Query 000637
Match_columns 1378
No_of_seqs 253 out of 363
Neff 3.1
Searched_HMMs 46136
Date Mon Apr 1 21:03:09 2013
Command hhsearch -i /work/01045/syshi/lefta3m/000637.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/leftcdd/000637hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1999 RNA polymerase II tran 100.0 1.2E-73 2.6E-78 675.4 30.9 343 1-357 352-822 (1024)
2 COG5164 SPT5 Transcription elo 100.0 5.4E-54 1.2E-58 479.9 27.0 273 2-298 38-402 (607)
3 KOG1999 RNA polymerase II tran 98.7 1.7E-07 3.7E-12 115.4 16.2 162 130-301 449-638 (1024)
4 PF00467 KOW: KOW motif; Inte 97.2 0.00045 9.8E-09 54.5 3.9 32 250-281 1-32 (32)
5 KOG0921 Dosage compensation co 97.0 0.0023 5E-08 80.1 9.8 50 144-197 390-441 (1282)
6 COG5164 SPT5 Transcription elo 96.9 0.0022 4.7E-08 75.7 8.0 156 1-174 202-382 (607)
7 PF00467 KOW: KOW motif; Inte 96.7 0.0018 3.9E-08 51.2 3.5 29 146-174 1-29 (32)
8 TIGR00405 L26e_arch ribosomal 96.3 0.0067 1.5E-07 61.3 5.7 51 248-298 87-141 (145)
9 KOG0921 Dosage compensation co 96.0 0.031 6.8E-07 70.6 10.3 6 277-282 527-532 (1282)
10 PRK08559 nusG transcription an 95.9 0.017 3.7E-07 59.6 6.6 52 247-298 94-149 (153)
11 smart00739 KOW KOW (Kyprides, 95.8 0.011 2.4E-07 44.0 3.4 26 144-169 2-27 (28)
12 KOG3973 Uncharacterized conser 95.5 0.065 1.4E-06 62.2 9.8 13 1105-1117 442-454 (465)
13 CHL00141 rpl24 ribosomal prote 95.5 0.017 3.7E-07 55.0 4.4 29 143-171 8-36 (83)
14 PRK12281 rplX 50S ribosomal pr 95.4 0.02 4.2E-07 53.9 4.4 28 143-170 6-33 (76)
15 PRK00004 rplX 50S ribosomal pr 95.3 0.023 5E-07 56.1 4.8 28 143-170 4-31 (105)
16 TIGR01956 NusG_myco NusG famil 95.2 0.066 1.4E-06 60.3 8.6 44 247-290 205-250 (258)
17 TIGR00922 nusG transcription t 94.5 0.061 1.3E-06 55.5 5.4 47 248-294 120-170 (172)
18 TIGR01955 RfaH transcriptional 94.4 0.071 1.5E-06 54.2 5.7 43 248-290 109-152 (159)
19 KOG3262 H/ACA small nucleolar 94.2 0.092 2E-06 56.8 6.3 20 1090-1110 194-213 (215)
20 PRK05609 nusG transcription an 94.1 0.083 1.8E-06 54.7 5.5 48 248-295 127-178 (181)
21 smart00739 KOW KOW (Kyprides, 94.0 0.075 1.6E-06 39.6 3.8 25 249-273 3-27 (28)
22 TIGR01079 rplX_bact ribosomal 93.9 0.072 1.6E-06 52.7 4.4 28 143-170 3-30 (104)
23 PRK01191 rpl24p 50S ribosomal 93.8 0.13 2.7E-06 52.5 6.0 34 143-176 45-80 (120)
24 KOG3262 H/ACA small nucleolar 93.5 0.13 2.9E-06 55.7 5.8 10 1055-1064 170-179 (215)
25 PRK09014 rfaH transcriptional 93.2 0.13 2.9E-06 52.7 5.2 43 248-290 110-153 (162)
26 PTZ00194 60S ribosomal protein 93.1 0.11 2.5E-06 54.1 4.5 29 143-171 46-74 (143)
27 COG0250 NusG Transcription ant 92.6 0.18 3.9E-06 53.9 5.4 44 247-290 123-168 (178)
28 TIGR01080 rplX_A_E ribosomal p 92.3 0.18 3.9E-06 51.0 4.5 29 143-171 41-69 (114)
29 PRK09014 rfaH transcriptional 91.7 0.46 1E-05 48.9 6.9 60 104-168 75-134 (162)
30 COG0198 RplX Ribosomal protein 91.7 0.23 5E-06 49.6 4.5 30 142-171 3-32 (104)
31 TIGR01955 RfaH transcriptional 91.7 0.42 9E-06 48.7 6.5 78 85-169 53-134 (159)
32 PRK05609 nusG transcription an 89.6 0.45 9.8E-06 49.4 4.7 37 141-177 124-162 (181)
33 TIGR00405 L26e_arch ribosomal 89.0 0.5 1.1E-05 48.0 4.4 34 142-175 85-120 (145)
34 TIGR01080 rplX_A_E ribosomal p 88.7 0.6 1.3E-05 47.3 4.6 36 249-284 43-78 (114)
35 TIGR00922 nusG transcription t 86.5 0.91 2E-05 47.0 4.6 34 142-175 118-153 (172)
36 PLN00208 translation initiatio 86.2 3.2 6.8E-05 43.9 8.3 78 78-170 19-97 (145)
37 PRK04313 30S ribosomal protein 85.9 2.3 4.9E-05 47.9 7.5 52 144-197 172-227 (237)
38 PRK00004 rplX 50S ribosomal pr 84.6 1.3 2.8E-05 44.1 4.4 35 250-284 7-41 (105)
39 PRK12281 rplX 50S ribosomal pr 84.4 1.5 3.2E-05 41.6 4.5 34 250-283 9-42 (76)
40 PRK08559 nusG transcription an 84.1 1.4 3E-05 45.9 4.6 29 142-170 93-121 (153)
41 PTZ00194 60S ribosomal protein 83.7 1.8 3.9E-05 45.6 5.1 33 249-281 48-80 (143)
42 smart00652 eIF1a eukaryotic tr 83.5 5.8 0.00013 38.2 8.1 65 90-169 5-69 (83)
43 CHL00141 rpl24 ribosomal prote 82.9 1.9 4.2E-05 41.4 4.7 35 249-283 10-44 (83)
44 KOG1708 Mitochondrial/chloropl 82.0 1.6 3.4E-05 48.3 4.2 31 141-171 70-100 (236)
45 TIGR01956 NusG_myco NusG famil 82.0 1.8 4E-05 49.1 4.8 34 143-176 205-240 (258)
46 COG0250 NusG Transcription ant 81.8 3.3 7.2E-05 44.6 6.4 35 136-170 116-150 (178)
47 PTZ00329 eukaryotic translatio 81.6 7 0.00015 41.8 8.5 78 78-170 19-97 (155)
48 PRK04012 translation initiatio 81.3 7.5 0.00016 38.8 8.1 75 80-169 10-85 (100)
49 TIGR01079 rplX_bact ribosomal 80.4 2.5 5.3E-05 42.2 4.6 35 250-284 6-40 (104)
50 PRK12442 translation initiatio 80.0 8.8 0.00019 37.8 8.0 69 83-169 4-72 (87)
51 PRK00276 infA translation init 79.9 11 0.00024 35.0 8.3 63 93-169 10-72 (72)
52 COG1471 RPS4A Ribosomal protei 79.9 5.5 0.00012 45.0 7.4 54 142-197 151-229 (241)
53 cd05793 S1_IF1A S1_IF1A: Trans 78.5 10 0.00022 36.1 7.8 64 92-170 2-65 (77)
54 PRK14635 hypothetical protein; 78.5 2.6 5.7E-05 44.5 4.4 50 247-296 95-155 (162)
55 CHL00010 infA translation init 78.4 14 0.0003 35.1 8.6 64 93-170 10-73 (78)
56 PTZ00223 40S ribosomal protein 78.3 6.9 0.00015 45.0 7.8 52 144-197 172-226 (273)
57 PRK14639 hypothetical protein; 77.6 4.2 9.1E-05 42.2 5.5 50 247-296 84-133 (140)
58 COG0198 RplX Ribosomal protein 77.2 3.2 7E-05 41.8 4.3 30 250-279 7-36 (104)
59 PF11623 DUF3252: Protein of u 76.9 7.9 0.00017 35.1 6.1 46 249-294 3-52 (53)
60 PTZ00118 40S ribosomal protein 76.9 7.1 0.00015 44.7 7.4 52 144-197 175-229 (262)
61 PRK03879 ribonuclease P protei 76.7 5.8 0.00013 39.2 5.9 46 248-295 12-60 (96)
62 PLN00036 40S ribosomal protein 76.7 8.2 0.00018 44.2 7.8 51 145-197 176-229 (261)
63 COG1588 POP4 RNase P/RNase MRP 76.1 5.7 0.00012 39.6 5.5 48 247-296 13-63 (95)
64 cd04456 S1_IF1A_like S1_IF1A_l 75.7 15 0.00032 35.2 8.0 65 91-170 1-66 (78)
65 PTZ00065 60S ribosomal protein 75.1 6.1 0.00013 41.3 5.7 34 249-283 9-42 (130)
66 PRK05585 yajC preprotein trans 74.3 4.5 9.8E-05 40.5 4.5 44 250-298 55-98 (106)
67 TIGR00523 eIF-1A eukaryotic/ar 74.2 11 0.00024 37.6 7.1 65 89-170 18-85 (99)
68 COG1862 YajC Preprotein transl 74.1 3.7 8E-05 40.8 3.8 45 251-300 47-91 (97)
69 PRK12288 GTPase RsgA; Reviewed 74.0 17 0.00036 42.8 9.6 87 92-197 40-128 (347)
70 PRK00092 ribosome maturation p 73.9 5.6 0.00012 41.5 5.2 49 248-296 95-147 (154)
71 PF02576 DUF150: Uncharacteris 73.4 6.1 0.00013 40.4 5.3 50 247-296 83-138 (141)
72 PF02736 Myosin_N: Myosin N-te 73.3 6.7 0.00014 33.2 4.6 28 265-293 15-42 (42)
73 PRK05886 yajC preprotein trans 73.1 7.5 0.00016 39.4 5.7 42 251-297 42-83 (109)
74 cd01734 YlxS_C YxlS is a Bacil 73.0 6.7 0.00015 37.1 5.1 49 248-296 22-76 (83)
75 TIGR00739 yajC preprotein tran 72.2 5.2 0.00011 38.5 4.2 42 250-296 40-81 (84)
76 PF01176 eIF-1a: Translation i 72.1 14 0.0003 33.8 6.7 62 91-167 4-65 (65)
77 PRK04333 50S ribosomal protein 70.2 6.2 0.00014 38.3 4.2 30 249-278 5-35 (84)
78 PF01868 UPF0086: Domain of un 69.1 13 0.00029 36.0 6.2 49 247-296 10-61 (89)
79 PRK14637 hypothetical protein; 68.9 9.5 0.00021 40.3 5.6 47 248-296 95-142 (151)
80 TIGR00008 infA translation ini 68.4 28 0.00061 32.9 7.9 65 84-166 3-67 (68)
81 PRK14634 hypothetical protein; 67.8 8.3 0.00018 40.7 5.0 48 248-297 97-148 (155)
82 PRK14638 hypothetical protein; 67.5 9 0.0002 40.3 5.1 48 247-296 96-143 (150)
83 PRK14644 hypothetical protein; 67.4 7.4 0.00016 40.4 4.4 49 247-295 81-135 (136)
84 PRK06531 yajC preprotein trans 67.2 11 0.00023 38.6 5.4 41 256-299 44-84 (113)
85 PRK01191 rpl24p 50S ribosomal 66.8 8.3 0.00018 39.8 4.6 31 249-279 47-79 (120)
86 PRK00098 GTPase RsgA; Reviewed 66.7 32 0.0007 39.2 9.7 86 94-197 3-88 (298)
87 PRK14643 hypothetical protein; 66.1 9.2 0.0002 40.9 4.9 51 247-297 100-158 (164)
88 smart00538 POP4 A domain found 65.6 16 0.00036 35.8 6.1 48 247-295 9-59 (92)
89 cd01854 YjeQ_engC YjeQ/EngC. 65.4 34 0.00074 38.8 9.5 85 94-197 1-86 (287)
90 PRK04950 ProP expression regul 64.4 10 0.00023 42.3 5.1 46 248-295 167-212 (213)
91 PRK14640 hypothetical protein; 63.0 13 0.00029 39.1 5.3 47 248-296 94-144 (152)
92 PF10842 DUF2642: Protein of u 61.2 23 0.00049 33.4 5.9 45 248-295 18-62 (66)
93 PRK01889 GTPase RsgA; Reviewed 60.7 27 0.00058 41.0 7.8 90 92-197 29-120 (356)
94 PRK14632 hypothetical protein; 59.3 16 0.00035 39.3 5.3 51 248-298 95-158 (172)
95 TIGR03630 arch_S17P archaeal r 59.2 17 0.00037 36.7 5.1 25 131-155 63-87 (102)
96 PRK14645 hypothetical protein; 59.0 14 0.00031 39.2 4.8 46 248-296 99-144 (154)
97 TIGR03635 S17_bact 30S ribosom 58.6 16 0.00035 34.5 4.5 24 131-155 37-60 (71)
98 PRK08572 rps17p 30S ribosomal 58.5 19 0.0004 36.8 5.2 26 131-156 65-90 (108)
99 PRK14633 hypothetical protein; 57.6 18 0.00039 38.1 5.2 49 248-297 91-143 (150)
100 PRK05610 rpsQ 30S ribosomal pr 56.2 19 0.00041 35.1 4.7 25 131-156 42-66 (84)
101 PRK14636 hypothetical protein; 55.9 18 0.00039 39.2 5.0 49 247-296 94-146 (176)
102 COG0361 InfA Translation initi 55.7 35 0.00075 33.0 6.2 64 93-170 10-73 (75)
103 PRK14630 hypothetical protein; 55.6 23 0.0005 37.1 5.6 46 248-296 94-139 (143)
104 PRK14647 hypothetical protein; 52.8 22 0.00047 37.7 4.9 48 248-296 96-152 (159)
105 PF02699 YajC: Preprotein tran 52.0 4.8 0.0001 38.4 0.0 42 250-296 39-80 (82)
106 PRK02001 hypothetical protein; 52.0 28 0.00061 37.0 5.6 48 248-295 87-146 (152)
107 PRK14646 hypothetical protein; 51.6 23 0.0005 37.5 4.9 49 247-297 96-148 (155)
108 COG2139 RPL21A Ribosomal prote 51.6 26 0.00057 35.3 4.9 50 248-297 33-94 (98)
109 PF13051 DUF3912: Protein of u 49.3 22 0.00047 33.1 3.6 52 248-301 3-57 (68)
110 CHL00142 rps17 ribosomal prote 46.1 32 0.00068 33.7 4.5 25 131-156 39-63 (84)
111 COG3109 ProQ Activator of osmo 46.1 27 0.00059 38.4 4.4 45 249-295 163-207 (208)
112 cd04451 S1_IF1 S1_IF1: Transla 46.0 91 0.002 28.1 7.1 59 94-166 5-63 (64)
113 PRK14631 hypothetical protein; 44.6 37 0.00079 36.9 5.1 47 248-295 114-166 (174)
114 cd05792 S1_eIF1AD_like S1_eIF1 44.3 1.2E+02 0.0025 29.6 7.8 64 92-170 2-66 (78)
115 COG0186 RpsQ Ribosomal protein 44.0 34 0.00073 33.9 4.3 24 131-155 44-67 (87)
116 PF00900 Ribosomal_S4e: Riboso 43.8 30 0.00064 33.2 3.9 63 85-154 7-71 (77)
117 COG1096 Predicted RNA-binding 43.8 67 0.0015 35.7 6.9 42 142-196 117-158 (188)
118 COG0779 Uncharacterized protei 43.0 42 0.00092 35.9 5.2 48 247-296 95-146 (153)
119 PRK09521 exosome complex RNA-b 42.2 79 0.0017 34.0 7.2 41 141-194 116-156 (189)
120 KOG1708 Mitochondrial/chloropl 41.6 24 0.00053 39.5 3.3 45 247-291 72-119 (236)
121 PF03144 GTP_EFTU_D2: Elongati 41.0 46 0.001 29.7 4.5 45 143-188 12-59 (74)
122 TIGR02760 TraI_TIGR conjugativ 40.9 97 0.0021 44.3 9.5 90 76-170 1326-1420(1960)
123 PRK13709 conjugal transfer nic 39.5 1.2E+02 0.0026 43.1 9.8 91 76-174 1272-1370(1747)
124 PRK11634 ATP-dependent RNA hel 37.8 62 0.0013 41.0 6.4 6 117-122 128-133 (629)
125 PF09643 YopX: YopX protein; 37.3 30 0.00064 33.0 2.8 22 136-157 54-75 (121)
126 PRK14712 conjugal transfer nic 36.6 1.4E+02 0.0031 42.0 9.8 94 76-175 1143-1242(1623)
127 PRK13709 conjugal transfer nic 36.0 1.3E+02 0.0028 42.8 9.3 92 77-176 646-748 (1747)
128 PTZ00241 40S ribosomal protein 35.8 55 0.0012 35.5 4.7 25 131-155 104-128 (158)
129 PRK10220 hypothetical protein; 35.5 54 0.0012 33.8 4.4 21 134-154 42-62 (111)
130 smart00743 Agenet Tudor-like d 35.2 55 0.0012 28.8 4.0 51 248-298 3-57 (61)
131 TIGR02760 TraI_TIGR conjugativ 35.1 1.4E+02 0.003 42.9 9.5 91 77-172 679-780 (1960)
132 TIGR00686 phnA alkylphosphonat 32.7 79 0.0017 32.6 5.0 36 134-169 41-82 (109)
133 COG4371 Predicted membrane pro 32.7 67 0.0015 37.3 5.0 7 1039-1045 54-60 (334)
134 KOG3416 Predicted nucleic acid 31.9 99 0.0021 32.8 5.7 47 133-187 51-99 (134)
135 PRK12289 GTPase RsgA; Reviewed 30.9 2.4E+02 0.0051 33.7 9.3 76 91-178 8-86 (352)
136 smart00333 TUDOR Tudor domain. 29.7 72 0.0016 27.3 3.7 50 249-298 4-54 (57)
137 PF02691 VacA: Vacuolating cyo 28.8 43 0.00093 43.2 3.0 55 136-195 314-371 (981)
138 PF05934 MCLC: Mid-1-related c 28.7 59 0.0013 40.6 4.0 48 246-293 395-443 (549)
139 PRK04333 50S ribosomal protein 27.9 81 0.0018 30.9 4.1 34 142-175 2-36 (84)
140 PRK08582 hypothetical protein; 27.8 2.8E+02 0.006 29.1 8.2 56 80-152 3-58 (139)
141 PF03831 PhnA: PhnA protein; 27.2 34 0.00074 31.6 1.3 20 135-154 1-20 (56)
142 KOG1740 Predicted mitochondria 26.5 52 0.0011 33.6 2.6 21 132-153 39-59 (107)
143 COG2163 RPL14A Ribosomal prote 26.3 86 0.0019 32.9 4.1 47 248-295 5-51 (125)
144 PF08605 Rad9_Rad53_bind: Fung 26.1 83 0.0018 33.0 4.1 46 142-197 58-103 (131)
145 PF14153 Spore_coat_CotO: Spor 25.7 72 0.0016 35.2 3.7 37 261-297 144-180 (185)
146 PRK06461 single-stranded DNA-b 25.5 2.1E+02 0.0046 29.4 6.8 50 115-175 39-88 (129)
147 PF12701 LSM14: Scd6-like Sm d 25.2 74 0.0016 31.8 3.4 35 247-281 4-38 (96)
148 PF14157 YmzC: YmzC-like prote 25.1 90 0.002 29.6 3.6 44 76-122 15-58 (63)
149 PRK14641 hypothetical protein; 24.8 1.2E+02 0.0027 33.0 5.2 36 248-283 101-145 (173)
150 PRK08059 general stress protei 24.8 3.4E+02 0.0074 27.5 8.0 58 79-153 4-61 (123)
151 KOG3591 Alpha crystallins [Pos 24.4 93 0.002 33.8 4.2 53 96-172 66-118 (173)
152 cd04370 BAH BAH, or Bromo Adja 24.1 1.1E+02 0.0025 29.0 4.4 97 80-189 4-109 (123)
153 cd05684 S1_DHX8_helicase S1_DH 23.8 4.5E+02 0.0098 24.0 7.9 35 138-182 43-77 (79)
154 cd05752 Ig1_FcgammaR_like Frst 23.2 1.9E+02 0.0041 26.9 5.4 24 168-193 45-68 (78)
155 PF04351 PilP: Pilus assembly 22.7 74 0.0016 33.3 3.0 30 250-279 99-129 (149)
156 PF00575 S1: S1 RNA binding do 22.5 1.6E+02 0.0035 26.2 4.7 58 79-153 1-58 (74)
157 PRK05807 hypothetical protein; 22.5 1.9E+02 0.0042 30.1 5.8 56 80-153 3-58 (136)
158 PF01157 Ribosomal_L21e: Ribos 22.4 1.1E+02 0.0025 30.9 4.0 60 134-194 23-96 (99)
159 PRK14712 conjugal transfer nic 22.0 3.3E+02 0.0072 38.7 9.4 91 78-176 515-616 (1623)
160 PRK11911 flgD flagellar basal 21.8 1.5E+02 0.0032 31.7 4.9 43 248-290 90-134 (140)
161 PF02237 BPL_C: Biotin protein 21.8 2.9E+02 0.0063 23.9 5.9 34 249-283 1-35 (48)
162 PF02756 GYR: GYR motif; Inte 21.0 58 0.0013 24.2 1.3 12 4-15 1-12 (18)
163 PF14001 YdfZ: YdfZ protein 21.0 1E+02 0.0022 29.3 3.1 33 136-171 2-34 (64)
164 COG3109 ProQ Activator of osmo 20.9 1.3E+02 0.0028 33.5 4.3 48 142-194 160-207 (208)
165 cd04508 TUDOR Tudor domains ar 20.3 1.1E+02 0.0024 25.4 3.0 31 264-294 15-46 (48)
166 cd05686 S1_pNO40 S1_pNO40: pNO 20.2 2.6E+02 0.0057 25.5 5.6 50 94-153 9-58 (73)
167 PRK04950 ProP expression regul 20.1 1.3E+02 0.0028 34.1 4.4 49 141-194 164-212 (213)
No 1
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=100.00 E-value=1.2e-73 Score=675.38 Aligned_cols=343 Identities=32% Similarity=0.438 Sum_probs=270.3
Q ss_pred CccccceeEEEEeeceEEecCCCCCHHHHhccCCCCCCcccchHHHHHHhhhccCCc-------EEEe------------
Q 000637 1 MMLKDGYLYKKVSIDSLSCWGVVPSEEELLKFQPSESNESADLEWLSQLYGERKKKR-------TTIV------------ 61 (1378)
Q Consensus 1 lmfkDGFLYKdVsIqSL~t~nVqPTLDEL~KF~~~~~de~~DLasLS~s~Geqkk~~-------vIVi------------ 61 (1378)
|||+||||||+|+|++|++++|+||||||+||+++ ++.+||+++++++.+++++| |+|+
T Consensus 352 ~~~~dGFLyK~v~i~sI~t~gV~PT~dELekF~~~--~e~~Dl~~~st~~~~r~~~~~F~~GD~VeV~~Gel~glkG~ve 429 (1024)
T KOG1999|consen 352 ELFKDGFLYKDVSISSIITDGVKPTLDELEKFNPS--NEEGDLEWVSTLKSNRKKKHLFSPGDAVEVIVGELKGLKGKVE 429 (1024)
T ss_pred ceeccceeeeeeecceeeecCcccCHHHHHhhcCC--CccccceeeeeeccccccccccCCCCeEEEeeeeeccceeEEE
Confidence 68999999999999999999999999999999987 45899999997777777776 2222
Q ss_pred -------------------------------ccCCC--------cC----------------------------------
Q 000637 62 -------------------------------GKGGD--------KG---------------------------------- 68 (1378)
Q Consensus 62 -------------------------------~~G~h--------kg---------------------------------- 68 (1378)
++|+| ++
T Consensus 430 ~vdg~~vti~~~~e~l~~pl~~~~~eLrKyF~~GDhVKVi~G~~eG~tGlVvrVe~~~vi~~Sd~t~eel~Vf~~dlq~c 509 (1024)
T KOG1999|consen 430 SVDGTIVTIMSKHEDLKGPLEVPASELRKYFEPGDHVKVIAGRYEGDTGLVVRVEQGDVILLSDLTMEELKVFARDLQLC 509 (1024)
T ss_pred eccCceEEEeeccccCCCccccchHhhhhhccCCCeEEEEeccccCCcceEEEEeCCeEEEEecCccceeeEEehhcccc
Confidence 13333 22
Q ss_pred -cCCCCCCCCCccEeceeEeecCCceEEEEEeccCCceEEccCCCCCCcEEEEeccccccCCCCCccccccCCCCeeccC
Q 000637 69 -EGSSGSSLENSFELYELVCFGRKDFGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLN 147 (1378)
Q Consensus 69 -EssTG~~slG~YELHDLVQLD~qTVGVIVrVEKDDsFKVLdqngDrGkVvtVKpseIk~Kr~dRR~vAlD~nGNtIrVg 147 (1378)
|++++++.+++||||||||||.++|||||++|+ +.|+||+.++ +|++|++++|.+|+..++++|+|+++|+|+++
T Consensus 510 ~ev~~gv~~~ge~e~hdlVqLd~~~vgvI~rle~-e~~~vl~~~g---~v~~i~~~~i~~kk~~r~~~~~D~~~n~I~~k 585 (1024)
T KOG1999|consen 510 SEVTLGVEKSGEYELHDLVQLDNQNVGVIVRLER-ETFQVLGMNG---KVVTIRKSSITKKKDNRKAVAVDRNGNEIRVK 585 (1024)
T ss_pred hheeecccccccccccceeecCCCcEEEEEEecc-hheeeecCcC---ceEEEeechhhhhhhhhhheeecccCCeeccc
Confidence 245677899999999999999999999999999 6999999984 99999999999888888899999999999999
Q ss_pred CeEEEecCCCCCceeEEEEEEcceEEEEeccccccccEEEEeCCceeecccccccCCCCCCCCCCCCC-CCCCCCCCCCC
Q 000637 148 DTARVSEGPSKDRQGIVKKIYRGILFIYDENETENGGYFCSKSQHCEKTKVEACEGKGGGSGASGFEE-FPSSPKSPLSP 226 (1378)
Q Consensus 148 DtVKVVdGP~KGRQG~VlHIyRg~LFL~sR~i~ENGGIFVvrArnVvlVgg~asnsK~g~s~~~~f~d-l~sSp~spmSP 226 (1378)
|+|+||+||+++|+|+|+||||.+||||||+++||+|||||+++||++++.. |.........++ .+|+|.--++|
T Consensus 586 D~Vkvi~Gp~~g~~G~v~~i~r~~~F~h~r~~~En~Gv~vck~k~~~~~g~~----~st~~~~~~~~~l~~msP~r~~sp 661 (1024)
T KOG1999|consen 586 DTVKVIGGPSKGREGEVLHIYRPFVFLHSRKNLENGGVFVCKEKNLILAGGK----KSTNSLAFNKGALAPMSPGRIQSP 661 (1024)
T ss_pred ceEEEecCCCCCccCccceeecceeeeeehhhcccCCeEEEecCCceecccc----CcccchhhcccccCCCCcccccCC
Confidence 9999999999999999999999999999999999999999999999999852 211101111111 23444211222
Q ss_pred ccchh--hcccCCCCCCCCCCCccccCcEEEEecCCCCCceeEEEeecCCeEEEEecCCceEEEEeCCcceeccCC----
Q 000637 227 KRSWQ--AREQNTEFKRGDRDGMFAVGQTLRIRVGPLKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLAEVRGK---- 300 (1378)
Q Consensus 227 ~rp~q--~rg~~r~fgRGGRd~D~LIGKTVKIrkGPYKGYlGiVKDaTgt~ARVELHSK~KtITVdKe~Lsvv~g~---- 300 (1378)
+.+.. ...+.+..+|++++++.||||||||+.||||||+|||||||+.+||||||++|++|+|++.+|.++...
T Consensus 662 ~~~~~~~ga~g~~gggrGg~rd~~l~GktVrI~~Gp~KG~~GivkD~~~~~arVELhs~~~ti~vd~~~~~~v~~~~~~g 741 (1024)
T KOG1999|consen 662 MGPSGGPGAFGGHGGGRGGNRDDSLLGKTVRIRLGPKKGYLGIVKDVNGDTARVELHSKCVTIKVDRLKRKIVGSTRDGG 741 (1024)
T ss_pred cCCCCCCCCcCcCccCccCcCcchhcCcEEEEecCCcccccceeEeccCCeeEEEEEeccEEEEechhhceEEeeccCCC
Confidence 22211 111122235666566899999999999999999999999999999999999999999999999876432
Q ss_pred ------------------------ccccccCCCCCCC-CCCCCCCCCCCCCCCCCCCCcccCCCCCCCCCC---CCCCCC
Q 000637 301 ------------------------SFITSTSDDQGSA-SFKPFDPLGAGGGSGDWMSAATTSAEGDRWNAG---GASAGR 352 (1378)
Q Consensus 301 ------------------------~t~~s~S~~P~s~-~~tP~~~~G~~~gs~~~~~G~~T~a~~~aWn~g---~~s~~~ 352 (1378)
.+++.++.+|.++ ++|||+ -++.+++|+|+|||||.+||++. +|+++.
