PRK02749 photosystem I reaction center subunit IV; Provisional
Probab=60.04 E-value=20 Score=25.14 Aligned_cols=30 Identities=23% Similarity=0.471 Sum_probs=24.8
Q ss_pred cceecCCEEEEeecC--CCCeEeeEEEEEecC
Q 032182 47 MPVRKDDEVQVVRGT--YKGREGKVVQVYRRK 76 (146)
Q Consensus 47 ~~IkkGD~V~Vi~G~--~KGk~GkV~~V~~k~ 76 (146)
|.|++||.|.|++=. +-...|+|..||...
T Consensus 1 m~i~rGskVrIlR~ESYWyn~vGtV~svD~sg 32 (71)
T PRK02749 1 MAISRGDKVRILRPESYWYNEVGTVASVDKSG 32 (71)
T ss_pred CccccCCEEEEccccceeecCcceEEEEccCC
Confidence 458999999999865 456689999999974
No 50
>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=59.98 E-value=11 Score=24.32 Aligned_cols=24 Identities=38% Similarity=0.574 Sum_probs=14.0
Q ss_pred eecCCEEEE-eecCCCC--eEeeEEEE
Q 032182 49 VRKDDEVQV-VRGTYKG--REGKVVQV 72 (146)
Q Consensus 49 IkkGD~V~V-i~G~~KG--k~GkV~~V 72 (146)
.--||+|.| +.....+ .+|+|++|
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 456999988 4444333 36999876
No 51
>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=59.84 E-value=20 Score=23.23 Aligned_cols=31 Identities=19% Similarity=0.344 Sum_probs=24.2
Q ss_pred ceecCCEEEEeecCCCCeE---eeEEEEEecCCEE
Q 032182 48 PVRKDDEVQVVRGTYKGRE---GKVVQVYRRKWVI 79 (146)
Q Consensus 48 ~IkkGD~V~Vi~G~~KGk~---GkV~~V~~k~~~V 79 (146)
.|++||+|.++. ..-++. ++|..+....+..
T Consensus 12 ~l~~gd~v~~~~-~~~~~~~~~~~I~~i~~~~~~~ 45 (74)
T PF03144_consen 12 TLKKGDKVRVLP-NGTGKKGQVVKIKSIFMFNGDV 45 (74)
T ss_dssp EEETTEEEEEES-TTTTEECEEEEEEEEEETTEEE
T ss_pred EEcCCCEEEECc-cCCcceeeeeecccccccccCc
Confidence 589999999998 666555 8888888876543
No 52
>KOG3418 consensus 60S ribosomal protein L27 [Translation, ribosomal structure and biogenesis]
Probab=58.66 E-value=17 Score=28.43 Aligned_cols=39 Identities=18% Similarity=0.296 Sum_probs=31.7
Q ss_pred eecCCEEEEeecCCCCeEeeEEEEEecC------CEEEEeeeeEE
Q 032182 49 VRKDDEVQVVRGTYKGREGKVVQVYRRK------WVIHIERITRE 87 (146)
Q Consensus 49 IkkGD~V~Vi~G~~KGk~GkV~~V~~k~------~~V~VEgin~~ 87 (146)
+++|-.|.|++|.+.|+...|++-.-+. +.+.|+||..-
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 6889999999999999998887665543 37899999654
No 53
>PTZ00223 40S ribosomal protein S4; Provisional
Probab=58.44 E-value=19 Score=30.99 Aligned_cols=56 Identities=18% Similarity=0.336 Sum_probs=40.1
Q ss_pred ccceecCCEEEEeecCCCCeEeeEEEEEecC---CEEEEeeeeEEeeCCcEEEeeccccceEEEcC
Q 032182 46 SMPVRKDDEVQVVRGTYKGREGKVVQVYRRK---WVIHIERITREKVNGSTVNVGINPSKVVITKL 108 (146)
Q Consensus 46 s~~IkkGD~V~Vi~G~~KGk~GkV~~V~~k~---~~V~VEgin~~K~~G~~~e~pIh~SNv~i~~~ 108 (146)
-+++..|..|.|+.|..-|..|+|..+.... +.|.+++ ++|..++ ...+||.++..
T Consensus 169 ~ikfe~G~l~~vtgG~n~GriG~I~~i~~~~~~~~iv~i~d-----~~g~~F~--T~~~~VfvIG~ 227 (273)
T PTZ00223 169 LIKNRNGKVVMVTGGANRGRIGEIVSIERHPGAFDIARLKD-----ASGHEFA--TRAANIFVIGK 227 (273)
T ss_pred EEecCCCCEEEEECCeeceeEEEEEEEEecCCCCCEEEEEe-----CCCCeEE--EEeeeEEEEeC
Confidence 4789999999999999999999999995543 3566663 3454432 34566766643
No 54
>PLN00036 40S ribosomal protein S4; Provisional
Probab=57.95 E-value=21 Score=30.61 Aligned_cols=56 Identities=20% Similarity=0.289 Sum_probs=40.3
Q ss_pred ccceecCCEEEEeecCCCCeEeeEEEEEecC---CEEEEeeeeEEeeCCcEEEeeccccceEEEcC
Q 032182 46 SMPVRKDDEVQVVRGTYKGREGKVVQVYRRK---WVIHIERITREKVNGSTVNVGINPSKVVITKL 108 (146)
Q Consensus 46 s~~IkkGD~V~Vi~G~~KGk~GkV~~V~~k~---~~V~VEgin~~K~~G~~~e~pIh~SNv~i~~~ 108 (146)
-+++..|..|.|+.|..-|..|+|..+.... +.|.|++ ++|..++ ...+||.++..
T Consensus 172 ~ikfe~G~l~~vtgG~n~GrvG~I~~i~~~~~~~~iV~i~d-----~~g~~F~--T~~~~vfvIG~ 230 (261)
T PLN00036 172 FIKFDVGNLVMVTGGRNRGRVGVIKNREKHKGSFEIIHVKD-----ATGHEFA--TRLGNVFVIGK 230 (261)
T ss_pred EEecCCCCEEEEECCeeceeEEEEEEEEecCCCCCEEEEEe-----CCCCeEE--EEeeeEEEEcc
Confidence 4789999999999999999999999998543 3466653 3554433 23466666653
No 55
>PF14505 DUF4438: Domain of unknown function (DUF4438); PDB: 3N99_N 3DCL_A.
Probab=57.43 E-value=20 Score=30.67 Aligned_cols=33 Identities=24% Similarity=0.250 Sum_probs=24.4
Q ss_pred ecCCEEEEeecCCCCeEeeEEEEEecCCEEEEe
Q 032182 50 RKDDEVQVVRGTYKGREGKVVQVYRRKWVIHIE 82 (146)
Q Consensus 50 kkGD~V~Vi~G~~KGk~GkV~~V~~k~~~V~VE 82 (146)
-.|.+..|++|.-||..|.|+-=.-.-+.|+|.
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 579999999999999999998776666677664
No 56
>COG1471 RPS4A Ribosomal protein S4E [Translation, ribosomal structure and biogenesis]
Probab=57.12 E-value=21 Score=30.29 Aligned_cols=38 Identities=21% Similarity=0.347 Sum_probs=32.4
Q ss_pred ccceecCCEEEEeecCCCCeEeeEEEEEecC----CEEEEee
Q 032182 46 SMPVRKDDEVQVVRGTYKGREGKVVQVYRRK----WVIHIER 83 (146)
Q Consensus 46 s~~IkkGD~V~Vi~G~~KGk~GkV~~V~~k~----~~V~VEg 83 (146)
-+++..|-.|.|+.|..-|..|+|..|.... +.|.||+
T Consensus 171 ~i~fe~g~~~~vtgG~h~G~~G~I~~I~~~~~~~~~~v~~e~ 212 (241)
T COG1471 171 HIKFEEGALVYVTGGRHVGRVGTIVEIEIQESSKPNLVTVED 212 (241)
T ss_pred EeccCCCcEEEEECCccccceEEEEEEEEecCCCccEEEEec
Confidence 3788999999999999999999999998764 4577774
No 57
>PF04014 Antitoxin-MazE: Antidote-toxin recognition MazE; InterPro: IPR007159 This domain is found in AbrB from Bacillus subtilis. The product of the abrB gene is an ambiactive repressor and activator of the transcription of genes expressed during the transition state between vegetative growth and the onset of stationary phase and sporulation []. AbrB is thought to interact directly with the transcription initiation regions of genes under its control []. AbrB contains a helix-turn-helix structure, but this domain ends before the helix-turn-helix begins []. The product of the B. subtilis gene spoVT is another member of this family and is also a transcriptional regulator []. DNA-binding activity in this AbrB homologue requires hexamerisation []. Another family member has been isolated from the Sulfolobus solfataricus and has been identified as a homologue of bacterial repressor-like proteins. The Escherichia coli family member SohA or Prl1F appears to be bifunctional and is able to regulate its own expression as well as relieve the export block imposed by high-level synthesis of beta-galactosidase hybrid proteins [].; PDB: 2L66_A 2GLW_A 3TND_D 2W1T_B 2RO5_B 2FY9_A 2RO3_B 1UB4_C 3ZVK_G 1YFB_B ....
Probab=57.12 E-value=10 Score=23.34 Aligned_cols=24 Identities=21% Similarity=0.484 Sum_probs=18.1
Q ss_pred ccCCHHHHhhhCCcccceecCCEEEEeec
Q 032182 32 APLSTDLRQKYNVRSMPVRKDDEVQVVRG 60 (146)
Q Consensus 32 a~Ls~eLr~ky~~rs~~IkkGD~V~Vi~G 60 (146)
-.||++++++++ |..||.|.+.--
T Consensus 9 v~iPk~~~~~l~-----l~~Gd~v~i~~~ 32 (47)
T PF04014_consen 9 VTIPKEIREKLG-----LKPGDEVEIEVE 32 (47)
T ss_dssp EEE-HHHHHHTT-----SSTTTEEEEEEE
T ss_pred EECCHHHHHHcC-----CCCCCEEEEEEe
Confidence 468999999984 566999998754
No 58
>PF02699 YajC: Preprotein translocase subunit; InterPro: IPR003849 Secretion across the inner membrane in some Gram-negative bacteria occurs via the preprotein translocase pathway. Proteins are produced in the cytoplasm as precursors, and require a chaperone subunit to direct them to the translocase component []. From there, the mature proteins are either targeted to the outer membrane, or remain as periplasmic proteins []. The translocase protein subunits are encoded on the bacterial chromosome. The translocase itself comprises 7 proteins, including a chaperone (SecB), ATPase (SecA), an integral membrane complex (SecY, SecE and SecG), and two additional membrane proteins that promote the release of the mature peptide into the periplasm (SecD and SecF) []. Other cytoplasmic/periplasmic proteins play a part in preprotein translocase activity, namely YidC and YajC []. The latter is bound in a complex to SecD and SecF, and plays a part in stabilising and regulating secretion through the SecYEG integral membrane component via SecA []. Homologues of the YajC gene have been found in a range of pathogenic and commensal microbes. Brucella abortis YajC- and SecD-like proteins were shown to stimulate a Th1 cell-mediated immune response in mice, and conferred protection when challenged with B.abortis []. Therefore, these proteins may have an antigenic role as well as a secretory one in virulent bacteria []. A number of previously uncharacterised "hypothetical" proteins also show similarity to E.coli YajC, suggesting that this family is wider than first thought []. More recently, the precise interactions between the E.coli SecYEG complex, SecD, SecF, YajC and YidC have been studied []. Rather than acting individually, the four proteins form a heterotetrameric complex and associate with the SecYEG heterotrimeric complex []. The SecF and YajC subunits link the complex to the integral membrane translocase. ; PDB: 2RDD_B.
Probab=56.82 E-value=3.6 Score=28.80 Aligned_cols=29 Identities=28% Similarity=0.470 Sum_probs=0.0
Q ss_pred ceecCCEEEEeecCCCCeEeeEEEEEecCCEEEEe
Q 032182 48 PVRKDDEVQVVRGTYKGREGKVVQVYRRKWVIHIE 82 (146)
Q Consensus 48 ~IkkGD~V~Vi~G~~KGk~GkV~~V~~k~~~V~VE 82 (146)
.+++||+|.-.+|= .|+|.++ +++.|.||
T Consensus 36 ~Lk~Gd~VvT~gGi----~G~V~~i--~~~~v~le 64 (82)
T PF02699_consen 36 SLKPGDEVVTIGGI----YGTVVEI--DDDTVVLE 64 (82)
T ss_dssp -----------------------------------
T ss_pred cCCCCCEEEECCcE----EEEEEEE--eCCEEEEE
Confidence 57999999988865 7999999 45667776
No 59
>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=56.48 E-value=11 Score=26.15 Aligned_cols=42 Identities=12% Similarity=0.231 Sum_probs=30.1
Q ss_pred eeccCCHHHHhhhCCcccceecCCEEEEeecCCCCeEeeEEEEEecC
Q 032182 30 MSAPLSTDLRQKYNVRSMPVRKDDEVQVVRGTYKGREGKVVQVYRRK 76 (146)
Q Consensus 30 msa~Ls~eLr~ky~~rs~~IkkGD~V~Vi~G~~KGk~GkV~~V~~k~ 76 (146)
.-+++|--+|. .+.|+.||.|.|--=++--..|.|+..+...
T Consensus 25 ~la~i~gK~rk-----~iwI~~GD~V~Ve~~~~d~~kg~Iv~r~~~~ 66 (77)
T cd05793 25 RLCRIRGKMRK-----RVWINEGDIVLVAPWDFQDDKADIIYKYTPD 66 (77)
T ss_pred EEEEEchhhcc-----cEEEcCCCEEEEEeccccCCEEEEEEEcCHH
Confidence 34667766663 3889999999995445555678888877643
No 60
>KOG4315 consensus G-patch nucleic acid binding protein [General function prediction only]
Probab=55.31 E-value=5 Score=36.65 Aligned_cols=38 Identities=26% Similarity=0.308 Sum_probs=32.7
Q ss_pred cceecCCEEEEeecCCCCeEeeEEEEEecCCEEEEeee
Q 032182 47 MPVRKDDEVQVVRGTYKGREGKVVQVYRRKWVIHIERI 84 (146)
Q Consensus 47 ~~IkkGD~V~Vi~G~~KGk~GkV~~V~~k~~~V~VEgi 84 (146)
++=.-|+.|.|++|+++|+.|-.+.=+..+.+..|..+
T Consensus 392 ~pr~~Ge~vmvv~gkhkg~~g~llskd~~Ke~~~v~~~ 429 (455)
T KOG4315|consen 392 LPRRGGEKVMVVSGKHKGVYGSLLSKDLDKETGVVRLV 429 (455)
T ss_pred cccccCceeEEEecccccchhhhhhhhhhhhhcceecc
Confidence 45578999999999999999999999988888877644
No 61
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=55.16 E-value=39 Score=21.41 Aligned_cols=34 Identities=21% Similarity=0.195 Sum_probs=24.1
Q ss_pred ceecCCEEEEeecCCCCe-EeeEEEEEecCCEEEEe
Q 032182 48 PVRKDDEVQVVRGTYKGR-EGKVVQVYRRKWVIHIE 82 (146)
Q Consensus 48 ~IkkGD~V~Vi~G~~KGk-~GkV~~V~~k~~~V~VE 82 (146)
.+++||.|.|..=.+.+= .|+|+++.. .++..|.
