Query 003213
Match_columns 838
No_of_seqs 309 out of 502
Neff 5.7
Searched_HMMs 46136
Date Thu Mar 28 19:12:52 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/003213.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/003213hhsearch_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 7E-189 2E-193 1618.3 64.5 809 1-838 185-1024(1024)
2 COG5164 SPT5 Transcription elo 100.0 9.1E-74 2E-78 617.8 34.6 397 130-556 4-403 (607)
3 KOG1999 RNA polymerase II tran 100.0 1E-35 2.2E-40 346.6 36.8 463 126-698 316-908 (1024)
4 COG5164 SPT5 Transcription elo 99.8 1.5E-18 3.2E-23 189.9 24.2 208 221-435 137-389 (607)
5 PRK08559 nusG transcription an 99.7 4.2E-16 9.1E-21 154.4 11.7 102 9-110 32-133 (153)
6 TIGR00405 L26e_arch ribosomal 99.6 9.6E-15 2.1E-19 143.2 10.9 102 9-110 24-125 (145)
7 PF03439 Spt5-NGN: Early trans 99.6 1.9E-15 4E-20 135.3 4.0 63 1-63 20-84 (84)
8 COG0250 NusG Transcription ant 99.1 8.6E-11 1.9E-15 119.2 6.6 96 12-107 51-159 (178)
9 PF12815 CTD: Spt5 C-terminal 99.0 7.8E-11 1.7E-15 112.5 0.0 57 562-620 2-68 (123)
10 PRK05609 nusG transcription an 98.7 8.3E-08 1.8E-12 97.3 9.3 85 22-106 64-161 (181)
11 TIGR01956 NusG_myco NusG famil 98.6 1.6E-07 3.5E-12 99.6 8.2 93 14-106 78-240 (258)
12 TIGR00922 nusG transcription t 98.4 8.9E-07 1.9E-11 89.3 9.9 90 17-106 52-154 (172)
13 KOG0260 RNA polymerase II, lar 98.2 2.1E-05 4.6E-10 95.6 16.7 18 301-318 1209-1226(1605)
14 KOG0260 RNA polymerase II, lar 98.2 2.9E-05 6.3E-10 94.5 16.7 11 541-551 1413-1423(1605)
15 PRK09014 rfaH transcriptional 98.0 6.4E-06 1.4E-10 82.4 5.0 88 17-105 46-142 (162)
16 PF12815 CTD: Spt5 C-terminal 98.0 1.4E-06 3E-11 83.6 0.0 43 563-605 14-67 (123)
17 TIGR01955 RfaH transcriptional 97.9 1.5E-05 3.3E-10 79.2 6.6 89 16-105 42-141 (159)
18 KOG2837 Protein containing a U 97.7 8E-07 1.7E-11 93.5 -6.7 55 742-804 254-309 (309)
19 PF00467 KOW: KOW motif; Inte 97.7 4.5E-05 9.7E-10 56.3 4.3 32 74-105 1-32 (32)
20 PF00467 KOW: KOW motif; Inte 96.9 0.00084 1.8E-08 49.6 3.2 31 508-538 2-32 (32)
21 smart00738 NGN In Spt5p, this 96.7 0.0011 2.3E-08 61.3 2.7 52 13-64 32-105 (106)
22 KOG4315 G-patch nucleic acid b 96.6 0.00059 1.3E-08 76.3 0.8 103 732-835 332-445 (455)
23 smart00739 KOW KOW (Kyprides, 96.2 0.0076 1.6E-07 42.4 3.9 28 223-250 1-28 (28)
24 smart00739 KOW KOW (Kyprides, 96.0 0.0095 2.1E-07 41.9 3.6 27 275-301 1-27 (28)
25 PRK01191 rpl24p 50S ribosomal 95.4 0.029 6.3E-07 53.8 5.6 39 69-107 43-81 (120)
26 CHL00141 rpl24 ribosomal prote 95.3 0.031 6.6E-07 50.4 5.2 37 69-105 6-42 (83)
27 TIGR00405 L26e_arch ribosomal 95.3 0.019 4.2E-07 56.5 4.3 58 223-280 86-145 (145)
28 PRK12281 rplX 50S ribosomal pr 94.8 0.051 1.1E-06 48.3 5.0 36 71-106 6-41 (76)
29 PRK09014 rfaH transcriptional 94.5 0.064 1.4E-06 53.7 5.6 52 223-274 109-161 (162)
30 PRK00004 rplX 50S ribosomal pr 94.4 0.064 1.4E-06 50.5 5.0 32 399-430 4-37 (105)
31 TIGR00922 nusG transcription t 94.4 0.073 1.6E-06 53.7 5.8 53 222-274 118-172 (172)
32 PRK12281 rplX 50S ribosomal pr 94.1 0.088 1.9E-06 46.7 4.9 34 787-820 8-41 (76)
33 TIGR01080 rplX_A_E ribosomal p 94.0 0.063 1.4E-06 51.2 4.2 28 276-303 42-69 (114)
34 COG0250 NusG Transcription ant 93.9 0.093 2E-06 53.9 5.5 54 221-274 121-176 (178)
35 CHL00141 rpl24 ribosomal prote 93.6 0.12 2.5E-06 46.8 5.0 34 787-820 10-43 (83)
36 PRK00004 rplX 50S ribosomal pr 93.6 0.12 2.6E-06 48.7 5.1 35 71-105 4-38 (105)
37 TIGR01080 rplX_A_E ribosomal p 93.5 0.14 3.1E-06 48.8 5.5 38 69-106 39-76 (114)
38 PRK05609 nusG transcription an 93.4 0.13 2.9E-06 52.1 5.7 53 222-274 125-179 (181)
39 PRK08559 nusG transcription an 93.1 0.12 2.7E-06 51.6 4.8 52 222-273 93-146 (153)
40 PTZ00194 60S ribosomal protein 93.1 0.17 3.7E-06 50.0 5.5 42 69-110 44-85 (143)
41 TIGR01955 RfaH transcriptional 93.0 0.18 3.9E-06 50.1 5.9 51 222-272 107-158 (159)
42 KOG1924 RhoA GTPase effector D 92.8 0.5 1.1E-05 57.2 9.8 12 349-360 222-233 (1102)
43 KOG1708 Mitochondrial/chloropl 92.7 0.21 4.5E-06 51.6 5.7 81 221-325 70-150 (236)
44 TIGR01079 rplX_bact ribosomal 92.0 0.25 5.4E-06 46.5 4.9 35 71-105 3-37 (104)
45 TIGR01956 NusG_myco NusG famil 91.8 0.29 6.4E-06 52.8 5.8 52 222-273 204-257 (258)
46 TIGR01079 rplX_bact ribosomal 91.2 0.34 7.5E-06 45.6 5.0 34 787-820 5-38 (104)
47 KOG1924 RhoA GTPase effector D 91.1 0.95 2.1E-05 54.9 9.5 12 291-302 222-233 (1102)
48 PRK01191 rpl24p 50S ribosomal 90.9 0.36 7.9E-06 46.4 4.9 34 787-820 47-80 (120)
49 PRK06763 F0F1 ATP synthase sub 89.9 1.7 3.7E-05 45.1 9.0 98 237-348 39-175 (213)
50 COG0198 RplX Ribosomal protein 89.7 0.49 1.1E-05 44.5 4.5 32 222-253 3-34 (104)
51 PTZ00194 60S ribosomal protein 88.6 0.65 1.4E-05 46.0 4.7 34 787-820 48-81 (143)
52 COG0198 RplX Ribosomal protein 87.7 0.78 1.7E-05 43.2 4.4 33 71-105 4-36 (104)
53 PRK12269 bifunctional cytidyla 86.5 27 0.00058 44.4 18.1 105 222-360 709-816 (863)
54 cd04467 S1_aIF5A S1_aIF5A: Arc 82.9 3.1 6.6E-05 35.2 5.3 45 240-286 4-49 (57)
55 PTZ00223 40S ribosomal protein 77.6 4.1 8.8E-05 44.6 5.6 40 276-315 172-215 (273)
56 COG1471 RPS4A Ribosomal protei 77.2 4.9 0.00011 42.8 5.9 36 266-301 162-199 (241)
57 cd04454 S1_Rrp4_like S1_Rrp4_l 76.7 6.7 0.00014 34.5 5.9 51 225-285 5-60 (82)
58 COG1862 YajC Preprotein transl 76.0 6.6 0.00014 36.6 5.8 54 222-282 42-95 (97)
59 PRK04313 30S ribosomal protein 75.1 5.6 0.00012 42.7 5.8 43 276-318 172-219 (237)
60 PLN00036 40S ribosomal protein 74.9 5.7 0.00012 43.2 5.8 25 276-300 175-199 (261)
61 PTZ00118 40S ribosomal protein 73.3 6.7 0.00014 42.7 5.9 25 276-300 175-199 (262)
62 PHA03378 EBNA-3B; Provisional 73.2 83 0.0018 38.5 15.0 18 267-284 327-344 (991)
63 smart00743 Agenet Tudor-like d 73.1 11 0.00024 31.4 6.0 55 223-277 2-58 (61)
64 PF11623 DUF3252: Protein of u 72.8 14 0.00031 30.5 6.2 44 508-551 5-52 (53)
65 KOG1708 Mitochondrial/chloropl 71.3 4 8.6E-05 42.5 3.4 29 275-303 72-100 (236)
66 PRK05585 yajC preprotein trans 68.4 14 0.00031 34.9 6.3 51 222-279 51-101 (106)
67 cd05705 S1_Rrp5_repeat_hs14 S1 68.2 13 0.00028 32.5 5.6 58 224-301 1-66 (74)
68 PRK04333 50S ribosomal protein 68.1 9.3 0.0002 34.7 4.7 33 71-104 3-35 (84)
69 PF11623 DUF3252: Protein of u 67.8 13 0.00027 30.8 4.9 49 224-272 2-52 (53)
70 PRK14635 hypothetical protein; 67.0 7.8 0.00017 39.3 4.5 49 504-552 95-154 (162)
71 PRK07400 30S ribosomal protein 65.6 1.2E+02 0.0026 34.1 13.9 156 222-409 74-249 (318)
72 PRK13709 conjugal transfer nic 65.0 36 0.00077 46.4 11.1 98 221-321 646-761 (1747)
73 CHL00010 infA translation init 64.5 57 0.0012 29.1 9.0 64 350-426 9-73 (78)
74 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 64.5 13 0.00027 33.0 4.9 52 224-285 4-64 (86)
75 PRK04313 30S ribosomal protein 64.4 29 0.00062 37.5 8.3 73 748-820 129-210 (237)
76 PRK05886 yajC preprotein trans 64.3 12 0.00026 35.7 4.9 42 507-553 41-82 (109)
77 PRK14639 hypothetical protein; 64.0 14 0.00031 36.6 5.6 49 504-552 84-132 (140)
78 TIGR00739 yajC preprotein tran 63.9 11 0.00023 34.3 4.3 41 507-552 40-80 (84)
79 COG1588 POP4 RNase P/RNase MRP 63.0 15 0.00032 34.1 5.0 50 502-553 11-63 (95)
80 PF01287 eIF-5a: Eukaryotic el 62.9 12 0.00025 32.8 4.2 43 240-282 5-52 (69)
81 PRK03879 ribonuclease P protei 62.8 18 0.00039 33.7 5.6 48 503-552 10-60 (96)
82 PRK00276 infA translation init 60.7 71 0.0015 27.9 8.8 62 351-425 10-72 (72)
83 COG2139 RPL21A Ribosomal prote 60.6 18 0.0004 33.6 5.2 53 222-274 31-93 (98)
84 cd04455 S1_NusA S1_NusA: N-uti 60.4 37 0.0008 28.8 6.9 42 240-285 7-50 (67)
85 PRK04333 50S ribosomal protein 59.1 14 0.0003 33.6 4.2 29 507-535 6-35 (84)
86 PF02736 Myosin_N: Myosin N-te 59.0 21 0.00047 28.0 4.7 28 522-550 15-42 (42)
87 PRK05585 yajC preprotein trans 58.1 14 0.00031 35.0 4.2 42 507-553 55-96 (106)
88 PF02357 NusG: Transcription t 57.7 11 0.00024 33.8 3.3 34 13-48 45-78 (92)
89 cd01734 YlxS_C YxlS is a Bacil 57.4 21 0.00045 32.0 5.0 51 225-275 23-77 (83)
90 PRK07400 30S ribosomal protein 57.1 2.3E+02 0.005 31.9 14.3 54 222-285 27-85 (318)
91 COG1862 YajC Preprotein transl 57.0 13 0.00028 34.7 3.7 41 508-553 47-87 (97)
92 cd05687 S1_RPS1_repeat_ec1_hs1 56.8 59 0.0013 27.4 7.5 43 240-285 4-54 (70)
93 cd05791 S1_CSL4 S1_CSL4: CSL4, 55.9 20 0.00044 32.8 4.7 50 225-284 5-69 (92)
94 smart00652 eIF1a eukaryotic tr 55.0 97 0.0021 28.1 8.8 65 348-426 5-70 (83)
95 PRK04914 ATP-dependent helicas 54.8 56 0.0012 42.0 9.9 65 749-818 18-82 (956)
96 PF11213 DUF3006: Protein of u 54.7 24 0.00053 30.8 4.8 42 241-284 1-42 (71)
97 TIGR00739 yajC preprotein tran 54.6 35 0.00077 30.9 6.0 44 270-318 32-75 (84)
98 PRK02749 photosystem I reactio 54.5 18 0.00039 31.5 3.8 38 72-111 3-42 (71)
99 CHL00125 psaE photosystem I su 54.4 21 0.00046 30.5 4.1 38 72-111 2-41 (64)
100 PLN00036 40S ribosomal protein 54.3 50 0.0011 36.1 8.1 72 748-820 133-212 (261)
101 PTZ00118 40S ribosomal protein 54.0 55 0.0012 35.9 8.3 72 748-820 133-212 (262)
102 PTZ00223 40S ribosomal protein 54.0 44 0.00096 36.8 7.7 72 748-820 130-209 (273)
103 KOG0307 Vesicle coat complex C 53.7 3.7E+02 0.0081 34.9 16.3 9 534-542 650-658 (1049)
104 PRK06763 F0F1 ATP synthase sub 53.0 1.3E+02 0.0029 31.7 10.5 27 292-318 42-68 (213)
105 TIGR02760 TraI_TIGR conjugativ 52.7 61 0.0013 45.0 10.4 96 221-323 1327-1440(1960)
106 PF11515 Cul7: Mouse developme 52.5 15 0.00032 32.9 3.1 30 70-99 16-48 (78)
107 PRK00092 ribosome maturation p 52.1 25 0.00055 35.2 5.2 50 504-553 94-147 (154)
108 PRK00087 4-hydroxy-3-methylbut 51.9 2.6E+02 0.0057 34.5 14.8 121 271-439 516-638 (647)
109 PRK14638 hypothetical protein; 51.6 27 0.00059 35.0 5.2 47 504-552 96-142 (150)
110 smart00361 RRM_1 RNA recogniti 51.4 28 0.00062 29.7 4.7 28 20-47 34-61 (70)
111 cd01734 YlxS_C YxlS is a Bacil 51.4 32 0.0007 30.8 5.2 50 504-553 21-76 (83)
112 PF02427 PSI_PsaE: Photosystem 51.1 33 0.00071 29.3 4.7 28 72-99 1-30 (61)
113 PF01868 UPF0086: Domain of un 51.0 46 0.00099 30.5 6.2 50 503-553 9-61 (89)
114 PRK06676 rpsA 30S ribosomal pr 51.0 2.6E+02 0.0057 31.9 13.8 45 52-107 44-88 (390)
115 PF02576 DUF150: Uncharacteris 51.0 31 0.00067 33.9 5.5 49 504-552 83-137 (141)
116 PRK14637 hypothetical protein; 50.5 35 0.00075 34.3 5.8 47 504-552 94-141 (151)
117 PRK14644 hypothetical protein; 50.1 25 0.00054 34.8 4.6 49 504-552 81-135 (136)
118 PRK14712 conjugal transfer nic 49.9 74 0.0016 43.1 10.1 85 222-309 515-617 (1623)
119 CHL00084 rpl19 ribosomal prote 49.7 61 0.0013 31.4 7.0 41 220-260 19-70 (117)
120 PRK14643 hypothetical protein; 49.7 29 0.00062 35.4 5.1 50 504-553 100-157 (164)
121 PRK07899 rpsA 30S ribosomal pr 49.6 4.9E+02 0.011 31.2 16.0 58 222-285 204-261 (486)
122 TIGR02760 TraI_TIGR conjugativ 49.1 1E+02 0.0022 42.9 11.6 96 221-320 679-795 (1960)
123 TIGR00037 eIF_5A translation i 48.7 32 0.00069 33.7 5.1 63 221-286 57-119 (130)
124 PF14944 TCRP1: Tongue Cancer 48.4 56 0.0012 32.9 6.7 27 659-685 54-81 (195)
125 PRK12269 bifunctional cytidyla 48.1 57 0.0012 41.6 8.4 51 222-285 317-367 (863)
126 cd05790 S1_Rrp40 S1_Rrp40: Rrp 47.7 21 0.00045 32.6 3.4 49 224-282 4-56 (86)
127 COG1471 RPS4A Ribosomal protei 47.5 51 0.0011 35.5 6.6 71 749-820 133-212 (241)
128 PTZ00065 60S ribosomal protein 47.4 25 0.00054 34.6 4.1 34 71-105 7-40 (130)
129 TIGR00717 rpsA ribosomal prote 47.2 3.9E+02 0.0085 31.7 15.0 101 271-409 400-500 (516)
130 PRK06299 rpsA 30S ribosomal pr 46.9 3.2E+02 0.0069 32.9 14.3 101 270-408 413-513 (565)
131 PF11746 DUF3303: Protein of u 46.6 42 0.00091 30.8 5.3 48 13-60 40-87 (91)
132 PLN00045 photosystem I reactio 46.6 18 0.00039 33.5 2.8 40 780-819 34-80 (101)
133 COG2139 RPL21A Ribosomal prote 46.4 40 0.00086 31.5 5.0 56 269-324 26-93 (98)
134 PRK06531 yajC preprotein trans 46.4 41 0.00088 32.4 5.3 51 222-280 35-87 (113)
135 PRK06531 yajC preprotein trans 46.2 26 0.00056 33.7 3.9 38 513-553 44-81 (113)
136 PRK14634 hypothetical protein; 44.6 37 0.00079 34.3 5.0 48 504-553 96-147 (155)
137 PRK05886 yajC preprotein trans 44.4 68 0.0015 30.7 6.4 49 270-323 33-81 (109)
138 cd04451 S1_IF1 S1_IF1: Transla 44.2 1.6E+02 0.0034 24.9 8.1 59 351-422 4-63 (64)
139 PRK12288 GTPase RsgA; Reviewed 43.8 1.6E+02 0.0036 33.4 10.6 88 350-454 40-129 (347)
140 PF10842 DUF2642: Protein of u 42.8 68 0.0015 28.0 5.6 45 504-551 17-61 (66)
141 PRK14645 hypothetical protein; 42.8 40 0.00087 34.0 4.9 46 504-552 98-143 (154)
142 cd04469 S1_Hex1 S1_Hex1: Hex1, 42.3 37 0.0008 30.3 4.0 38 243-280 6-48 (75)
143 smart00743 Agenet Tudor-like d 41.9 38 0.00082 28.1 3.9 39 749-787 21-59 (61)
144 cd05793 S1_IF1A S1_IF1A: Trans 41.8 1.9E+02 0.0041 25.9 8.5 63 350-426 2-65 (77)
145 PF09953 DUF2187: Uncharacteri 41.8 40 0.00086 28.6 3.8 28 225-256 5-32 (57)
146 PRK04950 ProP expression regul 41.5 44 0.00096 35.5 5.1 44 507-552 169-212 (213)
147 PRK14630 hypothetical protein; 41.0 60 0.0013 32.4 5.8 46 504-552 93-138 (143)
148 PRK09838 periplasmic copper-bi 40.5 67 0.0014 31.0 5.8 61 239-300 44-112 (115)
149 smart00538 POP4 A domain found 40.5 73 0.0016 29.4 5.8 48 503-551 8-58 (92)
150 PF14563 DUF4444: Domain of un 40.2 59 0.0013 25.9 4.3 33 799-832 7-39 (42)
151 PRK14640 hypothetical protein; 40.2 56 0.0012 32.8 5.5 47 504-552 93-143 (152)
152 PHA03378 EBNA-3B; Provisional 40.1 5.8E+02 0.013 31.8 14.3 22 772-793 907-928 (991)
153 PLN00045 photosystem I reactio 39.7 52 0.0011 30.6 4.6 32 67-98 35-68 (101)
154 PF02699 YajC: Preprotein tran 39.3 9.9 0.00021 34.2 0.0 41 507-552 39-79 (82)
155 PF09870 DUF2097: Uncharacteri 39.2 57 0.0012 29.9 4.8 52 222-274 17-68 (86)
156 PRK05338 rplS 50S ribosomal pr 39.0 1.2E+02 0.0026 29.4 7.2 48 221-268 16-74 (116)
157 PF11604 CusF_Ec: Copper bindi 38.9 1.4E+02 0.0031 25.9 7.1 58 242-299 1-66 (70)
158 PRK03999 translation initiatio 38.7 81 0.0017 30.9 6.2 62 221-286 56-118 (129)
159 COG0056 AtpA F0F1-type ATP syn 38.6 84 0.0018 37.0 7.1 49 291-365 26-74 (504)
160 PF09122 DUF1930: Domain of un 38.0 37 0.00079 29.3 3.1 25 84-111 44-68 (68)
161 cd05703 S1_Rrp5_repeat_hs12_sc 37.4 24 0.00052 30.6 2.1 46 240-285 4-56 (73)
162 TIGR01024 rplS_bact ribosomal 37.2 1.1E+02 0.0025 29.4 6.7 49 220-268 15-74 (113)
163 cd04456 S1_IF1A_like S1_IF1A_l 37.2 2.7E+02 0.0058 25.0 8.7 64 349-426 1-66 (78)
164 COG0231 Efp Translation elonga 36.9 89 0.0019 30.7 6.2 61 221-285 53-116 (131)
165 COG0779 Uncharacterized protei 36.9 56 0.0012 33.0 4.9 47 225-275 97-147 (153)
166 cd01854 YjeQ_engC YjeQ/EngC. 36.8 2.6E+02 0.0056 30.8 10.5 86 352-454 1-87 (287)
167 PRK07899 rpsA 30S ribosomal pr 36.3 1.3E+02 0.0029 35.9 8.6 51 222-285 31-89 (486)
168 cd00164 S1_like S1_like: Ribos 36.1 80 0.0017 25.1 5.0 42 241-285 2-51 (65)
169 TIGR00523 eIF-1A eukaryotic/ar 35.9 1.7E+02 0.0038 27.4 7.6 63 348-426 19-85 (99)
170 PTZ00065 60S ribosomal protein 35.8 35 0.00076 33.6 3.1 33 507-540 10-42 (130)
171 smart00316 S1 Ribosomal protei 35.7 1.8E+02 0.0038 23.5 7.1 44 52-106 28-71 (72)
172 cd03692 mtIF2_IVc mtIF2_IVc: t 35.6 59 0.0013 29.0 4.4 59 221-282 24-82 (84)
173 PRK00098 GTPase RsgA; Reviewed 35.6 2.9E+02 0.0063 30.5 10.7 88 351-454 2-89 (298)
174 PF02576 DUF150: Uncharacteris 35.1 54 0.0012 32.2 4.4 51 225-275 85-139 (141)
175 PF10447 EXOSC1: Exosome compo 34.9 1.3E+02 0.0029 27.2 6.5 14 271-284 64-77 (82)
176 COG0335 RplS Ribosomal protein 34.8 1.1E+02 0.0025 29.4 6.2 30 221-250 18-54 (115)
177 PF13051 DUF3912: Protein of u 34.7 62 0.0013 27.4 3.9 50 505-556 3-55 (68)
178 PF05641 Agenet: Agenet domain 34.6 96 0.0021 26.7 5.4 34 224-257 1-39 (68)
179 smart00357 CSP Cold shock prot 34.6 1.7E+02 0.0037 23.5 6.8 56 242-299 2-63 (64)
180 cd05690 S1_RPS1_repeat_ec5 S1_ 34.3 58 0.0013 27.1 3.9 43 52-104 26-68 (69)
181 PRK14633 hypothetical protein; 33.6 76 0.0016 31.8 5.2 49 504-553 90-142 (150)
182 PRK13806 rpsA 30S ribosomal pr 33.6 2.3E+02 0.005 33.8 10.1 49 223-284 31-84 (491)
183 CHL00010 infA translation init 33.5 1.5E+02 0.0033 26.4 6.5 56 240-298 9-69 (78)
184 PRK14632 hypothetical protein; 33.3 79 0.0017 32.5 5.4 50 504-553 94-156 (172)
185 PF00575 S1: S1 RNA binding do 32.9 2.1E+02 0.0046 24.1 7.3 42 241-285 9-58 (74)
186 PLN00208 translation initiatio 32.8 2.8E+02 0.006 28.0 8.8 76 337-426 20-97 (145)
187 PF00924 MS_channel: Mechanose 32.6 67 0.0015 32.8 4.9 46 221-274 58-103 (206)
188 PRK11642 exoribonuclease R; Pr 32.6 5.9E+02 0.013 32.5 13.9 115 240-358 85-214 (813)
189 cd05793 S1_IF1A S1_IF1A: Trans 32.5 2.4E+02 0.0051 25.2 7.6 58 240-299 2-62 (77)
190 TIGR00038 efp translation elon 32.4 4E+02 0.0086 27.6 10.4 70 222-300 51-123 (184)
191 PTZ00328 eukaryotic initiation 32.3 58 0.0013 33.3 4.1 45 239-283 89-145 (166)
192 PRK00092 ribosome maturation p 32.0 76 0.0017 31.8 5.0 49 225-275 96-148 (154)
193 PF02699 YajC: Preprotein tran 32.0 19 0.0004 32.5 0.5 44 270-318 31-74 (82)
194 PRK04012 translation initiatio 31.7 2.9E+02 0.0062 26.1 8.3 73 339-425 11-85 (100)
195 KOG1984 Vesicle coat complex C 31.6 8.4E+02 0.018 31.4 14.2 6 710-715 154-159 (1007)
196 PF13893 RRM_5: RNA recognitio 31.3 77 0.0017 25.4 4.1 36 12-47 10-45 (56)
197 PRK14647 hypothetical protein; 30.7 87 0.0019 31.7 5.1 48 504-552 95-151 (159)
198 PRK02001 hypothetical protein; 30.6 1.1E+02 0.0023 31.0 5.7 49 504-552 86-146 (152)
199 TIGR00358 3_prime_RNase VacB a 30.4 2.6E+02 0.0057 34.5 10.2 74 226-300 71-148 (654)
200 PRK14638 hypothetical protein; 30.4 90 0.0019 31.3 5.1 47 225-275 98-144 (150)
201 COG1532 Predicted RNA-binding 29.8 61 0.0013 27.2 3.1 41 59-105 14-56 (57)
202 COG0779 Uncharacterized protei 29.6 1.2E+02 0.0025 30.8 5.8 47 504-552 95-145 (153)
203 PTZ00329 eukaryotic translatio 29.4 3.9E+02 0.0085 27.2 9.3 76 222-299 16-94 (155)
204 PF07076 DUF1344: Protein of u 29.4 1.4E+02 0.003 25.8 5.2 44 239-285 4-47 (61)
205 PRK04163 exosome complex RNA-b 29.3 96 0.0021 33.3 5.5 50 225-284 62-120 (235)
206 PF12059 DUF3540: Protein of u 29.2 2E+02 0.0044 30.3 7.7 67 749-820 3-72 (202)
207 smart00333 TUDOR Tudor domain. 28.9 78 0.0017 25.5 3.7 39 747-787 18-56 (57)
208 PRK14639 hypothetical protein; 28.9 1E+02 0.0022 30.5 5.2 49 225-275 86-134 (140)
209 COG2163 RPL14A Ribosomal prote 28.9 75 0.0016 31.1 4.1 37 273-309 2-38 (125)
210 PRK04306 50S ribosomal protein 28.8 1.1E+02 0.0024 28.8 5.0 53 222-274 33-95 (98)
211 smart00333 TUDOR Tudor domain. 28.6 1.1E+02 0.0023 24.8 4.5 51 223-275 2-53 (57)
212 PRK14636 hypothetical protein; 28.5 95 0.0021 32.0 5.1 49 504-553 94-146 (176)
213 PRK09521 exosome complex RNA-b 28.4 1.4E+02 0.0029 30.9 6.2 54 222-285 60-128 (189)
214 PRK12442 translation initiatio 27.9 1.8E+02 0.0039 26.8 6.0 60 237-298 6-69 (87)
215 PRK13709 conjugal transfer nic 27.5 2.9E+02 0.0062 38.2 10.4 89 222-320 1274-1382(1747)
216 PRK04306 50S ribosomal protein 27.5 1.2E+02 0.0026 28.6 5.0 58 268-325 27-96 (98)
217 COG3109 ProQ Activator of osmo 27.4 89 0.0019 32.2 4.4 43 507-551 164-206 (208)
218 PRK14646 hypothetical protein; 27.3 1.1E+02 0.0024 30.9 5.2 47 504-552 96-146 (155)
219 TIGR01622 SF-CC1 splicing fact 27.0 1.3E+02 0.0028 34.8 6.5 52 12-63 398-454 (457)
220 cd05686 S1_pNO40 S1_pNO40: pNO 26.4 99 0.0022 26.6 4.1 44 51-106 29-72 (73)
221 cd05704 S1_Rrp5_repeat_hs13 S1 26.3 3.5E+02 0.0076 23.2 7.5 15 271-285 44-58 (72)
222 PRK10862 SoxR reducing system 26.0 1.3E+02 0.0029 30.2 5.5 19 239-257 3-21 (154)
223 COG4873 Uncharacterized protei 25.9 73 0.0016 27.8 3.0 29 223-255 23-51 (81)
224 PRK05807 hypothetical protein; 25.9 3.2E+02 0.007 26.8 8.1 15 271-285 44-58 (136)
225 cd05708 S1_Rrp5_repeat_sc12 S1 25.8 1.5E+02 0.0032 25.0 5.1 47 51-108 28-74 (77)
226 PRK04163 exosome complex RNA-b 25.7 6.1E+02 0.013 27.2 10.8 22 275-306 59-81 (235)
227 PTZ00329 eukaryotic translatio 25.6 4.2E+02 0.0092 27.0 8.8 74 339-426 22-97 (155)
228 KOG2893 Zn finger protein [Gen 25.5 6.5E+02 0.014 27.4 10.5 13 424-436 9-21 (341)
229 COG4873 Uncharacterized protei 25.5 97 0.0021 27.1 3.7 32 271-306 19-50 (81)
230 PF02427 PSI_PsaE: Photosystem 25.4 1.5E+02 0.0032 25.5 4.6 35 786-820 1-41 (61)
231 PRK00529 elongation factor P; 25.3 6.5E+02 0.014 26.1 10.6 71 221-300 51-124 (186)
232 PF14001 YdfZ: YdfZ protein 25.3 78 0.0017 27.4 3.1 32 392-426 2-33 (64)
233 PRK14630 hypothetical protein; 25.2 1.4E+02 0.003 29.8 5.4 46 225-275 95-140 (143)
234 smart00652 eIF1a eukaryotic tr 25.0 3.7E+02 0.008 24.4 7.6 58 240-299 7-67 (83)
235 PLN00208 translation initiatio 24.8 4.9E+02 0.011 26.3 9.0 71 227-299 21-94 (145)
236 smart00316 S1 Ribosomal protei 24.5 1.8E+02 0.0039 23.5 5.2 42 241-285 7-56 (72)
237 TIGR00008 infA translation ini 23.8 3.1E+02 0.0067 24.2 6.5 58 238-297 5-66 (68)
238 PLN02765 pyruvate kinase 23.8 2.7E+02 0.0058 33.7 8.3 44 248-291 112-157 (526)
239 KOG0917 Uncharacterized conser 23.8 4.6E+02 0.01 29.1 9.2 87 604-696 182-297 (338)
240 COG2163 RPL14A Ribosomal prote 23.8 1.2E+02 0.0025 29.8 4.4 32 71-103 4-35 (125)
241 PRK06299 rpsA 30S ribosomal pr 23.7 3.9E+02 0.0085 32.2 9.9 51 222-285 26-81 (565)
242 PF01176 eIF-1a: Translation i 23.6 2.2E+02 0.0048 24.3 5.7 56 240-298 5-64 (65)
243 PRK00409 recombination and DNA 23.5 1.2E+02 0.0026 38.4 5.6 47 222-275 635-682 (782)
244 cd05698 S1_Rrp5_repeat_hs6_sc5 23.5 1.5E+02 0.0033 24.8 4.7 45 51-106 25-69 (70)
245 PRK04012 translation initiatio 23.2 5.3E+02 0.011 24.3 8.5 60 238-299 21-83 (100)
246 PRK06676 rpsA 30S ribosomal pr 23.2 4.2E+02 0.0091 30.2 9.6 58 222-301 13-78 (390)
247 PRK14578 elongation factor P; 22.8 8.4E+02 0.018 25.5 10.7 71 221-300 53-126 (187)
248 cd04456 S1_IF1A_like S1_IF1A_l 22.6 4.5E+02 0.0097 23.6 7.6 58 240-299 2-63 (78)
249 PRK14640 hypothetical protein; 22.5 1.4E+02 0.0031 30.0 4.9 47 225-275 95-145 (152)
250 cd05705 S1_Rrp5_repeat_hs14 S1 22.5 1.4E+02 0.003 26.0 4.3 45 50-104 27-73 (74)
251 PRK05610 rpsQ 30S ribosomal pr 22.4 1.6E+02 0.0034 26.9 4.7 51 238-288 7-66 (84)
252 cd04508 TUDOR Tudor domains ar 22.4 88 0.0019 24.3 2.8 31 749-781 16-46 (48)
253 COG1097 RRP4 RNA-binding prote 22.4 1.1E+02 0.0024 33.1 4.3 50 224-283 62-120 (239)
254 PRK14631 hypothetical protein; 22.3 1.6E+02 0.0035 30.4 5.3 48 504-552 113-166 (174)
255 COG1096 Predicted RNA-binding 22.1 7.4E+02 0.016 26.0 10.0 127 224-377 20-151 (188)
256 TIGR03635 S17_bact 30S ribosom 22.1 1.7E+02 0.0037 25.9 4.7 49 239-287 3-60 (71)
257 KOG0132 RNA polymerase II C-te 22.1 3.1E+02 0.0067 34.5 8.3 28 503-530 479-506 (894)
258 PRK08582 hypothetical protein; 22.0 3.1E+02 0.0067 27.1 7.1 15 271-285 45-59 (139)
259 COG0290 InfC Translation initi 22.0 42 0.00092 34.5 1.1 33 251-285 92-124 (176)
260 cd04452 S1_IF2_alpha S1_IF2_al 21.9 1.8E+02 0.0039 24.6 4.9 45 51-106 30-74 (76)
261 PF01245 Ribosomal_L19: Riboso 21.9 1.6E+02 0.0035 28.3 4.9 38 220-257 15-63 (113)
262 PRK10334 mechanosensitive chan 21.6 1.7E+02 0.0036 32.4 5.7 45 221-273 127-171 (286)
263 PF02736 Myosin_N: Myosin N-te 21.6 1.9E+02 0.0042 22.6 4.5 29 292-321 14-42 (42)
264 cd05692 S1_RPS1_repeat_hs4 S1_ 21.6 2.1E+02 0.0046 23.2 5.1 42 241-285 5-54 (69)
265 cd05688 S1_RPS1_repeat_ec3 S1_ 21.5 1.4E+02 0.0031 24.4 4.1 42 52-104 26-67 (68)
266 PF13051 DUF3912: Protein of u 21.1 82 0.0018 26.7 2.4 23 402-424 5-27 (68)
267 PRK00276 infA translation init 21.1 3.9E+02 0.0083 23.3 6.8 55 240-297 9-68 (72)
268 PF08402 TOBE_2: TOBE domain; 21.0 2.9E+02 0.0062 22.8 5.9 48 238-285 16-66 (75)
269 PF09953 DUF2187: Uncharacteri 21.0 1.6E+02 0.0034 25.2 4.0 29 274-306 2-30 (57)
270 PF03831 PhnA: PhnA protein; 20.7 53 0.0012 27.8 1.2 20 392-411 2-21 (56)
271 cd05702 S1_Rrp5_repeat_hs11_sc 20.1 2.3E+02 0.0051 23.9 5.2 42 240-284 4-55 (70)
272 PLN02741 riboflavin synthase 20.1 5.1E+02 0.011 27.2 8.6 61 264-346 24-84 (194)
No 1
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=100.00 E-value=7.3e-189 Score=1618.35 Aligned_cols=809 Identities=50% Similarity=0.776 Sum_probs=709.7
Q ss_pred Ccccccc---CCCccEEEEEecCCCceEEEEEecChHHHHHHHhcCcceeeeeeeeeChhhhhhccccccccccCCCCCE
Q 003213 1 MQKCIDK---GSELQIRSVIALDHLKNYIYIEADKEAHVKEACKGLRNIYSQKVMLVPIREMTDVLAVESKAIDLSRDTW 77 (838)
Q Consensus 1 m~K~i~~---~~~l~I~Sv~~~~~lkGyIyVEA~~~~~V~~ai~g~~~v~~~~~~~Vpi~Em~~~L~~~~~~~~l~~G~~ 77 (838)
|||||++ +.||+|+|||++|||||||||||++|.||++||+||+|||.+++.||||+||++||+++|+.+.|++|+|
T Consensus 185 MrK~i~~~~t~~plqI~Sv~a~D~lkGyIYIEA~KqshV~~Ai~gv~niy~~~~~lVPikEM~dvLkV~K~~v~L~~gsw 264 (1024)
T KOG1999|consen 185 MRKFIELDKTDTPLQIKSVFAKDHLKGYIYIEADKQSHVKEAIEGVRNIYANRILLVPIKEMPDVLKVVKKVVQLSEGSW 264 (1024)
T ss_pred HHHHHhhcccCCCceEEEEEeccccceeEEEEechhHHHHHHHhhhhhheeccEEEEehhHhhhhhhhhhhhhccCccce
Confidence 8999996 4899999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEecCcCCCceEEEEEEeCCCCEEEEEEeeccchhhhhhhccccccccCCCCCCCCCCCCHHHHHhccccEeeecCCCC
Q 003213 78 VRMKIGNYKGDLAKVVDVDNVRQRVTVKLIPRIDLQALANKLEGREVAKKKPFVPPPRFMNVDEARELHIRVERRRDPMT 157 (838)
Q Consensus 78 VRik~G~ykGDlaqV~~vd~~~~~V~vkliPRiD~~~~~~~~~g~~~~kkk~~RPp~rlF~~~e~~~~~~~v~~~r~~~~ 157 (838)
||||+|+||||||||++|++++++|+|||||||||+++..+++ ...++|++||++|||+..+++++.++++.+|+..+
T Consensus 265 VRiKrG~YKgDLAqVd~Vd~~~n~v~lKlIPRIDyq~~~~~~~--~~~~~ka~~p~~R~~~~~~~~~~~ir~~~~~~~~~ 342 (1024)
T KOG1999|consen 265 VRIKRGKYKGDLAQVDDVDENRNRVRLKLIPRIDYQKLLGKLE--ETTDKKAFRPAPRRPNQKEFDEEAIRSEGRRDHSR 342 (1024)
T ss_pred EEEeccccccceeeeeeecccCCEEEEEEeccccHHhhhcccc--ccchhhccCCcccCCCccccchhhhhhcccccccc
Confidence 9999999999999999999999999999999999999998887 33456778999999999999999999999999999
Q ss_pred CccEEEeCCceeecceEEEEEeecceeecCCCCCHHhhhcccCCCCCCcchhhhhhhhhhccccc-ccCCCCEEEEecCc
Q 003213 158 GDYFENIGGMLFKDGFLYKTVSMKSISAQNIQPTFDELEKFRTPGENGESDIASLSTLFANRKKG-HFMKGDAVIVIKGD 236 (838)
Q Consensus 158 g~~~~~~~g~~y~dGfL~K~~~~~~l~~~~V~PTleEL~kF~~~~~~~~~dl~~ls~~~~~~~~~-~F~~GD~V~V~~Ge 236 (838)
|+||++++|++|+||||||.|+|++|++++|+|||+||+||++..+ +.||.++|+++.+++++ .|++||+|+||.||
T Consensus 343 Gd~l~~~gn~~~~dGFLyK~v~i~sI~t~gV~PT~dELekF~~~~e--~~Dl~~~st~~~~r~~~~~F~~GD~VeV~~Ge 420 (1024)
T KOG1999|consen 343 GDYLEFEGNELFKDGFLYKDVSISSIITDGVKPTLDELEKFNPSNE--EGDLEWVSTLKSNRKKKHLFSPGDAVEVIVGE 420 (1024)
T ss_pred CceEEecCCceeccceeeeeeecceeeecCcccCHHHHHhhcCCCc--cccceeeeeeccccccccccCCCCeEEEeeee
Confidence 9999888888999999999999999999999999999999999877 66777777666666554 59999999999999
Q ss_pred cCCceeEEEEEeCCeEEEeeCCCCCCceeEEcchhhhhhccCCCeEEEeccccCCceEEEEEEeCcEEEEEeCCCCCeEE
Q 003213 237 LKNLKGWVEKVDEENVHIRPEMKGLPKTLAVNSKELCKYFEPGNHVKVVSGTQAGATGMVLKVEQHVLIILSDTTKEDIR 316 (838)
Q Consensus 237 l~~l~G~V~~V~~d~V~i~~~~~~l~~~i~v~~~~LrK~F~~GDhVkVi~G~~~getGlVvkVe~~~v~vlSD~t~~ei~ 316 (838)
|+|++|+|++|++++|+|++++++|+.+|+|++++|||||++|||||||+|+|+|+|||||+|+++.|+||||++++|++
T Consensus 421 l~glkG~ve~vdg~~vti~~~~e~l~~pl~~~~~eLrKyF~~GDhVKVi~G~~eG~tGlVvrVe~~~vi~~Sd~t~eel~ 500 (1024)
T KOG1999|consen 421 LKGLKGKVESVDGTIVTIMSKHEDLKGPLEVPASELRKYFEPGDHVKVIAGRYEGDTGLVVRVEQGDVILLSDLTMEELK 500 (1024)
T ss_pred eccceeEEEeccCceEEEeeccccCCCccccchHhhhhhccCCCeEEEEeccccCCcceEEEEeCCeEEEEecCccceee
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EcccccccccccccccccCCceEecceEEeCCCcEEEEEEEecceEEEEecCCCCCcEEEEEccccccccc-cCccccCC
Q 003213 317 VFADDVVESSEVTTGITKIGDYELRDLVLLDNNSFGVIIRVESEAFQVLKGVPDRPEVALVKLREIKCKLE-KKSNVQDR 395 (838)
Q Consensus 317 V~~~dL~~~~e~~~g~d~~g~y~l~DLVqld~~~vGvIv~ier~~~~VL~~~~~~g~v~~vk~~~I~~K~~-~~~~a~D~ 395 (838)
||++||++|++++++++.+|+|+||||||||.++||||++++++.|+||++ ++.|++|++++|.+|++ ++++|+|+
T Consensus 501 Vf~~dlq~c~ev~~gv~~~ge~e~hdlVqLd~~~vgvI~rle~e~~~vl~~---~g~v~~i~~~~i~~kk~~r~~~~~D~ 577 (1024)
T KOG1999|consen 501 VFARDLQLCSEVTLGVEKSGEYELHDLVQLDNQNVGVIVRLERETFQVLGM---NGKVVTIRKSSITKKKDNRKAVAVDR 577 (1024)
T ss_pred EEehhcccchheeecccccccccccceeecCCCcEEEEEEecchheeeecC---cCceEEEeechhhhhhhhhhheeecc
Confidence 999999999999999999999999999999999999999999999999997 57999999999988886 45999999
Q ss_pred CCCeecCCCEEEEEcCCCCCceeeEEEEECCEEEEEeCceeccccEEEEeCCceEEecccCCCCCCCCCccccCCCCCCC
Q 003213 396 NKNTVAVKDVVRIVEGPCKGKQGPVEHIYRGILFIHDRHHLEHAGFICAKSSSCVVVGGSRANGDRNGDAYSRFNSLRTP 475 (838)
Q Consensus 396 ~gn~i~~gd~Vki~~Gp~kG~~G~Vkhi~r~~lFL~~~~~~En~Gifv~~a~~~~~~g~~~~~~~~~~~~~~~~~~~~~p 475 (838)
++|.|+++|+|+++.||++|++|.|+||||.++|||||+++||+|||||+++||.++|++++.. ......+.|++|+ |
T Consensus 578 ~~n~I~~kD~Vkvi~Gp~~g~~G~v~~i~r~~~F~h~r~~~En~Gv~vck~k~~~~~g~~~st~-~~~~~~~~l~~ms-P 655 (1024)
T KOG1999|consen 578 NGNEIRVKDTVKVIGGPSKGREGEVLHIYRPFVFLHSRKNLENGGVFVCKEKNLILAGGKKSTN-SLAFNKGALAPMS-P 655 (1024)
T ss_pred cCCeecccceEEEecCCCCCccCccceeecceeeeeehhhcccCCeEEEecCCceeccccCccc-chhhcccccCCCC-c
Confidence 9999999999999999999999999999999999999999999999999999999999976421 1112345566665 4
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCC-C-ccccCcEEEEeecCCCCceeEEEeecCCeEEEEeccCceEEEEecccccc
Q 003213 476 PRIPQSPGRYSRGGPPAGGRNRGGRGG-H-DALVGTTVKVRLGPYKGYRGRVVDVKGQSVRVELESQMKVVTVDRSMISD 553 (838)
Q Consensus 476 ~~~~~sp~~~~~~~~~~ggr~~~~~g~-r-d~liGktV~I~~GpyKG~~G~Vkdat~~~~rVELhs~~k~I~V~r~~l~~ 553 (838)
. ..++|++++.++ .++|+++++||| | |.+|||||+|+.||||||+|+|||+|+++||||||++|++|+|||.++..
T Consensus 656 ~-r~~sp~~~~~~~-ga~g~~gggrGg~rd~~l~GktVrI~~Gp~KG~~GivkD~~~~~arVELhs~~~ti~vd~~~~~~ 733 (1024)
T KOG1999|consen 656 G-RIQSPMGPSGGP-GAFGGHGGGRGGNRDDSLLGKTVRIRLGPKKGYLGIVKDVNGDTARVELHSKCVTIKVDRLKRKI 733 (1024)
T ss_pred c-cccCCcCCCCCC-CCcCcCccCccCcCcchhcCcEEEEecCCcccccceeEeccCCeeEEEEEeccEEEEechhhceE
Confidence 3 336666544332 222333444555 4 59999999999999999999999999999999999999999999999987
Q ss_pred ccc-----cccccc-------C-CCC-CCCCCCCCCCCCCCCCCC-CCCCCCCCCCCcCCCCCCCCCCCCCCCCCCCCCC
Q 003213 554 NVV-----VSTPYR-------D-TPR-YGMGSETPMHPSRTPLHP-YMTPMRDAGATPIHDGMRTPMRDRAWNPYTPMSP 618 (838)
Q Consensus 554 ~~~-----~~~~~~-------~-~~~-~~~g~~tp~~~s~TPm~~-~~TP~~~g~~TP~hdg~~tP~~~~aw~p~~p~tp 618 (838)
+.. ....|. + +|. |++||+||||||+||+|+ ++||++++++||+|||+||||+++||+|++++||
T Consensus 734 v~~~~~~g~~~sYg~~~~~~g~~~~~~~~~Gs~tp~~~s~tpl~~~s~tp~~~~~~Tp~~dG~rTP~r~~aW~~~~~~tP 813 (1024)
T KOG1999|consen 734 VGSTRDGGETSSYGERTPGYGRVTPARYGMGSSTPMYGSNTPLWGGSRTPARDGGATPSHDGSRTPARGRAWNPYNGKTP 813 (1024)
T ss_pred EeeccCCCCccccccccccccccCccccCCCCcCccCCCCCCCCCcccCccccCCCCcCCCCCcCCCCCCCcCCCCCCCC
Confidence 653 334454 1 333 478999999999999998 9999999999999999999999999999999999
Q ss_pred CC--CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCCCCC----cCCCCCCCCCCCCC
Q 003213 619 PR--DNWEDGNPGSWGTSPQYQPGSPPSRAYEAPTPGSGWASTPG-GNYSDAGTPRDSSSTY----VNAPSPYLPSTPGG 691 (838)
Q Consensus 619 ~r--~~~~~~~p~~~~~tp~y~~~tp~~~~~~~~TPg~~~~~Tpg-~~y~~~~tP~~~~~~y----~~~p~~y~p~tp~~ 691 (838)
+| ++|+++.++.|+.+|+|. |.|+|||+.|+.+++ +.|..+.||....|+| +++|++ ++++.
T Consensus 814 a~~~~~~~~g~~g~~g~sp~~~--------~~a~Tpg~~~~~~~~~~~~~~~g~~~~~gsa~~~~~~~sps~---sp~~~ 882 (1024)
T KOG1999|consen 814 ARNFDNREPGFEGSGGRSPQGY--------YSAPTPGSNWGSTGGGGAPAWPGTPNGNGSAWGPSGQNSPSP---SPWGY 882 (1024)
T ss_pred ccccCCcccCCCCCCCCCCCCC--------cCCCCCCCCCCcCCCCCCcCCCCCCCCCccccccccCCCCCC---CCccC
Confidence 99 789999998999888654 678999998886654 5566666665444444 344444 22222
Q ss_pred -CCCCCCCCCCCCCCCCC-CCCCCCCCCCCCCCcccCCCCCCCCccCcEEEEecCCCccEEEEEEeCCCCeEEEEeccCC
Q 003213 692 -QPMTPNSASYLPGTPGG-QPMTPGTGGLDAMSPVIGADNEGPWFMPDILVRRSGEESVVGVIREVLPDGSCRVVLGSSG 769 (838)
Q Consensus 692 -~p~tp~~~~y~p~tpg~-~p~tp~~~g~~~~~p~~~~~~~~~W~~~~I~V~~~g~~~~~gvI~~V~~dg~~~V~l~~~~ 769 (838)
.+||||+++|.|.|||+ +|||||+ +++.++... ++....| .+|..+ ...--++.++||+|.+ |.|+|+|.++
T Consensus 883 ~~~~tpss~s~~p~tpgg~~~~Tpgs-~~d~~~~~~-~~~~~~~-~~d~~~-~~~~~G~~~~ir~v~~-G~~sv~~~de- 956 (1024)
T KOG1999|consen 883 QNNPTPSSSSYGPKTPGGGNPMTPGS-GLDSGSGNG-GDGNSSW-GPDTSL-DTQLVGQTGIIRSVAD-GGCSVWLGDE- 956 (1024)
T ss_pred ccCCCCcccccCCCCCCCCCCCCCCc-cccccCCCC-CccceEe-cccccc-cceecccccceeeccC-CceeeecCCC-
Confidence 37799999999999998 9999999 466665322 1222233 333333 0001166889999977 9999999996
Q ss_pred CCceEEecCCCceEcCCCCCCcEEEEcCCCCCceEEEEEEeCCCeEEEecCCCceEEEeccccccccCC
Q 003213 770 NGDTITALPNEIEIVPPRKTDKIKIMGGPHRGATGKLIGVDGTDGIVKVDVSLDVKILDMAILAKLAQP 838 (838)
Q Consensus 770 ~g~~v~v~~~~Le~V~P~kgd~VkVi~G~~rG~tG~LisiD~~dgiVk~d~~~~~kil~~~~L~Kl~~~ 838 (838)
++++.++++||+++.|.++|.+||+.|.+||.+|+|+++|+.+||||+|.+.++|||++.+||||++|
T Consensus 957 -~~~~~~s~~~~a~~~p~~~d~~k~~~g~~~g~~~~~~~~dg~~g~~~~d~~~~~k~l~~~~~~k~~~~ 1024 (1024)
T KOG1999|consen 957 -GETISNSKPHLAPAPPCKGDDVKSIWGDDRGSTGKLVGNDGWDGIVRIDETSDIKILNLGLLCKMVSP 1024 (1024)
T ss_pred -CcccccccccCccCCCCCCCCccccccccccccccccCCCcccceecccccccchhhhhhhhhhccCC
Confidence 79999999999999999999999999999999999999999999999999999999999999999875
No 2
>COG5164 SPT5 Transcription elongation factor [Transcription]
Probab=100.00 E-value=9.1e-74 Score=617.85 Aligned_cols=397 Identities=23% Similarity=0.249 Sum_probs=345.0
Q ss_pred CCCCCCCCCHHHHHhccccEeeecCCCCCccEEEeCCceeecceEEEEEeecceeecCCCCCHHhhhcccCCCCCCcchh
Q 003213 130 FVPPPRFMNVDEARELHIRVERRRDPMTGDYFENIGGMLFKDGFLYKTVSMKSISAQNIQPTFDELEKFRTPGENGESDI 209 (838)
Q Consensus 130 ~RPp~rlF~~~e~~~~~~~v~~~r~~~~g~~~~~~~g~~y~dGfL~K~~~~~~l~~~~V~PTleEL~kF~~~~~~~~~dl 209 (838)
.|||+||||+.|+.++...-...|+++ .| .|.++.|.||||+|.|+++++++++++||+||+.+|....++ +||
T Consensus 4 ~r~~~~lfn~t~a~~~~~~~~~kr~~r---~f-~~~ne~~~dgflvk~~Ris~~et~~~~pt~de~~~F~~~~~d--ldl 77 (607)
T COG5164 4 HRAPPQLFNPTMALRLDQANLYKRDDR---HF-TYKNEDYIDGFLVKVKRISERETLMRIPTNDEKNVFSIICKD--LDL 77 (607)
T ss_pred ccCchhhcCchhhhhcChhhhhccCch---hc-cccCcccccceEEEEeeeceeeecccccccchhhhcCccccc--cch
Confidence 499999999999999887555556543 35 699999999999999999999999999999999999887554 788
Q ss_pred hhhhhhhhcccccccCCCCEEEEecCccCCceeEEEEEeCCeEEEeeCCCCCCceeEEcchhhhhhccCCCeEEEecccc
Q 003213 210 ASLSTLFANRKKGHFMKGDAVIVIKGDLKNLKGWVEKVDEENVHIRPEMKGLPKTLAVNSKELCKYFEPGNHVKVVSGTQ 289 (838)
Q Consensus 210 ~~ls~~~~~~~~~~F~~GD~V~V~~Gel~~l~G~V~~V~~d~V~i~~~~~~l~~~i~v~~~~LrK~F~~GDhVkVi~G~~ 289 (838)
.+++.+++... ..|||||+|||+.||+++..|.|.++.++..+|... +.+.|.++.+-|||.|..|||||||.|.|
T Consensus 78 ~s~~~s~kk~h-a~fqpgD~~Evl~Geqrg~~gVV~~~~~~I~tm~~~---~~~rl~~p~~~lRk~f~~gD~vkVI~g~~ 153 (607)
T COG5164 78 YSYVESFKKQH-AVFQPGDALEVLRGEQRGRVGVVPRQKEMIETMTYH---FEQRLCGPWGRLRKGFYKGDLVKVIEGGE 153 (607)
T ss_pred hHHHHHHhhcc-cccCCCCeeeeecceecccceeecccccceeeeeec---cCceeecchhhhhcccccCCeEEEecccc
Confidence 88887776543 459999999999999999999999999999998874 35789999999999999999999999999
Q ss_pred CCceEEEEEEeCcEEEEEeCCCCCeEEEcccccccccccccccccCCceEecceEEeCCCcEEEEEEEecceEEEEecCC
Q 003213 290 AGATGMVLKVEQHVLIILSDTTKEDIRVFADDVVESSEVTTGITKIGDYELRDLVLLDNNSFGVIIRVESEAFQVLKGVP 369 (838)
Q Consensus 290 ~getGlVvkVe~~~v~vlSD~t~~ei~V~~~dL~~~~e~~~g~d~~g~y~l~DLVqld~~~vGvIv~ier~~~~VL~~~~ 369 (838)
.+++|+|++|+++.++++||+.+.|++|++++|.++.+.+. ....|+|||+|+|+..+|.||..|++|.++|+++
T Consensus 154 ~~d~g~V~rI~~~~vtF~s~~~~~e~tI~sr~l~ks~~tta---~ss~Y~lhd~V~l~~~~vaci~sid~Dv~kvide-- 228 (607)
T COG5164 154 MVDIGTVPRIDGEKVTFNSENFKSESTIKSRGLSKSIDTTA---TSSIYKLHDYVDLFLEKVACINSIDFDVEKVIDE-- 228 (607)
T ss_pred ccccceEEEecCceeEEccccccccceEEeccccccccccc---hhhhhhhhhhhhhhhcceeEEeecccchhhhhhh--
Confidence 99999999999999999999999999999999999987632 3478999999999999999999999999999995
Q ss_pred CCCcEEEEEccccccccc-cC--ccccCCCCCeecCCCEEEEEcCCCCCceeeEEEEECCEEEEEeCceeccccEEEEeC
Q 003213 370 DRPEVALVKLREIKCKLE-KK--SNVQDRNKNTVAVKDVVRIVEGPCKGKQGPVEHIYRGILFIHDRHHLEHAGFICAKS 446 (838)
Q Consensus 370 ~~g~v~~vk~~~I~~K~~-~~--~~a~D~~gn~i~~gd~Vki~~Gp~kG~~G~Vkhi~r~~lFL~~~~~~En~Gifv~~a 446 (838)
.|+|.++-+.+|..|.+ +| .+++|++|++|++||.|++.-|. +++|+|+||++.|+|+|++++.||+|+||++.
