Query psy13744
Match_columns 296
No_of_seqs 150 out of 212
Neff 4.6
Searched_HMMs 46136
Date Fri Aug 16 19:24:55 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy13744.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/13744hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1999|consensus 100.0 1E-49 2.3E-54 413.2 21.6 277 3-296 650-1024(1024)
2 KOG4315|consensus 99.0 7E-11 1.5E-15 116.2 2.0 108 187-294 332-446 (455)
3 KOG2837|consensus 98.6 1.2E-09 2.6E-14 102.8 -6.1 61 194-261 247-308 (309)
4 KOG1999|consensus 97.9 6.6E-05 1.4E-09 80.7 10.0 17 56-72 787-805 (1024)
5 PF00467 KOW: KOW motif; Inte 97.4 0.00033 7.3E-09 45.8 4.4 31 246-276 1-31 (32)
6 PF12815 CTD: Spt5 C-terminal 97.2 7.2E-05 1.6E-09 63.4 0.0 32 56-87 32-70 (123)
7 smart00739 KOW KOW (Kyprides, 97.0 0.0012 2.7E-08 40.7 4.2 27 244-270 2-28 (28)
8 PRK12281 rplX 50S ribosomal pr 96.9 0.0018 4E-08 50.6 5.4 33 245-277 8-40 (76)
9 CHL00141 rpl24 ribosomal prote 96.9 0.0024 5.3E-08 50.7 5.5 33 245-277 10-42 (83)
10 TIGR01080 rplX_A_E ribosomal p 96.4 0.0053 1.1E-07 51.6 5.1 33 245-277 43-75 (114)
11 PRK00004 rplX 50S ribosomal pr 96.4 0.0074 1.6E-07 49.8 5.5 33 245-277 6-38 (105)
12 TIGR01079 rplX_bact ribosomal 96.3 0.0086 1.9E-07 49.4 5.5 33 245-277 5-37 (104)
13 PRK01191 rpl24p 50S ribosomal 96.1 0.011 2.4E-07 50.2 5.3 33 245-277 47-79 (120)
14 PF11623 DUF3252: Protein of u 95.9 0.025 5.4E-07 41.6 5.6 50 189-240 2-53 (53)
15 PTZ00194 60S ribosomal protein 95.6 0.019 4.1E-07 50.1 4.9 33 245-277 48-80 (143)
16 PRK05609 nusG transcription an 95.2 0.038 8.2E-07 48.1 5.3 50 244-293 127-180 (181)
17 TIGR00405 L26e_arch ribosomal 94.9 0.051 1.1E-06 46.2 5.2 51 244-294 87-141 (145)
18 COG0198 RplX Ribosomal protein 94.6 0.047 1E-06 45.3 4.2 27 245-271 6-32 (104)
19 TIGR00922 nusG transcription t 94.5 0.074 1.6E-06 46.1 5.3 32 244-275 120-151 (172)
20 PF15591 Imm17: Immunity prote 93.9 0.12 2.5E-06 40.6 4.8 48 194-241 10-63 (74)
21 COG5164 SPT5 Transcription elo 93.9 0.21 4.5E-06 51.2 7.8 87 205-291 293-399 (607)
22 PRK08559 nusG transcription an 93.1 0.22 4.8E-06 43.2 5.7 48 244-291 95-146 (153)
23 PF12815 CTD: Spt5 C-terminal 93.0 0.028 6.1E-07 47.8 0.0 28 56-84 12-46 (123)
24 PRK09014 rfaH transcriptional 92.8 0.24 5.2E-06 42.7 5.5 50 244-293 110-162 (162)
25 KOG0260|consensus 92.2 1.2 2.7E-05 50.2 11.0 11 41-51 1402-1412(1605)
26 TIGR01955 RfaH transcriptional 91.7 0.42 9.1E-06 40.7 5.7 34 244-277 109-143 (159)
27 COG5164 SPT5 Transcription elo 91.4 0.29 6.2E-06 50.2 5.0 45 192-240 355-399 (607)
28 COG0250 NusG Transcription ant 90.9 0.48 1E-05 42.5 5.4 52 242-293 122-177 (178)
29 PRK04313 30S ribosomal protein 90.7 2.2 4.7E-05 40.2 9.8 50 229-278 154-210 (237)
30 PTZ00223 40S ribosomal protein 90.3 2 4.2E-05 41.3 9.2 50 229-278 154-209 (273)
31 PLN00036 40S ribosomal protein 89.9 2.5 5.4E-05 40.4 9.5 50 229-278 157-212 (261)
32 PTZ00118 40S ribosomal protein 88.8 3.5 7.6E-05 39.4 9.6 70 208-278 132-212 (262)
33 COG1471 RPS4A Ribosomal protei 88.6 2.9 6.3E-05 39.5 8.8 42 237-278 167-212 (241)
34 PRK08559 nusG transcription an 86.2 2.9 6.2E-05 36.2 6.9 52 189-244 95-150 (153)
35 TIGR00405 L26e_arch ribosomal 83.9 3.4 7.4E-05 35.0 6.2 53 188-244 86-142 (145)
36 PRK04914 ATP-dependent helicas 82.8 7.7 0.00017 43.1 9.9 63 209-275 17-81 (956)
37 COG1862 YajC Preprotein transl 81.3 3.4 7.4E-05 33.9 5.0 43 245-292 45-87 (97)
38 PLN00045 photosystem I reactio 81.1 2.2 4.7E-05 35.2 3.7 44 235-278 31-81 (101)
39 TIGR00739 yajC preprotein tran 80.4 3.9 8.5E-05 32.4 4.9 43 245-292 39-81 (84)
40 smart00743 Agenet Tudor-like d 80.3 2.8 6.2E-05 30.2 3.8 53 190-245 4-59 (61)
41 PRK05585 yajC preprotein trans 80.3 3.8 8.1E-05 34.0 5.0 43 245-292 54-96 (106)
42 TIGR01956 NusG_myco NusG famil 79.1 4.7 0.0001 38.5 5.8 33 243-275 205-237 (258)
43 PF04717 Phage_base_V: Phage-r 77.9 4.7 0.0001 30.7 4.6 44 211-254 1-54 (79)
44 cd01734 YlxS_C YxlS is a Bacil 77.5 5.2 0.00011 31.2 4.8 49 245-293 23-77 (83)
45 smart00333 TUDOR Tudor domain. 75.0 9.4 0.0002 26.7 5.2 42 202-245 14-56 (57)
46 CHL00010 infA translation init 74.5 33 0.0007 26.7 8.5 58 209-266 9-69 (78)
47 PF00575 S1: S1 RNA binding do 74.3 26 0.00056 25.5 7.6 56 210-276 9-71 (74)
48 cd00164 S1_like S1_like: Ribos 73.6 15 0.00033 25.0 5.9 56 210-276 2-64 (65)
49 PF12059 DUF3540: Protein of u 73.2 22 0.00048 32.5 8.4 43 210-254 3-45 (202)
50 PF00467 KOW: KOW motif; Inte 72.1 5.2 0.00011 25.9 3.0 27 194-224 4-30 (32)
51 cd05708 S1_Rrp5_repeat_sc12 S1 71.8 27 0.0006 25.3 7.3 57 210-276 7-70 (77)
52 PF14563 DUF4444: Domain of un 70.5 8.2 0.00018 27.4 3.8 33 257-290 7-39 (42)
53 smart00333 TUDOR Tudor domain. 70.1 20 0.00042 25.1 5.9 53 243-295 2-55 (57)
54 PRK04333 50S ribosomal protein 69.9 11 0.00024 30.1 5.0 45 245-290 5-53 (84)
55 PRK06531 yajC preprotein trans 69.2 12 0.00027 31.5 5.4 29 245-277 38-66 (113)
56 cd05685 S1_Tex S1_Tex: The C-t 68.2 30 0.00064 24.2 6.6 23 244-276 45-67 (68)
57 PRK14639 hypothetical protein; 67.9 14 0.00031 31.8 5.6 49 245-293 86-134 (140)
58 cd04451 S1_IF1 S1_IF1: Transla 67.4 47 0.001 24.3 7.9 44 210-253 4-50 (64)
59 cd04452 S1_IF2_alpha S1_IF2_al 67.2 46 0.001 24.2 7.8 57 210-276 8-72 (76)
60 KOG1708|consensus 66.8 6.7 0.00015 36.6 3.6 30 246-275 75-106 (236)
61 cd05697 S1_Rrp5_repeat_hs5 S1_ 66.5 37 0.0008 24.6 6.9 56 210-276 5-67 (69)
62 PF01957 NfeD: NfeD-like C-ter 66.4 22 0.00047 29.0 6.3 45 204-254 87-132 (144)
63 cd05688 S1_RPS1_repeat_ec3 S1_ 66.3 38 0.00082 23.8 6.8 55 210-276 6-67 (68)
64 smart00357 CSP Cold shock prot 66.2 34 0.00073 23.7 6.5 58 210-267 1-63 (64)
65 COG1532 Predicted RNA-binding 65.9 19 0.00041 27.0 5.1 52 221-276 2-55 (57)
66 TIGR02760 TraI_TIGR conjugativ 65.1 42 0.00091 40.3 10.4 89 188-280 681-788 (1960)
67 cd05684 S1_DHX8_helicase S1_DH 64.4 44 0.00095 24.9 7.2 31 210-240 5-37 (79)
68 cd05686 S1_pNO40 S1_pNO40: pNO 63.4 49 0.0011 24.5 7.2 17 210-226 8-24 (73)
69 PF02699 YajC: Preprotein tran 63.4 2.4 5.1E-05 33.4 0.0 36 245-284 38-73 (82)
70 cd05707 S1_Rrp5_repeat_sc11 S1 63.2 41 0.00089 24.3 6.6 56 210-276 5-67 (68)
71 PF02427 PSI_PsaE: Photosystem 63.2 17 0.00037 27.6 4.6 35 244-278 1-41 (61)
72 PRK05886 yajC preprotein trans 63.1 16 0.00034 30.7 4.8 35 245-283 40-74 (109)
73 cd05691 S1_RPS1_repeat_ec6 S1_ 63.0 51 0.0011 23.7 7.1 56 210-276 5-67 (73)
74 PF02736 Myosin_N: Myosin N-te 62.8 17 0.00037 25.0 4.2 28 209-237 14-41 (42)
75 cd05689 S1_RPS1_repeat_ec4 S1_ 62.7 45 0.00098 24.2 6.9 18 210-227 8-25 (72)
76 TIGR01955 RfaH transcriptional 61.2 21 0.00045 30.3 5.4 50 187-240 107-159 (159)
77 PF09038 53-BP1_Tudor: Tumour 60.9 1.1E+02 0.0024 26.4 10.7 83 212-296 24-117 (122)
78 PF15057 DUF4537: Domain of un 60.7 58 0.0013 27.4 8.0 91 199-293 7-112 (124)
79 PRK14638 hypothetical protein; 60.2 22 0.00048 31.0 5.5 47 245-293 98-144 (150)
80 COG1585 Membrane protein impli 60.2 24 0.00053 30.5 5.7 45 203-254 83-129 (140)
81 cd05690 S1_RPS1_repeat_ec5 S1_ 59.4 50 0.0011 23.6 6.5 55 210-275 5-67 (69)
82 PF08863 YolD: YolD-like prote 59.4 24 0.00053 27.0 5.1 40 254-293 52-92 (92)
83 COG1588 POP4 RNase P/RNase MRP 59.2 51 0.0011 27.2 7.0 33 191-224 16-48 (95)
84 cd04466 S1_YloQ_GTPase S1_YloQ 59.1 64 0.0014 23.2 7.3 44 210-253 2-47 (68)
85 PRK00276 infA translation init 58.5 79 0.0017 24.0 8.4 44 210-253 10-56 (72)
86 PRK04950 ProP expression regul 58.4 23 0.0005 33.0 5.5 44 245-290 168-211 (213)
87 PRK14637 hypothetical protein; 58.1 28 0.0006 30.5 5.7 46 246-293 97-143 (151)
88 PRK14630 hypothetical protein; 57.6 26 0.00057 30.3 5.5 46 245-293 95-140 (143)
89 PRK03879 ribonuclease P protei 56.8 88 0.0019 25.5 8.1 69 192-275 15-83 (96)
90 PF07290 DUF1449: Protein of u 56.4 25 0.00055 32.3 5.4 49 204-254 134-188 (202)
91 TIGR00922 nusG transcription t 55.1 34 0.00074 29.5 5.8 50 187-240 118-171 (172)
92 PF07076 DUF1344: Protein of u 54.4 54 0.0012 25.0 6.0 44 209-255 5-49 (61)
93 COG0779 Uncharacterized protei 54.4 26 0.00057 31.0 5.0 46 246-293 98-147 (153)
94 CHL00125 psaE photosystem I su 54.1 20 0.00044 27.5 3.6 34 245-278 3-42 (64)
95 cd04508 TUDOR Tudor domains ar 54.0 13 0.00029 25.0 2.5 35 203-239 11-46 (48)
96 PRK09014 rfaH transcriptional 53.6 34 0.00074 29.3 5.6 50 188-241 109-161 (162)
97 TIGR01644 phage_P2_V phage bas 53.2 53 0.0011 29.1 6.8 46 209-254 10-62 (191)
98 cd04472 S1_PNPase S1_PNPase: P 52.7 75 0.0016 22.3 6.4 18 210-227 5-22 (68)
99 PRK02749 photosystem I reactio 52.7 20 0.00043 28.0 3.5 33 245-277 4-42 (71)
100 PRK00092 ribosome maturation p 52.2 30 0.00064 30.0 5.0 49 245-293 96-148 (154)
101 cd05698 S1_Rrp5_repeat_hs6_sc5 51.9 73 0.0016 22.9 6.4 56 210-276 5-67 (70)
102 PRK14633 hypothetical protein; 51.2 35 0.00076 29.7 5.3 47 246-293 93-143 (150)
103 cd04471 S1_RNase_R S1_RNase_R: 51.0 74 0.0016 23.4 6.4 14 263-276 67-80 (83)
104 COG0250 NusG Transcription ant 50.6 60 0.0013 29.2 6.7 50 189-242 124-177 (178)
105 PRK00409 recombination and DNA 50.5 27 0.0006 37.9 5.4 45 244-294 637-683 (782)
106 COG2139 RPL21A Ribosomal prote 49.4 18 0.00039 29.9 3.0 38 204-241 54-93 (98)
107 cd05705 S1_Rrp5_repeat_hs14 S1 49.3 89 0.0019 23.5 6.7 56 210-276 8-73 (74)
108 cd05695 S1_Rrp5_repeat_hs3 S1_ 48.5 1E+02 0.0022 22.6 6.7 56 210-276 5-65 (66)
109 TIGR01069 mutS2 MutS2 family p 48.2 30 0.00064 37.6 5.2 44 245-294 626-671 (771)
110 PRK14631 hypothetical protein; 48.0 45 0.00098 29.9 5.6 49 245-293 115-168 (174)
111 PRK00004 rplX 50S ribosomal pr 47.7 40 0.00086 27.8 4.8 26 189-218 5-30 (105)
112 PF00567 TUDOR: Tudor domain; 47.5 39 0.00084 25.9 4.5 35 210-244 70-105 (121)
113 PRK05609 nusG transcription an 47.3 62 0.0013 28.0 6.2 52 187-242 125-180 (181)
114 smart00743 Agenet Tudor-like d 47.1 51 0.0011 23.6 4.8 45 245-291 4-54 (61)
115 smart00316 S1 Ribosomal protei 47.1 92 0.002 21.3 6.9 56 210-276 7-69 (72)
116 PF02576 DUF150: Uncharacteris 47.1 38 0.00082 28.7 4.7 48 246-293 86-139 (141)
117 PF04319 NifZ: NifZ domain; I 46.3 40 0.00088 26.6 4.4 36 207-242 35-75 (75)
118 cd05696 S1_Rrp5_repeat_hs4 S1_ 46.0 82 0.0018 23.3 5.9 62 210-276 6-69 (71)
119 cd05687 S1_RPS1_repeat_ec1_hs1 45.8 1.1E+02 0.0024 22.0 7.2 55 210-276 5-67 (70)
120 PRK06763 F0F1 ATP synthase sub 45.7 37 0.0008 31.7 4.7 44 208-253 41-84 (213)
121 cd04461 S1_Rrp5_repeat_hs8_sc7 45.7 1.1E+02 0.0024 22.9 6.8 56 210-276 19-81 (83)
122 TIGR00739 yajC preprotein tran 45.6 61 0.0013 25.6 5.4 47 189-244 38-84 (84)
123 cd04458 CSP_CDS Cold-Shock Pro 45.2 1.1E+02 0.0024 22.0 6.4 54 210-263 2-61 (65)
124 COG1096 Predicted RNA-binding 44.2 1.1E+02 0.0024 28.1 7.5 59 209-269 29-89 (188)
125 PF15490 Ten1_2: Telomere-capp 43.2 1.4E+02 0.0029 25.4 7.4 42 226-275 47-89 (118)
126 PRK14646 hypothetical protein; 43.2 50 0.0011 28.9 5.0 47 245-293 98-148 (155)
127 PRK05585 yajC preprotein trans 43.1 71 0.0015 26.4 5.6 38 208-246 64-101 (106)
128 cd04467 S1_aIF5A S1_aIF5A: Arc 43.1 1.1E+02 0.0024 22.9 6.1 46 208-254 3-49 (57)
129 PRK14640 hypothetical protein; 43.0 52 0.0011 28.7 5.0 47 245-293 95-145 (152)
130 PRK08582 hypothetical protein; 42.4 1.4E+02 0.003 25.6 7.5 18 210-227 10-27 (139)
131 PF12701 LSM14: Scd6-like Sm d 42.1 61 0.0013 26.5 5.0 35 243-277 4-38 (96)
132 PRK14636 hypothetical protein; 41.8 58 0.0013 29.2 5.3 48 245-293 96-147 (176)
133 PRK14645 hypothetical protein; 41.6 53 0.0011 28.9 4.9 45 245-292 100-144 (154)
134 PF07076 DUF1344: Protein of u 40.4 40 0.00088 25.7 3.4 26 259-284 4-29 (61)
135 PRK13709 conjugal transfer nic 40.1 2.6E+02 0.0056 33.7 11.3 88 187-277 647-749 (1747)
136 PF02237 BPL_C: Biotin protein 40.0 94 0.002 21.6 5.1 40 246-287 2-42 (48)
137 PRK05807 hypothetical protein; 39.9 1.6E+02 0.0035 25.1 7.5 42 210-253 10-58 (136)
138 PRK02001 hypothetical protein; 39.1 78 0.0017 27.8 5.5 49 245-293 88-148 (152)
139 PRK14712 conjugal transfer nic 39.0 2.3E+02 0.0049 33.9 10.6 97 189-289 517-629 (1623)
140 PF09953 DUF2187: Uncharacteri 38.5 81 0.0018 23.8 4.7 40 245-288 5-44 (57)
141 cd05706 S1_Rrp5_repeat_sc10 S1 38.2 1.5E+02 0.0033 21.4 8.0 56 210-276 8-70 (73)
142 PF04452 Methyltrans_RNA: RNA 38.1 41 0.00089 30.5 3.8 41 237-277 9-50 (225)
143 PF08402 TOBE_2: TOBE domain; 37.8 1.3E+02 0.0028 21.1 5.8 45 208-253 17-66 (75)
144 PRK08059 general stress protei 37.6 1.6E+02 0.0035 24.4 7.0 18 210-227 12-29 (123)
145 TIGR02760 TraI_TIGR conjugativ 37.6 2.3E+02 0.005 34.4 10.6 71 210-280 1343-1430(1960)
146 COG2139 RPL21A Ribosomal prote 37.5 87 0.0019 26.0 5.2 37 257-293 56-94 (98)
147 PF01176 eIF-1a: Translation i 37.4 1.2E+02 0.0025 22.6 5.6 57 209-265 5-63 (65)
148 TIGR02768 TraA_Ti Ti-type conj 37.0 73 0.0016 34.5 6.0 46 245-291 609-659 (744)
149 PF06003 SMN: Survival motor n 37.0 59 0.0013 30.8 4.8 55 187-245 68-124 (264)
150 PRK07252 hypothetical protein; 36.7 2.1E+02 0.0044 24.0 7.5 8 245-252 49-56 (120)
151 PF00659 POLO_box: POLO box du 36.6 1.2E+02 0.0026 22.3 5.5 41 207-247 2-42 (68)
152 PRK14647 hypothetical protein; 36.5 81 0.0018 27.6 5.3 48 245-293 97-153 (159)
153 PF06003 SMN: Survival motor n 36.5 87 0.0019 29.7 5.8 47 245-291 70-119 (264)
154 COG1862 YajC Preprotein transl 35.3 44 0.00095 27.5 3.2 38 208-246 55-92 (97)
155 PF01455 HupF_HypC: HupF/HypC 35.3 92 0.002 23.7 4.8 42 210-255 6-49 (68)
156 PF12073 DUF3553: Protein of u 35.2 1.1E+02 0.0024 22.7 4.9 33 210-242 17-50 (52)
157 PTZ00065 60S ribosomal protein 34.2 57 0.0012 28.3 3.8 29 246-274 10-39 (130)
158 PRK13889 conjugal transfer rel 33.9 66 0.0014 36.2 5.2 45 245-290 602-651 (988)
159 PRK14643 hypothetical protein; 33.6 92 0.002 27.6 5.2 48 246-293 103-158 (164)
160 cd04473 S1_RecJ_like S1_RecJ_l 32.7 2.1E+02 0.0046 21.4 7.7 43 209-253 20-62 (77)
161 PF10133 RNA_bind_2: Predicted 32.7 90 0.0019 23.5 4.2 53 222-276 5-59 (61)
162 PRK15491 replication factor A; 32.4 1.9E+02 0.004 28.9 7.6 80 192-277 71-157 (374)
163 cd04465 S1_RPS1_repeat_ec2_hs2 32.0 1.9E+02 0.004 20.7 5.8 55 210-276 5-64 (67)
164 COG3109 ProQ Activator of osmo 31.9 82 0.0018 29.0 4.6 44 245-290 163-206 (208)
165 PRK14634 hypothetical protein; 31.7 81 0.0018 27.6 4.5 46 246-293 99-148 (155)
166 PRK14635 hypothetical protein; 31.1 81 0.0017 27.8 4.4 48 246-293 98-156 (162)
167 TIGR00046 RNA methyltransferas 30.9 81 0.0018 29.0 4.6 41 236-276 23-64 (240)
168 PF05641 Agenet: Agenet domain 30.6 1.8E+02 0.0039 21.6 5.7 54 190-245 2-66 (68)
169 PF08206 OB_RNB: Ribonuclease 30.3 70 0.0015 23.2 3.3 55 211-267 1-58 (58)
170 PRK10409 hydrogenase assembly 30.1 1.6E+02 0.0036 23.9 5.6 44 210-255 6-53 (90)
171 PF03947 Ribosomal_L2_C: Ribos 30.1 66 0.0014 27.6 3.6 44 247-293 26-69 (130)
172 TIGR02861 SASP_H small acid-so 30.0 78 0.0017 23.8 3.5 35 206-240 20-57 (58)
173 smart00538 POP4 A domain found 30.0 2.9E+02 0.0064 22.2 7.6 71 187-275 10-80 (92)
174 KOG1456|consensus 29.9 35 0.00077 34.7 2.1 12 43-54 56-67 (494)
175 PF08141 SspH: Small acid-solu 29.6 90 0.0019 23.4 3.8 35 206-240 20-57 (58)
176 TIGR02594 conserved hypothetic 29.6 1.1E+02 0.0025 25.8 4.9 36 243-279 73-109 (129)
177 PRK11642 exoribonuclease R; Pr 29.5 2.4E+02 0.0052 31.1 8.5 78 188-267 62-144 (813)
178 PRK14632 hypothetical protein; 29.5 1.2E+02 0.0026 27.0 5.3 48 246-293 97-157 (172)
179 PRK13826 Dtr system oriT relax 29.2 1.1E+02 0.0023 35.1 5.9 36 245-280 635-675 (1102)
180 PRK14644 hypothetical protein; 29.0 1.4E+02 0.003 25.7 5.4 48 245-292 83-136 (136)
181 TIGR02062 RNase_B exoribonucle 28.4 1.6E+02 0.0034 31.5 6.7 56 209-267 19-75 (639)
182 cd04455 S1_NusA S1_NusA: N-uti 27.8 1.2E+02 0.0025 22.2 4.1 10 245-254 42-51 (67)
183 cd05694 S1_Rrp5_repeat_hs2_sc2 27.7 2.7E+02 0.0058 21.0 7.5 58 209-276 8-66 (74)
184 PF11213 DUF3006: Protein of u 27.2 82 0.0018 23.9 3.3 42 210-252 1-42 (71)
185 TIGR00074 hypC_hupF hydrogenas 27.1 1.7E+02 0.0037 22.9 5.1 42 210-255 6-47 (76)
186 PTZ00471 60S ribosomal protein 26.9 83 0.0018 27.5 3.6 23 245-267 6-28 (134)
187 PRK06461 single-stranded DNA-b 26.8 2.4E+02 0.0053 23.6 6.4 34 245-278 66-100 (129)
188 TIGR00358 3_prime_RNase VacB a 26.4 1.8E+02 0.0038 31.0 6.7 57 209-267 17-77 (654)
189 cd03581 NTR_Sfrp3_like NTR dom 26.3 2.4E+02 0.0051 23.3 6.1 78 193-275 12-90 (111)
190 TIGR00008 infA translation ini 26.3 3.1E+02 0.0067 21.2 7.5 21 209-229 7-28 (68)
191 PF15436 PGBA_N: Plasminogen-b 26.2 1.6E+02 0.0034 27.7 5.5 55 210-270 47-103 (218)
192 PF06257 DUF1021: Protein of u 25.8 2.2E+02 0.0047 22.5 5.5 44 246-289 16-64 (76)
193 cd06541 ASCH ASC-1 homology or 25.8 1.3E+02 0.0029 24.2 4.5 27 242-268 29-55 (105)
194 PRK06955 biotin--protein ligas 25.6 1.4E+02 0.003 28.6 5.2 33 246-278 248-281 (300)
195 PRK11713 16S ribosomal RNA met 25.5 1.1E+02 0.0025 27.9 4.5 40 237-276 22-62 (234)
196 cd05692 S1_RPS1_repeat_hs4 S1_ 25.4 2.3E+02 0.005 19.5 6.6 18 210-227 5-22 (69)
197 TIGR02546 III_secr_ATP type II 25.3 3.3E+02 0.0072 27.5 8.1 28 207-234 3-32 (422)
198 TIGR00638 Mop molybdenum-pteri 25.2 1.6E+02 0.0035 21.0 4.5 47 208-254 8-59 (69)
199 PRK14132 riboflavin kinase; Pr 25.2 1.6E+02 0.0034 25.4 5.0 49 202-253 64-125 (126)
200 PF02239 Cytochrom_D1: Cytochr 25.2 5.2E+02 0.011 25.3 9.3 24 268-291 138-161 (369)
201 TIGR01956 NusG_myco NusG famil 24.6 1.9E+02 0.0042 27.8 6.0 50 187-240 204-257 (258)
202 PRK12442 translation initiatio 24.3 3.9E+02 0.0085 21.7 7.9 22 209-230 9-31 (87)
203 PRK12288 GTPase RsgA; Reviewed 24.0 3.8E+02 0.0083 26.3 8.1 58 209-269 40-100 (347)
204 cd04454 S1_Rrp4_like S1_Rrp4_l 24.0 1.8E+02 0.004 21.7 4.8 24 243-276 3-26 (82)
205 PF11948 DUF3465: Protein of u 23.5 2E+02 0.0043 25.1 5.3 37 220-257 60-98 (131)
206 TIGR01080 rplX_A_E ribosomal p 23.5 1.5E+02 0.0033 25.0 4.5 26 189-218 42-67 (114)
207 cd04453 S1_RNase_E S1_RNase_E: 23.4 2.1E+02 0.0045 22.4 5.1 42 210-252 12-65 (88)
208 PRK15464 cold shock-like prote 23.1 3.3E+02 0.0072 20.8 6.0 54 210-263 6-65 (70)
209 PRK00409 recombination and DNA 23.1 1.6E+02 0.0034 32.2 5.7 46 189-243 637-683 (782)
210 PF07930 DAP_B: D-aminopeptida 23.1 1.7E+02 0.0037 23.9 4.5 24 229-252 59-82 (88)
211 PF11623 DUF3252: Protein of u 22.9 2.9E+02 0.0062 20.6 5.2 45 246-290 4-52 (53)
212 PF01868 UPF0086: Domain of un 22.7 3.7E+02 0.0081 21.3 6.4 35 187-224 11-45 (89)
213 TIGR01069 mutS2 MutS2 family p 22.7 1.5E+02 0.0033 32.3 5.4 45 190-243 626-671 (771)
214 PRK01889 GTPase RsgA; Reviewed 22.5 3.3E+02 0.0072 26.6 7.3 44 209-253 29-78 (356)
215 PRK06936 type III secretion sy 22.4 4.9E+02 0.011 26.8 8.7 22 206-227 20-41 (439)
216 cd01722 Sm_F The eukaryotic Sm 22.2 1.6E+02 0.0035 21.9 4.1 28 246-273 10-37 (68)
217 cd06168 LSm9 The eukaryotic Sm 22.0 1.7E+02 0.0037 22.6 4.2 29 246-274 9-37 (75)
218 PRK04950 ProP expression regul 21.9 1.7E+02 0.0037 27.4 4.9 46 189-240 167-212 (213)
219 PF14444 S1-like: S1-like 21.8 2.2E+02 0.0048 21.5 4.6 36 210-254 5-44 (58)
220 PRK00737 small nuclear ribonuc 21.6 2.6E+02 0.0056 21.1 5.1 29 246-274 13-41 (72)
221 PRK05886 yajC preprotein trans 21.3 3.7E+02 0.0081 22.5 6.4 37 208-245 50-86 (109)
222 PRK09521 exosome complex RNA-b 21.2 3.2E+02 0.0069 24.2 6.4 41 209-251 29-69 (189)
223 PF11324 DUF3126: Protein of u 21.0 2.2E+02 0.0048 21.9 4.5 45 238-287 17-62 (63)
224 COG2163 RPL14A Ribosomal prote 20.9 1.8E+02 0.0039 25.0 4.5 26 245-270 6-32 (125)
225 PRK09507 cspE cold shock prote 20.7 3.8E+02 0.0081 20.2 6.1 55 208-262 3-63 (69)
226 COG1923 Hfq Uncharacterized ho 20.7 2.7E+02 0.0058 22.3 5.0 51 190-247 17-68 (77)
227 PRK04192 V-type ATP synthase s 20.5 4.3E+02 0.0094 28.3 8.1 50 209-276 3-52 (586)
228 cd01726 LSm6 The eukaryotic Sm 20.4 3.1E+02 0.0067 20.3 5.3 25 246-270 9-33 (67)
229 PF09962 DUF2196: Uncharacteri 20.1 2.4E+02 0.0052 21.6 4.5 40 189-228 9-54 (62)
No 1
>KOG1999|consensus
Probab=100.00 E-value=1e-49 Score=413.18 Aligned_cols=277 Identities=40% Similarity=0.639 Sum_probs=221.8
Q ss_pred CCCCCc-ccCCCCCCCCCCCCCCCCCCCcCCCCCccccccccceEEecCCccC---------------------------
Q psy13744 3 GGFMSP-RISSPMHPSGGRGGRGGGRGGHHGGNVRRDRELIGKTIKITGGPYK--------------------------- 54 (296)
Q Consensus 3 ~~~~sp-ri~sp~~~~~g~g~~~~~~~g~~~~~~rrd~~liG~tvkI~~GpyK--------------------------- 54 (296)
+++||| ||.|||||+++.|++|+.+|+||+ +||++|||+||||+.||||
T Consensus 650 l~~msP~r~~sp~~~~~~~ga~g~~gggrGg---~rd~~l~GktVrI~~Gp~KG~~GivkD~~~~~arVELhs~~~ti~v 726 (1024)
T KOG1999|consen 650 LAPMSPGRIQSPMGPSGGPGAFGGHGGGRGG---NRDDSLLGKTVRIRLGPKKGYLGIVKDVNGDTARVELHSKCVTIKV 726 (1024)
T ss_pred cCCCCcccccCCcCCCCCCCCcCcCccCccC---cCcchhcCcEEEEecCCcccccceeEeccCCeeEEEEEeccEEEEe
Confidence 688999 999999999864333333333222 2999999999999999999
Q ss_pred ------------------------------------CC---------------CCCCC--CCCCcCCCCCCCC---CCCC
Q psy13744 55 ------------------------------------VG---------------SRTPG--GGATPLHDGSRTP---GPWD 78 (296)
Q Consensus 55 ------------------------------------~g---------------srTP~--g~~TP~hdg~rTP---~awd 78 (296)
+| +|||+ +++||+|||+||| +|||
T Consensus 727 d~~~~~~v~~~~~~g~~~sYg~~~~~~g~~~~~~~~~Gs~tp~~~s~tpl~~~s~tp~~~~~~Tp~~dG~rTP~r~~aW~ 806 (1024)
T KOG1999|consen 727 DRLKRKIVGSTRDGGETSSYGERTPGYGRVTPARYGMGSSTPMYGSNTPLWGGSRTPARDGGATPSHDGSRTPARGRAWN 806 (1024)
T ss_pred chhhceEEeeccCCCCccccccccccccccCccccCCCCcCccCCCCCCCCCcccCccccCCCCcCCCCCcCCCCCCCcC
Confidence 23 45555 8999999999999 7999
Q ss_pred C--CCCCCCCC-----CCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC---CCccCCCCCCCCC
Q psy13744 79 P--SSTPARSI-----HND-AYPMDDSFNNSYPHTPGTMYGSSSEHTSYSPLQASPSPSGYQSH---SGVSSGSSSYLGA 147 (296)
Q Consensus 79 p--~~tP~r~~-----~~~-~p~tpg~~~~~~p~Tpg~~y~~~~~~~p~~~~~~spsp~~y~~~---~~~~~psp~~y~~ 147 (296)
| ++||+|++ +.+ .+ .+-|+-+|.++|||+.|++.. +...|+..-.|..|+.. +++.+|||
T Consensus 807 ~~~~~tPa~~~~~~~~g~~g~~-g~sp~~~~~a~Tpg~~~~~~~---~~~~~~~~g~~~~~gsa~~~~~~~sps~----- 877 (1024)
T KOG1999|consen 807 PYNGKTPARNFDNREPGFEGSG-GRSPQGYYSAPTPGSNWGSTG---GGGAPAWPGTPNGNGSAWGPSGQNSPSP----- 877 (1024)
T ss_pred CCCCCCCccccCCcccCCCCCC-CCCCCCCcCCCCCCCCCCcCC---CCCCcCCCCCCCCCccccccccCCCCCC-----
Confidence 9 89999953 111 11 011211258999998887622 33344444444333321 22334443
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCC---CCCCCCCCCCCCCCCcccCceEEEEecCCCCccccCCeEEEEEecCCeEEEE
Q psy13744 148 TPSPSSEAAPYGTPSPLSYSSRQAS---PFTPGTGLDQYPTPEWHTTDIEVRINENARDPEFRGQIGVIRHLGSGVCSVY 224 (296)
Q Consensus 148 tpsp~~~~~~~~tPsp~~y~p~tpg---p~TPg~g~d~~~~~~Wl~~dI~VkI~~~~~d~~yygqkGVVrsV~~g~c~V~ 224 (296)
||.+++ ..+|||+.+|.|.||| |||||+++|.++. +| ..++.+.+.+...|..+.|+.+|||+|.+|.|+|+
T Consensus 878 --sp~~~~-~~~tpss~s~~p~tpgg~~~~Tpgs~~d~~~~-~~-~~~~~~~~~d~~~~~~~~G~~~~ir~v~~G~~sv~ 952 (1024)
T KOG1999|consen 878 --SPWGYQ-NNPTPSSSSYGPKTPGGGNPMTPGSGLDSGSG-NG-GDGNSSWGPDTSLDTQLVGQTGIIRSVADGGCSVW 952 (1024)
T ss_pred --CCccCc-cCCCCcccccCCCCCCCCCCCCCCccccccCC-CC-CccceEecccccccceecccccceeeccCCceeee
Confidence 455665 4789999999999997 9999999999987 89 88899999988888999999999999999999999
Q ss_pred eCCCCeeeeeeCCceeEcCCCCCCeEEEEeCCCCCceEEEEEEeCCCcEEEEcCCCceeEeecchhhccCCC
Q psy13744 225 LAEEERTLSIEAHELEPVMPQPNDKVKVIVGEHKECTGVLLSVDNGEGVVKLTEEDDVKMIDVKFLCKYKPE 296 (296)
Q Consensus 225 L~d~~~vv~V~q~~LEtViP~kGd~VkVI~Ge~RG~tG~LisID~~dgiVkld~~~d~kil~~~~L~Kl~~~ 296 (296)
|.++++++++.+++|+++.|.++|.|||+.|++||.+|+|+++|..++|||+|+++++|||++.+||||+++
T Consensus 953 ~~de~~~~~~s~~~~a~~~p~~~d~~k~~~g~~~g~~~~~~~~dg~~g~~~~d~~~~~k~l~~~~~~k~~~~ 1024 (1024)
T KOG1999|consen 953 LGDEGETISNSKPHLAPAPPCKGDDVKSIWGDDRGSTGKLVGNDGWDGIVRIDETSDIKILNLGLLCKMVSP 1024 (1024)
T ss_pred cCCCCcccccccccCccCCCCCCCCccccccccccccccccCCCcccceecccccccchhhhhhhhhhccCC
Confidence 999999999999999999999999999999999999999999999999999998889999999999999864
No 2
>KOG4315|consensus
Probab=99.03 E-value=7e-11 Score=116.17 Aligned_cols=108 Identities=28% Similarity=0.501 Sum_probs=92.8
Q ss_pred CcccCceEEEEec-CCCCccccCCeEEEEEecC-CeEEEEeCCCCe-eee-eeCCceeEcCCCC-CCeEEEEeCCCCCce
Q psy13744 187 EWHTTDIEVRINE-NARDPEFRGQIGVIRHLGS-GVCSVYLAEEER-TLS-IEAHELEPVMPQP-NDKVKVIVGEHKECT 261 (296)
Q Consensus 187 ~Wl~~dI~VkI~~-~~~d~~yygqkGVVrsV~~-g~c~V~L~d~~~-vv~-V~q~~LEtViP~k-Gd~VkVI~Ge~RG~t 261 (296)
.|+..+|.|||++ ....++||.+|.+|.+|.+ .+|.|.+++..+ +-- |.|+-|||++|.. |++|+|+.|+|.|..
T Consensus 332 ~wlR~dl~VR~is~d~Kgg~ly~~K~~i~dv~gp~scd~r~Dedq~~~qg~irq~~lET~~pr~~Ge~vmvv~gkhkg~~ 411 (455)
T KOG4315|consen 332 SWLRSDLKVRFISKDVKGGRLYEKKVRIVDVVGPTSCDIRMDEDQELVQGNIRQELLETALPRRGGEKVMVVSGKHKGVY 411 (455)
T ss_pred hhhhcceeEEeeccccccchhhhcccceecccCCCccceeccccccccccchHHHHHhhhcccccCceeEEEecccccch
Confidence 7999999999996 5577899999999999985 789999988543 333 8999999999985 788999999999999
Q ss_pred EEEEEEeCC--CcEEEEcCCCceeEeecchhhccC
Q psy13744 262 GVLLSVDNG--EGVVKLTEEDDVKMIDVKFLCKYK 294 (296)
Q Consensus 262 G~LisID~~--dgiVkld~~~d~kil~~~~L~Kl~ 294 (296)
|.|++.|-+ .++|++-.+.|+..+-|++||.+.
T Consensus 412 g~llskd~~Ke~~~v~~~a~ndvv~~~~D~v~ey~ 446 (455)
T KOG4315|consen 412 GSLLSKDLDKETGVVRLVATNDVVTVYLDQVCEYM 446 (455)
T ss_pred hhhhhhhhhhhhcceecccccchhhhhHHHHHHhh
Confidence 999999664 788887555668789999999863
No 3
>KOG2837|consensus
Probab=98.58 E-value=1.2e-09 Score=102.82 Aligned_cols=61 Identities=18% Similarity=0.309 Sum_probs=52.6
Q ss_pred EEEEecCCCCccccCCeEEEEEecC-CeEEEEeCCCCeeeeeeCCceeEcCCCCCCeEEEEeCCCCCce
Q psy13744 194 EVRINENARDPEFRGQIGVIRHLGS-GVCSVYLAEEERTLSIEAHELEPVMPQPNDKVKVIVGEHKECT 261 (296)
Q Consensus 194 ~VkI~~~~~d~~yygqkGVVrsV~~-g~c~V~L~d~~~vv~V~q~~LEtViP~kGd~VkVI~Ge~RG~t 261 (296)
+|+|+.+....+ |++||||++|.| ++..|+ +|++.+|.|||+|||||||+ +||+|.|||..
T Consensus 247 ~vk~~sk~l~~k-~K~K~vv~~vid~y~~~~K-ld~g~~lk~dq~~lEtvip~-----~~vng~yRg~~ 308 (309)
T KOG2837|consen 247 VVKVISKSLGEK-YKQKGVVKKVIDDYTGQIK-LDSGTVLKVDQEHLETVIPQ-----MIVNGAYRGSE 308 (309)
T ss_pred EEEeehhhhhHH-hccccHHHHHHHhhhhhee-ccCCceecccHHHHHHHhHH-----HHhhhhhccCC
Confidence 899986444445 899999999976 677899 67889999999999999999 99999999975
No 4
>KOG1999|consensus
Probab=97.87 E-value=6.6e-05 Score=80.73 Aligned_cols=17 Identities=35% Similarity=0.616 Sum_probs=12.0
Q ss_pred CCCCCC--CCCCcCCCCCC
Q psy13744 56 GSRTPG--GGATPLHDGSR 72 (296)
Q Consensus 56 gsrTP~--g~~TP~hdg~r 72 (296)
+++||. |+|||..+++|
T Consensus 787 ~~~Tp~~dG~rTP~r~~aW 805 (1024)
T KOG1999|consen 787 GGATPSHDGSRTPARGRAW 805 (1024)
T ss_pred CCCCcCCCCCcCCCCCCCc
Confidence 567777 77777666666
No 5
>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=97.37 E-value=0.00033 Score=45.80 Aligned_cols=31 Identities=32% Similarity=0.440 Sum_probs=28.4
Q ss_pred CCCeEEEEeCCCCCceEEEEEEeCCCcEEEE
Q psy13744 246 PNDKVKVIVGEHKECTGVLLSVDNGEGVVKL 276 (296)
Q Consensus 246 kGd~VkVI~Ge~RG~tG~LisID~~dgiVkl 276 (296)
+||.|+|+.|.|+|..|+++.||.+...|.+
T Consensus 1 ~Gd~V~V~~G~~~G~~G~I~~i~~~~~~V~v 31 (32)
T PF00467_consen 1 VGDTVKVISGPFKGKIGKIVEIDRSKVRVTV 31 (32)
T ss_dssp TTSEEEESSSTTTTEEEEEEEEETTTTEEEE
T ss_pred CCCEEEEeEcCCCCceEEEEEEECCCCEEEE
Confidence 5899999999999999999999999877755
No 6
>PF12815 CTD: Spt5 C-terminal nonapeptide repeat binding Spt4; PDB: 2E70_A.