T Consensus 742 ~~~sYg~~~~~~g~~~~~~~~~Gs~tp~~~s~tpl~~~s~tp~~----~~~~Tp~~dG~rTP~r~~aW~~~~~~tPa~~~ 817 (1024)
T KOG1999|consen 742 ETSSYGERTPGYGRVTPARYGMGSSTPMYGSNTPLWGGSRTPAR----DGGATPSHDGSRTPARGRAWNPYNGKTPARNF 817 (1024)
T ss_pred CccccccccccccccCccccCCCCcCccCCCCCCCCCcccCccc----cCCCCcCCCCCcCCCCCCCcCCCCCCCCcccc
Confidence 1222244444444 444444 25667789999999999999987 566655
Q ss_pred CCCCC
Q 000637 353 SSWPS 357 (1378)
Q Consensus 353 ~~W~~ 357 (1378)
+.|.+
T Consensus 818 ~~~~~ 822 (1024)
T KOG1999|consen 818 DNREP 822 (1024)
T ss_pred CCccc
Confidence 66644
No 2
>COG5164 SPT5 Transcription elongation factor [Transcription]
Probab=100.00 E-value=5.4e-54 Score=479.90 Aligned_cols=273 Identities=22% Similarity=0.237 Sum_probs=220.2
Q ss_pred ccccceeEEEEeeceEEecCCCCCHHHHhccCCCCCCcccchHHHHHHh-----------------hhccCCcEEEe---
Q 000637 2 MLKDGYLYKKVSIDSLSCWGVVPSEEELLKFQPSESNESADLEWLSQLY-----------------GERKKKRTTIV--- 61 (1378)
Q Consensus 2 mfkDGFLYKdVsIqSL~t~nVqPTLDEL~KF~~~~~de~~DLasLS~s~-----------------Geqkk~~vIVi--- 61 (1378)
.|+||||||.|+|++++|++|+||+|||.+|.+. .+.+||.+++++| |||+....||+
T Consensus 38 ~~~dgflvk~~Ris~~et~~~~pt~de~~~F~~~--~~dldl~s~~~s~kk~ha~fqpgD~~Evl~Geqrg~~gVV~~~~ 115 (607)
T COG5164 38 DYIDGFLVKVKRISERETLMRIPTNDEKNVFSII--CKDLDLYSYVESFKKQHAVFQPGDALEVLRGEQRGRVGVVPRQK 115 (607)
T ss_pred ccccceEEEEeeeceeeecccccccchhhhcCcc--ccccchhHHHHHHhhcccccCCCCeeeeecceecccceeecccc
Confidence 4899999999999999999999999999999987 4459999999988 44433333332
Q ss_pred -------------------------cc--------CCCcCcC--------------------------------CCCCCC
Q 000637 62 -------------------------GK--------GGDKGEG--------------------------------SSGSSL 76 (1378)
Q Consensus 62 -------------------------~~--------G~hkgEs--------------------------------sTG~~s 76 (1378)
.+ |.|+++. .+.+.+
T Consensus 116 ~~I~tm~~~~~~rl~~p~~~lRk~f~~gD~vkVI~g~~~~d~g~V~rI~~~~vtF~s~~~~~e~tI~sr~l~ks~~tta~ 195 (607)
T COG5164 116 EMIETMTYHFEQRLCGPWGRLRKGFYKGDLVKVIEGGEMVDIGTVPRIDGEKVTFNSENFKSESTIKSRGLSKSIDTTAT 195 (607)
T ss_pred cceeeeeeccCceeecchhhhhcccccCCeEEEeccccccccceEEEecCceeEEccccccccceEEeccccccccccch
Confidence 12 2333221 112234
Q ss_pred CCccEeceeEeecCCceEEEEEeccCCceEEccCCCCCCcEEEEeccccccCCCCCc--cccccCCCCeeccCCeEEEec
Q 000637 77 ENSFELYELVCFGRKDFGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMK--FTALDQSMKVISLNDTARVSE 154 (1378)
Q Consensus 77 lG~YELHDLVQLD~qTVGVIVrVEKDDsFKVLdqngDrGkVvtVKpseIk~Kr~dRR--~vAlD~nGNtIrVgDtVKVVd 154 (1378)
...|+|||||+|+..+|.||+.|++ |.|+|+++. ++|.+|.|.+|..|+..+| ++++|+++++|+++|.|+|+-
T Consensus 196 ss~Y~lhd~V~l~~~~vaci~sid~-Dv~kvide~---g~v~t~~~~sI~~kv~~~Rg~~i~~d~ng~eI~igd~VvE~~ 271 (607)
T COG5164 196 SSIYKLHDYVDLFLEKVACINSIDF-DVEKVIDEL---GEVHTACPISIGDKVRVTRGELIGMDGNGREISIGDAVVESR 271 (607)
T ss_pred hhhhhhhhhhhhhhcceeEEeeccc-chhhhhhhc---CceeEecchhhhhhhecccceeEeeccccceEeeceeEEEec
Confidence 5889999999999999999999999 599999998 4899999999999987777 489999999999999999999
Q ss_pred CCCCCceeEEEEEEcceEEEEeccccccccEEEEeCCceeecccccccCCCCCCC-CCCCCCCCCCCCCCCCC--ccchh
Q 000637 155 GPSKDRQGIVKKIYRGILFIYDENETENGGYFCSKSQHCEKTKVEACEGKGGGSG-ASGFEEFPSSPKSPLSP--KRSWQ 231 (1378)
Q Consensus 155 GP~KGRQG~VlHIyRg~LFL~sR~i~ENGGIFVvrArnVvlVgg~asnsK~g~s~-~~~f~dl~sSp~spmSP--~rp~q 231 (1378)
| .++||+||||||.|+|+++++|.||+||||++.++|++|+. |+.... ..+| ..|+||+.- +.|
T Consensus 272 g--~~~egq~l~i~~~f~f~~t~~i~ennGVfv~~~~nv~~VAt-----kd~~~s~k~dl----~kmnp~v~~~~~~p-- 338 (607)
T COG5164 272 G--GKFEGQSLGIVKHFDFGETVSIKENNGVFVKIEGNVCIVAT-----KDFTESLKVDL----DKMNPPVTVNLQNP-- 338 (607)
T ss_pred C--CceeeEEEEEEEEEeeeeeeeeeccCceEEEecCceeEEEe-----ccchhhhcccH----hhcCchhhcCCCCC--
Confidence 9 45999999999999999999999999999999999999973 554321 1112 133433221 011
Q ss_pred hcccCCCCCC--CCCCCccccCcEEEEecCCCCCceeEEEeecCCeEEEEecCCceEEEEeCCcceecc
Q 000637 232 AREQNTEFKR--GDRDGMFAVGQTLRIRVGPLKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLAEVR 298 (1378)
Q Consensus 232 ~rg~~r~fgR--GGRd~D~LIGKTVKIrkGPYKGYlGiVKDaTgt~ARVELHSK~KtITVdKe~Lsvv~ 298 (1378)
.-..+.| ++| |++||||||||.|+|||+||+||||++..||||||+++|.|||+|+.|.+..
T Consensus 339 ---~~~~l~r~i~gR--d~aigktVrIr~g~yKG~lGVVKdv~~~~arVeLhs~nK~VTI~K~~l~y~~ 402 (607)
T COG5164 339 ---KTNELERKIVGR--DPAIGKTVRIRCGEYKGHLGVVKDVDRNIARVELHSNNKFVTIEKSRLAYLG 402 (607)
T ss_pred ---cchhhhcccccc--ccccCceEEEeecccccccceeeeccCceEEEEEecCCceEEeehhheEEec
Confidence 0112223 245 7999999999999999999999999999999999999999999999999753
No 3
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=98.72 E-value=1.7e-07 Score=115.41 Aligned_cols=162 Identities=19% Similarity=0.263 Sum_probs=99.2
Q ss_pred CCCccccccCCCCeeccCCeEEEecCCCCCceeEEEEEEcceEEEEeccccccccEEEEeCCceeecccccccCCCCCCC
Q 000637 130 FDMKFTALDQSMKVISLNDTARVSEGPSKDRQGIVKKIYRGILFIYDENETENGGYFCSKSQHCEKTKVEACEGKGGGSG 209 (1378)
Q Consensus 130 ~dRR~vAlD~nGNtIrVgDtVKVVdGP~KGRQG~VlHIyRg~LFL~sR~i~ENGGIFVvrArnVvlVgg~asnsK~g~s~ 209 (1378)
....+.+| .+.|+++|.||||.|+|+|.+|.|+.|++++|||++....|+..|||+.-..|+.|.+ ...+.+..
T Consensus 449 l~~~~~eL---rKyF~~GDhVKVi~G~~eG~tGlVvrVe~~~vi~~Sd~t~eel~Vf~~dlq~c~ev~~--gv~~~ge~- 522 (1024)
T KOG1999|consen 449 LEVPASEL---RKYFEPGDHVKVIAGRYEGDTGLVVRVEQGDVILLSDLTMEELKVFARDLQLCSEVTL--GVEKSGEY- 522 (1024)
T ss_pred cccchHhh---hhhccCCCeEEEEeccccCCcceEEEEeCCeEEEEecCccceeeEEehhcccchheee--cccccccc-
Confidence 34444555 7889999999999999999999999999999999999999999999999998887764 11121111
Q ss_pred CCCCCCCCC--------------------CCCCCCCCccchh--hcccCCCCC-CCCCCCccccCcEEEEecCCCCCcee
Q 000637 210 ASGFEEFPS--------------------SPKSPLSPKRSWQ--AREQNTEFK-RGDRDGMFAVGQTLRIRVGPLKGYLC 266 (1378)
Q Consensus 210 ~~~f~dl~s--------------------Sp~spmSP~rp~q--~rg~~r~fg-RGGRd~D~LIGKTVKIrkGPYKGYlG 266 (1378)
-+-+|.. .|......-++.. ..-..+... --.+...--|.-+|+++.||.|+-.|
T Consensus 523 --e~hdlVqLd~~~vgvI~rle~e~~~vl~~~g~v~~i~~~~i~~kk~~r~~~~~D~~~n~I~~kD~Vkvi~Gp~~g~~G 600 (1024)
T KOG1999|consen 523 --ELHDLVQLDNQNVGVIVRLERETFQVLGMNGKVVTIRKSSITKKKDNRKAVAVDRNGNEIRVKDTVKVIGGPSKGREG 600 (1024)
T ss_pred --cccceeecCCCcEEEEEEecchheeeecCcCceEEEeechhhhhhhhhhheeecccCCeecccceEEEecCCCCCccC
Confidence 0111111 0110000000000 000000000 00111133467899999999999999
Q ss_pred EEEeecCCeEEEEecCCc-----eEEEEeCCcceeccCCc
Q 000637 267 RVLAVRYSDVTVKLDSQQ-----KILTVKGEHLAEVRGKS 301 (1378)
Q Consensus 267 iVKDaTgt~ARVELHSK~-----KtITVdKe~Lsvv~g~~ 301 (1378)
-|+.+-...+ -||+.+ -++-++..+|.++..+.
T Consensus 601 ~v~~i~r~~~--F~h~r~~~En~Gv~vck~k~~~~~g~~~ 638 (1024)
T KOG1999|consen 601 EVLHIYRPFV--FLHSRKNLENGGVFVCKEKNLILAGGKK 638 (1024)
T ss_pred ccceeeccee--eeeehhhcccCCeEEEecCCceeccccC
Confidence 9999976543 344433 24445666666665544
No 4
>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=97.18 E-value=0.00045 Score=54.51 Aligned_cols=32 Identities=31% Similarity=0.675 Sum_probs=28.7
Q ss_pred cCcEEEEecCCCCCceeEEEeecCCeEEEEec
Q 000637 250 VGQTLRIRVGPLKGYLCRVLAVRYSDVTVKLD 281 (1378)
Q Consensus 250 IGKTVKIrkGPYKGYlGiVKDaTgt~ARVELH 281 (1378)
.|.+|+|+.|||||+.|+|+++....+||.++
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 37899999999999999999999998887764
No 5
>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]
Probab=97.02 E-value=0.0023 Score=80.12 Aligned_cols=50 Identities=10% Similarity=0.110 Sum_probs=23.0
Q ss_pred eccCCeEEEecCCCCCceeEEEEEEcce--EEEEeccccccccEEEEeCCceeecc
Q 000637 144 ISLNDTARVSEGPSKDRQGIVKKIYRGI--LFIYDENETENGGYFCSKSQHCEKTK 197 (1378)
Q Consensus 144 IrVgDtVKVVdGP~KGRQG~VlHIyRg~--LFL~sR~i~ENGGIFVvrArnVvlVg 197 (1378)
|..+|+|+|.-- . -.|.|+.|-.-+ .||.+-.. --.+++||..+.++.+.
T Consensus 390 v~dn~v~~I~ge-t--gcgk~tq~aq~iLe~~~~ns~g-~~~na~v~qprrisais 441 (1282)
T KOG0921|consen 390 VAENRVVIIKGE-T--GCGKSTQVAQFLLESFLENSNG-ASFNAVVSQPRRISAIS 441 (1282)
T ss_pred HhcCceeeEeec-c--cccchhHHHHHHHHHHhhcccc-ccccceeccccccchHH
Confidence 455677766532 1 245555554432 23332211 11234666666665543
No 6
>COG5164 SPT5 Transcription elongation factor [Transcription]
Probab=96.91 E-value=0.0022 Score=75.66 Aligned_cols=156 Identities=20% Similarity=0.196 Sum_probs=90.9
Q ss_pred CccccceeEEEEeeceEEecCCCCCHHHHhccCCCCCCcccchHHHHHHhhhccCCcEE--------------EeccCCC
Q 000637 1 MMLKDGYLYKKVSIDSLSCWGVVPSEEELLKFQPSESNESADLEWLSQLYGERKKKRTT--------------IVGKGGD 66 (1378)
Q Consensus 1 lmfkDGFLYKdVsIqSL~t~nVqPTLDEL~KF~~~~~de~~DLasLS~s~Geqkk~~vI--------------Vi~~G~h 66 (1378)
|-|+|.||.|.+-|-+|.. ||.|++|||.+|...- ..+|-.-+-.+ ..++| |+|.++.
T Consensus 202 hd~V~l~~~~vaci~sid~-Dv~kvide~g~v~t~~------~~sI~~kv~~~-Rg~~i~~d~ng~eI~igd~VvE~~g~ 273 (607)
T COG5164 202 HDYVDLFLEKVACINSIDF-DVEKVIDELGEVHTAC------PISIGDKVRVT-RGELIGMDGNGREISIGDAVVESRGG 273 (607)
T ss_pred hhhhhhhhcceeEEeeccc-chhhhhhhcCceeEec------chhhhhhhecc-cceeEeeccccceEeeceeEEEecCC
Confidence 4589999999999999887 9999999999997530 00111101011 11122 2233333
Q ss_pred cCcCCCCCCCCCccEeceeEeec--CCceEEEEEeccCCceEEcc-CCCCC--Cc------EEEEeccccccCCCCCccc
Q 000637 67 KGEGSSGSSLENSFELYELVCFG--RKDFGLIVGMEKDDHYKILK-EGSEG--PA------VVTVERRTLKNGPFDMKFT 135 (1378)
Q Consensus 67 kgEssTG~~slG~YELHDLVQLD--~qTVGVIVrVEKDDsFKVLd-qngDr--Gk------VvtVKpseIk~Kr~dRR~v 135 (1378)
+-|+ ..|+-|.-+|||.-- ...-||+|.++++ ...|-. ..-+. -. -++|+|+--+.+-..|.+
T Consensus 274 ~~eg----q~l~i~~~f~f~~t~~i~ennGVfv~~~~n-v~~VAtkd~~~s~k~dl~kmnp~v~~~~~~p~~~~l~r~i- 347 (607)
T COG5164 274 KFEG----QSLGIVKHFDFGETVSIKENNGVFVKIEGN-VCIVATKDFTESLKVDLDKMNPPVTVNLQNPKTNELERKI- 347 (607)
T ss_pred ceee----EEEEEEEEEeeeeeeeeeccCceEEEecCc-eeEEEeccchhhhcccHhhcCchhhcCCCCCcchhhhccc-
Confidence 3333 345666667776542 2467899998885 333322 11000 00 122222221111111112
Q ss_pred cccCCCCeeccCCeEEEecCCCCCceeEEEEEEcceEEE
Q 000637 136 ALDQSMKVISLNDTARVSEGPSKDRQGIVKKIYRGILFI 174 (1378)
Q Consensus 136 AlD~nGNtIrVgDtVKVVdGP~KGRQG~VlHIyRg~LFL 174 (1378)
-+....++-+|+|--|||||.-|+|+.+-+..+-|
T Consensus 348 ----~gRd~aigktVrIr~g~yKG~lGVVKdv~~~~arV 382 (607)
T COG5164 348 ----VGRDPAIGKTVRIRCGEYKGHLGVVKDVDRNIARV 382 (607)
T ss_pred ----cccccccCceEEEeecccccccceeeeccCceEEE
Confidence 25667899999999999999999999999987543
No 7
>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=96.69 E-value=0.0018 Score=51.17 Aligned_cols=29 Identities=31% Similarity=0.489 Sum_probs=25.8
Q ss_pred cCCeEEEecCCCCCceeEEEEEEcceEEE
Q 000637 146 LNDTARVSEGPSKDRQGIVKKIYRGILFI 174 (1378)
Q Consensus 146 VgDtVKVVdGP~KGRQG~VlHIyRg~LFL 174 (1378)
+||+|+|+.|||+|+.|+|++|.+...++
T Consensus 1 ~Gd~V~V~~G~~~G~~G~I~~i~~~~~~V 29 (32)
T PF00467_consen 1 VGDTVKVISGPFKGKIGKIVEIDRSKVRV 29 (32)
T ss_dssp TTSEEEESSSTTTTEEEEEEEEETTTTEE
T ss_pred CCCEEEEeEcCCCCceEEEEEEECCCCEE
Confidence 58999999999999999999999985333
No 8
>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=96.29 E-value=0.0067 Score=61.25 Aligned_cols=51 Identities=29% Similarity=0.468 Sum_probs=44.6
Q ss_pred cccCcEEEEecCCCCCceeEEEeec--CCeEEEEecCCceE--EEEeCCcceecc
Q 000637 248 FAVGQTLRIRVGPLKGYLCRVLAVR--YSDVTVKLDSQQKI--LTVKGEHLAEVR 298 (1378)
Q Consensus 248 ~LIGKTVKIrkGPYKGYlGiVKDaT--gt~ARVELHSK~Kt--ITVdKe~Lsvv~ 298 (1378)
..+|..|+|+.|||||+.|+|+++. ...|+|+|...... |+|+-+.|..+.
T Consensus 87 ~~~Gd~V~I~~GPf~G~~g~v~~~d~~k~~v~v~l~~~~~~~~v~v~~~~l~~~~ 141 (145)
T TIGR00405 87 IKKGDIVEIISGPFKGERAKVIRVDESKEEVTLELIEAAVPIPVTVKGDQVRIIQ 141 (145)
T ss_pred cCCCCEEEEeecCCCCCeEEEEEEcCCCCEEEEEEEEcCccceEEEeeeEEEEec
Confidence 4589999999999999999999995 56899999998888 999988887654
No 9
>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]
Probab=95.98 E-value=0.031 Score=70.64 Aligned_cols=6 Identities=50% Similarity=0.263 Sum_probs=2.4
Q ss_pred EEEecC
Q 000637 277 TVKLDS 282 (1378)
Q Consensus 277 RVELHS 282 (1378)
|||||+
T Consensus 527 ~v~lms 532 (1282)
T KOG0921|consen 527 RVVLMS 532 (1282)
T ss_pred hhhhhh
Confidence 344443
No 10
>PRK08559 nusG transcription antitermination protein NusG; Validated
Probab=95.92 E-value=0.017 Score=59.58 Aligned_cols=52 Identities=31% Similarity=0.463 Sum_probs=44.1
Q ss_pred ccccCcEEEEecCCCCCceeEEEeec--CCeEEEEecCCceE--EEEeCCcceecc
Q 000637 247 MFAVGQTLRIRVGPLKGYLCRVLAVR--YSDVTVKLDSQQKI--LTVKGEHLAEVR 298 (1378)
Q Consensus 247 D~LIGKTVKIrkGPYKGYlGiVKDaT--gt~ARVELHSK~Kt--ITVdKe~Lsvv~ 298 (1378)
...+|..|+|+.|||||+.|+|+++. ...|+|+|--+.-. |+|+.+.|.++.
T Consensus 94 ~~~~G~~V~I~~Gpf~g~~g~V~~vd~~k~~v~v~ll~~~~~~pv~v~~~~~~~~~ 149 (153)
T PRK08559 94 GIKEGDIVELIAGPFKGEKARVVRVDESKEEVTVELLEAAVPIPVTVRGDQVRVVK 149 (153)
T ss_pred CCCCCCEEEEeccCCCCceEEEEEEcCCCCEEEEEEECCcceeeEEEeccEEEEec
Confidence 36689999999999999999999996 45677887777755 999999998765
No 11
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=95.77 E-value=0.011 Score=44.03 Aligned_cols=26 Identities=35% Similarity=0.503 Sum_probs=24.4
Q ss_pred eccCCeEEEecCCCCCceeEEEEEEc
Q 000637 144 ISLNDTARVSEGPSKDRQGIVKKIYR 169 (1378)
Q Consensus 144 IrVgDtVKVVdGP~KGRQG~VlHIyR 169 (1378)
++++|.|+|+.||++|++|+|+.|.+
T Consensus 2 ~~~G~~V~I~~G~~~g~~g~i~~i~~ 27 (28)
T smart00739 2 FEVGDTVRVIAGPFKGKVGKVLEVDG 27 (28)
T ss_pred CCCCCEEEEeECCCCCcEEEEEEEcC
Confidence 68999999999999999999999975
No 12
>KOG3973 consensus Uncharacterized conserved glycine-rich protein [Function unknown]
Probab=95.51 E-value=0.065 Score=62.16 Aligned_cols=13 Identities=62% Similarity=1.247 Sum_probs=7.4
Q ss_pred CCCCCCCCCCCCC
Q 000637 1105 GGRGRGRRDQGGG 1117 (1378)
Q Consensus 1105 ggrg~~~~~~~gg 1117 (1378)
|||++++|+++||
T Consensus 442 ggr~gggrgrggg 454 (465)
T KOG3973|consen 442 GGRDGGGRGRGGG 454 (465)
T ss_pred CCCCCCCCCCCCC
Confidence 5565566666544
No 13
>CHL00141 rpl24 ribosomal protein L24; Validated
Probab=95.49 E-value=0.017 Score=55.00 Aligned_cols=29 Identities=28% Similarity=0.449 Sum_probs=27.2
Q ss_pred eeccCCeEEEecCCCCCceeEEEEEEcce
Q 000637 143 VISLNDTARVSEGPSKDRQGIVKKIYRGI 171 (1378)
Q Consensus 143 tIrVgDtVKVVdGP~KGRQG~VlHIyRg~ 171 (1378)
.|+.||+|.||.|+++|++|+|++|++..
T Consensus 8 ~I~~GD~V~Vi~G~dKGK~G~V~~V~~~~ 36 (83)
T CHL00141 8 HVKIGDTVKIISGSDKGKIGEVLKIIKKS 36 (83)
T ss_pred cccCCCEEEEeEcCCCCcEEEEEEEEcCC
Confidence 68999999999999999999999999853
No 14
>PRK12281 rplX 50S ribosomal protein L24; Reviewed
Probab=95.39 E-value=0.02 Score=53.88 Aligned_cols=28 Identities=21% Similarity=0.325 Sum_probs=26.5
Q ss_pred eeccCCeEEEecCCCCCceeEEEEEEcc
Q 000637 143 VISLNDTARVSEGPSKDRQGIVKKIYRG 170 (1378)
Q Consensus 143 tIrVgDtVKVVdGP~KGRQG~VlHIyRg 170 (1378)
.|+.+|+|+||.|+++|++|+|+.|++.
T Consensus 6 ~I~kGD~V~Vi~G~dKGK~G~V~~V~~~ 33 (76)
T PRK12281 6 KVKKGDMVKVIAGDDKGKTGKVLAVLPK 33 (76)
T ss_pred cccCCCEEEEeEcCCCCcEEEEEEEEcC
Confidence 6999999999999999999999999974
No 15
>PRK00004 rplX 50S ribosomal protein L24; Reviewed
Probab=95.31 E-value=0.023 Score=56.08 Aligned_cols=28 Identities=32% Similarity=0.374 Sum_probs=26.5
Q ss_pred eeccCCeEEEecCCCCCceeEEEEEEcc
Q 000637 143 VISLNDTARVSEGPSKDRQGIVKKIYRG 170 (1378)
Q Consensus 143 tIrVgDtVKVVdGP~KGRQG~VlHIyRg 170 (1378)
.|+.+|+|+||.|+++|++|+|+.|++.
T Consensus 4 ~i~kGD~V~Vi~G~dKGk~G~V~~V~~~ 31 (105)
T PRK00004 4 KIKKGDTVIVIAGKDKGKRGKVLKVLPK 31 (105)
T ss_pred cccCCCEEEEeEcCCCCcEEEEEEEEcC
Confidence 6899999999999999999999999964
No 16
>TIGR01956 NusG_myco NusG family protein. This model represents a family of Mycoplasma proteins orthologous to the bacterial transcription termination/antitermination factor NusG. These sequences from Mycoplasma are notably diverged (long branches in a Neighbor-joining phylogenetic tree) from the bacterial species. And although NusA and ribosomal protein S10 (NusE) appear to be present, NusB may be absent in Mycoplasmas calling into question whether these species have a functional Nus system including this family as a member.
Probab=95.24 E-value=0.066 Score=60.25 Aligned_cols=44 Identities=25% Similarity=0.441 Sum_probs=36.1
Q ss_pred ccccCcEEEEecCCCCCceeEEEeec--CCeEEEEecCCceEEEEe
Q 000637 247 MFAVGQTLRIRVGPLKGYLCRVLAVR--YSDVTVKLDSQQKILTVK 290 (1378)
Q Consensus 247 D~LIGKTVKIrkGPYKGYlGiVKDaT--gt~ARVELHSK~KtITVd 290 (1378)
+..+|.+|+|+.|||+|+.|+|.++. ...|+|+|+.-.|.+.|.
T Consensus 205 ~f~vGd~VrI~dGPF~GfeG~I~eid~~k~Rv~VlV~IfGR~TpVe 250 (258)
T TIGR01956 205 KFRVGNFVKIVDGPFKGIVGKIKKIDQEKKKAIVEVEILGKSVDVD 250 (258)
T ss_pred CCCCCCEEEEEecCCCCcEEEEEEEeCCCCEEEEEEEecCCcEEEE
Confidence 35689999999999999999999996 577888877766655544
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=94.45 E-value=0.061 Score=55.51 Aligned_cols=47 Identities=21% Similarity=0.372 Sum_probs=36.2
Q ss_pred cccCcEEEEecCCCCCceeEEEeec-C-CeEEEEecCCce--EEEEeCCcc
Q 000637 248 FAVGQTLRIRVGPLKGYLCRVLAVR-Y-SDVTVKLDSQQK--ILTVKGEHL 294 (1378)
Q Consensus 248 ~LIGKTVKIrkGPYKGYlGiVKDaT-g-t~ARVELHSK~K--tITVdKe~L 294 (1378)
..+|..|+|+.||++|+.|+|+.+. . ..|+|+|+--.+ .|.|+-++|
T Consensus 120 ~~~G~~V~I~~Gpf~G~~g~v~~~~~~~~r~~V~v~~~g~~~~v~v~~~~l 170 (172)
T TIGR00922 120 FEVGEQVRVNDGPFANFTGTVEEVDYEKSKLKVSVSIFGRETPVELEFSQV 170 (172)
T ss_pred CCCCCEEEEeecCCCCcEEEEEEEcCCCCEEEEEEEECCCceEEEEcHHHe
Confidence 3479999999999999999999996 3 477777776665 455555444
No 18
>TIGR01955 RfaH transcriptional activator RfaH. This model represents the transcriptional activator protein, RfaH. This protein is most closely related to the transcriptional termination/antitermination protein NusG (TIGR00922) and contains the KOW motif (pfam00467). This protein appears to be limited to the gamma proteobacteria. In E. coli, this gene appears to control the expression of haemolysin, sex factor and lipopolysaccharide genes.
Probab=94.41 E-value=0.071 Score=54.16 Aligned_cols=43 Identities=21% Similarity=0.221 Sum_probs=35.4
Q ss_pred cccCcEEEEecCCCCCceeEEEeecC-CeEEEEecCCceEEEEe
Q 000637 248 FAVGQTLRIRVGPLKGYLCRVLAVRY-SDVTVKLDSQQKILTVK 290 (1378)
Q Consensus 248 ~LIGKTVKIrkGPYKGYlGiVKDaTg-t~ARVELHSK~KtITVd 290 (1378)
..+|..|+|+.||++||.|+|+++.. ..|.|+|+--.+.+.|.
T Consensus 109 ~~~G~~V~V~~GPf~g~~g~v~~~~~~~r~~v~l~~~gr~~~v~ 152 (159)
T TIGR01955 109 PYKGDKVRITDGAFAGFEAIFLEPDGEKRSMLLLNMIGKQIKVS 152 (159)
T ss_pred CCCCCEEEEeccCCCCcEEEEEEECCCceEEEEEhhhCCceEEE
Confidence 45799999999999999999999974 46888888777765543
No 19
>KOG3262 consensus H/ACA small nucleolar RNP component GAR1 [Translation, ribosomal structure and biogenesis]
Probab=94.24 E-value=0.092 Score=56.82 Aligned_cols=20 Identities=75% Similarity=1.498 Sum_probs=8.2
Q ss_pred CCCCCCCCCCCCCCCCCCCCC
Q 000637 1090 RGGFGGRGSSDRGGFGGRGRG 1110 (1378)
Q Consensus 1090 rGG~gGrg~g~rgg~ggrg~~ 1110 (1378)
+++|.+|+ +.+++|.+|++.
T Consensus 194 rGG~~~Rg-g~ggg~rgrgR~ 213 (215)
T KOG3262|consen 194 RGGFRGRG-GHGGGFRGRGRG 213 (215)
T ss_pred CCCccccC-CCCCCCCCCCCC
Confidence 44443333 234444444443
No 20
>PRK05609 nusG transcription antitermination protein NusG; Validated
Probab=94.07 E-value=0.083 Score=54.75 Aligned_cols=48 Identities=21% Similarity=0.316 Sum_probs=36.8
Q ss_pred cccCcEEEEecCCCCCceeEEEeec--CCeEEEEecCCceE--EEEeCCcce
Q 000637 248 FAVGQTLRIRVGPLKGYLCRVLAVR--YSDVTVKLDSQQKI--LTVKGEHLA 295 (1378)
Q Consensus 248 ~LIGKTVKIrkGPYKGYlGiVKDaT--gt~ARVELHSK~Kt--ITVdKe~Ls 295 (1378)
...|..|+|+.|||+|+.|+|+.+. ...|+|+|+--.+. |.|+-+.|.
T Consensus 127 ~~~Gd~VrI~~GPf~G~~g~v~~i~~~~~r~~v~l~~~G~~~~v~l~~~~l~ 178 (181)
T PRK05609 127 FEVGEMVRVIDGPFADFNGTVEEVDYEKSKLKVLVSIFGRETPVELEFSQVE 178 (181)
T ss_pred CCCCCEEEEeccCCCCCEEEEEEEeCCCCEEEEEEEECCCceEEEEchHHEE
Confidence 3479999999999999999999996 34677777666654 555555554
No 21
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=94.05 E-value=0.075 Score=39.63 Aligned_cols=25 Identities=44% Similarity=0.715 Sum_probs=22.9
Q ss_pred ccCcEEEEecCCCCCceeEEEeecC
Q 000637 249 AVGQTLRIRVGPLKGYLCRVLAVRY 273 (1378)
Q Consensus 249 LIGKTVKIrkGPYKGYlGiVKDaTg 273 (1378)
.+|+.|+|+.|||+|+.|+|+++..
T Consensus 3 ~~G~~V~I~~G~~~g~~g~i~~i~~ 27 (28)
T smart00739 3 EVGDTVRVIAGPFKGKVGKVLEVDG 27 (28)
T ss_pred CCCCEEEEeECCCCCcEEEEEEEcC
Confidence 4789999999999999999999865
No 22
>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=93.90 E-value=0.072 Score=52.75 Aligned_cols=28 Identities=32% Similarity=0.437 Sum_probs=26.4
Q ss_pred eeccCCeEEEecCCCCCceeEEEEEEcc
Q 000637 143 VISLNDTARVSEGPSKDRQGIVKKIYRG 170 (1378)
Q Consensus 143 tIrVgDtVKVVdGP~KGRQG~VlHIyRg 170 (1378)
.|+.||+|.||.|+.+|++|+|++|++.
T Consensus 3 ~ikkGD~V~Vi~G~dKGK~G~V~~V~~~ 30 (104)
T TIGR01079 3 KIKKGDTVKVISGKDKGKRGKVLKVLPK 30 (104)
T ss_pred cccCCCEEEEeEcCCCCcEEEEEEEEcC
Confidence 5899999999999999999999999974
No 23
>PRK01191 rpl24p 50S ribosomal protein L24P; Validated
Probab=93.79 E-value=0.13 Score=52.50 Aligned_cols=34 Identities=21% Similarity=0.303 Sum_probs=29.7
Q ss_pred eeccCCeEEEecCCCCCceeEEEEEEcc--eEEEEe
Q 000637 143 VISLNDTARVSEGPSKDRQGIVKKIYRG--ILFIYD 176 (1378)
Q Consensus 143 tIrVgDtVKVVdGP~KGRQG~VlHIyRg--~LFL~s 176 (1378)
.|+++|+|+||.|++||++|+|+.|++. .|+|-.
T Consensus 45 ~IkkGD~V~VisG~~KGk~GkV~~V~~~~~~V~VeG 80 (120)
T PRK01191 45 PVRKGDTVKVMRGDFKGEEGKVVEVDLKRGRIYVEG 80 (120)
T ss_pred eEeCCCEEEEeecCCCCceEEEEEEEcCCCEEEEeC
Confidence 6999999999999999999999999875 465543
No 24
>KOG3262 consensus H/ACA small nucleolar RNP component GAR1 [Translation, ribosomal structure and biogenesis]
Probab=93.48 E-value=0.13 Score=55.65 Aligned_cols=10 Identities=80% Similarity=1.660 Sum_probs=4.8
Q ss_pred CCCCCCCCCC
Q 000637 1055 SDRGGFGGRG 1064 (1378)
Q Consensus 1055 ~~rGGfgGrg 1064 (1378)
..|++|++|+
T Consensus 170 ~~rGg~~grG 179 (215)
T KOG3262|consen 170 GGRGGFGGRG 179 (215)
T ss_pred CCcCCCCCCC
Confidence 3455554443
No 25
>PRK09014 rfaH transcriptional activator RfaH; Provisional
Probab=93.20 E-value=0.13 Score=52.74 Aligned_cols=43 Identities=14% Similarity=0.088 Sum_probs=34.9
Q ss_pred cccCcEEEEecCCCCCceeEEEeecC-CeEEEEecCCceEEEEe
Q 000637 248 FAVGQTLRIRVGPLKGYLCRVLAVRY-SDVTVKLDSQQKILTVK 290 (1378)
Q Consensus 248 ~LIGKTVKIrkGPYKGYlGiVKDaTg-t~ARVELHSK~KtITVd 290 (1378)
...|.+|+|+.||++|+.|+|+++.+ ..+.|+|+.-.+.+.|.
