Query 000247
Match_columns 1790
No_of_seqs 411 out of 950
Neff 3.7
Searched_HMMs 46136
Date Fri Mar 29 01:10:32 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/000247.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/000247hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1999 RNA polymerase II tran 100.0 6E-131 1E-135 1192.6 51.7 583 107-710 55-735 (1024)
2 COG5164 SPT5 Transcription elo 100.0 1E-51 2.3E-56 472.9 26.7 308 375-710 3-402 (607)
3 PRK08559 nusG transcription an 99.9 9.6E-24 2.1E-28 220.8 16.8 131 222-357 3-133 (153)
4 PF03439 Spt5-NGN: Early trans 99.9 3.4E-22 7.4E-27 190.9 6.8 84 226-310 1-84 (84)
5 KOG1999 RNA polymerase II tran 99.8 8.4E-17 1.8E-21 199.7 46.7 201 490-714 406-639 (1024)
6 TIGR00405 L26e_arch ribosomal 99.8 1.8E-19 3.8E-24 186.3 15.6 125 228-357 1-125 (145)
7 COG0250 NusG Transcription ant 99.7 1.1E-17 2.4E-22 179.7 13.2 133 224-356 2-163 (178)
8 PRK05609 nusG transcription an 99.6 1.7E-14 3.8E-19 153.3 15.7 130 224-356 5-166 (181)
9 TIGR01956 NusG_myco NusG famil 99.6 1.2E-14 2.6E-19 163.1 14.4 129 226-357 1-246 (258)
10 TIGR00922 nusG transcription t 99.5 5E-14 1.1E-18 149.1 14.4 127 227-356 1-159 (172)
11 COG5164 SPT5 Transcription elo 99.5 3.7E-15 8E-20 173.9 1.7 338 213-590 28-388 (607)
12 PF11942 Spt5_N: Spt5 transcri 99.5 5E-15 1.1E-19 145.6 1.9 92 119-220 1-97 (97)
13 PRK09014 rfaH transcriptional 99.3 3.1E-12 6.7E-17 134.7 10.3 127 226-356 3-148 (162)
14 TIGR01955 RfaH transcriptional 99.3 7.2E-12 1.6E-16 131.0 10.4 128 227-357 1-148 (159)
15 smart00738 NGN In Spt5p, this 99.2 4E-11 8.6E-16 117.0 9.2 83 226-311 1-105 (106)
16 PF02357 NusG: Transcription t 97.9 1.6E-05 3.4E-10 76.8 5.2 76 226-303 2-91 (92)
17 KOG3973 Uncharacterized conser 97.5 0.00038 8.3E-09 81.5 9.3 19 1511-1530 442-460 (465)
18 KOG0921 Dosage compensation co 97.3 0.00087 1.9E-08 85.8 10.3 10 71-80 92-101 (1282)
19 PF00467 KOW: KOW motif; Inte 97.2 0.00039 8.5E-09 56.6 4.2 32 321-352 1-32 (32)
20 PF00467 KOW: KOW motif; Inte 97.1 0.00066 1.4E-08 55.3 4.0 32 662-693 1-32 (32)
21 KOG3973 Uncharacterized conser 96.7 0.006 1.3E-07 72.0 9.0 9 351-359 139-147 (465)
22 TIGR00405 L26e_arch ribosomal 95.6 0.018 4E-07 60.7 5.5 50 660-709 87-140 (145)
23 smart00739 KOW KOW (Kyprides, 95.3 0.024 5.1E-07 43.9 3.9 27 555-581 1-27 (28)
24 PRK08559 nusG transcription an 95.1 0.042 9.2E-07 59.0 6.3 51 660-710 95-149 (153)
25 smart00739 KOW KOW (Kyprides, 94.5 0.052 1.1E-06 42.0 3.8 27 318-344 1-27 (28)
26 PRK01191 rpl24p 50S ribosomal 94.0 0.11 2.5E-06 54.5 6.2 50 304-355 33-82 (120)
27 CHL00141 rpl24 ribosomal prote 93.9 0.086 1.9E-06 52.1 4.9 28 555-582 8-35 (83)
28 TIGR01955 RfaH transcriptional 93.9 0.099 2.2E-06 55.5 5.7 42 660-701 109-151 (159)
29 PRK12281 rplX 50S ribosomal pr 93.8 0.091 2E-06 51.2 4.9 28 555-582 6-33 (76)
30 TIGR00922 nusG transcription t 93.7 0.11 2.3E-06 56.2 5.6 47 660-706 120-170 (172)
31 PRK00004 rplX 50S ribosomal pr 93.5 0.11 2.3E-06 53.4 5.0 28 555-582 4-31 (105)
32 PRK05609 nusG transcription an 93.1 0.14 3.1E-06 55.4 5.6 47 660-706 127-177 (181)
33 CHL00141 rpl24 ribosomal prote 92.5 0.19 4.2E-06 49.7 5.0 39 316-354 6-44 (83)
34 PF00524 PPV_E1_N: E1 Protein, 92.3 0.042 9E-07 58.2 0.2 69 116-198 14-86 (130)
35 PRK09014 rfaH transcriptional 92.1 0.22 4.7E-06 53.5 5.3 47 660-706 110-159 (162)
36 TIGR01079 rplX_bact ribosomal 91.5 0.28 6E-06 50.4 4.9 28 555-582 3-30 (104)
37 PRK12281 rplX 50S ribosomal pr 91.5 0.29 6.3E-06 47.8 4.8 38 317-354 5-42 (76)
38 TIGR01080 rplX_A_E ribosomal p 91.2 0.41 8.9E-06 50.0 5.9 39 316-354 39-77 (114)
39 PRK01191 rpl24p 50S ribosomal 91.1 0.43 9.4E-06 50.3 6.0 28 555-582 45-72 (120)
40 COG0250 NusG Transcription ant 90.9 0.35 7.6E-06 53.8 5.4 43 659-701 123-167 (178)
41 TIGR01956 NusG_myco NusG famil 90.9 0.36 7.9E-06 56.3 5.7 43 659-701 205-249 (258)
42 PTZ00194 60S ribosomal protein 90.7 0.48 1E-05 51.2 6.0 52 304-357 34-85 (143)
43 PRK00004 rplX 50S ribosomal pr 89.7 0.5 1.1E-05 48.6 4.9 37 318-354 4-40 (105)
44 PTZ00194 60S ribosomal protein 89.5 0.39 8.5E-06 51.9 4.2 28 555-582 46-73 (143)
45 COG0198 RplX Ribosomal protein 89.4 0.47 1E-05 49.0 4.5 30 554-583 3-32 (104)
46 KOG3262 H/ACA small nucleolar 89.3 0.76 1.6E-05 51.4 6.3 16 1207-1222 5-21 (215)
47 TIGR01080 rplX_A_E ribosomal p 88.7 0.53 1.2E-05 49.2 4.4 37 660-696 42-78 (114)
48 KOG3262 H/ACA small nucleolar 88.3 0.94 2E-05 50.7 6.1 11 1512-1522 203-213 (215)
49 PF11623 DUF3252: Protein of u 87.4 1.6 3.5E-05 40.2 6.0 47 660-706 2-52 (53)
50 TIGR01079 rplX_bact ribosomal 85.8 1.1 2.4E-05 46.2 4.7 37 318-354 3-39 (104)
51 COG2933 Predicted SAM-dependen 85.4 1.2 2.6E-05 52.5 5.2 57 229-292 5-61 (358)
52 PF04931 DNA_pol_phi: DNA poly 82.6 1.5 3.2E-05 58.2 5.1 16 236-251 764-779 (784)
53 KOG1708 Mitochondrial/chloropl 81.8 1.4 3E-05 49.9 3.8 30 553-582 70-99 (236)
54 PRK11760 putative 23S rRNA C24 80.8 2.4 5.1E-05 51.8 5.5 65 228-299 4-71 (357)
55 COG0198 RplX Ribosomal protein 79.0 2.9 6.3E-05 43.4 4.7 34 317-352 3-36 (104)
56 CHL00010 infA translation init 76.0 20 0.00043 35.4 9.2 65 504-582 9-73 (78)
57 PF09444 MRC1: MRC1-like domai 75.5 0.6 1.3E-05 50.6 -1.3 18 113-130 3-20 (145)
58 smart00652 eIF1a eukaryotic tr 74.8 15 0.00033 36.7 8.2 65 502-581 5-69 (83)
59 KOG1832 HIV-1 Vpr-binding prot 74.2 2.7 5.8E-05 55.6 3.6 9 184-192 1469-1477(1516)
60 PTZ00415 transmission-blocking 73.8 1.6 3.4E-05 60.5 1.5 15 224-238 313-327 (2849)
61 PTZ00061 DNA-directed RNA poly 73.8 20 0.00044 41.2 9.9 57 270-329 118-190 (205)
62 PHA02774 E1; Provisional 72.8 1.3 2.8E-05 57.0 0.4 31 298-332 177-207 (613)
63 TIGR01622 SF-CC1 splicing fact 72.2 9.5 0.00021 46.9 7.5 68 238-311 383-455 (457)
64 PLN00208 translation initiatio 71.6 13 0.00028 40.8 7.4 77 491-582 20-97 (145)
65 PF14632 SPT6_acidic: Acidic N 71.6 1.3 2.9E-05 44.9 0.1 9 143-151 20-28 (92)
66 KOG0299 U3 snoRNP-associated p 71.5 2.4 5.1E-05 52.8 2.2 19 180-198 98-116 (479)
67 PF14851 FAM176: FAM176 family 70.4 5.7 0.00012 43.8 4.5 17 179-195 114-130 (153)
68 KOG0415 Predicted peptidyl pro 70.4 9.7 0.00021 46.5 6.7 112 176-303 198-315 (479)
69 KOG0262 RNA polymerase I, larg 70.2 11 0.00024 51.7 7.8 70 226-296 1441-1520(1640)
70 cd05793 S1_IF1A S1_IF1A: Trans 69.6 22 0.00047 35.2 7.8 64 504-582 2-65 (77)
71 COG1588 POP4 RNase P/RNase MRP 68.7 9.8 0.00021 39.1 5.4 47 660-708 14-63 (95)
72 PRK04950 ProP expression regul 67.5 8.3 0.00018 44.5 5.2 46 660-707 167-212 (213)
73 cd04456 S1_IF1A_like S1_IF1A_l 67.0 29 0.00063 34.4 8.1 65 503-582 1-66 (78)
74 PF03115 Astro_capsid: Astrovi 66.7 1.9 4E-05 57.2 0.0 13 176-188 717-729 (787)
75 PF11746 DUF3303: Protein of u 66.1 19 0.00041 36.4 6.8 76 228-303 2-83 (91)
76 PRK12269 bifunctional cytidyla 65.5 57 0.0012 44.6 13.0 196 300-565 605-809 (863)
77 PRK00276 infA translation init 65.4 33 0.00072 33.1 8.1 63 505-581 10-72 (72)
78 PRK04333 50S ribosomal protein 65.1 10 0.00022 38.1 4.7 33 318-351 3-35 (84)
79 PTZ00329 eukaryotic translatio 65.1 23 0.0005 39.3 7.8 76 492-582 21-97 (155)
80 PLN03111 DNA-directed RNA poly 62.0 51 0.0011 38.2 10.0 55 273-329 121-191 (206)
81 PF02724 CDC45: CDC45-like pro 60.2 6.1 0.00013 51.5 2.8 31 280-310 235-266 (622)
82 PRK04012 translation initiatio 59.8 39 0.00085 35.1 7.9 72 495-581 13-85 (100)
83 PRK03879 ribonuclease P protei 59.3 19 0.0004 37.1 5.5 46 660-707 12-60 (96)
84 PF02736 Myosin_N: Myosin N-te 59.1 18 0.00039 31.7 4.6 30 675-705 12-42 (42)
85 smart00361 RRM_1 RNA recogniti 58.9 20 0.00043 33.6 5.3 29 267-295 34-62 (70)
86 PRK04333 50S ribosomal protein 58.8 13 0.00028 37.4 4.2 31 660-690 4-35 (84)
87 PF01176 eIF-1a: Translation i 58.0 35 0.00076 32.4 6.7 62 503-579 4-65 (65)
88 TIGR00739 yajC preprotein tran 57.4 24 0.00051 35.4 5.7 44 660-708 38-81 (84)
89 TIGR00523 eIF-1A eukaryotic/ar 57.2 35 0.00076 35.3 7.0 64 502-582 19-85 (99)
90 PRK14635 hypothetical protein; 57.1 13 0.00028 41.0 4.3 49 660-708 96-155 (162)
91 PF04931 DNA_pol_phi: DNA poly 56.5 9.5 0.00021 50.9 3.7 7 71-77 545-551 (784)
92 PRK05585 yajC preprotein trans 55.2 26 0.00057 36.5 5.8 44 661-709 54-97 (106)
93 PRK12442 translation initiatio 55.1 49 0.0011 33.8 7.4 63 505-581 10-72 (87)
94 PTZ00065 60S ribosomal protein 54.2 22 0.00048 38.4 5.3 35 660-695 8-42 (130)
95 PF02724 CDC45: CDC45-like pro 53.0 11 0.00024 49.2 3.5 13 184-196 199-211 (622)
96 COG1862 YajC Preprotein transl 52.9 25 0.00054 36.4 5.2 46 662-712 46-91 (97)
97 COG3109 ProQ Activator of osmo 52.5 20 0.00043 40.5 4.7 46 660-707 162-207 (208)
98 PTZ00065 60S ribosomal protein 52.4 19 0.00041 39.0 4.4 33 318-351 7-39 (130)
99 PTZ00415 transmission-blocking 52.2 6.9 0.00015 54.9 1.5 17 93-109 120-136 (2849)
100 KOG1708 Mitochondrial/chloropl 52.1 14 0.00029 42.5 3.4 39 660-698 73-114 (236)
101 cd05690 S1_RPS1_repeat_ec5 S1_ 51.5 21 0.00046 32.6 4.1 66 260-351 3-68 (69)
102 smart00316 S1 Ribosomal protei 50.8 37 0.00081 30.1 5.5 67 260-353 5-71 (72)
103 PRK14639 hypothetical protein; 49.9 27 0.00059 37.9 5.2 49 660-708 85-133 (140)
104 TIGR01659 sex-lethal sex-letha 49.5 55 0.0012 40.2 8.3 68 219-295 102-174 (346)
105 PRK12288 GTPase RsgA; Reviewed 48.3 95 0.002 38.2 10.0 86 504-608 40-127 (347)
106 PRK00092 ribosome maturation p 47.5 29 0.00064 37.8 5.1 49 660-708 95-147 (154)
107 TIGR01642 U2AF_lg U2 snRNP aux 46.5 30 0.00065 43.2 5.7 49 240-294 432-488 (509)
108 cd05698 S1_Rrp5_repeat_hs6_sc5 46.0 58 0.0013 30.0 6.1 67 260-353 3-69 (70)
109 PRK05886 yajC preprotein trans 45.5 47 0.001 35.1 5.9 43 661-708 40-82 (109)
110 TIGR02760 TraI_TIGR conjugativ 45.3 87 0.0019 46.5 10.4 93 489-586 1327-1424(1960)
111 PF01868 UPF0086: Domain of un 44.5 58 0.0013 32.9 6.2 48 660-708 11-61 (89)
112 PF10446 DUF2457: Protein of u 44.4 11 0.00025 47.1 1.5 7 226-232 123-129 (458)
113 PRK02749 photosystem I reactio 44.1 37 0.0008 33.3 4.5 43 319-362 3-49 (71)
114 smart00538 POP4 A domain found 44.1 52 0.0011 33.6 5.8 47 660-707 10-59 (92)
115 cd01734 YlxS_C YxlS is a Bacil 43.2 39 0.00085 33.3 4.7 49 660-708 22-76 (83)
116 PF13051 DUF3912: Protein of u 43.0 46 0.001 31.7 4.8 49 660-710 3-54 (68)
117 PF02576 DUF150: Uncharacteris 42.6 40 0.00087 36.1 5.1 49 660-708 84-138 (141)
118 cd04451 S1_IF1 S1_IF1: Transla 42.5 1.3E+02 0.0028 28.2 7.7 60 505-578 4-63 (64)
119 PRK14637 hypothetical protein; 42.2 44 0.00095 36.8 5.4 46 660-707 95-141 (151)
120 cd04461 S1_Rrp5_repeat_hs8_sc7 41.6 63 0.0014 31.2 5.8 69 258-353 15-83 (83)
121 KOG0107 Alternative splicing f 40.7 34 0.00073 38.9 4.2 34 259-292 36-69 (195)
122 PRK14638 hypothetical protein; 40.7 40 0.00086 37.0 4.8 47 660-708 97-143 (150)
123 PRK08572 rps17p 30S ribosomal 40.6 53 0.0012 34.7 5.4 25 543-567 65-89 (108)
124 PRK14643 hypothetical protein; 40.4 41 0.00089 37.5 4.9 50 660-709 101-158 (164)
125 KOG3218 RNA polymerase, 25-kDa 40.3 1.6E+02 0.0035 34.2 9.4 119 188-329 40-173 (208)
126 PRK14634 hypothetical protein; 40.3 39 0.00084 37.3 4.6 47 660-708 97-147 (155)
127 TIGR03630 arch_S17P archaeal r 40.3 53 0.0011 34.5 5.3 25 543-567 63-87 (102)
128 PF00575 S1: S1 RNA binding do 39.9 1E+02 0.0022 28.7 6.7 57 492-565 2-58 (74)
129 cd05703 S1_Rrp5_repeat_hs12_sc 39.8 66 0.0014 30.8 5.6 68 260-353 3-71 (73)
130 TIGR00008 infA translation ini 39.6 1.2E+02 0.0027 29.7 7.3 61 504-578 7-67 (68)
131 CHL00125 psaE photosystem I su 39.5 44 0.00096 32.3 4.2 41 319-360 2-46 (64)
132 PRK09521 exosome complex RNA-b 38.9 1.4E+02 0.003 33.7 8.7 90 491-606 61-156 (189)
133 PF10842 DUF2642: Protein of u 38.9 69 0.0015 31.3 5.4 45 660-707 18-62 (66)
134 PF10574 UPF0552: Uncharacteri 38.9 36 0.00077 39.7 4.2 98 226-340 58-176 (224)
135 COG0361 InfA Translation initi 38.8 1.2E+02 0.0026 30.4 7.1 65 504-582 9-73 (75)
136 PRK14644 hypothetical protein; 37.5 41 0.0009 36.4 4.2 48 660-707 82-135 (136)
137 cd01854 YjeQ_engC YjeQ/EngC. 37.4 1.9E+02 0.0041 34.5 9.9 84 506-608 1-85 (287)
138 PF10446 DUF2457: Protein of u 37.4 14 0.0003 46.5 0.7 10 572-581 399-408 (458)
139 COG2139 RPL21A Ribosomal prote 36.9 58 0.0013 33.9 4.8 49 660-708 33-93 (98)
140 PRK00098 GTPase RsgA; Reviewed 36.5 2E+02 0.0044 34.4 10.1 86 505-608 2-87 (298)
141 KOG4156 Claspin, protein media 36.0 8 0.00017 49.6 -1.5 13 118-130 1052-1064(1329)
142 KOG0130 RNA-binding protein RB 35.9 56 0.0012 36.0 4.8 61 226-292 71-136 (170)
143 cd05708 S1_Rrp5_repeat_sc12 S1 35.9 90 0.002 29.0 5.7 70 260-355 5-74 (77)
144 PF11515 Cul7: Mouse developme 35.8 56 0.0012 32.9 4.4 39 304-347 8-49 (78)
145 PF02427 PSI_PsaE: Photosystem 35.4 67 0.0014 31.0 4.6 40 319-359 1-44 (61)
146 PLN00045 photosystem I reactio 35.3 63 0.0014 33.5 4.8 45 315-360 36-85 (101)
147 PF13893 RRM_5: RNA recognitio 35.3 50 0.0011 29.3 3.8 36 259-294 10-45 (56)
148 TIGR02760 TraI_TIGR conjugativ 34.8 1.6E+02 0.0035 43.9 10.5 94 490-588 680-784 (1960)
149 PTZ00223 40S ribosomal protein 34.3 47 0.001 39.9 4.4 52 554-609 170-226 (273)
150 PLN00036 40S ribosomal protein 34.1 61 0.0013 38.7 5.2 52 554-609 173-229 (261)
151 COG1471 RPS4A Ribosomal protei 34.0 50 0.0011 38.9 4.4 52 554-609 172-229 (241)
152 PF04050 Upf2: Up-frameshift s 34.0 2.6 5.6E-05 46.4 -5.4 13 183-195 66-78 (170)
153 PRK14640 hypothetical protein; 33.2 65 0.0014 35.4 4.9 46 660-707 94-143 (152)
154 PTZ00118 40S ribosomal protein 32.7 65 0.0014 38.6 5.2 52 554-609 173-229 (262)
155 KOG3130 Uncharacterized conser 32.3 50 0.0011 41.3 4.2 11 219-229 358-369 (514)
156 PRK14712 conjugal transfer nic 32.1 2E+02 0.0043 42.2 10.3 92 490-589 515-617 (1623)
157 PRK08059 general stress protei 31.8 2.7E+02 0.0058 29.4 9.0 58 491-565 4-61 (123)
158 PRK13709 conjugal transfer nic 31.6 1.9E+02 0.0042 42.6 10.3 92 489-588 646-748 (1747)
159 PRK14630 hypothetical protein; 31.4 86 0.0019 34.3 5.4 45 660-708 94-139 (143)
160 cd05687 S1_RPS1_repeat_ec1_hs1 31.2 1.7E+02 0.0036 27.1 6.6 67 260-353 3-69 (70)
161 PRK14645 hypothetical protein; 31.1 66 0.0014 35.6 4.6 45 660-707 99-143 (154)
162 cd05688 S1_RPS1_repeat_ec3 S1_ 31.0 88 0.0019 28.2 4.7 64 260-351 4-67 (68)
163 PRK11634 ATP-dependent RNA hel 30.9 77 0.0017 41.8 5.9 11 301-311 279-289 (629)
164 COG1096 Predicted RNA-binding 30.8 1.6E+02 0.0036 33.9 7.6 42 553-607 116-157 (188)
165 PRK04313 30S ribosomal protein 30.7 56 0.0012 38.6 4.1 52 554-609 170-227 (237)
166 PRK13709 conjugal transfer nic 30.5 2.1E+02 0.0046 42.2 10.4 94 489-589 1273-1373(1747)
167 PRK11642 exoribonuclease R; Pr 30.5 1.3E+02 0.0029 41.1 8.0 81 259-354 645-725 (813)
168 PRK10486 autoinducer-2 (AI-2) 30.3 2.5E+02 0.0054 28.3 8.1 65 227-292 5-70 (96)
169 PF02699 YajC: Preprotein tran 29.9 17 0.00038 36.0 0.0 44 660-708 37-80 (82)
170 PF11623 DUF3252: Protein of u 29.8 83 0.0018 29.6 4.2 28 319-346 2-31 (53)
171 cd05697 S1_Rrp5_repeat_hs5 S1_ 28.5 1.3E+02 0.0029 27.8 5.5 68 259-353 2-69 (69)
172 cd05792 S1_eIF1AD_like S1_eIF1 28.3 2.6E+02 0.0057 28.2 7.6 64 504-582 2-66 (78)
173 KOG0123 Polyadenylate-binding 28.3 67 0.0015 39.9 4.5 71 216-295 67-140 (369)
174 cd05684 S1_DHX8_helicase S1_DH 28.3 3.2E+02 0.0069 26.1 8.1 15 551-565 44-58 (79)
175 COG2139 RPL21A Ribosomal prote 28.2 71 0.0015 33.3 3.9 49 488-537 29-91 (98)
176 KOG1819 FYVE finger-containing 28.2 35 0.00076 43.2 2.1 28 211-238 528-556 (990)
177 PRK12289 GTPase RsgA; Reviewed 27.9 3.1E+02 0.0067 34.1 9.9 75 503-589 8-85 (352)
178 PRK05807 hypothetical protein; 27.9 1.8E+02 0.0039 31.5 7.0 57 491-565 2-58 (136)
179 cd04471 S1_RNase_R S1_RNase_R: 27.9 70 0.0015 30.2 3.7 28 317-354 56-83 (83)
180 PRK06531 yajC preprotein trans 27.8 70 0.0015 34.0 3.9 47 662-712 39-85 (113)
181 COG0056 AtpA F0F1-type ATP syn 27.7 1E+02 0.0022 39.6 5.8 33 489-521 44-76 (504)
182 PRK14636 hypothetical protein; 27.5 82 0.0018 35.6 4.6 48 660-708 95-146 (176)
183 PF11424 DUF3195: Protein of u 26.8 60 0.0013 33.0 3.0 43 228-278 2-44 (89)
184 PRK08582 hypothetical protein; 26.7 2E+02 0.0044 31.2 7.2 57 492-565 3-59 (139)
185 PRK11634 ATP-dependent RNA hel 26.6 1.2E+02 0.0026 40.1 6.6 12 682-693 523-534 (629)
186 PRK14632 hypothetical protein; 26.6 1E+02 0.0022 34.8 5.0 49 660-708 95-156 (172)
187 PF06524 NOA36: NOA36 protein; 26.5 95 0.0021 37.2 5.0 6 81-86 206-211 (314)
188 PRK14633 hypothetical protein; 26.4 97 0.0021 34.1 4.8 48 660-708 91-142 (150)
189 cd05705 S1_Rrp5_repeat_hs14 S1 26.3 1.3E+02 0.0028 29.0 5.2 67 259-351 5-73 (74)
190 PRK14646 hypothetical protein; 26.2 93 0.002 34.4 4.7 47 660-708 97-147 (155)
191 PF05918 API5: Apoptosis inhib 26.2 22 0.00048 46.1 0.0 11 431-441 270-280 (556)
192 PRK14712 conjugal transfer nic 26.1 3.2E+02 0.0068 40.3 10.7 93 489-587 1144-1242(1623)
193 cd05691 S1_RPS1_repeat_ec6 S1_ 26.0 1.8E+02 0.0038 26.8 5.8 67 260-353 3-69 (73)
194 PLN03134 glycine-rich RNA-bind 25.9 1.4E+02 0.003 32.3 5.9 59 226-293 36-99 (144)
195 COG2163 RPL14A Ribosomal prote 25.8 89 0.0019 33.9 4.3 33 318-351 4-36 (125)
196 KOG0943 Predicted ubiquitin-pr 25.5 35 0.00076 47.0 1.5 24 268-291 1915-1938(3015)
197 COG1818 Predicted RNA-binding 25.2 2.6E+02 0.0057 31.9 7.9 76 227-311 3-83 (175)
198 COG0186 RpsQ Ribosomal protein 25.1 1.1E+02 0.0024 31.4 4.5 23 544-567 45-67 (87)
199 PRK12766 50S ribosomal protein 24.8 19 0.00042 42.1 -0.8 15 180-195 99-113 (232)
200 cd05706 S1_Rrp5_repeat_sc10 S1 24.7 2.2E+02 0.0047 26.6 6.2 68 259-353 5-72 (73)
201 KOG2055 WD40 repeat protein [G 24.7 61 0.0013 41.3 3.3 21 176-196 130-150 (514)
202 PF08595 RXT2_N: RXT2-like, N- 24.6 36 0.00078 37.6 1.2 6 119-124 54-59 (149)
203 cd05707 S1_Rrp5_repeat_sc11 S1 24.5 1.8E+02 0.0039 26.9 5.6 65 260-351 3-67 (68)
204 PRK02001 hypothetical protein; 24.4 1.3E+02 0.0028 33.5 5.3 48 660-707 87-146 (152)
205 smart00243 GAS2 Growth-Arrest- 24.2 1.6E+02 0.0035 29.4 5.3 50 304-356 5-55 (73)
206 KOG4211 Splicing factor hnRNP- 24.1 1.5E+02 0.0032 38.3 6.4 97 225-333 8-114 (510)
207 PLN03078 Putative tRNA pseudou 23.7 1.1E+02 0.0025 39.6 5.4 53 271-323 355-409 (513)
208 PRK05610 rpsQ 30S ribosomal pr 23.6 1.4E+02 0.0031 30.3 5.0 25 543-568 42-66 (84)
209 cd04461 S1_Rrp5_repeat_hs8_sc7 23.3 1.7E+02 0.0038 28.2 5.5 60 489-565 9-68 (83)
210 PRK14647 hypothetical protein; 22.6 1.2E+02 0.0026 33.6 4.8 48 660-708 96-152 (159)
211 COG1532 Predicted RNA-binding 22.6 50 0.0011 31.2 1.5 32 321-352 23-56 (57)
212 PRK06763 F0F1 ATP synthase sub 22.5 1.5E+02 0.0033 34.5 5.5 15 552-566 161-175 (213)
213 COG2163 RPL14A Ribosomal prote 22.4 1E+02 0.0022 33.5 3.9 46 660-706 5-50 (125)
214 cd05686 S1_pNO40 S1_pNO40: pNO 22.3 2.8E+02 0.0061 26.3 6.5 57 493-565 2-58 (73)
215 TIGR03635 S17_bact 30S ribosom 22.3 1.5E+02 0.0033 29.2 4.8 23 544-567 38-60 (71)
216 PF14001 YdfZ: YdfZ protein 22.3 94 0.002 30.3 3.2 32 548-582 2-33 (64)
217 PRK00321 rdgC recombination as 22.2 2.3E+02 0.0051 34.6 7.3 85 260-360 124-214 (303)
218 smart00743 Agenet Tudor-like d 22.2 1.9E+02 0.0041 26.5 5.2 48 491-538 2-54 (61)
219 PF02187 GAS2: Growth-Arrest-S 22.0 1.5E+02 0.0032 29.7 4.6 48 304-354 5-53 (73)
220 COG0779 Uncharacterized protei 21.7 1.5E+02 0.0033 33.1 5.2 47 660-708 96-146 (153)
221 COG5177 Uncharacterized conser 21.6 62 0.0013 41.6 2.5 18 175-192 437-454 (769)
222 PF00076 RRM_1: RNA recognitio 21.5 94 0.002 27.6 3.1 28 267-294 36-63 (70)
223 PRK12766 50S ribosomal protein 21.4 74 0.0016 37.5 2.9 9 123-131 58-66 (232)
224 PF03992 ABM: Antibiotic biosy 21.3 6E+02 0.013 23.2 8.3 56 227-282 5-61 (78)
225 KOG0339 ATP-dependent RNA heli 21.3 79 0.0017 41.0 3.3 18 406-423 372-391 (731)
226 PF10781 DSRB: Dextransucrase 21.1 2.2E+02 0.0047 27.5 5.2 34 556-590 1-38 (62)
227 smart00360 RRM RNA recognition 21.0 2.7E+02 0.0058 23.8 5.7 25 269-293 37-61 (71)
228 PRK01889 GTPase RsgA; Reviewed 21.0 3.2E+02 0.007 33.8 8.3 89 504-608 29-119 (356)
229 PF01037 AsnC_trans_reg: AsnC 20.9 5.2E+02 0.011 23.8 7.9 61 229-297 2-67 (74)
230 PRK08059 general stress protei 20.8 2.2E+02 0.0048 30.0 6.0 71 259-356 9-79 (123)
231 PTZ00287 6-phosphofructokinase 20.5 2.2E+02 0.0048 41.1 7.4 96 232-332 478-597 (1419)
232 PRK06531 yajC preprotein trans 20.5 2.3E+02 0.0051 30.3 6.0 42 303-355 27-68 (113)
233 PRK10708 hypothetical protein; 20.2 2E+02 0.0043 27.8 4.8 35 556-590 1-38 (62)
234 PLN00036 40S ribosomal protein 20.1 1.9E+02 0.0041 34.9 5.8 29 316-344 172-200 (261)
235 KOG2897 DNA-binding protein YL 20.1 65 0.0014 40.2 2.2 18 178-195 84-101 (390)
No 1
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=100.00 E-value=6.4e-131 Score=1192.60 Aligned_cols=583 Identities=35% Similarity=0.518 Sum_probs=468.6
Q ss_pred CccccccccccCcceeccccCCCCCchhhcCCCcCCC--CCCCCccchhhhhccCccccccccccCCCCCCCccccCCHH
Q 000247 107 HNRKRKNRSVLQFVEDAADVDYDDDDEEEVGNESDNS--GGFADDDFMEELFDAQPKVNNEMGQAHNLPFIPKEEEMDEE 184 (1790)
Q Consensus 107 r~rKRkrrr~n~FiDdEAEVDDDeEEEDEeeEe~e~~--~~Fi~dD~~~d~~e~~~~~~~d~r~~~~l~~r~~eEd~DaE 184 (1790)
..+|+|+.+...||+.|||||||+||+|+|+|++|+. ..||. +..+++++++ .++|.|++++ ++..+ .+|
T Consensus 55 ~~~~~k~~s~~gf~~~e~dvDdeveddd~~~edEed~~~~~~ie-~~e~~~~d~~----~~~R~~~~~~-~~~~~--~~e 126 (1024)
T KOG1999|consen 55 PDEKDKKESGGGFIDREADVDDEVEDDDDDEEDEEDIELHNDIE-ESEEDLPDER----GDRRLRRYWD-RQLNE--LEE 126 (1024)
T ss_pred hhhhccccccccccccccccccccccccchhccCcchhhcccch-hccccccccc----ccccchhhhh-hhhhH--HHH
Confidence 3455677888899999999999998876666554321 12221 1111222211 1122222222 12222 577
Q ss_pred HHHHHHHHHhccccchhhchhhHHHhhhcccccCCCCCCCCcEEEEEecCchhHHHHHHHHHHHHhhccCCCCCcEEEEE
Q 000247 185 EFDKMMEERYKSNKLIRYAEEDYEAKKMLEREYHMPCPEDPTIWKVKCMAGRERQSAFCLMQKFVDLQSLGSKMQIISAF 264 (1790)
Q Consensus 185 elAe~LkERY~r~s~~~y~~d~~e~~~~VpQqlLLPSVkDPkLWaVKCK~GkEReVV~~LmrKii~lq~~g~~L~I~SVF 264 (1790)
++|+.|+|||.... .|.+.+++++++|+||+|||+|+||+||+|||++|+||+||+|||+||++++++..||+|+|||
T Consensus 127 ~~~~r~aee~~~~~--~~~~~~~~~~d~I~Q~~LLPsvkDP~LW~VKC~iG~Er~~a~~LMrK~i~~~~t~~plqI~Sv~ 204 (1024)
T KOG1999|consen 127 ELAKRYAEEYIEKY--GFEDGDDEDSDDIPQQALLPSVKDPNLWIVKCKIGREREVAFCLMRKFIELDKTDTPLQIKSVF 204 (1024)
T ss_pred HHHHHHHHhhcccc--cccccchhcccchhHHhhCCCCCCCCeeEEEeccccHHHHHHHHHHHHHhhcccCCCceEEEEE
Confidence 77777777776532 1332333445889999999999999999999999999999999999999999999999999999
Q ss_pred EeCCCCcEEEEEeccchhHHHHhcCCCCEEeceeccCCHHHHHHHhhcccccccccCCCEEEEecCcCCCCcEEEEEEeC
Q 000247 265 AVDHIKGFIFIEADKQCDINEACKGLSGIYYSRLAPVPKNEVSHLLSAQIKRNEVSEGTWAYVKNGKYKGDLAQVVYVNN 344 (1790)
Q Consensus 265 vpd~lKGYIYVEA~kq~dVkeAIkGI~gVy~sK~~pVPikEM~dLLkvkkks~~Lk~GdwVRIKrGpYKGDLAQV~eVDe 344 (1790)
++++|+|||||||+++.||++||++|++||.++|+||||+||++||+|+++.+.|++|.|||||+|+||||||||++|++
T Consensus 205 a~D~lkGyIYIEA~KqshV~~Ai~gv~niy~~~~~lVPikEM~dvLkV~K~~v~L~~gswVRiKrG~YKgDLAqVd~Vd~ 284 (1024)
T KOG1999|consen 205 AKDHLKGYIYIEADKQSHVKEAIEGVRNIYANRILLVPIKEMPDVLKVVKKVVQLSEGSWVRIKRGKYKGDLAQVDDVDE 284 (1024)
T ss_pred eccccceeEEEEechhHHHHHHHhhhhhheeccEEEEehhHhhhhhhhhhhhhccCccceEEEeccccccceeeeeeecc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCEEEEEEeccCchhhHhhhcCCCcccCCCCCCCCCCCChhhHhhhcCceeecccCCCCceEEecCCceeecceEEEEE
Q 000247 345 ARKRATVKLIPRIDLQALAAKFGGGVAMKKTDSPAPRLISPSELEEFRPLIQYRRDRDTGKVFENLDGMMLKDGYLYKKV 424 (1790)
Q Consensus 345 nk~kVtVKLVPRIDy~~l~~k~~gg~~kKK~~RPPqRLFn~~Eark~~~~~~~rrd~~tG~~f~i~~G~~ykDGFLyK~f 424 (1790)
++++|+|||||||||+++..++. ....+|++||++|||+..|++.++++++.+++..++.+|+++.+++|+||||||.|
T Consensus 285 ~~n~v~lKlIPRIDyq~~~~~~~-~~~~~ka~~p~~R~~~~~~~~~~~ir~~~~~~~~~Gd~l~~~gn~~~~dGFLyK~v 363 (1024)
T KOG1999|consen 285 NRNRVRLKLIPRIDYQKLLGKLE-ETTDKKAFRPAPRRPNQKEFDEEAIRSEGRRDHSRGDYLEFEGNELFKDGFLYKDV 363 (1024)
T ss_pred cCCEEEEEEeccccHHhhhcccc-ccchhhccCCcccCCCccccchhhhhhccccccccCceEEecCCceeccceeeeee
Confidence 99999999999999999998887 56677889999999999999999988888999999999999988899999999999
Q ss_pred eccceEecCCCCCHHHHhhcCCCCCCccccHHHHHHHH-------------------hccc--cccEEEe----------
Q 000247 425 SIDSLSCWGVVPSEEELLKFQPSESNESADLEWLSQLY-------------------GERK--KKRTTIV---------- 473 (1790)
Q Consensus 425 kI~sL~tedVnPTLEEL~kF~~~~~de~~DL~~La~~~-------------------ge~k--k~~ii~v---------- 473 (1790)
+|++|++++|+|||+||+||++..+ .+||+.++.++ |+++ |+.|..|
T Consensus 364 ~i~sI~t~gV~PT~dELekF~~~~e--~~Dl~~~st~~~~r~~~~~F~~GD~VeV~~Gel~glkG~ve~vdg~~vti~~~ 441 (1024)
T KOG1999|consen 364 SISSIITDGVKPTLDELEKFNPSNE--EGDLEWVSTLKSNRKKKHLFSPGDAVEVIVGELKGLKGKVESVDGTIVTIMSK 441 (1024)
T ss_pred ecceeeecCcccCHHHHHhhcCCCc--cccceeeeeeccccccccccCCCCeEEEeeeeeccceeEEEeccCceEEEeec
Confidence 9999999999999999999998644 78888765221 1111 1111111
Q ss_pred ---------------------------ecCCCcc-----------------------------------cccCCCCcccc
Q 000247 474 ---------------------------GKGGDKG-----------------------------------EGSSGSSLENS 491 (1790)
Q Consensus 474 ---------------------------~kGg~kg-----------------------------------E~ssG~~slG~ 491 (1790)
+.|.+++ |+.++++.+++
T Consensus 442 ~e~l~~pl~~~~~eLrKyF~~GDhVKVi~G~~eG~tGlVvrVe~~~vi~~Sd~t~eel~Vf~~dlq~c~ev~~gv~~~ge 521 (1024)
T KOG1999|consen 442 HEDLKGPLEVPASELRKYFEPGDHVKVIAGRYEGDTGLVVRVEQGDVILLSDLTMEELKVFARDLQLCSEVTLGVEKSGE 521 (1024)
T ss_pred cccCCCccccchHhhhhhccCCCeEEEEeccccCCcceEEEEeCCeEEEEecCccceeeEEehhcccchheeeccccccc
Confidence 1121221 34566778899
Q ss_pred cccCcEEEecCCceEEEEEEecCceEEEccCCCCCCceEEEecccccCCCCCCcccccccCCCcccCCCeEEEecCCCCC
Q 000247 492 FELYELVCFGRKDFGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVSEGPSKD 571 (1790)
Q Consensus 492 FeLgDLVQLD~~TVGVIVrVEkDEsfkVLdq~gD~~~VvtVk~~eI~~K~~~rr~vAtD~~gn~I~vGD~VKVIdGphkG 571 (1790)
|||||||||+.++|||||++|+ +.|+||++++ +|++|++.+|..|+..++++|+|+++|+|+++|+|+||.||+++
T Consensus 522 ~e~hdlVqLd~~~vgvI~rle~-e~~~vl~~~g---~v~~i~~~~i~~kk~~r~~~~~D~~~n~I~~kD~Vkvi~Gp~~g 597 (1024)
T KOG1999|consen 522 YELHDLVQLDNQNVGVIVRLER-ETFQVLGMNG---KVVTIRKSSITKKKDNRKAVAVDRNGNEIRVKDTVKVIGGPSKG 597 (1024)
T ss_pred ccccceeecCCCcEEEEEEecc-hheeeecCcC---ceEEEeechhhhhhhhhhheeecccCCeecccceEEEecCCCCC
Confidence 9999999999999999999999 5999999985 79999999999998888999999999999999999999999999
Q ss_pred ceEEEEEEECCEEEEEeCcceeeccEEEEeCCceeecccccccCCCCCCCCCCCCCC-CCCCCCCCCCCcchhh--hccC
Q 000247 572 RQGIVKKIYRGILFIYDENETENGGYFCSKSQHCEKTKVEACEGKGGGSGASGFEEF-PSSPKSPLSPKRSWQA--REQN 648 (1790)
Q Consensus 572 RqG~VlHIyRs~VFL~Sr~~tENgGIFVvRArnv~tv~~~~~~~Kgg~~~~~~f~dl-~~sP~~~lsp~rp~~~--~~~~ 648 (1790)
++|.|+||||.+||||+++++||+||||||++||++++.... ..+.+...++| +|+|.-.++|+.|... ....