Probab=97.23 E-value=7.2e-05 Score=63.42 Aligned_cols=32 Identities=66% Similarity=0.987 Sum_probs=0.0
Q ss_pred CCCCCC---CCCCcC-CCCCCCC--CCC-CCCCCCCCCC
Q psy13744 56 GSRTPG---GGATPL-HDGSRTP--GPW-DPSSTPARSI 87 (296)
Q Consensus 56 gsrTP~---g~~TP~-hdg~rTP--~aw-dp~~tP~r~~ 87 (296)
|+|||+ |++||. |+|+||| .++ +..+||++.+
T Consensus 32 g~rTPa~~~gsrTP~~~~gsrTPa~~~~~~~~~TPa~~~ 70 (123)
T PF12815_consen 32 GSRTPAWGSGSRTPAFHDGSRTPAYGGSSSPSRTPAYGS 70 (123)
T ss_dssp ---------------------------------------
T ss_pred CCcCcccccCCcCcccCCCCCCCccCCCCCCCCCccCcC
Confidence 688888 899999 9999999 444 4477898753
No 7
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=97.04 E-value=0.0012 Score=40.70 Aligned_cols=27 Identities=37% Similarity=0.484 Sum_probs=24.6
Q ss_pred CCCCCeEEEEeCCCCCceEEEEEEeCC
Q psy13744 244 PQPNDKVKVIVGEHKECTGVLLSVDNG 270 (296)
Q Consensus 244 P~kGd~VkVI~Ge~RG~tG~LisID~~ 270 (296)
+++||+|+|+.|.++|..|++++||.+
T Consensus 2 ~~~G~~V~I~~G~~~g~~g~i~~i~~~ 28 (28)
T smart00739 2 FEVGDTVRVIAGPFKGKVGKVLEVDGE 28 (28)
T ss_pred CCCCCEEEEeECCCCCcEEEEEEEcCC
Confidence 468999999999999999999999863
No 8
>PRK12281 rplX 50S ribosomal protein L24; Reviewed
Probab=96.95 E-value=0.0018 Score=50.64 Aligned_cols=33 Identities=36% Similarity=0.428 Sum_probs=29.3
Q ss_pred CCCCeEEEEeCCCCCceEEEEEEeCCCcEEEEc
Q psy13744 245 QPNDKVKVIVGEHKECTGVLLSVDNGEGVVKLT 277 (296)
Q Consensus 245 ~kGd~VkVI~Ge~RG~tG~LisID~~dgiVkld 277 (296)
++||+|+||.|.++|.+|+++.||..+..|.++
T Consensus 8 ~kGD~V~Vi~G~dKGK~G~V~~V~~~~~~V~Ve 40 (76)
T PRK12281 8 KKGDMVKVIAGDDKGKTGKVLAVLPKKNRVIVE 40 (76)
T ss_pred cCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEEc
Confidence 579999999999999999999999888766554
No 9
>CHL00141 rpl24 ribosomal protein L24; Validated
Probab=96.85 E-value=0.0024 Score=50.69 Aligned_cols=33 Identities=27% Similarity=0.352 Sum_probs=29.7
Q ss_pred CCCCeEEEEeCCCCCceEEEEEEeCCCcEEEEc
Q psy13744 245 QPNDKVKVIVGEHKECTGVLLSVDNGEGVVKLT 277 (296)
Q Consensus 245 ~kGd~VkVI~Ge~RG~tG~LisID~~dgiVkld 277 (296)
++||+|+||.|.++|.+|+++.||.+...|.++
T Consensus 10 ~~GD~V~Vi~G~dKGK~G~V~~V~~~~~~V~Ve 42 (83)
T CHL00141 10 KIGDTVKIISGSDKGKIGEVLKIIKKSNKVIVK 42 (83)
T ss_pred cCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEEc
Confidence 579999999999999999999999988877654
No 10
>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=96.45 E-value=0.0053 Score=51.63 Aligned_cols=33 Identities=24% Similarity=0.354 Sum_probs=29.9
Q ss_pred CCCCeEEEEeCCCCCceEEEEEEeCCCcEEEEc
Q psy13744 245 QPNDKVKVIVGEHKECTGVLLSVDNGEGVVKLT 277 (296)
Q Consensus 245 ~kGd~VkVI~Ge~RG~tG~LisID~~dgiVkld 277 (296)
++||+|+||.|+++|.+|+++.||..+..|-++
T Consensus 43 kkGD~V~Vi~Gk~KGk~GkV~~V~~~~~~V~Ve 75 (114)
T TIGR01080 43 RKGDKVRIMRGDFKGHEGKVSKVDLKRYRIYVE 75 (114)
T ss_pred ecCCEEEEecCCCCCCEEEEEEEEcCCCEEEEc
Confidence 689999999999999999999999888877654
No 11
>PRK00004 rplX 50S ribosomal protein L24; Reviewed
Probab=96.38 E-value=0.0074 Score=49.77 Aligned_cols=33 Identities=30% Similarity=0.341 Sum_probs=29.2
Q ss_pred CCCCeEEEEeCCCCCceEEEEEEeCCCcEEEEc
Q psy13744 245 QPNDKVKVIVGEHKECTGVLLSVDNGEGVVKLT 277 (296)
Q Consensus 245 ~kGd~VkVI~Ge~RG~tG~LisID~~dgiVkld 277 (296)
++||+|+||.|.++|.+|+++.||.....|.++
T Consensus 6 ~kGD~V~Vi~G~dKGk~G~V~~V~~~~~~V~Ve 38 (105)
T PRK00004 6 KKGDTVIVIAGKDKGKRGKVLKVLPKKNKVIVE 38 (105)
T ss_pred cCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEEc
Confidence 579999999999999999999999887766554
No 12
>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=96.30 E-value=0.0086 Score=49.43 Aligned_cols=33 Identities=33% Similarity=0.370 Sum_probs=29.2
Q ss_pred CCCCeEEEEeCCCCCceEEEEEEeCCCcEEEEc
Q psy13744 245 QPNDKVKVIVGEHKECTGVLLSVDNGEGVVKLT 277 (296)
Q Consensus 245 ~kGd~VkVI~Ge~RG~tG~LisID~~dgiVkld 277 (296)
++||+|+||.|.++|.+|+++.||.....|.++
T Consensus 5 kkGD~V~Vi~G~dKGK~G~V~~V~~~~~~V~Ve 37 (104)
T TIGR01079 5 KKGDTVKVISGKDKGKRGKVLKVLPKTNKVIVE 37 (104)
T ss_pred cCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEEC
Confidence 579999999999999999999999887766554
No 13
>PRK01191 rpl24p 50S ribosomal protein L24P; Validated
Probab=96.10 E-value=0.011 Score=50.18 Aligned_cols=33 Identities=30% Similarity=0.461 Sum_probs=29.3
Q ss_pred CCCCeEEEEeCCCCCceEEEEEEeCCCcEEEEc
Q psy13744 245 QPNDKVKVIVGEHKECTGVLLSVDNGEGVVKLT 277 (296)
Q Consensus 245 ~kGd~VkVI~Ge~RG~tG~LisID~~dgiVkld 277 (296)
++||.|+||.|+++|.+|+++.||..+.-|.++
T Consensus 47 kkGD~V~VisG~~KGk~GkV~~V~~~~~~V~Ve 79 (120)
T PRK01191 47 RKGDTVKVMRGDFKGEEGKVVEVDLKRGRIYVE 79 (120)
T ss_pred eCCCEEEEeecCCCCceEEEEEEEcCCCEEEEe
Confidence 579999999999999999999999888766554
No 14
>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=95.91 E-value=0.025 Score=41.60 Aligned_cols=50 Identities=18% Similarity=0.349 Sum_probs=36.8
Q ss_pred ccCceEEEEecCCCCccccCCeEEEEEecCCeEEEEeCCC--CeeeeeeCCcee
Q psy13744 189 HTTDIEVRINENARDPEFRGQIGVIRHLGSGVCSVYLAEE--ERTLSIEAHELE 240 (296)
Q Consensus 189 l~~dI~VkI~~~~~d~~yygqkGVVrsV~~g~c~V~L~d~--~~vv~V~q~~LE 240 (296)
+.++..|+|++.. .-||+-+|.|.+|.|+.+.|-+... ++.|+..-++||
T Consensus 2 ilPG~~V~V~n~~--~~Y~~y~G~VQRvsdgkaaVLFEGGnWdKlvTf~l~eLe 53 (53)
T PF11623_consen 2 ILPGSTVRVKNPN--DIYYGYEGFVQRVSDGKAAVLFEGGNWDKLVTFRLSELE 53 (53)
T ss_dssp --TT-EEEE--TT--STTTT-EEEEEEEETTEEEEEEEETTEEEEEEEEGGGEE
T ss_pred ccCCCEEEEeCCC--CccchheEEEEEeeCCeEEEEecCCCceEEEEEEhhhCC
Confidence 4688899998532 3699999999999999998877443 789999999987
No 15
>PTZ00194 60S ribosomal protein L26; Provisional
Probab=95.63 E-value=0.019 Score=50.11 Aligned_cols=33 Identities=27% Similarity=0.424 Sum_probs=29.2
Q ss_pred CCCCeEEEEeCCCCCceEEEEEEeCCCcEEEEc
Q psy13744 245 QPNDKVKVIVGEHKECTGVLLSVDNGEGVVKLT 277 (296)
Q Consensus 245 ~kGd~VkVI~Ge~RG~tG~LisID~~dgiVkld 277 (296)
++||.|+||.|+++|.+|+++.||..++-|-++
T Consensus 48 kkGD~V~Vi~Gk~KGk~GkV~~V~~k~~~ViVE 80 (143)
T PTZ00194 48 RKDDEVMVVRGHHKGREGKVTAVYRKKWVIHIE 80 (143)
T ss_pred ecCCEEEEecCCCCCCceEEEEEEcCCCEEEEe
Confidence 679999999999999999999999888755443
No 16
>PRK05609 nusG transcription antitermination protein NusG; Validated
Probab=95.19 E-value=0.038 Score=48.12 Aligned_cols=50 Identities=18% Similarity=0.248 Sum_probs=36.4
Q ss_pred CCCCCeEEEEeCCCCCceEEEEEEeCCCcEEE--EcC-CCcee-Eeecchhhcc
Q psy13744 244 PQPNDKVKVIVGEHKECTGVLLSVDNGEGVVK--LTE-EDDVK-MIDVKFLCKY 293 (296)
Q Consensus 244 P~kGd~VkVI~Ge~RG~tG~LisID~~dgiVk--ld~-~~d~k-il~~~~L~Kl 293 (296)
.++||+|+|+.|.+.|..|+++.+|..+..|+ ++- +.... -|++++|-|+
T Consensus 127 ~~~Gd~VrI~~GPf~G~~g~v~~i~~~~~r~~v~l~~~G~~~~v~l~~~~l~~~ 180 (181)
T PRK05609 127 FEVGEMVRVIDGPFADFNGTVEEVDYEKSKLKVLVSIFGRETPVELEFSQVEKI 180 (181)
T ss_pred CCCCCEEEEeccCCCCCEEEEEEEeCCCCEEEEEEEECCCceEEEEchHHEEEc
Confidence 46899999999999999999999997665444 332 22222 3777777664
No 17
>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=94.91 E-value=0.051 Score=46.16 Aligned_cols=51 Identities=20% Similarity=0.187 Sum_probs=39.6
Q ss_pred CCCCCeEEEEeCCCCCceEEEEEEeCCCcEEEEcCC-Ccee---EeecchhhccC
Q psy13744 244 PQPNDKVKVIVGEHKECTGVLLSVDNGEGVVKLTEE-DDVK---MIDVKFLCKYK 294 (296)
Q Consensus 244 P~kGd~VkVI~Ge~RG~tG~LisID~~dgiVkld~~-~d~k---il~~~~L~Kl~ 294 (296)
.++||+|+|+.|.+.|..|+++.+|..+..|+++-- .... -+++++|-|+.
T Consensus 87 ~~~Gd~V~I~~GPf~G~~g~v~~~d~~k~~v~v~l~~~~~~~~v~v~~~~l~~~~ 141 (145)
T TIGR00405 87 IKKGDIVEIISGPFKGERAKVIRVDESKEEVTLELIEAAVPIPVTVKGDQVRIIQ 141 (145)
T ss_pred cCCCCEEEEeecCCCCCeEEEEEEcCCCCEEEEEEEEcCccceEEEeeeEEEEec
Confidence 678999999999999999999999988888875431 2222 37777776664
No 18
>COG0198 RplX Ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=94.65 E-value=0.047 Score=45.34 Aligned_cols=27 Identities=37% Similarity=0.462 Sum_probs=25.7
Q ss_pred CCCCeEEEEeCCCCCceEEEEEEeCCC
Q psy13744 245 QPNDKVKVIVGEHKECTGVLLSVDNGE 271 (296)
Q Consensus 245 ~kGd~VkVI~Ge~RG~tG~LisID~~d 271 (296)
.+||.|+||.|+++|..|+++.++..+
T Consensus 6 rkGD~V~Vi~GkdKGk~GkVl~v~~k~ 32 (104)
T COG0198 6 KKGDTVKVIAGKDKGKEGKVLKVLPKK 32 (104)
T ss_pred ecCCEEEEEecCCCCcceEEEEEecCe
Confidence 479999999999999999999999987
No 19
>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=94.50 E-value=0.074 Score=46.09 Aligned_cols=32 Identities=25% Similarity=0.307 Sum_probs=27.7
Q ss_pred CCCCCeEEEEeCCCCCceEEEEEEeCCCcEEE
Q psy13744 244 PQPNDKVKVIVGEHKECTGVLLSVDNGEGVVK 275 (296)
Q Consensus 244 P~kGd~VkVI~Ge~RG~tG~LisID~~dgiVk 275 (296)
.++||+|+|+.|.+.|..|+++.+|..+..|+
T Consensus 120 ~~~G~~V~I~~Gpf~G~~g~v~~~~~~~~r~~ 151 (172)
T TIGR00922 120 FEVGEQVRVNDGPFANFTGTVEEVDYEKSKLK 151 (172)
T ss_pred CCCCCEEEEeecCCCCcEEEEEEEcCCCCEEE
Confidence 46899999999999999999999997665444
No 20
>PF15591 Imm17: Immunity protein 17
Probab=93.94 E-value=0.12 Score=40.60 Aligned_cols=48 Identities=33% Similarity=0.419 Sum_probs=37.6
Q ss_pred EEEEec-CCCCccccCCeEEEEEecC---Ce--EEEEeCCCCeeeeeeCCceeE
Q psy13744 194 EVRINE-NARDPEFRGQIGVIRHLGS---GV--CSVYLAEEERTLSIEAHELEP 241 (296)
Q Consensus 194 ~VkI~~-~~~d~~yygqkGVVrsV~~---g~--c~V~L~d~~~vv~V~q~~LEt 241 (296)
+|+|++ -..|.+++|++|||.-+++ +. .+|.+.+.+....++.++|++
T Consensus 10 ~V~v~~s~p~~~ei~Gk~GVVlG~SeeD~~~~gY~Vli~d~e~~~~~ee~~l~~ 63 (74)
T PF15591_consen 10 EVEVVRSCPCDAEIWGKRGVVLGISEEDGGNFGYSVLIFDMECCWYIEEDELEA 63 (74)
T ss_pred EEEEeccCcchhhhcCceeEEEEEecCCCcEEEEEEEEeeeeeEEEechHHeee
Confidence 677875 2356689999999999972 22 378888888899999999886
No 21
>COG5164 SPT5 Transcription elongation factor [Transcription]
Probab=93.90 E-value=0.21 Score=51.22 Aligned_cols=87 Identities=25% Similarity=0.388 Sum_probs=60.3
Q ss_pred cccCCeEEEEEecCCeEEEEeCCCCeeeeee----------------CCceeEcC----CCCCCeEEEEeCCCCCceEEE
Q psy13744 205 EFRGQIGVIRHLGSGVCSVYLAEEERTLSIE----------------AHELEPVM----PQPNDKVKVIVGEHKECTGVL 264 (296)
Q Consensus 205 ~yygqkGVVrsV~~g~c~V~L~d~~~vv~V~----------------q~~LEtVi----P~kGd~VkVI~Ge~RG~tG~L 264 (296)
++...-||+..+....|.|+-.+.-..+++| ..+||--| |..|..|+|-.|+|+|+.|.+
T Consensus 293 ~i~ennGVfv~~~~nv~~VAtkd~~~s~k~dl~kmnp~v~~~~~~p~~~~l~r~i~gRd~aigktVrIr~g~yKG~lGVV 372 (607)
T COG5164 293 SIKENNGVFVKIEGNVCIVATKDFTESLKVDLDKMNPPVTVNLQNPKTNELERKIVGRDPAIGKTVRIRCGEYKGHLGVV 372 (607)
T ss_pred eeeccCceEEEecCceeEEEeccchhhhcccHhhcCchhhcCCCCCcchhhhccccccccccCceEEEeeccccccccee
Confidence 3445567777776777877765422221222 23444444 778999999999999999999
Q ss_pred EEEeCCCcEEEEcCCCceeEeecchhh
Q psy13744 265 LSVDNGEGVVKLTEEDDVKMIDVKFLC 291 (296)
Q Consensus 265 isID~~dgiVkld~~~d~kil~~~~L~ 291 (296)
..+|.+.+-|.|.++..+.-|+-+-|+
T Consensus 373 Kdv~~~~arVeLhs~nK~VTI~K~~l~ 399 (607)
T COG5164 373 KDVDRNIARVELHSNNKFVTIEKSRLA 399 (607)
T ss_pred eeccCceEEEEEecCCceEEeehhheE
Confidence 999999999999877555555555444
No 22
>PRK08559 nusG transcription antitermination protein NusG; Validated
Probab=93.09 E-value=0.22 Score=43.15 Aligned_cols=48 Identities=21% Similarity=0.223 Sum_probs=38.0
Q ss_pred CCCCCeEEEEeCCCCCceEEEEEEeCCCcEEEEcC-CCcee---Eeecchhh
Q psy13744 244 PQPNDKVKVIVGEHKECTGVLLSVDNGEGVVKLTE-EDDVK---MIDVKFLC 291 (296)
Q Consensus 244 P~kGd~VkVI~Ge~RG~tG~LisID~~dgiVkld~-~~d~k---il~~~~L~ 291 (296)
-+.||+|+|+.|.+.|..|+++.+|.....|+++. +..++ -|+++.|.
T Consensus 95 ~~~G~~V~I~~Gpf~g~~g~V~~vd~~k~~v~v~ll~~~~~~pv~v~~~~~~ 146 (153)
T PRK08559 95 IKEGDIVELIAGPFKGEKARVVRVDESKEEVTVELLEAAVPIPVTVRGDQVR 146 (153)
T ss_pred CCCCCEEEEeccCCCCceEEEEEEcCCCCEEEEEEECCcceeeEEEeccEEE
Confidence 56899999999999999999999999988888643 23333 26666663
No 23
>PF12815 CTD: Spt5 C-terminal nonapeptide repeat binding Spt4; PDB: 2E70_A.
Probab=92.99 E-value=0.028 Score=47.77 Aligned_cols=28 Identities=68% Similarity=1.143 Sum_probs=0.0
Q ss_pred CCCCCC----CCCCcCC--CCCCCCCCCCC-CCCCC
Q psy13744 56 GSRTPG----GGATPLH--DGSRTPGPWDP-SSTPA 84 (296)
Q Consensus 56 gsrTP~----g~~TP~h--dg~rTP~awdp-~~tP~ 84 (296)
|+|||+ |++||.+ ||+||| ||+- ..||+
T Consensus 12 g~rTPa~~~~gsrTP~~~~~g~rTP-a~~~gsrTP~ 46 (123)
T PF12815_consen 12 GSRTPAWGNDGSRTPAPGADGSRTP-AWGSGSRTPA 46 (123)
T ss_dssp ------------------------------------
T ss_pred CCCCcccccCCCCCcCCcCCCCcCc-ccccCCcCcc
Confidence 567776 6777776 467777 5643 44555
No 24
>PRK09014 rfaH transcriptional activator RfaH; Provisional
Probab=92.83 E-value=0.24 Score=42.66 Aligned_cols=50 Identities=24% Similarity=0.360 Sum_probs=36.1
Q ss_pred CCCCCeEEEEeCCCCCceEEEEEEeCCCc-EEEEcC-CCceeE-eecchhhcc
Q psy13744 244 PQPNDKVKVIVGEHKECTGVLLSVDNGEG-VVKLTE-EDDVKM-IDVKFLCKY 293 (296)
Q Consensus 244 P~kGd~VkVI~Ge~RG~tG~LisID~~dg-iVkld~-~~d~ki-l~~~~L~Kl 293 (296)
.++||+|+|+.|.+.|..|+++.+|..+- .|.++- +..+.+ |+.++|.|+
T Consensus 110 ~~~G~~V~I~~Gp~~g~eg~v~~~~~~~r~~v~v~~~gr~~~v~v~~~~~~~~ 162 (162)
T PRK09014 110 PKPGDKVIITEGAFEGLQAIYTEPDGEARSILLLNLLNKQVKHSVDNTQFRKI 162 (162)
T ss_pred CCCCCEEEEecCCCCCcEEEEEEeCCCeEEEEeehhhCCcEEEEECHHHeecC
Confidence 46899999999999999999999986644 344432 223333 777777553
No 25
>KOG0260|consensus
Probab=92.16 E-value=1.2 Score=50.16 Aligned_cols=11 Identities=18% Similarity=0.543 Sum_probs=4.5
Q ss_pred cccceEEecCC
Q psy13744 41 LIGKTIKITGG 51 (296)
Q Consensus 41 liG~tvkI~~G 51 (296)
+|||+-.+-.|
T Consensus 1402 mlgqlap~gTg 1412 (1605)
T KOG0260|consen 1402 MLGQLAPMGTG 1412 (1605)
T ss_pred eecccccCCCc
Confidence 33444444333
No 26
>TIGR01955 RfaH transcriptional activator RfaH. This model represents the transcriptional activator protein, RfaH. This protein is most closely related to the transcriptional termination/antitermination protein NusG (TIGR00922) and contains the KOW motif (pfam00467). This protein appears to be limited to the gamma proteobacteria. In E. coli, this gene appears to control the expression of haemolysin, sex factor and lipopolysaccharide genes.
Probab=91.71 E-value=0.42 Score=40.71 Aligned_cols=34 Identities=24% Similarity=0.427 Sum_probs=27.4
Q ss_pred CCCCCeEEEEeCCCCCceEEEEEEeCCC-cEEEEc
Q psy13744 244 PQPNDKVKVIVGEHKECTGVLLSVDNGE-GVVKLT 277 (296)
Q Consensus 244 P~kGd~VkVI~Ge~RG~tG~LisID~~d-giVkld 277 (296)
.++||+|+|+.|.+.|..|.++.+|... ..|.++
T Consensus 109 ~~~G~~V~V~~GPf~g~~g~v~~~~~~~r~~v~l~ 143 (159)
T TIGR01955 109 PYKGDKVRITDGAFAGFEAIFLEPDGEKRSMLLLN 143 (159)
T ss_pred CCCCCEEEEeccCCCCcEEEEEEECCCceEEEEEh
Confidence 4689999999999999999999998543 334443
No 27
>COG5164 SPT5 Transcription elongation factor [Transcription]
Probab=91.45 E-value=0.29 Score=50.22 Aligned_cols=45 Identities=27% Similarity=0.523 Sum_probs=39.4
Q ss_pred ceEEEEecCCCCccccCCeEEEEEecCCeEEEEeCCCCeeeeeeCCcee
Q psy13744 192 DIEVRINENARDPEFRGQIGVIRHLGSGVCSVYLAEEERTLSIEAHELE 240 (296)
Q Consensus 192 dI~VkI~~~~~d~~yygqkGVVrsV~~g~c~V~L~d~~~vv~V~q~~LE 240 (296)
+-.|||+. +.|.|+-|||++|.+..|+|+|-+..+.|+|+-+.|.
T Consensus 355 gktVrIr~----g~yKG~lGVVKdv~~~~arVeLhs~nK~VTI~K~~l~ 399 (607)
T COG5164 355 GKTVRIRC----GEYKGHLGVVKDVDRNIARVELHSNNKFVTIEKSRLA 399 (607)
T ss_pred CceEEEee----cccccccceeeeccCceEEEEEecCCceEEeehhheE
Confidence 56899985 4688999999999999999999999999999987663
No 28
>COG0250 NusG Transcription antiterminator [Transcription]
Probab=90.88 E-value=0.48 Score=42.49 Aligned_cols=52 Identities=21% Similarity=0.293 Sum_probs=40.1
Q ss_pred cCCCCCCeEEEEeCCCCCceEEEEEEeCCCcEEEEcC---CCceeE-eecchhhcc
Q psy13744 242 VMPQPNDKVKVIVGEHKECTGVLLSVDNGEGVVKLTE---EDDVKM-IDVKFLCKY 293 (296)
Q Consensus 242 ViP~kGd~VkVI~Ge~RG~tG~LisID~~dgiVkld~---~~d~ki-l~~~~L~Kl 293 (296)
+-..+||.|+|+.|.+.|..|+++.||.+...+++.- +....+ |+++++-|+
T Consensus 122 ~~~e~Gd~VrI~~GpFa~f~g~V~evd~ek~~~~v~v~ifgr~tPVel~~~qVek~ 177 (178)
T COG0250 122 VDFEPGDVVRIIDGPFAGFKAKVEEVDEEKGKLKVEVSIFGRPTPVELEFDQVEKL 177 (178)
T ss_pred ccCCCCCEEEEeccCCCCccEEEEEEcCcCcEEEEEEEEeCCceEEEEehhhEEEe
Confidence 3456799999999999999999999999988777532 222222 777777665
No 29
>PRK04313 30S ribosomal protein S4e; Validated
Probab=90.74 E-value=2.2 Score=40.24 Aligned_cols=50 Identities=14% Similarity=0.217 Sum_probs=37.0
Q ss_pred Ceeeeee---CCceeEcCCCCCCeEEEEeCCCCCceEEEEEEeCC----CcEEEEcC
Q psy13744 229 ERTLSIE---AHELEPVMPQPNDKVKVIVGEHKECTGVLLSVDNG----EGVVKLTE 278 (296)
Q Consensus 229 ~~vv~V~---q~~LEtViP~kGd~VkVI~Ge~RG~tG~LisID~~----dgiVkld~ 278 (296)
++++.|+ ++-++.+.=..|..|+|+.|.+.|.+|++++|+.. .-+|.|++
T Consensus 154 ~Dtv~i~l~~~kI~~~i~fe~G~l~~itgG~n~GriG~I~~i~~~~~~~~~~V~i~d 210 (237)
T PRK04313 154 GDSLLISLPEQEIVDHIPFEEGNLAIITGGKHVGEIGKIKEIEVTKSSKPNIVTLED 210 (237)
T ss_pred CCEEEEECCCCceeEEEecCCCCEEEEECCeeeeeEEEEEEEEEccCCCCcEEEEEc
Confidence 4444444 33455555678999999999999999999999643 46888863
No 30
>PTZ00223 40S ribosomal protein S4; Provisional
Probab=90.35 E-value=2 Score=41.35 Aligned_cols=50 Identities=16% Similarity=0.263 Sum_probs=37.6
Q ss_pred Ceeeeee---CCceeEcCCCCCCeEEEEeCCCCCceEEEEEEeCC---CcEEEEcC
Q psy13744 229 ERTLSIE---AHELEPVMPQPNDKVKVIVGEHKECTGVLLSVDNG---EGVVKLTE 278 (296)
Q Consensus 229 ~~vv~V~---q~~LEtViP~kGd~VkVI~Ge~RG~tG~LisID~~---dgiVkld~ 278 (296)
+++|.|+ ++-++.+.=..|..|+|+.|.+.|.+|+++.|+.. .-+|.+.+
T Consensus 154 ~Dtv~i~l~~~kI~~~ikfe~G~l~~vtgG~n~GriG~I~~i~~~~~~~~iv~i~d 209 (273)
T PTZ00223 154 GDTLVYNVKEKKVVDLIKNRNGKVVMVTGGANRGRIGEIVSIERHPGAFDIARLKD 209 (273)
T ss_pred CCEEEEECCCCeeeEEEecCCCCEEEEECCeeceeEEEEEEEEecCCCCCEEEEEe
Confidence 5555555 44556666688999999999999999999999543 34777753
No 31
>PLN00036 40S ribosomal protein S4; Provisional
Probab=89.92 E-value=2.5 Score=40.42 Aligned_cols=50 Identities=14% Similarity=0.244 Sum_probs=36.6
Q ss_pred Ceeeeee---CCceeEcCCCCCCeEEEEeCCCCCceEEEEEEeCC---CcEEEEcC
Q psy13744 229 ERTLSIE---AHELEPVMPQPNDKVKVIVGEHKECTGVLLSVDNG---EGVVKLTE 278 (296)
Q Consensus 229 ~~vv~V~---q~~LEtViP~kGd~VkVI~Ge~RG~tG~LisID~~---dgiVkld~ 278 (296)
+++|.|+ ++-++.+.=..|..|+|+.|.+.|.+|++++|+.. .-+|.+++
T Consensus 157 ~Dtv~i~l~~~kI~~~ikfe~G~l~~vtgG~n~GrvG~I~~i~~~~~~~~iV~i~d 212 (261)
T PLN00036 157 NDTIKIDLETNKIVDFIKFDVGNLVMVTGGRNRGRVGVIKNREKHKGSFEIIHVKD 212 (261)
T ss_pred CCEEEEeCCCCceeeEEecCCCCEEEEECCeeceeEEEEEEEEecCCCCCEEEEEe
Confidence 4555554 33445555578999999999999999999999732 34888754
No 32
>PTZ00118 40S ribosomal protein S4; Provisional
Probab=88.81 E-value=3.5 Score=39.42 Aligned_cols=70 Identities=14% Similarity=0.199 Sum_probs=45.2
Q ss_pred CCeEEEEEe-cCCeEEEEeCC----CCeeeeee--C-CceeEcCCCCCCeEEEEeCCCCCceEEEEEEeCC---CcEEEE
Q psy13744 208 GQIGVIRHL-GSGVCSVYLAE----EERTLSIE--A-HELEPVMPQPNDKVKVIVGEHKECTGVLLSVDNG---EGVVKL 276 (296)
Q Consensus 208 gqkGVVrsV-~~g~c~V~L~d----~~~vv~V~--q-~~LEtViP~kGd~VkVI~Ge~RG~tG~LisID~~---dgiVkl 276 (296)
.++|++.=+ .||.+ +...| .+++|.|+ . +-++.+.=..|..|+|+.|.+.|.+|++++++.. ..+|.|
T Consensus 132 ~~gg~~~l~~hDGrn-i~~~d~~ik~~Dtv~i~l~~~kI~~~ikfe~G~l~~vtgG~n~GriG~I~~~~~~~~~~~~V~i 210 (262)
T PTZ00118 132 GPKEVSIAVTHDGRT-IRYVHPDVKVGDSLRLDLETGKVLEFLKFEVGNLVMITGGHNVGRVGTIVSKEKHPGSFDLIHV 210 (262)
T ss_pred CCCCeEEEEecCcce-eccCCCcccCCCEEEEECCCCceeeEEecCCCCEEEEECCeeceeEEEEEEEEecCCCCcEEEE
Confidence 445555543 25555 33222 34555554 3 3445555578999999999999999999998643 348877
Q ss_pred cC
Q psy13744 277 TE 278 (296)
Q Consensus 277 d~ 278 (296)
++
T Consensus 211 ~d 212 (262)
T PTZ00118 211 KD 212 (262)
T ss_pred Ee
Confidence 54
No 33
>COG1471 RPS4A Ribosomal protein S4E [Translation, ribosomal structure and biogenesis]
Probab=88.57 E-value=2.9 Score=39.46 Aligned_cols=42 Identities=17% Similarity=0.251 Sum_probs=33.7
Q ss_pred CceeEcCCCCCCeEEEEeCCCCCceEEEEEEeCC----CcEEEEcC
Q psy13744 237 HELEPVMPQPNDKVKVIVGEHKECTGVLLSVDNG----EGVVKLTE 278 (296)
Q Consensus 237 ~~LEtViP~kGd~VkVI~Ge~RG~tG~LisID~~----dgiVkld~ 278 (296)
+-+|-+....|..|.|+.|.|.|.+|++.+|... .-+|.|++
T Consensus 167 ~I~~~i~fe~g~~~~vtgG~h~G~~G~I~~I~~~~~~~~~~v~~e~ 212 (241)
T COG1471 167 KIVEHIKFEEGALVYVTGGRHVGRVGTIVEIEIQESSKPNLVTVED 212 (241)
T ss_pred hheeEeccCCCcEEEEECCccccceEEEEEEEEecCCCccEEEEec
Confidence 3345556688999999999999999999999655 34788865
No 34
>PRK08559 nusG transcription antitermination protein NusG; Validated
Probab=86.16 E-value=2.9 Score=36.25 Aligned_cols=52 Identities=13% Similarity=0.171 Sum_probs=42.6
Q ss_pred ccCceEEEEecCCCCccccCCeEEEEEec--CCeEEEEeCCCCee--eeeeCCceeEcCC
Q psy13744 189 HTTDIEVRINENARDPEFRGQIGVIRHLG--SGVCSVYLAEEERT--LSIEAHELEPVMP 244 (296)
Q Consensus 189 l~~dI~VkI~~~~~d~~yygqkGVVrsV~--~g~c~V~L~d~~~v--v~V~q~~LEtViP 244 (296)
+.+|=.|+|++ +.|.+..|+|.++. ...+.|.|.+.... ++|+.++|.+|..
T Consensus 95 ~~~G~~V~I~~----Gpf~g~~g~V~~vd~~k~~v~v~ll~~~~~~pv~v~~~~~~~~~~ 150 (153)
T PRK08559 95 IKEGDIVELIA----GPFKGEKARVVRVDESKEEVTVELLEAAVPIPVTVRGDQVRVVKK 150 (153)
T ss_pred CCCCCEEEEec----cCCCCceEEEEEEcCCCCEEEEEEECCcceeeEEEeccEEEEecc
Confidence 55777889984 67889999999997 36678888887766 9999999988864
No 35
>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=83.85 E-value=3.4 Score=34.99 Aligned_cols=53 Identities=11% Similarity=0.148 Sum_probs=44.3
Q ss_pred cccCceEEEEecCCCCccccCCeEEEEEec--CCeEEEEeCCCCee--eeeeCCceeEcCC
Q psy13744 188 WHTTDIEVRINENARDPEFRGQIGVIRHLG--SGVCSVYLAEEERT--LSIEAHELEPVMP 244 (296)
Q Consensus 188 Wl~~dI~VkI~~~~~d~~yygqkGVVrsV~--~g~c~V~L~d~~~v--v~V~q~~LEtViP 244 (296)
.+.+|=.|+|++ +-|.|..|+|.+++ ...+.|.|.+.+.. ++|+.++|+.+-.
T Consensus 86 ~~~~Gd~V~I~~----GPf~G~~g~v~~~d~~k~~v~v~l~~~~~~~~v~v~~~~l~~~~~ 142 (145)
T TIGR00405 86 SIKKGDIVEIIS----GPFKGERAKVIRVDESKEEVTLELIEAAVPIPVTVKGDQVRIIQK 142 (145)
T ss_pred ccCCCCEEEEee----cCCCCCeEEEEEEcCCCCEEEEEEEEcCccceEEEeeeEEEEecc
Confidence 577888899984 67889999999997 36678888888888 9999999998763
No 36
>PRK04914 ATP-dependent helicase HepA; Validated
Probab=82.77 E-value=7.7 Score=43.15 Aligned_cols=63 Identities=16% Similarity=0.288 Sum_probs=52.8
Q ss_pred CeEEEEEecCCeEEEEeCCC--CeeeeeeCCceeEcCCCCCCeEEEEeCCCCCceEEEEEEeCCCcEEE
Q psy13744 209 QIGVIRHLGSGVCSVYLAEE--ERTLSIEAHELEPVMPQPNDKVKVIVGEHKECTGVLLSVDNGEGVVK 275 (296)
Q Consensus 209 qkGVVrsV~~g~c~V~L~d~--~~vv~V~q~~LEtViP~kGd~VkVI~Ge~RG~tG~LisID~~dgiVk 275 (296)
--|+|.+|.+.+|+|.++.+ .++..+...-|.-|+..+||+|.+..| ...++..|.+.+|++.
T Consensus 17 GlG~v~~~d~r~vtv~fpas~e~R~ya~~~apl~Rv~~~~g~~v~~~~~----~~~~v~~v~~~~gl~~ 81 (956)
T PRK04914 17 GLGTVVAVDGRTVTLLFPATGENRLYARNDAPLTRVMFNPGDTITSHEG----WQLTVEEVEEENGLLT 81 (956)
T ss_pred CcEEEEEEeCCEEEEEecCCCCceeeecCCCCceeeecCCCCEEEecCC----CEEEEEEEeccCCcEE
Confidence 37999999999999999775 567788999999999999999997665 4577777877777766
No 37
>COG1862 YajC Preprotein translocase subunit YajC [Intracellular trafficking and secretion]
Probab=81.27 E-value=3.4 Score=33.95 Aligned_cols=43 Identities=19% Similarity=0.335 Sum_probs=31.4
Q ss_pred CCCCeEEEEeCCCCCceEEEEEEeCCCcEEEEcCCCceeEeecchhhc
Q psy13744 245 QPNDKVKVIVGEHKECTGVLLSVDNGEGVVKLTEEDDVKMIDVKFLCK 292 (296)
Q Consensus 245 ~kGd~VkVI~Ge~RG~tG~LisID~~dgiVkld~~~d~kil~~~~L~K 292 (296)
++||+|+-+.| ..|++.+|++++..|+++++-.++ +.-+.++.
T Consensus 45 ~kGD~VvT~gG----i~G~V~~v~d~~v~I~l~~~~~i~-~~k~aI~~ 87 (97)
T COG1862 45 KKGDEVVTIGG----IVGTVTKVGDDTVEIELGDGTKIK-FEKEAIAT 87 (97)
T ss_pred cCCCEEEEcCC----eEEEEEEEecCcEEEEECCCeEEE-EEHHHHHh
Confidence 57999998876 899999999988777776443233 55555553
No 38
>PLN00045 photosystem I reaction center subunit IV; Provisional
Probab=81.05 E-value=2.2 Score=35.21 Aligned_cols=44 Identities=27% Similarity=0.453 Sum_probs=34.3
Q ss_pred eCCceeEcCCCCCCeEEEEeCC--CCCceEEEEEEeCCCc-----EEEEcC
Q psy13744 235 EAHELEPVMPQPNDKVKVIVGE--HKECTGVLLSVDNGEG-----VVKLTE 278 (296)
Q Consensus 235 ~q~~LEtViP~kGd~VkVI~Ge--~RG~tG~LisID~~dg-----iVkld~ 278 (296)
....-.++-|++|++|+||.=| |--.+|++.+||.+.+ +||+|.