T Consensus 229 -~g~v~t~~~~sI~~kv~~~Rg~~i~~d~ng~eI~igd~VvE~~g~--~~egq~l~i~~~f~f~~t~~i~ennGVfv~~~ 305 (607)
T COG5164 229 -LGEVHTACPISIGDKVRVTRGELIGMDGNGREISIGDAVVESRGG--KFEGQSLGIVKHFDFGETVSIKENNGVFVKIE 305 (607)
T ss_pred -cCceeEecchhhhhhhecccceeEeeccccceEeeceeEEEecCC--ceeeEEEEEEEEEeeeeeeeeeccCceEEEec
Confidence 69999999999999985 44 48999999999999999999885 68999999999999999999999999999999
Q ss_pred CceEEecccCCCCCCCCCccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccCcEEEEeecCCCCceeEEE
Q 003213 447 SSCVVVGGSRANGDRNGDAYSRFNSLRTPPRIPQSPGRYSRGGPPAGGRNRGGRGGHDALVGTTVKVRLGPYKGYRGRVV 526 (838)
Q Consensus 447 ~~~~~~g~~~~~~~~~~~~~~~~~~~~~p~~~~~sp~~~~~~~~~~ggr~~~~~g~rd~liGktV~I~~GpyKG~~G~Vk 526 (838)
+|+.+++.+.. .. ..-.+|++||+|- ...+..+ +..- -....+|||.+|||||+|+.|+|||++|+||
T Consensus 306 ~nv~~VAtkd~-~~---s~k~dl~kmnp~v--~~~~~~p----~~~~--l~r~i~gRd~aigktVrIr~g~yKG~lGVVK 373 (607)
T COG5164 306 GNVCIVATKDF-TE---SLKVDLDKMNPPV--TVNLQNP----KTNE--LERKIVGRDPAIGKTVRIRCGEYKGHLGVVK 373 (607)
T ss_pred CceeEEEeccc-hh---hhcccHhhcCchh--hcCCCCC----cchh--hhccccccccccCceEEEeecccccccceee
Confidence 99999988531 11 1225789999432 1222111 0000 0112358999999999999999999999999
Q ss_pred eecCCeEEEEeccCceEEEEeccccccccc
Q 003213 527 DVKGQSVRVELESQMKVVTVDRSMISDNVV 556 (838)
Q Consensus 527 dat~~~~rVELhs~~k~I~V~r~~l~~~~~ 556 (838)
|+++..|||||||++|.|||+|++|...+.
T Consensus 374 dv~~~~arVeLhs~nK~VTI~K~~l~y~~r 403 (607)
T COG5164 374 DVDRNIARVELHSNNKFVTIEKSRLAYLGR 403 (607)
T ss_pred eccCceEEEEEecCCceEEeehhheEEecc
Confidence 999999999999999999999999997654
No 3
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=100.00 E-value=1e-35 Score=346.64 Aligned_cols=463 Identities=23% Similarity=0.352 Sum_probs=301.9
Q ss_pred cCCCCCCCCCCCCHHHHHhccccEeeecCC---CCCccEEEeCCceeecceEEEEEeeccee-----ecCCCCCHHh--h
Q 003213 126 KKKPFVPPPRFMNVDEARELHIRVERRRDP---MTGDYFENIGGMLFKDGFLYKTVSMKSIS-----AQNIQPTFDE--L 195 (838)
Q Consensus 126 kkk~~RPp~rlF~~~e~~~~~~~v~~~r~~---~~g~~~~~~~g~~y~dGfL~K~~~~~~l~-----~~~V~PTleE--L 195 (838)
+++..||+|++|.+..++..+.++-.+=|. ..+.+ |..-+..+=|.++.+...-++ ++--+|.-+| |
T Consensus 316 ~p~~R~~~~~~~~~~~ir~~~~~~~~~Gd~l~~~gn~~---~~dGFLyK~v~i~sI~t~gV~PT~dELekF~~~~e~~Dl 392 (1024)
T KOG1999|consen 316 RPAPRRPNQKEFDEEAIRSEGRRDHSRGDYLEFEGNEL---FKDGFLYKDVSISSIITDGVKPTLDELEKFNPSNEEGDL 392 (1024)
T ss_pred CCcccCCCccccchhhhhhccccccccCceEEecCCce---eccceeeeeeecceeeecCcccCHHHHHhhcCCCccccc
Confidence 445569999999999999988776543211 12233 333333556888888877654 2333344331 1
Q ss_pred h---------c----ccCCCCCC--cchhh---------------------hhhhhh---hcccccccCCCCEEEEecCc
Q 003213 196 E---------K----FRTPGENG--ESDIA---------------------SLSTLF---ANRKKGHFMKGDAVIVIKGD 236 (838)
Q Consensus 196 ~---------k----F~~~~~~~--~~dl~---------------------~ls~~~---~~~~~~~F~~GD~V~V~~Ge 236 (838)
+ + |+..+.-. ..||. .|..-| ...-++.|++||||+|+.|.
T Consensus 393 ~~~st~~~~r~~~~~F~~GD~VeV~~Gel~glkG~ve~vdg~~vti~~~~e~l~~pl~~~~~eLrKyF~~GDhVKVi~G~ 472 (1024)
T KOG1999|consen 393 EWVSTLKSNRKKKHLFSPGDAVEVIVGELKGLKGKVESVDGTIVTIMSKHEDLKGPLEVPASELRKYFEPGDHVKVIAGR 472 (1024)
T ss_pred eeeeeeccccccccccCCCCeEEEeeeeeccceeEEEeccCceEEEeeccccCCCccccchHhhhhhccCCCeEEEEecc
Confidence 1 1 65542100 01110 011111 11226899999999999999
Q ss_pred cCCceeEEEEEeCCeEEEeeCCCCCCceeEEcchhhhhh------------ccCCCeEEEeccccCCceEEEEEEeCcEE
Q 003213 237 LKNLKGWVEKVDEENVHIRPEMKGLPKTLAVNSKELCKY------------FEPGNHVKVVSGTQAGATGMVLKVEQHVL 304 (838)
Q Consensus 237 l~~l~G~V~~V~~d~V~i~~~~~~l~~~i~v~~~~LrK~------------F~~GDhVkVi~G~~~getGlVvkVe~~~v 304 (838)
+++.+|+|++|+...|+|+++.. +++|+|++++|.+. |+.+|.|..-. ...|+|+++|++.+
T Consensus 473 ~eG~tGlVvrVe~~~vi~~Sd~t--~eel~Vf~~dlq~c~ev~~gv~~~ge~e~hdlVqLd~----~~vgvI~rle~e~~ 546 (1024)
T KOG1999|consen 473 YEGDTGLVVRVEQGDVILLSDLT--MEELKVFARDLQLCSEVTLGVEKSGEYELHDLVQLDN----QNVGVIVRLERETF 546 (1024)
T ss_pred ccCCcceEEEEeCCeEEEEecCc--cceeeEEehhcccchheeecccccccccccceeecCC----CcEEEEEEecchhe
Confidence 99999999999999999999876 89999999999954 67777776542 38999999999999
Q ss_pred EEEeCCCCCeEEEccccccccccc--cccccc-CCceEecceEEe--C--CCcEEEEEEEecceEEEEec-CCCCCcEEE
Q 003213 305 IILSDTTKEDIRVFADDVVESSEV--TTGITK-IGDYELRDLVLL--D--NNSFGVIIRVESEAFQVLKG-VPDRPEVAL 376 (838)
Q Consensus 305 ~vlSD~t~~ei~V~~~dL~~~~e~--~~g~d~-~g~y~l~DLVql--d--~~~vGvIv~ier~~~~VL~~-~~~~g~v~~ 376 (838)
.|| +.++.+++|.+.++..+.+. +..+|. .++++..|+|+. + .++.|-|++|.|..+|+.+. +.||+.|+.
T Consensus 547 ~vl-~~~g~v~~i~~~~i~~kk~~r~~~~~D~~~n~I~~kD~Vkvi~Gp~~g~~G~v~~i~r~~~F~h~r~~~En~Gv~v 625 (1024)
T KOG1999|consen 547 QVL-GMNGKVVTIRKSSITKKKDNRKAVAVDRNGNEIRVKDTVKVIGGPSKGREGEVLHIYRPFVFLHSRKNLENGGVFV 625 (1024)
T ss_pred eee-cCcCceEEEeechhhhhhhhhhheeecccCCeecccceEEEecCCCCCccCccceeecceeeeeehhhcccCCeEE
Confidence 999 88899999999999988777 445565 479999999997 3 35679999999999999985 678999999
Q ss_pred EEccccc---cccc------------cCcc------ccC-------------C--CCCeecCCCEEEEEcCCCCCceeeE
Q 003213 377 VKLREIK---CKLE------------KKSN------VQD-------------R--NKNTVAVKDVVRIVEGPCKGKQGPV 420 (838)
Q Consensus 377 vk~~~I~---~K~~------------~~~~------a~D-------------~--~gn~i~~gd~Vki~~Gp~kG~~G~V 420 (838)
|+++.+. .|.+ .+.. +.- + ++..-.+|++|+|..|||||..|.|
T Consensus 626 ck~k~~~~~g~~~st~~~~~~~~~l~~msP~r~~sp~~~~~~~ga~g~~gggrGg~rd~~l~GktVrI~~Gp~KG~~Giv 705 (1024)
T KOG1999|consen 626 CKEKNLILAGGKKSTNSLAFNKGALAPMSPGRIQSPMGPSGGPGAFGGHGGGRGGNRDDSLLGKTVRIRLGPKKGYLGIV 705 (1024)
T ss_pred EecCCceeccccCcccchhhcccccCCCCcccccCCcCCCCCCCCcCcCccCccCcCcchhcCcEEEEecCCccccccee
Confidence 9988642 1111 0100 000 0 0123788999999999999999999
Q ss_pred EEEECCE--EEEEeCceeccccEEEEeCCceEEecccCCCCCCCCCccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 003213 421 EHIYRGI--LFIHDRHHLEHAGFICAKSSSCVVVGGSRANGDRNGDAYSRFNSLRTPPRIPQSPGRYSRGGPPAGGRNRG 498 (838)
Q Consensus 421 khi~r~~--lFL~~~~~~En~Gifv~~a~~~~~~g~~~~~~~~~~~~~~~~~~~~~p~~~~~sp~~~~~~~~~~ggr~~~ 498 (838)
|++..++ +.||+...+ +- ++-.++..++..+.++..+ + .+.+. |+. |+..+
T Consensus 706 kD~~~~~arVELhs~~~t----i~-vd~~~~~~v~~~~~~g~~~--s---Yg~~~--------~~~---------g~~~~ 758 (1024)
T KOG1999|consen 706 KDVNGDTARVELHSKCVT----IK-VDRLKRKIVGSTRDGGETS--S---YGERT--------PGY---------GRVTP 758 (1024)
T ss_pred EeccCCeeEEEEEeccEE----EE-echhhceEEeeccCCCCcc--c---ccccc--------ccc---------cccCc
Confidence 9999997 799987765 22 4444455555432111100 0 00000 000 00000
Q ss_pred CCCCCccccCcEEEEeecCCCCceeEEEeecCCeEEEEeccCceEEEEecccccccccccccccCCCCCCCCCCCCCCC-
Q 003213 499 GRGGHDALVGTTVKVRLGPYKGYRGRVVDVKGQSVRVELESQMKVVTVDRSMISDNVVVSTPYRDTPRYGMGSETPMHP- 577 (838)
Q Consensus 499 ~~g~rd~liGktV~I~~GpyKG~~G~Vkdat~~~~rVELhs~~k~I~V~r~~l~~~~~~~~~~~~~~~~~~g~~tp~~~- 577 (838)
. |+ .++ +.+|+| |++||.|+
T Consensus 759 ~------------------~~---------------------------------~~G------s~tp~~--~s~tpl~~~ 779 (1024)
T KOG1999|consen 759 A------------------RY---------------------------------GMG------SSTPMY--GSNTPLWGG 779 (1024)
T ss_pred c------------------cc---------------------------------CCC------CcCccC--CCCCCCCCc
Confidence 0 00 011 234554 89999999
Q ss_pred CCCCC-CCCCCCCCCCCCCcCCCCCC------CCCC-CCCCCCCCCCCCCCCC---CCCCCCCC-CCCCCC-CCCCCCCC
Q 003213 578 SRTPL-HPYMTPMRDAGATPIHDGMR------TPMR-DRAWNPYTPMSPPRDN---WEDGNPGS-WGTSPQ-YQPGSPPS 644 (838)
Q Consensus 578 s~TPm-~~~~TP~~~g~~TP~hdg~~------tP~~-~~aw~p~~p~tp~r~~---~~~~~p~~-~~~tp~-y~~~tp~~ 644 (838)
|+||| |+++||.|||+|||++.++| ||++ .+.|.+..+..|.+.+ |.+++|++ |+++++ |.|
T Consensus 780 s~tp~~~~~~Tp~~dG~rTP~r~~aW~~~~~~tPa~~~~~~~~g~~g~~g~sp~~~~~a~Tpg~~~~~~~~~~~~----- 854 (1024)
T KOG1999|consen 780 SRTPARDGGATPSHDGSRTPARGRAWNPYNGKTPARNFDNREPGFEGSGGRSPQGYYSAPTPGSNWGSTGGGGAP----- 854 (1024)
T ss_pred ccCccccCCCCcCCCCCcCCCCCCCcCCCCCCCCccccCCcccCCCCCCCCCCCCCcCCCCCCCCCCcCCCCCCc-----
Confidence 99999 79999999999999766554 5554 3456677666666655 55666665 665432 333
Q ss_pred CCCCCCCCCCCC----CCCCCCCCCCCCCCCCCCCCCc----CCCCCCCCCCCCC-CCCCCCC
Q 003213 645 RAYEAPTPGSGW----ASTPGGNYSDAGTPRDSSSTYV----NAPSPYLPSTPGG-QPMTPNS 698 (838)
Q Consensus 645 ~~~~~~TPg~~~----~~Tpg~~y~~~~tP~~~~~~y~----~~p~~y~p~tp~~-~p~tp~~ 698 (838)
++||.++ +.+| +.+++|++++.+|+ |++++|.|.||++ +||||+.
T Consensus 855 -----~~~g~~~~~gsa~~~----~~~~sps~sp~~~~~~~tpss~s~~p~tpgg~~~~Tpgs 908 (1024)
T KOG1999|consen 855 -----AWPGTPNGNGSAWGP----SGQNSPSPSPWGYQNNPTPSSSSYGPKTPGGGNPMTPGS 908 (1024)
T ss_pred -----CCCCCCCCCcccccc----ccCCCCCCCCccCccCCCCcccccCCCCCCCCCCCCCCc
Confidence 3333211 1112 12333443444453 3334789999998 7888763
No 4
>COG5164 SPT5 Transcription elongation factor [Transcription]
Probab=99.82 E-value=1.5e-18 Score=189.94 Aligned_cols=208 Identities=21% Similarity=0.222 Sum_probs=169.4
Q ss_pred ccccCCCCEEEEecCccCCceeEEEEEeCCeEEEeeCCCCCCceeEEcchhhhhh---------ccCCCeEEEeccccCC
Q 003213 221 KGHFMKGDAVIVIKGDLKNLKGWVEKVDEENVHIRPEMKGLPKTLAVNSKELCKY---------FEPGNHVKVVSGTQAG 291 (838)
Q Consensus 221 ~~~F~~GD~V~V~~Gel~~l~G~V~~V~~d~V~i~~~~~~l~~~i~v~~~~LrK~---------F~~GDhVkVi~G~~~g 291 (838)
|+.|.+||+|+||+|+.+...|+|..|+++.|+++++ .++.++++++++|.|. ++..|.|.. +..
T Consensus 137 Rk~f~~gD~vkVI~g~~~~d~g~V~rI~~~~vtF~s~--~~~~e~tI~sr~l~ks~~tta~ss~Y~lhd~V~l----~~~ 210 (607)
T COG5164 137 RKGFYKGDLVKVIEGGEMVDIGTVPRIDGEKVTFNSE--NFKSESTIKSRGLSKSIDTTATSSIYKLHDYVDL----FLE 210 (607)
T ss_pred hcccccCCeEEEeccccccccceEEEecCceeEEccc--cccccceEEeccccccccccchhhhhhhhhhhhh----hhc
Confidence 6899999999999999999999999999999999997 4478999999999885 466676543 346
Q ss_pred ceEEEEEEeCcEEEEEeCCCCCeEEEccccccccccccc----ccccC-CceEecceEEe--CCCcEEEEEEEecceEEE
Q 003213 292 ATGMVLKVEQHVLIILSDTTKEDIRVFADDVVESSEVTT----GITKI-GDYELRDLVLL--DNNSFGVIIRVESEAFQV 364 (838)
Q Consensus 292 etGlVvkVe~~~v~vlSD~t~~ei~V~~~dL~~~~e~~~----g~d~~-g~y~l~DLVql--d~~~vGvIv~ier~~~~V 364 (838)
.+-||..|+.|+..++ |++++.-++++..+-.+.-++. ++|.. .+++++|-|.. +....|.|++|.+.+.++
T Consensus 211 ~vaci~sid~Dv~kvi-de~g~v~t~~~~sI~~kv~~~Rg~~i~~d~ng~eI~igd~VvE~~g~~~egq~l~i~~~f~f~ 289 (607)
T COG5164 211 KVACINSIDFDVEKVI-DELGEVHTACPISIGDKVRVTRGELIGMDGNGREISIGDAVVESRGGKFEGQSLGIVKHFDFG 289 (607)
T ss_pred ceeEEeecccchhhhh-hhcCceeEecchhhhhhhecccceeEeeccccceEeeceeEEEecCCceeeEEEEEEEEEeee
Confidence 7899999999999999 9999999999999987665543 35554 48999999998 678999999999998777
Q ss_pred Eec-CCCCCcEEEEEccc---cccc---------cccCccccCC--------------CCCeecCCCEEEEEcCCCCCce
Q 003213 365 LKG-VPDRPEVALVKLRE---IKCK---------LEKKSNVQDR--------------NKNTVAVKDVVRIVEGPCKGKQ 417 (838)
Q Consensus 365 L~~-~~~~g~v~~vk~~~---I~~K---------~~~~~~a~D~--------------~gn~i~~gd~Vki~~Gp~kG~~ 417 (838)
.+- ..++.+|+.+.+.. |+.| |+++..++-. -|++..+|.+|+|..|+|||..
T Consensus 290 ~t~~i~ennGVfv~~~~nv~~VAtkd~~~s~k~dl~kmnp~v~~~~~~p~~~~l~r~i~gRd~aigktVrIr~g~yKG~l 369 (607)
T COG5164 290 ETVSIKENNGVFVKIEGNVCIVATKDFTESLKVDLDKMNPPVTVNLQNPKTNELERKIVGRDPAIGKTVRIRCGEYKGHL 369 (607)
T ss_pred eeeeeeccCceEEEecCceeEEEeccchhhhcccHhhcCchhhcCCCCCcchhhhccccccccccCceEEEeeccccccc
Confidence 763 34566777776652 2333 3444322211 2788899999999999999999
Q ss_pred eeEEEEECCE--EEEEeCce
Q 003213 418 GPVEHIYRGI--LFIHDRHH 435 (838)
Q Consensus 418 G~Vkhi~r~~--lFL~~~~~ 435 (838)
|+||++.++. +.||+++.
T Consensus 370 GVVKdv~~~~arVeLhs~nK 389 (607)
T COG5164 370 GVVKDVDRNIARVELHSNNK 389 (607)
T ss_pred ceeeeccCceEEEEEecCCc
Confidence 9999999997 79998775
No 5
>PRK08559 nusG transcription antitermination protein NusG; Validated
Probab=99.66 E-value=4.2e-16 Score=154.36 Aligned_cols=102 Identities=26% Similarity=0.436 Sum_probs=93.3
Q ss_pred CCccEEEEEecCCCceEEEEEecChHHHHHHHhcCcceeeeeeeeeChhhhhhccccccccccCCCCCEEEEecCcCCCc
Q 003213 9 SELQIRSVIALDHLKNYIYIEADKEAHVKEACKGLRNIYSQKVMLVPIREMTDVLAVESKAIDLSRDTWVRMKIGNYKGD 88 (838)
Q Consensus 9 ~~l~I~Sv~~~~~lkGyIyVEA~~~~~V~~ai~g~~~v~~~~~~~Vpi~Em~~~L~~~~~~~~l~~G~~VRik~G~ykGD 88 (838)
.++.|+|||+|+.++|||||||...++++++|++++++++.-..+++.+||..+|+..+....+++|+||||++|+|+|+
T Consensus 32 ~~~~i~~i~vp~~fpGYVfVe~~~~~~~~~~i~~v~~v~g~lg~~l~~~Ei~~il~~~~~~~~~~~G~~V~I~~Gpf~g~ 111 (153)
T PRK08559 32 ENLPIYAILAPPELKGYVLVEAESKGAVEEAIRGIPHVRGVVPGEISFEEVEHFLKPKPIVEGIKEGDIVELIAGPFKGE 111 (153)
T ss_pred CCCcEEEEEccCCCCcEEEEEEEChHHHHHHHhcCCCEeeeCCCCCCHHHHHHHHhccCcccCCCCCCEEEEeccCCCCc
Confidence 46679999999999999999999999999999999999985446899999999998765556799999999999999999
Q ss_pred eEEEEEEeCCCCEEEEEEeecc
Q 003213 89 LAKVVDVDNVRQRVTVKLIPRI 110 (838)
Q Consensus 89 laqV~~vd~~~~~V~vkliPRi 110 (838)
.|+|.++|..+..++|+|+-|-
T Consensus 112 ~g~V~~vd~~k~~v~v~ll~~~ 133 (153)
T PRK08559 112 KARVVRVDESKEEVTVELLEAA 133 (153)
T ss_pred eEEEEEEcCCCCEEEEEEECCc
Confidence 9999999999999999998764
No 6
>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=99.57 E-value=9.6e-15 Score=143.18 Aligned_cols=102 Identities=25% Similarity=0.420 Sum_probs=91.0
Q ss_pred CCccEEEEEecCCCceEEEEEecChHHHHHHHhcCcceeeeeeeeeChhhhhhccccccccccCCCCCEEEEecCcCCCc
Q 003213 9 SELQIRSVIALDHLKNYIYIEADKEAHVKEACKGLRNIYSQKVMLVPIREMTDVLAVESKAIDLSRDTWVRMKIGNYKGD 88 (838)
Q Consensus 9 ~~l~I~Sv~~~~~lkGyIyVEA~~~~~V~~ai~g~~~v~~~~~~~Vpi~Em~~~L~~~~~~~~l~~G~~VRik~G~ykGD 88 (838)
..+.|+|+|+|..++||||||+....+++.+|++++++.+.-...||.+||.+++........+++|+||||++|||+|+
T Consensus 24 ~~~~~~~~~vp~~fpGYvFV~~~~~~~~~~~i~~~~gv~~~v~~~i~~~ei~~l~~~~~~~~~~~~Gd~V~I~~GPf~G~ 103 (145)
T TIGR00405 24 SGLEVYSILAPESLKGYILVEAETKIDMRNPIIGVPHVRGVVEGEIDFEEIERFLTPKKIIESIKKGDIVEIISGPFKGE 103 (145)
T ss_pred CCCcEEEEEccCCCCcEEEEEEECcHHHHHHHhCCCCEEeecCCCCCHHHHHHHhcccccccccCCCCEEEEeecCCCCC
Confidence 56889999999999999999999999999999999999985446799999999997533234589999999999999999
Q ss_pred eEEEEEEeCCCCEEEEEEeecc
Q 003213 89 LAKVVDVDNVRQRVTVKLIPRI 110 (838)
Q Consensus 89 laqV~~vd~~~~~V~vkliPRi 110 (838)
.|+|+++|..+..|+|+|+-+-
T Consensus 104 ~g~v~~~d~~k~~v~v~l~~~~ 125 (145)
T TIGR00405 104 RAKVIRVDESKEEVTLELIEAA 125 (145)
T ss_pred eEEEEEEcCCCCEEEEEEEEcC
Confidence 9999999999999999998743
No 7
>PF03439 Spt5-NGN: Early transcription elongation factor of RNA pol II, NGN section; InterPro: IPR005100 Spt5p and prokaryotic NusG are shown to contain a novel 'NGN' domain. The combined NGN and KOW motif regions of Spt5 form the binding domain with Spt4 []. Spt5 complexes with Spt4 as a 1:1 heterodimer snf this Spt5-Spt4 complex regulates early transcription elongation by RNA polymerase II and has an imputed role in pre-mRNA processing via its physical association with mRNA capping enzymes. The Schizosaccharomyces pombe core Spt5-Spt4 complex is a heterodimer bearing a trypsin-resistant Spt4-binding domain within the Spt5 subunit []. ; PDB: 3H7H_B 3QQC_D 3P8B_B 2EXU_A.
Probab=99.56 E-value=1.9e-15 Score=135.31 Aligned_cols=63 Identities=49% Similarity=0.748 Sum_probs=50.3
Q ss_pred Ccccccc--CCCccEEEEEecCCCceEEEEEecChHHHHHHHhcCcceeeeeeeeeChhhhhhcc
Q 003213 1 MQKCIDK--GSELQIRSVIALDHLKNYIYIEADKEAHVKEACKGLRNIYSQKVMLVPIREMTDVL 63 (838)
Q Consensus 1 m~K~i~~--~~~l~I~Sv~~~~~lkGyIyVEA~~~~~V~~ai~g~~~v~~~~~~~Vpi~Em~~~L 63 (838)
|+|+++. .+.++|+|||+++++||||||||++++||.+||+|++++|+..+++||++||+++|
T Consensus 20 ~~k~~~~~~~~~l~I~Si~~~~~lkGyIyVEA~~~~~V~~ai~gi~~i~~~~~~~vp~~E~~~~L 84 (84)
T PF03439_consen 20 MNKAEDLAKKNNLNIYSIFAPDSLKGYIYVEAERESDVKEAIRGIRHIRGSRPGLVPIEEMEDLL 84 (84)
T ss_dssp HHHHHHHHHHST----EEEE-TTSTSEEEEEESSHHHHHHHHTT-TTEEEECCEEB-GGGTCGGH
T ss_pred HHHHHHhhhcCCCceEEEEEeCCCceEEEEEeCCHHHHHHHHhcccceeeccceeECHHHHHhhC
Confidence 4666653 23499999999999999999999999999999999999999889999999999987
No 8
>COG0250 NusG Transcription antiterminator [Transcription]
Probab=99.11 E-value=8.6e-11 Score=119.18 Aligned_cols=96 Identities=18% Similarity=0.289 Sum_probs=84.0
Q ss_pred cEEEEEecCCCceEEEEEecChHHHHHHHhcCcceee------eeeeeeChhhhhh---cccc----ccccccCCCCCEE
Q 003213 12 QIRSVIALDHLKNYIYIEADKEAHVKEACKGLRNIYS------QKVMLVPIREMTD---VLAV----ESKAIDLSRDTWV 78 (838)
Q Consensus 12 ~I~Sv~~~~~lkGyIyVEA~~~~~V~~ai~g~~~v~~------~~~~~Vpi~Em~~---~L~~----~~~~~~l~~G~~V 78 (838)
..+.++.++-++|||||||....+.|..|+++++|.+ .++.+++.+|+.+ .+.. .+....+++|+.|
T Consensus 51 ~~~~~~e~~~fpGYVlVem~~~~~~w~~Vr~tpgV~GfVg~~~~~P~pi~~~ei~~~l~~~~~~~~~~~~~~~~e~Gd~V 130 (178)
T COG0250 51 KRKVIVERKLFPGYVLVEMDMTDEAWHLVRNTPGVTGFVGSGGAKPVPLSEEEIEHILGFLEEEVAPKKPKVDFEPGDVV 130 (178)
T ss_pred ceEEEEecccCCcEEEEEEEcCCceEEEEecCCCcEEEeccCCCCCcccCHHHHHHHHhhccccccCCcccccCCCCCEE
Confidence 4677799999999999999999999999999999985 3678999999999 4442 2235789999999
Q ss_pred EEecCcCCCceEEEEEEeCCCCEEEEEEe
Q 003213 79 RMKIGNYKGDLAKVVDVDNVRQRVTVKLI 107 (838)
Q Consensus 79 Rik~G~ykGDlaqV~~vd~~~~~V~vkli 107 (838)
||..|+|+|..|+|.+||.++.+++|.|.
T Consensus 131 rI~~GpFa~f~g~V~evd~ek~~~~v~v~ 159 (178)
T COG0250 131 RIIDGPFAGFKAKVEEVDEEKGKLKVEVS 159 (178)
T ss_pred EEeccCCCCccEEEEEEcCcCcEEEEEEE
Confidence 99999999999999999999999888763
No 9
>PF12815 CTD: Spt5 C-terminal nonapeptide repeat binding Spt4; PDB: 2E70_A.
Probab=98.98 E-value=7.8e-11 Score=112.49 Aligned_cols=57 Identities=42% Similarity=0.615 Sum_probs=0.0
Q ss_pred cCCCCCCC--CCCCCCC---CCCCCCC---CCCCCCCC-CCCCcC-CCCCCCCCCCCCCCCCCCCCCCC
Q 003213 562 RDTPRYGM--GSETPMH---PSRTPLH---PYMTPMRD-AGATPI-HDGMRTPMRDRAWNPYTPMSPPR 620 (838)
Q Consensus 562 ~~~~~~~~--g~~tp~~---~s~TPm~---~~~TP~~~-g~~TP~-hdg~~tP~~~~aw~p~~p~tp~r 620 (838)
.|||.|.. |++||+| ++|||++ ++.||.+. |++||+ |+|+|||+....|++ ..||++
T Consensus 2 ~rTPa~~~~~g~rTPa~~~~gsrTP~~~~~g~rTPa~~~gsrTP~~~~gsrTPa~~~~~~~--~~TPa~ 68 (123)
T PF12815_consen 2 SRTPAYGSASGSRTPAWGNDGSRTPAPGADGSRTPAWGSGSRTPAFHDGSRTPAYGGSSSP--SRTPAY 68 (123)
T ss_dssp ---------------------------------------------------------------------
T ss_pred CCCCcCcCCCCCCCcccccCCCCCcCCcCCCCcCcccccCCcCcccCCCCCCCccCCCCCC--CCCccC
Confidence 36888876 8999999 8999997 78899987 779999 999999987666654 667776
No 10
>PRK05609 nusG transcription antitermination protein NusG; Validated
Probab=98.65 E-value=8.3e-08 Score=97.32 Aligned_cols=85 Identities=14% Similarity=0.222 Sum_probs=71.3
Q ss_pred CceEEEEEecChHHHHHHHhcCcceee------eeeeeeChhhhhhcccc-c------cccccCCCCCEEEEecCcCCCc
Q 003213 22 LKNYIYIEADKEAHVKEACKGLRNIYS------QKVMLVPIREMTDVLAV-E------SKAIDLSRDTWVRMKIGNYKGD 88 (838)
Q Consensus 22 lkGyIyVEA~~~~~V~~ai~g~~~v~~------~~~~~Vpi~Em~~~L~~-~------~~~~~l~~G~~VRik~G~ykGD 88 (838)
++|||||++......+..|+.++++.+ ..+..||.+||..++.. . .....+++|+.|||..|||+|-
T Consensus 64 fpgYvFv~~~~~~~~~~~i~~~~gv~~~v~~~g~~p~~i~~~ei~~l~~~~~~~~~~~~~~~~~~~Gd~VrI~~GPf~G~ 143 (181)
T PRK05609 64 FPGYVLVKMVMTDESWHLVRNTPGVTGFVGSTGSKPTPLSEKEVEKILKQLQEGVEKPKPKVDFEVGEMVRVIDGPFADF 143 (181)
T ss_pred CCcEEEEEEEeCccHhHHhhcCCCeEEEecCCCCCcccCCHHHHHHHHHHhhcccccCccccCCCCCCEEEEeccCCCCC
Confidence 999999999988888999999999864 24678999999999862 1 1134688999999999999999
Q ss_pred eEEEEEEeCCCCEEEEEE
Q 003213 89 LAKVVDVDNVRQRVTVKL 106 (838)
Q Consensus 89 laqV~~vd~~~~~V~vkl 106 (838)
.|.|.+++..+.+|+|.|
T Consensus 144 ~g~v~~i~~~~~r~~v~l 161 (181)
T PRK05609 144 NGTVEEVDYEKSKLKVLV 161 (181)
T ss_pred EEEEEEEeCCCCEEEEEE
Confidence 999999998787877764
No 11
>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=98.55 E-value=1.6e-07 Score=99.64 Aligned_cols=93 Identities=16% Similarity=0.257 Sum_probs=75.3
Q ss_pred EEEEecCCCceEEEEEecChHHHHHHHhcCcceee---e-----eeeeeChhhh-hhcccccc-----------------
Q 003213 14 RSVIALDHLKNYIYIEADKEAHVKEACKGLRNIYS---Q-----KVMLVPIREM-TDVLAVES----------------- 67 (838)
Q Consensus 14 ~Sv~~~~~lkGyIyVEA~~~~~V~~ai~g~~~v~~---~-----~~~~Vpi~Em-~~~L~~~~----------------- 67 (838)
+-+..+.-++|||||+|...+++|.+|+++++|.| + +|.+++.+|. .++|+...
T Consensus 78 ~k~~er~~fPGYI~IkM~m~d~~W~~VRnt~gVTGFvGssg~g~kPiPls~~e~~~~ml~~~~~~~~~~~~~~~~~~~~~ 157 (258)
T TIGR01956 78 TKISEKNKYNGYIYIKMIMTEDAWFLIRNTENVTGLVGSSGKGAKPIPISADADKLKMLKGISENTKKRVLVTNTAIVEM 157 (258)
T ss_pred EEEEEeeecCcEEEEEEEecccHhhheecCCCCCeecCCCCCCCCCcCCCHHHHHHHHhhhhhhcccccccccccccccc
Confidence 34556667999999999999999999999999984 2 5788887777 56664211
Q ss_pred --------------------------------------------ccccCCCCCEEEEecCcCCCceEEEEEEeCCCCEEE
Q 003213 68 --------------------------------------------KAIDLSRDTWVRMKIGNYKGDLAKVVDVDNVRQRVT 103 (838)
Q Consensus 68 --------------------------------------------~~~~l~~G~~VRik~G~ykGDlaqV~~vd~~~~~V~ 103 (838)
....+++|+.|||..|+|+|..|+|.+++..+.+|.
T Consensus 158 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~vGd~VrI~dGPF~GfeG~I~eid~~k~Rv~ 237 (258)
T TIGR01956 158 EENKFDEKCQYILKHKQVKPEAIAQVSESGEIIDEIVEEFQLVDNLSKFRVGNFVKIVDGPFKGIVGKIKKIDQEKKKAI 237 (258)
T ss_pred cccccccccccccccccccccccccccccccccccccccccccccccCCCCCCEEEEEecCCCCcEEEEEEEeCCCCEEE
Confidence 123578999999999999999999999998788877
Q ss_pred EEE
Q 003213 104 VKL 106 (838)
Q Consensus 104 vkl 106 (838)
|.|
T Consensus 238 VlV 240 (258)
T TIGR01956 238 VEV 240 (258)
T ss_pred EEE
Confidence 764
No 12
>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=98.44 E-value=8.9e-07 Score=89.25 Aligned_cols=90 Identities=17% Similarity=0.234 Sum_probs=73.2
Q ss_pred EecCCCceEEEEEecChHHHHHHHhcCcceee-----eeeeeeCh-hhhhhcccccc-------ccccCCCCCEEEEecC
Q 003213 17 IALDHLKNYIYIEADKEAHVKEACKGLRNIYS-----QKVMLVPI-REMTDVLAVES-------KAIDLSRDTWVRMKIG 83 (838)
Q Consensus 17 ~~~~~lkGyIyVEA~~~~~V~~ai~g~~~v~~-----~~~~~Vpi-~Em~~~L~~~~-------~~~~l~~G~~VRik~G 83 (838)
+..+=++|||||++....+.+..|..+++|.+ ..+..||. +||..++.... ....+++|+.|||+.|
T Consensus 52 ~~~plfPgYvFv~~~~~~~~~~~i~~~~gv~~~v~~~~~p~~I~~~~ei~~l~~~~~~~~~~~~~~~~~~~G~~V~I~~G 131 (172)
T TIGR00922 52 VERKIFPGYVLVKMDLTDVSWHLVKNTPGVTGFVGSGGKPKALSEDEEVKNILNALEEGKDKPKPKIDFEVGEQVRVNDG 131 (172)
T ss_pred EEEecCCcEEEEEEEeCccHhHHhhcCCCccEEcCcCCeeeccCCHHHHHHHHHHhhcccccCccccCCCCCCEEEEeec
Confidence 33455799999999988888999999999874 36788999 99999875421 1234889999999999
Q ss_pred cCCCceEEEEEEeCCCCEEEEEE
Q 003213 84 NYKGDLAKVVDVDNVRQRVTVKL 106 (838)
Q Consensus 84 ~ykGDlaqV~~vd~~~~~V~vkl 106 (838)
||+|..|.|.++|..+.+|+|.|
T Consensus 132 pf~G~~g~v~~~~~~~~r~~V~v 154 (172)
T TIGR00922 132 PFANFTGTVEEVDYEKSKLKVSV 154 (172)
T ss_pred CCCCcEEEEEEEcCCCCEEEEEE
Confidence 99999999999997777777764
No 13
>KOG0260 consensus RNA polymerase II, large subunit [Transcription]
Probab=98.24 E-value=2.1e-05 Score=95.63 Aligned_cols=18 Identities=22% Similarity=0.309 Sum_probs=8.0
Q ss_pred CcEEEEEeCCCCCeEEEc
Q 003213 301 QHVLIILSDTTKEDIRVF 318 (838)
Q Consensus 301 ~~~v~vlSD~t~~ei~V~ 318 (838)
++.+.|++|-+-+.+.+|
T Consensus 1209 ~d~~~i~~ddna~klv~r 1226 (1605)
T KOG0260|consen 1209 SDLACIFSDDNAEKLVLR 1226 (1605)
T ss_pred CCCceeecccCCcceEEE
Confidence 344445555444433333
No 14
>KOG0260 consensus RNA polymerase II, large subunit [Transcription]
Probab=98.20 E-value=2.9e-05 Score=94.50 Aligned_cols=11 Identities=9% Similarity=0.051 Sum_probs=4.4
Q ss_pred ceEEEEecccc
Q 003213 541 MKVVTVDRSMI 551 (838)
Q Consensus 541 ~k~I~V~r~~l 551 (838)
|+-|-.|-+.|
T Consensus 1413 ~~d~~ld~e~l 1423 (1605)
T KOG0260|consen 1413 CFDLMLDAEKL 1423 (1605)
T ss_pred ceeeeccHHhh
Confidence 34344444433
No 15
>PRK09014 rfaH transcriptional activator RfaH; Provisional
Probab=98.00 E-value=6.4e-06 Score=82.38 Aligned_cols=88 Identities=16% Similarity=0.217 Sum_probs=67.5
Q ss_pred EecCCCceEEEEEecChHHHHHHHhcCccee-----eeeeeeeChhhhhhcccccc----ccccCCCCCEEEEecCcCCC
Q 003213 17 IALDHLKNYIYIEADKEAHVKEACKGLRNIY-----SQKVMLVPIREMTDVLAVES----KAIDLSRDTWVRMKIGNYKG 87 (838)
Q Consensus 17 ~~~~~lkGyIyVEA~~~~~V~~ai~g~~~v~-----~~~~~~Vpi~Em~~~L~~~~----~~~~l~~G~~VRik~G~ykG 87 (838)
...+=++|||||++..+...+..|+.++++. +..+..||-+||..++.... ....+++|+.|||+.|||+|
T Consensus 46 v~~plFPgYlFv~~~~~~~~~~~i~~~~gv~~~v~~g~~p~~I~~~ei~~l~~~~~~~~~~~~~~~~G~~V~I~~Gp~~g 125 (162)
T PRK09014 46 VSEPLFPNYLFVEFDPEVIHTTTIRSTRGVSHFVRFGAQPAIVPSDVIYQLSVYKPEKIVDPETPKPGDKVIITEGAFEG 125 (162)
T ss_pred EEEEcCCCeEEEEeccccCceEEEEecCCcceEeccCCCccccCHHHHHHHHhhcccccccccCCCCCCEEEEecCCCCC
Confidence 3445689999999987666666666666664 24688899999999875422 12357899999999999999
Q ss_pred ceEEEEEEeCCCCEEEEE
Q 003213 88 DLAKVVDVDNVRQRVTVK 105 (838)
Q Consensus 88 DlaqV~~vd~~~~~V~vk 105 (838)
-.|.|.+++ .+.++.|.
T Consensus 126 ~eg~v~~~~-~~~r~~v~ 142 (162)
T PRK09014 126 LQAIYTEPD-GEARSILL 142 (162)
T ss_pred cEEEEEEeC-CCeEEEEe
Confidence 999999998 56666554
No 16
>PF12815 CTD: Spt5 C-terminal nonapeptide repeat binding Spt4; PDB: 2E70_A.
Probab=97.99 E-value=1.4e-06 Score=83.62 Aligned_cols=43 Identities=44% Similarity=0.604 Sum_probs=0.0
Q ss_pred CCCCC-CCCCCCCCC---CCCCCCC--CCCCCC-CCCCCCcCCCC----CCCCC
Q 003213 563 DTPRY-GMGSETPMH---PSRTPLH--PYMTPM-RDAGATPIHDG----MRTPM 605 (838)
Q Consensus 563 ~~~~~-~~g~~tp~~---~s~TPm~--~~~TP~-~~g~~TP~hdg----~~tP~ 605 (838)
+||.| ..|++||++ ++|||.+ +++||. ++|++||+|.+ ++||+
T Consensus 14 rTPa~~~~gsrTP~~~~~g~rTPa~~~gsrTP~~~~gsrTPa~~~~~~~~~TPa 67 (123)
T PF12815_consen 14 RTPAWGNDGSRTPAPGADGSRTPAWGSGSRTPAFHDGSRTPAYGGSSSPSRTPA 67 (123)
T ss_dssp ------------------------------------------------------
T ss_pred CCcccccCCCCCcCCcCCCCcCcccccCCcCcccCCCCCCCccCCCCCCCCCcc
Confidence 56676 457777776 5777776 677777 77777777764 36664
No 17
>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=97.94 E-value=1.5e-05 Score=79.21 Aligned_cols=89 Identities=19% Similarity=0.217 Sum_probs=67.3
Q ss_pred EEecCCCceEEEEEecChHHHHHHHhcCcceee-----eeeeeeChhhhhhcccccc------ccccCCCCCEEEEecCc
Q 003213 16 VIALDHLKNYIYIEADKEAHVKEACKGLRNIYS-----QKVMLVPIREMTDVLAVES------KAIDLSRDTWVRMKIGN 84 (838)
Q Consensus 16 v~~~~~lkGyIyVEA~~~~~V~~ai~g~~~v~~-----~~~~~Vpi~Em~~~L~~~~------~~~~l~~G~~VRik~G~ 84 (838)
.+..+=++|||||+.....+.+..|..+.++.+ ..+..||-+||..+..... ....+++|+.|||+.||
T Consensus 42 ~~~~plfpgYvFv~~~~~~~~~~~i~~~~gv~~~v~~~~~p~~I~~~~i~~l~~~~~~~~~~~~~~~~~~G~~V~V~~GP 121 (159)
T TIGR01955 42 AVSEPLFPNYLFIEFDPEVDSWTTIRSTRGVSRFVRFGGHPAPVPDDLIHQLRQYEPKDSVPPATTLPYKGDKVRITDGA 121 (159)
T ss_pred EEEEecCCCeEEEEEccCCCceEEEecCCCcCEEECCCCCcccCCHHHHHHHHhccccccCCccccCCCCCCEEEEeccC
Confidence 345567999999999876666666666666543 4688899999998865321 12358899999999999
Q ss_pred CCCceEEEEEEeCCCCEEEEE
Q 003213 85 YKGDLAKVVDVDNVRQRVTVK 105 (838)
Q Consensus 85 ykGDlaqV~~vd~~~~~V~vk 105 (838)
|+|-.|.|.+++ .+.++.|.
T Consensus 122 f~g~~g~v~~~~-~~~r~~v~ 141 (159)
T TIGR01955 122 FAGFEAIFLEPD-GEKRSMLL 141 (159)
T ss_pred CCCcEEEEEEEC-CCceEEEE
Confidence 999999999998 45566664
No 18
>KOG2837 consensus Protein containing a U1-type Zn-finger and implicated in RNA splicing or processing [RNA processing and modification]
Probab=97.74 E-value=8e-07 Score=93.53 Aligned_cols=55 Identities=27% Similarity=0.452 Sum_probs=48.9
Q ss_pred ecCCC-ccEEEEEEeCCCCeEEEEeccCCCCceEEecCCCceEcCCCCCCcEEEEcCCCCCceE
Q 003213 742 RSGEE-SVVGVIREVLPDGSCRVVLGSSGNGDTITALPNEIEIVPPRKTDKIKIMGGPHRGATG 804 (838)
Q Consensus 742 ~~g~~-~~~gvI~~V~~dg~~~V~l~~~~~g~~v~v~~~~Le~V~P~kgd~VkVi~G~~rG~tG 804 (838)
.++++ +++|||++|.+++...|+ +|+ |.+|++||+|||+|||+ +|++|+|||..+
T Consensus 254 ~l~~k~K~K~vv~~vid~y~~~~K-ld~--g~~lk~dq~~lEtvip~-----~~vng~yRg~~~ 309 (309)
T KOG2837|consen 254 SLGEKYKQKGVVKKVIDDYTGQIK-LDS--GTVLKVDQEHLETVIPQ-----MIVNGAYRGSEA 309 (309)
T ss_pred hhhHHhccccHHHHHHHhhhhhee-ccC--CceecccHHHHHHHhHH-----HHhhhhhccCCC
Confidence 45666 999999999999999999 566 79999999999999999 999999999753
No 19
>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=97.73 E-value=4.5e-05 Score=56.31 Aligned_cols=32 Identities=34% Similarity=0.612 Sum_probs=30.0
Q ss_pred CCCEEEEecCcCCCceEEEEEEeCCCCEEEEE
Q 003213 74 RDTWVRMKIGNYKGDLAKVVDVDNVRQRVTVK 105 (838)
Q Consensus 74 ~G~~VRik~G~ykGDlaqV~~vd~~~~~V~vk 105 (838)
+|++|+|++|+|+|..|+|.+++.++.+|+|+
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 59999999999999999999999999998874
No 20
>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=96.93 E-value=0.00084 Score=49.56 Aligned_cols=31 Identities=48% Similarity=0.832 Sum_probs=27.8
Q ss_pred CcEEEEeecCCCCceeEEEeecCCeEEEEec
Q 003213 508 GTTVKVRLGPYKGYRGRVVDVKGQSVRVELE 538 (838)
Q Consensus 508 GktV~I~~GpyKG~~G~Vkdat~~~~rVELh 538 (838)
|.+|+|+.|||||..|.|.++.....+|.++
T Consensus 2 Gd~V~V~~G~~~G~~G~I~~i~~~~~~V~ve 32 (32)
T PF00467_consen 2 GDTVKVISGPFKGKIGKIVEIDRSKVRVTVE 32 (32)
T ss_dssp TSEEEESSSTTTTEEEEEEEEETTTTEEEES
T ss_pred CCEEEEeEcCCCCceEEEEEEECCCCEEEEC
Confidence 7899999999999999999999888777653
No 21
>smart00738 NGN In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold. In Spt5p, this domain may confer affinity for Spt4p.Spt4p
Probab=96.69 E-value=0.0011 Score=61.26 Aligned_cols=52 Identities=33% Similarity=0.492 Sum_probs=44.1
Q ss_pred EEEEEec-CCCc----------------eEEEEEecChHHHHHHHhcCcceee-----eeeeeeChhhhhhccc
Q 003213 13 IRSVIAL-DHLK----------------NYIYIEADKEAHVKEACKGLRNIYS-----QKVMLVPIREMTDVLA 64 (838)
Q Consensus 13 I~Sv~~~-~~lk----------------GyIyVEA~~~~~V~~ai~g~~~v~~-----~~~~~Vpi~Em~~~L~ 64 (838)
++++|+| ..++ ||||||++.+.+.+.+|+++++|++ ..+.+||.+||.++++
T Consensus 32 ~~~~~~P~~~~~~~~~g~~~~~~~plfpGYvFv~~~~~~~~~~~i~~~~~v~~~v~~~~~p~~v~~~e~~~l~~ 105 (106)
T smart00738 32 IVSILVPTEEVKEIRRGKKKVVERPLFPGYIFVEADLEDEVWTAIRGTPGVRGFVGGGGKPTPVPDDEIEKILK 105 (106)
T ss_pred cCEEEeeEEEEEEecCCEEEEEEEecCCCEEEEEEEeCCcHHHHHhcCCCccEECCCCCeeeECCHHHHHHHhh
Confidence 6777877 4444 9999999999999999999999875 3678999999999875
No 22
>KOG4315 consensus G-patch nucleic acid binding protein [General function prediction only]
Probab=96.65 E-value=0.00059 Score=76.25 Aligned_cols=103 Identities=21% Similarity=0.363 Sum_probs=82.5
Q ss_pred CCccCcEEE--E----ecCCC-ccEEEEEEeCCCCeEEEEeccCCCCceEE-ecCCCceEcCCC-CCCcEEEEcCCCCCc
Q 003213 732 PWFMPDILV--R----RSGEE-SVVGVIREVLPDGSCRVVLGSSGNGDTIT-ALPNEIEIVPPR-KTDKIKIMGGPHRGA 802 (838)
Q Consensus 732 ~W~~~~I~V--~----~~g~~-~~~gvI~~V~~dg~~~V~l~~~~~g~~v~-v~~~~Le~V~P~-kgd~VkVi~G~~rG~ 802 (838)
.|+..+|.| + +.|.. .++.+|.+|.+--+|.+.+.+.. +.+-- ++|+-|||++|. -|++|.|+.|.+.|.
T Consensus 332 ~wlR~dl~VR~is~d~Kgg~ly~~K~~i~dv~gp~scd~r~Dedq-~~~qg~irq~~lET~~pr~~Ge~vmvv~gkhkg~ 410 (455)
T KOG4315|consen 332 SWLRSDLKVRFISKDVKGGRLYEKKVRIVDVVGPTSCDIRMDEDQ-ELVQGNIRQELLETALPRRGGEKVMVVSGKHKGV 410 (455)
T ss_pred hhhhcceeEEeeccccccchhhhcccceecccCCCccceeccccc-cccccchHHHHHhhhcccccCceeEEEecccccc
Confidence 699999999 3 23333 78999999966568999997753 22323 899999999995 677799999999999
Q ss_pred eEEEEEEeCC--CeEEEecCCCceEEEeccccccc
Q 003213 803 TGKLIGVDGT--DGIVKVDVSLDVKILDMAILAKL 835 (838)
Q Consensus 803 tG~LisiD~~--dgiVk~d~~~~~kil~~~~L~Kl 835 (838)
.|.|++=|-. .++|++-.+.|+.-+-+..+|-.