T Consensus 598 ~~G~v~~i~r~~~F~h~r~~~En~Gv~vck~k~~~~~g~~~s----t~~~~~~~~~l~~msP~r~~sp~~~~~~~ga~g~ 673 (1024)
T KOG1999|consen 598 REGEVLHIYRPFVFLHSRKNLENGGVFVCKEKNLILAGGKKS----TNSLAFNKGALAPMSPGRIQSPMGPSGGPGAFGG 673 (1024)
T ss_pred ccCccceeecceeeeeehhhcccCCeEEEecCCceeccccCc----ccchhhcccccCCCCcccccCCcCCCCCCCCcCc
Confidence 999999999999999999999999999999999998764211 01111111112 2334222333333211 1111
Q ss_pred ccCcCCCCCCcccCCCEEEEccCCCCCceeEEEEEeCCeEEEEecCcceEEEEecCcccccc
Q 000247 649 TEFKRGDRDGMFAVGQTLRIRVGPLKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLAEVR 710 (1790)
Q Consensus 649 r~fgRGgRD~d~lIGKTVKIrkGPYKGylGiVKDaTdt~ARVELHSk~KtITVdKe~Ls~v~ 710 (1790)
+..+|++++++.|||+||+|+.||||||+|||||+|+++||||||++|++|+|++.+|.++.
T Consensus 674 ~gggrGg~rd~~l~GktVrI~~Gp~KG~~GivkD~~~~~arVELhs~~~ti~vd~~~~~~v~ 735 (1024)
T KOG1999|consen 674 HGGGRGGNRDDSLLGKTVRIRLGPKKGYLGIVKDVNGDTARVELHSKCVTIKVDRLKRKIVG 735 (1024)
T ss_pred CccCccCcCcchhcCcEEEEecCCcccccceeEeccCCeeEEEEEeccEEEEechhhceEEe
Confidence 22244553346899999999999999999999999999999999999999999999999864
No 2
>COG5164 SPT5 Transcription elongation factor [Transcription]
Probab=100.00 E-value=1e-51 Score=472.87 Aligned_cols=308 Identities=22% Similarity=0.254 Sum_probs=240.8
Q ss_pred CCCCCCCCCChhhHhhhcCceeecccCCCCceEEecCCceeecceEEEEEeccceEecCCCCCHHHHhhcCCCCCCcccc
Q 000247 375 TDSPAPRLISPSELEEFRPLIQYRRDRDTGKVFENLDGMMLKDGYLYKKVSIDSLSCWGVVPSEEELLKFQPSESNESAD 454 (1790)
Q Consensus 375 ~~RPPqRLFn~~Eark~~~~~~~rrd~~tG~~f~i~~G~~ykDGFLyK~fkI~sL~tedVnPTLEEL~kF~~~~~de~~D 454 (1790)
+.|||+|||||.|+.++.+...+.|+.. .| .|.++.|+||||||.|+|++++|++|+||+|||.+|..-+. .+|
T Consensus 3 a~r~~~~lfn~t~a~~~~~~~~~kr~~r---~f-~~~ne~~~dgflvk~~Ris~~et~~~~pt~de~~~F~~~~~--dld 76 (607)
T COG5164 3 AHRAPPQLFNPTMALRLDQANLYKRDDR---HF-TYKNEDYIDGFLVKVKRISERETLMRIPTNDEKNVFSIICK--DLD 76 (607)
T ss_pred cccCchhhcCchhhhhcChhhhhccCch---hc-cccCcccccceEEEEeeeceeeecccccccchhhhcCcccc--ccc
Confidence 5799999999999999988655555543 24 57799999999999999999999999999999999997654 488
Q ss_pred HHHHHHHH-----------------hcccc---------ccEE---------------------------EeecCCCccc
Q 000247 455 LEWLSQLY-----------------GERKK---------KRTT---------------------------IVGKGGDKGE 481 (1790)
Q Consensus 455 L~~La~~~-----------------ge~kk---------~~ii---------------------------~v~kGg~kgE 481 (1790)
|.++++.+ |+++. .-|+ .|+.++++.+
T Consensus 77 l~s~~~s~kk~ha~fqpgD~~Evl~Geqrg~~gVV~~~~~~I~tm~~~~~~rl~~p~~~lRk~f~~gD~vkVI~g~~~~d 156 (607)
T COG5164 77 LYSYVESFKKQHAVFQPGDALEVLRGEQRGRVGVVPRQKEMIETMTYHFEQRLCGPWGRLRKGFYKGDLVKVIEGGEMVD 156 (607)
T ss_pred hhHHHHHHhhcccccCCCCeeeeecceecccceeecccccceeeeeeccCceeecchhhhhcccccCCeEEEeccccccc
Confidence 88887654 22211 0010 0111222221
Q ss_pred cc------------------C-------C-------CCcccccccCcEEEecCCceEEEEEEecCceEEEccCCCCCCce
Q 000247 482 GS------------------S-------G-------SSLENSFELYELVCFGRKDFGLIVGMEKDDHYKILKEGSEGPAV 529 (1790)
Q Consensus 482 ~s------------------s-------G-------~~slG~FeLgDLVQLD~~TVGVIVrVEkDEsfkVLdq~gD~~~V 529 (1790)
.. + + ......|+|||||+|+..+|.||+.|++| .|+|+++.+ +|
T Consensus 157 ~g~V~rI~~~~vtF~s~~~~~e~tI~sr~l~ks~~tta~ss~Y~lhd~V~l~~~~vaci~sid~D-v~kvide~g---~v 232 (607)
T COG5164 157 IGTVPRIDGEKVTFNSENFKSESTIKSRGLSKSIDTTATSSIYKLHDYVDLFLEKVACINSIDFD-VEKVIDELG---EV 232 (607)
T ss_pred cceEEEecCceeEEccccccccceEEeccccccccccchhhhhhhhhhhhhhhcceeEEeecccc-hhhhhhhcC---ce
Confidence 10 0 0 11346899999999999999999999995 999999985 69
Q ss_pred EEEecccccCCCCCCcc--cccccCCCcccCCCeEEEecCCCCCceEEEEEEECCEEEEEeCcceeeccEEEEeCCceee
Q 000247 530 VTVERRTLKNGPFDMKF--TALDQSMKVISLNDTARVSEGPSKDRQGIVKKIYRGILFIYDENETENGGYFCSKSQHCEK 607 (1790)
Q Consensus 530 vtVk~~eI~~K~~~rr~--vAtD~~gn~I~vGD~VKVIdGphkGRqG~VlHIyRs~VFL~Sr~~tENgGIFVvRArnv~t 607 (1790)
.||.+.+|..|+..+|. +++|+++++|+++|.|+++.| .+++|+|+|||+.|+|++++.+.||.||||++.+||.+
T Consensus 233 ~t~~~~sI~~kv~~~Rg~~i~~d~ng~eI~igd~VvE~~g--~~~egq~l~i~~~f~f~~t~~i~ennGVfv~~~~nv~~ 310 (607)
T COG5164 233 HTACPISIGDKVRVTRGELIGMDGNGREISIGDAVVESRG--GKFEGQSLGIVKHFDFGETVSIKENNGVFVKIEGNVCI 310 (607)
T ss_pred eEecchhhhhhhecccceeEeeccccceEeeceeEEEecC--CceeeEEEEEEEEEeeeeeeeeeccCceEEEecCceeE
Confidence 99999999999877764 999999999999999999999 67999999999999999999999999999999999998
Q ss_pred cccccccCCCCCCC-CCCCCCCCCCCCCCCC--CCcchhhhccCccCcC--CCCCCcccCCCEEEEccCCCCCceeEEEE
Q 000247 608 TKVEACEGKGGGSG-ASGFEEFPSSPKSPLS--PKRSWQAREQNTEFKR--GDRDGMFAVGQTLRIRVGPLKGYLCRVLA 682 (1790)
Q Consensus 608 v~~~~~~~Kgg~~~-~~~f~dl~~sP~~~ls--p~rp~~~~~~~r~fgR--GgRD~d~lIGKTVKIrkGPYKGylGiVKD 682 (1790)
|+ +|+.+.. ..+|.+| +|++. +..|. -..+.| ++| +.+||+||+||.|+|||++|+|||
T Consensus 311 VA-----tkd~~~s~k~dl~km----np~v~~~~~~p~-----~~~l~r~i~gR--d~aigktVrIr~g~yKG~lGVVKd 374 (607)
T COG5164 311 VA-----TKDFTESLKVDLDKM----NPPVTVNLQNPK-----TNELERKIVGR--DPAIGKTVRIRCGEYKGHLGVVKD 374 (607)
T ss_pred EE-----eccchhhhcccHhhc----CchhhcCCCCCc-----chhhhcccccc--ccccCceEEEeecccccccceeee
Confidence 75 3554422 1233333 22221 11110 011222 245 489999999999999999999999
Q ss_pred EeCCeEEEEecCcceEEEEecCcccccc
Q 000247 683 VRYSDVTVKLDSQQKILTVKGEHLAEVR 710 (1790)
Q Consensus 683 aTdt~ARVELHSk~KtITVdKe~Ls~v~ 710 (1790)
++++.|||||||+||.|||+|++|++..
T Consensus 375 v~~~~arVeLhs~nK~VTI~K~~l~y~~ 402 (607)
T COG5164 375 VDRNIARVELHSNNKFVTIEKSRLAYLG 402 (607)
T ss_pred ccCceEEEEEecCCceEEeehhheEEec
Confidence 9999999999999999999999999853
No 3
>PRK08559 nusG transcription antitermination protein NusG; Validated
Probab=99.91 E-value=9.6e-24 Score=220.83 Aligned_cols=131 Identities=27% Similarity=0.446 Sum_probs=119.6
Q ss_pred CCCCcEEEEEecCchhHHHHHHHHHHHHhhccCCCCCcEEEEEEeCCCCcEEEEEeccchhHHHHhcCCCCEEeceeccC
Q 000247 222 PEDPTIWKVKCMAGRERQSAFCLMQKFVDLQSLGSKMQIISAFAVDHIKGFIFIEADKQCDINEACKGLSGIYYSRLAPV 301 (1790)
Q Consensus 222 VkDPkLWaVKCK~GkEReVV~~LmrKii~lq~~g~~L~I~SVFvpd~lKGYIYVEA~kq~dVkeAIkGI~gVy~sK~~pV 301 (1790)
-+||+||+|+|++|+|+.|+.+|++|+... ++.|++||+|+.|||||||||++.++++++|+++++|++.-..+|
T Consensus 3 ~~~~~WYvv~t~sG~E~~V~~~L~~~~~~~-----~~~i~~i~vp~~fpGYVfVe~~~~~~~~~~i~~v~~v~g~lg~~l 77 (153)
T PRK08559 3 PEMSMIFAVKTTAGQERNVALMLAMRAKKE-----NLPIYAILAPPELKGYVLVEAESKGAVEEAIRGIPHVRGVVPGEI 77 (153)
T ss_pred CCCCcEEEEEeECChHHHHHHHHHHHHHhC-----CCcEEEEEccCCCCcEEEEEEEChHHHHHHHhcCCCEeeeCCCCC
Confidence 368999999999999999999999998643 445999999999999999999999999999999999998655689
Q ss_pred CHHHHHHHhhcccccccccCCCEEEEecCcCCCCcEEEEEEeCCCCEEEEEEeccC
Q 000247 302 PKNEVSHLLSAQIKRNEVSEGTWAYVKNGKYKGDLAQVVYVNNARKRATVKLIPRI 357 (1790)
Q Consensus 302 PikEM~dLLkvkkks~~Lk~GdwVRIKrGpYKGDLAQV~eVDenk~kVtVKLVPRI 357 (1790)
+++||..||...+....|++|++|||++|||+|++|+|++|+.++..|+|+|+.|-
T Consensus 78 ~~~Ei~~il~~~~~~~~~~~G~~V~I~~Gpf~g~~g~V~~vd~~k~~v~v~ll~~~ 133 (153)
T PRK08559 78 SFEEVEHFLKPKPIVEGIKEGDIVELIAGPFKGEKARVVRVDESKEEVTVELLEAA 133 (153)
T ss_pred CHHHHHHHHhccCcccCCCCCCEEEEeccCCCCceEEEEEEcCCCCEEEEEEECCc
Confidence 99999999986654567999999999999999999999999999999999999874
No 4
>PF03439 Spt5-NGN: Early transcription elongation factor of RNA pol II, NGN section; InterPro: IPR005100 Spt5p and prokaryotic NusG are shown to contain a novel 'NGN' domain. The combined NGN and KOW motif regions of Spt5 form the binding domain with Spt4 []. Spt5 complexes with Spt4 as a 1:1 heterodimer snf this Spt5-Spt4 complex regulates early transcription elongation by RNA polymerase II and has an imputed role in pre-mRNA processing via its physical association with mRNA capping enzymes. The Schizosaccharomyces pombe core Spt5-Spt4 complex is a heterodimer bearing a trypsin-resistant Spt4-binding domain within the Spt5 subunit []. ; PDB: 3H7H_B 3QQC_D 3P8B_B 2EXU_A.
Probab=99.86 E-value=3.4e-22 Score=190.92 Aligned_cols=84 Identities=43% Similarity=0.727 Sum_probs=71.7
Q ss_pred cEEEEEecCchhHHHHHHHHHHHHhhccCCCCCcEEEEEEeCCCCcEEEEEeccchhHHHHhcCCCCEEeceeccCCHHH
Q 000247 226 TIWKVKCMAGRERQSAFCLMQKFVDLQSLGSKMQIISAFAVDHIKGFIFIEADKQCDINEACKGLSGIYYSRLAPVPKNE 305 (1790)
Q Consensus 226 kLWaVKCK~GkEReVV~~LmrKii~lq~~g~~L~I~SVFvpd~lKGYIYVEA~kq~dVkeAIkGI~gVy~sK~~pVPikE 305 (1790)
+||+|||++|+|++||++||+|++++..... +.|+|||+|+++||||||||+++++|.+||++|++||...+.+||++|
T Consensus 1 ~iw~Vkc~~G~E~~v~~~l~~k~~~~~~~~~-l~I~Si~~~~~lkGyIyVEA~~~~~V~~ai~gi~~i~~~~~~~vp~~E 79 (84)
T PF03439_consen 1 KIWAVKCKPGQEREVAISLMNKAEDLAKKNN-LNIYSIFAPDSLKGYIYVEAERESDVKEAIRGIRHIRGSRPGLVPIEE 79 (84)
T ss_dssp EEEEEEE-TTTHHHHHHHHHHHHHHHHHHST-----EEEE-TTSTSEEEEEESSHHHHHHHHTT-TTEEEECCEEB-GGG
T ss_pred CEEEEEeCCChHHHHHHHHHHHHHHhhhcCC-CceEEEEEeCCCceEEEEEeCCHHHHHHHHhcccceeeccceeECHHH
Confidence 5999999999999999999999988764444 999999999999999999999999999999999999999999999999
Q ss_pred HHHHh
Q 000247 306 VSHLL 310 (1790)
Q Consensus 306 M~dLL 310 (1790)
|++||
T Consensus 80 ~~~~L 84 (84)
T PF03439_consen 80 MEDLL 84 (84)
T ss_dssp TCGGH
T ss_pred HHhhC
Confidence 99997
No 5
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=99.83 E-value=8.4e-17 Score=199.73 Aligned_cols=201 Identities=18% Similarity=0.223 Sum_probs=139.3
Q ss_pred cccccCcEEEec----CCceEEEEEEecCceEEEccCCCCCCceEEEecccccCCCCCCcccccccCCCcccCCCeEEEe
Q 000247 490 NSFELYELVCFG----RKDFGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVS 565 (1790)
Q Consensus 490 G~FeLgDLVQLD----~~TVGVIVrVEkDEsfkVLdq~gD~~~VvtVk~~eI~~K~~~rr~vAtD~~gn~I~vGD~VKVI 565 (1790)
..|+++|.|+|. ....|+|++|+.+ +++|.....+++..+.|+.++| +|+|++|||||||
T Consensus 406 ~~F~~GD~VeV~~Gel~glkG~ve~vdg~-~vti~~~~e~l~~pl~~~~~eL---------------rKyF~~GDhVKVi 469 (1024)
T KOG1999|consen 406 HLFSPGDAVEVIVGELKGLKGKVESVDGT-IVTIMSKHEDLKGPLEVPASEL---------------RKYFEPGDHVKVI 469 (1024)
T ss_pred cccCCCCeEEEeeeeeccceeEEEeccCc-eEEEeeccccCCCccccchHhh---------------hhhccCCCeEEEE
Confidence 349999999984 4678999999984 5555544333444455555443 7999999999999
Q ss_pred cCCCCCceEEEEEEECCEEEEEeCcceeeccEEEEeCCceeecccccccCCCCCCCCCCCCCCCCCCCC-----------
Q 000247 566 EGPSKDRQGIVKKIYRGILFIYDENETENGGYFCSKSQHCEKTKVEACEGKGGGSGASGFEEFPSSPKS----------- 634 (1790)
Q Consensus 566 dGphkGRqG~VlHIyRs~VFL~Sr~~tENgGIFVvRArnv~tv~~~~~~~Kgg~~~~~~f~dl~~sP~~----------- 634 (1790)
.|+|+|.+|+|+.|++++|||+++.++|+..|||+.-.-|+.|.+. ..+.+ ...+.+|......
T Consensus 470 ~G~~eG~tGlVvrVe~~~vi~~Sd~t~eel~Vf~~dlq~c~ev~~g--v~~~g---e~e~hdlVqLd~~~vgvI~rle~e 544 (1024)
T KOG1999|consen 470 AGRYEGDTGLVVRVEQGDVILLSDLTMEELKVFARDLQLCSEVTLG--VEKSG---EYELHDLVQLDNQNVGVIVRLERE 544 (1024)
T ss_pred eccccCCcceEEEEeCCeEEEEecCccceeeEEehhcccchheeec--ccccc---cccccceeecCCCcEEEEEEecch
Confidence 9999999999999999999999999999999999999888876541 11211 1223333321100
Q ss_pred -----CCCCC----cch--hhhccCccCcC--CCCCCcccCCCEEEEccCCCCCceeEEEEEeCCeEEEEecCcce----
Q 000247 635 -----PLSPK----RSW--QAREQNTEFKR--GDRDGMFAVGQTLRIRVGPLKGYLCRVLAVRYSDVTVKLDSQQK---- 697 (1790)
Q Consensus 635 -----~lsp~----rp~--~~~~~~r~fgR--GgRD~d~lIGKTVKIrkGPYKGylGiVKDaTdt~ARVELHSk~K---- 697 (1790)
.|.+. ++. ...... ++.- -.......|+.+|+++.||.||-.|.|+.+....+. ||+++-
T Consensus 545 ~~~vl~~~g~v~~i~~~~i~~kk~~-r~~~~~D~~~n~I~~kD~Vkvi~Gp~~g~~G~v~~i~r~~~F--~h~r~~~En~ 621 (1024)
T KOG1999|consen 545 TFQVLGMNGKVVTIRKSSITKKKDN-RKAVAVDRNGNEIRVKDTVKVIGGPSKGREGEVLHIYRPFVF--LHSRKNLENG 621 (1024)
T ss_pred heeeecCcCceEEEeechhhhhhhh-hhheeecccCCeecccceEEEecCCCCCccCccceeecceee--eeehhhcccC
Confidence 00000 000 000000 1100 012234678999999999999999999999999988 887775
Q ss_pred -EEEEecCccccccCCcc
Q 000247 698 -ILTVKGEHLAEVRGKSF 714 (1790)
Q Consensus 698 -tITVdKe~Ls~v~~k~~ 714 (1790)
++.++..+|.++.++.+
T Consensus 622 Gv~vck~k~~~~~g~~~s 639 (1024)
T KOG1999|consen 622 GVFVCKEKNLILAGGKKS 639 (1024)
T ss_pred CeEEEecCCceeccccCc
Confidence 77889999998766543
No 6
>TIGR00405 L26e_arch ribosomal protein L24p/L26e, archaeal. This protein contains a KOW domain, shared by bacterial NusG and the L24p/L26e family of ribosomal proteins. Although called archaeal NusG in several publications, it is the only close homolog of eukaryotic L26e in archaeal genomes, shares an operon with L11 in many genomes, and has been sequenced from purified ribosomes. It is here designated as a ribosomal protein for these reasons.
Probab=99.82 E-value=1.8e-19 Score=186.28 Aligned_cols=125 Identities=22% Similarity=0.404 Sum_probs=111.2
Q ss_pred EEEEecCchhHHHHHHHHHHHHhhccCCCCCcEEEEEEeCCCCcEEEEEeccchhHHHHhcCCCCEEeceeccCCHHHHH
Q 000247 228 WKVKCMAGRERQSAFCLMQKFVDLQSLGSKMQIISAFAVDHIKGFIFIEADKQCDINEACKGLSGIYYSRLAPVPKNEVS 307 (1790)
Q Consensus 228 WaVKCK~GkEReVV~~LmrKii~lq~~g~~L~I~SVFvpd~lKGYIYVEA~kq~dVkeAIkGI~gVy~sK~~pVPikEM~ 307 (1790)
|+|+|++|+|+.|+..|.+|+.. ..+.|+++|+|..||||||||++...+++++|+++++|...-..+||.+||.