T Consensus 2 ~~~~G~~Ve~~~~~~~~W~~a~V~~~~~-~~~~~V~ 36 (61)
T smart00743 2 DFKKGDRVEVFSKEEDSWWEAVVTKVLG-DGKYLVR 36 (61)
T ss_pred CcCCCCEEEEEECCCCEEEEEEEEEECC-CCEEEEE
Confidence 478999999997443332 699999998 3344444
No 62
>PTZ00118 40S ribosomal protein S4; Provisional
Probab=54.57 E-value=23 Score=30.34 Aligned_cols=55 Identities=22% Similarity=0.309 Sum_probs=39.1
Q ss_pred ccceecCCEEEEeecCCCCeEeeEEEEEecC---CEEEEeeeeEEeeCCcEEEeeccccceEEEc
Q 032182 46 SMPVRKDDEVQVVRGTYKGREGKVVQVYRRK---WVIHIERITREKVNGSTVNVGINPSKVVITK 107 (146)
Q Consensus 46 s~~IkkGD~V~Vi~G~~KGk~GkV~~V~~k~---~~V~VEgin~~K~~G~~~e~pIh~SNv~i~~ 107 (146)
-+++..|..|.|+.|..-|..|+|..+.... +.|.||+ ++|..++ ...+||.++.
T Consensus 172 ~ikfe~G~l~~vtgG~n~GriG~I~~~~~~~~~~~~V~i~d-----~~g~~F~--T~~~~vfvIG 229 (262)
T PTZ00118 172 FLKFEVGNLVMITGGHNVGRVGTIVSKEKHPGSFDLIHVKD-----SRGKTFA--TRLSNVFVIG 229 (262)
T ss_pred EEecCCCCEEEEECCeeceeEEEEEEEEecCCCCcEEEEEe-----CCCCeEE--EEeeeEEEEc
Confidence 3789999999999999999999999866543 3466653 3454433 2345666664
No 63
>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed
Probab=52.21 E-value=21 Score=34.53 Aligned_cols=38 Identities=18% Similarity=0.343 Sum_probs=27.8
Q ss_pred cceecCCEEEEeecCCCCeEeeEEEEEecC-CEEEEeeeeEE
Q 032182 47 MPVRKDDEVQVVRGTYKGREGKVVQVYRRK-WVIHIERITRE 87 (146)
Q Consensus 47 ~~IkkGD~V~Vi~G~~KGk~GkV~~V~~k~-~~V~VEgin~~ 87 (146)
..++.||.|.|.+ -|+.|+|++|..++ ..|.+.++.+.
T Consensus 635 ~~~~~Gd~V~v~~---~~~~g~v~~i~~~~~~~V~~g~~k~~ 673 (782)
T PRK00409 635 EELKVGDEVKYLS---LGQKGEVLSIPDDKEAIVQAGIMKMK 673 (782)
T ss_pred cCCCCCCEEEEcc---CCceEEEEEEcCCCeEEEEECCEEEE
Confidence 4589999999966 56789999997532 34555566554
No 64
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=51.97 E-value=16 Score=25.76 Aligned_cols=41 Identities=17% Similarity=0.312 Sum_probs=29.7
Q ss_pred eccCCHHHHhhhCCcccceecCCEEEEeecCCCCeEeeEEEEEecC
Q 032182 31 SAPLSTDLRQKYNVRSMPVRKDDEVQVVRGTYKGREGKVVQVYRRK 76 (146)
Q Consensus 31 sa~Ls~eLr~ky~~rs~~IkkGD~V~Vi~G~~KGk~GkV~~V~~k~ 76 (146)
-+++|--+|. .+.|+.||.|.|---++--..|.|+.+..+.
T Consensus 31 la~ipgK~Rk-----~iwI~~GD~VlVe~~~~~~~kg~Iv~r~~~~ 71 (83)
T smart00652 31 LARIPGKMRK-----KVWIRRGDIVLVDPWDFQDVKADIIYKYTKD 71 (83)
T ss_pred EEEEchhhcc-----cEEEcCCCEEEEEecCCCCCEEEEEEEeCHH
Confidence 4667766663 4889999999997555544568888877643
No 65
>CHL00125 psaE photosystem I subunit IV; Reviewed
Probab=48.52 E-value=34 Score=23.55 Aligned_cols=28 Identities=21% Similarity=0.418 Sum_probs=23.2
Q ss_pred eecCCEEEEeecC--CCCeEeeEEEEEecC
Q 032182 49 VRKDDEVQVVRGT--YKGREGKVVQVYRRK 76 (146)
Q Consensus 49 IkkGD~V~Vi~G~--~KGk~GkV~~V~~k~ 76 (146)
|++||.|.|++-. +-...|+|..||...
T Consensus 2 i~rGskVrIlR~ESYWyn~vGtV~svd~~g 31 (64)
T CHL00125 2 VKRGSKVRILRKESYWYNEIGTVATVDQSG 31 (64)
T ss_pred cccCCEEEEccccceeecCcceEEEEcCCC
Confidence 7899999999865 445689999999963
No 66
>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=47.28 E-value=23 Score=24.73 Aligned_cols=42 Identities=14% Similarity=0.215 Sum_probs=29.5
Q ss_pred eeccCCHHHHhhhCCcccceecCCEEEEeecCC-CCeEeeEEEEEecC
Q 032182 30 MSAPLSTDLRQKYNVRSMPVRKDDEVQVVRGTY-KGREGKVVQVYRRK 76 (146)
Q Consensus 30 msa~Ls~eLr~ky~~rs~~IkkGD~V~Vi~G~~-KGk~GkV~~V~~k~ 76 (146)
.-+++|--+|. ++-|+.||.|.|-.=++ .-..|.|+.+....
T Consensus 25 ~l~~i~gK~Rk-----~iwI~~GD~VlV~~~~~~~~~kg~Iv~r~~~~ 67 (78)
T cd04456 25 RLVSIPGKLRK-----NIWIKRGDFLIVDPIEEGEDVKADIIFVYCKD 67 (78)
T ss_pred EEEEEchhhcc-----CEEEcCCCEEEEEecccCCCceEEEEEEeCHH
Confidence 33556655552 37899999999987666 34578888877654
No 67
>TIGR00523 eIF-1A eukaryotic/archaeal initiation factor 1A. Recommended nomenclature: eIF-1A for eukaryotes, aIF-1A for Archaea. Also called eIF-4C
Probab=46.78 E-value=14 Score=27.06 Aligned_cols=43 Identities=16% Similarity=0.242 Sum_probs=27.0
Q ss_pred eeeccCCHHHHhhhCCcccceecCCEEEEeecCCC-CeEeeEEEEEecC
Q 032182 29 LMSAPLSTDLRQKYNVRSMPVRKDDEVQVVRGTYK-GREGKVVQVYRRK 76 (146)
Q Consensus 29 ~msa~Ls~eLr~ky~~rs~~IkkGD~V~Vi~G~~K-Gk~GkV~~V~~k~ 76 (146)
..-|++|--+|. .+.|+.||.|.|-.=++- ...|.|+..+...
T Consensus 43 ~~la~i~GK~Rk-----~iwI~~GD~VlVsp~d~~~~~kg~Iv~r~~~~ 86 (99)
T TIGR00523 43 TRLGRIPGKLKK-----RIWIREGDVVIVKPWEFQGDDKCDIVWRYTKT 86 (99)
T ss_pred EEEEEEchhhcc-----cEEecCCCEEEEEEccCCCCccEEEEEEcCHH
Confidence 344667766663 488999999999211121 1258888776543
No 68
>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=46.36 E-value=23 Score=24.41 Aligned_cols=39 Identities=23% Similarity=0.379 Sum_probs=28.5
Q ss_pred eeeeccCCHHHHhhhCCcccceecCCEEEEeecCCCCeEeeEE
Q 032182 28 ILMSAPLSTDLRQKYNVRSMPVRKDDEVQVVRGTYKGREGKVV 70 (146)
Q Consensus 28 k~msa~Ls~eLr~ky~~rs~~IkkGD~V~Vi~G~~KGk~GkV~ 70 (146)
...-|++|--+|..+ +.|..||.|.|--=+|-=..|.|+
T Consensus 28 ~~vla~i~GKmr~~r----I~I~~GD~V~Ve~spyd~tkgrIi 66 (68)
T TIGR00008 28 HEVLAHISGKIRMHY----IRILPGDKVKVELSPYDLTRGRIT 66 (68)
T ss_pred CEEEEEecCcchhcc----EEECCCCEEEEEECcccCCcEeEE
Confidence 345578887777666 899999999997666654455554
No 69
>PLN00045 photosystem I reaction center subunit IV; Provisional
Probab=45.89 E-value=30 Score=25.67 Aligned_cols=31 Identities=23% Similarity=0.386 Sum_probs=25.6
Q ss_pred cccceecCCEEEEeecC--CCCeEeeEEEEEec
Q 032182 45 RSMPVRKDDEVQVVRGT--YKGREGKVVQVYRR 75 (146)
Q Consensus 45 rs~~IkkGD~V~Vi~G~--~KGk~GkV~~V~~k 75 (146)
.-+-+++||.|.|++-. +-...|+|..||..
T Consensus 36 p~ig~~RGskVrIlR~ESYWyn~vGtVvsVDq~ 68 (101)
T PLN00045 36 PPIGPKRGSKVKILRPESYWFNDVGKVVAVDQD 68 (101)
T ss_pred CCcccCCCCEEEEccccceeecCcceEEEEeCC
Confidence 34678999999999875 45668999999997
No 70
>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=45.40 E-value=55 Score=21.75 Aligned_cols=38 Identities=26% Similarity=0.234 Sum_probs=27.3
Q ss_pred eecCCEEEEeecC--CCCeEeeEEEEEecCCEEEEeeeeE
Q 032182 49 VRKDDEVQVVRGT--YKGREGKVVQVYRRKWVIHIERITR 86 (146)
Q Consensus 49 IkkGD~V~Vi~G~--~KGk~GkV~~V~~k~~~V~VEgin~ 86 (146)
|-+|-.|.|+.-. |-|-+|.|-+|.-.+--|..||=|.
T Consensus 2 ilPG~~V~V~n~~~~Y~~y~G~VQRvsdgkaaVLFEGGnW 41 (53)
T PF11623_consen 2 ILPGSTVRVKNPNDIYYGYEGFVQRVSDGKAAVLFEGGNW 41 (53)
T ss_dssp --TT-EEEE--TTSTTTT-EEEEEEEETTEEEEEEEETTE
T ss_pred ccCCCEEEEeCCCCccchheEEEEEeeCCeEEEEecCCCc
Confidence 6789999999764 7899999999999888899997554
No 71
>PRK05338 rplS 50S ribosomal protein L19; Provisional
Probab=45.26 E-value=98 Score=23.37 Aligned_cols=61 Identities=18% Similarity=0.155 Sum_probs=39.5
Q ss_pred ceecCCEEEEee---cCCCC----eEeeEEEEEecC--CEEEEeeeeEEeeCCcEEEeeccccceEEEcCCC
Q 032182 48 PVRKDDEVQVVR---GTYKG----REGKVVQVYRRK--WVIHIERITREKVNGSTVNVGINPSKVVITKLRL 110 (146)
Q Consensus 48 ~IkkGD~V~Vi~---G~~KG----k~GkV~~V~~k~--~~V~VEgin~~K~~G~~~e~pIh~SNv~i~~~~~ 110 (146)
.++.||.|.|-. ..+|. -+|.|+.+.... .+++|..+ ...-|-+.-.|+|..+|.=++.--
T Consensus 18 ~f~~GD~V~V~~~i~eg~k~R~q~f~GvvI~~~~~G~~~tftvRki--~~gvGVEr~fpl~SP~I~~IeV~r 87 (116)
T PRK05338 18 EFRPGDTVRVHVKVVEGNKERIQAFEGVVIARRGRGLNETFTVRKI--SYGVGVERTFPLHSPRIDSIEVVR 87 (116)
T ss_pred CcCCCCEEEEEEEEccCCceEeccEEEEEEEEeCCCCCceEEEEEc--ccCccEEEEecCCCCcccEEEEEE
Confidence 579999999843 22232 469999887643 35666654 112245777999998887555533
No 72
>PF15276 PP1_bind: Protein phosphatase 1 binding
Probab=44.89 E-value=17 Score=25.02 Aligned_cols=39 Identities=15% Similarity=0.187 Sum_probs=30.3
Q ss_pred cceeeeccCCHHHHhhhCCcccceecCCEEEEeecCCCC
Q 032182 26 RRILMSAPLSTDLRQKYNVRSMPVRKDDEVQVVRGTYKG 64 (146)
Q Consensus 26 r~k~msa~Ls~eLr~ky~~rs~~IkkGD~V~Vi~G~~KG 64 (146)
|+=-+..+||+||-.+.-.-+.++++|++=.--+.....
T Consensus 4 kRVsFG~~LSPElFD~~LPpnTPlkrG~tP~~~~~~~~~ 42 (64)
T PF15276_consen 4 KRVSFGEHLSPELFDKSLPPNTPLKRGATPVRRSDPSSS 42 (64)
T ss_pred ceeccCCCCCHHHhcccCCCCCCcCCCCCcccccCCCCC
Confidence 344578999999999999999999999986655544433
No 73
>COG3700 AphA Acid phosphatase (class B) [General function prediction only]
Probab=44.87 E-value=10 Score=31.66 Aligned_cols=40 Identities=20% Similarity=0.378 Sum_probs=33.6
Q ss_pred ccceecCCEEEEeecCCCCeEeeEEEEEecCCEEEEeeeeEE
Q 032182 46 SMPVRKDDEVQVVRGTYKGREGKVVQVYRRKWVIHIERITRE 87 (146)
Q Consensus 46 s~~IkkGD~V~Vi~G~~KGk~GkV~~V~~k~~~V~VEgin~~ 87 (146)
.|+.++||.|..++|.-.|+.-.|.+...+...+ .+.|-+
T Consensus 124 ~MHq~RGD~i~FvTGRt~gk~d~vsk~Lak~F~i--~~m~pv 163 (237)
T COG3700 124 DMHQRRGDAIYFVTGRTPGKTDTVSKTLAKNFHI--TNMNPV 163 (237)
T ss_pred HHHHhcCCeEEEEecCCCCcccccchhHHhhccc--CCCcce
Confidence 5789999999999999999999999999888766 444433
No 74
>COG1193 Mismatch repair ATPase (MutS family) [DNA replication, recombination, and repair]
Probab=43.42 E-value=25 Score=34.14 Aligned_cols=33 Identities=24% Similarity=0.397 Sum_probs=27.3
Q ss_pred ccceecCCEEEEeecCCCCeEeeEEEEEecCCEEEEe
Q 032182 46 SMPVRKDDEVQVVRGTYKGREGKVVQVYRRKWVIHIE 82 (146)
Q Consensus 46 s~~IkkGD~V~Vi~G~~KGk~GkV~~V~~k~~~V~VE 82 (146)
.-.++.||+|.|++ |..|.|++|..+.+.+.|+
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 45789999999999 7789999999766666665
No 75
>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=43.03 E-value=36 Score=22.51 Aligned_cols=36 Identities=17% Similarity=0.305 Sum_probs=21.4
Q ss_pred eccCCHHHHhhhCCcccceecCCEEEEeecCCCCeEeeEEE
Q 032182 31 SAPLSTDLRQKYNVRSMPVRKDDEVQVVRGTYKGREGKVVQ 71 (146)
Q Consensus 31 sa~Ls~eLr~ky~~rs~~IkkGD~V~Vi~G~~KGk~GkV~~ 71 (146)
-+.||-- +. +.+.|+.||.|.|---++--..|.|+.