T Consensus 110 ~~~G~~V~I~~Gp~~g~eg~v~~~~~~~r~~v~v~~~gr~~~v~ 153 (162)
T PRK09014 110 PKPGDKVIITEGAFEGLQAIYTEPDGEARSILLLNLLNKQVKHS 153 (162)
T ss_pred CCCCCEEEEecCCCCCcEEEEEEeCCCeEEEEeehhhCCcEEEE
Confidence 34799999999999999999999964 47778888777655543
No 26
>PTZ00194 60S ribosomal protein L26; Provisional
Probab=93.06 E-value=0.11 Score=54.11 Aligned_cols=29 Identities=31% Similarity=0.484 Sum_probs=27.3
Q ss_pred eeccCCeEEEecCCCCCceeEEEEEEcce
Q 000637 143 VISLNDTARVSEGPSKDRQGIVKKIYRGI 171 (1378)
Q Consensus 143 tIrVgDtVKVVdGP~KGRQG~VlHIyRg~ 171 (1378)
.|+.+|+|+||.|.++|++|.|+.|++..
T Consensus 46 ~IkkGD~V~Vi~Gk~KGk~GkV~~V~~k~ 74 (143)
T PTZ00194 46 PVRKDDEVMVVRGHHKGREGKVTAVYRKK 74 (143)
T ss_pred eeecCCEEEEecCCCCCCceEEEEEEcCC
Confidence 69999999999999999999999998864
No 27
>COG0250 NusG Transcription antiterminator [Transcription]
Probab=92.65 E-value=0.18 Score=53.91 Aligned_cols=44 Identities=25% Similarity=0.396 Sum_probs=37.5
Q ss_pred ccccCcEEEEecCCCCCceeEEEeecCC--eEEEEecCCceEEEEe
Q 000637 247 MFAVGQTLRIRVGPLKGYLCRVLAVRYS--DVTVKLDSQQKILTVK 290 (1378)
Q Consensus 247 D~LIGKTVKIrkGPYKGYlGiVKDaTgt--~ARVELHSK~KtITVd 290 (1378)
+..+|..|+|+.|||+|+.|+|.++... .++|+|..-.+.+.|.
T Consensus 123 ~~e~Gd~VrI~~GpFa~f~g~V~evd~ek~~~~v~v~ifgr~tPVe 168 (178)
T COG0250 123 DFEPGDVVRIIDGPFAGFKAKVEEVDEEKGKLKVEVSIFGRPTPVE 168 (178)
T ss_pred cCCCCCEEEEeccCCCCccEEEEEEcCcCcEEEEEEEEeCCceEEE
Confidence 5778999999999999999999999876 7788887777766653
No 28
>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=92.30 E-value=0.18 Score=50.96 Aligned_cols=29 Identities=24% Similarity=0.296 Sum_probs=27.0
Q ss_pred eeccCCeEEEecCCCCCceeEEEEEEcce
Q 000637 143 VISLNDTARVSEGPSKDRQGIVKKIYRGI 171 (1378)
Q Consensus 143 tIrVgDtVKVVdGP~KGRQG~VlHIyRg~ 171 (1378)
.|+.||+|+||.|+++|++|+|+.|.+.-
T Consensus 41 ~IkkGD~V~Vi~Gk~KGk~GkV~~V~~~~ 69 (114)
T TIGR01080 41 PVRKGDKVRIMRGDFKGHEGKVSKVDLKR 69 (114)
T ss_pred eeecCCEEEEecCCCCCCEEEEEEEEcCC
Confidence 79999999999999999999999998653
No 29
>PRK09014 rfaH transcriptional activator RfaH; Provisional
Probab=91.73 E-value=0.46 Score=48.89 Aligned_cols=60 Identities=13% Similarity=0.009 Sum_probs=37.4
Q ss_pred ceEEccCCCCCCcEEEEeccccccCCCCCccccccCCCCeeccCCeEEEecCCCCCceeEEEEEE
Q 000637 104 HYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVSEGPSKDRQGIVKKIY 168 (1378)
Q Consensus 104 sFKVLdqngDrGkVvtVKpseIk~Kr~dRR~vAlD~nGNtIrVgDtVKVVdGP~KGRQG~VlHIy 168 (1378)
...+|... .+...|...+|.. +..... .....-..+.+||.|+|++||++|.+|+|+.|-
T Consensus 75 v~~~v~~g---~~p~~I~~~ei~~-l~~~~~-~~~~~~~~~~~G~~V~I~~Gp~~g~eg~v~~~~ 134 (162)
T PRK09014 75 VSHFVRFG---AQPAIVPSDVIYQ-LSVYKP-EKIVDPETPKPGDKVIITEGAFEGLQAIYTEPD 134 (162)
T ss_pred cceEeccC---CCccccCHHHHHH-HHhhcc-cccccccCCCCCCEEEEecCCCCCcEEEEEEeC
Confidence 55566532 1345677777742 111100 000112348899999999999999999999984
No 30
>COG0198 RplX Ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=91.71 E-value=0.23 Score=49.60 Aligned_cols=30 Identities=27% Similarity=0.359 Sum_probs=27.6
Q ss_pred CeeccCCeEEEecCCCCCceeEEEEEEcce
Q 000637 142 KVISLNDTARVSEGPSKDRQGIVKKIYRGI 171 (1378)
Q Consensus 142 NtIrVgDtVKVVdGP~KGRQG~VlHIyRg~ 171 (1378)
..|+.+|+|+||.|.+||++|.|+-++.-.
T Consensus 3 ~~IrkGD~V~Vi~GkdKGk~GkVl~v~~k~ 32 (104)
T COG0198 3 MKVKKGDTVKVIAGKDKGKEGKVLKVLPKK 32 (104)
T ss_pred cceecCCEEEEEecCCCCcceEEEEEecCe
Confidence 468999999999999999999999998765
No 31
>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=91.66 E-value=0.42 Score=48.70 Aligned_cols=78 Identities=10% Similarity=0.080 Sum_probs=45.2
Q ss_pred eEeecCC--ceEEEEEeccCCceEEccCCCCCCcEEEEeccccccC--CCCCccccccCCCCeeccCCeEEEecCCCCCc
Q 000637 85 LVCFGRK--DFGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNG--PFDMKFTALDQSMKVISLNDTARVSEGPSKDR 160 (1378)
Q Consensus 85 LVQLD~q--TVGVIVrVEKDDsFKVLdqngDrGkVvtVKpseIk~K--r~dRR~vAlD~nGNtIrVgDtVKVVdGP~KGR 160 (1378)
+|+++.. .+-.|.++.. ...+|... ++...|...+|..- +..... +......+++||.|+|++||++|.
T Consensus 53 Fv~~~~~~~~~~~i~~~~g--v~~~v~~~---~~p~~I~~~~i~~l~~~~~~~~--~~~~~~~~~~G~~V~V~~GPf~g~ 125 (159)
T TIGR01955 53 FIEFDPEVDSWTTIRSTRG--VSRFVRFG---GHPAPVPDDLIHQLRQYEPKDS--VPPATTLPYKGDKVRITDGAFAGF 125 (159)
T ss_pred EEEEccCCCceEEEecCCC--cCEEECCC---CCcccCCHHHHHHHHhcccccc--CCccccCCCCCCEEEEeccCCCCc
Confidence 3554432 3444544433 45555532 23456666666421 111111 112234588999999999999999
Q ss_pred eeEEEEEEc
Q 000637 161 QGIVKKIYR 169 (1378)
Q Consensus 161 QG~VlHIyR 169 (1378)
+|.|+.|-.
T Consensus 126 ~g~v~~~~~ 134 (159)
T TIGR01955 126 EAIFLEPDG 134 (159)
T ss_pred EEEEEEECC
Confidence 999999853
No 32
>PRK05609 nusG transcription antitermination protein NusG; Validated
Probab=89.59 E-value=0.45 Score=49.41 Aligned_cols=37 Identities=22% Similarity=0.326 Sum_probs=30.3
Q ss_pred CCeeccCCeEEEecCCCCCceeEEEEEE--cceEEEEec
Q 000637 141 MKVISLNDTARVSEGPSKDRQGIVKKIY--RGILFIYDE 177 (1378)
Q Consensus 141 GNtIrVgDtVKVVdGP~KGRQG~VlHIy--Rg~LFL~sR 177 (1378)
...+++||.|+|++||++|.+|+|++|- +..++|...
T Consensus 124 ~~~~~~Gd~VrI~~GPf~G~~g~v~~i~~~~~r~~v~l~ 162 (181)
T PRK05609 124 KVDFEVGEMVRVIDGPFADFNGTVEEVDYEKSKLKVLVS 162 (181)
T ss_pred ccCCCCCCEEEEeccCCCCCEEEEEEEeCCCCEEEEEEE
Confidence 3568899999999999999999999996 345666543
No 33
>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=89.04 E-value=0.5 Score=47.99 Aligned_cols=34 Identities=18% Similarity=0.265 Sum_probs=28.0
Q ss_pred CeeccCCeEEEecCCCCCceeEEEEEE--cceEEEE
Q 000637 142 KVISLNDTARVSEGPSKDRQGIVKKIY--RGILFIY 175 (1378)
Q Consensus 142 NtIrVgDtVKVVdGP~KGRQG~VlHIy--Rg~LFL~ 175 (1378)
..+++||.|+|++||++|.+|+|+++- +..|.|.
T Consensus 85 ~~~~~Gd~V~I~~GPf~G~~g~v~~~d~~k~~v~v~ 120 (145)
T TIGR00405 85 ESIKKGDIVEIISGPFKGERAKVIRVDESKEEVTLE 120 (145)
T ss_pred cccCCCCEEEEeecCCCCCeEEEEEEcCCCCEEEEE
Confidence 349999999999999999999999995 3444443
No 34
>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=88.70 E-value=0.6 Score=47.29 Aligned_cols=36 Identities=22% Similarity=0.302 Sum_probs=29.5
Q ss_pred ccCcEEEEecCCCCCceeEEEeecCCeEEEEecCCc
Q 000637 249 AVGQTLRIRVGPLKGYLCRVLAVRYSDVTVKLDSQQ 284 (1378)
Q Consensus 249 LIGKTVKIrkGPYKGYlGiVKDaTgt~ARVELHSK~ 284 (1378)
-.|.+|+|+.|.|||..|.|+.|.....+|.++--+
T Consensus 43 kkGD~V~Vi~Gk~KGk~GkV~~V~~~~~~V~Vegvn 78 (114)
T TIGR01080 43 RKGDKVRIMRGDFKGHEGKVSKVDLKRYRIYVEGVT 78 (114)
T ss_pred ecCCEEEEecCCCCCCEEEEEEEEcCCCEEEEcCeE
Confidence 357899999999999999999998666666666533
No 35
>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=86.54 E-value=0.91 Score=47.04 Aligned_cols=34 Identities=21% Similarity=0.329 Sum_probs=28.4
Q ss_pred CeeccCCeEEEecCCCCCceeEEEEEEc--ceEEEE
Q 000637 142 KVISLNDTARVSEGPSKDRQGIVKKIYR--GILFIY 175 (1378)
Q Consensus 142 NtIrVgDtVKVVdGP~KGRQG~VlHIyR--g~LFL~ 175 (1378)
..+++||.|+|++||++|.+|+|++|-+ ..+.|.
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 5588999999999999999999999962 345444
No 36
>PLN00208 translation initiation factor (eIF); Provisional
Probab=86.24 E-value=3.2 Score=43.91 Aligned_cols=78 Identities=15% Similarity=0.085 Sum_probs=58.1
Q ss_pred CccEeceeEeecC-CceEEEEEeccCCceEEccCCCCCCcEEEEeccccccCCCCCccccccCCCCeeccCCeEEEecCC
Q 000637 78 NSFELYELVCFGR-KDFGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVSEGP 156 (1378)
Q Consensus 78 G~YELHDLVQLD~-qTVGVIVrVEKDDsFKVLdqngDrGkVvtVKpseIk~Kr~dRR~vAlD~nGNtIrVgDtVKVVdGP 156 (1378)
...+.++|+.... +.+|+|+++..+..|+|.+.++ ..+++. |.-|+ +++ -=|.+||+|.|---|
T Consensus 19 ~~~~~~el~~p~egq~~g~V~~~lGn~~~~V~c~dG---~~rLa~---IpGKm-RKr--------IWI~~GD~VlVel~~ 83 (145)
T PLN00208 19 ADDEKRELIFKEDGQEYAQVLRMLGNGRCEALCIDG---TKRLCH---IRGKM-RKK--------VWIAAGDIILVGLRD 83 (145)
T ss_pred CccceeecccCCCCcEEEEEEEEcCCCEEEEEECCC---CEEEEE---Eeccc-eee--------EEecCCCEEEEEccC
Confidence 4577899998864 5799999999878999998753 444433 43332 122 248899999998888
Q ss_pred CCCceeEEEEEEcc
Q 000637 157 SKDRQGIVKKIYRG 170 (1378)
Q Consensus 157 ~KGRQG~VlHIyRg 170 (1378)
|.--.|.|+|.|..
T Consensus 84 ~d~~KgdIv~ry~~ 97 (145)
T PLN00208 84 YQDDKADVILKYMP 97 (145)
T ss_pred CCCCEEEEEEEcCH
Confidence 88889999998874
No 37
>PRK04313 30S ribosomal protein S4e; Validated
Probab=85.94 E-value=2.3 Score=47.94 Aligned_cols=52 Identities=15% Similarity=0.099 Sum_probs=37.0
Q ss_pred eccCCeEEEecCCCCCceeEEEEEEcce----EEEEeccccccccEEEEeCCceeecc
Q 000637 144 ISLNDTARVSEGPSKDRQGIVKKIYRGI----LFIYDENETENGGYFCSKSQHCEKTK 197 (1378)
Q Consensus 144 IrVgDtVKVVdGP~KGRQG~VlHIyRg~----LFL~sR~i~ENGGIFVvrArnVvlVg 197 (1378)
+.+|.+|.|+.|.+.||.|+|.+|-+.. --|+.++ .++=-|-++..+|.+|+
T Consensus 172 fe~G~l~~itgG~n~GriG~I~~i~~~~~~~~~~V~i~d--~~G~~F~T~~~~vfvIG 227 (237)
T PRK04313 172 FEEGNLAIITGGKHVGEIGKIKEIEVTKSSKPNIVTLED--KDGEKFETILDYVFVIG 227 (237)
T ss_pred cCCCCEEEEECCeeeeeEEEEEEEEEccCCCCcEEEEEc--CCCCEEEEEeeeEEEEc
Confidence 3567777778899999999999996543 2233221 23335999999999996
No 38
>PRK00004 rplX 50S ribosomal protein L24; Reviewed
Probab=84.64 E-value=1.3 Score=44.13 Aligned_cols=35 Identities=26% Similarity=0.246 Sum_probs=29.2
Q ss_pred cCcEEEEecCCCCCceeEEEeecCCeEEEEecCCc
Q 000637 250 VGQTLRIRVGPLKGYLCRVLAVRYSDVTVKLDSQQ 284 (1378)
Q Consensus 250 IGKTVKIrkGPYKGYlGiVKDaTgt~ARVELHSK~ 284 (1378)
.|-+|.|+.|++||.+|+|..|....-+|.++--+
T Consensus 7 kGD~V~Vi~G~dKGk~G~V~~V~~~~~~V~Vegvn 41 (105)
T PRK00004 7 KGDTVIVIAGKDKGKRGKVLKVLPKKNKVIVEGVN 41 (105)
T ss_pred CCCEEEEeEcCCCCcEEEEEEEEcCCCEEEEcCcE
Confidence 56799999999999999999998776676666533
No 39
>PRK12281 rplX 50S ribosomal protein L24; Reviewed
Probab=84.42 E-value=1.5 Score=41.64 Aligned_cols=34 Identities=26% Similarity=0.299 Sum_probs=28.0
Q ss_pred cCcEEEEecCCCCCceeEEEeecCCeEEEEecCC
Q 000637 250 VGQTLRIRVGPLKGYLCRVLAVRYSDVTVKLDSQ 283 (1378)
Q Consensus 250 IGKTVKIrkGPYKGYlGiVKDaTgt~ARVELHSK 283 (1378)
.|-+|.|+.|++||..|+|+.|....-+|.++--
T Consensus 9 kGD~V~Vi~G~dKGK~G~V~~V~~~~~~V~Vegv 42 (76)
T PRK12281 9 KGDMVKVIAGDDKGKTGKVLAVLPKKNRVIVEGV 42 (76)
T ss_pred CCCEEEEeEcCCCCcEEEEEEEEcCCCEEEEcCc
Confidence 4669999999999999999999876666666553
No 40
>PRK08559 nusG transcription antitermination protein NusG; Validated
Probab=84.15 E-value=1.4 Score=45.88 Aligned_cols=29 Identities=21% Similarity=0.282 Sum_probs=26.0
Q ss_pred CeeccCCeEEEecCCCCCceeEEEEEEcc
Q 000637 142 KVISLNDTARVSEGPSKDRQGIVKKIYRG 170 (1378)
Q Consensus 142 NtIrVgDtVKVVdGP~KGRQG~VlHIyRg 170 (1378)
..+++||.|+|++||++|..|+|.++.+.
T Consensus 93 ~~~~~G~~V~I~~Gpf~g~~g~V~~vd~~ 121 (153)
T PRK08559 93 EGIKEGDIVELIAGPFKGEKARVVRVDES 121 (153)
T ss_pred cCCCCCCEEEEeccCCCCceEEEEEEcCC
Confidence 34999999999999999999999999643
No 41
>PTZ00194 60S ribosomal protein L26; Provisional
Probab=83.67 E-value=1.8 Score=45.60 Aligned_cols=33 Identities=18% Similarity=0.192 Sum_probs=26.5
Q ss_pred ccCcEEEEecCCCCCceeEEEeecCCeEEEEec
Q 000637 249 AVGQTLRIRVGPLKGYLCRVLAVRYSDVTVKLD 281 (1378)
Q Consensus 249 LIGKTVKIrkGPYKGYlGiVKDaTgt~ARVELH 281 (1378)
-.|.+|+|+.|.|||..|.|+.|....-+|-++
T Consensus 48 kkGD~V~Vi~Gk~KGk~GkV~~V~~k~~~ViVE 80 (143)
T PTZ00194 48 RKDDEVMVVRGHHKGREGKVTAVYRKKWVIHIE 80 (143)
T ss_pred ecCCEEEEecCCCCCCceEEEEEEcCCCEEEEe
Confidence 358899999999999999999997655444443
No 42
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=83.54 E-value=5.8 Score=38.16 Aligned_cols=65 Identities=11% Similarity=0.053 Sum_probs=47.8
Q ss_pred CCceEEEEEeccCCceEEccCCCCCCcEEEEeccccccCCCCCccccccCCCCeeccCCeEEEecCCCCCceeEEEEEEc
Q 000637 90 RKDFGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVSEGPSKDRQGIVKKIYR 169 (1378)
Q Consensus 90 ~qTVGVIVrVEKDDsFKVLdqngDrGkVvtVKpseIk~Kr~dRR~vAlD~nGNtIrVgDtVKVVdGP~KGRQG~VlHIyR 169 (1378)
.+.+|.|+++..+..|+|.+.++ +++.+. |..|+ ++ .==|+.||.|.|-.=||.-..|.|.|+|+
T Consensus 5 ~q~~g~V~~~lG~~~~~V~~~dG---~~~la~---ipgK~-Rk--------~iwI~~GD~VlVe~~~~~~~kg~Iv~r~~ 69 (83)
T smart00652 5 GQEIAQVVKMLGNGRLEVMCADG---KERLAR---IPGKM-RK--------KVWIRRGDIVLVDPWDFQDVKADIIYKYT 69 (83)
T ss_pred CcEEEEEEEEcCCCEEEEEECCC---CEEEEE---Echhh-cc--------cEEEcCCCEEEEEecCCCCCEEEEEEEeC
Confidence 46789999999888999998763 445433 43332 11 22488999999987787778899999886
No 43
>CHL00141 rpl24 ribosomal protein L24; Validated
Probab=82.92 E-value=1.9 Score=41.40 Aligned_cols=35 Identities=26% Similarity=0.343 Sum_probs=28.9
Q ss_pred ccCcEEEEecCCCCCceeEEEeecCCeEEEEecCC
Q 000637 249 AVGQTLRIRVGPLKGYLCRVLAVRYSDVTVKLDSQ 283 (1378)
Q Consensus 249 LIGKTVKIrkGPYKGYlGiVKDaTgt~ARVELHSK 283 (1378)
..|-+|.|+.|++||.+|+|..|....-+|.++--
T Consensus 10 ~~GD~V~Vi~G~dKGK~G~V~~V~~~~~~V~Vegv 44 (83)
T CHL00141 10 KIGDTVKIISGSDKGKIGEVLKIIKKSNKVIVKGI 44 (83)
T ss_pred cCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEEcCc
Confidence 35779999999999999999999876666666554
No 44
>KOG1708 consensus Mitochondrial/chloroplast ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=81.98 E-value=1.6 Score=48.26 Aligned_cols=31 Identities=29% Similarity=0.288 Sum_probs=27.7
Q ss_pred CCeeccCCeEEEecCCCCCceeEEEEEEcce
Q 000637 141 MKVISLNDTARVSEGPSKDRQGIVKKIYRGI 171 (1378)
Q Consensus 141 GNtIrVgDtVKVVdGP~KGRQG~VlHIyRg~ 171 (1378)
-=.+.+||+|+|+.|.-|||||.|+.|+|.-
T Consensus 70 dw~ff~GDtVeVlvGkDkGkqG~Vtqv~r~~ 100 (236)
T KOG1708|consen 70 DWHFFFGDTVEVLVGKDKGKQGEVTQVIRHR 100 (236)
T ss_pred ceeEecCCEEEEEecccCCccceEEEEeecC
Confidence 3468899999999999999999999998853
No 45
>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=81.95 E-value=1.8 Score=49.12 Aligned_cols=34 Identities=21% Similarity=0.312 Sum_probs=28.7
Q ss_pred eeccCCeEEEecCCCCCceeEEEEEE--cceEEEEe
Q 000637 143 VISLNDTARVSEGPSKDRQGIVKKIY--RGILFIYD 176 (1378)
Q Consensus 143 tIrVgDtVKVVdGP~KGRQG~VlHIy--Rg~LFL~s 176 (1378)
.+.+||.|+|++||++|.+|+|++|. +..|.|..
T Consensus 205 ~f~vGd~VrI~dGPF~GfeG~I~eid~~k~Rv~VlV 240 (258)
T TIGR01956 205 KFRVGNFVKIVDGPFKGIVGKIKKIDQEKKKAIVEV 240 (258)
T ss_pred CCCCCCEEEEEecCCCCcEEEEEEEeCCCCEEEEEE
Confidence 37899999999999999999999997 45565543
No 46
>COG0250 NusG Transcription antiterminator [Transcription]
Probab=81.79 E-value=3.3 Score=44.61 Aligned_cols=35 Identities=17% Similarity=0.219 Sum_probs=31.2
Q ss_pred cccCCCCeeccCCeEEEecCCCCCceeEEEEEEcc
Q 000637 136 ALDQSMKVISLNDTARVSEGPSKDRQGIVKKIYRG 170 (1378)
Q Consensus 136 AlD~nGNtIrVgDtVKVVdGP~KGRQG~VlHIyRg 170 (1378)
+....-..|.+||+|+|++|||++-.|+|+-|-..
T Consensus 116 ~~~~~~~~~e~Gd~VrI~~GpFa~f~g~V~evd~e 150 (178)
T COG0250 116 APKKPKVDFEPGDVVRIIDGPFAGFKAKVEEVDEE 150 (178)
T ss_pred cCCcccccCCCCCEEEEeccCCCCccEEEEEEcCc
Confidence 45667789999999999999999999999998765
No 47
>PTZ00329 eukaryotic translation initiation factor 1A; Provisional
Probab=81.60 E-value=7 Score=41.85 Aligned_cols=78 Identities=17% Similarity=0.096 Sum_probs=56.6
Q ss_pred CccEeceeEeec-CCceEEEEEeccCCceEEccCCCCCCcEEEEeccccccCCCCCccccccCCCCeeccCCeEEEecCC
Q 000637 78 NSFELYELVCFG-RKDFGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVSEGP 156 (1378)
Q Consensus 78 G~YELHDLVQLD-~qTVGVIVrVEKDDsFKVLdqngDrGkVvtVKpseIk~Kr~dRR~vAlD~nGNtIrVgDtVKVVdGP 156 (1378)
...+..+|+.=. .+.+|+|+++..+..|+|++.++ .++++ -|.-|+ +++ -=|.+||+|+|--=|
T Consensus 19 ~~~~~rel~~~eegq~~g~V~~~LGn~~f~V~c~dG---~~rLa---~I~GKm-RK~--------IWI~~GD~VlVel~~ 83 (155)
T PTZ00329 19 NEGEKRELVFKEEGQEYAQVLRMLGNGRLEAYCFDG---VKRLC---HIRGKM-RKR--------VWINIGDIILVSLRD 83 (155)
T ss_pred CccceeeeccCCCCcEEEEEEEEcCCCEEEEEECCC---CEEEE---Eeeccc-eee--------EEecCCCEEEEeccC
Confidence 345677777664 46899999999878999998763 44443 344442 122 248899999998888
Q ss_pred CCCceeEEEEEEcc
Q 000637 157 SKDRQGIVKKIYRG 170 (1378)
Q Consensus 157 ~KGRQG~VlHIyRg 170 (1378)
|.--.|.|+|.|+.
T Consensus 84 yd~~KgdIi~Ry~~ 97 (155)
T PTZ00329 84 FQDSKADVILKYTP 97 (155)
T ss_pred CCCCEEEEEEEcCH
Confidence 88888999988874
No 48
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=81.27 E-value=7.5 Score=38.81 Aligned_cols=75 Identities=12% Similarity=0.032 Sum_probs=53.2
Q ss_pred cEeceeEeecC-CceEEEEEeccCCceEEccCCCCCCcEEEEeccccccCCCCCccccccCCCCeeccCCeEEEecCCCC
Q 000637 80 FELYELVCFGR-KDFGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVSEGPSK 158 (1378)
Q Consensus 80 YELHDLVQLD~-qTVGVIVrVEKDDsFKVLdqngDrGkVvtVKpseIk~Kr~dRR~vAlD~nGNtIrVgDtVKVVdGP~K 158 (1378)
-..++|+.+.. +.+|+|+++..+..|+|...++ ..+.+. |.-|+ +++ ==|..||.|.|--=||.
T Consensus 10 ~~~~~~~~p~e~e~~g~V~~~lG~~~~~V~~~dG---~~~la~---i~GK~-Rk~--------IwI~~GD~VlVe~~~~~ 74 (100)
T PRK04012 10 VTRVRLPMPEEGEVFGVVEQMLGANRVRVRCMDG---VERMGR---IPGKM-KKR--------MWIREGDVVIVAPWDFQ 74 (100)
T ss_pred ceeEEccCCCCCEEEEEEEEEcCCCEEEEEeCCC---CEEEEE---Echhh-ccc--------EEecCCCEEEEEecccC
Confidence 34577888854 5789999999878999987653 444433 33332 122 24779999999877777
Q ss_pred CceeEEEEEEc
Q 000637 159 DRQGIVKKIYR 169 (1378)
Q Consensus 159 GRQG~VlHIyR 169 (1378)
--.|.|.|+|+
T Consensus 75 ~~kg~Iv~r~~ 85 (100)
T PRK04012 75 DEKADIIWRYT 85 (100)
T ss_pred CCEEEEEEEcC
Confidence 67899999986
No 49
>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=80.38 E-value=2.5 Score=42.24 Aligned_cols=35 Identities=26% Similarity=0.280 Sum_probs=29.1
Q ss_pred cCcEEEEecCCCCCceeEEEeecCCeEEEEecCCc
Q 000637 250 VGQTLRIRVGPLKGYLCRVLAVRYSDVTVKLDSQQ 284 (1378)
Q Consensus 250 IGKTVKIrkGPYKGYlGiVKDaTgt~ARVELHSK~ 284 (1378)
.|-+|.|+.|++||..|+|+.|....-+|.++--+
T Consensus 6 kGD~V~Vi~G~dKGK~G~V~~V~~~~~~V~VegvN 40 (104)
T TIGR01079 6 KGDTVKVISGKDKGKRGKVLKVLPKTNKVIVEGVN 40 (104)
T ss_pred CCCEEEEeEcCCCCcEEEEEEEEcCCCEEEECCcE
Confidence 46799999999999999999998776676666543
No 50
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=80.04 E-value=8.8 Score=37.82 Aligned_cols=69 Identities=14% Similarity=0.171 Sum_probs=47.4
Q ss_pred ceeEeecCCceEEEEEeccCCceEEccCCCCCCcEEEEeccccccCCCCCccccccCCCCeeccCCeEEEecCCCCCcee
Q 000637 83 YELVCFGRKDFGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVSEGPSKDRQG 162 (1378)
Q Consensus 83 HDLVQLD~qTVGVIVrVEKDDsFKVLdqngDrGkVvtVKpseIk~Kr~dRR~vAlD~nGNtIrVgDtVKVVdGP~KGRQG 162 (1378)
.|++++. |+|+.+..+..|+|...++ .++. .-|.-|+...++ -|.+||.|+|--=||.-..|
T Consensus 4 e~~ie~~----G~V~e~Lp~~~frV~LenG---~~vl---a~isGKmR~~rI--------rIl~GD~V~VE~spYDltkG 65 (87)
T PRK12442 4 EELIELD----GIVDEVLPDSRFRVTLENG---VEVG---AYASGRMRKHRI--------RILAGDRVTLELSPYDLTKG 65 (87)
T ss_pred cceEEEE----EEEEEECCCCEEEEEeCCC---CEEE---EEeccceeeeeE--------EecCCCEEEEEECcccCCce
Confidence 3677665 9999999988999886653 3333 234334322122 37799999998889987778
Q ss_pred EEEEEEc
Q 000637 163 IVKKIYR 169 (1378)
Q Consensus 163 ~VlHIyR 169 (1378)
.|.|=|+
T Consensus 66 RIiyR~~ 72 (87)
T PRK12442 66 RINFRHK 72 (87)
T ss_pred eEEEEec
Confidence 8876665
No 51
>PRK00276 infA translation initiation factor IF-1; Validated
Probab=79.90 E-value=11 Score=35.00 Aligned_cols=63 Identities=14% Similarity=0.073 Sum_probs=40.8
Q ss_pred eEEEEEeccCCceEEccCCCCCCcEEEEeccccccCCCCCccccccCCCCeeccCCeEEEecCCCCCceeEEEEEEc
Q 000637 93 FGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVSEGPSKDRQGIVKKIYR 169 (1378)
Q Consensus 93 VGVIVrVEKDDsFKVLdqngDrGkVvtVKpseIk~Kr~dRR~vAlD~nGNtIrVgDtVKVVdGP~KGRQG~VlHIyR 169 (1378)
.|+|+++-.+..|.|.+.+ ++++.+++.-..++ +...|.+||.|.|---|+....|.|.|=||
T Consensus 10 ~G~Vi~~~~~~~y~V~~~~---g~~~~c~~~Gklr~-----------~~i~i~vGD~V~ve~~~~~~~~g~Iv~r~~ 72 (72)
T PRK00276 10 EGTVVEALPNAMFRVELEN---GHEVLAHISGKMRK-----------NYIRILPGDKVTVELSPYDLTKGRITYRHK 72 (72)
T ss_pred EEEEEEEcCCCEEEEEeCC---CCEEEEEEccceee-----------CCcccCCCCEEEEEEcccCCCeEEEEEEeC
Confidence 3899999873378875543 35666653322111 122389999999985556556788888775
No 52
>COG1471 RPS4A Ribosomal protein S4E [Translation, ribosomal structure and biogenesis]
Probab=79.88 E-value=5.5 Score=45.00 Aligned_cols=54 Identities=19% Similarity=0.185 Sum_probs=37.5
Q ss_pred CeeccCCeEEE---------------------ecCCCCCceeEEEEEEcce----EEEEeccccccccEEEEeCCceeec
Q 000637 142 KVISLNDTARV---------------------SEGPSKDRQGIVKKIYRGI----LFIYDENETENGGYFCSKSQHCEKT 196 (1378)
Q Consensus 142 NtIrVgDtVKV---------------------VdGP~KGRQG~VlHIyRg~----LFL~sR~i~ENGGIFVvrArnVvlV 196 (1378)
+.|+++|+|++ +-|.+.|+.|+|.||-..- =-|+..+ +.+=-|.|...+|.+|
T Consensus 151 ~~~k~~Dtv~i~lp~~~I~~~i~fe~g~~~~vtgG~h~G~~G~I~~I~~~~~~~~~~v~~e~--~~g~~F~T~~~yVfvI 228 (241)
T COG1471 151 DNYKTGDTVKISLPEQKIVEHIKFEEGALVYVTGGRHVGRVGTIVEIEIQESSKPNLVTVED--EEGNTFQTIKDYVFVI 228 (241)
T ss_pred CccccccEEEEeCCChhheeEeccCCCcEEEEECCccccceEEEEEEEEecCCCccEEEEec--CCCCceEEeeeEEEEE
Confidence 66777777765 4588899999999998642 1122221 1223799999999999
Q ss_pred c
Q 000637 197 K 197 (1378)
Q Consensus 197 g 197 (1378)
+
T Consensus 229 G 229 (241)
T COG1471 229 G 229 (241)
T ss_pred c
Confidence 7
No 53
>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=78.54 E-value=10 Score=36.11 Aligned_cols=64 Identities=11% Similarity=0.058 Sum_probs=46.9
Q ss_pred ceEEEEEeccCCceEEccCCCCCCcEEEEeccccccCCCCCccccccCCCCeeccCCeEEEecCCCCCceeEEEEEEcc
Q 000637 92 DFGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVSEGPSKDRQGIVKKIYRG 170 (1378)
Q Consensus 92 TVGVIVrVEKDDsFKVLdqngDrGkVvtVKpseIk~Kr~dRR~vAlD~nGNtIrVgDtVKVVdGP~KGRQG~VlHIyRg 170 (1378)
.+|.|+++..+..|+|...++ +++.+ .|..|+. ++ ==|..||.|.|--=||.-..|.|.|.|+.