T Consensus 31 ~~~kpp~ig~~RGskVrIlR~ESYWyn~vGtVvsVDq~~girYPVvVRF~k 81 (101)
T PLN00045 31 AKPKPPPIGPKRGSKVKILRPESYWFNDVGKVVAVDQDPGVRYPVVVRFEK 81 (101)
T ss_pred ccCCCCCcccCCCCEEEEccccceeecCcceEEEEeCCCCcccceEEEeee
Confidence 3444567778999999999976 5778999999999855 667653
No 39
>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=80.41 E-value=3.9 Score=32.44 Aligned_cols=43 Identities=19% Similarity=0.364 Sum_probs=31.0
Q ss_pred CCCCeEEEEeCCCCCceEEEEEEeCCCcEEEEcCCCceeEeecchhhc
Q psy13744 245 QPNDKVKVIVGEHKECTGVLLSVDNGEGVVKLTEEDDVKMIDVKFLCK 292 (296)
Q Consensus 245 ~kGd~VkVI~Ge~RG~tG~LisID~~dgiVkld~~~d~kil~~~~L~K 292 (296)
++||+|+-..| ..|++.+||++..+|++.++-.++ ++-..+++
T Consensus 39 ~~Gd~VvT~gG----i~G~V~~i~d~~v~vei~~g~~i~-~~r~aI~~ 81 (84)
T TIGR00739 39 KKGDKVLTIGG----IIGTVTKIAENTIVIELNDNTEIT-FSKNAIVE 81 (84)
T ss_pred CCCCEEEECCC----eEEEEEEEeCCEEEEEECCCeEEE-EEhHHhhh
Confidence 46999998876 889999999887777775543333 55555554
No 40
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=80.30 E-value=2.8 Score=30.19 Aligned_cols=53 Identities=15% Similarity=0.177 Sum_probs=38.8
Q ss_pred cCceEEEEecCCCCccccCCeEEEEEecC-CeEEEEeCC--CCeeeeeeCCceeEcCCC
Q psy13744 190 TTDIEVRINENARDPEFRGQIGVIRHLGS-GVCSVYLAE--EERTLSIEAHELEPVMPQ 245 (296)
Q Consensus 190 ~~dI~VkI~~~~~d~~yygqkGVVrsV~~-g~c~V~L~d--~~~vv~V~q~~LEtViP~ 245 (296)
..|-+|.+..+. ++.++ .|+|++|.+ +.|.|++.+ .+..++++.++|.+..|-
T Consensus 4 ~~G~~Ve~~~~~-~~~W~--~a~V~~~~~~~~~~V~~~~~~~~~~e~v~~~~LRp~~~w 59 (61)
T smart00743 4 KKGDRVEVFSKE-EDSWW--EAVVTKVLGDGKYLVRYLTESEPLKETVDWSDLRPHPPW 59 (61)
T ss_pred CCCCEEEEEECC-CCEEE--EEEEEEECCCCEEEEEECCCCcccEEEEeHHHcccCCCC
Confidence 445555555322 33443 589999986 889999988 888999999999987764
No 41
>PRK05585 yajC preprotein translocase subunit YajC; Validated
Probab=80.28 E-value=3.8 Score=33.97 Aligned_cols=43 Identities=19% Similarity=0.307 Sum_probs=30.1
Q ss_pred CCCCeEEEEeCCCCCceEEEEEEeCCCcEEEEcCCCceeEeecchhhc
Q psy13744 245 QPNDKVKVIVGEHKECTGVLLSVDNGEGVVKLTEEDDVKMIDVKFLCK 292 (296)
Q Consensus 245 ~kGd~VkVI~Ge~RG~tG~LisID~~dgiVkld~~~d~kil~~~~L~K 292 (296)
++||+|+-+.| ..|++++||++..+|++.++..++ ++-..+.+
T Consensus 54 k~Gd~VvT~gG----i~G~Vv~i~~~~v~lei~~g~~i~-~~r~aI~~ 96 (106)
T PRK05585 54 AKGDEVVTNGG----IIGKVTKVSEDFVIIELNDDTEIK-IQKSAIAA 96 (106)
T ss_pred CCCCEEEECCC----eEEEEEEEeCCEEEEEECCCeEEE-EEhHHhhh
Confidence 46999998886 889999999876777775553344 33334443
No 42
>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=79.11 E-value=4.7 Score=38.54 Aligned_cols=33 Identities=18% Similarity=0.212 Sum_probs=28.0
Q ss_pred CCCCCCeEEEEeCCCCCceEEEEEEeCCCcEEE
Q psy13744 243 MPQPNDKVKVIVGEHKECTGVLLSVDNGEGVVK 275 (296)
Q Consensus 243 iP~kGd~VkVI~Ge~RG~tG~LisID~~dgiVk 275 (296)
...+||.|+|+.|.+.|..|+++.+|.+..-|+
T Consensus 205 ~f~vGd~VrI~dGPF~GfeG~I~eid~~k~Rv~ 237 (258)
T TIGR01956 205 KFRVGNFVKIVDGPFKGIVGKIKKIDQEKKKAI 237 (258)
T ss_pred CCCCCCEEEEEecCCCCcEEEEEEEeCCCCEEE
Confidence 356899999999999999999999986555444
No 43
>PF04717 Phage_base_V: Phage-related baseplate assembly protein; InterPro: IPR006531 This domain occurs in a family of phage (and bacteriocin) proteins related to the phage P2 V gene product, which forms the small spike at the tip of the tail []. Homologs in general are annotated as baseplate assembly protein V. At least one member is encoded within a region of Pectobacterium carotovorum (Erwinia carotovora) described as a bacteriocin, a phage tail-derived module able to kill bacteria closely related to the host strain. It is also found in Vgr-related proteins. Genes encoding type VI secretion systems (T6SS) are widely distributed in pathogenic Gram-negative bacterial species. In Vibrio cholerae, T6SS have been found to secrete three related proteins extracellularly, VgrG-1, VgrG-2, and VgrG-3. VgrG-1 can covalently cross-link actin in vitro, and this activity was used to demonstrate that V. cholerae can translocate VgrG-1 into macrophages by a T6SS-dependent mechanism. VgrG-related proteins likely assemble into a trimeric complex that is analogous to that formed by the two trimeric proteins gp27 and gp5 that make up the baseplate "tail spike" of Escherichia coli bacteriophage T4. The VgrG components of the T6SS apparatus might assemble a "cell-puncturing device" analogous to phage tail spikes to deliver effector protein domains through membranes of target host cells []. Gp5 is an integral component of the virion baseplate of bacteriophage T4. T4 Gp5 consists of 3 domains connected via long linkers: the N-terminal oligosaccharide/oligonucleotide-binding (OB)-fold domain, the middle lysozyme domain, and the C-terminal triplestranded-helix. The equivalent of the Gp5 OB-fold domain in the structure of VgrG is the domain of unknown function comprising residues 380-470 and conserved in all known VgrGs. This entry represents the OB-fold domain which consists of a 5-stranded antiparallel-barrel with a Greek-key topology [].; PDB: 3AQJ_C 3QR8_A 2P5Z_X.
Probab=77.94 E-value=4.7 Score=30.66 Aligned_cols=44 Identities=16% Similarity=0.243 Sum_probs=21.6
Q ss_pred EEEEEec--CCeEEEEeCCCCeeee----eeCC---ce-eEcCCCCCCeEEEEe
Q psy13744 211 GVIRHLG--SGVCSVYLAEEERTLS----IEAH---EL-EPVMPQPNDKVKVIV 254 (296)
Q Consensus 211 GVVrsV~--~g~c~V~L~d~~~vv~----V~q~---~L-EtViP~kGd~VkVI~ 254 (296)
|+|.+|. +++|+|+|.+.+..++ +-+. .. .-..|.+|+.|+|+.
T Consensus 1 G~V~~v~~~~grvrV~~~~~~~~~s~Wl~~~~~~ag~~g~~~~P~iGeqV~v~~ 54 (79)
T PF04717_consen 1 GTVTAVDPDKGRVRVRFPDDGDIVSDWLPVLQPRAGGWGFWFPPEIGEQVLVLF 54 (79)
T ss_dssp EEEEEEETTTTEEEEE-B-CTTEEEEEEEE--S-BSSSB------TT-EEEEEE
T ss_pred CeEEEEECCCCEEEEEEecCCCccceEEEeeehhccCCeeEccCCCCcEEEEEc
Confidence 6788886 3789999844333322 2221 12 234688999999987
No 44
>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=77.49 E-value=5.2 Score=31.15 Aligned_cols=49 Identities=22% Similarity=0.268 Sum_probs=33.9
Q ss_pred CCCCeEEEEe----CCCCCceEEEEEEeCCCcEEEEcCC--CceeEeecchhhcc
Q psy13744 245 QPNDKVKVIV----GEHKECTGVLLSVDNGEGVVKLTEE--DDVKMIDVKFLCKY 293 (296)
Q Consensus 245 ~kGd~VkVI~----Ge~RG~tG~LisID~~dgiVkld~~--~d~kil~~~~L~Kl 293 (296)
.+|..|+|.. +..+..+|.|+++|++.-++..+.. .....|++++|.|.
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 3588888843 3345679999999998776666421 22445899998875
No 45
>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=75.01 E-value=9.4 Score=26.73 Aligned_cols=42 Identities=14% Similarity=0.266 Sum_probs=33.1
Q ss_pred CCccccCCeEEEEEecC-CeEEEEeCCCCeeeeeeCCceeEcCCC
Q psy13744 202 RDPEFRGQIGVIRHLGS-GVCSVYLAEEERTLSIEAHELEPVMPQ 245 (296)
Q Consensus 202 ~d~~yygqkGVVrsV~~-g~c~V~L~d~~~vv~V~q~~LEtViP~ 245 (296)
+|+.+| .|.|+++.+ +.|.|.+.|-+....|..++|-+..+.
T Consensus 14 ~d~~wy--ra~I~~~~~~~~~~V~f~D~G~~~~v~~~~l~~l~~~ 56 (57)
T smart00333 14 EDGEWY--RARIIKVDGEQLYEVFFIDYGNEEVVPPSDLRPLPEE 56 (57)
T ss_pred CCCCEE--EEEEEEECCCCEEEEEEECCCccEEEeHHHeecCCCC
Confidence 345555 479999986 889999998788889999988876553
No 46
>CHL00010 infA translation initiation factor 1
Probab=74.54 E-value=33 Score=26.71 Aligned_cols=58 Identities=19% Similarity=0.197 Sum_probs=32.8
Q ss_pred CeEEEEEec-CCeEEEEeCCCCee-eeeeCCce-eEcCCCCCCeEEEEeCCCCCceEEEEE
Q psy13744 209 QIGVIRHLG-SGVCSVYLAEEERT-LSIEAHEL-EPVMPQPNDKVKVIVGEHKECTGVLLS 266 (296)
Q Consensus 209 qkGVVrsV~-~g~c~V~L~d~~~v-v~V~q~~L-EtViP~kGd~VkVI~Ge~RG~tG~Lis 266 (296)
.+|+|.++. ++.+.|++.++... ..+....- ..+.|..||+|.|--=.+-...|.++-
T Consensus 9 ~~G~Vik~lg~~~y~V~~~~g~~~~c~~rGklr~~~i~~~vGD~V~ve~~~~~~~~g~Ii~ 69 (78)
T CHL00010 9 MEGLVTESLPNGMFRVRLDNGCQVLGYISGKIRRNSIRILPGDRVKVELSPYDLTKGRIIY 69 (78)
T ss_pred EEEEEEEEcCCCEEEEEeCCCCEEEEEeccceecCCcccCCCCEEEEEEcccCCCeEEEEE
Confidence 468899888 58888887544322 22222211 256688899987753222233444443
No 47
>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=74.25 E-value=26 Score=25.54 Aligned_cols=56 Identities=21% Similarity=0.194 Sum_probs=38.8
Q ss_pred eEEEEEecCCeEEEEeCCCCeeeeeeCCceeEc-------CCCCCCeEEEEeCCCCCceEEEEEEeCCCcEEEE
Q psy13744 210 IGVIRHLGSGVCSVYLAEEERTLSIEAHELEPV-------MPQPNDKVKVIVGEHKECTGVLLSVDNGEGVVKL 276 (296)
Q Consensus 210 kGVVrsV~~g~c~V~L~d~~~vv~V~q~~LEtV-------iP~kGd~VkVI~Ge~RG~tG~LisID~~dgiVkl 276 (296)
.|+|.+|.+.-|-|.|. .+..--|+.++|..- .-.+|++|.| +++++|.+.+.+.|
T Consensus 9 ~g~V~~v~~~g~~V~l~-~~~~g~ip~~~l~~~~~~~~~~~~~~G~~v~v----------~v~~vd~~~~~i~l 71 (74)
T PF00575_consen 9 EGKVTSVEDFGVFVDLG-NGIEGFIPISELSDDRIDDPSEVYKIGQTVRV----------KVIKVDKEKGRIRL 71 (74)
T ss_dssp EEEEEEEETTEEEEEES-TSSEEEEEGGGSSSSEESSSHGTCETTCEEEE----------EEEEEETTTTEEEE
T ss_pred EEEEEEEECCEEEEEEC-CcEEEEEEeehhcCccccccccccCCCCEEEE----------EEEEEECCCCeEEE
Confidence 68899998888889988 454555666666642 2234666554 57888888887765
No 48
>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=73.57 E-value=15 Score=24.96 Aligned_cols=56 Identities=23% Similarity=0.205 Sum_probs=29.8
Q ss_pred eEEEEEecCCeEEEEeCCCCeeeeeeCCceeE--c-----CCCCCCeEEEEeCCCCCceEEEEEEeCCCcEEEE
Q psy13744 210 IGVIRHLGSGVCSVYLAEEERTLSIEAHELEP--V-----MPQPNDKVKVIVGEHKECTGVLLSVDNGEGVVKL 276 (296)
Q Consensus 210 kGVVrsV~~g~c~V~L~d~~~vv~V~q~~LEt--V-----iP~kGd~VkVI~Ge~RG~tG~LisID~~dgiVkl 276 (296)
.|+|++|.+..+.|.|... ..--++.++|.- + .-+.||.| .++++++|.+++.+.|
T Consensus 2 ~g~V~~v~~~g~~v~l~~~-~~g~~~~~~~~~~~~~~~~~~~~~G~~v----------~~~v~~~d~~~~~i~l 64 (65)
T cd00164 2 TGKVVSITKFGVFVELEDG-VEGLVHISELSDKFVKDPSEVFKVGDEV----------EVKVLEVDPEKGRISL 64 (65)
T ss_pred EEEEEEEEeeeEEEEecCC-CEEEEEHHHCCCccccCHhhEeCCCCEE----------EEEEEEEcCCcCEEec
Confidence 4677777766666776633 223333333321 0 11334444 4467777777666654
No 49
>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=73.17 E-value=22 Score=32.54 Aligned_cols=43 Identities=16% Similarity=0.001 Sum_probs=29.7
Q ss_pred eEEEEEecCCeEEEEeCCCCeeeeeeCCceeEcCCCCCCeEEEEe
Q psy13744 210 IGVIRHLGSGVCSVYLAEEERTLSIEAHELEPVMPQPNDKVKVIV 254 (296)
Q Consensus 210 kGVVrsV~~g~c~V~L~d~~~vv~V~q~~LEtViP~kGd~VkVI~ 254 (296)
.|.|..+.++.|.|...+.. +.+-...==.+.|..||+|+|..
T Consensus 3 ~g~V~~~~~~~~~v~~~~G~--~~arrAaSCLl~P~~GD~VLv~~ 45 (202)
T PF12059_consen 3 SGTVVGREGDGLVVVDDDGE--WRARRAASCLLEPAVGDTVLVSG 45 (202)
T ss_pred eEEEEEEeCCeEEEEcCCCE--EEEEeccccccCCCCCCEEEEee
Confidence 57788887776766665443 44444444457899999999976
No 50
>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=72.10 E-value=5.2 Score=25.89 Aligned_cols=27 Identities=26% Similarity=0.448 Sum_probs=19.7
Q ss_pred EEEEecCCCCccccCCeEEEEEecCCeEEEE
Q psy13744 194 EVRINENARDPEFRGQIGVIRHLGSGVCSVY 224 (296)
Q Consensus 194 ~VkI~~~~~d~~yygqkGVVrsV~~g~c~V~ 224 (296)
.|+|++ ++|.|+.|+|.+|......|.
T Consensus 4 ~V~V~~----G~~~G~~G~I~~i~~~~~~V~ 30 (32)
T PF00467_consen 4 TVKVIS----GPFKGKIGKIVEIDRSKVRVT 30 (32)
T ss_dssp EEEESS----STTTTEEEEEEEEETTTTEEE
T ss_pred EEEEeE----cCCCCceEEEEEEECCCCEEE
Confidence 577874 578899999999975444443
No 51
>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=71.75 E-value=27 Score=25.29 Aligned_cols=57 Identities=16% Similarity=0.179 Sum_probs=29.5
Q ss_pred eEEEEEecCCeEEEEeCCCCeeeeeeCCceeEc-------CCCCCCeEEEEeCCCCCceEEEEEEeCCCcEEEE
Q psy13744 210 IGVIRHLGSGVCSVYLAEEERTLSIEAHELEPV-------MPQPNDKVKVIVGEHKECTGVLLSVDNGEGVVKL 276 (296)
Q Consensus 210 kGVVrsV~~g~c~V~L~d~~~vv~V~q~~LEtV-------iP~kGd~VkVI~Ge~RG~tG~LisID~~dgiVkl 276 (296)
.|.|.+|.+.-+-|.|.+.+..--+..++|..- .-+.||.|+| +++++|.+.+-+.+
T Consensus 7 ~g~V~~i~~~g~~v~l~~~~~~g~i~~~~l~~~~~~~~~~~~~~Gd~v~v----------~i~~vd~~~~~i~l 70 (77)
T cd05708 7 DGTVRRVEDYGVFIDIDGTNVSGLCHKSEISDNRVADASKLFRVGDKVRA----------KVLKIDAEKKRISL 70 (77)
T ss_pred EEEEEEEEcceEEEEECCCCeEEEEEHHHCCCCccCCHhHeecCCCEEEE----------EEEEEeCCCCEEEE
Confidence 466666665555566653222223333333210 1155666665 57788877665544
No 52
>PF14563 DUF4444: Domain of unknown function (DUF4444); PDB: 3BFM_A.
Probab=70.50 E-value=8.2 Score=27.37 Aligned_cols=33 Identities=30% Similarity=0.509 Sum_probs=21.9
Q ss_pred CCCceEEEEEEeCCCcEEEEcCCCceeEeecchh
Q psy13744 257 HKECTGVLLSVDNGEGVVKLTEEDDVKMIDVKFL 290 (296)
Q Consensus 257 ~RG~tG~LisID~~dgiVkld~~~d~kil~~~~L 290 (296)
.+|.+|+.+++|++=|.+ |.++.+-++|++.+|
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 444556888998876
No 53
>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=70.14 E-value=20 Score=25.07 Aligned_cols=53 Identities=13% Similarity=0.018 Sum_probs=36.5
Q ss_pred CCCCCCeEEEEeCCCCCceEEEEEEeC-CCcEEEEcCCCceeEeecchhhccCC
Q psy13744 243 MPQPNDKVKVIVGEHKECTGVLLSVDN-GEGVVKLTEEDDVKMIDVKFLCKYKP 295 (296)
Q Consensus 243 iP~kGd~VkVI~Ge~RG~tG~LisID~-~dgiVkld~~~d~kil~~~~L~Kl~~ 295 (296)
.++.|+.|++..-+.+=.+|++++++. ....|.+.+-.....++.++|..|..
T Consensus 2 ~~~~G~~~~a~~~d~~wyra~I~~~~~~~~~~V~f~D~G~~~~v~~~~l~~l~~ 55 (57)
T smart00333 2 TFKVGDKVAARWEDGEWYRARIIKVDGEQLYEVFFIDYGNEEVVPPSDLRPLPE 55 (57)
T ss_pred CCCCCCEEEEEeCCCCEEEEEEEEECCCCEEEEEEECCCccEEEeHHHeecCCC
Confidence 467899999986222347899999988 55667754422355788888877643
No 54
>PRK04333 50S ribosomal protein L14e; Validated
Probab=69.91 E-value=11 Score=30.11 Aligned_cols=45 Identities=13% Similarity=0.130 Sum_probs=31.1
Q ss_pred CCCCeEEEEeCCCCCceEEEEEEeCCCcEEEEcCC----CceeEeecchh
Q psy13744 245 QPNDKVKVIVGEHKECTGVLLSVDNGEGVVKLTEE----DDVKMIDVKFL 290 (296)
Q Consensus 245 ~kGd~VkVI~Ge~RG~tG~LisID~~dgiVkld~~----~d~kil~~~~L 290 (296)
+.|.-|+++.|.|.|..+.++.|-.++.++ +|.. ..-+..++.+|
T Consensus 5 ~~GrvV~~~~Grd~gk~~vIv~i~d~~~vl-Vdg~~~~~~~rk~kn~khl 53 (84)
T PRK04333 5 EVGRVCVKTAGREAGRKCVIVDIIDKNFVL-VTGPSLTGVKRRRCNIKHL 53 (84)
T ss_pred cccEEEEEeccCCCCCEEEEEEEecCCEEE-EECCCcCCCCCeeechHHE
Confidence 358899999999999999999995454444 4543 22344555554
No 55
>PRK06531 yajC preprotein translocase subunit YajC; Validated
Probab=69.17 E-value=12 Score=31.49 Aligned_cols=29 Identities=31% Similarity=0.354 Sum_probs=23.6
Q ss_pred CCCCeEEEEeCCCCCceEEEEEEeCCCcEEEEc
Q psy13744 245 QPNDKVKVIVGEHKECTGVLLSVDNGEGVVKLT 277 (296)
Q Consensus 245 ~kGd~VkVI~Ge~RG~tG~LisID~~dgiVkld 277 (296)
++||+|+-+.| ..|++..||.++..|.|+
T Consensus 38 k~GD~VvT~GG----i~G~V~~I~~~~~~v~le 66 (113)
T PRK06531 38 QKGDEVVTIGG----LYGTVDEVDTEAKTIVLD 66 (113)
T ss_pred CCCCEEEECCC----cEEEEEEEecCCCEEEEE
Confidence 47999988875 889999999877767665
No 56
>cd05685 S1_Tex S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin expression. Tex has two functional domains, an N-terminal domain homologous to the Escherichia coli maltose repression protein, which is a poorly defined transcriptional factor, and a C-terminal S1 RNA-binding domain. Tex is found in prokaryotes, eukaryotes, and archaea.
Probab=68.24 E-value=30 Score=24.18 Aligned_cols=23 Identities=30% Similarity=0.476 Sum_probs=15.5
Q ss_pred CCCCCeEEEEeCCCCCceEEEEEEeCCCcEEEE
Q psy13744 244 PQPNDKVKVIVGEHKECTGVLLSVDNGEGVVKL 276 (296)
Q Consensus 244 P~kGd~VkVI~Ge~RG~tG~LisID~~dgiVkl 276 (296)
.+.||+|+| +++++|.+++.|.|
T Consensus 45 ~~~Gd~v~v----------~i~~vd~~~~~i~l 67 (68)
T cd05685 45 VSVGDIVEV----------KVISIDEERGRISL 67 (68)
T ss_pred cCCCCEEEE----------EEEEEECCCCEEec
Confidence 466777776 46777877666543
No 57
>PRK14639 hypothetical protein; Provisional
Probab=67.88 E-value=14 Score=31.83 Aligned_cols=49 Identities=20% Similarity=0.268 Sum_probs=35.7
Q ss_pred CCCCeEEEEeCCCCCceEEEEEEeCCCcEEEEcCCCceeEeecchhhcc
Q psy13744 245 QPNDKVKVIVGEHKECTGVLLSVDNGEGVVKLTEEDDVKMIDVKFLCKY 293 (296)
Q Consensus 245 ~kGd~VkVI~Ge~RG~tG~LisID~~dgiVkld~~~d~kil~~~~L~Kl 293 (296)
.+|.+|+|-...-+-.+|+|+++|++...+...++.....|+++++.|.
T Consensus 86 ~~G~~v~v~l~~~~~~~G~L~~~~~~~i~l~~~~~~~~~~i~~~~I~ka 134 (140)
T PRK14639 86 SIGELVKITTNEKEKFEGKIVSVDDENITLENLENKEKTTINFNDIKKA 134 (140)
T ss_pred hCCCEEEEEECCCcEEEEEEEEEeCCEEEEEEccCCcEEEEEhHHeeeE
Confidence 4699999976557889999999998766664322222345899998875
No 58
>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=67.35 E-value=47 Score=24.33 Aligned_cols=44 Identities=23% Similarity=0.261 Sum_probs=25.3
Q ss_pred eEEEEEec-CCeEEEEeCCCCeeeeeeCCce--eEcCCCCCCeEEEE
Q psy13744 210 IGVIRHLG-SGVCSVYLAEEERTLSIEAHEL--EPVMPQPNDKVKVI 253 (296)
Q Consensus 210 kGVVrsV~-~g~c~V~L~d~~~vv~V~q~~L--EtViP~kGd~VkVI 253 (296)
+|+|.+.. ++.+.|++.++....-..-..| .-+.|..||+|.+-
T Consensus 4 ~G~Vi~~~~g~~~~V~~~~g~~~~c~~rGklr~~~~~~~vGD~V~~~ 50 (64)
T cd04451 4 EGVVTEALPNAMFRVELENGHEVLAHISGKMRMNYIRILPGDRVKVE 50 (64)
T ss_pred EEEEEEEeCCCEEEEEeCCCCEEEEEECceeecCCcccCCCCEEEEE
Confidence 56777776 4777777644332222222223 34457889999775
No 59
>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=67.22 E-value=46 Score=24.22 Aligned_cols=57 Identities=21% Similarity=0.161 Sum_probs=32.5
Q ss_pred eEEEEEecCCeEEEEeCCC-CeeeeeeCCceeEcCC-------CCCCeEEEEeCCCCCceEEEEEEeCCCcEEEE
Q psy13744 210 IGVIRHLGSGVCSVYLAEE-ERTLSIEAHELEPVMP-------QPNDKVKVIVGEHKECTGVLLSVDNGEGVVKL 276 (296)
Q Consensus 210 kGVVrsV~~g~c~V~L~d~-~~vv~V~q~~LEtViP-------~kGd~VkVI~Ge~RG~tG~LisID~~dgiVkl 276 (296)
+|+|.+|.+.-|-|.|.+. +..-.|..++|..=.- +.||.|+| +++++|...+-+.|
T Consensus 8 ~g~V~~v~~~g~~v~l~~~~~~~gll~~s~l~~~~~~~~~~~~~~Gd~v~v----------kv~~~d~~~~~i~l 72 (76)
T cd04452 8 VVTVKSIADMGAYVSLLEYGNIEGMILLSELSRRRIRSIRKLVKVGRKEVV----------KVIRVDKEKGYIDL 72 (76)
T ss_pred EEEEEEEEccEEEEEEcCCCCeEEEEEhHHcCCcccCCHHHeeCCCCEEEE----------EEEEEECCCCEEEE
Confidence 6788888877788888642 2333444444432110 34555554 56777776654443
No 60
>KOG1708|consensus
Probab=66.83 E-value=6.7 Score=36.60 Aligned_cols=30 Identities=37% Similarity=0.398 Sum_probs=23.9
Q ss_pred CCCeEEEEeCCCCCceEEEEEE--eCCCcEEE
Q psy13744 246 PNDKVKVIVGEHKECTGVLLSV--DNGEGVVK 275 (296)
Q Consensus 246 kGd~VkVI~Ge~RG~tG~LisI--D~~dgiVk 275 (296)
.||.|.||.|++.|..|++..| +.+.-||+
T Consensus 75 ~GDtVeVlvGkDkGkqG~Vtqv~r~~s~VvV~ 106 (236)
T KOG1708|consen 75 FGDTVEVLVGKDKGKQGEVTQVIRHRSWVVVK 106 (236)
T ss_pred cCCEEEEEecccCCccceEEEEeecCceEEEc
Confidence 4999999999999999999888 44444543
No 61
>cd05697 S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 5 (hs5) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=66.51 E-value=37 Score=24.60 Aligned_cols=56 Identities=27% Similarity=0.240 Sum_probs=31.0
Q ss_pred eEEEEEecCCeEEEEeCCCCeeeeeeCCceeE--c-----CCCCCCeEEEEeCCCCCceEEEEEEeCCCcEEEE
Q psy13744 210 IGVIRHLGSGVCSVYLAEEERTLSIEAHELEP--V-----MPQPNDKVKVIVGEHKECTGVLLSVDNGEGVVKL 276 (296)
Q Consensus 210 kGVVrsV~~g~c~V~L~d~~~vv~V~q~~LEt--V-----iP~kGd~VkVI~Ge~RG~tG~LisID~~dgiVkl 276 (296)
+|.|++|.+.-|.|.|.+. ..--|+.++|.- + .=++||++++ +++++|.++..+.|
T Consensus 5 ~g~V~~v~~~Gv~V~l~~~-v~g~i~~~~l~~~~~~~~~~~~~~Gd~i~~----------~V~~id~~~~~i~l 67 (69)
T cd05697 5 KGTIRKLRPSGIFVKLSDH-IKGLVPPMHLADVRLKHPEKKFKPGLKVKC----------RVLSVEPERKRLVL 67 (69)
T ss_pred EEEEEEEeccEEEEEecCC-cEEEEEHHHCCCccccCHHHcCCCCCEEEE----------EEEEEECCCCEEEE
Confidence 4667777766666776543 333344333321 1 1233565555 67788887776654
No 62
>PF01957 NfeD: NfeD-like C-terminal, partner-binding; InterPro: IPR002810 The nfe genes (nfeA, nfeB, and nfeD) are involved in the nodulation efficiency and competitiveness of Rhizobium meliloti (Sinorhizobium meliloti) (Rhizobium meliloti) on alfalfa roots []. The specific function of this family is unknown although it is unlikely that NfeD is specifically involved in nodulation as the family contains several different archaeal and bacterial species most of which are not symbionts. This entry describes archaeal and bacterial proteins which are variously described, examples are: nodulation protein, nodulation efficiency protein D (nfeD), hypothetical protein and membrane-bound serine protease (ClpP class). A number of these proteins are classified in MEROPS peptidase family S49 as non-peptidase homologues or as unassigned peptidases. ; PDB: 2K5H_A 3CP0_A 2EXD_A.
Probab=66.35 E-value=22 Score=29.03 Aligned_cols=45 Identities=16% Similarity=0.213 Sum_probs=28.2
Q ss_pred ccccCCeEEE-EEecCCeEEEEeCCCCeeeeeeCCceeEcCCCCCCeEEEEe
Q psy13744 204 PEFRGQIGVI-RHLGSGVCSVYLAEEERTLSIEAHELEPVMPQPNDKVKVIV 254 (296)
Q Consensus 204 ~~yygqkGVV-rsV~~g~c~V~L~d~~~vv~V~q~~LEtViP~kGd~VkVI~ 254 (296)
..+.|++|+| ....++..+|++.. +.-++..++= =++|++|+|+.
T Consensus 87 ~~liG~~g~v~~~~~~~~G~V~~~G--~~w~A~s~~~----i~~G~~V~Vv~ 132 (144)
T PF01957_consen 87 DDLIGKEGTVIEIPLNGSGRVKVDG--ERWRARSEDE----IPKGDRVRVVG 132 (144)
T ss_dssp GGGTTSEEEEEEEBSSS-EEEEETT--EEEEEEESST----B-TT-EEEEEE
T ss_pred HHHcCCeEEEEEeecCCcEEEEECC--eEEEEEeCCC----CCCCCEEEEEE
Confidence 5689999999 44457888888863 3444332221 34699999986
No 63
>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=66.32 E-value=38 Score=23.76 Aligned_cols=55 Identities=20% Similarity=0.238 Sum_probs=29.1
Q ss_pred eEEEEEecCCeEEEEeCCCCeeeeeeCCceeE--c-CC----CCCCeEEEEeCCCCCceEEEEEEeCCCcEEEE
Q psy13744 210 IGVIRHLGSGVCSVYLAEEERTLSIEAHELEP--V-MP----QPNDKVKVIVGEHKECTGVLLSVDNGEGVVKL 276 (296)
Q Consensus 210 kGVVrsV~~g~c~V~L~d~~~vv~V~q~~LEt--V-iP----~kGd~VkVI~Ge~RG~tG~LisID~~dgiVkl 276 (296)
+|+|.+|.+..+-|.|.. ..-.+..++|.. + .+ +.||+|+| +++++|.+++.+.|
T Consensus 6 ~g~V~~v~~~g~~v~l~~--~~g~l~~~e~~~~~~~~~~~~~~~Gd~v~v----------~i~~vd~~~~~i~l 67 (68)
T cd05688 6 EGTVKSITDFGAFVDLGG--VDGLLHISDMSWGRVKHPSEVVNVGDEVEV----------KVLKIDKERKRISL 67 (68)
T ss_pred EEEEEEEEeeeEEEEECC--eEEEEEhHHCCCccccCHhHEECCCCEEEE----------EEEEEECCCCEEec
Confidence 567777776556666652 223333333321 1 11 44565555 46777776665543
No 64
>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=66.21 E-value=34 Score=23.72 Aligned_cols=58 Identities=10% Similarity=0.153 Sum_probs=29.9
Q ss_pred eEEEEEecCCeEEEEeCCCCeeeeeeCCceeE--cCCCCCCeEEEEe-C--CCCCceEEEEEE
Q psy13744 210 IGVIRHLGSGVCSVYLAEEERTLSIEAHELEP--VMPQPNDKVKVIV-G--EHKECTGVLLSV 267 (296)
Q Consensus 210 kGVVrsV~~g~c~V~L~d~~~vv~V~q~~LEt--ViP~kGd~VkVI~-G--e~RG~tG~LisI 267 (296)
+|+|+...++.+-|.-.+.+..+-|..+.|+. --...||+|.+-- - ...+..|.++.|
T Consensus 1 ~G~i~~~~~g~gfv~~~~~~~~i~v~~~~~~~~~~~~~~Gd~V~~~i~~~~~~~~~~a~~v~~ 63 (64)
T smart00357 1 TGVVKWFNKGFGFIRPDDGGKDVFVHPSQIQGGLKSLREGDEVEFKVVSPRGGGKPEAENVVK 63 (64)
T ss_pred CeEEEEEcCCeeEEecCCCCccEEEEhHHhhcCCCcCCCCCEEEEEEEEccCCCCcEEEEEEe
Confidence 35566555555544433332355666666433 1234599998842 2 234456665543
No 65
>COG1532 Predicted RNA-binding protein [General function prediction only]
Probab=65.88 E-value=19 Score=27.00 Aligned_cols=52 Identities=23% Similarity=0.340 Sum_probs=34.1
Q ss_pred EEEEeCCCCeeeeeeCCceeEcCCCCCCeEEE--EeCCCCCceEEEEEEeCCCcEEEE
Q psy13744 221 CSVYLAEEERTLSIEAHELEPVMPQPNDKVKV--IVGEHKECTGVLLSVDNGEGVVKL 276 (296)
Q Consensus 221 c~V~L~d~~~vv~V~q~~LEtViP~kGd~VkV--I~Ge~RG~tG~LisID~~dgiVkl 276 (296)
|+-.|..+++++.=|.=.|| .+++.|+. |.|+++...|++..||-++-.|-|
T Consensus 2 Ce~nly~~GelimEDV~~ie----v~~e~V~a~Dilgd~ke~~G~vkriDldehkI~l 55 (57)
T COG1532 2 CEFNLYLGGELIMEDVLYIE----VTEEGVVARDILGDEKEFEGQVKRIDLDEHKIEL 55 (57)
T ss_pred ceEEEEECCEEEEeEEEEEE----EecCcEEEEeccCCceEecceEEEEEccccEEEe
Confidence 43333333555544433333 35788877 559999999999999988776654
No 66
>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=65.13 E-value=42 Score=40.33 Aligned_cols=89 Identities=8% Similarity=0.086 Sum_probs=61.0
Q ss_pred cccCceEEEEecCCCCccccCCeEEEEEecC--CeEEEEeCCCCeeeeeeCCcee-----------EcCC-CCCCeEEEE
Q psy13744 188 WHTTDIEVRINENARDPEFRGQIGVIRHLGS--GVCSVYLAEEERTLSIEAHELE-----------PVMP-QPNDKVKVI 253 (296)
Q Consensus 188 Wl~~dI~VkI~~~~~d~~yygqkGVVrsV~~--g~c~V~L~d~~~vv~V~q~~LE-----------tViP-~kGd~VkVI 253 (296)
.+.+|-+|+.- ++..+.+..++|.+|.. +.+.|.. +.++.+.++.++|. -+++ .+||++++.
T Consensus 681 ~Yr~Gdvv~~y---~~~~~~~~~y~V~~V~~~~n~L~l~~-~dG~~~~~~p~~l~~~~~~~svy~~~~l~ia~Gdrl~~t 756 (1960)
T TIGR02760 681 HYKQGMVIRFW---QKGKIPHDDYVVTNVNKHNNTLTLKD-AQGKTQKFKPSSLKDLERPFSVYRPEQLEVAAGERLQVT 756 (1960)
T ss_pred hcCCCCEEEee---cccCccCCcEEEEEEeCCCCEEEEEc-CCCCEEEECHHHhcccccceeeeccccccccCCCEEEEc
Confidence 46778777663 33456666789999974 5555544 35677788887772 2244 369999997
Q ss_pred eCC-----CCCceEEEEEEeCCCcEEEEcCCC
Q psy13744 254 VGE-----HKECTGVLLSVDNGEGVVKLTEED 280 (296)
Q Consensus 254 ~Ge-----~RG~tG~LisID~~dgiVkld~~~ 280 (296)
.-. -+|...++.+|+...-.|+.+++.
T Consensus 757 rn~~~~gl~ng~~~tV~~i~~~~i~l~~~~g~ 788 (1960)
T TIGR02760 757 GNHFHSRVRNGELLTVSSINNEGITLITEDGQ 788 (1960)
T ss_pred cCCcccCccCCCEEEEEEEcCCeEEEEeCCCc
Confidence 743 488999999999987777765443
No 67
>cd05684 S1_DHX8_helicase S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH (Asp-Glu-Ala-His) box polypeptide. The DEAH-box RNA helicases are thought to play key roles in pre-mRNA splicing and DHX8 facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. DHX8 is also known as HRH1 (human RNA helicase 1) in Homo sapiens and PRP22 in Saccharomyces cerevisiae.
Probab=64.43 E-value=44 Score=24.93 Aligned_cols=31 Identities=16% Similarity=0.136 Sum_probs=16.7
Q ss_pred eEEEEEecCCeEEEEeCCC--CeeeeeeCCcee
Q psy13744 210 IGVIRHLGSGVCSVYLAEE--ERTLSIEAHELE 240 (296)
Q Consensus 210 kGVVrsV~~g~c~V~L~d~--~~vv~V~q~~LE 240 (296)
+|.|.+|.+.-|-|.|.+. +..--+..++|+
T Consensus 5 ~g~V~~v~~~G~fv~l~~~~~~~~gll~~s~l~ 37 (79)
T cd05684 5 KGKVTSIMDFGCFVQLEGLKGRKEGLVHISQLS 37 (79)
T ss_pred EEEEEEEEeeeEEEEEeCCCCCcEEEEEhHhcc
Confidence 5677777765566666532 223334444443
No 68
>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=63.41 E-value=49 Score=24.52 Aligned_cols=17 Identities=12% Similarity=0.014 Sum_probs=11.5
Q ss_pred eEEEEEecCCeEEEEeC
Q psy13744 210 IGVIRHLGSGVCSVYLA 226 (296)
Q Consensus 210 kGVVrsV~~g~c~V~L~ 226 (296)
+|.|.+|.+.-|-|.|.
T Consensus 8 ~g~V~~i~~fG~fv~l~ 24 (73)
T cd05686 8 KGEVASVTEYGAFVKIP 24 (73)
T ss_pred EEEEEEEEeeeEEEEEC
Confidence 56777777655666664
No 69
>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=63.38 E-value=2.4 Score=33.37 Aligned_cols=36 Identities=22% Similarity=0.479 Sum_probs=0.0
Q ss_pred CCCCeEEEEeCCCCCceEEEEEEeCCCcEEEEcCCCceeE
Q psy13744 245 QPNDKVKVIVGEHKECTGVLLSVDNGEGVVKLTEEDDVKM 284 (296)
Q Consensus 245 ~kGd~VkVI~Ge~RG~tG~LisID~~dgiVkld~~~d~ki 284 (296)
++||+|+-..| ..|+++++|++..+|+++++..+++
T Consensus 38 k~Gd~VvT~gG----i~G~V~~i~~~~v~lei~~g~~i~v 73 (82)
T PF02699_consen 38 KPGDEVVTIGG----IYGTVVEIDDDTVVLEIAPGVEITV 73 (82)
T ss_dssp ----------------------------------------
T ss_pred CCCCEEEECCc----EEEEEEEEeCCEEEEEECCCeEEEE
Confidence 46999999886 8899999988888888876544443
No 70
>cd05707 S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 11 (sc11). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=63.22 E-value=41 Score=24.28 Aligned_cols=56 Identities=18% Similarity=0.261 Sum_probs=30.3
Q ss_pred eEEEEEecCCeEEEEeCCCCeeeeeeCCcee--EcC-----CCCCCeEEEEeCCCCCceEEEEEEeCCCcEEEE
Q psy13744 210 IGVIRHLGSGVCSVYLAEEERTLSIEAHELE--PVM-----PQPNDKVKVIVGEHKECTGVLLSVDNGEGVVKL 276 (296)
Q Consensus 210 kGVVrsV~~g~c~V~L~d~~~vv~V~q~~LE--tVi-----P~kGd~VkVI~Ge~RG~tG~LisID~~dgiVkl 276 (296)
.|.|++|.+.-+-|.|.+. ..--|..++|. .+. =+.||.|++ +++++|.+.+-|.|
T Consensus 5 ~g~V~~v~~~Gv~V~l~~~-~~G~v~~s~l~~~~~~~~~~~~~~Gd~v~~----------~v~~~d~~~~~i~l 67 (68)
T cd05707 5 RGFVKNIANNGVFVTLGRG-VDARVRVSELSDSYLKDWKKRFKVGQLVKG----------KIVSIDPDNGRIEM 67 (68)
T ss_pred EEEEEEEECccEEEEeCCC-CEEEEEHHHCCchhhcCHhhccCCCCEEEE----------EEEEEeCCCCEEec
Confidence 5677787766677777643 23333333331 111 134555554 66777776665543
No 71
>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=63.20 E-value=17 Score=27.65 Aligned_cols=35 Identities=26% Similarity=0.352 Sum_probs=26.1
Q ss_pred CCCCCeEEEEeCC--CCCceEEEEEEeCCC----cEEEEcC
Q psy13744 244 PQPNDKVKVIVGE--HKECTGVLLSVDNGE----GVVKLTE 278 (296)
Q Consensus 244 P~kGd~VkVI~Ge--~RG~tG~LisID~~d----giVkld~ 278 (296)
+++|++|+|+.=| +--.+|++.+||.+. -+||++.