T Consensus 29 l~~i~gK-~r----~~iwI~~GD~V~V~~~~~d~~kG~Ii~ 64 (65)
T PF01176_consen 29 LARIPGK-FR----KRIWIKRGDFVLVEPSPYDKVKGRIIY 64 (65)
T ss_dssp EEEE-HH-HH----TCC---TTEEEEEEESTTCTTEEEEEE
T ss_pred EEEeccc-ee----eeEecCCCCEEEEEecccCCCeEEEEE
Confidence 3555554 22 347899999999986666566787764
No 76
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=42.94 E-value=24 Score=25.88 Aligned_cols=41 Identities=15% Similarity=0.313 Sum_probs=29.3
Q ss_pred eeccCCHHHHhhhCCcccceecCCEEEEeecCCCCeEeeEEEEEec
Q 032182 30 MSAPLSTDLRQKYNVRSMPVRKDDEVQVVRGTYKGREGKVVQVYRR 75 (146)
Q Consensus 30 msa~Ls~eLr~ky~~rs~~IkkGD~V~Vi~G~~KGk~GkV~~V~~k 75 (146)
.-|++|--+|. .+.|+.||.|.|--=++--..|.|+..+..
T Consensus 46 ~la~i~GK~Rk-----~IwI~~GD~VlVe~~~~~~~kg~Iv~r~~~ 86 (100)
T PRK04012 46 RMGRIPGKMKK-----RMWIREGDVVIVAPWDFQDEKADIIWRYTK 86 (100)
T ss_pred EEEEEchhhcc-----cEEecCCCEEEEEecccCCCEEEEEEEcCH
Confidence 44667766664 378999999999754544557888887764
No 77
>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=42.90 E-value=36 Score=32.87 Aligned_cols=35 Identities=26% Similarity=0.565 Sum_probs=25.2
Q ss_pred ecCCEEEEeecCCCCeEeeEEEEEe-cCCEEEEeeeeEE
Q 032182 50 RKDDEVQVVRGTYKGREGKVVQVYR-RKWVIHIERITRE 87 (146)
Q Consensus 50 kkGD~V~Vi~G~~KGk~GkV~~V~~-k~~~V~VEgin~~ 87 (146)
+.||.|.|.+ -|..|+|+++.. +...|.+.++.+.
T Consensus 626 ~~Gd~V~v~~---~~~~g~v~~i~~~~~~~V~~g~~k~~ 661 (771)
T TIGR01069 626 KIGDKVRIRY---FGQKGKIVQILGGNKWNVTVGGMRMK 661 (771)
T ss_pred CCCCEEEEcc---CCceEEEEEEcCCCeEEEEECCEEEE
Confidence 8999999954 678899999974 2224555566554
No 78
>PF01245 Ribosomal_L19: Ribosomal protein L19; InterPro: IPR001857 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L19 is one of the proteins from the large ribosomal subunit [, ]. In Escherichia coli, L19 is known to be located at the 30S-50S ribosomal subunit interface [] and may play a role in the structure and function of the aminoacyl-tRNA binding site. It belongs to a family of ribosomal proteins, including L19 from bacteria and the chloroplasts of red algae. L19 is a protein of 120 to 130 amino-acid residues.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3HUZ_T 3V2D_T 3I8I_R 2XG2_T 2V49_T 2XUX_T 3HUX_T 3I9C_R 3V25_T 3UZ2_R ....
Probab=40.45 E-value=1e+02 Score=22.95 Aligned_cols=59 Identities=22% Similarity=0.222 Sum_probs=39.0
Q ss_pred ceecCCEEEEee---cCCCCe----EeeEEEEEecC--CEEEEeeeeEEeeCCcEEEeeccccceEEEcC
Q 032182 48 PVRKDDEVQVVR---GTYKGR----EGKVVQVYRRK--WVIHIERITREKVNGSTVNVGINPSKVVITKL 108 (146)
Q Consensus 48 ~IkkGD~V~Vi~---G~~KGk----~GkV~~V~~k~--~~V~VEgin~~K~~G~~~e~pIh~SNv~i~~~ 108 (146)
.++.||.|.|.. ...|.. +|.|+.+.... .+++|.++ ....|-+.-+|+|...|.-++.
T Consensus 18 ~f~~GD~v~V~~~i~e~~k~r~q~f~GvvIa~~~~g~~ssftlR~~--~~g~gVE~~f~l~SP~I~~IeV 85 (113)
T PF01245_consen 18 EFRVGDTVRVTYKISEGNKERIQVFEGVVIARRRRGLNSSFTLRNI--SQGVGVERVFPLYSPLIKSIEV 85 (113)
T ss_dssp SSSSSSEEEEEEEEESSSSEEEEEEEEEEEEEEBSSTSSEEEEEEE--ETTEEEEEEEETTSTTEEEEEE
T ss_pred CcCCCCEEEEEEEEecCCCceeEEEEEEEEEEECCCCCeeEEEEEE--ecCccEEEEEEcCCCCeEEEEE
Confidence 589999999964 233333 58888888753 35666544 1112346678999998876554
No 79
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=40.32 E-value=22 Score=25.82 Aligned_cols=43 Identities=16% Similarity=0.226 Sum_probs=32.5
Q ss_pred eeeeccCCHHHHhhhCCcccceecCCEEEEeecCCCCeEeeEEEEEe
Q 032182 28 ILMSAPLSTDLRQKYNVRSMPVRKDDEVQVVRGTYKGREGKVVQVYR 74 (146)
Q Consensus 28 k~msa~Ls~eLr~ky~~rs~~IkkGD~V~Vi~G~~KGk~GkV~~V~~ 74 (146)
..+-|++|--+|..+ +.|..||.|.|---+|-=..|.|+.-..
T Consensus 30 ~~vla~isGKmR~~r----IrIl~GD~V~VE~spYDltkGRIiyR~~ 72 (87)
T PRK12442 30 VEVGAYASGRMRKHR----IRILAGDRVTLELSPYDLTKGRINFRHK 72 (87)
T ss_pred CEEEEEeccceeeee----EEecCCCEEEEEECcccCCceeEEEEec
Confidence 445688887777766 8999999999987777666677765543
No 80
>COG1385 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=40.21 E-value=67 Score=26.83 Aligned_cols=50 Identities=14% Similarity=0.255 Sum_probs=38.2
Q ss_pred CCHHHHhhhCCcccceecCCEEEEeecCCCCeEeeEEEEEecCCEEEEeee
Q 032182 34 LSTDLRQKYNVRSMPVRKDDEVQVVRGTYKGREGKVVQVYRRKWVIHIERI 84 (146)
Q Consensus 34 Ls~eLr~ky~~rs~~IkkGD~V~Vi~G~~KGk~GkV~~V~~k~~~V~VEgi 84 (146)
|+.+ .-.|=.+-++++.||++.+..|.+.=-.++|.++..+.-.+.+...
T Consensus 20 l~~~-~~~Hl~~VlRl~~gd~l~l~~g~g~~~~a~i~~~~kk~~~~~i~~~ 69 (246)
T COG1385 20 LTGD-EAHHLKRVLRLKEGDELRLFDGSGGEFLAEITKIGKKEALLKIVEQ 69 (246)
T ss_pred ECch-hhhhHHheeecCCCCEEEEEeCCCcEEEEEEeecCCCceEEEEEee
Confidence 3444 6677677889999999999999876667789888887766655543
No 81
>PRK08577 hypothetical protein; Provisional
Probab=39.83 E-value=38 Score=25.16 Aligned_cols=28 Identities=18% Similarity=0.284 Sum_probs=22.4
Q ss_pred cCCHHHHhhhCCcccceecCCEEEEeecCCCCe
Q 032182 33 PLSTDLRQKYNVRSMPVRKDDEVQVVRGTYKGR 65 (146)
Q Consensus 33 ~Ls~eLr~ky~~rs~~IkkGD~V~Vi~G~~KGk 65 (146)
.+|+++|+++ .|+.||.|.+..-.++|.
T Consensus 16 ~ip~~~r~~l-----~~~~g~~~~~~~~~~~~~ 43 (136)
T PRK08577 16 TIPLEIREAL-----GIREGMYVLLIADTDKKE 43 (136)
T ss_pred EecHHHHHHc-----CcCCCCEEEEEEECCCCE
Confidence 5889999887 468899999987666664
No 82
>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=39.64 E-value=56 Score=21.45 Aligned_cols=24 Identities=4% Similarity=0.238 Sum_probs=19.7
Q ss_pred ceecCCEEEEeecCCCCeEeeEEEEEecCCEEEE
Q 032182 48 PVRKDDEVQVVRGTYKGREGKVVQVYRRKWVIHI 81 (146)
Q Consensus 48 ~IkkGD~V~Vi~G~~KGk~GkV~~V~~k~~~V~V 81 (146)
.++.||+|.+ +|+.+++++.++.+
T Consensus 46 ~~~vG~~v~~----------kV~~id~~~~~i~l 69 (71)
T cd05696 46 PFKAGTTHKA----------RIIGYSPMDGLLQL 69 (71)
T ss_pred ccCCCCEEEE----------EEEEEeCCCCEEEE
Confidence 4789999876 78999998888775
No 83
>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=39.42 E-value=61 Score=22.14 Aligned_cols=30 Identities=27% Similarity=0.327 Sum_probs=19.4
Q ss_pred ceecCCEEEEeecCCCCeEeeEEEEEecCC
Q 032182 48 PVRKDDEVQVVRGTYKGREGKVVQVYRRKW 77 (146)
Q Consensus 48 ~IkkGD~V~Vi~G~~KGk~GkV~~V~~k~~ 77 (146)
.|++|+.|.|+++..-=..|+|.++...+.
T Consensus 26 ~l~~g~~v~vlr~~~~~~~g~i~sl~~~~~ 55 (84)
T cd03692 26 KIKRNAKVRVLRNGEVIYEGKISSLKRFKD 55 (84)
T ss_pred EEeCCCEEEEEcCCCEEEEEEEEEEEEcCc
Confidence 578899999998741113566666665443
No 84
>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=39.27 E-value=46 Score=21.23 Aligned_cols=24 Identities=17% Similarity=0.151 Sum_probs=19.5
Q ss_pred ceecCCEEEEeecCCCCeEeeEEEEEecCCEEEE
Q 032182 48 PVRKDDEVQVVRGTYKGREGKVVQVYRRKWVIHI 81 (146)
Q Consensus 48 ~IkkGD~V~Vi~G~~KGk~GkV~~V~~k~~~V~V 81 (146)
.++.||.|.+ +|++++++++++.+
T Consensus 44 ~~~~Gd~v~~----------~v~~~d~~~~~i~l 67 (68)
T cd05707 44 RFKVGQLVKG----------KIVSIDPDNGRIEM 67 (68)
T ss_pred ccCCCCEEEE----------EEEEEeCCCCEEec
Confidence 3789999987 78888888877764
No 85
>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=39.26 E-value=55 Score=21.73 Aligned_cols=25 Identities=16% Similarity=0.254 Sum_probs=20.5
Q ss_pred ceecCCEEEEeecCCCCeEeeEEEEEecCCEEEEe
Q 032182 48 PVRKDDEVQVVRGTYKGREGKVVQVYRRKWVIHIE 82 (146)
Q Consensus 48 ~IkkGD~V~Vi~G~~KGk~GkV~~V~~k~~~V~VE 82 (146)
.++.||.|.+ +|+.+++++.+|.+.
T Consensus 46 ~~~vG~~v~~----------kV~~id~~~~~i~Ls 70 (73)
T cd05703 46 KFPIGQALKA----------KVVGVDKEHKLLRLS 70 (73)
T ss_pred hCCCCCEEEE----------EEEEEeCCCCEEEEE
Confidence 3689999865 799999999888764
No 86
>KOG1728 consensus 40S ribosomal protein S11 [Translation, ribosomal structure and biogenesis]
Probab=38.57 E-value=20 Score=28.45 Aligned_cols=26 Identities=31% Similarity=0.332 Sum_probs=21.1
Q ss_pred cccceeeeccCCHHHHhhhCCcccceecCCEEEE
Q 032182 24 SVRRILMSAPLSTDLRQKYNVRSMPVRKDDEVQV 57 (146)
Q Consensus 24 h~r~k~msa~Ls~eLr~ky~~rs~~IkkGD~V~V 57 (146)
..|.+-||+++|+-.| .|..||.|.|
T Consensus 101 ekrHkN~svh~SPcFr--------di~~gDiVtv 126 (156)
T KOG1728|consen 101 EKRHKNMSVHVSPCFR--------DIQEGDIVTV 126 (156)
T ss_pred HHhccCCccccchhhh--------ccccCCEEEE
Confidence 4578889999999743 3889999987
No 87
>COG2139 RPL21A Ribosomal protein L21E [Translation, ribosomal structure and biogenesis]
Probab=38.50 E-value=50 Score=24.49 Aligned_cols=44 Identities=30% Similarity=0.554 Sum_probs=31.8
Q ss_pred eccCCHHHHhhhCCcccceecCCEEEEeec----------CCCCeEeeEEEEEecCCEEEEe
Q 032182 31 SAPLSTDLRQKYNVRSMPVRKDDEVQVVRG----------TYKGREGKVVQVYRRKWVIHIE 82 (146)
Q Consensus 31 sa~Ls~eLr~ky~~rs~~IkkGD~V~Vi~G----------~~KGk~GkV~~V~~k~~~V~VE 82 (146)
.++||.-|+ +| +.||.|-|.-- .|-|++|.|.-+--..+.|.|.
T Consensus 23 ~~plsr~l~-ey-------~~Gd~V~I~IdpSv~kGmPh~rf~G~TG~Vvg~~g~ay~V~v~ 76 (98)
T COG2139 23 LSPLSRYLQ-EY-------KVGDKVHIDIDPSVHKGMPHPRFQGKTGTVVGVRGRAYKVEVY 76 (98)
T ss_pred CcchhhHHh-hc-------cCCCEEEEEeCcccccCCCCccccCcceEEEeccCCEEEEEEe
Confidence 455776554 33 89999987644 3789999999987776666665
No 88
>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=38.35 E-value=59 Score=20.63 Aligned_cols=25 Identities=20% Similarity=0.207 Sum_probs=19.9
Q ss_pred ceecCCEEEEeecCCCCeEeeEEEEEecCCEEEEe
Q 032182 48 PVRKDDEVQVVRGTYKGREGKVVQVYRRKWVIHIE 82 (146)
Q Consensus 48 ~IkkGD~V~Vi~G~~KGk~GkV~~V~~k~~~V~VE 82 (146)
.++.||.|.| +|++++++.+++.+.
T Consensus 44 ~~~~G~~i~v----------~v~~~d~~~~~i~ls 68 (70)
T cd05698 44 HFRVGQVVKV----------KVLSCDPEQQRLLLS 68 (70)
T ss_pred cccCCCEEEE----------EEEEEcCCCCEEEEE
Confidence 3788999988 688888887777653
No 89
>cd05697 S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 5 (hs5) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=37.17 E-value=72 Score=20.35 Aligned_cols=25 Identities=12% Similarity=0.173 Sum_probs=20.7
Q ss_pred ceecCCEEEEeecCCCCeEeeEEEEEecCCEEEEe
Q 032182 48 PVRKDDEVQVVRGTYKGREGKVVQVYRRKWVIHIE 82 (146)
Q Consensus 48 ~IkkGD~V~Vi~G~~KGk~GkV~~V~~k~~~V~VE 82 (146)
.++.||.+.+ +|+++++++.++.+.