T Consensus 2 ~~g~V~~~~g~~~~~V~~~~g---~~~la---~i~gK~r-k~--------iwI~~GD~V~Ve~~~~d~~kg~Iv~r~~~ 65 (77)
T cd05793 2 EYGQVEKMLGNGRLEVRCFDG---KKRLC---RIRGKMR-KR--------VWINEGDIVLVAPWDFQDDKADIIYKYTP 65 (77)
T ss_pred EEEEEEEEcCCCEEEEEECCC---CEEEE---EEchhhc-cc--------EEEcCCCEEEEEeccccCCEEEEEEEcCH
Confidence 468999999878999998763 44443 3433321 12 25889999999877888889999999863
No 54
>PRK14635 hypothetical protein; Provisional
Probab=78.53 E-value=2.6 Score=44.53 Aligned_cols=50 Identities=12% Similarity=0.065 Sum_probs=38.9
Q ss_pred ccccCcEEEEec---C--CCCCceeEEEeecCCeEEEEecCC------ceEEEEeCCccee
Q 000637 247 MFAVGQTLRIRV---G--PLKGYLCRVLAVRYSDVTVKLDSQ------QKILTVKGEHLAE 296 (1378)
Q Consensus 247 D~LIGKTVKIrk---G--PYKGYlGiVKDaTgt~ARVELHSK------~KtITVdKe~Lsv 296 (1378)
..++|+.|+|+. + .|+|++|+++++++..+++++..+ .++|+|+.+.|.-
T Consensus 95 ~r~~G~~v~v~~~~~~~~~~~g~~g~L~~~~~~~v~l~~~~k~~~~~~~~~~~ip~~~I~k 155 (162)
T PRK14635 95 DRFRGIPVRLVFRSEESEKWQEGIFRLVNRDGDQVELEKFQKGKKSKVKKQTTLNLKDILK 155 (162)
T ss_pred HHhCCCEEEEEEecCCCcEEEecceEEEEEcCCEEEEEEecccccccCCeEEEEEhHHeee
Confidence 357899988863 2 566888899999999999998543 6678888887764
No 55
>CHL00010 infA translation initiation factor 1
Probab=78.36 E-value=14 Score=35.10 Aligned_cols=64 Identities=14% Similarity=0.083 Sum_probs=41.8
Q ss_pred eEEEEEeccCCceEEccCCCCCCcEEEEeccccccCCCCCccccccCCCCeeccCCeEEEecCCCCCceeEEEEEEcc
Q 000637 93 FGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVSEGPSKDRQGIVKKIYRG 170 (1378)
Q Consensus 93 VGVIVrVEKDDsFKVLdqngDrGkVvtVKpseIk~Kr~dRR~vAlD~nGNtIrVgDtVKVVdGP~KGRQG~VlHIyRg 170 (1378)
.|+||++-....|.|...+ ++++++++.-..+ .+...|.+||.|.|--=|+....|.|.|=|+.
T Consensus 10 ~G~Vik~lg~~~y~V~~~~---g~~~~c~~rGklr-----------~~~i~~~vGD~V~ve~~~~~~~~g~Ii~r~~~ 73 (78)
T CHL00010 10 EGLVTESLPNGMFRVRLDN---GCQVLGYISGKIR-----------RNSIRILPGDRVKVELSPYDLTKGRIIYRLRN 73 (78)
T ss_pred EEEEEEEcCCCEEEEEeCC---CCEEEEEecccee-----------cCCcccCCCCEEEEEEcccCCCeEEEEEEecC
Confidence 5999999842478885533 3566665322211 11344789999999755555567999998875
No 56
>PTZ00223 40S ribosomal protein S4; Provisional
Probab=78.27 E-value=6.9 Score=45.02 Aligned_cols=52 Identities=15% Similarity=0.158 Sum_probs=37.9
Q ss_pred eccCCeEEEecCCCCCceeEEEEEEcc---eEEEEeccccccccEEEEeCCceeecc
Q 000637 144 ISLNDTARVSEGPSKDRQGIVKKIYRG---ILFIYDENETENGGYFCSKSQHCEKTK 197 (1378)
Q Consensus 144 IrVgDtVKVVdGP~KGRQG~VlHIyRg---~LFL~sR~i~ENGGIFVvrArnVvlVg 197 (1378)
+.+|.+|.|+.|.+.||.|+|.||-+. +--||.++ .++--|.++..+|.+|+
T Consensus 172 fe~G~l~~vtgG~n~GriG~I~~i~~~~~~~~iv~i~d--~~g~~F~T~~~~VfvIG 226 (273)
T PTZ00223 172 NRNGKVVMVTGGANRGRIGEIVSIERHPGAFDIARLKD--ASGHEFATRAANIFVIG 226 (273)
T ss_pred cCCCCEEEEECCeeceeEEEEEEEEecCCCCCEEEEEe--CCCCeEEEEeeeEEEEe
Confidence 356777778889999999999999543 12233332 24447999999999997
No 57
>PRK14639 hypothetical protein; Provisional
Probab=77.64 E-value=4.2 Score=42.25 Aligned_cols=50 Identities=10% Similarity=0.222 Sum_probs=41.2
Q ss_pred ccccCcEEEEecCCCCCceeEEEeecCCeEEEEecCCceEEEEeCCccee
Q 000637 247 MFAVGQTLRIRVGPLKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLAE 296 (1378)
Q Consensus 247 D~LIGKTVKIrkGPYKGYlGiVKDaTgt~ARVELHSK~KtITVdKe~Lsv 296 (1378)
.+++|+.|+|+..--|=+.|++++++++.++||+-...++|+|+.+.|.-
T Consensus 84 ~r~~G~~v~v~l~~~~~~~G~L~~~~~~~i~l~~~~~~~~~~i~~~~I~k 133 (140)
T PRK14639 84 AKSIGELVKITTNEKEKFEGKIVSVDDENITLENLENKEKTTINFNDIKK 133 (140)
T ss_pred HHhCCCEEEEEECCCcEEEEEEEEEeCCEEEEEEccCCcEEEEEhHHeee
Confidence 35899999998755688999999999999999875445678888888764
No 58
>COG0198 RplX Ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=77.22 E-value=3.2 Score=41.76 Aligned_cols=30 Identities=33% Similarity=0.389 Sum_probs=27.3
Q ss_pred cCcEEEEecCCCCCceeEEEeecCCeEEEE
Q 000637 250 VGQTLRIRVGPLKGYLCRVLAVRYSDVTVK 279 (1378)
Q Consensus 250 IGKTVKIrkGPYKGYlGiVKDaTgt~ARVE 279 (1378)
.|-+|+|+.|.+||..|.|..|....|.||
T Consensus 7 kGD~V~Vi~GkdKGk~GkVl~v~~k~V~VE 36 (104)
T COG0198 7 KGDTVKVIAGKDKGKEGKVLKVLPKKVVVE 36 (104)
T ss_pred cCCEEEEEecCCCCcceEEEEEecCeEEEE
Confidence 467999999999999999999998887777
No 59
>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=76.93 E-value=7.9 Score=35.08 Aligned_cols=46 Identities=24% Similarity=0.297 Sum_probs=36.1
Q ss_pred ccCcEEEEec--CCCCCceeEEEeecCCeEEEEecCCc--eEEEEeCCcc
Q 000637 249 AVGQTLRIRV--GPLKGYLCRVLAVRYSDVTVKLDSQQ--KILTVKGEHL 294 (1378)
Q Consensus 249 LIGKTVKIrk--GPYKGYlGiVKDaTgt~ARVELHSK~--KtITVdKe~L 294 (1378)
|=|-+|+|+- =+|-+|.|+|..|++..|-|.++--+ |.||+..++|
T Consensus 3 lPG~~V~V~n~~~~Y~~y~G~VQRvsdgkaaVLFEGGnWdKlvTf~l~eL 52 (53)
T PF11623_consen 3 LPGSTVRVKNPNDIYYGYEGFVQRVSDGKAAVLFEGGNWDKLVTFRLSEL 52 (53)
T ss_dssp -TT-EEEE--TTSTTTT-EEEEEEEETTEEEEEEEETTEEEEEEEEGGGE
T ss_pred cCCCEEEEeCCCCccchheEEEEEeeCCeEEEEecCCCceEEEEEEhhhC
Confidence 3466888875 46999999999999999999999888 9999988776
No 60
>PTZ00118 40S ribosomal protein S4; Provisional
Probab=76.92 E-value=7.1 Score=44.72 Aligned_cols=52 Identities=12% Similarity=0.156 Sum_probs=37.6
Q ss_pred eccCCeEEEecCCCCCceeEEEEEEcce---EEEEeccccccccEEEEeCCceeecc
Q 000637 144 ISLNDTARVSEGPSKDRQGIVKKIYRGI---LFIYDENETENGGYFCSKSQHCEKTK 197 (1378)
Q Consensus 144 IrVgDtVKVVdGP~KGRQG~VlHIyRg~---LFL~sR~i~ENGGIFVvrArnVvlVg 197 (1378)
+.+|.+|.|+.|.+-||.|+|.|+-+.. --||.++ .++--|.++..+|.+|+
T Consensus 175 fe~G~l~~vtgG~n~GriG~I~~~~~~~~~~~~V~i~d--~~g~~F~T~~~~vfvIG 229 (262)
T PTZ00118 175 FEVGNLVMITGGHNVGRVGTIVSKEKHPGSFDLIHVKD--SRGKTFATRLSNVFVIG 229 (262)
T ss_pred cCCCCEEEEECCeeceeEEEEEEEEecCCCCcEEEEEe--CCCCeEEEEeeeEEEEc
Confidence 3567777778899999999999976531 2223222 24447999999999996
No 61
>PRK03879 ribonuclease P protein component 1; Validated
Probab=76.73 E-value=5.8 Score=39.21 Aligned_cols=46 Identities=15% Similarity=0.174 Sum_probs=40.6
Q ss_pred cccCcEEEEecCC---CCCceeEEEeecCCeEEEEecCCceEEEEeCCcce
Q 000637 248 FAVGQTLRIRVGP---LKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLA 295 (1378)
Q Consensus 248 ~LIGKTVKIrkGP---YKGYlGiVKDaTgt~ARVELHSK~KtITVdKe~Ls 295 (1378)
.|||-.|+|..-+ |-|+.|+|++=|..++.|+ ...+.++|+|+...
T Consensus 12 eliGl~v~Vv~S~npslvGi~GiVv~ETknt~~I~--~~~~~~~VPK~~~i 60 (96)
T PRK03879 12 ELIGLKVEVVDSTNPSLVGIKGRVVDETRNTLVIE--TDGKEWMVPKDGAT 60 (96)
T ss_pred HhcCCEEEEEEcCCCCcccceEEEEEeceeEEEEE--cCCcEEEEeCCCeE
Confidence 6999999999876 5689999999999999999 77889999999855
No 62
>PLN00036 40S ribosomal protein S4; Provisional
Probab=76.68 E-value=8.2 Score=44.23 Aligned_cols=51 Identities=16% Similarity=0.255 Sum_probs=37.2
Q ss_pred ccCCeEEEecCCCCCceeEEEEEEcc---eEEEEeccccccccEEEEeCCceeecc
Q 000637 145 SLNDTARVSEGPSKDRQGIVKKIYRG---ILFIYDENETENGGYFCSKSQHCEKTK 197 (1378)
Q Consensus 145 rVgDtVKVVdGP~KGRQG~VlHIyRg---~LFL~sR~i~ENGGIFVvrArnVvlVg 197 (1378)
.+|.+|.|+.|.+-||.|+|.||-+. +=-||.++ .++--|.++..+|.+|+
T Consensus 176 e~G~l~~vtgG~n~GrvG~I~~i~~~~~~~~iV~i~d--~~g~~F~T~~~~vfvIG 229 (261)
T PLN00036 176 DVGNLVMVTGGRNRGRVGVIKNREKHKGSFEIIHVKD--ATGHEFATRLGNVFVIG 229 (261)
T ss_pred CCCCEEEEECCeeceeEEEEEEEEecCCCCCEEEEEe--CCCCeEEEEeeeEEEEc
Confidence 56677777889999999999999853 11233222 24447999999999996
No 63
>COG1588 POP4 RNase P/RNase MRP subunit p29 [Translation, ribosomal structure and biogenesis]
Probab=76.11 E-value=5.7 Score=39.60 Aligned_cols=48 Identities=15% Similarity=0.111 Sum_probs=40.4
Q ss_pred ccccCcEEEEecCC---CCCceeEEEeecCCeEEEEecCCceEEEEeCCccee
Q 000637 247 MFAVGQTLRIRVGP---LKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLAE 296 (1378)
Q Consensus 247 D~LIGKTVKIrkGP---YKGYlGiVKDaTgt~ARVELHSK~KtITVdKe~Lsv 296 (1378)
..|||..|+|..-+ |-|..|+|+|-|-.+++|+-.. +.++|+|....+
T Consensus 13 hEliGl~vrVv~s~~~s~vGI~G~VVdETkNtLvi~t~~--~~~~VpK~~~vf 63 (95)
T COG1588 13 HELIGLEVRVVRSTNPSYVGIEGRVVDETKNTLVIDTGS--REKVVPKDGAVF 63 (95)
T ss_pred HHhcCcEEEEEecCCCCccceeEEEEeeeccEEEEECCC--ceEEEecCcEEE
Confidence 47999999999876 5677788999999998888776 888888888763
No 64
>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=75.72 E-value=15 Score=35.17 Aligned_cols=65 Identities=11% Similarity=0.018 Sum_probs=46.5
Q ss_pred CceEEEEEeccCCceEEccCCCCCCcEEEEeccccccCCCCCccccccCCCCeeccCCeEEEecCCC-CCceeEEEEEEc
Q 000637 91 KDFGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVSEGPS-KDRQGIVKKIYR 169 (1378)
Q Consensus 91 qTVGVIVrVEKDDsFKVLdqngDrGkVvtVKpseIk~Kr~dRR~vAlD~nGNtIrVgDtVKVVdGP~-KGRQG~VlHIyR 169 (1378)
+.+|.|+++..+..|+|...++ +.+.+. |..|+ +++ ==|+.||.|.|--=|| .--.|.|.|+|+
T Consensus 1 q~i~~V~~~lG~~~~~V~~~dg---~~~l~~---i~gK~-Rk~--------iwI~~GD~VlV~~~~~~~~~kg~Iv~r~~ 65 (78)
T cd04456 1 QQIVRVLRMLGNNRHEVECADG---QRRLVS---IPGKL-RKN--------IWIKRGDFLIVDPIEEGEDVKADIIFVYC 65 (78)
T ss_pred CeEEEEEEECCCCEEEEEECCC---CEEEEE---Echhh-ccC--------EEEcCCCEEEEEecccCCCceEEEEEEeC
Confidence 4689999999878999987653 445443 33332 121 2488999999987777 567899999987
Q ss_pred c
Q 000637 170 G 170 (1378)
Q Consensus 170 g 170 (1378)
.
T Consensus 66 ~ 66 (78)
T cd04456 66 K 66 (78)
T ss_pred H
Confidence 4
No 65
>PTZ00065 60S ribosomal protein L14; Provisional
Probab=75.11 E-value=6.1 Score=41.25 Aligned_cols=34 Identities=26% Similarity=0.435 Sum_probs=27.6
Q ss_pred ccCcEEEEecCCCCCceeEEEeecCCeEEEEecCC
Q 000637 249 AVGQTLRIRVGPLKGYLCRVLAVRYSDVTVKLDSQ 283 (1378)
Q Consensus 249 LIGKTVKIrkGPYKGYlGiVKDaTgt~ARVELHSK 283 (1378)
=||+-|.|..|||+|-|+.|+||-+.. ||.++-.
T Consensus 9 EiGRVvli~~Gp~~GKL~vIVDIID~n-RvLVDGP 42 (130)
T PTZ00065 9 EPGRLCLIQYGPDAGKLCFIVDIVTPT-RVLVDGA 42 (130)
T ss_pred eeceEEEEecCCCCCCEEEEEEEEcCC-eEEEeCC
Confidence 478899999999999999999997643 5555544
No 66
>PRK05585 yajC preprotein translocase subunit YajC; Validated
Probab=74.29 E-value=4.5 Score=40.51 Aligned_cols=44 Identities=20% Similarity=0.310 Sum_probs=35.0
Q ss_pred cCcEEEEecCCCCCceeEEEeecCCeEEEEecCCceEEEEeCCcceecc
Q 000637 250 VGQTLRIRVGPLKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLAEVR 298 (1378)
Q Consensus 250 IGKTVKIrkGPYKGYlGiVKDaTgt~ARVELHSK~KtITVdKe~Lsvv~ 298 (1378)
+|..|. +.| |+.|+|+++.+++|.||+ +..-+|+|+|..|..+-
T Consensus 55 ~Gd~Vv-T~g---Gi~G~Vv~i~~~~v~lei-~~g~~i~~~r~aI~~v~ 98 (106)
T PRK05585 55 KGDEVV-TNG---GIIGKVTKVSEDFVIIEL-NDDTEIKIQKSAIAAVL 98 (106)
T ss_pred CCCEEE-ECC---CeEEEEEEEeCCEEEEEE-CCCeEEEEEhHHhhhhc
Confidence 455664 444 789999999999999999 45688999999998654
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=74.25 E-value=11 Score=37.56 Aligned_cols=65 Identities=14% Similarity=-0.008 Sum_probs=44.3
Q ss_pred cCCceEEEEEeccCCceEEccCCCCCCcEEEEeccccccCCCCCccccccCCCCeeccCCeEEEecCCCCCc---eeEEE
Q 000637 89 GRKDFGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVSEGPSKDR---QGIVK 165 (1378)
Q Consensus 89 D~qTVGVIVrVEKDDsFKVLdqngDrGkVvtVKpseIk~Kr~dRR~vAlD~nGNtIrVgDtVKVVdGP~KGR---QG~Vl 165 (1378)
+.+.+|.|+++..+..|+|+..++ .++.+. |..|+. ++ ==|..||.|.| -||.-- .|.|.
T Consensus 18 e~e~~g~V~~~lG~~~~~V~~~dG---~~~la~---i~GK~R-k~--------iwI~~GD~VlV--sp~d~~~~~kg~Iv 80 (99)
T TIGR00523 18 EGEILGVIEQMLGAGRVKVRCLDG---KTRLGR---IPGKLK-KR--------IWIREGDVVIV--KPWEFQGDDKCDIV 80 (99)
T ss_pred CCEEEEEEEEEcCCCEEEEEeCCC---CEEEEE---Echhhc-cc--------EEecCCCEEEE--EEccCCCCccEEEE
Confidence 456899999999878999987653 444433 433321 12 24889999999 465433 59999
Q ss_pred EEEcc
Q 000637 166 KIYRG 170 (1378)
Q Consensus 166 HIyRg 170 (1378)
|+|..
T Consensus 81 ~r~~~ 85 (99)
T TIGR00523 81 WRYTK 85 (99)
T ss_pred EEcCH
Confidence 98864
No 68
>COG1862 YajC Preprotein translocase subunit YajC [Intracellular trafficking and secretion]
Probab=74.11 E-value=3.7 Score=40.82 Aligned_cols=45 Identities=24% Similarity=0.396 Sum_probs=36.5
Q ss_pred CcEEEEecCCCCCceeEEEeecCCeEEEEecCCceEEEEeCCcceeccCC
Q 000637 251 GQTLRIRVGPLKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLAEVRGK 300 (1378)
Q Consensus 251 GKTVKIrkGPYKGYlGiVKDaTgt~ARVELHSK~KtITVdKe~Lsvv~g~ 300 (1378)
|..| |+.| |+.|+|+.|.++++.|||. ..-.|+|.|+.|..+..+
T Consensus 47 GD~V-vT~g---Gi~G~V~~v~d~~v~I~l~-~~~~i~~~k~aI~~v~~~ 91 (97)
T COG1862 47 GDEV-VTIG---GIVGTVTKVGDDTVEIELG-DGTKIKFEKEAIATVLEK 91 (97)
T ss_pred CCEE-EEcC---CeEEEEEEEecCcEEEEEC-CCeEEEEEHHHHHhhccC
Confidence 3344 4555 7999999999999999999 888899999999865443
No 69
>PRK12288 GTPase RsgA; Reviewed
Probab=73.98 E-value=17 Score=42.77 Aligned_cols=87 Identities=8% Similarity=0.046 Sum_probs=58.1
Q ss_pred ceEEEEEeccCCceEEccCCCCCCcEEEEeccccccCCCCCccccccCCCCeeccCCeEEEec--CCCCCceeEEEEEEc
Q 000637 92 DFGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVSE--GPSKDRQGIVKKIYR 169 (1378)
Q Consensus 92 TVGVIVrVEKDDsFKVLdqngDrGkVvtVKpseIk~Kr~dRR~vAlD~nGNtIrVgDtVKVVd--GP~KGRQG~VlHIyR 169 (1378)
..|.||++.+ ..|.|++.. ++++.++++.. + ..+-|||.|.+-. .......|.|++|+-
T Consensus 40 ~~g~Vi~~~~-~~~~v~~~~---g~~~~~~~~g~---~------------~~~~vGD~V~~~~~~~~~~~~~~~I~~il~ 100 (347)
T PRK12288 40 QEGIVISRFG-QHADVEAAD---GEVHRCNIRRT---I------------RSLVTGDRVVWRPGKEALEGVSGVVEAVHP 100 (347)
T ss_pred cceEEEEEEC-CEEEEEeCC---CcEEEEEeccc---C------------CCCCCCcEEEEEeCCCcccccceEEEEEec
Confidence 3599999999 588888754 35555442221 1 1289999999852 111012499999998
Q ss_pred ceEEEEeccccccccEEEEeCCceeecc
Q 000637 170 GILFIYDENETENGGYFCSKSQHCEKTK 197 (1378)
Q Consensus 170 g~LFL~sR~i~ENGGIFVvrArnVvlVg 197 (1378)
-+=+|.-+.+....-+||++...|++|-
T Consensus 101 R~n~L~R~~~~~~~q~iaANvD~vlIV~ 128 (347)
T PRK12288 101 RTSVLTRPDYYDGVKPIAANIDQIVIVS 128 (347)
T ss_pred ccceEECCCcccccceEEEEccEEEEEE
Confidence 8755554544444468999999988885
No 70
>PRK00092 ribosome maturation protein RimP; Reviewed
Probab=73.86 E-value=5.6 Score=41.53 Aligned_cols=49 Identities=18% Similarity=0.352 Sum_probs=39.5
Q ss_pred cccCcEEEEe----cCCCCCceeEEEeecCCeEEEEecCCceEEEEeCCccee
Q 000637 248 FAVGQTLRIR----VGPLKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLAE 296 (1378)
Q Consensus 248 ~LIGKTVKIr----kGPYKGYlGiVKDaTgt~ARVELHSK~KtITVdKe~Lsv 296 (1378)
.+||+.|+|+ ...-|=|.|++++++++.+++++..+.|+|+|+.+.|..
T Consensus 95 r~~G~~v~V~~~~~~~~~~~~~G~L~~~~~~~i~l~~~~~~~~~~i~~~~I~~ 147 (154)
T PRK00092 95 RFIGREVKVKLYEPIDGRKKFQGILLAVDGETVTLEVEGKEKEVEIPLDNIAK 147 (154)
T ss_pred HhCCCeEEEEEEcccCCceEEEEEEEEeeCCEEEEEECCCeEEEEEEHHHcce
Confidence 5899999998 344567789999999999998876544589998888864
No 71
>PF02576 DUF150: Uncharacterised BCR, YhbC family COG0779; InterPro: IPR003728 The RimP protein facilitates maturation of the 30S ribsomal subunit, and is required for the efficient production of translationally competent ribosmomes [].; PDB: 1IB8_A.
Probab=73.37 E-value=6.1 Score=40.41 Aligned_cols=50 Identities=14% Similarity=0.430 Sum_probs=36.1
Q ss_pred ccccCcEEEEec-CCCCC---ceeEEEeecCCeEEEEecCC--ceEEEEeCCccee
Q 000637 247 MFAVGQTLRIRV-GPLKG---YLCRVLAVRYSDVTVKLDSQ--QKILTVKGEHLAE 296 (1378)
Q Consensus 247 D~LIGKTVKIrk-GPYKG---YlGiVKDaTgt~ARVELHSK--~KtITVdKe~Lsv 296 (1378)
..+||+.|+|+- -|..+ +.|+++++++..++|++..+ .++|+|+.++|.-
T Consensus 83 ~~~iG~~v~v~~~~~~~~~~~~~G~L~~~~~~~i~l~~~~~~~~~~~~I~~~~I~k 138 (141)
T PF02576_consen 83 ERFIGRKVKVKLKQPVNGRKEFEGKLLEVDEDEITLEVEGKGKKKEVEIPFSDIKK 138 (141)
T ss_dssp HHH-SEEEEEE-SS-SSS-SEEEEEEEEEETTEEEEEEE-SS-EEEEEE-SS--SS
T ss_pred HHhcCCeEEEEEeccCCCcEEEEEEEEEEeCCEEEEEECCccceEEEEEEHHHCce
Confidence 468999999995 44444 79999999999999999888 4689999888764
No 72
>PF02736 Myosin_N: Myosin N-terminal SH3-like domain; InterPro: IPR004009 This domain has an SH3-like fold. It is found at the N terminus of many but not all myosins. The function of this domain is unknown.; GO: 0003774 motor activity, 0005524 ATP binding, 0016459 myosin complex; PDB: 2EC6_A 2W4H_M 1O1E_P 1O1D_D 1O18_A 1O1C_P 1O1B_D 1O1F_A 2W4A_M 2W4G_M ....
Probab=73.27 E-value=6.7 Score=33.21 Aligned_cols=28 Identities=29% Similarity=0.293 Sum_probs=25.6
Q ss_pred eeEEEeecCCeEEEEecCCceEEEEeCCc
Q 000637 265 LCRVLAVRYSDVTVKLDSQQKILTVKGEH 293 (1378)
Q Consensus 265 lGiVKDaTgt~ARVELHSK~KtITVdKe~ 293 (1378)
+|.|+++.+..|+|+|.. .++++|++++
T Consensus 15 ~g~I~~~~g~~vtV~~~~-G~~~tv~~dd 42 (42)
T PF02736_consen 15 KGEIIEEEGDKVTVKTED-GKEVTVKKDD 42 (42)
T ss_dssp EEEEEEEESSEEEEEETT-TEEEEEEGGG
T ss_pred EEEEEEEcCCEEEEEECC-CCEEEeCCCC
Confidence 689999999999999999 9999999864
No 73
>PRK05886 yajC preprotein translocase subunit YajC; Validated
Probab=73.08 E-value=7.5 Score=39.44 Aligned_cols=42 Identities=10% Similarity=0.176 Sum_probs=33.9
Q ss_pred CcEEEEecCCCCCceeEEEeecCCeEEEEecCCceEEEEeCCcceec
Q 000637 251 GQTLRIRVGPLKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLAEV 297 (1378)
Q Consensus 251 GKTVKIrkGPYKGYlGiVKDaTgt~ARVELHSK~KtITVdKe~Lsvv 297 (1378)
|..| |+.| |+.|+|+++++.+|.||+. ..-.|+|.|..|..+
T Consensus 42 GD~V-vT~g---Gi~G~V~~I~d~~v~leia-~gv~i~~~r~AI~~v 83 (109)
T PRK05886 42 GDRV-HTTS---GLQATIVGITDDTVDLEIA-PGVVTTWMKLAVRDR 83 (109)
T ss_pred CCEE-EECC---CeEEEEEEEeCCEEEEEEC-CCeEEEEEhhheeee
Confidence 4444 5555 8999999999999999994 567799999999843
No 74
>cd01734 YlxS_C YxlS is a Bacillus subtilis gene of unknown function with two domains that each have an alpha/beta fold. The N-terminal domain is composed of two alpha-helices and a three-stranded beta-sheet, while the C-terminal domain is composed of one alpha-helix and a five-stranded beta-sheet. This CD represents the C-terminal domain which has a fold similar to the Sm fold of proteins like Sm-D3.
Probab=73.00 E-value=6.7 Score=37.07 Aligned_cols=49 Identities=22% Similarity=0.352 Sum_probs=38.5
Q ss_pred cccCcEEEEec----CCCCCceeEEEeecCCeEEEEecCC--ceEEEEeCCccee
Q 000637 248 FAVGQTLRIRV----GPLKGYLCRVLAVRYSDVTVKLDSQ--QKILTVKGEHLAE 296 (1378)
Q Consensus 248 ~LIGKTVKIrk----GPYKGYlGiVKDaTgt~ARVELHSK--~KtITVdKe~Lsv 296 (1378)
.+||+.|+|+- +.-|=+.|+++++++..++|+++.+ .++|+|+.++|.-
T Consensus 22 r~~G~~v~v~~~~~~~~~~~~~G~L~~~~~~~v~l~~~~~~~~~~~~i~~~~I~k 76 (83)
T cd01734 22 RAVGKYVHVKLYQPIDGQKEFEGTLLGVDDDTVTLEVDIKTRGKTVEIPLDKIAK 76 (83)
T ss_pred HhCCCEEEEEEEcccCCeEEEEEEEEeEeCCEEEEEEecCCCCeEEEEEhHHeeE
Confidence 58999999964 3345689999999999999888743 5688888888764
No 75
>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=72.19 E-value=5.2 Score=38.55 Aligned_cols=42 Identities=17% Similarity=0.375 Sum_probs=33.4
Q ss_pred cCcEEEEecCCCCCceeEEEeecCCeEEEEecCCceEEEEeCCccee
Q 000637 250 VGQTLRIRVGPLKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLAE 296 (1378)
Q Consensus 250 IGKTVKIrkGPYKGYlGiVKDaTgt~ARVELHSK~KtITVdKe~Lsv 296 (1378)
.|..|.. .| |+.|+|+++.++++.||+. ..-+|+|+|..|..