T Consensus 1 Yvv~t~~g~E~~v~~~L~~~~~~-----~~~~~~~~~vp~~fpGYvFV~~~~~~~~~~~i~~~~gv~~~v~~~i~~~ei~ 75 (145)
T TIGR00405 1 FAVKTSVGQEKNVARLMARKARK-----SGLEVYSILAPESLKGYILVEAETKIDMRNPIIGVPHVRGVVEGEIDFEEIE 75 (145)
T ss_pred CeEEeeCChHHHHHHHHHHHHhh-----CCCcEEEEEccCCCCcEEEEEEECcHHHHHHHhCCCCEEeecCCCCCHHHHH
Confidence 89999999999999999988743 3467999999999999999999999999999999999988655679999999
Q ss_pred HHhhcccccccccCCCEEEEecCcCCCCcEEEEEEeCCCCEEEEEEeccC
Q 000247 308 HLLSAQIKRNEVSEGTWAYVKNGKYKGDLAQVVYVNNARKRATVKLIPRI 357 (1790)
Q Consensus 308 dLLkvkkks~~Lk~GdwVRIKrGpYKGDLAQV~eVDenk~kVtVKLVPRI 357 (1790)
.||........|++|++|||++|||+|++|+|++++.++..|+|.|+-+-
T Consensus 76 ~l~~~~~~~~~~~~Gd~V~I~~GPf~G~~g~v~~~d~~k~~v~v~l~~~~ 125 (145)
T TIGR00405 76 RFLTPKKIIESIKKGDIVEIISGPFKGERAKVIRVDESKEEVTLELIEAA 125 (145)
T ss_pred HHhcccccccccCCCCEEEEeecCCCCCeEEEEEEcCCCCEEEEEEEEcC
Confidence 99975332345899999999999999999999999999999999998743
No 7
>COG0250 NusG Transcription antiterminator [Transcription]
Probab=99.74 E-value=1.1e-17 Score=179.74 Aligned_cols=133 Identities=17% Similarity=0.233 Sum_probs=111.0
Q ss_pred CCcEEEEEecCchhHHHHHHHHHHHHhhccCCC------C-C-------cEEEEEEeCCCCcEEEEEeccchhHHHHhcC
Q 000247 224 DPTIWKVKCMAGRERQSAFCLMQKFVDLQSLGS------K-M-------QIISAFAVDHIKGFIFIEADKQCDINEACKG 289 (1790)
Q Consensus 224 DPkLWaVKCK~GkEReVV~~LmrKii~lq~~g~------~-L-------~I~SVFvpd~lKGYIYVEA~kq~dVkeAIkG 289 (1790)
.++||+|+|++|+|+.|+..|++++..+..... | . ..+.++.++.|||||||||.+.++++++|++
T Consensus 2 ~~~Wyvv~~~sg~E~~V~~~l~~~~~~~~~~~~~~~v~vp~E~v~e~~~~~~~~~e~~~fpGYVlVem~~~~~~w~~Vr~ 81 (178)
T COG0250 2 MKRWYVVQTYSGQEKKVKENLERKAELLGMEDLIFEVLVPTEEVVEVKGKRKVIVERKLFPGYVLVEMDMTDEAWHLVRN 81 (178)
T ss_pred CceEEEEEeeccHHHHHHHHHHHHHHhcCCccceeeEEeceEEEEEecCceEEEEecccCCcEEEEEEEcCCceEEEEec
Confidence 578999999999999999999999988764311 0 0 2344477899999999999999999999999
Q ss_pred CCCEEe------ceeccCCHHHHHHHhhcc-------cccccccCCCEEEEecCcCCCCcEEEEEEeCCCCE--EEEEEe
Q 000247 290 LSGIYY------SRLAPVPKNEVSHLLSAQ-------IKRNEVSEGTWAYVKNGKYKGDLAQVVYVNNARKR--ATVKLI 354 (1790)
Q Consensus 290 I~gVy~------sK~~pVPikEM~dLLkvk-------kks~~Lk~GdwVRIKrGpYKGDLAQV~eVDenk~k--VtVKLV 354 (1790)
+++|.+ .+|.+|+.+||.++|... +..+.|++|+.|||+.|||+++.|+|.+||.++.+ |.|.++
T Consensus 82 tpgV~GfVg~~~~~P~pi~~~ei~~~l~~~~~~~~~~~~~~~~e~Gd~VrI~~GpFa~f~g~V~evd~ek~~~~v~v~if 161 (178)
T COG0250 82 TPGVTGFVGSGGAKPVPLSEEEIEHILGFLEEEVAPKKPKVDFEPGDVVRIIDGPFAGFKAKVEEVDEEKGKLKVEVSIF 161 (178)
T ss_pred CCCcEEEeccCCCCCcccCHHHHHHHHhhccccccCCcccccCCCCCEEEEeccCCCCccEEEEEEcCcCcEEEEEEEEe
Confidence 999875 478999999999966532 23578999999999999999999999999999775 555566
Q ss_pred cc
Q 000247 355 PR 356 (1790)
Q Consensus 355 PR 356 (1790)
.|
T Consensus 162 gr 163 (178)
T COG0250 162 GR 163 (178)
T ss_pred CC
Confidence 65
No 8
>PRK05609 nusG transcription antitermination protein NusG; Validated
Probab=99.59 E-value=1.7e-14 Score=153.28 Aligned_cols=130 Identities=15% Similarity=0.222 Sum_probs=103.4
Q ss_pred CCcEEEEEecCchhHHHHHHHHHHHHhhccCCCCCcEEEEEEe-----------------CCCCcEEEEEeccchhHHHH
Q 000247 224 DPTIWKVKCMAGRERQSAFCLMQKFVDLQSLGSKMQIISAFAV-----------------DHIKGFIFIEADKQCDINEA 286 (1790)
Q Consensus 224 DPkLWaVKCK~GkEReVV~~LmrKii~lq~~g~~L~I~SVFvp-----------------d~lKGYIYVEA~kq~dVkeA 286 (1790)
+.+||+|+|++|+|+.|+..|.+++.... -...++.+|+| +.|||||||+++....+...
T Consensus 5 ~~~WYvl~~~~~~E~~v~~~L~~~~~~~~---i~~~~~~~~~P~~~~~~~~~g~~~~~~~plfpgYvFv~~~~~~~~~~~ 81 (181)
T PRK05609 5 KKRWYVVQTYSGYEKKVKENLENRIETLG---MEDLIGEVLVPTEEVVEVKNGKKKKVERKFFPGYVLVKMVMTDESWHL 81 (181)
T ss_pred CCeEEEEEeECCcHHHHHHHHHHHHHHCC---CcceeeEEEeeeEEEEEccCCEEEEEEEecCCcEEEEEEEeCccHhHH
Confidence 45799999999999999999999864322 11114455655 46999999999988888999
Q ss_pred hcCCCCEEe------ceeccCCHHHHHHHhhcc-------cccccccCCCEEEEecCcCCCCcEEEEEEeCCCC--EEEE
Q 000247 287 CKGLSGIYY------SRLAPVPKNEVSHLLSAQ-------IKRNEVSEGTWAYVKNGKYKGDLAQVVYVNNARK--RATV 351 (1790)
Q Consensus 287 IkGI~gVy~------sK~~pVPikEM~dLLkvk-------kks~~Lk~GdwVRIKrGpYKGDLAQV~eVDenk~--kVtV 351 (1790)
|+.+++|.. .+|.+||.+||..|+... .....|++|+.|||+.|||+|..|+|++|+..+. .|.|
T Consensus 82 i~~~~gv~~~v~~~g~~p~~i~~~ei~~l~~~~~~~~~~~~~~~~~~~Gd~VrI~~GPf~G~~g~v~~i~~~~~r~~v~l 161 (181)
T PRK05609 82 VRNTPGVTGFVGSTGSKPTPLSEKEVEKILKQLQEGVEKPKPKVDFEVGEMVRVIDGPFADFNGTVEEVDYEKSKLKVLV 161 (181)
T ss_pred hhcCCCeEEEecCCCCCcccCCHHHHHHHHHHhhcccccCccccCCCCCCEEEEeccCCCCCEEEEEEEeCCCCEEEEEE
Confidence 999998743 368899999999998731 1235688999999999999999999999996665 5677
Q ss_pred EEecc
Q 000247 352 KLIPR 356 (1790)
Q Consensus 352 KLVPR 356 (1790)
.|+.|
T Consensus 162 ~~~G~ 166 (181)
T PRK05609 162 SIFGR 166 (181)
T ss_pred EECCC
Confidence 77776
No 9
>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=99.58 E-value=1.2e-14 Score=163.11 Aligned_cols=129 Identities=13% Similarity=0.203 Sum_probs=104.9
Q ss_pred cEEEEEecCchhHHHHHHHHHHHHhhccCCCCCcEEEEEEe---------------------------------------
Q 000247 226 TIWKVKCMAGRERQSAFCLMQKFVDLQSLGSKMQIISAFAV--------------------------------------- 266 (1790)
Q Consensus 226 kLWaVKCK~GkEReVV~~LmrKii~lq~~g~~L~I~SVFvp--------------------------------------- 266 (1790)
+||+|+|.+|+|..|+..|++|+..+... ..|+.|++|
T Consensus 1 kWYvv~t~sG~E~kV~~~l~~kv~~~~~e---d~i~~v~Vp~e~~ve~~v~e~k~~~~p~~~k~~~~~~w~~~~~gk~~k 77 (258)
T TIGR01956 1 QWYIATTINGNEDEVIENIKAKVRALGLE---NYISDFKILKEREIEEKVFEPKNGQAPRSMKNTATTKWETLDETKYKK 77 (258)
T ss_pred CeEEEEeeCCcHHHHHHHHHHHHHhCCCc---cEEEEEEEeeeEEEEEEEEEeecCcccccccccccccceeccCCcccc
Confidence 59999999999999999999999887632 234444333
Q ss_pred ------CCCCcEEEEEeccchhHHHHhcCCCCEEe--------ceeccCCHHHH-HHHhhccc-----------------
Q 000247 267 ------DHIKGFIFIEADKQCDINEACKGLSGIYY--------SRLAPVPKNEV-SHLLSAQI----------------- 314 (1790)
Q Consensus 267 ------d~lKGYIYVEA~kq~dVkeAIkGI~gVy~--------sK~~pVPikEM-~dLLkvkk----------------- 314 (1790)
+.|||||||+|.+.++++++|+++++|.+ .+|+||+.+|+ .+||....
T Consensus 78 ~k~~er~~fPGYI~IkM~m~d~~W~~VRnt~gVTGFvGssg~g~kPiPls~~e~~~~ml~~~~~~~~~~~~~~~~~~~~~ 157 (258)
T TIGR01956 78 TKISEKNKYNGYIYIKMIMTEDAWFLIRNTENVTGLVGSSGKGAKPIPISADADKLKMLKGISENTKKRVLVTNTAIVEM 157 (258)
T ss_pred EEEEEeeecCcEEEEEEEecccHhhheecCCCCCeecCCCCCCCCCcCCCHHHHHHHHhhhhhhcccccccccccccccc
Confidence 46999999999999999999999999864 26999999888 78885211
Q ss_pred --------------------------------------------ccccccCCCEEEEecCcCCCCcEEEEEEeCCCC--E
Q 000247 315 --------------------------------------------KRNEVSEGTWAYVKNGKYKGDLAQVVYVNNARK--R 348 (1790)
Q Consensus 315 --------------------------------------------ks~~Lk~GdwVRIKrGpYKGDLAQV~eVDenk~--k 348 (1790)
..+.|++|+.|||+.|||+|+.|+|++|+.++. .
T Consensus 158 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~vGd~VrI~dGPF~GfeG~I~eid~~k~Rv~ 237 (258)
T TIGR01956 158 EENKFDEKCQYILKHKQVKPEAIAQVSESGEIIDEIVEEFQLVDNLSKFRVGNFVKIVDGPFKGIVGKIKKIDQEKKKAI 237 (258)
T ss_pred cccccccccccccccccccccccccccccccccccccccccccccccCCCCCCEEEEEecCCCCcEEEEEEEeCCCCEEE
Confidence 124578999999999999999999999996555 5
Q ss_pred EEEEEeccC
Q 000247 349 ATVKLIPRI 357 (1790)
Q Consensus 349 VtVKLVPRI 357 (1790)
|.|.||.|.
T Consensus 238 VlV~IfGR~ 246 (258)
T TIGR01956 238 VEVEILGKS 246 (258)
T ss_pred EEEEecCCc
Confidence 777777763
No 10
>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=99.55 E-value=5e-14 Score=149.09 Aligned_cols=127 Identities=17% Similarity=0.212 Sum_probs=100.5
Q ss_pred EEEEEecCchhHHHHHHHHHHHHhhccCCCCCcEEEEEEe-----------------CCCCcEEEEEeccchhHHHHhcC
Q 000247 227 IWKVKCMAGRERQSAFCLMQKFVDLQSLGSKMQIISAFAV-----------------DHIKGFIFIEADKQCDINEACKG 289 (1790)
Q Consensus 227 LWaVKCK~GkEReVV~~LmrKii~lq~~g~~L~I~SVFvp-----------------d~lKGYIYVEA~kq~dVkeAIkG 289 (1790)
||+|+|++|+|+.|+..|.+++..+. .+..++.+|+| +.|||||||++....+.+..|+.
T Consensus 1 WYvl~~~~~~E~~v~~~L~~~~~~~g---~~~~~~~~~~P~~~~~~~~~g~~~~~~~plfPgYvFv~~~~~~~~~~~i~~ 77 (172)
T TIGR00922 1 WYVVQTYSGYEKKVKQNLEELIELLG---MGDYIFEVIVPTEEVVEIKKGKKKVVERKIFPGYVLVKMDLTDVSWHLVKN 77 (172)
T ss_pred CEEEEeECChHHHHHHHHHHHHHHCC---CccceeEEEcceEEEEEEcCCEEEEEEEecCCcEEEEEEEeCccHhHHhhc
Confidence 89999999999999999999864322 11113344444 68999999999988888999999
Q ss_pred CCCEEe-----ceeccCCH-HHHHHHhhccc-------ccccccCCCEEEEecCcCCCCcEEEEEEeCCCC--EEEEEEe
Q 000247 290 LSGIYY-----SRLAPVPK-NEVSHLLSAQI-------KRNEVSEGTWAYVKNGKYKGDLAQVVYVNNARK--RATVKLI 354 (1790)
Q Consensus 290 I~gVy~-----sK~~pVPi-kEM~dLLkvkk-------ks~~Lk~GdwVRIKrGpYKGDLAQV~eVDenk~--kVtVKLV 354 (1790)
+++|.. .+|.+||. +||..|+.... ....|++|+.|||+.|||+|..|.|++|+..+. .|.|.|+
T Consensus 78 ~~gv~~~v~~~~~p~~I~~~~ei~~l~~~~~~~~~~~~~~~~~~~G~~V~I~~Gpf~G~~g~v~~~~~~~~r~~V~v~~~ 157 (172)
T TIGR00922 78 TPGVTGFVGSGGKPKALSEDEEVKNILNALEEGKDKPKPKIDFEVGEQVRVNDGPFANFTGTVEEVDYEKSKLKVSVSIF 157 (172)
T ss_pred CCCccEEcCcCCeeeccCCHHHHHHHHHHhhcccccCccccCCCCCCEEEEeecCCCCcEEEEEEEcCCCCEEEEEEEEC
Confidence 998764 36899999 99999986421 123488999999999999999999999996655 4667777
Q ss_pred cc
Q 000247 355 PR 356 (1790)
Q Consensus 355 PR 356 (1790)
.|
T Consensus 158 g~ 159 (172)
T TIGR00922 158 GR 159 (172)
T ss_pred CC
Confidence 76
No 11
>COG5164 SPT5 Transcription elongation factor [Transcription]
Probab=99.50 E-value=3.7e-15 Score=173.91 Aligned_cols=338 Identities=21% Similarity=0.252 Sum_probs=207.0
Q ss_pred cccccCCCCCCCCcEEEEEecCchhHHHHHHHHHHHHhhccCCCCCcEEEEEEeCCCCcEEEEEeccchhHH----HHhc
Q 000247 213 LEREYHMPCPEDPTIWKVKCMAGRERQSAFCLMQKFVDLQSLGSKMQIISAFAVDHIKGFIFIEADKQCDIN----EACK 288 (1790)
Q Consensus 213 VpQqlLLPSVkDPkLWaVKCK~GkEReVV~~LmrKii~lq~~g~~L~I~SVFvpd~lKGYIYVEA~kq~dVk----eAIk 288 (1790)
.+|.+|.|--+-+..|+||++...|+++.+. +. +..++.++++.+-+ |+.|.|+|+.+..|+. ++|+
T Consensus 28 ~~r~f~~~ne~~~dgflvk~~Ris~~et~~~----~p----t~de~~~F~~~~~d-ldl~s~~~s~kk~ha~fqpgD~~E 98 (607)
T COG5164 28 DDRHFTYKNEDYIDGFLVKVKRISERETLMR----IP----TNDEKNVFSIICKD-LDLYSYVESFKKQHAVFQPGDALE 98 (607)
T ss_pred CchhccccCcccccceEEEEeeeceeeeccc----cc----ccchhhhcCccccc-cchhHHHHHHhhcccccCCCCeee
Confidence 6788889998999999999999999987442 22 23466777777766 9999999999999998 8888
Q ss_pred CCCCEEeceeccCC-HHHHHHHhhcccccccccCCCEEEEecCcCCCCcEEEEEEeCCCCEEEEEEeccCchhhHhhhcC
Q 000247 289 GLSGIYYSRLAPVP-KNEVSHLLSAQIKRNEVSEGTWAYVKNGKYKGDLAQVVYVNNARKRATVKLIPRIDLQALAAKFG 367 (1790)
Q Consensus 289 GI~gVy~sK~~pVP-ikEM~dLLkvkkks~~Lk~GdwVRIKrGpYKGDLAQV~eVDenk~kVtVKLVPRIDy~~l~~k~~ 367 (1790)
=++++-....-.|| .+||...|... ...-..+-|-||+.+.|+||+++|++= +.++.+.||||||-..
T Consensus 99 vl~Geqrg~~gVV~~~~~~I~tm~~~--~~~rl~~p~~~lRk~f~~gD~vkVI~g---~~~~d~g~V~rI~~~~------ 167 (607)
T COG5164 99 VLRGEQRGRVGVVPRQKEMIETMTYH--FEQRLCGPWGRLRKGFYKGDLVKVIEG---GEMVDIGTVPRIDGEK------ 167 (607)
T ss_pred eecceecccceeecccccceeeeeec--cCceeecchhhhhcccccCCeEEEecc---ccccccceEEEecCce------
Confidence 88887665555666 77777766543 112235678888889999999888864 5578889999998431
Q ss_pred CCcccCCCCCCCCCCCChhhHhhhcCceeecc---cCCCCceEEecCCceeecceEEEEEeccceEecCCCCCHHHHhhc
Q 000247 368 GGVAMKKTDSPAPRLISPSELEEFRPLIQYRR---DRDTGKVFENLDGMMLKDGYLYKKVSIDSLSCWGVVPSEEELLKF 444 (1790)
Q Consensus 368 gg~~kKK~~RPPqRLFn~~Eark~~~~~~~rr---d~~tG~~f~i~~G~~ykDGFLyK~fkI~sL~tedVnPTLEEL~kF 444 (1790)
.+|+++....- ..+..+. ..++.-+-++|.-..|+++||.|..-|.+|-. ||.|++|||.+|
T Consensus 168 -------------vtF~s~~~~~e-~tI~sr~l~ks~~tta~ss~Y~lhd~V~l~~~~vaci~sid~-Dv~kvide~g~v 232 (607)
T COG5164 168 -------------VTFNSENFKSE-STIKSRGLSKSIDTTATSSIYKLHDYVDLFLEKVACINSIDF-DVEKVIDELGEV 232 (607)
T ss_pred -------------eEEcccccccc-ceEEeccccccccccchhhhhhhhhhhhhhhcceeEEeeccc-chhhhhhhcCce
Confidence 25666543210 0111111 01222233467778999999999999988864 899999999999
Q ss_pred CCCCCCccccHHHH--HHHH-----hccccccEEEeecCCCcccccCCCCcccccccCcEEEecCCceEEEEEEecCceE
Q 000247 445 QPSESNESADLEWL--SQLY-----GERKKKRTTIVGKGGDKGEGSSGSSLENSFELYELVCFGRKDFGLIVGMEKDDHY 517 (1790)
Q Consensus 445 ~~~~~de~~DL~~L--a~~~-----ge~kk~~ii~v~kGg~kgE~ssG~~slG~FeLgDLVQLD~~TVGVIVrVEkDEsf 517 (1790)
.....-...+-... ++++ +.+.+....++++.+.+.|+.+- -...+|.++..|-| ...-||+|.++++...
T Consensus 233 ~t~~~~sI~~kv~~~Rg~~i~~d~ng~eI~igd~VvE~~g~~~egq~l-~i~~~f~f~~t~~i-~ennGVfv~~~~nv~~ 310 (607)
T COG5164 233 HTACPISIGDKVRVTRGELIGMDGNGREISIGDAVVESRGGKFEGQSL-GIVKHFDFGETVSI-KENNGVFVKIEGNVCI 310 (607)
T ss_pred eEecchhhhhhhecccceeEeeccccceEeeceeEEEecCCceeeEEE-EEEEEEeeeeeeee-eccCceEEEecCceeE
Confidence 85432111111000 0011 11111111122333333333211 12234444444433 3566999999986333
Q ss_pred EEccCCCCCCceEEEecccc----cCCCCCCccccccc--CCCcccCCCeEEEecCCCCCceEEEEEEECCEE--EEEeC
Q 000247 518 KILKEGSEGPAVVTVERRTL----KNGPFDMKFTALDQ--SMKVISLNDTARVSEGPSKDRQGIVKKIYRGIL--FIYDE 589 (1790)
Q Consensus 518 kVLdq~gD~~~VvtVk~~eI----~~K~~~rr~vAtD~--~gn~I~vGD~VKVIdGphkGRqG~VlHIyRs~V--FL~Sr 589 (1790)
+..+..-. -+.|.+..+ ..++..-+...+-+ -+....+|-+|+|-.|+|||.-|+|+.+.++++ -||+.
T Consensus 311 VAtkd~~~---s~k~dl~kmnp~v~~~~~~p~~~~l~r~i~gRd~aigktVrIr~g~yKG~lGVVKdv~~~~arVeLhs~ 387 (607)
T COG5164 311 VATKDFTE---SLKVDLDKMNPPVTVNLQNPKTNELERKIVGRDPAIGKTVRIRCGEYKGHLGVVKDVDRNIARVELHSN 387 (607)
T ss_pred EEeccchh---hhcccHhhcCchhhcCCCCCcchhhhccccccccccCceEEEeecccccccceeeeccCceEEEEEecC
Confidence 32232210 111222211 11111000000000 355678999999999999999999999999975 45554
Q ss_pred c
Q 000247 590 N 590 (1790)
Q Consensus 590 ~ 590 (1790)
.
T Consensus 388 n 388 (607)
T COG5164 388 N 388 (607)
T ss_pred C
Confidence 3
No 12
>PF11942 Spt5_N: Spt5 transcription elongation factor, acidic N-terminal; InterPro: IPR022581 This is the very acidic N-terminal domain of the early transcription elongation factor Spt5 []. The Spt5-Spt4 complex regulates early transcription elongation by RNA polymerase II and has an imputed role in pre-mRNA processing via its physical association with mRNA capping enzymes. The actual function of this N-terminal domain is not known although it is dispensable for binding to Spt4 [], nor is it essential for RNA polymerase II binding [].
Probab=99.50 E-value=5e-15 Score=145.63 Aligned_cols=92 Identities=27% Similarity=0.452 Sum_probs=57.3
Q ss_pred cceeccccCCCCCchhhcCCCcCCCCCCCCcc--chhhhhccCccccccccccCCCC-CCCccccCCHHHHHHHHH--HH
Q 000247 119 FVEDAADVDYDDDDEEEVGNESDNSGGFADDD--FMEELFDAQPKVNNEMGQAHNLP-FIPKEEEMDEEEFDKMME--ER 193 (1790)
Q Consensus 119 FiDdEAEVDDDeEEEDEeeEe~e~~~~Fi~dD--~~~d~~e~~~~~~~d~r~~~~l~-~r~~eEd~DaEelAe~Lk--ER 193 (1790)
|||+||+||||+|||||++++. .||... +.++. . ...+.++|+.++ +++++++|++|+||++|+ +|
T Consensus 1 Fid~EAeVDddeEEeee~ed~~----~~~~~~~~~~~~~---~--~~~~d~~~r~~d~~r~~~~~~dae~lae~~k~~~R 71 (97)
T PF11942_consen 1 FIDDEAEVDDDEEEEEEDEDEA----DEIGEEDDEIEDA---E--AEEDDRRHRRLDRRREMEEEEDAEELAEYLKLSER 71 (97)
T ss_pred CchhhcccCCcccccccccccc----hhhhccccccccc---c--cchhHhhhhhhhhhHHHHhccCHHHHHHHHHHHHH
Confidence 9999999999988777555442 222111 11100 0 111223344444 468889999999999999 99
Q ss_pred hccccchhhchhhHHHhhhcccccCCC
Q 000247 194 YKSNKLIRYAEEDYEAKKMLEREYHMP 220 (1790)
Q Consensus 194 Y~r~s~~~y~~d~~e~~~~VpQqlLLP 220 (1790)
|++++...+... .+...+||||+|||
T Consensus 72 Y~~~~~~~~~~~-~~~~~~v~q~~LLP 97 (97)
T PF11942_consen 72 YARSSESRYDGD-DEDSDEVPQQLLLP 97 (97)
T ss_pred hccccccccccc-ccccccchHhccCc
Confidence 998641112111 12347899999999
No 13
>PRK09014 rfaH transcriptional activator RfaH; Provisional
Probab=99.34 E-value=3.1e-12 Score=134.70 Aligned_cols=127 Identities=15% Similarity=0.209 Sum_probs=93.0
Q ss_pred cEEEEEecCchhHHHHHHHHHHHHhhccCCCCCc--------EEEEEEeCCCCcEEEEEeccchhHHHHhcCCCCEEe--
Q 000247 226 TIWKVKCMAGRERQSAFCLMQKFVDLQSLGSKMQ--------IISAFAVDHIKGFIFIEADKQCDINEACKGLSGIYY-- 295 (1790)
Q Consensus 226 kLWaVKCK~GkEReVV~~LmrKii~lq~~g~~L~--------I~SVFvpd~lKGYIYVEA~kq~dVkeAIkGI~gVy~-- 295 (1790)
+||+|+|++++|+.++..|.++-++.- .|+. -.-....+.|||||||++..+...+..|+.+++|..
T Consensus 3 ~WYvl~t~~~~E~~v~~~L~~~gi~~~---~P~~~~~~~~~gk~~~v~~plFPgYlFv~~~~~~~~~~~i~~~~gv~~~v 79 (162)
T PRK09014 3 SWYLLYCKRGQLQRAQEHLERQGVECL---YPMITLEKIVRGKRTEVSEPLFPNYLFVEFDPEVIHTTTIRSTRGVSHFV 79 (162)
T ss_pred eEEEEEecCchHHHHHHHHHHCCCEEE---CCCEEEEEEECCeEEEEEEEcCCCeEEEEeccccCceEEEEecCCcceEe
Confidence 799999999999999998877532210 1110 112233368999999999876666666777777643
Q ss_pred ---ceeccCCHHHHHHHhhccc----ccccccCCCEEEEecCcCCCCcEEEEEEeCCCCE--EEEEEecc
Q 000247 296 ---SRLAPVPKNEVSHLLSAQI----KRNEVSEGTWAYVKNGKYKGDLAQVVYVNNARKR--ATVKLIPR 356 (1790)
Q Consensus 296 ---sK~~pVPikEM~dLLkvkk----ks~~Lk~GdwVRIKrGpYKGDLAQV~eVDenk~k--VtVKLVPR 356 (1790)
.+|.+||.+||..|+.... ....+++|+.|||+.|||+|.+|.|++++. +.+ |.|.|+.|
T Consensus 80 ~~g~~p~~I~~~ei~~l~~~~~~~~~~~~~~~~G~~V~I~~Gp~~g~eg~v~~~~~-~~r~~v~v~~~gr 148 (162)
T PRK09014 80 RFGAQPAIVPSDVIYQLSVYKPEKIVDPETPKPGDKVIITEGAFEGLQAIYTEPDG-EARSILLLNLLNK 148 (162)
T ss_pred ccCCCccccCHHHHHHHHhhcccccccccCCCCCCEEEEecCCCCCcEEEEEEeCC-CeEEEEeehhhCC
Confidence 4799999999999986422 123578999999999999999999999984 444 55555553
No 14
>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=99.31 E-value=7.2e-12 Score=130.95 Aligned_cols=128 Identities=17% Similarity=0.234 Sum_probs=93.4
Q ss_pred EEEEEecCchhHHHHHHHHHHHHhhccCCCCC--------cEEEEEEeCCCCcEEEEEeccchhHHHHhcCCCCEEe---
Q 000247 227 IWKVKCMAGRERQSAFCLMQKFVDLQSLGSKM--------QIISAFAVDHIKGFIFIEADKQCDINEACKGLSGIYY--- 295 (1790)
Q Consensus 227 LWaVKCK~GkEReVV~~LmrKii~lq~~g~~L--------~I~SVFvpd~lKGYIYVEA~kq~dVkeAIkGI~gVy~--- 295 (1790)
||+|+|++++|+.++..|.++-++.- .|+ .-...+..+.|||||||+++...+....|..+++|..
T Consensus 1 WYvl~~~~~~E~~v~~~L~~~gi~~~---~P~~~~~~~~~g~~~~~~~plfpgYvFv~~~~~~~~~~~i~~~~gv~~~v~ 77 (159)
T TIGR01955 1 WYLLYCKPRQEQRAQEHLERQAVECY---LPMITVEKIVRGKRQAVSEPLFPNYLFIEFDPEVDSWTTIRSTRGVSRFVR 77 (159)
T ss_pred CEEEEEcCchHHHHHHHHHHCCCEEE---ccCEEEEEEECCcEEEEEEecCCCeEEEEEccCCCceEEEecCCCcCEEEC
Confidence 89999999999999998877532210 111 0112334479999999999987766666677776643
Q ss_pred --ceeccCCHHHHHHHhhccc------ccccccCCCEEEEecCcCCCCcEEEEEEeCCC-CEEEEEEeccC
Q 000247 296 --SRLAPVPKNEVSHLLSAQI------KRNEVSEGTWAYVKNGKYKGDLAQVVYVNNAR-KRATVKLIPRI 357 (1790)
Q Consensus 296 --sK~~pVPikEM~dLLkvkk------ks~~Lk~GdwVRIKrGpYKGDLAQV~eVDenk-~kVtVKLVPRI 357 (1790)
.+|.+||.+||..|+.... ....|++|+.|||+.|||+|..|.|++++..+ -.|.|.|+.|.
T Consensus 78 ~~~~p~~I~~~~i~~l~~~~~~~~~~~~~~~~~~G~~V~V~~GPf~g~~g~v~~~~~~~r~~v~l~~~gr~ 148 (159)
T TIGR01955 78 FGGHPAPVPDDLIHQLRQYEPKDSVPPATTLPYKGDKVRITDGAFAGFEAIFLEPDGEKRSMLLLNMIGKQ 148 (159)
T ss_pred CCCCcccCCHHHHHHHHhccccccCCccccCCCCCCEEEEeccCCCCcEEEEEEECCCceEEEEEhhhCCc
Confidence 4799999999998875421 12458899999999999999999999998443 13555666653
No 15
>smart00738 NGN In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold. In Spt5p, this domain may confer affinity for Spt4p.Spt4p
Probab=99.21 E-value=4e-11 Score=117.00 Aligned_cols=83 Identities=28% Similarity=0.464 Sum_probs=71.1
Q ss_pred cEEEEEecCchhHHHHHHHHHHHHhhccCCCCCcEEEEEEe-----------------CCCCcEEEEEeccchhHHHHhc
Q 000247 226 TIWKVKCMAGRERQSAFCLMQKFVDLQSLGSKMQIISAFAV-----------------DHIKGFIFIEADKQCDINEACK 288 (1790)
Q Consensus 226 kLWaVKCK~GkEReVV~~LmrKii~lq~~g~~L~I~SVFvp-----------------d~lKGYIYVEA~kq~dVkeAIk 288 (1790)
+||+|+|++|+|++|+..|++++.++.. +..++++|+| +.|||||||+++...++..+|+
T Consensus 1 ~Wyvv~~~~g~E~~v~~~L~~~~~~~~~---~~~~~~~~~P~~~~~~~~~g~~~~~~~plfpGYvFv~~~~~~~~~~~i~ 77 (106)
T smart00738 1 NWYAVRTTSGQEKRVAENLERKAEALGL---EDKIVSILVPTEEVKEIRRGKKKVVERPLFPGYIFVEADLEDEVWTAIR 77 (106)
T ss_pred CEEEEEEeCCcHHHHHHHHHHHHHhcCC---ccccCEEEeeEEEEEEecCCEEEEEEEecCCCEEEEEEEeCCcHHHHHh
Confidence 5999999999999999999999865432 3346677777 4788999999999999999999
Q ss_pred CCCCEEe-----ceeccCCHHHHHHHhh
Q 000247 289 GLSGIYY-----SRLAPVPKNEVSHLLS 311 (1790)
Q Consensus 289 GI~gVy~-----sK~~pVPikEM~dLLk 311 (1790)
.+++|+. .+|.+||.+||.+|++
T Consensus 78 ~~~~v~~~v~~~~~p~~v~~~e~~~l~~ 105 (106)
T smart00738 78 GTPGVRGFVGGGGKPTPVPDDEIEKILK 105 (106)
T ss_pred cCCCccEECCCCCeeeECCHHHHHHHhh
Confidence 9999875 3688999999999986
No 16
>PF02357 NusG: Transcription termination factor nusG; InterPro: IPR006645 This sequence is identified by the NGN domain and is represented by the bacterial antitermination protein NusG. This protein influences transcription termination and anti-termination and acts as a component of the transcription complex. In addition to this, it interacts with the termination factor Rho and RNA polymerase [, ].; GO: 0032968 positive regulation of transcription elongation from RNA polymerase II promoter; PDB: 1NZ8_A 2OUG_C 1NPP_B 1M1G_D 1NPR_A 1M1H_A 2XHA_A 2XHC_A 2K06_A.
Probab=97.88 E-value=1.6e-05 Score=76.78 Aligned_cols=76 Identities=16% Similarity=0.319 Sum_probs=51.8
Q ss_pred cEEEEEecCchhHHHHHHHHHH-HHhhccC----CC---CC-cEEEEEEeCCCCcEEEEEeccchhHHHHhcCCCCEEe-
Q 000247 226 TIWKVKCMAGRERQSAFCLMQK-FVDLQSL----GS---KM-QIISAFAVDHIKGFIFIEADKQCDINEACKGLSGIYY- 295 (1790)
Q Consensus 226 kLWaVKCK~GkEReVV~~LmrK-ii~lq~~----g~---~L-~I~SVFvpd~lKGYIYVEA~kq~dVkeAIkGI~gVy~- 295 (1790)
+||+|+|++++|..|+..|.++ +..+-.. .. .- .+.. ...+.|||||||++...+++ ..|+.+++|+.
T Consensus 2 ~WYvl~~~~~~E~~v~~~L~~~~i~~~~P~~~~~~~~~~~g~~~~~-~~~plfpgYvFv~~~~~~~~-~~i~~~~gv~~~ 79 (92)
T PF02357_consen 2 RWYVLRTKPGKEQKVAERLERQGIEAFLPMREVIRRRKPRGKKVKR-VERPLFPGYVFVRMDMEDEL-WKIRSTPGVSGF 79 (92)
T ss_dssp EEEEEEESTTTHHHHHHHHCHHHHHHE-SEEEEEECSSSSSCSEEE-EEEESSTTEEEEEE-TTHHH-HHHHHSTTEEEE
T ss_pred EEEEEEEECChHHHHHHHHHHcCCceeccEEEEEEEEecCCceEEE-EEEEecCcEEEEEEEcchhh-hhhhcCCCeEEE
Confidence 6999999999999999999554 4332200 00 11 3444 56679999999999999665 44488888765
Q ss_pred ----ceeccCCH
Q 000247 296 ----SRLAPVPK 303 (1790)
Q Consensus 296 ----sK~~pVPi 303 (1790)
.+|++||.