T Consensus 44 ~~~~Gd~i~~----------~V~~id~~~~~i~ls 68 (69)
T cd05697 44 KFKPGLKVKC----------RVLSVEPERKRLVLT 68 (69)
T ss_pred cCCCCCEEEE----------EEEEEECCCCEEEEE
Confidence 4789999988 789999988888753
No 90
>KOG0171 consensus Mitochondrial inner membrane protease, subunit IMP1 [Posttranslational modification, protein turnover, chaperones]
Probab=36.47 E-value=50 Score=26.87 Aligned_cols=69 Identities=16% Similarity=0.127 Sum_probs=45.1
Q ss_pred ccCCCCcccceeeeccCCHHHHhhhCCcccceecCCEEEEeecCCCCe---EeeEEEEEecCCEEEEeeeeEEee
Q 032182 18 HFTAPSSVRRILMSAPLSTDLRQKYNVRSMPVRKDDEVQVVRGTYKGR---EGKVVQVYRRKWVIHIERITREKV 89 (146)
Q Consensus 18 ~~~Ap~h~r~k~msa~Ls~eLr~ky~~rs~~IkkGD~V~Vi~G~~KGk---~GkV~~V~~k~~~V~VEgin~~K~ 89 (146)
+|+-| .+..++.+.=|+++. ++-++.+-=..||-|.|.-|+-.+- ++-++.+.--.+.|.|+|=|..+.
T Consensus 62 ~f~~~--~~gDIVi~~sP~~~~-~~~cKRIva~eGD~v~v~~~~~~~n~~~e~~~~~i~VP~GhVfv~GDN~~nS 133 (176)
T KOG0171|consen 62 RFRKP--QVGDIVIAKSPPDPK-EHICKRIVAMEGDLVEVHDGPLVVNDLVEKFSTPIRVPEGHVFVEGDNRNNS 133 (176)
T ss_pred hhcCC--CCCCEEEEeCCCCch-hhhhheeeccCCceEEEecCCcccchhhhhccceeeccCceEEEecCCCCCc
Confidence 44444 344455554444433 3446666677899999999987654 444455666678999999988764
No 91
>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=36.23 E-value=80 Score=20.11 Aligned_cols=25 Identities=28% Similarity=0.339 Sum_probs=20.1
Q ss_pred ceecCCEEEEeecCCCCeEeeEEEEEecCCEEEEe
Q 032182 48 PVRKDDEVQVVRGTYKGREGKVVQVYRRKWVIHIE 82 (146)
Q Consensus 48 ~IkkGD~V~Vi~G~~KGk~GkV~~V~~k~~~V~VE 82 (146)
.++.||.|.| +|+++++..+++.++
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 3699999988 588888888887765
No 92
>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=36.04 E-value=59 Score=21.08 Aligned_cols=24 Identities=13% Similarity=0.279 Sum_probs=19.4
Q ss_pred ceecCCEEEEeecCCCCeEeeEEEEEecCCEEEE
Q 032182 48 PVRKDDEVQVVRGTYKGREGKVVQVYRRKWVIHI 81 (146)
Q Consensus 48 ~IkkGD~V~Vi~G~~KGk~GkV~~V~~k~~~V~V 81 (146)
.++.||+|.+ +|+.+++++.+|.+
T Consensus 42 ~~~~G~~i~~----------kVi~id~~~~~i~L 65 (66)
T cd05695 42 TYKEGQKVRA----------RILYVDPSTKVVGL 65 (66)
T ss_pred CcCCCCEEEE----------EEEEEeCCCCEEec
Confidence 3688998876 89999998877654
No 93
>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=35.99 E-value=54 Score=26.92 Aligned_cols=28 Identities=39% Similarity=0.334 Sum_probs=15.7
Q ss_pred cceecCCEEEEe-ecCCCCeEeeEEEEEe
Q 032182 47 MPVRKDDEVQVV-RGTYKGREGKVVQVYR 74 (146)
Q Consensus 47 ~~IkkGD~V~Vi-~G~~KGk~GkV~~V~~ 74 (146)
-.|+.||.|.+. .+......-+|+.|..
T Consensus 104 ~~V~~Gd~v~~~~~~~~~~~~~~V~~v~~ 132 (217)
T PF01079_consen 104 SDVRVGDCVLVSDEGGGKLRPSRVVRVST 132 (217)
T ss_dssp GG--TT-EEEEE-TTT--EEEEEEEEEEE
T ss_pred hhCCCCCEEEEEEcCCCcEEEEEEEEEEE
Confidence 368999999993 4444445577777754
No 94
>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=34.88 E-value=26 Score=26.90 Aligned_cols=24 Identities=29% Similarity=0.569 Sum_probs=16.8
Q ss_pred ceecCCEEEEeecCCCCeEeeEEEEEecC
Q 032182 48 PVRKDDEVQVVRGTYKGREGKVVQVYRRK 76 (146)
Q Consensus 48 ~IkkGD~V~Vi~G~~KGk~GkV~~V~~k~ 76 (146)
+++.||.|+|= |..|.|.+|....
T Consensus 60 pf~vGD~I~i~-----~~~G~V~~I~l~~ 83 (206)
T PF00924_consen 60 PFKVGDRIEIG-----GVEGRVEEIGLRS 83 (206)
T ss_dssp SS-TT-EEESS-----S-EEEEEEE-SSE
T ss_pred CccCCCEEEEE-----EeehHHHhcCcce
Confidence 78999999885 8899999997753
No 95
>TIGR01448 recD_rel helicase, putative, RecD/TraA family. This model describes a family similar to RecD, the exodeoxyribonuclease V alpha chain of TIGR01447. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD.
Probab=34.63 E-value=1.1e+02 Score=29.37 Aligned_cols=37 Identities=22% Similarity=0.335 Sum_probs=27.6
Q ss_pred ccceecCCEEEEeecC-----CCCeEeeEEEEEecC----CEEEEe
Q 032182 46 SMPVRKDDEVQVVRGT-----YKGREGKVVQVYRRK----WVIHIE 82 (146)
Q Consensus 46 s~~IkkGD~V~Vi~G~-----~KGk~GkV~~V~~k~----~~V~VE 82 (146)
...++.||.|..+.=. +-|-.|.|+.++... ..+.|+
T Consensus 584 ~~~~~~GDkVm~~~N~~~~~v~NGdiG~I~~i~~~~~~~~~~i~v~ 629 (720)
T TIGR01448 584 EGEYRKGDRVMQTKNDYNNEIFNGDLGMIVKIEGAKQGKKDQVVVD 629 (720)
T ss_pred CceecCCCEEEEeeecchhccccCCeeEEEeccccccCCCceEEEE
Confidence 4578999999998654 568899999997743 345554
No 96
>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=34.14 E-value=49 Score=22.58 Aligned_cols=33 Identities=15% Similarity=0.427 Sum_probs=23.9
Q ss_pred eecCCEEEEeecC--CCCeEeeEEEEEecC--CEEEE
Q 032182 49 VRKDDEVQVVRGT--YKGREGKVVQVYRRK--WVIHI 81 (146)
Q Consensus 49 IkkGD~V~Vi~G~--~KGk~GkV~~V~~k~--~~V~V 81 (146)
|.+|+.|.|++=. +-...|+|..||... +-|+|
T Consensus 1 i~rgskVrIlR~ESYWyn~vGtV~svdqs~i~YPV~V 37 (61)
T PF02427_consen 1 IKRGSKVRILRKESYWYNEVGTVASVDQSGIRYPVVV 37 (61)
T ss_dssp S-TTSEEEE-SSSSTTTTSEEEEEEETTSSSSSSEEE
T ss_pred CCCCCEEEEccccceeecccceEEEEccCCccccEEE
Confidence 5789999999865 557789999999874 33544
No 97
>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=34.06 E-value=73 Score=21.23 Aligned_cols=25 Identities=24% Similarity=0.240 Sum_probs=19.8
Q ss_pred ceecCCEEEEeecCCCCeEeeEEEEEecCCEEEEe
Q 032182 48 PVRKDDEVQVVRGTYKGREGKVVQVYRRKWVIHIE 82 (146)
Q Consensus 48 ~IkkGD~V~Vi~G~~KGk~GkV~~V~~k~~~V~VE 82 (146)
.++.||.|.| +|++++...+++.+.
T Consensus 58 ~~~~Gd~v~v----------kV~~id~~~~~i~ls 82 (83)
T cd04461 58 GFKKGQSVTA----------KVTSVDEEKQRFLLS 82 (83)
T ss_pred hcCCCCEEEE----------EEEEEcCCCCEEEEe
Confidence 3689999988 788888887877653
No 98
>cd03450 NodN NodN (nodulation factor N) contains a single hot dog fold similar to those of the peroxisomal Hydratase-Dehydrogenase-Epimerase (HDE) protein, and the fatty acid synthase beta subunit. Rhizobium and related species form nodules on the roots of their legume hosts, a symbiotic process that requires production of Nod factors, which are signal molecules involved in root hair deformation and meristematic cell division. The nodulation gene products, including NodN, are involved in producing the Nod factors, however the role played by NodN is unclear.
Probab=32.90 E-value=1.7e+02 Score=22.24 Aligned_cols=45 Identities=13% Similarity=0.113 Sum_probs=26.8
Q ss_pred ceecCCEEEEeecCCCCeEeeEEEEEecCCE-EEEeeeeEEeeCCcEEEeeccc
Q 032182 48 PVRKDDEVQVVRGTYKGREGKVVQVYRRKWV-IHIERITREKVNGSTVNVGINP 100 (146)
Q Consensus 48 ~IkkGD~V~Vi~G~~KGk~GkV~~V~~k~~~-V~VEgin~~K~~G~~~e~pIh~ 100 (146)
|+..||+|.+ .++|+++..+.+. +.|.==+.+.-.|...++++--
T Consensus 97 PV~~GDtl~~--------~~~V~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~ 142 (149)
T cd03450 97 PVPVGSRVRG--------RFTLLSVEELKGGGVQVTLEVTVEIEGEDKPACVAE 142 (149)
T ss_pred ceeCCcEEEE--------EEEEEEEEEcCCCeEEEEEEEEEEEeCCCCceEEEE
Confidence 6889999988 6689998887763 3332111122345555555443
No 99
>PRK11713 16S ribosomal RNA methyltransferase RsmE; Provisional
Probab=32.48 E-value=71 Score=25.91 Aligned_cols=48 Identities=15% Similarity=0.266 Sum_probs=32.4
Q ss_pred cCCHHHHhhhCCcccceecCCEEEEeecCCCCeEeeEEEEEecCCEEEE
Q 032182 33 PLSTDLRQKYNVRSMPVRKDDEVQVVRGTYKGREGKVVQVYRRKWVIHI 81 (146)
Q Consensus 33 ~Ls~eLr~ky~~rs~~IkkGD~V~Vi~G~~KGk~GkV~~V~~k~~~V~V 81 (146)
.|+.+ ...|=.+-++++.||.|.|..|...=-.|+|..++++.-.+.|
T Consensus 15 ~l~~~-~~~Hl~~VlR~~~Gd~i~v~~g~g~~~~~~i~~i~~~~~~~~i 62 (234)
T PRK11713 15 ILDGE-EAHHLVRVLRLKEGDELRLFDGDGGEYLAEITEIGKKEVELEI 62 (234)
T ss_pred EEChH-HHhHHHhhccCCCCCEEEEEeCCCCEEEEEEEEecCcEEEEEE
Confidence 45554 3355467789999999999988642235889888765444433
No 100
>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=32.35 E-value=76 Score=22.75 Aligned_cols=35 Identities=23% Similarity=0.279 Sum_probs=24.2
Q ss_pred cccceecCCEEEEeecC------------CCCeEeeEEEEEe-cCCEE
Q 032182 45 RSMPVRKDDEVQVVRGT------------YKGREGKVVQVYR-RKWVI 79 (146)
Q Consensus 45 rs~~IkkGD~V~Vi~G~------------~KGk~GkV~~V~~-k~~~V 79 (146)
..+-|++||.|.|+.-. .-|..|.+++|.- .++++
T Consensus 62 ~~~~V~~G~~V~i~~~~~~~~i~~~g~Al~~g~~G~~I~V~N~~s~k~ 109 (122)
T TIGR03170 62 PPWLVKRGDTVTVIARGGGLSVTTEGKALEDGAVGDQIRVRNLSSGKI 109 (122)
T ss_pred CccEEcCCCEEEEEEecCCEEEEEEEEEccccCCCCEEEEEECCCCCE
Confidence 34579999999998543 3477777777773 44544
No 101
>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=32.14 E-value=81 Score=19.41 Aligned_cols=24 Identities=33% Similarity=0.476 Sum_probs=18.4
Q ss_pred ceecCCEEEEeecCCCCeEeeEEEEEecCCEEEE
Q 032182 48 PVRKDDEVQVVRGTYKGREGKVVQVYRRKWVIHI 81 (146)
Q Consensus 48 ~IkkGD~V~Vi~G~~KGk~GkV~~V~~k~~~V~V 81 (146)
.++.||.|.| +|+++++.++++.+
T Consensus 44 ~~~~Gd~v~v----------~i~~vd~~~~~i~l 67 (68)
T cd05688 44 VVNVGDEVEV----------KVLKIDKERKRISL 67 (68)
T ss_pred EECCCCEEEE----------EEEEEECCCCEEec
Confidence 3799999988 57888877776654
No 102
>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=31.89 E-value=89 Score=21.94 Aligned_cols=40 Identities=18% Similarity=0.322 Sum_probs=28.3
Q ss_pred ccCCHHHHhhhCCcccceecCCEEEEeecCCCCe-EeeEEEEEecC
Q 032182 32 APLSTDLRQKYNVRSMPVRKDDEVQVVRGTYKGR-EGKVVQVYRRK 76 (146)
Q Consensus 32 a~Ls~eLr~ky~~rs~~IkkGD~V~Vi~G~~KGk-~GkV~~V~~k~ 76 (146)
+.+|.-+|. ++=|+.||-|.|-.-++-.+ .|.|+.+..+.
T Consensus 27 ~~iP~KfRk-----~iWIkrGd~VlV~p~~~~~kvkgeIv~i~~~~ 67 (78)
T cd05792 27 VSMPTKFRK-----NIWIKRGDFVLVEPIEEGDKVKAEIVKILTRD 67 (78)
T ss_pred EEechhhcc-----cEEEEeCCEEEEEecccCCceEEEEEEEECHH
Confidence 445544443 35599999999987776544 68998887754
No 103
>COG1153 FwdD Formylmethanofuran dehydrogenase subunit D [Energy production and conversion]
Probab=31.82 E-value=1.3e+02 Score=23.23 Aligned_cols=56 Identities=16% Similarity=0.197 Sum_probs=35.9
Q ss_pred ccCCHHHHhhhCCcccceecCCEEEEeecCCCCeEeeEEEEEecCCEEEEeeeeEEeeCC----cEEEeeccccceEEEc
Q 032182 32 APLSTDLRQKYNVRSMPVRKDDEVQVVRGTYKGREGKVVQVYRRKWVIHIERITREKVNG----STVNVGINPSKVVITK 107 (146)
Q Consensus 32 a~Ls~eLr~ky~~rs~~IkkGD~V~Vi~G~~KGk~GkV~~V~~k~~~V~VEgin~~K~~G----~~~e~pIh~SNv~i~~ 107 (146)
+-++++.-++ +-+..||.|+|.+-- +.|+|. .+.++ +.+.+|.-|--=++++
T Consensus 33 ~~inp~D~~~-----Lgv~EGD~VkVkse~---------------GeVVV~----Ak~~~~~~pG~vfiPmgpWaN~vi~ 88 (128)
T COG1153 33 CEINPEDMKQ-----LGVSEGDKVKVKSEF---------------GEVVVK----AKEADGVQPGMVFIPMGPWANVVID 88 (128)
T ss_pred EEECHHHHHH-----hCCCcCCeEEEEecC---------------ccEEEE----EeeCCCCCCCeEEecCCcccceeeC
Confidence 3455554333 457899999997632 345553 23222 5678898887777889
Q ss_pred CCCc
Q 032182 108 LRLD 111 (146)
Q Consensus 108 ~~~~ 111 (146)
++++
T Consensus 89 P~T~ 92 (128)
T COG1153 89 PDTD 92 (128)
T ss_pred CCCC
Confidence 9885
No 104
>cd04452 S1_IF2_alpha S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Eukaryotic and archaeal Initiation Factor 2 (e- and aIF2, respectively) are heterotrimeric proteins with three subunits (alpha, beta, and gamma). IF2 plays a crucial role in the process of translation initiation. The IF2 gamma subunit contains a GTP-binding site. The IF2 beta and gamma subunits together are thought to be responsible for binding methionyl-initiator tRNA. The ternary complex consisting of IF2, GTP, and the methionyl-initiator tRNA binds to the small subunit of the ribosome, as part of a pre-initiation complex that scans the mRNA to find the AUG start codon. The IF2-bound GTP is hydrolyzed to GDP when the methionyl-initiator tRNA binds the AUG start codon, at which time the IF2 is released with its bound GDP. The large ribosomal subunit then joins with the small subunit to c
Probab=31.71 E-value=1e+02 Score=19.68 Aligned_cols=24 Identities=29% Similarity=0.360 Sum_probs=18.3
Q ss_pred eecCCEEEEeecCCCCeEeeEEEEEecCCEEEEe
Q 032182 49 VRKDDEVQVVRGTYKGREGKVVQVYRRKWVIHIE 82 (146)
Q Consensus 49 IkkGD~V~Vi~G~~KGk~GkV~~V~~k~~~V~VE 82 (146)
++.||.|.| +|++++...+.+.+.