T Consensus 40 ~Gd~VvT-~g---Gi~G~V~~i~d~~v~vei~-~g~~i~~~r~aI~~ 81 (84)
T TIGR00739 40 KGDKVLT-IG---GIIGTVTKIAENTIVIELN-DNTEITFSKNAIVE 81 (84)
T ss_pred CCCEEEE-CC---CeEEEEEEEeCCEEEEEEC-CCeEEEEEhHHhhh
Confidence 4556644 44 7899999999999999984 56779999998864
No 76
>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=72.07 E-value=14 Score=33.77 Aligned_cols=62 Identities=15% Similarity=0.126 Sum_probs=42.5
Q ss_pred CceEEEEEeccCCceEEccCCCCCCcEEEEeccccccCCCCCccccccCCCCeeccCCeEEEecCCCCCceeEEEEE
Q 000637 91 KDFGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVSEGPSKDRQGIVKKI 167 (1378)
Q Consensus 91 qTVGVIVrVEKDDsFKVLdqngDrGkVvtVKpseIk~Kr~dRR~vAlD~nGNtIrVgDtVKVVdGP~KGRQG~VlHI 167 (1378)
+.+|+|+++..+..|+|...++ +.+.+.... | +.++ --|+.||.|.|---|+.-..|.|.|.
T Consensus 4 e~~~~V~~~lG~~~~~V~~~dg---~~~l~~i~g---K-~r~~--------iwI~~GD~V~V~~~~~d~~kG~Ii~r 65 (65)
T PF01176_consen 4 EVIGRVTEMLGNNLFEVECEDG---EERLARIPG---K-FRKR--------IWIKRGDFVLVEPSPYDKVKGRIIYR 65 (65)
T ss_dssp EEEEEEEEEESSSEEEEEETTS---EEEEEEE-H---H-HHTC--------C---TTEEEEEEESTTCTTEEEEEEE
T ss_pred EEEEEEEEECCCCEEEEEeCCC---CEEEEEecc---c-eeee--------EecCCCCEEEEEecccCCCeEEEEEC
Confidence 5679999999888999988763 555544332 2 1112 24899999999888888889999874
No 77
>PRK04333 50S ribosomal protein L14e; Validated
Probab=70.16 E-value=6.2 Score=38.26 Aligned_cols=30 Identities=23% Similarity=0.309 Sum_probs=25.9
Q ss_pred ccCcEEEEecCCCCCceeEEEee-cCCeEEE
Q 000637 249 AVGQTLRIRVGPLKGYLCRVLAV-RYSDVTV 278 (1378)
Q Consensus 249 LIGKTVKIrkGPYKGYlGiVKDa-Tgt~ARV 278 (1378)
-+|+-|+|+.|+|+|-+.+|+++ .+..|.|
T Consensus 5 ~~GrvV~~~~Grd~gk~~vIv~i~d~~~vlV 35 (84)
T PRK04333 5 EVGRVCVKTAGREAGRKCVIVDIIDKNFVLV 35 (84)
T ss_pred cccEEEEEeccCCCCCEEEEEEEecCCEEEE
Confidence 47899999999999999999999 4556666
No 78
>PF01868 UPF0086: Domain of unknown function UPF0086; InterPro: IPR002730 The p29 subunit (also known as Rpp29 or Pop4) of the related ribonucleoproteins ribonuclease (RNase) P and RNase MRP can be found in both eukaryotes and arachea []. The structure of the RNase P subunit, Rpp29, from Methanobacterium thermoautotrophicum has been determined. Mth Rpp29 is a member of the oligonucleotide/oligosaccharide binding fold family. It contains a structured beta-barrel core and unstructured N- and C-terminal extensions bearing several highly conserved amino acid residues that could be involved in RNA contacts in the protein-RNA complex []. Rpp29 (3.1.26.5 from EC) catalyses the endonucleolytic cleavage of RNA, removing 5'-extranucleotides from tRNA precursor. It interacts with the Rpp25 and Pop5 subunits. RNase P is a ubiquitous ribonucleoprotein enzyme primarily responsible for cleaving the 5' leader sequence during maturation of tRNAs in all three domains of life. In eubacteria, this enzyme is made up of two subunits: a large RNA (approximately 120 kDa) responsible for mediating catalysis, and a small protein cofactor (approximately 15 kDa) that modulates substrate recognition and is required for efficient in vivo catalysis. In contrast, multiple proteins are associated with eukaryotic and archaeal RNase P, and these proteins exhibit no recognizable homology to the conserved bacterial protein subunit. In reconstitution experiments with recombinantly expressed and purified protein subunits Mth Rpp29, a homologue of the Rpp29 protein subunit from eukaryotic RNase P, is an essential protein component of the archaeal holoenzyme []. In Saccharomyces cerevisiae (Baker's yeast), RNase P consists of 9 protein subunits (Pop1, Pop3-8, Rpr2 and Rpp1), while in humans there are 10 subunits (Rpp14, 20, 21, 25, 29, 30, 38, 40, hPop1, 5). RNase MRP (mitochondrial RNA processing) is an rRNA processing enzyme that cleaves a specific site within precursor rRNA to generate the mature 5'-end of 5.8S rRNA []. RNase MRP also cleaves primers for mitochondrial DNA replication and CLB2 mRNA. In yeast, RNase MRP possesses one putatively catalytic RNA and at least 9 protein subunits and is highly related to RNase P (Pop1, Pop3-Pop8, Rpp1, Snm1 and Rmp1).; GO: 0003723 RNA binding, 0004540 ribonuclease activity, 0006364 rRNA processing, 0006379 mRNA cleavage, 0008033 tRNA processing, 0000172 ribonuclease MRP complex, 0030677 ribonuclease P complex; PDB: 1V76_B 2ZAE_C 1OQK_A 2KI7_A 1TSF_A 1TS9_A 1PC0_A.
Probab=69.12 E-value=13 Score=36.01 Aligned_cols=49 Identities=12% Similarity=0.072 Sum_probs=38.4
Q ss_pred ccccCcEEEEecCC---CCCceeEEEeecCCeEEEEecCCceEEEEeCCccee
Q 000637 247 MFAVGQTLRIRVGP---LKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLAE 296 (1378)
Q Consensus 247 D~LIGKTVKIrkGP---YKGYlGiVKDaTgt~ARVELHSK~KtITVdKe~Lsv 296 (1378)
.+|+|-.|+|..=+ |-|+.|||++=|..+++|+ ....|+++|+|.+..+
T Consensus 10 ~dl~G~~i~V~~s~~pslvG~~GiVV~ETknt~~I~-t~~~~~~~IpK~~~vF 61 (89)
T PF01868_consen 10 ADLIGAKIEVVRSKNPSLVGIEGIVVDETKNTFVIV-TEDGKVKTIPKAGSVF 61 (89)
T ss_dssp S--TT-EEEEEEESSCCCTTEEEEEEEEETTEEEEE-ETTEEEEEEESTTEEE
T ss_pred hhhcCCEEEEEEcCCCCccCCEEEEEEcccceEEEE-ecCCcEEEEecCCEEE
Confidence 36999999998766 7899999999999999987 3344799999998764
No 79
>PRK14637 hypothetical protein; Provisional
Probab=68.91 E-value=9.5 Score=40.28 Aligned_cols=47 Identities=9% Similarity=0.120 Sum_probs=37.3
Q ss_pred cccCcEEEEecCCCCCc-eeEEEeecCCeEEEEecCCceEEEEeCCccee
Q 000637 248 FAVGQTLRIRVGPLKGY-LCRVLAVRYSDVTVKLDSQQKILTVKGEHLAE 296 (1378)
Q Consensus 248 ~LIGKTVKIrkGPYKGY-lGiVKDaTgt~ARVELHSK~KtITVdKe~Lsv 296 (1378)
.+||+.|+|+...-|-+ .|++++++++.+++++ ..+++.|+.++|.-
T Consensus 95 r~~G~~V~V~l~~~~~~~~G~L~~~~d~~v~l~~--~~~~~~i~~~~I~k 142 (151)
T PRK14637 95 IFVGETVKVWFECTGQWQVGTIAEADETCLVLTS--DGVPVTIPYVQITK 142 (151)
T ss_pred HhCCCEEEEEECCCCcEEEEEEEEEeCCEEEEEE--CCEEEEEEHHHeee
Confidence 58999999986323567 5999999999999885 56788888877764
No 80
>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=68.37 E-value=28 Score=32.94 Aligned_cols=65 Identities=12% Similarity=0.087 Sum_probs=43.8
Q ss_pred eeEeecCCceEEEEEeccCCceEEccCCCCCCcEEEEeccccccCCCCCccccccCCCCeeccCCeEEEecCCCCCceeE
Q 000637 84 ELVCFGRKDFGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVSEGPSKDRQGI 163 (1378)
Q Consensus 84 DLVQLD~qTVGVIVrVEKDDsFKVLdqngDrGkVvtVKpseIk~Kr~dRR~vAlD~nGNtIrVgDtVKVVdGP~KGRQG~ 163 (1378)
|++++. |+|+++-.+..|+|...++ ..+. .-|.-|+..++ =-|.+||+|+|--=||.--.|.
T Consensus 3 ~~ie~~----G~V~e~L~~~~f~V~l~ng---~~vl---a~i~GKmr~~r--------I~I~~GD~V~Ve~spyd~tkgr 64 (68)
T TIGR00008 3 DKIEME----GKVTESLPNAMFRVELENG---HEVL---AHISGKIRMHY--------IRILPGDKVKVELSPYDLTRGR 64 (68)
T ss_pred cEEEEE----EEEEEECCCCEEEEEECCC---CEEE---EEecCcchhcc--------EEECCCCEEEEEECcccCCcEe
Confidence 556544 9999999888899876653 3333 23433432222 2478999999998898767777
Q ss_pred EEE
Q 000637 164 VKK 166 (1378)
Q Consensus 164 VlH 166 (1378)
|.|
T Consensus 65 Ii~ 67 (68)
T TIGR00008 65 ITY 67 (68)
T ss_pred EEe
Confidence 764
No 81
>PRK14634 hypothetical protein; Provisional
Probab=67.84 E-value=8.3 Score=40.74 Aligned_cols=48 Identities=8% Similarity=0.099 Sum_probs=38.7
Q ss_pred cccCcEEEEe-cCCC---CCceeEEEeecCCeEEEEecCCceEEEEeCCcceec
Q 000637 248 FAVGQTLRIR-VGPL---KGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLAEV 297 (1378)
Q Consensus 248 ~LIGKTVKIr-kGPY---KGYlGiVKDaTgt~ARVELHSK~KtITVdKe~Lsvv 297 (1378)
++||+.|+|+ ..|. |=|.|++++++++.+++++ ..++|+|+.+.|.-+
T Consensus 97 r~~G~~V~V~l~~~~~~~k~~~G~L~~~~~~~v~l~~--~~~~~~i~~~~I~ka 148 (155)
T PRK14634 97 TFRGFPVEVSHRDDDGSEQRLEGLLLERNEDHLQINI--RGRIKRIPRDSVISV 148 (155)
T ss_pred HhCCCeEEEEEecCCCCeEEEEEEEEEEeCCEEEEEE--CCEEEEEEHHHeeeE
Confidence 5899999996 4443 6799999999999999887 467788888887754
No 82
>PRK14638 hypothetical protein; Provisional
Probab=67.48 E-value=9 Score=40.31 Aligned_cols=48 Identities=10% Similarity=0.150 Sum_probs=39.0
Q ss_pred ccccCcEEEEecCCCCCceeEEEeecCCeEEEEecCCceEEEEeCCccee
Q 000637 247 MFAVGQTLRIRVGPLKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLAE 296 (1378)
Q Consensus 247 D~LIGKTVKIrkGPYKGYlGiVKDaTgt~ARVELHSK~KtITVdKe~Lsv 296 (1378)
..+||+.|+|+----|=+.|+++++++..++|++ ..++|.|+.+.|.-
T Consensus 96 ~r~~G~~v~V~~~~~k~~~G~L~~~~~~~i~l~~--~~~~~~i~~~~I~~ 143 (150)
T PRK14638 96 VRFTGKLAKIVTKDGKTFIGRIESFVDGTITISD--EKEKYEINIDDVKR 143 (150)
T ss_pred HHhCCCEEEEEECCCcEEEEEEEEEeCCEEEEEE--CCcEEEEEhHHcce
Confidence 3589999999864458899999999999999885 45778888887764
No 83
>PRK14644 hypothetical protein; Provisional
Probab=67.38 E-value=7.4 Score=40.45 Aligned_cols=49 Identities=12% Similarity=0.173 Sum_probs=37.3
Q ss_pred ccccCcEEEEec-CC---CCCceeEEEeecCCeEEEEe--cCCceEEEEeCCcce
Q 000637 247 MFAVGQTLRIRV-GP---LKGYLCRVLAVRYSDVTVKL--DSQQKILTVKGEHLA 295 (1378)
Q Consensus 247 D~LIGKTVKIrk-GP---YKGYlGiVKDaTgt~ARVEL--HSK~KtITVdKe~Ls 295 (1378)
..+||+.|+|+- -| -|=+.|+++++.+..+++++ ..+.|.|+++++.|.
T Consensus 81 ~r~~G~~v~V~l~~~~~~~~~~~G~L~~v~~~~i~l~~~~k~~~~~i~~~~~~i~ 135 (136)
T PRK14644 81 ENHIGEIIDVSLNKEVNKTDFITGELLENNPETITLKWNCKGQFRKVEINKENIK 135 (136)
T ss_pred HHhCCCeEEEEEccCcCCeEEEEEEEEEEeCCEEEEEEecCCcEEEEEECHHHhc
Confidence 458999999974 33 36688999999999999964 444567778877764
No 84
>PRK06531 yajC preprotein translocase subunit YajC; Validated
Probab=67.16 E-value=11 Score=38.58 Aligned_cols=41 Identities=24% Similarity=0.246 Sum_probs=30.9
Q ss_pred EecCCCCCceeEEEeecCCeEEEEecCCceEEEEeCCcceeccC
Q 000637 256 IRVGPLKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLAEVRG 299 (1378)
Q Consensus 256 IrkGPYKGYlGiVKDaTgt~ARVELHSK~KtITVdKe~Lsvv~g 299 (1378)
|+.| |++|+|+++.++..+|+|....-.|+|.|..|..+..
T Consensus 44 vT~G---Gi~G~V~~I~~~~~~v~le~~gv~i~v~r~AI~~Vv~ 84 (113)
T PRK06531 44 VTIG---GLYGTVDEVDTEAKTIVLDVDGVYLTFELAAIKRVVP 84 (113)
T ss_pred EECC---CcEEEEEEEecCCCEEEEEECCEEEEEEhhHhhhhcC
Confidence 6666 8999999998765455554456789999999986543
No 85
>PRK01191 rpl24p 50S ribosomal protein L24P; Validated
Probab=66.81 E-value=8.3 Score=39.79 Aligned_cols=31 Identities=26% Similarity=0.414 Sum_probs=25.6
Q ss_pred ccCcEEEEecCCCCCceeEEEeecCCe--EEEE
Q 000637 249 AVGQTLRIRVGPLKGYLCRVLAVRYSD--VTVK 279 (1378)
Q Consensus 249 LIGKTVKIrkGPYKGYlGiVKDaTgt~--ARVE 279 (1378)
-.|-+|.|+.|++||-.|+|+.|.... |.||
T Consensus 47 kkGD~V~VisG~~KGk~GkV~~V~~~~~~V~Ve 79 (120)
T PRK01191 47 RKGDTVKVMRGDFKGEEGKVVEVDLKRGRIYVE 79 (120)
T ss_pred eCCCEEEEeecCCCCceEEEEEEEcCCCEEEEe
Confidence 358899999999999999999996544 4444
No 86
>PRK00098 GTPase RsgA; Reviewed
Probab=66.68 E-value=32 Score=39.18 Aligned_cols=86 Identities=13% Similarity=0.126 Sum_probs=56.3
Q ss_pred EEEEEeccCCceEEccCCCCCCcEEEEeccccccCCCCCccccccCCCCeeccCCeEEEecCCCCCceeEEEEEEcceEE
Q 000637 94 GLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVSEGPSKDRQGIVKKIYRGILF 173 (1378)
Q Consensus 94 GVIVrVEKDDsFKVLdqngDrGkVvtVKpseIk~Kr~dRR~vAlD~nGNtIrVgDtVKVVdGP~KGRQG~VlHIyRg~LF 173 (1378)
|.||++.+ ..|.|++.. +++++++++...+ + ....+-|||.|.|-. + ...+|.|++|+.-.-+
T Consensus 3 g~v~~~~~-~~~~v~~~~---~~~~~~~~~g~~~---------~--~~~~~~vGD~V~~~~-~-~~~~g~i~~i~~R~~~ 65 (298)
T PRK00098 3 GLIIKALG-GFYYVESED---GQVYQCRARGKFR---------K--KTNTPAVGDRVEFSA-E-NNDEGVILEIHERKNL 65 (298)
T ss_pred EEEEEEEC-CEEEEEECC---CCEEEEEeccccc---------c--CCCCcCCCCEEEEEE-C-CCCcEEEEEEeCCCce
Confidence 88999999 588888643 2456655333211 0 235678999998842 1 2246899999998877
Q ss_pred EEeccccccccEEEEeCCceeecc
Q 000637 174 IYDENETENGGYFCSKSQHCEKTK 197 (1378)
Q Consensus 174 L~sR~i~ENGGIFVvrArnVvlVg 197 (1378)
|..+.+ ...-++++++..|++|-
T Consensus 66 l~R~~~-~~~q~iaaniD~vllV~ 88 (298)
T PRK00098 66 LVRPPI-FKSKLIAANVDQAVLVF 88 (298)
T ss_pred EECCCC-ccccceeecCCEEEEEE
Confidence 777665 23345677777766664
No 87
>PRK14643 hypothetical protein; Provisional
Probab=66.13 E-value=9.2 Score=40.92 Aligned_cols=51 Identities=22% Similarity=0.241 Sum_probs=40.2
Q ss_pred ccccCcEEEEec-CCC---CCceeEEEeecCCeEEEEec----CCceEEEEeCCcceec
Q 000637 247 MFAVGQTLRIRV-GPL---KGYLCRVLAVRYSDVTVKLD----SQQKILTVKGEHLAEV 297 (1378)
Q Consensus 247 D~LIGKTVKIrk-GPY---KGYlGiVKDaTgt~ARVELH----SK~KtITVdKe~Lsvv 297 (1378)
..++|+.|+|+- -|+ |=+.|+++++.+..++|+|+ ...++|.|+++.|.-+
T Consensus 100 ~r~~G~~V~V~l~~~~~g~k~~~G~L~~~~~~~~~l~l~~~~~~~~~~~~ip~~~I~ka 158 (164)
T PRK14643 100 VKALNQWVYVQLNNEIKKVKEFEGYVTKYNVNTNTFRFTFFIKGQKKKLDVKYEQIKFI 158 (164)
T ss_pred HHhcCCeEEEEEecccCCceEEEEEEEEEeCCcEEEEEEeeccCcCcEEEEeHHHhhhe
Confidence 358999999974 444 44899999999999998864 3467899999888753
No 88
>smart00538 POP4 A domain found in a protein subunit of human RNase MRP and RNase P ribonucleoprotein complexes and archaeal proteins.
Probab=65.56 E-value=16 Score=35.79 Aligned_cols=48 Identities=15% Similarity=0.175 Sum_probs=39.9
Q ss_pred ccccCcEEEEecCC---CCCceeEEEeecCCeEEEEecCCceEEEEeCCcce
Q 000637 247 MFAVGQTLRIRVGP---LKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLA 295 (1378)
Q Consensus 247 D~LIGKTVKIrkGP---YKGYlGiVKDaTgt~ARVELHSK~KtITVdKe~Ls 295 (1378)
..|||-.|+|..-+ |-|+.|+|++=|..+++|+... .++++|+|....
T Consensus 9 ~el~G~~v~Vv~s~~ps~vGi~GiVv~ET~nt~~I~t~~-~~~~~IpK~~~v 59 (92)
T smart00538 9 HELIGLKVRVVASKNPSLVGIEGIVVDETRNTLKIETKE-GRVKTVPKDGAV 59 (92)
T ss_pred hhhcCCEEEEEEcCCCCccCcEEEEEEeeeeEEEEEeCC-CcEEEEECCCeE
Confidence 36999999998876 5789999999999999998654 578888888854
No 89
>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=65.36 E-value=34 Score=38.80 Aligned_cols=85 Identities=12% Similarity=0.151 Sum_probs=54.4
Q ss_pred EEEEEeccCCceEEccCCCCCCcEEEEeccccccCCCCCccccccCCCCeeccCCeEEEecCCCCCceeEEEEEEc-ceE
Q 000637 94 GLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVSEGPSKDRQGIVKKIYR-GIL 172 (1378)
Q Consensus 94 GVIVrVEKDDsFKVLdqngDrGkVvtVKpseIk~Kr~dRR~vAlD~nGNtIrVgDtVKVVdGP~KGRQG~VlHIyR-g~L 172 (1378)
|.||++.+ ..|.|++.+ .++.++++....+ ....+-|||.|.+..- ...++.|..|+- ..+
T Consensus 1 g~v~~~~~-~~~~v~~~~----~~~~~~~~g~~~~-----------~~~~~~vGD~V~~~~~--~~~~~~i~~i~~R~~~ 62 (287)
T cd01854 1 GRVIAVHG-GFYDVETEG----GELRCRARGKLRK-----------KGIKPVVGDWVEVEPD--DDGEGVIVRVLPRKNL 62 (287)
T ss_pred CEEEEEEC-CEEEEEECC----eEEEEEecccccc-----------CCCCccCCCEEEEEec--CCCcEEEEEEECCCce
Confidence 56888888 588888753 4555554332211 1455999999987532 236799999994 445
Q ss_pred EEEeccccccccEEEEeCCceeecc
Q 000637 173 FIYDENETENGGYFCSKSQHCEKTK 197 (1378)
Q Consensus 173 FL~sR~i~ENGGIFVvrArnVvlVg 197 (1378)
|+.-..... .-++++++..|++|-
T Consensus 63 l~R~~~~~~-~~~i~anvD~vllV~ 86 (287)
T cd01854 63 LSRPAAGGR-EQVIAANVDQLVIVV 86 (287)
T ss_pred EEccCCCCc-ceeEEEeCCEEEEEE
Confidence 444332222 567888888777774
No 90
>PRK04950 ProP expression regulator; Provisional
Probab=64.36 E-value=10 Score=42.32 Aligned_cols=46 Identities=35% Similarity=0.574 Sum_probs=37.3
Q ss_pred cccCcEEEEecCCCCCceeEEEeecCCeEEEEecCCceEEEEeCCcce
Q 000637 248 FAVGQTLRIRVGPLKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLA 295 (1378)
Q Consensus 248 ~LIGKTVKIrkGPYKGYlGiVKDaTgt~ARVELHSK~KtITVdKe~Ls 295 (1378)
--+||.|+|..|.- =.-++|+||+-+.|||+|.+-+. |.|.-+||.
T Consensus 167 l~~gq~v~vk~g~~-~~~a~i~ei~kd~v~vql~~Gl~-~~v~ae~l~ 212 (213)
T PRK04950 167 LTVGQAVKVKAGKS-AMDATVLEITKDDVRVQLDSGLS-MIVRAEHLV 212 (213)
T ss_pred hccCCEEEEeccCC-CCceEEEEEecCcEEEEcCCCcE-EEEeHhhhc
Confidence 35799999998853 35689999999999999999775 677777774
No 91
>PRK14640 hypothetical protein; Provisional
Probab=63.00 E-value=13 Score=39.09 Aligned_cols=47 Identities=17% Similarity=0.147 Sum_probs=36.7
Q ss_pred cccCcEEEEec----CCCCCceeEEEeecCCeEEEEecCCceEEEEeCCccee
Q 000637 248 FAVGQTLRIRV----GPLKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLAE 296 (1378)
Q Consensus 248 ~LIGKTVKIrk----GPYKGYlGiVKDaTgt~ARVELHSK~KtITVdKe~Lsv 296 (1378)
.+||+.|+|+- .--|=+.|++++++++.+++++. .+++.|+.+.|.-
T Consensus 94 r~~G~~v~V~l~~~~~~~k~~~G~L~~v~~~~v~l~~~--~~~~~i~~~~I~k 144 (152)
T PRK14640 94 KYVGQEAAVTLRMATNNRRKFKGVIKAVQGDMITLTVD--GKDEVLAFTNIQK 144 (152)
T ss_pred HhCCCeEEEEEecccCCceEEEEEEEEEeCCEEEEEEC--CeEEEEEhHHeee
Confidence 58999999984 33477899999999999998875 5567777776653
No 92
>PF10842 DUF2642: Protein of unknown function (DUF2642); InterPro: IPR020139 This entry contains proteins with no known function.
Probab=61.21 E-value=23 Score=33.43 Aligned_cols=45 Identities=7% Similarity=0.124 Sum_probs=34.9
Q ss_pred cccCcEEEEecCCCCCceeEEEeecCCeEEEEecCCceEEEEeCCcce
Q 000637 248 FAVGQTLRIRVGPLKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLA 295 (1378)
Q Consensus 248 ~LIGKTVKIrkGPYKGYlGiVKDaTgt~ARVELHSK~KtITVdKe~Ls 295 (1378)
.||||+|.|.. ..-=++|+++||..+++.||-+ .+.+.|.-.+|.
T Consensus 18 ~liG~~vvV~T-~~g~v~G~L~~V~pDhIvl~~~--~~~~~IR~~~IV 62 (66)
T PF10842_consen 18 SLIGQRVVVQT-TRGSVRGILVDVKPDHIVLEEN--GTPFFIRIAQIV 62 (66)
T ss_pred HhcCCEEEEEE-cCCcEEEEEEeecCCEEEEEeC--CcEEEEEeeeEE
Confidence 58999999987 3444689999999999999988 555555555554
No 93
>PRK01889 GTPase RsgA; Reviewed
Probab=60.66 E-value=27 Score=40.99 Aligned_cols=90 Identities=8% Similarity=0.038 Sum_probs=55.2
Q ss_pred ceEEEEEeccCCceEEccCCCCCCcEEEEeccccccCCCCCccccccCCCCeeccCCeEEEecCCCCCceeEEEEEEcce
Q 000637 92 DFGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVSEGPSKDRQGIVKKIYRGI 171 (1378)
Q Consensus 92 TVGVIVrVEKDDsFKVLdqngDrGkVvtVKpseIk~Kr~dRR~vAlD~nGNtIrVgDtVKVVdGP~KGRQG~VlHIyRg~ 171 (1378)
..|.||++.+ ..|.|++.+ +.++ .. ++.|+. . ........+-|||.|.+-. ...|.|++|+--.
T Consensus 29 ~~g~v~~~~~-~~~~v~~~~---~~~~-~~---~~gk~~---~-~~~~~~~~~~vGD~V~~~~----~~~g~I~~i~pR~ 92 (356)
T PRK01889 29 EPGRVVEEHR-SGYVVATEE---GEVR-AE---VSGKWR---H-EAFPPGDRPAVGDWVLLDN----EKKARIVRLLPRR 92 (356)
T ss_pred ccEEEEEEEC-CEEEEEECC---cEEE-EE---ecchhh---c-cccccCCCCccCcEEEEec----CCceEEEEEECCC
Confidence 4699999999 588888643 2322 22 222211 0 1111244589999998753 2468999998765
Q ss_pred EEEEeccc--cccccEEEEeCCceeecc
Q 000637 172 LFIYDENE--TENGGYFCSKSQHCEKTK 197 (1378)
Q Consensus 172 LFL~sR~i--~ENGGIFVvrArnVvlVg 197 (1378)
=+|.-+.. ....-+|+++...|++|-
T Consensus 93 ~~L~R~~~~~~~~~q~iaANvD~vliV~ 120 (356)
T PRK01889 93 SLFSRKAAGTRSEEQLIAANVDTVFIVC 120 (356)
T ss_pred ceEEcCCCCCCccceeEEEeCCEEEEEE
Confidence 45554443 223357888888887774
No 94
>PRK14632 hypothetical protein; Provisional
Probab=59.33 E-value=16 Score=39.28 Aligned_cols=51 Identities=16% Similarity=0.316 Sum_probs=40.0
Q ss_pred cccCcEEEEe-cCCC------CCceeEEEeecCCeEEEEecCC------ceEEEEeCCcceecc
Q 000637 248 FAVGQTLRIR-VGPL------KGYLCRVLAVRYSDVTVKLDSQ------QKILTVKGEHLAEVR 298 (1378)
Q Consensus 248 ~LIGKTVKIr-kGPY------KGYlGiVKDaTgt~ARVELHSK------~KtITVdKe~Lsvv~ 298 (1378)
.+||+.|+|+ ..|+ |=|.|+++++++..++|++..+ ..+|+|+.+.|..+.
T Consensus 95 r~iG~~V~V~l~~~~~~~~g~k~~~G~L~~v~~~~i~l~~~~~~~~~~~~~~~~i~~~~I~ka~ 158 (172)
T PRK14632 95 PYVGRQIELTLIDPTPEWPGRRKFRGELLAVEGDTVVLRPEGAPAPEAEEAVLRTSWQGVRKAN 158 (172)
T ss_pred HhCCCEEEEEEeccccccCCceEEEEEEEEEeCCEEEEEEcCcccccCCceeEEEEhHHccEEE
Confidence 5899999996 3443 6788999999999999998653 247888888887543
No 95
>TIGR03630 arch_S17P archaeal ribosomal protein S17P. This model describes exclusively the archaeal ribosomal protein S17P. It excludes homologous ribosomal proteins S11 from eukaryotes and S17 from bacteria.
Probab=59.25 E-value=17 Score=36.73 Aligned_cols=25 Identities=16% Similarity=0.106 Sum_probs=21.5
Q ss_pred CCccccccCCCCeeccCCeEEEecC
Q 000637 131 DMKFTALDQSMKVISLNDTARVSEG 155 (1378)
Q Consensus 131 dRR~vAlD~nGNtIrVgDtVKVVdG 155 (1378)
.+++.|-|.+-|+.++||+|+|.+-
T Consensus 63 ~kky~aHDe~cn~~kvGD~V~I~E~ 87 (102)
T TIGR03630 63 RSKIHAHNPPCIDVKEGDIVIIGET 87 (102)
T ss_pred eeeEEEECCCCCCCCCCCEEEEEEc
Confidence 4457899998899999999999884
No 96
>PRK14645 hypothetical protein; Provisional
Probab=58.97 E-value=14 Score=39.15 Aligned_cols=46 Identities=17% Similarity=0.122 Sum_probs=37.8
Q ss_pred cccCcEEEEecCCCCCceeEEEeecCCeEEEEecCCceEEEEeCCccee
Q 000637 248 FAVGQTLRIRVGPLKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLAE 296 (1378)
Q Consensus 248 ~LIGKTVKIrkGPYKGYlGiVKDaTgt~ARVELHSK~KtITVdKe~Lsv 296 (1378)
.++|+.|+|+.+ -|=|.|+++++++..++|++ ..+++.|+.+.|..
T Consensus 99 r~~G~~v~v~~~-~k~~~G~L~~~~d~~i~l~~--~~~~~~i~~~~I~~ 144 (154)
T PRK14645 99 RFAGLKAKVRGP-GENFTGRIKAVSGDQVTFDV--GGEDRTLRIGTFQA 144 (154)
T ss_pred HhCCCEEEEEcC-CeEEEEEEEEEeCCEEEEEE--CCeEEEEEHHHhhh
Confidence 589999999863 57889999999999988876 45778888888753
No 97
>TIGR03635 S17_bact 30S ribosomal protein S17. This model describes the bacterial ribosomal small subunit protein S17, while excluding cytosolic eukaryotic homologs and archaeal homologs. The model finds many, but not, chloroplast and mitochondrial counterparts to bacterial S17.