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 4689999999976 578899999999874 3777764
No 72
>PRK05886 yajC preprotein translocase subunit YajC; Validated
Probab=63.06 E-value=16 Score=30.69 Aligned_cols=35 Identities=14% Similarity=0.284 Sum_probs=25.7
Q ss_pred CCCCeEEEEeCCCCCceEEEEEEeCCCcEEEEcCCCcee
Q psy13744 245 QPNDKVKVIVGEHKECTGVLLSVDNGEGVVKLTEEDDVK 283 (296)
Q Consensus 245 ~kGd~VkVI~Ge~RG~tG~LisID~~dgiVkld~~~d~k 283 (296)
++||+|+-+.| ..|++++|+++..+|++..+-.++
T Consensus 40 k~GD~VvT~gG----i~G~V~~I~d~~v~leia~gv~i~ 74 (109)
T PRK05886 40 QPGDRVHTTSG----LQATIVGITDDTVDLEIAPGVVTT 74 (109)
T ss_pred CCCCEEEECCC----eEEEEEEEeCCEEEEEECCCeEEE
Confidence 46999988876 889999998776666665443343
No 73
>cd05691 S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 6 (ec6) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=62.95 E-value=51 Score=23.66 Aligned_cols=56 Identities=21% Similarity=0.240 Sum_probs=29.5
Q ss_pred eEEEEEecCCeEEEEeCCCCeeeeeeCCceeE--cC-----CCCCCeEEEEeCCCCCceEEEEEEeCCCcEEEE
Q psy13744 210 IGVIRHLGSGVCSVYLAEEERTLSIEAHELEP--VM-----PQPNDKVKVIVGEHKECTGVLLSVDNGEGVVKL 276 (296)
Q Consensus 210 kGVVrsV~~g~c~V~L~d~~~vv~V~q~~LEt--Vi-----P~kGd~VkVI~Ge~RG~tG~LisID~~dgiVkl 276 (296)
.|.|++|.+..+.|.|.+. ..-.+..++|.. +. =++||.|++ +++++|.....+.|
T Consensus 5 ~g~V~~v~~~g~~v~l~~~-~~g~i~~~~~~~~~~~~~~~~~~~Gd~v~~----------~v~~~d~~~~~i~l 67 (73)
T cd05691 5 TGKVTEVDAKGATVKLGDG-VEGFLRAAELSRDRVEDATERFKVGDEVEA----------KITNVDRKNRKISL 67 (73)
T ss_pred EEEEEEEECCeEEEEeCCC-CEEEEEHHHCCCccccCHHHccCCCCEEEE----------EEEEEeCCCCEEEE
Confidence 4667777666666666543 222233333321 10 134555554 57788887666554
No 74
>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=62.78 E-value=17 Score=24.99 Aligned_cols=28 Identities=11% Similarity=0.144 Sum_probs=23.4
Q ss_pred CeEEEEEecCCeEEEEeCCCCeeeeeeCC
Q psy13744 209 QIGVIRHLGSGVCSVYLAEEERTLSIEAH 237 (296)
Q Consensus 209 qkGVVrsV~~g~c~V~L~d~~~vv~V~q~ 237 (296)
.+|.|++..++.|.|++.+ ++.++|..+
T Consensus 14 v~g~I~~~~g~~vtV~~~~-G~~~tv~~d 41 (42)
T PF02736_consen 14 VKGEIIEEEGDKVTVKTED-GKEVTVKKD 41 (42)
T ss_dssp EEEEEEEEESSEEEEEETT-TEEEEEEGG
T ss_pred EEEEEEEEcCCEEEEEECC-CCEEEeCCC
Confidence 4788888889999999998 778888765
No 75
>cd05689 S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (ec4) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=62.73 E-value=45 Score=24.19 Aligned_cols=18 Identities=33% Similarity=0.429 Sum_probs=11.7
Q ss_pred eEEEEEecCCeEEEEeCC
Q psy13744 210 IGVIRHLGSGVCSVYLAE 227 (296)
Q Consensus 210 kGVVrsV~~g~c~V~L~d 227 (296)
+|.|++|.+.-+-|.|.+
T Consensus 8 ~g~V~~i~~~G~fv~l~~ 25 (72)
T cd05689 8 FGKVTNLTDYGCFVELEE 25 (72)
T ss_pred EEEEEEEEeeEEEEEcCC
Confidence 567777766556666654
No 76
>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=61.22 E-value=21 Score=30.29 Aligned_cols=50 Identities=16% Similarity=0.190 Sum_probs=37.5
Q ss_pred CcccCceEEEEecCCCCccccCCeEEEEEecC-CeEEEEe--CCCCeeeeeeCCcee
Q psy13744 187 EWHTTDIEVRINENARDPEFRGQIGVIRHLGS-GVCSVYL--AEEERTLSIEAHELE 240 (296)
Q Consensus 187 ~Wl~~dI~VkI~~~~~d~~yygqkGVVrsV~~-g~c~V~L--~d~~~vv~V~q~~LE 240 (296)
..+.+|=.|+|++ +-|.|..|+|.++.+ ..+.|.| ......++|+.++||
T Consensus 107 ~~~~~G~~V~V~~----GPf~g~~g~v~~~~~~~r~~v~l~~~gr~~~v~~~~~~~~ 159 (159)
T TIGR01955 107 TLPYKGDKVRITD----GAFAGFEAIFLEPDGEKRSMLLLNMIGKQIKVSVPNTSVE 159 (159)
T ss_pred cCCCCCCEEEEec----cCCCCcEEEEEEECCCceEEEEEhhhCCceEEEecHHHcC
Confidence 4678898999984 567899999999974 5555554 444566888888876
No 77
>PF09038 53-BP1_Tudor: Tumour suppressor p53-binding protein-1 Tudor; InterPro: IPR015125 This domain consist of ten beta-strands and a carboxy-terminal alpha-helix. The amino-terminal five beta-strands and the C-terminal five beta-strands adopt folds that are identical to each other. The domain is essential for the recruitment of proteins to double stranded breaks in DNA, which is mediated by interaction with methylated Lys 79 of histone H3 []. ; PDB: 3LGL_A 1XNI_B 3LGF_A 2G3R_A 2IG0_A 3LH0_A 1SSF_A.
Probab=60.91 E-value=1.1e+02 Score=26.38 Aligned_cols=83 Identities=12% Similarity=0.173 Sum_probs=59.2
Q ss_pred EEEEecCCeEEEEeCCCCeeeeeeCCceeEcCCC-CCCeEEEEeCCCCCceEEEEEE--eCCC--cEEEEcCCCce----
Q psy13744 212 VIRHLGSGVCSVYLAEEERTLSIEAHELEPVMPQ-PNDKVKVIVGEHKECTGVLLSV--DNGE--GVVKLTEEDDV---- 282 (296)
Q Consensus 212 VVrsV~~g~c~V~L~d~~~vv~V~q~~LEtViP~-kGd~VkVI~Ge~RG~tG~LisI--D~~d--giVkld~~~d~---- 282 (296)
|+++..++.|.|.+.|.. .-+|-+++|-.+.|. .+..|.-+..++-...|.++.. |.++ .+|++| +...
T Consensus 24 I~~~~~~~kykv~FdDG~-~~~v~~~div~~dplpl~~eV~A~~eddY~~~GvV~~h~~~~~e~yY~Ve~d-G~~~~~~r 101 (122)
T PF09038_consen 24 ITSDKGKNKYKVLFDDGY-ECRVLGKDIVVCDPLPLGTEVTALSEDDYFSPGVVKGHKTDSGEVYYCVETD-GQRKRYQR 101 (122)
T ss_dssp EEEEETTTEEEEEETTS--EEEEECCCEEEESSS-TTEEEEECCTTCTSEEEEEEEEEEETTEEEEEEEET-TEEEEEEG
T ss_pred EeecCCCCeEEEEecCCc-cceeccCcEEEEcceeccceeEEeecCCcccccEEEEEEccCCcEEEEEEEC-CCEEEEEe
Confidence 455666899999988654 457888888888776 4888999888888889998887 4333 367777 3221
Q ss_pred --eEeecchhhccCCC
Q psy13744 283 --KMIDVKFLCKYKPE 296 (296)
Q Consensus 283 --kil~~~~L~Kl~~~ 296 (296)
.||..+.-|+|..|
T Consensus 102 ~~viLs~~Q~~~Lre~ 117 (122)
T PF09038_consen 102 KDVILSADQANRLREQ 117 (122)
T ss_dssp GGEEEEHHHHHCCCCC
T ss_pred eeEEEcHHHHHHHHHh
Confidence 24788888887643
No 78
>PF15057 DUF4537: Domain of unknown function (DUF4537)
Probab=60.75 E-value=58 Score=27.40 Aligned_cols=91 Identities=14% Similarity=0.148 Sum_probs=52.0
Q ss_pred cCCCCccccCCeEEEEEec-CCeEEEEeCCCCeeeeeeCCceeEcCC------CCCCeEEEEeC--CCCCceEEEEE---
Q psy13744 199 ENARDPEFRGQIGVIRHLG-SGVCSVYLAEEERTLSIEAHELEPVMP------QPNDKVKVIVG--EHKECTGVLLS--- 266 (296)
Q Consensus 199 ~~~~d~~yygqkGVVrsV~-~g~c~V~L~d~~~vv~V~q~~LEtViP------~kGd~VkVI~G--e~RG~tG~Lis--- 266 (296)
+...|+-|| .|+|++.. .+...|.+. .+++..|..+++=.+-. +.||+|+...= .++=.=|+++.
T Consensus 7 R~~~DG~YY--~GtV~~~~~~~~~lV~f~-~~~~~~v~~~~iI~~~~~~~~~L~~GD~VLA~~~~~~~~Y~Pg~V~~~~~ 83 (124)
T PF15057_consen 7 RREEDGFYY--PGTVKKCVSSGQFLVEFD-DGDTQEVPISDIIALSDAMRHSLQVGDKVLAPWEPDDCRYGPGTVIAGPE 83 (124)
T ss_pred eeCCCCcEE--eEEEEEccCCCEEEEEEC-CCCEEEeChHHeEEccCcccCcCCCCCEEEEecCcCCCEEeCEEEEECcc
Confidence 455666554 58888885 466678874 34444455544433322 25999999852 23323388885
Q ss_pred --E-eCCCcEEEEcCCCceeEeecchhhcc
Q psy13744 267 --V-DNGEGVVKLTEEDDVKMIDVKFLCKY 293 (296)
Q Consensus 267 --I-D~~dgiVkld~~~d~kil~~~~L~Kl 293 (296)
. +...-.|++-++. ...++.+.+.||
T Consensus 84 ~~~~~~~~~~V~f~ng~-~~~vp~~~~~~I 112 (124)
T PF15057_consen 84 RRASEDKEYTVRFYNGK-TAKVPRGEVIWI 112 (124)
T ss_pred ccccCCceEEEEEECCC-CCccchhhEEEC
Confidence 2 4445567664443 233565555555
No 79
>PRK14638 hypothetical protein; Provisional
Probab=60.25 E-value=22 Score=30.99 Aligned_cols=47 Identities=15% Similarity=0.150 Sum_probs=33.3
Q ss_pred CCCCeEEEEeCCCCCceEEEEEEeCCCcEEEEcCCCceeEeecchhhcc
Q psy13744 245 QPNDKVKVIVGEHKECTGVLLSVDNGEGVVKLTEEDDVKMIDVKFLCKY 293 (296)
Q Consensus 245 ~kGd~VkVI~Ge~RG~tG~LisID~~dgiVkld~~~d~kil~~~~L~Kl 293 (296)
.+|.+|+|-....+-.+|+|.++|++.-.+.. +.....|++++|.|.
T Consensus 98 ~~G~~v~V~~~~~k~~~G~L~~~~~~~i~l~~--~~~~~~i~~~~I~~a 144 (150)
T PRK14638 98 FTGKLAKIVTKDGKTFIGRIESFVDGTITISD--EKEKYEINIDDVKRA 144 (150)
T ss_pred hCCCEEEEEECCCcEEEEEEEEEeCCEEEEEE--CCcEEEEEhHHcceE
Confidence 35999999654468899999999875544432 223455899998875
No 80
>COG1585 Membrane protein implicated in regulation of membrane protease activity [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=60.21 E-value=24 Score=30.45 Aligned_cols=45 Identities=22% Similarity=0.374 Sum_probs=32.7
Q ss_pred CccccCCeEEEEE-ecCCeEEEEeCCCCeeeeeeC-CceeEcCCCCCCeEEEEe
Q psy13744 203 DPEFRGQIGVIRH-LGSGVCSVYLAEEERTLSIEA-HELEPVMPQPNDKVKVIV 254 (296)
Q Consensus 203 d~~yygqkGVVrs-V~~g~c~V~L~d~~~vv~V~q-~~LEtViP~kGd~VkVI~ 254 (296)
+.++.|++|+|.+ +.++...|+++++ .=++.. ++|. +||+|+|+.
T Consensus 83 ~~~l~G~~g~v~e~i~~g~g~Vkv~g~--~Wra~~~~~l~-----~G~~V~Vv~ 129 (140)
T COG1585 83 GEQLVGRRGVVVEDIVEGRGRVKVEGE--SWRARSDEDLP-----AGDRVEVVG 129 (140)
T ss_pred hhHhcCcEEEEEeeccCCeEEEEECCe--EeEEecCCCCC-----CCCEEEEEE
Confidence 3467899999998 4679999999754 344444 3343 899999986
No 81
>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=59.43 E-value=50 Score=23.57 Aligned_cols=55 Identities=16% Similarity=0.195 Sum_probs=30.7
Q ss_pred eEEEEEecCCeEEEEeCCCCeeeeeeCCcee-Ec-C--C----CCCCeEEEEeCCCCCceEEEEEEeCCCcEEE
Q psy13744 210 IGVIRHLGSGVCSVYLAEEERTLSIEAHELE-PV-M--P----QPNDKVKVIVGEHKECTGVLLSVDNGEGVVK 275 (296)
Q Consensus 210 kGVVrsV~~g~c~V~L~d~~~vv~V~q~~LE-tV-i--P----~kGd~VkVI~Ge~RG~tG~LisID~~dgiVk 275 (296)
+|.|++|.+.-+-|.|.+. ..--|..++|. .. . + +.||+|+| ++++||.+..-+.
T Consensus 5 ~g~V~~i~~~G~fv~l~~~-~~Glv~~~~l~~~~~~~~~~~~~~~G~~v~v----------~v~~id~~~~~i~ 67 (69)
T cd05690 5 SGKIKSITDFGIFVGLDGG-IDGLVHISDISWTQRVRHPSEIYKKGQEVEA----------VVLNIDVERERIS 67 (69)
T ss_pred EEEEEEEEeeeEEEEeCCC-CEEEEEHHHCCCccccCChhhEECCCCEEEE----------EEEEEECCcCEEe
Confidence 5778888765566777543 23334555554 11 1 1 34555555 4777777665544
No 82
>PF08863 YolD: YolD-like protein; InterPro: IPR014962 These proteins are functionally uncharacterised. However it has been predicted that these proteins are functionally equivalent to the UmuD subunit of polymerase V from Gram-negative bacteria [].
Probab=59.39 E-value=24 Score=27.00 Aligned_cols=40 Identities=18% Similarity=0.274 Sum_probs=33.4
Q ss_pred eCCCCCceEEEEEEeCCCcEEEEcC-CCceeEeecchhhcc
Q psy13744 254 VGEHKECTGVLLSVDNGEGVVKLTE-EDDVKMIDVKFLCKY 293 (296)
Q Consensus 254 ~Ge~RG~tG~LisID~~dgiVkld~-~~d~kil~~~~L~Kl 293 (296)
+|.+.-.+|++..||...-.+++.+ +.+...|++++|+.+
T Consensus 52 ~g~~~~~~G~I~~id~~~~~l~~~~~~~~~~~I~~~~I~~I 92 (92)
T PF08863_consen 52 DGYYQSVTGTIHKIDEINRTLKLKDEDGETEKIPFDDIIDI 92 (92)
T ss_pred CCeeEEEEEEEEEEcCCCCEEEEEeCCCCEEEEEhhhEEEC
Confidence 3888999999999999999999865 456778999998753
No 83
>COG1588 POP4 RNase P/RNase MRP subunit p29 [Translation, ribosomal structure and biogenesis]
Probab=59.15 E-value=51 Score=27.25 Aligned_cols=33 Identities=18% Similarity=0.321 Sum_probs=22.1
Q ss_pred CceEEEEecCCCCccccCCeEEEEEecCCeEEEE
Q psy13744 191 TDIEVRINENARDPEFRGQIGVIRHLGSGVCSVY 224 (296)
Q Consensus 191 ~dI~VkI~~~~~d~~yygqkGVVrsV~~g~c~V~ 224 (296)
.+++|+|+++ .+..|.|-+|-|.+=..++..|.
T Consensus 16 iGl~vrVv~s-~~~s~vGI~G~VVdETkNtLvi~ 48 (95)
T COG1588 16 IGLEVRVVRS-TNPSYVGIEGRVVDETKNTLVID 48 (95)
T ss_pred cCcEEEEEec-CCCCccceeEEEEeeeccEEEEE
Confidence 3999999853 34578888888876554444333
No 84
>cd04466 S1_YloQ_GTPase S1_YloQ_GTPase: YloQ GTase family (also known as YjeQ and CpgA), S1-like RNA-binding domain. Proteins in the YloQ GTase family bind the ribosome and have GTPase activity. The precise role of this family is unknown. The protein structure is composed of three domains: an N-terminal S1 domain, a central GTPase domain, and a C-terminal zinc finger domain. This N-terminal S1 domain binds ssRNA. The central GTPase domain contains nucleotide-binding signature motifs: G1 (walker A), G3 (walker B) and G4 motifs. Experiments show that the bacterial YloQ and YjeQ proteins have low intrinsic GTPase activity. The C-terminal zinc-finger domain has structural similarity to a portion of the DNA-repair protein Rad51. This suggests a possible role for this GTPase as a regulator of translation, perhaps as a translation initiation factor. This family is classified based on the N-terminal S1 domain.
Probab=59.09 E-value=64 Score=23.16 Aligned_cols=44 Identities=16% Similarity=0.130 Sum_probs=23.6
Q ss_pred eEEEEEecCCeEEEEeCCCC-eeeeeeCCce-eEcCCCCCCeEEEE
Q psy13744 210 IGVIRHLGSGVCSVYLAEEE-RTLSIEAHEL-EPVMPQPNDKVKVI 253 (296)
Q Consensus 210 kGVVrsV~~g~c~V~L~d~~-~vv~V~q~~L-EtViP~kGd~VkVI 253 (296)
.|.|.++..+.+.|...+++ ....+..... +...|..||+|.+-
T Consensus 2 ~grVv~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~VGD~V~~~ 47 (68)
T cd04466 2 EGLIIKAIGGFYYVETEDGKIYECRLRGKFRKDKNPPAVGDRVEFE 47 (68)
T ss_pred CEEEEEEECCEEEEEeCCCeEEEEEEccccccCCCCCCCCcEEEEE
Confidence 45666666666666654222 2222222211 23568889999773
No 85
>PRK00276 infA translation initiation factor IF-1; Validated
Probab=58.53 E-value=79 Score=24.00 Aligned_cols=44 Identities=20% Similarity=0.166 Sum_probs=25.3
Q ss_pred eEEEEEecC-CeEEEEeCCCCee-eeeeCCce-eEcCCCCCCeEEEE
Q psy13744 210 IGVIRHLGS-GVCSVYLAEEERT-LSIEAHEL-EPVMPQPNDKVKVI 253 (296)
Q Consensus 210 kGVVrsV~~-g~c~V~L~d~~~v-v~V~q~~L-EtViP~kGd~VkVI 253 (296)
+|+|.++.. +.+.|.+.+.... ..+....= .-+.|..||.|.|-
T Consensus 10 ~G~Vi~~~~~~~y~V~~~~g~~~~c~~~Gklr~~~i~i~vGD~V~ve 56 (72)
T PRK00276 10 EGTVVEALPNAMFRVELENGHEVLAHISGKMRKNYIRILPGDKVTVE 56 (72)
T ss_pred EEEEEEEcCCCEEEEEeCCCCEEEEEEccceeeCCcccCCCCEEEEE
Confidence 578888764 4888877543222 22222111 13447888888775
No 86
>PRK04950 ProP expression regulator; Provisional
Probab=58.42 E-value=23 Score=33.03 Aligned_cols=44 Identities=18% Similarity=0.259 Sum_probs=36.4
Q ss_pred CCCCeEEEEeCCCCCceEEEEEEeCCCcEEEEcCCCceeEeecchh
Q psy13744 245 QPNDKVKVIVGEHKECTGVLLSVDNGEGVVKLTEEDDVKMIDVKFL 290 (296)
Q Consensus 245 ~kGd~VkVI~Ge~RG~tG~LisID~~dgiVkld~~~d~kil~~~~L 290 (296)
++|..|+|..|+. =.-|+++.|..+|--|+|+++..++ +..|+|
T Consensus 168 ~~gq~v~vk~g~~-~~~a~i~ei~kd~v~vql~~Gl~~~-v~ae~l 211 (213)
T PRK04950 168 TVGQAVKVKAGKS-AMDATVLEITKDDVRVQLDSGLSMI-VRAEHL 211 (213)
T ss_pred ccCCEEEEeccCC-CCceEEEEEecCcEEEEcCCCcEEE-EeHhhh
Confidence 4699999999954 6889999999999999999987554 565555
No 87
>PRK14637 hypothetical protein; Provisional
Probab=58.14 E-value=28 Score=30.49 Aligned_cols=46 Identities=17% Similarity=0.056 Sum_probs=32.3
Q ss_pred CCCeEEEEeCCCCCc-eEEEEEEeCCCcEEEEcCCCceeEeecchhhcc
Q psy13744 246 PNDKVKVIVGEHKEC-TGVLLSVDNGEGVVKLTEEDDVKMIDVKFLCKY 293 (296)
Q Consensus 246 kGd~VkVI~Ge~RG~-tG~LisID~~dgiVkld~~~d~kil~~~~L~Kl 293 (296)
+|.+|+|.....+.. +|+|+++|++.-++..+ + ....|++++|.|.
T Consensus 97 ~G~~V~V~l~~~~~~~~G~L~~~~d~~v~l~~~-~-~~~~i~~~~I~ka 143 (151)
T PRK14637 97 VGETVKVWFECTGQWQVGTIAEADETCLVLTSD-G-VPVTIPYVQITKA 143 (151)
T ss_pred CCCEEEEEECCCCcEEEEEEEEEeCCEEEEEEC-C-EEEEEEHHHeeeE
Confidence 489999965223456 69999998876655543 2 3455899998875
No 88
>PRK14630 hypothetical protein; Provisional
Probab=57.56 E-value=26 Score=30.33 Aligned_cols=46 Identities=13% Similarity=0.085 Sum_probs=32.5
Q ss_pred CCCCeEEEEeCCCCCceEEEEEEeCCCcEEEEcCCCceeEeecchhhcc
Q psy13744 245 QPNDKVKVIVGEHKECTGVLLSVDNGEGVVKLTEEDDVKMIDVKFLCKY 293 (296)
Q Consensus 245 ~kGd~VkVI~Ge~RG~tG~LisID~~dgiVkld~~~d~kil~~~~L~Kl 293 (296)
.+|.+|+|...+-. .+|+|+++|++.-.+.++ .....|+++++.|.
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 35899999654433 389999998766666553 23456899998875
No 89
>PRK03879 ribonuclease P protein component 1; Validated
Probab=56.81 E-value=88 Score=25.49 Aligned_cols=69 Identities=16% Similarity=0.230 Sum_probs=38.4
Q ss_pred ceEEEEecCCCCccccCCeEEEEEecCCeEEEEeCCCCeeeeeeCCceeEcCCCCCCeEEEEeCCCCCceEEEEEEeCCC
Q psy13744 192 DIEVRINENARDPEFRGQIGVIRHLGSGVCSVYLAEEERTLSIEAHELEPVMPQPNDKVKVIVGEHKECTGVLLSVDNGE 271 (296)
Q Consensus 192 dI~VkI~~~~~d~~yygqkGVVrsV~~g~c~V~L~d~~~vv~V~q~~LEtViP~kGd~VkVI~Ge~RG~tG~LisID~~d 271 (296)
|..|+|.++ .+..|.|.+|+|..=...+..|. .+++ +-++|+.+-...+-.. ...++.+.|+++.
T Consensus 15 Gl~v~Vv~S-~npslvGi~GiVv~ETknt~~I~--~~~~---------~~~VPK~~~iF~f~~~---~~~~~~v~I~G~~ 79 (96)
T PRK03879 15 GLKVEVVDS-TNPSLVGIKGRVVDETRNTLVIE--TDGK---------EWMVPKDGATFEFELG---RDDVVKVKVDGRL 79 (96)
T ss_pred CCEEEEEEc-CCCCcccceEEEEEeceeEEEEE--cCCc---------EEEEeCCCeEEEEEEc---CCCCeEEEEECce
Confidence 778888753 34678899998877555555554 2233 3345666655555431 1123445555554
Q ss_pred cEEE
Q psy13744 272 GVVK 275 (296)
Q Consensus 272 giVk 275 (296)
.+.|
T Consensus 80 l~~R 83 (96)
T PRK03879 80 LVGR 83 (96)
T ss_pred eecC
Confidence 4443
No 90
>PF07290 DUF1449: Protein of unknown function (DUF1449); InterPro: IPR010840 This family consists of several bacterial proteins of around 210 residues in length. The function of this family is unknown.
Probab=56.44 E-value=25 Score=32.27 Aligned_cols=49 Identities=6% Similarity=0.104 Sum_probs=36.4
Q ss_pred ccccCCeEEEEEec---CCeEEEEeCCC---CeeeeeeCCceeEcCCCCCCeEEEEe
Q psy13744 204 PEFRGQIGVIRHLG---SGVCSVYLAEE---ERTLSIEAHELEPVMPQPNDKVKVIV 254 (296)
Q Consensus 204 ~~yygqkGVVrsV~---~g~c~V~L~d~---~~vv~V~q~~LEtViP~kGd~VkVI~ 254 (296)
.+|-|+.|+|..-. +.-|++++.|. .+.|+|..+ +.+..++|++|+||.
T Consensus 134 ~~LiGr~a~Vt~g~a~~g~~aqa~V~D~~Gq~hyv~veP~--~~~~~~~G~~VLlv~ 188 (202)
T PF07290_consen 134 DDLIGRVATVTSGTARQGSPAQARVKDQFGQLHYVMVEPE--AGEEFKQGTEVLLVD 188 (202)
T ss_pred hhcCcceEEEEecccCCCCceEEEEEecCCCEEEEEEeeC--CCCCCCCCCEEEEEE
Confidence 46889999998732 34667776552 356777765 777889999999995
No 91
>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=55.10 E-value=34 Score=29.48 Aligned_cols=50 Identities=18% Similarity=0.256 Sum_probs=38.3
Q ss_pred CcccCceEEEEecCCCCccccCCeEEEEEec-C-CeEEEE--eCCCCeeeeeeCCcee
Q psy13744 187 EWHTTDIEVRINENARDPEFRGQIGVIRHLG-S-GVCSVY--LAEEERTLSIEAHELE 240 (296)
Q Consensus 187 ~Wl~~dI~VkI~~~~~d~~yygqkGVVrsV~-~-g~c~V~--L~d~~~vv~V~q~~LE 240 (296)
..+.+|=.|+|++ +.|.|..|+|+++. + +.+.|. +......++|+.++||
T Consensus 118 ~~~~~G~~V~I~~----Gpf~G~~g~v~~~~~~~~r~~V~v~~~g~~~~v~v~~~~l~ 171 (172)
T TIGR00922 118 IDFEVGEQVRVND----GPFANFTGTVEEVDYEKSKLKVSVSIFGRETPVELEFSQVE 171 (172)
T ss_pred cCCCCCCEEEEee----cCCCCcEEEEEEEcCCCCEEEEEEEECCCceEEEEcHHHee
Confidence 4578898999984 57889999999997 3 566555 4555677888888886
No 92
>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=54.36 E-value=54 Score=25.02 Aligned_cols=44 Identities=16% Similarity=0.305 Sum_probs=30.9
Q ss_pred CeEEEEEecCCeEEEEeCCCCeeeeeeCCc-eeEcCCCCCCeEEEEeC
Q psy13744 209 QIGVIRHLGSGVCSVYLAEEERTLSIEAHE-LEPVMPQPNDKVKVIVG 255 (296)
Q Consensus 209 qkGVVrsV~~g~c~V~L~d~~~vv~V~q~~-LEtViP~kGd~VkVI~G 255 (296)
-+|+|++|...+.+|.|.|.+ ..+++.+. |+-+ +.|.+|+|..=
T Consensus 5 veG~I~~id~~~~titLdDGk-sy~lp~ef~~~~L--~~G~kV~V~yd 49 (61)
T PF07076_consen 5 VEGTIKSIDPETMTITLDDGK-SYKLPEEFDFDGL--KPGMKVVVFYD 49 (61)
T ss_pred ceEEEEEEcCCceEEEecCCC-EEECCCccccccc--CCCCEEEEEEE
Confidence 579999999888999998754 44444432 3333 35899999864
No 93
>COG0779 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=54.36 E-value=26 Score=30.96 Aligned_cols=46 Identities=22% Similarity=0.274 Sum_probs=35.8
Q ss_pred CCCeEEEEe----CCCCCceEEEEEEeCCCcEEEEcCCCceeEeecchhhcc
Q psy13744 246 PNDKVKVIV----GEHKECTGVLLSVDNGEGVVKLTEEDDVKMIDVKFLCKY 293 (296)
Q Consensus 246 kGd~VkVI~----Ge~RG~tG~LisID~~dgiVkld~~~d~kil~~~~L~Kl 293 (296)
+|..|+|.. ..-+-..|+|+.+|+++-++.++. .+ ..|+|..++|-
T Consensus 98 ~G~~Vkv~l~~~~~~~k~~~G~i~~~d~~~v~~~~~~-k~-v~Ip~~~i~kA 147 (153)
T COG0779 98 IGEKVKVKLRLPIEGRKKFEGKIVAVDGETVTLEVDG-KE-VEIPFSDIAKA 147 (153)
T ss_pred cCcEEEEEEecccCCceEEEEEEEEEcCCeEEEEECC-EE-EEEEcccchhh
Confidence 499999977 446778999999999997776543 33 55899998875
No 94
>CHL00125 psaE photosystem I subunit IV; Reviewed
Probab=54.10 E-value=20 Score=27.49 Aligned_cols=34 Identities=21% Similarity=0.358 Sum_probs=26.9
Q ss_pred CCCCeEEEEeCC--CCCceEEEEEEeCCC----cEEEEcC
Q psy13744 245 QPNDKVKVIVGE--HKECTGVLLSVDNGE----GVVKLTE 278 (296)
Q Consensus 245 ~kGd~VkVI~Ge--~RG~tG~LisID~~d----giVkld~ 278 (296)
++|++|+|+.=| +--.+|++.+||.+. -+||+|.
T Consensus 3 ~rGskVrIlR~ESYWyn~vGtV~svd~~gi~YPV~VRF~k 42 (64)
T CHL00125 3 KRGSKVRILRKESYWYNEIGTVATVDQSGIRYPVLVRFEK 42 (64)
T ss_pred ccCCEEEEccccceeecCcceEEEEcCCCCCccEEEEEee
Confidence 579999999976 567899999999872 2677654
No 95
>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=53.96 E-value=13 Score=25.03 Aligned_cols=35 Identities=17% Similarity=0.257 Sum_probs=26.1
Q ss_pred CccccCCeEEEEEec-CCeEEEEeCCCCeeeeeeCCce
Q psy13744 203 DPEFRGQIGVIRHLG-SGVCSVYLAEEERTLSIEAHEL 239 (296)
Q Consensus 203 d~~yygqkGVVrsV~-~g~c~V~L~d~~~vv~V~q~~L 239 (296)
|+++| .|+|+++. +..|.|.+.|-+....|+.++|
T Consensus 11 d~~wy--ra~V~~~~~~~~~~V~f~DyG~~~~v~~~~l 46 (48)
T cd04508 11 DGKWY--RAKITSILSDGKVEVFFVDYGNTEVVPLSDL 46 (48)
T ss_pred CCeEE--EEEEEEECCCCcEEEEEEcCCCcEEEeHHHc
Confidence 45555 48899997 7889999988666666776655
No 96
>PRK09014 rfaH transcriptional activator RfaH; Provisional
Probab=53.61 E-value=34 Score=29.29 Aligned_cols=50 Identities=14% Similarity=0.167 Sum_probs=37.7
Q ss_pred cccCceEEEEecCCCCccccCCeEEEEEecC-CeEEEEe--CCCCeeeeeeCCceeE
Q psy13744 188 WHTTDIEVRINENARDPEFRGQIGVIRHLGS-GVCSVYL--AEEERTLSIEAHELEP 241 (296)
Q Consensus 188 Wl~~dI~VkI~~~~~d~~yygqkGVVrsV~~-g~c~V~L--~d~~~vv~V~q~~LEt 241 (296)
.+..|=.|+|++ +-|.|..|+|.++.+ ..+.|.| ..-...++|+.++||.
T Consensus 109 ~~~~G~~V~I~~----Gp~~g~eg~v~~~~~~~r~~v~v~~~gr~~~v~v~~~~~~~ 161 (162)
T PRK09014 109 TPKPGDKVIITE----GAFEGLQAIYTEPDGEARSILLLNLLNKQVKHSVDNTQFRK 161 (162)
T ss_pred CCCCCCEEEEec----CCCCCcEEEEEEeCCCeEEEEeehhhCCcEEEEECHHHeec
Confidence 467888899984 568899999999974 4554444 4456788888888874
No 97
>TIGR01644 phage_P2_V phage baseplate assembly protein V. This model describes a family of phage (and bacteriocin) proteins related to the phage P2 V gene product, which forms the small spike at the tip of the tail. Homologs in general are annotated as baseplate assembly protein V. At least one member is encoded within a region of Pectobacterium carotovorum (Erwinia carotovora) described as a bacteriocin, a phage tail-derived module able to kill bacteria closely related to the host strain.
Probab=53.19 E-value=53 Score=29.09 Aligned_cols=46 Identities=20% Similarity=0.247 Sum_probs=31.5
Q ss_pred CeEEEEEecC--CeEEEEeCCC-Ceeeeee----CCceeEcCCCCCCeEEEEe
Q psy13744 209 QIGVIRHLGS--GVCSVYLAEE-ERTLSIE----AHELEPVMPQPNDKVKVIV 254 (296)
Q Consensus 209 qkGVVrsV~~--g~c~V~L~d~-~~vv~V~----q~~LEtViP~kGd~VkVI~ 254 (296)
+.|+|.+|.+ ..|+|...+. ..-+.+. +++=....|.+|+.|+||.
T Consensus 10 r~G~V~~vd~~~~~vrv~~~~~~t~wl~~~~~~ag~~~~~~~P~vGeqv~vl~ 62 (191)
T TIGR01644 10 RRGVVAEVDDAAARVRVLQGELLTGWLPWDVERAGNYRHWSAPSPGEQVVVLS 62 (191)
T ss_pred EEEEEEEEcCCCCcEEEecCCccccchhhhhHhhCCCceEcCCCCCCEEEEEc
Confidence 5799999974 4788876542 1222222 4444678999999999987
No 98
>cd04472 S1_PNPase S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA. It is a trimeric multidomain protein. The C-terminus contains the S1 domain which binds ssRNA. This family is classified based on the S1 domain. PNPase nonspecifically removes the 3' nucleotides from mRNA, but is stalled by double-stranded RNA structures such as a stem-loop. Evidence shows that a minimum of 7-10 unpaired nucleotides at the 3' end, is required for PNPase degradation. It is suggested that PNPase also dephosphorylates the RNA 5' end. This additional activity may regulate the 5'-dependent activity of RNaseE in vivo.
Probab=52.74 E-value=75 Score=22.28 Aligned_cols=18 Identities=11% Similarity=-0.051 Sum_probs=10.8
Q ss_pred eEEEEEecCCeEEEEeCC
Q psy13744 210 IGVIRHLGSGVCSVYLAE 227 (296)
Q Consensus 210 kGVVrsV~~g~c~V~L~d 227 (296)
+|.|.+|.+.-|-|.|.+
T Consensus 5 ~g~V~~v~~~G~~v~l~~ 22 (68)
T cd04472 5 EGKVVKIKDFGAFVEILP 22 (68)
T ss_pred EEEEEEEEEeEEEEEeCC
Confidence 466666665556666653
No 99
>PRK02749 photosystem I reaction center subunit IV; Provisional
Probab=52.65 E-value=20 Score=28.02 Aligned_cols=33 Identities=27% Similarity=0.409 Sum_probs=26.4
Q ss_pred CCCCeEEEEeCC--CCCceEEEEEEeCCC----cEEEEc
Q psy13744 245 QPNDKVKVIVGE--HKECTGVLLSVDNGE----GVVKLT 277 (296)
Q Consensus 245 ~kGd~VkVI~Ge--~RG~tG~LisID~~d----giVkld 277 (296)
++|++|+|+.=| +-..+|++.+||.+. -+||+|
T Consensus 4 ~rGskVrIlR~ESYWyn~vGtV~svD~sgi~YPV~VRF~ 42 (71)
T PRK02749 4 SRGDKVRILRPESYWYNEVGTVASVDKSGIKYPVIVRFD 42 (71)
T ss_pred ccCCEEEEccccceeecCcceEEEEccCCCeeeEEEEee
Confidence 579999999976 577899999999883 256654
No 100
>PRK00092 ribosome maturation protein RimP; Reviewed
Probab=52.25 E-value=30 Score=29.97 Aligned_cols=49 Identities=22% Similarity=0.287 Sum_probs=34.4
Q ss_pred CCCCeEEEEe----CCCCCceEEEEEEeCCCcEEEEcCCCceeEeecchhhcc
Q psy13744 245 QPNDKVKVIV----GEHKECTGVLLSVDNGEGVVKLTEEDDVKMIDVKFLCKY 293 (296)
Q Consensus 245 ~kGd~VkVI~----Ge~RG~tG~LisID~~dgiVkld~~~d~kil~~~~L~Kl 293 (296)
.+|..|+|.. +.-+-.+|+|+++|.+...+.++.......|+|++|.|.
T Consensus 96 ~~G~~v~V~~~~~~~~~~~~~G~L~~~~~~~i~l~~~~~~~~~~i~~~~I~~a 148 (154)
T PRK00092 96 FIGREVKVKLYEPIDGRKKFQGILLAVDGETVTLEVEGKEKEVEIPLDNIAKA 148 (154)
T ss_pred hCCCeEEEEEEcccCCceEEEEEEEEeeCCEEEEEECCCeEEEEEEHHHcceE
Confidence 4699999963 445667999999998776666543211445899998875
No 101
>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=51.93 E-value=73 Score=22.87 Aligned_cols=56 Identities=23% Similarity=0.221 Sum_probs=30.1
Q ss_pred eEEEEEecCCeEEEEeCCCCeeeeeeCCceeE--cC-----CCCCCeEEEEeCCCCCceEEEEEEeCCCcEEEE
Q psy13744 210 IGVIRHLGSGVCSVYLAEEERTLSIEAHELEP--VM-----PQPNDKVKVIVGEHKECTGVLLSVDNGEGVVKL 276 (296)
Q Consensus 210 kGVVrsV~~g~c~V~L~d~~~vv~V~q~~LEt--Vi-----P~kGd~VkVI~Ge~RG~tG~LisID~~dgiVkl 276 (296)
.|.|++|.+.-+-|.|.+. ..--|+.++|.- +. =+.||.|+| +++++|.+.+.|.|
T Consensus 5 ~g~V~~v~~~G~~V~l~~~-~~gli~~s~l~~~~~~~~~~~~~~G~~i~v----------~v~~~d~~~~~i~l 67 (70)
T cd05698 5 HGTIVKVKPNGCIVSFYNN-VKGFLPKSELSEAFIKDPEEHFRVGQVVKV----------KVLSCDPEQQRLLL 67 (70)
T ss_pred EEEEEEEecCcEEEEECCC-CEEEEEHHHcChhhcCCHHHcccCCCEEEE----------EEEEEcCCCCEEEE
Confidence 5677777766666777543 222333333321 11 123555554 56777777665554
No 102
>PRK14633 hypothetical protein; Provisional
Probab=51.22 E-value=35 Score=29.70 Aligned_cols=47 Identities=23% Similarity=0.301 Sum_probs=33.0
Q ss_pred CCCeEEEEe----CCCCCceEEEEEEeCCCcEEEEcCCCceeEeecchhhcc
Q psy13744 246 PNDKVKVIV----GEHKECTGVLLSVDNGEGVVKLTEEDDVKMIDVKFLCKY 293 (296)
Q Consensus 246 kGd~VkVI~----Ge~RG~tG~LisID~~dgiVkld~~~d~kil~~~~L~Kl 293 (296)
+|.+|+|.. +..+-.+|+|++++++.-.+.+..+. ...|+++++.|.
T Consensus 93 ~G~~v~V~~~~~~~~~~~~~G~L~~v~~~~i~l~~~~~~-~~~i~~~~I~ka 143 (150)
T PRK14633 93 VGFNVKAVTLAPVGSQTKFKGVLERVEGNNVILNLEDGK-EISFDFDELKKL 143 (150)
T ss_pred CCCeEEEEEecccCCcEEEEEEEEEEeCCEEEEEEcCCc-EEEEEhHHeeeE
Confidence 589999954 34677899999997765544443333 345899998875
No 103
>cd04471 S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase play an important role in the degradation of RNA with extensive secondary structure, such as rRNA, tRNA, and certain mRNA which contains repetitive extragenic palindromic sequences. The C-terminal S1 domain binds ssRNA.
Probab=50.98 E-value=74 Score=23.39 Aligned_cols=14 Identities=14% Similarity=0.237 Sum_probs=7.7
Q ss_pred EEEEEeCCCcEEEE
Q psy13744 263 VLLSVDNGEGVVKL 276 (296)
Q Consensus 263 ~LisID~~dgiVkl 276 (296)
+++++|.+.+.+.+
T Consensus 67 ~v~~vd~~~~~i~~ 80 (83)
T cd04471 67 RVVRVDLDRRKIDF 80 (83)
T ss_pred EEEEeccccCEEEE
Confidence 46666665554443
No 104
>COG0250 NusG Transcription antiterminator [Transcription]
Probab=50.56 E-value=60 Score=29.17 Aligned_cols=50 Identities=18% Similarity=0.244 Sum_probs=36.8
Q ss_pred ccCceEEEEecCCCCccccCCeEEEEEecC--CeEEEEeCC--CCeeeeeeCCceeEc
Q psy13744 189 HTTDIEVRINENARDPEFRGQIGVIRHLGS--GVCSVYLAE--EERTLSIEAHELEPV 242 (296)
Q Consensus 189 l~~dI~VkI~~~~~d~~yygqkGVVrsV~~--g~c~V~L~d--~~~vv~V~q~~LEtV 242 (296)
|.+|=.|||++ +-|.+.+|.|.+|+. +..+|.|.. -...++++.+++|-+
T Consensus 124 ~e~Gd~VrI~~----GpFa~f~g~V~evd~ek~~~~v~v~ifgr~tPVel~~~qVek~ 177 (178)
T COG0250 124 FEPGDVVRIID----GPFAGFKAKVEEVDEEKGKLKVEVSIFGRPTPVELEFDQVEKL 177 (178)
T ss_pred CCCCCEEEEec----cCCCCccEEEEEEcCcCcEEEEEEEEeCCceEEEEehhhEEEe
Confidence 56777899984 678999999999974 455555544 345667888888754
No 105
>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed
Probab=50.49 E-value=27 Score=37.92 Aligned_cols=45 Identities=27% Similarity=0.320 Sum_probs=33.3
Q ss_pred CCCCCeEEEEeCCCCCceEEEEEEeC-CCcEEEEcCCCceeE-eecchhhccC
Q psy13744 244 PQPNDKVKVIVGEHKECTGVLLSVDN-GEGVVKLTEEDDVKM-IDVKFLCKYK 294 (296)
Q Consensus 244 P~kGd~VkVI~Ge~RG~tG~LisID~-~dgiVkld~~~d~ki-l~~~~L~Kl~ 294 (296)
.+.||+|+|.. -|+.|++++|+. .+..|++.. +|+ +++++|-++.