T Consensus 80 l~~g~~p~~vpd 91 (92)
T PF02357_consen 80 LRFGGKPAPVPD 91 (92)
T ss_dssp EESSSSSBEB-H
T ss_pred EcCCCEEeecCC
Confidence 36777774
No 17
>KOG3973 consensus Uncharacterized conserved glycine-rich protein [Function unknown]
Probab=97.47 E-value=0.00038 Score=81.52 Aligned_cols=19 Identities=53% Similarity=1.071 Sum_probs=9.4
Q ss_pred CCCCCCCCCCCCCCCCCCCC
Q 000247 1511 SDRGGFGGRGRGRRDQGGGW 1530 (1790)
Q Consensus 1511 g~RGg~gGrg~~~~~~~~~~ 1530 (1790)
|+|+| ||||+|++|++||+
T Consensus 442 ggr~g-ggrgrgggggrg~y 460 (465)
T KOG3973|consen 442 GGRDG-GGRGRGGGGGRGGY 460 (465)
T ss_pred CCCCC-CCCCCCCCCCCccc
Confidence 34444 45555555555553
No 18
>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]
Probab=97.30 E-value=0.00087 Score=85.84 Aligned_cols=10 Identities=40% Similarity=0.149 Sum_probs=4.9
Q ss_pred eecCcccccc
Q 000247 71 IVCDPEMATD 80 (1790)
Q Consensus 71 ~~~~~~~~~~ 80 (1790)
-..|-|||++
T Consensus 92 ~l~~~~~a~~ 101 (1282)
T KOG0921|consen 92 TWQDSETATM 101 (1282)
T ss_pred cccccccccc
Confidence 3445555554
No 19
>PF00467 KOW: KOW motif; InterPro: IPR005824 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The KOW (Kyprides, Ouzounis, Woese) motif is found in a variety of ribosomal proteins and the bacterial transcription antitermination proteins NusG []. ; PDB: 3BBO_W 2HGJ_X 2HGQ_X 2HGU_X 1NPP_B 1M1G_D 1NPR_A 2XHC_A 2KVQ_G 2JVV_A ....
Probab=97.23 E-value=0.00039 Score=56.63 Aligned_cols=32 Identities=28% Similarity=0.532 Sum_probs=30.0
Q ss_pred CCCEEEEecCcCCCCcEEEEEEeCCCCEEEEE
Q 000247 321 EGTWAYVKNGKYKGDLAQVVYVNNARKRATVK 352 (1790)
Q Consensus 321 ~GdwVRIKrGpYKGDLAQV~eVDenk~kVtVK 352 (1790)
+|++|+|++|+|+|..|+|++|++++.+|+|+
T Consensus 1 ~Gd~V~V~~G~~~G~~G~I~~i~~~~~~V~ve 32 (32)
T PF00467_consen 1 VGDTVKVISGPFKGKIGKIVEIDRSKVRVTVE 32 (32)
T ss_dssp TTSEEEESSSTTTTEEEEEEEEETTTTEEEES
T ss_pred CCCEEEEeEcCCCCceEEEEEEECCCCEEEEC
Confidence 69999999999999999999999999888873
No 20
>PF00467 KOW: KOW motif; InterPro: IPR005824 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The KOW (Kyprides, Ouzounis, Woese) motif is found in a variety of ribosomal proteins and the bacterial transcription antitermination proteins NusG []. ; PDB: 3BBO_W 2HGJ_X 2HGQ_X 2HGU_X 1NPP_B 1M1G_D 1NPR_A 2XHC_A 2KVQ_G 2JVV_A ....
Probab=97.06 E-value=0.00066 Score=55.33 Aligned_cols=32 Identities=31% Similarity=0.675 Sum_probs=28.6
Q ss_pred CCCEEEEccCCCCCceeEEEEEeCCeEEEEec
Q 000247 662 VGQTLRIRVGPLKGYLCRVLAVRYSDVTVKLD 693 (1790)
Q Consensus 662 IGKTVKIrkGPYKGylGiVKDaTdt~ARVELH 693 (1790)
.|++|+|+.|||||+.|+|+++....+||.++
T Consensus 1 ~Gd~V~V~~G~~~G~~G~I~~i~~~~~~V~ve 32 (32)
T PF00467_consen 1 VGDTVKVISGPFKGKIGKIVEIDRSKVRVTVE 32 (32)
T ss_dssp TTSEEEESSSTTTTEEEEEEEEETTTTEEEES
T ss_pred CCCEEEEeEcCCCCceEEEEEEECCCCEEEEC
Confidence 37899999999999999999999998887664
No 21
>KOG3973 consensus Uncharacterized conserved glycine-rich protein [Function unknown]
Probab=96.67 E-value=0.006 Score=71.99 Aligned_cols=9 Identities=22% Similarity=0.313 Sum_probs=4.2
Q ss_pred EEEeccCch
Q 000247 351 VKLIPRIDL 359 (1790)
Q Consensus 351 VKLVPRIDy 359 (1790)
++|+|-||-
T Consensus 139 ~ev~q~i~~ 147 (465)
T KOG3973|consen 139 LEVTQLIDS 147 (465)
T ss_pred chHHHHHHH
Confidence 344455543
No 22
>TIGR00405 L26e_arch ribosomal protein L24p/L26e, archaeal. This protein contains a KOW domain, shared by bacterial NusG and the L24p/L26e family of ribosomal proteins. Although called archaeal NusG in several publications, it is the only close homolog of eukaryotic L26e in archaeal genomes, shares an operon with L11 in many genomes, and has been sequenced from purified ribosomes. It is here designated as a ribosomal protein for these reasons.
Probab=95.57 E-value=0.018 Score=60.66 Aligned_cols=50 Identities=30% Similarity=0.468 Sum_probs=43.7
Q ss_pred ccCCCEEEEccCCCCCceeEEEEEe--CCeEEEEecCcceE--EEEecCccccc
Q 000247 660 FAVGQTLRIRVGPLKGYLCRVLAVR--YSDVTVKLDSQQKI--LTVKGEHLAEV 709 (1790)
Q Consensus 660 ~lIGKTVKIrkGPYKGylGiVKDaT--dt~ARVELHSk~Kt--ITVdKe~Ls~v 709 (1790)
..+|+.|+|+.|||||+.|+|+++. ...|+|+|...... |+|+-+.|..+
T Consensus 87 ~~~Gd~V~I~~GPf~G~~g~v~~~d~~k~~v~v~l~~~~~~~~v~v~~~~l~~~ 140 (145)
T TIGR00405 87 IKKGDIVEIISGPFKGERAKVIRVDESKEEVTLELIEAAVPIPVTVKGDQVRII 140 (145)
T ss_pred cCCCCEEEEeecCCCCCeEEEEEEcCCCCEEEEEEEEcCccceEEEeeeEEEEe
Confidence 5689999999999999999999984 56888999888888 99998888754
No 23
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=95.29 E-value=0.024 Score=43.90 Aligned_cols=27 Identities=33% Similarity=0.464 Sum_probs=25.0
Q ss_pred cccCCCeEEEecCCCCCceEEEEEEEC
Q 000247 555 VISLNDTARVSEGPSKDRQGIVKKIYR 581 (1790)
Q Consensus 555 ~I~vGD~VKVIdGphkGRqG~VlHIyR 581 (1790)
.|++||.|+|+.|+++|+.|+|++|.+
T Consensus 1 ~~~~G~~V~I~~G~~~g~~g~i~~i~~ 27 (28)
T smart00739 1 KFEVGDTVRVIAGPFKGKVGKVLEVDG 27 (28)
T ss_pred CCCCCCEEEEeECCCCCcEEEEEEEcC
Confidence 378999999999999999999999975
No 24
>PRK08559 nusG transcription antitermination protein NusG; Validated
Probab=95.08 E-value=0.042 Score=59.02 Aligned_cols=51 Identities=31% Similarity=0.494 Sum_probs=43.5
Q ss_pred ccCCCEEEEccCCCCCceeEEEEEe--CCeEEEEecCcceE--EEEecCcccccc
Q 000247 660 FAVGQTLRIRVGPLKGYLCRVLAVR--YSDVTVKLDSQQKI--LTVKGEHLAEVR 710 (1790)
Q Consensus 660 ~lIGKTVKIrkGPYKGylGiVKDaT--dt~ARVELHSk~Kt--ITVdKe~Ls~v~ 710 (1790)
+.+|+.|+|+.|||+|+.|+|+++. ...|+|+|-.+... |||+.+.|.++.
T Consensus 95 ~~~G~~V~I~~Gpf~g~~g~V~~vd~~k~~v~v~ll~~~~~~pv~v~~~~~~~~~ 149 (153)
T PRK08559 95 IKEGDIVELIAGPFKGEKARVVRVDESKEEVTVELLEAAVPIPVTVRGDQVRVVK 149 (153)
T ss_pred CCCCCEEEEeccCCCCceEEEEEEcCCCCEEEEEEECCcceeeEEEeccEEEEec
Confidence 6789999999999999999999996 55678887777755 999999998753
No 25
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=94.48 E-value=0.052 Score=42.03 Aligned_cols=27 Identities=26% Similarity=0.442 Sum_probs=24.8
Q ss_pred cccCCCEEEEecCcCCCCcEEEEEEeC
Q 000247 318 EVSEGTWAYVKNGKYKGDLAQVVYVNN 344 (1790)
Q Consensus 318 ~Lk~GdwVRIKrGpYKGDLAQV~eVDe 344 (1790)
.|++|+.|+|+.|+|++..|+|++|+.
T Consensus 1 ~~~~G~~V~I~~G~~~g~~g~i~~i~~ 27 (28)
T smart00739 1 KFEVGDTVRVIAGPFKGKVGKVLEVDG 27 (28)
T ss_pred CCCCCCEEEEeECCCCCcEEEEEEEcC
Confidence 368999999999999999999999975
No 26
>PRK01191 rpl24p 50S ribosomal protein L24P; Validated
Probab=93.99 E-value=0.11 Score=54.46 Aligned_cols=50 Identities=26% Similarity=0.326 Sum_probs=40.8
Q ss_pred HHHHHHhhcccccccccCCCEEEEecCcCCCCcEEEEEEeCCCCEEEEEEec
Q 000247 304 NEVSHLLSAQIKRNEVSEGTWAYVKNGKYKGDLAQVVYVNNARKRATVKLIP 355 (1790)
Q Consensus 304 kEM~dLLkvkkks~~Lk~GdwVRIKrGpYKGDLAQV~eVDenk~kVtVKLVP 355 (1790)
+|+..-+.+. ...|+.||.|.|++|+|||-.|+|+.|++.+.+|+|+=|=
T Consensus 33 keLr~~y~ir--~~~IkkGD~V~VisG~~KGk~GkV~~V~~~~~~V~VeGvn 82 (120)
T PRK01191 33 KELREKYGIR--SLPVRKGDTVKVMRGDFKGEEGKVVEVDLKRGRIYVEGVT 82 (120)
T ss_pred HHHHHHhCCc--cceEeCCCEEEEeecCCCCceEEEEEEEcCCCEEEEeCcE
Confidence 4444444433 5689999999999999999999999999999999997543
No 27
>CHL00141 rpl24 ribosomal protein L24; Validated
Probab=93.88 E-value=0.086 Score=52.07 Aligned_cols=28 Identities=29% Similarity=0.487 Sum_probs=26.7
Q ss_pred cccCCCeEEEecCCCCCceEEEEEEECC
Q 000247 555 VISLNDTARVSEGPSKDRQGIVKKIYRG 582 (1790)
Q Consensus 555 ~I~vGD~VKVIdGphkGRqG~VlHIyRs 582 (1790)
.|+.||.|.||.|+++|++|+|++|++.
T Consensus 8 ~I~~GD~V~Vi~G~dKGK~G~V~~V~~~ 35 (83)
T CHL00141 8 HVKIGDTVKIISGSDKGKIGEVLKIIKK 35 (83)
T ss_pred cccCCCEEEEeEcCCCCcEEEEEEEEcC
Confidence 6899999999999999999999999885
No 28
>TIGR01955 RfaH transcriptional activator RfaH. This model represents the transcriptional activator protein, RfaH. This protein is most closely related to the transcriptional termination/antitermination protein NusG (TIGR00922) and contains the KOW motif (pfam00467). This protein appears to be limited to the gamma proteobacteria. In E. coli, this gene appears to control the expression of haemolysin, sex factor and lipopolysaccharide genes.
Probab=93.85 E-value=0.099 Score=55.55 Aligned_cols=42 Identities=21% Similarity=0.236 Sum_probs=34.9
Q ss_pred ccCCCEEEEccCCCCCceeEEEEEe-CCeEEEEecCcceEEEE
Q 000247 660 FAVGQTLRIRVGPLKGYLCRVLAVR-YSDVTVKLDSQQKILTV 701 (1790)
Q Consensus 660 ~lIGKTVKIrkGPYKGylGiVKDaT-dt~ARVELHSk~KtITV 701 (1790)
..+|+.|+|+.||++|+.|+|+++. ...|.|+|+.-.+.+.|
T Consensus 109 ~~~G~~V~V~~GPf~g~~g~v~~~~~~~r~~v~l~~~gr~~~v 151 (159)
T TIGR01955 109 PYKGDKVRITDGAFAGFEAIFLEPDGEKRSMLLLNMIGKQIKV 151 (159)
T ss_pred CCCCCEEEEeccCCCCcEEEEEEECCCceEEEEEhhhCCceEE
Confidence 4589999999999999999999997 44688888877776444
No 29
>PRK12281 rplX 50S ribosomal protein L24; Reviewed
Probab=93.83 E-value=0.091 Score=51.19 Aligned_cols=28 Identities=21% Similarity=0.325 Sum_probs=26.4
Q ss_pred cccCCCeEEEecCCCCCceEEEEEEECC
Q 000247 555 VISLNDTARVSEGPSKDRQGIVKKIYRG 582 (1790)
Q Consensus 555 ~I~vGD~VKVIdGphkGRqG~VlHIyRs 582 (1790)
.|+.||.|.|+.|+++|++|+|+.|++.
T Consensus 6 ~I~kGD~V~Vi~G~dKGK~G~V~~V~~~ 33 (76)
T PRK12281 6 KVKKGDMVKVIAGDDKGKTGKVLAVLPK 33 (76)
T ss_pred cccCCCEEEEeEcCCCCcEEEEEEEEcC
Confidence 6899999999999999999999999874
No 30
>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=93.66 E-value=0.11 Score=56.20 Aligned_cols=47 Identities=21% Similarity=0.376 Sum_probs=36.6
Q ss_pred ccCCCEEEEccCCCCCceeEEEEEe--CCeEEEEecCcce--EEEEecCcc
Q 000247 660 FAVGQTLRIRVGPLKGYLCRVLAVR--YSDVTVKLDSQQK--ILTVKGEHL 706 (1790)
Q Consensus 660 ~lIGKTVKIrkGPYKGylGiVKDaT--dt~ARVELHSk~K--tITVdKe~L 706 (1790)
+.+|+.|+|+.||++|+.|+|+.+. ...|+|+|+.-.+ .|+|+-++|
T Consensus 120 ~~~G~~V~I~~Gpf~G~~g~v~~~~~~~~r~~V~v~~~g~~~~v~v~~~~l 170 (172)
T TIGR00922 120 FEVGEQVRVNDGPFANFTGTVEEVDYEKSKLKVSVSIFGRETPVELEFSQV 170 (172)
T ss_pred CCCCCEEEEeecCCCCcEEEEEEEcCCCCEEEEEEEECCCceEEEEcHHHe
Confidence 4579999999999999999999996 3477777776665 455555544
No 31
>PRK00004 rplX 50S ribosomal protein L24; Reviewed
Probab=93.52 E-value=0.11 Score=53.36 Aligned_cols=28 Identities=32% Similarity=0.374 Sum_probs=26.4
Q ss_pred cccCCCeEEEecCCCCCceEEEEEEECC
Q 000247 555 VISLNDTARVSEGPSKDRQGIVKKIYRG 582 (1790)
Q Consensus 555 ~I~vGD~VKVIdGphkGRqG~VlHIyRs 582 (1790)
.|+.||.|.||.|+++|++|+|+.|++.
T Consensus 4 ~i~kGD~V~Vi~G~dKGk~G~V~~V~~~ 31 (105)
T PRK00004 4 KIKKGDTVIVIAGKDKGKRGKVLKVLPK 31 (105)
T ss_pred cccCCCEEEEeEcCCCCcEEEEEEEEcC
Confidence 6899999999999999999999999864
No 32
>PRK05609 nusG transcription antitermination protein NusG; Validated
Probab=93.10 E-value=0.14 Score=55.42 Aligned_cols=47 Identities=21% Similarity=0.323 Sum_probs=36.5
Q ss_pred ccCCCEEEEccCCCCCceeEEEEEe--CCeEEEEecCcceE--EEEecCcc
Q 000247 660 FAVGQTLRIRVGPLKGYLCRVLAVR--YSDVTVKLDSQQKI--LTVKGEHL 706 (1790)
Q Consensus 660 ~lIGKTVKIrkGPYKGylGiVKDaT--dt~ARVELHSk~Kt--ITVdKe~L 706 (1790)
+..|+.|+|+.||++|+.|+|+.+. ...|+|+|+--.+. |.|+-+.|
T Consensus 127 ~~~Gd~VrI~~GPf~G~~g~v~~i~~~~~r~~v~l~~~G~~~~v~l~~~~l 177 (181)
T PRK05609 127 FEVGEMVRVIDGPFADFNGTVEEVDYEKSKLKVLVSIFGRETPVELEFSQV 177 (181)
T ss_pred CCCCCEEEEeccCCCCCEEEEEEEeCCCCEEEEEEEECCCceEEEEchHHE
Confidence 4579999999999999999999996 34677777766654 55555444
No 33
>CHL00141 rpl24 ribosomal protein L24; Validated
Probab=92.50 E-value=0.19 Score=49.68 Aligned_cols=39 Identities=23% Similarity=0.315 Sum_probs=35.4
Q ss_pred cccccCCCEEEEecCcCCCCcEEEEEEeCCCCEEEEEEe
Q 000247 316 RNEVSEGTWAYVKNGKYKGDLAQVVYVNNARKRATVKLI 354 (1790)
Q Consensus 316 s~~Lk~GdwVRIKrGpYKGDLAQV~eVDenk~kVtVKLV 354 (1790)
...|.+||.|.|.+|+|||-.+.|..|+..+++|+|+=|
T Consensus 6 ~~~I~~GD~V~Vi~G~dKGK~G~V~~V~~~~~~V~Vegv 44 (83)
T CHL00141 6 KMHVKIGDTVKIISGSDKGKIGEVLKIIKKSNKVIVKGI 44 (83)
T ss_pred eCcccCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEEcCc
Confidence 457899999999999999999999999999999988643
No 34
>PF00524 PPV_E1_N: E1 Protein, N terminal domain; InterPro: IPR014000 Papillomaviruses are a large family of DNA tumour viruses which give rise to warts in their host species. The helicase E1 protein is an ATP-dependent DNA helicase required for initiation of viral DNA replication []. It forms a complex with the viral E2 protein, which is a site-specific DNA-binding transcriptional activator. The E1-E2 complex binds to the replication origin which contains binding sites for both proteins []. The E1 protein is a 70 kDa polypeptide with a centrally-located DNA-binding domain and a C-terminal ATPase/helicase domain. It binds specific 18 bp DNA sequences at the origin of replication, melts the DNA duplex and functions as a 3' to 5' helicase []. In addition to E2 it also interacts with DNA polymerase alpha and replication protein A to effect DNA replication. The DNA-binding domain forms a five-stranded antiparallel beta sheet bordered by four loosely packed alpha helices on one side and two tightly packed helices on the other []. Two structural modules within this domain, an extended loop and a helix, contain conserved residues and are critical for DNA binding. In solution E1 is a monomer, but binds DNA as a dimer. Recruitment of more E1 subunits to the complex leads to melting of the origin and ultimately to the formation of an E1 hexamer with helicase activity []. This entry represents the N-terminal region of E1, which contains the nuclear localisation signal.; GO: 0016817 hydrolase activity, acting on acid anhydrides
Probab=92.30 E-value=0.042 Score=58.24 Aligned_cols=69 Identities=23% Similarity=0.312 Sum_probs=33.1
Q ss_pred ccCcceeccccCCCC----CchhhcCCCcCCCCCCCCccchhhhhccCccccccccccCCCCCCCccccCCHHHHHHHHH
Q 000247 116 VLQFVEDAADVDYDD----DDEEEVGNESDNSGGFADDDFMEELFDAQPKVNNEMGQAHNLPFIPKEEEMDEEEFDKMME 191 (1790)
Q Consensus 116 ~n~FiDdEAEVDDDe----EEEDEeeEe~e~~~~Fi~dD~~~d~~e~~~~~~~d~r~~~~l~~r~~eEd~DaEelAe~Lk 191 (1790)
.+.+|.+|||++||. |.|+..++++ .+.+||.+.... +.+. ++.| |.+.+.+.+ ++....||
T Consensus 14 ~~gw~~vEAec~dd~~s~de~E~~~d~~s-d~~dfIDd~~~~---~qgn--------slaL-f~~Q~~~~d-~~~v~~LK 79 (130)
T PF00524_consen 14 CGGWFIVEAECSDDDISEDEDEDLFDSGS-DISDFIDDSEVS---EQGN--------SLAL-FNQQEAEDD-ERAVQALK 79 (130)
T ss_pred cCcEEEEEEEEcCCCCCCCcccccccCCc-cccccccCCCcc---cccH--------HHHH-HHHHHHHHH-HHHHHHHH
Confidence 355666799998822 2222222222 235787543321 1010 1111 112233333 45556899
Q ss_pred HHhcccc
Q 000247 192 ERYKSNK 198 (1790)
Q Consensus 192 ERY~r~s 198 (1790)
.+|-.++
T Consensus 80 RK~~~SP 86 (130)
T PF00524_consen 80 RKYLGSP 86 (130)
T ss_pred HHHcCCc
Confidence 9998654
No 35
>PRK09014 rfaH transcriptional activator RfaH; Provisional
Probab=92.15 E-value=0.22 Score=53.48 Aligned_cols=47 Identities=15% Similarity=0.165 Sum_probs=36.4
Q ss_pred ccCCCEEEEccCCCCCceeEEEEEe-CCeEEEEecCcceEE--EEecCcc
Q 000247 660 FAVGQTLRIRVGPLKGYLCRVLAVR-YSDVTVKLDSQQKIL--TVKGEHL 706 (1790)
Q Consensus 660 ~lIGKTVKIrkGPYKGylGiVKDaT-dt~ARVELHSk~KtI--TVdKe~L 706 (1790)
+..|++|+|+.||++|+.|+|+++. ...|.|+|+.-.+.+ .|+-+.|
T Consensus 110 ~~~G~~V~I~~Gp~~g~eg~v~~~~~~~r~~v~v~~~gr~~~v~v~~~~~ 159 (162)
T PRK09014 110 PKPGDKVIITEGAFEGLQAIYTEPDGEARSILLLNLLNKQVKHSVDNTQF 159 (162)
T ss_pred CCCCCEEEEecCCCCCcEEEEEEeCCCeEEEEeehhhCCcEEEEECHHHe
Confidence 4579999999999999999999996 446777777776644 4454444
No 36
>TIGR01079 rplX_bact ribosomal protein L24, bacterial/organelle. This model recognizes bacterial and organellar forms of ribosomal protein L24. It excludes eukaryotic and archaeal forms, designated L26 in eukaryotes.
Probab=91.49 E-value=0.28 Score=50.44 Aligned_cols=28 Identities=32% Similarity=0.437 Sum_probs=26.3
Q ss_pred cccCCCeEEEecCCCCCceEEEEEEECC
Q 000247 555 VISLNDTARVSEGPSKDRQGIVKKIYRG 582 (1790)
Q Consensus 555 ~I~vGD~VKVIdGphkGRqG~VlHIyRs 582 (1790)
.|+.||.|.||.|+.+|++|+|++|++.
T Consensus 3 ~ikkGD~V~Vi~G~dKGK~G~V~~V~~~ 30 (104)
T TIGR01079 3 KIKKGDTVKVISGKDKGKRGKVLKVLPK 30 (104)
T ss_pred cccCCCEEEEeEcCCCCcEEEEEEEEcC
Confidence 5899999999999999999999999874
No 37
>PRK12281 rplX 50S ribosomal protein L24; Reviewed
Probab=91.47 E-value=0.29 Score=47.81 Aligned_cols=38 Identities=26% Similarity=0.316 Sum_probs=34.8
Q ss_pred ccccCCCEEEEecCcCCCCcEEEEEEeCCCCEEEEEEe
Q 000247 317 NEVSEGTWAYVKNGKYKGDLAQVVYVNNARKRATVKLI 354 (1790)
Q Consensus 317 ~~Lk~GdwVRIKrGpYKGDLAQV~eVDenk~kVtVKLV 354 (1790)
..|..||.|.|.+|++||-.+.|..|+..+.+|+|+=|
T Consensus 5 ~~I~kGD~V~Vi~G~dKGK~G~V~~V~~~~~~V~Vegv 42 (76)
T PRK12281 5 LKVKKGDMVKVIAGDDKGKTGKVLAVLPKKNRVIVEGV 42 (76)
T ss_pred ccccCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEEcCc
Confidence 36889999999999999999999999999999998744
No 38
>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=91.23 E-value=0.41 Score=50.05 Aligned_cols=39 Identities=26% Similarity=0.307 Sum_probs=35.1
Q ss_pred cccccCCCEEEEecCcCCCCcEEEEEEeCCCCEEEEEEe
Q 000247 316 RNEVSEGTWAYVKNGKYKGDLAQVVYVNNARKRATVKLI 354 (1790)
Q Consensus 316 s~~Lk~GdwVRIKrGpYKGDLAQV~eVDenk~kVtVKLV 354 (1790)
...|+.||.|+|+.|+|+|-.|.|+.|+..+..|+|+=|
T Consensus 39 ~~~IkkGD~V~Vi~Gk~KGk~GkV~~V~~~~~~V~Vegv 77 (114)
T TIGR01080 39 ALPVRKGDKVRIMRGDFKGHEGKVSKVDLKRYRIYVEGV 77 (114)
T ss_pred cceeecCCEEEEecCCCCCCEEEEEEEEcCCCEEEEcCe
Confidence 458999999999999999999999999998888888644
No 39
>PRK01191 rpl24p 50S ribosomal protein L24P; Validated
Probab=91.10 E-value=0.43 Score=50.28 Aligned_cols=28 Identities=25% Similarity=0.296 Sum_probs=26.5
Q ss_pred cccCCCeEEEecCCCCCceEEEEEEECC
Q 000247 555 VISLNDTARVSEGPSKDRQGIVKKIYRG 582 (1790)
Q Consensus 555 ~I~vGD~VKVIdGphkGRqG~VlHIyRs 582 (1790)
.|+.||.|+||.|+++|++|.|+.|++.
T Consensus 45 ~IkkGD~V~VisG~~KGk~GkV~~V~~~ 72 (120)
T PRK01191 45 PVRKGDTVKVMRGDFKGEEGKVVEVDLK 72 (120)
T ss_pred eEeCCCEEEEeecCCCCceEEEEEEEcC
Confidence 6999999999999999999999999875
No 40
>COG0250 NusG Transcription antiterminator [Transcription]
Probab=90.93 E-value=0.35 Score=53.75 Aligned_cols=43 Identities=26% Similarity=0.396 Sum_probs=36.4
Q ss_pred cccCCCEEEEccCCCCCceeEEEEEeCC--eEEEEecCcceEEEE
Q 000247 659 MFAVGQTLRIRVGPLKGYLCRVLAVRYS--DVTVKLDSQQKILTV 701 (1790)
Q Consensus 659 d~lIGKTVKIrkGPYKGylGiVKDaTdt--~ARVELHSk~KtITV 701 (1790)
++.+|+.|+|+.|||+|+.|+|.++... .++|+|..-.+.+.|
T Consensus 123 ~~e~Gd~VrI~~GpFa~f~g~V~evd~ek~~~~v~v~ifgr~tPV 167 (178)
T COG0250 123 DFEPGDVVRIIDGPFAGFKAKVEEVDEEKGKLKVEVSIFGRPTPV 167 (178)
T ss_pred cCCCCCEEEEeccCCCCccEEEEEEcCcCcEEEEEEEEeCCceEE
Confidence 5788999999999999999999999876 677777776665555
No 41
>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=90.88 E-value=0.36 Score=56.35 Aligned_cols=43 Identities=26% Similarity=0.448 Sum_probs=35.5
Q ss_pred cccCCCEEEEccCCCCCceeEEEEEe--CCeEEEEecCcceEEEE
Q 000247 659 MFAVGQTLRIRVGPLKGYLCRVLAVR--YSDVTVKLDSQQKILTV 701 (1790)
Q Consensus 659 d~lIGKTVKIrkGPYKGylGiVKDaT--dt~ARVELHSk~KtITV 701 (1790)
++.+|++|+|+.||++|+.|+|.++. ...|+|+|+.-.+.+.|
T Consensus 205 ~f~vGd~VrI~dGPF~GfeG~I~eid~~k~Rv~VlV~IfGR~TpV 249 (258)
T TIGR01956 205 KFRVGNFVKIVDGPFKGIVGKIKKIDQEKKKAIVEVEILGKSVDV 249 (258)
T ss_pred CCCCCCEEEEEecCCCCcEEEEEEEeCCCCEEEEEEEecCCcEEE
Confidence 35689999999999999999999996 67888887776665444
No 42
>PTZ00194 60S ribosomal protein L26; Provisional
Probab=90.72 E-value=0.48 Score=51.25 Aligned_cols=52 Identities=19% Similarity=0.169 Sum_probs=42.7
Q ss_pred HHHHHHhhcccccccccCCCEEEEecCcCCCCcEEEEEEeCCCCEEEEEEeccC
Q 000247 304 NEVSHLLSAQIKRNEVSEGTWAYVKNGKYKGDLAQVVYVNNARKRATVKLIPRI 357 (1790)
Q Consensus 304 kEM~dLLkvkkks~~Lk~GdwVRIKrGpYKGDLAQV~eVDenk~kVtVKLVPRI 357 (1790)
+|+...+.+. ...|+.||.|.|++|.|+|-.|+|+.|+....+|+|+=|.++
T Consensus 34 keLr~k~~~R--s~~IkkGD~V~Vi~Gk~KGk~GkV~~V~~k~~~ViVEgvn~~ 85 (143)
T PTZ00194 34 KELRAKYNVR--SMPVRKDDEVMVVRGHHKGREGKVTAVYRKKWVIHIEKITRE 85 (143)
T ss_pred HHHHHHhCCc--cceeecCCEEEEecCCCCCCceEEEEEEcCCCEEEEeCeEEE
Confidence 4444444333 568999999999999999999999999999999999877655
No 43
>PRK00004 rplX 50S ribosomal protein L24; Reviewed
Probab=89.66 E-value=0.5 Score=48.62 Aligned_cols=37 Identities=24% Similarity=0.338 Sum_probs=34.5
Q ss_pred cccCCCEEEEecCcCCCCcEEEEEEeCCCCEEEEEEe
Q 000247 318 EVSEGTWAYVKNGKYKGDLAQVVYVNNARKRATVKLI 354 (1790)
Q Consensus 318 ~Lk~GdwVRIKrGpYKGDLAQV~eVDenk~kVtVKLV 354 (1790)
.|.+||.|.|++|++||-.+.|..|+..+.+|+|+=|
T Consensus 4 ~i~kGD~V~Vi~G~dKGk~G~V~~V~~~~~~V~Vegv 40 (105)
T PRK00004 4 KIKKGDTVIVIAGKDKGKRGKVLKVLPKKNKVIVEGV 40 (105)
T ss_pred cccCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEEcCc
Confidence 6889999999999999999999999999999999754
No 44
>PTZ00194 60S ribosomal protein L26; Provisional
Probab=89.49 E-value=0.39 Score=51.86 Aligned_cols=28 Identities=32% Similarity=0.526 Sum_probs=26.6
Q ss_pred cccCCCeEEEecCCCCCceEEEEEEECC
Q 000247 555 VISLNDTARVSEGPSKDRQGIVKKIYRG 582 (1790)
Q Consensus 555 ~I~vGD~VKVIdGphkGRqG~VlHIyRs 582 (1790)
.|+.||+|+||.|.++|++|.|+.|++.