T Consensus 411 ~g~llskd~~Ke~~~v~~~a~ndvv~~~~D~v~ey 445 (455)
T KOG4315|consen 411 YGSLLSKDLDKETGVVRLVATNDVVTVYLDQVCEY 445 (455)
T ss_pred hhhhhhhhhhhhhcceecccccchhhhhHHHHHHh
Confidence 9999988775 89998777777777777777754
No 23
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=96.17 E-value=0.0076 Score=42.39 Aligned_cols=28 Identities=46% Similarity=0.564 Sum_probs=25.7
Q ss_pred ccCCCCEEEEecCccCCceeEEEEEeCC
Q 003213 223 HFMKGDAVIVIKGDLKNLKGWVEKVDEE 250 (838)
Q Consensus 223 ~F~~GD~V~V~~Gel~~l~G~V~~V~~d 250 (838)
.|++||.|+|+.|.+++..|.|.+++.+
T Consensus 1 ~~~~G~~V~I~~G~~~g~~g~i~~i~~~ 28 (28)
T smart00739 1 KFEVGDTVRVIAGPFKGKVGKVLEVDGE 28 (28)
T ss_pred CCCCCCEEEEeECCCCCcEEEEEEEcCC
Confidence 3789999999999999999999999863
No 24
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=95.96 E-value=0.0095 Score=41.88 Aligned_cols=27 Identities=41% Similarity=0.712 Sum_probs=25.1
Q ss_pred hccCCCeEEEeccccCCceEEEEEEeC
Q 003213 275 YFEPGNHVKVVSGTQAGATGMVLKVEQ 301 (838)
Q Consensus 275 ~F~~GDhVkVi~G~~~getGlVvkVe~ 301 (838)
.|++||.|+|++|.|+|..|.|+++++
T Consensus 1 ~~~~G~~V~I~~G~~~g~~g~i~~i~~ 27 (28)
T smart00739 1 KFEVGDTVRVIAGPFKGKVGKVLEVDG 27 (28)
T ss_pred CCCCCCEEEEeECCCCCcEEEEEEEcC
Confidence 378999999999999999999999975
No 25
>PRK01191 rpl24p 50S ribosomal protein L24P; Validated
Probab=95.38 E-value=0.029 Score=53.79 Aligned_cols=39 Identities=31% Similarity=0.523 Sum_probs=35.7
Q ss_pred cccCCCCCEEEEecCcCCCceEEEEEEeCCCCEEEEEEe
Q 003213 69 AIDLSRDTWVRMKIGNYKGDLAKVVDVDNVRQRVTVKLI 107 (838)
Q Consensus 69 ~~~l~~G~~VRik~G~ykGDlaqV~~vd~~~~~V~vkli 107 (838)
...|+.||.|.|++|.|||-.|+|..|+..+++|.|+=|
T Consensus 43 ~~~IkkGD~V~VisG~~KGk~GkV~~V~~~~~~V~VeGv 81 (120)
T PRK01191 43 SLPVRKGDTVKVMRGDFKGEEGKVVEVDLKRGRIYVEGV 81 (120)
T ss_pred cceEeCCCEEEEeecCCCCceEEEEEEEcCCCEEEEeCc
Confidence 457999999999999999999999999999999999743
No 26
>CHL00141 rpl24 ribosomal protein L24; Validated
Probab=95.31 E-value=0.031 Score=50.44 Aligned_cols=37 Identities=22% Similarity=0.357 Sum_probs=34.8
Q ss_pred cccCCCCCEEEEecCcCCCceEEEEEEeCCCCEEEEE
Q 003213 69 AIDLSRDTWVRMKIGNYKGDLAKVVDVDNVRQRVTVK 105 (838)
Q Consensus 69 ~~~l~~G~~VRik~G~ykGDlaqV~~vd~~~~~V~vk 105 (838)
...|.+||-|.|.+|+|||-.|+|.+|+..++.|.|+
T Consensus 6 ~~~I~~GD~V~Vi~G~dKGK~G~V~~V~~~~~~V~Ve 42 (83)
T CHL00141 6 KMHVKIGDTVKIISGSDKGKIGEVLKIIKKSNKVIVK 42 (83)
T ss_pred eCcccCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEEc
Confidence 4579999999999999999999999999999999987
No 27
>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=95.31 E-value=0.019 Score=56.51 Aligned_cols=58 Identities=24% Similarity=0.341 Sum_probs=44.2
Q ss_pred ccCCCCEEEEecCccCCceeEEEEEeCCe--EEEeeCCCCCCceeEEcchhhhhhccCCC
Q 003213 223 HFMKGDAVIVIKGDLKNLKGWVEKVDEEN--VHIRPEMKGLPKTLAVNSKELCKYFEPGN 280 (838)
Q Consensus 223 ~F~~GD~V~V~~Gel~~l~G~V~~V~~d~--V~i~~~~~~l~~~i~v~~~~LrK~F~~GD 280 (838)
.|++||.|+|++|-++|+.|.|+.++++. |++.-......-+++++.++|+|.=+.||
T Consensus 86 ~~~~Gd~V~I~~GPf~G~~g~v~~~d~~k~~v~v~l~~~~~~~~v~v~~~~l~~~~~~~~ 145 (145)
T TIGR00405 86 SIKKGDIVEIISGPFKGERAKVIRVDESKEEVTLELIEAAVPIPVTVKGDQVRIIQKEAD 145 (145)
T ss_pred ccCCCCEEEEeecCCCCCeEEEEEEcCCCCEEEEEEEEcCccceEEEeeeEEEEecccCC
Confidence 49999999999999999999999998663 44433333334458999999987655554
No 28
>PRK12281 rplX 50S ribosomal protein L24; Reviewed
Probab=94.77 E-value=0.051 Score=48.26 Aligned_cols=36 Identities=28% Similarity=0.376 Sum_probs=34.1
Q ss_pred cCCCCCEEEEecCcCCCceEEEEEEeCCCCEEEEEE
Q 003213 71 DLSRDTWVRMKIGNYKGDLAKVVDVDNVRQRVTVKL 106 (838)
Q Consensus 71 ~l~~G~~VRik~G~ykGDlaqV~~vd~~~~~V~vkl 106 (838)
.|..||-|.|.+|++||-.|+|..|+..+++|.|+=
T Consensus 6 ~I~kGD~V~Vi~G~dKGK~G~V~~V~~~~~~V~Veg 41 (76)
T PRK12281 6 KVKKGDMVKVIAGDDKGKTGKVLAVLPKKNRVIVEG 41 (76)
T ss_pred cccCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEEcC
Confidence 688999999999999999999999999999999873
No 29
>PRK09014 rfaH transcriptional activator RfaH; Provisional
Probab=94.46 E-value=0.064 Score=53.72 Aligned_cols=52 Identities=19% Similarity=0.256 Sum_probs=42.4
Q ss_pred ccCCCCEEEEecCccCCceeEEEEEeCC-eEEEeeCCCCCCceeEEcchhhhh
Q 003213 223 HFMKGDAVIVIKGDLKNLKGWVEKVDEE-NVHIRPEMKGLPKTLAVNSKELCK 274 (838)
Q Consensus 223 ~F~~GD~V~V~~Gel~~l~G~V~~V~~d-~V~i~~~~~~l~~~i~v~~~~LrK 274 (838)
.|++||+|+|++|-++|+.|.|..++++ .+.|.-+.=+..-+++++..+|.|
T Consensus 109 ~~~~G~~V~I~~Gp~~g~eg~v~~~~~~~r~~v~v~~~gr~~~v~v~~~~~~~ 161 (162)
T PRK09014 109 TPKPGDKVIITEGAFEGLQAIYTEPDGEARSILLLNLLNKQVKHSVDNTQFRK 161 (162)
T ss_pred CCCCCCEEEEecCCCCCcEEEEEEeCCCeEEEEeehhhCCcEEEEECHHHeec
Confidence 4999999999999999999999999866 555665544445678888888865
No 30
>PRK00004 rplX 50S ribosomal protein L24; Reviewed
Probab=94.38 E-value=0.064 Score=50.49 Aligned_cols=32 Identities=25% Similarity=0.431 Sum_probs=28.2
Q ss_pred eecCCCEEEEEcCCCCCceeeEEEEECC--EEEE
Q 003213 399 TVAVKDVVRIVEGPCKGKQGPVEHIYRG--ILFI 430 (838)
Q Consensus 399 ~i~~gd~Vki~~Gp~kG~~G~Vkhi~r~--~lFL 430 (838)
.|..||+|.|+.|++||++|+|+.|++. .+++
T Consensus 4 ~i~kGD~V~Vi~G~dKGk~G~V~~V~~~~~~V~V 37 (105)
T PRK00004 4 KIKKGDTVIVIAGKDKGKRGKVLKVLPKKNKVIV 37 (105)
T ss_pred cccCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEE
Confidence 5889999999999999999999999954 3555
No 31
>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=94.37 E-value=0.073 Score=53.74 Aligned_cols=53 Identities=26% Similarity=0.387 Sum_probs=43.0
Q ss_pred cccCCCCEEEEecCccCCceeEEEEEe-CC-eEEEeeCCCCCCceeEEcchhhhh
Q 003213 222 GHFMKGDAVIVIKGDLKNLKGWVEKVD-EE-NVHIRPEMKGLPKTLAVNSKELCK 274 (838)
Q Consensus 222 ~~F~~GD~V~V~~Gel~~l~G~V~~V~-~d-~V~i~~~~~~l~~~i~v~~~~LrK 274 (838)
..|++||.|+|++|-|+|+.|.|++++ ++ .++|.-+.=+....+++...+|+|
T Consensus 118 ~~~~~G~~V~I~~Gpf~G~~g~v~~~~~~~~r~~V~v~~~g~~~~v~v~~~~l~~ 172 (172)
T TIGR00922 118 IDFEVGEQVRVNDGPFANFTGTVEEVDYEKSKLKVSVSIFGRETPVELEFSQVEK 172 (172)
T ss_pred cCCCCCCEEEEeecCCCCcEEEEEEEcCCCCEEEEEEEECCCceEEEEcHHHeeC
Confidence 459999999999999999999999998 34 777777654445568888888764
No 32
>PRK12281 rplX 50S ribosomal protein L24; Reviewed
Probab=94.06 E-value=0.088 Score=46.74 Aligned_cols=34 Identities=32% Similarity=0.526 Sum_probs=30.9
Q ss_pred CCCCcEEEEcCCCCCceEEEEEEeCCCeEEEecC
Q 003213 787 RKTDKIKIMGGPHRGATGKLIGVDGTDGIVKVDV 820 (838)
Q Consensus 787 ~kgd~VkVi~G~~rG~tG~LisiD~~dgiVk~d~ 820 (838)
.+||+|+||.|.++|.+|+++.||..++-|-+++
T Consensus 8 ~kGD~V~Vi~G~dKGK~G~V~~V~~~~~~V~Veg 41 (76)
T PRK12281 8 KKGDMVKVIAGDDKGKTGKVLAVLPKKNRVIVEG 41 (76)
T ss_pred cCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEEcC
Confidence 6899999999999999999999999988776654
No 33
>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=94.02 E-value=0.063 Score=51.23 Aligned_cols=28 Identities=29% Similarity=0.501 Sum_probs=25.3
Q ss_pred ccCCCeEEEeccccCCceEEEEEEeCcE
Q 003213 276 FEPGNHVKVVSGTQAGATGMVLKVEQHV 303 (838)
Q Consensus 276 F~~GDhVkVi~G~~~getGlVvkVe~~~ 303 (838)
++.||.|+|++|.+.|.+|.|++|....
T Consensus 42 IkkGD~V~Vi~Gk~KGk~GkV~~V~~~~ 69 (114)
T TIGR01080 42 VRKGDKVRIMRGDFKGHEGKVSKVDLKR 69 (114)
T ss_pred eecCCEEEEecCCCCCCEEEEEEEEcCC
Confidence 4899999999999999999999997543
No 34
>COG0250 NusG Transcription antiterminator [Transcription]
Probab=93.93 E-value=0.093 Score=53.86 Aligned_cols=54 Identities=31% Similarity=0.499 Sum_probs=44.6
Q ss_pred ccccCCCCEEEEecCccCCceeEEEEEeCC--eEEEeeCCCCCCceeEEcchhhhh
Q 003213 221 KGHFMKGDAVIVIKGDLKNLKGWVEKVDEE--NVHIRPEMKGLPKTLAVNSKELCK 274 (838)
Q Consensus 221 ~~~F~~GD~V~V~~Gel~~l~G~V~~V~~d--~V~i~~~~~~l~~~i~v~~~~LrK 274 (838)
...|.+||.|+|+.|-++|..|+|+.|+.+ .++++-..-+..-++++..++++|
T Consensus 121 ~~~~e~Gd~VrI~~GpFa~f~g~V~evd~ek~~~~v~v~ifgr~tPVel~~~qVek 176 (178)
T COG0250 121 KVDFEPGDVVRIIDGPFAGFKAKVEEVDEEKGKLKVEVSIFGRPTPVELEFDQVEK 176 (178)
T ss_pred cccCCCCCEEEEeccCCCCccEEEEEEcCcCcEEEEEEEEeCCceEEEEehhhEEE
Confidence 478999999999999999999999999998 566665555555677888777765
No 35
>CHL00141 rpl24 ribosomal protein L24; Validated
Probab=93.64 E-value=0.12 Score=46.77 Aligned_cols=34 Identities=24% Similarity=0.428 Sum_probs=31.2
Q ss_pred CCCCcEEEEcCCCCCceEEEEEEeCCCeEEEecC
Q 003213 787 RKTDKIKIMGGPHRGATGKLIGVDGTDGIVKVDV 820 (838)
Q Consensus 787 ~kgd~VkVi~G~~rG~tG~LisiD~~dgiVk~d~ 820 (838)
.+||+|.||.|.++|.+|+++.||...+-|-+++
T Consensus 10 ~~GD~V~Vi~G~dKGK~G~V~~V~~~~~~V~Veg 43 (83)
T CHL00141 10 KIGDTVKIISGSDKGKIGEVLKIIKKSNKVIVKG 43 (83)
T ss_pred cCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEEcC
Confidence 6899999999999999999999999988777764
No 36
>PRK00004 rplX 50S ribosomal protein L24; Reviewed
Probab=93.55 E-value=0.12 Score=48.70 Aligned_cols=35 Identities=26% Similarity=0.333 Sum_probs=33.6
Q ss_pred cCCCCCEEEEecCcCCCceEEEEEEeCCCCEEEEE
Q 003213 71 DLSRDTWVRMKIGNYKGDLAKVVDVDNVRQRVTVK 105 (838)
Q Consensus 71 ~l~~G~~VRik~G~ykGDlaqV~~vd~~~~~V~vk 105 (838)
.|..||.|.|.+|.+||-.|+|.+|+..+++|.|+
T Consensus 4 ~i~kGD~V~Vi~G~dKGk~G~V~~V~~~~~~V~Ve 38 (105)
T PRK00004 4 KIKKGDTVIVIAGKDKGKRGKVLKVLPKKNKVIVE 38 (105)
T ss_pred cccCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEEc
Confidence 68899999999999999999999999999999997
No 37
>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=93.46 E-value=0.14 Score=48.84 Aligned_cols=38 Identities=34% Similarity=0.462 Sum_probs=34.6
Q ss_pred cccCCCCCEEEEecCcCCCceEEEEEEeCCCCEEEEEE
Q 003213 69 AIDLSRDTWVRMKIGNYKGDLAKVVDVDNVRQRVTVKL 106 (838)
Q Consensus 69 ~~~l~~G~~VRik~G~ykGDlaqV~~vd~~~~~V~vkl 106 (838)
...|+.||-|+|++|.|||-.|+|.+|+..++.|.|+=
T Consensus 39 ~~~IkkGD~V~Vi~Gk~KGk~GkV~~V~~~~~~V~Veg 76 (114)
T TIGR01080 39 ALPVRKGDKVRIMRGDFKGHEGKVSKVDLKRYRIYVEG 76 (114)
T ss_pred cceeecCCEEEEecCCCCCCEEEEEEEEcCCCEEEEcC
Confidence 34799999999999999999999999999999888863
No 38
>PRK05609 nusG transcription antitermination protein NusG; Validated
Probab=93.44 E-value=0.13 Score=52.13 Aligned_cols=53 Identities=25% Similarity=0.376 Sum_probs=42.7
Q ss_pred cccCCCCEEEEecCccCCceeEEEEEeC-C-eEEEeeCCCCCCceeEEcchhhhh
Q 003213 222 GHFMKGDAVIVIKGDLKNLKGWVEKVDE-E-NVHIRPEMKGLPKTLAVNSKELCK 274 (838)
Q Consensus 222 ~~F~~GD~V~V~~Gel~~l~G~V~~V~~-d-~V~i~~~~~~l~~~i~v~~~~LrK 274 (838)
..|++||.|+|++|-|+|+.|.|++++. . .+++.-+.=+-.-.+++...+|+|
T Consensus 125 ~~~~~Gd~VrI~~GPf~G~~g~v~~i~~~~~r~~v~l~~~G~~~~v~l~~~~l~~ 179 (181)
T PRK05609 125 VDFEVGEMVRVIDGPFADFNGTVEEVDYEKSKLKVLVSIFGRETPVELEFSQVEK 179 (181)
T ss_pred cCCCCCCEEEEeccCCCCCEEEEEEEeCCCCEEEEEEEECCCceEEEEchHHEEE
Confidence 5699999999999999999999999973 3 677776654444567888877765
No 39
>PRK08559 nusG transcription antitermination protein NusG; Validated
Probab=93.11 E-value=0.12 Score=51.56 Aligned_cols=52 Identities=27% Similarity=0.374 Sum_probs=38.5
Q ss_pred cccCCCCEEEEecCccCCceeEEEEEeCCe--EEEeeCCCCCCceeEEcchhhh
Q 003213 222 GHFMKGDAVIVIKGDLKNLKGWVEKVDEEN--VHIRPEMKGLPKTLAVNSKELC 273 (838)
Q Consensus 222 ~~F~~GD~V~V~~Gel~~l~G~V~~V~~d~--V~i~~~~~~l~~~i~v~~~~Lr 273 (838)
..|++||.|+|++|-++|..|.|++++.+. +++.--.....-+++++.++|+
T Consensus 93 ~~~~~G~~V~I~~Gpf~g~~g~V~~vd~~k~~v~v~ll~~~~~~pv~v~~~~~~ 146 (153)
T PRK08559 93 EGIKEGDIVELIAGPFKGEKARVVRVDESKEEVTVELLEAAVPIPVTVRGDQVR 146 (153)
T ss_pred cCCCCCCEEEEeccCCCCceEEEEEEcCCCCEEEEEEECCcceeeEEEeccEEE
Confidence 469999999999999999999999998763 3333222222334888888773
No 40
>PTZ00194 60S ribosomal protein L26; Provisional
Probab=93.07 E-value=0.17 Score=49.99 Aligned_cols=42 Identities=24% Similarity=0.273 Sum_probs=37.6
Q ss_pred cccCCCCCEEEEecCcCCCceEEEEEEeCCCCEEEEEEeecc
Q 003213 69 AIDLSRDTWVRMKIGNYKGDLAKVVDVDNVRQRVTVKLIPRI 110 (838)
Q Consensus 69 ~~~l~~G~~VRik~G~ykGDlaqV~~vd~~~~~V~vkliPRi 110 (838)
...|+.||-|.|++|.|||-.|+|..|+..+++|.|+=|-+.
T Consensus 44 s~~IkkGD~V~Vi~Gk~KGk~GkV~~V~~k~~~ViVEgvn~~ 85 (143)
T PTZ00194 44 SMPVRKDDEVMVVRGHHKGREGKVTAVYRKKWVIHIEKITRE 85 (143)
T ss_pred cceeecCCEEEEecCCCCCCceEEEEEEcCCCEEEEeCeEEE
Confidence 347899999999999999999999999999999999866554
No 41
>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=93.04 E-value=0.18 Score=50.09 Aligned_cols=51 Identities=20% Similarity=0.234 Sum_probs=39.7
Q ss_pred cccCCCCEEEEecCccCCceeEEEEEeCC-eEEEeeCCCCCCceeEEcchhh
Q 003213 222 GHFMKGDAVIVIKGDLKNLKGWVEKVDEE-NVHIRPEMKGLPKTLAVNSKEL 272 (838)
Q Consensus 222 ~~F~~GD~V~V~~Gel~~l~G~V~~V~~d-~V~i~~~~~~l~~~i~v~~~~L 272 (838)
..|++||.|+|++|-++|+.|.|+.+++. .+.+.-+.=+..-.+++..++|
T Consensus 107 ~~~~~G~~V~V~~GPf~g~~g~v~~~~~~~r~~v~l~~~gr~~~v~~~~~~~ 158 (159)
T TIGR01955 107 TLPYKGDKVRITDGAFAGFEAIFLEPDGEKRSMLLLNMIGKQIKVSVPNTSV 158 (159)
T ss_pred cCCCCCCEEEEeccCCCCcEEEEEEECCCceEEEEEhhhCCceEEEecHHHc
Confidence 46999999999999999999999999855 5666665443334577776665
No 42
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=92.83 E-value=0.5 Score=57.16 Aligned_cols=12 Identities=33% Similarity=0.800 Sum_probs=5.8
Q ss_pred CcEEEEEEEecc
Q 003213 349 NSFGVIIRVESE 360 (838)
Q Consensus 349 ~~vGvIv~ier~ 360 (838)
+++|.++-+.++
T Consensus 222 n~~Gl~~vL~~e 233 (1102)
T KOG1924|consen 222 NKFGLVLVLRRE 233 (1102)
T ss_pred cccceeeeecCC
Confidence 455555444444
No 43
>KOG1708 consensus Mitochondrial/chloroplast ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=92.73 E-value=0.21 Score=51.63 Aligned_cols=81 Identities=25% Similarity=0.332 Sum_probs=55.1
Q ss_pred ccccCCCCEEEEecCccCCceeEEEEEeCCeEEEeeCCCCCCceeEEcchhhhhhccCCCeEEEeccccCCceEEEEEEe
Q 003213 221 KGHFMKGDAVIVIKGDLKNLKGWVEKVDEENVHIRPEMKGLPKTLAVNSKELCKYFEPGNHVKVVSGTQAGATGMVLKVE 300 (838)
Q Consensus 221 ~~~F~~GD~V~V~~Gel~~l~G~V~~V~~d~V~i~~~~~~l~~~i~v~~~~LrK~F~~GDhVkVi~G~~~getGlVvkVe 300 (838)
...|..||.|+|+.|.-+|-+|.|+.|.-+.-.|..+ +|+- |-+-+++.-+|+-|.|++.|
T Consensus 70 dw~ff~GDtVeVlvGkDkGkqG~Vtqv~r~~s~VvV~--gln~-----------------k~r~~gsekeg~pgtivk~E 130 (236)
T KOG1708|consen 70 DWHFFFGDTVEVLVGKDKGKQGEVTQVIRHRSWVVVK--GLNT-----------------KYRHMGSEKEGEPGTIVKSE 130 (236)
T ss_pred ceeEecCCEEEEEecccCCccceEEEEeecCceEEEc--ccch-----------------hhhhhcccccCCCceEEeec
Confidence 3689999999999999999999999997653333322 3321 11234667789999999998
Q ss_pred CcEEEEEeCCCCCeEEEcccccccc
Q 003213 301 QHVLIILSDTTKEDIRVFADDVVES 325 (838)
Q Consensus 301 ~~~v~vlSD~t~~ei~V~~~dL~~~ 325 (838)
.-.- .+++..-|-|+|.+-|
T Consensus 131 aPlh-----vsk~VmLvdp~d~q~t 150 (236)
T KOG1708|consen 131 APLH-----VSKQVMLVDPEDDQPT 150 (236)
T ss_pred CCce-----ecceeEEECccccCCc
Confidence 6321 1234455666666554
No 44
>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=91.99 E-value=0.25 Score=46.50 Aligned_cols=35 Identities=26% Similarity=0.344 Sum_probs=33.2
Q ss_pred cCCCCCEEEEecCcCCCceEEEEEEeCCCCEEEEE
Q 003213 71 DLSRDTWVRMKIGNYKGDLAKVVDVDNVRQRVTVK 105 (838)
Q Consensus 71 ~l~~G~~VRik~G~ykGDlaqV~~vd~~~~~V~vk 105 (838)
.|..||-|.|.+|++||-.|.|..|+..+++|.|+
T Consensus 3 ~ikkGD~V~Vi~G~dKGK~G~V~~V~~~~~~V~Ve 37 (104)
T TIGR01079 3 KIKKGDTVKVISGKDKGKRGKVLKVLPKTNKVIVE 37 (104)
T ss_pred cccCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEEC
Confidence 57899999999999999999999999999999987
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=91.78 E-value=0.29 Score=52.78 Aligned_cols=52 Identities=25% Similarity=0.448 Sum_probs=42.8
Q ss_pred cccCCCCEEEEecCccCCceeEEEEEeC--CeEEEeeCCCCCCceeEEcchhhh
Q 003213 222 GHFMKGDAVIVIKGDLKNLKGWVEKVDE--ENVHIRPEMKGLPKTLAVNSKELC 273 (838)
Q Consensus 222 ~~F~~GD~V~V~~Gel~~l~G~V~~V~~--d~V~i~~~~~~l~~~i~v~~~~Lr 273 (838)
..|.+||.|+|++|-+.|+.|.|+.++. ..+.|+-+.-+...++++...+|.
T Consensus 204 ~~f~vGd~VrI~dGPF~GfeG~I~eid~~k~Rv~VlV~IfGR~TpVeL~~~qVe 257 (258)
T TIGR01956 204 SKFRVGNFVKIVDGPFKGIVGKIKKIDQEKKKAIVEVEILGKSVDVDLNFKHLK 257 (258)
T ss_pred cCCCCCCEEEEEecCCCCcEEEEEEEeCCCCEEEEEEEecCCcEEEEEchHHEE
Confidence 4699999999999999999999999984 478877765555567888777764
No 46
>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=91.22 E-value=0.34 Score=45.56 Aligned_cols=34 Identities=29% Similarity=0.497 Sum_probs=30.7
Q ss_pred CCCCcEEEEcCCCCCceEEEEEEeCCCeEEEecC
Q 003213 787 RKTDKIKIMGGPHRGATGKLIGVDGTDGIVKVDV 820 (838)
Q Consensus 787 ~kgd~VkVi~G~~rG~tG~LisiD~~dgiVk~d~ 820 (838)
.+||+|.||.|.+.|.+|+++.|+...+-|-+++
T Consensus 5 kkGD~V~Vi~G~dKGK~G~V~~V~~~~~~V~Veg 38 (104)
T TIGR01079 5 KKGDTVKVISGKDKGKRGKVLKVLPKTNKVIVEG 38 (104)
T ss_pred cCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEECC
Confidence 5899999999999999999999999988776754
No 47
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=91.14 E-value=0.95 Score=54.90 Aligned_cols=12 Identities=25% Similarity=0.473 Sum_probs=5.9
Q ss_pred CceEEEEEEeCc
Q 003213 291 GATGMVLKVEQH 302 (838)
Q Consensus 291 getGlVvkVe~~ 302 (838)
+..|+++-..++
T Consensus 222 n~~Gl~~vL~~e 233 (1102)
T KOG1924|consen 222 NKFGLVLVLRRE 233 (1102)
T ss_pred cccceeeeecCC
Confidence 455555544433
No 48
>PRK01191 rpl24p 50S ribosomal protein L24P; Validated
Probab=90.94 E-value=0.36 Score=46.45 Aligned_cols=34 Identities=38% Similarity=0.635 Sum_probs=30.7
Q ss_pred CCCCcEEEEcCCCCCceEEEEEEeCCCeEEEecC
Q 003213 787 RKTDKIKIMGGPHRGATGKLIGVDGTDGIVKVDV 820 (838)
Q Consensus 787 ~kgd~VkVi~G~~rG~tG~LisiD~~dgiVk~d~ 820 (838)
.+||.|+||.|.+.|.+|+++.||..++-|-+++
T Consensus 47 kkGD~V~VisG~~KGk~GkV~~V~~~~~~V~VeG 80 (120)
T PRK01191 47 RKGDTVKVMRGDFKGEEGKVVEVDLKRGRIYVEG 80 (120)
T ss_pred eCCCEEEEeecCCCCceEEEEEEEcCCCEEEEeC
Confidence 6899999999999999999999999988776654
No 49
>PRK06763 F0F1 ATP synthase subunit alpha; Validated
Probab=89.92 E-value=1.7 Score=45.15 Aligned_cols=98 Identities=19% Similarity=0.249 Sum_probs=64.0
Q ss_pred cCCceeEEEEEeCCeEEEeeCCCCCCceeEEcchhhhhhccCCCeEEEe----------------------cccc-----
Q 003213 237 LKNLKGWVEKVDEENVHIRPEMKGLPKTLAVNSKELCKYFEPGNHVKVV----------------------SGTQ----- 289 (838)
Q Consensus 237 l~~l~G~V~~V~~d~V~i~~~~~~l~~~i~v~~~~LrK~F~~GDhVkVi----------------------~G~~----- 289 (838)
+.-..|+|+.|+.+.+.|.++.- .+++.+- -+....+++||.||+. .|.|
T Consensus 39 ~~tiEGrVvEV~~~~i~iesk~y--n~~v~i~-~d~~~nvKVGD~VKaTG~m~rnf~~ym~A~sVEk~~~~~G~h~~e~g 115 (213)
T PRK06763 39 FSTIEGRVVEVDNGVIVIKSKQY--EEPVSVY-IDSLSNVKVGDEVKATGSMMRNFTEYMVATAVENTTNKLGMHMKEDG 115 (213)
T ss_pred cceeeeEEEEEeCCEEEEEeccC--CCceEEE-ecCCCCcccCcEEEEchHHHHhhHHhhhhhhheeeccCcceeecccC
Confidence 45678999999999999998743 6777776 4555667999999998 2444
Q ss_pred --CCceEEEEEEeCc---------EEEE-EeCCCCCeEEEcccccccccccccccccCCceEecceEEeCC
Q 003213 290 --AGATGMVLKVEQH---------VLII-LSDTTKEDIRVFADDVVESSEVTTGITKIGDYELRDLVLLDN 348 (838)
Q Consensus 290 --~getGlVvkVe~~---------~v~v-lSD~t~~ei~V~~~dL~~~~e~~~g~d~~g~y~l~DLVqld~ 348 (838)
+=..|-|.+|... .|.| ..+..++...| -.-+.....|.++|.|+++.
T Consensus 116 ~pdYvIG~Iskv~k~~~~~~~~~dyVvV~YP~~~G~~~~V-----------~V~LT~GQkFnVGDkVKV~~ 175 (213)
T PRK06763 116 SPDYVIGEVSKVYTMEDDGDGATKYVVVEYPSLNGKKLII-----------DVFLTKGQVFHVGDKVKVDM 175 (213)
T ss_pred CcceEEEEEEEecccccCCCCcccEEEEEcCCCCCCeeEE-----------EEEeccCCEEecCCEEEEEe
Confidence 4567888888541 2222 23333332222 12233346799999999863
No 50
>COG0198 RplX Ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=89.65 E-value=0.49 Score=44.47 Aligned_cols=32 Identities=41% Similarity=0.358 Sum_probs=28.3
Q ss_pred cccCCCCEEEEecCccCCceeEEEEEeCCeEE
Q 003213 222 GHFMKGDAVIVIKGDLKNLKGWVEKVDEENVH 253 (838)
Q Consensus 222 ~~F~~GD~V~V~~Gel~~l~G~V~~V~~d~V~ 253 (838)
..++.||.|.|+.|..+|-+|+|++|....|.
T Consensus 3 ~~IrkGD~V~Vi~GkdKGk~GkVl~v~~k~V~ 34 (104)
T COG0198 3 MKVKKGDTVKVIAGKDKGKEGKVLKVLPKKVV 34 (104)
T ss_pred cceecCCEEEEEecCCCCcceEEEEEecCeEE
Confidence 46789999999999999999999999877633
No 51
>PTZ00194 60S ribosomal protein L26; Provisional
Probab=88.57 E-value=0.65 Score=46.00 Aligned_cols=34 Identities=26% Similarity=0.568 Sum_probs=30.5
Q ss_pred CCCCcEEEEcCCCCCceEEEEEEeCCCeEEEecC
Q 003213 787 RKTDKIKIMGGPHRGATGKLIGVDGTDGIVKVDV 820 (838)
Q Consensus 787 ~kgd~VkVi~G~~rG~tG~LisiD~~dgiVk~d~ 820 (838)
.+||.|+||.|.++|.+|+++.||..++-|-+++
T Consensus 48 kkGD~V~Vi~Gk~KGk~GkV~~V~~k~~~ViVEg 81 (143)
T PTZ00194 48 RKDDEVMVVRGHHKGREGKVTAVYRKKWVIHIEK 81 (143)
T ss_pred ecCCEEEEecCCCCCCceEEEEEEcCCCEEEEeC
Confidence 6899999999999999999999999988665654
No 52
>COG0198 RplX Ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=87.69 E-value=0.78 Score=43.18 Aligned_cols=33 Identities=27% Similarity=0.360 Sum_probs=29.8
Q ss_pred cCCCCCEEEEecCcCCCceEEEEEEeCCCCEEEEE
Q 003213 71 DLSRDTWVRMKIGNYKGDLAKVVDVDNVRQRVTVK 105 (838)
Q Consensus 71 ~l~~G~~VRik~G~ykGDlaqV~~vd~~~~~V~vk 105 (838)
.|..||.|.|++|.+||-.|+|.+|+... |.|+
T Consensus 4 ~IrkGD~V~Vi~GkdKGk~GkVl~v~~k~--V~VE 36 (104)
T COG0198 4 KVKKGDTVKVIAGKDKGKEGKVLKVLPKK--VVVE 36 (104)
T ss_pred ceecCCEEEEEecCCCCcceEEEEEecCe--EEEE
Confidence 57789999999999999999999999876 7765
No 53
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=86.45 E-value=27 Score=44.39 Aligned_cols=105 Identities=15% Similarity=0.198 Sum_probs=55.8
Q ss_pred cccCCCCEEEEecCccCCceeEEEEEeCC--eEEEeeCCCCCCceeEEcchhhhhhccCCCeEEEeccccCCceEEEEEE
Q 003213 222 GHFMKGDAVIVIKGDLKNLKGWVEKVDEE--NVHIRPEMKGLPKTLAVNSKELCKYFEPGNHVKVVSGTQAGATGMVLKV 299 (838)
Q Consensus 222 ~~F~~GD~V~V~~Gel~~l~G~V~~V~~d--~V~i~~~~~~l~~~i~v~~~~LrK~F~~GDhVkVi~G~~~getGlVvkV 299 (838)
..|++||.|+| +|+.|+.+ .+.+..+.. +.+ +...+-+.|++||.| +|.|+++
T Consensus 709 ~~~kvGq~Vkv----------kVl~ID~e~rrI~LS~K~l-~~d----pw~~~~~~~~vG~iV----------~GkV~~v 763 (863)
T PRK12269 709 HELEVGKEIEC----------MVIECDPQARRIRLGVKQL-SDN----PWQVFANAYGVGSTV----------EGEVSSV 763 (863)
T ss_pred hccCCCCEEEE----------EEEEEeccCCEEEEEeccc-ccC----hHHHHHhhCCCCCEE----------EEEEEEE
Confidence 46999999987 68999865 344443311 012 344455668899975 4556666
Q ss_pred eCcEEEE-EeCCCCCeEEEcccccccccccccccccCCceEecceEEeCCCcEEEEEEEecc
Q 003213 300 EQHVLII-LSDTTKEDIRVFADDVVESSEVTTGITKIGDYELRDLVLLDNNSFGVIIRVESE 360 (838)
Q Consensus 300 e~~~v~v-lSD~t~~ei~V~~~dL~~~~e~~~g~d~~g~y~l~DLVqld~~~vGvIv~ier~ 360 (838)
.+.-+.| |.+ +-+-.|..++|........ .+....|++||.|.+ +|+.++.+
T Consensus 764 ~~~GvFVeL~~--gVeGlI~~s~lsdd~~~~~-~~~~~~f~vGD~V~v------~Vl~iD~~ 816 (863)
T PRK12269 764 TDFGIFVRVPG--GVEGLVRKQHLVENRDGDP-GEALRKYAVGDRVKA------VIVDMNVK 816 (863)
T ss_pred ecCeEEEEcCC--CeEEEEEHHHcCCcccccc-hhhccccCCCCEEEE------EEEEEEcC
Confidence 5543322 212 2233333344432111000 011235888888874 66666654
No 54
>cd04467 S1_aIF5A S1_aIF5A: Archaeal translation Initiation Factor 5A (aIF5A), S1-like RNA-binding domain. aIF5A is a homolog of eukaryotic eIF5A. IF5A is the only protein known to have the unusual amino acid hypusine. Hypusine is a post-translationally modified lysine and is essential for IF5A function. In yeast, eIF5A interacts with components of the 80S ribosome and translation elongation factors 2 (eEF2) in a hypusine-dependent manner. This C-terminal S1 domain resembles the cold-shock domain which binds RNA. Moreover, IF5A prefers binding to the actively translating ribosome. This evidence suggests that IF5A plays a role in translation elongation instead of translation initiation as previously proposed.
Probab=82.89 E-value=3.1 Score=35.15 Aligned_cols=45 Identities=22% Similarity=0.315 Sum_probs=34.3
Q ss_pred ceeEEEEEeCCeEEEeeCCCCCCceeEEcc-hhhhhhccCCCeEEEec
Q 003213 240 LKGWVEKVDEENVHIRPEMKGLPKTLAVNS-KELCKYFEPGNHVKVVS 286 (838)
Q Consensus 240 l~G~V~~V~~d~V~i~~~~~~l~~~i~v~~-~~LrK~F~~GDhVkVi~ 286 (838)
-+|.|++|.+|.|.+| |.+. -++++++. .+++-.+++|+.|.++.
T Consensus 4 ~~aqVisi~g~~vQlM-D~eT-YeT~ev~~p~~~~~~i~~G~eV~y~~ 49 (57)
T cd04467 4 KTGQVLSIMGDVVQLM-DLET-YETFEVPIPEEIKDKLEPGKEVEYWE 49 (57)
T ss_pred eEEEEEEEcCCEEEEe-cccc-ceeEEEecchhhcccCCCCCEEEEEe
Confidence 3689999999999999 5553 34566665 45656699999998875
No 55
>PTZ00223 40S ribosomal protein S4; Provisional
Probab=77.56 E-value=4.1 Score=44.57 Aligned_cols=40 Identities=25% Similarity=0.457 Sum_probs=30.1
Q ss_pred ccCCCeEEEeccccCCceEEEEEEeCc----EEEEEeCCCCCeE
Q 003213 276 FEPGNHVKVVSGTQAGATGMVLKVEQH----VLIILSDTTKEDI 315 (838)
Q Consensus 276 F~~GDhVkVi~G~~~getGlVvkVe~~----~v~vlSD~t~~ei 315 (838)
|++|..|-|++|+|.|.+|.|+.++.. ..+.+.|..++++
T Consensus 172 fe~G~l~~vtgG~n~GriG~I~~i~~~~~~~~iv~i~d~~g~~F 215 (273)
T PTZ00223 172 NRNGKVVMVTGGANRGRIGEIVSIERHPGAFDIARLKDASGHEF 215 (273)
T ss_pred cCCCCEEEEECCeeceeEEEEEEEEecCCCCCEEEEEeCCCCeE
Confidence 799999999999999999999998642 2344445444433
No 56
>COG1471 RPS4A Ribosomal protein S4E [Translation, ribosomal structure and biogenesis]
Probab=77.18 E-value=4.9 Score=42.81 Aligned_cols=36 Identities=25% Similarity=0.528 Sum_probs=29.1
Q ss_pred EEcchhhhhh--ccCCCeEEEeccccCCceEEEEEEeC
Q 003213 266 AVNSKELCKY--FEPGNHVKVVSGTQAGATGMVLKVEQ 301 (838)
Q Consensus 266 ~v~~~~LrK~--F~~GDhVkVi~G~~~getGlVvkVe~ 301 (838)
+++.+++..+ |++|..|-|++|+|.|++|.|+.++-
T Consensus 162 ~lp~~~I~~~i~fe~g~~~~vtgG~h~G~~G~I~~I~~ 199 (241)
T COG1471 162 SLPEQKIVEHIKFEEGALVYVTGGRHVGRVGTIVEIEI 199 (241)
T ss_pred eCCChhheeEeccCCCcEEEEECCccccceEEEEEEEE
Confidence 3444555554 78999999999999999999999973
No 57
>cd04454 S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein, and Rrp40 and Csl4 proteins, also represented in this group, are subunits of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=76.68 E-value=6.7 Score=34.55 Aligned_cols=51 Identities=22% Similarity=0.247 Sum_probs=31.6
Q ss_pred CCCCEEEEecCccCCceeEEEEEeCCeEEEeeCC--CCCC--ceeE-EcchhhhhhccCCCeEEEe
Q 003213 225 MKGDAVIVIKGDLKNLKGWVEKVDEENVHIRPEM--KGLP--KTLA-VNSKELCKYFEPGNHVKVV 285 (838)
Q Consensus 225 ~~GD~V~V~~Gel~~l~G~V~~V~~d~V~i~~~~--~~l~--~~i~-v~~~~LrK~F~~GDhVkVi 285 (838)
++||.| .|+|++|.++.+.+.... +.+- .++. -..++++..|++||.+++.
T Consensus 5 ~~GdiV----------~G~V~~v~~~~~~V~i~~~~~g~l~~~~~~~~~~~~~~~~~~~GD~i~~~ 60 (82)
T cd04454 5 DVGDIV----------IGIVTEVNSRFWKVDILSRGTARLEDSSATEKDKKEIRKSLQPGDLILAK 60 (82)
T ss_pred CCCCEE----------EEEEEEEcCCEEEEEeCCCceEEeechhccCcchHHHHhcCCCCCEEEEE
Confidence 567766 588999999976665431 1110 1111 1245677889999997653
No 58
>COG1862 YajC Preprotein translocase subunit YajC [Intracellular trafficking and secretion]
Probab=76.04 E-value=6.6 Score=36.64 Aligned_cols=54 Identities=26% Similarity=0.450 Sum_probs=42.7
Q ss_pred cccCCCCEEEEecCccCCceeEEEEEeCCeEEEeeCCCCCCceeEEcchhhhhhccCCCeE
Q 003213 222 GHFMKGDAVIVIKGDLKNLKGWVEKVDEENVHIRPEMKGLPKTLAVNSKELCKYFEPGNHV 282 (838)
Q Consensus 222 ~~F~~GD~V~V~~Gel~~l~G~V~~V~~d~V~i~~~~~~l~~~i~v~~~~LrK~F~~GDhV 282 (838)
..+++||.|.-+.| +.|+|++|.++.++|... + .-+++|.-+.+....+.|+.+
T Consensus 42 ~sL~kGD~VvT~gG----i~G~V~~v~d~~v~I~l~-~--~~~i~~~k~aI~~v~~~~~~~ 95 (97)
T COG1862 42 NSLKKGDEVVTIGG----IVGTVTKVGDDTVEIELG-D--GTKIKFEKEAIATVLEKGDLK 95 (97)
T ss_pred HhccCCCEEEEcCC----eEEEEEEEecCcEEEEEC-C--CeEEEEEHHHHHhhccCcccc
Confidence 57999999988755 899999999998888886 3 356788877777766666643
No 59
>PRK04313 30S ribosomal protein S4e; Validated
Probab=75.11 E-value=5.6 Score=42.73 Aligned_cols=43 Identities=26% Similarity=0.496 Sum_probs=32.6
Q ss_pred ccCCCeEEEeccccCCceEEEEEEeCc-----EEEEEeCCCCCeEEEc
Q 003213 276 FEPGNHVKVVSGTQAGATGMVLKVEQH-----VLIILSDTTKEDIRVF 318 (838)
Q Consensus 276 F~~GDhVkVi~G~~~getGlVvkVe~~-----~v~vlSD~t~~ei~V~ 318 (838)
|++|..|-|++|+|.|++|.|+.++.. ..+.+.|..++++.-.
T Consensus 172 fe~G~l~~itgG~n~GriG~I~~i~~~~~~~~~~V~i~d~~G~~F~T~ 219 (237)
T PRK04313 172 FEEGNLAIITGGKHVGEIGKIKEIEVTKSSKPNIVTLEDKDGEKFETI 219 (237)
T ss_pred cCCCCEEEEECCeeeeeEEEEEEEEEccCCCCcEEEEEcCCCCEEEEE
Confidence 799999999999999999999999631 2333446666655443
No 60
>PLN00036 40S ribosomal protein S4; Provisional
Probab=74.93 E-value=5.7 Score=43.25 Aligned_cols=25 Identities=36% Similarity=0.618 Sum_probs=24.0
Q ss_pred ccCCCeEEEeccccCCceEEEEEEe
Q 003213 276 FEPGNHVKVVSGTQAGATGMVLKVE 300 (838)
Q Consensus 276 F~~GDhVkVi~G~~~getGlVvkVe 300 (838)
|++|..|-|++|+|.|.+|.|+.++
T Consensus 175 fe~G~l~~vtgG~n~GrvG~I~~i~ 199 (261)
T PLN00036 175 FDVGNLVMVTGGRNRGRVGVIKNRE 199 (261)
T ss_pred cCCCCEEEEECCeeceeEEEEEEEE
Confidence 7999999999999999999999987
No 61
>PTZ00118 40S ribosomal protein S4; Provisional
Probab=73.26 E-value=6.7 Score=42.72 Aligned_cols=25 Identities=36% Similarity=0.651 Sum_probs=23.5
Q ss_pred ccCCCeEEEeccccCCceEEEEEEe
Q 003213 276 FEPGNHVKVVSGTQAGATGMVLKVE 300 (838)
Q Consensus 276 F~~GDhVkVi~G~~~getGlVvkVe 300 (838)
|++|..|-|++|+|.|++|.|+.++
T Consensus 175 fe~G~l~~vtgG~n~GriG~I~~~~ 199 (262)
T PTZ00118 175 FEVGNLVMITGGHNVGRVGTIVSKE 199 (262)
T ss_pred cCCCCEEEEECCeeceeEEEEEEEE
Confidence 7999999999999999999998876
No 62
>PHA03378 EBNA-3B; Provisional
Probab=73.17 E-value=83 Score=38.55 Aligned_cols=18 Identities=17% Similarity=0.325 Sum_probs=10.9
Q ss_pred EcchhhhhhccCCCeEEE
Q 003213 267 VNSKELCKYFEPGNHVKV 284 (838)
Q Consensus 267 v~~~~LrK~F~~GDhVkV 284 (838)
+.+.++.+.|..|-.--+
T Consensus 327 Ltsedi~~AfarGqamGL 344 (991)
T PHA03378 327 LTSEEIDLAYARGLAMEI 344 (991)
T ss_pred chHHHHHHHHHHHHhhcc
Confidence 455677777766664333
No 63
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=73.09 E-value=11 Score=31.38 Aligned_cols=55 Identities=24% Similarity=0.141 Sum_probs=39.5
Q ss_pred ccCCCCEEEEecC-ccCCceeEEEEEeC-CeEEEeeCCCCCCceeEEcchhhhhhcc
Q 003213 223 HFMKGDAVIVIKG-DLKNLKGWVEKVDE-ENVHIRPEMKGLPKTLAVNSKELCKYFE 277 (838)
Q Consensus 223 ~F~~GD~V~V~~G-el~~l~G~V~~V~~-d~V~i~~~~~~l~~~i~v~~~~LrK~F~ 277 (838)
.|++||.|+|.-= +-.=-.|+|+++.+ +...|.-...+..+..+|+.++||-+..
T Consensus 2 ~~~~G~~Ve~~~~~~~~W~~a~V~~~~~~~~~~V~~~~~~~~~~e~v~~~~LRp~~~ 58 (61)
T smart00743 2 DFKKGDRVEVFSKEEDSWWEAVVTKVLGDGKYLVRYLTESEPLKETVDWSDLRPHPP 58 (61)
T ss_pred CcCCCCEEEEEECCCCEEEEEEEEEECCCCEEEEEECCCCcccEEEEeHHHcccCCC
Confidence 6999999999853 22345799999988 5555555442235678899999996653
No 64
>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=72.84 E-value=14 Score=30.48 Aligned_cols=44 Identities=36% Similarity=0.442 Sum_probs=34.7
Q ss_pred CcEEEEeec--CCCCceeEEEeecCCeEEEEeccCc--eEEEEecccc
Q 003213 508 GTTVKVRLG--PYKGYRGRVVDVKGQSVRVELESQM--KVVTVDRSMI 551 (838)
Q Consensus 508 GktV~I~~G--pyKG~~G~Vkdat~~~~rVELhs~~--k~I~V~r~~l 551 (838)
|.+|+++.- +|-||.|.|..+++..|-|..+-.| |.||..-++|
T Consensus 5 G~~V~V~n~~~~Y~~y~G~VQRvsdgkaaVLFEGGnWdKlvTf~l~eL 52 (53)
T PF11623_consen 5 GSTVRVKNPNDIYYGYEGFVQRVSDGKAAVLFEGGNWDKLVTFRLSEL 52 (53)
T ss_dssp T-EEEE--TTSTTTT-EEEEEEEETTEEEEEEEETTEEEEEEEEGGGE
T ss_pred CCEEEEeCCCCccchheEEEEEeeCCeEEEEecCCCceEEEEEEhhhC
Confidence 567777654 6999999999999999999999888 8888877665
No 65
>KOG1708 consensus Mitochondrial/chloroplast ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=71.25 E-value=4 Score=42.53 Aligned_cols=29 Identities=34% Similarity=0.486 Sum_probs=26.1
Q ss_pred hccCCCeEEEeccccCCceEEEEEEeCcE
Q 003213 275 YFEPGNHVKVVSGTQAGATGMVLKVEQHV 303 (838)
Q Consensus 275 ~F~~GDhVkVi~G~~~getGlVvkVe~~~ 303 (838)
+|..||.|+|+.|+-+|.-|.|++|-.+.
T Consensus 72 ~ff~GDtVeVlvGkDkGkqG~Vtqv~r~~ 100 (236)
T KOG1708|consen 72 HFFFGDTVEVLVGKDKGKQGEVTQVIRHR 100 (236)
T ss_pred eEecCCEEEEEecccCCccceEEEEeecC
Confidence 68899999999999999999999996543
No 66
>PRK05585 yajC preprotein translocase subunit YajC; Validated
Probab=68.43 E-value=14 Score=34.93 Aligned_cols=51 Identities=25% Similarity=0.386 Sum_probs=37.9
Q ss_pred cccCCCCEEEEecCccCCceeEEEEEeCCeEEEeeCCCCCCceeEEcchhhhhhccCC
Q 003213 222 GHFMKGDAVIVIKGDLKNLKGWVEKVDEENVHIRPEMKGLPKTLAVNSKELCKYFEPG 279 (838)
Q Consensus 222 ~~F~~GD~V~V~~Gel~~l~G~V~~V~~d~V~i~~~~~~l~~~i~v~~~~LrK~F~~G 279 (838)
..+++||.|.-+.| +.|+|++|++++|++.... .-.++|.-+.+.+..+.+
T Consensus 51 ~~Lk~Gd~VvT~gG----i~G~Vv~i~~~~v~lei~~---g~~i~~~r~aI~~v~~~~ 101 (106)
T PRK05585 51 SSLAKGDEVVTNGG----IIGKVTKVSEDFVIIELND---DTEIKIQKSAIAAVLPKG 101 (106)
T ss_pred HhcCCCCEEEECCC----eEEEEEEEeCCEEEEEECC---CeEEEEEhHHhhhhcCCC
Confidence 58999999998865 8999999999988887532 235667666666554433
No 67
>cd05705 S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 14 (hs14). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=68.19 E-value=13 Score=32.53 Aligned_cols=58 Identities=21% Similarity=0.418 Sum_probs=32.7
Q ss_pred cCCCCEEEEecCccCCceeEEEEEeCCe--EEEeeCCCCC------CceeEEcchhhhhhccCCCeEEEeccccCCceEE
Q 003213 224 FMKGDAVIVIKGDLKNLKGWVEKVDEEN--VHIRPEMKGL------PKTLAVNSKELCKYFEPGNHVKVVSGTQAGATGM 295 (838)
Q Consensus 224 F~~GD~V~V~~Gel~~l~G~V~~V~~d~--V~i~~~~~~l------~~~i~v~~~~LrK~F~~GDhVkVi~G~~~getGl 295 (838)
|++||.| .|+|.+|.+.- |.+.+..+++ .+..--..+++.++|++||.|++ .
T Consensus 1 ~k~G~~V----------~g~V~~i~~~G~fV~l~~~v~G~v~~~~ls~~~~~~~~~~~~~~~~G~~v~~----------k 60 (74)
T cd05705 1 IKEGQLL----------RGYVSSVTKQGVFFRLSSSIVGRVLFQNVTKYFVSDPSLYNKYLPEGKLLTA----------K 60 (74)
T ss_pred CCCCCEE----------EEEEEEEeCCcEEEEeCCCCEEEEEHHHccCccccChhhHhcccCCCCEEEE----------E
Confidence 4567666 46777776553 3333332222 11110123457789999999865 4
Q ss_pred EEEEeC
Q 003213 296 VLKVEQ 301 (838)
Q Consensus 296 VvkVe~ 301 (838)
|+.++.
T Consensus 61 Vl~id~ 66 (74)
T cd05705 61 VLSVNS 66 (74)
T ss_pred EEEEEC
Confidence 777764
No 68
>PRK04333 50S ribosomal protein L14e; Validated
Probab=68.13 E-value=9.3 Score=34.73 Aligned_cols=33 Identities=18% Similarity=0.195 Sum_probs=27.9
Q ss_pred cCCCCCEEEEecCcCCCceEEEEEEeCCCCEEEE
Q 003213 71 DLSRDTWVRMKIGNYKGDLAKVVDVDNVRQRVTV 104 (838)
Q Consensus 71 ~l~~G~~VRik~G~ykGDlaqV~~vd~~~~~V~v 104 (838)
.+++|..|.+..|.|+|-+|.|+++.+ .+.|.|
T Consensus 3 ~v~~GrvV~~~~Grd~gk~~vIv~i~d-~~~vlV 35 (84)
T PRK04333 3 AIEVGRVCVKTAGREAGRKCVIVDIID-KNFVLV 35 (84)
T ss_pred cccccEEEEEeccCCCCCEEEEEEEec-CCEEEE
Confidence 578999999999999999999999854 355554
No 69
>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=67.79 E-value=13 Score=30.79 Aligned_cols=49 Identities=20% Similarity=0.297 Sum_probs=36.4
Q ss_pred cCCCCEEEEecCc--cCCceeEEEEEeCCeEEEeeCCCCCCceeEEcchhh
Q 003213 224 FMKGDAVIVIKGD--LKNLKGWVEKVDEENVHIRPEMKGLPKTLAVNSKEL 272 (838)
Q Consensus 224 F~~GD~V~V~~Ge--l~~l~G~V~~V~~d~V~i~~~~~~l~~~i~v~~~~L 272 (838)
+.||-.|+|+.-+ +-+.+|.|.+|.++.+-++=+-....+-++|..++|
T Consensus 2 ilPG~~V~V~n~~~~Y~~y~G~VQRvsdgkaaVLFEGGnWdKlvTf~l~eL 52 (53)
T PF11623_consen 2 ILPGSTVRVKNPNDIYYGYEGFVQRVSDGKAAVLFEGGNWDKLVTFRLSEL 52 (53)
T ss_dssp --TT-EEEE--TTSTTTT-EEEEEEEETTEEEEEEEETTEEEEEEEEGGGE
T ss_pred ccCCCEEEEeCCCCccchheEEEEEeeCCeEEEEecCCCceEEEEEEhhhC
Confidence 5689999999884 478999999999999988877665567789998887
No 70
>PRK14635 hypothetical protein; Provisional
Probab=67.05 E-value=7.8 Score=39.29 Aligned_cols=49 Identities=22% Similarity=0.251 Sum_probs=38.7
Q ss_pred ccccCcEEEEee-----cCCCCceeEEEeecCCeEEEEeccC------ceEEEEeccccc
Q 003213 504 DALVGTTVKVRL-----GPYKGYRGRVVDVKGQSVRVELESQ------MKVVTVDRSMIS 552 (838)
Q Consensus 504 d~liGktV~I~~-----GpyKG~~G~Vkdat~~~~rVELhs~------~k~I~V~r~~l~ 552 (838)
..++|+.|+|+- ..|+|++|++++++++.+++++..+ .++++++.+.|+
T Consensus 95 ~r~~G~~v~v~~~~~~~~~~~g~~g~L~~~~~~~v~l~~~~k~~~~~~~~~~~ip~~~I~ 154 (162)
T PRK14635 95 DRFRGIPVRLVFRSEESEKWQEGIFRLVNRDGDQVELEKFQKGKKSKVKKQTTLNLKDIL 154 (162)
T ss_pred HHhCCCEEEEEEecCCCcEEEecceEEEEEcCCEEEEEEecccccccCCeEEEEEhHHee
Confidence 578899988862 2577888899999999999988543 667888887775
No 71
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=65.58 E-value=1.2e+02 Score=34.10 Aligned_cols=156 Identities=12% Similarity=0.133 Sum_probs=76.7
Q ss_pred cccCCCCEEEEecCccCCceeEEEEEeCC--eEEEeeCCCCCCceeEEcchhhhhhccCCCeEEEe-ccccCCceEEEEE
Q 003213 222 GHFMKGDAVIVIKGDLKNLKGWVEKVDEE--NVHIRPEMKGLPKTLAVNSKELCKYFEPGNHVKVV-SGTQAGATGMVLK 298 (838)
Q Consensus 222 ~~F~~GD~V~V~~Gel~~l~G~V~~V~~d--~V~i~~~~~~l~~~i~v~~~~LrK~F~~GDhVkVi-~G~~~getGlVvk 298 (838)
..|++||.|+|+ |++++.+ .+++...... ..-....|++.++.|+.|++. .+ ...-|++|.
T Consensus 74 ~~~~~G~~v~~~----------Vi~~~~~~~~i~lS~k~~~----~~~~w~~l~~~~~~~~~V~g~V~~--~~~~G~~V~ 137 (318)
T PRK07400 74 EVLQPNETREFF----------ILSDENEDGQLTLSIRRIE----YMRAWERVRQLQKEDATVRSEVFA--TNRGGALVR 137 (318)
T ss_pred HccCCCCEEEEE----------EEEEeCCCCeEEEehhhhh----hhhHHHHHHHhccCCCEEEEEEEE--EECCeEEEE
Confidence 469999999886 6666543 4444332110 012356777888889877653 22 223478888
Q ss_pred EeCcEEEE----EeC------CCCCeEEEcccccc-------cccccccccccCCceEecceEEeCCCcEEEEEEEecce
Q 003213 299 VEQHVLII----LSD------TTKEDIRVFADDVV-------ESSEVTTGITKIGDYELRDLVLLDNNSFGVIIRVESEA 361 (838)
Q Consensus 299 Ve~~~v~v----lSD------~t~~ei~V~~~dL~-------~~~e~~~g~d~~g~y~l~DLVqld~~~vGvIv~ier~~ 361 (838)
+++=...| +|+ .-++++++.--++. .|.-.+..-....+|+.+|.|. |.|.+|....
T Consensus 138 l~Gv~gfip~s~ls~~~~~~~~vG~~i~~kVl~id~~~~~i~lS~K~~~~~~~~~~~k~G~vv~------G~V~~I~~~G 211 (318)
T PRK07400 138 IEGLRGFIPGSHISTRKPKEELVGEELPLKFLEVDEERNRLVLSHRRALVERKMNRLEVGEVVV------GTVRGIKPYG 211 (318)
T ss_pred ECCEEEEEEHHHcCccCCccccCCCEEEEEEEEEEcccCEEEEEhhHhhhhhhhccCCCCCEEE------EEEEEEECCe
Confidence 85322111 122 12344444322221 1110000001234566666654 7888888776
Q ss_pred EEEEecCCCCCcEEEEEccccccccccCccccCCCCCeecCCCEEEEE
Q 003213 362 FQVLKGVPDRPEVALVKLREIKCKLEKKSNVQDRNKNTVAVKDVVRIV 409 (838)
Q Consensus 362 ~~VL~~~~~~g~v~~vk~~~I~~K~~~~~~a~D~~gn~i~~gd~Vki~ 409 (838)
++|--. |-.-.+..+++..+. ...-...+++||.|++.
T Consensus 212 ~fV~i~----gv~Gllhisels~~~------~~~~~~~~~vGd~Vkvk 249 (318)
T PRK07400 212 AFIDIG----GVSGLLHISEISHEH------IETPHSVFNVNDEMKVM 249 (318)
T ss_pred EEEEEC----CEEEEEEHHHccccc------ccChhhccCCCCEEEEE
Confidence 665431 211122223333221 11234568899998874
No 72
>PRK13709 conjugal transfer nickase/helicase TraI; Provisional
Probab=64.98 E-value=36 Score=46.41 Aligned_cols=98 Identities=15% Similarity=0.196 Sum_probs=70.9
Q ss_pred ccccCCCCEEEEecCc-cCCceeEEEEEeCC--eEEEeeCCCCCCceeEEcchhhhh----------hccCCCeEEEecc
Q 003213 221 KGHFMKGDAVIVIKGD-LKNLKGWVEKVDEE--NVHIRPEMKGLPKTLAVNSKELCK----------YFEPGNHVKVVSG 287 (838)
Q Consensus 221 ~~~F~~GD~V~V~~Ge-l~~l~G~V~~V~~d--~V~i~~~~~~l~~~i~v~~~~LrK----------~F~~GDhVkVi~G 287 (838)
...|++||.|+-.... +++...+|+.|+.+ .+++.... .+.++|.++.+.+ .+..||.+++...