T Consensus 637 ~~~Gd~V~v~~---~~~~g~v~~i~~~~~~~V~~g~---~k~~v~~~~l~~~~ 683 (782)
T PRK00409 637 LKVGDEVKYLS---LGQKGEVLSIPDDKEAIVQAGI---MKMKVPLSDLEKIQ 683 (782)
T ss_pred CCCCCEEEEcc---CCceEEEEEEcCCCeEEEEECC---EEEEEeHHHceeCc
Confidence 56899999986 368999999964 466777642 444 8888876653
No 106
>COG2139 RPL21A Ribosomal protein L21E [Translation, ribosomal structure and biogenesis]
Probab=49.43 E-value=18 Score=29.95 Aligned_cols=38 Identities=29% Similarity=0.601 Sum_probs=28.6
Q ss_pred ccccCCeEEEEEecCCeEE--EEeCCCCeeeeeeCCceeE
Q psy13744 204 PEFRGQIGVIRHLGSGVCS--VYLAEEERTLSIEAHELEP 241 (296)
Q Consensus 204 ~~yygqkGVVrsV~~g~c~--V~L~d~~~vv~V~q~~LEt 241 (296)
.+|-|++|+|..+.+.... |++.+-.+.|-|..+||.+
T Consensus 54 ~rf~G~TG~Vvg~~g~ay~V~v~~G~k~K~liv~peHLk~ 93 (98)
T COG2139 54 PRFQGKTGTVVGVRGRAYKVEVYDGNKEKTLIVRPEHLKP 93 (98)
T ss_pred ccccCcceEEEeccCCEEEEEEecCCceEEEEeCHHHccc
Confidence 6789999999999875554 4455556778888888764
No 107
>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=49.31 E-value=89 Score=23.53 Aligned_cols=56 Identities=16% Similarity=0.176 Sum_probs=32.0
Q ss_pred eEEEEEecCCeEEEEeCCCCeeeeeeCCceeEcC---C-------CCCCeEEEEeCCCCCceEEEEEEeCCCcEEEE
Q psy13744 210 IGVIRHLGSGVCSVYLAEEERTLSIEAHELEPVM---P-------QPNDKVKVIVGEHKECTGVLLSVDNGEGVVKL 276 (296)
Q Consensus 210 kGVVrsV~~g~c~V~L~d~~~vv~V~q~~LEtVi---P-------~kGd~VkVI~Ge~RG~tG~LisID~~dgiVkl 276 (296)
.|.|+++.+.-|-|.|.. +..-.|+-.+|.--. | +.|+. ..+++++||.++.-|.|
T Consensus 8 ~g~V~~i~~~G~fV~l~~-~v~G~v~~~~ls~~~~~~~~~~~~~~~~G~~----------v~~kVl~id~~~~~i~L 73 (74)
T cd05705 8 RGYVSSVTKQGVFFRLSS-SIVGRVLFQNVTKYFVSDPSLYNKYLPEGKL----------LTAKVLSVNSEKNLVEL 73 (74)
T ss_pred EEEEEEEeCCcEEEEeCC-CCEEEEEHHHccCccccChhhHhcccCCCCE----------EEEEEEEEECCCCEEec
Confidence 577888877667777753 222233433332211 1 22444 45678899988776654
No 108
>cd05695 S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 3 (hs3). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=48.54 E-value=1e+02 Score=22.56 Aligned_cols=56 Identities=21% Similarity=0.196 Sum_probs=29.6
Q ss_pred eEEEEEecCCeEEEEeCCCCeeeeeeCCceeEcC--C---CCCCeEEEEeCCCCCceEEEEEEeCCCcEEEE
Q psy13744 210 IGVIRHLGSGVCSVYLAEEERTLSIEAHELEPVM--P---QPNDKVKVIVGEHKECTGVLLSVDNGEGVVKL 276 (296)
Q Consensus 210 kGVVrsV~~g~c~V~L~d~~~vv~V~q~~LEtVi--P---~kGd~VkVI~Ge~RG~tG~LisID~~dgiVkl 276 (296)
.|.|++|.+.-+.|.|.+ +-.-.|+..||.... + +.|++| .++++.+|.++.-|.|
T Consensus 5 ~g~V~~i~~~G~~v~l~~-~v~g~v~~~~l~~~~~~~~~~~~G~~i----------~~kVi~id~~~~~i~L 65 (66)
T cd05695 5 NARVKKVLSNGLILDFLS-SFTGTVDFLHLDPEKSSKSTYKEGQKV----------RARILYVDPSTKVVGL 65 (66)
T ss_pred EEEEEEEeCCcEEEEEcC-CceEEEEHHHcCCccCcccCcCCCCEE----------EEEEEEEeCCCCEEec
Confidence 456677765446666654 233345555553211 1 124444 4578888877655543
No 109
>TIGR01069 mutS2 MutS2 family protein. Function of MutS2 is unknown. It should not be considered a DNA mismatch repair protein. It is likely a DNA mismatch binding protein of unknown cellular function.
Probab=48.25 E-value=30 Score=37.64 Aligned_cols=44 Identities=18% Similarity=0.182 Sum_probs=33.3
Q ss_pred CCCCeEEEEeCCCCCceEEEEEEeC-CCcEEEEcCCCceeE-eecchhhccC
Q psy13744 245 QPNDKVKVIVGEHKECTGVLLSVDN-GEGVVKLTEEDDVKM-IDVKFLCKYK 294 (296)
Q Consensus 245 ~kGd~VkVI~Ge~RG~tG~LisID~-~dgiVkld~~~d~ki-l~~~~L~Kl~ 294 (296)
+.||+|+|.. -++.|++++|+. ++..|++.. +|+ +++++|.++.
T Consensus 626 ~~Gd~V~v~~---~~~~g~v~~i~~~~~~~V~~g~---~k~~v~~~~l~~~~ 671 (771)
T TIGR01069 626 KIGDKVRIRY---FGQKGKIVQILGGNKWNVTVGG---MRMKVHGSELEKIN 671 (771)
T ss_pred CCCCEEEEcc---CCceEEEEEEcCCCeEEEEECC---EEEEEeHHHceecc
Confidence 7899999975 578999999964 566777742 554 8888886653
No 110
>PRK14631 hypothetical protein; Provisional
Probab=48.01 E-value=45 Score=29.90 Aligned_cols=49 Identities=18% Similarity=0.177 Sum_probs=33.2
Q ss_pred CCCCeEEEEe----CCCCCceEEEEEEeCCCcEEEEcC-CCceeEeecchhhcc
Q psy13744 245 QPNDKVKVIV----GEHKECTGVLLSVDNGEGVVKLTE-EDDVKMIDVKFLCKY 293 (296)
Q Consensus 245 ~kGd~VkVI~----Ge~RG~tG~LisID~~dgiVkld~-~~d~kil~~~~L~Kl 293 (296)
.+|..|+|.. +..+-.+|+|+++|.++..|.+.. +.....|++++|.|.
T Consensus 115 ~~G~~V~V~l~~~~~~~k~~~G~L~~v~~~~~~v~l~~~~~~~~~i~~~~I~ka 168 (174)
T PRK14631 115 YIGQQVALRLIAAVENRRKFQAKLLAVDLENEEIQVEVEGKHVLDIDSNNIDKA 168 (174)
T ss_pred hCCCeEEEEEecccCCceEEEEEEEEeecCCCEEEEEEcCCcEEEEEhHHcceE
Confidence 4589999964 345889999999994444444432 222345899998875
No 111
>PRK00004 rplX 50S ribosomal protein L24; Reviewed
Probab=47.73 E-value=40 Score=27.81 Aligned_cols=26 Identities=12% Similarity=0.043 Sum_probs=18.8
Q ss_pred ccCceEEEEecCCCCccccCCeEEEEEecC
Q psy13744 189 HTTDIEVRINENARDPEFRGQIGVIRHLGS 218 (296)
Q Consensus 189 l~~dI~VkI~~~~~d~~yygqkGVVrsV~~ 218 (296)
+..|=.|+|+. +++.|+.|.|.+|.-
T Consensus 5 i~kGD~V~Vi~----G~dKGk~G~V~~V~~ 30 (105)
T PRK00004 5 IKKGDTVIVIA----GKDKGKRGKVLKVLP 30 (105)
T ss_pred ccCCCEEEEeE----cCCCCcEEEEEEEEc
Confidence 44555677774 345799999999973
No 112
>PF00567 TUDOR: Tudor domain; InterPro: IPR008191 There are multiple copies of this domain in the Drosophila melanogaster tudor protein and it has been identified in several RNA-binding proteins []. Although the function of this domain is unknown, in Drosophila melanogaster the tudor protein is required during oogenesis for the formation of primordial germ cells and for normal abdominal segmentation [].; PDB: 3NTI_A 3NTK_B 3NTH_A 2DIQ_A 3FDR_A 3PNW_O 3S6W_A 3PMT_A 2WAC_A 2O4X_A ....
Probab=47.48 E-value=39 Score=25.89 Aligned_cols=35 Identities=26% Similarity=0.417 Sum_probs=27.5
Q ss_pred eEEE-EEecCCeEEEEeCCCCeeeeeeCCceeEcCC
Q psy13744 210 IGVI-RHLGSGVCSVYLAEEERTLSIEAHELEPVMP 244 (296)
Q Consensus 210 kGVV-rsV~~g~c~V~L~d~~~vv~V~q~~LEtViP 244 (296)
.|+| ....+..+.|++.|.|.++.|..++|-...+
T Consensus 70 Ra~I~~~~~~~~~~V~~iD~G~~~~v~~~~l~~l~~ 105 (121)
T PF00567_consen 70 RAVITVDIDENQYKVFLIDYGNTEKVSASDLRPLPP 105 (121)
T ss_dssp EEEEEEEECTTEEEEEETTTTEEEEEEGGGEEE--H
T ss_pred eEEEEEecccceeEEEEEecCceEEEcHHHhhhhCH
Confidence 5677 5556799999999999999999999877653
No 113
>PRK05609 nusG transcription antitermination protein NusG; Validated
Probab=47.27 E-value=62 Score=27.98 Aligned_cols=52 Identities=15% Similarity=0.198 Sum_probs=39.4
Q ss_pred CcccCceEEEEecCCCCccccCCeEEEEEec-C-CeEEEE--eCCCCeeeeeeCCceeEc
Q psy13744 187 EWHTTDIEVRINENARDPEFRGQIGVIRHLG-S-GVCSVY--LAEEERTLSIEAHELEPV 242 (296)
Q Consensus 187 ~Wl~~dI~VkI~~~~~d~~yygqkGVVrsV~-~-g~c~V~--L~d~~~vv~V~q~~LEtV 242 (296)
..+.+|=.|+|.+ +-|.|..|+|.++. + ..+.|. +......+.|+.++||.+
T Consensus 125 ~~~~~Gd~VrI~~----GPf~G~~g~v~~i~~~~~r~~v~l~~~G~~~~v~l~~~~l~~~ 180 (181)
T PRK05609 125 VDFEVGEMVRVID----GPFADFNGTVEEVDYEKSKLKVLVSIFGRETPVELEFSQVEKI 180 (181)
T ss_pred cCCCCCCEEEEec----cCCCCCEEEEEEEeCCCCEEEEEEEECCCceEEEEchHHEEEc
Confidence 4678888999984 57889999999996 3 456544 455667888988888753
No 114
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=47.10 E-value=51 Score=23.56 Aligned_cols=45 Identities=22% Similarity=0.225 Sum_probs=30.6
Q ss_pred CCCCeEEEEe---CCCCCceEEEEEEeC-CCcEEEEcC--CCceeEeecchhh
Q psy13744 245 QPNDKVKVIV---GEHKECTGVLLSVDN-GEGVVKLTE--EDDVKMIDVKFLC 291 (296)
Q Consensus 245 ~kGd~VkVI~---Ge~RG~tG~LisID~-~dgiVkld~--~~d~kil~~~~L~ 291 (296)
++|++|-+.. +.+ ..|+++.++. ....|+++. ..+...++..+|-
T Consensus 4 ~~G~~Ve~~~~~~~~W--~~a~V~~~~~~~~~~V~~~~~~~~~~e~v~~~~LR 54 (61)
T smart00743 4 KKGDRVEVFSKEEDSW--WEAVVTKVLGDGKYLVRYLTESEPLKETVDWSDLR 54 (61)
T ss_pred CCCCEEEEEECCCCEE--EEEEEEEECCCCEEEEEECCCCcccEEEEeHHHcc
Confidence 4688998884 444 5788999977 557888765 3334556665553
No 115
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=47.10 E-value=92 Score=21.35 Aligned_cols=56 Identities=29% Similarity=0.261 Sum_probs=29.9
Q ss_pred eEEEEEecCCeEEEEeCCCCeeeeeeCCceeEc-------CCCCCCeEEEEeCCCCCceEEEEEEeCCCcEEEE
Q psy13744 210 IGVIRHLGSGVCSVYLAEEERTLSIEAHELEPV-------MPQPNDKVKVIVGEHKECTGVLLSVDNGEGVVKL 276 (296)
Q Consensus 210 kGVVrsV~~g~c~V~L~d~~~vv~V~q~~LEtV-------iP~kGd~VkVI~Ge~RG~tG~LisID~~dgiVkl 276 (296)
.|.|.+|.+..+.|.+... ..--++.++|..- .-+.||.|++ +++++|.+.+.+.+
T Consensus 7 ~g~V~~v~~~g~~v~i~~~-~~g~l~~~~~~~~~~~~~~~~~~~G~~v~~----------~V~~~~~~~~~i~l 69 (72)
T smart00316 7 EGTVTEITPFGAFVDLGNG-VEGLIPISELSDKRVKDPEEVLKVGDEVKV----------KVLSVDEEKGRIIL 69 (72)
T ss_pred EEEEEEEEccEEEEEeCCC-CEEEEEHHHCCccccCCHHHeecCCCEEEE----------EEEEEeCCCCEEEE
Confidence 4667777665566666532 2333444444332 1345666655 56777766555443
No 116
>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=47.06 E-value=38 Score=28.67 Aligned_cols=48 Identities=29% Similarity=0.265 Sum_probs=29.5
Q ss_pred CCCeEEEEe----CCCCCceEEEEEEeCCCcEEEEcCCC--ceeEeecchhhcc
Q psy13744 246 PNDKVKVIV----GEHKECTGVLLSVDNGEGVVKLTEED--DVKMIDVKFLCKY 293 (296)
Q Consensus 246 kGd~VkVI~----Ge~RG~tG~LisID~~dgiVkld~~~--d~kil~~~~L~Kl 293 (296)
.|.+|+|.. ...+-.+|+|+++|++.-+++++... ...-|+|+++.|.
T Consensus 86 iG~~v~v~~~~~~~~~~~~~G~L~~~~~~~i~l~~~~~~~~~~~~I~~~~I~ka 139 (141)
T PF02576_consen 86 IGRKVKVKLKQPVNGRKEFEGKLLEVDEDEITLEVEGKGKKKEVEIPFSDIKKA 139 (141)
T ss_dssp -SEEEEEE-SS-SSS-SEEEEEEEEEETTEEEEEEE-SS-EEEEEE-SS--SS-
T ss_pred cCCeEEEEEeccCCCcEEEEEEEEEEeCCEEEEEECCccceEEEEEEHHHCceE
Confidence 488999975 23455699999999988887765432 1334888888774
No 117
>PF04319 NifZ: NifZ domain; InterPro: IPR007415 NifZ is a short protein is found in the nif (nitrogen fixation) operon. It is required for the maturation of the nitrogenase MoFe protein. In the absence of NifZ, only one of the two P-clusters of the MoFe protein is matured to the ultimate [8Fe-7S] structure. The other P-cluster site in the protein contains a [4Fe-4S] cluster pair, suggesting that NifZ is specifically required for the formation of the second P-cluster [, , ].; GO: 0009399 nitrogen fixation
Probab=46.28 E-value=40 Score=26.58 Aligned_cols=36 Identities=31% Similarity=0.557 Sum_probs=28.1
Q ss_pred cCCeEEEEEec----C-CeEEEEeCCCCeeeeeeCCceeEc
Q psy13744 207 RGQIGVIRHLG----S-GVCSVYLAEEERTLSIEAHELEPV 242 (296)
Q Consensus 207 ygqkGVVrsV~----~-g~c~V~L~d~~~vv~V~q~~LEtV 242 (296)
.|..|+|++|- + ....|.+.+.+.+|-.-.++|++|
T Consensus 35 ~G~~G~V~~iG~flq~~~IY~V~F~~~~~vVGcre~EL~~~ 75 (75)
T PF04319_consen 35 KGDVGYVVSIGTFLQDFYIYLVHFLERGRVVGCREEELEPV 75 (75)
T ss_pred CCCcEEEEEeeEEcceeEEEEEEEcCCCCEEeEcHHHcccC
Confidence 57789999983 2 334677888899999999999876
No 118
>cd05696 S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 4 (hs4). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=45.98 E-value=82 Score=23.32 Aligned_cols=62 Identities=11% Similarity=0.111 Sum_probs=31.5
Q ss_pred eEEEEEe-cCCeEEEEeCCCCeeeeeeCCceeEc-CCCCCCeEEEEeCCCCCceEEEEEEeCCCcEEEE
Q psy13744 210 IGVIRHL-GSGVCSVYLAEEERTLSIEAHELEPV-MPQPNDKVKVIVGEHKECTGVLLSVDNGEGVVKL 276 (296)
Q Consensus 210 kGVVrsV-~~g~c~V~L~d~~~vv~V~q~~LEtV-iP~kGd~VkVI~Ge~RG~tG~LisID~~dgiVkl 276 (296)
.|.|++| .+.-+-|.|.+. ..--|..++|.-- .....++++| | ....++++++|..+..+.|
T Consensus 6 ~g~V~~v~~~~G~~V~l~~g-v~G~i~~s~l~~~~~~~~~~~~~v--G--~~v~~kV~~id~~~~~i~l 69 (71)
T cd05696 6 SVKVTKVEPDLGAVFELKDG-LLGFVHISHLSDDKVPSDTGPFKA--G--TTHKARIIGYSPMDGLLQL 69 (71)
T ss_pred eeEEEEEccCceEEEEeCCC-CEEEEEHHHCCcchhcCcccccCC--C--CEEEEEEEEEeCCCCEEEE
Confidence 4677777 355566777653 3334444454211 1111111111 2 1245667888888887765
No 119
>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=45.85 E-value=1.1e+02 Score=21.96 Aligned_cols=55 Identities=24% Similarity=0.267 Sum_probs=29.3
Q ss_pred eEEEEEecCCeEEEEeCCCCeeeeeeCCcee--------EcCCCCCCeEEEEeCCCCCceEEEEEEeCCCcEEEE
Q psy13744 210 IGVIRHLGSGVCSVYLAEEERTLSIEAHELE--------PVMPQPNDKVKVIVGEHKECTGVLLSVDNGEGVVKL 276 (296)
Q Consensus 210 kGVVrsV~~g~c~V~L~d~~~vv~V~q~~LE--------tViP~kGd~VkVI~Ge~RG~tG~LisID~~dgiVkl 276 (296)
.|.|.+|.+..+.|.|... ..-.++.++|. -+ -++||+|++. ++++|...+.+.|
T Consensus 5 ~g~V~~i~~~~~~v~l~~~-~~g~l~~~e~~~~~~~~~~~~-~~~Gd~i~~~----------i~~~~~~~~~i~l 67 (70)
T cd05687 5 KGTVVSVDDDEVLVDIGYK-SEGIIPISEFSDDPIENGEDE-VKVGDEVEVY----------VLRVEDEEGNVVL 67 (70)
T ss_pred EEEEEEEeCCEEEEEeCCC-ceEEEEHHHhCccccCCHhHc-CCCCCEEEEE----------EEEEECCCCeEEE
Confidence 5677777766677777532 22223333332 11 2557666654 6677755554444
No 120
>PRK06763 F0F1 ATP synthase subunit alpha; Validated
Probab=45.73 E-value=37 Score=31.65 Aligned_cols=44 Identities=23% Similarity=0.272 Sum_probs=36.5
Q ss_pred CCeEEEEEecCCeEEEEeCCCCeeeeeeCCceeEcCCCCCCeEEEE
Q psy13744 208 GQIGVIRHLGSGVCSVYLAEEERTLSIEAHELEPVMPQPNDKVKVI 253 (296)
Q Consensus 208 gqkGVVrsV~~g~c~V~L~d~~~vv~V~q~~LEtViP~kGd~VkVI 253 (296)
.-+|.|.+|.++...|+..+..+-++|.-+.+.-| +.||.||+.
T Consensus 41 tiEGrVvEV~~~~i~iesk~yn~~v~i~~d~~~nv--KVGD~VKaT 84 (213)
T PRK06763 41 TIEGRVVEVDNGVIVIKSKQYEEPVSVYIDSLSNV--KVGDEVKAT 84 (213)
T ss_pred eeeeEEEEEeCCEEEEEeccCCCceEEEecCCCCc--ccCcEEEEc
Confidence 46788999998888888877677788888877777 889999997
No 121
>cd04461 S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains. Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in S. cerevisiae Rrp5 and 14 S1 repeats in H. sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 8 and S. cerevisiae S1 repeat 7. Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=45.66 E-value=1.1e+02 Score=22.95 Aligned_cols=56 Identities=20% Similarity=0.111 Sum_probs=31.7
Q ss_pred eEEEEEecCCeEEEEeCCCCeeeeeeCCcee--EcC-C----CCCCeEEEEeCCCCCceEEEEEEeCCCcEEEE
Q psy13744 210 IGVIRHLGSGVCSVYLAEEERTLSIEAHELE--PVM-P----QPNDKVKVIVGEHKECTGVLLSVDNGEGVVKL 276 (296)
Q Consensus 210 kGVVrsV~~g~c~V~L~d~~~vv~V~q~~LE--tVi-P----~kGd~VkVI~Ge~RG~tG~LisID~~dgiVkl 276 (296)
.|+|++|.+.-|-|.|.+. ..--|+.++|. .+. + +.||.|+| +++++|.+.+-|.|
T Consensus 19 ~g~V~~v~~~G~fv~l~~~-~~g~v~~~el~~~~~~~~~~~~~~Gd~v~v----------kV~~id~~~~~i~l 81 (83)
T cd04461 19 HGYVRNITPYGVFVEFLGG-LTGLAPKSYISDEFVTDPSFGFKKGQSVTA----------KVTSVDEEKQRFLL 81 (83)
T ss_pred EEEEEEEeeceEEEEcCCC-CEEEEEHHHCCcccccCHHHhcCCCCEEEE----------EEEEEcCCCCEEEE
Confidence 6889999887788888643 23334433331 111 1 22555554 56677776665554
No 122
>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=45.59 E-value=61 Score=25.64 Aligned_cols=47 Identities=15% Similarity=0.293 Sum_probs=34.1
Q ss_pred ccCceEEEEecCCCCccccCCeEEEEEecCCeEEEEeCCCCeeeeeeCCceeEcCC
Q psy13744 189 HTTDIEVRINENARDPEFRGQIGVIRHLGSGVCSVYLAEEERTLSIEAHELEPVMP 244 (296)
Q Consensus 189 l~~dI~VkI~~~~~d~~yygqkGVVrsV~~g~c~V~L~d~~~vv~V~q~~LEtViP 244 (296)
|.+|=+|... .|-.|.|.+|.|.++.|++. .+..++++-+.+.-|+|
T Consensus 38 L~~Gd~VvT~--------gGi~G~V~~i~d~~v~vei~-~g~~i~~~r~aI~~v~~ 84 (84)
T TIGR00739 38 LKKGDKVLTI--------GGIIGTVTKIAENTIVIELN-DNTEITFSKNAIVEVLP 84 (84)
T ss_pred CCCCCEEEEC--------CCeEEEEEEEeCCEEEEEEC-CCeEEEEEhHHhhhcCC
Confidence 4556666443 26788999999888888885 46778888887766654
No 123
>cd04458 CSP_CDS Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein. CSP expression is up-regulated by an abrupt drop in growth temperature. CSP's are also expressed under normal condition at lower level. The function of cold-shock proteins is not fully understood. They preferentially bind poly-pyrimidine region of single-stranded RNA and DNA. CSP's are thought to bind mRNA and regulate ribosomal translation, mRNA degradation, and the rate of transcription termination. The human Y-box protein, which contains a CSD, regulates transcription and translation of genes that contain the Y-box sequence in their promoters. This specific ssDNA-binding properties of CSD are required for the binding of Y-box protein to the promoter's Y-box sequence, thereby regulating transcription.
Probab=45.19 E-value=1.1e+02 Score=22.04 Aligned_cols=54 Identities=17% Similarity=0.222 Sum_probs=39.6
Q ss_pred eEEEEEecC--CeEEEEeCCCCeeeeeeCCceeEc---CCCCCCeEEEEeCC-CCCceEE
Q psy13744 210 IGVIRHLGS--GVCSVYLAEEERTLSIEAHELEPV---MPQPNDKVKVIVGE-HKECTGV 263 (296)
Q Consensus 210 kGVVrsV~~--g~c~V~L~d~~~vv~V~q~~LEtV---iP~kGd~VkVI~Ge-~RG~tG~ 263 (296)
+|+|+...+ +.--|...+.++.+-+..+.|+-. .|+.|++|...... .+|..+.
T Consensus 2 ~G~Vk~~~~~kGfGFI~~~~~g~diffh~~~~~~~~~~~~~~G~~V~f~~~~~~~g~~A~ 61 (65)
T cd04458 2 TGTVKWFDDEKGFGFITPDDGGEDVFVHISALEGDGFRSLEEGDRVEFELEEGDKGPQAV 61 (65)
T ss_pred cEEEEEEECCCCeEEEecCCCCcCEEEEhhHhhccCCCcCCCCCEEEEEEEECCCCCeEE
Confidence 678888753 666677777677788999999874 78999999986654 3555443
No 124
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=44.17 E-value=1.1e+02 Score=28.09 Aligned_cols=59 Identities=22% Similarity=0.324 Sum_probs=40.2
Q ss_pred CeEEEEEecCCeEEEEeCCCCeeeeeeCCceeEcCCCCCCeEE--EEeCCCCCceEEEEEEeC
Q psy13744 209 QIGVIRHLGSGVCSVYLAEEERTLSIEAHELEPVMPQPNDKVK--VIVGEHKECTGVLLSVDN 269 (296)
Q Consensus 209 qkGVVrsV~~g~c~V~L~d~~~vv~V~q~~LEtViP~kGd~Vk--VI~Ge~RG~tG~LisID~ 269 (296)
+.|.|++..-+ .|..++.++++.|.....++.+|+.||.|. |+.-..+-..-++++|++
T Consensus 29 ~~g~i~Aa~~G--~~~~d~~n~~~~V~p~~~~~~~~K~GdiV~grV~~v~~~~a~V~i~~ve~ 89 (188)
T COG1096 29 EGGEIRAAATG--VVRRDDKNRVISVKPGKKTPPLPKGGDIVYGRVTDVREQRALVRIVGVEG 89 (188)
T ss_pred ECCEEEEeecc--cEEEcccceEEEeccCCCCCCCCCCCCEEEEEEeeccceEEEEEEEEEec
Confidence 35555555433 345566788999999988999999999986 444444555555666665
No 125
>PF15490 Ten1_2: Telomere-capping, CST complex subunit
Probab=43.25 E-value=1.4e+02 Score=25.38 Aligned_cols=42 Identities=24% Similarity=0.395 Sum_probs=33.4
Q ss_pred CCCCeeeeeeCCceeEcCCCCCCeEEEEeCCCCCceEEEEEE-eCCCcEEE
Q psy13744 226 AEEERTLSIEAHELEPVMPQPNDKVKVIVGEHKECTGVLLSV-DNGEGVVK 275 (296)
Q Consensus 226 ~d~~~vv~V~q~~LEtViP~kGd~VkVI~Ge~RG~tG~LisI-D~~dgiVk 275 (296)
.+.+..+.|+-++||++..+.|..+.|| |+|... +..+.+++
T Consensus 47 ~~~~~~l~V~t~~l~~~~~~~gslyq~i--------GEl~~~~~~~~~~L~ 89 (118)
T PF15490_consen 47 ESDQHSLKVDTKLLEPFQARVGSLYQFI--------GELEHQPQDGGIVLK 89 (118)
T ss_pred cCCCcEEEEEeeEccccccCCCCEEEEE--------EEEEEEcCCCcEEEE
Confidence 6678899999999999999999999988 456555 55555554
No 126
>PRK14646 hypothetical protein; Provisional
Probab=43.16 E-value=50 Score=28.91 Aligned_cols=47 Identities=17% Similarity=0.114 Sum_probs=31.7
Q ss_pred CCCCeEEEEe-C---CCCCceEEEEEEeCCCcEEEEcCCCceeEeecchhhcc
Q psy13744 245 QPNDKVKVIV-G---EHKECTGVLLSVDNGEGVVKLTEEDDVKMIDVKFLCKY 293 (296)
Q Consensus 245 ~kGd~VkVI~-G---e~RG~tG~LisID~~dgiVkld~~~d~kil~~~~L~Kl 293 (296)
.+|.+|+|-. . ..+-.+|+|+++|++.-.+.++ .....|++++|.|.
T Consensus 98 ~~G~~v~V~l~~~~~~~~~~~G~L~~~~~~~v~l~~~--g~~~~i~~~~I~ka 148 (155)
T PRK14646 98 FKGFPVNVELNQKNSKIKFLNGLLYEKSKDYLAINIK--GKIKKIPFNEVLKI 148 (155)
T ss_pred hCCCEEEEEEecCcCCeEEEEEEEEEEeCCEEEEEEC--CEEEEEEHHHeeeE
Confidence 3599999953 2 2355679999998865444433 23455899999886
No 127
>PRK05585 yajC preprotein translocase subunit YajC; Validated
Probab=43.13 E-value=71 Score=26.42 Aligned_cols=38 Identities=18% Similarity=0.456 Sum_probs=31.5
Q ss_pred CCeEEEEEecCCeEEEEeCCCCeeeeeeCCceeEcCCCC
Q psy13744 208 GQIGVIRHLGSGVCSVYLAEEERTLSIEAHELEPVMPQP 246 (296)
Q Consensus 208 gqkGVVrsV~~g~c~V~L~d~~~vv~V~q~~LEtViP~k 246 (296)
|-.|.|.+|.+.++.|++. ++.+++++-..+.-|+.+.
T Consensus 64 Gi~G~Vv~i~~~~v~lei~-~g~~i~~~r~aI~~v~~~~ 101 (106)
T PRK05585 64 GIIGKVTKVSEDFVIIELN-DDTEIKIQKSAIAAVLPKG 101 (106)
T ss_pred CeEEEEEEEeCCEEEEEEC-CCeEEEEEhHHhhhhcCCC
Confidence 6788999999899999985 4578899999888887654
No 128
>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=43.12 E-value=1.1e+02 Score=22.86 Aligned_cols=46 Identities=15% Similarity=0.176 Sum_probs=27.8
Q ss_pred CCeEEEEEecCCeEEEEeCCCCeeeeeeC-CceeEcCCCCCCeEEEEe
Q psy13744 208 GQIGVIRHLGSGVCSVYLAEEERTLSIEA-HELEPVMPQPNDKVKVIV 254 (296)
Q Consensus 208 gqkGVVrsV~~g~c~V~L~d~~~vv~V~q-~~LEtViP~kGd~VkVI~ 254 (296)
+++|.|.++.++.+.|-=.++-++..|+- +++ -.-.+.|+.|.++.
T Consensus 3 k~~aqVisi~g~~vQlMD~eTYeT~ev~~p~~~-~~~i~~G~eV~y~~ 49 (57)
T cd04467 3 RKTGQVLSIMGDVVQLMDLETYETFEVPIPEEI-KDKLEPGKEVEYWE 49 (57)
T ss_pred ceEEEEEEEcCCEEEEeccccceeEEEecchhh-cccCCCCCEEEEEe
Confidence 68999999998744433222333444443 221 13466789999887
No 129
>PRK14640 hypothetical protein; Provisional
Probab=43.05 E-value=52 Score=28.68 Aligned_cols=47 Identities=11% Similarity=0.164 Sum_probs=32.8
Q ss_pred CCCCeEEEEe----CCCCCceEEEEEEeCCCcEEEEcCCCceeEeecchhhcc
Q psy13744 245 QPNDKVKVIV----GEHKECTGVLLSVDNGEGVVKLTEEDDVKMIDVKFLCKY 293 (296)
Q Consensus 245 ~kGd~VkVI~----Ge~RG~tG~LisID~~dgiVkld~~~d~kil~~~~L~Kl 293 (296)
.+|.+|+|.. ...+-.+|+|+++|++.-.+.++ +. ...+++++|.|.
T Consensus 95 ~~G~~v~V~l~~~~~~~k~~~G~L~~v~~~~v~l~~~-~~-~~~i~~~~I~ka 145 (152)
T PRK14640 95 YVGQEAAVTLRMATNNRRKFKGVIKAVQGDMITLTVD-GK-DEVLAFTNIQKA 145 (152)
T ss_pred hCCCeEEEEEecccCCceEEEEEEEEEeCCEEEEEEC-Ce-EEEEEhHHeeeE
Confidence 3589999954 34578899999998755444433 22 345899988875
No 130
>PRK08582 hypothetical protein; Provisional
Probab=42.37 E-value=1.4e+02 Score=25.57 Aligned_cols=18 Identities=22% Similarity=0.093 Sum_probs=10.4
Q ss_pred eEEEEEecCCeEEEEeCC
Q psy13744 210 IGVIRHLGSGVCSVYLAE 227 (296)
Q Consensus 210 kGVVrsV~~g~c~V~L~d 227 (296)
.|+|.+|.+.-+-|.|.+
T Consensus 10 ~G~V~~I~~fG~fV~L~~ 27 (139)
T PRK08582 10 QGKVTGITNFGAFVELPE 27 (139)
T ss_pred EEEEEEEECCeEEEEECC
Confidence 456666665545556643
No 131
>PF12701 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC8_A 2VXF_A 2VXE_A.
Probab=42.13 E-value=61 Score=26.50 Aligned_cols=35 Identities=23% Similarity=0.414 Sum_probs=30.6
Q ss_pred CCCCCCeEEEEeCCCCCceEEEEEEeCCCcEEEEc
Q psy13744 243 MPQPNDKVKVIVGEHKECTGVLLSVDNGEGVVKLT 277 (296)
Q Consensus 243 iP~kGd~VkVI~Ge~RG~tG~LisID~~dgiVkld 277 (296)
.+-.|.+|-++...+-...|+|..||.++..|.|.
T Consensus 4 ~~~IGs~ISlisk~~iRYeG~L~~Id~~~sTItL~ 38 (96)
T PF12701_consen 4 DPYIGSKISLISKSDIRYEGILYSIDTEDSTITLK 38 (96)
T ss_dssp CCCTTCEEEEEETTTEEEEEEEEEEETTTTEEEEE
T ss_pred ccccCCEEEEEECCCcEEEEEEEEEcCCCCEEEee
Confidence 35579999999999999999999999999988763
No 132
>PRK14636 hypothetical protein; Provisional
Probab=41.77 E-value=58 Score=29.23 Aligned_cols=48 Identities=8% Similarity=0.138 Sum_probs=33.0
Q ss_pred CCCCeEEE-Ee---CCCCCceEEEEEEeCCCcEEEEcCCCceeEeecchhhcc
Q psy13744 245 QPNDKVKV-IV---GEHKECTGVLLSVDNGEGVVKLTEEDDVKMIDVKFLCKY 293 (296)
Q Consensus 245 ~kGd~VkV-I~---Ge~RG~tG~LisID~~dgiVkld~~~d~kil~~~~L~Kl 293 (296)
.+|.+|+| ++ ...+-.+|+|+++|++.-.+.+..+. ...|++++|.|.
T Consensus 96 ~~G~~V~V~l~~~~~g~k~~~G~L~~v~~~~v~l~~~~~~-~~~i~~~~I~kA 147 (176)
T PRK14636 96 WAGHEARIALSEPLDGRKQFRGELKGIDGDTVTIADNKAG-EVILPFAAIESA 147 (176)
T ss_pred hCCCeEEEEEecccCCeEEEEEEEEEEeCCEEEEEEcCCc-EEEEEhHHcceE
Confidence 35999999 44 23466799999998876555543333 345899888875
No 133
>PRK14645 hypothetical protein; Provisional
Probab=41.60 E-value=53 Score=28.88 Aligned_cols=45 Identities=13% Similarity=0.107 Sum_probs=32.0
Q ss_pred CCCCeEEEEeCCCCCceEEEEEEeCCCcEEEEcCCCceeEeecchhhc
Q psy13744 245 QPNDKVKVIVGEHKECTGVLLSVDNGEGVVKLTEEDDVKMIDVKFLCK 292 (296)
Q Consensus 245 ~kGd~VkVI~Ge~RG~tG~LisID~~dgiVkld~~~d~kil~~~~L~K 292 (296)
.+|.+|+|.. ..+-.+|+|+++|++.-.+..+ .....|++++|.|
T Consensus 100 ~~G~~v~v~~-~~k~~~G~L~~~~d~~i~l~~~--~~~~~i~~~~I~~ 144 (154)
T PRK14645 100 FAGLKAKVRG-PGENFTGRIKAVSGDQVTFDVG--GEDRTLRIGTFQA 144 (154)
T ss_pred hCCCEEEEEc-CCeEEEEEEEEEeCCEEEEEEC--CeEEEEEHHHhhh
Confidence 3589999965 3577899999998765544443 2355689988854
No 134
>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=40.44 E-value=40 Score=25.69 Aligned_cols=26 Identities=19% Similarity=0.381 Sum_probs=21.6
Q ss_pred CceEEEEEEeCCCcEEEEcCCCceeE
Q psy13744 259 ECTGVLLSVDNGEGVVKLTEEDDVKM 284 (296)
Q Consensus 259 G~tG~LisID~~dgiVkld~~~d~ki 284 (296)
...|++.+||.....|.||++...+.
T Consensus 4 ~veG~I~~id~~~~titLdDGksy~l 29 (61)
T PF07076_consen 4 DVEGTIKSIDPETMTITLDDGKSYKL 29 (61)
T ss_pred cceEEEEEEcCCceEEEecCCCEEEC
Confidence 46899999999999999998765543
No 135
>PRK13709 conjugal transfer nickase/helicase TraI; Provisional
Probab=40.12 E-value=2.6e+02 Score=33.72 Aligned_cols=88 Identities=11% Similarity=0.048 Sum_probs=56.2
Q ss_pred CcccCceEEEEecCCCCccccCCeEEEEEecCCeEEEEe-CCCCeeeeeeCC----ceeEcCCC-----CCCeEEEEeCC
Q psy13744 187 EWHTTDIEVRINENARDPEFRGQIGVIRHLGSGVCSVYL-AEEERTLSIEAH----ELEPVMPQ-----PNDKVKVIVGE 256 (296)
Q Consensus 187 ~Wl~~dI~VkI~~~~~d~~yygqkGVVrsV~~g~c~V~L-~d~~~vv~V~q~----~LEtViP~-----kGd~VkVI~Ge 256 (296)
.++.+|.+|+..+.. ...+..-+|..|....-.|.| .+.++.+.++.. .++.-.+. +||++++...+
T Consensus 647 ~~Y~~G~vi~~~~~~---~~~~~~y~V~~v~~~~n~LtL~~~~G~~~~~~p~~~~~~~~vy~~~~ieiA~GDrLr~T~nd 723 (1747)
T PRK13709 647 DMYRPGMVMEQWNPE---TRSHDRYVIDRVTAQSHSLTLRDAQGETQVVKISSLDSSWSLFRPEKMPVADGERLRVLGKI 723 (1747)
T ss_pred hcCCCCcEEEeeccc---cccCccEEEEEEcCCCCEEEEEcCCCCEEEeChHHhcccceeccccccccCCCCEEEEccCC
Confidence 467889888775321 122344588888753233333 445666677743 34555554 59999998743
Q ss_pred -----CCCceEEEEEEeCCCcEEEEc
Q psy13744 257 -----HKECTGVLLSVDNGEGVVKLT 277 (296)
Q Consensus 257 -----~RG~tG~LisID~~dgiVkld 277 (296)
..|...++++|++..-.|+.+
T Consensus 724 ~~~~l~Ngd~~tV~~i~~~~i~l~~~ 749 (1747)
T PRK13709 724 PGLRLKGGDRLQVTSVSEDGLTVVVP 749 (1747)
T ss_pred cccCccCCCEEEEEEecCCeEEEEEC
Confidence 367899999998866666654
No 136
>PF02237 BPL_C: Biotin protein ligase C terminal domain; InterPro: IPR003142 This C-terminal domain has an SH3-like barrel fold, the function of which is unknown. It is found associated with prokaryotic bifunctional transcriptional repressors [] and eukaryotic enzymes involved in biotin utilization [, ]. In Escherichia coli the biotin operon repressor (BirA) is a bifunctional protein. BirA acts both as the acetyl-coA carboxylase biotin holoenzyme synthetase (6.3.4.15 from EC) and as the biotin operon repressor. DNA sequence analysis of mutations indicates that the helix-turn-helix DNA binding region is located at the N terminus while mutations affecting enzyme function, although mapping over a large region, are found mainly in the central part of the protein's primary sequence [].; GO: 0006464 protein modification process; PDB: 3RUX_A 2CGH_A 3L1A_B 3L2Z_A 1HXD_A 1BIB_A 2EWN_B 1BIA_A 2EJ9_A 3FJP_A ....