T Consensus 46 ~IkkGD~V~Vi~Gk~KGk~GkV~~V~~k 73 (143)
T PTZ00194 46 PVRKDDEVMVVRGHHKGREGKVTAVYRK 73 (143)
T ss_pred eeecCCEEEEecCCCCCCceEEEEEEcC
Confidence 6999999999999999999999999875
No 45
>COG0198 RplX Ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=89.38 E-value=0.47 Score=48.97 Aligned_cols=30 Identities=27% Similarity=0.359 Sum_probs=27.5
Q ss_pred CcccCCCeEEEecCCCCCceEEEEEEECCE
Q 000247 554 KVISLNDTARVSEGPSKDRQGIVKKIYRGI 583 (1790)
Q Consensus 554 n~I~vGD~VKVIdGphkGRqG~VlHIyRs~ 583 (1790)
..|+.||+|+||.|..+|++|.|+.|+..-
T Consensus 3 ~~IrkGD~V~Vi~GkdKGk~GkVl~v~~k~ 32 (104)
T COG0198 3 MKVKKGDTVKVIAGKDKGKEGKVLKVLPKK 32 (104)
T ss_pred cceecCCEEEEEecCCCCcceEEEEEecCe
Confidence 468999999999999999999999998865
No 46
>KOG3262 consensus H/ACA small nucleolar RNP component GAR1 [Translation, ribosomal structure and biogenesis]
Probab=89.33 E-value=0.76 Score=51.38 Aligned_cols=16 Identities=56% Similarity=1.124 Sum_probs=8.4
Q ss_pred CCCCCCCCCcC-CCCCC
Q 000247 1207 DGGRGSGGRWG-QGGGQ 1222 (1790)
Q Consensus 1207 ~~~~~~~~~~~-~~~~~ 1222 (1790)
++|.|.+++.| |++++
T Consensus 5 rgggg~~g~~gfRgg~g 21 (215)
T KOG3262|consen 5 RGGGGGGGGGGFRGGGG 21 (215)
T ss_pred cCCCCCCCCCCcccCCC
Confidence 35556666655 44433
No 47
>TIGR01080 rplX_A_E ribosomal protein L24p/L26e, archaeal/eukaryotic. This model represents the archaeal and eukaryotic branch of the ribosomal protein L24p/L26e family. Bacterial and organellar forms are represented by the related TIGR01079.
Probab=88.74 E-value=0.53 Score=49.24 Aligned_cols=37 Identities=22% Similarity=0.294 Sum_probs=29.5
Q ss_pred ccCCCEEEEccCCCCCceeEEEEEeCCeEEEEecCcc
Q 000247 660 FAVGQTLRIRVGPLKGYLCRVLAVRYSDVTVKLDSQQ 696 (1790)
Q Consensus 660 ~lIGKTVKIrkGPYKGylGiVKDaTdt~ARVELHSk~ 696 (1790)
.-.|++|+|+.|+|||..|.|+.|.....+|.++--+
T Consensus 42 IkkGD~V~Vi~Gk~KGk~GkV~~V~~~~~~V~Vegvn 78 (114)
T TIGR01080 42 VRKGDKVRIMRGDFKGHEGKVSKVDLKRYRIYVEGVT 78 (114)
T ss_pred eecCCEEEEecCCCCCCEEEEEEEEcCCCEEEEcCeE
Confidence 3468999999999999999999997655555555444
No 48
>KOG3262 consensus H/ACA small nucleolar RNP component GAR1 [Translation, ribosomal structure and biogenesis]
Probab=88.30 E-value=0.94 Score=50.69 Aligned_cols=11 Identities=73% Similarity=1.446 Sum_probs=5.5
Q ss_pred CCCCCCCCCCC
Q 000247 1512 DRGGFGGRGRG 1522 (1790)
Q Consensus 1512 ~RGg~gGrg~~ 1522 (1790)
.++++.+++|.
T Consensus 203 ~ggg~rgrgR~ 213 (215)
T KOG3262|consen 203 HGGGFRGRGRG 213 (215)
T ss_pred CCCCCCCCCCC
Confidence 34555555554
No 49
>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=87.44 E-value=1.6 Score=40.19 Aligned_cols=47 Identities=23% Similarity=0.286 Sum_probs=36.9
Q ss_pred ccCCCEEEEccC--CCCCceeEEEEEeCCeEEEEecCcc--eEEEEecCcc
Q 000247 660 FAVGQTLRIRVG--PLKGYLCRVLAVRYSDVTVKLDSQQ--KILTVKGEHL 706 (1790)
Q Consensus 660 ~lIGKTVKIrkG--PYKGylGiVKDaTdt~ARVELHSk~--KtITVdKe~L 706 (1790)
.|-|-+|+|+.- +|-+|.|+|-.+++..|-|...-.+ |.||.+-++|
T Consensus 2 ilPG~~V~V~n~~~~Y~~y~G~VQRvsdgkaaVLFEGGnWdKlvTf~l~eL 52 (53)
T PF11623_consen 2 ILPGSTVRVKNPNDIYYGYEGFVQRVSDGKAAVLFEGGNWDKLVTFRLSEL 52 (53)
T ss_dssp --TT-EEEE--TTSTTTT-EEEEEEEETTEEEEEEEETTEEEEEEEEGGGE
T ss_pred ccCCCEEEEeCCCCccchheEEEEEeeCCeEEEEecCCCceEEEEEEhhhC
Confidence 456789999877 8999999999999999999999887 8999887766
No 50
>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=85.81 E-value=1.1 Score=46.16 Aligned_cols=37 Identities=24% Similarity=0.311 Sum_probs=33.9
Q ss_pred cccCCCEEEEecCcCCCCcEEEEEEeCCCCEEEEEEe
Q 000247 318 EVSEGTWAYVKNGKYKGDLAQVVYVNNARKRATVKLI 354 (1790)
Q Consensus 318 ~Lk~GdwVRIKrGpYKGDLAQV~eVDenk~kVtVKLV 354 (1790)
.|..||.|.|++|++||=.+.|..|+..+++|+|+=|
T Consensus 3 ~ikkGD~V~Vi~G~dKGK~G~V~~V~~~~~~V~Vegv 39 (104)
T TIGR01079 3 KIKKGDTVKVISGKDKGKRGKVLKVLPKTNKVIVEGV 39 (104)
T ss_pred cccCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEECCc
Confidence 5789999999999999999999999999999998643
No 51
>COG2933 Predicted SAM-dependent methyltransferase [General function prediction only]
Probab=85.39 E-value=1.2 Score=52.48 Aligned_cols=57 Identities=21% Similarity=0.306 Sum_probs=48.5
Q ss_pred EEEecCchhHHHHHHHHHHHHhhccCCCCCcEEEEEEeCCCCcEEEEEeccchhHHHHhcCCCC
Q 000247 229 KVKCMAGRERQSAFCLMQKFVDLQSLGSKMQIISAFAVDHIKGFIFIEADKQCDINEACKGLSG 292 (1790)
Q Consensus 229 aVKCK~GkEReVV~~LmrKii~lq~~g~~L~I~SVFvpd~lKGYIYVEA~kq~dVkeAIkGI~g 292 (1790)
++.|++|.|+|++.-|-.|+..+. |+-..-.+.-.|||..|++..+++..+|+.|+.
T Consensus 5 ~lyCRpGFEkE~aAEi~d~Aa~l~-------IfGfarvk~n~gyV~feCyq~d~adrL~r~lpf 61 (358)
T COG2933 5 ALYCRPGFEKECAAEITDKAAQLE-------IFGFARVKENSGYVIFECYQPDDADRLIRELPF 61 (358)
T ss_pred eeeecCCCcHHHHHHHHHhhhhhc-------cccceeecccCceEEEEEcCcccHHHHHHhCcH
Confidence 578999999999999999986553 554444467889999999999999999999986
No 52
>PF04931 DNA_pol_phi: DNA polymerase phi; InterPro: IPR007015 Proteins of this family are predominantly nucleolar. The majority are described as transcription factor transactivators. The family also includes the fifth essential DNA polymerase (Pol5p) of Schizosaccharomyces pombe (Fission yeast) and Saccharomyces cerevisiae (Baker's yeast) (2.7.7.7 from EC). Pol5p is localized exclusively to the nucleolus and binds near or at the enhancer region of rRNA-encoding DNA repeating units.; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006351 transcription, DNA-dependent
Probab=82.55 E-value=1.5 Score=58.21 Aligned_cols=16 Identities=13% Similarity=0.420 Sum_probs=10.4
Q ss_pred hhHHHHHHHHHHHHhh
Q 000247 236 RERQSAFCLMQKFVDL 251 (1790)
Q Consensus 236 kEReVV~~LmrKii~l 251 (1790)
.+++.++.+..|++++
T Consensus 764 ~~~~~~~~Fk~RvlDL 779 (784)
T PF04931_consen 764 EAKENVIHFKNRVLDL 779 (784)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 4555666677777765
No 53
>KOG1708 consensus Mitochondrial/chloroplast ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=81.79 E-value=1.4 Score=49.92 Aligned_cols=30 Identities=30% Similarity=0.324 Sum_probs=27.6
Q ss_pred CCcccCCCeEEEecCCCCCceEEEEEEECC
Q 000247 553 MKVISLNDTARVSEGPSKDRQGIVKKIYRG 582 (1790)
Q Consensus 553 gn~I~vGD~VKVIdGphkGRqG~VlHIyRs 582 (1790)
-=+|.+||+|+|+.|.-+|++|.|+.|.++
T Consensus 70 dw~ff~GDtVeVlvGkDkGkqG~Vtqv~r~ 99 (236)
T KOG1708|consen 70 DWHFFFGDTVEVLVGKDKGKQGEVTQVIRH 99 (236)
T ss_pred ceeEecCCEEEEEecccCCccceEEEEeec
Confidence 457899999999999999999999999875
No 54
>PRK11760 putative 23S rRNA C2498 ribose 2'-O-ribose methyltransferase; Provisional
Probab=80.80 E-value=2.4 Score=51.80 Aligned_cols=65 Identities=18% Similarity=0.300 Sum_probs=51.2
Q ss_pred EEEEecCchhHHHHHHHHHHHHhhccCCCCCcEEEEEEeCCCCcEEEEEeccchhHHHHhcCCCC---EEeceec
Q 000247 228 WKVKCMAGRERQSAFCLMQKFVDLQSLGSKMQIISAFAVDHIKGFIFIEADKQCDINEACKGLSG---IYYSRLA 299 (1790)
Q Consensus 228 WaVKCK~GkEReVV~~LmrKii~lq~~g~~L~I~SVFvpd~lKGYIYVEA~kq~dVkeAIkGI~g---Vy~sK~~ 299 (1790)
+++.|++|.|++++.-|..++.++. |+-..-...-.|||..|++...+...+++.|+. |+..+++
T Consensus 4 l~lyCR~GFE~e~aaEi~~~a~~~~-------~~G~~~~~~~sgyv~f~~~~~~~~~~l~~~l~~~~LiFaRq~~ 71 (357)
T PRK11760 4 LLLYCRPGFEKECAAEITDKAAELG-------VFGYARVKENSGYVIFECYQPDDADRLARELPFSELIFARQMF 71 (357)
T ss_pred EEEEeCCCchHHHHHHHHHHHHhcC-------CcccccccCCCeEEEEEecCcchHHHHHhhCCchhceehhHHH
Confidence 6899999999999999999986643 333333355679999999999999999998885 5655543
No 55
>COG0198 RplX Ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=78.98 E-value=2.9 Score=43.40 Aligned_cols=34 Identities=29% Similarity=0.314 Sum_probs=30.3
Q ss_pred ccccCCCEEEEecCcCCCCcEEEEEEeCCCCEEEEE
Q 000247 317 NEVSEGTWAYVKNGKYKGDLAQVVYVNNARKRATVK 352 (1790)
Q Consensus 317 ~~Lk~GdwVRIKrGpYKGDLAQV~eVDenk~kVtVK 352 (1790)
..|..||.|+|++|++||-.|+|++|++.. |+|+
T Consensus 3 ~~IrkGD~V~Vi~GkdKGk~GkVl~v~~k~--V~VE 36 (104)
T COG0198 3 MKVKKGDTVKVIAGKDKGKEGKVLKVLPKK--VVVE 36 (104)
T ss_pred cceecCCEEEEEecCCCCcceEEEEEecCe--EEEE
Confidence 357889999999999999999999999976 7665
No 56
>CHL00010 infA translation initiation factor 1
Probab=76.01 E-value=20 Score=35.35 Aligned_cols=65 Identities=14% Similarity=0.061 Sum_probs=42.6
Q ss_pred ceEEEEEEecCceEEEccCCCCCCceEEEecccccCCCCCCcccccccCCCcccCCCeEEEecCCCCCceEEEEEEECC
Q 000247 504 DFGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVSEGPSKDRQGIVKKIYRG 582 (1790)
Q Consensus 504 TVGVIVrVEkDEsfkVLdq~gD~~~VvtVk~~eI~~K~~~rr~vAtD~~gn~I~vGD~VKVIdGphkGRqG~VlHIyRs 582 (1790)
..|+|+++-....|.|.+.++ .++.+.+.- |+. .....|.+||+|.|--=++....|.|+|=|++
T Consensus 9 ~~G~Vik~lg~~~y~V~~~~g---~~~~c~~rG---klr--------~~~i~~~vGD~V~ve~~~~~~~~g~Ii~r~~~ 73 (78)
T CHL00010 9 MEGLVTESLPNGMFRVRLDNG---CQVLGYISG---KIR--------RNSIRILPGDRVKVELSPYDLTKGRIIYRLRN 73 (78)
T ss_pred EEEEEEEEcCCCEEEEEeCCC---CEEEEEecc---cee--------cCCcccCCCCEEEEEEcccCCCeEEEEEEecC
Confidence 469999998434788765432 456666432 111 11344789999999744455678999998875
No 57
>PF09444 MRC1: MRC1-like domain; InterPro: IPR018564 This putative domain is found in the most conserved region in mediator of replication checkpoint protein 1. This protein is a component of the replisome and is required for Rad3-dependent activation of the checkpoint kinase Cds1 in response to replication fork arrest [].
Probab=75.50 E-value=0.6 Score=50.65 Aligned_cols=18 Identities=28% Similarity=0.479 Sum_probs=14.1
Q ss_pred cccccCcceeccccCCCC
Q 000247 113 NRSVLQFVEDAADVDYDD 130 (1790)
Q Consensus 113 rrr~n~FiDdEAEVDDDe 130 (1790)
|.....||+.|||..|||
T Consensus 3 k~~~~~~vE~EAEESeDE 20 (145)
T PF09444_consen 3 KSGASEFVEEEAEESEDE 20 (145)
T ss_pred chhHHHHHHHHHhcchhh
Confidence 345678999999987765
No 58
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=74.85 E-value=15 Score=36.69 Aligned_cols=65 Identities=11% Similarity=0.018 Sum_probs=47.5
Q ss_pred CCceEEEEEEecCceEEEccCCCCCCceEEEecccccCCCCCCcccccccCCCcccCCCeEEEecCCCCCceEEEEEEEC
Q 000247 502 RKDFGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVSEGPSKDRQGIVKKIYR 581 (1790)
Q Consensus 502 ~~TVGVIVrVEkDEsfkVLdq~gD~~~VvtVk~~eI~~K~~~rr~vAtD~~gn~I~vGD~VKVIdGphkGRqG~VlHIyR 581 (1790)
.+.+|.|+++..+..|.|.+.++ ..+.+.+. -|+. ..=-|+.||.|.|--=++.-..|.|+|+|.
T Consensus 5 ~q~~g~V~~~lG~~~~~V~~~dG---~~~la~ip---gK~R---------k~iwI~~GD~VlVe~~~~~~~kg~Iv~r~~ 69 (83)
T smart00652 5 GQEIAQVVKMLGNGRLEVMCADG---KERLARIP---GKMR---------KKVWIRRGDIVLVDPWDFQDVKADIIYKYT 69 (83)
T ss_pred CcEEEEEEEEcCCCEEEEEECCC---CEEEEEEc---hhhc---------ccEEEcCCCEEEEEecCCCCCEEEEEEEeC
Confidence 35789999999888999998764 34444432 2321 234689999999987777778899999886
No 59
>KOG1832 consensus HIV-1 Vpr-binding protein [Cell cycle control, cell division, chromosome partitioning]
Probab=74.23 E-value=2.7 Score=55.58 Aligned_cols=9 Identities=33% Similarity=0.560 Sum_probs=4.9
Q ss_pred HHHHHHHHH
Q 000247 184 EEFDKMMEE 192 (1790)
Q Consensus 184 EelAe~LkE 192 (1790)
+++++.|+|
T Consensus 1469 ~df~~elee 1477 (1516)
T KOG1832|consen 1469 GDFMEELEE 1477 (1516)
T ss_pred hHHHHHHhh
Confidence 455555554
No 60
>PTZ00415 transmission-blocking target antigen s230; Provisional
Probab=73.84 E-value=1.6 Score=60.52 Aligned_cols=15 Identities=27% Similarity=0.331 Sum_probs=8.7
Q ss_pred CCcEEEEEecCchhH
Q 000247 224 DPTIWKVKCMAGRER 238 (1790)
Q Consensus 224 DPkLWaVKCK~GkER 238 (1790)
-|-+-+|+.+.|.|.
T Consensus 313 apyv~l~~~~~~~~e 327 (2849)
T PTZ00415 313 APYVTLTKANEGSEE 327 (2849)
T ss_pred CceEEEEccCCcchh
Confidence 455666666666543
No 61
>PTZ00061 DNA-directed RNA polymerase; Provisional
Probab=73.84 E-value=20 Score=41.23 Aligned_cols=57 Identities=14% Similarity=0.103 Sum_probs=36.3
Q ss_pred CcEEEEEeccchhHHHHhcCCCCEEeceeccCCHHHHHHHhhc---cc-------------ccccccCCCEEEEec
Q 000247 270 KGFIFIEADKQCDINEACKGLSGIYYSRLAPVPKNEVSHLLSA---QI-------------KRNEVSEGTWAYVKN 329 (1790)
Q Consensus 270 KGYIYVEA~kq~dVkeAIkGI~gVy~sK~~pVPikEM~dLLkv---kk-------------ks~~Lk~GdwVRIKr 329 (1790)
+.| .||...++++.- +=+.|+..-+-.+++.+|...||+. +. +...+++|+.|+|+|
T Consensus 118 ~~~-~iE~F~E~eLlv--nit~H~lVPkH~~Ls~eEk~~lL~~y~i~~~qLPrI~~~DPvary~g~k~G~vvkI~R 190 (205)
T PTZ00061 118 PRH-IIENFLETELLV--NITKHELVPKHIPLTDDEKLNLLQRYKVKESQLPRIQSADPVARYFGLSKGQVVKIIR 190 (205)
T ss_pred CCc-EEEEeeehheEE--ecccceecCCeEEcCHHHHHHHHHHhCCCHHHCCcccccChhhHhcCCCCCCEEEEEE
Confidence 444 477776655421 2223455556677889999999962 11 134678899998887
No 62
>PHA02774 E1; Provisional
Probab=72.78 E-value=1.3 Score=57.05 Aligned_cols=31 Identities=13% Similarity=0.133 Sum_probs=21.4
Q ss_pred eccCCHHHHHHHhhcccccccccCCCEEEEecCcC
Q 000247 298 LAPVPKNEVSHLLSAQIKRNEVSEGTWAYVKNGKY 332 (1790)
Q Consensus 298 ~~pVPikEM~dLLkvkkks~~Lk~GdwVRIKrGpY 332 (1790)
..-|+..|+++.++-.|. --.+||-..-|.+
T Consensus 177 ~fgvsf~eLtR~FKSdKT----cc~dWVv~v~gv~ 207 (613)
T PHA02774 177 AFGVSFTELTRPFKSDKT----CCNDWVVAVFGVS 207 (613)
T ss_pred HhcccHHHheecccCCCc----cchhheEEEEecC
Confidence 456788888888875442 2358888887754
No 63
>TIGR01622 SF-CC1 splicing factor, CC1-like family. A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the model.
Probab=72.17 E-value=9.5 Score=46.86 Aligned_cols=68 Identities=12% Similarity=0.102 Sum_probs=50.7
Q ss_pred HHHHHHHHHHHHhhccCCCCCcEEEEEEe-CCCCcEEEEEeccchhHHHHhcCCCCEEe----ceeccCCHHHHHHHhh
Q 000247 238 RQSAFCLMQKFVDLQSLGSKMQIISAFAV-DHIKGFIFIEADKQCDINEACKGLSGIYY----SRLAPVPKNEVSHLLS 311 (1790)
Q Consensus 238 ReVV~~LmrKii~lq~~g~~L~I~SVFvp-d~lKGYIYVEA~kq~dVkeAIkGI~gVy~----sK~~pVPikEM~dLLk 311 (1790)
.+|..-|+..|..+. .|.+|++. +...||||||-...++...||+.|.+-+. ..+..+|.+++..++.
T Consensus 383 ~~~~~dv~~e~~k~G------~v~~v~v~~~~~~G~~fV~F~~~e~A~~A~~~lnGr~f~gr~i~~~~~~~~~~~~~~~ 455 (457)
T TIGR01622 383 NEILDDVKEECSKYG------GVVHIYVDTKNSAGKIYLKFSSVDAALAAFQALNGRYFGGKMITAAFVVNDVYDMSCL 455 (457)
T ss_pred HHHHHHHHHHHHhcC------CeeEEEEeCCCCceeEEEEECCHHHHHHHHHHhcCcccCCeEEEEEEEcHHHHHhhcC
Confidence 445555665655443 47888887 67899999999999999999999999653 2466778877766653
No 64
>PLN00208 translation initiation factor (eIF); Provisional
Probab=71.60 E-value=13 Score=40.79 Aligned_cols=77 Identities=14% Similarity=0.040 Sum_probs=55.3
Q ss_pred ccccCcEEEecC-CceEEEEEEecCceEEEccCCCCCCceEEEecccccCCCCCCcccccccCCCcccCCCeEEEecCCC
Q 000247 491 SFELYELVCFGR-KDFGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVSEGPS 569 (1790)
Q Consensus 491 ~FeLgDLVQLD~-~TVGVIVrVEkDEsfkVLdq~gD~~~VvtVk~~eI~~K~~~rr~vAtD~~gn~I~vGD~VKVIdGph 569 (1790)
.-+..+|+.... +.+|+|+++-.+..|.|.+.++ ..+.+.+ .-|+.. .--|.+||+|.|---+|
T Consensus 20 ~~~~~el~~p~egq~~g~V~~~lGn~~~~V~c~dG---~~rLa~I---pGKmRK---------rIWI~~GD~VlVel~~~ 84 (145)
T PLN00208 20 DDEKRELIFKEDGQEYAQVLRMLGNGRCEALCIDG---TKRLCHI---RGKMRK---------KVWIAAGDIILVGLRDY 84 (145)
T ss_pred ccceeecccCCCCcEEEEEEEEcCCCEEEEEECCC---CEEEEEE---ecccee---------eEEecCCCEEEEEccCC
Confidence 345666766643 6789999999888999998764 2444432 233211 24589999999987788
Q ss_pred CCceEEEEEEECC
Q 000247 570 KDRQGIVKKIYRG 582 (1790)
Q Consensus 570 kGRqG~VlHIyRs 582 (1790)
.-..|.|+|+|..
T Consensus 85 d~~KgdIv~ry~~ 97 (145)
T PLN00208 85 QDDKADVILKYMP 97 (145)
T ss_pred CCCEEEEEEEcCH
Confidence 8889999998864
No 65
>PF14632 SPT6_acidic: Acidic N-terminal SPT6
Probab=71.57 E-value=1.3 Score=44.89 Aligned_cols=9 Identities=44% Similarity=0.534 Sum_probs=6.6
Q ss_pred CCCCCCccc
Q 000247 143 SGGFADDDF 151 (1790)
Q Consensus 143 ~~~Fi~dD~ 151 (1790)
+.+||.++.
T Consensus 20 ~eGFIvDde 28 (92)
T PF14632_consen 20 REGFIVDDE 28 (92)
T ss_pred hcCCccCCc
Confidence 479998753
No 66
>KOG0299 consensus U3 snoRNP-associated protein (contains WD40 repeats) [RNA processing and modification]
Probab=71.52 E-value=2.4 Score=52.81 Aligned_cols=19 Identities=16% Similarity=0.300 Sum_probs=15.1
Q ss_pred cCCHHHHHHHHHHHhcccc
Q 000247 180 EMDEEEFDKMMEERYKSNK 198 (1790)
Q Consensus 180 d~DaEelAe~LkERY~r~s 198 (1790)
++|.|.||+.|+|-|..++
T Consensus 98 ~~~~e~va~rLked~le~~ 116 (479)
T KOG0299|consen 98 DLDDELVASRLKEDVLEQS 116 (479)
T ss_pred hhhHHHHHHHHHHHHHHhc
Confidence 5566889999999998655
No 67
>PF14851 FAM176: FAM176 family
Probab=70.44 E-value=5.7 Score=43.76 Aligned_cols=17 Identities=29% Similarity=0.345 Sum_probs=11.4
Q ss_pred ccCCHHHHHHHHHHHhc
Q 000247 179 EEMDEEEFDKMMEERYK 195 (1790)
Q Consensus 179 Ed~DaEelAe~LkERY~ 195 (1790)
-...|-|+|+.|+||-+
T Consensus 114 ~sae~~e~A~rlEeRe~ 130 (153)
T PF14851_consen 114 TSAEELERAQRLEERER 130 (153)
T ss_pred ccHHHHHHHHHHHHHHH
Confidence 34445578888888865
No 68
>KOG0415 consensus Predicted peptidyl prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]
Probab=70.42 E-value=9.7 Score=46.47 Aligned_cols=112 Identities=16% Similarity=0.202 Sum_probs=71.6
Q ss_pred CccccCCHHHHHHHHHHHhccccchhhchhhHHHhhhcccccCCCCCCCCcEEEEEecCchhHHHHHHHHHHHHhhccCC
Q 000247 176 PKEEEMDEEEFDKMMEERYKSNKLIRYAEEDYEAKKMLEREYHMPCPEDPTIWKVKCMAGRERQSAFCLMQKFVDLQSLG 255 (1790)
Q Consensus 176 ~~eEd~DaEelAe~LkERY~r~s~~~y~~d~~e~~~~VpQqlLLPSVkDPkLWaVKCK~GkEReVV~~LmrKii~lq~~g 255 (1790)
+.++.+.||||+++|+||-+...+. .-|+-..+|--.+.|- +--||+.|..|=-+-+=+..|.-||=
T Consensus 198 d~~~g~saeel~e~~~e~ea~~~A~-----iLEmvGDlpdAd~~PP--eNVLFVCKLNPVTtDeDLeiIFSrFG------ 264 (479)
T KOG0415|consen 198 DDDEGLSAEELEEVLAEKEAKAQAV-----ILEMVGDLPDADVKPP--ENVLFVCKLNPVTTDEDLEIIFSRFG------ 264 (479)
T ss_pred ccccccCHHHHHHHHHHHHHHhhHh-----HHHHhcCCcccccCCC--cceEEEEecCCcccccchhhHHhhcc------
Confidence 4557889999999999998764432 1122234444444442 23488888877666555555555552
Q ss_pred CCCcEEEEEE-eC----CCCcEEEEEeccchhHHHHhcCCCCEEe-ceeccCCH
Q 000247 256 SKMQIISAFA-VD----HIKGFIFIEADKQCDINEACKGLSGIYY-SRLAPVPK 303 (1790)
Q Consensus 256 ~~L~I~SVFv-pd----~lKGYIYVEA~kq~dVkeAIkGI~gVy~-sK~~pVPi 303 (1790)
.|.|+-+ ++ ..-=|-|||-+.+..+..|.=.|.+|.. ...+-|.+
T Consensus 265 ---~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHVDF 315 (479)
T KOG0415|consen 265 ---KIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHVDF 315 (479)
T ss_pred ---cceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEeeh
Confidence 1444433 33 2335999999999999999999999876 34444543
No 69
>KOG0262 consensus RNA polymerase I, large subunit [Transcription]
Probab=70.22 E-value=11 Score=51.73 Aligned_cols=70 Identities=7% Similarity=0.102 Sum_probs=37.6
Q ss_pred cEEEEEec--CchhHHHHHHHHHHHHhhccCCCCCcEEEEEEeC------CCCcEEEEEeccchhHHHHhc--CCCCEEe
Q 000247 226 TIWKVKCM--AGRERQSAFCLMQKFVDLQSLGSKMQIISAFAVD------HIKGFIFIEADKQCDINEACK--GLSGIYY 295 (1790)
Q Consensus 226 kLWaVKCK--~GkEReVV~~LmrKii~lq~~g~~L~I~SVFvpd------~lKGYIYVEA~kq~dVkeAIk--GI~gVy~ 295 (1790)
+|..|+.+ ..+|+..+.+|.+++...--.-.--.|..+++.+ ..+ ++.-|...-.++++..+ .|..||.
T Consensus 1441 ~wcev~~~lp~~~~k~~mssiVe~~~~~~vI~q~~gIeRc~~~~~~~~~k~~~-~l~TeGVnl~a~~~~~d~LDv~~lyS 1519 (1640)
T KOG0262|consen 1441 KWCEVELKLPLDKEKLDMSSIVESIAPKSVIHQVPGIERCVVSEPQDDVKEKS-VLLTEGVNLPALFDHADILDVNRLYS 1519 (1640)
T ss_pred cEEEEEEEecCCCcchHHHHHHHHHhcceeeeccCCceeeeccCCcccccccc-eehhcCccHHHHHHHHhhhhhhhhcc
Confidence 34445443 5788888888888876432111223566777663 122 55555555555554332 3445554
Q ss_pred c
Q 000247 296 S 296 (1790)
Q Consensus 296 s 296 (1790)
+
T Consensus 1520 N 1520 (1640)
T KOG0262|consen 1520 N 1520 (1640)
T ss_pred c
Confidence 3
No 70
>cd05793 S1_IF1A S1_IF1A: Translation initiation factor IF1A, also referred to as eIF1A in eukaryotes and aIF1A in archaea, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea.
Probab=69.58 E-value=22 Score=35.16 Aligned_cols=64 Identities=11% Similarity=0.019 Sum_probs=46.8
Q ss_pred ceEEEEEEecCceEEEccCCCCCCceEEEecccccCCCCCCcccccccCCCcccCCCeEEEecCCCCCceEEEEEEECC
Q 000247 504 DFGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVSEGPSKDRQGIVKKIYRG 582 (1790)
Q Consensus 504 TVGVIVrVEkDEsfkVLdq~gD~~~VvtVk~~eI~~K~~~rr~vAtD~~gn~I~vGD~VKVIdGphkGRqG~VlHIyRs 582 (1790)
..|.|+++-.+..|.|.+.++ ..+.+.+ ..|+. ..--|.+||.|.|--=|+.-..|.|+|+|..
T Consensus 2 ~~g~V~~~~g~~~~~V~~~~g---~~~la~i---~gK~r---------k~iwI~~GD~V~Ve~~~~d~~kg~Iv~r~~~ 65 (77)
T cd05793 2 EYGQVEKMLGNGRLEVRCFDG---KKRLCRI---RGKMR---------KRVWINEGDIVLVAPWDFQDDKADIIYKYTP 65 (77)
T ss_pred EEEEEEEEcCCCEEEEEECCC---CEEEEEE---chhhc---------ccEEEcCCCEEEEEeccccCCEEEEEEEcCH
Confidence 468999998888999998764 2344432 23321 2346899999999777888889999999863
No 71
>COG1588 POP4 RNase P/RNase MRP subunit p29 [Translation, ribosomal structure and biogenesis]
Probab=68.74 E-value=9.8 Score=39.10 Aligned_cols=47 Identities=15% Similarity=0.123 Sum_probs=39.6
Q ss_pred ccCCCEEEEccCC---CCCceeEEEEEeCCeEEEEecCcceEEEEecCcccc
Q 000247 660 FAVGQTLRIRVGP---LKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLAE 708 (1790)
Q Consensus 660 ~lIGKTVKIrkGP---YKGylGiVKDaTdt~ARVELHSk~KtITVdKe~Ls~ 708 (1790)
.|||..|+|+.=+ |-|..|+|+|-|.++..|+-.+ +.++|+|+...+
T Consensus 14 EliGl~vrVv~s~~~s~vGI~G~VVdETkNtLvi~t~~--~~~~VpK~~~vf 63 (95)
T COG1588 14 ELIGLEVRVVRSTNPSYVGIEGRVVDETKNTLVIDTGS--REKVVPKDGAVF 63 (95)
T ss_pred HhcCcEEEEEecCCCCccceeEEEEeeeccEEEEECCC--ceEEEecCcEEE
Confidence 6999999999885 5677888999999999987776 778888887664
No 72
>PRK04950 ProP expression regulator; Provisional
Probab=67.51 E-value=8.3 Score=44.46 Aligned_cols=46 Identities=35% Similarity=0.590 Sum_probs=38.2
Q ss_pred ccCCCEEEEccCCCCCceeEEEEEeCCeEEEEecCcceEEEEecCccc
Q 000247 660 FAVGQTLRIRVGPLKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLA 707 (1790)
Q Consensus 660 ~lIGKTVKIrkGPYKGylGiVKDaTdt~ARVELHSk~KtITVdKe~Ls 707 (1790)
..+|+.|+|.-|. -=.-+.|++|+-+.|||+|.+.+. |.|..+||.