Probab=58.61 E-value=16 Score=34.50 Aligned_cols=24 Identities=25% Similarity=0.345 Sum_probs=19.8
Q ss_pred CCccccccCCCCeeccCCeEEEecC
Q 000637 131 DMKFTALDQSMKVISLNDTARVSEG 155 (1378)
Q Consensus 131 dRR~vAlD~nGNtIrVgDtVKVVdG 155 (1378)
.+++.|-|. .|++++||+|+|.+-
T Consensus 37 ~kk~~aHD~-~~~~k~GD~V~I~ec 60 (71)
T TIGR03635 37 TKKYHAHDE-NNECKVGDVVRIIET 60 (71)
T ss_pred cEEEEEECC-CCCCCCCCEEEEEEc
Confidence 345789999 468999999999875
No 98
>PRK08572 rps17p 30S ribosomal protein S17P; Reviewed
Probab=58.47 E-value=19 Score=36.79 Aligned_cols=26 Identities=12% Similarity=0.165 Sum_probs=22.1
Q ss_pred CCccccccCCCCeeccCCeEEEecCC
Q 000637 131 DMKFTALDQSMKVISLNDTARVSEGP 156 (1378)
Q Consensus 131 dRR~vAlD~nGNtIrVgDtVKVVdGP 156 (1378)
.+++.|-|.+-|+.++||+|+|.+-.
T Consensus 65 ~kky~aHDe~cn~~kvGD~V~I~E~R 90 (108)
T PRK08572 65 RSRIHAHNPPCIDAKVGDKVKIAECR 90 (108)
T ss_pred eeeEEEECCCCCCCCCCCEEEEEEcC
Confidence 44588999988999999999999853
No 99
>PRK14633 hypothetical protein; Provisional
Probab=57.59 E-value=18 Score=38.09 Aligned_cols=49 Identities=14% Similarity=0.180 Sum_probs=38.7
Q ss_pred cccCcEEEEec-C---CCCCceeEEEeecCCeEEEEecCCceEEEEeCCcceec
Q 000637 248 FAVGQTLRIRV-G---PLKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLAEV 297 (1378)
Q Consensus 248 ~LIGKTVKIrk-G---PYKGYlGiVKDaTgt~ARVELHSK~KtITVdKe~Lsvv 297 (1378)
.+||+.|+|+- - --|=+.|++++++++.+++++.. .++|.|+.++|.-.
T Consensus 91 r~~G~~v~V~~~~~~~~~~~~~G~L~~v~~~~i~l~~~~-~~~~~i~~~~I~ka 143 (150)
T PRK14633 91 ALVGFNVKAVTLAPVGSQTKFKGVLERVEGNNVILNLED-GKEISFDFDELKKL 143 (150)
T ss_pred HhCCCeEEEEEecccCCcEEEEEEEEEEeCCEEEEEEcC-CcEEEEEhHHeeeE
Confidence 58999999965 3 34668899999999999998753 36788888887753
No 100
>PRK05610 rpsQ 30S ribosomal protein S17; Reviewed
Probab=56.21 E-value=19 Score=35.05 Aligned_cols=25 Identities=24% Similarity=0.348 Sum_probs=20.6
Q ss_pred CCccccccCCCCeeccCCeEEEecCC
Q 000637 131 DMKFTALDQSMKVISLNDTARVSEGP 156 (1378)
Q Consensus 131 dRR~vAlD~nGNtIrVgDtVKVVdGP 156 (1378)
.+++.|-|. .|++++||+|+|.+..
T Consensus 42 ~kk~~aHD~-~n~~k~GD~V~I~e~r 66 (84)
T PRK05610 42 SKKYHAHDE-NNEAKIGDVVRIMETR 66 (84)
T ss_pred ceEEEEECC-CCCCCCCCEEEEEEcc
Confidence 445789999 4689999999999864
No 101
>PRK14636 hypothetical protein; Provisional
Probab=55.93 E-value=18 Score=39.18 Aligned_cols=49 Identities=16% Similarity=0.164 Sum_probs=37.2
Q ss_pred ccccCcEEEEec-CCC---CCceeEEEeecCCeEEEEecCCceEEEEeCCccee
Q 000637 247 MFAVGQTLRIRV-GPL---KGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLAE 296 (1378)
Q Consensus 247 D~LIGKTVKIrk-GPY---KGYlGiVKDaTgt~ARVELHSK~KtITVdKe~Lsv 296 (1378)
.++||+.|+|+. .|+ |=|.|+++++++..++|++.. .++|+|+.+.|.-
T Consensus 94 ~r~~G~~V~V~l~~~~~g~k~~~G~L~~v~~~~v~l~~~~-~~~~~i~~~~I~k 146 (176)
T PRK14636 94 ADWAGHEARIALSEPLDGRKQFRGELKGIDGDTVTIADNK-AGEVILPFAAIES 146 (176)
T ss_pred HHhCCCeEEEEEecccCCeEEEEEEEEEEeCCEEEEEEcC-CcEEEEEhHHcce
Confidence 358999999964 444 446899999999999988742 3567888777764
No 102
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=55.68 E-value=35 Score=33.01 Aligned_cols=64 Identities=14% Similarity=0.134 Sum_probs=46.5
Q ss_pred eEEEEEeccCCceEEccCCCCCCcEEEEeccccccCCCCCccccccCCCCeeccCCeEEEecCCCCCceeEEEEEEcc
Q 000637 93 FGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVSEGPSKDRQGIVKKIYRG 170 (1378)
Q Consensus 93 VGVIVrVEKDDsFKVLdqngDrGkVvtVKpseIk~Kr~dRR~vAlD~nGNtIrVgDtVKVVdGP~KGRQG~VlHIyRg 170 (1378)
.|+|+++..+..|+|...++ .+++ .-|.-|+...+ ==|.+||+|.|--=||.-..|.|.|=|+.
T Consensus 10 ~g~V~e~L~~~~f~v~~edg---~~~~---ahI~GKmr~~~--------i~I~~GD~V~Ve~~~~d~~kg~I~~Ry~~ 73 (75)
T COG0361 10 EGTVIEMLPNGRFRVELENG---HERL---AHISGKMRKNR--------IRILPGDVVLVELSPYDLTKGRIVYRYKK 73 (75)
T ss_pred EEEEEEecCCCEEEEEecCC---cEEE---EEccCcchhee--------EEeCCCCEEEEEecccccccccEEEEecC
Confidence 59999999988999998874 4444 33433321112 24889999999999998788989887763
No 103
>PRK14630 hypothetical protein; Provisional
Probab=55.62 E-value=23 Score=37.14 Aligned_cols=46 Identities=13% Similarity=0.096 Sum_probs=35.8
Q ss_pred cccCcEEEEecCCCCCceeEEEeecCCeEEEEecCCceEEEEeCCccee
Q 000637 248 FAVGQTLRIRVGPLKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLAE 296 (1378)
Q Consensus 248 ~LIGKTVKIrkGPYKGYlGiVKDaTgt~ARVELHSK~KtITVdKe~Lsv 296 (1378)
.+||+.|+|+...-. +.|+++++.+..+++++. .++|.|+.+.|.-
T Consensus 94 r~~G~~v~V~l~~~~-~~G~L~~~~d~~i~l~~~--~~~~~i~~~~I~k 139 (143)
T PRK14630 94 IFEGKKIKLMLDNDF-EEGFILEAKADSFIFKTD--SKEVNVLYSDVKK 139 (143)
T ss_pred HhCCCEEEEEEcCcc-eEEEEEEEeCCEEEEEEC--CEEEEEEhHhcce
Confidence 589999999753322 489999999999998864 4678888877764
No 104
>PRK14647 hypothetical protein; Provisional
Probab=52.81 E-value=22 Score=37.73 Aligned_cols=48 Identities=17% Similarity=0.223 Sum_probs=37.9
Q ss_pred cccCcEEEEec-CC--------CCCceeEEEeecCCeEEEEecCCceEEEEeCCccee
Q 000637 248 FAVGQTLRIRV-GP--------LKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLAE 296 (1378)
Q Consensus 248 ~LIGKTVKIrk-GP--------YKGYlGiVKDaTgt~ARVELHSK~KtITVdKe~Lsv 296 (1378)
.+||+.|+|+- -| -|=|.|+++++++..++|+++- .++|+|+.+.|.-
T Consensus 96 r~~G~~v~V~l~~~~~~~~~~~~~~~~G~L~~~~~~~v~l~~~~-~~~~~i~~~~I~k 152 (159)
T PRK14647 96 RYAGRLVKVRTFELLADEAGNKRKTFLGELEGLADGVVTIALKE-GQQARIPLDKIAK 152 (159)
T ss_pred HhCCcEEEEEEeccccccccCCceEEEEEEEeecCCEEEEEEcC-CcEEEEEHHHCCE
Confidence 58999999974 33 3778999999999999998852 4578888887764
No 105
>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=52.02 E-value=4.8 Score=38.40 Aligned_cols=42 Identities=17% Similarity=0.210 Sum_probs=0.0
Q ss_pred cCcEEEEecCCCCCceeEEEeecCCeEEEEecCCceEEEEeCCccee
Q 000637 250 VGQTLRIRVGPLKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLAE 296 (1378)
Q Consensus 250 IGKTVKIrkGPYKGYlGiVKDaTgt~ARVELHSK~KtITVdKe~Lsv 296 (1378)
+|..|.... |+.|+|+++++++|.||+.. .-+|+|.|..|..
T Consensus 39 ~Gd~VvT~g----Gi~G~V~~i~~~~v~lei~~-g~~i~v~k~aI~~ 80 (82)
T PF02699_consen 39 PGDEVVTIG----GIYGTVVEIDDDTVVLEIAP-GVEITVEKSAIAR 80 (82)
T ss_dssp -----------------------------------------------
T ss_pred CCCEEEECC----cEEEEEEEEeCCEEEEEECC-CeEEEEEHHHhHh
Confidence 456665444 78899999999999999988 5678999988864
No 106
>PRK02001 hypothetical protein; Validated
Probab=52.01 E-value=28 Score=37.03 Aligned_cols=48 Identities=15% Similarity=0.189 Sum_probs=37.6
Q ss_pred cccCcEEEEecCCCCCceeEEEeecCCeEEEEecCC------------ceEEEEeCCcce
Q 000637 248 FAVGQTLRIRVGPLKGYLCRVLAVRYSDVTVKLDSQ------------QKILTVKGEHLA 295 (1378)
Q Consensus 248 ~LIGKTVKIrkGPYKGYlGiVKDaTgt~ARVELHSK------------~KtITVdKe~Ls 295 (1378)
++||+.|+|+----|=|.|+++++++..++|+++.+ .+.++|+.+.|.
T Consensus 87 r~~G~~v~V~l~~~~~~~G~L~~~~~~~i~l~~~~~~~~~~~k~~~~~~~~~~i~~~~I~ 146 (152)
T PRK02001 87 KNIGRELEVLTKNGKKIEGELKSADENDITLEVKAREPKEGGKGKVTVEKEETITYDDIK 146 (152)
T ss_pred HhCCCEEEEEECCCCEEEEEEEEEeCCEEEEEEcccccccccccccccceeEEEEhHhee
Confidence 589999999864447899999999999999998753 235777666664
No 107
>PRK14646 hypothetical protein; Provisional
Probab=51.64 E-value=23 Score=37.52 Aligned_cols=49 Identities=8% Similarity=0.022 Sum_probs=38.0
Q ss_pred ccccCcEEEEec-CCC---CCceeEEEeecCCeEEEEecCCceEEEEeCCcceec
Q 000637 247 MFAVGQTLRIRV-GPL---KGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLAEV 297 (1378)
Q Consensus 247 D~LIGKTVKIrk-GPY---KGYlGiVKDaTgt~ARVELHSK~KtITVdKe~Lsvv 297 (1378)
..++|+.|+|+- .|+ |=|.|+++++.+..++|++. .+++.|+.+.|.-+
T Consensus 96 ~r~~G~~v~V~l~~~~~~~~~~~G~L~~~~~~~v~l~~~--g~~~~i~~~~I~ka 148 (155)
T PRK14646 96 KTFKGFPVNVELNQKNSKIKFLNGLLYEKSKDYLAINIK--GKIKKIPFNEVLKI 148 (155)
T ss_pred HHhCCCEEEEEEecCcCCeEEEEEEEEEEeCCEEEEEEC--CEEEEEEHHHeeeE
Confidence 358999999974 343 45679999999999999874 67788888877643
No 108
>COG2139 RPL21A Ribosomal protein L21E [Translation, ribosomal structure and biogenesis]
Probab=51.55 E-value=26 Score=35.31 Aligned_cols=50 Identities=30% Similarity=0.519 Sum_probs=38.9
Q ss_pred cccCcEEEEecCC----------CCCceeEEEeecCCeEEEEe--cCCceEEEEeCCcceec
Q 000637 248 FAVGQTLRIRVGP----------LKGYLCRVLAVRYSDVTVKL--DSQQKILTVKGEHLAEV 297 (1378)
Q Consensus 248 ~LIGKTVKIrkGP----------YKGYlGiVKDaTgt~ARVEL--HSK~KtITVdKe~Lsvv 297 (1378)
.-+|+.|.|..=| |-|+.|+|+.+++.-+-||| -.+.|+|.|--+||.-.
T Consensus 33 y~~Gd~V~I~IdpSv~kGmPh~rf~G~TG~Vvg~~g~ay~V~v~~G~k~K~liv~peHLk~~ 94 (98)
T COG2139 33 YKVGDKVHIDIDPSVHKGMPHPRFQGKTGTVVGVRGRAYKVEVYDGNKEKTLIVRPEHLKPQ 94 (98)
T ss_pred ccCCCEEEEEeCcccccCCCCccccCcceEEEeccCCEEEEEEecCCceEEEEeCHHHcccc
Confidence 3467777776543 78999999999999887775 55668999999998753
No 109
>PF13051 DUF3912: Protein of unknown function (DUF3912)
Probab=49.33 E-value=22 Score=33.12 Aligned_cols=52 Identities=19% Similarity=0.200 Sum_probs=37.4
Q ss_pred cccCcEEEEecCCCCCceeEEEeec---CCeEEEEecCCceEEEEeCCcceeccCCc
Q 000637 248 FAVGQTLRIRVGPLKGYLCRVLAVR---YSDVTVKLDSQQKILTVKGEHLAEVRGKS 301 (1378)
Q Consensus 248 ~LIGKTVKIrkGPYKGYlGiVKDaT---gt~ARVELHSK~KtITVdKe~Lsvv~g~~ 301 (1378)
.++||..-|..|||.--+||||.-. +.++-|-+. .+.|.|+..+|.+|..+.
T Consensus 3 di~gqkayikdgp~rnrigivk~~e~q~~~~f~ivi~--~q~i~velkdivlvgvdv 57 (68)
T PF13051_consen 3 DIVGQKAYIKDGPYRNRIGIVKKNEKQLESHFAIVIG--EQSIDVELKDIVLVGVDV 57 (68)
T ss_pred cccccEeeeccCCccceeEEEecchhhcCCcEEEEEC--CeEEEEEeeeEEEEEecH
Confidence 4789999999999999999999754 233444333 356777777777665443
No 110
>CHL00142 rps17 ribosomal protein S17; Validated
Probab=46.13 E-value=32 Score=33.70 Aligned_cols=25 Identities=16% Similarity=0.217 Sum_probs=19.8
Q ss_pred CCccccccCCCCeeccCCeEEEecCC
Q 000637 131 DMKFTALDQSMKVISLNDTARVSEGP 156 (1378)
Q Consensus 131 dRR~vAlD~nGNtIrVgDtVKVVdGP 156 (1378)
.+++.|=| ..|++++||+|+|.+-+
T Consensus 39 ~kk~~aHD-e~n~~~~GD~V~I~e~R 63 (84)
T CHL00142 39 TKKYLVHD-EENECNIGDQVLIEETR 63 (84)
T ss_pred eEEEEEeC-CCCCCCCCCEEEEEEcC
Confidence 34577889 46689999999999754
No 111
>COG3109 ProQ Activator of osmoprotectant transporter ProP [Signal transduction mechanisms]
Probab=46.07 E-value=27 Score=38.39 Aligned_cols=45 Identities=33% Similarity=0.533 Sum_probs=36.5
Q ss_pred ccCcEEEEecCCCCCceeEEEeecCCeEEEEecCCceEEEEeCCcce
Q 000637 249 AVGQTLRIRVGPLKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLA 295 (1378)
Q Consensus 249 LIGKTVKIrkGPYKGYlGiVKDaTgt~ARVELHSK~KtITVdKe~Ls 295 (1378)
-||+.|+|..|.- -...+|++|+-+.|||+|.+-.. +.|.-+||.
T Consensus 163 ~~g~~~kVk~G~~-a~~AtvlEv~Kd~vRVqL~~Gl~-m~V~AehL~ 207 (208)
T COG3109 163 TVGQALKVKAGQN-AMDATVLEITKDGVRVQLNSGLS-MIVRAEHLV 207 (208)
T ss_pred hccceeeeccccc-cccceEEEEeccceEEeecCCce-EEEehhhhc
Confidence 4799999999863 45689999999999999998654 667777764
No 112
>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=46.01 E-value=91 Score=28.09 Aligned_cols=59 Identities=14% Similarity=0.099 Sum_probs=34.4
Q ss_pred EEEEEeccCCceEEccCCCCCCcEEEEeccccccCCCCCccccccCCCCeeccCCeEEEecCCCCCceeEEEE
Q 000637 94 GLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVSEGPSKDRQGIVKK 166 (1378)
Q Consensus 94 GVIVrVEKDDsFKVLdqngDrGkVvtVKpseIk~Kr~dRR~vAlD~nGNtIrVgDtVKVVdGP~KGRQG~VlH 166 (1378)
|+||+.-....|.|.+.. ++++++++....++ ....+.+||.|.+---++...+|.|.|
T Consensus 5 G~Vi~~~~g~~~~V~~~~---g~~~~c~~rGklr~-----------~~~~~~vGD~V~~~~~~~~~~~g~I~~ 63 (64)
T cd04451 5 GVVTEALPNAMFRVELEN---GHEVLAHISGKMRM-----------NYIRILPGDRVKVELSPYDLTKGRIVY 63 (64)
T ss_pred EEEEEEeCCCEEEEEeCC---CCEEEEEECceeec-----------CCcccCCCCEEEEEEeecCCCEEEEEE
Confidence 778877631367775533 35666664332111 234489999998874443345677765
No 113
>PRK14631 hypothetical protein; Provisional
Probab=44.63 E-value=37 Score=36.88 Aligned_cols=47 Identities=17% Similarity=0.466 Sum_probs=36.0
Q ss_pred cccCcEEEEec-CC---CCCceeEEEeec--CCeEEEEecCCceEEEEeCCcce
Q 000637 248 FAVGQTLRIRV-GP---LKGYLCRVLAVR--YSDVTVKLDSQQKILTVKGEHLA 295 (1378)
Q Consensus 248 ~LIGKTVKIrk-GP---YKGYlGiVKDaT--gt~ARVELHSK~KtITVdKe~Ls 295 (1378)
+++|+.|+|+- .| -|=|.|+++.++ +..++|++.-+ ++|.|+...|.
T Consensus 114 r~~G~~V~V~l~~~~~~~k~~~G~L~~v~~~~~~v~l~~~~~-~~~~i~~~~I~ 166 (174)
T PRK14631 114 GYIGQQVALRLIAAVENRRKFQAKLLAVDLENEEIQVEVEGK-HVLDIDSNNID 166 (174)
T ss_pred HhCCCeEEEEEecccCCceEEEEEEEEeecCCCEEEEEEcCC-cEEEEEhHHcc
Confidence 58999999985 23 366889999999 99999988533 45777766665
No 114
>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=44.32 E-value=1.2e+02 Score=29.60 Aligned_cols=64 Identities=14% Similarity=0.098 Sum_probs=40.1
Q ss_pred ceEEEEEeccCCceEEccCCCCCCcEEEEeccccccCCCCCccccccCCCCeeccCCeEEEecCCCCC-ceeEEEEEEcc
Q 000637 92 DFGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVSEGPSKD-RQGIVKKIYRG 170 (1378)
Q Consensus 92 TVGVIVrVEKDDsFKVLdqngDrGkVvtVKpseIk~Kr~dRR~vAlD~nGNtIrVgDtVKVVdGP~KG-RQG~VlHIyRg 170 (1378)
.+..||++.-++.|.|.+..+ +.+.|. |-.| +++ .-=|+.||.|.|.-=++.. -.|+|.|||..
T Consensus 2 ~i~rV~~~~G~n~~~V~~~dG---~~~l~~---iP~K-fRk--------~iWIkrGd~VlV~p~~~~~kvkgeIv~i~~~ 66 (78)
T cd05792 2 QIVRVLGSKGNNLHEVETPNG---SRYLVS---MPTK-FRK--------NIWIKRGDFVLVEPIEEGDKVKAEIVKILTR 66 (78)
T ss_pred eEEEEEEcCCCcEEEEEcCCC---CEEEEE---echh-hcc--------cEEEEeCCEEEEEecccCCceEEEEEEEECH
Confidence 456677777656788887653 455544 3233 122 2248899999996544433 38999999873
No 115
>COG0186 RpsQ Ribosomal protein S17 [Translation, ribosomal structure and biogenesis]
Probab=43.97 E-value=34 Score=33.92 Aligned_cols=24 Identities=25% Similarity=0.385 Sum_probs=20.1
Q ss_pred CCccccccCCCCeeccCCeEEEecC
Q 000637 131 DMKFTALDQSMKVISLNDTARVSEG 155 (1378)
Q Consensus 131 dRR~vAlD~nGNtIrVgDtVKVVdG 155 (1378)
.+++-|-| .-|.+++||+|+|.+=
T Consensus 44 ~kK~~aHd-e~~~~k~GD~V~I~Et 67 (87)
T COG0186 44 SKKYHAHD-ECNEAKVGDIVRIAET 67 (87)
T ss_pred EeeeEeec-ccccCCCCCEEEEEEc
Confidence 34577999 8899999999999873
No 116
>PF00900 Ribosomal_S4e: Ribosomal family S4e; InterPro: IPR013845 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 [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families includes yeast S7 (YS6); archaeal S4e; and mammalian and plant cytoplasmic S4 []. Two highly similar isoforms of mammalian S4 exist, one coded by a gene on chromosome Y, and the other on chromosome X. These proteins have 233 to 264 amino acids. This entry represents the central region of these proteins.; PDB: 2XZM_W 2XZN_W 3IZ6_D 3KBG_A 3U5G_E 3U5C_E 3IZB_D.
Probab=43.84 E-value=30 Score=33.16 Aligned_cols=63 Identities=19% Similarity=0.133 Sum_probs=35.9
Q ss_pred eEeecCCceEEEEEeccCCc-eEEccCCCCCCcEEEEeccccccCCCCCcc-ccccCCCCeeccCCeEEEec
Q 000637 85 LVCFGRKDFGLIVGMEKDDH-YKILKEGSEGPAVVTVERRTLKNGPFDMKF-TALDQSMKVISLNDTARVSE 154 (1378)
Q Consensus 85 LVQLD~qTVGVIVrVEKDDs-FKVLdqngDrGkVvtVKpseIk~Kr~dRR~-vAlD~nGNtIrVgDtVKVVd 154 (1378)
.|.+|.+-.=++++|+.+|+ ||++.-. ...+|+-.-++-.+-+-|. .+-| ..|+++|+|+|--
T Consensus 7 Rvl~d~kgr~~l~~I~~eea~~KLckV~----~k~~~~gG~~ql~~hDGrni~~~~---~~~k~~Dtv~i~l 71 (77)
T PF00900_consen 7 RVLYDTKGRFVLHPISEEEAKYKLCKVR----NKTTGKGGKPQLNTHDGRNIRYPD---PDIKTNDTVVIDL 71 (77)
T ss_dssp EEEE-TTS-EEEEEE-TTGGGEEEEEEE----EEEEEGGGEEEEEETTTEEEES-S---ST--TTEEEEEET
T ss_pred EEEECCCCcEEEEECCHHHccCeEEEEe----EEEEecCCcEEEEecCceEEEcCc---CCccCCCEEEEEC
Confidence 36677766667778887654 7777653 3455555555544444443 3444 8899999999854
No 117
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=43.80 E-value=67 Score=35.69 Aligned_cols=42 Identities=12% Similarity=0.225 Sum_probs=31.4
Q ss_pred CeeccCCeEEEecCCCCCceeEEEEEEcceEEEEeccccccccEEEEeCCceeec
Q 000637 142 KVISLNDTARVSEGPSKDRQGIVKKIYRGILFIYDENETENGGYFCSKSQHCEKT 196 (1378)
Q Consensus 142 NtIrVgDtVKVVdGP~KGRQG~VlHIyRg~LFL~sR~i~ENGGIFVvrArnVvlV 196 (1378)
+.|+++|+|| +.|+-++ ..+||.-+ -.+.||+-++|.+|-..
T Consensus 117 d~f~~GDivr----------A~Vis~~-~~~~Lst~--~~dlGVI~A~CsrC~~~ 158 (188)
T COG1096 117 DAFRIGDIVR----------ARVISTG-DPIQLSTK--GNDLGVIYARCSRCRAP 158 (188)
T ss_pred cccccccEEE----------EEEEecC-CCeEEEec--CCcceEEEEEccCCCcc
Confidence 7899999998 5677777 55666654 35789999988888633
No 118
>COG0779 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=42.98 E-value=42 Score=35.94 Aligned_cols=48 Identities=19% Similarity=0.326 Sum_probs=38.8
Q ss_pred ccccCcEEEEec----CCCCCceeEEEeecCCeEEEEecCCceEEEEeCCccee
Q 000637 247 MFAVGQTLRIRV----GPLKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLAE 296 (1378)
Q Consensus 247 D~LIGKTVKIrk----GPYKGYlGiVKDaTgt~ARVELHSK~KtITVdKe~Lsv 296 (1378)
..++|+.|+|.. ---|=+.|+|+.+.+++++|++.- |.|.|+...|.-
T Consensus 95 ~r~~G~~Vkv~l~~~~~~~k~~~G~i~~~d~~~v~~~~~~--k~v~Ip~~~i~k 146 (153)
T COG0779 95 ARFIGEKVKVKLRLPIEGRKKFEGKIVAVDGETVTLEVDG--KEVEIPFSDIAK 146 (153)
T ss_pred HHhcCcEEEEEEecccCCceEEEEEEEEEcCCeEEEEECC--EEEEEEcccchh
Confidence 358999999998 556789999999999999998554 558887777653
No 119
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=42.17 E-value=79 Score=34.05 Aligned_cols=41 Identities=15% Similarity=0.237 Sum_probs=26.8
Q ss_pred CCeeccCCeEEEecCCCCCceeEEEEEEcceEEEEeccccccccEEEEeCCcee
Q 000637 141 MKVISLNDTARVSEGPSKDRQGIVKKIYRGILFIYDENETENGGYFCSKSQHCE 194 (1378)
Q Consensus 141 GNtIrVgDtVKVVdGP~KGRQG~VlHIyRg~LFL~sR~i~ENGGIFVvrArnVv 194 (1378)
...+++||+|++ .|+.|. ..+.|..++ +..|++.+++..|-
T Consensus 116 ~~~~~~GD~V~a----------kV~~i~-~~i~LS~k~--~~lGvv~a~~~~~g 156 (189)
T PRK09521 116 TDAFKIGDIVRA----------KVISYT-DPLQLSTKG--KDLGVIYAMCSRCR 156 (189)
T ss_pred HhccCCCCEEEE----------EEEecC-CcEEEEEec--CCceEEEEEccccC
Confidence 556899999985 345554 344455443 45788888777664
No 120
>KOG1708 consensus Mitochondrial/chloroplast ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=41.58 E-value=24 Score=39.50 Aligned_cols=45 Identities=31% Similarity=0.323 Sum_probs=35.4
Q ss_pred ccccCcEEEEecCCCCCceeEEEeec--CCeEEEE-ecCCceEEEEeC
Q 000637 247 MFAVGQTLRIRVGPLKGYLCRVLAVR--YSDVTVK-LDSQQKILTVKG 291 (1378)
Q Consensus 247 D~LIGKTVKIrkGPYKGYlGiVKDaT--gt~ARVE-LHSK~KtITVdK 291 (1378)
-++.|.||.|+.|.-||.+|+|..|- .+.|-|+ ||++-+++--.+
T Consensus 72 ~ff~GDtVeVlvGkDkGkqG~Vtqv~r~~s~VvV~gln~k~r~~gsek 119 (236)
T KOG1708|consen 72 HFFFGDTVEVLVGKDKGKQGEVTQVIRHRSWVVVKGLNTKYRHMGSEK 119 (236)
T ss_pred eEecCCEEEEEecccCCccceEEEEeecCceEEEcccchhhhhhcccc
Confidence 45679999999999999999999985 4577777 887776554333
No 121
>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=40.96 E-value=46 Score=29.68 Aligned_cols=45 Identities=16% Similarity=0.135 Sum_probs=27.4
Q ss_pred eeccCCeEEEecCCCCCce---eEEEEEEcceEEEEeccccccccEEEE
Q 000637 143 VISLNDTARVSEGPSKDRQ---GIVKKIYRGILFIYDENETENGGYFCS 188 (1378)
Q Consensus 143 tIrVgDtVKVVdGP~KGRQ---G~VlHIyRg~LFL~sR~i~ENGGIFVv 188 (1378)
+|+++|.|+++. ....++ .+|.+||.-.--......-.+.|++|.
T Consensus 12 ~l~~gd~v~~~~-~~~~~~~~~~~I~~i~~~~~~~~~~~~~~~~G~~~~ 59 (74)
T PF03144_consen 12 TLKKGDKVRVLP-NGTGKKGQVVKIKSIFMFNGDVQEAVAGANAGDIVA 59 (74)
T ss_dssp EEETTEEEEEES-TTTTEECEEEEEEEEEETTEEESEEETTEEEEEEEE
T ss_pred EEcCCCEEEECc-cCCcceeeeeecccccccccCccEeCCceeeEEEEE
Confidence 689999999977 434444 788887765332233333345555554
No 122
>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI. This protein is a component of the relaxosome complex. In the process of conjugative plasmid transfer the realaxosome binds to the plasmid at the oriT (origin of transfer) site. The relaxase protein TraI mediates the single-strand nicking and ATP-dependent unwinding (relaxation, helicase activity) of the plasmid molecule. These two activities reside in separate domains of the protein.
Probab=40.88 E-value=97 Score=44.27 Aligned_cols=90 Identities=12% Similarity=0.138 Sum_probs=62.3
Q ss_pred CCCccEeceeEeecCCceEEEEEeccCCceEEccCCCCCCcEEEEeccccccCCCCCccccccCCCCeeccCCeEEEec-
Q 000637 76 LENSFELYELVCFGRKDFGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVSE- 154 (1378)
Q Consensus 76 slG~YELHDLVQLD~qTVGVIVrVEKDDsFKVLdqngDrGkVvtVKpseIk~Kr~dRR~vAlD~nGNtIrVgDtVKVVd- 154 (1378)
....|+..|+|+|.....-.|+.|++++...+|... ..|+.+.+.|.++.. +.+.+-....-+|.+||.|++..
T Consensus 1326 ~~~~Y~~G~vv~~~~~~y~~V~~vd~~~~~v~l~~~-~~G~~~~~~p~~~~~----~~~~~y~~~~~~l~~GDri~~t~~ 1400 (1960)
T TIGR02760 1326 TMMPFEKGAVLRLKKDAYLTIADIDREHGKLTVADI-KTGSERDILPRQLDH----TFTSLYSDSELPLAKGDKIRLRAT 1400 (1960)
T ss_pred hccccCCCcEEEecCCcEEEEEEecCCCCEEEEEec-CCCCeEeeChhhcCc----ccceeeccccccccCCCEEEEeec
Confidence 357788999999888888889999886444444320 125778888877642 23446677788899999999864
Q ss_pred ----CCCCCceeEEEEEEcc
Q 000637 155 ----GPSKDRQGIVKKIYRG 170 (1378)
Q Consensus 155 ----GP~KGRQG~VlHIyRg 170 (1378)
|-..+-.++|..|-.+
T Consensus 1401 d~~~g~~n~~~~~V~~v~~~ 1420 (1960)
T TIGR02760 1401 DKNRGIKANEVYTVTQVVNG 1420 (1960)
T ss_pred CcccccccCCeEEEEEEcCC
Confidence 2234667888888554
No 123
>PRK13709 conjugal transfer nickase/helicase TraI; Provisional
Probab=39.47 E-value=1.2e+02 Score=43.08 Aligned_cols=91 Identities=14% Similarity=0.137 Sum_probs=60.8
Q ss_pred CCCccEe--ceeEeecCCceEEEEEeccCCc-eEEccCCCCCCcEEEEeccccccCCCCCccccccCCCCeeccCCeEEE
Q 000637 76 LENSFEL--YELVCFGRKDFGLIVGMEKDDH-YKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARV 152 (1378)
Q Consensus 76 slG~YEL--HDLVQLD~qTVGVIVrVEKDDs-FKVLdqngDrGkVvtVKpseIk~Kr~dRR~vAlD~nGNtIrVgDtVKV 152 (1378)
....|+. .|+|++. ...--|+.|++++. +.|.+.. |+.+.+.|.++.. .++.+-.....+|.+||.|+.