Probab=40.00 E-value=94 Score=21.65 Aligned_cols=40 Identities=18% Similarity=0.346 Sum_probs=27.3
Q ss_pred CCCeEEEEeCCCCCceEEEEEEeCCCc-EEEEcCCCceeEeec
Q psy13744 246 PNDKVKVIVGEHKECTGVLLSVDNGEG-VVKLTEEDDVKMIDV 287 (296)
Q Consensus 246 kGd~VkVI~Ge~RG~tG~LisID~~dg-iVkld~~~d~kil~~ 287 (296)
.|.+|+|.. ...-.+|+...||.+-. +|+.+++ .++.+.-
T Consensus 2 lG~~V~v~~-~~~~~~G~~~gId~~G~L~v~~~~g-~~~~i~s 42 (48)
T PF02237_consen 2 LGQEVRVET-GDGEIEGIAEGIDDDGALLVRTEDG-SIRTISS 42 (48)
T ss_dssp TTSEEEEEE-TSCEEEEEEEEEETTSEEEEEETTE-EEEEESS
T ss_pred CCCEEEEEE-CCeEEEEEEEEECCCCEEEEEECCC-CEEEEEE
Confidence 478899988 46677999999988765 5555443 2444433
No 137
>PRK05807 hypothetical protein; Provisional
Probab=39.94 E-value=1.6e+02 Score=25.06 Aligned_cols=42 Identities=21% Similarity=0.142 Sum_probs=23.1
Q ss_pred eEEEEEecCCeEEEEeCCCCeeeeeeCCceeE-------cCCCCCCeEEEE
Q psy13744 210 IGVIRHLGSGVCSVYLAEEERTLSIEAHELEP-------VMPQPNDKVKVI 253 (296)
Q Consensus 210 kGVVrsV~~g~c~V~L~d~~~vv~V~q~~LEt-------ViP~kGd~VkVI 253 (296)
+|+|..|.+.-+-|.|. +..--|.-++|.. -.-+.||.|+|.
T Consensus 10 ~G~Vt~i~~~GafV~L~--~~~Glvhiseis~~~v~~~~~~~kvGd~V~Vk 58 (136)
T PRK05807 10 EGTVVNITNFGAFVEVE--GKTGLVHISEVADTYVKDIREHLKEQDKVKVK 58 (136)
T ss_pred EEEEEEEECCeEEEEEC--CEEEEEEhhhcccccccCccccCCCCCEEEEE
Confidence 56777777666667772 2333344444421 123567777763
No 138
>PRK02001 hypothetical protein; Validated
Probab=39.05 E-value=78 Score=27.83 Aligned_cols=49 Identities=14% Similarity=0.195 Sum_probs=34.2
Q ss_pred CCCCeEEEEeCCCCCceEEEEEEeCCCcEEEEcCC------------CceeEeecchhhcc
Q psy13744 245 QPNDKVKVIVGEHKECTGVLLSVDNGEGVVKLTEE------------DDVKMIDVKFLCKY 293 (296)
Q Consensus 245 ~kGd~VkVI~Ge~RG~tG~LisID~~dgiVkld~~------------~d~kil~~~~L~Kl 293 (296)
.+|..|+|..-..+-.+|+|.++|++.-.+.++.. .....|+|+++.|.
T Consensus 88 ~~G~~v~V~l~~~~~~~G~L~~~~~~~i~l~~~~~~~~~~~k~~~~~~~~~~i~~~~I~ka 148 (152)
T PRK02001 88 NIGRELEVLTKNGKKIEGELKSADENDITLEVKAREPKEGGKGKVTVEKEETITYDDIKEA 148 (152)
T ss_pred hCCCEEEEEECCCCEEEEEEEEEeCCEEEEEEcccccccccccccccceeEEEEhHheeeE
Confidence 35999999664468899999999977555544321 01345899988875
No 139
>PRK14712 conjugal transfer nickase/helicase TraI; Provisional
Probab=38.98 E-value=2.3e+02 Score=33.94 Aligned_cols=97 Identities=11% Similarity=0.060 Sum_probs=59.6
Q ss_pred ccCceEEE-EecCCCCccccCCeEEEEEecC-CeEEEEeCCCCeeeeeeCCce----eEcCCC-----CCCeEEEEeCC-
Q psy13744 189 HTTDIEVR-INENARDPEFRGQIGVIRHLGS-GVCSVYLAEEERTLSIEAHEL----EPVMPQ-----PNDKVKVIVGE- 256 (296)
Q Consensus 189 l~~dI~Vk-I~~~~~d~~yygqkGVVrsV~~-g~c~V~L~d~~~vv~V~q~~L----EtViP~-----kGd~VkVI~Ge- 256 (296)
+.+|.+|+ +.+.... +..-+|..|.. ..|.+-..+.++.++++...| +.-.|. +||+|++...+
T Consensus 517 Y~~GmVl~~~~r~~k~----~~~y~V~~V~~~~n~LtL~~~dG~~~~~~p~~~~~~~~vy~~e~lelA~GDrlr~t~nd~ 592 (1623)
T PRK14712 517 YRPGMVMEQWNPETRS----HDRYVTERVTAQSHSLTLRNAQGETQVVRISSLDSSWSLFRPEKMPVADGERLRVTGKIP 592 (1623)
T ss_pred CCCCCEEEecccCcCc----CceEEEEEEcCCCceEEEEcCCCcEEEechHHcccceeeecccccccCCCCEEEEccCCc
Confidence 37788886 4432111 23338888874 334333355567777777665 555554 59999999864
Q ss_pred ----CCCceEEEEEEeCCCcEEEEcCCCceeEeecch
Q psy13744 257 ----HKECTGVLLSVDNGEGVVKLTEEDDVKMIDVKF 289 (296)
Q Consensus 257 ----~RG~tG~LisID~~dgiVkld~~~d~kil~~~~ 289 (296)
..|...++.+|+++.-+|+.+.......|++++
T Consensus 593 ~~~L~ngd~~tV~~i~~~~itl~~~G~~~~~~l~~~~ 629 (1623)
T PRK14712 593 GLRVSGGDRLQVASVSEDAMTVVVPGRAEPATLPVSD 629 (1623)
T ss_pred ccCccCCCEEEEEEecCCeEEEEECCcceeecccccc
Confidence 256889999999888888765322223344433
No 140
>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=38.52 E-value=81 Score=23.76 Aligned_cols=40 Identities=18% Similarity=0.321 Sum_probs=27.6
Q ss_pred CCCCeEEEEeCCCCCceEEEEEEeCCCcEEEEcCCCceeEeecc
Q psy13744 245 QPNDKVKVIVGEHKECTGVLLSVDNGEGVVKLTEEDDVKMIDVK 288 (296)
Q Consensus 245 ~kGd~VkVI~Ge~RG~tG~LisID~~dgiVkld~~~d~kil~~~ 288 (296)
..||-+.. .+|.+|++..+-++..+|.+..-++++.++++
T Consensus 5 ~vGdiIef----k~g~~G~V~kv~eNSVIVdIT~m~~~~e~~l~ 44 (57)
T PF09953_consen 5 KVGDIIEF----KDGFTGIVEKVYENSVIVDITIMENFDELDLE 44 (57)
T ss_pred ccCcEEEE----cCCcEEEEEEEecCcEEEEEEecCCccccCCC
Confidence 45777765 35799999999999999997442233344443
No 141
>cd05706 S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 10 (sc10). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=38.17 E-value=1.5e+02 Score=21.38 Aligned_cols=56 Identities=21% Similarity=0.150 Sum_probs=28.5
Q ss_pred eEEEEEecCCeEEEEeCCCCeeeeeeCCceeE--c-----CCCCCCeEEEEeCCCCCceEEEEEEeCCCcEEEE
Q psy13744 210 IGVIRHLGSGVCSVYLAEEERTLSIEAHELEP--V-----MPQPNDKVKVIVGEHKECTGVLLSVDNGEGVVKL 276 (296)
Q Consensus 210 kGVVrsV~~g~c~V~L~d~~~vv~V~q~~LEt--V-----iP~kGd~VkVI~Ge~RG~tG~LisID~~dgiVkl 276 (296)
.|.|++|.+..+.|.|.+. ..-.|..++|.- + .=+.||.|+ ++++++|.+...+.|
T Consensus 8 ~g~V~~v~~~gi~v~l~~~-~~g~v~~s~l~~~~~~~~~~~~~~Gd~v~----------~~V~~~d~~~~~i~l 70 (73)
T cd05706 8 PGRVTKVNDRYVLVQLGNK-VTGPSFITDALDDYSEALPYKFKKNDIVR----------ACVLSVDVPNKKIAL 70 (73)
T ss_pred EEEEEEEeCCeEEEEeCCC-cEEEEEhhhccCccccccccccCCCCEEE----------EEEEEEeCCCCEEEE
Confidence 4666776665566666542 222233333321 1 013355554 467788877666554
No 142
>PF04452 Methyltrans_RNA: RNA methyltransferase; InterPro: IPR006700 Methyltransferases (Mtases) are responsible for the transfer of methyl groups between two molecules. The transfer of the methyl group from the ubiquitous S-adenosyl-L-methionine (AdoMet) to either nitrogen, oxygen or carbon atoms is frequently employed in diverse organisms. The reaction is catalyzed by Mtases and modifies DNA, RNA, proteins or small molecules, such as catechol, for regulatory purposes. Proteins in this entry belong to the RsmE family of Mtases, this is supported by crystal structural studying, which show a close structural homology to other known methyltransferases []. This entry contains RsmE of Escherichia coli, which specifically methylates the uridine in position 1498 of 16S rRNA in the fully assembled 30S ribosomal subunit [, ].; GO: 0008168 methyltransferase activity, 0006364 rRNA processing; PDB: 1NXZ_B 1VHY_B 2EGW_A 2EGV_A 2Z0Y_A 2CX8_A 3KW2_A 1VHK_D 1Z85_B 1V6Z_A ....
Probab=38.05 E-value=41 Score=30.50 Aligned_cols=41 Identities=17% Similarity=0.321 Sum_probs=31.9
Q ss_pred CceeEc-CCCCCCeEEEEeCCCCCceEEEEEEeCCCcEEEEc
Q psy13744 237 HELEPV-MPQPNDKVKVIVGEHKECTGVLLSVDNGEGVVKLT 277 (296)
Q Consensus 237 ~~LEtV-iP~kGd~VkVI~Ge~RG~tG~LisID~~dgiVkld 277 (296)
.||--| +=+.||.|.|++|.-+-..++|..|+.....+++.
T Consensus 9 ~Hl~~VlR~k~Gd~i~v~dg~g~~~~a~i~~i~~~~~~~~i~ 50 (225)
T PF04452_consen 9 HHLVKVLRLKEGDSIEVFDGDGGEYRAEITEISKKSATLRIL 50 (225)
T ss_dssp HHHHTTST--TT-EEEEEESSSEEEEEEEEEEESSEEEEEEE
T ss_pred HHHHHhcCCCCCCEEEEEECCCCEEEEEEEECcCcEEEEEEe
Confidence 456444 45789999999999999999999999998877764
No 143
>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=37.80 E-value=1.3e+02 Score=21.15 Aligned_cols=45 Identities=16% Similarity=0.222 Sum_probs=27.4
Q ss_pred CCeEEEEEec--CCeE--EEEeCCCCe-eeeeeCCceeEcCCCCCCeEEEE
Q psy13744 208 GQIGVIRHLG--SGVC--SVYLAEEER-TLSIEAHELEPVMPQPNDKVKVI 253 (296)
Q Consensus 208 gqkGVVrsV~--~g~c--~V~L~d~~~-vv~V~q~~LEtViP~kGd~VkVI 253 (296)
.-.|.|+++. +..+ .|.+.+... ++....... ...++.|++|.|-
T Consensus 17 ~~~g~V~~~~~~G~~~~~~v~~~~~~~~~~~~~~~~~-~~~~~~G~~v~l~ 66 (75)
T PF08402_consen 17 RLPGTVVSVEFLGSETRYTVRLEGGEELVVRVPNSQR-DSPLEPGDEVRLS 66 (75)
T ss_dssp EEEEEEEEEEEESSEEEEEEEETTSSEEEEEEESSG--TTT--TTSEEEEE
T ss_pred eEEEEEEEEEECCCEEEEEEEECCCCEEEEEecCccc-cCCCCCCCEEEEE
Confidence 5688999986 5555 445555544 444444444 4678899999874
No 144
>PRK08059 general stress protein 13; Validated
Probab=37.57 E-value=1.6e+02 Score=24.36 Aligned_cols=18 Identities=22% Similarity=0.130 Sum_probs=10.9
Q ss_pred eEEEEEecCCeEEEEeCC
Q psy13744 210 IGVIRHLGSGVCSVYLAE 227 (296)
Q Consensus 210 kGVVrsV~~g~c~V~L~d 227 (296)
.|+|.+|.+.-|.|.|.+
T Consensus 12 ~G~V~~i~~~G~fV~i~~ 29 (123)
T PRK08059 12 TGKVTGIQPYGAFVALDE 29 (123)
T ss_pred EEEEEEEecceEEEEECC
Confidence 466666666556666653
No 145
>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=37.56 E-value=2.3e+02 Score=34.37 Aligned_cols=71 Identities=17% Similarity=0.149 Sum_probs=42.2
Q ss_pred eEEEEEec--CCeEEEEeCCCCeeeeeeCCcee-----EcC----C-CCCCeEEEEeCC-----CCCceEEEEEEeCCCc
Q psy13744 210 IGVIRHLG--SGVCSVYLAEEERTLSIEAHELE-----PVM----P-QPNDKVKVIVGE-----HKECTGVLLSVDNGEG 272 (296)
Q Consensus 210 kGVVrsV~--~g~c~V~L~d~~~vv~V~q~~LE-----tVi----P-~kGd~VkVI~Ge-----~RG~tG~LisID~~dg 272 (296)
...|.+|. ++.+.|.-.+.++...++..++. .-. + .+||+|++..-+ -.|..+++.+|+.++-
T Consensus 1343 y~~V~~vd~~~~~v~l~~~~~G~~~~~~p~~~~~~~~~~y~~~~~~l~~GDri~~t~~d~~~g~~n~~~~~V~~v~~~~~ 1422 (1960)
T TIGR02760 1343 YLTIADIDREHGKLTVADIKTGSERDILPRQLDHTFTSLYSDSELPLAKGDKIRLRATDKNRGIKANEVYTVTQVVNGLS 1422 (1960)
T ss_pred EEEEEEecCCCCEEEEEecCCCCeEeeChhhcCcccceeeccccccccCCCEEEEeecCcccccccCCeEEEEEEcCCcE
Confidence 34466664 34444443234545555444332 111 2 469999998732 3568899999998887
Q ss_pred EEEEcCCC
Q psy13744 273 VVKLTEED 280 (296)
Q Consensus 273 iVkld~~~ 280 (296)
+++.+.+.
T Consensus 1423 ~~~~~~~~ 1430 (1960)
T TIGR02760 1423 VQLSKVKN 1430 (1960)
T ss_pred EEEcCCCc
Confidence 77665543
No 146
>COG2139 RPL21A Ribosomal protein L21E [Translation, ribosomal structure and biogenesis]
Probab=37.48 E-value=87 Score=26.02 Aligned_cols=37 Identities=14% Similarity=0.166 Sum_probs=27.5
Q ss_pred CCCceEEEEEEeCCCcEEEEcCCCc--eeEeecchhhcc
Q psy13744 257 HKECTGVLLSVDNGEGVVKLTEEDD--VKMIDVKFLCKY 293 (296)
Q Consensus 257 ~RG~tG~LisID~~dgiVkld~~~d--~kil~~~~L~Kl 293 (296)
|-|.||+++.+-+...+|.+..+.. ..|+--++|-..
T Consensus 56 f~G~TG~Vvg~~g~ay~V~v~~G~k~K~liv~peHLk~~ 94 (98)
T COG2139 56 FQGKTGTVVGVRGRAYKVEVYDGNKEKTLIVRPEHLKPQ 94 (98)
T ss_pred ccCcceEEEeccCCEEEEEEecCCceEEEEeCHHHcccc
Confidence 6899999999999999998755432 445666776544
No 147
>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=37.36 E-value=1.2e+02 Score=22.58 Aligned_cols=57 Identities=18% Similarity=0.169 Sum_probs=36.2
Q ss_pred CeEEEEEec-CCeEEEEeCCC-CeeeeeeCCceeEcCCCCCCeEEEEeCCCCCceEEEE
Q psy13744 209 QIGVIRHLG-SGVCSVYLAEE-ERTLSIEAHELEPVMPQPNDKVKVIVGEHKECTGVLL 265 (296)
Q Consensus 209 qkGVVrsV~-~g~c~V~L~d~-~~vv~V~q~~LEtViP~kGd~VkVI~Ge~RG~tG~Li 265 (296)
..|+|.+.. ++.+.|.+.+. .....++...-..|-=+.||.|+|---++--..|.++
T Consensus 5 ~~~~V~~~lG~~~~~V~~~dg~~~l~~i~gK~r~~iwI~~GD~V~V~~~~~d~~kG~Ii 63 (65)
T PF01176_consen 5 VIGRVTEMLGNNLFEVECEDGEERLARIPGKFRKRIWIKRGDFVLVEPSPYDKVKGRII 63 (65)
T ss_dssp EEEEEEEEESSSEEEEEETTSEEEEEEE-HHHHTCC---TTEEEEEEESTTCTTEEEEE
T ss_pred EEEEEEEECCCCEEEEEeCCCCEEEEEeccceeeeEecCCCCEEEEEecccCCCeEEEE
Confidence 356777776 48889999875 4566777776666666678888876555545666554
No 148
>TIGR02768 TraA_Ti Ti-type conjugative transfer relaxase TraA. This protein contains domains distinctive of a single strand exonuclease (N-terminus, MobA/MobL, pfam03389) as well as a helicase domain (central region, homologous to the corresponding region of the F-type relaxase TraI, TIGR02760). This protein likely fills the same role as TraI(F), nicking (at the oriT site) and unwinding the coiled plasmid prior to conjugative transfer.
Probab=37.04 E-value=73 Score=34.45 Aligned_cols=46 Identities=17% Similarity=0.299 Sum_probs=32.8
Q ss_pred CCCCeEEEEe-----CCCCCceEEEEEEeCCCcEEEEcCCCceeEeecchhh
Q psy13744 245 QPNDKVKVIV-----GEHKECTGVLLSVDNGEGVVKLTEEDDVKMIDVKFLC 291 (296)
Q Consensus 245 ~kGd~VkVI~-----Ge~RG~tG~LisID~~dgiVkld~~~d~kil~~~~L~ 291 (296)
++||+|+++. |-+-|.+|++++|+.+.-+|+++++. ...++.+.+.
T Consensus 609 ~~GDrV~~~~N~~~~gv~NGd~g~V~~i~~~~i~v~~~~G~-~v~~~~~~~~ 659 (744)
T TIGR02768 609 AAGDRIVFLENNRDLGVKNGMLGTVEEIEDGRLVVQLDSGE-LVIIPQAEYD 659 (744)
T ss_pred cCCCEEEEEecccccCCcCCCEEEEEEecCCeEEEEECCCC-EEEECHHHhC
Confidence 6899999986 34578999999998777777777543 3334444443
No 149
>PF06003 SMN: Survival motor neuron protein (SMN); InterPro: IPR010304 This family consists of several eukaryotic survival motor neuron (SMN) proteins. The Survival of Motor Neurons (SMN) protein, the product of the spinal muscular atrophy-determining gene, is part of a large macromolecular complex (SMN complex) that functions in the assembly of spliceosomal small nuclear ribonucleoproteins (snRNPs). The SMN complex functions as a specificity factor essential for the efficient assembly of Sm proteins on U snRNAs and likely protects cells from illicit, and potentially deleterious, non-specific binding of Sm proteins to RNAs.; GO: 0003723 RNA binding, 0006397 mRNA processing, 0005634 nucleus, 0005737 cytoplasm; PDB: 1MHN_A 4A4G_A 3S6N_M 4A4E_A 1G5V_A 4A4H_A 4A4F_A 2D9T_A.
Probab=37.00 E-value=59 Score=30.83 Aligned_cols=55 Identities=16% Similarity=0.324 Sum_probs=35.8
Q ss_pred CcccCceEEEEecCCCCccccCCeEEEEEec--CCeEEEEeCCCCeeeeeeCCceeEcCCC
Q psy13744 187 EWHTTDIEVRINENARDPEFRGQIGVIRHLG--SGVCSVYLAEEERTLSIEAHELEPVMPQ 245 (296)
Q Consensus 187 ~Wl~~dI~VkI~~~~~d~~yygqkGVVrsV~--~g~c~V~L~d~~~vv~V~q~~LEtViP~ 245 (296)
.|-.=|-+ ..+ -.+|+.|| .++|.+|. +++|.|.+..-+....|.-++|.+.-..
T Consensus 68 ~WkvGd~C-~A~-~s~Dg~~Y--~A~I~~i~~~~~~~~V~f~gYgn~e~v~l~dL~~~~~~ 124 (264)
T PF06003_consen 68 KWKVGDKC-MAV-YSEDGQYY--PATIESIDEEDGTCVVVFTGYGNEEEVNLSDLKPSEGD 124 (264)
T ss_dssp ---TT-EE-EEE--TTTSSEE--EEEEEEEETTTTEEEEEETTTTEEEEEEGGGEEETT--
T ss_pred CCCCCCEE-EEE-ECCCCCEE--EEEEEEEcCCCCEEEEEEcccCCeEeeehhhhcccccc
Confidence 58544444 444 23567777 48999997 4899999887777777888888887665
No 150
>PRK07252 hypothetical protein; Provisional
Probab=36.66 E-value=2.1e+02 Score=23.96 Aligned_cols=8 Identities=25% Similarity=0.364 Sum_probs=5.7
Q ss_pred CCCCeEEE
Q psy13744 245 QPNDKVKV 252 (296)
Q Consensus 245 ~kGd~VkV 252 (296)
+.||.|+|
T Consensus 49 ~vGD~V~V 56 (120)
T PRK07252 49 KVGEEVLV 56 (120)
T ss_pred CCCCEEEE
Confidence 56787776
No 151
>PF00659 POLO_box: POLO box duplicated region; InterPro: IPR000959 A subgroup of serine/threonine protein kinases, Polo or Polo-like kinases play multiple roles during the cell cycle. Polo kinases are required at several key points through mitosis, starting from control of the G2/M transition through phosphorylation of Cdc25C and mitotic cyclins. Polo kinases are characterised by an amino terminal catalytic domain, and a carboxy terminal non-catalytic domain consisting of three blocks of conserved sequences known as polo boxes which form one single functional domain []. The domain is named after its founding member encoded by the polo gene of Drosophila melanogaster []. This domain of around 70 amino acids has been found in species ranging from yeast to mammals. Polo boxes appear to mediate interaction with multiple proteins through protein:protein interactions; some but not all of these proteins are substrates for the kinase domain of the molecule []. The crystal structure of the polo domain of the murine protein, Sak, is dimeric, consisting of two alpha-helices and two six-stranded beta-sheets []. The topology of one polypeptide subunit of the dimer consists of, from its N- to C terminus, an extended strand segment, five beta-strands, one alpha-helix (A) and a C-terminal beta-strand. Beta-strands from one subunit form a contiguous antiparallel beta-sheet with beta-strands from the second subunit. The two beta-sheets pack with a crossing angle of 110 degrees, orienting the hydrophobic surfaces inward and the hydrophilic surfaces outward. Helix A, which is colinear with beta-strand 6 of the same polypeptide, buries a large portion of the non-overlapping hydrophobic beta-sheet surfaces. Interactions involving helices A comprise a majority of the hydrophobic core structure and also the dimer interface. Point mutations in the Polo box of the budding yeast Cdc5 protein abolish the ability of overexpressed Cdc5 to interact with the spindle poles and to organise cytokinetic structures [].; GO: 0005515 protein binding; PDB: 1MBY_B 3P37_A 3MHN_A 1Q4K_A 3HIK_A 3Q1I_A 3P35_A 3MHQ_A 1UMW_B 3MQ8_B ....
Probab=36.63 E-value=1.2e+02 Score=22.27 Aligned_cols=41 Identities=15% Similarity=0.246 Sum_probs=26.8
Q ss_pred cCCeEEEEEecCCeEEEEeCCCCeeeeeeCCceeEcCCCCC
Q psy13744 207 RGQIGVIRHLGSGVCSVYLAEEERTLSIEAHELEPVMPQPN 247 (296)
Q Consensus 207 ygqkGVVrsV~~g~c~V~L~d~~~vv~V~q~~LEtViP~kG 247 (296)
..+.|++-..+|+.+.|.+.|..+++--+...+-+.+.+.+
T Consensus 2 ~~k~gi~~~LSng~vqv~FnD~tkivl~~~~~~v~yi~~~~ 42 (68)
T PF00659_consen 2 RTKYGIGYQLSNGTVQVNFNDHTKIVLSPDGRLVTYIDRDG 42 (68)
T ss_dssp EECSEEEEEETTSEEEEEETTS-EEEEETTCCEEEEE-TTS
T ss_pred ccceEEEEEEeCCCEEEEEeCCCEEEECCCCCEEEEECCCC
Confidence 35788888999999999988877666544444444444433
No 152
>PRK14647 hypothetical protein; Provisional
Probab=36.50 E-value=81 Score=27.63 Aligned_cols=48 Identities=25% Similarity=0.269 Sum_probs=32.9
Q ss_pred CCCCeEEEEe--------C-CCCCceEEEEEEeCCCcEEEEcCCCceeEeecchhhcc
Q psy13744 245 QPNDKVKVIV--------G-EHKECTGVLLSVDNGEGVVKLTEEDDVKMIDVKFLCKY 293 (296)
Q Consensus 245 ~kGd~VkVI~--------G-e~RG~tG~LisID~~dgiVkld~~~d~kil~~~~L~Kl 293 (296)
.+|.+|+|.. | ..+-.+|+|.++|.+.-.+.+..+. ...|++++|.|.
T Consensus 97 ~~G~~v~V~l~~~~~~~~~~~~~~~~G~L~~~~~~~v~l~~~~~~-~~~i~~~~I~ka 153 (159)
T PRK14647 97 YAGRLVKVRTFELLADEAGNKRKTFLGELEGLADGVVTIALKEGQ-QARIPLDKIAKA 153 (159)
T ss_pred hCCcEEEEEEeccccccccCCceEEEEEEEeecCCEEEEEEcCCc-EEEEEHHHCCEE
Confidence 3589999953 1 3578899999998655444443333 345899999885
No 153
>PF06003 SMN: Survival motor neuron protein (SMN); InterPro: IPR010304 This family consists of several eukaryotic survival motor neuron (SMN) proteins. The Survival of Motor Neurons (SMN) protein, the product of the spinal muscular atrophy-determining gene, is part of a large macromolecular complex (SMN complex) that functions in the assembly of spliceosomal small nuclear ribonucleoproteins (snRNPs). The SMN complex functions as a specificity factor essential for the efficient assembly of Sm proteins on U snRNAs and likely protects cells from illicit, and potentially deleterious, non-specific binding of Sm proteins to RNAs.; GO: 0003723 RNA binding, 0006397 mRNA processing, 0005634 nucleus, 0005737 cytoplasm; PDB: 1MHN_A 4A4G_A 3S6N_M 4A4E_A 1G5V_A 4A4H_A 4A4F_A 2D9T_A.
Probab=36.46 E-value=87 Score=29.72 Aligned_cols=47 Identities=17% Similarity=0.184 Sum_probs=30.8
Q ss_pred CCCCeEEEEe-CCCCCceEEEEEEeCC--CcEEEEcCCCceeEeecchhh
Q psy13744 245 QPNDKVKVIV-GEHKECTGVLLSVDNG--EGVVKLTEEDDVKMIDVKFLC 291 (296)
Q Consensus 245 ~kGd~VkVI~-Ge~RG~tG~LisID~~--dgiVkld~~~d~kil~~~~L~ 291 (296)
++||+++.+. ++..=..|+|.+||.+ .++|+.+.=..-.++.|.+|-
T Consensus 70 kvGd~C~A~~s~Dg~~Y~A~I~~i~~~~~~~~V~f~gYgn~e~v~l~dL~ 119 (264)
T PF06003_consen 70 KVGDKCMAVYSEDGQYYPATIESIDEEDGTCVVVFTGYGNEEEVNLSDLK 119 (264)
T ss_dssp -TT-EEEEE-TTTSSEEEEEEEEEETTTTEEEEEETTTTEEEEEEGGGEE
T ss_pred CCCCEEEEEECCCCCEEEEEEEEEcCCCCEEEEEEcccCCeEeeehhhhc
Confidence 3799999998 3445578999999986 467776542334556666664
No 154
>COG1862 YajC Preprotein translocase subunit YajC [Intracellular trafficking and secretion]
Probab=35.31 E-value=44 Score=27.48 Aligned_cols=38 Identities=16% Similarity=0.438 Sum_probs=32.1
Q ss_pred CCeEEEEEecCCeEEEEeCCCCeeeeeeCCceeEcCCCC
Q psy13744 208 GQIGVIRHLGSGVCSVYLAEEERTLSIEAHELEPVMPQP 246 (296)
Q Consensus 208 gqkGVVrsV~~g~c~V~L~d~~~vv~V~q~~LEtViP~k 246 (296)
|-.|.|.+|.+...+|++. .+..+++.-+.+-.|+++.
T Consensus 55 Gi~G~V~~v~d~~v~I~l~-~~~~i~~~k~aI~~v~~~~ 92 (97)
T COG1862 55 GIVGTVTKVGDDTVEIELG-DGTKIKFEKEAIATVLEKG 92 (97)
T ss_pred CeEEEEEEEecCcEEEEEC-CCeEEEEEHHHHHhhccCc
Confidence 6899999999877999998 7778889888888877763
No 155
>PF01455 HupF_HypC: HupF/HypC family; InterPro: IPR001109 The large subunit of [NiFe]-hydrogenase, as well as other nickel metalloenzymes, is synthesised as a precursor devoid of the metalloenzyme active site. This precursor then undergoes a complex post-translational maturation process that requires a number of accessory proteins. The hydrogenase expression/formation proteins (HupF/HypC) form a family of small proteins that are hydrogenase precursor-specific chaperones required for this maturation process []. They are believed to keep the hydrogenase precursor in a conformation accessible for metal incorporation [, ].; PDB: 3D3R_A 2Z1C_C 2OT2_A.
Probab=35.28 E-value=92 Score=23.74 Aligned_cols=42 Identities=17% Similarity=0.167 Sum_probs=29.1
Q ss_pred eEEEEEec--CCeEEEEeCCCCeeeeeeCCceeEcCCCCCCeEEEEeC
Q psy13744 210 IGVIRHLG--SGVCSVYLAEEERTLSIEAHELEPVMPQPNDKVKVIVG 255 (296)
Q Consensus 210 kGVVrsV~--~g~c~V~L~d~~~vv~V~q~~LEtViP~kGd~VkVI~G 255 (296)
-+.|.+|. +..+.|... +...+|+-..|.. .+.||.|+|=.|
T Consensus 6 P~~Vv~v~~~~~~A~v~~~--G~~~~V~~~lv~~--v~~Gd~VLVHaG 49 (68)
T PF01455_consen 6 PGRVVEVDEDGGMAVVDFG--GVRREVSLALVPD--VKVGDYVLVHAG 49 (68)
T ss_dssp EEEEEEEETTTTEEEEEET--TEEEEEEGTTCTS--B-TT-EEEEETT
T ss_pred cEEEEEEeCCCCEEEEEcC--CcEEEEEEEEeCC--CCCCCEEEEecC
Confidence 35677775 577788776 5666777777766 677999999776
No 156
>PF12073 DUF3553: Protein of unknown function (DUF3553); InterPro: IPR021938 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are about 60 amino acids in length. This protein has two conserved sequence motifs: GQVQS and TVNF.
Probab=35.15 E-value=1.1e+02 Score=22.72 Aligned_cols=33 Identities=21% Similarity=0.261 Sum_probs=22.9
Q ss_pred eEEEEEecCCeEEEEeCCCCee-eeeeCCceeEc
Q psy13744 210 IGVIRHLGSGVCSVYLAEEERT-LSIEAHELEPV 242 (296)
Q Consensus 210 kGVVrsV~~g~c~V~L~d~~~v-v~V~q~~LEtV 242 (296)
.|.|.++.++.++|.+.+.+++ +....-.||.|
T Consensus 17 ~GqVqS~i~~rvTVnF~~aGK~vI~~~~v~L~~v 50 (52)
T PF12073_consen 17 IGQVQSNIGGRVTVNFEHAGKKVIDGSRVALEKV 50 (52)
T ss_pred ceEEEEecCCeEEEeeccCCeEEEeccEEEEEEc
Confidence 6889999999999999886644 33333344443
No 157
>PTZ00065 60S ribosomal protein L14; Provisional
Probab=34.18 E-value=57 Score=28.32 Aligned_cols=29 Identities=10% Similarity=0.133 Sum_probs=23.9
Q ss_pred CCCeEEEEeCCCCCceEEEEEE-eCCCcEE
Q psy13744 246 PNDKVKVIVGEHKECTGVLLSV-DNGEGVV 274 (296)
Q Consensus 246 kGd~VkVI~Ge~RG~tG~LisI-D~~dgiV 274 (296)
.|.-|+|..|++.|..+.++.| |.+-..|
T Consensus 10 iGRVvli~~Gp~~GKL~vIVDIID~nRvLV 39 (130)
T PTZ00065 10 PGRLCLIQYGPDAGKLCFIVDIVTPTRVLV 39 (130)
T ss_pred eceEEEEecCCCCCCEEEEEEEEcCCeEEE
Confidence 4788888899999999999999 6665554
No 158
>PRK13889 conjugal transfer relaxase TraA; Provisional
Probab=33.88 E-value=66 Score=36.20 Aligned_cols=45 Identities=20% Similarity=0.252 Sum_probs=33.1
Q ss_pred CCCCeEEEEeCC-----CCCceEEEEEEeCCCcEEEEcCCCceeEeecchh
Q psy13744 245 QPNDKVKVIVGE-----HKECTGVLLSVDNGEGVVKLTEEDDVKMIDVKFL 290 (296)
Q Consensus 245 ~kGd~VkVI~Ge-----~RG~tG~LisID~~dgiVkld~~~d~kil~~~~L 290 (296)
.+||+|+++.-+ ..|.+|++++|+.+..+|++|++. ...++..++
T Consensus 602 ~vGDrVm~~rNd~~lgV~NGd~GtV~~I~~~~i~V~~d~gr-~V~~~~~~~ 651 (988)
T PRK13889 602 ASGDRVMFLQNERGLGVKNGTLGTIEQVSAQSMSVRLDDGR-SVAFDLKDY 651 (988)
T ss_pred cCCCEEEEeecCCcCCEeCCCeEEEEEecCCeEEEEECCCe-EEEecHHHc
Confidence 679999998743 478999999999988888887543 223444433
No 159
>PRK14643 hypothetical protein; Provisional
Probab=33.58 E-value=92 Score=27.64 Aligned_cols=48 Identities=17% Similarity=0.117 Sum_probs=33.1
Q ss_pred CCCeEEEEe-CC---CCCceEEEEEEeCCCcEEEEc----CCCceeEeecchhhcc
Q psy13744 246 PNDKVKVIV-GE---HKECTGVLLSVDNGEGVVKLT----EEDDVKMIDVKFLCKY 293 (296)
Q Consensus 246 kGd~VkVI~-Ge---~RG~tG~LisID~~dgiVkld----~~~d~kil~~~~L~Kl 293 (296)
+|.+|+|-. .. -+-.+|+|+++|++.-.+.++ .......+++++|.|.
T Consensus 103 ~G~~V~V~l~~~~~g~k~~~G~L~~~~~~~~~l~l~~~~~~~~~~~~ip~~~I~ka 158 (164)
T PRK14643 103 LNQWVYVQLNNEIKKVKEFEGYVTKYNVNTNTFRFTFFIKGQKKKLDVKYEQIKFI 158 (164)
T ss_pred cCCeEEEEEecccCCceEEEEEEEEEeCCcEEEEEEeeccCcCcEEEEeHHHhhhe
Confidence 499999953 21 366899999999887666531 1122445899998875
No 160
>cd04473 S1_RecJ_like S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease. The function of this family is not fully understood. In Escherichia coli, RecJ degrades single-stranded DNA in the 5'-3' direction and participates in homologous recombination and mismatch repair.
Probab=32.72 E-value=2.1e+02 Score=21.37 Aligned_cols=43 Identities=19% Similarity=0.016 Sum_probs=27.9
Q ss_pred CeEEEEEecCCeEEEEeCCCCeeeeeeCCceeEcCCCCCCeEEEE
Q psy13744 209 QIGVIRHLGSGVCSVYLAEEERTLSIEAHELEPVMPQPNDKVKVI 253 (296)
Q Consensus 209 qkGVVrsV~~g~c~V~L~d~~~vv~V~q~~LEtViP~kGd~VkVI 253 (296)
-+|.|.++.+.-|-|.|.+. ..--+..++|.- ..+.||+|+|.
T Consensus 20 ~~g~V~~i~~~G~fV~l~~~-~~Glv~~se~~~-~~~iGd~v~v~ 62 (77)
T cd04473 20 YKGKVNGVAKYGVFVDLNDH-VRGLIHRSNLLR-DYEVGDEVIVQ 62 (77)
T ss_pred EEEEEEeEecceEEEEECCC-cEEEEEchhccC-cCCCCCEEEEE
Confidence 46888998887777888653 333455555542 25678887774
No 161
>PF10133 RNA_bind_2: Predicted RNA-binding protein; InterPro: IPR019300 This entry represents a family of bacterial proteins predicted to have RNA-binding properties, though their exact function has not yet been defined.
Probab=32.67 E-value=90 Score=23.52 Aligned_cols=53 Identities=26% Similarity=0.509 Sum_probs=33.8
Q ss_pred EEEeCCCCeeeeeeCCceeEcCCCCCCeEEE--EeCCCCCceEEEEEEeCCCcEEEE
Q psy13744 222 SVYLAEEERTLSIEAHELEPVMPQPNDKVKV--IVGEHKECTGVLLSVDNGEGVVKL 276 (296)
Q Consensus 222 ~V~L~d~~~vv~V~q~~LEtViP~kGd~VkV--I~Ge~RG~tG~LisID~~dgiVkl 276 (296)
.|+|.+.+. ..+--+..-.|.|. +|.|++ |.|+.+-..|++..||-.+.-|-|
T Consensus 5 ~vyl~~~~~-eelime~V~~i~~~-~~~i~l~dIfG~~k~v~g~I~~idl~~hkIil 59 (61)
T PF10133_consen 5 NVYLLKGGK-EELIMEDVDRIEPE-GDKIRLTDIFGEQKEVEGRIKEIDLVDHKIIL 59 (61)
T ss_pred EEEEecCCC-cEEEEecccEEEEe-CCEEEEEeccCCeEEEEEEEEEEEccCCEEEE
Confidence 677743322 22333444455555 566766 559999999999999887765543
No 162
>PRK15491 replication factor A; Provisional
Probab=32.39 E-value=1.9e+02 Score=28.91 Aligned_cols=80 Identities=13% Similarity=0.223 Sum_probs=42.6
Q ss_pred ceEEEEecCCCCccc---cCCeEEEEEec--C--CeEEEEeCCCCeeeeeeCCceeEcCCCCCCeEEEEeCCCCCceEEE
Q psy13744 192 DIEVRINENARDPEF---RGQIGVIRHLG--S--GVCSVYLAEEERTLSIEAHELEPVMPQPNDKVKVIVGEHKECTGVL 264 (296)
Q Consensus 192 dI~VkI~~~~~d~~y---ygqkGVVrsV~--~--g~c~V~L~d~~~vv~V~q~~LEtViP~kGd~VkVI~Ge~RG~tG~L 264 (296)
.|.+||.+..+-..| .|..|.|.++. | |.+++.|-++. .-.+....|| +|+.|+|-...-.+..|.=
T Consensus 71 ~i~arVl~~~~~R~f~r~dGs~g~v~~~~v~DeTG~ir~tlW~~~-a~~~~~~~le-----~G~v~~I~~~~~~~y~g~E 144 (374)
T PRK15491 71 NFTAKVVSIFEPKEFNRNDGTTGRVGNIIVADETGSIRLTLWDDL-ADLIKTGDIE-----VGKSLNISGYAKEGYSGIE 144 (374)
T ss_pred EEEEEEeeccCCeeeecCCCCceEEEEEEEEcCCCeEEEEEECch-hhhhccCCcC-----CCCEEEEeeeeccCcccEE
Confidence 788888754443334 34567888653 3 66666665422 1112222233 6888887543223555644
Q ss_pred EEEeCCCcEEEEc
Q psy13744 265 LSVDNGEGVVKLT 277 (296)
Q Consensus 265 isID~~dgiVkld 277 (296)
++++...-+.+.+
T Consensus 145 i~i~~~~~i~~~~ 157 (374)
T PRK15491 145 VNIGRYGGISESD 157 (374)
T ss_pred EEeCCCceeeecc
Confidence 5555544444443
No 163
>cd04465 S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: 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 2 of the Escherichia coli and Homo sapiens RPS1 (ec2 and hs2, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=32.04 E-value=1.9e+02 Score=20.74 Aligned_cols=55 Identities=13% Similarity=0.059 Sum_probs=30.3
Q ss_pred eEEEEEecCCeEEEEeCCCCeeeeeeCCceeEcC---C--CCCCeEEEEeCCCCCceEEEEEEeCCCcEEEE
Q psy13744 210 IGVIRHLGSGVCSVYLAEEERTLSIEAHELEPVM---P--QPNDKVKVIVGEHKECTGVLLSVDNGEGVVKL 276 (296)
Q Consensus 210 kGVVrsV~~g~c~V~L~d~~~vv~V~q~~LEtVi---P--~kGd~VkVI~Ge~RG~tG~LisID~~dgiVkl 276 (296)
+|.|++|.++-+.|.| + +..--|+.++|..-. + .+|++ ...+++++|.+...+.|
T Consensus 5 ~g~V~~v~~~G~~v~l-~-g~~gfip~s~~~~~~~~~~~~~vG~~----------i~~~i~~vd~~~~~i~l 64 (67)
T cd04465 5 EGKVTEKVKGGLIVDI-E-GVRAFLPASQVDLRPVEDLDEYVGKE----------LKFKIIEIDRERNNIVL 64 (67)
T ss_pred EEEEEEEECCeEEEEE-C-CEEEEEEHHHCCCcccCChHHhCCCE----------EEEEEEEEeCCCCEEEE
Confidence 4667777766676777 2 444455555554211 1 12443 34556777876665544
No 164
>COG3109 ProQ Activator of osmoprotectant transporter ProP [Signal transduction mechanisms]
Probab=31.92 E-value=82 Score=29.03 Aligned_cols=44 Identities=16% Similarity=0.251 Sum_probs=35.1
Q ss_pred CCCCeEEEEeCCCCCceEEEEEEeCCCcEEEEcCCCceeEeecchh
Q psy13744 245 QPNDKVKVIVGEHKECTGVLLSVDNGEGVVKLTEEDDVKMIDVKFL 290 (296)
Q Consensus 245 ~kGd~VkVI~Ge~RG~tG~LisID~~dgiVkld~~~d~kil~~~~L 290 (296)
.+|+.|||-.|+. -..++++.|..++.-|+|.++.. -++.-|+|
T Consensus 163 ~~g~~~kVk~G~~-a~~AtvlEv~Kd~vRVqL~~Gl~-m~V~AehL 206 (208)
T COG3109 163 TVGQALKVKAGQN-AMDATVLEITKDGVRVQLNSGLS-MIVRAEHL 206 (208)
T ss_pred hccceeeeccccc-cccceEEEEeccceEEeecCCce-EEEehhhh
Confidence 4699999998854 57899999999999999998873 34665554
No 165
>PRK14634 hypothetical protein; Provisional
Probab=31.68 E-value=81 Score=27.63 Aligned_cols=46 Identities=15% Similarity=0.155 Sum_probs=31.7
Q ss_pred CCCeEEE-EeC---CCCCceEEEEEEeCCCcEEEEcCCCceeEeecchhhcc
Q psy13744 246 PNDKVKV-IVG---EHKECTGVLLSVDNGEGVVKLTEEDDVKMIDVKFLCKY 293 (296)
Q Consensus 246 kGd~VkV-I~G---e~RG~tG~LisID~~dgiVkld~~~d~kil~~~~L~Kl 293 (296)
+|.+|+| +.. ..+-.+|+|+++|++.-.+.++ .....|++++|.|.