T Consensus 167 l~~gq~v~vk~g~-~~~~a~i~ei~kd~v~vql~~Gl~-~~v~ae~l~ 212 (213)
T PRK04950 167 LTVGQAVKVKAGK-SAMDATVLEITKDDVRVQLDSGLS-MIVRAEHLV 212 (213)
T ss_pred hccCCEEEEeccC-CCCceEEEEEecCcEEEEcCCCcE-EEEeHhhhc
Confidence 4689999999982 234589999999999999999886 678888875
No 73
>cd04456 S1_IF1A_like S1_IF1A_like: Translation initiation factor IF1A-like, S1-like RNA-binding domain. IF1A is also referred to as eIF1A in eukaryotes and aIF1A in archaea. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea.
Probab=67.00 E-value=29 Score=34.41 Aligned_cols=65 Identities=11% Similarity=-0.032 Sum_probs=46.6
Q ss_pred CceEEEEEEecCceEEEccCCCCCCceEEEecccccCCCCCCcccccccCCCcccCCCeEEEecCCC-CCceEEEEEEEC
Q 000247 503 KDFGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVSEGPS-KDRQGIVKKIYR 581 (1790)
Q Consensus 503 ~TVGVIVrVEkDEsfkVLdq~gD~~~VvtVk~~eI~~K~~~rr~vAtD~~gn~I~vGD~VKVIdGph-kGRqG~VlHIyR 581 (1790)
+.+|.|+++..+..|.|.+.++ ..+.+.+. .|+. ..--|+.||.|.|--=++ .-..|.|+|+|.
T Consensus 1 q~i~~V~~~lG~~~~~V~~~dg---~~~l~~i~---gK~R---------k~iwI~~GD~VlV~~~~~~~~~kg~Iv~r~~ 65 (78)
T cd04456 1 QQIVRVLRMLGNNRHEVECADG---QRRLVSIP---GKLR---------KNIWIKRGDFLIVDPIEEGEDVKADIIFVYC 65 (78)
T ss_pred CeEEEEEEECCCCEEEEEECCC---CEEEEEEc---hhhc---------cCEEEcCCCEEEEEecccCCCceEEEEEEeC
Confidence 3579999999888999988764 34444432 2321 124689999999987677 567899999987
Q ss_pred C
Q 000247 582 G 582 (1790)
Q Consensus 582 s 582 (1790)
.
T Consensus 66 ~ 66 (78)
T cd04456 66 K 66 (78)
T ss_pred H
Confidence 4
No 74
>PF03115 Astro_capsid: Astrovirus capsid protein precursor; InterPro: IPR004337 The astrovirus genome is apparently organised with nonstructural proteins encoded at the 5' end and structural proteins at the 3' end []. Proteins in this family are encoded by astrovirus ORF2, one of the three astrovirus ORFs (1a, 1b, 2). The proteins contain a viral RNA-dependent RNA polymerase motif []. The 87kDa precursor polyprotein undergoes an intracellular cleavage to form a 79kDa protein. Subsequently, extracellular trypsin cleavage yields the three proteins forming the infectious virion [].; PDB: 3QSQ_A 3TS3_D.
Probab=66.67 E-value=1.9 Score=57.22 Aligned_cols=13 Identities=15% Similarity=0.189 Sum_probs=0.0
Q ss_pred CccccCCHHHHHH
Q 000247 176 PKEEEMDEEEFDK 188 (1790)
Q Consensus 176 ~~eEd~DaEelAe 188 (1790)
..++-+++|+-++
T Consensus 717 LVNqGi~eerAar 729 (787)
T PF03115_consen 717 LVNQGIPEERAAR 729 (787)
T ss_dssp -------------
T ss_pred HHHcCCCHHHHHh
Confidence 3445555554443
No 75
>PF11746 DUF3303: Protein of unknown function (DUF3303); InterPro: IPR021734 Several members are annotated as being LysM domain-like proteins, but these did not match any LysM domains reported in the literature.
Probab=66.14 E-value=19 Score=36.45 Aligned_cols=76 Identities=16% Similarity=0.240 Sum_probs=49.7
Q ss_pred EEEEec--CchhHHHHHHHHHHHHhhccCC-CC--C-cEEEEEEeCCCCcEEEEEeccchhHHHHhcCCCCEEeceeccC
Q 000247 228 WKVKCM--AGRERQSAFCLMQKFVDLQSLG-SK--M-QIISAFAVDHIKGFIFIEADKQCDINEACKGLSGIYYSRLAPV 301 (1790)
Q Consensus 228 WaVKCK--~GkEReVV~~LmrKii~lq~~g-~~--L-~I~SVFvpd~lKGYIYVEA~kq~dVkeAIkGI~gVy~sK~~pV 301 (1790)
|+|.+. ++....-...++.|+++..... .+ + -|..++.|....|||.|||+....+.+.+.--+.+++..+..+
T Consensus 2 flv~w~f~~~~~~~~~~~~~~~~~~~G~~~~~peG~~~l~rw~~~~~g~g~~i~eadd~~~l~~~~~~W~~~fg~~~ei~ 81 (91)
T PF11746_consen 2 FLVIWQFPPGESQQEAYKAFERFMESGAPGDPPEGFKVLGRWHDPGGGRGFAIVEADDAKALFKHFAPWRDLFGMEFEIT 81 (91)
T ss_pred EEEEEEeCCcccchhHHHHHHHHHhcCCCCCCCCCEEEEEEEEecCCCcEEEEEEeCCHHHHHHHHhhhhhccCceEEEE
Confidence 666664 4555533344555665543111 11 2 2567888889999999999999999999988888755444444
Q ss_pred CH
Q 000247 302 PK 303 (1790)
Q Consensus 302 Pi 303 (1790)
|+
T Consensus 82 Pv 83 (91)
T PF11746_consen 82 PV 83 (91)
T ss_pred ec
Confidence 43
No 76
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=65.47 E-value=57 Score=44.59 Aligned_cols=196 Identities=13% Similarity=0.111 Sum_probs=0.0
Q ss_pred cCCHHHHHHHhhcccccccccCCCEEEEecCcCCCCcEEEEEEeCCCCEEEEEEeccCchhhHhhhcCCCcccCCCCCCC
Q 000247 300 PVPKNEVSHLLSAQIKRNEVSEGTWAYVKNGKYKGDLAQVVYVNNARKRATVKLIPRIDLQALAAKFGGGVAMKKTDSPA 379 (1790)
Q Consensus 300 pVPikEM~dLLkvkkks~~Lk~GdwVRIKrGpYKGDLAQV~eVDenk~kVtVKLVPRIDy~~l~~k~~gg~~kKK~~RPP 379 (1790)
+|++.||...-++......|++|+.|++ +|+.||.++.++.|.+ ++....|-
T Consensus 605 LvhiSEls~~~~~~~p~~~~kvGd~V~v----------kVl~iD~e~~rIsLS~------------------K~l~~~Pw 656 (863)
T PRK12269 605 LAHISEFSWVKKTSKPSDMVKIGDEVEC----------MILGYDIQAGRVSLGL------------------KQVTANPW 656 (863)
T ss_pred eeEHHHhcCccccCCHHHcCCCCCEEEE----------EEEEEecccCceEEEe------------------hhcccCch
Q ss_pred CCCCChhhHhhhcCcee--ecccCCCCceEEecCCceeecceEEEEEeccceEecCCCCCHHHHhhcCCCCCCccccHHH
Q 000247 380 PRLISPSELEEFRPLIQ--YRRDRDTGKVFENLDGMMLKDGYLYKKVSIDSLSCWGVVPSEEELLKFQPSESNESADLEW 457 (1790)
Q Consensus 380 qRLFn~~Eark~~~~~~--~rrd~~tG~~f~i~~G~~ykDGFLyK~fkI~sL~tedVnPTLEEL~kF~~~~~de~~DL~~ 457 (1790)
..| .+....+..++ +..-...|-+..+..| ++|||. ++.|....+...++++ |.
T Consensus 657 ~~~---~~~~~vG~~v~G~V~~i~~~G~fV~l~~g---V~GlIh----~sels~~~~~~~~~~~--~k------------ 712 (863)
T PRK12269 657 EEI---EARYPVGARFTRRIVKVTNAGAFIEMEEG---IDGFLH----VDDLSWVKRTRPADHE--LE------------ 712 (863)
T ss_pred HHH---HHhCCCCCEEEEEEEEEecceEEEEeCCC---cEEEEE----hHHhhccccccchhhc--cC------------
Q ss_pred HHHHHhccccccEEEeecCCCcccccCCCCcc-------cccccCcEEEecCCceEEEEEEecCceEEEccCCCCCCceE
Q 000247 458 LSQLYGERKKKRTTIVGKGGDKGEGSSGSSLE-------NSFELYELVCFGRKDFGLIVGMEKDDHYKILKEGSEGPAVV 530 (1790)
Q Consensus 458 La~~~ge~kk~~ii~v~kGg~kgE~ssG~~sl-------G~FeLgDLVQLD~~TVGVIVrVEkDEsfkVLdq~gD~~~Vv 530 (1790)
.|..-+.+|+.+.....+-..+.=.... ..|.+||.|. |.|++|...-.|+=|..+ ..-
T Consensus 713 ----vGq~VkvkVl~ID~e~rrI~LS~K~l~~dpw~~~~~~~~vG~iV~------GkV~~v~~~GvFVeL~~g----VeG 778 (863)
T PRK12269 713 ----VGKEIECMVIECDPQARRIRLGVKQLSDNPWQVFANAYGVGSTVE------GEVSSVTDFGIFVRVPGG----VEG 778 (863)
T ss_pred ----CCCEEEEEEEEEeccCCEEEEEecccccChHHHHHhhCCCCCEEE------EEEEEEecCeEEEEcCCC----eEE
Q ss_pred EEecccccCCCCCCcccccccCCCcccCCCeEEEe
Q 000247 531 TVERRTLKNGPFDMKFTALDQSMKVISLNDTARVS 565 (1790)
Q Consensus 531 tVk~~eI~~K~~~rr~vAtD~~gn~I~vGD~VKVI 565 (1790)
.|...+|....... .....+.|++||.|+|+
T Consensus 779 lI~~s~lsdd~~~~----~~~~~~~f~vGD~V~v~ 809 (863)
T PRK12269 779 LVRKQHLVENRDGD----PGEALRKYAVGDRVKAV 809 (863)
T ss_pred EEEHHHcCCccccc----chhhccccCCCCEEEEE
No 77
>PRK00276 infA translation initiation factor IF-1; Validated
Probab=65.41 E-value=33 Score=33.15 Aligned_cols=63 Identities=14% Similarity=0.073 Sum_probs=40.9
Q ss_pred eEEEEEEecCceEEEccCCCCCCceEEEecccccCCCCCCcccccccCCCcccCCCeEEEecCCCCCceEEEEEEEC
Q 000247 505 FGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVSEGPSKDRQGIVKKIYR 581 (1790)
Q Consensus 505 VGVIVrVEkDEsfkVLdq~gD~~~VvtVk~~eI~~K~~~rr~vAtD~~gn~I~vGD~VKVIdGphkGRqG~VlHIyR 581 (1790)
.|+|+++-.+..|.|.+.++ .++.+.+.- |+.. ....|.+||.|.|--=++....|.|+|=|+
T Consensus 10 ~G~Vi~~~~~~~y~V~~~~g---~~~~c~~~G---klr~--------~~i~i~vGD~V~ve~~~~~~~~g~Iv~r~~ 72 (72)
T PRK00276 10 EGTVVEALPNAMFRVELENG---HEVLAHISG---KMRK--------NYIRILPGDKVTVELSPYDLTKGRITYRHK 72 (72)
T ss_pred EEEEEEEcCCCEEEEEeCCC---CEEEEEEcc---ceee--------CCcccCCCCEEEEEEcccCCCeEEEEEEeC
Confidence 58999998654777765432 356666432 2111 123389999999985455566799998775
No 78
>PRK04333 50S ribosomal protein L14e; Validated
Probab=65.12 E-value=10 Score=38.10 Aligned_cols=33 Identities=15% Similarity=0.181 Sum_probs=28.4
Q ss_pred cccCCCEEEEecCcCCCCcEEEEEEeCCCCEEEE
Q 000247 318 EVSEGTWAYVKNGKYKGDLAQVVYVNNARKRATV 351 (1790)
Q Consensus 318 ~Lk~GdwVRIKrGpYKGDLAQV~eVDenk~kVtV 351 (1790)
++++|..|+++.|+|+|-++.|++|.++ ++|.|
T Consensus 3 ~v~~GrvV~~~~Grd~gk~~vIv~i~d~-~~vlV 35 (84)
T PRK04333 3 AIEVGRVCVKTAGREAGRKCVIVDIIDK-NFVLV 35 (84)
T ss_pred cccccEEEEEeccCCCCCEEEEEEEecC-CEEEE
Confidence 6789999999999999999999999554 55655
No 79
>PTZ00329 eukaryotic translation initiation factor 1A; Provisional
Probab=65.05 E-value=23 Score=39.29 Aligned_cols=76 Identities=16% Similarity=0.060 Sum_probs=53.4
Q ss_pred cccCcEEEec-CCceEEEEEEecCceEEEccCCCCCCceEEEecccccCCCCCCcccccccCCCcccCCCeEEEecCCCC
Q 000247 492 FELYELVCFG-RKDFGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVSEGPSK 570 (1790)
Q Consensus 492 FeLgDLVQLD-~~TVGVIVrVEkDEsfkVLdq~gD~~~VvtVk~~eI~~K~~~rr~vAtD~~gn~I~vGD~VKVIdGphk 570 (1790)
-+..+|+.=. -+.+|+|+++-.+..|.|.+.++ ..+.+. |.-|+.. .--|.+||+|.|--=+|.
T Consensus 21 ~~~rel~~~eegq~~g~V~~~LGn~~f~V~c~dG---~~rLa~---I~GKmRK---------~IWI~~GD~VlVel~~yd 85 (155)
T PTZ00329 21 GEKRELVFKEEGQEYAQVLRMLGNGRLEAYCFDG---VKRLCH---IRGKMRK---------RVWINIGDIILVSLRDFQ 85 (155)
T ss_pred cceeeeccCCCCcEEEEEEEEcCCCEEEEEECCC---CEEEEE---eecccee---------eEEecCCCEEEEeccCCC
Confidence 3444555433 36789999999888999998764 234433 3233321 245899999999888888
Q ss_pred CceEEEEEEECC
Q 000247 571 DRQGIVKKIYRG 582 (1790)
Q Consensus 571 GRqG~VlHIyRs 582 (1790)
-..|.|+|.|..
T Consensus 86 ~~KgdIi~Ry~~ 97 (155)
T PTZ00329 86 DSKADVILKYTP 97 (155)
T ss_pred CCEEEEEEEcCH
Confidence 889999998864
No 80
>PLN03111 DNA-directed RNA polymerase II subunit family protein; Provisional
Probab=62.01 E-value=51 Score=38.19 Aligned_cols=55 Identities=11% Similarity=0.085 Sum_probs=34.9
Q ss_pred EEEEeccchhHHHHhcCCCCEEeceeccCCHHHHHHHhhc---cc-------------ccccccCCCEEEEec
Q 000247 273 IFIEADKQCDINEACKGLSGIYYSRLAPVPKNEVSHLLSA---QI-------------KRNEVSEGTWAYVKN 329 (1790)
Q Consensus 273 IYVEA~kq~dVkeAIkGI~gVy~sK~~pVPikEM~dLLkv---kk-------------ks~~Lk~GdwVRIKr 329 (1790)
..||.+.++++.-- =+.|+..-+-.+++.+|...||+. +. +...+++|+.|+|+|
T Consensus 121 ~~iE~F~e~eLlvn--it~H~lVPkH~~ls~eEk~~lL~~y~i~~~qLPrI~~~DPvary~g~k~G~vvkI~R 191 (206)
T PLN03111 121 FKIEVFQETELLVN--ITKHVLVPKHQVLTDEEKKTLLKRYTVKETQLPRIQVSDPIARYYGLKRGQVVKIIR 191 (206)
T ss_pred ceEEEeehhHheec--cccceecCCeEEcCHHHHHHHHHHcCCCHHHCCcccccChhhHhcCCCCCCEEEEEE
Confidence 35677666654322 223445556677889999999962 11 134678888888876
No 81
>PF02724 CDC45: CDC45-like protein; InterPro: IPR003874 CDC45 is an essential gene required for initiation of DNA replication in Saccharomyces cerevisiae (cell division control protein 45), forming a complex with MCM5/CDC46. Homologs of CDC45 have been identified in human [], mouse and the smut fungus, Melampsora spp., (tsd2 protein) among others.; GO: 0006270 DNA-dependent DNA replication initiation
Probab=60.22 E-value=6.1 Score=51.54 Aligned_cols=31 Identities=23% Similarity=0.198 Sum_probs=16.9
Q ss_pred chhHHHHhcCCCCEEec-eeccCCHHHHHHHh
Q 000247 280 QCDINEACKGLSGIYYS-RLAPVPKNEVSHLL 310 (1790)
Q Consensus 280 q~dVkeAIkGI~gVy~s-K~~pVPikEM~dLL 310 (1790)
.+.++.||=|+...|.. ++..-....+..+|
T Consensus 235 ~d~LW~AIvGlT~q~i~~~i~~~~Y~~~~~~L 266 (622)
T PF02724_consen 235 NDLLWLAIVGLTDQYIHERISSERYDRYVPLL 266 (622)
T ss_pred hHHHHHHHHhhhHHhhhcccchhhHHHHHHHH
Confidence 35678888888776542 33333333334444
No 82
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=59.83 E-value=39 Score=35.10 Aligned_cols=72 Identities=13% Similarity=-0.013 Sum_probs=50.2
Q ss_pred CcEEEecC-CceEEEEEEecCceEEEccCCCCCCceEEEecccccCCCCCCcccccccCCCcccCCCeEEEecCCCCCce
Q 000247 495 YELVCFGR-KDFGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVSEGPSKDRQ 573 (1790)
Q Consensus 495 gDLVQLD~-~TVGVIVrVEkDEsfkVLdq~gD~~~VvtVk~~eI~~K~~~rr~vAtD~~gn~I~vGD~VKVIdGphkGRq 573 (1790)
.+++.... +.+|+|+++-.+..|.|.+.++ ..+.+.+. -|+. ..--|.+||.|.|--=++.-..
T Consensus 13 ~~~~~p~e~e~~g~V~~~lG~~~~~V~~~dG---~~~la~i~---GK~R---------k~IwI~~GD~VlVe~~~~~~~k 77 (100)
T PRK04012 13 VRLPMPEEGEVFGVVEQMLGANRVRVRCMDG---VERMGRIP---GKMK---------KRMWIREGDVVIVAPWDFQDEK 77 (100)
T ss_pred EEccCCCCCEEEEEEEEEcCCCEEEEEeCCC---CEEEEEEc---hhhc---------ccEEecCCCEEEEEecccCCCE
Confidence 44555543 5679999999888999998764 24444432 2321 1245789999999877777778
Q ss_pred EEEEEEEC
Q 000247 574 GIVKKIYR 581 (1790)
Q Consensus 574 G~VlHIyR 581 (1790)
|.|+|+|.
T Consensus 78 g~Iv~r~~ 85 (100)
T PRK04012 78 ADIIWRYT 85 (100)
T ss_pred EEEEEEcC
Confidence 99999986
No 83
>PRK03879 ribonuclease P protein component 1; Validated
Probab=59.30 E-value=19 Score=37.06 Aligned_cols=46 Identities=15% Similarity=0.174 Sum_probs=40.1
Q ss_pred ccCCCEEEEccCC---CCCceeEEEEEeCCeEEEEecCcceEEEEecCccc
Q 000247 660 FAVGQTLRIRVGP---LKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLA 707 (1790)
Q Consensus 660 ~lIGKTVKIrkGP---YKGylGiVKDaTdt~ARVELHSk~KtITVdKe~Ls 707 (1790)
.|||-.|+|+.=+ |-|..|+|++-|..+..|+ ..++.++|+|++-.
T Consensus 12 eliGl~v~Vv~S~npslvGi~GiVv~ETknt~~I~--~~~~~~~VPK~~~i 60 (96)
T PRK03879 12 ELIGLKVEVVDSTNPSLVGIKGRVVDETRNTLVIE--TDGKEWMVPKDGAT 60 (96)
T ss_pred HhcCCEEEEEEcCCCCcccceEEEEEeceeEEEEE--cCCcEEEEeCCCeE
Confidence 5899999999874 5789999999999999998 77888899998844
No 84
>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=59.11 E-value=18 Score=31.71 Aligned_cols=30 Identities=30% Similarity=0.403 Sum_probs=26.4
Q ss_pred Cc-eeEEEEEeCCeEEEEecCcceEEEEecCc
Q 000247 675 GY-LCRVLAVRYSDVTVKLDSQQKILTVKGEH 705 (1790)
Q Consensus 675 Gy-lGiVKDaTdt~ARVELHSk~KtITVdKe~ 705 (1790)
|| +|.|+++.+..|+|+|.. .++++|++++
T Consensus 12 gfv~g~I~~~~g~~vtV~~~~-G~~~tv~~dd 42 (42)
T PF02736_consen 12 GFVKGEIIEEEGDKVTVKTED-GKEVTVKKDD 42 (42)
T ss_dssp SEEEEEEEEEESSEEEEEETT-TEEEEEEGGG
T ss_pred cEEEEEEEEEcCCEEEEEECC-CCEEEeCCCC
Confidence 44 699999999999999999 8899998763
No 85
>smart00361 RRM_1 RNA recognition motif.
Probab=58.89 E-value=20 Score=33.59 Aligned_cols=29 Identities=28% Similarity=0.580 Sum_probs=25.3
Q ss_pred CCCCcEEEEEeccchhHHHHhcCCCCEEe
Q 000247 267 DHIKGFIFIEADKQCDINEACKGLSGIYY 295 (1790)
Q Consensus 267 d~lKGYIYVEA~kq~dVkeAIkGI~gVy~ 295 (1790)
.+.+||+||+-...++...||+.|.+-+.
T Consensus 34 ~~~rG~~fV~f~~~~dA~~A~~~l~g~~~ 62 (70)
T smart00361 34 NHKRGNVYITFERSEDAARAIVDLNGRYF 62 (70)
T ss_pred CCCcEEEEEEECCHHHHHHHHHHhCCCEE
Confidence 35799999999999999999999888543
No 86
>PRK04333 50S ribosomal protein L14e; Validated
Probab=58.78 E-value=13 Score=37.38 Aligned_cols=31 Identities=23% Similarity=0.310 Sum_probs=26.2
Q ss_pred ccCCCEEEEccCCCCCceeEEEEE-eCCeEEE
Q 000247 660 FAVGQTLRIRVGPLKGYLCRVLAV-RYSDVTV 690 (1790)
Q Consensus 660 ~lIGKTVKIrkGPYKGylGiVKDa-Tdt~ARV 690 (1790)
.-+|+-|.|..|+|+|.+.+|+++ .+.+|-|
T Consensus 4 v~~GrvV~~~~Grd~gk~~vIv~i~d~~~vlV 35 (84)
T PRK04333 4 IEVGRVCVKTAGREAGRKCVIVDIIDKNFVLV 35 (84)
T ss_pred ccccEEEEEeccCCCCCEEEEEEEecCCEEEE
Confidence 357899999999999999999999 4555665
No 87
>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=58.00 E-value=35 Score=32.38 Aligned_cols=62 Identities=15% Similarity=0.128 Sum_probs=43.1
Q ss_pred CceEEEEEEecCceEEEccCCCCCCceEEEecccccCCCCCCcccccccCCCcccCCCeEEEecCCCCCceEEEEEE
Q 000247 503 KDFGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVSEGPSKDRQGIVKKI 579 (1790)
Q Consensus 503 ~TVGVIVrVEkDEsfkVLdq~gD~~~VvtVk~~eI~~K~~~rr~vAtD~~gn~I~vGD~VKVIdGphkGRqG~VlHI 579 (1790)
+.+|+|+++..+..|.|...++ ..+.+.+. .| . ++.--|+.||.|.|---++.-..|.|+|.
T Consensus 4 e~~~~V~~~lG~~~~~V~~~dg---~~~l~~i~---gK-~--------r~~iwI~~GD~V~V~~~~~d~~kG~Ii~r 65 (65)
T PF01176_consen 4 EVIGRVTEMLGNNLFEVECEDG---EERLARIP---GK-F--------RKRIWIKRGDFVLVEPSPYDKVKGRIIYR 65 (65)
T ss_dssp EEEEEEEEEESSSEEEEEETTS---EEEEEEE----HH-H--------HTCC---TTEEEEEEESTTCTTEEEEEEE
T ss_pred EEEEEEEEECCCCEEEEEeCCC---CEEEEEec---cc-e--------eeeEecCCCCEEEEEecccCCCeEEEEEC
Confidence 4579999999988999998764 34444433 12 1 23446899999999878888889999884
No 88
>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=57.39 E-value=24 Score=35.39 Aligned_cols=44 Identities=14% Similarity=0.254 Sum_probs=35.9
Q ss_pred ccCCCEEEEccCCCCCceeEEEEEeCCeEEEEecCcceEEEEecCcccc
Q 000247 660 FAVGQTLRIRVGPLKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLAE 708 (1790)
Q Consensus 660 ~lIGKTVKIrkGPYKGylGiVKDaTdt~ARVELHSk~KtITVdKe~Ls~ 708 (1790)
-..|+.|....| ..|+|+++.++++.||+. ..-.|+|+|..++.
T Consensus 38 L~~Gd~VvT~gG----i~G~V~~i~d~~v~vei~-~g~~i~~~r~aI~~ 81 (84)
T TIGR00739 38 LKKGDKVLTIGG----IIGTVTKIAENTIVIELN-DNTEITFSKNAIVE 81 (84)
T ss_pred CCCCCEEEECCC----eEEEEEEEeCCEEEEEEC-CCeEEEEEhHHhhh
Confidence 346788877765 789999999999999985 56679999998764
No 89
>TIGR00523 eIF-1A eukaryotic/archaeal initiation factor 1A. Recommended nomenclature: eIF-1A for eukaryotes, aIF-1A for Archaea. Also called eIF-4C
Probab=57.19 E-value=35 Score=35.33 Aligned_cols=64 Identities=14% Similarity=-0.049 Sum_probs=43.4
Q ss_pred CCceEEEEEEecCceEEEccCCCCCCceEEEecccccCCCCCCcccccccCCCcccCCCeEEEecCCCCC---ceEEEEE
Q 000247 502 RKDFGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVSEGPSKD---RQGIVKK 578 (1790)
Q Consensus 502 ~~TVGVIVrVEkDEsfkVLdq~gD~~~VvtVk~~eI~~K~~~rr~vAtD~~gn~I~vGD~VKVIdGphkG---RqG~VlH 578 (1790)
.+.+|.|+++-.+..|.|.+.++ ..+.+.+ .-|+. ..--|..||.|.|- |+.- ..|.|+|
T Consensus 19 ~e~~g~V~~~lG~~~~~V~~~dG---~~~la~i---~GK~R---------k~iwI~~GD~VlVs--p~d~~~~~kg~Iv~ 81 (99)
T TIGR00523 19 GEILGVIEQMLGAGRVKVRCLDG---KTRLGRI---PGKLK---------KRIWIREGDVVIVK--PWEFQGDDKCDIVW 81 (99)
T ss_pred CEEEEEEEEEcCCCEEEEEeCCC---CEEEEEE---chhhc---------ccEEecCCCEEEEE--EccCCCCccEEEEE
Confidence 45789999999888999998664 3444432 23321 13468999999993 5432 3699999
Q ss_pred EECC
Q 000247 579 IYRG 582 (1790)
Q Consensus 579 IyRs 582 (1790)
+|..
T Consensus 82 r~~~ 85 (99)
T TIGR00523 82 RYTK 85 (99)
T ss_pred EcCH
Confidence 8863
No 90
>PRK14635 hypothetical protein; Provisional
Probab=57.13 E-value=13 Score=41.01 Aligned_cols=49 Identities=12% Similarity=0.087 Sum_probs=37.7
Q ss_pred ccCCCEEEEcc---C--CCCCceeEEEEEeCCeEEEEecCc------ceEEEEecCcccc
Q 000247 660 FAVGQTLRIRV---G--PLKGYLCRVLAVRYSDVTVKLDSQ------QKILTVKGEHLAE 708 (1790)
Q Consensus 660 ~lIGKTVKIrk---G--PYKGylGiVKDaTdt~ARVELHSk------~KtITVdKe~Ls~ 708 (1790)
.++|+.|+|+- + .|+|++|++++++++.+++++..+ .++++++.+.|.-
T Consensus 96 r~~G~~v~v~~~~~~~~~~~g~~g~L~~~~~~~v~l~~~~k~~~~~~~~~~~ip~~~I~k 155 (162)
T PRK14635 96 RFRGIPVRLVFRSEESEKWQEGIFRLVNRDGDQVELEKFQKGKKSKVKKQTTLNLKDILK 155 (162)
T ss_pred HhCCCEEEEEEecCCCcEEEecceEEEEEcCCEEEEEEecccccccCCeEEEEEhHHeee
Confidence 47889988752 2 566888899999999999988543 5678888877763
No 91
>PF04931 DNA_pol_phi: DNA polymerase phi; InterPro: IPR007015 Proteins of this family are predominantly nucleolar. The majority are described as transcription factor transactivators. The family also includes the fifth essential DNA polymerase (Pol5p) of Schizosaccharomyces pombe (Fission yeast) and Saccharomyces cerevisiae (Baker's yeast) (2.7.7.7 from EC). Pol5p is localized exclusively to the nucleolus and binds near or at the enhancer region of rRNA-encoding DNA repeating units.; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006351 transcription, DNA-dependent
Probab=56.48 E-value=9.5 Score=50.91 Aligned_cols=7 Identities=29% Similarity=0.439 Sum_probs=3.0
Q ss_pred eecCccc
Q 000247 71 IVCDPEM 77 (1790)
Q Consensus 71 ~~~~~~~ 77 (1790)
+.|+|+.
T Consensus 545 ~~~~~~~ 551 (784)
T PF04931_consen 545 LYNGPEE 551 (784)
T ss_pred HhcCChH
Confidence 3444443
No 92
>PRK05585 yajC preprotein translocase subunit YajC; Validated
Probab=55.24 E-value=26 Score=36.54 Aligned_cols=44 Identities=20% Similarity=0.286 Sum_probs=36.7
Q ss_pred cCCCEEEEccCCCCCceeEEEEEeCCeEEEEecCcceEEEEecCccccc
Q 000247 661 AVGQTLRIRVGPLKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLAEV 709 (1790)
Q Consensus 661 lIGKTVKIrkGPYKGylGiVKDaTdt~ARVELHSk~KtITVdKe~Ls~v 709 (1790)
-+|+.|.-+.| ..|+|+++.+++|.||+ +..-+|+|+|.-|..+
T Consensus 54 k~Gd~VvT~gG----i~G~Vv~i~~~~v~lei-~~g~~i~~~r~aI~~v 97 (106)
T PRK05585 54 AKGDEVVTNGG----IIGKVTKVSEDFVIIEL-NDDTEIKIQKSAIAAV 97 (106)
T ss_pred CCCCEEEECCC----eEEEEEEEeCCEEEEEE-CCCeEEEEEhHHhhhh
Confidence 46888877665 77999999999999999 4567899999998854
No 93
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=55.06 E-value=49 Score=33.82 Aligned_cols=63 Identities=13% Similarity=0.081 Sum_probs=45.7
Q ss_pred eEEEEEEecCceEEEccCCCCCCceEEEecccccCCCCCCcccccccCCCcccCCCeEEEecCCCCCceEEEEEEEC
Q 000247 505 FGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVSEGPSKDRQGIVKKIYR 581 (1790)
Q Consensus 505 VGVIVrVEkDEsfkVLdq~gD~~~VvtVk~~eI~~K~~~rr~vAtD~~gn~I~vGD~VKVIdGphkGRqG~VlHIyR 581 (1790)
.|+|+.+-.+..|+|...++. ++... |.-|+.. +.=-|.+||.|+|--=||.-..|.|++=|+
T Consensus 10 ~G~V~e~Lp~~~frV~LenG~---~vla~---isGKmR~--------~rIrIl~GD~V~VE~spYDltkGRIiyR~~ 72 (87)
T PRK12442 10 DGIVDEVLPDSRFRVTLENGV---EVGAY---ASGRMRK--------HRIRILAGDRVTLELSPYDLTKGRINFRHK 72 (87)
T ss_pred EEEEEEECCCCEEEEEeCCCC---EEEEE---eccceee--------eeEEecCCCEEEEEECcccCCceeEEEEec
Confidence 599999999889999877642 33332 3333321 234578999999998899888899988776
No 94
>PTZ00065 60S ribosomal protein L14; Provisional
Probab=54.23 E-value=22 Score=38.45 Aligned_cols=35 Identities=26% Similarity=0.424 Sum_probs=28.1
Q ss_pred ccCCCEEEEccCCCCCceeEEEEEeCCeEEEEecCc
Q 000247 660 FAVGQTLRIRVGPLKGYLCRVLAVRYSDVTVKLDSQ 695 (1790)
Q Consensus 660 ~lIGKTVKIrkGPYKGylGiVKDaTdt~ARVELHSk 695 (1790)
.-||..|.|..|||+|-|+.|+||-|.. ||.++..