T Consensus 50 ~~~Gd~v~v----------kv~~~d~~~~~i~ls 73 (76)
T cd04452 50 VKVGRKEVV----------KVIRVDKEKGYIDLS 73 (76)
T ss_pred eCCCCEEEE----------EEEEEECCCCEEEEE
Confidence 699999988 577888776666553
No 105
>PF11717 Tudor-knot: RNA binding activity-knot of a chromodomain ; PDB: 2EKO_A 2RO0_A 2RNZ_A 1WGS_A 3E9G_A 3E9F_A 2K3X_A 2K3Y_A 2EFI_A 2F5K_F ....
Probab=31.33 E-value=69 Score=20.37 Aligned_cols=29 Identities=10% Similarity=0.071 Sum_probs=21.9
Q ss_pred eecCCEEEEeecCCCCeEeeEEEEEecCC
Q 032182 49 VRKDDEVQVVRGTYKGREGKVVQVYRRKW 77 (146)
Q Consensus 49 IkkGD~V~Vi~G~~KGk~GkV~~V~~k~~ 77 (146)
|..|+.|.+..+...-..++|+++..+.+
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 46899999999665566799999988663
No 106
>cd05791 S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. ScCSL4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In S. cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=31.27 E-value=63 Score=22.72 Aligned_cols=44 Identities=11% Similarity=0.047 Sum_probs=29.6
Q ss_pred ecCCEEEEeecCCCCeEeeEEEEEecCCEEEEeeeeEEeeCCcEEEeeccccceE
Q 032182 50 RKDDEVQVVRGTYKGREGKVVQVYRRKWVIHIERITREKVNGSTVNVGINPSKVV 104 (146)
Q Consensus 50 kkGD~V~Vi~G~~KGk~GkV~~V~~k~~~V~VEgin~~K~~G~~~e~pIh~SNv~ 104 (146)
++||.| .|+|++|......|-|-.++- .+-.....+-||.|++.
T Consensus 5 ~~GDiV----------ig~V~~v~~~~~~v~I~~v~~-~~l~~~~~g~l~~~dv~ 48 (92)
T cd05791 5 KVGSIV----------IARVTRINPRFAKVDILCVGG-RPLKESFRGVIRKEDIR 48 (92)
T ss_pred CCCCEE----------EEEEEEEcCCEEEEEEEEecC-eecCCCcccEEEHHHcc
Confidence 678887 589999988776666655541 11223456778888875
No 107
>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=30.88 E-value=1.7e+02 Score=21.15 Aligned_cols=43 Identities=12% Similarity=-0.053 Sum_probs=30.9
Q ss_pred cceecCCEEEEeecC--CCCeEeeEEEEEecC-CEEEEeeeeEEee
Q 032182 47 MPVRKDDEVQVVRGT--YKGREGKVVQVYRRK-WVIHIERITREKV 89 (146)
Q Consensus 47 ~~IkkGD~V~Vi~G~--~KGk~GkV~~V~~k~-~~V~VEgin~~K~ 89 (146)
..++.||-|.|.+.. ..-..|.|.++.... +...+.+.=...+
T Consensus 2 ~~~~vGD~V~v~~~~~~~~~~i~~I~~i~~~~~g~~~~~~~Wf~rP 47 (121)
T cd04717 2 LQYRVGDCVYVANPEDPSKPIIFRIERLWKDEDGEKFFFGCWFYRP 47 (121)
T ss_pred CEEECCCEEEEeCCCCCCCCEEEEEeEEEECCCCCEEEEEEEEeCh
Confidence 347899999999866 445589999998864 6666665544433
No 108
>PRK00276 infA translation initiation factor IF-1; Validated
Probab=30.85 E-value=45 Score=22.49 Aligned_cols=39 Identities=21% Similarity=0.313 Sum_probs=24.7
Q ss_pred eeeeccCCHHHHhhhCCcccceecCCEEEEeecCCCCeEeeEE
Q 032182 28 ILMSAPLSTDLRQKYNVRSMPVRKDDEVQVVRGTYKGREGKVV 70 (146)
Q Consensus 28 k~msa~Ls~eLr~ky~~rs~~IkkGD~V~Vi~G~~KGk~GkV~ 70 (146)
....++++--||.. .+.+..||.|.|---.+-...|.|+
T Consensus 30 ~~~~c~~~Gklr~~----~i~i~vGD~V~ve~~~~~~~~g~Iv 68 (72)
T PRK00276 30 HEVLAHISGKMRKN----YIRILPGDKVTVELSPYDLTKGRIT 68 (72)
T ss_pred CEEEEEEccceeeC----CcccCCCCEEEEEEcccCCCeEEEE
Confidence 45667777666632 3558999999997444444445554
No 109
>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=30.71 E-value=1e+02 Score=19.70 Aligned_cols=24 Identities=25% Similarity=0.242 Sum_probs=18.8
Q ss_pred eecCCEEEEeecCCCCeEeeEEEEEecCCEEEEe
Q 032182 49 VRKDDEVQVVRGTYKGREGKVVQVYRRKWVIHIE 82 (146)
Q Consensus 49 IkkGD~V~Vi~G~~KGk~GkV~~V~~k~~~V~VE 82 (146)
++.||.|.+ +|+++++++..+.+.
T Consensus 48 ~~~Gd~v~~----------~V~~~d~~~~~i~ls 71 (73)
T cd05706 48 FKKNDIVRA----------CVLSVDVPNKKIALS 71 (73)
T ss_pred cCCCCEEEE----------EEEEEeCCCCEEEEE
Confidence 688999877 788888877777654
No 110
>PRK10334 mechanosensitive channel MscS; Provisional
Probab=30.54 E-value=60 Score=27.49 Aligned_cols=24 Identities=29% Similarity=0.418 Sum_probs=20.1
Q ss_pred ceecCCEEEEeecCCCCeEeeEEEEEecC
Q 032182 48 PVRKDDEVQVVRGTYKGREGKVVQVYRRK 76 (146)
Q Consensus 48 ~IkkGD~V~Vi~G~~KGk~GkV~~V~~k~ 76 (146)
|++.||.|+| .|..|.|.+|....
T Consensus 129 pf~vGD~I~i-----~~~~G~V~~I~~r~ 152 (286)
T PRK10334 129 PFRAGEYVDL-----GGVAGTVLSVQIFS 152 (286)
T ss_pred CCCCCCEEEE-----CCEEEEEEEEEeEE
Confidence 6899999998 37899999987654
No 111
>cd01737 LSm16_N LSm16 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. LSm16 has, in addition to its N-terminal Sm-like domain, a C-terminal Yjef_N-type rossman fold domain of unknown function.
Probab=30.40 E-value=89 Score=21.38 Aligned_cols=31 Identities=23% Similarity=0.241 Sum_probs=26.3
Q ss_pred CCEEEEeecCCCCe-EeeEEEEEecCCEEEEe
Q 032182 52 DDEVQVVRGTYKGR-EGKVVQVYRRKWVIHIE 82 (146)
Q Consensus 52 GD~V~Vi~G~~KGk-~GkV~~V~~k~~~V~VE 82 (146)
|-.|-+--|++-|- +|.|.+|++...+|.+.
T Consensus 6 Gs~VSI~C~~~lGVyQG~i~~V~~~~qTI~l~ 37 (62)
T cd01737 6 GSIVSINCGETLGVYQGLVSAVDQESQTISLA 37 (62)
T ss_pred ceEEEEecCCceEEEEEEEEEeCccceEEEEe
Confidence 66788888888887 79999999999888775
No 112
>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=30.34 E-value=81 Score=22.53 Aligned_cols=39 Identities=18% Similarity=0.008 Sum_probs=25.1
Q ss_pred ccceecCCEEEE--eecCCCCeEeeEEEEEecCCEEEEeeee
Q 032182 46 SMPVRKDDEVQV--VRGTYKGREGKVVQVYRRKWVIHIERIT 85 (146)
Q Consensus 46 s~~IkkGD~V~V--i~G~~KGk~GkV~~V~~k~~~V~VEgin 85 (146)
.-..++||.|.. -.+..-|..|.|.+|.. .+.|+|-.-|
T Consensus 60 ~~~P~~Gdivv~~~~~~~~~GHVaIV~~v~~-~~~i~v~e~N 100 (124)
T PF05257_consen 60 GSTPQPGDIVVWDSGSGGGYGHVAIVESVND-GGTITVIEQN 100 (124)
T ss_dssp CS---TTEEEEEEECTTTTT-EEEEEEEE-T-TSEEEEEECS
T ss_pred CcccccceEEEeccCCCCCCCeEEEEEEECC-CCEEEEEECC
Confidence 346789999887 46667889999999944 4566665544
No 113
>cd05685 S1_Tex S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin expression. Tex has two functional domains, an N-terminal domain homologous to the Escherichia coli maltose repression protein, which is a poorly defined transcriptional factor, and a C-terminal S1 RNA-binding domain. Tex is found in prokaryotes, eukaryotes, and archaea.
Probab=29.91 E-value=87 Score=19.14 Aligned_cols=23 Identities=30% Similarity=0.384 Sum_probs=17.7
Q ss_pred eecCCEEEEeecCCCCeEeeEEEEEecCCEEEE
Q 032182 49 VRKDDEVQVVRGTYKGREGKVVQVYRRKWVIHI 81 (146)
Q Consensus 49 IkkGD~V~Vi~G~~KGk~GkV~~V~~k~~~V~V 81 (146)
++.||.|.| +|+++++..+++.+
T Consensus 45 ~~~Gd~v~v----------~i~~vd~~~~~i~l 67 (68)
T cd05685 45 VSVGDIVEV----------KVISIDEERGRISL 67 (68)
T ss_pred cCCCCEEEE----------EEEEEECCCCEEec
Confidence 689999988 57888877766643
No 114
>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=29.91 E-value=32 Score=24.65 Aligned_cols=19 Identities=37% Similarity=0.529 Sum_probs=14.8
Q ss_pred eecCCEEEEeecCCCCeEe
Q 032182 49 VRKDDEVQVVRGTYKGREG 67 (146)
Q Consensus 49 IkkGD~V~Vi~G~~KGk~G 67 (146)
+..||.|.|++|..-|..|
T Consensus 90 ~~~gd~vVv~~g~~~~~~g 108 (117)
T PF02887_consen 90 LKPGDKVVVVAGMPFGTPG 108 (117)
T ss_dssp S-TTSEEEEEEESSTTTTS
T ss_pred CCCCCEEEEEeCCCCCCCC
Confidence 7999999999996656555
No 115
>PF00575 S1: S1 RNA binding domain; InterPro: IPR003029 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The S1 domain was originally identified in ribosomal protein S1 but is found in a large number of RNA-associated proteins. The structure of the S1 RNA-binding domain from the Escherichia coli polynucleotide phosphorylase has been determined using NMR methods and consists of a five-stranded antiparallel beta barrel. Conserved residues on one face of the barrel and adjacent loops form the putative RNA-binding site []. The structure of the S1 domain is very similar to that of cold shock proteins. This suggests that they may both be derived from an ancient nucleic acid-binding protein []. More information about these proteins can be found at Protein of the Month: RNA Exosomes []. This entry does not include translation initiation factor IF-1 S1 domains.; GO: 0003723 RNA binding; PDB: 3L7Z_F 2JE6_I 2JEA_I 2JEB_I 1E3P_A 2Y0S_E 1WI5_A 2BH8_A 2CQO_A 2EQS_A ....
Probab=29.86 E-value=1.1e+02 Score=19.48 Aligned_cols=26 Identities=27% Similarity=0.317 Sum_probs=21.2
Q ss_pred cceecCCEEEEeecCCCCeEeeEEEEEecCCEEEEe
Q 032182 47 MPVRKDDEVQVVRGTYKGREGKVVQVYRRKWVIHIE 82 (146)
Q Consensus 47 ~~IkkGD~V~Vi~G~~KGk~GkV~~V~~k~~~V~VE 82 (146)
-.++.||.|.| +|++++++.+++.+.