T Consensus 99 ~G~~V~V~l~~~~~~~k~~~G~L~~~~~~~v~l~~~--~~~~~i~~~~I~ka 148 (155)
T PRK14634 99 RGFPVEVSHRDDDGSEQRLEGLLLERNEDHLQINIR--GRIKRIPRDSVISV 148 (155)
T ss_pred CCCeEEEEEecCCCCeEEEEEEEEEEeCCEEEEEEC--CEEEEEEHHHeeeE
Confidence 4899999 432 2467899999998755444332 23455899999886
No 166
>PRK14635 hypothetical protein; Provisional
Probab=31.09 E-value=81 Score=27.77 Aligned_cols=48 Identities=13% Similarity=0.079 Sum_probs=29.9
Q ss_pred CCCeEEEEe---C--CCCCceEEEEEEeCCCcEEEEcC------CCceeEeecchhhcc
Q psy13744 246 PNDKVKVIV---G--EHKECTGVLLSVDNGEGVVKLTE------EDDVKMIDVKFLCKY 293 (296)
Q Consensus 246 kGd~VkVI~---G--e~RG~tG~LisID~~dgiVkld~------~~d~kil~~~~L~Kl 293 (296)
+|..|+|.. | +++|.+|+|+++|++.-.+.+.. ......|++++|.|.
T Consensus 98 ~G~~v~v~~~~~~~~~~~g~~g~L~~~~~~~v~l~~~~k~~~~~~~~~~~ip~~~I~ka 156 (162)
T PRK14635 98 RGIPVRLVFRSEESEKWQEGIFRLVNRDGDQVELEKFQKGKKSKVKKQTTLNLKDILKG 156 (162)
T ss_pred CCCEEEEEEecCCCcEEEecceEEEEEcCCEEEEEEecccccccCCeEEEEEhHHeeee
Confidence 488887742 2 34455569999987654444421 122455899998875
No 167
>TIGR00046 RNA methyltransferase, RsmE family. Members of this protein family, previously called conserved hypothetical protein TIGR00046, include the YggJ protein of E. coli, which has now been shown to methylate U1498 in 16S rRNA.
Probab=30.86 E-value=81 Score=29.02 Aligned_cols=41 Identities=22% Similarity=0.188 Sum_probs=31.8
Q ss_pred CCceeEc-CCCCCCeEEEEeCCCCCceEEEEEEeCCCcEEEE
Q psy13744 236 AHELEPV-MPQPNDKVKVIVGEHKECTGVLLSVDNGEGVVKL 276 (296)
Q Consensus 236 q~~LEtV-iP~kGd~VkVI~Ge~RG~tG~LisID~~dgiVkl 276 (296)
..||--| +=+.||.|+|.+|+..-..++|..++.+...+++
T Consensus 23 ~~Hl~~VlR~~~Gd~v~v~~g~g~~~~a~i~~~~~~~~~~~i 64 (240)
T TIGR00046 23 AHHLVRVLRLKKGDKLKLLDGDGFIYHCEIKKISKKFVKCEL 64 (240)
T ss_pred HhHHHHcccCCCCCEEEEEeCCCCEEEEEEEEEcCCeEEEEE
Confidence 3466545 4567999999999777788999999988776665
No 168
>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=30.58 E-value=1.8e+02 Score=21.57 Aligned_cols=54 Identities=13% Similarity=0.148 Sum_probs=29.0
Q ss_pred cCceEEEEec--CCCCccccCCeEEEEEecCC-eEEEEeCC---C---C--eeeeeeCCceeEcCCC
Q psy13744 190 TTDIEVRINE--NARDPEFRGQIGVIRHLGSG-VCSVYLAE---E---E--RTLSIEAHELEPVMPQ 245 (296)
Q Consensus 190 ~~dI~VkI~~--~~~d~~yygqkGVVrsV~~g-~c~V~L~d---~---~--~vv~V~q~~LEtViP~ 245 (296)
.+|-+|.|.. .+..+.+ -.|+|++..+. .|.|+..+ + . -...|+..+|.|+.|.
T Consensus 2 ~~G~~VEV~s~e~g~~gaW--f~a~V~~~~~~~~~~V~Y~~~~~~~~~~~~l~e~V~~~~iRP~pP~ 66 (68)
T PF05641_consen 2 KKGDEVEVSSDEDGFRGAW--FPATVLKENGDDKYLVEYDDLPDEDGESPPLKEWVDARRIRPCPPP 66 (68)
T ss_dssp -TT-EEEEEE-SBTT--EE--EEEEEEEEETT-EEEEEETT-SS--------EEEEEGGGEEE----
T ss_pred CCCCEEEEEEcCCCCCcEE--EEEEEEEeCCCcEEEEEECCcccccccccccEEEechheEECcCcC
Confidence 4566666653 1111222 25788888765 88888643 1 1 3778999999999885
No 169
>PF08206 OB_RNB: Ribonuclease B OB domain; InterPro: IPR013223 This domain includes the N-terminal OB domain found in ribonuclease B proteins in one or two copies.; PDB: 2ID0_D 2IX1_A 2IX0_A.
Probab=30.32 E-value=70 Score=23.16 Aligned_cols=55 Identities=25% Similarity=0.293 Sum_probs=32.4
Q ss_pred EEEEEecCCeEEEEeCCCCeeeeeeCCceeEcCCCCCCeEEE-EeCC--CCCceEEEEEE
Q psy13744 211 GVIRHLGSGVCSVYLAEEERTLSIEAHELEPVMPQPNDKVKV-IVGE--HKECTGVLLSV 267 (296)
Q Consensus 211 GVVrsV~~g~c~V~L~d~~~vv~V~q~~LEtViP~kGd~VkV-I~Ge--~RG~tG~LisI 267 (296)
|+|+-..++++=|...+.++-+-|+.++|.-++. ||+|+| |... .+...|+++.|
T Consensus 1 G~~~~~~~GfGFv~~~~~~~DifIp~~~l~~A~~--gD~V~v~i~~~~~~~~~eg~vv~V 58 (58)
T PF08206_consen 1 GTLKIHPKGFGFVIPDDGGEDIFIPPRNLNGAMD--GDKVLVRITPPSRGKRPEGEVVEV 58 (58)
T ss_dssp EEEEE-SSS-EEEEECT-TEEEEE-HHHHTTS-T--T-EEEEEEEESSSEEEEEEEEEE-
T ss_pred CEEEEEcCCCEEEEECCCCCCEEECHHHHCCCCC--CCEEEEEEecCCCCCCCCEEEEeC
Confidence 4555556677777777667777899998887765 788887 3332 35566776654
No 170
>PRK10409 hydrogenase assembly chaperone; Provisional
Probab=30.14 E-value=1.6e+02 Score=23.86 Aligned_cols=44 Identities=20% Similarity=0.238 Sum_probs=26.9
Q ss_pred eEEEEEecCCeEEEEeCCCCeeeeeeCCceeEc----CCCCCCeEEEEeC
Q psy13744 210 IGVIRHLGSGVCSVYLAEEERTLSIEAHELEPV----MPQPNDKVKVIVG 255 (296)
Q Consensus 210 kGVVrsV~~g~c~V~L~d~~~vv~V~q~~LEtV----iP~kGd~VkVI~G 255 (296)
-|.|+++.+.++.|.+.. ....|+-..|.-+ -.+.||.|+|=.|
T Consensus 6 P~kVv~i~~~~A~vd~~G--v~reV~l~Lv~~~~~~~~~~vGDyVLVHaG 53 (90)
T PRK10409 6 PGQIRTIDGNQAKVDVCG--IQRDVDLTLVGSCDENGQPRVGQWVLVHVG 53 (90)
T ss_pred ceEEEEEcCCeEEEEcCC--eEEEEEEeeecccCCCCccCCCCEEEEecC
Confidence 356777766667777763 3333443333221 3578999999776
No 171
>PF03947 Ribosomal_L2_C: Ribosomal Proteins L2, C-terminal domain; InterPro: IPR022669 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 L2 is one of the proteins from the large ribosomal subunit. This entry represents the best conserved region located in the C-terminal section of these proteins.In Escherichia coli, L2 is known to bind to the 23S rRNA and to have peptidyltransferase activity. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities [, ], groups: Eubacterial L2. Algal and plant chloroplast L2. Cyanelle L2. Archaebacterial L2. Plant L2. Slime mold L2. Marchantia polymorpha mitochondrial L2. Paramecium tetraurelia mitochondrial L2. Fission yeast K5, K37 and KD4. Yeast YL6. Vertebrate L8. ; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3MRZ_C 3F1H_D 3PYO_C 3F1F_D 3PYV_C 3PYR_C 1VSA_B 3D5B_D 3PYT_C 3MS1_C ....
Probab=30.11 E-value=66 Score=27.57 Aligned_cols=44 Identities=16% Similarity=0.202 Sum_probs=33.1
Q ss_pred CCeEEEEeCCCCCceEEEEEEeCCCcEEEEcCCCceeEeecchhhcc
Q psy13744 247 NDKVKVIVGEHKECTGVLLSVDNGEGVVKLTEEDDVKMIDVKFLCKY 293 (296)
Q Consensus 247 Gd~VkVI~Ge~RG~tG~LisID~~dgiVkld~~~d~kil~~~~L~Kl 293 (296)
|+.-+++. -.|.-++|+..+++..+|||-+++ ++.|+.+.+|=+
T Consensus 26 g~g~~~~R--aAGt~a~ii~k~~~~~~ikLPSG~-~k~v~~~c~Ati 69 (130)
T PF03947_consen 26 GDGGKLAR--AAGTYAQIISKEGNYVVIKLPSGE-IKLVSSNCRATI 69 (130)
T ss_dssp TSSEEBSS--STTBBEEEEEEESSEEEEEETTSE-EEEEETTSEEEE
T ss_pred CCCceEEe--eCCCEEEEEEeccceeEEEecCCC-eEeecccceEEE
Confidence 55555544 467999999999999999998765 677877776643
No 172
>TIGR02861 SASP_H small acid-soluble spore protein, H-type. This model is derived from pfam08141 but has been expanded to include in the seed corresponding proteins from three species of Clostridium. Members of this family should occur only in endospore-forming bacteria, typically with two members per genome, but may be absent from the genomes of some endospore-forming bacteria. SspH (previously designated YfjU) was shown to be expressed specifically in spores of Bacillus subtilis.
Probab=30.02 E-value=78 Score=23.76 Aligned_cols=35 Identities=26% Similarity=0.499 Sum_probs=27.5
Q ss_pred ccCCeEEEEEec--CCeEEEEeCC-CCeeeeeeCCcee
Q psy13744 206 FRGQIGVIRHLG--SGVCSVYLAE-EERTLSIEAHELE 240 (296)
Q Consensus 206 yygqkGVVrsV~--~g~c~V~L~d-~~~vv~V~q~~LE 240 (296)
|.|+.=.|..|. +++|+|++.+ .++...|+-+.|+
T Consensus 20 Y~G~pV~Ie~vde~~~tA~V~~l~~p~~~~~Vpv~~L~ 57 (58)
T TIGR02861 20 YKGVPVYIEHVDEQSGTARVYSLDNPGKEQDVPVNDLE 57 (58)
T ss_pred ECCEEEEEEEEcCCCCeEEEEECCCCCcEEEEEHHHcc
Confidence 457777888896 4899999876 4888888887774
No 173
>smart00538 POP4 A domain found in a protein subunit of human RNase MRP and RNase P ribonucleoprotein complexes and archaeal proteins.
Probab=29.97 E-value=2.9e+02 Score=22.17 Aligned_cols=71 Identities=17% Similarity=0.292 Sum_probs=40.4
Q ss_pred CcccCceEEEEecCCCCccccCCeEEEEEecCCeEEEEeCCCCeeeeeeCCceeEcCCCCCCeEEEEeCCCCCceEEEEE
Q psy13744 187 EWHTTDIEVRINENARDPEFRGQIGVIRHLGSGVCSVYLAEEERTLSIEAHELEPVMPQPNDKVKVIVGEHKECTGVLLS 266 (296)
Q Consensus 187 ~Wl~~dI~VkI~~~~~d~~yygqkGVVrsV~~g~c~V~L~d~~~vv~V~q~~LEtViP~kGd~VkVI~Ge~RG~tG~Lis 266 (296)
+|+ |..|+|.++ .+..|.|.+|+|..=...+..|...+ ++ +-++|+.+-...+-... |..+.
T Consensus 10 el~--G~~v~Vv~s-~~ps~vGi~GiVv~ET~nt~~I~t~~-~~---------~~~IpK~~~vF~f~l~~-----~~~~~ 71 (92)
T smart00538 10 ELI--GLKVRVVAS-KNPSLVGIEGIVVDETRNTLKIETKE-GR---------VKTVPKDGAVFEFELPG-----GEIVR 71 (92)
T ss_pred hhc--CCEEEEEEc-CCCCccCcEEEEEEeeeeEEEEEeCC-Cc---------EEEEECCCeEEEEEECC-----CeEEE
Confidence 465 677777753 35678999999987555555554432 22 34456665555553321 14555
Q ss_pred EeCCCcEEE
Q psy13744 267 VDNGEGVVK 275 (296)
Q Consensus 267 ID~~dgiVk 275 (296)
|+++..+.|
T Consensus 72 i~G~~l~~r 80 (92)
T smart00538 72 IDGDRLVGR 80 (92)
T ss_pred EECceeeeC
Confidence 555555544
No 174
>KOG1456|consensus
Probab=29.85 E-value=35 Score=34.75 Aligned_cols=12 Identities=33% Similarity=0.313 Sum_probs=9.7
Q ss_pred cceEEecCCccC
Q psy13744 43 GKTIKITGGPYK 54 (296)
Q Consensus 43 G~tvkI~~GpyK 54 (296)
|-++-++-+|+|
T Consensus 56 G~i~yvt~~P~~ 67 (494)
T KOG1456|consen 56 GPIAYVTCMPHK 67 (494)
T ss_pred CceEEEEecccc
Confidence 777788888887
No 175
>PF08141 SspH: Small acid-soluble spore protein H family; InterPro: IPR012610 This family consists of the small acid-soluble spore proteins (SASP) of the H type (sspH). SspH are unique to spores of Bacillus subtilis and are expressed only in the forespore compartment during sporulation of this organism. The sspH genes are monocistronic and are recognised by the forespore-specific sigma factor for RNA polymerase - sigma-G. The specific role of this protein is unclear but is thought to play a role in sporulation under conditions different from that of the common laboratory tests of spore properties [].; GO: 0030436 asexual sporulation, 0042601 endospore-forming forespore
Probab=29.58 E-value=90 Score=23.43 Aligned_cols=35 Identities=23% Similarity=0.353 Sum_probs=27.5
Q ss_pred ccCCeEEEEEec--CCeEEEEeC-CCCeeeeeeCCcee
Q psy13744 206 FRGQIGVIRHLG--SGVCSVYLA-EEERTLSIEAHELE 240 (296)
Q Consensus 206 yygqkGVVrsV~--~g~c~V~L~-d~~~vv~V~q~~LE 240 (296)
|.|+.=.|.+|. +++|+|++. ..+....|+-++|+
T Consensus 20 y~G~pV~Ie~vde~~~tA~V~~l~~p~~~~~Vpv~~L~ 57 (58)
T PF08141_consen 20 YNGVPVWIEHVDEENGTARVHPLDNPEEEQEVPVNDLE 57 (58)
T ss_pred ECCEEEEEEEEcCCCCeEEEEECCCCCcEEEEEHHHcc
Confidence 557777888995 499999987 56778888887774
No 176
>TIGR02594 conserved hypothetical protein TIGR02594. Members of this protein family known so far are restricted to the bacteria, and for the most to the proteobacteria. The function is unknown.
Probab=29.58 E-value=1.1e+02 Score=25.80 Aligned_cols=36 Identities=17% Similarity=0.153 Sum_probs=26.0
Q ss_pred CCCCCCeEEEEeCCCCCceEEEEEEeCCCcEEE-EcCC
Q psy13744 243 MPQPNDKVKVIVGEHKECTGVLLSVDNGEGVVK-LTEE 279 (296)
Q Consensus 243 iP~kGd~VkVI~Ge~RG~tG~LisID~~dgiVk-ld~~ 279 (296)
.|+.||-|..=.+ ..+++|.+++.|.+.+.|. |..+
T Consensus 73 ~p~~GDiv~f~~~-~~~HVGi~~g~~~~~g~i~~lgGN 109 (129)
T TIGR02594 73 KPAYGCIAVKRRG-GGGHVGFVVGKDKQTGTIIVLGGN 109 (129)
T ss_pred CCCccEEEEEECC-CCCEEEEEEeEcCCCCEEEEeeCC
Confidence 4788998876444 3789999999988766555 5443
No 177
>PRK11642 exoribonuclease R; Provisional
Probab=29.54 E-value=2.4e+02 Score=31.11 Aligned_cols=78 Identities=12% Similarity=0.126 Sum_probs=49.6
Q ss_pred cccCceEEEEecC-CCCc-cccCCeEEEEEecCCeEEEEeCCCCeeeeeeCCceeEcCCCCCCeEEEE-eCCC--CCceE
Q psy13744 188 WHTTDIEVRINEN-ARDP-EFRGQIGVIRHLGSGVCSVYLAEEERTLSIEAHELEPVMPQPNDKVKVI-VGEH--KECTG 262 (296)
Q Consensus 188 Wl~~dI~VkI~~~-~~d~-~yygqkGVVrsV~~g~c~V~L~d~~~vv~V~q~~LEtViP~kGd~VkVI-~Ge~--RG~tG 262 (296)
....+++++..+. ..-. ...-..|+|+--.+|+|=|...+.++-+-|+.++|.-++. ||+|+|. ..+. +...|
T Consensus 62 L~~~g~l~~~~~~~~~~~~~~~~~~G~v~~~~~GfgFv~~e~~~~difI~~~~l~~A~~--GD~V~v~i~~~~~~~r~eg 139 (813)
T PRK11642 62 MERDGQLVFTRRQCYALPERLDLLKGTVIGHRDGYGFLRVEGRKDDLYLSSEQMKTCIH--GDQVLAQPLGADRKGRREA 139 (813)
T ss_pred HHHCCCEEEcCCceEecCCcCceEEEEEEECCCccEEEEECCCCCCEEEChHHHccCCC--CCEEEEEEccCCCCCCcEE
Confidence 4566777765531 1000 1112458888777888877655444567789999888876 9999774 4422 33588
Q ss_pred EEEEE
Q psy13744 263 VLLSV 267 (296)
Q Consensus 263 ~LisI 267 (296)
+++.|
T Consensus 140 ~Vv~I 144 (813)
T PRK11642 140 RIVRV 144 (813)
T ss_pred EEEEE
Confidence 88888
No 178
>PRK14632 hypothetical protein; Provisional
Probab=29.51 E-value=1.2e+02 Score=27.01 Aligned_cols=48 Identities=15% Similarity=0.195 Sum_probs=32.1
Q ss_pred CCCeEEEEe-C------CCCCceEEEEEEeCCCcEEEEcCC------CceeEeecchhhcc
Q psy13744 246 PNDKVKVIV-G------EHKECTGVLLSVDNGEGVVKLTEE------DDVKMIDVKFLCKY 293 (296)
Q Consensus 246 kGd~VkVI~-G------e~RG~tG~LisID~~dgiVkld~~------~d~kil~~~~L~Kl 293 (296)
+|..|+|.. . ..+-.+|+|+++|++.-.+.++.. .....|++++|.|.
T Consensus 97 iG~~V~V~l~~~~~~~~g~k~~~G~L~~v~~~~i~l~~~~~~~~~~~~~~~~i~~~~I~ka 157 (172)
T PRK14632 97 VGRQIELTLIDPTPEWPGRRKFRGELLAVEGDTVVLRPEGAPAPEAEEAVLRTSWQGVRKA 157 (172)
T ss_pred CCCEEEEEEeccccccCCceEEEEEEEEEeCCEEEEEEcCcccccCCceeEEEEhHHccEE
Confidence 589999943 3 146788999999876555544321 12345888888775
No 179
>PRK13826 Dtr system oriT relaxase; Provisional
Probab=29.24 E-value=1.1e+02 Score=35.11 Aligned_cols=36 Identities=14% Similarity=0.269 Sum_probs=29.2
Q ss_pred CCCCeEEEEe-----CCCCCceEEEEEEeCCCcEEEEcCCC
Q psy13744 245 QPNDKVKVIV-----GEHKECTGVLLSVDNGEGVVKLTEED 280 (296)
Q Consensus 245 ~kGd~VkVI~-----Ge~RG~tG~LisID~~dgiVkld~~~ 280 (296)
.+||+|+++. |-.-|..|++++++.+..+|+++++.
T Consensus 635 ~vGDrV~f~rNd~~lgV~NGd~GtV~~i~~~~i~v~~d~g~ 675 (1102)
T PRK13826 635 AAGDQIVFLKNEGSLGVKNGMIGKVVEAAPNRIVAEIGEGE 675 (1102)
T ss_pred cCCCEEEEeeecCccCccCCCeEEEEEecCCeEEEEEcCCC
Confidence 6799999987 44588999999998877778786553
No 180
>PRK14644 hypothetical protein; Provisional
Probab=28.98 E-value=1.4e+02 Score=25.72 Aligned_cols=48 Identities=19% Similarity=0.120 Sum_probs=29.5
Q ss_pred CCCCeEEEEe-C---CCCCceEEEEEEeCCCcEEEEcC-CCceeE-eecchhhc
Q psy13744 245 QPNDKVKVIV-G---EHKECTGVLLSVDNGEGVVKLTE-EDDVKM-IDVKFLCK 292 (296)
Q Consensus 245 ~kGd~VkVI~-G---e~RG~tG~LisID~~dgiVkld~-~~d~ki-l~~~~L~K 292 (296)
.+|.+|+|.. - ..+-.+|.|+++|++.-.+.++. +...++ +++++|++
T Consensus 83 ~~G~~v~V~l~~~~~~~~~~~G~L~~v~~~~i~l~~~~k~~~~~i~~~~~~i~~ 136 (136)
T PRK14644 83 HIGEIIDVSLNKEVNKTDFITGELLENNPETITLKWNCKGQFRKVEINKENIKK 136 (136)
T ss_pred hCCCeEEEEEccCcCCeEEEEEEEEEEeCCEEEEEEecCCcEEEEEECHHHhcC
Confidence 3599999953 2 24678999999987654444332 222332 55576653
No 181
>TIGR02062 RNase_B exoribonuclease II. This family consists of exoribonuclease II, the product of the rnb gene, as found in a number of gamma proteobacteria. In Escherichia coli, it is one of eight different exoribonucleases. It is involved in mRNA degradation and tRNA precursor end processing.
Probab=28.40 E-value=1.6e+02 Score=31.48 Aligned_cols=56 Identities=16% Similarity=0.237 Sum_probs=39.0
Q ss_pred CeEEEEEecCCeEEEEeCCCCeeeeeeCCceeEcCCCCCCeEEEE-eCCCCCceEEEEEE
Q psy13744 209 QIGVIRHLGSGVCSVYLAEEERTLSIEAHELEPVMPQPNDKVKVI-VGEHKECTGVLLSV 267 (296)
Q Consensus 209 qkGVVrsV~~g~c~V~L~d~~~vv~V~q~~LEtViP~kGd~VkVI-~Ge~RG~tG~LisI 267 (296)
..|+|+--..|+|=|...+ ++-+-|..++|..+.. ||+|+|. ..+.....|+++.|
T Consensus 19 ~~G~i~~~~kGfgFv~~~~-~~difI~~~~l~~A~~--GD~V~v~i~~~~~r~~~~v~~i 75 (639)
T TIGR02062 19 VEGVVKATEKGFGFLEVDA-QKSYFIPPPQMKKVMH--GDKIIAVIHSEKERESAEPEEL 75 (639)
T ss_pred EEEEEEECCCccEEEEECC-CCcEEEChHHHccCCC--CCEEEEEEecCCCCcEEEEEEE
Confidence 3577776678889775443 4467899999999887 9999773 33333346777666
No 182
>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=27.76 E-value=1.2e+02 Score=22.20 Aligned_cols=10 Identities=40% Similarity=0.866 Sum_probs=7.1
Q ss_pred CCCCeEEEEe
Q psy13744 245 QPNDKVKVIV 254 (296)
Q Consensus 245 ~kGd~VkVI~ 254 (296)
+.||+|+++-
T Consensus 42 ~~Gd~v~v~v 51 (67)
T cd04455 42 RPGDRIKAYV 51 (67)
T ss_pred CCCCEEEEEE
Confidence 6788877753
No 183
>cd05694 S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: 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 2 (hs2) and S. cerevisiae S1 repeat 2 (sc2). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=27.73 E-value=2.7e+02 Score=20.99 Aligned_cols=58 Identities=12% Similarity=0.028 Sum_probs=34.2
Q ss_pred CeEEEEEecCCeEEEEeCCCCeeeeeeCCceeEc-CCCCCCeEEEEeCCCCCceEEEEEEeCCCcEEEE
Q psy13744 209 QIGVIRHLGSGVCSVYLAEEERTLSIEAHELEPV-MPQPNDKVKVIVGEHKECTGVLLSVDNGEGVVKL 276 (296)
Q Consensus 209 qkGVVrsV~~g~c~V~L~d~~~vv~V~q~~LEtV-iP~kGd~VkVI~Ge~RG~tG~LisID~~dgiVkl 276 (296)
-+|.|++|.+.-|-|.+.-.+-.=-++.++|.-- .=++|+. ...++++||.+...|.|
T Consensus 8 v~g~V~si~d~G~~v~~g~~gv~Gfl~~~~~~~~~~~~~Gq~----------v~~~V~~vd~~~~~v~l 66 (74)
T cd05694 8 LSGCVSSVEDHGYILDIGIPGTTGFLPKKDAGNFSKLKVGQL----------LLCVVEKVKDDGRVVSL 66 (74)
T ss_pred EEEEEEEEeCCEEEEEeCCCCcEEEEEHHHCCcccccCCCCE----------EEEEEEEEECCCCEEEE
Confidence 3678899988777777753333333455554321 0122333 45667888888777765
No 184
>PF11213 DUF3006: Protein of unknown function (DUF3006); InterPro: IPR021377 This family of proteins has no known function.
Probab=27.17 E-value=82 Score=23.89 Aligned_cols=42 Identities=10% Similarity=0.264 Sum_probs=29.1
Q ss_pred eEEEEEecCCeEEEEeCCCCeeeeeeCCceeEcCCCCCCeEEE
Q psy13744 210 IGVIRHLGSGVCSVYLAEEERTLSIEAHELEPVMPQPNDKVKV 252 (296)
Q Consensus 210 kGVVrsV~~g~c~V~L~d~~~vv~V~q~~LEtViP~kGd~VkV 252 (296)
|+||-.+.++.+.+.+.+.+..+.|+.+.|=.= =+.||.+.|
T Consensus 1 k~ivDRiE~~~AVl~~~~~~~~~~vp~~~LP~~-~keGDvl~i 42 (71)
T PF11213_consen 1 KAIVDRIEGDYAVLELEDGEKEIDVPRSRLPEG-AKEGDVLEI 42 (71)
T ss_pred CeEEEEEeCCEEEEEECCCeEEEEEEHHHCCCC-CCcccEEEE
Confidence 578888888888777777666888988876221 125885555
No 185
>TIGR00074 hypC_hupF hydrogenase assembly chaperone HypC/HupF. An additional proposed function is to shuttle the iron atom that has been liganded at the HypC/HypD complex to the precursor of the large hydrogenase (HycE) subunit. PubMed:12441107.
Probab=27.09 E-value=1.7e+02 Score=22.90 Aligned_cols=42 Identities=17% Similarity=0.157 Sum_probs=26.1
Q ss_pred eEEEEEecCCeEEEEeCCCCeeeeeeCCceeEcCCCCCCeEEEEeC
Q psy13744 210 IGVIRHLGSGVCSVYLAEEERTLSIEAHELEPVMPQPNDKVKVIVG 255 (296)
Q Consensus 210 kGVVrsV~~g~c~V~L~d~~~vv~V~q~~LEtViP~kGd~VkVI~G 255 (296)
-+.|.+|.++.+.|... +....|+-..|. -.+.||.|+|=.|
T Consensus 6 P~~V~~i~~~~A~v~~~--G~~~~v~l~lv~--~~~vGD~VLVH~G 47 (76)
T TIGR00074 6 PGQVVEIDENIALVEFC--GIKRDVSLDLVG--EVKVGDYVLVHVG 47 (76)
T ss_pred ceEEEEEcCCEEEEEcC--CeEEEEEEEeeC--CCCCCCEEEEecC
Confidence 35677777777777765 333344433332 2467999999776
No 186
>PTZ00471 60S ribosomal protein L27; Provisional
Probab=26.95 E-value=83 Score=27.51 Aligned_cols=23 Identities=22% Similarity=0.283 Sum_probs=20.2
Q ss_pred CCCCeEEEEeCCCCCceEEEEEE
Q psy13744 245 QPNDKVKVIVGEHKECTGVLLSV 267 (296)
Q Consensus 245 ~kGd~VkVI~Ge~RG~tG~LisI 267 (296)
+.|.-|+||.|.|.|..+.++..
T Consensus 6 kpgkVVivL~GR~AGkKaVivk~ 28 (134)
T PTZ00471 6 KPGKVVIVTSGRYAGRKAVIVQN 28 (134)
T ss_pred cCCEEEEEEccccCCcEEEEEee
Confidence 35778889999999999999987
No 187
>PRK06461 single-stranded DNA-binding protein; Reviewed
Probab=26.82 E-value=2.4e+02 Score=23.60 Aligned_cols=34 Identities=12% Similarity=0.131 Sum_probs=18.4
Q ss_pred CCCCeEEEEeCCCCCceEEE-EEEeCCCcEEEEcC
Q psy13744 245 QPNDKVKVIVGEHKECTGVL-LSVDNGEGVVKLTE 278 (296)
Q Consensus 245 ~kGd~VkVI~Ge~RG~tG~L-isID~~dgiVkld~ 278 (296)
++||-|+|.++.-+...|+| |+|+...-|.++++
T Consensus 66 ~~GdvV~I~na~v~~f~G~lqL~i~~~~~i~~~~~ 100 (129)
T PRK06461 66 KEGEVVEIENAWTTLYRGKVQLNVGKYGSISESDD 100 (129)
T ss_pred CCCCEEEEECcEEeeeCCEEEEEECCCEEEEECCc
Confidence 46999999877433444442 44444333434443
No 188
>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=26.40 E-value=1.8e+02 Score=31.03 Aligned_cols=57 Identities=14% Similarity=0.242 Sum_probs=40.2
Q ss_pred CeEEEEEecCCeEEEEeCC-CCeeeeeeCCceeEcCCCCCCeEEEE-eCCC-CC-ceEEEEEE
Q psy13744 209 QIGVIRHLGSGVCSVYLAE-EERTLSIEAHELEPVMPQPNDKVKVI-VGEH-KE-CTGVLLSV 267 (296)
Q Consensus 209 qkGVVrsV~~g~c~V~L~d-~~~vv~V~q~~LEtViP~kGd~VkVI-~Ge~-RG-~tG~LisI 267 (296)
.+|+|+-..+|+|-|...+ +++.+-|+.++|.-++. ||+|+|. ..+. ++ ..|+++.|
T Consensus 17 ~~G~i~~~~~gfgFv~~~~~~~~difI~~~~~~~a~~--GD~V~v~i~~~~~~~~~~g~v~~i 77 (654)
T TIGR00358 17 VKGVVKAHNKGFGFLRPDDDDKKDYFIPPPQMKKVMH--GDLVEACPLSQPQRGRFEAEVERI 77 (654)
T ss_pred EEEEEEECCCccEEEEeCCCCCCcEEEchHHhCcCCC--CCEEEEEEeecCCCCCceEEEEEE
Confidence 4688887778888776654 24567888888888876 9999763 3322 23 37888887
No 189
>cd03581 NTR_Sfrp3_like NTR domain, Secreted frizzled-related protein (Sfrp) 3-like subfamily; composed of proteins similar to human Sfrp3 and Sfrp4. Sfrps are soluble proteins containing an NTR domain C-terminal to a cysteine-rich Frizzled domain. They show diverse functions and are thought to work in Wnt signaling indirectly, as modulators or antagonists by binding Wnt ligands, and directly, via the Wnt receptor, Frizzled. They participate in regulating the patterning along the anteroposterior axis in vertebrates. Human Sfrp3 may suppress the growth and invasiveness of androgen-independent prostate cancer cells.
Probab=26.31 E-value=2.4e+02 Score=23.30 Aligned_cols=78 Identities=18% Similarity=0.204 Sum_probs=39.8
Q ss_pred eEEEEecCCCCccccCCeEEEEEecC-CeEEEEeCCCCeeeeeeCCceeEcCCCCCCeEEEEeCCCCCceEEEEEEeCCC
Q psy13744 193 IEVRINENARDPEFRGQIGVIRHLGS-GVCSVYLAEEERTLSIEAHELEPVMPQPNDKVKVIVGEHKECTGVLLSVDNGE 271 (296)
Q Consensus 193 I~VkI~~~~~d~~yygqkGVVrsV~~-g~c~V~L~d~~~vv~V~q~~LEtViP~kGd~VkVI~Ge~RG~tG~LisID~~d 271 (296)
+.|+|......+.+..-.-.|++|.. +.- .+..+...+-+...+..+.+ .+|..-+|+.- ..+....|+ +|.+.
T Consensus 12 ~kv~V~~~~~~~~~~~y~v~V~~V~K~g~~--~i~~~~~~l~~~~~C~cp~l-~~gk~YLImG~-~~~~~~~~~-ld~~S 86 (111)
T cd03581 12 IRAKVKEVKRGCHEVTAVVEVKEILKSSLV--NIPRDTVTLYTNSGCLCPPL-TPNEEYIIMGY-EDEERSRLL-LVEGS 86 (111)
T ss_pred EEEEEEEEEecCCEEEEEEEEEEEEecCCC--ccCCceEEEEEcCCCCCccc-cCCCEEEEEec-CCCCcceEE-eCCce
Confidence 55666543333455555666777742 221 23444555555555555544 36777777754 333334443 45544
Q ss_pred cEEE
Q psy13744 272 GVVK 275 (296)
Q Consensus 272 giVk 275 (296)
.|..
T Consensus 87 ~Ve~ 90 (111)
T cd03581 87 LAEK 90 (111)
T ss_pred EEEE
Confidence 4443
No 190
>TIGR00008 infA translation initiation factor IF-1. This family consists of translation initiation factor IF-1 as found in bacteria and chloroplasts. This protein, about 70 residues in length, consists largely of an S1 RNA binding domain (pfam00575).
Probab=26.30 E-value=3.1e+02 Score=21.19 Aligned_cols=21 Identities=14% Similarity=0.085 Sum_probs=16.2
Q ss_pred CeEEEEEec-CCeEEEEeCCCC
Q psy13744 209 QIGVIRHLG-SGVCSVYLAEEE 229 (296)
Q Consensus 209 qkGVVrsV~-~g~c~V~L~d~~ 229 (296)
..|+|.++. ++...|+|.+..
T Consensus 7 ~~G~V~e~L~~~~f~V~l~ng~ 28 (68)
T TIGR00008 7 MEGKVTESLPNAMFRVELENGH 28 (68)
T ss_pred EEEEEEEECCCCEEEEEECCCC
Confidence 468899986 588899997643
No 191
>PF15436 PGBA_N: Plasminogen-binding protein pgbA N-terminal
Probab=26.15 E-value=1.6e+02 Score=27.69 Aligned_cols=55 Identities=16% Similarity=0.213 Sum_probs=32.4
Q ss_pred eEEEEEecCCeEEEEeCCCCeeeeeeCCceeE--cCCCCCCeEEEEeCCCCCceEEEEEEeCC
Q psy13744 210 IGVIRHLGSGVCSVYLAEEERTLSIEAHELEP--VMPQPNDKVKVIVGEHKECTGVLLSVDNG 270 (296)
Q Consensus 210 kGVVrsV~~g~c~V~L~d~~~vv~V~q~~LEt--ViP~kGd~VkVI~Ge~RG~tG~LisID~~ 270 (296)
.++|.++.++.+.+++. .-..+.|++|-+ +.|++||+|+.=..-+ ++.||.=|.+
T Consensus 47 ~a~V~~~~~g~A~~kf~---~fd~L~Q~aLP~p~~~pk~GD~vil~~~Y~---rallIAPn~e 103 (218)
T PF15436_consen 47 RAVVISKKNGVAKAKFS---VFDSLKQDALPTPKMVPKKGDEVILNYLYN---RALLIAPNQE 103 (218)
T ss_pred EEEEEEecCCeeEEEEe---ehhhhhhhcCCCCccccCCCCEEEEeeccc---ceEEEcCCHH
Confidence 34444455566666553 233567888765 5799999987644433 3455544443
No 192
>PF06257 DUF1021: Protein of unknown function (DUF1021); InterPro: IPR009366 This entry consists of several hypothetical bacterial proteins of unknown function.; PDB: 3FB9_A.
Probab=25.80 E-value=2.2e+02 Score=22.50 Aligned_cols=44 Identities=23% Similarity=0.259 Sum_probs=0.0
Q ss_pred CCCeEEEEe----CCCCCceEEEEEEeCCCcEEEEcC-CCceeEeecch
Q psy13744 246 PNDKVKVIV----GEHKECTGVLLSVDNGEGVVKLTE-EDDVKMIDVKF 289 (296)
Q Consensus 246 kGd~VkVI~----Ge~RG~tG~LisID~~dgiVkld~-~~d~kil~~~~ 289 (296)
+|++|+|.. -+.....|.|.+.-.+=|+|++|. ......+-|..
T Consensus 16 vG~~V~l~a~~GRkK~~~r~GvL~~tYPsvFvV~l~~~~~~~~rvSySY 64 (76)
T PF06257_consen 16 VGKRVKLKANKGRKKIIEREGVLEETYPSVFVVELDQEENQFERVSYSY 64 (76)
T ss_dssp TTSEEEEEE--SSS--S-EEEEEEEE-SSEEEEEES-S-SS-EEEEEEH
T ss_pred CCCEEEEEEcCCceEEEEEEEEEEeecCcEEEEEEccCCCceEEEEEEe
No 193
>cd06541 ASCH ASC-1 homology or ASCH domain, a small beta-barrel domain found in all three kingdoms of life. ASCH resembles the RNA-binding PUA domain and may also interact with RNA. ASCH has been proposed to function as an RNA-binding domain during coactivation, RNA-processing and the regulation of prokaryotic translation. The domain has been named after the ASC-1 protein, the activating signal cointegrator 1 or thyroid hormone receptor interactor protein 4 (TRIP4). ASC-1 is conserved in many eukaryotes and has been suggested to participate in a protein complex that interacts with RNA. It has been shown that ASC-1 mediates the interaction between various transciption factors and the basal transcriptional machinery.