T Consensus 646 a~~Y~~G~vi~~~~~~~~~~~~y~V~~v~~~~n~LtL~~~~---G~~~~~~p~~~~~~~~vy~~~~ieiA~GDrLr~T~n 722 (1747)
T PRK13709 646 RDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQ---GETQVVKISSLDSSWSLFRPEKMPVADGERLRVLGK 722 (1747)
T ss_pred hhcCCCCcEEEeeccccccCccEEEEEEcCCCCEEEEEcCC---CCEEEeChHHhcccceeccccccccCCCCEEEEccC
Confidence 4689999999876543 24656799999876 45554432 3456788777632 3689999999854
Q ss_pred c-----cCCceEEEEEEeCcEEEEEeCCCCCeEEEcccc
Q 003213 288 T-----QAGATGMVLKVEQHVLIILSDTTKEDIRVFADD 321 (838)
Q Consensus 288 ~-----~~getGlVvkVe~~~v~vlSD~t~~ei~V~~~d 321 (838)
. ..|+...|++|+++.++|-.|-.++++++-...
T Consensus 723 d~~~~l~Ngd~~tV~~i~~~~i~l~~~~~gk~~~L~~~~ 761 (1747)
T PRK13709 723 IPGLRLKGGDRLQVTSVSEDGLTVVVPGRAEPATLPVDD 761 (1747)
T ss_pred CcccCccCCCEEEEEEecCCeEEEEECCCceEEEeCCcc
Confidence 3 458999999999999999876556777774444
No 73
>CHL00010 infA translation initiation factor 1
Probab=64.55 E-value=57 Score=29.09 Aligned_cols=64 Identities=20% Similarity=0.203 Sum_probs=43.4
Q ss_pred cEEEEEEEe-cceEEEEecCCCCCcEEEEEccccccccccCccccCCCCCeecCCCEEEEEcCCCCCceeeEEEEECC
Q 003213 350 SFGVIIRVE-SEAFQVLKGVPDRPEVALVKLREIKCKLEKKSNVQDRNKNTVAVKDVVRIVEGPCKGKQGPVEHIYRG 426 (838)
Q Consensus 350 ~vGvIv~ie-r~~~~VL~~~~~~g~v~~vk~~~I~~K~~~~~~a~D~~gn~i~~gd~Vki~~Gp~kG~~G~Vkhi~r~ 426 (838)
-.|+|+++- .+.|.|.. ++|+++.++..- |+. .+..-+.+||.|.+---++....|.|.|=|++
T Consensus 9 ~~G~Vik~lg~~~y~V~~---~~g~~~~c~~rG---klr-------~~~i~~~vGD~V~ve~~~~~~~~g~Ii~r~~~ 73 (78)
T CHL00010 9 MEGLVTESLPNGMFRVRL---DNGCQVLGYISG---KIR-------RNSIRILPGDRVKVELSPYDLTKGRIIYRLRN 73 (78)
T ss_pred EEEEEEEEcCCCEEEEEe---CCCCEEEEEecc---cee-------cCCcccCCCCEEEEEEcccCCCeEEEEEEecC
Confidence 359999999 57787755 356777777432 211 11334789999999855555567999888775
No 74
>cd05789 S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=64.54 E-value=13 Score=33.00 Aligned_cols=52 Identities=15% Similarity=0.228 Sum_probs=29.9
Q ss_pred cCCCCEEEEecCccCCceeEEEEEeCCeEEEeeC--CCCC--Ccee-----EEcchhhhhhccCCCeEEEe
Q 003213 224 FMKGDAVIVIKGDLKNLKGWVEKVDEENVHIRPE--MKGL--PKTL-----AVNSKELCKYFEPGNHVKVV 285 (838)
Q Consensus 224 F~~GD~V~V~~Gel~~l~G~V~~V~~d~V~i~~~--~~~l--~~~i-----~v~~~~LrK~F~~GDhVkVi 285 (838)
+++||.| .|+|++|.++.+.+.-. .+++ ..++ .-..+++.+.|++||.+++-
T Consensus 4 p~~GdiV----------~g~V~~i~~~g~~v~i~~~~~G~l~~se~~~~~~~~~~~~~~~~l~vGd~i~~~ 64 (86)
T cd05789 4 PEVGDVV----------IGRVTEVGFKRWKVDINSPYDAVLPLSEVNLPRTDEDELNMRSYLDEGDLIVAE 64 (86)
T ss_pred CCCCCEE----------EEEEEEECCCEEEEECCCCeEEEEEHHHccCCCCccchHHHHhhCCCCCEEEEE
Confidence 4677777 47788888775554432 1111 0111 11234566689999998653
No 75
>PRK04313 30S ribosomal protein S4e; Validated
Probab=64.40 E-value=29 Score=37.47 Aligned_cols=73 Identities=26% Similarity=0.396 Sum_probs=51.4
Q ss_pred cEEEEEEeCCCCeEEEEe--ccCCCCceEEec-CCC--ceEcCCCCCCcEEEEcCCCCCceEEEEEEeC----CCeEEEe
Q 003213 748 VVGVIREVLPDGSCRVVL--GSSGNGDTITAL-PNE--IEIVPPRKTDKIKIMGGPHRGATGKLIGVDG----TDGIVKV 818 (838)
Q Consensus 748 ~~gvI~~V~~dg~~~V~l--~~~~~g~~v~v~-~~~--Le~V~P~kgd~VkVi~G~~rG~tG~LisiD~----~dgiVk~ 818 (838)
+.|++.=++-||.+-.+- .+-..+|+|.++ .++ ++.+.-..|..+.|+.|.+.|.+|++.+|.. ..-+|.+
T Consensus 129 ~gG~~ql~~hDGrni~~~~~~~~k~~Dtv~i~l~~~kI~~~i~fe~G~l~~itgG~n~GriG~I~~i~~~~~~~~~~V~i 208 (237)
T PRK04313 129 KGGKIQLNLHDGRNILVDVEDDYKTGDSLLISLPEQEIVDHIPFEEGNLAIITGGKHVGEIGKIKEIEVTKSSKPNIVTL 208 (237)
T ss_pred cCCEEEEEecCCceEEccCccccccCCEEEEECCCCceeEEEecCCCCEEEEECCeeeeeEEEEEEEEEccCCCCcEEEE
Confidence 355666566678774442 121126777776 233 6677779999999999999999999999984 4567777
Q ss_pred cC
Q 003213 819 DV 820 (838)
Q Consensus 819 d~ 820 (838)
.+
T Consensus 209 ~d 210 (237)
T PRK04313 209 ED 210 (237)
T ss_pred Ec
Confidence 74
No 76
>PRK05886 yajC preprotein translocase subunit YajC; Validated
Probab=64.29 E-value=12 Score=35.65 Aligned_cols=42 Identities=21% Similarity=0.313 Sum_probs=32.7
Q ss_pred cCcEEEEeecCCCCceeEEEeecCCeEEEEeccCceEEEEecccccc
Q 003213 507 VGTTVKVRLGPYKGYRGRVVDVKGQSVRVELESQMKVVTVDRSMISD 553 (838)
Q Consensus 507 iGktV~I~~GpyKG~~G~Vkdat~~~~rVELhs~~k~I~V~r~~l~~ 553 (838)
.|..| |+.| |+.|+|++++++++.||+. ..-.|+++|..|+-
T Consensus 41 ~GD~V-vT~g---Gi~G~V~~I~d~~v~leia-~gv~i~~~r~AI~~ 82 (109)
T PRK05886 41 PGDRV-HTTS---GLQATIVGITDDTVDLEIA-PGVVTTWMKLAVRD 82 (109)
T ss_pred CCCEE-EECC---CeEEEEEEEeCCEEEEEEC-CCeEEEEEhhheee
Confidence 34454 4445 7999999999999999995 45568999999873
No 77
>PRK14639 hypothetical protein; Provisional
Probab=63.96 E-value=14 Score=36.58 Aligned_cols=49 Identities=18% Similarity=0.329 Sum_probs=40.6
Q ss_pred ccccCcEEEEeecCCCCceeEEEeecCCeEEEEeccCceEEEEeccccc
Q 003213 504 DALVGTTVKVRLGPYKGYRGRVVDVKGQSVRVELESQMKVVTVDRSMIS 552 (838)
Q Consensus 504 d~liGktV~I~~GpyKG~~G~Vkdat~~~~rVELhs~~k~I~V~r~~l~ 552 (838)
..++|+.|+|+-.--|-+.|++++++++.+++|+-...+++.++.++|+
T Consensus 84 ~r~~G~~v~v~l~~~~~~~G~L~~~~~~~i~l~~~~~~~~~~i~~~~I~ 132 (140)
T PRK14639 84 AKSIGELVKITTNEKEKFEGKIVSVDDENITLENLENKEKTTINFNDIK 132 (140)
T ss_pred HHhCCCEEEEEECCCcEEEEEEEEEeCCEEEEEEccCCcEEEEEhHHee
Confidence 5789999999875568899999999999999987445567888888775
No 78
>TIGR00739 yajC preprotein translocase, YajC subunit. While this protein is part of the preprotein translocase in Escherichia coli, it is not essential for viability or protein secretion. The N-terminus region contains a predicted membrane-spanning region followed by a region consisting almost entirely of residues with charged (acidic, basic, or zwitterionic) side chains. This small protein is about 100 residues in length, and is restricted to bacteria; however, this protein is absent from some lineages, including spirochetes and Mycoplasmas.
Probab=63.90 E-value=11 Score=34.28 Aligned_cols=41 Identities=24% Similarity=0.409 Sum_probs=32.3
Q ss_pred cCcEEEEeecCCCCceeEEEeecCCeEEEEeccCceEEEEeccccc
Q 003213 507 VGTTVKVRLGPYKGYRGRVVDVKGQSVRVELESQMKVVTVDRSMIS 552 (838)
Q Consensus 507 iGktV~I~~GpyKG~~G~Vkdat~~~~rVELhs~~k~I~V~r~~l~ 552 (838)
.|..|.-. | |..|+|+++.++++.||+. ..-.++++|+.|+
T Consensus 40 ~Gd~VvT~-g---Gi~G~V~~i~d~~v~vei~-~g~~i~~~r~aI~ 80 (84)
T TIGR00739 40 KGDKVLTI-G---GIIGTVTKIAENTIVIELN-DNTEITFSKNAIV 80 (84)
T ss_pred CCCEEEEC-C---CeEEEEEEEeCCEEEEEEC-CCeEEEEEhHHhh
Confidence 45555544 4 6899999999999999995 4556999999876
No 79
>COG1588 POP4 RNase P/RNase MRP subunit p29 [Translation, ribosomal structure and biogenesis]
Probab=62.96 E-value=15 Score=34.12 Aligned_cols=50 Identities=26% Similarity=0.335 Sum_probs=40.6
Q ss_pred CCccccCcEEEEeecC---CCCceeEEEeecCCeEEEEeccCceEEEEecccccc
Q 003213 502 GHDALVGTTVKVRLGP---YKGYRGRVVDVKGQSVRVELESQMKVVTVDRSMISD 553 (838)
Q Consensus 502 ~rd~liGktV~I~~Gp---yKG~~G~Vkdat~~~~rVELhs~~k~I~V~r~~l~~ 553 (838)
-+.+|||..|+|..-+ |-|..|.|.|-|.++..++-.+ +.+.|.|....+
T Consensus 11 ~~hEliGl~vrVv~s~~~s~vGI~G~VVdETkNtLvi~t~~--~~~~VpK~~~vf 63 (95)
T COG1588 11 IRHELIGLEVRVVRSTNPSYVGIEGRVVDETKNTLVIDTGS--REKVVPKDGAVF 63 (95)
T ss_pred ChHHhcCcEEEEEecCCCCccceeEEEEeeeccEEEEECCC--ceEEEecCcEEE
Confidence 3589999999999876 5677889999999999988776 666777766543
No 80
>PF01287 eIF-5a: Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold; InterPro: IPR020189 A five-stranded beta-barrel was first noted as a common structure among four proteins binding single-stranded nucleic acids (staphylococcal nuclease and aspartyl-tRNA synthetase) or oligosaccharides (B subunits of enterotoxin and verotoxin-1), and has been termed the oligonucleotide/oligosaccharide binding motif, or OB fold, a five-stranded beta-sheet coiled to form a closed beta-barrel capped by an alpha helix located between the third and fourth strands []. Two ribosomal proteins, S17 and S1, are members of this class, and have different variations of the OB fold theme. Comparisons with other OB fold nucleic acid binding proteins suggest somewhat different mechanisms of nucleic acid recognition in each case []. There are many nucleic acid-binding proteins that contain domains with this OB-fold structure, including anticodon-binding tRNA synthetases, ssDNA-binding proteins (CDC13, telomere-end binding proteins), phage ssDNA-binding proteins (gp32, gp2.5, gpV), cold shock proteins, DNA ligases, RNA-capping enzymes, DNA replication initiators and RNA polymerase subunit RBP8 []. This entry represents the RNA-binding domain of translation elongation factor IF5A [].; GO: 0003723 RNA binding, 0003746 translation elongation factor activity, 0043022 ribosome binding, 0006452 translational frameshifting, 0045901 positive regulation of translational elongation, 0045905 positive regulation of translational termination; PDB: 1IZ6_B 3CPF_A 1KHI_A 1BKB_A 1XTD_A 3ER0_A 3HKS_B 1X6O_A 2EIF_A 1EIF_A.
Probab=62.86 E-value=12 Score=32.85 Aligned_cols=43 Identities=19% Similarity=0.210 Sum_probs=33.4
Q ss_pred ceeEEEEEeCC-eEEEeeCCCCCCceeEEc----chhhhhhccCCCeE
Q 003213 240 LKGWVEKVDEE-NVHIRPEMKGLPKTLAVN----SKELCKYFEPGNHV 282 (838)
Q Consensus 240 l~G~V~~V~~d-~V~i~~~~~~l~~~i~v~----~~~LrK~F~~GDhV 282 (838)
-.+.|++|++| .+++|-+..+..+.|.+| .++++..|+.|..+
T Consensus 5 ~eyqli~I~~Dg~lsLMde~get~eDl~lP~~el~~ei~~~~~~g~~~ 52 (69)
T PF01287_consen 5 KEYQLIDIDGDGFLSLMDEDGETREDLKLPDGELGEEIKAKFEEGKEV 52 (69)
T ss_dssp EEEEEEEEETTTEEEEEETTS-EEEEEECCSHHHHHHHHHHHHTTCEE
T ss_pred EEEEEEEEccCcEEEEEcCCCCeeccEEecccchhHHHHhhccCCCeE
Confidence 35789999877 999998655555668899 57788899999883
No 81
>PRK03879 ribonuclease P protein component 1; Validated
Probab=62.76 E-value=18 Score=33.71 Aligned_cols=48 Identities=27% Similarity=0.360 Sum_probs=41.1
Q ss_pred CccccCcEEEEeecC---CCCceeEEEeecCCeEEEEeccCceEEEEeccccc
Q 003213 503 HDALVGTTVKVRLGP---YKGYRGRVVDVKGQSVRVELESQMKVVTVDRSMIS 552 (838)
Q Consensus 503 rd~liGktV~I~~Gp---yKG~~G~Vkdat~~~~rVELhs~~k~I~V~r~~l~ 552 (838)
+.+|+|-.|+|.+=+ +-|..|+|.+-|..++.|+ +.++..+|+|+.-.
T Consensus 10 ~~eliGl~v~Vv~S~npslvGi~GiVv~ETknt~~I~--~~~~~~~VPK~~~i 60 (96)
T PRK03879 10 RHELIGLKVEVVDSTNPSLVGIKGRVVDETRNTLVIE--TDGKEWMVPKDGAT 60 (96)
T ss_pred HHHhcCCEEEEEEcCCCCcccceEEEEEeceeEEEEE--cCCcEEEEeCCCeE
Confidence 468999999998766 5689999999999999999 77788889998843
No 82
>PRK00276 infA translation initiation factor IF-1; Validated
Probab=60.66 E-value=71 Score=27.92 Aligned_cols=62 Identities=18% Similarity=0.230 Sum_probs=41.0
Q ss_pred EEEEEEEecc-eEEEEecCCCCCcEEEEEccccccccccCccccCCCCCeecCCCEEEEEcCCCCCceeeEEEEEC
Q 003213 351 FGVIIRVESE-AFQVLKGVPDRPEVALVKLREIKCKLEKKSNVQDRNKNTVAVKDVVRIVEGPCKGKQGPVEHIYR 425 (838)
Q Consensus 351 vGvIv~ier~-~~~VL~~~~~~g~v~~vk~~~I~~K~~~~~~a~D~~gn~i~~gd~Vki~~Gp~kG~~G~Vkhi~r 425 (838)
.|.|+++-.+ .|.|.. ++|.++.++..- |+.+ +...+.+||.|.+---++....|.|.|=||
T Consensus 10 ~G~Vi~~~~~~~y~V~~---~~g~~~~c~~~G---klr~-------~~i~i~vGD~V~ve~~~~~~~~g~Iv~r~~ 72 (72)
T PRK00276 10 EGTVVEALPNAMFRVEL---ENGHEVLAHISG---KMRK-------NYIRILPGDKVTVELSPYDLTKGRITYRHK 72 (72)
T ss_pred EEEEEEEcCCCEEEEEe---CCCCEEEEEEcc---ceee-------CCcccCCCCEEEEEEcccCCCeEEEEEEeC
Confidence 5899999877 677755 356777777542 2111 123389999999985555556788877554
No 83
>COG2139 RPL21A Ribosomal protein L21E [Translation, ribosomal structure and biogenesis]
Probab=60.61 E-value=18 Score=33.60 Aligned_cols=53 Identities=25% Similarity=0.238 Sum_probs=40.7
Q ss_pred cccCCCCEEEEe------cC----ccCCceeEEEEEeCCeEEEeeCCCCCCceeEEcchhhhh
Q 003213 222 GHFMKGDAVIVI------KG----DLKNLKGWVEKVDEENVHIRPEMKGLPKTLAVNSKELCK 274 (838)
Q Consensus 222 ~~F~~GD~V~V~------~G----el~~l~G~V~~V~~d~V~i~~~~~~l~~~i~v~~~~LrK 274 (838)
..|.+||.|-|. +| .+.|.+|+|+.+.++...+.....+..+.|-+.+..|+.
T Consensus 31 ~ey~~Gd~V~I~IdpSv~kGmPh~rf~G~TG~Vvg~~g~ay~V~v~~G~k~K~liv~peHLk~ 93 (98)
T COG2139 31 QEYKVGDKVHIDIDPSVHKGMPHPRFQGKTGTVVGVRGRAYKVEVYDGNKEKTLIVRPEHLKP 93 (98)
T ss_pred hhccCCCEEEEEeCcccccCCCCccccCcceEEEeccCCEEEEEEecCCceEEEEeCHHHccc
Confidence 579999999763 33 678999999999999766666566666777777777764
No 84
>cd04455 S1_NusA S1_NusA: N-utilizing substance A protein (NusA), S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. NusA is a transcription elongation factor containing an N-terminal catalytic domain and three RNA binding domains (RBD's). The RBD's include one S1 domain and two KH domains that form an RNA binding surface. DNA transcription by RNA polymerase (RNAP) includes three phases - initiation, elongation, and termination. During initiation, sigma factors bind RNAP and target RNAP to specific promoters. During elongation, N-utilization substances (NusA, B, E, and G) replace sigma factors and regulate pausing, termination, and antitermination. NusA is cold-shock-inducible.
Probab=60.42 E-value=37 Score=28.81 Aligned_cols=42 Identities=26% Similarity=0.425 Sum_probs=28.9
Q ss_pred ceeEEEEEeCCeEEEeeCCCCCCceeEEcchhhh--hhccCCCeEEEe
Q 003213 240 LKGWVEKVDEENVHIRPEMKGLPKTLAVNSKELC--KYFEPGNHVKVV 285 (838)
Q Consensus 240 l~G~V~~V~~d~V~i~~~~~~l~~~i~v~~~~Lr--K~F~~GDhVkVi 285 (838)
.+|+|++++.+.+.+.- .+ -+--++.+++. ..|++||+|++.
T Consensus 7 V~G~V~~~~~~~~~vdi--g~--~eg~lp~~e~~~~~~~~~Gd~v~v~ 50 (67)
T cd04455 7 VTGIVKRVDRGNVIVDL--GK--VEAILPKKEQIPGESYRPGDRIKAY 50 (67)
T ss_pred EEEEEEEEcCCCEEEEc--CC--eEEEeeHHHCCCCCcCCCCCEEEEE
Confidence 36889999888666543 22 23456666664 579999999875
No 85
>PRK04333 50S ribosomal protein L14e; Validated
Probab=59.14 E-value=14 Score=33.59 Aligned_cols=29 Identities=28% Similarity=0.286 Sum_probs=24.7
Q ss_pred cCcEEEEeecCCCCceeEEEeec-CCeEEE
Q 003213 507 VGTTVKVRLGPYKGYRGRVVDVK-GQSVRV 535 (838)
Q Consensus 507 iGktV~I~~GpyKG~~G~Vkdat-~~~~rV 535 (838)
+|+-|.+..|+++|-+.+|.|+- +..|-|
T Consensus 6 ~GrvV~~~~Grd~gk~~vIv~i~d~~~vlV 35 (84)
T PRK04333 6 VGRVCVKTAGREAGRKCVIVDIIDKNFVLV 35 (84)
T ss_pred ccEEEEEeccCCCCCEEEEEEEecCCEEEE
Confidence 78999999999999999999994 445554
No 86
>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=58.95 E-value=21 Score=27.96 Aligned_cols=28 Identities=32% Similarity=0.523 Sum_probs=25.2
Q ss_pred eeEEEeecCCeEEEEeccCceEEEEeccc
Q 003213 522 RGRVVDVKGQSVRVELESQMKVVTVDRSM 550 (838)
Q Consensus 522 ~G~Vkdat~~~~rVELhs~~k~I~V~r~~ 550 (838)
.|.|++..+..++|++.. .++++|.+++
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 589999999999999999 8899998764
No 87
>PRK05585 yajC preprotein translocase subunit YajC; Validated
Probab=58.12 E-value=14 Score=34.96 Aligned_cols=42 Identities=26% Similarity=0.357 Sum_probs=33.9
Q ss_pred cCcEEEEeecCCCCceeEEEeecCCeEEEEeccCceEEEEecccccc
Q 003213 507 VGTTVKVRLGPYKGYRGRVVDVKGQSVRVELESQMKVVTVDRSMISD 553 (838)
Q Consensus 507 iGktV~I~~GpyKG~~G~Vkdat~~~~rVELhs~~k~I~V~r~~l~~ 553 (838)
.|..|.-.. |..|+|+++.++++.||+. ..-.|+++|..|.-
T Consensus 55 ~Gd~VvT~g----Gi~G~Vv~i~~~~v~lei~-~g~~i~~~r~aI~~ 96 (106)
T PRK05585 55 KGDEVVTNG----GIIGKVTKVSEDFVIIELN-DDTEIKIQKSAIAA 96 (106)
T ss_pred CCCEEEECC----CeEEEEEEEeCCEEEEEEC-CCeEEEEEhHHhhh
Confidence 566665444 6899999999999999994 55779999999874
No 88
>PF02357 NusG: Transcription termination factor nusG; InterPro: IPR006645 This sequence is identified by the NGN domain and is represented by the bacterial antitermination protein NusG. This protein influences transcription termination and anti-termination and acts as a component of the transcription complex. In addition to this, it interacts with the termination factor Rho and RNA polymerase [, ].; GO: 0032968 positive regulation of transcription elongation from RNA polymerase II promoter; PDB: 1NZ8_A 2OUG_C 1NPP_B 1M1G_D 1NPR_A 1M1H_A 2XHA_A 2XHC_A 2K06_A.
Probab=57.73 E-value=11 Score=33.83 Aligned_cols=34 Identities=9% Similarity=0.326 Sum_probs=24.7
Q ss_pred EEEEEecCCCceEEEEEecChHHHHHHHhcCcceee
Q 003213 13 IRSVIALDHLKNYIYIEADKEAHVKEACKGLRNIYS 48 (838)
Q Consensus 13 I~Sv~~~~~lkGyIyVEA~~~~~V~~ai~g~~~v~~ 48 (838)
++- ...+=++|||||++...+++++. +.+.++++
T Consensus 45 ~~~-~~~plfpgYvFv~~~~~~~~~~i-~~~~gv~~ 78 (92)
T PF02357_consen 45 VKR-VERPLFPGYVFVRMDMEDELWKI-RSTPGVSG 78 (92)
T ss_dssp EEE-EEEESSTTEEEEEE-TTHHHHHH-HHSTTEEE
T ss_pred EEE-EEEEecCcEEEEEEEcchhhhhh-hcCCCeEE
Confidence 444 45567999999999999666444 88888875
No 89
>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=57.41 E-value=21 Score=31.98 Aligned_cols=51 Identities=24% Similarity=0.298 Sum_probs=37.7
Q ss_pred CCCCEEEEec----CccCCceeEEEEEeCCeEEEeeCCCCCCceeEEcchhhhhh
Q 003213 225 MKGDAVIVIK----GDLKNLKGWVEKVDEENVHIRPEMKGLPKTLAVNSKELCKY 275 (838)
Q Consensus 225 ~~GD~V~V~~----Gel~~l~G~V~~V~~d~V~i~~~~~~l~~~i~v~~~~LrK~ 275 (838)
..|-.|+|.- +..+...|.+.+++++.|+|..+...-.+++.++-.+++|+
T Consensus 23 ~~G~~v~v~~~~~~~~~~~~~G~L~~~~~~~v~l~~~~~~~~~~~~i~~~~I~ka 77 (83)
T cd01734 23 AVGKYVHVKLYQPIDGQKEFEGTLLGVDDDTVTLEVDIKTRGKTVEIPLDKIAKA 77 (83)
T ss_pred hCCCEEEEEEEcccCCeEEEEEEEEeEeCCEEEEEEecCCCCeEEEEEhHHeeEE
Confidence 3567777742 44577899999999999999876433346788888888774
No 90
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=57.12 E-value=2.3e+02 Score=31.85 Aligned_cols=54 Identities=17% Similarity=0.255 Sum_probs=31.5
Q ss_pred cccCCCCEEEEecCccCCceeEEEEEeCCeEEEeeCC--CCC--CceeEE-cchhhhhhccCCCeEEEe
Q 003213 222 GHFMKGDAVIVIKGDLKNLKGWVEKVDEENVHIRPEM--KGL--PKTLAV-NSKELCKYFEPGNHVKVV 285 (838)
Q Consensus 222 ~~F~~GD~V~V~~Gel~~l~G~V~~V~~d~V~i~~~~--~~l--~~~i~v-~~~~LrK~F~~GDhVkVi 285 (838)
..|++||.| .|+|++|..+-+.|.-.. .++ ..++.. ...++.++|++||.|++.
T Consensus 27 ~~~~~G~iv----------~G~V~~i~~~g~~Vdig~k~~g~lp~sEis~~~~~~~~~~~~~G~~v~~~ 85 (318)
T PRK07400 27 YHFKPGDIV----------NGTVFSLEPRGALIDIGAKTAAFMPIQEMSINRVEGPEEVLQPNETREFF 85 (318)
T ss_pred hhcCCCCEE----------EEEEEEEECCEEEEEECCCeEEEEEHHHhccccccCHHHccCCCCEEEEE
Confidence 358899987 577888877755444321 111 111111 124456679999988764
No 91
>COG1862 YajC Preprotein translocase subunit YajC [Intracellular trafficking and secretion]
Probab=57.01 E-value=13 Score=34.75 Aligned_cols=41 Identities=27% Similarity=0.482 Sum_probs=33.9
Q ss_pred CcEEEEeecCCCCceeEEEeecCCeEEEEeccCceEEEEecccccc
Q 003213 508 GTTVKVRLGPYKGYRGRVVDVKGQSVRVELESQMKVVTVDRSMISD 553 (838)
Q Consensus 508 GktV~I~~GpyKG~~G~Vkdat~~~~rVELhs~~k~I~V~r~~l~~ 553 (838)
|..|. +.| |+.|+|..+.++++.|||. .+-.+++.|+.|+.
T Consensus 47 GD~Vv-T~g---Gi~G~V~~v~d~~v~I~l~-~~~~i~~~k~aI~~ 87 (97)
T COG1862 47 GDEVV-TIG---GIVGTVTKVGDDTVEIELG-DGTKIKFEKEAIAT 87 (97)
T ss_pred CCEEE-EcC---CeEEEEEEEecCcEEEEEC-CCeEEEEEHHHHHh
Confidence 44554 344 7999999999999999999 77789999999874
No 92
>cd05687 S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 1 of the Escherichia coli and Homo sapiens RPS1 (ec1 and hs1, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=56.85 E-value=59 Score=27.38 Aligned_cols=43 Identities=23% Similarity=0.277 Sum_probs=27.2
Q ss_pred ceeEEEEEeCCeEEEeeCCCCCCceeEEcchhh--------hhhccCCCeEEEe
Q 003213 240 LKGWVEKVDEENVHIRPEMKGLPKTLAVNSKEL--------CKYFEPGNHVKVV 285 (838)
Q Consensus 240 l~G~V~~V~~d~V~i~~~~~~l~~~i~v~~~~L--------rK~F~~GDhVkVi 285 (838)
.+|+|++|.++.+.+.-.. ..+=.++.+++ .+.|++||.+++.
T Consensus 4 v~g~V~~i~~~~~~v~l~~---~~~g~l~~~e~~~~~~~~~~~~~~~Gd~i~~~ 54 (70)
T cd05687 4 VKGTVVSVDDDEVLVDIGY---KSEGIIPISEFSDDPIENGEDEVKVGDEVEVY 54 (70)
T ss_pred EEEEEEEEeCCEEEEEeCC---CceEEEEHHHhCccccCCHhHcCCCCCEEEEE
Confidence 3789999988765554321 12233444555 4569999998765
No 93
>cd05791 S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. ScCSL4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In S. cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=55.87 E-value=20 Score=32.80 Aligned_cols=50 Identities=22% Similarity=0.329 Sum_probs=29.2
Q ss_pred CCCCEEEEecCccCCceeEEEEEeCCeE--EEeeCC-CCCCc----ee--------EEcchhhhhhccCCCeEEE
Q 003213 225 MKGDAVIVIKGDLKNLKGWVEKVDEENV--HIRPEM-KGLPK----TL--------AVNSKELCKYFEPGNHVKV 284 (838)
Q Consensus 225 ~~GD~V~V~~Gel~~l~G~V~~V~~d~V--~i~~~~-~~l~~----~i--------~v~~~~LrK~F~~GDhVkV 284 (838)
++||.| .|+|++|....+ .|..-. ..+.. -| ++...+++++|++||.|+.
T Consensus 5 ~~GDiV----------ig~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~~dv~~~~~d~~~~~~~f~~GDiV~A 69 (92)
T cd05791 5 KVGSIV----------IARVTRINPRFAKVDILCVGGRPLKESFRGVIRKEDIRATEKDKVEMYKCFRPGDIVRA 69 (92)
T ss_pred CCCCEE----------EEEEEEEcCCEEEEEEEEecCeecCCCcccEEEHHHccccccchHHHHhhcCCCCEEEE
Confidence 678887 578888877743 332211 11111 11 2233378999999998864
No 94
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=54.98 E-value=97 Score=28.08 Aligned_cols=65 Identities=12% Similarity=0.185 Sum_probs=44.7
Q ss_pred CCcEEEEEEEecce-EEEEecCCCCCcEEEEEccccccccccCccccCCCCCeecCCCEEEEEcCCCCCceeeEEEEECC
Q 003213 348 NNSFGVIIRVESEA-FQVLKGVPDRPEVALVKLREIKCKLEKKSNVQDRNKNTVAVKDVVRIVEGPCKGKQGPVEHIYRG 426 (838)
Q Consensus 348 ~~~vGvIv~ier~~-~~VL~~~~~~g~v~~vk~~~I~~K~~~~~~a~D~~gn~i~~gd~Vki~~Gp~kG~~G~Vkhi~r~ 426 (838)
.+..|.|++...+. |.|... +|..+.+.. ..|+.+ .==|..||.|.|---||.-..|.|.|+|..
T Consensus 5 ~q~~g~V~~~lG~~~~~V~~~---dG~~~la~i---pgK~Rk--------~iwI~~GD~VlVe~~~~~~~kg~Iv~r~~~ 70 (83)
T smart00652 5 GQEIAQVVKMLGNGRLEVMCA---DGKERLARI---PGKMRK--------KVWIRRGDIVLVDPWDFQDVKADIIYKYTK 70 (83)
T ss_pred CcEEEEEEEEcCCCEEEEEEC---CCCEEEEEE---chhhcc--------cEEEcCCCEEEEEecCCCCCEEEEEEEeCH
Confidence 46789999998664 777773 566666553 223221 225789999999877776678999888853
No 95
>PRK04914 ATP-dependent helicase HepA; Validated
Probab=54.84 E-value=56 Score=42.05 Aligned_cols=65 Identities=14% Similarity=0.161 Sum_probs=55.5
Q ss_pred EEEEEEeCCCCeEEEEeccCCCCceEEecCCCceEcCCCCCCcEEEEcCCCCCceEEEEEEeCCCeEEEe
Q 003213 749 VGVIREVLPDGSCRVVLGSSGNGDTITALPNEIEIVPPRKTDKIKIMGGPHRGATGKLIGVDGTDGIVKV 818 (838)
Q Consensus 749 ~gvI~~V~~dg~~~V~l~~~~~g~~v~v~~~~Le~V~P~kgd~VkVi~G~~rG~tG~LisiD~~dgiVk~ 818 (838)
-|+|.+|.+ .+++|..+.+++.+...++..-|.-|.+.+||+|.+..| ...++..|.+.+|++..
T Consensus 18 lG~v~~~d~-r~vtv~fpas~e~R~ya~~~apl~Rv~~~~g~~v~~~~~----~~~~v~~v~~~~gl~~y 82 (956)
T PRK04914 18 LGTVVAVDG-RTVTLLFPATGENRLYARNDAPLTRVMFNPGDTITSHEG----WQLTVEEVEEENGLLTY 82 (956)
T ss_pred cEEEEEEeC-CEEEEEecCCCCceeeecCCCCceeeecCCCCEEEecCC----CEEEEEEEeccCCcEEE
Confidence 789999965 889999999987788888999999999999999997665 45777778888888775
No 96
>PF11213 DUF3006: Protein of unknown function (DUF3006); InterPro: IPR021377 This family of proteins has no known function.
Probab=54.66 E-value=24 Score=30.78 Aligned_cols=42 Identities=17% Similarity=0.260 Sum_probs=35.4
Q ss_pred eeEEEEEeCCeEEEeeCCCCCCceeEEcchhhhhhccCCCeEEE
Q 003213 241 KGWVEKVDEENVHIRPEMKGLPKTLAVNSKELCKYFEPGNHVKV 284 (838)
Q Consensus 241 ~G~V~~V~~d~V~i~~~~~~l~~~i~v~~~~LrK~F~~GDhVkV 284 (838)
++.|.+++++.+.+..+... +.+.|+.+.|=.-.++||.+.+
T Consensus 1 k~ivDRiE~~~AVl~~~~~~--~~~~vp~~~LP~~~keGDvl~i 42 (71)
T PF11213_consen 1 KAIVDRIEGDYAVLELEDGE--KEIDVPRSRLPEGAKEGDVLEI 42 (71)
T ss_pred CeEEEEEeCCEEEEEECCCe--EEEEEEHHHCCCCCCcccEEEE
Confidence 36889999998888876553 5799999999999999997776
No 97
>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=54.64 E-value=35 Score=30.92 Aligned_cols=44 Identities=23% Similarity=0.437 Sum_probs=32.9
Q ss_pred hhhhhhccCCCeEEEeccccCCceEEEEEEeCcEEEEEeCCCCCeEEEc
Q 003213 270 KELCKYFEPGNHVKVVSGTQAGATGMVLKVEQHVLIILSDTTKEDIRVF 318 (838)
Q Consensus 270 ~~LrK~F~~GDhVkVi~G~~~getGlVvkVe~~~v~vlSD~t~~ei~V~ 318 (838)
+++....++||.|...+| --|.|++++++.++|-.. .+-++++.
T Consensus 32 ~~m~~~L~~Gd~VvT~gG----i~G~V~~i~d~~v~vei~-~g~~i~~~ 75 (84)
T TIGR00739 32 KKLIESLKKGDKVLTIGG----IIGTVTKIAENTIVIELN-DNTEITFS 75 (84)
T ss_pred HHHHHhCCCCCEEEECCC----eEEEEEEEeCCEEEEEEC-CCeEEEEE
Confidence 577788999999998887 669999999988866432 23445443
No 98
>PRK02749 photosystem I reaction center subunit IV; Provisional
Probab=54.48 E-value=18 Score=31.55 Aligned_cols=38 Identities=26% Similarity=0.385 Sum_probs=29.8
Q ss_pred CCCCCEEEEecC--cCCCceEEEEEEeCCCCEEEEEEeeccc
Q 003213 72 LSRDTWVRMKIG--NYKGDLAKVVDVDNVRQRVTVKLIPRID 111 (838)
Q Consensus 72 l~~G~~VRik~G--~ykGDlaqV~~vd~~~~~V~vkliPRiD 111 (838)
|+.|+.|||+|- -.=+|.|.|..||.++ +.--++=|+|
T Consensus 3 i~rGskVrIlR~ESYWyn~vGtV~svD~sg--i~YPV~VRF~ 42 (71)
T PRK02749 3 ISRGDKVRILRPESYWYNEVGTVASVDKSG--IKYPVIVRFD 42 (71)
T ss_pred cccCCEEEEccccceeecCcceEEEEccCC--CeeeEEEEee
Confidence 678999999983 5679999999999886 4444555555
No 99
>CHL00125 psaE photosystem I subunit IV; Reviewed
Probab=54.44 E-value=21 Score=30.54 Aligned_cols=38 Identities=18% Similarity=0.361 Sum_probs=28.2
Q ss_pred CCCCCEEEEec--CcCCCceEEEEEEeCCCCEEEEEEeeccc
Q 003213 72 LSRDTWVRMKI--GNYKGDLAKVVDVDNVRQRVTVKLIPRID 111 (838)
Q Consensus 72 l~~G~~VRik~--G~ykGDlaqV~~vd~~~~~V~vkliPRiD 111 (838)
++.|+.|||+| --.=+|.|.|..||.++ +.--++=|+|
T Consensus 2 i~rGskVrIlR~ESYWyn~vGtV~svd~~g--i~YPV~VRF~ 41 (64)
T CHL00125 2 VKRGSKVRILRKESYWYNEIGTVATVDQSG--IRYPVLVRFE 41 (64)
T ss_pred cccCCEEEEccccceeecCcceEEEEcCCC--CCccEEEEEe
Confidence 57899999998 35678999999999875 3333344555
No 100
>PLN00036 40S ribosomal protein S4; Provisional
Probab=54.27 E-value=50 Score=36.14 Aligned_cols=72 Identities=19% Similarity=0.251 Sum_probs=50.1
Q ss_pred cEEEEEEeCCCCeEEEEeccC--CCCceEEec--CC-CceEcCCCCCCcEEEEcCCCCCceEEEEEEeC---CCeEEEec
Q 003213 748 VVGVIREVLPDGSCRVVLGSS--GNGDTITAL--PN-EIEIVPPRKTDKIKIMGGPHRGATGKLIGVDG---TDGIVKVD 819 (838)
Q Consensus 748 ~~gvI~~V~~dg~~~V~l~~~--~~g~~v~v~--~~-~Le~V~P~kgd~VkVi~G~~rG~tG~LisiD~---~dgiVk~d 819 (838)
+.|++.=++.||.+ +...+. ..+|+|.++ .. =++.+.-..|..+.|+.|.+.|.+|+++.|.. ..-+|.+.
T Consensus 133 ~gG~~ql~~hDGrn-i~~~d~~~k~~Dtv~i~l~~~kI~~~ikfe~G~l~~vtgG~n~GrvG~I~~i~~~~~~~~iV~i~ 211 (261)
T PLN00036 133 QKGIPYLNTHDGRT-IRYPDPLIKANDTIKIDLETNKIVDFIKFDVGNLVMVTGGRNRGRVGVIKNREKHKGSFEIIHVK 211 (261)
T ss_pred cCCeEEEEecCCce-eccCCCccccCCEEEEeCCCCceeeEEecCCCCEEEEECCeeceeEEEEEEEEecCCCCCEEEEE
Confidence 35566666667877 332221 126777775 22 26666779999999999999999999999983 23477776
Q ss_pred C
Q 003213 820 V 820 (838)
Q Consensus 820 ~ 820 (838)
+
T Consensus 212 d 212 (261)
T PLN00036 212 D 212 (261)
T ss_pred e
Confidence 4
No 101
>PTZ00118 40S ribosomal protein S4; Provisional
Probab=53.97 E-value=55 Score=35.86 Aligned_cols=72 Identities=18% Similarity=0.247 Sum_probs=50.2
Q ss_pred cEEEEEEeCCCCeEEEEeccC--CCCceEEec-CCC--ceEcCCCCCCcEEEEcCCCCCceEEEEEEeC---CCeEEEec
Q 003213 748 VVGVIREVLPDGSCRVVLGSS--GNGDTITAL-PNE--IEIVPPRKTDKIKIMGGPHRGATGKLIGVDG---TDGIVKVD 819 (838)
Q Consensus 748 ~~gvI~~V~~dg~~~V~l~~~--~~g~~v~v~-~~~--Le~V~P~kgd~VkVi~G~~rG~tG~LisiD~---~dgiVk~d 819 (838)
+.|++.=++-||.+ +...|. ..+|+|.++ .++ ++.+.-..|..+.|+.|.+.|.+|+++.+.. +.-+|.++
T Consensus 133 ~gg~~~l~~hDGrn-i~~~d~~ik~~Dtv~i~l~~~kI~~~ikfe~G~l~~vtgG~n~GriG~I~~~~~~~~~~~~V~i~ 211 (262)
T PTZ00118 133 PKEVSIAVTHDGRT-IRYVHPDVKVGDSLRLDLETGKVLEFLKFEVGNLVMITGGHNVGRVGTIVSKEKHPGSFDLIHVK 211 (262)
T ss_pred CCCeEEEEecCcce-eccCCCcccCCCEEEEECCCCceeeEEecCCCCEEEEECCeeceeEEEEEEEEecCCCCcEEEEE
Confidence 35566656667877 332221 126777776 222 6666679999999999999999999998774 34577776
Q ss_pred C
Q 003213 820 V 820 (838)
Q Consensus 820 ~ 820 (838)
+
T Consensus 212 d 212 (262)
T PTZ00118 212 D 212 (262)
T ss_pred e
Confidence 4
No 102
>PTZ00223 40S ribosomal protein S4; Provisional
Probab=53.97 E-value=44 Score=36.75 Aligned_cols=72 Identities=18% Similarity=0.366 Sum_probs=50.6
Q ss_pred cEEEEEEeCCCCeEEEEecc--CCCCceEEec---CCCceEcCCCCCCcEEEEcCCCCCceEEEEEEeCC---CeEEEec
Q 003213 748 VVGVIREVLPDGSCRVVLGS--SGNGDTITAL---PNEIEIVPPRKTDKIKIMGGPHRGATGKLIGVDGT---DGIVKVD 819 (838)
Q Consensus 748 ~~gvI~~V~~dg~~~V~l~~--~~~g~~v~v~---~~~Le~V~P~kgd~VkVi~G~~rG~tG~LisiD~~---dgiVk~d 819 (838)
+.|++.=++-||.+ +...+ -..+|+|.++ +.=++.+.-..|..+.|+.|.+.|.+|++..|... .-+|.+.
T Consensus 130 ~gG~~ql~~hDGrn-I~~~d~~~k~~Dtv~i~l~~~kI~~~ikfe~G~l~~vtgG~n~GriG~I~~i~~~~~~~~iv~i~ 208 (273)
T PTZ00223 130 TGRIPVAVTHDGHR-IRYPDPRTSRGDTLVYNVKEKKVVDLIKNRNGKVVMVTGGANRGRIGEIVSIERHPGAFDIARLK 208 (273)
T ss_pred cCCeeEEEecCCce-eccCCccccCCCEEEEECCCCeeeEEEecCCCCEEEEECCeeceeEEEEEEEEecCCCCCEEEEE
Confidence 35566666667877 33222 1126777776 33367777799999999999999999999999643 3467766
Q ss_pred C
Q 003213 820 V 820 (838)
Q Consensus 820 ~ 820 (838)
+
T Consensus 209 d 209 (273)
T PTZ00223 209 D 209 (273)
T ss_pred e
Confidence 4
No 103
>KOG0307 consensus Vesicle coat complex COPII, subunit SEC31 [Intracellular trafficking, secretion, and vesicular transport]
Probab=53.65 E-value=3.7e+02 Score=34.93 Aligned_cols=9 Identities=22% Similarity=0.076 Sum_probs=3.4
Q ss_pred EEEeccCce
Q 003213 534 RVELESQMK 542 (838)
Q Consensus 534 rVELhs~~k 542 (838)
++++-+.++
T Consensus 650 ~l~~~~~~~ 658 (1049)
T KOG0307|consen 650 KLAQFSANK 658 (1049)
T ss_pred hhhhcccCc
Confidence 333333333
No 104
>PRK06763 F0F1 ATP synthase subunit alpha; Validated
Probab=52.98 E-value=1.3e+02 Score=31.67 Aligned_cols=27 Identities=30% Similarity=0.535 Sum_probs=20.8
Q ss_pred ceEEEEEEeCcEEEEEeCCCCCeEEEc
Q 003213 292 ATGMVLKVEQHVLIILSDTTKEDIRVF 318 (838)
Q Consensus 292 etGlVvkVe~~~v~vlSD~t~~ei~V~ 318 (838)
--|-||.|+.+.+.|=|.+..+.++|.
T Consensus 42 iEGrVvEV~~~~i~iesk~yn~~v~i~ 68 (213)
T PRK06763 42 IEGRVVEVDNGVIVIKSKQYEEPVSVY 68 (213)
T ss_pred eeeEEEEEeCCEEEEEeccCCCceEEE
Confidence 457888888888888888777776663
No 105
>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=52.74 E-value=61 Score=45.00 Aligned_cols=96 Identities=15% Similarity=0.153 Sum_probs=67.1
Q ss_pred ccccCCCCEEEEecCccCCceeEEEEEeCC--eEEEeeCCCCCCceeEEcchhhhh-----------hccCCCeEEEecc
Q 003213 221 KGHFMKGDAVIVIKGDLKNLKGWVEKVDEE--NVHIRPEMKGLPKTLAVNSKELCK-----------YFEPGNHVKVVSG 287 (838)
Q Consensus 221 ~~~F~~GD~V~V~~Gel~~l~G~V~~V~~d--~V~i~~~~~~l~~~i~v~~~~LrK-----------~F~~GDhVkVi~G 287 (838)
...|++||.|+.-.| ....|+.|+.+ .|++..-.. .....+.++++.+ .|..||.++....
T Consensus 1327 ~~~Y~~G~vv~~~~~----~y~~V~~vd~~~~~v~l~~~~~--G~~~~~~p~~~~~~~~~~y~~~~~~l~~GDri~~t~~ 1400 (1960)
T TIGR02760 1327 MMPFEKGAVLRLKKD----AYLTIADIDREHGKLTVADIKT--GSERDILPRQLDHTFTSLYSDSELPLAKGDKIRLRAT 1400 (1960)
T ss_pred ccccCCCcEEEecCC----cEEEEEEecCCCCEEEEEecCC--CCeEeeChhhcCcccceeeccccccccCCCEEEEeec
Confidence 368999999995544 55668888744 555543122 2456666666653 5789999988753
Q ss_pred -----ccCCceEEEEEEeCcEEEEEeCCCCCeEEEcccccc
Q 003213 288 -----TQAGATGMVLKVEQHVLIILSDTTKEDIRVFADDVV 323 (838)
Q Consensus 288 -----~~~getGlVvkVe~~~v~vlSD~t~~ei~V~~~dL~ 323 (838)
.-.|+.+.|+.|+.+.+++.+|. ++++++.+.+..
T Consensus 1401 d~~~g~~n~~~~~V~~v~~~~~~~~~~~-~~~~~l~~~~~~ 1440 (1960)
T TIGR02760 1401 DKNRGIKANEVYTVTQVVNGLSVQLSKV-KNSLSLKPIQAK 1440 (1960)
T ss_pred CcccccccCCeEEEEEEcCCcEEEEcCC-CceEEecCchhh
Confidence 33589999999988888888776 577888776543
No 106
>PF11515 Cul7: Mouse development and cellular proliferation protein Cullin-7; InterPro: IPR021097 The CPH domain is found in the Cullin-7, PARC and HERC2 proteins, which are all components of known or predicted E3-ubiquitin ligases. The CPH domain is a protein-protein interaction module that binds the teramerisation domain of the tumour suppressor protein p53 []. Structurally it forms a beta-barrel fold similar to the SH3, Tudor and KOW and domains. Unlike the SH3 and Tudor domains, which bind to small peptides, the CPH domain appears to bind to an extended surface on p53.; PDB: 2JUF_A 2JNG_A.
Probab=52.53 E-value=15 Score=32.94 Aligned_cols=30 Identities=20% Similarity=0.102 Sum_probs=19.6
Q ss_pred ccCCCCCEEEEec---CcCCCceEEEEEEeCCC
Q 003213 70 IDLSRDTWVRMKI---GNYKGDLAKVVDVDNVR 99 (838)
Q Consensus 70 ~~l~~G~~VRik~---G~ykGDlaqV~~vd~~~ 99 (838)
..|++|+.||+.+ ...+||.|+|..++.++
T Consensus 16 ~~i~~GM~VRc~~~yeeV~~GD~G~V~k~~~dg 48 (78)
T PF11515_consen 16 DNIQPGMRVRCCRDYEEVRAGDEGEVFKQDRDG 48 (78)
T ss_dssp HH--TT-EEEESS-BTTB-TT-EEE-EEEE-TT
T ss_pred HhCCCCcEEEEecccccccccccceeEeeccCC
Confidence 4789999999986 58999999999988665
No 107
>PRK00092 ribosome maturation protein RimP; Reviewed
Probab=52.08 E-value=25 Score=35.16 Aligned_cols=50 Identities=28% Similarity=0.502 Sum_probs=39.0
Q ss_pred ccccCcEEEEe----ecCCCCceeEEEeecCCeEEEEeccCceEEEEecccccc
Q 003213 504 DALVGTTVKVR----LGPYKGYRGRVVDVKGQSVRVELESQMKVVTVDRSMISD 553 (838)
Q Consensus 504 d~liGktV~I~----~GpyKG~~G~Vkdat~~~~rVELhs~~k~I~V~r~~l~~ 553 (838)
..++|+.|+|+ .+.-|=+.|++.+++++.+.++...+.++++++.++|+-
T Consensus 94 ~r~~G~~v~V~~~~~~~~~~~~~G~L~~~~~~~i~l~~~~~~~~~~i~~~~I~~ 147 (154)
T PRK00092 94 RRFIGREVKVKLYEPIDGRKKFQGILLAVDGETVTLEVEGKEKEVEIPLDNIAK 147 (154)
T ss_pred HHhCCCeEEEEEEcccCCceEEEEEEEEeeCCEEEEEECCCeEEEEEEHHHcce
Confidence 57899999997 244466789999999999988876543488888888763
No 108
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=51.89 E-value=2.6e+02 Score=34.50 Aligned_cols=121 Identities=14% Similarity=0.229 Sum_probs=57.7
Q ss_pred hhhhhccCCCeEEEeccccCCceEEEEEEeCcEEEEEeCCCCCeEEEcccccccccccccccccCCceEecceEEeCCCc
Q 003213 271 ELCKYFEPGNHVKVVSGTQAGATGMVLKVEQHVLIILSDTTKEDIRVFADDVVESSEVTTGITKIGDYELRDLVLLDNNS 350 (838)
Q Consensus 271 ~LrK~F~~GDhVkVi~G~~~getGlVvkVe~~~v~vlSD~t~~ei~V~~~dL~~~~e~~~g~d~~g~y~l~DLVqld~~~ 350 (838)
...+.|++||.|++. |++++.+ .+.+.+..+++....-. .-...|+.++.|+
T Consensus 516 ~~~~~~~vGd~V~vk----------V~~id~~---------~~~I~lS~K~~~~~p~~----~~~~~~~~G~~v~----- 567 (647)
T PRK00087 516 KPSDVLKVGDEIKVY----------ILDIDKE---------NKKLSLSLKKLLPDPWE----NVEEKYPVGSIVL----- 567 (647)
T ss_pred CHHHhcCCCCEEEEE----------EEEEECC---------CCEEEEEeeccccChhh----hhhhhccCCeEEE-----
Confidence 355789999998763 5566431 22222222333221100 0113456666655
Q ss_pred EEEEEEEecceEEEEecCCCCCcEEEEEccccccccccCccccCCCCCeecCCCEEEEEcCCCCCceeeEEEEEC--CEE
Q 003213 351 FGVIIRVESEAFQVLKGVPDRPEVALVKLREIKCKLEKKSNVQDRNKNTVAVKDVVRIVEGPCKGKQGPVEHIYR--GIL 428 (838)
Q Consensus 351 vGvIv~ier~~~~VL~~~~~~g~v~~vk~~~I~~K~~~~~~a~D~~gn~i~~gd~Vki~~Gp~kG~~G~Vkhi~r--~~l 428 (838)
|.|.++.+-.++|--. .+-.-.+..+++... + .......+++||.|++. |+.|.. ..+
T Consensus 568 -g~V~~i~~~G~fV~l~---~~i~Gli~~sel~~~---~---~~~~~~~~kvGd~V~vk----------V~~id~e~~rI 627 (647)
T PRK00087 568 -GKVVRIAPFGAFVELE---PGVDGLVHISQISWK---R---IDKPEDVLSEGEEVKAK----------ILEVDPEEKRI 627 (647)
T ss_pred -EEEEEEECCeEEEEEC---CCCEEEEEhhhcCcc---c---cCCHhhcCCCCCEEEEE----------EEEEeCCCCEE
Confidence 7777777665554321 111112333333211 1 11223467899988764 444432 335
Q ss_pred EEEeCceeccc
Q 003213 429 FIHDRHHLEHA 439 (838)
Q Consensus 429 FL~~~~~~En~ 439 (838)
-|.-+...+|-
T Consensus 628 ~lslk~~~~~~ 638 (647)
T PRK00087 628 RLSIKEVEEEP 638 (647)
T ss_pred EEEEeecccCc
Confidence 55555555544
No 109
>PRK14638 hypothetical protein; Provisional
Probab=51.59 E-value=27 Score=35.02 Aligned_cols=47 Identities=11% Similarity=0.161 Sum_probs=38.5
Q ss_pred ccccCcEEEEeecCCCCceeEEEeecCCeEEEEeccCceEEEEeccccc
Q 003213 504 DALVGTTVKVRLGPYKGYRGRVVDVKGQSVRVELESQMKVVTVDRSMIS 552 (838)
Q Consensus 504 d~liGktV~I~~GpyKG~~G~Vkdat~~~~rVELhs~~k~I~V~r~~l~ 552 (838)
..++|+.|+|+-.--|-+.|++++++++.++++. ..+++.++.++|+
T Consensus 96 ~r~~G~~v~V~~~~~k~~~G~L~~~~~~~i~l~~--~~~~~~i~~~~I~ 142 (150)
T PRK14638 96 VRFTGKLAKIVTKDGKTFIGRIESFVDGTITISD--EKEKYEINIDDVK 142 (150)
T ss_pred HHhCCCEEEEEECCCcEEEEEEEEEeCCEEEEEE--CCcEEEEEhHHcc
Confidence 5789999999753348899999999999999874 5677888887775
No 110
>smart00361 RRM_1 RNA recognition motif.
Probab=51.44 E-value=28 Score=29.65 Aligned_cols=28 Identities=21% Similarity=0.432 Sum_probs=25.0
Q ss_pred CCCceEEEEEecChHHHHHHHhcCccee
Q 003213 20 DHLKNYIYIEADKEAHVKEACKGLRNIY 47 (838)
Q Consensus 20 ~~lkGyIyVEA~~~~~V~~ai~g~~~v~ 47 (838)
.+.+||.||+-.+..+...|++.|.+-.
T Consensus 34 ~~~rG~~fV~f~~~~dA~~A~~~l~g~~ 61 (70)
T smart00361 34 NHKRGNVYITFERSEDAARAIVDLNGRY 61 (70)
T ss_pred CCCcEEEEEEECCHHHHHHHHHHhCCCE
Confidence 3579999999999999999999988854
No 111
>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=51.44 E-value=32 Score=30.76 Aligned_cols=50 Identities=26% Similarity=0.462 Sum_probs=38.4
Q ss_pred ccccCcEEEEe-ecC---CCCceeEEEeecCCeEEEEeccC--ceEEEEecccccc
Q 003213 504 DALVGTTVKVR-LGP---YKGYRGRVVDVKGQSVRVELESQ--MKVVTVDRSMISD 553 (838)
Q Consensus 504 d~liGktV~I~-~Gp---yKG~~G~Vkdat~~~~rVELhs~--~k~I~V~r~~l~~ 553 (838)
..++|+.|+|. +.+ -|-+.|++.+++++.++++++.+ .+.++++.++|.-
T Consensus 21 ~r~~G~~v~v~~~~~~~~~~~~~G~L~~~~~~~v~l~~~~~~~~~~~~i~~~~I~k 76 (83)
T cd01734 21 ERAVGKYVHVKLYQPIDGQKEFEGTLLGVDDDTVTLEVDIKTRGKTVEIPLDKIAK 76 (83)
T ss_pred HHhCCCEEEEEEEcccCCeEEEEEEEEeEeCCEEEEEEecCCCCeEEEEEhHHeeE
Confidence 57899999995 433 35578999999999999887642 5678888877753
No 112
>PF02427 PSI_PsaE: Photosystem I reaction centre subunit IV / PsaE; InterPro: IPR003375 PsaE is a 69 amino acid polypeptide from photosystem I present on the stromal side of the thylakoid membrane. The structure is comprised of a well-defined five-stranded beta-sheet similar to SH3 domains []. This subunit may form complexes with ferredoxin and ferredoxin-oxidoreductase in the photosystem I reaction centre.; GO: 0015979 photosynthesis, 0009522 photosystem I, 0009538 photosystem I reaction center; PDB: 1PSF_A 1PSE_A 2WSF_E 2WSC_E 2O01_E 2WSE_E 1GXI_E 1JB0_E 3PCQ_E 1QP2_A ....