T Consensus 8 VEiGRVvli~~Gp~~GKL~vIVDIID~n-RvLVDGP 42 (130)
T PTZ00065 8 VEPGRLCLIQYGPDAGKLCFIVDIVTPT-RVLVDGA 42 (130)
T ss_pred eeeceEEEEecCCCCCCEEEEEEEEcCC-eEEEeCC
Confidence 4589999999999999999999997543 4555554
No 95
>PF02724 CDC45: CDC45-like protein; InterPro: IPR003874 CDC45 is an essential gene required for initiation of DNA replication in Saccharomyces cerevisiae (cell division control protein 45), forming a complex with MCM5/CDC46. Homologs of CDC45 have been identified in human [], mouse and the smut fungus, Melampsora spp., (tsd2 protein) among others.; GO: 0006270 DNA-dependent DNA replication initiation
Probab=53.01 E-value=11 Score=49.24 Aligned_cols=13 Identities=31% Similarity=0.636 Sum_probs=6.6
Q ss_pred HHHHHHHHHHhcc
Q 000247 184 EEFDKMMEERYKS 196 (1790)
Q Consensus 184 EelAe~LkERY~r 196 (1790)
++..+.|++.|..
T Consensus 199 ~~~~~~i~~yY~~ 211 (622)
T PF02724_consen 199 EEYREEIEKYYSQ 211 (622)
T ss_pred HHHHHHHHHHHhc
Confidence 3445555555643
No 96
>COG1862 YajC Preprotein translocase subunit YajC [Intracellular trafficking and secretion]
Probab=52.88 E-value=25 Score=36.38 Aligned_cols=46 Identities=22% Similarity=0.224 Sum_probs=38.1
Q ss_pred CCCEEEEccCCCCCceeEEEEEeCCeEEEEecCcceEEEEecCccccccCC
Q 000247 662 VGQTLRIRVGPLKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLAEVRGK 712 (1790)
Q Consensus 662 IGKTVKIrkGPYKGylGiVKDaTdt~ARVELHSk~KtITVdKe~Ls~v~~k 712 (1790)
-|+.|.-..| +.|+|+.+.++++.|||. .+-.|+|.|+.++.+..+
T Consensus 46 kGD~VvT~gG----i~G~V~~v~d~~v~I~l~-~~~~i~~~k~aI~~v~~~ 91 (97)
T COG1862 46 KGDEVVTIGG----IVGTVTKVGDDTVEIELG-DGTKIKFEKEAIATVLEK 91 (97)
T ss_pred CCCEEEEcCC----eEEEEEEEecCcEEEEEC-CCeEEEEEHHHHHhhccC
Confidence 4677766654 889999999999999999 888899999999865443
No 97
>COG3109 ProQ Activator of osmoprotectant transporter ProP [Signal transduction mechanisms]
Probab=52.49 E-value=20 Score=40.46 Aligned_cols=46 Identities=33% Similarity=0.563 Sum_probs=38.1
Q ss_pred ccCCCEEEEccCCCCCceeEEEEEeCCeEEEEecCcceEEEEecCccc
Q 000247 660 FAVGQTLRIRVGPLKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLA 707 (1790)
Q Consensus 660 ~lIGKTVKIrkGPYKGylGiVKDaTdt~ARVELHSk~KtITVdKe~Ls 707 (1790)
..||+.|+|..|. --+--+|++|+-+.|||+|.+... ++|..+||.
T Consensus 162 l~~g~~~kVk~G~-~a~~AtvlEv~Kd~vRVqL~~Gl~-m~V~AehL~ 207 (208)
T COG3109 162 LTVGQALKVKAGQ-NAMDATVLEITKDGVRVQLNSGLS-MIVRAEHLV 207 (208)
T ss_pred hhccceeeecccc-ccccceEEEEeccceEEeecCCce-EEEehhhhc
Confidence 3589999999993 345679999999999999998876 678888874
No 98
>PTZ00065 60S ribosomal protein L14; Provisional
Probab=52.35 E-value=19 Score=38.99 Aligned_cols=33 Identities=24% Similarity=0.333 Sum_probs=28.2
Q ss_pred cccCCCEEEEecCcCCCCcEEEEEEeCCCCEEEE
Q 000247 318 EVSEGTWAYVKNGKYKGDLAQVVYVNNARKRATV 351 (1790)
Q Consensus 318 ~Lk~GdwVRIKrGpYKGDLAQV~eVDenk~kVtV 351 (1790)
-+++|=.|.|..|||+|-||.|++|-+. ++|+|
T Consensus 7 fVEiGRVvli~~Gp~~GKL~vIVDIID~-nRvLV 39 (130)
T PTZ00065 7 FVEPGRLCLIQYGPDAGKLCFIVDIVTP-TRVLV 39 (130)
T ss_pred ceeeceEEEEecCCCCCCEEEEEEEEcC-CeEEE
Confidence 4688999999999999999999999764 56665
No 99
>PTZ00415 transmission-blocking target antigen s230; Provisional
Probab=52.17 E-value=6.9 Score=54.88 Aligned_cols=17 Identities=24% Similarity=0.184 Sum_probs=8.0
Q ss_pred CccccCCCCCCCCCCcc
Q 000247 93 GKRKRNDGSSGVKPHNR 109 (1790)
Q Consensus 93 ~~~~~~~~~~~~~~r~r 109 (1790)
||.++.+-+.-+-.|||
T Consensus 120 g~~~~~~~d~~i~~~~~ 136 (2849)
T PTZ00415 120 GKAEIGDLDMIIIKRRR 136 (2849)
T ss_pred chhhcCCcceEEeehHH
Confidence 45555555544443333
No 100
>KOG1708 consensus Mitochondrial/chloroplast ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=52.06 E-value=14 Score=42.48 Aligned_cols=39 Identities=36% Similarity=0.376 Sum_probs=31.4
Q ss_pred ccCCCEEEEccCCCCCceeEEEEEe--CCeEEEE-ecCcceE
Q 000247 660 FAVGQTLRIRVGPLKGYLCRVLAVR--YSDVTVK-LDSQQKI 698 (1790)
Q Consensus 660 ~lIGKTVKIrkGPYKGylGiVKDaT--dt~ARVE-LHSk~Kt 698 (1790)
++.|+||.|+.|.-||.+|+|..+. .+.|-|+ ||++-++
T Consensus 73 ff~GDtVeVlvGkDkGkqG~Vtqv~r~~s~VvV~gln~k~r~ 114 (236)
T KOG1708|consen 73 FFFGDTVEVLVGKDKGKQGEVTQVIRHRSWVVVKGLNTKYRH 114 (236)
T ss_pred EecCCEEEEEecccCCccceEEEEeecCceEEEcccchhhhh
Confidence 5679999999999999999999986 4456665 6666553
No 101
>cd05690 S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 5 (ec5) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=51.51 E-value=21 Score=32.62 Aligned_cols=66 Identities=17% Similarity=0.179 Sum_probs=40.8
Q ss_pred EEEEEEeCCCCcEEEEEeccchhHHHHhcCCCCEEeceeccCCHHHHHHHhhcccccccccCCCEEEEecCcCCCCcEEE
Q 000247 260 IISAFAVDHIKGFIFIEADKQCDINEACKGLSGIYYSRLAPVPKNEVSHLLSAQIKRNEVSEGTWAYVKNGKYKGDLAQV 339 (1790)
Q Consensus 260 I~SVFvpd~lKGYIYVEA~kq~dVkeAIkGI~gVy~sK~~pVPikEM~dLLkvkkks~~Lk~GdwVRIKrGpYKGDLAQV 339 (1790)
|+.+.+....+-.||||... ++. .+|++.||............|++|+.|+++ |
T Consensus 3 ~~~g~V~~i~~~G~fv~l~~---------~~~-------Glv~~~~l~~~~~~~~~~~~~~~G~~v~v~----------v 56 (69)
T cd05690 3 VVSGKIKSITDFGIFVGLDG---------GID-------GLVHISDISWTQRVRHPSEIYKKGQEVEAV----------V 56 (69)
T ss_pred EEEEEEEEEEeeeEEEEeCC---------CCE-------EEEEHHHCCCccccCChhhEECCCCEEEEE----------E
Confidence 45555555556668888753 122 245566665212222223458999999985 8
Q ss_pred EEEeCCCCEEEE
Q 000247 340 VYVNNARKRATV 351 (1790)
Q Consensus 340 ~eVDenk~kVtV 351 (1790)
++|+.++.++.+
T Consensus 57 ~~id~~~~~i~l 68 (69)
T cd05690 57 LNIDVERERISL 68 (69)
T ss_pred EEEECCcCEEeC
Confidence 999988877754
No 102
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=50.82 E-value=37 Score=30.07 Aligned_cols=67 Identities=16% Similarity=0.234 Sum_probs=42.5
Q ss_pred EEEEEEeCCCCcEEEEEeccchhHHHHhcCCCCEEeceeccCCHHHHHHHhhcccccccccCCCEEEEecCcCCCCcEEE
Q 000247 260 IISAFAVDHIKGFIFIEADKQCDINEACKGLSGIYYSRLAPVPKNEVSHLLSAQIKRNEVSEGTWAYVKNGKYKGDLAQV 339 (1790)
Q Consensus 260 I~SVFvpd~lKGYIYVEA~kq~dVkeAIkGI~gVy~sK~~pVPikEM~dLLkvkkks~~Lk~GdwVRIKrGpYKGDLAQV 339 (1790)
|+.+++....+.++||+... ++. ..||+.||.+-.. .+....|++|+.|++ +|
T Consensus 5 ~v~g~V~~v~~~g~~v~i~~---------~~~-------g~l~~~~~~~~~~-~~~~~~~~~G~~v~~----------~V 57 (72)
T smart00316 5 VVEGTVTEITPFGAFVDLGN---------GVE-------GLIPISELSDKRV-KDPEEVLKVGDEVKV----------KV 57 (72)
T ss_pred EEEEEEEEEEccEEEEEeCC---------CCE-------EEEEHHHCCcccc-CCHHHeecCCCEEEE----------EE
Confidence 55566666666788887753 111 2445555554321 111235889999986 69
Q ss_pred EEEeCCCCEEEEEE
Q 000247 340 VYVNNARKRATVKL 353 (1790)
Q Consensus 340 ~eVDenk~kVtVKL 353 (1790)
..|+....++.|.+
T Consensus 58 ~~~~~~~~~i~ls~ 71 (72)
T smart00316 58 LSVDEEKGRIILSL 71 (72)
T ss_pred EEEeCCCCEEEEEe
Confidence 99998878877765
No 103
>PRK14639 hypothetical protein; Provisional
Probab=49.94 E-value=27 Score=37.86 Aligned_cols=49 Identities=10% Similarity=0.231 Sum_probs=39.2
Q ss_pred ccCCCEEEEccCCCCCceeEEEEEeCCeEEEEecCcceEEEEecCcccc
Q 000247 660 FAVGQTLRIRVGPLKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLAE 708 (1790)
Q Consensus 660 ~lIGKTVKIrkGPYKGylGiVKDaTdt~ARVELHSk~KtITVdKe~Ls~ 708 (1790)
.++|+.|+|+-.--|=+.|++++++++.++||+-...++|+|+.+.|.-
T Consensus 85 r~~G~~v~v~l~~~~~~~G~L~~~~~~~i~l~~~~~~~~~~i~~~~I~k 133 (140)
T PRK14639 85 KSIGELVKITTNEKEKFEGKIVSVDDENITLENLENKEKTTINFNDIKK 133 (140)
T ss_pred HhCCCEEEEEECCCcEEEEEEEEEeCCEEEEEEccCCcEEEEEhHHeee
Confidence 4799999998644588899999999999999764345678888877763
No 104
>TIGR01659 sex-lethal sex-lethal family splicing factor. This model describes the sex-lethal family of splicing factors found in Dipteran insects. The sex-lethal phenotype, however, may be limited to the Melanogasters and closely related species. In Drosophila the protein acts as an inhibitor of splicing. This subfamily is most closely related to the ELAV/HUD subfamily of splicing factors (TIGR01661).
Probab=49.55 E-value=55 Score=40.19 Aligned_cols=68 Identities=16% Similarity=0.201 Sum_probs=44.4
Q ss_pred CCCCCCCcEEEEEecCchhHHHHHHHHHHHHhhccCCCCCcEEEEEEe-C----CCCcEEEEEeccchhHHHHhcCCCCE
Q 000247 219 MPCPEDPTIWKVKCMAGRERQSAFCLMQKFVDLQSLGSKMQIISAFAV-D----HIKGFIFIEADKQCDINEACKGLSGI 293 (1790)
Q Consensus 219 LPSVkDPkLWaVKCK~GkEReVV~~LmrKii~lq~~g~~L~I~SVFvp-d----~lKGYIYVEA~kq~dVkeAIkGI~gV 293 (1790)
.+...+-+||+=.+-.--..+.+..|...+ . .|.+|.+. + ..+||-|||-..++++..||+.|.++
T Consensus 102 ~~~~~~~~LfVgnLp~~~te~~L~~lF~~~---G------~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~ 172 (346)
T TIGR01659 102 DTNNSGTNLIVNYLPQDMTDRELYALFRTI---G------PINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGI 172 (346)
T ss_pred CCCCCCcEEEEeCCCCCCCHHHHHHHHHhc---C------CEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCC
Confidence 344556677776665444444444444332 1 36666554 2 35699999999999999999988875
Q ss_pred Ee
Q 000247 294 YY 295 (1790)
Q Consensus 294 y~ 295 (1790)
..
T Consensus 173 ~l 174 (346)
T TIGR01659 173 TV 174 (346)
T ss_pred cc
Confidence 43
No 105
>PRK12288 GTPase RsgA; Reviewed
Probab=48.25 E-value=95 Score=38.24 Aligned_cols=86 Identities=9% Similarity=0.081 Sum_probs=55.7
Q ss_pred ceEEEEEEecCceEEEccCCCCCCceEEEecccccCCCCCCcccccccCCCcccCCCeEEEecCCCC--CceEEEEEEEC
Q 000247 504 DFGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVSEGPSK--DRQGIVKKIYR 581 (1790)
Q Consensus 504 TVGVIVrVEkDEsfkVLdq~gD~~~VvtVk~~eI~~K~~~rr~vAtD~~gn~I~vGD~VKVIdGphk--GRqG~VlHIyR 581 (1790)
..|.||++.+. .+.|++..+ .++.+.++.. + +.+-|||.|.+-.-... ...|+|.+|+.
T Consensus 40 ~~g~Vi~~~~~-~~~v~~~~g---~~~~~~~~g~---~------------~~~~vGD~V~~~~~~~~~~~~~~~I~~il~ 100 (347)
T PRK12288 40 QEGIVISRFGQ-HADVEAADG---EVHRCNIRRT---I------------RSLVTGDRVVWRPGKEALEGVSGVVEAVHP 100 (347)
T ss_pred cceEEEEEECC-EEEEEeCCC---cEEEEEeccc---C------------CCCCCCcEEEEEeCCCcccccceEEEEEec
Confidence 46999999994 888876443 3555554321 1 23899999998521100 12499999998
Q ss_pred CEEEEEeCcceeeccEEEEeCCceeec
Q 000247 582 GILFIYDENETENGGYFCSKSQHCEKT 608 (1790)
Q Consensus 582 s~VFL~Sr~~tENgGIFVvRArnv~tv 608 (1790)
-+-.|.-.......-+++++...|++|
T Consensus 101 R~n~L~R~~~~~~~q~iaANvD~vlIV 127 (347)
T PRK12288 101 RTSVLTRPDYYDGVKPIAANIDQIVIV 127 (347)
T ss_pred ccceEECCCcccccceEEEEccEEEEE
Confidence 765555444444446788888887765
No 106
>PRK00092 ribosome maturation protein RimP; Reviewed
Probab=47.52 E-value=29 Score=37.80 Aligned_cols=49 Identities=18% Similarity=0.352 Sum_probs=38.2
Q ss_pred ccCCCEEEEc----cCCCCCceeEEEEEeCCeEEEEecCcceEEEEecCcccc
Q 000247 660 FAVGQTLRIR----VGPLKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLAE 708 (1790)
Q Consensus 660 ~lIGKTVKIr----kGPYKGylGiVKDaTdt~ARVELHSk~KtITVdKe~Ls~ 708 (1790)
.++|+.|+|+ ...-|=+.|++++++++.+++++..+.++++|+.+.|..
T Consensus 95 r~~G~~v~V~~~~~~~~~~~~~G~L~~~~~~~i~l~~~~~~~~~~i~~~~I~~ 147 (154)
T PRK00092 95 RFIGREVKVKLYEPIDGRKKFQGILLAVDGETVTLEVEGKEKEVEIPLDNIAK 147 (154)
T ss_pred HhCCCeEEEEEEcccCCceEEEEEEEEeeCCEEEEEECCCeEEEEEEHHHcce
Confidence 4799999997 234466689999999999998876443488998888764
No 107
>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor. Members of this subfamily are found in plants, metazoa and fungi.
Probab=46.55 E-value=30 Score=43.17 Aligned_cols=49 Identities=16% Similarity=0.162 Sum_probs=36.2
Q ss_pred HHHHHHHHHHhhccCCCCCcEEEEEEeCC--------CCcEEEEEeccchhHHHHhcCCCCEE
Q 000247 240 SAFCLMQKFVDLQSLGSKMQIISAFAVDH--------IKGFIFIEADKQCDINEACKGLSGIY 294 (1790)
Q Consensus 240 VV~~LmrKii~lq~~g~~L~I~SVFvpd~--------lKGYIYVEA~kq~dVkeAIkGI~gVy 294 (1790)
|+..|.+.|..+. .|.+|+++.. -.||||||-...++...||..|.+..
T Consensus 432 ~~edl~~~f~~~G------~v~~v~i~~~~~~~~~~~~~G~~fV~F~~~e~A~~A~~~lnGr~ 488 (509)
T TIGR01642 432 IYEDVKTEFSKYG------PLINIVIPRPNGDRNSTPGVGKVFLEYADVRSAEKAMEGMNGRK 488 (509)
T ss_pred HHHHHHHHHHhcC------CeeEEEeeccCcCCCcCCCcceEEEEECCHHHHHHHHHHcCCCE
Confidence 3344555554443 4888888742 25999999999999999999999853
No 108
>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=46.02 E-value=58 Score=30.05 Aligned_cols=67 Identities=13% Similarity=0.083 Sum_probs=42.7
Q ss_pred EEEEEEeCCCCcEEEEEeccchhHHHHhcCCCCEEeceeccCCHHHHHHHhhcccccccccCCCEEEEecCcCCCCcEEE
Q 000247 260 IISAFAVDHIKGFIFIEADKQCDINEACKGLSGIYYSRLAPVPKNEVSHLLSAQIKRNEVSEGTWAYVKNGKYKGDLAQV 339 (1790)
Q Consensus 260 I~SVFvpd~lKGYIYVEA~kq~dVkeAIkGI~gVy~sK~~pVPikEM~dLLkvkkks~~Lk~GdwVRIKrGpYKGDLAQV 339 (1790)
|+.+.+....+.-||||... + ...+||+.||.+=. +......|++|+.|++ +|
T Consensus 3 ~~~g~V~~v~~~G~~V~l~~---------~-------~~gli~~s~l~~~~-~~~~~~~~~~G~~i~v----------~v 55 (70)
T cd05698 3 KTHGTIVKVKPNGCIVSFYN---------N-------VKGFLPKSELSEAF-IKDPEEHFRVGQVVKV----------KV 55 (70)
T ss_pred EEEEEEEEEecCcEEEEECC---------C-------CEEEEEHHHcChhh-cCCHHHcccCCCEEEE----------EE
Confidence 45555555667778888642 1 13466777764322 1122335788999887 68
Q ss_pred EEEeCCCCEEEEEE
Q 000247 340 VYVNNARKRATVKL 353 (1790)
Q Consensus 340 ~eVDenk~kVtVKL 353 (1790)
++|++...++.|.+
T Consensus 56 ~~~d~~~~~i~ls~ 69 (70)
T cd05698 56 LSCDPEQQRLLLSC 69 (70)
T ss_pred EEEcCCCCEEEEEe
Confidence 99999888888765
No 109
>PRK05886 yajC preprotein translocase subunit YajC; Validated
Probab=45.52 E-value=47 Score=35.06 Aligned_cols=43 Identities=9% Similarity=0.178 Sum_probs=35.1
Q ss_pred cCCCEEEEccCCCCCceeEEEEEeCCeEEEEecCcceEEEEecCcccc
Q 000247 661 AVGQTLRIRVGPLKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLAE 708 (1790)
Q Consensus 661 lIGKTVKIrkGPYKGylGiVKDaTdt~ARVELHSk~KtITVdKe~Ls~ 708 (1790)
-.|+.|.-+. |+.|+|+++++++|.||+. ..-.|+|.|..|..
T Consensus 40 k~GD~VvT~g----Gi~G~V~~I~d~~v~leia-~gv~i~~~r~AI~~ 82 (109)
T PRK05886 40 QPGDRVHTTS----GLQATIVGITDDTVDLEIA-PGVVTTWMKLAVRD 82 (109)
T ss_pred CCCCEEEECC----CeEEEEEEEeCCEEEEEEC-CCeEEEEEhhheee
Confidence 4577776655 4889999999999999995 45679999999984
No 110
>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=45.34 E-value=87 Score=46.50 Aligned_cols=93 Identities=11% Similarity=0.113 Sum_probs=65.7
Q ss_pred ccccccCcEEEecCCceEEEEEEecCceEEEccCCCCCCceEEEecccccCCCCCCcccccccCCCcccCCCeEEEecCC
Q 000247 489 ENSFELYELVCFGRKDFGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVSEGP 568 (1790)
Q Consensus 489 lG~FeLgDLVQLD~~TVGVIVrVEkDEsfkVLdq~gD~~~VvtVk~~eI~~K~~~rr~vAtD~~gn~I~vGD~VKVIdGp 568 (1790)
...|+.||+|+|.....-.|+.|+++...++|....+ +..+.+.|.++.. ..+........+|..||.|+...-.
T Consensus 1327 ~~~Y~~G~vv~~~~~~y~~V~~vd~~~~~v~l~~~~~-G~~~~~~p~~~~~----~~~~~y~~~~~~l~~GDri~~t~~d 1401 (1960)
T TIGR02760 1327 MMPFEKGAVLRLKKDAYLTIADIDREHGKLTVADIKT-GSERDILPRQLDH----TFTSLYSDSELPLAKGDKIRLRATD 1401 (1960)
T ss_pred ccccCCCcEEEecCCcEEEEEEecCCCCEEEEEecCC-CCeEeeChhhcCc----ccceeeccccccccCCCEEEEeecC
Confidence 4689999999999999999999999777776644111 3567788776532 1233455567789999999987542
Q ss_pred -----CCCceEEEEEEECCEEEE
Q 000247 569 -----SKDRQGIVKKIYRGILFI 586 (1790)
Q Consensus 569 -----hkGRqG~VlHIyRs~VFL 586 (1790)
..+..++|+.|..+.+.+
T Consensus 1402 ~~~g~~n~~~~~V~~v~~~~~~~ 1424 (1960)
T TIGR02760 1402 KNRGIKANEVYTVTQVVNGLSVQ 1424 (1960)
T ss_pred cccccccCCeEEEEEEcCCcEEE
Confidence 246788899886554333
No 111
>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=44.53 E-value=58 Score=32.94 Aligned_cols=48 Identities=13% Similarity=0.070 Sum_probs=37.5
Q ss_pred ccCCCEEEEccCC---CCCceeEEEEEeCCeEEEEecCcceEEEEecCcccc
Q 000247 660 FAVGQTLRIRVGP---LKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLAE 708 (1790)
Q Consensus 660 ~lIGKTVKIrkGP---YKGylGiVKDaTdt~ARVELHSk~KtITVdKe~Ls~ 708 (1790)
.|+|-.|+|+.=+ |.|..|||++-|..+..|+- ...++++|+|.+-.+
T Consensus 11 dl~G~~i~V~~s~~pslvG~~GiVV~ETknt~~I~t-~~~~~~~IpK~~~vF 61 (89)
T PF01868_consen 11 DLIGAKIEVVRSKNPSLVGIEGIVVDETKNTFVIVT-EDGKVKTIPKAGSVF 61 (89)
T ss_dssp --TT-EEEEEEESSCCCTTEEEEEEEEETTEEEEEE-TTEEEEEEESTTEEE
T ss_pred hhcCCEEEEEEcCCCCccCCEEEEEEcccceEEEEe-cCCcEEEEecCCEEE
Confidence 5899999999873 78999999999999999863 344789999988664
No 112
>PF10446 DUF2457: Protein of unknown function (DUF2457); InterPro: IPR018853 This entry represents a family of uncharacterised proteins.
Probab=44.37 E-value=11 Score=47.15 Aligned_cols=7 Identities=14% Similarity=0.610 Sum_probs=3.0
Q ss_pred cEEEEEe
Q 000247 226 TIWKVKC 232 (1790)
Q Consensus 226 kLWaVKC 232 (1790)
.||+-..
T Consensus 123 ~~WtP~~ 129 (458)
T PF10446_consen 123 EFWTPGA 129 (458)
T ss_pred eeecccc
Confidence 3444443
No 113
>PRK02749 photosystem I reaction center subunit IV; Provisional
Probab=44.13 E-value=37 Score=33.34 Aligned_cols=43 Identities=12% Similarity=0.295 Sum_probs=32.0
Q ss_pred ccCCCEEEEecC--cCCCCcEEEEEEeCCCCE--EEEEEeccCchhhH
Q 000247 319 VSEGTWAYVKNG--KYKGDLAQVVYVNNARKR--ATVKLIPRIDLQAL 362 (1790)
Q Consensus 319 Lk~GdwVRIKrG--pYKGDLAQV~eVDenk~k--VtVKLVPRIDy~~l 362 (1790)
|+.|+.|||+|. -+=+|++.|..||...-+ |+|+ |-.++|..+
T Consensus 3 i~rGskVrIlR~ESYWyn~vGtV~svD~sgi~YPV~VR-F~kvNY~g~ 49 (71)
T PRK02749 3 ISRGDKVRILRPESYWYNEVGTVASVDKSGIKYPVIVR-FDKVNYNGF 49 (71)
T ss_pred cccCCEEEEccccceeecCcceEEEEccCCCeeeEEEE-eeeeecccc
Confidence 678999999996 467899999999998643 4444 345566543
No 114
>smart00538 POP4 A domain found in a protein subunit of human RNase MRP and RNase P ribonucleoprotein complexes and archaeal proteins.
Probab=44.08 E-value=52 Score=33.62 Aligned_cols=47 Identities=15% Similarity=0.188 Sum_probs=38.9
Q ss_pred ccCCCEEEEccCC---CCCceeEEEEEeCCeEEEEecCcceEEEEecCccc
Q 000247 660 FAVGQTLRIRVGP---LKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLA 707 (1790)
Q Consensus 660 ~lIGKTVKIrkGP---YKGylGiVKDaTdt~ARVELHSk~KtITVdKe~Ls 707 (1790)
.|||-.|+|+.=+ |-|..|||++-|..+..|+... .++.+|+|.+-.
T Consensus 10 el~G~~v~Vv~s~~ps~vGi~GiVv~ET~nt~~I~t~~-~~~~~IpK~~~v 59 (92)
T smart00538 10 ELIGLKVRVVASKNPSLVGIEGIVVDETRNTLKIETKE-GRVKTVPKDGAV 59 (92)
T ss_pred hhcCCEEEEEEcCCCCccCcEEEEEEeeeeEEEEEeCC-CcEEEEECCCeE
Confidence 5899999999874 6789999999999999988654 477888888844
No 115
>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=43.23 E-value=39 Score=33.31 Aligned_cols=49 Identities=22% Similarity=0.352 Sum_probs=37.4
Q ss_pred ccCCCEEEEcc----CCCCCceeEEEEEeCCeEEEEecCc--ceEEEEecCcccc
Q 000247 660 FAVGQTLRIRV----GPLKGYLCRVLAVRYSDVTVKLDSQ--QKILTVKGEHLAE 708 (1790)
Q Consensus 660 ~lIGKTVKIrk----GPYKGylGiVKDaTdt~ARVELHSk--~KtITVdKe~Ls~ 708 (1790)
..||+.|+|+- +.-|=+.|+++++.++.++|+++.+ .++|+|+.++|..
T Consensus 22 r~~G~~v~v~~~~~~~~~~~~~G~L~~~~~~~v~l~~~~~~~~~~~~i~~~~I~k 76 (83)
T cd01734 22 RAVGKYVHVKLYQPIDGQKEFEGTLLGVDDDTVTLEVDIKTRGKTVEIPLDKIAK 76 (83)
T ss_pred HhCCCEEEEEEEcccCCeEEEEEEEEeEeCCEEEEEEecCCCCeEEEEEhHHeeE
Confidence 47899999953 3345579999999999999887643 5688888777764
No 116
>PF13051 DUF3912: Protein of unknown function (DUF3912)
Probab=42.95 E-value=46 Score=31.72 Aligned_cols=49 Identities=20% Similarity=0.238 Sum_probs=35.0
Q ss_pred ccCCCEEEEccCCCCCceeEEEEEe---CCeEEEEecCcceEEEEecCcccccc
Q 000247 660 FAVGQTLRIRVGPLKGYLCRVLAVR---YSDVTVKLDSQQKILTVKGEHLAEVR 710 (1790)
Q Consensus 660 ~lIGKTVKIrkGPYKGylGiVKDaT---dt~ARVELHSk~KtITVdKe~Ls~v~ 710 (1790)
.++||...|..|||.-.+||||.-. +.+..|-+. -+.|.|...+|.+|.
T Consensus 3 di~gqkayikdgp~rnrigivk~~e~q~~~~f~ivi~--~q~i~velkdivlvg 54 (68)
T PF13051_consen 3 DIVGQKAYIKDGPYRNRIGIVKKNEKQLESHFAIVIG--EQSIDVELKDIVLVG 54 (68)
T ss_pred cccccEeeeccCCccceeEEEecchhhcCCcEEEEEC--CeEEEEEeeeEEEEE
Confidence 3789999999999999999999753 334443333 445667667776653
No 117
>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=42.55 E-value=40 Score=36.08 Aligned_cols=49 Identities=14% Similarity=0.452 Sum_probs=35.2
Q ss_pred ccCCCEEEEcc-CCCCC---ceeEEEEEeCCeEEEEecCc--ceEEEEecCcccc
Q 000247 660 FAVGQTLRIRV-GPLKG---YLCRVLAVRYSDVTVKLDSQ--QKILTVKGEHLAE 708 (1790)
Q Consensus 660 ~lIGKTVKIrk-GPYKG---ylGiVKDaTdt~ARVELHSk--~KtITVdKe~Ls~ 708 (1790)
..||+.|+|+- -|..+ +.|++++++++.++|+++.+ .++++|+.++|.-
T Consensus 84 ~~iG~~v~v~~~~~~~~~~~~~G~L~~~~~~~i~l~~~~~~~~~~~~I~~~~I~k 138 (141)
T PF02576_consen 84 RFIGRKVKVKLKQPVNGRKEFEGKLLEVDEDEITLEVEGKGKKKEVEIPFSDIKK 138 (141)
T ss_dssp HH-SEEEEEE-SS-SSS-SEEEEEEEEEETTEEEEEEE-SS-EEEEEE-SS--SS
T ss_pred HhcCCeEEEEEeccCCCcEEEEEEEEEEeCCEEEEEECCccceEEEEEEHHHCce
Confidence 47999999995 34444 69999999999999999887 4689998888763
No 118
>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=42.46 E-value=1.3e+02 Score=28.25 Aligned_cols=60 Identities=13% Similarity=0.071 Sum_probs=35.9
Q ss_pred eEEEEEEecCceEEEccCCCCCCceEEEecccccCCCCCCcccccccCCCcccCCCeEEEecCCCCCceEEEEE
Q 000247 505 FGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVSEGPSKDRQGIVKK 578 (1790)
Q Consensus 505 VGVIVrVEkDEsfkVLdq~gD~~~VvtVk~~eI~~K~~~rr~vAtD~~gn~I~vGD~VKVIdGphkGRqG~VlH 578 (1790)
.|+|++.-....|.|.+..+ .++++.++. ++.. ....+.+||.|.+---++...+|.|+|
T Consensus 4 ~G~Vi~~~~g~~~~V~~~~g---~~~~c~~rG---klr~--------~~~~~~vGD~V~~~~~~~~~~~g~I~~ 63 (64)
T cd04451 4 EGVVTEALPNAMFRVELENG---HEVLAHISG---KMRM--------NYIRILPGDRVKVELSPYDLTKGRIVY 63 (64)
T ss_pred EEEEEEEeCCCEEEEEeCCC---CEEEEEECc---eeec--------CCcccCCCCEEEEEEeecCCCEEEEEE
Confidence 48888887323677755332 366666543 2110 234489999998874443445688876
No 119
>PRK14637 hypothetical protein; Provisional
Probab=42.16 E-value=44 Score=36.80 Aligned_cols=46 Identities=9% Similarity=0.114 Sum_probs=35.8
Q ss_pred ccCCCEEEEccCCCCCc-eeEEEEEeCCeEEEEecCcceEEEEecCccc
Q 000247 660 FAVGQTLRIRVGPLKGY-LCRVLAVRYSDVTVKLDSQQKILTVKGEHLA 707 (1790)
Q Consensus 660 ~lIGKTVKIrkGPYKGy-lGiVKDaTdt~ARVELHSk~KtITVdKe~Ls 707 (1790)
..+|+.|+|+-..-+-+ .|++++++++.++++. ..+++.|+.+.|.