T Consensus 1272 ~~~~Y~~~~G~vv~~~-~~y~~V~~vd~~~~~ltl~~~~---G~~~~~~P~~~~~----~~~~vy~~~~~ela~GDrIr~ 1343 (1747)
T PRK13709 1272 RLSTWEAHRGALALVD-NVYHRIAGIDKDDGLITLRDAE---GNTRLISPREAVA----EGVTLYTPDTIRVGTGDRMRF 1343 (1747)
T ss_pred hhhhcccCCCcEEEec-CceEEEEEEcCCCCEEEEEcCC---CCEEEeChhhccc----ccccccccccccccCCCEEEE
Confidence 3567888 7888886 45567888887533 3333443 6788888877632 245677788899999999999
Q ss_pred ec-----CCCCCceeEEEEEEcceEEE
Q 000637 153 SE-----GPSKDRQGIVKKIYRGILFI 174 (1378)
Q Consensus 153 Vd-----GP~KGRQG~VlHIyRg~LFL 174 (1378)
.. |-+.|.+++|+.|-...|-|
T Consensus 1344 TrnDk~~G~~Ng~~~tV~~I~~~~I~l 1370 (1747)
T PRK13709 1344 TKSDRERGYVANSVWTVTAVSGDSVTL 1370 (1747)
T ss_pred cccCcccccccCCEEEEEEEcCCeEEE
Confidence 64 33345566777665544333
No 124
>PRK11634 ATP-dependent RNA helicase DeaD; Provisional
Probab=37.83 E-value=62 Score=40.95 Aligned_cols=6 Identities=17% Similarity=0.124 Sum_probs=2.3
Q ss_pred EEEEec
Q 000637 117 VVTVER 122 (1378)
Q Consensus 117 VvtVKp 122 (1378)
|+..+|
T Consensus 128 IVVgTP 133 (629)
T PRK11634 128 IVVGTP 133 (629)
T ss_pred EEEECH
Confidence 333333
No 125
>PF09643 YopX: YopX protein; InterPro: IPR019096 YopX is a protein of plasmid origin found in bacteria. It is of approx. 135 residues and is largely helical, with three identical chains probably complexing into a twelve-chain structure. Yop proteins are a subset of pathogenicity factors known as (Yersinia) outer proteins - Yops - which act as chaperones for other proteins such as X. They are exported by the type III secretion system (TTSS) upon bacterial infection of host cells. The TTSS is encoded on a virulence plasmid and is necessary for the survival and replication of the bacterium within host lymphoid tissues []. ; PDB: 2QYZ_A 2P84_A 2OX7_D 2I2L_B.
Probab=37.34 E-value=30 Score=32.95 Aligned_cols=22 Identities=23% Similarity=0.235 Sum_probs=18.4
Q ss_pred cccCCCCeeccCCeEEEecCCC
Q 000637 136 ALDQSMKVISLNDTARVSEGPS 157 (1378)
Q Consensus 136 AlD~nGNtIrVgDtVKVVdGP~ 157 (1378)
.+|.++++|-.||+|++...+.
T Consensus 54 lkDknGkeIyEGDIv~~~~~~~ 75 (121)
T PF09643_consen 54 LKDKNGKEIYEGDIVKFEDGEY 75 (121)
T ss_dssp EE-TTSEEEETTEEEEETTSSC
T ss_pred cEecCCCEeccCCEEEEecCcc
Confidence 5799999999999999977654
No 126
>PRK14712 conjugal transfer nickase/helicase TraI; Provisional
Probab=36.62 E-value=1.4e+02 Score=41.99 Aligned_cols=94 Identities=14% Similarity=0.131 Sum_probs=66.4
Q ss_pred CCCccEe-ceeEeecCCceEEEEEeccCCceEEccCCCCCCcEEEEeccccccCCCCCccccccCCCCeeccCCeEEEec
Q 000637 76 LENSFEL-YELVCFGRKDFGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVSE 154 (1378)
Q Consensus 76 slG~YEL-HDLVQLD~qTVGVIVrVEKDDsFKVLdqngDrGkVvtVKpseIk~Kr~dRR~vAlD~nGNtIrVgDtVKVVd 154 (1378)
....|+. .|.|.|.....-.|+.|++++.+.+|... .|+.+.+.|..... .++.+-.....+|.+||.|+...
T Consensus 1143 ~a~~Y~~~~~~i~l~~~~y~~V~~vd~~~~~vtl~d~--~G~~~~~~P~~~~~----~~~~vy~~~~~ela~GD~Ir~Tr 1216 (1623)
T PRK14712 1143 RLSTWENNPDALALVDNVYHRIAGISKDDGLITLQDA--EGNTRLISPREAVA----EGVTLYTPDTIRVGTGDRIRFTK 1216 (1623)
T ss_pred hhhccccCCceeeecCCceEEEEEEcCCCCEEEEEcC--CCCEEEeChhhccc----cceeeecccccccCCCCEEEEcc
Confidence 3567887 57777887788888999985445445322 25788888866532 24567788899999999999964
Q ss_pred -----CCCCCceeEEEEEEcceEEEE
Q 000637 155 -----GPSKDRQGIVKKIYRGILFIY 175 (1378)
Q Consensus 155 -----GP~KGRQG~VlHIyRg~LFL~ 175 (1378)
|-..+-..+|..|....|-|.
T Consensus 1217 nD~~~G~~Ng~~~tV~~i~~~~i~l~ 1242 (1623)
T PRK14712 1217 SDRERGYVANSVWTVTAVSGDSVTLS 1242 (1623)
T ss_pred CCcccccccCceEEEEEEcCCeEEEe
Confidence 334567788888877766554
No 127
>PRK13709 conjugal transfer nickase/helicase TraI; Provisional
Probab=36.02 E-value=1.3e+02 Score=42.80 Aligned_cols=92 Identities=9% Similarity=0.006 Sum_probs=65.5
Q ss_pred CCccEeceeEeecC-----CceEEEEEeccC-CceEEccCCCCCCcEEEEeccccccCCCCCccccccCCCCeeccCCeE
Q 000637 77 ENSFELYELVCFGR-----KDFGLIVGMEKD-DHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTA 150 (1378)
Q Consensus 77 lG~YELHDLVQLD~-----qTVGVIVrVEKD-DsFKVLdqngDrGkVvtVKpseIk~Kr~dRR~vAlD~nGNtIrVgDtV 150 (1378)
...|+..|+|++-. ...-+|++|+++ ..+.|.+.. |++++++|..+.. ++.+-....-+|.+||.|
T Consensus 646 a~~Y~~G~vi~~~~~~~~~~~~y~V~~v~~~~n~LtL~~~~---G~~~~~~p~~~~~-----~~~vy~~~~ieiA~GDrL 717 (1747)
T PRK13709 646 RDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQ---GETQVVKISSLDS-----SWSLFRPEKMPVADGERL 717 (1747)
T ss_pred hhcCCCCcEEEeeccccccCccEEEEEEcCCCCEEEEEcCC---CCEEEeChHHhcc-----cceeccccccccCCCCEE
Confidence 57899999999832 224589999985 244555554 5788888888742 345667778899999999
Q ss_pred EEecCC-----CCCceeEEEEEEcceEEEEe
Q 000637 151 RVSEGP-----SKDRQGIVKKIYRGILFIYD 176 (1378)
Q Consensus 151 KVVdGP-----~KGRQG~VlHIyRg~LFL~s 176 (1378)
++..-- ..|-..+|+.|-...|-|..
T Consensus 718 r~T~nd~~~~l~Ngd~~tV~~i~~~~i~l~~ 748 (1747)
T PRK13709 718 RVLGKIPGLRLKGGDRLQVTSVSEDGLTVVV 748 (1747)
T ss_pred EEccCCcccCccCCCEEEEEEecCCeEEEEE
Confidence 997532 24678889988887766653
No 128
>PTZ00241 40S ribosomal protein S11; Provisional
Probab=35.82 E-value=55 Score=35.51 Aligned_cols=25 Identities=8% Similarity=-0.052 Sum_probs=20.4
Q ss_pred CCccccccCCCCeeccCCeEEEecC
Q 000637 131 DMKFTALDQSMKVISLNDTARVSEG 155 (1378)
Q Consensus 131 dRR~vAlD~nGNtIrVgDtVKVVdG 155 (1378)
.+++.|-|..-+.+++||+|+|.+=
T Consensus 104 ~kk~~aHd~~~~~~kvGD~V~I~Ec 128 (158)
T PTZ00241 104 HKNIPVHCSPCFDVKEGDIVVVGQC 128 (158)
T ss_pred eecEEEeCCccCCCCCCCEEEEEEc
Confidence 3457788877788999999999873
No 129
>PRK10220 hypothetical protein; Provisional
Probab=35.46 E-value=54 Score=33.79 Aligned_cols=21 Identities=10% Similarity=0.218 Sum_probs=18.7
Q ss_pred cccccCCCCeeccCCeEEEec
Q 000637 134 FTALDQSMKVISLNDTARVSE 154 (1378)
Q Consensus 134 ~vAlD~nGNtIrVgDtVKVVd 154 (1378)
.+.+|++||++.-||.|.||.
T Consensus 42 ~~vkDsnG~~L~dGDsV~viK 62 (111)
T PRK10220 42 LIVKDANGNLLADGDSVTIVK 62 (111)
T ss_pred ceEEcCCCCCccCCCEEEEEe
Confidence 357999999999999999975
No 130
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=35.23 E-value=55 Score=28.76 Aligned_cols=51 Identities=16% Similarity=0.055 Sum_probs=38.7
Q ss_pred cccCcEEEEecCCCCC-ceeEEEeecC-CeEEEEecC--CceEEEEeCCcceecc
Q 000637 248 FAVGQTLRIRVGPLKG-YLCRVLAVRY-SDVTVKLDS--QQKILTVKGEHLAEVR 298 (1378)
Q Consensus 248 ~LIGKTVKIrkGPYKG-YlGiVKDaTg-t~ARVELHS--K~KtITVdKe~Lsvv~ 298 (1378)
..+|..|.+..=.-.. |.|+|+.+.. ..+.|.|.. .....+|+..+|..+.
T Consensus 3 ~~~G~~Ve~~~~~~~~W~~a~V~~~~~~~~~~V~~~~~~~~~~e~v~~~~LRp~~ 57 (61)
T smart00743 3 FKKGDRVEVFSKEEDSWWEAVVTKVLGDGKYLVRYLTESEPLKETVDWSDLRPHP 57 (61)
T ss_pred cCCCCEEEEEECCCCEEEEEEEEEECCCCEEEEEECCCCcccEEEEeHHHcccCC
Confidence 4577788887421222 6699999988 789999999 8889999999887643
No 131
>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI. This protein is a component of the relaxosome complex. In the process of conjugative plasmid transfer the realaxosome binds to the plasmid at the oriT (origin of transfer) site. The relaxase protein TraI mediates the single-strand nicking and ATP-dependent unwinding (relaxation, helicase activity) of the plasmid molecule. These two activities reside in separate domains of the protein.
Probab=35.10 E-value=1.4e+02 Score=42.93 Aligned_cols=91 Identities=11% Similarity=0.113 Sum_probs=60.8
Q ss_pred CCccEeceeEeecCC-----ceEEEEEeccC-CceEEccCCCCCCcEEEEeccccccCCCCCccccccCCCCeeccCCeE
Q 000637 77 ENSFELYELVCFGRK-----DFGLIVGMEKD-DHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTA 150 (1378)
Q Consensus 77 lG~YELHDLVQLD~q-----TVGVIVrVEKD-DsFKVLdqngDrGkVvtVKpseIk~Kr~dRR~vAlD~nGNtIrVgDtV 150 (1378)
...|...|.|++-.. ...+|+.|+++ ..+.|.+.. |+.++++|.++..+. ..+.+--...-+|.++|.|
T Consensus 679 ~~~Yr~Gdvv~~y~~~~~~~~~y~V~~V~~~~n~L~l~~~d---G~~~~~~p~~l~~~~--~~~svy~~~~l~ia~Gdrl 753 (1960)
T TIGR02760 679 AAHYKQGMVIRFWQKGKIPHDDYVVTNVNKHNNTLTLKDAQ---GKTQKFKPSSLKDLE--RPFSVYRPEQLEVAAGERL 753 (1960)
T ss_pred HhhcCCCCEEEeecccCccCCcEEEEEEeCCCCEEEEEcCC---CCEEEECHHHhcccc--cceeeeccccccccCCCEE
Confidence 467999999998422 34799999984 356655543 588999999885321 2344555666788889998
Q ss_pred EEecCC-----CCCceeEEEEEEcceE
Q 000637 151 RVSEGP-----SKDRQGIVKKIYRGIL 172 (1378)
Q Consensus 151 KVVdGP-----~KGRQG~VlHIyRg~L 172 (1378)
++..-- ..|...+|..|-...|
T Consensus 754 ~~trn~~~~gl~ng~~~tV~~i~~~~i 780 (1960)
T TIGR02760 754 QVTGNHFHSRVRNGELLTVSSINNEGI 780 (1960)
T ss_pred EEccCCcccCccCCCEEEEEEEcCCeE
Confidence 886422 2456666766655433
No 132
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=32.73 E-value=79 Score=32.60 Aligned_cols=36 Identities=17% Similarity=0.170 Sum_probs=25.0
Q ss_pred cccccCCCCeeccCCeEEEec-----CC-CCCceeEEEEEEc
Q 000637 134 FTALDQSMKVISLNDTARVSE-----GP-SKDRQGIVKKIYR 169 (1378)
Q Consensus 134 ~vAlD~nGNtIrVgDtVKVVd-----GP-~KGRQG~VlHIyR 169 (1378)
.+.+|+|||++.-||+|.||. |. .-=|+|++....|
T Consensus 41 ~~~kDsnG~~L~dGDsV~liKDLkVKGss~~~K~GTkVknIr 82 (109)
T TIGR00686 41 LIVKDCNGNLLANGDSVILIKDLKVKGSSLVLKKGTKIKNIR 82 (109)
T ss_pred ceEEcCCCCCccCCCEEEEEeeccccCcccceeCccEEEEEE
Confidence 357999999999999999975 21 1234555554444
No 133
>COG4371 Predicted membrane protein [Function unknown]
Probab=32.70 E-value=67 Score=37.27 Aligned_cols=7 Identities=57% Similarity=1.270 Sum_probs=3.0
Q ss_pred CCCCcCC
Q 000637 1039 GSGNFRG 1045 (1378)
Q Consensus 1039 ~~g~~~g 1045 (1378)
++++||.
T Consensus 54 GGgSfra 60 (334)
T COG4371 54 GGGSFRA 60 (334)
T ss_pred cCCCCCC
Confidence 4444443
No 134
>KOG3416 consensus Predicted nucleic acid binding protein [General function prediction only]
Probab=31.95 E-value=99 Score=32.80 Aligned_cols=47 Identities=28% Similarity=0.521 Sum_probs=31.7
Q ss_pred ccccccCCCCeeccCCeEEEecCCCCCceeEEEEEEcceEEEE--eccccccccEEE
Q 000637 133 KFTALDQSMKVISLNDTARVSEGPSKDRQGIVKKIYRGILFIY--DENETENGGYFC 187 (1378)
Q Consensus 133 R~vAlD~nGNtIrVgDtVKVVdGP~KGRQG~VlHIyRg~LFL~--sR~i~ENGGIFV 187 (1378)
.+..-|..+..|++||+||...|= --|||+-|-|| -+-.++.-|=||
T Consensus 51 ~isvW~e~~~~~~PGDIirLt~Gy--------~Si~qg~LtL~~GK~Ge~~KiGef~ 99 (134)
T KOG3416|consen 51 NISVWDEEGCLIQPGDIIRLTGGY--------ASIFQGCLTLYVGKGGEVQKIGEFC 99 (134)
T ss_pred EEEEecCcCcccCCccEEEecccc--------hhhhcCceEEEecCCceEeEeeeeE
Confidence 456889999999999999988773 35777754444 333444444443
No 135
>PRK12289 GTPase RsgA; Reviewed
Probab=30.88 E-value=2.4e+02 Score=33.71 Aligned_cols=76 Identities=14% Similarity=0.296 Sum_probs=44.0
Q ss_pred CceEEEEEeccCCceEEccCCCC---CCcEEEEeccccccCCCCCccccccCCCCeeccCCeEEEecCCCCCceeEEEEE
Q 000637 91 KDFGLIVGMEKDDHYKILKEGSE---GPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVSEGPSKDRQGIVKKI 167 (1378)
Q Consensus 91 qTVGVIVrVEKDDsFKVLdqngD---rGkVvtVKpseIk~Kr~dRR~vAlD~nGNtIrVgDtVKVVdGP~KGRQG~VlHI 167 (1378)
+..|.||++.+ ..|.|+...++ .++++.++... ++. ..+..+-|||.|.+-.-+.....+.|.+|
T Consensus 8 ~~~g~V~~~~~-~~y~V~~~~~~~~~~~~~~~~~~r~--------~lk---~~~~~~~vGD~V~~~~~~~~~~~~~I~~v 75 (352)
T PRK12289 8 QLLGTVVAVQA-NFYRVQLDEPQNLNPPSLLLCTRRT--------RLK---KIGQQVMVGDRVIVEEPDWQGQRGAIAEV 75 (352)
T ss_pred cccEEEEEEEC-CEEEEEECCCcccCcceEEEEEccc--------ccc---cCCCCcccCCEEEEeecCCCCCceEEEEE
Confidence 45799999999 48888753211 12333333211 111 13445899999988532223457899999
Q ss_pred EcceEEEEecc
Q 000637 168 YRGILFIYDEN 178 (1378)
Q Consensus 168 yRg~LFL~sR~ 178 (1378)
+--.=+|..+.
T Consensus 76 lpR~~~L~R~~ 86 (352)
T PRK12289 76 LPRKTELDRPP 86 (352)
T ss_pred eccccceechh
Confidence 87644444333
No 136
>smart00333 TUDOR Tudor domain. Domain of unknown function present in several RNA-binding proteins. 10 copies in the Drosophila Tudor protein. Initial proposal that the survival motor neuron gene product contain a Tudor domain are corroborated by more recent database search techniques such as PSI-BLAST (unpublished).
Probab=29.71 E-value=72 Score=27.31 Aligned_cols=50 Identities=18% Similarity=0.081 Sum_probs=35.8
Q ss_pred ccCcEEEEecCCCCCceeEEEeecC-CeEEEEecCCceEEEEeCCcceecc
Q 000637 249 AVGQTLRIRVGPLKGYLCRVLAVRY-SDVTVKLDSQQKILTVKGEHLAEVR 298 (1378)
Q Consensus 249 LIGKTVKIrkGPYKGYlGiVKDaTg-t~ARVELHSK~KtITVdKe~Lsvv~ 298 (1378)
-+|+.|.++---=.=|+++|++++. ..+.|.+.--..+..|++++|..+.
T Consensus 4 ~~G~~~~a~~~d~~wyra~I~~~~~~~~~~V~f~D~G~~~~v~~~~l~~l~ 54 (57)
T smart00333 4 KVGDKVAARWEDGEWYRARIIKVDGEQLYEVFFIDYGNEEVVPPSDLRPLP 54 (57)
T ss_pred CCCCEEEEEeCCCCEEEEEEEEECCCCEEEEEEECCCccEEEeHHHeecCC
Confidence 4666666664111238999999998 8899987776666788888887643
No 137
>PF02691 VacA: Vacuolating cyotoxin; InterPro: IPR003842 Helicobacter pylori is a micro-aerophilic bacterium with the extraordinary ability to establish infections in human stomachs that can last for years or decades, despite immune and inflammatory responses and normal turnover of the gastric epithelium and overlying mucin layer in which it resides. Most H. pylori strains secrete a toxin (VacA) that induces multiple structural and functional alterations in eukaryotic cells. The most prominent effect of VacA is its capacity to induce the formation of large cytoplasmic vacuoles in eukaryotic cells. In addition, VacA interferes with the process of antigen presentation, increases permeability of polarised epithelial cell monolayers, and forms anion-selective membrane channels. Formation of channels in endosomal membranes of cells may be an important feature of the mechanism by which VacA induces cell vacuolation. H. pylori vacA encodes a ~139kDa protoxin, which undergoes cleavage of a 33-residue N-terminal signal sequence and C-terminal proteolytic processing to yield a mature secreted toxin. Purified VacA degrades during prolonged storage into two fragments (of ~34 and 58kDa), which are derived from the N- and the C terminus of the toxin respectively. The mass of the experimentally intact toxin (~88.2kDa) corresponds closely to the sum of the masses of the two proteolytic fragments []. Secondary structure predictions suggest that a 35kDa portion of the VacA C-terminal domain is rich in amphipathic beta-sheets, and this region exhibits low-level similarity to members of the family of autotransporter proteins. In addition, at the C terminus of VacA, there is a phenylalanine- containing motif that is commonly found in autotransporter proteins, as well as in numerous Gram-negative bacterial outer membrane proteins. An intact N-terminal portion of VacA is not required for proteolytic processing of the protoxin. However, the N-terminal 32 amino acids of the mature VacA are predicted to form the only contiguous hydrophobic region in the protein that is long enough to span the membrane. What is more, isogenic H. pylori mutant strains in which the C-terminal VacA domain is disrupted, fail to express or secrete any detectable VacA, which is probably attributable to the degradation of export-incompetent toxin precursors within the periplasm. It is speculated that the VacA protoxin may undergo proteolytic cleavage at multiple sites downstream from amino acid 854 of the protoxin, which would yield a 33kDa cell-associated domain, as well as a fragment of ~15kDa []. ; GO: 0009405 pathogenesis, 0005576 extracellular region; PDB: 2QV3_A.
Probab=28.80 E-value=43 Score=43.20 Aligned_cols=55 Identities=16% Similarity=0.265 Sum_probs=10.3
Q ss_pred cccCCCCeeccCCeEEEecCCCCCceeEEEEEEcceEEEEeccccccccE---EEEeCCceee
Q 000637 136 ALDQSMKVISLNDTARVSEGPSKDRQGIVKKIYRGILFIYDENETENGGY---FCSKSQHCEK 195 (1378)
Q Consensus 136 AlD~nGNtIrVgDtVKVVdGP~KGRQG~VlHIyRg~LFL~sR~i~ENGGI---FVvrArnVvl 195 (1378)
.-+.+..+|++ |.||+||+.|-.++|+||.| |=....-.+..+|| ++++|.++.+
T Consensus 314 ~NssQK~EvQp---tqVInGpfag~K~tVv~I~~--~Nt~~dgti~~gg~~a~l~tna~~l~i 371 (981)
T PF02691_consen 314 PNSSQKTEVQP---TQVINGPFAGAKDTVVNINR--LNTNSDGTIRVGGFKASLTTNAANLNI 371 (981)
T ss_dssp -----------------------------EEEEE--EE--------------EEEE-SSEEEE
T ss_pred CccccccccCC---ceeecCCCCCCcceEEEeee--ecccccceeeecceeeeeeccccceee
Confidence 34566677777 99999999999999999998 33344444555555 4555665554
No 138
>PF05934 MCLC: Mid-1-related chloride channel (MCLC); InterPro: IPR009231 This entry consists of several Chloride channel CLIC-like proteins, which function as a chloride channel when incorporated in the planar lipid bilayer [].
Probab=28.69 E-value=59 Score=40.59 Aligned_cols=48 Identities=25% Similarity=0.323 Sum_probs=41.9
Q ss_pred CccccCcEEEEecCCC-CCceeEEEeecCCeEEEEecCCceEEEEeCCc
Q 000637 246 GMFAVGQTLRIRVGPL-KGYLCRVLAVRYSDVTVKLDSQQKILTVKGEH 293 (1378)
Q Consensus 246 ~D~LIGKTVKIrkGPY-KGYlGiVKDaTgt~ARVELHSK~KtITVdKe~ 293 (1378)
+..+-++.-.|-+||| |.|.|+---.++.+|++++++.+|-+-|-|..
T Consensus 395 d~~~~~~~~~~~~g~~~~~~~~~~~~~r~~d~~~~~~t~~~~~e~l~a~ 443 (549)
T PF05934_consen 395 DFYYRGHVGSIEQGPYDKTYEGRRDVLRERDVDLRFQTGNKSPEVLRAF 443 (549)
T ss_pred CCcccCCCCccccCccccccccccccchhhhhhhhcccCCCCcccccCC
Confidence 4667788888999999 99999977778999999999999999988765
No 139
>PRK04333 50S ribosomal protein L14e; Validated
Probab=27.88 E-value=81 Score=30.88 Aligned_cols=34 Identities=12% Similarity=0.306 Sum_probs=27.4
Q ss_pred CeeccCCeEEEecCCCCCceeEEEEEE-cceEEEE
Q 000637 142 KVISLNDTARVSEGPSKDRQGIVKKIY-RGILFIY 175 (1378)
Q Consensus 142 NtIrVgDtVKVVdGP~KGRQG~VlHIy-Rg~LFL~ 175 (1378)
-.|++|-+|++..|+++|+..+|+-|. .++|.|-
T Consensus 2 ~~v~~GrvV~~~~Grd~gk~~vIv~i~d~~~vlVd 36 (84)
T PRK04333 2 PAIEVGRVCVKTAGREAGRKCVIVDIIDKNFVLVT 36 (84)
T ss_pred CcccccEEEEEeccCCCCCEEEEEEEecCCEEEEE
Confidence 368899999999999999999998764 4466553
No 140
>PRK08582 hypothetical protein; Provisional
Probab=27.83 E-value=2.8e+02 Score=29.08 Aligned_cols=56 Identities=18% Similarity=0.205 Sum_probs=32.9
Q ss_pred cEeceeEeecCCceEEEEEeccCCceEEccCCCCCCcEEEEeccccccCCCCCccccccCCCCeeccCCeEEE
Q 000637 80 FELYELVCFGRKDFGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARV 152 (1378)
Q Consensus 80 YELHDLVQLD~qTVGVIVrVEKDDsFKVLdqngDrGkVvtVKpseIk~Kr~dRR~vAlD~nGNtIrVgDtVKV 152 (1378)
|++.+.|. |+|+.|..--+|.-|... ..-.|..++|.... + .| ....|+++|.|+|
T Consensus 3 ~kvG~iv~------G~V~~I~~fG~fV~L~~~----~~GlVhiSels~~~-----v-~~-~~~~l~vGD~Vkv 58 (139)
T PRK08582 3 IEVGSKLQ------GKVTGITNFGAFVELPEG----KTGLVHISEVADNY-----V-KD-INDHLKVGDEVEV 58 (139)
T ss_pred CcCCCEEE------EEEEEEECCeEEEEECCC----CEEEEEeeccCccc-----c-cc-cccccCCCCEEEE
Confidence 45555554 788888775455555532 23455556664321 1 12 1367999999987
No 141
>PF03831 PhnA: PhnA protein; InterPro: IPR013988 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the C-terminal domain of PhnA.; PDB: 2AKK_A 2AKL_A.
Probab=27.18 E-value=34 Score=31.60 Aligned_cols=20 Identities=10% Similarity=0.101 Sum_probs=13.5
Q ss_pred ccccCCCCeeccCCeEEEec
Q 000637 135 TALDQSMKVISLNDTARVSE 154 (1378)
Q Consensus 135 vAlD~nGNtIrVgDtVKVVd 154 (1378)
+..|++||++.-+|.|.+|.
T Consensus 1 vv~DsnGn~L~dGDsV~~iK 20 (56)
T PF03831_consen 1 VVKDSNGNELQDGDSVTLIK 20 (56)
T ss_dssp S-B-TTS-B--TTEEEEESS
T ss_pred CeEcCCCCCccCCCEEEEEe
Confidence 46899999999999999975
No 142
>KOG1740 consensus Predicted mitochondrial/chloroplast ribosomal protein S17 [Translation, ribosomal structure and biogenesis]
Probab=26.52 E-value=52 Score=33.56 Aligned_cols=21 Identities=24% Similarity=0.376 Sum_probs=17.1
Q ss_pred CccccccCCCCeeccCCeEEEe
Q 000637 132 MKFTALDQSMKVISLNDTARVS 153 (1378)
Q Consensus 132 RR~vAlD~nGNtIrVgDtVKVV 153 (1378)
+++.|.|. .|...+||.|++-
T Consensus 39 ~kymahD~-~n~cnvGD~Vrle 59 (107)
T KOG1740|consen 39 SKYMAHDD-KNQCNVGDRVRLE 59 (107)
T ss_pred hheeecCc-cccccccceEEec
Confidence 34678886 8899999999984
No 143
>COG2163 RPL14A Ribosomal protein L14E/L6E/L27E [Translation, ribosomal structure and biogenesis]
Probab=26.26 E-value=86 Score=32.89 Aligned_cols=47 Identities=15% Similarity=0.293 Sum_probs=33.2
Q ss_pred cccCcEEEEecCCCCCceeEEEeecCCeEEEEecCCceEEEEeCCcce
Q 000637 248 FAVGQTLRIRVGPLKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLA 295 (1378)
Q Consensus 248 ~LIGKTVKIrkGPYKGYlGiVKDaTgt~ARVELHSK~KtITVdKe~Ls 295 (1378)
.-+|+-|.|+.|.|.|-++.|+++-|.. .|...-..++--|++..+.
T Consensus 5 l~~GrVvvv~~GR~aGkk~VIv~~iDd~-~v~i~gp~~v~gv~r~r~n 51 (125)
T COG2163 5 LEVGRVVVVTAGRFAGKKVVIVKIIDDN-FVLITGPKKVKGVPRRRIN 51 (125)
T ss_pred ccCCeEEEEecceeCCceEEEEEEccCC-EEEEeCCccccCCcccccc
Confidence 4689999999999999999999998876 4444433333334444443
No 144
>PF08605 Rad9_Rad53_bind: Fungal Rad9-like Rad53-binding; InterPro: IPR013914 In Saccharomyces cerevisiae (Baker s yeast), the Rad9 is a key adaptor protein in DNA damage checkpoint pathways. DNA damage induces Rad9 phosphorylation, and Rad53 specifically associates with this region of Rad9, when phosphorylated, via the Rad53 IPR000253 from INTERPRO domain []. There is no clear higher eukaryotic ortholog to Rad9.
Probab=26.10 E-value=83 Score=33.02 Aligned_cols=46 Identities=22% Similarity=0.257 Sum_probs=32.2
Q ss_pred CeeccCCeEEEecCCCCCceeEEEEEEcceEEEEeccccccccEEEEeCCceeecc
Q 000637 142 KVISLNDTARVSEGPSKDRQGIVKKIYRGILFIYDENETENGGYFCSKSQHCEKTK 197 (1378)
Q Consensus 142 NtIrVgDtVKVVdGP~KGRQG~VlHIyRg~LFL~sR~i~ENGGIFVvrArnVvlVg 197 (1378)
-.|+|||+|||-. | .++||-.++-.... .+...|-|+|-.+.+.+.