Probab=51.13 E-value=33 Score=29.26 Aligned_cols=28 Identities=21% Similarity=0.348 Sum_probs=22.7
Q ss_pred CCCCCEEEEec--CcCCCceEEEEEEeCCC
Q 003213 72 LSRDTWVRMKI--GNYKGDLAKVVDVDNVR 99 (838)
Q Consensus 72 l~~G~~VRik~--G~ykGDlaqV~~vd~~~ 99 (838)
++.|+.|||+| --.=+|+|.|..||.++
T Consensus 1 i~rgskVrIlR~ESYWyn~vGtV~svdqs~ 30 (61)
T PF02427_consen 1 IKRGSKVRILRKESYWYNEVGTVASVDQSG 30 (61)
T ss_dssp S-TTSEEEE-SSSSTTTTSEEEEEEETTSS
T ss_pred CCCCCEEEEccccceeecccceEEEEccCC
Confidence 46899999998 35689999999999887
No 113
>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=51.03 E-value=46 Score=30.48 Aligned_cols=50 Identities=22% Similarity=0.248 Sum_probs=38.2
Q ss_pred CccccCcEEEEeecC---CCCceeEEEeecCCeEEEEeccCceEEEEecccccc
Q 003213 503 HDALVGTTVKVRLGP---YKGYRGRVVDVKGQSVRVELESQMKVVTVDRSMISD 553 (838)
Q Consensus 503 rd~liGktV~I~~Gp---yKG~~G~Vkdat~~~~rVELhs~~k~I~V~r~~l~~ 553 (838)
+-+|+|-.|+|.+=+ |-|..|+|.+-|..+++|+ ...+++.+|.|..-.+
T Consensus 9 ~~dl~G~~i~V~~s~~pslvG~~GiVV~ETknt~~I~-t~~~~~~~IpK~~~vF 61 (89)
T PF01868_consen 9 KADLIGAKIEVVRSKNPSLVGIEGIVVDETKNTFVIV-TEDGKVKTIPKAGSVF 61 (89)
T ss_dssp TS--TT-EEEEEEESSCCCTTEEEEEEEEETTEEEEE-ETTEEEEEEESTTEEE
T ss_pred hhhhcCCEEEEEEcCCCCccCCEEEEEEcccceEEEE-ecCCcEEEEecCCEEE
Confidence 357899999998765 6799999999999999987 4455788999888543
No 114
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=51.00 E-value=2.6e+02 Score=31.90 Aligned_cols=45 Identities=13% Similarity=0.164 Sum_probs=31.0
Q ss_pred eeeChhhhhhccccccccccCCCCCEEEEecCcCCCceEEEEEEeCCCCEEEEEEe
Q 003213 52 MLVPIREMTDVLAVESKAIDLSRDTWVRMKIGNYKGDLAKVVDVDNVRQRVTVKLI 107 (838)
Q Consensus 52 ~~Vpi~Em~~~L~~~~~~~~l~~G~~VRik~G~ykGDlaqV~~vd~~~~~V~vkli 107 (838)
..+|..||.+-. .+.....+++|+.|++ .|..++.++.++.|-+-
T Consensus 44 g~lp~~e~~~~~-~~~~~~~~~vGd~v~~----------~V~~v~~~~~~i~lS~k 88 (390)
T PRK06676 44 GVIPISELSNDH-IEDINDVVKVGDELEV----------YVLKVEDGEGNLLLSKR 88 (390)
T ss_pred EEEEHHHhcccc-ccCcccccCCCCEEEE----------EEEEEECCCCCEEEEHH
Confidence 578999997642 2222335789999885 78999888876666543
No 115
>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=50.97 E-value=31 Score=33.89 Aligned_cols=49 Identities=31% Similarity=0.564 Sum_probs=35.4
Q ss_pred ccccCcEEEEee-cCC---CCceeEEEeecCCeEEEEeccCc--eEEEEeccccc
Q 003213 504 DALVGTTVKVRL-GPY---KGYRGRVVDVKGQSVRVELESQM--KVVTVDRSMIS 552 (838)
Q Consensus 504 d~liGktV~I~~-Gpy---KG~~G~Vkdat~~~~rVELhs~~--k~I~V~r~~l~ 552 (838)
..++|+.|+|.- -+. |=+.|++.+++++.+.+++..+. ++++|+.++|.
T Consensus 83 ~~~iG~~v~v~~~~~~~~~~~~~G~L~~~~~~~i~l~~~~~~~~~~~~I~~~~I~ 137 (141)
T PF02576_consen 83 ERFIGRKVKVKLKQPVNGRKEFEGKLLEVDEDEITLEVEGKGKKKEVEIPFSDIK 137 (141)
T ss_dssp HHH-SEEEEEE-SS-SSS-SEEEEEEEEEETTEEEEEEE-SS-EEEEEE-SS--S
T ss_pred HHhcCCeEEEEEeccCCCcEEEEEEEEEEeCCEEEEEECCccceEEEEEEHHHCc
Confidence 478999999995 333 44799999999999999998884 68888888875
No 116
>PRK14637 hypothetical protein; Provisional
Probab=50.50 E-value=35 Score=34.35 Aligned_cols=47 Identities=21% Similarity=0.244 Sum_probs=37.2
Q ss_pred ccccCcEEEEeecCCCCc-eeEEEeecCCeEEEEeccCceEEEEeccccc
Q 003213 504 DALVGTTVKVRLGPYKGY-RGRVVDVKGQSVRVELESQMKVVTVDRSMIS 552 (838)
Q Consensus 504 d~liGktV~I~~GpyKG~-~G~Vkdat~~~~rVELhs~~k~I~V~r~~l~ 552 (838)
..++|+.|+|+-..-|.+ .|++++++++.+.++. ..+++.++.++|+
T Consensus 94 ~r~~G~~V~V~l~~~~~~~~G~L~~~~d~~v~l~~--~~~~~~i~~~~I~ 141 (151)
T PRK14637 94 SIFVGETVKVWFECTGQWQVGTIAEADETCLVLTS--DGVPVTIPYVQIT 141 (151)
T ss_pred HHhCCCEEEEEECCCCcEEEEEEEEEeCCEEEEEE--CCEEEEEEHHHee
Confidence 578999999986223567 5999999999999885 5677888887775
No 117
>PRK14644 hypothetical protein; Provisional
Probab=50.07 E-value=25 Score=34.77 Aligned_cols=49 Identities=14% Similarity=0.343 Sum_probs=37.2
Q ss_pred ccccCcEEEEee-cC---CCCceeEEEeecCCeEEEEe--ccCceEEEEeccccc
Q 003213 504 DALVGTTVKVRL-GP---YKGYRGRVVDVKGQSVRVEL--ESQMKVVTVDRSMIS 552 (838)
Q Consensus 504 d~liGktV~I~~-Gp---yKG~~G~Vkdat~~~~rVEL--hs~~k~I~V~r~~l~ 552 (838)
..++|+.|+|+- .+ -|=+.|+++++.+..++++. ..+-+.|++++++|+
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 477999999963 33 36688999999999999864 444567778888775
No 118
>PRK14712 conjugal transfer nickase/helicase TraI; Provisional
Probab=49.88 E-value=74 Score=43.14 Aligned_cols=85 Identities=14% Similarity=0.182 Sum_probs=63.7
Q ss_pred cccCCCCEEEEecCcc-CCceeEEEEEeCC--eEEEeeCCCCCCceeEEcchhhhh----------hccCCCeEEEeccc
Q 003213 222 GHFMKGDAVIVIKGDL-KNLKGWVEKVDEE--NVHIRPEMKGLPKTLAVNSKELCK----------YFEPGNHVKVVSGT 288 (838)
Q Consensus 222 ~~F~~GD~V~V~~Gel-~~l~G~V~~V~~d--~V~i~~~~~~l~~~i~v~~~~LrK----------~F~~GDhVkVi~G~ 288 (838)
.+|++|+.|+....+. +...-.|++|+.+ .+++... . .+..+|.++.+-+ .+..||.+++....
T Consensus 515 ~~Y~~GmVl~~~~r~~k~~~~y~V~~V~~~~n~LtL~~~-d--G~~~~~~p~~~~~~~~vy~~e~lelA~GDrlr~t~nd 591 (1623)
T PRK14712 515 DMYRPGMVMEQWNPETRSHDRYVTERVTAQSHSLTLRNA-Q--GETQVVRISSLDSSWSLFRPEKMPVADGERLRVTGKI 591 (1623)
T ss_pred hcCCCCCEEEecccCcCcCceEEEEEEcCCCceEEEEcC-C--CcEEEechHHcccceeeecccccccCCCCEEEEccCC
Confidence 6899999999666654 4666699999877 5554332 2 3456777777632 26899999998664
Q ss_pred c-----CCceEEEEEEeCcEEEEEeC
Q 003213 289 Q-----AGATGMVLKVEQHVLIILSD 309 (838)
Q Consensus 289 ~-----~getGlVvkVe~~~v~vlSD 309 (838)
. .|+...|++++++.++|..+
T Consensus 592 ~~~~L~ngd~~tV~~i~~~~itl~~~ 617 (1623)
T PRK14712 592 PGLRVSGGDRLQVASVSEDAMTVVVP 617 (1623)
T ss_pred cccCccCCCEEEEEEecCCeEEEEEC
Confidence 3 57999999999999999866
No 119
>CHL00084 rpl19 ribosomal protein L19
Probab=49.72 E-value=61 Score=31.37 Aligned_cols=41 Identities=22% Similarity=0.351 Sum_probs=29.6
Q ss_pred cccccCCCCEEEE----ecCc---cCCceeEEEEEeCC----eEEEeeCCCC
Q 003213 220 KKGHFMKGDAVIV----IKGD---LKNLKGWVEKVDEE----NVHIRPEMKG 260 (838)
Q Consensus 220 ~~~~F~~GD~V~V----~~Ge---l~~l~G~V~~V~~d----~V~i~~~~~~ 260 (838)
.-..|++||.|+| .+|+ .+...|.|+++.+. ++|+.--..+
T Consensus 19 ~~p~f~~GDtV~V~~~i~eg~k~R~q~F~GvvI~~r~~G~~~tftvRki~~g 70 (117)
T CHL00084 19 NLPKIRVGDTVKVGVLIQEGNKERVQFYEGTVIAKKNSGLNTTITVRKVFQG 70 (117)
T ss_pred CCCccCCCCEEEEEEEEecCCeeEeceEEEEEEEEeCCCCCeeEEEEEeccC
Confidence 3468999999998 4675 45788999999754 5666654433
No 120
>PRK14643 hypothetical protein; Provisional
Probab=49.71 E-value=29 Score=35.42 Aligned_cols=50 Identities=20% Similarity=0.167 Sum_probs=39.4
Q ss_pred ccccCcEEEEee-cCC---CCceeEEEeecCCeEEEEec----cCceEEEEecccccc
Q 003213 504 DALVGTTVKVRL-GPY---KGYRGRVVDVKGQSVRVELE----SQMKVVTVDRSMISD 553 (838)
Q Consensus 504 d~liGktV~I~~-Gpy---KG~~G~Vkdat~~~~rVELh----s~~k~I~V~r~~l~~ 553 (838)
..++|+.|+|+- .|+ |-+.|+++++.++.++++|+ ...+++.+++++|+-
T Consensus 100 ~r~~G~~V~V~l~~~~~g~k~~~G~L~~~~~~~~~l~l~~~~~~~~~~~~ip~~~I~k 157 (164)
T PRK14643 100 VKALNQWVYVQLNNEIKKVKEFEGYVTKYNVNTNTFRFTFFIKGQKKKLDVKYEQIKF 157 (164)
T ss_pred HHhcCCeEEEEEecccCCceEEEEEEEEEeCCcEEEEEEeeccCcCcEEEEeHHHhhh
Confidence 478999999963 444 44889999999999988864 446789999888864
No 121
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=49.57 E-value=4.9e+02 Score=31.21 Aligned_cols=58 Identities=17% Similarity=0.125 Sum_probs=28.5
Q ss_pred cccCCCCEEEEecCccCCceeEEEEEeCCeEEEeeCCCCCCceeEEcchhhhhhccCCCeEEEe
Q 003213 222 GHFMKGDAVIVIKGDLKNLKGWVEKVDEENVHIRPEMKGLPKTLAVNSKELCKYFEPGNHVKVV 285 (838)
Q Consensus 222 ~~F~~GD~V~V~~Gel~~l~G~V~~V~~d~V~i~~~~~~l~~~i~v~~~~LrK~F~~GDhVkVi 285 (838)
..+++||.|+..==...+ .|..+.+. + |.-+.-.++|.. -..+++.++|++||.|+|.
T Consensus 204 ~~lk~G~iv~G~V~~i~~-~G~FVdlg-g-v~Glv~~Sels~---~~v~~~~~~~kvGd~V~vk 261 (486)
T PRK07899 204 NQLQKGQVRKGVVSSIVN-FGAFVDLG-G-VDGLVHVSELSW---KHIDHPSEVVEVGQEVTVE 261 (486)
T ss_pred HhccCCCEEEEEEEEEEC-CeEEEEEC-C-EEEEEEHHHCCC---cccCCHHHhcCCCCEEEEE
Confidence 468899887533222221 24444442 2 211111122211 1124566889999998775
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=49.14 E-value=1e+02 Score=42.91 Aligned_cols=96 Identities=11% Similarity=0.208 Sum_probs=66.9
Q ss_pred ccccCCCCEEEEecCc-cCCceeEEEEEeC--CeEEEeeCCCCCCceeEEcchhhh-------------hhccCCCeEEE
Q 003213 221 KGHFMKGDAVIVIKGD-LKNLKGWVEKVDE--ENVHIRPEMKGLPKTLAVNSKELC-------------KYFEPGNHVKV 284 (838)
Q Consensus 221 ~~~F~~GD~V~V~~Ge-l~~l~G~V~~V~~--d~V~i~~~~~~l~~~i~v~~~~Lr-------------K~F~~GDhVkV 284 (838)
...|++||.|+-..-. +.+-.++|+.|+. +.++|.... .+.++|..++|. ..+..||.+++
T Consensus 679 ~~~Yr~Gdvv~~y~~~~~~~~~y~V~~V~~~~n~L~l~~~d---G~~~~~~p~~l~~~~~~~svy~~~~l~ia~Gdrl~~ 755 (1960)
T TIGR02760 679 AAHYKQGMVIRFWQKGKIPHDDYVVTNVNKHNNTLTLKDAQ---GKTQKFKPSSLKDLERPFSVYRPEQLEVAAGERLQV 755 (1960)
T ss_pred HhhcCCCCEEEeecccCccCCcEEEEEEeCCCCEEEEEcCC---CCEEEECHHHhcccccceeeeccccccccCCCEEEE
Confidence 3689999999975432 3455589999986 567765532 245677777762 24788999988
Q ss_pred ecc-----ccCCceEEEEEEeCcEEEEEeCCCCCeEEEccc
Q 003213 285 VSG-----TQAGATGMVLKVEQHVLIILSDTTKEDIRVFAD 320 (838)
Q Consensus 285 i~G-----~~~getGlVvkVe~~~v~vlSD~t~~ei~V~~~ 320 (838)
... ...|+...|..++.+.++|-.+. ++++++-..
T Consensus 756 trn~~~~gl~ng~~~tV~~i~~~~i~l~~~~-g~~~~L~~~ 795 (1960)
T TIGR02760 756 TGNHFHSRVRNGELLTVSSINNEGITLITED-GQTLHLPHG 795 (1960)
T ss_pred ccCCcccCccCCCEEEEEEEcCCeEEEEeCC-CceEEccCC
Confidence 754 23589999999999888877554 456665433
No 123
>TIGR00037 eIF_5A translation initiation factor eIF-5A. Observed in eukaryotes and archaea.
Probab=48.68 E-value=32 Score=33.74 Aligned_cols=63 Identities=17% Similarity=0.028 Sum_probs=47.7
Q ss_pred ccccCCCCEEEEecCccCCceeEEEEEeCCeEEEeeCCCCCCceeEEcchhhhhhccCCCeEEEec
Q 003213 221 KGHFMKGDAVIVIKGDLKNLKGWVEKVDEENVHIRPEMKGLPKTLAVNSKELCKYFEPGNHVKVVS 286 (838)
Q Consensus 221 ~~~F~~GD~V~V~~Gel~~l~G~V~~V~~d~V~i~~~~~~l~~~i~v~~~~LrK~F~~GDhVkVi~ 286 (838)
...|..+|.|++. .+.--.....-+++|..++|-...--..+|..+. ++.+++++|..|.|++
T Consensus 57 e~~f~s~~~ve~~--~ve~~~~qylY~dg~~~~fMd~etyeq~~i~~~~-~~~~~Lke~~~V~v~~ 119 (130)
T TIGR00037 57 EFVSPSTSKVEVP--IVDRREYQVLAIMGGMVQLMDLDTYETDELPIPE-ELGDSLEPGFEVEYIE 119 (130)
T ss_pred EEEECCCCEEEEe--EEEEEEEEEEEecCCEEEEEcCCCcEEEEecCCh-hHHHHhhcCCEEEEEe
Confidence 4689999999987 5556666778889999999976441122455555 9999999999998886
No 124
>PF14944 TCRP1: Tongue Cancer Chemotherapy Resistant Protein 1
Probab=48.42 E-value=56 Score=32.90 Aligned_cols=27 Identities=26% Similarity=0.549 Sum_probs=13.5
Q ss_pred CCCCCCCCCCCCCCC-CCCCcCCCCCCC
Q 003213 659 TPGGNYSDAGTPRDS-SSTYVNAPSPYL 685 (838)
Q Consensus 659 Tpg~~y~~~~tP~~~-~~~y~~~p~~y~ 685 (838)
|||..|--..||+.. .++|+++|.||+
T Consensus 54 t~gTPyKv~~s~s~~~~ppys~sPnPY~ 81 (195)
T PF14944_consen 54 TAGTPYKVSPSQSNGTVPPYSPSPNPYQ 81 (195)
T ss_pred CCCCcccccCCCCCCCCCCCCCCCCccc
Confidence 344444434444432 455776666663
No 125
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=48.13 E-value=57 Score=41.58 Aligned_cols=51 Identities=20% Similarity=0.102 Sum_probs=40.2
Q ss_pred cccCCCCEEEEecCccCCceeEEEEEeCCeEEEeeCCCCCCceeEEcchhhhhhccCCCeEEEe
Q 003213 222 GHFMKGDAVIVIKGDLKNLKGWVEKVDEENVHIRPEMKGLPKTLAVNSKELCKYFEPGNHVKVV 285 (838)
Q Consensus 222 ~~F~~GD~V~V~~Gel~~l~G~V~~V~~d~V~i~~~~~~l~~~i~v~~~~LrK~F~~GDhVkVi 285 (838)
..|++||.| +|+|++|++|.|.|--. .+.+=-++.+++.+-+++||.|+|.
T Consensus 317 ~~~~~G~iV----------~G~Vv~i~~~~v~VdiG---~K~eGiI~~~E~~~~~kvGd~i~~~ 367 (863)
T PRK12269 317 EAPEPGSVR----------MGTVVQVNAGTVFVDIG---GKSEGRVPVEEFEAPPKAGDGVRVY 367 (863)
T ss_pred ccCCCCCEE----------EEEEEEEECCEEEEEeC---CCceEEeEHHHhccCCCCCCEEEEE
Confidence 568888877 68999999998887763 2344567888888888999998765
No 126
>cd05790 S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=47.66 E-value=21 Score=32.64 Aligned_cols=49 Identities=27% Similarity=0.212 Sum_probs=31.8
Q ss_pred cCCCCEEEEecCccCCceeEEEEEeCC--eEEEeeCCCCCCceeEEc--chhhhhhccCCCeE
Q 003213 224 FMKGDAVIVIKGDLKNLKGWVEKVDEE--NVHIRPEMKGLPKTLAVN--SKELCKYFEPGNHV 282 (838)
Q Consensus 224 F~~GD~V~V~~Gel~~l~G~V~~V~~d--~V~i~~~~~~l~~~i~v~--~~~LrK~F~~GDhV 282 (838)
-++||.| .|+|+.+..+ .|-|.+....+-.-+.|+ .+..|.+|++||.|
T Consensus 4 P~~gD~V----------IG~V~~~~~~~~~VdI~s~~~a~L~~~~f~gatk~~rp~L~~GDlV 56 (86)
T cd05790 4 PAKGDHV----------IGIVVAKAGDFFKVDIGGSEPASLSYLAFEGATKRNRPNLNVGDLV 56 (86)
T ss_pred CCCCCEE----------EEEEEEEcCCeEEEEcCCCcceEechHHcccccccccccCCCCCEE
Confidence 3678887 4788888877 555555433221122332 56789999999986
No 127
>COG1471 RPS4A Ribosomal protein S4E [Translation, ribosomal structure and biogenesis]
Probab=47.47 E-value=51 Score=35.45 Aligned_cols=71 Identities=25% Similarity=0.394 Sum_probs=49.3
Q ss_pred EEEEEEeCCCCeEEEEecc--CCCCceEEecCCC---ceEcCCCCCCcEEEEcCCCCCceEEEEEEeCCC----eEEEec
Q 003213 749 VGVIREVLPDGSCRVVLGS--SGNGDTITALPNE---IEIVPPRKTDKIKIMGGPHRGATGKLIGVDGTD----GIVKVD 819 (838)
Q Consensus 749 ~gvI~~V~~dg~~~V~l~~--~~~g~~v~v~~~~---Le~V~P~kgd~VkVi~G~~rG~tG~LisiD~~d----giVk~d 819 (838)
.|.|.=+.-||+- +.+.| -.-|+++.++-.+ +|.....+|..|.|+.|.+.|.+|++..|.-.. -+|.++
T Consensus 133 gG~~QLn~hDGrn-i~~~d~~~k~~Dtv~i~lp~~~I~~~i~fe~g~~~~vtgG~h~G~~G~I~~I~~~~~~~~~~v~~e 211 (241)
T COG1471 133 GGRIQLNLHDGRN-IRLEDDNYKTGDTVKISLPEQKIVEHIKFEEGALVYVTGGRHVGRVGTIVEIEIQESSKPNLVTVE 211 (241)
T ss_pred CCEEEEEecCCce-eeccCCccccccEEEEeCCChhheeEeccCCCcEEEEECCccccceEEEEEEEEecCCCccEEEEe
Confidence 4455555555653 34333 1125666554333 677788999999999999999999999998764 577777
Q ss_pred C
Q 003213 820 V 820 (838)
Q Consensus 820 ~ 820 (838)
+
T Consensus 212 ~ 212 (241)
T COG1471 212 D 212 (241)
T ss_pred c
Confidence 6
No 128
>PTZ00065 60S ribosomal protein L14; Provisional
Probab=47.38 E-value=25 Score=34.56 Aligned_cols=34 Identities=24% Similarity=0.290 Sum_probs=28.5
Q ss_pred cCCCCCEEEEecCcCCCceEEEEEEeCCCCEEEEE
Q 003213 71 DLSRDTWVRMKIGNYKGDLAKVVDVDNVRQRVTVK 105 (838)
Q Consensus 71 ~l~~G~~VRik~G~ykGDlaqV~~vd~~~~~V~vk 105 (838)
.+++|=.|.|..|+|+|-||.|++|-+ +++|.|-
T Consensus 7 fVEiGRVvli~~Gp~~GKL~vIVDIID-~nRvLVD 40 (130)
T PTZ00065 7 FVEPGRLCLIQYGPDAGKLCFIVDIVT-PTRVLVD 40 (130)
T ss_pred ceeeceEEEEecCCCCCCEEEEEEEEc-CCeEEEe
Confidence 468999999999999999999999954 5666653
No 129
>TIGR00717 rpsA ribosomal protein S1. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned.
Probab=47.16 E-value=3.9e+02 Score=31.68 Aligned_cols=101 Identities=18% Similarity=0.244 Sum_probs=49.1
Q ss_pred hhhhhccCCCeEEEeccccCCceEEEEEEeCcEEEEEeCCCCCeEEEcccccccccccccccccCCceEecceEEeCCCc
Q 003213 271 ELCKYFEPGNHVKVVSGTQAGATGMVLKVEQHVLIILSDTTKEDIRVFADDVVESSEVTTGITKIGDYELRDLVLLDNNS 350 (838)
Q Consensus 271 ~LrK~F~~GDhVkVi~G~~~getGlVvkVe~~~v~vlSD~t~~ei~V~~~dL~~~~e~~~g~d~~g~y~l~DLVqld~~~ 350 (838)
...+.|++||.|++. |+.++. ..+.+.+..+++....-. .....|..+|.|.
T Consensus 400 ~~~~~~~~G~~V~~~----------Vl~vd~---------~~~~i~ls~K~~~~~p~~----~~~~~~~~G~~v~----- 451 (516)
T TIGR00717 400 EADHLYKKGDEIEAV----------VLAVDK---------EKKRISLGVKQLTENPWE----KFAAKYKVGSVVK----- 451 (516)
T ss_pred CHhHccCCCCEEEEE----------EEEEeC---------cCCEEEEeeccccCCchh----hhhhccCcceEEE-----
Confidence 345789999988653 566642 222333333333221100 0013456666665
Q ss_pred EEEEEEEecceEEEEecCCCCCcEEEEEccccccccccCccccCCCCCeecCCCEEEEE
Q 003213 351 FGVIIRVESEAFQVLKGVPDRPEVALVKLREIKCKLEKKSNVQDRNKNTVAVKDVVRIV 409 (838)
Q Consensus 351 vGvIv~ier~~~~VL~~~~~~g~v~~vk~~~I~~K~~~~~~a~D~~gn~i~~gd~Vki~ 409 (838)
|.|.++.+..++|--. ++---.|..+++.... .+.-...+++||.|++.
T Consensus 452 -g~V~~v~~~G~fV~l~---~~~~Glv~~s~l~~~~------~~~~~~~~~~Gd~v~~~ 500 (516)
T TIGR00717 452 -GKVTEIKDFGAFVELP---GGVEGLIRNSELSENR------DEDKTDEIKVGDEVEAK 500 (516)
T ss_pred -EEEEEEecceEEEEcC---CCeEEEEEHHHcCccc------cccccccCCCCCEEEEE
Confidence 6777777665554432 1111123333433211 11234467888888763
No 130
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=46.86 E-value=3.2e+02 Score=32.92 Aligned_cols=101 Identities=21% Similarity=0.236 Sum_probs=49.9
Q ss_pred hhhhhhccCCCeEEEeccccCCceEEEEEEeCcEEEEEeCCCCCeEEEcccccccccccccccccCCceEecceEEeCCC
Q 003213 270 KELCKYFEPGNHVKVVSGTQAGATGMVLKVEQHVLIILSDTTKEDIRVFADDVVESSEVTTGITKIGDYELRDLVLLDNN 349 (838)
Q Consensus 270 ~~LrK~F~~GDhVkVi~G~~~getGlVvkVe~~~v~vlSD~t~~ei~V~~~dL~~~~e~~~g~d~~g~y~l~DLVqld~~ 349 (838)
+++.+.|++||+|++. |+.++. ..+.+.+..+.+..... ......++.+|.|.
T Consensus 413 ~~~~~~~~~Gd~v~v~----------Il~vd~---------~~~~i~ls~k~~~~~p~----~~~~~~~~~G~vV~---- 465 (565)
T PRK06299 413 EEAVELYKKGDEVEAV----------VLKVDV---------EKERISLGIKQLEEDPF----EEFAKKHKKGSIVT---- 465 (565)
T ss_pred cChHhhCCCCCEEEEE----------EEEEeC---------CCCEEEEEEehhhcCch----hHHHhhcCCCCEEE----
Confidence 5666889999998753 556642 22233333333321110 01123456667665
Q ss_pred cEEEEEEEecceEEEEecCCCCCcEEEEEccccccccccCccccCCCCCeecCCCEEEE
Q 003213 350 SFGVIIRVESEAFQVLKGVPDRPEVALVKLREIKCKLEKKSNVQDRNKNTVAVKDVVRI 408 (838)
Q Consensus 350 ~vGvIv~ier~~~~VL~~~~~~g~v~~vk~~~I~~K~~~~~~a~D~~gn~i~~gd~Vki 408 (838)
|.|+++.+..++|--. ++-.-.|..+++... ........+.+||.|+.
T Consensus 466 --G~V~~v~~~G~fV~l~---~gi~g~i~~se~s~~------~~~~~~~~~~~Gd~v~~ 513 (565)
T PRK06299 466 --GTVTEVKDKGAFVELE---DGVEGLIRASELSRD------RVEDATEVLKVGDEVEA 513 (565)
T ss_pred --EEEEEEecCceEEecC---CCcEEEEEHHHhcch------hccCccccCCCCCEEEE
Confidence 6777777666554432 121122333333211 01122345788888875
No 131
>PF11746 DUF3303: Protein of unknown function (DUF3303); InterPro: IPR021734 Several members are annotated as being LysM domain-like proteins, but these did not match any LysM domains reported in the literature.
Probab=46.61 E-value=42 Score=30.82 Aligned_cols=48 Identities=10% Similarity=0.181 Sum_probs=40.6
Q ss_pred EEEEEecCCCceEEEEEecChHHHHHHHhcCcceeeeeeeeeChhhhh
Q 003213 13 IRSVIALDHLKNYIYIEADKEAHVKEACKGLRNIYSQKVMLVPIREMT 60 (838)
Q Consensus 13 I~Sv~~~~~lkGyIyVEA~~~~~V~~ai~g~~~v~~~~~~~Vpi~Em~ 60 (838)
|..++.+.+-.||+.+||++...+.+.+.--+.++|.....+|+=+-.
T Consensus 40 l~rw~~~~~g~g~~i~eadd~~~l~~~~~~W~~~fg~~~ei~Pv~~d~ 87 (91)
T PF11746_consen 40 LGRWHDPGGGRGFAIVEADDAKALFKHFAPWRDLFGMEFEITPVMTDE 87 (91)
T ss_pred EEEEEecCCCcEEEEEEeCCHHHHHHHHhhhhhccCceEEEEecccHH
Confidence 667888889999999999999999999999999988777777654433
No 132
>PLN00045 photosystem I reaction center subunit IV; Provisional
Probab=46.60 E-value=18 Score=33.45 Aligned_cols=40 Identities=25% Similarity=0.492 Sum_probs=32.8
Q ss_pred CceEcCCCCCCcEEEEcCC--CCCceEEEEEEeCCCe-----EEEec
Q 003213 780 EIEIVPPRKTDKIKIMGGP--HRGATGKLIGVDGTDG-----IVKVD 819 (838)
Q Consensus 780 ~Le~V~P~kgd~VkVi~G~--~rG~tG~LisiD~~dg-----iVk~d 819 (838)
--.++-|++|++|+|+.=| |--.+|++.+||.+.| +||+|
T Consensus 34 kpp~ig~~RGskVrIlR~ESYWyn~vGtVvsVDq~~girYPVvVRF~ 80 (101)
T PLN00045 34 KPPPIGPKRGSKVKILRPESYWFNDVGKVVAVDQDPGVRYPVVVRFE 80 (101)
T ss_pred CCCCcccCCCCEEEEccccceeecCcceEEEEeCCCCcccceEEEee
Confidence 3456779999999999877 5678999999999877 56765
No 133
>COG2139 RPL21A Ribosomal protein L21E [Translation, ribosomal structure and biogenesis]
Probab=46.37 E-value=40 Score=31.48 Aligned_cols=56 Identities=16% Similarity=0.287 Sum_probs=40.0
Q ss_pred chhhhhhccCCCeEEEe------cc----ccCCceEEEEEEeCcEEEE--EeCCCCCeEEEccccccc
Q 003213 269 SKELCKYFEPGNHVKVV------SG----TQAGATGMVLKVEQHVLII--LSDTTKEDIRVFADDVVE 324 (838)
Q Consensus 269 ~~~LrK~F~~GDhVkVi------~G----~~~getGlVvkVe~~~v~v--lSD~t~~ei~V~~~dL~~ 324 (838)
.+-+-+-|++||.|-++ .| +|.|-||.|+-+-++.+.| ......+.+-|.|.+|+.
T Consensus 26 lsr~l~ey~~Gd~V~I~IdpSv~kGmPh~rf~G~TG~Vvg~~g~ay~V~v~~G~k~K~liv~peHLk~ 93 (98)
T COG2139 26 LSRYLQEYKVGDKVHIDIDPSVHKGMPHPRFQGKTGTVVGVRGRAYKVEVYDGNKEKTLIVRPEHLKP 93 (98)
T ss_pred hhhHHhhccCCCEEEEEeCcccccCCCCccccCcceEEEeccCCEEEEEEecCCceEEEEeCHHHccc
Confidence 44455569999988554 23 6789999999999887554 333446777888888864
No 134
>PRK06531 yajC preprotein translocase subunit YajC; Validated
Probab=46.36 E-value=41 Score=32.37 Aligned_cols=51 Identities=25% Similarity=0.372 Sum_probs=35.9
Q ss_pred cccCCCCEEEEecCccCCceeEEEEEeCC--eEEEeeCCCCCCceeEEcchhhhhhccCCC
Q 003213 222 GHFMKGDAVIVIKGDLKNLKGWVEKVDEE--NVHIRPEMKGLPKTLAVNSKELCKYFEPGN 280 (838)
Q Consensus 222 ~~F~~GD~V~V~~Gel~~l~G~V~~V~~d--~V~i~~~~~~l~~~i~v~~~~LrK~F~~GD 280 (838)
..+++||.|.-+.| +.|+|++|+++ .|++.. + .-.++|.-+.+......++
T Consensus 35 ~sLk~GD~VvT~GG----i~G~V~~I~~~~~~v~le~--~--gv~i~v~r~AI~~Vv~~~~ 87 (113)
T PRK06531 35 NAIQKGDEVVTIGG----LYGTVDEVDTEAKTIVLDV--D--GVYLTFELAAIKRVVPKAE 87 (113)
T ss_pred HhcCCCCEEEECCC----cEEEEEEEecCCCEEEEEE--C--CEEEEEEhhHhhhhcCCCC
Confidence 47999999988855 89999999875 566654 2 2456666666665554444
No 135
>PRK06531 yajC preprotein translocase subunit YajC; Validated
Probab=46.21 E-value=26 Score=33.68 Aligned_cols=38 Identities=24% Similarity=0.364 Sum_probs=27.7
Q ss_pred EeecCCCCceeEEEeecCCeEEEEeccCceEEEEecccccc
Q 003213 513 VRLGPYKGYRGRVVDVKGQSVRVELESQMKVVTVDRSMISD 553 (838)
Q Consensus 513 I~~GpyKG~~G~Vkdat~~~~rVELhs~~k~I~V~r~~l~~ 553 (838)
|+.| |+.|+|.++.++..+|+|....-.|++.|+.|+-
T Consensus 44 vT~G---Gi~G~V~~I~~~~~~v~le~~gv~i~v~r~AI~~ 81 (113)
T PRK06531 44 VTIG---GLYGTVDEVDTEAKTIVLDVDGVYLTFELAAIKR 81 (113)
T ss_pred EECC---CcEEEEEEEecCCCEEEEEECCEEEEEEhhHhhh
Confidence 4556 8999999998764444444456679999999874
No 136
>PRK14634 hypothetical protein; Provisional
Probab=44.59 E-value=37 Score=34.28 Aligned_cols=48 Identities=10% Similarity=0.269 Sum_probs=38.3
Q ss_pred ccccCcEEEEe-ecCC---CCceeEEEeecCCeEEEEeccCceEEEEecccccc
Q 003213 504 DALVGTTVKVR-LGPY---KGYRGRVVDVKGQSVRVELESQMKVVTVDRSMISD 553 (838)
Q Consensus 504 d~liGktV~I~-~Gpy---KG~~G~Vkdat~~~~rVELhs~~k~I~V~r~~l~~ 553 (838)
..++|+.|+|+ ..+. |=+.|++++++++.+++++ ..+.+.++.+.|+-
T Consensus 96 ~r~~G~~V~V~l~~~~~~~k~~~G~L~~~~~~~v~l~~--~~~~~~i~~~~I~k 147 (155)
T PRK14634 96 QTFRGFPVEVSHRDDDGSEQRLEGLLLERNEDHLQINI--RGRIKRIPRDSVIS 147 (155)
T ss_pred HHhCCCeEEEEEecCCCCeEEEEEEEEEEeCCEEEEEE--CCEEEEEEHHHeee
Confidence 57899999996 4443 6789999999999999886 46778888877753
No 137
>PRK05886 yajC preprotein translocase subunit YajC; Validated
Probab=44.35 E-value=68 Score=30.68 Aligned_cols=49 Identities=14% Similarity=0.192 Sum_probs=35.2
Q ss_pred hhhhhhccCCCeEEEeccccCCceEEEEEEeCcEEEEEeCCCCCeEEEcccccc
Q 003213 270 KELCKYFEPGNHVKVVSGTQAGATGMVLKVEQHVLIILSDTTKEDIRVFADDVV 323 (838)
Q Consensus 270 ~~LrK~F~~GDhVkVi~G~~~getGlVvkVe~~~v~vlSD~t~~ei~V~~~dL~ 323 (838)
++++...++||.|..++| --|.|++|+++.++|=... +-.+++.-.-++
T Consensus 33 ~~m~~~Lk~GD~VvT~gG----i~G~V~~I~d~~v~leia~-gv~i~~~r~AI~ 81 (109)
T PRK05886 33 IDLHESLQPGDRVHTTSG----LQATIVGITDDTVDLEIAP-GVVTTWMKLAVR 81 (109)
T ss_pred HHHHHhcCCCCEEEECCC----eEEEEEEEeCCEEEEEECC-CeEEEEEhhhee
Confidence 467788999999998877 6799999999887774322 445555444443
No 138
>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=44.22 E-value=1.6e+02 Score=24.89 Aligned_cols=59 Identities=19% Similarity=0.224 Sum_probs=37.1
Q ss_pred EEEEEEEec-ceEEEEecCCCCCcEEEEEccccccccccCccccCCCCCeecCCCEEEEEcCCCCCceeeEEE
Q 003213 351 FGVIIRVES-EAFQVLKGVPDRPEVALVKLREIKCKLEKKSNVQDRNKNTVAVKDVVRIVEGPCKGKQGPVEH 422 (838)
Q Consensus 351 vGvIv~ier-~~~~VL~~~~~~g~v~~vk~~~I~~K~~~~~~a~D~~gn~i~~gd~Vki~~Gp~kG~~G~Vkh 422 (838)
.|.|++... ..+.|.. +.++++.++.+. |+.+ +...+.+||.|.+.--++...+|.|.|
T Consensus 4 ~G~Vi~~~~g~~~~V~~---~~g~~~~c~~rG---klr~-------~~~~~~vGD~V~~~~~~~~~~~g~I~~ 63 (64)
T cd04451 4 EGVVTEALPNAMFRVEL---ENGHEVLAHISG---KMRM-------NYIRILPGDRVKVELSPYDLTKGRIVY 63 (64)
T ss_pred EEEEEEEeCCCEEEEEe---CCCCEEEEEECc---eeec-------CCcccCCCCEEEEEEeecCCCEEEEEE
Confidence 488888884 7777765 246677777543 2211 233489999998874443344677765
No 139
>PRK12288 GTPase RsgA; Reviewed
Probab=43.83 E-value=1.6e+02 Score=33.42 Aligned_cols=88 Identities=19% Similarity=0.211 Sum_probs=58.6
Q ss_pred cEEEEEEEecceEEEEecCCCCCcEEEEEccccccccccCccccCCCCCeecCCCEEEEEcC--CCCCceeeEEEEECCE
Q 003213 350 SFGVIIRVESEAFQVLKGVPDRPEVALVKLREIKCKLEKKSNVQDRNKNTVAVKDVVRIVEG--PCKGKQGPVEHIYRGI 427 (838)
Q Consensus 350 ~vGvIv~ier~~~~VL~~~~~~g~v~~vk~~~I~~K~~~~~~a~D~~gn~i~~gd~Vki~~G--p~kG~~G~Vkhi~r~~ 427 (838)
..|.|+++.+..+.|.+. .|+++.++.+. ++ ..+.+||.|.+... ......|.|.+|.--+
T Consensus 40 ~~g~Vi~~~~~~~~v~~~---~g~~~~~~~~g---~~-----------~~~~vGD~V~~~~~~~~~~~~~~~I~~il~R~ 102 (347)
T PRK12288 40 QEGIVISRFGQHADVEAA---DGEVHRCNIRR---TI-----------RSLVTGDRVVWRPGKEALEGVSGVVEAVHPRT 102 (347)
T ss_pred cceEEEEEECCEEEEEeC---CCcEEEEEecc---cC-----------CCCCCCcEEEEEeCCCcccccceEEEEEeccc
Confidence 569999999999999873 46666665432 11 13899999998521 1101249999999776
Q ss_pred EEEEeCceeccccEEEEeCCceEEecc
Q 003213 428 LFIHDRHHLEHAGFICAKSSSCVVVGG 454 (838)
Q Consensus 428 lFL~~~~~~En~Gifv~~a~~~~~~g~ 454 (838)
=.|.-+......-+++++...+.++-+
T Consensus 103 n~L~R~~~~~~~q~iaANvD~vlIV~s 129 (347)
T PRK12288 103 SVLTRPDYYDGVKPIAANIDQIVIVSA 129 (347)
T ss_pred ceEECCCcccccceEEEEccEEEEEEe
Confidence 444433333333578888888887765
No 140
>PF10842 DUF2642: Protein of unknown function (DUF2642); InterPro: IPR020139 This entry contains proteins with no known function.
Probab=42.84 E-value=68 Score=28.02 Aligned_cols=45 Identities=27% Similarity=0.316 Sum_probs=33.4
Q ss_pred ccccCcEEEEeecCCCCceeEEEeecCCeEEEEeccCceEEEEecccc
Q 003213 504 DALVGTTVKVRLGPYKGYRGRVVDVKGQSVRVELESQMKVVTVDRSMI 551 (838)
Q Consensus 504 d~liGktV~I~~GpyKG~~G~Vkdat~~~~rVELhs~~k~I~V~r~~l 551 (838)
..++||.|.|.-- .--++|+++|+..+++.||-+ .+..-|.-++|
T Consensus 17 q~liG~~vvV~T~-~g~v~G~L~~V~pDhIvl~~~--~~~~~IR~~~I 61 (66)
T PF10842_consen 17 QSLIGQRVVVQTT-RGSVRGILVDVKPDHIVLEEN--GTPFFIRIAQI 61 (66)
T ss_pred HHhcCCEEEEEEc-CCcEEEEEEeecCCEEEEEeC--CcEEEEEeeeE
Confidence 4689999999763 334589999999999999888 55455544444
No 141
>PRK14645 hypothetical protein; Provisional
Probab=42.78 E-value=40 Score=34.01 Aligned_cols=46 Identities=22% Similarity=0.315 Sum_probs=38.1
Q ss_pred ccccCcEEEEeecCCCCceeEEEeecCCeEEEEeccCceEEEEeccccc
Q 003213 504 DALVGTTVKVRLGPYKGYRGRVVDVKGQSVRVELESQMKVVTVDRSMIS 552 (838)
Q Consensus 504 d~liGktV~I~~GpyKG~~G~Vkdat~~~~rVELhs~~k~I~V~r~~l~ 552 (838)
..++|+.|+|+.| -|=+.|+++++++..++++. ..+++.++.+.|+
T Consensus 98 ~r~~G~~v~v~~~-~k~~~G~L~~~~d~~i~l~~--~~~~~~i~~~~I~ 143 (154)
T PRK14645 98 ERFAGLKAKVRGP-GENFTGRIKAVSGDQVTFDV--GGEDRTLRIGTFQ 143 (154)
T ss_pred HHhCCCEEEEEcC-CeEEEEEEEEEeCCEEEEEE--CCeEEEEEHHHhh
Confidence 5789999999864 47789999999999988775 5677888888885
No 142
>cd04469 S1_Hex1 S1_Hex1: Hex1, S1-like RNA-binding domain. Hex1 protein is the major component of the Woronin body in filamentous fungi. The Woronin body is a dense vesicle and plays a vital role in filamentous fungi cell integrity. When cell damage occurs, Woronin bodies seal the septal pore to prevent further cytoplasmic bleeding. Hex1 protein self-assembles to form the solid core of the Woronin body vesicle. The Hex1 sequence and structure are similar to eukaryotic initiation factor 5A (eIF5A), suggesting they share a common ancestor during evolution. All members of the EF superfamily to which Hex1 belongs, contain an S1 domain, which has been shown to bind RNA or single-stranded DNA and often interacts with the ribosome.
Probab=42.27 E-value=37 Score=30.33 Aligned_cols=38 Identities=21% Similarity=0.245 Sum_probs=31.4
Q ss_pred EEEEEeCCeEEEeeCCCCCCceeEEc-----chhhhhhccCCC
Q 003213 243 WVEKVDEENVHIRPEMKGLPKTLAVN-----SKELCKYFEPGN 280 (838)
Q Consensus 243 ~V~~V~~d~V~i~~~~~~l~~~i~v~-----~~~LrK~F~~GD 280 (838)
.++.|+++.+++|.+..+.++.|.+| .++|+..|+.|.
T Consensus 6 qLidI~DG~lsLM~e~G~~kdDl~lP~~~~l~~~I~~~f~~gk 48 (75)
T cd04469 6 RVLDIQDGSIVAMTETGDVKQGLPVIDQSNLWTRLKTAFESGR 48 (75)
T ss_pred EEEEecCCeEEEEcCCCCcccCccCCCcchHHHHHHHHHHCCC
Confidence 46778677999999888888889999 567788899998
No 143
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=41.85 E-value=38 Score=28.11 Aligned_cols=39 Identities=23% Similarity=0.188 Sum_probs=32.0
Q ss_pred EEEEEEeCCCCeEEEEeccCCCCceEEecCCCceEcCCC
Q 003213 749 VGVIREVLPDGSCRVVLGSSGNGDTITALPNEIEIVPPR 787 (838)
Q Consensus 749 ~gvI~~V~~dg~~~V~l~~~~~g~~v~v~~~~Le~V~P~ 787 (838)
.|+|.++.+++.+.|++.+.+.+..++++.++|-+..|-
T Consensus 21 ~a~V~~~~~~~~~~V~~~~~~~~~~e~v~~~~LRp~~~w 59 (61)
T smart00743 21 EAVVTKVLGDGKYLVRYLTESEPLKETVDWSDLRPHPPW 59 (61)
T ss_pred EEEEEEECCCCEEEEEECCCCcccEEEEeHHHcccCCCC
Confidence 789999988778999998822268999999999887764
No 144
>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=41.78 E-value=1.9e+02 Score=25.85 Aligned_cols=63 Identities=13% Similarity=0.188 Sum_probs=43.2
Q ss_pred cEEEEEEEecc-eEEEEecCCCCCcEEEEEccccccccccCccccCCCCCeecCCCEEEEEcCCCCCceeeEEEEECC
Q 003213 350 SFGVIIRVESE-AFQVLKGVPDRPEVALVKLREIKCKLEKKSNVQDRNKNTVAVKDVVRIVEGPCKGKQGPVEHIYRG 426 (838)
Q Consensus 350 ~vGvIv~ier~-~~~VL~~~~~~g~v~~vk~~~I~~K~~~~~~a~D~~gn~i~~gd~Vki~~Gp~kG~~G~Vkhi~r~ 426 (838)
..|.|+++-.+ .|.|... +|..+.+.- ..|+.+ .=-|..||.|.|--=||.-..|.|.|.|..
T Consensus 2 ~~g~V~~~~g~~~~~V~~~---~g~~~la~i---~gK~rk--------~iwI~~GD~V~Ve~~~~d~~kg~Iv~r~~~ 65 (77)
T cd05793 2 EYGQVEKMLGNGRLEVRCF---DGKKRLCRI---RGKMRK--------RVWINEGDIVLVAPWDFQDDKADIIYKYTP 65 (77)
T ss_pred EEEEEEEEcCCCEEEEEEC---CCCEEEEEE---chhhcc--------cEEEcCCCEEEEEeccccCCEEEEEEEcCH
Confidence 35788888755 4777774 466555542 233221 126789999999877887789999998863
No 145
>PF09953 DUF2187: Uncharacterized protein conserved in bacteria (DUF2187); InterPro: IPR018690 This family consists of various hypothetical bacterial proteins with known function. It includes the uncharacterised YkvS protein from Bacillus subtilis.
Probab=41.76 E-value=40 Score=28.63 Aligned_cols=28 Identities=32% Similarity=0.373 Sum_probs=22.2
Q ss_pred CCCCEEEEecCccCCceeEEEEEeCCeEEEee
Q 003213 225 MKGDAVIVIKGDLKNLKGWVEKVDEENVHIRP 256 (838)
Q Consensus 225 ~~GD~V~V~~Gel~~l~G~V~~V~~d~V~i~~ 256 (838)
.+||.++.- .+++|.|++|.++.|.+.-
T Consensus 5 ~vGdiIefk----~g~~G~V~kv~eNSVIVdI 32 (57)
T PF09953_consen 5 KVGDIIEFK----DGFTGIVEKVYENSVIVDI 32 (57)
T ss_pred ccCcEEEEc----CCcEEEEEEEecCcEEEEE
Confidence 589999963 4699999999999765543
No 146
>PRK04950 ProP expression regulator; Provisional
Probab=41.45 E-value=44 Score=35.48 Aligned_cols=44 Identities=30% Similarity=0.517 Sum_probs=36.0
Q ss_pred cCcEEEEeecCCCCceeEEEeecCCeEEEEeccCceEEEEeccccc
Q 003213 507 VGTTVKVRLGPYKGYRGRVVDVKGQSVRVELESQMKVVTVDRSMIS 552 (838)
Q Consensus 507 iGktV~I~~GpyKG~~G~Vkdat~~~~rVELhs~~k~I~V~r~~l~ 552 (838)
+||.|+|.-|. --.-|.|.|++.+.|||+|.+... |.|.-+||.
T Consensus 169 ~gq~v~vk~g~-~~~~a~i~ei~kd~v~vql~~Gl~-~~v~ae~l~ 212 (213)
T PRK04950 169 VGQAVKVKAGK-SAMDATVLEITKDDVRVQLDSGLS-MIVRAEHLV 212 (213)
T ss_pred cCCEEEEeccC-CCCceEEEEEecCcEEEEcCCCcE-EEEeHhhhc
Confidence 79999999883 345689999999999999999886 567777663
No 147
>PRK14630 hypothetical protein; Provisional
Probab=40.99 E-value=60 Score=32.36 Aligned_cols=46 Identities=22% Similarity=0.218 Sum_probs=35.7
Q ss_pred ccccCcEEEEeecCCCCceeEEEeecCCeEEEEeccCceEEEEeccccc
Q 003213 504 DALVGTTVKVRLGPYKGYRGRVVDVKGQSVRVELESQMKVVTVDRSMIS 552 (838)
Q Consensus 504 d~liGktV~I~~GpyKG~~G~Vkdat~~~~rVELhs~~k~I~V~r~~l~ 552 (838)
..++|+.|+|+-..-. ..|+++++.++.++++.. .+.+.++.++|+
T Consensus 93 ~r~~G~~v~V~l~~~~-~~G~L~~~~d~~i~l~~~--~~~~~i~~~~I~ 138 (143)
T PRK14630 93 KIFEGKKIKLMLDNDF-EEGFILEAKADSFIFKTD--SKEVNVLYSDVK 138 (143)
T ss_pred HHhCCCEEEEEEcCcc-eEEEEEEEeCCEEEEEEC--CEEEEEEhHhcc
Confidence 5789999999753322 489999999999998864 567888877765
No 148
>PRK09838 periplasmic copper-binding protein; Provisional
Probab=40.47 E-value=67 Score=30.95 Aligned_cols=61 Identities=15% Similarity=0.245 Sum_probs=38.0
Q ss_pred CceeEEEEEeCCe--EEEeeC-CCCCC-----ceeEEcchhhhhhccCCCeEEEeccccCCceEEEEEEe
Q 003213 239 NLKGWVEKVDEEN--VHIRPE-MKGLP-----KTLAVNSKELCKYFEPGNHVKVVSGTQAGATGMVLKVE 300 (838)
Q Consensus 239 ~l~G~V~~V~~d~--V~i~~~-~~~l~-----~~i~v~~~~LrK~F~~GDhVkVi~G~~~getGlVvkVe 300 (838)
-.+|+|.+|+.+. |+|.-. .++|. =.+.+....+.+.+++||.|..--=+..+ .-+|++|+
T Consensus 44 ~~~G~V~~vd~~~~~iti~H~pIp~l~wPaMTM~F~v~~~~~l~~lk~G~~V~F~~~~~~~-~~~i~~i~ 112 (115)
T PRK09838 44 SGTGVVKGIDLESKKITIHHEPIPAVNWPEMTMRFTITPQTKMSEIKTGDKVAFNFVQQGN-LSLLQDIK 112 (115)
T ss_pred EEEEEEEEEeCCCCEEEEeecccccCCCCCccccccCCChhhhccCCCCCEEEEEEEEcCC-cEEEEEEe
Confidence 4579999998875 666533 22331 13666677777889999998764222222 22666654
No 149
>smart00538 POP4 A domain found in a protein subunit of human RNase MRP and RNase P ribonucleoprotein complexes and archaeal proteins.
Probab=40.46 E-value=73 Score=29.41 Aligned_cols=48 Identities=27% Similarity=0.387 Sum_probs=39.3
Q ss_pred CccccCcEEEEeecC---CCCceeEEEeecCCeEEEEeccCceEEEEecccc
Q 003213 503 HDALVGTTVKVRLGP---YKGYRGRVVDVKGQSVRVELESQMKVVTVDRSMI 551 (838)
Q Consensus 503 rd~liGktV~I~~Gp---yKG~~G~Vkdat~~~~rVELhs~~k~I~V~r~~l 551 (838)
+.+|+|-.|+|.+=+ |-|..|+|.+-|..++.|+-.. ++...|+|+.-
T Consensus 8 ~~el~G~~v~Vv~s~~ps~vGi~GiVv~ET~nt~~I~t~~-~~~~~IpK~~~ 58 (92)
T smart00538 8 RHELIGLKVRVVASKNPSLVGIEGIVVDETRNTLKIETKE-GRVKTVPKDGA 58 (92)
T ss_pred hhhhcCCEEEEEEcCCCCccCcEEEEEEeeeeEEEEEeCC-CcEEEEECCCe
Confidence 357899999998765 6799999999999999998664 46677888774
No 150
>PF14563 DUF4444: Domain of unknown function (DUF4444); PDB: 3BFM_A.