T Consensus 47 ~~~~~G~~v~v----------~v~~vd~~~~~i~lS 72 (74)
T PF00575_consen 47 EVYKIGQTVRV----------KVIKVDKEKGRIRLS 72 (74)
T ss_dssp GTCETTCEEEE----------EEEEEETTTTEEEEE
T ss_pred cccCCCCEEEE----------EEEEEECCCCeEEEE
Confidence 45799999987 689999998888763
No 116
>cd04451 S1_IF1 S1_IF1: Translation Initiation Factor IF1, S1-like RNA-binding domain. IF1 contains an S1-like RNA-binding domain, which is found in a wide variety of RNA-associated proteins. Translation initiation includes a number of interrelated steps preceding the formation of the first peptide bond. In Escherichia coli, the initiation mechanism requires, in addition to mRNA, fMet-tRNA, and ribosomal subunits, the presence of three additional proteins (initiation factors IF1, IF2, and IF3) and at least one GTP molecule. The three initiation factors influence both the kinetics and the stability of ternary complex formation. IF1 is the smallest of the three factors. IF1 enhances the rate of 70S ribosome subunit association and dissociation and the interaction of 30S ribosomal subunit with IF2 and IF3. It stimulates 30S complex formation. In addition, by binding to the A-site of the 30S ribosomal subunit, IF1 may contribute to the fidelity of the selection of the initiation site of th
Probab=29.48 E-value=53 Score=21.27 Aligned_cols=37 Identities=22% Similarity=0.329 Sum_probs=21.5
Q ss_pred eeeccCCHHHHhhhCCcccceecCCEEEEeecCCCCeEeeE
Q 032182 29 LMSAPLSTDLRQKYNVRSMPVRKDDEVQVVRGTYKGREGKV 69 (146)
Q Consensus 29 ~msa~Ls~eLr~ky~~rs~~IkkGD~V~Vi~G~~KGk~GkV 69 (146)
...+.+.-.||. ...++..||.|.+-.-.+-+.+|.|
T Consensus 25 ~~~c~~rGklr~----~~~~~~vGD~V~~~~~~~~~~~g~I 61 (64)
T cd04451 25 EVLAHISGKMRM----NYIRILPGDRVKVELSPYDLTKGRI 61 (64)
T ss_pred EEEEEECceeec----CCcccCCCCEEEEEEeecCCCEEEE
Confidence 445555554542 2456899999988754333334544
No 117
>PRK07018 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=29.35 E-value=76 Score=25.94 Aligned_cols=34 Identities=18% Similarity=0.219 Sum_probs=25.2
Q ss_pred ccceecCCEEEEeecC------------CCCeEeeEEEEE-ecCCEE
Q 032182 46 SMPVRKDDEVQVVRGT------------YKGREGKVVQVY-RRKWVI 79 (146)
Q Consensus 46 s~~IkkGD~V~Vi~G~------------~KGk~GkV~~V~-~k~~~V 79 (146)
-+-|++||.|.|+... .-|..|..++|. ..++++
T Consensus 174 ~~~V~~G~~V~i~~~~g~~~i~~~G~Al~~G~~Gd~IrVrN~~Sgk~ 220 (235)
T PRK07018 174 AWVVCKGQTVSIIARGDGFSVKTEGEALNDGAVGQQIRVRNMASGQV 220 (235)
T ss_pred ccEeCCCCEEEEEEecCCEEEEEEEEEcCCCCCCCeEEEEECCCCCE
Confidence 4679999999999654 447778888887 555554
No 118
>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=29.29 E-value=88 Score=20.88 Aligned_cols=23 Identities=17% Similarity=0.296 Sum_probs=18.8
Q ss_pred eecCCEEEEeecCCCCeEeeEEEEEecCCEEEE
Q 032182 49 VRKDDEVQVVRGTYKGREGKVVQVYRRKWVIHI 81 (146)
Q Consensus 49 IkkGD~V~Vi~G~~KGk~GkV~~V~~k~~~V~V 81 (146)
++.||.|.+ +|++|+++++++.+
T Consensus 51 ~~~G~~v~~----------kVl~id~~~~~i~L 73 (74)
T cd05705 51 LPEGKLLTA----------KVLSVNSEKNLVEL 73 (74)
T ss_pred cCCCCEEEE----------EEEEEECCCCEEec
Confidence 689999865 79999998887754
No 119
>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=28.84 E-value=71 Score=19.24 Aligned_cols=17 Identities=18% Similarity=0.384 Sum_probs=12.5
Q ss_pred ccceecCCEEEEeecCC
Q 032182 46 SMPVRKDDEVQVVRGTY 62 (146)
Q Consensus 46 s~~IkkGD~V~Vi~G~~ 62 (146)
.+.+++||.+.|+.=.+
T Consensus 13 eLs~~~Gd~i~v~~~~~ 29 (48)
T PF00018_consen 13 ELSFKKGDIIEVLEKSD 29 (48)
T ss_dssp BSEB-TTEEEEEEEESS
T ss_pred EEeEECCCEEEEEEecC
Confidence 47799999999986443
No 120
>TIGR01439 lp_hng_hel_AbrB looped-hinge helix DNA binding domain, AbrB family. This DNA-binding domain family includes AbrB, a transition state regulator in Bacillus subtilis, whose DNA-binding domain structure in solution was determined by NMR. The domain binds DNA as a dimer in what is termed a looped-hinge helix fold. Some members of the family have two copies of the domain in tandem. The domain is found usually at the N-terminus of a small protein. This model excludes members of family TIGR02609.
Probab=28.77 E-value=71 Score=18.47 Aligned_cols=26 Identities=19% Similarity=0.470 Sum_probs=19.7
Q ss_pred eccCCHHHHhhhCCcccceecCCEEEEeecC
Q 032182 31 SAPLSTDLRQKYNVRSMPVRKDDEVQVVRGT 61 (146)
Q Consensus 31 sa~Ls~eLr~ky~~rs~~IkkGD~V~Vi~G~ 61 (146)
.-.||.++|+.+ .+..||.+.+....
T Consensus 8 ri~iP~~~r~~l-----~~~~gd~~~i~~~~ 33 (43)
T TIGR01439 8 QIVIPKEIREKL-----GLKEGDRLEVIRVE 33 (43)
T ss_pred eEEecHHHHHHc-----CcCCCCEEEEEEeC
Confidence 346888888876 56789999988653
No 121
>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=28.27 E-value=44 Score=20.80 Aligned_cols=13 Identities=23% Similarity=0.572 Sum_probs=10.0
Q ss_pred ccceecCCEEEEe
Q 032182 46 SMPVRKDDEVQVV 58 (146)
Q Consensus 46 s~~IkkGD~V~Vi 58 (146)
.+.+.+||.|.|+
T Consensus 15 ~Ls~~~Gd~i~v~ 27 (55)
T PF07653_consen 15 ELSFKKGDVIEVL 27 (55)
T ss_dssp B-EB-TTEEEEEE
T ss_pred ceEEecCCEEEEE
Confidence 3789999999999
No 122
>PRK08515 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=28.12 E-value=87 Score=25.58 Aligned_cols=34 Identities=26% Similarity=0.323 Sum_probs=25.2
Q ss_pred ccceecCCEEEEeecC------------CCCeEeeEEEEEecCCEE
Q 032182 46 SMPVRKDDEVQVVRGT------------YKGREGKVVQVYRRKWVI 79 (146)
Q Consensus 46 s~~IkkGD~V~Vi~G~------------~KGk~GkV~~V~~k~~~V 79 (146)
-+-|++||.|.|+.-. .-|..|.+++|--.++++
T Consensus 163 ~~lV~rGd~V~i~~~~gg~~I~~~G~Al~~G~~Gd~IrVrN~Sgki 208 (222)
T PRK08515 163 LILVRKNDIINGVLKEGGVSIEISLKALQDGNLGDIIQAKNKSNKI 208 (222)
T ss_pred cceEecCCEEEEEEECCCEEEEEEEEEcccCCCCCEEEEEeCCCCE
Confidence 4579999999998654 447788888887755544
No 123
>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=27.41 E-value=99 Score=18.29 Aligned_cols=23 Identities=39% Similarity=0.398 Sum_probs=16.9
Q ss_pred ceecCCEEEEeecCCCCeEeeEEEEEecCCEEE
Q 032182 48 PVRKDDEVQVVRGTYKGREGKVVQVYRRKWVIH 80 (146)
Q Consensus 48 ~IkkGD~V~Vi~G~~KGk~GkV~~V~~k~~~V~ 80 (146)
.++.||.|.+ +|+++++..+.+.
T Consensus 41 ~~~~G~~v~~----------~v~~~d~~~~~i~ 63 (65)
T cd00164 41 VFKVGDEVEV----------KVLEVDPEKGRIS 63 (65)
T ss_pred EeCCCCEEEE----------EEEEEcCCcCEEe
Confidence 3799999977 6777777666654
No 124
>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=27.24 E-value=90 Score=26.03 Aligned_cols=32 Identities=28% Similarity=0.315 Sum_probs=24.2
Q ss_pred ccceecCCEEEEeecCCCCeEeeEEEEEecCCEE
Q 032182 46 SMPVRKDDEVQVVRGTYKGREGKVVQVYRRKWVI 79 (146)
Q Consensus 46 s~~IkkGD~V~Vi~G~~KGk~GkV~~V~~k~~~V 79 (146)
+..+-.||.|.+-.-. +..|.|.+|.+.++.+
T Consensus 32 ~~~~~vGD~V~~~~~~--~~~~~i~~i~~R~~~l 63 (287)
T cd01854 32 GIKPVVGDWVEVEPDD--DGEGVIVRVLPRKNLL 63 (287)
T ss_pred CCCccCCCEEEEEecC--CCcEEEEEEECCCceE
Confidence 4568999999986422 4579999999887754
No 125
>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=27.21 E-value=64 Score=18.58 Aligned_cols=16 Identities=19% Similarity=0.466 Sum_probs=13.2
Q ss_pred ccceecCCEEEEeecC
Q 032182 46 SMPVRKDDEVQVVRGT 61 (146)
Q Consensus 46 s~~IkkGD~V~Vi~G~ 61 (146)
.+.+.+||.|.|+...
T Consensus 15 ~l~~~~Gd~v~v~~~~ 30 (54)
T cd00174 15 ELSFKKGDIIEVLEKS 30 (54)
T ss_pred CCCCCCCCEEEEEEcC
Confidence 4678999999999773
No 126
>CHL00010 infA translation initiation factor 1
Probab=26.64 E-value=97 Score=21.31 Aligned_cols=43 Identities=21% Similarity=0.337 Sum_probs=26.6
Q ss_pred eeeeccCCHHHHhhhCCcccceecCCEEEEeecCCCCeEeeEEEEEe
Q 032182 28 ILMSAPLSTDLRQKYNVRSMPVRKDDEVQVVRGTYKGREGKVVQVYR 74 (146)
Q Consensus 28 k~msa~Ls~eLr~ky~~rs~~IkkGD~V~Vi~G~~KGk~GkV~~V~~ 74 (146)
....++++--||. +.+.+..||.|.|--=.+-...|.|+.=+.
T Consensus 30 ~~~~c~~rGklr~----~~i~~~vGD~V~ve~~~~~~~~g~Ii~r~~ 72 (78)
T CHL00010 30 CQVLGYISGKIRR----NSIRILPGDRVKVELSPYDLTKGRIIYRLR 72 (78)
T ss_pred CEEEEEeccceec----CCcccCCCCEEEEEEcccCCCeEEEEEEec
Confidence 3556666666552 357789999999974333344566654433
No 127
>cd05690 S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 5 (ec5) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=26.45 E-value=1.1e+02 Score=19.11 Aligned_cols=23 Identities=22% Similarity=0.221 Sum_probs=18.4
Q ss_pred ceecCCEEEEeecCCCCeEeeEEEEEecCCEEE
Q 032182 48 PVRKDDEVQVVRGTYKGREGKVVQVYRRKWVIH 80 (146)
Q Consensus 48 ~IkkGD~V~Vi~G~~KGk~GkV~~V~~k~~~V~ 80 (146)
.++.||.|.| +|+.|++++.++.
T Consensus 45 ~~~~G~~v~v----------~v~~id~~~~~i~ 67 (69)
T cd05690 45 IYKKGQEVEA----------VVLNIDVERERIS 67 (69)
T ss_pred EECCCCEEEE----------EEEEEECCcCEEe
Confidence 3699999998 4888888877764
No 128
>PRK11509 hydrogenase-1 operon protein HyaE; Provisional
Probab=26.37 E-value=71 Score=24.46 Aligned_cols=29 Identities=17% Similarity=0.308 Sum_probs=23.3
Q ss_pred cCCHHHHhhhCCcccc----eecCCEEEEeecC
Q 032182 33 PLSTDLRQKYNVRSMP----VRKDDEVQVVRGT 61 (146)
Q Consensus 33 ~Ls~eLr~ky~~rs~~----IkkGD~V~Vi~G~ 61 (146)
--.++|..+||++++| ++-|..|-.+.|-
T Consensus 78 D~~~~LA~~fgV~siPTLl~FkdGk~v~~i~G~ 110 (132)
T PRK11509 78 EQSEAIGDRFGVFRFPATLVFTGGNYRGVLNGI 110 (132)
T ss_pred CCCHHHHHHcCCccCCEEEEEECCEEEEEEeCc
Confidence 3568899999999997 6778777777773
No 129
>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=26.23 E-value=2.4e+02 Score=21.16 Aligned_cols=43 Identities=12% Similarity=0.019 Sum_probs=28.8
Q ss_pred ccceecCCEEEEeecCCCCeEeeEEEEEecC-CEEEEeeeeEEe
Q 032182 46 SMPVRKDDEVQVVRGTYKGREGKVVQVYRRK-WVIHIERITREK 88 (146)
Q Consensus 46 s~~IkkGD~V~Vi~G~~KGk~GkV~~V~~k~-~~V~VEgin~~K 88 (146)
.+.|+.||-|.|.+-..+=-.|.|.++.... +...|.+.=...
T Consensus 5 ~~~i~vGD~V~v~~~~~~~~va~Ie~i~ed~~g~~~v~v~WF~~ 48 (130)
T cd04721 5 GVTISVHDFVYVLSEEEDRYVAYIEDLYEDKKGSKMVKVRWFHT 48 (130)
T ss_pred CEEEECCCEEEEeCCCCCcEEEEEEEEEEcCCCCEEEEEEEecC
Confidence 4569999999999754333479999988854 444554443333
No 130
>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=26.20 E-value=1.3e+02 Score=19.51 Aligned_cols=25 Identities=36% Similarity=0.437 Sum_probs=17.8
Q ss_pred ceecCCEEEEeecCCCCeEeeEEEEEecCCEEEEe
Q 032182 48 PVRKDDEVQVVRGTYKGREGKVVQVYRRKWVIHIE 82 (146)
Q Consensus 48 ~IkkGD~V~Vi~G~~KGk~GkV~~V~~k~~~V~VE 82 (146)
.++.||.|.| +|..++....++.+.
T Consensus 57 ~~~~gd~v~v----------~v~~vd~~~~~i~~~ 81 (83)
T cd04471 57 VFRLGDKVKV----------RVVRVDLDRRKIDFE 81 (83)
T ss_pred EEcCCCEEEE----------EEEEeccccCEEEEE
Confidence 4688999988 477777766666543
No 131
>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=26.08 E-value=73 Score=22.11 Aligned_cols=24 Identities=38% Similarity=0.495 Sum_probs=13.0
Q ss_pred cCCEEEEeec--------------CCCCeEeeEEEEEe
Q 032182 51 KDDEVQVVRG--------------TYKGREGKVVQVYR 74 (146)
Q Consensus 51 kGD~V~Vi~G--------------~~KGk~GkV~~V~~ 74 (146)
.||+|.|.+- +.+|.+|+|.++..
T Consensus 1 vGdrVrV~~sv~Vyh~P~hr~~~fDl~G~EGev~~~v~ 38 (67)
T PF02941_consen 1 VGDRVRVKASVVVYHHPEHRNPPFDLKGMEGEVKQIVT 38 (67)
T ss_dssp TT-EEEE-S--EES--TTSTTS-EE-TT-EEEEEEE-S
T ss_pred CCCeEEEeeeEEEEeCCcccCCCccccCCEEEEEEEEe
Confidence 3788877643 25688898888764
No 132
>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=25.78 E-value=1.5e+02 Score=18.67 Aligned_cols=24 Identities=29% Similarity=0.473 Sum_probs=18.9
Q ss_pred eecCCEEEEeecCCCCeEeeEEEEEecCCEEEEe
Q 032182 49 VRKDDEVQVVRGTYKGREGKVVQVYRRKWVIHIE 82 (146)
Q Consensus 49 IkkGD~V~Vi~G~~KGk~GkV~~V~~k~~~V~VE 82 (146)
++.||.|.+ +|+++++.++.+.+.
T Consensus 45 ~~~Gd~v~~----------~v~~~d~~~~~i~ls 68 (73)
T cd05691 45 FKVGDEVEA----------KITNVDRKNRKISLS 68 (73)
T ss_pred cCCCCEEEE----------EEEEEeCCCCEEEEE
Confidence 688999987 688888887776654
No 133
>cd04715 BAH_Orc1p_like BAH, or Bromo Adjacent Homology domain, as present in the Schizosaccharomyces pombe homolog of Saccharomyces cerevisiae Orc1p and similar proteins. Orc1 is part of the Yeast Sir1-origin recognition complex, the Orc1p BAH doman functions in epigenetic silencing. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=25.71 E-value=1.8e+02 Score=22.77 Aligned_cols=33 Identities=24% Similarity=0.381 Sum_probs=27.9
Q ss_pred CcccceecCCEEEEeecCCCCeEeeEEEEEecC
Q 032182 44 VRSMPVRKDDEVQVVRGTYKGREGKVVQVYRRK 76 (146)
Q Consensus 44 ~rs~~IkkGD~V~Vi~G~~KGk~GkV~~V~~k~ 76 (146)
+....++.||-|.|-+|..+--.|+|.++....