T Consensus 58 LDlRIGD~Vkv~~-~------k~~yiV~Gl~~~~~---~~~~~i~cirGy~tV~Lk 103 (131)
T PF08605_consen 58 LDLRIGDTVKVDG-P------KVTYIVVGLECKIS---SEDNIITCIRGYNTVYLK 103 (131)
T ss_pred eeeecCCEEEECC-C------CccEEEEEeeecCC---CCCCceEEcCCCcEEEEE
Confidence 4699999999865 3 35677776553322 223339999999999885
No 145
>PF14153 Spore_coat_CotO: Spore coat protein CotO
Probab=25.67 E-value=72 Score=35.19 Aligned_cols=37 Identities=14% Similarity=0.177 Sum_probs=33.7
Q ss_pred CCCceeEEEeecCCeEEEEecCCceEEEEeCCcceec
Q 000637 261 LKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLAEV 297 (1378)
Q Consensus 261 YKGYlGiVKDaTgt~ARVELHSK~KtITVdKe~Lsvv 297 (1378)
-+=|+|+|++.++..|.|.......++.|.+++|.-|
T Consensus 144 ~~~Y~G~I~~~~~~~v~i~~~~~~~~~~i~~~~I~sI 180 (185)
T PF14153_consen 144 DKSYRGIILSYDEGEVSIMPFNQGEEIEIPIDDITSI 180 (185)
T ss_pred CceEEEEEEeccCCEEEEeccCCCcceEeehhheeee
Confidence 4689999999999999999999999999999999754
No 146
>PRK06461 single-stranded DNA-binding protein; Reviewed
Probab=25.47 E-value=2.1e+02 Score=29.35 Aligned_cols=50 Identities=10% Similarity=0.184 Sum_probs=31.2
Q ss_pred CcEEEEeccccccCCCCCccccccCCCCeeccCCeEEEecCCCCCceeEEEEEEcceEEEE
Q 000637 115 PAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVSEGPSKDRQGIVKKIYRGILFIY 175 (1378)
Q Consensus 115 GkVvtVKpseIk~Kr~dRR~vAlD~nGNtIrVgDtVKVVdGP~KGRQG~VlHIyRg~LFL~ 175 (1378)
+.++.+.+.+-.-. -++++=|.+-..|+++|+|+|..+ .| ..|++.|=|+
T Consensus 39 ~~v~~~~l~D~TG~---I~~tlW~~~a~~l~~GdvV~I~na-------~v-~~f~G~lqL~ 88 (129)
T PRK06461 39 RTISEAVVGDETGR---VKLTLWGEQAGSLKEGEVVEIENA-------WT-TLYRGKVQLN 88 (129)
T ss_pred eEEEEEEEECCCCE---EEEEEeCCccccCCCCCEEEEECc-------EE-eeeCCEEEEE
Confidence 35666665555432 245556666667999999999755 22 3577765555
No 147
>PF12701 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC8_A 2VXF_A 2VXE_A.
Probab=25.20 E-value=74 Score=31.81 Aligned_cols=35 Identities=14% Similarity=0.133 Sum_probs=30.8
Q ss_pred ccccCcEEEEecCCCCCceeEEEeecCCeEEEEec
Q 000637 247 MFAVGQTLRIRVGPLKGYLCRVLAVRYSDVTVKLD 281 (1378)
Q Consensus 247 D~LIGKTVKIrkGPYKGYlGiVKDaTgt~ARVELH 281 (1378)
+++||++|.|+.-.---|.|++..++....+|-|.
T Consensus 4 ~~~IGs~ISlisk~~iRYeG~L~~Id~~~sTItL~ 38 (96)
T PF12701_consen 4 DPYIGSKISLISKSDIRYEGILYSIDTEDSTITLK 38 (96)
T ss_dssp CCCTTCEEEEEETTTEEEEEEEEEEETTTTEEEEE
T ss_pred ccccCCEEEEEECCCcEEEEEEEEEcCCCCEEEee
Confidence 57999999999999999999999999876666665
No 148
>PF14157 YmzC: YmzC-like protein; PDB: 3KVP_E.
Probab=25.07 E-value=90 Score=29.57 Aligned_cols=44 Identities=11% Similarity=0.245 Sum_probs=28.8
Q ss_pred CCCccEeceeEeecCCceEEEEEeccCCceEEccCCCCCCcEEEEec
Q 000637 76 LENSFELYELVCFGRKDFGLIVGMEKDDHYKILKEGSEGPAVVTVER 122 (1378)
Q Consensus 76 slG~YELHDLVQLD~qTVGVIVrVEKDDsFKVLdqngDrGkVvtVKp 122 (1378)
+.-...+--+|||...+|||+ ..+..+||..=++++.+|..||-
T Consensus 15 s~~~~~ts~m~ql~~N~Fav~---~e~~~iKIfkyd~~tNei~L~KE 58 (63)
T PF14157_consen 15 SDPEPNTSNMTQLEHNHFAVV---DEDGQIKIFKYDEDTNEITLKKE 58 (63)
T ss_dssp -------EEEEE-STTEEEEE----ETTEEEEEEEETTTTEEEEEEE
T ss_pred cccccCcCceEEecCCEEEEE---ecCCeEEEEEeCCCCCeEEEEEe
Confidence 344566778999999999998 33368999987777788887763
No 149
>PRK14641 hypothetical protein; Provisional
Probab=24.76 E-value=1.2e+02 Score=33.04 Aligned_cols=36 Identities=17% Similarity=0.181 Sum_probs=27.7
Q ss_pred cccCcEEEEe-cCCCCC---ceeEEEeec-----CCeEEEEecCC
Q 000637 248 FAVGQTLRIR-VGPLKG---YLCRVLAVR-----YSDVTVKLDSQ 283 (1378)
Q Consensus 248 ~LIGKTVKIr-kGPYKG---YlGiVKDaT-----gt~ARVELHSK 283 (1378)
.+||+.|+|+ .-|+.+ +.|++++++ +..++|++...
T Consensus 101 r~~G~~V~V~l~~~~~~~~~~~G~L~~~~~~~~~~~~v~~~~~~~ 145 (173)
T PRK14641 101 RHVGRLLRVTYRDEEGSEHEVTGHLQEVSLTEGEGASIVLKPEQK 145 (173)
T ss_pred HhCCCEEEEEEecccCCeEEEEEEEEeeecccCCCCcEEEEeccc
Confidence 5899999996 455554 889999885 77888877764
No 150
>PRK08059 general stress protein 13; Validated
Probab=24.76 E-value=3.4e+02 Score=27.53 Aligned_cols=58 Identities=19% Similarity=0.323 Sum_probs=33.7
Q ss_pred ccEeceeEeecCCceEEEEEeccCCceEEccCCCCCCcEEEEeccccccCCCCCccccccCCCCeeccCCeEEEe
Q 000637 79 SFELYELVCFGRKDFGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVS 153 (1378)
Q Consensus 79 ~YELHDLVQLD~qTVGVIVrVEKDDsFKVLdqngDrGkVvtVKpseIk~Kr~dRR~vAlD~nGNtIrVgDtVKVV 153 (1378)
.|+..++|. |+|++|.+.-.|..|... ..-.|..++|... +. ..-...|++||+|+|.
T Consensus 4 ~~k~G~iv~------G~V~~i~~~G~fV~i~~~----~~Gli~~sel~~~----~~---~~~~~~~~vGD~I~vk 61 (123)
T PRK08059 4 QYEVGSVVT------GKVTGIQPYGAFVALDEE----TQGLVHISEITHG----FV---KDIHDFLSVGDEVKVK 61 (123)
T ss_pred cCCCCCEEE------EEEEEEecceEEEEECCC----CEEEEEHHHCCcc----cc---cCHHHcCCCCCEEEEE
Confidence 466667664 888888885445545432 2234444555332 11 1124578999999973
No 151
>KOG3591 consensus Alpha crystallins [Posttranslational modification, protein turnover, chaperones]
Probab=24.44 E-value=93 Score=33.84 Aligned_cols=53 Identities=17% Similarity=0.251 Sum_probs=36.4
Q ss_pred EEEeccCCceEEccCCCCCCcEEEEeccccccCCCCCccccccCCCCeeccCCeEEEecCCCCCceeEEEEEEcceE
Q 000637 96 IVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVSEGPSKDRQGIVKKIYRGIL 172 (1378)
Q Consensus 96 IVrVEKDDsFKVLdqngDrGkVvtVKpseIk~Kr~dRR~vAlD~nGNtIrVgDtVKVVdGP~KGRQG~VlHIyRg~L 172 (1378)
-|.+.+ +.|+|.-. |...+|.+|+-| +.|.+.||+|.|.-|+-..-+|.|.|+
T Consensus 66 ~~~~~~-~~F~V~lD------V~~F~PeEl~Vk-----------------~~~~~l~V~gkHeer~d~~G~v~R~F~ 118 (173)
T KOG3591|consen 66 EIVNDK-DKFEVNLD------VHQFKPEELKVK-----------------TDDNTLEVEGKHEEKEDEHGYVSRSFV 118 (173)
T ss_pred ccccCC-CcEEEEEE------cccCcccceEEE-----------------eCCCEEEEEeeeccccCCCCeEEEEEE
Confidence 344555 47877544 566778887544 445578899998888877777778664
No 152
>cd04370 BAH BAH, or Bromo Adjacent Homology domain (also called ELM1 and BAM for Bromo Adjacent Motif). BAH domains have first been described as domains found in the polybromo protein and Yeast Rsc1/Rsc2 (Remodeling of the Structure of Chromatin). They also occur in mammalian DNA methyltransferases and the MTA1 subunits of histone deacetylase complexes. A BAH domain is also found in Yeast Sir3p and in the origin receptor complex protein 1 (Orc1p), where it was found to interact with the N-terminal lobe of the silence information regulator 1 protein (Sir1p), confirming the initial hypothesis that BAH plays a role in protein-protein interactions.
Probab=24.13 E-value=1.1e+02 Score=29.02 Aligned_cols=97 Identities=13% Similarity=-0.032 Sum_probs=0.0
Q ss_pred cEeceeEeecCCc--------eEEEEEeccC-CceEEccCCCCCCcEEEEeccccccCCCCCccccccCCCCeeccCCeE
Q 000637 80 FELYELVCFGRKD--------FGLIVGMEKD-DHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTA 150 (1378)
Q Consensus 80 YELHDLVQLD~qT--------VGVIVrVEKD-DsFKVLdqngDrGkVvtVKpseIk~Kr~dRR~vAlD~nGNtIrVgDtV 150 (1378)
|.++|-|.|.+.. ||.|.+|-.+ +..+.|.-. .-.+|++|...... ...-|+|-.-+..
T Consensus 4 y~vgd~V~v~~~~~~~~~~~~i~~I~~i~~~~~~~~~~~v~------wf~rp~e~~~~~~~------~~~~~Elf~s~~~ 71 (123)
T cd04370 4 YEVGDSVYVEPDDSIKSDPPYIARIEELWEDTNGSKQVKVR------WFYRPEETPKGLSP------FALRRELFLSDHL 71 (123)
T ss_pred EecCCEEEEecCCcCCCCCCEEEEEeeeeECCCCCEEEEEE------EEEchhHhcccccc------ccccceeEEecCc
Q ss_pred EEecCCCCCceeEEEEEEcceEEEEeccccccccEEEEe
Q 000637 151 RVSEGPSKDRQGIVKKIYRGILFIYDENETENGGYFCSK 189 (1378)
Q Consensus 151 KVVdGP~KGRQG~VlHIyRg~LFL~sR~i~ENGGIFVvr 189 (1378)
.++.=..--....|+|+-.-.-... +...+...+|+|+
T Consensus 72 ~~i~v~~I~gkc~V~~~~~~~~~~~-~~~~~~~~~f~~r 109 (123)
T cd04370 72 DEIPVESIIGKCKVLFVSEFEGLKQ-RPNKIDTDDFFCR 109 (123)
T ss_pred cccCHHHhccccEEEechHhhcccc-ccccCCCCeEEEE
No 153
>cd05684 S1_DHX8_helicase S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH (Asp-Glu-Ala-His) box polypeptide. The DEAH-box RNA helicases are thought to play key roles in pre-mRNA splicing and DHX8 facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. DHX8 is also known as HRH1 (human RNA helicase 1) in Homo sapiens and PRP22 in Saccharomyces cerevisiae.
Probab=23.76 E-value=4.5e+02 Score=24.03 Aligned_cols=35 Identities=14% Similarity=0.228 Sum_probs=21.8
Q ss_pred cCCCCeeccCCeEEEecCCCCCceeEEEEEEcceEEEEecccccc
Q 000637 138 DQSMKVISLNDTARVSEGPSKDRQGIVKKIYRGILFIYDENETEN 182 (1378)
Q Consensus 138 D~nGNtIrVgDtVKVVdGP~KGRQG~VlHIyRg~LFL~sR~i~EN 182 (1378)
+...+.++++|.|+|. |+.|-+..+-|..+.+.++
T Consensus 43 ~~~~~~~~~Gd~v~v~----------v~~vd~~~i~~s~k~~~~~ 77 (79)
T cd05684 43 ANPSDVVKRGQKVKVK----------VISIQNGKISLSMKDVDQD 77 (79)
T ss_pred CChhheeCCCCEEEEE----------EEEEeCCEEEEEEEecccC
Confidence 3446789999999984 3333345555555555444
No 154
>cd05752 Ig1_FcgammaR_like Frst immunoglobulin (Ig)-like domain of Fcgamma-receptors (FcgammaRs) and similar proteins. Ig1_FcgammaR_like: domain similar to the first immunoglobulin (Ig)-like domain of Fcgamma-receptors (FcgammaRs). Interactions between IgG and FcgammaR are important to the initiation of cellular and humoral response. IgG binding to FcgammaR leads to a cascade of signals and ultimately to functions such as antibody-dependent-cellular-cytotoxicity (ADCC), endocytosis, phagocytosis, release of inflammatory mediators, etc. FcgammaR has two Ig-like domains. This group also contains FcepsilonRI, which binds IgE with high affinity.
Probab=23.21 E-value=1.9e+02 Score=26.86 Aligned_cols=24 Identities=13% Similarity=0.148 Sum_probs=17.1
Q ss_pred EcceEEEEeccccccccEEEEeCCce
Q 000637 168 YRGILFIYDENETENGGYFCSKSQHC 193 (1378)
Q Consensus 168 yRg~LFL~sR~i~ENGGIFVvrArnV 193 (1378)
..+.|.|.+- .++.|.+.|+|.+-
T Consensus 45 ~~~~l~i~~~--~~dsG~Y~C~a~~~ 68 (78)
T cd05752 45 TTNSYRIRAA--NNDSGEYRCQTQGS 68 (78)
T ss_pred cCCeEEEeec--ccCCEEeEEECCCC
Confidence 3445566655 88889999988764
No 155
>PF04351 PilP: Pilus assembly protein, PilP; InterPro: IPR007446 The PilP family are periplasmic proteins involved in the biogenesis of type IV pili [].; PDB: 2Y4Y_B 2Y4X_A 2IVW_A 2LC4_A.
Probab=22.72 E-value=74 Score=33.34 Aligned_cols=30 Identities=20% Similarity=0.420 Sum_probs=26.8
Q ss_pred cCcEEEEecCCCCCc-eeEEEeecCCeEEEE
Q 000637 250 VGQTLRIRVGPLKGY-LCRVLAVRYSDVTVK 279 (1378)
Q Consensus 250 IGKTVKIrkGPYKGY-lGiVKDaTgt~ARVE 279 (1378)
-|+..+|+.|-|=|. .|+|+.|+++.|.|+
T Consensus 99 dg~v~~V~~G~yiG~n~G~I~~Is~~~I~l~ 129 (149)
T PF04351_consen 99 DGKVYRVKVGDYIGQNYGRITSISEDSIELV 129 (149)
T ss_dssp TTEEEEEETTEEETTTTEEEEEEETTEEEEE
T ss_pred CCCEEEecCCCEeccCCCEEEEEeCCeEEEE
Confidence 388999999999998 999999999988775
No 156
>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=22.54 E-value=1.6e+02 Score=26.20 Aligned_cols=58 Identities=19% Similarity=0.252 Sum_probs=0.0
Q ss_pred ccEeceeEeecCCceEEEEEeccCCceEEccCCCCCCcEEEEeccccccCCCCCccccccCCCCeeccCCeEEEe
Q 000637 79 SFELYELVCFGRKDFGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVS 153 (1378)
Q Consensus 79 ~YELHDLVQLD~qTVGVIVrVEKDDsFKVLdqngDrGkVvtVKpseIk~Kr~dRR~vAlD~nGNtIrVgDtVKVV 153 (1378)
.|+..|+|. |.|++|++...|.=|... -.-.|...+|... ..+.....++++|+|+++
T Consensus 1 k~~~G~iv~------g~V~~v~~~g~~V~l~~~----~~g~ip~~~l~~~-------~~~~~~~~~~~G~~v~v~ 58 (74)
T PF00575_consen 1 KLKEGDIVE------GKVTSVEDFGVFVDLGNG----IEGFIPISELSDD-------RIDDPSEVYKIGQTVRVK 58 (74)
T ss_dssp -SSTTSEEE------EEEEEEETTEEEEEESTS----SEEEEEGGGSSSS-------EESSSHGTCETTCEEEEE
T ss_pred CCCCCCEEE------EEEEEEECCEEEEEECCc----EEEEEEeehhcCc-------cccccccccCCCCEEEEE
No 157
>PRK05807 hypothetical protein; Provisional
Probab=22.47 E-value=1.9e+02 Score=30.08 Aligned_cols=56 Identities=13% Similarity=0.157 Sum_probs=35.5
Q ss_pred cEeceeEeecCCceEEEEEeccCCceEEccCCCCCCcEEEEeccccccCCCCCccccccCCCCeeccCCeEEEe
Q 000637 80 FELYELVCFGRKDFGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVS 153 (1378)
Q Consensus 80 YELHDLVQLD~qTVGVIVrVEKDDsFKVLdqngDrGkVvtVKpseIk~Kr~dRR~vAlD~nGNtIrVgDtVKVV 153 (1378)
|++.+.|. |+|+.|...-+|..|. + ..-.|..++|.... ..|. ...+++||+|+|+
T Consensus 3 ~~vG~vv~------G~Vt~i~~~GafV~L~-~----~~Glvhiseis~~~------v~~~-~~~~kvGd~V~Vk 58 (136)
T PRK05807 3 LKAGSILE------GTVVNITNFGAFVEVE-G----KTGLVHISEVADTY------VKDI-REHLKEQDKVKVK 58 (136)
T ss_pred ccCCCEEE------EEEEEEECCeEEEEEC-C----EEEEEEhhhccccc------ccCc-cccCCCCCEEEEE
Confidence 66677775 8888888765677673 2 34566666764321 1111 3468999999984
No 158
>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=22.36 E-value=1.1e+02 Score=30.86 Aligned_cols=60 Identities=12% Similarity=0.251 Sum_probs=30.0
Q ss_pred cccccCCCCeeccCCeEEEecCC----------CCCceeEEEEEEcce---EEEE-eccccccccEEEEeCCcee
Q 000637 134 FTALDQSMKVISLNDTARVSEGP----------SKDRQGIVKKIYRGI---LFIY-DENETENGGYFCSKSQHCE 194 (1378)
Q Consensus 134 ~vAlD~nGNtIrVgDtVKVVdGP----------~KGRQG~VlHIyRg~---LFL~-sR~i~ENGGIFVvrArnVv 194 (1378)
.+.+.....++++||.|-|+-=| |-||.|+|..|.+.. +++. .+.-... =.|+|++.||.
T Consensus 23 ~~~ls~~l~~yk~GD~V~I~id~sv~kGmPh~~yHGkTG~V~~v~~~~~G~~~~~~v~~~~~~-K~i~vr~eHlk 96 (99)
T PF01157_consen 23 MIPLSTYLQEYKVGDKVDIKIDPSVHKGMPHKRYHGKTGRVFNVTKGARGVAYNKQVKDRIKE-KRIIVRPEHLK 96 (99)
T ss_dssp S--CHHHH----TT-EEEE---TTSSSSS--GGGTTEEEEEEEE-SSCEEEEEEEECSSSCEE-EEEEEEGGGEE
T ss_pred CCcHHHHHHHccCCCEEEEEecCccccCCCcceECCCceeEEEeCCCceEEEEEEEecCCccc-EEEEECHHHcc
Confidence 45566667899999999996433 368899999988863 3222 2221111 13666777765
No 159
>PRK14712 conjugal transfer nickase/helicase TraI; Provisional
Probab=22.03 E-value=3.3e+02 Score=38.73 Aligned_cols=91 Identities=7% Similarity=0.039 Sum_probs=64.6
Q ss_pred CccEeceeEe-ecCC----ceEEEEEeccCC-ceEEccCCCCCCcEEEEeccccccCCCCCccccccCCCCeeccCCeEE
Q 000637 78 NSFELYELVC-FGRK----DFGLIVGMEKDD-HYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTAR 151 (1378)
Q Consensus 78 G~YELHDLVQ-LD~q----TVGVIVrVEKDD-sFKVLdqngDrGkVvtVKpseIk~Kr~dRR~vAlD~nGNtIrVgDtVK 151 (1378)
..|+-.++|+ ++.. .-=+|++|.++. .+.|.+.. |++++++|+.+. +++.+-....-+|.+||.|+
T Consensus 515 ~~Y~~GmVl~~~~r~~k~~~~y~V~~V~~~~n~LtL~~~d---G~~~~~~p~~~~-----~~~~vy~~e~lelA~GDrlr 586 (1623)
T PRK14712 515 DMYRPGMVMEQWNPETRSHDRYVTERVTAQSHSLTLRNAQ---GETQVVRISSLD-----SSWSLFRPEKMPVADGERLR 586 (1623)
T ss_pred hcCCCCCEEEecccCcCcCceEEEEEEcCCCceEEEEcCC---CcEEEechHHcc-----cceeeecccccccCCCCEEE
Confidence 7899999997 6642 223999999853 44444554 589999998874 24567777888999999999
Q ss_pred EecCCC-----CCceeEEEEEEcceEEEEe
Q 000637 152 VSEGPS-----KDRQGIVKKIYRGILFIYD 176 (1378)
Q Consensus 152 VVdGP~-----KGRQG~VlHIyRg~LFL~s 176 (1378)
+...-. .+-..+|.+|-...|-|..
T Consensus 587 ~t~nd~~~~L~ngd~~tV~~i~~~~itl~~ 616 (1623)
T PRK14712 587 VTGKIPGLRVSGGDRLQVASVSEDAMTVVV 616 (1623)
T ss_pred EccCCcccCccCCCEEEEEEecCCeEEEEE
Confidence 976432 3467788888876655543
No 160
>PRK11911 flgD flagellar basal body rod modification protein; Provisional
Probab=21.78 E-value=1.5e+02 Score=31.73 Aligned_cols=43 Identities=14% Similarity=0.130 Sum_probs=29.8
Q ss_pred cccCcEEEEecCCCCCceeEEEeec--CCeEEEEecCCceEEEEe
Q 000637 248 FAVGQTLRIRVGPLKGYLCRVLAVR--YSDVTVKLDSQQKILTVK 290 (1378)
Q Consensus 248 ~LIGKTVKIrkGPYKGYlGiVKDaT--gt~ARVELHSK~KtITVd 290 (1378)
.||||+|......=.-+.|+|..|+ ...++|.|+...++|.+.
T Consensus 90 ~lIGk~V~~~~~~g~~~tG~V~sV~~~~~~~~~~v~d~~~~v~l~ 134 (140)
T PRK11911 90 NFIGKDIKGVSLNGEVISGKVESVQQTTNGVMLKLKDNDSLVPMT 134 (140)
T ss_pred HhhCceeEEEecCCCEEEEEEEEEEEcCCceEEEEEcCCEEEEcc
Confidence 5999999754444345778887665 357777777777776653
No 161
>PF02237 BPL_C: Biotin protein ligase C terminal domain; InterPro: IPR003142 This C-terminal domain has an SH3-like barrel fold, the function of which is unknown. It is found associated with prokaryotic bifunctional transcriptional repressors [] and eukaryotic enzymes involved in biotin utilization [, ]. In Escherichia coli the biotin operon repressor (BirA) is a bifunctional protein. BirA acts both as the acetyl-coA carboxylase biotin holoenzyme synthetase (6.3.4.15 from EC) and as the biotin operon repressor. DNA sequence analysis of mutations indicates that the helix-turn-helix DNA binding region is located at the N terminus while mutations affecting enzyme function, although mapping over a large region, are found mainly in the central part of the protein's primary sequence [].; GO: 0006464 protein modification process; PDB: 3RUX_A 2CGH_A 3L1A_B 3L2Z_A 1HXD_A 1BIB_A 2EWN_B 1BIA_A 2EJ9_A 3FJP_A ....
Probab=21.77 E-value=2.9e+02 Score=23.92 Aligned_cols=34 Identities=12% Similarity=0.117 Sum_probs=27.2
Q ss_pred ccCcEEEEecCCCCCceeEEEeecCC-eEEEEecCC
Q 000637 249 AVGQTLRIRVGPLKGYLCRVLAVRYS-DVTVKLDSQ 283 (1378)
Q Consensus 249 LIGKTVKIrkGPYKGYlGiVKDaTgt-~ARVELHSK 283 (1378)
.|||.|+|.. +-.=+.|+++++++. ...|++...
T Consensus 1 ~lG~~V~v~~-~~~~~~G~~~gId~~G~L~v~~~~g 35 (48)
T PF02237_consen 1 TLGQEVRVET-GDGEIEGIAEGIDDDGALLVRTEDG 35 (48)
T ss_dssp STTSEEEEEE-TSCEEEEEEEEEETTSEEEEEETTE
T ss_pred CCCCEEEEEE-CCeEEEEEEEEECCCCEEEEEECCC
Confidence 4899999999 667779999999864 666666655
No 162
>PF02756 GYR: GYR motif; InterPro: IPR004011 The GYR motif is found in several Drosophila melanogaster proteins, in either single or multiple copies. Its function is unknown, however the presence of completely conserved tyrosine residues may suggest it could be a substrate for tyrosine kinases.
Probab=21.05 E-value=58 Score=24.23 Aligned_cols=12 Identities=50% Similarity=0.703 Sum_probs=9.9
Q ss_pred ccceeEEEEeec
Q 000637 4 KDGYLYKKVSID 15 (1378)
Q Consensus 4 kDGFLYKdVsIq 15 (1378)
.|||-||+|+--
T Consensus 1 ddGYrYkTvrrl 12 (18)
T PF02756_consen 1 DDGYRYKTVRRL 12 (18)
T ss_pred CCcceeeEeEEE
Confidence 489999999753
No 163
>PF14001 YdfZ: YdfZ protein
Probab=21.00 E-value=1e+02 Score=29.34 Aligned_cols=33 Identities=15% Similarity=0.260 Sum_probs=27.6
Q ss_pred cccCCCCeeccCCeEEEecCCCCCceeEEEEEEcce
Q 000637 136 ALDQSMKVISLNDTARVSEGPSKDRQGIVKKIYRGI 171 (1378)
Q Consensus 136 AlD~nGNtIrVgDtVKVVdGP~KGRQG~VlHIyRg~ 171 (1378)
+-|+|.|.|.+|..|.|-. .|..|+|+-||---
T Consensus 2 tYDRnRN~i~~G~rVMiag---tG~~gvikAih~~g 34 (64)
T PF14001_consen 2 TYDRNRNAITTGSRVMIAG---TGATGVIKAIHADG 34 (64)
T ss_pred ccccccCcCCCCCEEEEcC---CCcccEEeeeecCC
Confidence 5699999999999998864 47899999887643
No 164
>COG3109 ProQ Activator of osmoprotectant transporter ProP [Signal transduction mechanisms]
Probab=20.94 E-value=1.3e+02 Score=33.54 Aligned_cols=48 Identities=13% Similarity=0.214 Sum_probs=40.9
Q ss_pred CeeccCCeEEEecCCCCCceeEEEEEEcceEEEEeccccccccEEEEeCCcee
Q 000637 142 KVISLNDTARVSEGPSKDRQGIVKKIYRGILFIYDENETENGGYFCSKSQHCE 194 (1378)
Q Consensus 142 NtIrVgDtVKVVdGP~KGRQG~VlHIyRg~LFL~sR~i~ENGGIFVvrArnVv 194 (1378)
..+.+|+.|+|.-|.. -+..+|+.|-+--+-|. ++|+=+++|++.|+.
T Consensus 160 s~l~~g~~~kVk~G~~-a~~AtvlEv~Kd~vRVq----L~~Gl~m~V~AehL~ 207 (208)
T COG3109 160 SALTVGQALKVKAGQN-AMDATVLEITKDGVRVQ----LNSGLSMIVRAEHLV 207 (208)
T ss_pred Hhhhccceeeeccccc-cccceEEEEeccceEEe----ecCCceEEEehhhhc
Confidence 4678999999999975 48899999999877665 789989999998875
No 165
>cd04508 TUDOR Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to symmetrically dimethylated arginines of arginine-glycine (RG) rich sequences found in the C-terminal tails of Sm proteins. The SMN protein is linked to spinal muscular atrophy. Another example is the tandem tudor domains of 53BP1, which bind to histone H4 specifically dimethylated at Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA damage checkpoint signal.
Probab=20.31 E-value=1.1e+02 Score=25.41 Aligned_cols=31 Identities=16% Similarity=0.125 Sum_probs=21.5
Q ss_pred ceeEEEeec-CCeEEEEecCCceEEEEeCCcc
Q 000637 264 YLCRVLAVR-YSDVTVKLDSQQKILTVKGEHL 294 (1378)
Q Consensus 264 YlGiVKDaT-gt~ARVELHSK~KtITVdKe~L 294 (1378)
|+++|+.+. ...+.|.+---..+-.|++++|
T Consensus 15 yra~V~~~~~~~~~~V~f~DyG~~~~v~~~~l 46 (48)
T cd04508 15 YRAKITSILSDGKVEVFFVDYGNTEVVPLSDL 46 (48)
T ss_pred EEEEEEEECCCCcEEEEEEcCCCcEEEeHHHc
Confidence 899999998 7788888655444444555554
No 166
>cd05686 S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function with an N-terminal S1 RNA binding domain, a CCHC type zinc finger, and clusters of basic amino acids representing a potential nucleolar targeting signal. pNO40 was identified through a yeast two-hybrid interaction screen of a human kidney cDNA library using the pinin (pnn) protein as bait. pNO40 is thought to play a role in ribosome maturation and/or biogenesis.
Probab=20.22 E-value=2.6e+02 Score=25.46 Aligned_cols=50 Identities=10% Similarity=0.215 Sum_probs=26.3
Q ss_pred EEEEEeccCCceEEccCCCCCCcEEEEeccccccCCCCCccccccCCCCeeccCCeEEEe
Q 000637 94 GLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVS 153 (1378)
Q Consensus 94 GVIVrVEKDDsFKVLdqngDrGkVvtVKpseIk~Kr~dRR~vAlD~nGNtIrVgDtVKVV 153 (1378)
|+|++|..--.|.=|... +..-.|..++|... + .++-...+++||.|+|.
T Consensus 9 g~V~~i~~fG~fv~l~~~---~~eGlvh~sel~~~----~---~~~~~~~~~~Gd~v~vk 58 (73)
T cd05686 9 GEVASVTEYGAFVKIPGC---RKQGLVHKSHMSSC----R---VDDPSEVVDVGEKVWVK 58 (73)
T ss_pred EEEEEEEeeeEEEEECCC---CeEEEEEchhhCCC----c---ccCHhhEECCCCEEEEE
Confidence 666666653233333221 01234455566443 2 23446678999999874
No 167
>PRK04950 ProP expression regulator; Provisional
Probab=20.15 E-value=1.3e+02 Score=34.08 Aligned_cols=49 Identities=14% Similarity=0.245 Sum_probs=42.4
Q ss_pred CCeeccCCeEEEecCCCCCceeEEEEEEcceEEEEeccccccccEEEEeCCcee
Q 000637 141 MKVISLNDTARVSEGPSKDRQGIVKKIYRGILFIYDENETENGGYFCSKSQHCE 194 (1378)
Q Consensus 141 GNtIrVgDtVKVVdGP~KGRQG~VlHIyRg~LFL~sR~i~ENGGIFVvrArnVv 194 (1378)
-.+|.++..|+|.-|-. -..++|+-|-+.-|-|. ++|+-+++|++.||.
T Consensus 164 ~~~l~~gq~v~vk~g~~-~~~a~i~ei~kd~v~vq----l~~Gl~~~v~ae~l~ 212 (213)
T PRK04950 164 ISELTVGQAVKVKAGKS-AMDATVLEITKDDVRVQ----LDSGLSMIVRAEHLV 212 (213)
T ss_pred HHHhccCCEEEEeccCC-CCceEEEEEecCcEEEE----cCCCcEEEEeHhhhc
Confidence 37899999999999864 48999999999888665 789999999998875
Done!