Probab=40.21 E-value=59 Score=25.88 Aligned_cols=33 Identities=24% Similarity=0.450 Sum_probs=21.9
Q ss_pred CCCceEEEEEEeCCCeEEEecCCCceEEEecccc
Q 003213 799 HRGATGKLIGVDGTDGIVKVDVSLDVKILDMAIL 832 (838)
Q Consensus 799 ~rG~tG~LisiD~~dgiVk~d~~~~~kil~~~~L 832 (838)
.+|.+|+.+++|+.=|.+ +.++.+-.++++..|
T Consensus 7 ~~g~tGtFlGvDE~FGmL-Lr~~~~T~LIPLT~l 39 (42)
T PF14563_consen 7 VAGLTGTFLGVDEDFGML-LRDDDTTHLIPLTTL 39 (42)
T ss_dssp ETTEEEEEEEE-TT--EE-EE-SS-EEEE-GGGG
T ss_pred EcCcceeEEeeccccceE-EEeCCccEEEEchHh
Confidence 478999999999998876 455567888988765
No 151
>PRK14640 hypothetical protein; Provisional
Probab=40.15 E-value=56 Score=32.84 Aligned_cols=47 Identities=19% Similarity=0.319 Sum_probs=36.4
Q ss_pred ccccCcEEEEee-c---CCCCceeEEEeecCCeEEEEeccCceEEEEeccccc
Q 003213 504 DALVGTTVKVRL-G---PYKGYRGRVVDVKGQSVRVELESQMKVVTVDRSMIS 552 (838)
Q Consensus 504 d~liGktV~I~~-G---pyKG~~G~Vkdat~~~~rVELhs~~k~I~V~r~~l~ 552 (838)
..++|+.|+|+- . --|=+.|++++++++.+++++. .+++.++.+.|+
T Consensus 93 ~r~~G~~v~V~l~~~~~~~k~~~G~L~~v~~~~v~l~~~--~~~~~i~~~~I~ 143 (152)
T PRK14640 93 EKYVGQEAAVTLRMATNNRRKFKGVIKAVQGDMITLTVD--GKDEVLAFTNIQ 143 (152)
T ss_pred HHhCCCeEEEEEecccCCceEEEEEEEEEeCCEEEEEEC--CeEEEEEhHHee
Confidence 578999999974 2 3477889999999999998864 556677766665
No 152
>PHA03378 EBNA-3B; Provisional
Probab=40.11 E-value=5.8e+02 Score=31.78 Aligned_cols=22 Identities=23% Similarity=0.273 Sum_probs=11.3
Q ss_pred ceEEecCCCceEcCCCCCCcEE
Q 003213 772 DTITALPNEIEIVPPRKTDKIK 793 (838)
Q Consensus 772 ~~v~v~~~~Le~V~P~kgd~Vk 793 (838)
+.--+-.-|-+-+.|+|.-|.+
T Consensus 907 err~~gpm~~~~i~p~kr~k~~ 928 (991)
T PHA03378 907 ERRGVGPMHPTDIPPSKRAKTD 928 (991)
T ss_pred cccCCCCCChhhCCCchhcccc
Confidence 3334444555666666654443
No 153
>PLN00045 photosystem I reaction center subunit IV; Provisional
Probab=39.68 E-value=52 Score=30.57 Aligned_cols=32 Identities=28% Similarity=0.332 Sum_probs=27.1
Q ss_pred cccccCCCCCEEEEec--CcCCCceEEEEEEeCC
Q 003213 67 SKAIDLSRDTWVRMKI--GNYKGDLAKVVDVDNV 98 (838)
Q Consensus 67 ~~~~~l~~G~~VRik~--G~ykGDlaqV~~vd~~ 98 (838)
+....++.|+.|||+| --+=+|.|.|+.||.+
T Consensus 35 pp~ig~~RGskVrIlR~ESYWyn~vGtVvsVDq~ 68 (101)
T PLN00045 35 PPPIGPKRGSKVKILRPESYWFNDVGKVVAVDQD 68 (101)
T ss_pred CCCcccCCCCEEEEccccceeecCcceEEEEeCC
Confidence 3456899999999998 3567999999999986
No 154
>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=39.31 E-value=9.9 Score=34.21 Aligned_cols=41 Identities=29% Similarity=0.425 Sum_probs=0.0
Q ss_pred cCcEEEEeecCCCCceeEEEeecCCeEEEEeccCceEEEEeccccc
Q 003213 507 VGTTVKVRLGPYKGYRGRVVDVKGQSVRVELESQMKVVTVDRSMIS 552 (838)
Q Consensus 507 iGktV~I~~GpyKG~~G~Vkdat~~~~rVELhs~~k~I~V~r~~l~ 552 (838)
.|..|.-.. |+.|+|++++++++.||+... -.++++|+.|+
T Consensus 39 ~Gd~VvT~g----Gi~G~V~~i~~~~v~lei~~g-~~i~v~k~aI~ 79 (82)
T PF02699_consen 39 PGDEVVTIG----GIYGTVVEIDDDTVVLEIAPG-VEITVEKSAIA 79 (82)
T ss_dssp ----------------------------------------------
T ss_pred CCCEEEECC----cEEEEEEEEeCCEEEEEECCC-eEEEEEHHHhH
Confidence 344554333 689999999999999999984 55889998775
No 155
>PF09870 DUF2097: Uncharacterized protein conserved in archaea (DUF2097); InterPro: IPR019208 This domain, found in various hypothetical prokaryotic proteins, has no known function.
Probab=39.17 E-value=57 Score=29.92 Aligned_cols=52 Identities=15% Similarity=0.244 Sum_probs=42.5
Q ss_pred cccCCCCEEEEecCccCCceeEEEEEeCCeEEEeeCCCCCCceeEEcchhhhh
Q 003213 222 GHFMKGDAVIVIKGDLKNLKGWVEKVDEENVHIRPEMKGLPKTLAVNSKELCK 274 (838)
Q Consensus 222 ~~F~~GD~V~V~~Gel~~l~G~V~~V~~d~V~i~~~~~~l~~~i~v~~~~LrK 274 (838)
..++.||.+++.=|. ...-|.|++++.-.+.+..+.+-+++.++|...++..
T Consensus 17 ~nV~e~D~lEisygR-v~vpG~V~~~~~~~~~l~~~~~~~~g~ve~DleeI~d 68 (86)
T PF09870_consen 17 NNVKEGDYLEISYGR-VHVPGEVLSIEDGFLRLQLDGELINGTVEVDLEEIKD 68 (86)
T ss_pred hcCCCCCEEEEEeeE-EEeeeEEEEeeeeEEEEEEcCccccCcEEEEHHHHHH
Confidence 479999999999885 5788999999998888887765556788888877664
No 156
>PRK05338 rplS 50S ribosomal protein L19; Provisional
Probab=39.01 E-value=1.2e+02 Score=29.40 Aligned_cols=48 Identities=21% Similarity=0.267 Sum_probs=32.6
Q ss_pred ccccCCCCEEEEe----cCc---cCCceeEEEEEeCC----eEEEeeCCCCCCceeEEc
Q 003213 221 KGHFMKGDAVIVI----KGD---LKNLKGWVEKVDEE----NVHIRPEMKGLPKTLAVN 268 (838)
Q Consensus 221 ~~~F~~GD~V~V~----~Ge---l~~l~G~V~~V~~d----~V~i~~~~~~l~~~i~v~ 268 (838)
-..|.+||.|+|- +|+ .+...|.|+++.+. ++++.--..+..-|..|+
T Consensus 16 ~p~f~~GD~V~V~~~i~eg~k~R~q~f~GvvI~~~~~G~~~tftvRki~~gvGVEr~fp 74 (116)
T PRK05338 16 IPEFRPGDTVRVHVKVVEGNKERIQAFEGVVIARRGRGLNETFTVRKISYGVGVERTFP 74 (116)
T ss_pred CCCcCCCCEEEEEEEEccCCceEeccEEEEEEEEeCCCCCceEEEEEcccCccEEEEec
Confidence 4689999999983 664 46799999999744 666665544333333333
No 157
>PF11604 CusF_Ec: Copper binding periplasmic protein CusF; InterPro: IPR021647 CusF is a periplasmic protein involved in copper and silver resistance in Escherichia coil. CusF forms a five-stranded beta-barrel OB fold. Cu(I) binds to H36, M47 and M49 which are conserved residues in the protein []. ; PDB: 2L55_A 2VB3_X 1ZEQ_X 2QCP_X 3E6Z_X 2VB2_X.
Probab=38.90 E-value=1.4e+02 Score=25.93 Aligned_cols=58 Identities=19% Similarity=0.276 Sum_probs=34.1
Q ss_pred eEEEEEe--CCeEEEeeC-CCCCC-----ceeEEcchhhhhhccCCCeEEEeccccCCceEEEEEE
Q 003213 242 GWVEKVD--EENVHIRPE-MKGLP-----KTLAVNSKELCKYFEPGNHVKVVSGTQAGATGMVLKV 299 (838)
Q Consensus 242 G~V~~V~--~d~V~i~~~-~~~l~-----~~i~v~~~~LrK~F~~GDhVkVi~G~~~getGlVvkV 299 (838)
|.|.+|+ ..+|+|.-+ ..+|. -.+.+....+-.-|++||.|...--+.++..=.|+++
T Consensus 1 G~V~~vd~~~~~iti~H~pIp~l~wpaMTM~F~v~~~~~l~~l~~Gd~V~F~~~~~~~~~~~I~~i 66 (70)
T PF11604_consen 1 GVVKSVDPEAGTITISHEPIPELGWPAMTMDFPVADPVDLAGLKPGDKVRFTFERTDDGSYVITAI 66 (70)
T ss_dssp EEEEEEETTTTEEEEEE--BCCCTB-SEEEEEE--TTSEESS-STT-EEEEEEEEETTCEEEEEEE
T ss_pred CEEEEEecCCCEEEEecCccccCCCCCeEEEEEcCChhhhhcCCCCCEEEEEEEECCCCcEEEEEE
Confidence 7899999 558888754 23331 2466777778889999999987643333333344444
No 158
>PRK03999 translation initiation factor IF-5A; Provisional
Probab=38.73 E-value=81 Score=30.90 Aligned_cols=62 Identities=19% Similarity=0.110 Sum_probs=45.8
Q ss_pred ccccCCCCEEEEecCccCCceeEEEEEeCCeEEEeeCCCCCCceeEEcc-hhhhhhccCCCeEEEec
Q 003213 221 KGHFMKGDAVIVIKGDLKNLKGWVEKVDEENVHIRPEMKGLPKTLAVNS-KELCKYFEPGNHVKVVS 286 (838)
Q Consensus 221 ~~~F~~GD~V~V~~Gel~~l~G~V~~V~~d~V~i~~~~~~l~~~i~v~~-~~LrK~F~~GDhVkVi~ 286 (838)
...|..+|.|++. .+.-.....+.++++.+.+|-. +. -+.++++. .+..++|++|+.|.|+.
T Consensus 56 e~~~~s~d~~e~~--~ve~~~~qylY~dg~~~~fMd~-eT-yeq~~i~~~~d~~~~l~eg~~v~v~~ 118 (129)
T PRK03999 56 SLVQPVDAKVEVP--IIEKKTGQVLSIMGDVVQLMDL-ET-YETFEIPIPEELKDKLEPGVEVEYWE 118 (129)
T ss_pred EEEecCCCceeee--eEEeEEEEEEEecCCEEEEecC-CC-ceEEEecCChhHHhhCcCCCEEEEEh
Confidence 3578888887775 5567777889999999999942 22 23456655 45778999999999885
No 159
>COG0056 AtpA F0F1-type ATP synthase, alpha subunit [Energy production and conversion]
Probab=38.56 E-value=84 Score=37.02 Aligned_cols=49 Identities=14% Similarity=0.258 Sum_probs=40.7
Q ss_pred CceEEEEEEeCcEEEEEeCCCCCeEEEcccccccccccccccccCCceEecceEEeCCCcEEEEEEEecceEEEE
Q 003213 291 GATGMVLKVEQHVLIILSDTTKEDIRVFADDVVESSEVTTGITKIGDYELRDLVLLDNNSFGVIIRVESEAFQVL 365 (838)
Q Consensus 291 getGlVvkVe~~~v~vlSD~t~~ei~V~~~dL~~~~e~~~g~d~~g~y~l~DLVqld~~~vGvIv~ier~~~~VL 365 (838)
.++|.|++|-+..+.|. .+.++..+.+|++..+..|+.+.+|.+.+-++
T Consensus 26 ~~~g~V~sv~DgIa~v~--------------------------Gl~~~~~~E~~ef~~~v~G~alnle~d~VG~v 74 (504)
T COG0056 26 KEVGTVISVGDGIARVS--------------------------GLENVMAGELVEFPGGVKGMALNLEEDSVGAV 74 (504)
T ss_pred hccceEEEEecceEEEe--------------------------cCchhhcCceEEecCCcEEEEEeccccceeEE
Confidence 48999999998888765 24578899999999999999999999875443
No 160
>PF09122 DUF1930: Domain of unknown function (DUF1930); InterPro: IPR015206 This entry represents a domain found in 3-mercaptopyruvate sulphurtransferase which has no known function. This domain adopts a structure consisting of a four-stranded antiparallel beta-sheet and an alpha-helix, arranged in a beta(2)-alpha-beta(2) fashion, and bearing a remarkable structural similarity to the FK506-binding protein class of peptidylprolyl cis/trans-isomerase []. ; PDB: 1OKG_A.
Probab=37.99 E-value=37 Score=29.33 Aligned_cols=25 Identities=28% Similarity=0.412 Sum_probs=16.2
Q ss_pred cCCCceEEEEEEeCCCCEEEEEEeeccc
Q 003213 84 NYKGDLAKVVDVDNVRQRVTVKLIPRID 111 (838)
Q Consensus 84 ~ykGDlaqV~~vd~~~~~V~vkliPRiD 111 (838)
..-|+.|+|.. +++..++++. ||||
T Consensus 44 lH~GEkA~V~F--kS~Rv~~iEv-P~i~ 68 (68)
T PF09122_consen 44 LHIGEKAQVFF--KSQRVAVIEV-PRID 68 (68)
T ss_dssp -BTT-EEEEEE--TTS-EEEEE---SS-
T ss_pred hhcCceeEEEE--ecCcEEEEEc-cCCC
Confidence 45789999974 7889999998 9997
No 161
>cd05703 S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 12 (hs12) and S. cerevisiae S1 repeat 9 (sc9). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=37.43 E-value=24 Score=30.63 Aligned_cols=46 Identities=28% Similarity=0.377 Sum_probs=26.1
Q ss_pred ceeEEEEEeCCeEEEe--eCCCCCC--ceeEE---cchhhhhhccCCCeEEEe
Q 003213 240 LKGWVEKVDEENVHIR--PEMKGLP--KTLAV---NSKELCKYFEPGNHVKVV 285 (838)
Q Consensus 240 l~G~V~~V~~d~V~i~--~~~~~l~--~~i~v---~~~~LrK~F~~GDhVkVi 285 (838)
.+|+|.++.+.-+.+. +..+++- .+|.- ..+++.+.|++||.|++.
T Consensus 4 V~g~V~~i~~~g~~V~l~~~i~G~i~~~~ls~~~~~~~~~~~~~~vG~~v~~k 56 (73)
T cd05703 4 VTGFVNNVSKEFVWLTISPDVKGRIPLLDLSDDVSVLEHPEKKFPIGQALKAK 56 (73)
T ss_pred EEEEEEEEeCCEEEEEeCCCcEEEEEHHHcCCccccccCHHHhCCCCCEEEEE
Confidence 3688888887744333 3222221 11110 134677889999998653
No 162
>TIGR01024 rplS_bact ribosomal protein L19, bacterial type. This model describes bacterial ribosomoal protein L19 and its chloroplast equivalent. Putative mitochondrial L19 are found in several species (but not Saccharomyces cerevisiae) and score between trusted and noise cutoffs.
Probab=37.18 E-value=1.1e+02 Score=29.39 Aligned_cols=49 Identities=20% Similarity=0.246 Sum_probs=32.2
Q ss_pred cccccCCCCEEEE----ecC---ccCCceeEEEEEeCC----eEEEeeCCCCCCceeEEc
Q 003213 220 KKGHFMKGDAVIV----IKG---DLKNLKGWVEKVDEE----NVHIRPEMKGLPKTLAVN 268 (838)
Q Consensus 220 ~~~~F~~GD~V~V----~~G---el~~l~G~V~~V~~d----~V~i~~~~~~l~~~i~v~ 268 (838)
.-..|.+||.|+| .+| ..+...|.|+++.+. ++++.-...+..-|..|+
T Consensus 15 ~ip~f~~GD~v~V~~~i~eg~k~R~q~f~GvvI~~~~~G~~~tftvR~i~~gvGVEr~fp 74 (113)
T TIGR01024 15 DLPDFRVGDTVRVHVKIVEGKKERIQVFEGVVIARRGGGIGETFTVRKISYGVGVERIFP 74 (113)
T ss_pred CCCccCCCCEEEEEEEEccCCceEcccEEEEEEEEeCCCCceEEEEEEeccCccEEEEEE
Confidence 3468999999998 244 345688999999743 566665544443343333
No 163
>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=37.17 E-value=2.7e+02 Score=24.98 Aligned_cols=64 Identities=14% Similarity=0.112 Sum_probs=42.5
Q ss_pred CcEEEEEEEecc-eEEEEecCCCCCcEEEEEccccccccccCccccCCCCCeecCCCEEEEEcCCC-CCceeeEEEEECC
Q 003213 349 NSFGVIIRVESE-AFQVLKGVPDRPEVALVKLREIKCKLEKKSNVQDRNKNTVAVKDVVRIVEGPC-KGKQGPVEHIYRG 426 (838)
Q Consensus 349 ~~vGvIv~ier~-~~~VL~~~~~~g~v~~vk~~~I~~K~~~~~~a~D~~gn~i~~gd~Vki~~Gp~-kG~~G~Vkhi~r~ 426 (838)
+..|.|++.-.+ .|.|... +|..+.+.. ..|+.+ .==|..||.|.|---|| .--.|.|.|.|..
T Consensus 1 q~i~~V~~~lG~~~~~V~~~---dg~~~l~~i---~gK~Rk--------~iwI~~GD~VlV~~~~~~~~~kg~Iv~r~~~ 66 (78)
T cd04456 1 QQIVRVLRMLGNNRHEVECA---DGQRRLVSI---PGKLRK--------NIWIKRGDFLIVDPIEEGEDVKADIIFVYCK 66 (78)
T ss_pred CeEEEEEEECCCCEEEEEEC---CCCEEEEEE---chhhcc--------CEEEcCCCEEEEEecccCCCceEEEEEEeCH
Confidence 356888888755 4677763 566666553 223221 12578999999987777 4568999998864
No 164
>COG0231 Efp Translation elongation factor P (EF-P)/translation initiation factor 5A (eIF-5A) [Translation, ribosomal structure and biogenesis]
Probab=36.94 E-value=89 Score=30.73 Aligned_cols=61 Identities=15% Similarity=0.147 Sum_probs=49.5
Q ss_pred ccccCCCCEEEEecCccCCceeEEEEEeCCeEEEeeCCCCCCceeEEcch---hhhhhccCCCeEEEe
Q 003213 221 KGHFMKGDAVIVIKGDLKNLKGWVEKVDEENVHIRPEMKGLPKTLAVNSK---ELCKYFEPGNHVKVV 285 (838)
Q Consensus 221 ~~~F~~GD~V~V~~Gel~~l~G~V~~V~~d~V~i~~~~~~l~~~i~v~~~---~LrK~F~~GDhVkVi 285 (838)
...|+.+|.|++. .+..-......++||...+|-... -+.++++.. +..+++++|-.|.|+
T Consensus 53 e~~f~~~~kve~a--~ie~~~~q~lY~dg~~~~FMD~et--yeq~~v~~~~~~d~~~~l~eg~~v~v~ 116 (131)
T COG0231 53 EKTFKADDKVEVA--IVERKTAQYLYIDGDFYVFMDLET--YEQYELPKDQIGDAAKFLKEGMEVEVL 116 (131)
T ss_pred EEEEcCCCEEEEe--EEeeeeEEEEEcCCCeEEEccCCC--ceEEEecchhhhhHHHhcCCCCEEEEE
Confidence 4689999999998 566667789999999999996533 466888876 788899999988776
No 165
>COG0779 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=36.87 E-value=56 Score=33.04 Aligned_cols=47 Identities=23% Similarity=0.311 Sum_probs=39.3
Q ss_pred CCCCEEEEec----CccCCceeEEEEEeCCeEEEeeCCCCCCceeEEcchhhhhh
Q 003213 225 MKGDAVIVIK----GDLKNLKGWVEKVDEENVHIRPEMKGLPKTLAVNSKELCKY 275 (838)
Q Consensus 225 ~~GD~V~V~~----Gel~~l~G~V~~V~~d~V~i~~~~~~l~~~i~v~~~~LrK~ 275 (838)
..|-.|+|.- ...+..+|+|+.++++.|++..+.+ +++++-+++.|+
T Consensus 97 ~~G~~Vkv~l~~~~~~~k~~~G~i~~~d~~~v~~~~~~k----~v~Ip~~~i~kA 147 (153)
T COG0779 97 FIGEKVKVKLRLPIEGRKKFEGKIVAVDGETVTLEVDGK----EVEIPFSDIAKA 147 (153)
T ss_pred hcCcEEEEEEecccCCceEEEEEEEEEcCCeEEEEECCE----EEEEEcccchhh
Confidence 5799999987 6789999999999999999986544 488888777764
No 166
>cd01854 YjeQ_engC YjeQ/EngC. YjeQ (YloQ in Bacillus subtilis) represents a protein family whose members are broadly conserved in bacteria and have been shown to be essential to the growth of E. coli and B. subtilis. Proteins of the YjeQ family contain all sequence motifs typical of the vast class of P-loop-containing GTPases, but show a circular permutation, with a G4-G1-G3 pattern of motifs as opposed to the regular G1-G3-G4 pattern seen in most GTPases. All YjeQ family proteins display a unique domain architecture, which includes an N-terminal OB-fold RNA-binding domain, the central permuted GTPase domain, and a zinc knuckle-like C-terminal cysteine domain. This domain architecture suggests a role for YjeQ as a regulator of translation.
Probab=36.80 E-value=2.6e+02 Score=30.75 Aligned_cols=86 Identities=20% Similarity=0.177 Sum_probs=56.0
Q ss_pred EEEEEEecceEEEEecCCCCCcEEEEEccccccccccCccccCCCCCeecCCCEEEEEcCCCCCceeeEEEEEC-CEEEE
Q 003213 352 GVIIRVESEAFQVLKGVPDRPEVALVKLREIKCKLEKKSNVQDRNKNTVAVKDVVRIVEGPCKGKQGPVEHIYR-GILFI 430 (838)
Q Consensus 352 GvIv~ier~~~~VL~~~~~~g~v~~vk~~~I~~K~~~~~~a~D~~gn~i~~gd~Vki~~Gp~kG~~G~Vkhi~r-~~lFL 430 (838)
|.|++..++.+.|++. ++++.++.+. ++.+ ....+.+||.|.+..-. +.+|.|..|+- ...+.
T Consensus 1 g~v~~~~~~~~~v~~~----~~~~~~~~~g---~~~~-------~~~~~~vGD~V~~~~~~--~~~~~i~~i~~R~~~l~ 64 (287)
T cd01854 1 GRVIAVHGGFYDVETE----GGELRCRARG---KLRK-------KGIKPVVGDWVEVEPDD--DGEGVIVRVLPRKNLLS 64 (287)
T ss_pred CEEEEEECCEEEEEEC----CeEEEEEecc---cccc-------CCCCccCCCEEEEEecC--CCcEEEEEEECCCceEE
Confidence 6789999999988872 5566666543 1111 14468999999885322 45799999994 44555
Q ss_pred EeCceeccccEEEEeCCceEEecc
Q 003213 431 HDRHHLEHAGFICAKSSSCVVVGG 454 (838)
Q Consensus 431 ~~~~~~En~Gifv~~a~~~~~~g~ 454 (838)
+-..... .-+++.++..+.++-+
T Consensus 65 R~~~~~~-~~~i~anvD~vllV~d 87 (287)
T cd01854 65 RPAAGGR-EQVIAANVDQLVIVVS 87 (287)
T ss_pred ccCCCCc-ceeEEEeCCEEEEEEE
Confidence 4332222 4577778877777755
No 167
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=36.28 E-value=1.3e+02 Score=35.85 Aligned_cols=51 Identities=31% Similarity=0.414 Sum_probs=33.4
Q ss_pred cccCCCCEEEEecCccCCceeEEEEEeCCeEEEeeCCCCCCceeEEcchhh--------hhhccCCCeEEEe
Q 003213 222 GHFMKGDAVIVIKGDLKNLKGWVEKVDEENVHIRPEMKGLPKTLAVNSKEL--------CKYFEPGNHVKVV 285 (838)
Q Consensus 222 ~~F~~GD~V~V~~Gel~~l~G~V~~V~~d~V~i~~~~~~l~~~i~v~~~~L--------rK~F~~GDhVkVi 285 (838)
..|++||.| .|+|++|+.+.|.|.-.. +-+=.++.++| .+.|++||.|++.
T Consensus 31 ~~~~~GdiV----------~G~V~~v~~~gv~VdIg~---k~eG~Ip~~Els~~~~~~~~~~~~vGd~Ie~~ 89 (486)
T PRK07899 31 KYFNDGDIV----------EGTVVKVDRDEVLLDIGY---KTEGVIPSRELSIKHDVDPNEVVEVGDEVEAL 89 (486)
T ss_pred hcCCCCCEE----------EEEEEEEECCcEEEEECC---CcEEEEEHHHhcccccCChhhcCCCCCEEEEE
Confidence 459999988 478999988876655421 11122344443 5679999998754
No 168
>cd00164 S1_like S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.
Probab=36.15 E-value=80 Score=25.10 Aligned_cols=42 Identities=24% Similarity=0.228 Sum_probs=25.8
Q ss_pred eeEEEEEeCCeEEEeeCCCCCCceeEEcchh--------hhhhccCCCeEEEe
Q 003213 241 KGWVEKVDEENVHIRPEMKGLPKTLAVNSKE--------LCKYFEPGNHVKVV 285 (838)
Q Consensus 241 ~G~V~~V~~d~V~i~~~~~~l~~~i~v~~~~--------LrK~F~~GDhVkVi 285 (838)
.|.|+++..+-+.+..... .+--++.++ ..++|++||.|++.
T Consensus 2 ~g~V~~v~~~g~~v~l~~~---~~g~~~~~~~~~~~~~~~~~~~~~G~~v~~~ 51 (65)
T cd00164 2 TGKVVSITKFGVFVELEDG---VEGLVHISELSDKFVKDPSEVFKVGDEVEVK 51 (65)
T ss_pred EEEEEEEEeeeEEEEecCC---CEEEEEHHHCCCccccCHhhEeCCCCEEEEE
Confidence 5788888877665554311 122333333 45679999998764
No 169
>TIGR00523 eIF-1A eukaryotic/archaeal initiation factor 1A. Recommended nomenclature: eIF-1A for eukaryotes, aIF-1A for Archaea. Also called eIF-4C
Probab=35.89 E-value=1.7e+02 Score=27.42 Aligned_cols=63 Identities=21% Similarity=0.197 Sum_probs=40.9
Q ss_pred CCcEEEEEEEecc-eEEEEecCCCCCcEEEEEccccccccccCccccCCCCCeecCCCEEEEEcCCCCCc---eeeEEEE
Q 003213 348 NNSFGVIIRVESE-AFQVLKGVPDRPEVALVKLREIKCKLEKKSNVQDRNKNTVAVKDVVRIVEGPCKGK---QGPVEHI 423 (838)
Q Consensus 348 ~~~vGvIv~ier~-~~~VL~~~~~~g~v~~vk~~~I~~K~~~~~~a~D~~gn~i~~gd~Vki~~Gp~kG~---~G~Vkhi 423 (838)
.+..|.|+++-.+ .|.|... +|..+.+.- ..|+.+ .==|..||.|.| .||.-- .|.|.|.
T Consensus 19 ~e~~g~V~~~lG~~~~~V~~~---dG~~~la~i---~GK~Rk--------~iwI~~GD~VlV--sp~d~~~~~kg~Iv~r 82 (99)
T TIGR00523 19 GEILGVIEQMLGAGRVKVRCL---DGKTRLGRI---PGKLKK--------RIWIREGDVVIV--KPWEFQGDDKCDIVWR 82 (99)
T ss_pred CEEEEEEEEEcCCCEEEEEeC---CCCEEEEEE---chhhcc--------cEEecCCCEEEE--EEccCCCCccEEEEEE
Confidence 4678999998855 4777763 466665552 233221 125789999999 465433 6889888
Q ss_pred ECC
Q 003213 424 YRG 426 (838)
Q Consensus 424 ~r~ 426 (838)
|..
T Consensus 83 ~~~ 85 (99)
T TIGR00523 83 YTK 85 (99)
T ss_pred cCH
Confidence 753
No 170
>PTZ00065 60S ribosomal protein L14; Provisional
Probab=35.82 E-value=35 Score=33.58 Aligned_cols=33 Identities=24% Similarity=0.372 Sum_probs=26.9
Q ss_pred cCcEEEEeecCCCCceeEEEeecCCeEEEEeccC
Q 003213 507 VGTTVKVRLGPYKGYRGRVVDVKGQSVRVELESQ 540 (838)
Q Consensus 507 iGktV~I~~GpyKG~~G~Vkdat~~~~rVELhs~ 540 (838)
||.-|.|..|||+|-++.|+|+-|.. ||.++..
T Consensus 10 iGRVvli~~Gp~~GKL~vIVDIID~n-RvLVDGP 42 (130)
T PTZ00065 10 PGRLCLIQYGPDAGKLCFIVDIVTPT-RVLVDGA 42 (130)
T ss_pred eceEEEEecCCCCCCEEEEEEEEcCC-eEEEeCC
Confidence 78899999999999999999997643 4555544
No 171
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=35.67 E-value=1.8e+02 Score=23.52 Aligned_cols=44 Identities=30% Similarity=0.423 Sum_probs=30.7
Q ss_pred eeeChhhhhhccccccccccCCCCCEEEEecCcCCCceEEEEEEeCCCCEEEEEE
Q 003213 52 MLVPIREMTDVLAVESKAIDLSRDTWVRMKIGNYKGDLAKVVDVDNVRQRVTVKL 106 (838)
Q Consensus 52 ~~Vpi~Em~~~L~~~~~~~~l~~G~~VRik~G~ykGDlaqV~~vd~~~~~V~vkl 106 (838)
..+|..|+.+-.. .+....+++|++|++ +|.+++..+.++.|.+
T Consensus 28 g~l~~~~~~~~~~-~~~~~~~~~G~~v~~----------~V~~~~~~~~~i~ls~ 71 (72)
T smart00316 28 GLIPISELSDKRV-KDPEEVLKVGDEVKV----------KVLSVDEEKGRIILSL 71 (72)
T ss_pred EEEEHHHCCcccc-CCHHHeecCCCEEEE----------EEEEEeCCCCEEEEEe
Confidence 5777777776531 122345899999986 7888888777777764
No 172
>cd03692 mtIF2_IVc mtIF2_IVc: this family represents the C2 subdomain of domain IV of mitochondrial translation initiation factor 2 (mtIF2) which adopts a beta-barrel fold displaying a high degree of structural similarity with domain II of the translation elongation factor EF-Tu. The C-terminal part of mtIF2 contains the entire fMet-tRNAfmet binding site of IF-2 and is resistant to proteolysis. This C-terminal portion consists of two domains, IF2 C1 and IF2 C2. IF2 C2 been shown to contain all molecular determinants necessary and sufficient for the recognition and binding of fMet-tRNAfMet. Like IF2 from certain prokaryotes such as Thermus thermophilus, mtIF2lacks domain II which is thought to be involved in binding of E.coli IF-2 to 30S subunits.
Probab=35.62 E-value=59 Score=29.03 Aligned_cols=59 Identities=10% Similarity=0.166 Sum_probs=34.4
Q ss_pred ccccCCCCEEEEecCccCCceeEEEEEeCCeEEEeeCCCCCCceeEEcchhhhhhccCCCeE
Q 003213 221 KGHFMKGDAVIVIKGDLKNLKGWVEKVDEENVHIRPEMKGLPKTLAVNSKELCKYFEPGNHV 282 (838)
Q Consensus 221 ~~~F~~GD~V~V~~Gel~~l~G~V~~V~~d~V~i~~~~~~l~~~i~v~~~~LrK~F~~GDhV 282 (838)
...+++|+.|+|+.+.-.-.+|+|.++.-..-.+..-.. .++..+..+++- .|+.||.+
T Consensus 24 ~G~l~~g~~v~vlr~~~~~~~g~i~sl~~~~~~v~~a~~--G~ecgi~l~~~~-d~~~Gdvi 82 (84)
T cd03692 24 DGKIKRNAKVRVLRNGEVIYEGKISSLKRFKDDVKEVKK--GYECGITLENFN-DIKVGDII 82 (84)
T ss_pred ECEEeCCCEEEEEcCCCEEEEEEEEEEEEcCcccCEECC--CCEEEEEEeCcc-cCCCCCEE
Confidence 368999999999987422256888887633111111111 344444445555 67777754
No 173
>PRK00098 GTPase RsgA; Reviewed
Probab=35.56 E-value=2.9e+02 Score=30.51 Aligned_cols=88 Identities=23% Similarity=0.216 Sum_probs=57.4
Q ss_pred EEEEEEEecceEEEEecCCCCCcEEEEEccccccccccCccccCCCCCeecCCCEEEEEcCCCCCceeeEEEEECCEEEE
Q 003213 351 FGVIIRVESEAFQVLKGVPDRPEVALVKLREIKCKLEKKSNVQDRNKNTVAVKDVVRIVEGPCKGKQGPVEHIYRGILFI 430 (838)
Q Consensus 351 vGvIv~ier~~~~VL~~~~~~g~v~~vk~~~I~~K~~~~~~a~D~~gn~i~~gd~Vki~~Gp~kG~~G~Vkhi~r~~lFL 430 (838)
.|.|+++.++.+.|++. .++++.++.+. ++.. ....+.+||.|.+-. + ....|.|..|....-+|
T Consensus 2 ~g~v~~~~~~~~~v~~~---~~~~~~~~~~g---~~~~-------~~~~~~vGD~V~~~~-~-~~~~g~i~~i~~R~~~l 66 (298)
T PRK00098 2 EGLIIKALGGFYYVESE---DGQVYQCRARG---KFRK-------KTNTPAVGDRVEFSA-E-NNDEGVILEIHERKNLL 66 (298)
T ss_pred eEEEEEEECCEEEEEEC---CCCEEEEEecc---cccc-------CCCCcCCCCEEEEEE-C-CCCcEEEEEEeCCCceE
Confidence 48999999999999873 35666666542 1110 234578999998842 1 22469999999887666
Q ss_pred EeCceeccccEEEEeCCceEEecc
Q 003213 431 HDRHHLEHAGFICAKSSSCVVVGG 454 (838)
Q Consensus 431 ~~~~~~En~Gifv~~a~~~~~~g~ 454 (838)
..+.. ...-+++.++..+.++-.
T Consensus 67 ~R~~~-~~~q~iaaniD~vllV~d 89 (298)
T PRK00098 67 VRPPI-FKSKLIAANVDQAVLVFA 89 (298)
T ss_pred ECCCC-ccccceeecCCEEEEEEE
Confidence 66664 222356666766666644
No 174
>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=35.11 E-value=54 Score=32.21 Aligned_cols=51 Identities=25% Similarity=0.326 Sum_probs=34.3
Q ss_pred CCCCEEEEec----CccCCceeEEEEEeCCeEEEeeCCCCCCceeEEcchhhhhh
Q 003213 225 MKGDAVIVIK----GDLKNLKGWVEKVDEENVHIRPEMKGLPKTLAVNSKELCKY 275 (838)
Q Consensus 225 ~~GD~V~V~~----Gel~~l~G~V~~V~~d~V~i~~~~~~l~~~i~v~~~~LrK~ 275 (838)
..|-.|+|.- ...+...|++.+++++.|++....++.+++++++-+++.|+
T Consensus 85 ~iG~~v~v~~~~~~~~~~~~~G~L~~~~~~~i~l~~~~~~~~~~~~I~~~~I~ka 139 (141)
T PF02576_consen 85 FIGRKVKVKLKQPVNGRKEFEGKLLEVDEDEITLEVEGKGKKKEVEIPFSDIKKA 139 (141)
T ss_dssp H-SEEEEEE-SS-SSS-SEEEEEEEEEETTEEEEEEE-SS-EEEEEE-SS--SS-
T ss_pred hcCCeEEEEEeccCCCcEEEEEEEEEEeCCEEEEEECCccceEEEEEEHHHCceE
Confidence 4788999985 33456799999999999999776554456889998888774
No 175
>PF10447 EXOSC1: Exosome component EXOSC1/CSL4; InterPro: IPR019495 The exosome mediates degradation of unstable mRNAs that contain AU-rich elements (AREs) within their 3' untranslated regions []. The proteins in this entry are components of the exosome 3'->5' exoribonuclease complex. They do not have exonuclease activity, but are required for the 3'-processing of the 7S pre-RNA to the mature 5.8S rRNA and for mRNA decay [, ].; PDB: 2NN6_I.
Probab=34.89 E-value=1.3e+02 Score=27.23 Aligned_cols=14 Identities=29% Similarity=0.745 Sum_probs=8.7
Q ss_pred hhhhhccCCCeEEE
Q 003213 271 ELCKYFEPGNHVKV 284 (838)
Q Consensus 271 ~LrK~F~~GDhVkV 284 (838)
++.+.|++||.|+.
T Consensus 64 ~~~~~FrpGDIVrA 77 (82)
T PF10447_consen 64 KMYDCFRPGDIVRA 77 (82)
T ss_dssp -GGGT--SSSEEEE
T ss_pred hHHhccCCCCEEEE
Confidence 45778999998864
No 176
>COG0335 RplS Ribosomal protein L19 [Translation, ribosomal structure and biogenesis]
Probab=34.77 E-value=1.1e+02 Score=29.41 Aligned_cols=30 Identities=23% Similarity=0.392 Sum_probs=22.8
Q ss_pred ccccCCCCEEE----EecC---ccCCceeEEEEEeCC
Q 003213 221 KGHFMKGDAVI----VIKG---DLKNLKGWVEKVDEE 250 (838)
Q Consensus 221 ~~~F~~GD~V~----V~~G---el~~l~G~V~~V~~d 250 (838)
-..|.+||+|+ |++| .++.-.|.|+++.+.
T Consensus 18 iP~f~~GDtvrv~vki~Eg~keR~Q~FeGvVia~r~~ 54 (115)
T COG0335 18 IPSFRPGDTVRVHVKIVEGSKERVQAFEGVVIARRGR 54 (115)
T ss_pred CCCCCCCCEEEEEEEEEeCCeEEEeeeeEEEEEECCC
Confidence 46899999865 4777 456778889888764
No 177
>PF13051 DUF3912: Protein of unknown function (DUF3912)
Probab=34.74 E-value=62 Score=27.43 Aligned_cols=50 Identities=20% Similarity=0.269 Sum_probs=35.3
Q ss_pred cccCcEEEEeecCCCCceeEEEeec---CCeEEEEeccCceEEEEeccccccccc
Q 003213 505 ALVGTTVKVRLGPYKGYRGRVVDVK---GQSVRVELESQMKVVTVDRSMISDNVV 556 (838)
Q Consensus 505 ~liGktV~I~~GpyKG~~G~Vkdat---~~~~rVELhs~~k~I~V~r~~l~~~~~ 556 (838)
.+.||..-|..|||.--+|+||.-. +.++-+-+. -+.|.|+..+|..++.
T Consensus 3 di~gqkayikdgp~rnrigivk~~e~q~~~~f~ivi~--~q~i~velkdivlvgv 55 (68)
T PF13051_consen 3 DIVGQKAYIKDGPYRNRIGIVKKNEKQLESHFAIVIG--EQSIDVELKDIVLVGV 55 (68)
T ss_pred cccccEeeeccCCccceeEEEecchhhcCCcEEEEEC--CeEEEEEeeeEEEEEe
Confidence 4789999999999999999999754 333433333 4456666667665543
No 178
>PF05641 Agenet: Agenet domain; InterPro: IPR008395 This domain is related to the TUDOR domain IPR008191 from INTERPRO []. The function of the agenet domain is unknown. This signature matches one of the two Agenet domains in the FMR proteins [].; GO: 0003723 RNA binding; PDB: 2BKD_N 3O8V_A 3KUF_A 3H8Z_A.
Probab=34.63 E-value=96 Score=26.65 Aligned_cols=34 Identities=24% Similarity=0.223 Sum_probs=22.9
Q ss_pred cCCCCEEEEecCcc----CCceeEEEEEeCC-eEEEeeC
Q 003213 224 FMKGDAVIVIKGDL----KNLKGWVEKVDEE-NVHIRPE 257 (838)
Q Consensus 224 F~~GD~V~V~~Gel----~~l~G~V~~V~~d-~V~i~~~ 257 (838)
|++||.|||..-+- .=..++|++..++ .+.|.-+
T Consensus 1 F~~G~~VEV~s~e~g~~gaWf~a~V~~~~~~~~~~V~Y~ 39 (68)
T PF05641_consen 1 FKKGDEVEVSSDEDGFRGAWFPATVLKENGDDKYLVEYD 39 (68)
T ss_dssp --TT-EEEEEE-SBTT--EEEEEEEEEEETT-EEEEEET
T ss_pred CCCCCEEEEEEcCCCCCcEEEEEEEEEeCCCcEEEEEEC
Confidence 89999999987542 2356899999988 7777654
No 179
>smart00357 CSP Cold shock protein domain. RNA-binding domain that functions as a RNA-chaperone in bacteria and is involved in regulating translation in eukaryotes. Contains sub-family of RNA-binding domains in the Rho transcription termination factor.
Probab=34.56 E-value=1.7e+02 Score=23.53 Aligned_cols=56 Identities=18% Similarity=0.188 Sum_probs=32.8
Q ss_pred eEEEEEeCCeEEEeeCCCCCCceeEEcchhh---hhhccCCCeEEEeccc---cCCceEEEEEE
Q 003213 242 GWVEKVDEENVHIRPEMKGLPKTLAVNSKEL---CKYFEPGNHVKVVSGT---QAGATGMVLKV 299 (838)
Q Consensus 242 G~V~~V~~d~V~i~~~~~~l~~~i~v~~~~L---rK~F~~GDhVkVi~G~---~~getGlVvkV 299 (838)
|.|...+...--+.++.. .+.+-|+.+++ ...+..||.|.+---. ..+..+.|++|
T Consensus 2 G~i~~~~~g~gfv~~~~~--~~~i~v~~~~~~~~~~~~~~Gd~V~~~i~~~~~~~~~~a~~v~~ 63 (64)
T smart00357 2 GVVKWFNKGFGFIRPDDG--GKDVFVHPSQIQGGLKSLREGDEVEFKVVSPRGGGKPEAENVVK 63 (64)
T ss_pred eEEEEEcCCeeEEecCCC--CccEEEEhHHhhcCCCcCCCCCEEEEEEEEccCCCCcEEEEEEe
Confidence 555555544444555433 24688888886 5556779999775322 23445566554
No 180
>cd05690 S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 5 (ec5) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=34.31 E-value=58 Score=27.14 Aligned_cols=43 Identities=21% Similarity=0.251 Sum_probs=29.3
Q ss_pred eeeChhhhhhccccccccccCCCCCEEEEecCcCCCceEEEEEEeCCCCEEEE
Q 003213 52 MLVPIREMTDVLAVESKAIDLSRDTWVRMKIGNYKGDLAKVVDVDNVRQRVTV 104 (838)
Q Consensus 52 ~~Vpi~Em~~~L~~~~~~~~l~~G~~VRik~G~ykGDlaqV~~vd~~~~~V~v 104 (838)
.++++.|+..-.........+++||.|+++ |.++|.++.++.+
T Consensus 26 Glv~~~~l~~~~~~~~~~~~~~~G~~v~v~----------v~~id~~~~~i~l 68 (69)
T cd05690 26 GLVHISDISWTQRVRHPSEIYKKGQEVEAV----------VLNIDVERERISL 68 (69)
T ss_pred EEEEHHHCCCccccCChhhEECCCCEEEEE----------EEEEECCcCEEeC
Confidence 577777876322223333458999999884 8899988887754
No 181
>PRK14633 hypothetical protein; Provisional
Probab=33.62 E-value=76 Score=31.83 Aligned_cols=49 Identities=29% Similarity=0.407 Sum_probs=38.0
Q ss_pred ccccCcEEEEee-c---CCCCceeEEEeecCCeEEEEeccCceEEEEecccccc
Q 003213 504 DALVGTTVKVRL-G---PYKGYRGRVVDVKGQSVRVELESQMKVVTVDRSMISD 553 (838)
Q Consensus 504 d~liGktV~I~~-G---pyKG~~G~Vkdat~~~~rVELhs~~k~I~V~r~~l~~ 553 (838)
..++|+.|+|+- . --|=+.|+.++++++.+++++.. .+.+.++.++|+-
T Consensus 90 ~r~~G~~v~V~~~~~~~~~~~~~G~L~~v~~~~i~l~~~~-~~~~~i~~~~I~k 142 (150)
T PRK14633 90 QALVGFNVKAVTLAPVGSQTKFKGVLERVEGNNVILNLED-GKEISFDFDELKK 142 (150)
T ss_pred HHhCCCeEEEEEecccCCcEEEEEEEEEEeCCEEEEEEcC-CcEEEEEhHHeee
Confidence 578999999964 3 34667899999999999988743 4677888887753
No 182
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=33.58 E-value=2.3e+02 Score=33.76 Aligned_cols=49 Identities=22% Similarity=0.322 Sum_probs=33.3
Q ss_pred ccCCCCEEEEecCccCCceeEEEEEeCCeEEEeeCCCCCCceeEEcchhhhh-----hccCCCeEEE
Q 003213 223 HFMKGDAVIVIKGDLKNLKGWVEKVDEENVHIRPEMKGLPKTLAVNSKELCK-----YFEPGNHVKV 284 (838)
Q Consensus 223 ~F~~GD~V~V~~Gel~~l~G~V~~V~~d~V~i~~~~~~l~~~i~v~~~~LrK-----~F~~GDhVkV 284 (838)
.|++||.| +|+|++|+.+.|.|.-. .+.+=.++.+++.. .+++||.+++
T Consensus 31 ~~~~G~~v----------~G~V~~v~~~~v~Vdig---~k~eg~ip~~e~~~~~~~~~~~~G~~i~~ 84 (491)
T PRK13806 31 ELRVGDKI----------TGTVIAITEDSVFVDTG---SKVDGVVDRAELLDADGELTVAVGDEVEL 84 (491)
T ss_pred cCCCCCEE----------EEEEEEEECCEEEEEEC---CCcEEEEEHHHhcCccccccccCCCEEEE
Confidence 48888887 68899999997776652 22334456666542 3788888754
No 183
>CHL00010 infA translation initiation factor 1
Probab=33.46 E-value=1.5e+02 Score=26.42 Aligned_cols=56 Identities=18% Similarity=0.206 Sum_probs=33.8
Q ss_pred ceeEEEEEeC-CeEEEeeCCCCCCceeE-Ecchhhhhh---ccCCCeEEEeccccCCceEEEEE
Q 003213 240 LKGWVEKVDE-ENVHIRPEMKGLPKTLA-VNSKELCKY---FEPGNHVKVVSGTQAGATGMVLK 298 (838)
Q Consensus 240 l~G~V~~V~~-d~V~i~~~~~~l~~~i~-v~~~~LrK~---F~~GDhVkVi~G~~~getGlVvk 298 (838)
+.|+|+++-+ +...+.++.. ..+. ....-||+. ..+||.|.|--=.++.+.|.|+-
T Consensus 9 ~~G~Vik~lg~~~y~V~~~~g---~~~~c~~rGklr~~~i~~~vGD~V~ve~~~~~~~~g~Ii~ 69 (78)
T CHL00010 9 MEGLVTESLPNGMFRVRLDNG---CQVLGYISGKIRRNSIRILPGDRVKVELSPYDLTKGRIIY 69 (78)
T ss_pred EEEEEEEEcCCCEEEEEeCCC---CEEEEEeccceecCCcccCCCCEEEEEEcccCCCeEEEEE
Confidence 6789998884 6556654221 2332 223334432 46799999874455677787764
No 184
>PRK14632 hypothetical protein; Provisional
Probab=33.28 E-value=79 Score=32.49 Aligned_cols=50 Identities=20% Similarity=0.448 Sum_probs=39.2
Q ss_pred ccccCcEEEEe-ecCC------CCceeEEEeecCCeEEEEeccC------ceEEEEecccccc
Q 003213 504 DALVGTTVKVR-LGPY------KGYRGRVVDVKGQSVRVELESQ------MKVVTVDRSMISD 553 (838)
Q Consensus 504 d~liGktV~I~-~Gpy------KG~~G~Vkdat~~~~rVELhs~------~k~I~V~r~~l~~ 553 (838)
..++|+.|+|+ ..+. |=+.|++++++++.+.+++..+ ..++.++.++|+-
T Consensus 94 ~r~iG~~V~V~l~~~~~~~~g~k~~~G~L~~v~~~~i~l~~~~~~~~~~~~~~~~i~~~~I~k 156 (172)
T PRK14632 94 SPYVGRQIELTLIDPTPEWPGRRKFRGELLAVEGDTVVLRPEGAPAPEAEEAVLRTSWQGVRK 156 (172)
T ss_pred HHhCCCEEEEEEeccccccCCceEEEEEEEEEeCCEEEEEEcCcccccCCceeEEEEhHHccE
Confidence 57899999995 4433 6688999999999999998643 2478888888864
No 185
>PF00575 S1: S1 RNA binding domain; InterPro: IPR003029 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The S1 domain was originally identified in ribosomal protein S1 but is found in a large number of RNA-associated proteins. The structure of the S1 RNA-binding domain from the Escherichia coli polynucleotide phosphorylase has been determined using NMR methods and consists of a five-stranded antiparallel beta barrel. Conserved residues on one face of the barrel and adjacent loops form the putative RNA-binding site []. The structure of the S1 domain is very similar to that of cold shock proteins. This suggests that they may both be derived from an ancient nucleic acid-binding protein []. More information about these proteins can be found at Protein of the Month: RNA Exosomes []. This entry does not include translation initiation factor IF-1 S1 domains.; GO: 0003723 RNA binding; PDB: 3L7Z_F 2JE6_I 2JEA_I 2JEB_I 1E3P_A 2Y0S_E 1WI5_A 2BH8_A 2CQO_A 2EQS_A ....
Probab=32.91 E-value=2.1e+02 Score=24.06 Aligned_cols=42 Identities=21% Similarity=0.279 Sum_probs=26.4
Q ss_pred eeEEEEEeCCeEEEeeCCCCCCceeEEcchh--------hhhhccCCCeEEEe
Q 003213 241 KGWVEKVDEENVHIRPEMKGLPKTLAVNSKE--------LCKYFEPGNHVKVV 285 (838)
Q Consensus 241 ~G~V~~V~~d~V~i~~~~~~l~~~i~v~~~~--------LrK~F~~GDhVkVi 285 (838)
.|+|.+|+..-+.+.-. .+ -+--++.++ ..+.|++||.|+|.
T Consensus 9 ~g~V~~v~~~g~~V~l~-~~--~~g~ip~~~l~~~~~~~~~~~~~~G~~v~v~ 58 (74)
T PF00575_consen 9 EGKVTSVEDFGVFVDLG-NG--IEGFIPISELSDDRIDDPSEVYKIGQTVRVK 58 (74)
T ss_dssp EEEEEEEETTEEEEEES-TS--SEEEEEGGGSSSSEESSSHGTCETTCEEEEE
T ss_pred EEEEEEEECCEEEEEEC-Cc--EEEEEEeehhcCccccccccccCCCCEEEEE
Confidence 57788888776666554 11 122334443 45789999998775
No 186
>PLN00208 translation initiation factor (eIF); Provisional
Probab=32.78 E-value=2.8e+02 Score=27.99 Aligned_cols=76 Identities=18% Similarity=0.253 Sum_probs=52.0
Q ss_pred ceEecceEEeC-CCcEEEEEEEecc-eEEEEecCCCCCcEEEEEccccccccccCccccCCCCCeecCCCEEEEEcCCCC
Q 003213 337 DYELRDLVLLD-NNSFGVIIRVESE-AFQVLKGVPDRPEVALVKLREIKCKLEKKSNVQDRNKNTVAVKDVVRIVEGPCK 414 (838)
Q Consensus 337 ~y~l~DLVqld-~~~vGvIv~ier~-~~~VL~~~~~~g~v~~vk~~~I~~K~~~~~~a~D~~gn~i~~gd~Vki~~Gp~k 414 (838)
+-+..+|+..+ .+..|.|+++-.+ .|.|.+. +|..+.+.- ..|+.++ ==|..||.|.|---+|.
T Consensus 20 ~~~~~el~~p~egq~~g~V~~~lGn~~~~V~c~---dG~~rLa~I---pGKmRKr--------IWI~~GD~VlVel~~~d 85 (145)
T PLN00208 20 DDEKRELIFKEDGQEYAQVLRMLGNGRCEALCI---DGTKRLCHI---RGKMRKK--------VWIAAGDIILVGLRDYQ 85 (145)
T ss_pred ccceeecccCCCCcEEEEEEEEcCCCEEEEEEC---CCCEEEEEE---eccceee--------EEecCCCEEEEEccCCC
Confidence 34556666653 5688999999855 5778874 466666553 2332221 25889999999877787
Q ss_pred CceeeEEEEECC
Q 003213 415 GKQGPVEHIYRG 426 (838)
Q Consensus 415 G~~G~Vkhi~r~ 426 (838)
--.|.|.|.|..
T Consensus 86 ~~KgdIv~ry~~ 97 (145)
T PLN00208 86 DDKADVILKYMP 97 (145)
T ss_pred CCEEEEEEEcCH
Confidence 778999888864
No 187
>PF00924 MS_channel: Mechanosensitive ion channel; InterPro: IPR006685 Mechanosensitive (MS) channels provide protection against hypo-osmotic shock, responding both to stretching of the cell membrane and to membrane depolarisation. They are present in the membranes of organisms from the three domains of life: bacteria, archaea, and eukarya []. There are two families of MS channels: large-conductance MS channels (MscL) and small-conductance MS channels (MscS or YGGB). The pressure threshold for MscS opening is 50% that of MscL []. The MscS family is much larger and more variable in size and sequence than the MscL family. Much of the diversity in MscS proteins occurs in the size of the transmembrane regions, which ranges from three to eleven transmembrane helices, although the three C-terminal helices are conserved. This family contains sequences form the MscS family of proteins. MscS folds as a homo-heptamer with a cylindrical shape, and can be divided into transmembrane and extramembrane regions: an N-terminal periplasmic region, a transmembrane region, and a C-terminal cytoplasmic region (middle and C-terminal domains). The transmembrane region forms a channel through the membrane that opens into a chamber enclosed by the extramembrane portion, the latter connecting to the cytoplasm through distinct portals [].; GO: 0055085 transmembrane transport, 0016020 membrane; PDB: 2OAU_E 2VV5_F.
Probab=32.63 E-value=67 Score=32.81 Aligned_cols=46 Identities=17% Similarity=0.286 Sum_probs=31.7
Q ss_pred ccccCCCCEEEEecCccCCceeEEEEEeCCeEEEeeCCCCCCceeEEcchhhhh
Q 003213 221 KGHFMKGDAVIVIKGDLKNLKGWVEKVDEENVHIRPEMKGLPKTLAVNSKELCK 274 (838)
Q Consensus 221 ~~~F~~GD~V~V~~Gel~~l~G~V~~V~~d~V~i~~~~~~l~~~i~v~~~~LrK 274 (838)
.+.|+.||.|+|- +..|+|++|.--.++++... .+.+.+|-+.|..
T Consensus 58 ~~pf~vGD~I~i~-----~~~G~V~~I~l~~t~l~~~~---g~~v~IPNs~l~~ 103 (206)
T PF00924_consen 58 ERPFKVGDRIEIG-----GVEGRVEEIGLRSTRLRTWD---GEIVIIPNSKLIS 103 (206)
T ss_dssp C-SS-TT-EEESS-----S-EEEEEEE-SSEEEEEETT---S-EEEEEHHHHHC
T ss_pred cCCccCCCEEEEE-----EeehHHHhcCcceeeeecCC---CCEEEEEchheee
Confidence 4699999999876 99999999998888887542 3567888777763
No 188
>PRK11642 exoribonuclease R; Provisional
Probab=32.58 E-value=5.9e+02 Score=32.52 Aligned_cols=115 Identities=19% Similarity=0.173 Sum_probs=65.0
Q ss_pred ceeEEEEEeCCeEEEeeCCCCCCceeEEcchhhhhhccCCCeEEEe-cc--ccCCceEEEEEE-eCc---EEEEEeCCCC
Q 003213 240 LKGWVEKVDEENVHIRPEMKGLPKTLAVNSKELCKYFEPGNHVKVV-SG--TQAGATGMVLKV-EQH---VLIILSDTTK 312 (838)
Q Consensus 240 l~G~V~~V~~d~V~i~~~~~~l~~~i~v~~~~LrK~F~~GDhVkVi-~G--~~~getGlVvkV-e~~---~v~vlSD~t~ 312 (838)
+.|+|..-...---+.++.. .+.|-++.++|..++. ||.|.|. .+ .-....|.|++| |+. .+=.+ ....