T Consensus 25 ~~g~~y~lGD~Vlv~s~~~~~yIgkI~~iwe~~ 57 (159)
T cd04715 25 YDGVEYRLYDDVYVHNGDSEPYIGKIIKIYETA 57 (159)
T ss_pred ECCEEEeCCCEEEEeCCCCCCEEEEEEEEEEcC
Confidence 455668999999999998777799999998764
No 134
>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=25.58 E-value=1.1e+02 Score=24.88 Aligned_cols=48 Identities=13% Similarity=0.210 Sum_probs=31.2
Q ss_pred cCCHHHHhhhCCcccceecCCEEEEeecCCCCeEeeEEEEEecCCEEEE
Q 032182 33 PLSTDLRQKYNVRSMPVRKDDEVQVVRGTYKGREGKVVQVYRRKWVIHI 81 (146)
Q Consensus 33 ~Ls~eLr~ky~~rs~~IkkGD~V~Vi~G~~KGk~GkV~~V~~k~~~V~V 81 (146)
.|+.+ ...|=.+-++++.||.|.|.-|.-.=-.++|..+..+.-.+.|
T Consensus 17 ~l~~~-~~~Hl~~VlR~~~Gd~v~v~~g~g~~~~a~i~~~~~~~~~~~i 64 (240)
T TIGR00046 17 SLTEE-EAHHLVRVLRLKKGDKLKLLDGDGFIYHCEIKKISKKFVKCEL 64 (240)
T ss_pred EEChH-HHhHHHHcccCCCCCEEEEEeCCCCEEEEEEEEEcCCeEEEEE
Confidence 34443 3345456789999999999998421124678887766544444
No 135
>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=25.50 E-value=1.1e+02 Score=19.57 Aligned_cols=23 Identities=30% Similarity=0.362 Sum_probs=17.5
Q ss_pred ceecCCEEEEeecCCCCeEeeEEEEEecCCEEE
Q 032182 48 PVRKDDEVQVVRGTYKGREGKVVQVYRRKWVIH 80 (146)
Q Consensus 48 ~IkkGD~V~Vi~G~~KGk~GkV~~V~~k~~~V~ 80 (146)
.++.||.|.| +|++++.+..++.
T Consensus 48 ~~~~Gd~v~v----------~v~~id~~~~~i~ 70 (72)
T cd05689 48 VVSLGDEVEV----------MVLDIDEERRRIS 70 (72)
T ss_pred EeCCCCEEEE----------EEEEeeCCcCEEe
Confidence 3789999998 4778887776654
No 136
>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=25.34 E-value=1.5e+02 Score=18.73 Aligned_cols=23 Identities=30% Similarity=0.372 Sum_probs=17.1
Q ss_pred eecCCEEEEeecCCCCeEeeEEEEEecCCEEEE
Q 032182 49 VRKDDEVQVVRGTYKGREGKVVQVYRRKWVIHI 81 (146)
Q Consensus 49 IkkGD~V~Vi~G~~KGk~GkV~~V~~k~~~V~V 81 (146)
++.||.|.+ +|+.++++.+++.+
T Consensus 45 ~~~Gd~i~~----------~i~~~~~~~~~i~l 67 (70)
T cd05687 45 VKVGDEVEV----------YVLRVEDEEGNVVL 67 (70)
T ss_pred CCCCCEEEE----------EEEEEECCCCeEEE
Confidence 689999977 47777776666655
No 137
>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=25.25 E-value=74 Score=22.39 Aligned_cols=26 Identities=19% Similarity=0.234 Sum_probs=15.5
Q ss_pred ccceeeeccCCHHHHhhhCCcccceecCCEEEEee
Q 032182 25 VRRILMSAPLSTDLRQKYNVRSMPVRKDDEVQVVR 59 (146)
Q Consensus 25 ~r~k~msa~Ls~eLr~ky~~rs~~IkkGD~V~Vi~ 59 (146)
...-.+|+.+ ||.+.++.||.|.-..
T Consensus 28 ~~DvYVs~~q---------Irrf~LR~GD~V~G~v 53 (78)
T PF07497_consen 28 PDDVYVSPSQ---------IRRFGLRTGDLVEGQV 53 (78)
T ss_dssp TTSEEE-CCC---------CCCTT--TTEEEEEEE
T ss_pred CCCEEECHHH---------HHHcCCCCCCEEEEEE
Confidence 3345555555 5789999999998443
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=25.02 E-value=73 Score=18.48 Aligned_cols=16 Identities=19% Similarity=0.430 Sum_probs=13.4
Q ss_pred ccceecCCEEEEeecC
Q 032182 46 SMPVRKDDEVQVVRGT 61 (146)
Q Consensus 46 s~~IkkGD~V~Vi~G~ 61 (146)
.+.+.+||.|.|+...
T Consensus 18 ~l~~~~Gd~v~v~~~~ 33 (58)
T smart00326 18 ELSFKKGDIITVLEKS 33 (58)
T ss_pred CCCCCCCCEEEEEEcC
Confidence 3678999999999775
No 139
>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=24.26 E-value=1.4e+02 Score=22.34 Aligned_cols=40 Identities=20% Similarity=0.109 Sum_probs=28.9
Q ss_pred hCCcccceecCCEEEEeecCCCCeEeeEEEEEecCCEEEEe
Q 032182 42 YNVRSMPVRKDDEVQVVRGTYKGREGKVVQVYRRKWVIHIE 82 (146)
Q Consensus 42 y~~rs~~IkkGD~V~Vi~G~~KGk~GkV~~V~~k~~~V~VE 82 (146)
+|.+--.-++||.|..-.|. .|..|.|+..+...+.|++=
T Consensus 67 ~G~~v~~p~~GDiv~f~~~~-~~HVGi~~g~~~~~g~i~~l 106 (129)
T TIGR02594 67 YGTKLSKPAYGCIAVKRRGG-GGHVGFVVGKDKQTGTIIVL 106 (129)
T ss_pred cCCcCCCCCccEEEEEECCC-CCEEEEEEeEcCCCCEEEEe
Confidence 44332345899999876654 78899999998876776654
No 140
>cd05789 S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=24.25 E-value=83 Score=20.97 Aligned_cols=38 Identities=24% Similarity=0.241 Sum_probs=24.1
Q ss_pred ceecCCEEEEeecCCCCeEeeEEEEEecCCEEEEeeeeEEeeCCcEEEeeccccceE
Q 032182 48 PVRKDDEVQVVRGTYKGREGKVVQVYRRKWVIHIERITREKVNGSTVNVGINPSKVV 104 (146)
Q Consensus 48 ~IkkGD~V~Vi~G~~KGk~GkV~~V~~k~~~V~VEgin~~K~~G~~~e~pIh~SNv~ 104 (146)
..++||.| .|+|++|.... +.|+ + +...++-||.|.+.
T Consensus 3 ~p~~GdiV----------~g~V~~i~~~g--~~v~-i------~~~~~G~l~~se~~ 40 (86)
T cd05789 3 IPEVGDVV----------IGRVTEVGFKR--WKVD-I------NSPYDAVLPLSEVN 40 (86)
T ss_pred cCCCCCEE----------EEEEEEECCCE--EEEE-C------CCCeEEEEEHHHcc
Confidence 34678877 57888886644 3332 1 23477778888774
No 141
>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=24.18 E-value=38 Score=23.48 Aligned_cols=16 Identities=31% Similarity=0.522 Sum_probs=13.4
Q ss_pred eecCCEEEEeecCCCC
Q 032182 49 VRKDDEVQVVRGTYKG 64 (146)
Q Consensus 49 IkkGD~V~Vi~G~~KG 64 (146)
|++|+.|.|++.++-|
T Consensus 1 lKKG~lVrv~re~~~n 16 (67)
T PF11910_consen 1 LKKGSLVRVNREKYEN 16 (67)
T ss_pred CCcceEEEeehHhhcC
Confidence 5899999999888765
No 142
>PRK07252 hypothetical protein; Provisional
Probab=24.14 E-value=1.3e+02 Score=22.21 Aligned_cols=25 Identities=20% Similarity=0.183 Sum_probs=21.4
Q ss_pred ceecCCEEEEeecCCCCeEeeEEEEEecCCEEEEe
Q 032182 48 PVRKDDEVQVVRGTYKGREGKVVQVYRRKWVIHIE 82 (146)
Q Consensus 48 ~IkkGD~V~Vi~G~~KGk~GkV~~V~~k~~~V~VE 82 (146)
.++.||.|.| +|+++++..+++.++
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 3799999988 788999988888876
No 143
>PRK12617 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=23.60 E-value=1.3e+02 Score=24.60 Aligned_cols=32 Identities=25% Similarity=0.225 Sum_probs=23.2
Q ss_pred cceecCCEEEEeecC------------CCCeEeeEEEEEe-cCCE
Q 032182 47 MPVRKDDEVQVVRGT------------YKGREGKVVQVYR-RKWV 78 (146)
Q Consensus 47 ~~IkkGD~V~Vi~G~------------~KGk~GkV~~V~~-k~~~ 78 (146)
+-|++||.|.|++.. .-|..|..++|-- .+++
T Consensus 154 ~lV~rG~~V~I~a~~~g~~Vs~~G~AL~~G~~Ge~IrVrN~~Sgr 198 (214)
T PRK12617 154 RLVRRGDTVPLVSRNGGLEVRMSGRALSDAGENERVSVENSSSRR 198 (214)
T ss_pred ceEcCCCEEEEEEecCCEEEEEEEEEccCCCCCCEEEEEECCCCC
Confidence 569999999999764 3477777777774 4443
No 144
>COG1792 MreC Cell shape-determining protein [Cell envelope biogenesis, outer membrane]
Probab=23.57 E-value=1.1e+02 Score=25.90 Aligned_cols=40 Identities=23% Similarity=0.234 Sum_probs=30.1
Q ss_pred HHHhhhCCcccceecCCEEEEeecCC----CCe-EeeEEEEEecCC
Q 032182 37 DLRQKYNVRSMPVRKDDEVQVVRGTY----KGR-EGKVVQVYRRKW 77 (146)
Q Consensus 37 eLr~ky~~rs~~IkkGD~V~Vi~G~~----KGk-~GkV~~V~~k~~ 77 (146)
+|.-.|-..+-.|+.|| ..|.+|-. .|. .|+|.+|..++.
T Consensus 201 ~l~~~~~~~~~~i~~GD-~vvTSGlgg~fP~Gl~Vg~V~~v~~~~~ 245 (284)
T COG1792 201 LLLLVYLPPNSDIKEGD-LVVTSGLGGVFPAGLPVGEVSSVKLDDY 245 (284)
T ss_pred ceeeeeccCCCCccCCC-EEEecCCCCcCCCCcEEEEEEEEEeCCC
Confidence 34445666778999999 77888864 566 599999998874
No 145
>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=23.47 E-value=1.8e+02 Score=18.31 Aligned_cols=31 Identities=23% Similarity=0.298 Sum_probs=20.9
Q ss_pred cceecCCEEEEeecCCCCeEeeEEEEEecCCEE
Q 032182 47 MPVRKDDEVQVVRGTYKGREGKVVQVYRRKWVI 79 (146)
Q Consensus 47 ~~IkkGD~V~Vi~G~~KGk~GkV~~V~~k~~~V 79 (146)
..+..||.|.+-. .+ +-.|.|.+|.+.++.+
T Consensus 36 ~~~~VGD~V~~~~-~~-~~~~~I~~vl~R~s~l 66 (68)
T cd04466 36 NPPAVGDRVEFEP-ED-DGEGVIEEILPRKNLL 66 (68)
T ss_pred CCCCCCcEEEEEE-CC-CCcEEEEEEeccceEE
Confidence 4578999998742 22 2357788888877643
No 146
>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=23.23 E-value=1.2e+02 Score=20.68 Aligned_cols=18 Identities=17% Similarity=0.335 Sum_probs=16.2
Q ss_pred eEeeEEEEEecCCEEEEe
Q 032182 65 REGKVVQVYRRKWVIHIE 82 (146)
Q Consensus 65 k~GkV~~V~~k~~~V~VE 82 (146)
.+|+|.+|++....|..+
T Consensus 5 veG~I~~id~~~~titLd 22 (61)
T PF07076_consen 5 VEGTIKSIDPETMTITLD 22 (61)
T ss_pred ceEEEEEEcCCceEEEec
Confidence 379999999999999988
No 147
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=23.01 E-value=1.8e+02 Score=17.40 Aligned_cols=25 Identities=36% Similarity=0.397 Sum_probs=19.1
Q ss_pred ceecCCEEEEeecCCCCeEeeEEEEEecCCEEEEe
Q 032182 48 PVRKDDEVQVVRGTYKGREGKVVQVYRRKWVIHIE 82 (146)
Q Consensus 48 ~IkkGD~V~Vi~G~~KGk~GkV~~V~~k~~~V~VE 82 (146)
.++.||.|.+ .|+.+++.++.+.+.
T Consensus 46 ~~~~G~~v~~----------~V~~~~~~~~~i~ls 70 (72)
T smart00316 46 VLKVGDEVKV----------KVLSVDEEKGRIILS 70 (72)
T ss_pred eecCCCEEEE----------EEEEEeCCCCEEEEE
Confidence 3799999987 688888877776653
No 148
>PF09926 DUF2158: Uncharacterized small protein (DUF2158); InterPro: IPR019226 This entry represents a family of predominantly prokaryotic proteins with no known function.
Probab=22.67 E-value=53 Score=21.42 Aligned_cols=13 Identities=31% Similarity=0.388 Sum_probs=10.9
Q ss_pred eecCCEEEEeecC
Q 032182 49 VRKDDEVQVVRGT 61 (146)
Q Consensus 49 IkkGD~V~Vi~G~ 61 (146)
++.||.|+..+|-
T Consensus 1 f~~GDvV~LKSGG 13 (53)
T PF09926_consen 1 FKIGDVVQLKSGG 13 (53)
T ss_pred CCCCCEEEEccCC
Confidence 3689999999985
No 149
>cd04714 BAH_BAHCC1 BAH, or Bromo Adjacent Homology domain, as present in mammalian BAHCC1 and similar proteins. BAHCC1 stands for BAH domain and coiled-coil containing 1. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=22.62 E-value=2.8e+02 Score=20.30 Aligned_cols=37 Identities=8% Similarity=-0.024 Sum_probs=27.2
Q ss_pred ceecCCEEEEeecCC--CCeEeeEEEEEecC-CEEEEeee
Q 032182 48 PVRKDDEVQVVRGTY--KGREGKVVQVYRRK-WVIHIERI 84 (146)
Q Consensus 48 ~IkkGD~V~Vi~G~~--KGk~GkV~~V~~k~-~~V~VEgi 84 (146)
.++.||-|.|.+... .=-.|+|.++.... +...|...