Probab=25.80 E-value=1.3e+02 Score=24.17 Aligned_cols=27 Identities=15% Similarity=0.381 Sum_probs=19.0
Q ss_pred cCCCCCCeEEEEeCCCCCceEEEEEEe
Q psy13744 242 VMPQPNDKVKVIVGEHKECTGVLLSVD 268 (296)
Q Consensus 242 ViP~kGd~VkVI~Ge~RG~tG~LisID 268 (296)
-.|++||.++|++|+..=+..++++|+
T Consensus 29 ~~~k~Gd~~i~~~~~~~~~~i~v~~V~ 55 (105)
T cd06541 29 QLPKAGDYLIILDGQQPLAIAEVVKVE 55 (105)
T ss_pred cCCCCCCEEEEecCCCcEEEEEEEEEE
Confidence 678999999999997222455555553
No 194
>PRK06955 biotin--protein ligase; Provisional
Probab=25.64 E-value=1.4e+02 Score=28.58 Aligned_cols=33 Identities=12% Similarity=0.196 Sum_probs=23.1
Q ss_pred CCCeEEEEeCCCCCceEEEEEEeCCCcE-EEEcC
Q psy13744 246 PNDKVKVIVGEHKECTGVLLSVDNGEGV-VKLTE 278 (296)
Q Consensus 246 kGd~VkVI~Ge~RG~tG~LisID~~dgi-Vkld~ 278 (296)
.|++|.|+....+-.+|++++||.+-.. |+.++
T Consensus 248 ~g~~V~v~~~~~~~~~G~~~gId~~G~L~v~~~~ 281 (300)
T PRK06955 248 AGREVVLLEDGAELARGVAHGIDETGQLLLDTPA 281 (300)
T ss_pred CCCeEEEEECCCcEEEEEEeeECCCceEEEEeCC
Confidence 4889998765444579999999976554 44333
No 195
>PRK11713 16S ribosomal RNA methyltransferase RsmE; Provisional
Probab=25.53 E-value=1.1e+02 Score=27.88 Aligned_cols=40 Identities=18% Similarity=0.291 Sum_probs=31.1
Q ss_pred CceeEc-CCCCCCeEEEEeCCCCCceEEEEEEeCCCcEEEE
Q psy13744 237 HELEPV-MPQPNDKVKVIVGEHKECTGVLLSVDNGEGVVKL 276 (296)
Q Consensus 237 ~~LEtV-iP~kGd~VkVI~Ge~RG~tG~LisID~~dgiVkl 276 (296)
.||--| +=+.||.|.|++|+..-..|+|..||.....+++
T Consensus 22 ~Hl~~VlR~~~Gd~i~v~~g~g~~~~~~i~~i~~~~~~~~i 62 (234)
T PRK11713 22 HHLVRVLRLKEGDELRLFDGDGGEYLAEITEIGKKEVELEI 62 (234)
T ss_pred hHHHhhccCCCCCEEEEEeCCCCEEEEEEEEecCcEEEEEE
Confidence 455344 5778999999999876678999999888776665
No 196
>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=25.37 E-value=2.3e+02 Score=19.47 Aligned_cols=18 Identities=22% Similarity=0.082 Sum_probs=11.1
Q ss_pred eEEEEEecCCeEEEEeCC
Q psy13744 210 IGVIRHLGSGVCSVYLAE 227 (296)
Q Consensus 210 kGVVrsV~~g~c~V~L~d 227 (296)
+|.|.++.+..+-|.|.+
T Consensus 5 ~g~V~~i~~~g~~v~i~~ 22 (69)
T cd05692 5 EGTVTRLKPFGAFVELGG 22 (69)
T ss_pred EEEEEEEEeeeEEEEECC
Confidence 456677766556666653
No 197
>TIGR02546 III_secr_ATP type III secretion apparatus H+-transporting two-sector ATPase.
Probab=25.31 E-value=3.3e+02 Score=27.52 Aligned_cols=28 Identities=11% Similarity=0.051 Sum_probs=19.0
Q ss_pred cCCeEEEEEecCCeEEEEeCCC--Ceeeee
Q psy13744 207 RGQIGVIRHLGSGVCSVYLAEE--ERTLSI 234 (296)
Q Consensus 207 ygqkGVVrsV~~g~c~V~L~d~--~~vv~V 234 (296)
+.+.|.|.+|.+..++|.+..- ++++.|
T Consensus 3 ~~~~G~V~~v~g~~v~v~~~~~~~ge~~~i 32 (422)
T TIGR02546 3 VRVRGRVTEVSGTLLKAVLPGARVGELCLI 32 (422)
T ss_pred cceeEEEEEEECcEEEEEECCCCCCCEEEE
Confidence 4567889999888888876431 445555
No 198
>TIGR00638 Mop molybdenum-pterin binding domain. This model describes a multigene family of molybdenum-pterin binding proteins of about 70 amino acids in Clostridium pasteurianum, as a tandemly-repeated domain C-terminal to an unrelated domain in ModE, a molybdate transport gene repressor of E. coli, and in single or tandemly paired domains in several related proteins.
Probab=25.24 E-value=1.6e+02 Score=20.97 Aligned_cols=47 Identities=15% Similarity=0.135 Sum_probs=30.1
Q ss_pred CCeEEEEEec--CCeEEEEeC--CC-CeeeeeeCCceeEcCCCCCCeEEEEe
Q psy13744 208 GQIGVIRHLG--SGVCSVYLA--EE-ERTLSIEAHELEPVMPQPNDKVKVIV 254 (296)
Q Consensus 208 gqkGVVrsV~--~g~c~V~L~--d~-~~vv~V~q~~LEtViP~kGd~VkVI~ 254 (296)
--.|.|++|. +..|.|.|. +. .-...|..+.++..--++|++|.+.-
T Consensus 8 ~l~g~I~~i~~~g~~~~v~l~~~~~~~l~a~i~~~~~~~l~l~~G~~v~~~i 59 (69)
T TIGR00638 8 QLKGKVVAIEDGDVNAEVDLLLGGGTKLTAVITLESVAELGLKPGKEVYAVI 59 (69)
T ss_pred EEEEEEEEEEECCCeEEEEEEECCCCEEEEEecHHHHhhCCCCCCCEEEEEE
Confidence 3467888884 456766653 33 22336667777666667899988753
No 199
>PRK14132 riboflavin kinase; Provisional
Probab=25.18 E-value=1.6e+02 Score=25.39 Aligned_cols=49 Identities=16% Similarity=0.151 Sum_probs=32.4
Q ss_pred CCccccCCeEEEEEecC----CeEEEEeCCCCeeeeeeCCceeEcCCCC---------CCeEEEE
Q psy13744 202 RDPEFRGQIGVIRHLGS----GVCSVYLAEEERTLSIEAHELEPVMPQP---------NDKVKVI 253 (296)
Q Consensus 202 ~d~~yygqkGVVrsV~~----g~c~V~L~d~~~vv~V~q~~LEtViP~k---------Gd~VkVI 253 (296)
++.++++-+.....+.+ -.|.|.+++ ...-+.+.||.+.|.+ ||+|+|.
T Consensus 64 ~~~r~fGv~~~~~~i~~~~~~i~~aiV~P~---rT~h~~~~lEiIAp~~LR~~L~LkDGD~V~I~ 125 (126)
T PRK14132 64 NGKKFFGVKVLPIAILNKGKEIDGAIVFPK---KTDHSKNVLEIIAPIKLRKFLNLKDGDVVKIV 125 (126)
T ss_pred cCCceEEEEEEEEEEecCCCceeEEEEEec---cCCCCCCeEEEECCcchHhhcCCCCCCEEEEE
Confidence 55678887777777742 257777774 2235567788888865 6777663
No 200
>PF02239 Cytochrom_D1: Cytochrome D1 heme domain; PDB: 1NNO_B 1HZU_A 1N15_B 1N50_A 1GJQ_A 1BL9_B 1NIR_B 1N90_B 1HZV_A 1AOQ_A ....
Probab=25.17 E-value=5.2e+02 Score=25.34 Aligned_cols=24 Identities=21% Similarity=0.178 Sum_probs=17.0
Q ss_pred eCCCcEEEEcCCCceeEeecchhh
Q psy13744 268 DNGEGVVKLTEEDDVKMIDVKFLC 291 (296)
Q Consensus 268 D~~dgiVkld~~~d~kil~~~~L~ 291 (296)
+..++||-+.+..++.+|||+++.
T Consensus 138 ~~~~fVv~lkd~~~I~vVdy~d~~ 161 (369)
T PF02239_consen 138 GRPEFVVNLKDTGEIWVVDYSDPK 161 (369)
T ss_dssp SSSEEEEEETTTTEEEEEETTTSS
T ss_pred CCCEEEEEEccCCeEEEEEecccc
Confidence 444588887666668888888764
No 201
>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=24.59 E-value=1.9e+02 Score=27.75 Aligned_cols=50 Identities=16% Similarity=0.253 Sum_probs=37.4
Q ss_pred CcccCceEEEEecCCCCccccCCeEEEEEec--CCeEEEE--eCCCCeeeeeeCCcee
Q psy13744 187 EWHTTDIEVRINENARDPEFRGQIGVIRHLG--SGVCSVY--LAEEERTLSIEAHELE 240 (296)
Q Consensus 187 ~Wl~~dI~VkI~~~~~d~~yygqkGVVrsV~--~g~c~V~--L~d~~~vv~V~q~~LE 240 (296)
..|..|=.|+|.+ +-|.+..|+|.++. ...+.|. +..-...+.|+.++||
T Consensus 204 ~~f~vGd~VrI~d----GPF~GfeG~I~eid~~k~Rv~VlV~IfGR~TpVeL~~~qVe 257 (258)
T TIGR01956 204 SKFRVGNFVKIVD----GPFKGIVGKIKKIDQEKKKAIVEVEILGKSVDVDLNFKHLK 257 (258)
T ss_pred cCCCCCCEEEEEe----cCCCCcEEEEEEEeCCCCEEEEEEEecCCcEEEEEchHHEE
Confidence 3567888999984 56889999999997 3666555 4545667888888776
No 202
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=24.31 E-value=3.9e+02 Score=21.74 Aligned_cols=22 Identities=14% Similarity=0.107 Sum_probs=16.5
Q ss_pred CeEEEEEec-CCeEEEEeCCCCe
Q psy13744 209 QIGVIRHLG-SGVCSVYLAEEER 230 (296)
Q Consensus 209 qkGVVrsV~-~g~c~V~L~d~~~ 230 (296)
..|+|.++. ++.+.|.|.+...
T Consensus 9 ~~G~V~e~Lp~~~frV~LenG~~ 31 (87)
T PRK12442 9 LDGIVDEVLPDSRFRVTLENGVE 31 (87)
T ss_pred EEEEEEEECCCCEEEEEeCCCCE
Confidence 478888886 6888999976443
No 203
>PRK12288 GTPase RsgA; Reviewed
Probab=24.05 E-value=3.8e+02 Score=26.28 Aligned_cols=58 Identities=22% Similarity=0.182 Sum_probs=27.5
Q ss_pred CeEEEEEecCCeEEEEeCCCCe-eeeeeCCceeEcCCCCCCeEEEEeC-CCC-CceEEEEEEeC
Q psy13744 209 QIGVIRHLGSGVCSVYLAEEER-TLSIEAHELEPVMPQPNDKVKVIVG-EHK-ECTGVLLSVDN 269 (296)
Q Consensus 209 qkGVVrsV~~g~c~V~L~d~~~-vv~V~q~~LEtViP~kGd~VkVI~G-e~R-G~tG~LisID~ 269 (296)
..|.|..+..+.+.|...+... ...+.. .|+ .|..||+|.+-.. +.. ...|.+..|.+
T Consensus 40 ~~g~Vi~~~~~~~~v~~~~g~~~~~~~~g-~~~--~~~vGD~V~~~~~~~~~~~~~~~I~~il~ 100 (347)
T PRK12288 40 QEGIVISRFGQHADVEAADGEVHRCNIRR-TIR--SLVTGDRVVWRPGKEALEGVSGVVEAVHP 100 (347)
T ss_pred cceEEEEEECCEEEEEeCCCcEEEEEecc-cCC--CCCCCcEEEEEeCCCcccccceEEEEEec
Confidence 4556666655555555432221 111222 122 2778888888432 111 12366666643
No 204
>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=24.02 E-value=1.8e+02 Score=21.69 Aligned_cols=24 Identities=25% Similarity=0.373 Sum_probs=12.1
Q ss_pred CCCCCCeEEEEeCCCCCceEEEEEEeCCCcEEEE
Q psy13744 243 MPQPNDKVKVIVGEHKECTGVLLSVDNGEGVVKL 276 (296)
Q Consensus 243 iP~kGd~VkVI~Ge~RG~tG~LisID~~dgiVkl 276 (296)
.|++||.|. |++++++.+...|.+
T Consensus 3 ~p~~GdiV~----------G~V~~v~~~~~~V~i 26 (82)
T cd04454 3 LPDVGDIVI----------GIVTEVNSRFWKVDI 26 (82)
T ss_pred CCCCCCEEE----------EEEEEEcCCEEEEEe
Confidence 356666553 444455444444444
No 205
>PF11948 DUF3465: Protein of unknown function (DUF3465); InterPro: IPR021856 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 131 to 151 amino acids in length. This protein has a conserved HWTH sequence motif.
Probab=23.55 E-value=2e+02 Score=25.07 Aligned_cols=37 Identities=30% Similarity=0.398 Sum_probs=26.4
Q ss_pred eEEEEeCCCCeeeeeeCCceeEcCC--CCCCeEEEEeCCC
Q psy13744 220 VCSVYLAEEERTLSIEAHELEPVMP--QPNDKVKVIVGEH 257 (296)
Q Consensus 220 ~c~V~L~d~~~vv~V~q~~LEtViP--~kGd~VkVI~Ge~ 257 (296)
..-|.|.+...++-+..-.|-+-+| ++||.|-+- |+|
T Consensus 60 ~Fiv~l~~g~tllIahNIDlaprip~l~~GD~V~f~-GeY 98 (131)
T PF11948_consen 60 RFIVRLSSGQTLLIAHNIDLAPRIPWLQKGDQVEFY-GEY 98 (131)
T ss_pred EEEEEeCCCCEEEEEeccCccccCcCcCCCCEEEEE-EEE
Confidence 3456676666666677777888888 578988764 776
No 206
>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=23.55 E-value=1.5e+02 Score=24.98 Aligned_cols=26 Identities=23% Similarity=0.383 Sum_probs=19.4
Q ss_pred ccCceEEEEecCCCCccccCCeEEEEEecC
Q psy13744 189 HTTDIEVRINENARDPEFRGQIGVIRHLGS 218 (296)
Q Consensus 189 l~~dI~VkI~~~~~d~~yygqkGVVrsV~~ 218 (296)
+..|=+|+|+. +++.|++|.|.+|..
T Consensus 42 IkkGD~V~Vi~----Gk~KGk~GkV~~V~~ 67 (114)
T TIGR01080 42 VRKGDKVRIMR----GDFKGHEGKVSKVDL 67 (114)
T ss_pred eecCCEEEEec----CCCCCCEEEEEEEEc
Confidence 55666788874 456689999999963
No 207
>cd04453 S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain. RNase E is an essential endoribonuclease in the processing and degradation of RNA. In addition to its role in mRNA degradation, RNase E has also been implicated in the processing of rRNA, and the maturation of tRNA, 10Sa RNA and the M1 precursor of RNase P. RNase E associates with PNPase (3' to 5' exonuclease), Rhl B (DEAD-box RNA helicase) and enolase (glycolytic enzyme) to form the RNA degradosome. RNase E tends to cut mRNA within single-stranded regions that are rich in A/U nucleotides. The N-terminal region of RNase E contains the catalytic site. Within the conserved N-terminal domain of RNAse E and RNase G, there is an S1-like subdomain, which is an ancient single-stranded RNA-binding domain. S1 domain is an RNA-binding module originally identified in the ribosomal protein S1. The S1 domain is required for RNA cleavage by RNase E. RNase G is paralogous to RNase E with an N-terminal catalytic domain th
Probab=23.44 E-value=2.1e+02 Score=22.39 Aligned_cols=42 Identities=12% Similarity=0.263 Sum_probs=25.2
Q ss_pred eEEEEEecCC--eEEEEeCCCCeeeeeeCCceeE-----c-----CCCCCCeEEE
Q psy13744 210 IGVIRHLGSG--VCSVYLAEEERTLSIEAHELEP-----V-----MPQPNDKVKV 252 (296)
Q Consensus 210 kGVVrsV~~g--~c~V~L~d~~~vv~V~q~~LEt-----V-----iP~kGd~VkV 252 (296)
+|.|+++.+. -|-|.|.+. ..--|..++|.- | .-++||.|+|
T Consensus 12 ~g~V~~i~~~~~GaFV~l~~g-~~Gllh~seis~~~~~~v~~~~~~~~~Gd~v~V 65 (88)
T cd04453 12 LGRVKKIVPGLQAAFVDIGLG-KNGFLHLSDILPAYFKKHKKIAKLLKEGQEILV 65 (88)
T ss_pred EEEEEEeccCCcEEEEEeCCC-CEEEEEhHHcCchhccccCCHHHcCCCCCEEEE
Confidence 5677777764 566777653 344566666632 1 2456887776
No 208
>PRK15464 cold shock-like protein CspH; Provisional
Probab=23.13 E-value=3.3e+02 Score=20.77 Aligned_cols=54 Identities=11% Similarity=0.239 Sum_probs=38.9
Q ss_pred eEEEEEecC--CeEEEEeCCCCeeeeeeCCceeEc---CCCCCCeEEEEeCCC-CCceEE
Q psy13744 210 IGVIRHLGS--GVCSVYLAEEERTLSIEAHELEPV---MPQPNDKVKVIVGEH-KECTGV 263 (296)
Q Consensus 210 kGVVrsV~~--g~c~V~L~d~~~vv~V~q~~LEtV---iP~kGd~VkVI~Ge~-RG~tG~ 263 (296)
+|+|+.-.+ |+-=|...+.++-|-|..+.|+.- .|..|++|..-..+. ||..+.
T Consensus 6 ~G~Vk~fn~~KGfGFI~~~~g~~DvFvH~s~l~~~g~~~l~~G~~V~f~v~~~~kG~~A~ 65 (70)
T PRK15464 6 TGIVKTFDRKSGKGFIIPSDGRKEVQVHISAFTPRDAEVLIPGLRVEFCRVNGLRGPTAA 65 (70)
T ss_pred eEEEEEEECCCCeEEEccCCCCccEEEEehhehhcCCCCCCCCCEEEEEEEECCCCceeE
Confidence 688888753 555577777777778889999754 588999998866553 576544
No 209
>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed
Probab=23.13 E-value=1.6e+02 Score=32.24 Aligned_cols=46 Identities=17% Similarity=0.155 Sum_probs=37.4
Q ss_pred ccCceEEEEecCCCCccccCCeEEEEEec-CCeEEEEeCCCCeeeeeeCCceeEcC
Q psy13744 189 HTTDIEVRINENARDPEFRGQIGVIRHLG-SGVCSVYLAEEERTLSIEAHELEPVM 243 (296)
Q Consensus 189 l~~dI~VkI~~~~~d~~yygqkGVVrsV~-~g~c~V~L~d~~~vv~V~q~~LEtVi 243 (296)
+..|=.|+|.+ ++++|+|.+|. ++.+.|.++ .-.++|+.++|+.+.
T Consensus 637 ~~~Gd~V~v~~-------~~~~g~v~~i~~~~~~~V~~g--~~k~~v~~~~l~~~~ 683 (782)
T PRK00409 637 LKVGDEVKYLS-------LGQKGEVLSIPDDKEAIVQAG--IMKMKVPLSDLEKIQ 683 (782)
T ss_pred CCCCCEEEEcc-------CCceEEEEEEcCCCeEEEEEC--CEEEEEeHHHceeCc
Confidence 56777888874 47899999996 467888885 678899999999886
No 210
>PF07930 DAP_B: D-aminopeptidase, domain B; InterPro: IPR012856 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. D-aminopeptidase (Q9ZBA9 from SWISSPROT) is a dimeric enzyme with each monomer being composed of three domains. Domain B is organised to form a beta barrel made up of eight antiparallel beta strands. It is connected to domain A, the catalytic domain, by an eight-residue sequence, and also interacts with both domains A and C via non-covalent bonds. Domain B probably functions in maintaining domain C in a good position to interact with the catalytic domain []. This domain is found in peptidases that belong to MEROPS peptidase family S12 (D-Ala-D-Ala carboxypeptidase B family, clan ME).; GO: 0004177 aminopeptidase activity; PDB: 1EI5_A.
Probab=23.12 E-value=1.7e+02 Score=23.93 Aligned_cols=24 Identities=13% Similarity=0.039 Sum_probs=15.9
Q ss_pred CeeeeeeCCceeEcCCCCCCeEEE
Q psy13744 229 ERTLSIEAHELEPVMPQPNDKVKV 252 (296)
Q Consensus 229 ~~vv~V~q~~LEtViP~kGd~VkV 252 (296)
..++.+|-+.|+...+..+..+.+
T Consensus 59 ~~~~~rDGd~l~m~R~~ENltl~~ 82 (88)
T PF07930_consen 59 GTVLRRDGDMLRMERLDENLTLNM 82 (88)
T ss_dssp S-EEEEETTEEEEEEGGGTEEEEE
T ss_pred ceEEEEcCCeEEEeecccceEEEe
Confidence 567777777777777776655543
No 211
>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=22.95 E-value=2.9e+02 Score=20.61 Aligned_cols=45 Identities=18% Similarity=0.207 Sum_probs=28.8
Q ss_pred CCCeEEEEeCC--CCCceEEEEEEeCCCcEEEEcCC-C-ceeEeecchh
Q psy13744 246 PNDKVKVIVGE--HKECTGVLLSVDNGEGVVKLTEE-D-DVKMIDVKFL 290 (296)
Q Consensus 246 kGd~VkVI~Ge--~RG~tG~LisID~~dgiVkld~~-~-d~kil~~~~L 290 (296)
.|-.|+|++-. |.+.+|.+--|-...+-|-++.+ . ++.-+.+++|
T Consensus 4 PG~~V~V~n~~~~Y~~y~G~VQRvsdgkaaVLFEGGnWdKlvTf~l~eL 52 (53)
T PF11623_consen 4 PGSTVRVKNPNDIYYGYEGFVQRVSDGKAAVLFEGGNWDKLVTFRLSEL 52 (53)
T ss_dssp TT-EEEE--TTSTTTT-EEEEEEEETTEEEEEEEETTEEEEEEEEGGGE
T ss_pred CCCEEEEeCCCCccchheEEEEEeeCCeEEEEecCCCceEEEEEEhhhC
Confidence 37789998855 79999999999776666657655 2 2444666665
No 212
>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=22.69 E-value=3.7e+02 Score=21.29 Aligned_cols=35 Identities=9% Similarity=0.275 Sum_probs=22.8
Q ss_pred CcccCceEEEEecCCCCccccCCeEEEEEecCCeEEEE
Q psy13744 187 EWHTTDIEVRINENARDPEFRGQIGVIRHLGSGVCSVY 224 (296)
Q Consensus 187 ~Wl~~dI~VkI~~~~~d~~yygqkGVVrsV~~g~c~V~ 224 (296)
+|+ |..|+|.++ .+..|.|.+|+|..=...+..|.
T Consensus 11 dl~--G~~i~V~~s-~~pslvG~~GiVV~ETknt~~I~ 45 (89)
T PF01868_consen 11 DLI--GAKIEVVRS-KNPSLVGIEGIVVDETKNTFVIV 45 (89)
T ss_dssp --T--T-EEEEEEE-SSCCCTTEEEEEEEEETTEEEEE
T ss_pred hhc--CCEEEEEEc-CCCCccCCEEEEEEcccceEEEE
Confidence 566 677777743 34678999999988666666554
No 213
>TIGR01069 mutS2 MutS2 family protein. Function of MutS2 is unknown. It should not be considered a DNA mismatch repair protein. It is likely a DNA mismatch binding protein of unknown cellular function.
Probab=22.67 E-value=1.5e+02 Score=32.34 Aligned_cols=45 Identities=24% Similarity=0.265 Sum_probs=35.9
Q ss_pred cCceEEEEecCCCCccccCCeEEEEEec-CCeEEEEeCCCCeeeeeeCCceeEcC
Q psy13744 190 TTDIEVRINENARDPEFRGQIGVIRHLG-SGVCSVYLAEEERTLSIEAHELEPVM 243 (296)
Q Consensus 190 ~~dI~VkI~~~~~d~~yygqkGVVrsV~-~g~c~V~L~d~~~vv~V~q~~LEtVi 243 (296)
..|=.|+|.. ++++|.|.+|. ++.|.|.++ .-.++|+.++|+.+.
T Consensus 626 ~~Gd~V~v~~-------~~~~g~v~~i~~~~~~~V~~g--~~k~~v~~~~l~~~~ 671 (771)
T TIGR01069 626 KIGDKVRIRY-------FGQKGKIVQILGGNKWNVTVG--GMRMKVHGSELEKIN 671 (771)
T ss_pred CCCCEEEEcc-------CCceEEEEEEcCCCeEEEEEC--CEEEEEeHHHceecc
Confidence 3455677763 57899999997 488899987 677899999999876
No 214
>PRK01889 GTPase RsgA; Reviewed
Probab=22.46 E-value=3.3e+02 Score=26.63 Aligned_cols=44 Identities=14% Similarity=-0.037 Sum_probs=25.3
Q ss_pred CeEEEEEecCCeEEEEeCCCCeeeeeeCCcee------EcCCCCCCeEEEE
Q psy13744 209 QIGVIRHLGSGVCSVYLAEEERTLSIEAHELE------PVMPQPNDKVKVI 253 (296)
Q Consensus 209 qkGVVrsV~~g~c~V~L~d~~~vv~V~q~~LE------tViP~kGd~VkVI 253 (296)
.+|.|..+..+.+.|...+ +..+-+-...|. .-.|..||+|.|-
T Consensus 29 ~~g~v~~~~~~~~~v~~~~-~~~~~~~~gk~~~~~~~~~~~~~vGD~V~~~ 78 (356)
T PRK01889 29 EPGRVVEEHRSGYVVATEE-GEVRAEVSGKWRHEAFPPGDRPAVGDWVLLD 78 (356)
T ss_pred ccEEEEEEECCEEEEEECC-cEEEEEecchhhccccccCCCCccCcEEEEe
Confidence 5677877777777776533 333222222232 2457788888774
No 215
>PRK06936 type III secretion system ATPase; Provisional
Probab=22.44 E-value=4.9e+02 Score=26.81 Aligned_cols=22 Identities=5% Similarity=0.078 Sum_probs=17.0
Q ss_pred ccCCeEEEEEecCCeEEEEeCC
Q psy13744 206 FRGQIGVIRHLGSGVCSVYLAE 227 (296)
Q Consensus 206 yygqkGVVrsV~~g~c~V~L~d 227 (296)
.+...|.|.+|.+..++|.+..
T Consensus 20 ~~~~~G~V~~v~g~~v~~~~~~ 41 (439)
T PRK06936 20 LIQIRGRVTQVTGTILKAVVPG 41 (439)
T ss_pred ccceeeEEEEEECcEEEEEeCC
Confidence 4567899999998888887653
No 216
>cd01722 Sm_F The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit F is capable of forming both homo- and hetero-heptamer ring structures. To form the hetero-heptamer, Sm subunit F initially binds subunits E and G to form a trimer which then assembles onto snRNA along with the D3/B and D1/D2 heterodimers.
Probab=22.15 E-value=1.6e+02 Score=21.91 Aligned_cols=28 Identities=29% Similarity=0.235 Sum_probs=22.7
Q ss_pred CCCeEEEEeCCCCCceEEEEEEeCCCcE
Q psy13744 246 PNDKVKVIVGEHKECTGVLLSVDNGEGV 273 (296)
Q Consensus 246 kGd~VkVI~Ge~RG~tG~LisID~~dgi 273 (296)
+|.+|.|..=..|-..|+|+++|..=-+
T Consensus 10 ~g~~V~V~Lk~g~~~~G~L~~~D~~mNi 37 (68)
T cd01722 10 TGKPVIVKLKWGMEYKGTLVSVDSYMNL 37 (68)
T ss_pred CCCEEEEEECCCcEEEEEEEEECCCEEE
Confidence 6888998776789999999999976333
No 217
>cd06168 LSm9 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm9 proteins have a single Sm-like domain structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=22.01 E-value=1.7e+02 Score=22.64 Aligned_cols=29 Identities=14% Similarity=0.355 Sum_probs=24.9
Q ss_pred CCCeEEEEeCCCCCceEEEEEEeCCCcEE
Q psy13744 246 PNDKVKVIVGEHKECTGVLLSVDNGEGVV 274 (296)
Q Consensus 246 kGd~VkVI~Ge~RG~tG~LisID~~dgiV 274 (296)
.+.+|+|..=.-|-.+|+|.+.|..--+|
T Consensus 9 l~~~v~V~l~dgR~~~G~l~~~D~~~Niv 37 (75)
T cd06168 9 LGRTMRIHMTDGRTLVGVFLCTDRDCNII 37 (75)
T ss_pred cCCeEEEEEcCCeEEEEEEEEEcCCCcEE
Confidence 47788888877899999999999987776
No 218
>PRK04950 ProP expression regulator; Provisional
Probab=21.95 E-value=1.7e+02 Score=27.38 Aligned_cols=46 Identities=13% Similarity=0.164 Sum_probs=34.5
Q ss_pred ccCceEEEEecCCCCccccCCeEEEEEecCCeEEEEeCCCCeeeeeeCCcee
Q psy13744 189 HTTDIEVRINENARDPEFRGQIGVIRHLGSGVCSVYLAEEERTLSIEAHELE 240 (296)
Q Consensus 189 l~~dI~VkI~~~~~d~~yygqkGVVrsV~~g~c~V~L~d~~~vv~V~q~~LE 240 (296)
|..+=.|+|+ .+.. -..|+|.+|....+.|+|. ++-++.|-.+||-
T Consensus 167 l~~gq~v~vk-~g~~----~~~a~i~ei~kd~v~vql~-~Gl~~~v~ae~l~ 212 (213)
T PRK04950 167 LTVGQAVKVK-AGKS----AMDATVLEITKDDVRVQLD-SGLSMIVRAEHLV 212 (213)
T ss_pred hccCCEEEEe-ccCC----CCceEEEEEecCcEEEEcC-CCcEEEEeHhhhc
Confidence 5667778876 2221 4789999999877999987 5777888888874
No 219
>PF14444 S1-like: S1-like
Probab=21.78 E-value=2.2e+02 Score=21.53 Aligned_cols=36 Identities=25% Similarity=0.454 Sum_probs=22.1
Q ss_pred eEEEEEecC--CeE--EEEeCCCCeeeeeeCCceeEcCCCCCCeEEEEe
Q psy13744 210 IGVIRHLGS--GVC--SVYLAEEERTLSIEAHELEPVMPQPNDKVKVIV 254 (296)
Q Consensus 210 kGVVrsV~~--g~c--~V~L~d~~~vv~V~q~~LEtViP~kGd~VkVI~ 254 (296)
+|+|.++.+ |.. .|++. -+.+.=.+|+.||+|.+..
T Consensus 5 ~GvVTkl~~~yG~IDe~vFF~---------~~vv~G~~P~vGdrV~v~A 44 (58)
T PF14444_consen 5 TGVVTKLCDDYGFIDEDVFFQ---------TDVVKGNVPKVGDRVLVEA 44 (58)
T ss_pred EEEEEEEeCCcceEcccEEEE---------cccEecCCCccCCEEEEEE
Confidence 678888754 322 23322 2224566899999999854
No 220
>PRK00737 small nuclear ribonucleoprotein; Provisional
Probab=21.56 E-value=2.6e+02 Score=21.09 Aligned_cols=29 Identities=28% Similarity=0.209 Sum_probs=21.6
Q ss_pred CCCeEEEEeCCCCCceEEEEEEeCCCcEE
Q psy13744 246 PNDKVKVIVGEHKECTGVLLSVDNGEGVV 274 (296)
Q Consensus 246 kGd~VkVI~Ge~RG~tG~LisID~~dgiV 274 (296)
.+.+|.|..=..|...|+|+++|..=-+|
T Consensus 13 ~~k~V~V~lk~g~~~~G~L~~~D~~mNlv 41 (72)
T PRK00737 13 LNSPVLVRLKGGREFRGELQGYDIHMNLV 41 (72)
T ss_pred CCCEEEEEECCCCEEEEEEEEEcccceeE
Confidence 47788885544688999999999863333
No 221
>PRK05886 yajC preprotein translocase subunit YajC; Validated
Probab=21.32 E-value=3.7e+02 Score=22.52 Aligned_cols=37 Identities=8% Similarity=0.017 Sum_probs=30.1
Q ss_pred CCeEEEEEecCCeEEEEeCCCCeeeeeeCCceeEcCCC
Q psy13744 208 GQIGVIRHLGSGVCSVYLAEEERTLSIEAHELEPVMPQ 245 (296)
Q Consensus 208 gqkGVVrsV~~g~c~V~L~d~~~vv~V~q~~LEtViP~ 245 (296)
|-.|+|.+|.+.++.|++. .+..+++.-..+..|+..
T Consensus 50 Gi~G~V~~I~d~~v~leia-~gv~i~~~r~AI~~v~~p 86 (109)
T PRK05886 50 GLQATIVGITDDTVDLEIA-PGVVTTWMKLAVRDRILP 86 (109)
T ss_pred CeEEEEEEEeCCEEEEEEC-CCeEEEEEhhheeeecCC
Confidence 6788999999888999985 467888998888877643
No 222
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=21.22 E-value=3.2e+02 Score=24.20 Aligned_cols=41 Identities=17% Similarity=0.191 Sum_probs=23.1
Q ss_pred CeEEEEEecCCeEEEEeCCCCeeeeeeCCceeEcCCCCCCeEE
Q psy13744 209 QIGVIRHLGSGVCSVYLAEEERTLSIEAHELEPVMPQPNDKVK 251 (296)
Q Consensus 209 qkGVVrsV~~g~c~V~L~d~~~vv~V~q~~LEtViP~kGd~Vk 251 (296)
..|.|.+-.-|.++ ++..++.+.|+.-..-...|++||.|.
T Consensus 29 ~~~~i~as~~G~~~--id~~~~~Isv~P~~~~~~~~~~GdiV~ 69 (189)
T PRK09521 29 DNGEVYASVVGKVF--IDDINRKISVIPFKKTPPLLKKGDIVY 69 (189)
T ss_pred eCCEEEEEeeEEEE--EcCCCCEEEEecCcCCCCCCCCCCEEE
Confidence 34556665434443 344566677764333346778888764
No 223
>PF11324 DUF3126: Protein of unknown function (DUF3126); InterPro: IPR021473 This family of proteins with unknown function appear to be restricted to Alphaproteobacteria.
Probab=21.01 E-value=2.2e+02 Score=21.85 Aligned_cols=45 Identities=27% Similarity=0.474 Sum_probs=25.8
Q ss_pred ceeEc-CCCCCCeEEEEeCCCCCceEEEEEEeCCCcEEEEcCCCceeEeec
Q psy13744 238 ELEPV-MPQPNDKVKVIVGEHKECTGVLLSVDNGEGVVKLTEEDDVKMIDV 287 (296)
Q Consensus 238 ~LEtV-iP~kGd~VkVI~Ge~RG~tG~LisID~~dgiVkld~~~d~kil~~ 287 (296)
.|+.. .|+++|.|-|..|+ +..|+| ..|.++|-+.. ...+.||+.
T Consensus 17 ~i~v~~rpk~~dsaEV~~g~--EfiGvi-~~DedeGe~Sy--~f~M~ILd~ 62 (63)
T PF11324_consen 17 GITVKARPKKDDSAEVYIGD--EFIGVI-YRDEDEGEVSY--NFQMAILDE 62 (63)
T ss_pred ceEEEcCCCCCCceEEEeCC--EEEEEE-EeecCCCcEEE--EEEEEEecC
Confidence 34444 47889999998775 355544 44666654332 123556553
No 224
>COG2163 RPL14A Ribosomal protein L14E/L6E/L27E [Translation, ribosomal structure and biogenesis]
Probab=20.92 E-value=1.8e+02 Score=25.00 Aligned_cols=26 Identities=19% Similarity=0.272 Sum_probs=22.3
Q ss_pred CCCCeEEEEeCCCCCceEEEEEE-eCC
Q psy13744 245 QPNDKVKVIVGEHKECTGVLLSV-DNG 270 (296)
Q Consensus 245 ~kGd~VkVI~Ge~RG~tG~LisI-D~~ 270 (296)
..|.-|+|+.|.++|....++.| |..
T Consensus 6 ~~GrVvvv~~GR~aGkk~VIv~~iDd~ 32 (125)
T COG2163 6 EVGRVVVVTAGRFAGKKVVIVKIIDDN 32 (125)
T ss_pred cCCeEEEEecceeCCceEEEEEEccCC
Confidence 46888999999999999999999 544
No 225
>PRK09507 cspE cold shock protein CspE; Reviewed
Probab=20.69 E-value=3.8e+02 Score=20.17 Aligned_cols=55 Identities=7% Similarity=0.128 Sum_probs=38.5
Q ss_pred CCeEEEEEecC--CeEEEEeCCCCeeeeeeCCceeEc---CCCCCCeEEEEeCC-CCCceE
Q psy13744 208 GQIGVIRHLGS--GVCSVYLAEEERTLSIEAHELEPV---MPQPNDKVKVIVGE-HKECTG 262 (296)
Q Consensus 208 gqkGVVrsV~~--g~c~V~L~d~~~vv~V~q~~LEtV---iP~kGd~VkVI~Ge-~RG~tG 262 (296)
..+|+|+.-.+ |+-=|.-.+.++-|-|..+.|+.- .++.|++|.....+ .+|..+
T Consensus 3 ~~~G~Vk~f~~~kGyGFI~~~~g~~dvfvH~s~l~~~g~~~l~~G~~V~f~~~~~~~G~~A 63 (69)
T PRK09507 3 KIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNGFKTLAEGQRVEFEITNGAKGPSA 63 (69)
T ss_pred ccceEEEEEeCCCCcEEEecCCCCeeEEEEeecccccCCCCCCCCCEEEEEEEECCCCccc
Confidence 35788888753 665677777777788888888863 57899999886533 245433
No 226
>COG1923 Hfq Uncharacterized host factor I protein [General function prediction only]
Probab=20.66 E-value=2.7e+02 Score=22.28 Aligned_cols=51 Identities=18% Similarity=0.222 Sum_probs=37.2
Q ss_pred cCceEEEEe-cCCCCccccCCeEEEEEecCCeEEEEeCCCCeeeeeeCCceeEcCCCCC
Q psy13744 190 TTDIEVRIN-ENARDPEFRGQIGVIRHLGSGVCSVYLAEEERTLSIEAHELEPVMPQPN 247 (296)
Q Consensus 190 ~~dI~VkI~-~~~~d~~yygqkGVVrsV~~g~c~V~L~d~~~vv~V~q~~LEtViP~kG 247 (296)
.+.|.|+|- -++- +-+|.|++.++. +|-|.++++...|.-..+.|+.|+..
T Consensus 17 k~~i~VtIfLvNG~-----~L~G~V~sfD~f--~VlL~~~g~qqlVYKHAISTi~p~~~ 68 (77)
T COG1923 17 KEKIPVTIFLVNGF-----KLQGQVESFDNF--VVLLKNTGKQQLVYKHAISTIVPSRP 68 (77)
T ss_pred hcCCeEEEEEEcCE-----EEEEEEEeeeeE--EEEEEcCCeeEEEEeeeeeEEccccc
Confidence 356888884 3332 468899998643 46666677888899999999999863
No 227
>PRK04192 V-type ATP synthase subunit A; Provisional
Probab=20.48 E-value=4.3e+02 Score=28.29 Aligned_cols=50 Identities=12% Similarity=0.243 Sum_probs=31.6
Q ss_pred CeEEEEEecCCeEEEEeCCCCeeeeeeCCceeEcCCCCCCeEEEEeCCCCCceEEEEEEeCCCcEEEE
Q psy13744 209 QIGVIRHLGSGVCSVYLAEEERTLSIEAHELEPVMPQPNDKVKVIVGEHKECTGVLLSVDNGEGVVKL 276 (296)
Q Consensus 209 qkGVVrsV~~g~c~V~L~d~~~vv~V~q~~LEtViP~kGd~VkVI~Ge~RG~tG~LisID~~dgiVkl 276 (296)
.+|.|.+|.+..+.|..... .+.++.|+| | ..+..|+++.++++...+++
T Consensus 3 ~~G~I~~V~Gpvv~~~~~~~---------------~~~~E~v~v--~-~~~l~gEVi~~~~d~a~iqv 52 (586)
T PRK04192 3 TKGKIVRVSGPLVVAEGMGG---------------ARMYEVVRV--G-EEGLIGEIIRIEGDKATIQV 52 (586)
T ss_pred ceeEEEEEECcEEEEEeCCC---------------CCccCEEEE--C-CCcEEEEEEEEeCCceEEEE
Confidence 47888888877776664321 334555555 3 23467777777777776664
No 228
>cd01726 LSm6 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm6 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=20.40 E-value=3.1e+02 Score=20.27 Aligned_cols=25 Identities=20% Similarity=0.224 Sum_probs=19.4
Q ss_pred CCCeEEEEeCCCCCceEEEEEEeCC
Q psy13744 246 PNDKVKVIVGEHKECTGVLLSVDNG 270 (296)
Q Consensus 246 kGd~VkVI~Ge~RG~tG~LisID~~ 270 (296)
+|.+|.|-.=..+...|+|.++|..
T Consensus 9 ~~~~V~V~Lk~g~~~~G~L~~~D~~ 33 (67)
T cd01726 9 IGRPVVVKLNSGVDYRGILACLDGY 33 (67)
T ss_pred CCCeEEEEECCCCEEEEEEEEEccc
Confidence 5778888433367899999999976
No 229
>PF09962 DUF2196: Uncharacterized conserved protein (DUF2196); InterPro: IPR019240 A pair of adjacent genes, ablAB (acetyl-beta-lysine biosynthesis) encodes lysine 2,3-aminomutase and beta-lysine acetyltransferase in methanogenic archaea. Homologous pairs, possibly with identical function, occur in a wide range of species, including Bacillus subtilis. This model describes a conserved hypothetical protein, small in size, with a phylogenetic distribution moderately well correlated to that of the acetyltransferase family. This protein family is also described as DUF2196 and COG4895 from COG. The function is unknown.
Probab=20.06 E-value=2.4e+02 Score=21.63 Aligned_cols=40 Identities=15% Similarity=0.106 Sum_probs=24.0
Q ss_pred ccCceEEEEecCCCCccccCCeEEEEEec-C-----CeEEEEeCCC
Q psy13744 189 HTTDIEVRINENARDPEFRGQIGVIRHLG-S-----GVCSVYLAEE 228 (296)
Q Consensus 189 l~~dI~VkI~~~~~d~~yygqkGVVrsV~-~-----g~c~V~L~d~ 228 (296)
+..++.|.|+-+.+...=.--.|+|+++. + .-.+|.|.+.
T Consensus 9 I~~G~~V~IVlK~dQ~tg~lt~GiV~~iLT~s~~HP~GIKVrL~~G 54 (62)
T PF09962_consen 9 IKPGITVEIVLKQDQRTGKLTEGIVKDILTNSPTHPHGIKVRLEDG 54 (62)
T ss_pred ccCCCEEEEEECCCCCcCccccEEhheeecCCCCCCCCcEEEecCC
Confidence 66788888874333222235678998885 1 2246666643
Done!