T Consensus 85 ~~G~v~~~~~GfgFv~~e~~--~~difI~~~~l~~A~~-GD~V~v~i~~~~~~~r~eg~Vv~IleR~~~~~vG~~-~~~~ 160 (813)
T PRK11642 85 LKGTVIGHRDGYGFLRVEGR--KDDLYLSSEQMKTCIH-GDQVLAQPLGADRKGRREARIVRVLVPKTSQIVGRY-FTDA 160 (813)
T ss_pred EEEEEEECCCccEEEEECCC--CCCEEEChHHHccCCC-CCEEEEEEccCCCCCCcEEEEEEEEecCCCEEEEEE-EEeC
Confidence 56777766555333344322 3478889999999887 9999775 22 112247888888 332 12112 1223
Q ss_pred CeEEEcccccccccccccccccCCceEecceEEe--C------CCcEEEEEEEe
Q 003213 313 EDIRVFADDVVESSEVTTGITKIGDYELRDLVLL--D------NNSFGVIIRVE 358 (838)
Q Consensus 313 ~ei~V~~~dL~~~~e~~~g~d~~g~y~l~DLVql--d------~~~vGvIv~ie 358 (838)
...-|.|.|-+...++--........+.+|+|.. . ..-.|.|+++-
T Consensus 161 ~~~~v~P~d~r~~~~i~i~~~~~~~~~~gd~V~v~I~~~p~~~~~~~g~iv~vL 214 (813)
T PRK11642 161 GVGFVVPDDSRLSFDILIPPEQIMGARMGFVVVVELTQRPTRRTKAVGKIVEVL 214 (813)
T ss_pred CeEEEEECCCCCCCcEEeccccccCCCCCCEEEEEEecCCCcCCCCCEEEEEEe
Confidence 4456777776655544322223345666788765 2 12357776654
No 189
>cd05793 S1_IF1A S1_IF1A: Translation initiation factor IF1A, also referred to as eIF1A in eukaryotes and aIF1A in archaea, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea.
Probab=32.55 E-value=2.4e+02 Score=25.22 Aligned_cols=58 Identities=19% Similarity=0.094 Sum_probs=38.1
Q ss_pred ceeEEEEEeCC-eEEEeeCCCCCCceeEEcchhhhhh--ccCCCeEEEeccccCCceEEEEEE
Q 003213 240 LKGWVEKVDEE-NVHIRPEMKGLPKTLAVNSKELCKY--FEPGNHVKVVSGTQAGATGMVLKV 299 (838)
Q Consensus 240 l~G~V~~V~~d-~V~i~~~~~~l~~~i~v~~~~LrK~--F~~GDhVkVi~G~~~getGlVvkV 299 (838)
+.|+|++.-++ ...+.+... ..-+---+.-+||. +..||.|.|---.|+...|-|+..
T Consensus 2 ~~g~V~~~~g~~~~~V~~~~g--~~~la~i~gK~rk~iwI~~GD~V~Ve~~~~d~~kg~Iv~r 62 (77)
T cd05793 2 EYGQVEKMLGNGRLEVRCFDG--KKRLCRIRGKMRKRVWINEGDIVLVAPWDFQDDKADIIYK 62 (77)
T ss_pred EEEEEEEEcCCCEEEEEECCC--CEEEEEEchhhcccEEEcCCCEEEEEeccccCCEEEEEEE
Confidence 35888888776 445555422 23343334445664 589999999766788888888765
No 190
>TIGR00038 efp translation elongation factor P. function: involved in peptide bond synthesis. stimulate efficient translation and peptide-bond synthesis on native or reconstituted 70S ribosomes in vitro. probably functions indirectly by altering the affinity of the ribosome for aminoacyl-tRNA, thus increasing their reactivity as acceptors for peptidyl transferase (by similarity). The trusted cutoff of this model is set high enough to exclude members of TIGR02178, an EFP-like protein of certain Gammaproteobacteria.
Probab=32.41 E-value=4e+02 Score=27.62 Aligned_cols=70 Identities=17% Similarity=0.181 Sum_probs=52.4
Q ss_pred cccCCCCEEEEecCccCCceeEEEEEeCCeEEEeeCCCCCCceeEEcchhh---hhhccCCCeEEEeccccCCceEEEEE
Q 003213 222 GHFMKGDAVIVIKGDLKNLKGWVEKVDEENVHIRPEMKGLPKTLAVNSKEL---CKYFEPGNHVKVVSGTQAGATGMVLK 298 (838)
Q Consensus 222 ~~F~~GD~V~V~~Gel~~l~G~V~~V~~d~V~i~~~~~~l~~~i~v~~~~L---rK~F~~GDhVkVi~G~~~getGlVvk 298 (838)
..|+.+|.|++. ++.--...++..++|.+.+|-. +. -+.++++.+.| .+++++|..|.|. -|+++ ++.
T Consensus 51 ~~f~~~~kve~~--~~e~~~~q~ly~dgd~~~fMD~-et-yeq~~i~~~~l~~~~~~L~eg~~v~v~--~~~~~---~i~ 121 (184)
T TIGR00038 51 KTFRSGEKVEKA--DVEEREMQYLYKDGDSYVFMDT-ET-YEQIELPKDLLGDAAKFLKENMEVSVT--FYNGE---PIG 121 (184)
T ss_pred EEeCCCCEEEcc--cEEeEEEEEEEECCCEEEEeCC-CC-ccceEcCHHHHHHHHhhcCCCCEEEEE--EECCE---EEE
Confidence 588999987777 5666777899999999999943 22 45688887754 7889999998876 35544 667
Q ss_pred Ee
Q 003213 299 VE 300 (838)
Q Consensus 299 Ve 300 (838)
|+
T Consensus 122 v~ 123 (184)
T TIGR00038 122 VE 123 (184)
T ss_pred EE
Confidence 66
No 191
>PTZ00328 eukaryotic initiation factor 5a; Provisional
Probab=32.32 E-value=58 Score=33.33 Aligned_cols=45 Identities=11% Similarity=0.178 Sum_probs=35.8
Q ss_pred CceeEEEEEeCCe-------EEEeeCCCCCCceeEEcc-hh----hhhhccCCCeEE
Q 003213 239 NLKGWVEKVDEEN-------VHIRPEMKGLPKTLAVNS-KE----LCKYFEPGNHVK 283 (838)
Q Consensus 239 ~l~G~V~~V~~d~-------V~i~~~~~~l~~~i~v~~-~~----LrK~F~~GDhVk 283 (838)
.-.+.|++|++|. +.+|-+....++.|.++. .+ |+..|+.|..|.
T Consensus 89 r~~yqli~I~~d~~~~~~g~v~LMd~~g~~k~dl~lp~~~el~~~ik~~f~~g~ev~ 145 (166)
T PTZ00328 89 TFTYSVLDIQPNEDPSLPAHLSLMDDEGESREDLDMPPDAALATQIKEQFDSGKEVL 145 (166)
T ss_pred eeEEEEEEEcCCCcccccceEEEEcCCCCeeecccCCChhHHHHHHHHHhcCCCeEE
Confidence 4567899998875 999987666677888875 56 788999999776
No 192
>PRK00092 ribosome maturation protein RimP; Reviewed
Probab=32.02 E-value=76 Score=31.77 Aligned_cols=49 Identities=27% Similarity=0.303 Sum_probs=38.5
Q ss_pred CCCCEEEEe----cCccCCceeEEEEEeCCeEEEeeCCCCCCceeEEcchhhhhh
Q 003213 225 MKGDAVIVI----KGDLKNLKGWVEKVDEENVHIRPEMKGLPKTLAVNSKELCKY 275 (838)
Q Consensus 225 ~~GD~V~V~----~Gel~~l~G~V~~V~~d~V~i~~~~~~l~~~i~v~~~~LrK~ 275 (838)
..|..|+|. -+..+..+|.+.+++++.|++..+.+. ++++++-++++|+
T Consensus 96 ~~G~~v~V~~~~~~~~~~~~~G~L~~~~~~~i~l~~~~~~--~~~~i~~~~I~~a 148 (154)
T PRK00092 96 FIGREVKVKLYEPIDGRKKFQGILLAVDGETVTLEVEGKE--KEVEIPLDNIAKA 148 (154)
T ss_pred hCCCeEEEEEEcccCCceEEEEEEEEeeCCEEEEEECCCe--EEEEEEHHHcceE
Confidence 579999997 355678899999999999998865331 4788888888774
No 193
>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=32.01 E-value=19 Score=32.47 Aligned_cols=44 Identities=20% Similarity=0.445 Sum_probs=3.3
Q ss_pred hhhhhhccCCCeEEEeccccCCceEEEEEEeCcEEEEEeCCCCCeEEEc
Q 003213 270 KELCKYFEPGNHVKVVSGTQAGATGMVLKVEQHVLIILSDTTKEDIRVF 318 (838)
Q Consensus 270 ~~LrK~F~~GDhVkVi~G~~~getGlVvkVe~~~v~vlSD~t~~ei~V~ 318 (838)
.++....++||.|...+| --|.|++++++.+.|=.+. +-++++.
T Consensus 31 ~~m~~~Lk~Gd~VvT~gG----i~G~V~~i~~~~v~lei~~-g~~i~v~ 74 (82)
T PF02699_consen 31 QEMLASLKPGDEVVTIGG----IYGTVVEIDDDTVVLEIAP-GVEITVE 74 (82)
T ss_dssp TTGGG--------------------------------------------
T ss_pred HHHHHcCCCCCEEEECCc----EEEEEEEEeCCEEEEEECC-CeEEEEE
Confidence 466778899999998887 5588999999888775443 3444443
No 194
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=31.69 E-value=2.9e+02 Score=26.08 Aligned_cols=73 Identities=15% Similarity=0.153 Sum_probs=48.2
Q ss_pred EecceEEeC-CCcEEEEEEEecc-eEEEEecCCCCCcEEEEEccccccccccCccccCCCCCeecCCCEEEEEcCCCCCc
Q 003213 339 ELRDLVLLD-NNSFGVIIRVESE-AFQVLKGVPDRPEVALVKLREIKCKLEKKSNVQDRNKNTVAVKDVVRIVEGPCKGK 416 (838)
Q Consensus 339 ~l~DLVqld-~~~vGvIv~ier~-~~~VL~~~~~~g~v~~vk~~~I~~K~~~~~~a~D~~gn~i~~gd~Vki~~Gp~kG~ 416 (838)
...+++..+ .+..|.|+++-.+ .|.|... +|..+.+... .|+.+ .==|..||.|.|--=||.--
T Consensus 11 ~~~~~~~p~e~e~~g~V~~~lG~~~~~V~~~---dG~~~la~i~---GK~Rk--------~IwI~~GD~VlVe~~~~~~~ 76 (100)
T PRK04012 11 TRVRLPMPEEGEVFGVVEQMLGANRVRVRCM---DGVERMGRIP---GKMKK--------RMWIREGDVVIVAPWDFQDE 76 (100)
T ss_pred eeEEccCCCCCEEEEEEEEEcCCCEEEEEeC---CCCEEEEEEc---hhhcc--------cEEecCCCEEEEEecccCCC
Confidence 345566654 4578999988755 4777763 5666665532 23221 12578999999976677656
Q ss_pred eeeEEEEEC
Q 003213 417 QGPVEHIYR 425 (838)
Q Consensus 417 ~G~Vkhi~r 425 (838)
.|.|.|.|.
T Consensus 77 kg~Iv~r~~ 85 (100)
T PRK04012 77 KADIIWRYT 85 (100)
T ss_pred EEEEEEEcC
Confidence 799988886
No 195
>KOG1984 consensus Vesicle coat complex COPII, subunit SFB3 [Intracellular trafficking, secretion, and vesicular transport]
Probab=31.65 E-value=8.4e+02 Score=31.38 Aligned_cols=6 Identities=33% Similarity=0.905 Sum_probs=3.5
Q ss_pred CCCCCC
Q 003213 710 PMTPGT 715 (838)
Q Consensus 710 p~tp~~ 715 (838)
.|+|+.
T Consensus 154 ~f~p~~ 159 (1007)
T KOG1984|consen 154 AFPPGP 159 (1007)
T ss_pred cCCCCc
Confidence 466665
No 196
>PF13893 RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); PDB: 2PE8_A 2PEH_A 2D9O_A 1A9N_D 2DIT_A 3S6E_A 2LQ5_A 1SJQ_A 2AD9_A 1X4D_A ....
Probab=31.30 E-value=77 Score=25.42 Aligned_cols=36 Identities=8% Similarity=0.269 Sum_probs=29.4
Q ss_pred cEEEEEecCCCceEEEEEecChHHHHHHHhcCccee
Q 003213 12 QIRSVIALDHLKNYIYIEADKEAHVKEACKGLRNIY 47 (838)
Q Consensus 12 ~I~Sv~~~~~lkGyIyVEA~~~~~V~~ai~g~~~v~ 47 (838)
.|.++...+.-+|+.|||-.+..+...|++.+.+..
T Consensus 10 ~V~~i~~~~~~~~~a~V~f~~~~~A~~a~~~l~~~~ 45 (56)
T PF13893_consen 10 EVKKIKIFKKKRGFAFVEFASVEDAQKAIEQLNGRQ 45 (56)
T ss_dssp -EEEEEEETTSTTEEEEEESSHHHHHHHHHHHTTSE
T ss_pred cEEEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCE
Confidence 377777766557999999999999999999887654
No 197
>PRK14647 hypothetical protein; Provisional
Probab=30.73 E-value=87 Score=31.68 Aligned_cols=48 Identities=21% Similarity=0.278 Sum_probs=37.6
Q ss_pred ccccCcEEEEee-cC--------CCCceeEEEeecCCeEEEEeccCceEEEEeccccc
Q 003213 504 DALVGTTVKVRL-GP--------YKGYRGRVVDVKGQSVRVELESQMKVVTVDRSMIS 552 (838)
Q Consensus 504 d~liGktV~I~~-Gp--------yKG~~G~Vkdat~~~~rVELhs~~k~I~V~r~~l~ 552 (838)
..++|+.|+|+- .+ -|=+.|++++++++.+++++.. .+.+.++.++|+
T Consensus 95 ~r~~G~~v~V~l~~~~~~~~~~~~~~~~G~L~~~~~~~v~l~~~~-~~~~~i~~~~I~ 151 (159)
T PRK14647 95 ERYAGRLVKVRTFELLADEAGNKRKTFLGELEGLADGVVTIALKE-GQQARIPLDKIA 151 (159)
T ss_pred HHhCCcEEEEEEeccccccccCCceEEEEEEEeecCCEEEEEEcC-CcEEEEEHHHCC
Confidence 578999999973 22 3678999999999999998752 456788887775
No 198
>PRK02001 hypothetical protein; Validated
Probab=30.56 E-value=1.1e+02 Score=30.98 Aligned_cols=49 Identities=16% Similarity=0.209 Sum_probs=37.9
Q ss_pred ccccCcEEEEeecCCCCceeEEEeecCCeEEEEeccC------------ceEEEEeccccc
Q 003213 504 DALVGTTVKVRLGPYKGYRGRVVDVKGQSVRVELESQ------------MKVVTVDRSMIS 552 (838)
Q Consensus 504 d~liGktV~I~~GpyKG~~G~Vkdat~~~~rVELhs~------------~k~I~V~r~~l~ 552 (838)
..++|+.|+|+-.--|=+.|++.++++..+.++++.+ .+.++++.++|+
T Consensus 86 ~r~~G~~v~V~l~~~~~~~G~L~~~~~~~i~l~~~~~~~~~~~k~~~~~~~~~~i~~~~I~ 146 (152)
T PRK02001 86 KKNIGRELEVLTKNGKKIEGELKSADENDITLEVKAREPKEGGKGKVTVEKEETITYDDIK 146 (152)
T ss_pred HHhCCCEEEEEECCCCEEEEEEEEEeCCEEEEEEcccccccccccccccceeEEEEhHhee
Confidence 5789999999753348899999999999999998753 235666666654
No 199
>TIGR00358 3_prime_RNase VacB and RNase II family 3'-5' exoribonucleases. This model is defined to identify a pair of paralogous 3-prime exoribonucleases in E. coli, plus the set of proteins apparently orthologous to one or the other in other eubacteria. VacB was characterized originally as required for the expression of virulence genes, but is now recognized as the exoribonuclease RNase R (Rnr). Its paralog in E. coli and H. influenzae is designated exoribonuclease II (Rnb). Both are involved in the degradation of mRNA, and consequently have strong pleiotropic effects that may be difficult to disentangle. Both these proteins share domain-level similarity (RNB, S1) with a considerable number of other proteins, and full-length similarity scoring below the trusted cutoff to proteins associated with various phenotypes but uncertain biochemistry; it may be that these latter proteins are also 3-prime exoribonucleases.
Probab=30.45 E-value=2.6e+02 Score=34.54 Aligned_cols=74 Identities=11% Similarity=0.108 Sum_probs=45.3
Q ss_pred CCCEEEEecCccCCceeEEEEEeCCeEEEeeCCCCCCceeEEcchhhhhhccCCCeEEEecccc----CCceEEEEEEe
Q 003213 226 KGDAVIVIKGDLKNLKGWVEKVDEENVHIRPEMKGLPKTLAVNSKELCKYFEPGNHVKVVSGTQ----AGATGMVLKVE 300 (838)
Q Consensus 226 ~GD~V~V~~Gel~~l~G~V~~V~~d~V~i~~~~~~l~~~i~v~~~~LrK~F~~GDhVkVi~G~~----~getGlVvkVe 300 (838)
.|-.|+|++=..+.+.|.+.. .++...+.|+...+...|.++.++..+.++.||.|+|-==+| ..-.|-|+++=
T Consensus 71 ~g~v~~il~r~~~~~vG~~~~-~~~~~~v~p~~~~~~~~i~i~~~~~~~~~~~g~~V~v~i~~~p~~~~~~~g~i~~~l 148 (654)
T TIGR00358 71 EAEVERILEPALTRFVGKFLG-ENDFGFVVPDDPRIYLDIIVPKASVKNELAEGDKVVVELTEYPLRRNLFYGEITQIL 148 (654)
T ss_pred eEEEEEEeccCCCEEEEEEEE-eCCeEEEEECCCCCCCcEEEcCCccccCCCCCCEEEEEEccCCCCCCCceEEEEEEE
Confidence 344444444444445554432 234455677777777778888776555788999987753333 23478888874
No 200
>PRK14638 hypothetical protein; Provisional
Probab=30.44 E-value=90 Score=31.34 Aligned_cols=47 Identities=17% Similarity=0.314 Sum_probs=38.1
Q ss_pred CCCCEEEEecCccCCceeEEEEEeCCeEEEeeCCCCCCceeEEcchhhhhh
Q 003213 225 MKGDAVIVIKGDLKNLKGWVEKVDEENVHIRPEMKGLPKTLAVNSKELCKY 275 (838)
Q Consensus 225 ~~GD~V~V~~Gel~~l~G~V~~V~~d~V~i~~~~~~l~~~i~v~~~~LrK~ 275 (838)
..|-.|+|.-.+-+..+|++.+++++.|++..+ +++++++.++++|+
T Consensus 98 ~~G~~v~V~~~~~k~~~G~L~~~~~~~i~l~~~----~~~~~i~~~~I~~a 144 (150)
T PRK14638 98 FTGKLAKIVTKDGKTFIGRIESFVDGTITISDE----KEKYEINIDDVKRA 144 (150)
T ss_pred hCCCEEEEEECCCcEEEEEEEEEeCCEEEEEEC----CcEEEEEhHHcceE
Confidence 579999996555689999999999999998743 35688888888774
No 201
>COG1532 Predicted RNA-binding protein [General function prediction only]
Probab=29.77 E-value=61 Score=27.21 Aligned_cols=41 Identities=24% Similarity=0.336 Sum_probs=31.7
Q ss_pred hhhccccccccccCCCCCEEEEe--cCcCCCceEEEEEEeCCCCEEEEE
Q 003213 59 MTDVLAVESKAIDLSRDTWVRMK--IGNYKGDLAKVVDVDNVRQRVTVK 105 (838)
Q Consensus 59 m~~~L~~~~~~~~l~~G~~VRik--~G~ykGDlaqV~~vd~~~~~V~vk 105 (838)
|+|++.++. .|+-|+.+ -|-||-..|||.++|-++.++.++
T Consensus 14 mEDV~~iev------~~e~V~a~Dilgd~ke~~G~vkriDldehkI~lE 56 (57)
T COG1532 14 MEDVLYIEV------TEEGVVARDILGDEKEFEGQVKRIDLDEHKIELE 56 (57)
T ss_pred EeEEEEEEE------ecCcEEEEeccCCceEecceEEEEEccccEEEec
Confidence 567776654 35666665 499999999999999999888764
No 202
>COG0779 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=29.56 E-value=1.2e+02 Score=30.79 Aligned_cols=47 Identities=34% Similarity=0.540 Sum_probs=38.9
Q ss_pred ccccCcEEEEee----cCCCCceeEEEeecCCeEEEEeccCceEEEEeccccc
Q 003213 504 DALVGTTVKVRL----GPYKGYRGRVVDVKGQSVRVELESQMKVVTVDRSMIS 552 (838)
Q Consensus 504 d~liGktV~I~~----GpyKG~~G~Vkdat~~~~rVELhs~~k~I~V~r~~l~ 552 (838)
..++|+.|+|.- .--|=+.|.+..+.++++.++. ..|.|.|+...|+
T Consensus 95 ~r~~G~~Vkv~l~~~~~~~k~~~G~i~~~d~~~v~~~~--~~k~v~Ip~~~i~ 145 (153)
T COG0779 95 ARFIGEKVKVKLRLPIEGRKKFEGKIVAVDGETVTLEV--DGKEVEIPFSDIA 145 (153)
T ss_pred HHhcCcEEEEEEecccCCceEEEEEEEEEcCCeEEEEE--CCEEEEEEcccch
Confidence 578999999998 5568899999999999988884 4556888877775
No 203
>PTZ00329 eukaryotic translation initiation factor 1A; Provisional
Probab=29.43 E-value=3.9e+02 Score=27.23 Aligned_cols=76 Identities=11% Similarity=-0.046 Sum_probs=50.7
Q ss_pred cccCCCCEEEEecCccCCceeEEEEEeCC-eEEEeeCCCCCCceeEEcchhhhhh--ccCCCeEEEeccccCCceEEEEE
Q 003213 222 GHFMKGDAVIVIKGDLKNLKGWVEKVDEE-NVHIRPEMKGLPKTLAVNSKELCKY--FEPGNHVKVVSGTQAGATGMVLK 298 (838)
Q Consensus 222 ~~F~~GD~V~V~~Gel~~l~G~V~~V~~d-~V~i~~~~~~l~~~i~v~~~~LrK~--F~~GDhVkVi~G~~~getGlVvk 298 (838)
+.-.-+...+++--+---+.|+|++.-++ .+.+++... ..-|---+--+||. ..+||.|.|---.|..+.|-|+.
T Consensus 16 k~~~~~~~rel~~~eegq~~g~V~~~LGn~~f~V~c~dG--~~rLa~I~GKmRK~IWI~~GD~VlVel~~yd~~KgdIi~ 93 (155)
T PTZ00329 16 KNDNEGEKRELVFKEEGQEYAQVLRMLGNGRLEAYCFDG--VKRLCHIRGKMRKRVWINIGDIILVSLRDFQDSKADVIL 93 (155)
T ss_pred cccCccceeeeccCCCCcEEEEEEEEcCCCEEEEEECCC--CEEEEEeeccceeeEEecCCCEEEEeccCCCCCEEEEEE
Confidence 34444455555554445578999999776 667776532 33444444556664 68999999987788888888876
Q ss_pred E
Q 003213 299 V 299 (838)
Q Consensus 299 V 299 (838)
.
T Consensus 94 R 94 (155)
T PTZ00329 94 K 94 (155)
T ss_pred E
Confidence 5
No 204
>PF07076 DUF1344: Protein of unknown function (DUF1344); InterPro: IPR009780 This family consists of several short, hypothetical bacterial proteins of around 80 residues in length. Members of this family are found in Rhizobium, Agrobacterium and Brucella species. The function of this family is unknown.
Probab=29.43 E-value=1.4e+02 Score=25.84 Aligned_cols=44 Identities=20% Similarity=0.311 Sum_probs=28.5
Q ss_pred CceeEEEEEeCCeEEEeeCCCCCCceeEEcchhhhhhccCCCeEEEe
Q 003213 239 NLKGWVEKVDEENVHIRPEMKGLPKTLAVNSKELCKYFEPGNHVKVV 285 (838)
Q Consensus 239 ~l~G~V~~V~~d~V~i~~~~~~l~~~i~v~~~~LrK~F~~GDhVkVi 285 (838)
..+|+|.+|+.+.-+|.-+.. +.+.++..-=-...++|.-|.|.
T Consensus 4 ~veG~I~~id~~~~titLdDG---ksy~lp~ef~~~~L~~G~kV~V~ 47 (61)
T PF07076_consen 4 DVEGTIKSIDPETMTITLDDG---KSYKLPEEFDFDGLKPGMKVVVF 47 (61)
T ss_pred cceEEEEEEcCCceEEEecCC---CEEECCCcccccccCCCCEEEEE
Confidence 468999999999877776533 33333333223345788877765
No 205
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=29.31 E-value=96 Score=33.30 Aligned_cols=50 Identities=26% Similarity=0.359 Sum_probs=31.0
Q ss_pred CCCCEEEEecCccCCceeEEEEEeCCeE--EEeeCCCCC-------CceeEEcchhhhhhccCCCeEEE
Q 003213 225 MKGDAVIVIKGDLKNLKGWVEKVDEENV--HIRPEMKGL-------PKTLAVNSKELCKYFEPGNHVKV 284 (838)
Q Consensus 225 ~~GD~V~V~~Gel~~l~G~V~~V~~d~V--~i~~~~~~l-------~~~i~v~~~~LrK~F~~GDhVkV 284 (838)
++||.| .|+|++|..+.. .|-+....+ ...++...++++++|++||.|++
T Consensus 62 ~vGDiV----------iG~V~~i~~~~~~vdI~~~~~g~L~~s~i~~~~~~~d~~~~~~~~~~GDlV~a 120 (235)
T PRK04163 62 KVGDLV----------IGKVTDVTFSGWEVDINSPYKAYLPVSEVLGRPVNVEGTDLRKYLDIGDYIIA 120 (235)
T ss_pred CCCCEE----------EEEEEEEeCceEEEEeCCCceeEEEHHHcCCCccccchhhhHhhCCCCCEEEE
Confidence 789988 478888877743 333222111 11122234788899999999865
No 206
>PF12059 DUF3540: Protein of unknown function (DUF3540); InterPro: IPR021927 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 212 to 238 amino acids in length. This protein has a conserved SCL sequence motif.
Probab=29.25 E-value=2e+02 Score=30.30 Aligned_cols=67 Identities=19% Similarity=0.164 Sum_probs=40.6
Q ss_pred EEEEEEeCCCCeEEEEeccCCCCceEEecCCCceEcCCCCCCcEEEEcCCCCC---ceEEEEEEeCCCeEEEecC
Q 003213 749 VGVIREVLPDGSCRVVLGSSGNGDTITALPNEIEIVPPRKTDKIKIMGGPHRG---ATGKLIGVDGTDGIVKVDV 820 (838)
Q Consensus 749 ~gvI~~V~~dg~~~V~l~~~~~g~~v~v~~~~Le~V~P~kgd~VkVi~G~~rG---~tG~LisiD~~dgiVk~d~ 820 (838)
.|.|....+++.+ |... . |. +.+-..-==.+.|+.||+|.|....+-+ ..+.|.--++....+.+++
T Consensus 3 ~g~V~~~~~~~~~-v~~~-~--G~-~~arrAaSCLl~P~~GD~VLv~~~~d~~~~yILAVL~r~~~~~a~L~~~G 72 (202)
T PF12059_consen 3 SGTVVGREGDGLV-VVDD-D--GE-WRARRAASCLLEPAVGDTVLVSGVADEERVYILAVLERADPGPATLSVPG 72 (202)
T ss_pred eEEEEEEeCCeEE-EEcC-C--CE-EEEEeccccccCCCCCCEEEEeecCCCCcEEEEEEEecCCCCcceEecCC
Confidence 5778877775543 3322 2 55 6665555556889999999997633222 4566655555555555544
No 207
>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=28.92 E-value=78 Score=25.55 Aligned_cols=39 Identities=15% Similarity=0.145 Sum_probs=31.4
Q ss_pred ccEEEEEEeCCCCeEEEEeccCCCCceEEecCCCceEcCCC
Q 003213 747 SVVGVIREVLPDGSCRVVLGSSGNGDTITALPNEIEIVPPR 787 (838)
Q Consensus 747 ~~~gvI~~V~~dg~~~V~l~~~~~g~~v~v~~~~Le~V~P~ 787 (838)
=..|.|.++.+++.|.|...|. |....+..++|-+..+.
T Consensus 18 wyra~I~~~~~~~~~~V~f~D~--G~~~~v~~~~l~~l~~~ 56 (57)
T smart00333 18 WYRARIIKVDGEQLYEVFFIDY--GNEEVVPPSDLRPLPEE 56 (57)
T ss_pred EEEEEEEEECCCCEEEEEEECC--CccEEEeHHHeecCCCC
Confidence 3488999998778899999987 57888888888776653
No 208
>PRK14639 hypothetical protein; Provisional
Probab=28.91 E-value=1e+02 Score=30.54 Aligned_cols=49 Identities=18% Similarity=0.321 Sum_probs=38.1
Q ss_pred CCCCEEEEecCccCCceeEEEEEeCCeEEEeeCCCCCCceeEEcchhhhhh
Q 003213 225 MKGDAVIVIKGDLKNLKGWVEKVDEENVHIRPEMKGLPKTLAVNSKELCKY 275 (838)
Q Consensus 225 ~~GD~V~V~~Gel~~l~G~V~~V~~d~V~i~~~~~~l~~~i~v~~~~LrK~ 275 (838)
..|-.|+|.-.+-+..+|++.+++++.+++..... .+.++++-++++|+
T Consensus 86 ~~G~~v~v~l~~~~~~~G~L~~~~~~~i~l~~~~~--~~~~~i~~~~I~ka 134 (140)
T PRK14639 86 SIGELVKITTNEKEKFEGKIVSVDDENITLENLEN--KEKTTINFNDIKKA 134 (140)
T ss_pred hCCCEEEEEECCCcEEEEEEEEEeCCEEEEEEccC--CcEEEEEhHHeeeE
Confidence 57999999766678999999999999999853212 34578888888774
No 209
>COG2163 RPL14A Ribosomal protein L14E/L6E/L27E [Translation, ribosomal structure and biogenesis]
Probab=28.89 E-value=75 Score=31.14 Aligned_cols=37 Identities=22% Similarity=0.372 Sum_probs=29.7
Q ss_pred hhhccCCCeEEEeccccCCceEEEEEEeCcEEEEEeC
Q 003213 273 CKYFEPGNHVKVVSGTQAGATGMVLKVEQHVLIILSD 309 (838)
Q Consensus 273 rK~F~~GDhVkVi~G~~~getGlVvkVe~~~v~vlSD 309 (838)
++.+++|--|.+.+|+++|.-.+|+++=++.+.+.++
T Consensus 2 ~~~l~~GrVvvv~~GR~aGkk~VIv~~iDd~~v~i~g 38 (125)
T COG2163 2 RASLEVGRVVVVTAGRFAGKKVVIVKIIDDNFVLITG 38 (125)
T ss_pred CccccCCeEEEEecceeCCceEEEEEEccCCEEEEeC
Confidence 5678999999999999999999999985443444444
No 210
>PRK04306 50S ribosomal protein L21e; Reviewed
Probab=28.78 E-value=1.1e+02 Score=28.78 Aligned_cols=53 Identities=23% Similarity=0.251 Sum_probs=37.2
Q ss_pred cccCCCCEEEEe-cC---------ccCCceeEEEEEeCCeEEEeeCCCCCCceeEEcchhhhh
Q 003213 222 GHFMKGDAVIVI-KG---------DLKNLKGWVEKVDEENVHIRPEMKGLPKTLAVNSKELCK 274 (838)
Q Consensus 222 ~~F~~GD~V~V~-~G---------el~~l~G~V~~V~~d~V~i~~~~~~l~~~i~v~~~~LrK 274 (838)
..|+.||.|-|. .| -+-+-+|.|.++.+.-+.|.....+..+.|-+.+..|++
T Consensus 33 ~~y~~Gd~V~I~~d~sv~kGmPh~~yhGkTG~V~~v~~~A~~V~v~vg~k~Kri~vr~eHlk~ 95 (98)
T PRK04306 33 QEFEEGDKVHIVIDPSVHKGMPHPRFHGKTGTVVGKRGRAYIVEVKDGGKEKTLIVRPEHLRP 95 (98)
T ss_pred HhccCCCEEEEEecCceecCCccccccCCCEEEEeecCeEEEEEEEECCceeEEEcCHHHcCc
Confidence 469999999763 33 456789999999999555444444445667777777665
No 211
>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=28.63 E-value=1.1e+02 Score=24.75 Aligned_cols=51 Identities=20% Similarity=0.105 Sum_probs=36.2
Q ss_pred ccCCCCEEEEecCccCCceeEEEEEeC-CeEEEeeCCCCCCceeEEcchhhhhh
Q 003213 223 HFMKGDAVIVIKGDLKNLKGWVEKVDE-ENVHIRPEMKGLPKTLAVNSKELCKY 275 (838)
Q Consensus 223 ~F~~GD~V~V~~Gel~~l~G~V~~V~~-d~V~i~~~~~~l~~~i~v~~~~LrK~ 275 (838)
.|++|+.|.+.--+-.=-+++|+++++ +.+.|.=. |......|+.++||..
T Consensus 2 ~~~~G~~~~a~~~d~~wyra~I~~~~~~~~~~V~f~--D~G~~~~v~~~~l~~l 53 (57)
T smart00333 2 TFKVGDKVAARWEDGEWYRARIIKVDGEQLYEVFFI--DYGNEEVVPPSDLRPL 53 (57)
T ss_pred CCCCCCEEEEEeCCCCEEEEEEEEECCCCEEEEEEE--CCCccEEEeHHHeecC
Confidence 588999999986455678999999998 45544433 3345567777777753
No 212
>PRK14636 hypothetical protein; Provisional
Probab=28.52 E-value=95 Score=32.04 Aligned_cols=49 Identities=18% Similarity=0.356 Sum_probs=37.0
Q ss_pred ccccCcEEEEe-ecCC---CCceeEEEeecCCeEEEEeccCceEEEEecccccc
Q 003213 504 DALVGTTVKVR-LGPY---KGYRGRVVDVKGQSVRVELESQMKVVTVDRSMISD 553 (838)
Q Consensus 504 d~liGktV~I~-~Gpy---KG~~G~Vkdat~~~~rVELhs~~k~I~V~r~~l~~ 553 (838)
..++|+.|+|+ ..+. |=+.|+++++++..+++++.. .++++++.+.|+-
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 57899999996 3444 446899999999999988742 3467888877753
No 213
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=28.40 E-value=1.4e+02 Score=30.90 Aligned_cols=54 Identities=26% Similarity=0.323 Sum_probs=31.6
Q ss_pred cccCCCCEEEEecCccCCceeEEEEEeCCeEEEeeC--C---CCCCc--eeEEcc--------hhhhhhccCCCeEEEe
Q 003213 222 GHFMKGDAVIVIKGDLKNLKGWVEKVDEENVHIRPE--M---KGLPK--TLAVNS--------KELCKYFEPGNHVKVV 285 (838)
Q Consensus 222 ~~F~~GD~V~V~~Gel~~l~G~V~~V~~d~V~i~~~--~---~~l~~--~i~v~~--------~~LrK~F~~GDhVkVi 285 (838)
..+++||.| .|+|++|.++.+.+.-. . ..+.. +--++. +++++.|++||.|++-
T Consensus 60 ~~~~~GdiV----------~GkV~~i~~~g~~V~I~~~~~~~~~l~~~~~G~l~~s~i~~~~~~~~~~~~~~GD~V~ak 128 (189)
T PRK09521 60 PLLKKGDIV----------YGRVVDVKEQRALVRIVSIEGSERELATSKLAYIHISQVSDGYVESLTDAFKIGDIVRAK 128 (189)
T ss_pred CCCCCCCEE----------EEEEEEEcCCeEEEEEEEecccccccCCCceeeEEhhHcChhhhhhHHhccCCCCEEEEE
Confidence 467889987 47899998885443321 0 00111 112222 3457889999998653
No 214
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=27.86 E-value=1.8e+02 Score=26.83 Aligned_cols=60 Identities=20% Similarity=0.156 Sum_probs=39.3
Q ss_pred cCCceeEEEEEeCC-eEEEeeCCCCCCceeEEcchhhhhh---ccCCCeEEEeccccCCceEEEEE
Q 003213 237 LKNLKGWVEKVDEE-NVHIRPEMKGLPKTLAVNSKELCKY---FEPGNHVKVVSGTQAGATGMVLK 298 (838)
Q Consensus 237 l~~l~G~V~~V~~d-~V~i~~~~~~l~~~i~v~~~~LrK~---F~~GDhVkVi~G~~~getGlVvk 298 (838)
+.-+.|+|+.+-.+ ...+..+.. .+-+-.-+--+||+ ..+||.|+|---.|+-+-|.|+-
T Consensus 6 ~ie~~G~V~e~Lp~~~frV~LenG--~~vla~isGKmR~~rIrIl~GD~V~VE~spYDltkGRIiy 69 (87)
T PRK12442 6 LIELDGIVDEVLPDSRFRVTLENG--VEVGAYASGRMRKHRIRILAGDRVTLELSPYDLTKGRINF 69 (87)
T ss_pred eEEEEEEEEEECCCCEEEEEeCCC--CEEEEEeccceeeeeEEecCCCEEEEEECcccCCceeEEE
Confidence 34456888888544 445444322 23344445566664 48999999988889888888764
No 215
>PRK13709 conjugal transfer nickase/helicase TraI; Provisional
Probab=27.55 E-value=2.9e+02 Score=38.25 Aligned_cols=89 Identities=13% Similarity=0.218 Sum_probs=57.9
Q ss_pred cccCC--CCEEEEecCccCCceeEEEEEeCC--eEEEeeCCCCCCceeEEcchhh-----------hhhccCCCeEEEec
Q 003213 222 GHFMK--GDAVIVIKGDLKNLKGWVEKVDEE--NVHIRPEMKGLPKTLAVNSKEL-----------CKYFEPGNHVKVVS 286 (838)
Q Consensus 222 ~~F~~--GD~V~V~~Gel~~l~G~V~~V~~d--~V~i~~~~~~l~~~i~v~~~~L-----------rK~F~~GDhVkVi~ 286 (838)
..|++ ||.|.. .+ ..-.|+.|+.+ .|++... + .+...|+++.+ ...|..||.|+...
T Consensus 1274 ~~Y~~~~G~vv~~-~~----~y~~V~~vd~~~~~ltl~~~-~--G~~~~~~P~~~~~~~~~vy~~~~~ela~GDrIr~Tr 1345 (1747)
T PRK13709 1274 STWEAHRGALALV-DN----VYHRIAGIDKDDGLITLRDA-E--GNTRLISPREAVAEGVTLYTPDTIRVGTGDRMRFTK 1345 (1747)
T ss_pred hhcccCCCcEEEe-cC----ceEEEEEEcCCCCEEEEEcC-C--CCEEEeChhhcccccccccccccccccCCCEEEEcc
Confidence 46777 888875 33 34678888754 5666543 2 34556666554 23589999998874
Q ss_pred -----cccCCceEEEEEEeCcEEEEEeCCCCCeEEEccc
Q 003213 287 -----GTQAGATGMVLKVEQHVLIILSDTTKEDIRVFAD 320 (838)
Q Consensus 287 -----G~~~getGlVvkVe~~~v~vlSD~t~~ei~V~~~ 320 (838)
|...|+.+.|+.|+++.+++- |-.+ ++.+.+.
T Consensus 1346 nDk~~G~~Ng~~~tV~~I~~~~I~l~-~~~~-~~~l~~~ 1382 (1747)
T PRK13709 1346 SDRERGYVANSVWTVTAVSGDSVTLS-DGQQ-TRVIRPG 1382 (1747)
T ss_pred cCcccccccCCEEEEEEEcCCeEEEE-cCCc-eEEeccc
Confidence 445689999999999885544 4433 3555444
No 216
>PRK04306 50S ribosomal protein L21e; Reviewed
Probab=27.49 E-value=1.2e+02 Score=28.59 Aligned_cols=58 Identities=21% Similarity=0.283 Sum_probs=38.7
Q ss_pred cchhhhhhccCCCeEEEe-cc---------ccCCceEEEEEEeCcEEEEE-eCCC-CCeEEEcccccccc
Q 003213 268 NSKELCKYFEPGNHVKVV-SG---------TQAGATGMVLKVEQHVLIIL-SDTT-KEDIRVFADDVVES 325 (838)
Q Consensus 268 ~~~~LrK~F~~GDhVkVi-~G---------~~~getGlVvkVe~~~v~vl-SD~t-~~ei~V~~~dL~~~ 325 (838)
+.+..-..|++||.|-+. .| .|-|-||.|+.+.+..+.|. -|-+ .+.|.|.+.+|..+
T Consensus 27 ~ls~~l~~y~~Gd~V~I~~d~sv~kGmPh~~yhGkTG~V~~v~~~A~~V~v~vg~k~Kri~vr~eHlk~~ 96 (98)
T PRK04306 27 PLSRALQEFEEGDKVHIVIDPSVHKGMPHPRFHGKTGTVVGKRGRAYIVEVKDGGKEKTLIVRPEHLRPQ 96 (98)
T ss_pred cHHHHHHhccCCCEEEEEecCceecCCccccccCCCEEEEeecCeEEEEEEEECCceeEEEcCHHHcCcc
Confidence 345555569999988554 33 56799999999998765443 3322 45666777776544
No 217
>COG3109 ProQ Activator of osmoprotectant transporter ProP [Signal transduction mechanisms]
Probab=27.37 E-value=89 Score=32.22 Aligned_cols=43 Identities=28% Similarity=0.518 Sum_probs=34.9
Q ss_pred cCcEEEEeecCCCCceeEEEeecCCeEEEEeccCceEEEEecccc
Q 003213 507 VGTTVKVRLGPYKGYRGRVVDVKGQSVRVELESQMKVVTVDRSMI 551 (838)
Q Consensus 507 iGktV~I~~GpyKG~~G~Vkdat~~~~rVELhs~~k~I~V~r~~l 551 (838)
+|+.|++..|. -..-.+|.+++.+.|||+|.+... +.|.-+||
T Consensus 164 ~g~~~kVk~G~-~a~~AtvlEv~Kd~vRVqL~~Gl~-m~V~AehL 206 (208)
T COG3109 164 VGQALKVKAGQ-NAMDATVLEITKDGVRVQLNSGLS-MIVRAEHL 206 (208)
T ss_pred ccceeeecccc-ccccceEEEEeccceEEeecCCce-EEEehhhh
Confidence 79999999984 345689999999999999998776 45666665
No 218
>PRK14646 hypothetical protein; Provisional
Probab=27.35 E-value=1.1e+02 Score=30.90 Aligned_cols=47 Identities=15% Similarity=0.194 Sum_probs=36.9
Q ss_pred ccccCcEEEEee-cCC---CCceeEEEeecCCeEEEEeccCceEEEEeccccc
Q 003213 504 DALVGTTVKVRL-GPY---KGYRGRVVDVKGQSVRVELESQMKVVTVDRSMIS 552 (838)
Q Consensus 504 d~liGktV~I~~-Gpy---KG~~G~Vkdat~~~~rVELhs~~k~I~V~r~~l~ 552 (838)
..++|+.|+|+- .+. |=+.|+++++.++.+.+++ ..+++.++.++|+
T Consensus 96 ~r~~G~~v~V~l~~~~~~~~~~~G~L~~~~~~~v~l~~--~g~~~~i~~~~I~ 146 (155)
T PRK14646 96 KTFKGFPVNVELNQKNSKIKFLNGLLYEKSKDYLAINI--KGKIKKIPFNEVL 146 (155)
T ss_pred HHhCCCEEEEEEecCcCCeEEEEEEEEEEeCCEEEEEE--CCEEEEEEHHHee
Confidence 578999999973 333 4567999999999999886 4677888887775
No 219
>TIGR01622 SF-CC1 splicing factor, CC1-like family. A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the model.
Probab=27.05 E-value=1.3e+02 Score=34.77 Aligned_cols=52 Identities=12% Similarity=0.064 Sum_probs=42.0
Q ss_pred cEEEEEec-CCCceEEEEEecChHHHHHHHhcCccee--e--eeeeeeChhhhhhcc
Q 003213 12 QIRSVIAL-DHLKNYIYIEADKEAHVKEACKGLRNIY--S--QKVMLVPIREMTDVL 63 (838)
Q Consensus 12 ~I~Sv~~~-~~lkGyIyVEA~~~~~V~~ai~g~~~v~--~--~~~~~Vpi~Em~~~L 63 (838)
.|.+|++. ....|++|||-.+..+...|+++|.|-+ + .....+|.+++...+
T Consensus 398 ~v~~v~v~~~~~~G~~fV~F~~~e~A~~A~~~lnGr~f~gr~i~~~~~~~~~~~~~~ 454 (457)
T TIGR01622 398 GVVHIYVDTKNSAGKIYLKFSSVDAALAAFQALNGRYFGGKMITAAFVVNDVYDMSC 454 (457)
T ss_pred CeeEEEEeCCCCceeEEEEECCHHHHHHHHHHhcCcccCCeEEEEEEEcHHHHHhhc
Confidence 46777666 6778999999999999999999999965 3 466788887776654
No 220
>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=26.42 E-value=99 Score=26.55 Aligned_cols=44 Identities=18% Similarity=0.179 Sum_probs=28.8
Q ss_pred eeeeChhhhhhccccccccccCCCCCEEEEecCcCCCceEEEEEEeCCCCEEEEEE
Q 003213 51 VMLVPIREMTDVLAVESKAIDLSRDTWVRMKIGNYKGDLAKVVDVDNVRQRVTVKL 106 (838)
Q Consensus 51 ~~~Vpi~Em~~~L~~~~~~~~l~~G~~VRik~G~ykGDlaqV~~vd~~~~~V~vkl 106 (838)
-.++++.|+.+- .+.....-+++||.|++ +|.++|..+ ++.|.+
T Consensus 29 eGlvh~sel~~~-~~~~~~~~~~~Gd~v~v----------kv~~vd~~~-ki~ls~ 72 (73)
T cd05686 29 QGLVHKSHMSSC-RVDDPSEVVDVGEKVWV----------KVIGREMKD-KMKLSL 72 (73)
T ss_pred EEEEEchhhCCC-cccCHhhEECCCCEEEE----------EEEEECCCC-cEEEEe
Confidence 357788888663 33222334789999988 578888765 665543
No 221
>cd05704 S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 13 (hs13). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=26.34 E-value=3.5e+02 Score=23.18 Aligned_cols=15 Identities=27% Similarity=0.476 Sum_probs=11.4
Q ss_pred hhhhhccCCCeEEEe
Q 003213 271 ELCKYFEPGNHVKVV 285 (838)
Q Consensus 271 ~LrK~F~~GDhVkVi 285 (838)
.+..+|++||.|++.
T Consensus 44 ~~~~~~~~Gd~v~~k 58 (72)
T cd05704 44 NPLEGFKPGKIVRCC 58 (72)
T ss_pred CHHHhCCCCCEEEEE
Confidence 345679999998864
No 222
>PRK10862 SoxR reducing system protein RseC; Provisional
Probab=25.98 E-value=1.3e+02 Score=30.21 Aligned_cols=19 Identities=16% Similarity=-0.086 Sum_probs=16.1
Q ss_pred CceeEEEEEeCCeEEEeeC
Q 003213 239 NLKGWVEKVDEENVHIRPE 257 (838)
Q Consensus 239 ~l~G~V~~V~~d~V~i~~~ 257 (838)
..+|+|++++++.+++...
T Consensus 3 ee~~~Vv~v~~~~a~Ve~~ 21 (154)
T PRK10862 3 KEWATVVSWQNGIALLRCE 21 (154)
T ss_pred ceEEEEEEEECCEEEEEEe
Confidence 4689999999998888765
No 223
>COG4873 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.94 E-value=73 Score=27.82 Aligned_cols=29 Identities=31% Similarity=0.381 Sum_probs=23.2
Q ss_pred ccCCCCEEEEecCccCCceeEEEEEeCCeEEEe
Q 003213 223 HFMKGDAVIVIKGDLKNLKGWVEKVDEENVHIR 255 (838)
Q Consensus 223 ~F~~GD~V~V~~Gel~~l~G~V~~V~~d~V~i~ 255 (838)
.-..||.|+... ||+|.|++++++.|.+.
T Consensus 23 ~a~vgniief~d----gl~g~vek~nensvivd 51 (81)
T COG4873 23 IAKVGNIIEFKD----GLTGVVEKVNENSVIVD 51 (81)
T ss_pred eeeccceEEEcc----cceeeeeeecCCcEEEE
Confidence 446899998874 59999999999976544
No 224
>PRK05807 hypothetical protein; Provisional
Probab=25.90 E-value=3.2e+02 Score=26.83 Aligned_cols=15 Identities=20% Similarity=0.337 Sum_probs=11.7
Q ss_pred hhhhhccCCCeEEEe
Q 003213 271 ELCKYFEPGNHVKVV 285 (838)
Q Consensus 271 ~LrK~F~~GDhVkVi 285 (838)
++..+|++||.|+|.
T Consensus 44 ~~~~~~kvGd~V~Vk 58 (136)
T PRK05807 44 DIREHLKEQDKVKVK 58 (136)
T ss_pred CccccCCCCCEEEEE
Confidence 346789999998874
No 225
>cd05708 S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 12 (sc12). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=25.83 E-value=1.5e+02 Score=25.03 Aligned_cols=47 Identities=23% Similarity=0.265 Sum_probs=32.4
Q ss_pred eeeeChhhhhhccccccccccCCCCCEEEEecCcCCCceEEEEEEeCCCCEEEEEEee
Q 003213 51 VMLVPIREMTDVLAVESKAIDLSRDTWVRMKIGNYKGDLAKVVDVDNVRQRVTVKLIP 108 (838)
Q Consensus 51 ~~~Vpi~Em~~~L~~~~~~~~l~~G~~VRik~G~ykGDlaqV~~vd~~~~~V~vkliP 108 (838)
..++|+.|+.+-. .......+++||.|++ +|.+++.++.++.+.+-+
T Consensus 28 ~g~i~~~~l~~~~-~~~~~~~~~~Gd~v~v----------~i~~vd~~~~~i~ls~k~ 74 (77)
T cd05708 28 SGLCHKSEISDNR-VADASKLFRVGDKVRA----------KVLKIDAEKKRISLGLKA 74 (77)
T ss_pred EEEEEHHHCCCCc-cCCHhHeecCCCEEEE----------EEEEEeCCCCEEEEEEEe
Confidence 4677777776422 1112345789999987 588999988888887643
No 226
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=25.70 E-value=6.1e+02 Score=27.22 Aligned_cols=22 Identities=27% Similarity=0.344 Sum_probs=16.0
Q ss_pred hc-cCCCeEEEeccccCCceEEEEEEeCcEEEE
Q 003213 275 YF-EPGNHVKVVSGTQAGATGMVLKVEQHVLII 306 (838)
Q Consensus 275 ~F-~~GDhVkVi~G~~~getGlVvkVe~~~v~v 306 (838)
|. ++||.| .|.|+++..+.+.+
T Consensus 59 y~P~vGDiV----------iG~V~~i~~~~~~v 81 (235)
T PRK04163 59 YIPKVGDLV----------IGKVTDVTFSGWEV 81 (235)
T ss_pred ccCCCCCEE----------EEEEEEEeCceEEE
Confidence 55 899986 57888887776544
No 227
>PTZ00329 eukaryotic translation initiation factor 1A; Provisional
Probab=25.56 E-value=4.2e+02 Score=26.98 Aligned_cols=74 Identities=16% Similarity=0.254 Sum_probs=50.3
Q ss_pred EecceEEe-CCCcEEEEEEEecc-eEEEEecCCCCCcEEEEEccccccccccCccccCCCCCeecCCCEEEEEcCCCCCc
Q 003213 339 ELRDLVLL-DNNSFGVIIRVESE-AFQVLKGVPDRPEVALVKLREIKCKLEKKSNVQDRNKNTVAVKDVVRIVEGPCKGK 416 (838)
Q Consensus 339 ~l~DLVql-d~~~vGvIv~ier~-~~~VL~~~~~~g~v~~vk~~~I~~K~~~~~~a~D~~gn~i~~gd~Vki~~Gp~kG~ 416 (838)
+..+|+.= ..+..|+|+++-.+ .|.|... +|..+.+. |..|+.++ ==|..||.|.|---||.--
T Consensus 22 ~~rel~~~eegq~~g~V~~~LGn~~f~V~c~---dG~~rLa~---I~GKmRK~--------IWI~~GD~VlVel~~yd~~ 87 (155)
T PTZ00329 22 EKRELVFKEEGQEYAQVLRMLGNGRLEAYCF---DGVKRLCH---IRGKMRKR--------VWINIGDIILVSLRDFQDS 87 (155)
T ss_pred ceeeeccCCCCcEEEEEEEEcCCCEEEEEEC---CCCEEEEE---eeccceee--------EEecCCCEEEEeccCCCCC
Confidence 34444443 35789999999855 5788874 46665554 33343221 2588999999988888777
Q ss_pred eeeEEEEECC
Q 003213 417 QGPVEHIYRG 426 (838)
Q Consensus 417 ~G~Vkhi~r~ 426 (838)
.|.|.|.|..
T Consensus 88 KgdIi~Ry~~ 97 (155)
T PTZ00329 88 KADVILKYTP 97 (155)
T ss_pred EEEEEEEcCH
Confidence 8999888864
No 228
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=25.53 E-value=6.5e+02 Score=27.43 Aligned_cols=13 Identities=8% Similarity=-0.003 Sum_probs=7.4
Q ss_pred ECCEEEEEeCcee
Q 003213 424 YRGILFIHDRHHL 436 (838)
Q Consensus 424 ~r~~lFL~~~~~~ 436 (838)
-+-++|..+|++-
T Consensus 9 ~kpwcwycnrefd 21 (341)
T KOG2893|consen 9 DKPWCWYCNREFD 21 (341)
T ss_pred CCceeeecccccc
Confidence 3445666666644
No 229
>COG4873 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.49 E-value=97 Score=27.08 Aligned_cols=32 Identities=34% Similarity=0.525 Sum_probs=25.2
Q ss_pred hhhhhccCCCeEEEeccccCCceEEEEEEeCcEEEE
Q 003213 271 ELCKYFEPGNHVKVVSGTQAGATGMVLKVEQHVLII 306 (838)
Q Consensus 271 ~LrK~F~~GDhVkVi~G~~~getGlVvkVe~~~v~v 306 (838)
-+.+..++||.+.... |-+|.|-|+++++|.|
T Consensus 19 ~~m~~a~vgniief~d----gl~g~vek~nensviv 50 (81)
T COG4873 19 KLMKIAKVGNIIEFKD----GLTGVVEKVNENSVIV 50 (81)
T ss_pred eEeeeeeccceEEEcc----cceeeeeeecCCcEEE
Confidence 3455678899887764 5899999999998865
No 230
>PF02427 PSI_PsaE: Photosystem I reaction centre subunit IV / PsaE; InterPro: IPR003375 PsaE is a 69 amino acid polypeptide from photosystem I present on the stromal side of the thylakoid membrane. The structure is comprised of a well-defined five-stranded beta-sheet similar to SH3 domains []. This subunit may form complexes with ferredoxin and ferredoxin-oxidoreductase in the photosystem I reaction centre.; GO: 0015979 photosynthesis, 0009522 photosystem I, 0009538 photosystem I reaction center; PDB: 1PSF_A 1PSE_A 2WSF_E 2WSC_E 2O01_E 2WSE_E 1GXI_E 1JB0_E 3PCQ_E 1QP2_A ....
Probab=25.38 E-value=1.5e+02 Score=25.51 Aligned_cols=35 Identities=20% Similarity=0.373 Sum_probs=26.3
Q ss_pred CCCCCcEEEEcCC--CCCceEEEEEEeCCC----eEEEecC
Q 003213 786 PRKTDKIKIMGGP--HRGATGKLIGVDGTD----GIVKVDV 820 (838)
Q Consensus 786 P~kgd~VkVi~G~--~rG~tG~LisiD~~d----giVk~d~ 820 (838)
+++|++|+|+.=| +--.+|++.+||.+. -+||+|.