T Consensus 3 ~~~vGD~V~v~~~~~~~~pyIgrI~~i~e~~~g~~~~~v~ 42 (121)
T cd04714 3 IIRVGDCVLFKSPGRPSLPYVARIESLWEDPEGNMVVRVK 42 (121)
T ss_pred EEEcCCEEEEeCCCCCCCCEEEEEEEEEEcCCCCEEEEEE
Confidence 378999999998654 44589999998743 55666544
No 150
>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=22.43 E-value=92 Score=21.25 Aligned_cols=20 Identities=25% Similarity=0.227 Sum_probs=14.4
Q ss_pred CcccceecCCEEEEeecCCC
Q 032182 44 VRSMPVRKDDEVQVVRGTYK 63 (146)
Q Consensus 44 ~rs~~IkkGD~V~Vi~G~~K 63 (146)
||.+.++.||.|.-..-+-+
T Consensus 36 Irr~~LR~GD~V~G~vr~p~ 55 (68)
T cd04459 36 IRRFNLRTGDTVVGQIRPPK 55 (68)
T ss_pred HHHhCCCCCCEEEEEEeCCC
Confidence 45678999999987654433
No 151
>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=22.40 E-value=1.4e+02 Score=20.67 Aligned_cols=29 Identities=14% Similarity=0.139 Sum_probs=22.7
Q ss_pred ceecCCEEEEeecCCCC--eEeeEEEEEecC
Q 032182 48 PVRKDDEVQVVRGTYKG--REGKVVQVYRRK 76 (146)
Q Consensus 48 ~IkkGD~V~Vi~G~~KG--k~GkV~~V~~k~ 76 (146)
.++.||-|.|..+...+ ..|.|..+....
T Consensus 2 ~~~vGD~V~v~~~~~~~~~~v~~I~~i~~~~ 32 (119)
T PF01426_consen 2 TYKVGDFVYVKPDDPPEPPYVARIEEIWEDK 32 (119)
T ss_dssp EEETTSEEEEECTSTTSEEEEEEEEEEEEET
T ss_pred EEeCCCEEEEeCCCCCCCCEEEEEEEEEcCC
Confidence 47899999999999443 469999887643
No 152
>COG0668 MscS Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]
Probab=22.26 E-value=1.6e+02 Score=23.80 Aligned_cols=29 Identities=28% Similarity=0.362 Sum_probs=21.5
Q ss_pred cceecCCEEEEeecCCCCeEeeEEEEEecCCEE
Q 032182 47 MPVRKDDEVQVVRGTYKGREGKVVQVYRRKWVI 79 (146)
Q Consensus 47 ~~IkkGD~V~Vi~G~~KGk~GkV~~V~~k~~~V 79 (146)
=+++.||.|++-. |..|.|..+.-..-++
T Consensus 146 ~~f~vGD~I~i~~----~~~G~V~~i~~~~T~i 174 (316)
T COG0668 146 RPFKVGDWIEIGS----GVEGTVEDIGLRSTTI 174 (316)
T ss_pred cCcCcCCEEEECC----CceEEEEEEEEEEEEE
Confidence 3678999999965 7788888887654333
No 153
>KOG3421 consensus 60S ribosomal protein L14 [Translation, ribosomal structure and biogenesis]
Probab=21.76 E-value=96 Score=24.27 Aligned_cols=35 Identities=17% Similarity=0.090 Sum_probs=29.0
Q ss_pred eecCCEEEEeecCCCCeEeeEEEEEecCCEEEEeee
Q 032182 49 VRKDDEVQVVRGTYKGREGKVVQVYRRKWVIHIERI 84 (146)
Q Consensus 49 IkkGD~V~Vi~G~~KGk~GkV~~V~~k~~~V~VEgi 84 (146)
+..|-.+.|..|+|.|+---|+.|+-. +++.|+|-
T Consensus 7 veVGrva~v~~G~~~GkL~AIVdviDq-nr~lvDGp 41 (136)
T KOG3421|consen 7 VEVGRVALVSFGPDAGKLVAIVDVIDQ-NRALVDGP 41 (136)
T ss_pred hhcceEEEEEecCCCceEEEEEEeecc-hhhhccCc
Confidence 567899999999999999888888764 68888754
No 154
>PLN00208 translation initiation factor (eIF); Provisional
Probab=21.49 E-value=1.2e+02 Score=23.81 Aligned_cols=30 Identities=17% Similarity=0.217 Sum_probs=21.1
Q ss_pred cceecCCEEEEeecCCCCeEeeEEEEEecC
Q 032182 47 MPVRKDDEVQVVRGTYKGREGKVVQVYRRK 76 (146)
Q Consensus 47 ~~IkkGD~V~Vi~G~~KGk~GkV~~V~~k~ 76 (146)
+.|+.||.|.|---+|--..|.|+.++...
T Consensus 69 IWI~~GD~VlVel~~~d~~KgdIv~ry~~d 98 (145)
T PLN00208 69 VWIAAGDIILVGLRDYQDDKADVILKYMPD 98 (145)
T ss_pred EEecCCCEEEEEccCCCCCEEEEEEEcCHH
Confidence 778889988886555555567777766544
No 155
>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=21.48 E-value=1.6e+02 Score=19.70 Aligned_cols=13 Identities=23% Similarity=0.452 Sum_probs=7.4
Q ss_pred ceecCCEEEEeec
Q 032182 48 PVRKDDEVQVVRG 60 (146)
Q Consensus 48 ~IkkGD~V~Vi~G 60 (146)
.|++||.|.+...
T Consensus 26 ~i~~Gd~v~i~P~ 38 (83)
T cd03698 26 SIQKGDTLLVMPS 38 (83)
T ss_pred EEeCCCEEEEeCC
Confidence 3566666666543
No 156
>cd05686 S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function with an N-terminal S1 RNA binding domain, a CCHC type zinc finger, and clusters of basic amino acids representing a potential nucleolar targeting signal. pNO40 was identified through a yeast two-hybrid interaction screen of a human kidney cDNA library using the pinin (pnn) protein as bait. pNO40 is thought to play a role in ribosome maturation and/or biogenesis.
Probab=21.43 E-value=1.4e+02 Score=19.41 Aligned_cols=22 Identities=23% Similarity=0.293 Sum_probs=15.9
Q ss_pred eecCCEEEEeecCCCCeEeeEEEEEecCCEEEE
Q 032182 49 VRKDDEVQVVRGTYKGREGKVVQVYRRKWVIHI 81 (146)
Q Consensus 49 IkkGD~V~Vi~G~~KGk~GkV~~V~~k~~~V~V 81 (146)
++.||+|.| +|++++..+ ++.+
T Consensus 49 ~~~Gd~v~v----------kv~~vd~~~-ki~l 70 (73)
T cd05686 49 VDVGEKVWV----------KVIGREMKD-KMKL 70 (73)
T ss_pred ECCCCEEEE----------EEEEECCCC-cEEE
Confidence 688999988 577777754 5443
No 157
>PRK12618 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=21.42 E-value=1.7e+02 Score=22.32 Aligned_cols=28 Identities=18% Similarity=0.259 Sum_probs=21.5
Q ss_pred cceecCCEEEEeecC------------CCCeEeeEEEEEe
Q 032182 47 MPVRKDDEVQVVRGT------------YKGREGKVVQVYR 74 (146)
Q Consensus 47 ~~IkkGD~V~Vi~G~------------~KGk~GkV~~V~~ 74 (146)
+-|.+||.|.|+... .-|..|..++|..
T Consensus 80 ~lV~rG~~V~i~~~~ggl~i~~~G~AL~~G~~Gd~IrV~N 119 (141)
T PRK12618 80 AIVDRNQLVPLAYRLGGLEIRTEGRALSRGGVGDEIRVMN 119 (141)
T ss_pred cEEeCCCEEEEEEecCCEEEEEEEEEcccCCCCCEEEEEE
Confidence 569999999999654 4477788887744
No 158
>PF06701 MIB_HERC2: Mib_herc2; InterPro: IPR010606 Mib is a RING ubiquitin ligase in the Notch pathway. Mib interacts with the intracellular domain of Delta to promote its ubiquitylation and internalisation. Cell transplantation studies suggest that mib function is essential in the signalling cell for efficient activation of Notch in neighbouring cells. This domain has been named 'mib/herc2 domain' in []and usually the protein also contains an E3 ligase domain (either Ring or Hect).; GO: 0004842 ubiquitin-protein ligase activity, 0046872 metal ion binding, 0016567 protein ubiquitination; PDB: 2DK3_A 3DKM_A.
Probab=21.36 E-value=1.1e+02 Score=20.84 Aligned_cols=27 Identities=30% Similarity=0.448 Sum_probs=13.5
Q ss_pred EEeecCC---------CCeEeeEEEE-----EecCCEEEEe
Q 032182 56 QVVRGTY---------KGREGKVVQV-----YRRKWVIHIE 82 (146)
Q Consensus 56 ~Vi~G~~---------KGk~GkV~~V-----~~k~~~V~VE 82 (146)
.|++|+| .|..|+|++| ....+.|.|.
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 4778863 3688999997 4455666664
No 159
>cd04472 S1_PNPase S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA. It is a trimeric multidomain protein. The C-terminus contains the S1 domain which binds ssRNA. This family is classified based on the S1 domain. PNPase nonspecifically removes the 3' nucleotides from mRNA, but is stalled by double-stranded RNA structures such as a stem-loop. Evidence shows that a minimum of 7-10 unpaired nucleotides at the 3' end, is required for PNPase degradation. It is suggested that PNPase also dephosphorylates the RNA 5' end. This additional activity may regulate the 5'-dependent activity of RNaseE in vivo.
Probab=21.24 E-value=1.4e+02 Score=18.36 Aligned_cols=23 Identities=35% Similarity=0.475 Sum_probs=16.6
Q ss_pred ceecCCEEEEeecCCCCeEeeEEEEEecCCEEEE
Q 032182 48 PVRKDDEVQVVRGTYKGREGKVVQVYRRKWVIHI 81 (146)
Q Consensus 48 ~IkkGD~V~Vi~G~~KGk~GkV~~V~~k~~~V~V 81 (146)
.++.||.|.| +|+++++ .+.+.+
T Consensus 44 ~~~~Gd~v~v----------~v~~~d~-~~~i~l 66 (68)
T cd04472 44 VLKVGDEVKV----------KVIEVDD-RGRISL 66 (68)
T ss_pred ccCCCCEEEE----------EEEEECC-CCcEEe
Confidence 3689999988 4777777 666554
No 160
>TIGR02609 doc_partner putative addiction module antidote. Members of this protein family are putative addiction module antidote proteins that appear recurringly in two-gene operons with members of the Doc (death-on-curing) family TIGR01550. Members of this family contain a SpoVT/AbrB-like domain (pfam04014). Note that the gene pairs with a member of this family tend to be found on bacterial chromosomes, not on plasmids.
Probab=21.02 E-value=1.2e+02 Score=20.60 Aligned_cols=26 Identities=12% Similarity=0.279 Sum_probs=19.9
Q ss_pred eeccCCHHHHhhhCCcccceecCCEEEEeec
Q 032182 30 MSAPLSTDLRQKYNVRSMPVRKDDEVQVVRG 60 (146)
Q Consensus 30 msa~Ls~eLr~ky~~rs~~IkkGD~V~Vi~G 60 (146)
..-+||+++++.+| |..||.|.|...
T Consensus 10 ~~vtIPk~i~~~lg-----l~~Gd~v~v~~~ 35 (74)
T TIGR02609 10 LVVTLPKEVLESLG-----LKEGDTLYVDEE 35 (74)
T ss_pred eEEEECHHHHHHcC-----cCCCCEEEEEEE
Confidence 45678999998875 569999987644
No 161
>COG0335 RplS Ribosomal protein L19 [Translation, ribosomal structure and biogenesis]
Probab=20.70 E-value=3e+02 Score=20.97 Aligned_cols=63 Identities=21% Similarity=0.234 Sum_probs=37.2
Q ss_pred ceecCCEEEEe----ecCC---CCeEeeEEEEEecC--CEEEEeeeeEEeeCC--cEEEeeccccceEEEcCCC-cchh
Q 032182 48 PVRKDDEVQVV----RGTY---KGREGKVVQVYRRK--WVIHIERITREKVNG--STVNVGINPSKVVITKLRL-DKDR 114 (146)
Q Consensus 48 ~IkkGD~V~Vi----~G~~---KGk~GkV~~V~~k~--~~V~VEgin~~K~~G--~~~e~pIh~SNv~i~~~~~-~~~R 114 (146)
.+.+||+|.|- -|.- ---+|.|+.+.-.. .+++|..+ ..| -+.-.|+|..++.=++.-. .+.|
T Consensus 20 ~f~~GDtvrv~vki~Eg~keR~Q~FeGvVia~r~~G~~~tftvRki----s~G~GVEr~Fp~~SP~Ie~IeV~rrGkVR 94 (115)
T COG0335 20 SFRPGDTVRVHVKIVEGSKERVQAFEGVVIARRGRGISETFTVRKI----SYGVGVERVFPLHSPLIESIEVVRRGKVR 94 (115)
T ss_pred CCCCCCEEEEEEEEEeCCeEEEeeeeEEEEEECCCCccceEEEEEe----ecCceEEEEeecCCCceeEEEEEecCcee
Confidence 46899998753 3331 12357777765532 24555433 234 4667999999997655544 4444
No 162
>PHA00653 mtd major tropism determinant
Probab=20.49 E-value=2.1e+02 Score=25.82 Aligned_cols=56 Identities=20% Similarity=0.248 Sum_probs=37.7
Q ss_pred ceecCCEEEEeecCCCCeEeeEEEEEecCCEEEEeeeeEEeeCC---------cEEEeeccccceEEEcC
Q 032182 48 PVRKDDEVQVVRGTYKGREGKVVQVYRRKWVIHIERITREKVNG---------STVNVGINPSKVVITKL 108 (146)
Q Consensus 48 ~IkkGD~V~Vi~G~~KGk~GkV~~V~~k~~~V~VEgin~~K~~G---------~~~e~pIh~SNv~i~~~ 108 (146)
.+|.|-+-+. -.|+|..|+|+ |+..+++++|.+..-. .| .....-.++|||.|+.-
T Consensus 6 ~~r~gt~~~~--asf~ga~~ei~-~~t~~~~l~v~Dgtt~--gg~~L~kl~~~~~~~~~~~~s~~~~~~t 70 (381)
T PHA00653 6 QFRGGTTAQH--ATFTGAAREIT-VDTDKNTVVVHDGATA--GGFPLARHDLVKTAFIKADKSAVAFTRT 70 (381)
T ss_pred EEccCcccce--eeecccceeEE-EccCCceEEEecCccc--CCceeeccccccceeeeecccceeEEec
Confidence 3444544444 35899999986 7888999999987432 22 13455667888888754
No 163
>PRK13922 rod shape-determining protein MreC; Provisional
Probab=20.25 E-value=2e+02 Score=23.57 Aligned_cols=40 Identities=33% Similarity=0.403 Sum_probs=28.1
Q ss_pred HHhhhCCcccceecCCEEEEeecCC----CCe-EeeEEEEEecCCE
Q 032182 38 LRQKYNVRSMPVRKDDEVQVVRGTY----KGR-EGKVVQVYRRKWV 78 (146)
Q Consensus 38 Lr~ky~~rs~~IkkGD~V~Vi~G~~----KGk-~GkV~~V~~k~~~ 78 (146)
+.=.|=.+..+|++||.| |.+|-+ +|- .|+|.+|.+..+.
T Consensus 204 l~l~~i~~~~~i~~GD~V-vTSGl~g~fP~Gi~VG~V~~v~~~~~~ 248 (276)
T PRK13922 204 LKLEFIPRSADIKVGDLV-VTSGLGGIFPAGLPVGKVTSVERDDYG 248 (276)
T ss_pred eEEEecCCCCCCCCCCEE-EECCCCCcCCCCCEEEEEEEEEeCCCC
Confidence 344454556789999985 678863 465 6999999776543
Done!