T Consensus 1 i~rgskVrIlR~ESYWyn~vGtV~svdqs~i~YPV~VRF~k 41 (61)
T PF02427_consen 1 IKRGSKVRILRKESYWYNEVGTVASVDQSGIRYPVVVRFDK 41 (61)
T ss_dssp S-TTSEEEE-SSSSTTTTSEEEEEEETTSSSSSSEEEE-SS
T ss_pred CCCCCEEEEccccceeecccceEEEEccCCccccEEEEEEE
Confidence 5789999999877 567899999999874 5677764
No 231
>PRK00529 elongation factor P; Validated
Probab=25.34 E-value=6.5e+02 Score=26.07 Aligned_cols=71 Identities=21% Similarity=0.247 Sum_probs=53.2
Q ss_pred ccccCCCCEEEEecCccCCceeEEEEEeCCeEEEeeCCCCCCceeEEcchhh---hhhccCCCeEEEeccccCCceEEEE
Q 003213 221 KGHFMKGDAVIVIKGDLKNLKGWVEKVDEENVHIRPEMKGLPKTLAVNSKEL---CKYFEPGNHVKVVSGTQAGATGMVL 297 (838)
Q Consensus 221 ~~~F~~GD~V~V~~Gel~~l~G~V~~V~~d~V~i~~~~~~l~~~i~v~~~~L---rK~F~~GDhVkVi~G~~~getGlVv 297 (838)
...|..+|.|++. ++.--...+..+++|.+.+|-. + --+.++++...| .+++++|..|.|. -|++ -++
T Consensus 51 e~~f~~~e~ve~~--~ve~~~~q~ly~dgd~~~fMD~-e-tyeq~~l~~~~lg~~~~~L~eg~~v~v~--~~~~---~~i 121 (186)
T PRK00529 51 EKTFKAGDKVERA--DVERREMQYLYNDGDGYVFMDT-E-TYEQIEVPADQVGDAAKFLKEGMEVTVV--FYNG---EPI 121 (186)
T ss_pred EEEeCCCCEEEec--cEEeEEEEEEEECCCEEEEecC-C-CceeeEcCHHHhHHHHhhccCCCEEEEE--EECC---EEE
Confidence 3588999998877 5667777899999999888843 2 245688888755 7889999998887 3543 466
Q ss_pred EEe
Q 003213 298 KVE 300 (838)
Q Consensus 298 kVe 300 (838)
.|+
T Consensus 122 ~v~ 124 (186)
T PRK00529 122 SVE 124 (186)
T ss_pred EEE
Confidence 766
No 232
>PF14001 YdfZ: YdfZ protein
Probab=25.28 E-value=78 Score=27.44 Aligned_cols=32 Identities=28% Similarity=0.424 Sum_probs=27.1
Q ss_pred ccCCCCCeecCCCEEEEEcCCCCCceeeEEEEECC
Q 003213 392 VQDRNKNTVAVKDVVRIVEGPCKGKQGPVEHIYRG 426 (838)
Q Consensus 392 a~D~~gn~i~~gd~Vki~~Gp~kG~~G~Vkhi~r~ 426 (838)
+-|+|.|.|..|..|.|-. .|..|+|+-|+-.
T Consensus 2 tYDRnRN~i~~G~rVMiag---tG~~gvikAih~~ 33 (64)
T PF14001_consen 2 TYDRNRNAITTGSRVMIAG---TGATGVIKAIHAD 33 (64)
T ss_pred ccccccCcCCCCCEEEEcC---CCcccEEeeeecC
Confidence 4599999999999999865 3789999998754
No 233
>PRK14630 hypothetical protein; Provisional
Probab=25.21 E-value=1.4e+02 Score=29.79 Aligned_cols=46 Identities=11% Similarity=0.239 Sum_probs=35.8
Q ss_pred CCCCEEEEecCccCCceeEEEEEeCCeEEEeeCCCCCCceeEEcchhhhhh
Q 003213 225 MKGDAVIVIKGDLKNLKGWVEKVDEENVHIRPEMKGLPKTLAVNSKELCKY 275 (838)
Q Consensus 225 ~~GD~V~V~~Gel~~l~G~V~~V~~d~V~i~~~~~~l~~~i~v~~~~LrK~ 275 (838)
..|-.|+|.-.+-. .+|++.+++++.|++..+ .++++++-+++.|+
T Consensus 95 ~~G~~v~V~l~~~~-~~G~L~~~~d~~i~l~~~----~~~~~i~~~~I~ka 140 (143)
T PRK14630 95 FEGKKIKLMLDNDF-EEGFILEAKADSFIFKTD----SKEVNVLYSDVKKA 140 (143)
T ss_pred hCCCEEEEEEcCcc-eEEEEEEEeCCEEEEEEC----CEEEEEEhHhcceE
Confidence 57999999654433 389999999999998753 35788888888764
No 234
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=25.04 E-value=3.7e+02 Score=24.37 Aligned_cols=58 Identities=14% Similarity=-0.005 Sum_probs=37.8
Q ss_pred ceeEEEEEeCC-eEEEeeCCCCCCceeEEcchhhhhh--ccCCCeEEEeccccCCceEEEEEE
Q 003213 240 LKGWVEKVDEE-NVHIRPEMKGLPKTLAVNSKELCKY--FEPGNHVKVVSGTQAGATGMVLKV 299 (838)
Q Consensus 240 l~G~V~~V~~d-~V~i~~~~~~l~~~i~v~~~~LrK~--F~~GDhVkVi~G~~~getGlVvkV 299 (838)
..|+|+...++ ...+++... ..-+---+.-+||. ...||.|.|---.|+...|-|+.+
T Consensus 7 ~~g~V~~~lG~~~~~V~~~dG--~~~la~ipgK~Rk~iwI~~GD~VlVe~~~~~~~kg~Iv~r 67 (83)
T smart00652 7 EIAQVVKMLGNGRLEVMCADG--KERLARIPGKMRKKVWIRRGDIVLVDPWDFQDVKADIIYK 67 (83)
T ss_pred EEEEEEEEcCCCEEEEEECCC--CEEEEEEchhhcccEEEcCCCEEEEEecCCCCCEEEEEEE
Confidence 56888888776 556665433 23343344455664 589999998766677777776654
No 235
>PLN00208 translation initiation factor (eIF); Provisional
Probab=24.80 E-value=4.9e+02 Score=26.29 Aligned_cols=71 Identities=11% Similarity=-0.057 Sum_probs=47.6
Q ss_pred CCEEEEecCccCCceeEEEEEeCC-eEEEeeCCCCCCceeEEcchhhhhh--ccCCCeEEEeccccCCceEEEEEE
Q 003213 227 GDAVIVIKGDLKNLKGWVEKVDEE-NVHIRPEMKGLPKTLAVNSKELCKY--FEPGNHVKVVSGTQAGATGMVLKV 299 (838)
Q Consensus 227 GD~V~V~~Gel~~l~G~V~~V~~d-~V~i~~~~~~l~~~i~v~~~~LrK~--F~~GDhVkVi~G~~~getGlVvkV 299 (838)
++..++.--+--...|.|++.-++ .+.+++... ...+---+.-+||. ..+||+|.|---.|+.+.|-|+..
T Consensus 21 ~~~~el~~p~egq~~g~V~~~lGn~~~~V~c~dG--~~rLa~IpGKmRKrIWI~~GD~VlVel~~~d~~KgdIv~r 94 (145)
T PLN00208 21 DEKRELIFKEDGQEYAQVLRMLGNGRCEALCIDG--TKRLCHIRGKMRKKVWIAAGDIILVGLRDYQDDKADVILK 94 (145)
T ss_pred cceeecccCCCCcEEEEEEEEcCCCEEEEEECCC--CEEEEEEeccceeeEEecCCCEEEEEccCCCCCEEEEEEE
Confidence 334455444444578999999776 667776532 33444444555664 689999999777788888888776
No 236
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=24.48 E-value=1.8e+02 Score=23.46 Aligned_cols=42 Identities=19% Similarity=0.165 Sum_probs=23.3
Q ss_pred eeEEEEEeCCeEEEeeCCCCCCceeEEcchhh--------hhhccCCCeEEEe
Q 003213 241 KGWVEKVDEENVHIRPEMKGLPKTLAVNSKEL--------CKYFEPGNHVKVV 285 (838)
Q Consensus 241 ~G~V~~V~~d~V~i~~~~~~l~~~i~v~~~~L--------rK~F~~GDhVkVi 285 (838)
.|+|.++...-+.+.-.. .-.--++.+++ .+.|++||.|++.
T Consensus 7 ~g~V~~v~~~g~~v~i~~---~~~g~l~~~~~~~~~~~~~~~~~~~G~~v~~~ 56 (72)
T smart00316 7 EGTVTEITPFGAFVDLGN---GVEGLIPISELSDKRVKDPEEVLKVGDEVKVK 56 (72)
T ss_pred EEEEEEEEccEEEEEeCC---CCEEEEEHHHCCccccCCHHHeecCCCEEEEE
Confidence 577777776644443321 11122333333 4559999998764
No 237
>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=23.83 E-value=3.1e+02 Score=24.17 Aligned_cols=58 Identities=21% Similarity=0.170 Sum_probs=38.7
Q ss_pred CCceeEEEEEeCC-eEEEeeCCCCCCceeEEcchhhhhh---ccCCCeEEEeccccCCceEEEE
Q 003213 238 KNLKGWVEKVDEE-NVHIRPEMKGLPKTLAVNSKELCKY---FEPGNHVKVVSGTQAGATGMVL 297 (838)
Q Consensus 238 ~~l~G~V~~V~~d-~V~i~~~~~~l~~~i~v~~~~LrK~---F~~GDhVkVi~G~~~getGlVv 297 (838)
.-+.|+|+..-++ ...+..+.. .+-+-.-+--+||+ ..+||.|+|---.|+-+.|-|+
T Consensus 5 ie~~G~V~e~L~~~~f~V~l~ng--~~vla~i~GKmr~~rI~I~~GD~V~Ve~spyd~tkgrIi 66 (68)
T TIGR00008 5 IEMEGKVTESLPNAMFRVELENG--HEVLAHISGKIRMHYIRILPGDKVKVELSPYDLTRGRIT 66 (68)
T ss_pred EEEEEEEEEECCCCEEEEEECCC--CEEEEEecCcchhccEEECCCCEEEEEECcccCCcEeEE
Confidence 3456888888655 455554322 33344555666763 5899999998778888888775
No 238
>PLN02765 pyruvate kinase
Probab=23.82 E-value=2.7e+02 Score=33.70 Aligned_cols=44 Identities=23% Similarity=0.348 Sum_probs=31.7
Q ss_pred eCCeEEEeeCC--CCCCceeEEcchhhhhhccCCCeEEEeccccCC
Q 003213 248 DEENVHIRPEM--KGLPKTLAVNSKELCKYFEPGNHVKVVSGTQAG 291 (838)
Q Consensus 248 ~~d~V~i~~~~--~~l~~~i~v~~~~LrK~F~~GDhVkVi~G~~~g 291 (838)
.|+.+++..+. .+-.+.|.++-++|-+.+++||.|-+-.|.+.|
T Consensus 112 ~G~~~~l~~~~~~~g~~~~i~v~~~~l~~~v~~Gd~IlidDG~~~g 157 (526)
T PLN02765 112 AGNTVTLTPDQSKEASSEVLPINFPGLAKAVKPGDTIFVGQYLFTG 157 (526)
T ss_pred CCCEEEEecccccCCCCCEEeechHHHHhhcCCCCEEEECCccccc
Confidence 45566665442 122456888889999999999999998876655
No 239
>KOG0917 consensus Uncharacterized conserved protein [Function unknown]
Probab=23.80 E-value=4.6e+02 Score=29.12 Aligned_cols=87 Identities=25% Similarity=0.364 Sum_probs=0.0
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC---------------------CCCCCCCCCCCCCCCCCCCCCCCC
Q 003213 604 PMRDRAWNPYTPMSPPRDNWEDGNPGSWGTSPQYQ---------------------PGSPPSRAYEAPTPGSGWASTPGG 662 (838)
Q Consensus 604 P~~~~aw~p~~p~tp~r~~~~~~~p~~~~~tp~y~---------------------~~tp~~~~~~~~TPg~~~~~Tpg~ 662 (838)
|..+++-++..|.++...++.-+-+..-..+-.|- |.|||..+...++|...+.+|+
T Consensus 182 P~~tGp~~~syp~Py~p~p~~q~p~p~~p~~~~yiS~~~S~ns~~qs~~s~s~s~~~S~pP~~pa~~nnP~p~ySst~-- 259 (338)
T KOG0917|consen 182 PTQTGPTQPSYPSPYDPSPYHQDPMPSGPYTGIYISHEPSPNSLPQSYPSFSESSLPSTPPGAPAPANNPAPVYSSTG-- 259 (338)
T ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcceeecccCcccccccccccccccCCCCCCCCccccCCCCCCCCCCC--
Q ss_pred CCCCCCCCCCCCCCCcCCCCC--------CCCCCCCCCCCCC
Q 003213 663 NYSDAGTPRDSSSTYVNAPSP--------YLPSTPGGQPMTP 696 (838)
Q Consensus 663 ~y~~~~tP~~~~~~y~~~p~~--------y~p~tp~~~p~tp 696 (838)
+.+.|+ .+.++.|.|.| ++|-.+++...||
T Consensus 260 ---~ap~ps-~f~~~~P~~qP~~a~d~~~~qPV~~~g~qptp 297 (338)
T KOG0917|consen 260 ---VAPNPS-TFFTIQPTPQPIPAIDPALFQPVSQGGVQPTP 297 (338)
T ss_pred ---CCCCCC-CCCCCCCCCCCCCcccccccccccCCCCccCH
No 240
>COG2163 RPL14A Ribosomal protein L14E/L6E/L27E [Translation, ribosomal structure and biogenesis]
Probab=23.78 E-value=1.2e+02 Score=29.81 Aligned_cols=32 Identities=19% Similarity=0.232 Sum_probs=27.2
Q ss_pred cCCCCCEEEEecCcCCCceEEEEEEeCCCCEEE
Q 003213 71 DLSRDTWVRMKIGNYKGDLAKVVDVDNVRQRVT 103 (838)
Q Consensus 71 ~l~~G~~VRik~G~ykGDlaqV~~vd~~~~~V~ 103 (838)
.|.+|..|-+++|.|+|-++.|+.+-+.+ .|.
T Consensus 4 ~l~~GrVvvv~~GR~aGkk~VIv~~iDd~-~v~ 35 (125)
T COG2163 4 SLEVGRVVVVTAGRFAGKKVVIVKIIDDN-FVL 35 (125)
T ss_pred cccCCeEEEEecceeCCceEEEEEEccCC-EEE
Confidence 57899999999999999999999886654 444
No 241
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=23.75 E-value=3.9e+02 Score=32.16 Aligned_cols=51 Identities=22% Similarity=0.277 Sum_probs=33.6
Q ss_pred cccCCCCEEEEecCccCCceeEEEEEeCCeEEEeeCCCCCCceeEEcchhhhh-----hccCCCeEEEe
Q 003213 222 GHFMKGDAVIVIKGDLKNLKGWVEKVDEENVHIRPEMKGLPKTLAVNSKELCK-----YFEPGNHVKVV 285 (838)
Q Consensus 222 ~~F~~GD~V~V~~Gel~~l~G~V~~V~~d~V~i~~~~~~l~~~i~v~~~~LrK-----~F~~GDhVkVi 285 (838)
..+.+|+.| +|+|+++..+.+.|.-.. +-+--++.++|.. .|++||.+++.
T Consensus 26 ~~~~~G~~v----------~G~V~~v~~~~~~Vdig~---k~~g~lp~~e~~~~~~~~~~~vG~~i~~~ 81 (565)
T PRK06299 26 SETREGSIV----------KGTVVAIDKDYVLVDVGL---KSEGRIPLEEFKNEQGELEVKVGDEVEVY 81 (565)
T ss_pred ccCCCCCEE----------EEEEEEEECCEEEEEeCC---CeEEEEEHHHhcCccccccCCCCCEEEEE
Confidence 456778776 578999988876665421 2233456666643 58999988764
No 242
>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=23.61 E-value=2.2e+02 Score=24.30 Aligned_cols=56 Identities=16% Similarity=0.178 Sum_probs=37.7
Q ss_pred ceeEEEEEeCC-eEEEeeCCCCCCce-eEEcchhhhhh--ccCCCeEEEeccccCCceEEEEE
Q 003213 240 LKGWVEKVDEE-NVHIRPEMKGLPKT-LAVNSKELCKY--FEPGNHVKVVSGTQAGATGMVLK 298 (838)
Q Consensus 240 l~G~V~~V~~d-~V~i~~~~~~l~~~-i~v~~~~LrK~--F~~GDhVkVi~G~~~getGlVvk 298 (838)
..|+|++.-++ .+.+..... .+- ..++.+ .++. .+.||.|.|---.|+.+.|-|+.
T Consensus 5 ~~~~V~~~lG~~~~~V~~~dg--~~~l~~i~gK-~r~~iwI~~GD~V~V~~~~~d~~kG~Ii~ 64 (65)
T PF01176_consen 5 VIGRVTEMLGNNLFEVECEDG--EERLARIPGK-FRKRIWIKRGDFVLVEPSPYDKVKGRIIY 64 (65)
T ss_dssp EEEEEEEEESSSEEEEEETTS--EEEEEEE-HH-HHTCC---TTEEEEEEESTTCTTEEEEEE
T ss_pred EEEEEEEECCCCEEEEEeCCC--CEEEEEeccc-eeeeEecCCCCEEEEEecccCCCeEEEEE
Confidence 56889999877 556665432 122 356777 6664 58999999987778888888874
No 243
>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed
Probab=23.48 E-value=1.2e+02 Score=38.40 Aligned_cols=47 Identities=19% Similarity=0.203 Sum_probs=35.3
Q ss_pred cccCCCCEEEEecCccCCceeEEEEEeC-CeEEEeeCCCCCCceeEEcchhhhhh
Q 003213 222 GHFMKGDAVIVIKGDLKNLKGWVEKVDE-ENVHIRPEMKGLPKTLAVNSKELCKY 275 (838)
Q Consensus 222 ~~F~~GD~V~V~~Gel~~l~G~V~~V~~-d~V~i~~~~~~l~~~i~v~~~~LrK~ 275 (838)
..|++||.|+|.. -|..|.|++|.+ +.++|... . =.+.|+.++|++.
T Consensus 635 ~~~~~Gd~V~v~~---~~~~g~v~~i~~~~~~~V~~g--~--~k~~v~~~~l~~~ 682 (782)
T PRK00409 635 EELKVGDEVKYLS---LGQKGEVLSIPDDKEAIVQAG--I--MKMKVPLSDLEKI 682 (782)
T ss_pred cCCCCCCEEEEcc---CCceEEEEEEcCCCeEEEEEC--C--EEEEEeHHHceeC
Confidence 4599999999986 456799999964 56666653 2 2478888998754
No 244
>cd05698 S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 6 (hs6) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=23.47 E-value=1.5e+02 Score=24.76 Aligned_cols=45 Identities=18% Similarity=0.328 Sum_probs=30.7
Q ss_pred eeeeChhhhhhccccccccccCCCCCEEEEecCcCCCceEEEEEEeCCCCEEEEEE
Q 003213 51 VMLVPIREMTDVLAVESKAIDLSRDTWVRMKIGNYKGDLAKVVDVDNVRQRVTVKL 106 (838)
Q Consensus 51 ~~~Vpi~Em~~~L~~~~~~~~l~~G~~VRik~G~ykGDlaqV~~vd~~~~~V~vkl 106 (838)
..++|+.|+.+=- .......+++|+.+++ +|.++|..+.++.|.+
T Consensus 25 ~gli~~s~l~~~~-~~~~~~~~~~G~~i~v----------~v~~~d~~~~~i~ls~ 69 (70)
T cd05698 25 KGFLPKSELSEAF-IKDPEEHFRVGQVVKV----------KVLSCDPEQQRLLLSC 69 (70)
T ss_pred EEEEEHHHcChhh-cCCHHHcccCCCEEEE----------EEEEEcCCCCEEEEEe
Confidence 4688888886422 1112335889999987 6788888878777654
No 245
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=23.23 E-value=5.3e+02 Score=24.32 Aligned_cols=60 Identities=15% Similarity=0.114 Sum_probs=39.4
Q ss_pred CCceeEEEEEeCC-eEEEeeCCCCCCceeEEcchhhhh--hccCCCeEEEeccccCCceEEEEEE
Q 003213 238 KNLKGWVEKVDEE-NVHIRPEMKGLPKTLAVNSKELCK--YFEPGNHVKVVSGTQAGATGMVLKV 299 (838)
Q Consensus 238 ~~l~G~V~~V~~d-~V~i~~~~~~l~~~i~v~~~~LrK--~F~~GDhVkVi~G~~~getGlVvkV 299 (838)
--..|+|+..-++ .+.+++... ..-+---+.-+|| .+..||.|.|--=.|+.+.|-|+..
T Consensus 21 ~e~~g~V~~~lG~~~~~V~~~dG--~~~la~i~GK~Rk~IwI~~GD~VlVe~~~~~~~kg~Iv~r 83 (100)
T PRK04012 21 GEVFGVVEQMLGANRVRVRCMDG--VERMGRIPGKMKKRMWIREGDVVIVAPWDFQDEKADIIWR 83 (100)
T ss_pred CEEEEEEEEEcCCCEEEEEeCCC--CEEEEEEchhhcccEEecCCCEEEEEecccCCCEEEEEEE
Confidence 3467888888766 556665432 2333333344455 4689999999876788888888765
No 246
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=23.16 E-value=4.2e+02 Score=30.23 Aligned_cols=58 Identities=31% Similarity=0.357 Sum_probs=35.1
Q ss_pred cccCCCCEEEEecCccCCceeEEEEEeCCeEEEeeCCCCCCceeEEcchhh--------hhhccCCCeEEEeccccCCce
Q 003213 222 GHFMKGDAVIVIKGDLKNLKGWVEKVDEENVHIRPEMKGLPKTLAVNSKEL--------CKYFEPGNHVKVVSGTQAGAT 293 (838)
Q Consensus 222 ~~F~~GD~V~V~~Gel~~l~G~V~~V~~d~V~i~~~~~~l~~~i~v~~~~L--------rK~F~~GDhVkVi~G~~~get 293 (838)
..+++||.| .|+|.+++.+-+.|.-... .-+-.++.+++ .+.|++||.|++
T Consensus 13 ~~~~~G~iv----------~G~V~~i~~~g~~V~i~~~--~~~g~lp~~e~~~~~~~~~~~~~~vGd~v~~--------- 71 (390)
T PRK06676 13 KEVEVGDVV----------TGEVLKVEDKQVFVNIEGY--KVEGVIPISELSNDHIEDINDVVKVGDELEV--------- 71 (390)
T ss_pred hcccCCCEE----------EEEEEEEECCeEEEEEecC--CcEEEEEHHHhccccccCcccccCCCCEEEE---------
Confidence 457888877 4678888776554432101 11233444444 457999999876
Q ss_pred EEEEEEeC
Q 003213 294 GMVLKVEQ 301 (838)
Q Consensus 294 GlVvkVe~ 301 (838)
.|+.++.
T Consensus 72 -~V~~v~~ 78 (390)
T PRK06676 72 -YVLKVED 78 (390)
T ss_pred -EEEEEEC
Confidence 4667654
No 247
>PRK14578 elongation factor P; Provisional
Probab=22.82 E-value=8.4e+02 Score=25.54 Aligned_cols=71 Identities=17% Similarity=0.237 Sum_probs=50.0
Q ss_pred ccccCCCCEEEEecCccCCceeEEEEEeCCeEEEeeCCCCCCceeEEcchhh---hhhccCCCeEEEeccccCCceEEEE
Q 003213 221 KGHFMKGDAVIVIKGDLKNLKGWVEKVDEENVHIRPEMKGLPKTLAVNSKEL---CKYFEPGNHVKVVSGTQAGATGMVL 297 (838)
Q Consensus 221 ~~~F~~GD~V~V~~Gel~~l~G~V~~V~~d~V~i~~~~~~l~~~i~v~~~~L---rK~F~~GDhVkVi~G~~~getGlVv 297 (838)
...|+.||.|+.. ++..-...-.--+++...+|-... -+.++++...| .+++++|..|.|. -|+|+ ++
T Consensus 53 e~tf~s~d~ve~a--~ve~~~~qylY~dg~~~~FMD~et--yEQ~~i~~~~~g~~~~fL~e~~~v~v~--~~~~~---~i 123 (187)
T PRK14578 53 EKTFRSGDKVEEA--DFERHKGQFLYADGDRGVFMDLET--YEQFEMEEDAFSAIAPFLLDGTEVQLG--LFQGR---MV 123 (187)
T ss_pred EEEECCCCEEEEe--EEEEeEeEEEEeCCCEEEEecCCC--cEEEEecHHHhhhHHhhccCCCEEEEE--EECCE---EE
Confidence 4689999999887 444444445555788888885422 35588887765 7789999999887 45554 66
Q ss_pred EEe
Q 003213 298 KVE 300 (838)
Q Consensus 298 kVe 300 (838)
.|+
T Consensus 124 ~v~ 126 (187)
T PRK14578 124 NVD 126 (187)
T ss_pred EEE
Confidence 666
No 248
>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=22.62 E-value=4.5e+02 Score=23.56 Aligned_cols=58 Identities=12% Similarity=0.035 Sum_probs=37.1
Q ss_pred ceeEEEEEeCC-eEEEeeCCCCCCceeEEcchhhhhh--ccCCCeEEEecccc-CCceEEEEEE
Q 003213 240 LKGWVEKVDEE-NVHIRPEMKGLPKTLAVNSKELCKY--FEPGNHVKVVSGTQ-AGATGMVLKV 299 (838)
Q Consensus 240 l~G~V~~V~~d-~V~i~~~~~~l~~~i~v~~~~LrK~--F~~GDhVkVi~G~~-~getGlVvkV 299 (838)
..|+|+..-++ ..++.+... ..-+---+.-+||. .+.||.|.|---.| +...|-|+.+
T Consensus 2 ~i~~V~~~lG~~~~~V~~~dg--~~~l~~i~gK~Rk~iwI~~GD~VlV~~~~~~~~~kg~Iv~r 63 (78)
T cd04456 2 QIVRVLRMLGNNRHEVECADG--QRRLVSIPGKLRKNIWIKRGDFLIVDPIEEGEDVKADIIFV 63 (78)
T ss_pred eEEEEEEECCCCEEEEEECCC--CEEEEEEchhhccCEEEcCCCEEEEEecccCCCceEEEEEE
Confidence 35788888776 556665432 23333334445554 68999999976667 5677777665
No 249
>PRK14640 hypothetical protein; Provisional
Probab=22.49 E-value=1.4e+02 Score=29.96 Aligned_cols=47 Identities=15% Similarity=0.235 Sum_probs=36.9
Q ss_pred CCCCEEEEec----CccCCceeEEEEEeCCeEEEeeCCCCCCceeEEcchhhhhh
Q 003213 225 MKGDAVIVIK----GDLKNLKGWVEKVDEENVHIRPEMKGLPKTLAVNSKELCKY 275 (838)
Q Consensus 225 ~~GD~V~V~~----Gel~~l~G~V~~V~~d~V~i~~~~~~l~~~i~v~~~~LrK~ 275 (838)
..|-.|+|.- +..+..+|++.+++++.|++..+ .++++++-+++.|+
T Consensus 95 ~~G~~v~V~l~~~~~~~k~~~G~L~~v~~~~v~l~~~----~~~~~i~~~~I~ka 145 (152)
T PRK14640 95 YVGQEAAVTLRMATNNRRKFKGVIKAVQGDMITLTVD----GKDEVLAFTNIQKA 145 (152)
T ss_pred hCCCeEEEEEecccCCceEEEEEEEEEeCCEEEEEEC----CeEEEEEhHHeeeE
Confidence 5799999963 35589999999999999998764 34677787777764
No 250
>cd05705 S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 14 (hs14). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=22.46 E-value=1.4e+02 Score=26.00 Aligned_cols=45 Identities=20% Similarity=0.174 Sum_probs=32.1
Q ss_pred eeeeeChhhhhhcc-cccc-ccccCCCCCEEEEecCcCCCceEEEEEEeCCCCEEEE
Q 003213 50 KVMLVPIREMTDVL-AVES-KAIDLSRDTWVRMKIGNYKGDLAKVVDVDNVRQRVTV 104 (838)
Q Consensus 50 ~~~~Vpi~Em~~~L-~~~~-~~~~l~~G~~VRik~G~ykGDlaqV~~vd~~~~~V~v 104 (838)
...+||+.||.+-. +..+ ....+++|+-|+. +|.++|++++++.|
T Consensus 27 v~G~v~~~~ls~~~~~~~~~~~~~~~~G~~v~~----------kVl~id~~~~~i~L 73 (74)
T cd05705 27 IVGRVLFQNVTKYFVSDPSLYNKYLPEGKLLTA----------KVLSVNSEKNLVEL 73 (74)
T ss_pred CEEEEEHHHccCccccChhhHhcccCCCCEEEE----------EEEEEECCCCEEec
Confidence 34688888988765 2111 2346899999975 79999998887764
No 251
>PRK05610 rpsQ 30S ribosomal protein S17; Reviewed
Probab=22.40 E-value=1.6e+02 Score=26.93 Aligned_cols=51 Identities=16% Similarity=0.156 Sum_probs=33.4
Q ss_pred CCceeEEEEEeCC-eEEEeeC----CCCCCc----eeEEcchhhhhhccCCCeEEEeccc
Q 003213 238 KNLKGWVEKVDEE-NVHIRPE----MKGLPK----TLAVNSKELCKYFEPGNHVKVVSGT 288 (838)
Q Consensus 238 ~~l~G~V~~V~~d-~V~i~~~----~~~l~~----~i~v~~~~LrK~F~~GDhVkVi~G~ 288 (838)
+-+.|.|++...+ +|++..+ |.-+.. .=.+.+.|=....++||.|++...+
T Consensus 7 ~~l~G~Vvs~km~KTvvV~v~r~~~h~kY~K~~~r~kk~~aHD~~n~~k~GD~V~I~e~r 66 (84)
T PRK05610 7 KTLQGRVVSDKMDKTIVVLVERRVKHPLYGKIVKRSKKYHAHDENNEAKIGDVVRIMETR 66 (84)
T ss_pred CEEEEEEEcccCCceEEEEEEEEEEeccccEEEEcceEEEEECCCCCCCCCCEEEEEEcc
Confidence 4588999998776 5666654 332222 2245555555678999999887654
No 252
>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=22.38 E-value=88 Score=24.33 Aligned_cols=31 Identities=23% Similarity=0.339 Sum_probs=23.6
Q ss_pred EEEEEEeCCCCeEEEEeccCCCCceEEecCCCc
Q 003213 749 VGVIREVLPDGSCRVVLGSSGNGDTITALPNEI 781 (838)
Q Consensus 749 ~gvI~~V~~dg~~~V~l~~~~~g~~v~v~~~~L 781 (838)
.|.|.++.+++.|.|.+.|. |....|..++|
T Consensus 16 ra~V~~~~~~~~~~V~f~Dy--G~~~~v~~~~l 46 (48)
T cd04508 16 RAKITSILSDGKVEVFFVDY--GNTEVVPLSDL 46 (48)
T ss_pred EEEEEEECCCCcEEEEEEcC--CCcEEEeHHHc
Confidence 78899998668999999998 45555655544
No 253
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=22.37 E-value=1.1e+02 Score=33.10 Aligned_cols=50 Identities=24% Similarity=0.318 Sum_probs=33.8
Q ss_pred cCCCCEEEEecCccCCceeEEEEEeCC--eEEEeeCCCC-------CCceeEEcchhhhhhccCCCeEE
Q 003213 224 FMKGDAVIVIKGDLKNLKGWVEKVDEE--NVHIRPEMKG-------LPKTLAVNSKELCKYFEPGNHVK 283 (838)
Q Consensus 224 F~~GD~V~V~~Gel~~l~G~V~~V~~d--~V~i~~~~~~-------l~~~i~v~~~~LrK~F~~GDhVk 283 (838)
=+.||.| .|+|+.|..+ .|-|.+.+.. +...++--..++|.+|++||+|.
T Consensus 62 P~~gD~V----------IG~I~~v~~~~W~VDI~sp~~A~L~ls~~~~r~~~~~~~~~r~~l~vGD~v~ 120 (239)
T COG1097 62 PEVGDVV----------IGKIIEVGPSGWKVDIGSPYPALLSLSDFLRRKFENAEKDLRPFLNVGDLVY 120 (239)
T ss_pred CCCCCEE----------EEEEEEEcccceEEEcCCccceEeehhhhhcccccccccccccccccCCEEE
Confidence 3678887 4888888766 5555554322 12233444789999999999974
No 254
>PRK14631 hypothetical protein; Provisional
Probab=22.35 E-value=1.6e+02 Score=30.40 Aligned_cols=48 Identities=23% Similarity=0.548 Sum_probs=36.3
Q ss_pred ccccCcEEEEee-c---CCCCceeEEEeec--CCeEEEEeccCceEEEEeccccc
Q 003213 504 DALVGTTVKVRL-G---PYKGYRGRVVDVK--GQSVRVELESQMKVVTVDRSMIS 552 (838)
Q Consensus 504 d~liGktV~I~~-G---pyKG~~G~Vkdat--~~~~rVELhs~~k~I~V~r~~l~ 552 (838)
..++|+.|+|+- . --|=+.|++.+++ ++.+++++.-+ +++.++.++|.
T Consensus 113 ~r~~G~~V~V~l~~~~~~~k~~~G~L~~v~~~~~~v~l~~~~~-~~~~i~~~~I~ 166 (174)
T PRK14631 113 QGYIGQQVALRLIAAVENRRKFQAKLLAVDLENEEIQVEVEGK-HVLDIDSNNID 166 (174)
T ss_pred HHhCCCeEEEEEecccCCceEEEEEEEEeecCCCEEEEEEcCC-cEEEEEhHHcc
Confidence 578999999984 2 2366889999999 99999887533 45777776664
No 255
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=22.10 E-value=7.4e+02 Score=26.04 Aligned_cols=127 Identities=18% Similarity=0.206 Sum_probs=0.0
Q ss_pred cCCCCEEEEecCccCCceeEEEEEeCCeEEEeeCCCCCCceeEEcchhhhhhccCCCeEEEeccccCCceEEEEEEeCcE
Q 003213 224 FMKGDAVIVIKGDLKNLKGWVEKVDEENVHIRPEMKGLPKTLAVNSKELCKYFEPGNHVKVVSGTQAGATGMVLKVEQHV 303 (838)
Q Consensus 224 F~~GD~V~V~~Gel~~l~G~V~~V~~d~V~i~~~~~~l~~~i~v~~~~LrK~F~~GDhVkVi~G~~~getGlVvkVe~~~ 303 (838)
|.+|+-+..-+|++.-..==++.++.....+..+ +.+..--.-+.||.| -|.|+++.++.
T Consensus 20 ~~~G~gt~~~~g~i~Aa~~G~~~~d~~n~~~~V~----------p~~~~~~~~K~GdiV----------~grV~~v~~~~ 79 (188)
T COG1096 20 FLPGEGTYEEGGEIRAAATGVVRRDDKNRVISVK----------PGKKTPPLPKGGDIV----------YGRVTDVREQR 79 (188)
T ss_pred eecCCCeEeECCEEEEeecccEEEcccceEEEec----------cCCCCCCCCCCCCEE----------EEEEeeccceE
Q ss_pred EEE----EeCCCCCeEEEcccccccccccccccccC-CceEecceEEeCCCcEEEEEEEecceEEEEecCCCCCcEEEE
Q 003213 304 LII----LSDTTKEDIRVFADDVVESSEVTTGITKI-GDYELRDLVLLDNNSFGVIIRVESEAFQVLKGVPDRPEVALV 377 (838)
Q Consensus 304 v~v----lSD~t~~ei~V~~~dL~~~~e~~~g~d~~-g~y~l~DLVqld~~~vGvIv~ier~~~~VL~~~~~~g~v~~v 377 (838)
+.| .-|...+--.-++-+|..+.-...-...+ ..|+.+|+|+ +-|+... +.+++-+..++-|-|+..
T Consensus 80 a~V~i~~ve~~~r~~~~~~~~~ihvs~~~~~~~~~~~d~f~~GDivr------A~Vis~~-~~~~Lst~~~dlGVI~A~ 151 (188)
T COG1096 80 ALVRIVGVEGKERELATSGAADIHVSQVRDGYVEKLSDAFRIGDIVR------ARVISTG-DPIQLSTKGNDLGVIYAR 151 (188)
T ss_pred EEEEEEEEecccccCCCCceeeEEEEecccccccccccccccccEEE------EEEEecC-CCeEEEecCCcceEEEEE
No 256
>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=22.08 E-value=1.7e+02 Score=25.85 Aligned_cols=49 Identities=14% Similarity=0.146 Sum_probs=30.4
Q ss_pred CceeEEEEEeCC-eEEEeeC----CCCCCce----eEEcchhhhhhccCCCeEEEecc
Q 003213 239 NLKGWVEKVDEE-NVHIRPE----MKGLPKT----LAVNSKELCKYFEPGNHVKVVSG 287 (838)
Q Consensus 239 ~l~G~V~~V~~d-~V~i~~~----~~~l~~~----i~v~~~~LrK~F~~GDhVkVi~G 287 (838)
-++|.|++...+ +|+|..+ +.-+... =.+.+.|=....++||.|.+...
T Consensus 3 ~l~G~Vvs~km~KTvvV~v~~~~~h~ky~k~~~r~kk~~aHD~~~~~k~GD~V~I~ec 60 (71)
T TIGR03635 3 TLQGVVVSDKMDKTIVVLVERRVKHPLYGKIVKRTKKYHAHDENNECKVGDVVRIIET 60 (71)
T ss_pred EEEEEEEcccCCceEEEEEEEEEEeccccEEEEccEEEEEECCCCCCCCCCEEEEEEc
Confidence 478999999766 5555544 3322222 23445444556899999988654
No 257
>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]
Probab=22.06 E-value=3.1e+02 Score=34.48 Aligned_cols=28 Identities=18% Similarity=0.156 Sum_probs=20.4
Q ss_pred CccccCcEEEEeecCCCCceeEEEeecC
Q 003213 503 HDALVGTTVKVRLGPYKGYRGRVVDVKG 530 (838)
Q Consensus 503 rd~liGktV~I~~GpyKG~~G~Vkdat~ 530 (838)
...+..|+|||.=|-=||-+---||.-+
T Consensus 479 n~kv~~k~Iki~Wa~g~G~kse~k~~wD 506 (894)
T KOG0132|consen 479 NVKVADKTIKIAWAVGKGPKSEYKDYWD 506 (894)
T ss_pred cccccceeeEEeeeccCCcchhhhhhhh
Confidence 4678899999999988887654444443
No 258
>PRK08582 hypothetical protein; Provisional
Probab=22.00 E-value=3.1e+02 Score=27.09 Aligned_cols=15 Identities=20% Similarity=0.421 Sum_probs=11.7
Q ss_pred hhhhhccCCCeEEEe
Q 003213 271 ELCKYFEPGNHVKVV 285 (838)
Q Consensus 271 ~LrK~F~~GDhVkVi 285 (838)
++.+.|++||.|+|.
T Consensus 45 ~~~~~l~vGD~Vkvk 59 (139)
T PRK08582 45 DINDHLKVGDEVEVK 59 (139)
T ss_pred ccccccCCCCEEEEE
Confidence 445889999998874
No 259
>COG0290 InfC Translation initiation factor 3 (IF-3) [Translation, ribosomal structure and biogenesis]
Probab=21.96 E-value=42 Score=34.47 Aligned_cols=33 Identities=24% Similarity=0.562 Sum_probs=27.0
Q ss_pred eEEEeeCCCCCCceeEEcchhhhhhccCCCeEEEe
Q 003213 251 NVHIRPEMKGLPKTLAVNSKELCKYFEPGNHVKVV 285 (838)
Q Consensus 251 ~V~i~~~~~~l~~~i~v~~~~LrK~F~~GDhVkVi 285 (838)
.|.+.|... ...+.+.++.+++.++.||+|||.
T Consensus 92 Eik~rp~Id--~hD~~~K~k~~~rFLe~GdkVKvt 124 (176)
T COG0290 92 EIKLRPKID--EHDYETKLKNARRFLEKGDKVKVT 124 (176)
T ss_pred EEEeecCcC--cchHHHHHHHHHHHHHCCCeEEEE
Confidence 567777655 345889999999999999999986
No 260
>cd04452 S1_IF2_alpha S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Eukaryotic and archaeal Initiation Factor 2 (e- and aIF2, respectively) are heterotrimeric proteins with three subunits (alpha, beta, and gamma). IF2 plays a crucial role in the process of translation initiation. The IF2 gamma subunit contains a GTP-binding site. The IF2 beta and gamma subunits together are thought to be responsible for binding methionyl-initiator tRNA. The ternary complex consisting of IF2, GTP, and the methionyl-initiator tRNA binds to the small subunit of the ribosome, as part of a pre-initiation complex that scans the mRNA to find the AUG start codon. The IF2-bound GTP is hydrolyzed to GDP when the methionyl-initiator tRNA binds the AUG start codon, at which time the IF2 is released with its bound GDP. The large ribosomal subunit then joins with the small subunit to c
Probab=21.86 E-value=1.8e+02 Score=24.63 Aligned_cols=45 Identities=13% Similarity=0.108 Sum_probs=30.2
Q ss_pred eeeeChhhhhhccccccccccCCCCCEEEEecCcCCCceEEEEEEeCCCCEEEEEE
Q 003213 51 VMLVPIREMTDVLAVESKAIDLSRDTWVRMKIGNYKGDLAKVVDVDNVRQRVTVKL 106 (838)
Q Consensus 51 ~~~Vpi~Em~~~L~~~~~~~~l~~G~~VRik~G~ykGDlaqV~~vd~~~~~V~vkl 106 (838)
..++|+.|+.+-. .......+++||+|++ +|.++|..+.++.|.+
T Consensus 30 ~gll~~s~l~~~~-~~~~~~~~~~Gd~v~v----------kv~~~d~~~~~i~ls~ 74 (76)
T cd04452 30 EGMILLSELSRRR-IRSIRKLVKVGRKEVV----------KVIRVDKEKGYIDLSK 74 (76)
T ss_pred EEEEEhHHcCCcc-cCCHHHeeCCCCEEEE----------EEEEEECCCCEEEEEE
Confidence 4677888875421 1112335799999987 5888888777777654
No 261
>PF01245 Ribosomal_L19: Ribosomal protein L19; InterPro: IPR001857 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L19 is one of the proteins from the large ribosomal subunit [, ]. In Escherichia coli, L19 is known to be located at the 30S-50S ribosomal subunit interface [] and may play a role in the structure and function of the aminoacyl-tRNA binding site. It belongs to a family of ribosomal proteins, including L19 from bacteria and the chloroplasts of red algae. L19 is a protein of 120 to 130 amino-acid residues.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3HUZ_T 3V2D_T 3I8I_R 2XG2_T 2V49_T 2XUX_T 3HUX_T 3I9C_R 3V25_T 3UZ2_R ....
Probab=21.85 E-value=1.6e+02 Score=28.30 Aligned_cols=38 Identities=24% Similarity=0.316 Sum_probs=26.4
Q ss_pred cccccCCCCEEEEec----Cc---cCCceeEEEEEeCC----eEEEeeC
Q 003213 220 KKGHFMKGDAVIVIK----GD---LKNLKGWVEKVDEE----NVHIRPE 257 (838)
Q Consensus 220 ~~~~F~~GD~V~V~~----Ge---l~~l~G~V~~V~~d----~V~i~~~ 257 (838)
.-..|.+||.|+|.- |+ .+..+|.|+++.+. +++|.--
T Consensus 15 ~~p~f~~GD~v~V~~~i~e~~k~r~q~f~GvvIa~~~~g~~ssftlR~~ 63 (113)
T PF01245_consen 15 DIPEFRVGDTVRVTYKISEGNKERIQVFEGVVIARRRRGLNSSFTLRNI 63 (113)
T ss_dssp SSSSSSSSSEEEEEEEEESSSSEEEEEEEEEEEEEEBSSTSSEEEEEEE
T ss_pred CCCCcCCCCEEEEEEEEecCCCceeEEEEEEEEEEECCCCCeeEEEEEE
Confidence 346899999999843 42 35678999988763 5555543
No 262
>PRK10334 mechanosensitive channel MscS; Provisional
Probab=21.58 E-value=1.7e+02 Score=32.43 Aligned_cols=45 Identities=18% Similarity=0.179 Sum_probs=31.9
Q ss_pred ccccCCCCEEEEecCccCCceeEEEEEeCCeEEEeeCCCCCCceeEEcchhhh
Q 003213 221 KGHFMKGDAVIVIKGDLKNLKGWVEKVDEENVHIRPEMKGLPKTLAVNSKELC 273 (838)
Q Consensus 221 ~~~F~~GD~V~V~~Gel~~l~G~V~~V~~d~V~i~~~~~~l~~~i~v~~~~Lr 273 (838)
.+.|++||.|++ .+..|.|++|.=-..+|+... ...+.+|-+.+-
T Consensus 127 ~rpf~vGD~I~i-----~~~~G~V~~I~~r~T~i~t~d---~~~v~IPNs~~~ 171 (286)
T PRK10334 127 FRPFRAGEYVDL-----GGVAGTVLSVQIFSTTMRTAD---GKIIVIPNGKII 171 (286)
T ss_pred cCCCCCCCEEEE-----CCEEEEEEEEEeEEEEEEcCC---CCEEEEcchHhc
Confidence 368999999998 378999999976555555422 345667766654
No 263
>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=21.57 E-value=1.9e+02 Score=22.61 Aligned_cols=29 Identities=17% Similarity=0.375 Sum_probs=23.1
Q ss_pred ceEEEEEEeCcEEEEEeCCCCCeEEEcccc
Q 003213 292 ATGMVLKVEQHVLIILSDTTKEDIRVFADD 321 (838)
Q Consensus 292 etGlVvkVe~~~v~vlSD~t~~ei~V~~~d 321 (838)
..|.|++.+++.++|-... +++++|...|
T Consensus 14 v~g~I~~~~g~~vtV~~~~-G~~~tv~~dd 42 (42)
T PF02736_consen 14 VKGEIIEEEGDKVTVKTED-GKEVTVKKDD 42 (42)
T ss_dssp EEEEEEEEESSEEEEEETT-TEEEEEEGGG
T ss_pred EEEEEEEEcCCEEEEEECC-CCEEEeCCCC
Confidence 4688999999998887555 8888887654
No 264
>cd05692 S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (hs4) of the H. sapiens RPS1 homolog. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=21.57 E-value=2.1e+02 Score=23.17 Aligned_cols=42 Identities=17% Similarity=0.181 Sum_probs=23.1
Q ss_pred eeEEEEEeCCeEEEeeCCCCCCceeEEcchhh--------hhhccCCCeEEEe
Q 003213 241 KGWVEKVDEENVHIRPEMKGLPKTLAVNSKEL--------CKYFEPGNHVKVV 285 (838)
Q Consensus 241 ~G~V~~V~~d~V~i~~~~~~l~~~i~v~~~~L--------rK~F~~GDhVkVi 285 (838)
.|+|+++...-+.+.-... .+--++.++| .+.|++||.|+|.
T Consensus 5 ~g~V~~i~~~g~~v~i~~~---~~g~l~~~~l~~~~~~~~~~~~~~Gd~v~v~ 54 (69)
T cd05692 5 EGTVTRLKPFGAFVELGGG---ISGLVHISQIAHKRVKDVKDVLKEGDKVKVK 54 (69)
T ss_pred EEEEEEEEeeeEEEEECCC---CEEEEEhHHcCCcccCCHHHccCCCCEEEEE
Confidence 5777777765444433211 1122333333 3779999998764
No 265
>cd05688 S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 3 (ec3) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=21.54 E-value=1.4e+02 Score=24.36 Aligned_cols=42 Identities=24% Similarity=0.298 Sum_probs=27.4
Q ss_pred eeeChhhhhhccccccccccCCCCCEEEEecCcCCCceEEEEEEeCCCCEEEE
Q 003213 52 MLVPIREMTDVLAVESKAIDLSRDTWVRMKIGNYKGDLAKVVDVDNVRQRVTV 104 (838)
Q Consensus 52 ~~Vpi~Em~~~L~~~~~~~~l~~G~~VRik~G~ykGDlaqV~~vd~~~~~V~v 104 (838)
.++|..|+.. -........+++||+|++ +|.+++..++++.|
T Consensus 26 g~l~~~e~~~-~~~~~~~~~~~~Gd~v~v----------~i~~vd~~~~~i~l 67 (68)
T cd05688 26 GLLHISDMSW-GRVKHPSEVVNVGDEVEV----------KVLKIDKERKRISL 67 (68)
T ss_pred EEEEhHHCCC-ccccCHhHEECCCCEEEE----------EEEEEECCCCEEec
Confidence 5677777652 122222345899999987 57888877777654
No 266
>PF13051 DUF3912: Protein of unknown function (DUF3912)
Probab=21.12 E-value=82 Score=26.70 Aligned_cols=23 Identities=26% Similarity=0.380 Sum_probs=18.7
Q ss_pred CCCEEEEEcCCCCCceeeEEEEE
Q 003213 402 VKDVVRIVEGPCKGKQGPVEHIY 424 (838)
Q Consensus 402 ~gd~Vki~~Gp~kG~~G~Vkhi~ 424 (838)
+|..--|.+|||.+|.|+||.--
T Consensus 5 ~gqkayikdgp~rnrigivk~~e 27 (68)
T PF13051_consen 5 VGQKAYIKDGPYRNRIGIVKKNE 27 (68)
T ss_pred cccEeeeccCCccceeEEEecch
Confidence 45667788999999999998643
No 267
>PRK00276 infA translation initiation factor IF-1; Validated
Probab=21.06 E-value=3.9e+02 Score=23.33 Aligned_cols=55 Identities=18% Similarity=0.196 Sum_probs=30.8
Q ss_pred ceeEEEEEeCC-eEEEeeCCCCCCceeEEc-chhhhh---hccCCCeEEEeccccCCceEEEE
Q 003213 240 LKGWVEKVDEE-NVHIRPEMKGLPKTLAVN-SKELCK---YFEPGNHVKVVSGTQAGATGMVL 297 (838)
Q Consensus 240 l~G~V~~V~~d-~V~i~~~~~~l~~~i~v~-~~~LrK---~F~~GDhVkVi~G~~~getGlVv 297 (838)
+.|+|++.-++ ...+.... ...+.-. .--||+ ...+||.|.+---.++.+.|.||
T Consensus 9 ~~G~Vi~~~~~~~y~V~~~~---g~~~~c~~~Gklr~~~i~i~vGD~V~ve~~~~~~~~g~Iv 68 (72)
T PRK00276 9 MEGTVVEALPNAMFRVELEN---GHEVLAHISGKMRKNYIRILPGDKVTVELSPYDLTKGRIT 68 (72)
T ss_pred EEEEEEEEcCCCEEEEEeCC---CCEEEEEEccceeeCCcccCCCCEEEEEEcccCCCeEEEE
Confidence 45778877644 44554321 1222222 222332 15789999987555667778776
No 268
>PF08402 TOBE_2: TOBE domain; InterPro: IPR013611 The TOBE domain [] (Transport-associated OB) always occurs as a dimer as the C-terminal strand of each domain is supplied by the partner. Probably involved in the recognition of small ligands such as molybdenum (e.g. P46930 from SWISSPROT) and sulphate (P16676 from SWISSPROT). Found in ABC transporters immediately after the ATPase domain. A strong RPE motif is found at the presumed N terminus of the domain. ; GO: 0005215 transporter activity, 0005524 ATP binding, 0016820 hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances, 0006810 transport, 0043190 ATP-binding cassette (ABC) transporter complex; PDB: 1Q12_A 1Q1B_C 2AWN_D 3RLF_B 3PUX_B 2R6G_B 3PUV_B 1Q1E_A 3PV0_B 2AWO_A ....
Probab=21.03 E-value=2.9e+02 Score=22.81 Aligned_cols=48 Identities=21% Similarity=0.335 Sum_probs=27.5
Q ss_pred CCceeEEEEEe--CCeEEEeeCCCCCCc-eeEEcchhhhhhccCCCeEEEe
Q 003213 238 KNLKGWVEKVD--EENVHIRPEMKGLPK-TLAVNSKELCKYFEPGNHVKVV 285 (838)
Q Consensus 238 ~~l~G~V~~V~--~d~V~i~~~~~~l~~-~i~v~~~~LrK~F~~GDhVkVi 285 (838)
..+.|+|+++. |+...+.....+-.. .+..+.......|++||.|.+-
T Consensus 16 ~~~~g~V~~~~~~G~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~G~~v~l~ 66 (75)
T PF08402_consen 16 NRLPGTVVSVEFLGSETRYTVRLEGGEELVVRVPNSQRDSPLEPGDEVRLS 66 (75)
T ss_dssp TEEEEEEEEEEEESSEEEEEEEETTSSEEEEEEESSG-TTT--TTSEEEEE
T ss_pred CeEEEEEEEEEECCCEEEEEEEECCCCEEEEEecCccccCCCCCCCEEEEE
Confidence 47889999985 776555555443222 2333333335689999988763
No 269
>PF09953 DUF2187: Uncharacterized protein conserved in bacteria (DUF2187); InterPro: IPR018690 This family consists of various hypothetical bacterial proteins with known function. It includes the uncharacterised YkvS protein from Bacillus subtilis.
Probab=20.97 E-value=1.6e+02 Score=25.18 Aligned_cols=29 Identities=31% Similarity=0.442 Sum_probs=23.2
Q ss_pred hhccCCCeEEEeccccCCceEEEEEEeCcEEEE
Q 003213 274 KYFEPGNHVKVVSGTQAGATGMVLKVEQHVLII 306 (838)
Q Consensus 274 K~F~~GDhVkVi~G~~~getGlVvkVe~~~v~v 306 (838)
|..++||.+..- .|-+|.|.+|-+|+|.|
T Consensus 2 ~~a~vGdiIefk----~g~~G~V~kv~eNSVIV 30 (57)
T PF09953_consen 2 KKAKVGDIIEFK----DGFTGIVEKVYENSVIV 30 (57)
T ss_pred cccccCcEEEEc----CCcEEEEEEEecCcEEE
Confidence 456889987753 46899999999998876
No 270
>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=20.74 E-value=53 Score=27.75 Aligned_cols=20 Identities=30% Similarity=0.459 Sum_probs=12.8
Q ss_pred ccCCCCCeecCCCEEEEEcC
Q 003213 392 VQDRNKNTVAVKDVVRIVEG 411 (838)
Q Consensus 392 a~D~~gn~i~~gd~Vki~~G 411 (838)
..|+|||.+.-||.|.+++.
T Consensus 2 v~DsnGn~L~dGDsV~~iKD 21 (56)
T PF03831_consen 2 VKDSNGNELQDGDSVTLIKD 21 (56)
T ss_dssp -B-TTS-B--TTEEEEESS-
T ss_pred eEcCCCCCccCCCEEEEEee
Confidence 57999999999999999753
No 271
>cd05702 S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 11 (hs11) and S. cerevisiae S1 repeat 8 (sc8). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=20.12 E-value=2.3e+02 Score=23.89 Aligned_cols=42 Identities=17% Similarity=0.262 Sum_probs=24.4
Q ss_pred ceeEEEEEeCCeEEEeeCCCCCCceeEEc----------chhhhhhccCCCeEEE
Q 003213 240 LKGWVEKVDEENVHIRPEMKGLPKTLAVN----------SKELCKYFEPGNHVKV 284 (838)
Q Consensus 240 l~G~V~~V~~d~V~i~~~~~~l~~~i~v~----------~~~LrK~F~~GDhVkV 284 (838)
..|+|++|.+..+.+.... ++ +-.++ ..++...|++||.|++
T Consensus 4 V~g~V~~i~~~gi~v~l~~-~i--~g~i~~~~i~~~~~~~~~~~~~~~~Gd~i~~ 55 (70)
T cd05702 4 VKAKVKSVKPTQLNVQLAD-NV--HGRIHVSEVFDEWPDGKNPLSKFKIGQKIKA 55 (70)
T ss_pred EEEEEEEEECCcEEEEeCC-Cc--EEEEEHHHhccccccccChhHhCCCCCEEEE
Confidence 4688999988855544321 11 11122 2334566999998764
No 272
>PLN02741 riboflavin synthase
Probab=20.12 E-value=5.1e+02 Score=27.18 Aligned_cols=61 Identities=16% Similarity=0.254 Sum_probs=37.3
Q ss_pred eeEEcchhhhhhccCCCeEEEeccccCCceEEEEEEeCcEEEEEeCCCCCeEEEcccccccccccccccccCCceEecce
Q 003213 264 TLAVNSKELCKYFEPGNHVKVVSGTQAGATGMVLKVEQHVLIILSDTTKEDIRVFADDVVESSEVTTGITKIGDYELRDL 343 (838)
Q Consensus 264 ~i~v~~~~LrK~F~~GDhVkVi~G~~~getGlVvkVe~~~v~vlSD~t~~ei~V~~~dL~~~~e~~~g~d~~g~y~l~DL 343 (838)
.+.|.++.+.++.+.||.|-|- |-.=.|++++++.+.+- +.|.-| ....++.++.+|.
T Consensus 24 ~l~i~~~~~~~~l~~G~SIAvn-----GvCLTV~~~~~~~f~vd---------vipETl--------~~T~L~~l~~G~~ 81 (194)
T PLN02741 24 DLKIEASTVLDGVKLGDSIAVN-----GTCLTVTEFDGDEFTVG---------LAPETL--------RKTSLGELKTGSL 81 (194)
T ss_pred EEEEEcchhhcccccCCEEEEC-----cEEEEEEEECCCEEEEE---------EEHHHh--------hhCccccCCCCCE
Confidence 4666666777889999998653 34555666665544331 111111 1234688888888
Q ss_pred EEe
Q 003213 344 VLL 346 (838)
Q Consensus 344 Vql 346 (838)
|-|
T Consensus 82 VNL 84 (194)
T PLN02741 82 VNL 84 (194)
T ss_pred Eee
Confidence 876
Done!