T Consensus 95 r~~G~~V~V~l~~~~~~~~G~L~~~~d~~v~l~~--~~~~~~i~~~~I~ 141 (151)
T PRK14637 95 IFVGETVKVWFECTGQWQVGTIAEADETCLVLTS--DGVPVTIPYVQIT 141 (151)
T ss_pred HhCCCEEEEEECCCCcEEEEEEEEEeCCEEEEEE--CCEEEEEEHHHee
Confidence 47999999986223557 5999999999999885 4677888777765
No 120
>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=41.58 E-value=63 Score=31.17 Aligned_cols=69 Identities=17% Similarity=0.213 Sum_probs=46.6
Q ss_pred CcEEEEEEeCCCCcEEEEEeccchhHHHHhcCCCCEEeceeccCCHHHHHHHhhcccccccccCCCEEEEecCcCCCCcE
Q 000247 258 MQIISAFAVDHIKGFIFIEADKQCDINEACKGLSGIYYSRLAPVPKNEVSHLLSAQIKRNEVSEGTWAYVKNGKYKGDLA 337 (1790)
Q Consensus 258 L~I~SVFvpd~lKGYIYVEA~kq~dVkeAIkGI~gVy~sK~~pVPikEM~dLLkvkkks~~Lk~GdwVRIKrGpYKGDLA 337 (1790)
-.|+.+.+....+--|||+... ++. .+||+.||.+-. +......|++|+.|++
T Consensus 15 G~i~~g~V~~v~~~G~fv~l~~---------~~~-------g~v~~~el~~~~-~~~~~~~~~~Gd~v~v---------- 67 (83)
T cd04461 15 GMVVHGYVRNITPYGVFVEFLG---------GLT-------GLAPKSYISDEF-VTDPSFGFKKGQSVTA---------- 67 (83)
T ss_pred CCEEEEEEEEEeeceEEEEcCC---------CCE-------EEEEHHHCCccc-ccCHHHhcCCCCEEEE----------
Confidence 3688888887788888888742 222 345666654321 1122345788999987
Q ss_pred EEEEEeCCCCEEEEEE
Q 000247 338 QVVYVNNARKRATVKL 353 (1790)
Q Consensus 338 QV~eVDenk~kVtVKL 353 (1790)
+|+.++.++.++.|.|
T Consensus 68 kV~~id~~~~~i~lsl 83 (83)
T cd04461 68 KVTSVDEEKQRFLLSL 83 (83)
T ss_pred EEEEEcCCCCEEEEeC
Confidence 6999999988888864
No 121
>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]
Probab=40.74 E-value=34 Score=38.94 Aligned_cols=34 Identities=26% Similarity=0.478 Sum_probs=31.3
Q ss_pred cEEEEEEeCCCCcEEEEEeccchhHHHHhcCCCC
Q 000247 259 QIISAFAVDHIKGFIFIEADKQCDINEACKGLSG 292 (1790)
Q Consensus 259 ~I~SVFvpd~lKGYIYVEA~kq~dVkeAIkGI~g 292 (1790)
.|.+|.+--..|||-|||-+...|..+||..|-+
T Consensus 36 ~lrsvWvArnPPGfAFVEFed~RDA~DAvr~LDG 69 (195)
T KOG0107|consen 36 PLRSVWVARNPPGFAFVEFEDPRDAEDAVRYLDG 69 (195)
T ss_pred cceeEEEeecCCCceEEeccCcccHHHHHhhcCC
Confidence 4888998889999999999999999999999887
No 122
>PRK14638 hypothetical protein; Provisional
Probab=40.69 E-value=40 Score=37.03 Aligned_cols=47 Identities=11% Similarity=0.142 Sum_probs=37.7
Q ss_pred ccCCCEEEEccCCCCCceeEEEEEeCCeEEEEecCcceEEEEecCcccc
Q 000247 660 FAVGQTLRIRVGPLKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLAE 708 (1790)
Q Consensus 660 ~lIGKTVKIrkGPYKGylGiVKDaTdt~ARVELHSk~KtITVdKe~Ls~ 708 (1790)
+.+|+.|+|+----|=+.|++++++++.++|++ ..++|.|+.+.|..
T Consensus 97 r~~G~~v~V~~~~~k~~~G~L~~~~~~~i~l~~--~~~~~~i~~~~I~~ 143 (150)
T PRK14638 97 RFTGKLAKIVTKDGKTFIGRIESFVDGTITISD--EKEKYEINIDDVKR 143 (150)
T ss_pred HhCCCEEEEEECCCcEEEEEEEEEeCCEEEEEE--CCcEEEEEhHHcce
Confidence 479999999753347799999999999999874 45778888777764
No 123
>PRK08572 rps17p 30S ribosomal protein S17P; Reviewed
Probab=40.60 E-value=53 Score=34.72 Aligned_cols=25 Identities=12% Similarity=0.183 Sum_probs=21.6
Q ss_pred CCcccccccCCCcccCCCeEEEecC
Q 000247 543 DMKFTALDQSMKVISLNDTARVSEG 567 (1790)
Q Consensus 543 ~rr~vAtD~~gn~I~vGD~VKVIdG 567 (1790)
..++.|-|...++.++||.|+|.+-
T Consensus 65 ~kky~aHDe~cn~~kvGD~V~I~E~ 89 (108)
T PRK08572 65 RSRIHAHNPPCIDAKVGDKVKIAEC 89 (108)
T ss_pred eeeEEEECCCCCCCCCCCEEEEEEc
Confidence 3458899988899999999999875
No 124
>PRK14643 hypothetical protein; Provisional
Probab=40.38 E-value=41 Score=37.50 Aligned_cols=50 Identities=22% Similarity=0.235 Sum_probs=39.0
Q ss_pred ccCCCEEEEcc-CCC---CCceeEEEEEeCCeEEEEec----CcceEEEEecCccccc
Q 000247 660 FAVGQTLRIRV-GPL---KGYLCRVLAVRYSDVTVKLD----SQQKILTVKGEHLAEV 709 (1790)
Q Consensus 660 ~lIGKTVKIrk-GPY---KGylGiVKDaTdt~ARVELH----Sk~KtITVdKe~Ls~v 709 (1790)
.++|+.|+|+- -|+ |=+.|+++++.++.++|+|+ ...++|.|+.+.|.-+
T Consensus 101 r~~G~~V~V~l~~~~~g~k~~~G~L~~~~~~~~~l~l~~~~~~~~~~~~ip~~~I~ka 158 (164)
T PRK14643 101 KALNQWVYVQLNNEIKKVKEFEGYVTKYNVNTNTFRFTFFIKGQKKKLDVKYEQIKFI 158 (164)
T ss_pred HhcCCeEEEEEecccCCceEEEEEEEEEeCCcEEEEEEeeccCcCcEEEEeHHHhhhe
Confidence 47999999974 454 44799999999999998864 3467899988887743
No 125
>KOG3218 consensus RNA polymerase, 25-kDa subunit (common to polymerases I, II and III) [Transcription]
Probab=40.30 E-value=1.6e+02 Score=34.19 Aligned_cols=119 Identities=15% Similarity=0.147 Sum_probs=60.4
Q ss_pred HHHHHHhccccchhhchhhHHHhhhcccccCCCCCCCCc--EEEEEecCchhHHHHHHHHHHHHhhccCCCCCcEEE-EE
Q 000247 188 KMMEERYKSNKLIRYAEEDYEAKKMLEREYHMPCPEDPT--IWKVKCMAGRERQSAFCLMQKFVDLQSLGSKMQIIS-AF 264 (1790)
Q Consensus 188 e~LkERY~r~s~~~y~~d~~e~~~~VpQqlLLPSVkDPk--LWaVKCK~GkEReVV~~LmrKii~lq~~g~~L~I~S-VF 264 (1790)
+.|++||....-.+ ++ =+.+.+-.+||. ||++.|... +.-|..|..-++.++. ..|.. |+
T Consensus 40 e~F~~~yg~~~p~r--~~---------L~~~~~~~~dp~~ki~V~F~~~~--kvgvk~~k~~~~~~~~----~ni~~~Il 102 (208)
T KOG3218|consen 40 EEFKARYGDKMPDR--ED---------LRILAAHRDDPTDKIYVFFPEEP--KVGVKTMKTYVIQMQS----ENIFRAIL 102 (208)
T ss_pred HHHHHHhccCCcch--hh---------EEEEeccCCCCcCcEEEEeCCCC--cccHHHHHHHHHHHHh----cCceEEEE
Confidence 45788998642100 01 123455667776 999998533 2222222222222221 12332 22
Q ss_pred Ee------------CCCCcEEEEEeccchhHHHHhcCCCCEEeceeccCCHHHHHHHhhcccccccccCCCEEEEec
Q 000247 265 AV------------DHIKGFIFIEADKQCDINEACKGLSGIYYSRLAPVPKNEVSHLLSAQIKRNEVSEGTWAYVKN 329 (1790)
Q Consensus 265 vp------------d~lKGYIYVEA~kq~dVkeAIkGI~gVy~sK~~pVPikEM~dLLkvkkks~~Lk~GdwVRIKr 329 (1790)
+. ..|+.-.-||.+..+++.- +=..|+...+-..+..+|-..||+. +.|++.+.=||-.
T Consensus 103 V~q~~mt~~A~k~i~~~~p~f~iE~F~e~eLlv--NIT~H~lvPkH~vL~~eEK~~LL~r----y~l~e~qLPRIq~ 173 (208)
T KOG3218|consen 103 VVQNGMTPSALKALSDFTPKFTIEVFLEAELLV--NITEHELVPKHQVLTDEEKEELLRR----YKLKETQLPRIQK 173 (208)
T ss_pred EecCCCChHHHHHHHhcCCceEEEeeehhhhee--eccceeecCceEEcCHHHHHHHHHH----hcCCcccCCeeec
Confidence 22 2456666677776655422 1122444455666788999999963 2344444445543
No 126
>PRK14634 hypothetical protein; Provisional
Probab=40.28 E-value=39 Score=37.30 Aligned_cols=47 Identities=6% Similarity=0.064 Sum_probs=37.3
Q ss_pred ccCCCEEEEc-cCCC---CCceeEEEEEeCCeEEEEecCcceEEEEecCcccc
Q 000247 660 FAVGQTLRIR-VGPL---KGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLAE 708 (1790)
Q Consensus 660 ~lIGKTVKIr-kGPY---KGylGiVKDaTdt~ARVELHSk~KtITVdKe~Ls~ 708 (1790)
+.+|+.|+|+ ..|. |=+.|+++++.++.+++++. .++|+|+.+.|.-
T Consensus 97 r~~G~~V~V~l~~~~~~~k~~~G~L~~~~~~~v~l~~~--~~~~~i~~~~I~k 147 (155)
T PRK14634 97 TFRGFPVEVSHRDDDGSEQRLEGLLLERNEDHLQINIR--GRIKRIPRDSVIS 147 (155)
T ss_pred HhCCCeEEEEEecCCCCeEEEEEEEEEEeCCEEEEEEC--CEEEEEEHHHeee
Confidence 4789999996 3443 66899999999999998874 6778888777764
No 127
>TIGR03630 arch_S17P archaeal ribosomal protein S17P. This model describes exclusively the archaeal ribosomal protein S17P. It excludes homologous ribosomal proteins S11 from eukaryotes and S17 from bacteria.
Probab=40.27 E-value=53 Score=34.45 Aligned_cols=25 Identities=16% Similarity=0.106 Sum_probs=21.3
Q ss_pred CCcccccccCCCcccCCCeEEEecC
Q 000247 543 DMKFTALDQSMKVISLNDTARVSEG 567 (1790)
Q Consensus 543 ~rr~vAtD~~gn~I~vGD~VKVIdG 567 (1790)
..++.|-|...++.++||+|+|.+-
T Consensus 63 ~kky~aHDe~cn~~kvGD~V~I~E~ 87 (102)
T TIGR03630 63 RSKIHAHNPPCIDVKEGDIVIIGET 87 (102)
T ss_pred eeeEEEECCCCCCCCCCCEEEEEEc
Confidence 3458899988789999999999875
No 128
>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=39.94 E-value=1e+02 Score=28.70 Aligned_cols=57 Identities=19% Similarity=0.256 Sum_probs=37.2
Q ss_pred cccCcEEEecCCceEEEEEEecCceEEEccCCCCCCceEEEecccccCCCCCCcccccccCCCcccCCCeEEEe
Q 000247 492 FELYELVCFGRKDFGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVS 565 (1790)
Q Consensus 492 FeLgDLVQLD~~TVGVIVrVEkDEsfkVLdq~gD~~~VvtVk~~eI~~K~~~rr~vAtD~~gn~I~vGD~VKVI 565 (1790)
|+.+|.|. |.|++|+....|.=|..+ ..--|..++|... ..+.....|++||.|++.
T Consensus 2 ~~~G~iv~------g~V~~v~~~g~~V~l~~~----~~g~ip~~~l~~~-------~~~~~~~~~~~G~~v~v~ 58 (74)
T PF00575_consen 2 LKEGDIVE------GKVTSVEDFGVFVDLGNG----IEGFIPISELSDD-------RIDDPSEVYKIGQTVRVK 58 (74)
T ss_dssp SSTTSEEE------EEEEEEETTEEEEEESTS----SEEEEEGGGSSSS-------EESSSHGTCETTCEEEEE
T ss_pred CCCCCEEE------EEEEEEECCEEEEEECCc----EEEEEEeehhcCc-------cccccccccCCCCEEEEE
Confidence 56777775 899999986444444422 2355666666432 234456789999999874
No 129
>cd05703 S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 12 (hs12) and S. cerevisiae S1 repeat 9 (sc9). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=39.81 E-value=66 Score=30.79 Aligned_cols=68 Identities=16% Similarity=0.218 Sum_probs=43.6
Q ss_pred EEEEEEeCCCCcEEEEEeccchhHHHHhcCCCCEEeceeccCCHHHHHHHh-hcccccccccCCCEEEEecCcCCCCcEE
Q 000247 260 IISAFAVDHIKGFIFIEADKQCDINEACKGLSGIYYSRLAPVPKNEVSHLL-SAQIKRNEVSEGTWAYVKNGKYKGDLAQ 338 (1790)
Q Consensus 260 I~SVFvpd~lKGYIYVEA~kq~dVkeAIkGI~gVy~sK~~pVPikEM~dLL-kvkkks~~Lk~GdwVRIKrGpYKGDLAQ 338 (1790)
|...++....+..||||... +| ..+||+.|+.+-. .+......|++|+.|. |+
T Consensus 3 ~V~g~V~~i~~~g~~V~l~~---------~i-------~G~i~~~~ls~~~~~~~~~~~~~~vG~~v~----------~k 56 (73)
T cd05703 3 EVTGFVNNVSKEFVWLTISP---------DV-------KGRIPLLDLSDDVSVLEHPEKKFPIGQALK----------AK 56 (73)
T ss_pred EEEEEEEEEeCCEEEEEeCC---------Cc-------EEEEEHHHcCCccccccCHHHhCCCCCEEE----------EE
Confidence 45566666667777877521 11 2355666665431 1222344688999987 46
Q ss_pred EEEEeCCCCEEEEEE
Q 000247 339 VVYVNNARKRATVKL 353 (1790)
Q Consensus 339 V~eVDenk~kVtVKL 353 (1790)
|++||+++.+|.|.+
T Consensus 57 V~~id~~~~~i~Ls~ 71 (73)
T cd05703 57 VVGVDKEHKLLRLSA 71 (73)
T ss_pred EEEEeCCCCEEEEEe
Confidence 999999999998876
No 130
>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=39.64 E-value=1.2e+02 Score=29.74 Aligned_cols=61 Identities=13% Similarity=0.071 Sum_probs=43.1
Q ss_pred ceEEEEEEecCceEEEccCCCCCCceEEEecccccCCCCCCcccccccCCCcccCCCeEEEecCCCCCceEEEEE
Q 000247 504 DFGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVSEGPSKDRQGIVKK 578 (1790)
Q Consensus 504 TVGVIVrVEkDEsfkVLdq~gD~~~VvtVk~~eI~~K~~~rr~vAtD~~gn~I~vGD~VKVIdGphkGRqG~VlH 578 (1790)
..|+|+++-.+..|+|...++ ..+... |.-|+.. +.=-|.+||.|+|--=||.-..|.|+|
T Consensus 7 ~~G~V~e~L~~~~f~V~l~ng---~~vla~---i~GKmr~--------~rI~I~~GD~V~Ve~spyd~tkgrIi~ 67 (68)
T TIGR00008 7 MEGKVTESLPNAMFRVELENG---HEVLAH---ISGKIRM--------HYIRILPGDKVKVELSPYDLTRGRITY 67 (68)
T ss_pred EEEEEEEECCCCEEEEEECCC---CEEEEE---ecCcchh--------ccEEECCCCEEEEEECcccCCcEeEEe
Confidence 359999999888999887664 233333 3333321 234589999999998888877888875
No 131
>CHL00125 psaE photosystem I subunit IV; Reviewed
Probab=39.54 E-value=44 Score=32.26 Aligned_cols=41 Identities=15% Similarity=0.315 Sum_probs=30.3
Q ss_pred ccCCCEEEEecC--cCCCCcEEEEEEeCCCCE--EEEEEeccCchh
Q 000247 319 VSEGTWAYVKNG--KYKGDLAQVVYVNNARKR--ATVKLIPRIDLQ 360 (1790)
Q Consensus 319 Lk~GdwVRIKrG--pYKGDLAQV~eVDenk~k--VtVKLVPRIDy~ 360 (1790)
|+.|+.|||+|- -+=.|++.|..||..+-+ |+|++ -.++|.
T Consensus 2 i~rGskVrIlR~ESYWyn~vGtV~svd~~gi~YPV~VRF-~kvNY~ 46 (64)
T CHL00125 2 VKRGSKVRILRKESYWYNEIGTVATVDQSGIRYPVLVRF-EKVNYS 46 (64)
T ss_pred cccCCEEEEccccceeecCcceEEEEcCCCCCccEEEEE-eeeecc
Confidence 577999999996 467899999999997543 55543 344553
No 132
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=38.94 E-value=1.4e+02 Score=33.67 Aligned_cols=90 Identities=11% Similarity=0.199 Sum_probs=48.1
Q ss_pred ccccCcEEEecCCceEEEEEEecCceEEEccCCC------CCCceEEEecccccCCCCCCcccccccCCCcccCCCeEEE
Q 000247 491 SFELYELVCFGRKDFGLIVGMEKDDHYKILKEGS------EGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARV 564 (1790)
Q Consensus 491 ~FeLgDLVQLD~~TVGVIVrVEkDEsfkVLdq~g------D~~~VvtVk~~eI~~K~~~rr~vAtD~~gn~I~vGD~VKV 564 (1790)
.+++||+|. |.|++|..+-.|.-|..-. ..+..-.+..++|... ..+.....|++||.|++
T Consensus 61 ~~~~GdiV~------GkV~~i~~~g~~V~I~~~~~~~~~l~~~~~G~l~~s~i~~~-------~~~~~~~~~~~GD~V~a 127 (189)
T PRK09521 61 LLKKGDIVY------GRVVDVKEQRALVRIVSIEGSERELATSKLAYIHISQVSDG-------YVESLTDAFKIGDIVRA 127 (189)
T ss_pred CCCCCCEEE------EEEEEEcCCeEEEEEEEecccccccCCCceeeEEhhHcChh-------hhhhHHhccCCCCEEEE
Confidence 677899985 8899987643333331100 0001122223333211 11223567999999985
Q ss_pred ecCCCCCceEEEEEEECCEEEEEeCcceeeccEEEEeCCcee
Q 000247 565 SEGPSKDRQGIVKKIYRGILFIYDENETENGGYFCSKSQHCE 606 (1790)
Q Consensus 565 IdGphkGRqG~VlHIyRs~VFL~Sr~~tENgGIFVvRArnv~ 606 (1790)
. |+.|. ..+.|..+. +..|++.+++..|-
T Consensus 128 k----------V~~i~-~~i~LS~k~--~~lGvv~a~~~~~g 156 (189)
T PRK09521 128 K----------VISYT-DPLQLSTKG--KDLGVIYAMCSRCR 156 (189)
T ss_pred E----------EEecC-CcEEEEEec--CCceEEEEEccccC
Confidence 3 44444 334444443 55788888777654
No 133
>PF10842 DUF2642: Protein of unknown function (DUF2642); InterPro: IPR020139 This entry contains proteins with no known function.
Probab=38.89 E-value=69 Score=31.29 Aligned_cols=45 Identities=7% Similarity=0.115 Sum_probs=35.0
Q ss_pred ccCCCEEEEccCCCCCceeEEEEEeCCeEEEEecCcceEEEEecCccc
Q 000247 660 FAVGQTLRIRVGPLKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLA 707 (1790)
Q Consensus 660 ~lIGKTVKIrkGPYKGylGiVKDaTdt~ARVELHSk~KtITVdKe~Ls 707 (1790)
.+||+.|.|..- .-=+.|+++|+..+++.||-+ .+.+-|.-.+|.
T Consensus 18 ~liG~~vvV~T~-~g~v~G~L~~V~pDhIvl~~~--~~~~~IR~~~IV 62 (66)
T PF10842_consen 18 SLIGQRVVVQTT-RGSVRGILVDVKPDHIVLEEN--GTPFFIRIAQIV 62 (66)
T ss_pred HhcCCEEEEEEc-CCcEEEEEEeecCCEEEEEeC--CcEEEEEeeeEE
Confidence 489999999773 333589999999999998888 666666666655
No 134
>PF10574 UPF0552: Uncharacterised protein family UPF0552; InterPro: IPR018889 This family of proteins has no known function.
Probab=38.87 E-value=36 Score=39.70 Aligned_cols=98 Identities=14% Similarity=0.177 Sum_probs=0.0
Q ss_pred cEEEEEecCchhHHHHHHHHHHHHhhccCCCCCcEEEEEEeCCCCcEEE----EEec------cchhHHHHhc--CCCCE
Q 000247 226 TIWKVKCMAGRERQSAFCLMQKFVDLQSLGSKMQIISAFAVDHIKGFIF----IEAD------KQCDINEACK--GLSGI 293 (1790)
Q Consensus 226 kLWaVKCK~GkEReVV~~LmrKii~lq~~g~~L~I~SVFvpd~lKGYIY----VEA~------kq~dVkeAIk--GI~gV 293 (1790)
++|+|.|++- .|.+|-++.. +.++.-..--....-.||+. |||. .++++..+|. .+..|
T Consensus 58 Ry~vl~i~~~-------~~hrR~fd~~--G~EIepnfs~T~kVntGyL~SsykveAkg~tDrls~~~L~~~V~k~~ll~l 128 (224)
T PF10574_consen 58 RYYVLYIRPS-------RIHRRKFDAK--GNEIEPNFSDTTKVNTGYLNSSYKVEAKGDTDRLSPEQLKALVNKPELLAL 128 (224)
T ss_pred EEEEEEEeec-------hhhhhcccCC--CcCcCCCccceeeeeecccCcccEEEecCCccccCHHHHHHHhCchhhccc
Q ss_pred Eec------eeccCCHHHHHHHhhcccccccccCCCEEEEec---CcCCCCcEEEE
Q 000247 294 YYS------RLAPVPKNEVSHLLSAQIKRNEVSEGTWAYVKN---GKYKGDLAQVV 340 (1790)
Q Consensus 294 y~s------K~~pVPikEM~dLLkvkkks~~Lk~GdwVRIKr---GpYKGDLAQV~ 340 (1790)
... -...+|..||.++ +|++|+-||||. +||-.-||+|+
T Consensus 129 t~~~~~~~~~aFW~~e~~~~~~--------ele~G~~vRlKT~GDspFieSlaKlD 176 (224)
T PF10574_consen 129 TESHTPDQTFAFWMPEAEMEKM--------ELELGDEVRLKTRGDSPFIESLAKLD 176 (224)
T ss_pred ccccCCCCeEEEeechhhccce--------ecccCCeEEEEecCCchhheeeeeec
No 135
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=38.80 E-value=1.2e+02 Score=30.43 Aligned_cols=65 Identities=14% Similarity=0.118 Sum_probs=47.8
Q ss_pred ceEEEEEEecCceEEEccCCCCCCceEEEecccccCCCCCCcccccccCCCcccCCCeEEEecCCCCCceEEEEEEECC
Q 000247 504 DFGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVSEGPSKDRQGIVKKIYRG 582 (1790)
Q Consensus 504 TVGVIVrVEkDEsfkVLdq~gD~~~VvtVk~~eI~~K~~~rr~vAtD~~gn~I~vGD~VKVIdGphkGRqG~VlHIyRs 582 (1790)
..|+|+++-.+..|+|.+.++ .++.-. |.-|+.. +.--|.+||.|.|--=||.-..|.|++=|+.
T Consensus 9 ~~g~V~e~L~~~~f~v~~edg---~~~~ah---I~GKmr~--------~~i~I~~GD~V~Ve~~~~d~~kg~I~~Ry~~ 73 (75)
T COG0361 9 MEGTVIEMLPNGRFRVELENG---HERLAH---ISGKMRK--------NRIRILPGDVVLVELSPYDLTKGRIVYRYKK 73 (75)
T ss_pred EEEEEEEecCCCEEEEEecCC---cEEEEE---ccCcchh--------eeEEeCCCCEEEEEecccccccccEEEEecC
Confidence 459999999999999999875 233333 4344321 2346899999999988998888999887763
No 136
>PRK14644 hypothetical protein; Provisional
Probab=37.52 E-value=41 Score=36.45 Aligned_cols=48 Identities=13% Similarity=0.202 Sum_probs=36.2
Q ss_pred ccCCCEEEEcc-CC---CCCceeEEEEEeCCeEEEEec--CcceEEEEecCccc
Q 000247 660 FAVGQTLRIRV-GP---LKGYLCRVLAVRYSDVTVKLD--SQQKILTVKGEHLA 707 (1790)
Q Consensus 660 ~lIGKTVKIrk-GP---YKGylGiVKDaTdt~ARVELH--Sk~KtITVdKe~Ls 707 (1790)
.+||+.|+|+- -| -|=+.|+++++.++.+++++. .+-++|++++++|.
T Consensus 82 r~~G~~v~V~l~~~~~~~~~~~G~L~~v~~~~i~l~~~~k~~~~~i~~~~~~i~ 135 (136)
T PRK14644 82 NHIGEIIDVSLNKEVNKTDFITGELLENNPETITLKWNCKGQFRKVEINKENIK 135 (136)
T ss_pred HhCCCeEEEEEccCcCCeEEEEEEEEEEeCCEEEEEEecCCcEEEEEECHHHhc
Confidence 47999999963 33 366789999999999999654 44467777777664
No 137
>cd01854 YjeQ_engC YjeQ/EngC. YjeQ (YloQ in Bacillus subtilis) represents a protein family whose members are broadly conserved in bacteria and have been shown to be essential to the growth of E. coli and B. subtilis. Proteins of the YjeQ family contain all sequence motifs typical of the vast class of P-loop-containing GTPases, but show a circular permutation, with a G4-G1-G3 pattern of motifs as opposed to the regular G1-G3-G4 pattern seen in most GTPases. All YjeQ family proteins display a unique domain architecture, which includes an N-terminal OB-fold RNA-binding domain, the central permuted GTPase domain, and a zinc knuckle-like C-terminal cysteine domain. This domain architecture suggests a role for YjeQ as a regulator of translation.
Probab=37.38 E-value=1.9e+02 Score=34.50 Aligned_cols=84 Identities=12% Similarity=0.171 Sum_probs=51.8
Q ss_pred EEEEEEecCceEEEccCCCCCCceEEEecccccCCCCCCcccccccCCCcccCCCeEEEecCCCCCceEEEEEEECC-EE
Q 000247 506 GLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVSEGPSKDRQGIVKKIYRG-IL 584 (1790)
Q Consensus 506 GVIVrVEkDEsfkVLdq~gD~~~VvtVk~~eI~~K~~~rr~vAtD~~gn~I~vGD~VKVIdGphkGRqG~VlHIyRs-~V 584 (1790)
|.||++.+ ..+.|++.+ .++..+++.... .....+-|||.|.+..- ...++.|.+|+.- -+
T Consensus 1 g~v~~~~~-~~~~v~~~~----~~~~~~~~g~~~-----------~~~~~~~vGD~V~~~~~--~~~~~~i~~i~~R~~~ 62 (287)
T cd01854 1 GRVIAVHG-GFYDVETEG----GELRCRARGKLR-----------KKGIKPVVGDWVEVEPD--DDGEGVIVRVLPRKNL 62 (287)
T ss_pred CEEEEEEC-CEEEEEECC----eEEEEEeccccc-----------cCCCCccCCCEEEEEec--CCCcEEEEEEECCCce
Confidence 57888888 488888753 355665543211 01456899999987532 2467999999854 34
Q ss_pred EEEeCcceeeccEEEEeCCceeec
Q 000247 585 FIYDENETENGGYFCSKSQHCEKT 608 (1790)
Q Consensus 585 FL~Sr~~tENgGIFVvRArnv~tv 608 (1790)
++.-..... .-+++.++..|++|
T Consensus 63 l~R~~~~~~-~~~i~anvD~vllV 85 (287)
T cd01854 63 LSRPAAGGR-EQVIAANVDQLVIV 85 (287)
T ss_pred EEccCCCCc-ceeEEEeCCEEEEE
Confidence 444332222 55677777666554
No 138
>PF10446 DUF2457: Protein of unknown function (DUF2457); InterPro: IPR018853 This entry represents a family of uncharacterised proteins.
Probab=37.36 E-value=14 Score=46.51 Aligned_cols=10 Identities=40% Similarity=0.551 Sum_probs=4.0
Q ss_pred ceEEEEEEEC
Q 000247 572 RQGIVKKIYR 581 (1790)
Q Consensus 572 RqG~VlHIyR 581 (1790)
||-.=...|+
T Consensus 399 RQrRKEKf~r 408 (458)
T PF10446_consen 399 RQRRKEKFWR 408 (458)
T ss_pred hhhhhHHHHH
Confidence 4433333333
No 139
>COG2139 RPL21A Ribosomal protein L21E [Translation, ribosomal structure and biogenesis]
Probab=36.87 E-value=58 Score=33.91 Aligned_cols=49 Identities=33% Similarity=0.551 Sum_probs=38.4
Q ss_pred ccCCCEEEEc------cC-C---CCCceeEEEEEeCCeEEEEe--cCcceEEEEecCcccc
Q 000247 660 FAVGQTLRIR------VG-P---LKGYLCRVLAVRYSDVTVKL--DSQQKILTVKGEHLAE 708 (1790)
Q Consensus 660 ~lIGKTVKIr------kG-P---YKGylGiVKDaTdt~ARVEL--HSk~KtITVdKe~Ls~ 708 (1790)
+-+|+.|.|. +| | |-|+.|+|+.+++.-.-||+ -.+.|+|.|-.+||.-
T Consensus 33 y~~Gd~V~I~IdpSv~kGmPh~rf~G~TG~Vvg~~g~ay~V~v~~G~k~K~liv~peHLk~ 93 (98)
T COG2139 33 YKVGDKVHIDIDPSVHKGMPHPRFQGKTGTVVGVRGRAYKVEVYDGNKEKTLIVRPEHLKP 93 (98)
T ss_pred ccCCCEEEEEeCcccccCCCCccccCcceEEEeccCCEEEEEEecCCceEEEEeCHHHccc
Confidence 4578888875 44 3 57899999999999877775 4566789999999874
No 140
>PRK00098 GTPase RsgA; Reviewed
Probab=36.49 E-value=2e+02 Score=34.37 Aligned_cols=86 Identities=13% Similarity=0.130 Sum_probs=53.5
Q ss_pred eEEEEEEecCceEEEccCCCCCCceEEEecccccCCCCCCcccccccCCCcccCCCeEEEecCCCCCceEEEEEEECCEE
Q 000247 505 FGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVSEGPSKDRQGIVKKIYRGIL 584 (1790)
Q Consensus 505 VGVIVrVEkDEsfkVLdq~gD~~~VvtVk~~eI~~K~~~rr~vAtD~~gn~I~vGD~VKVIdGphkGRqG~VlHIyRs~V 584 (1790)
.|.||++.+. .+.|++..+ .+++++++.. +. .....+-+||.|.|-. + ....|.|.+|+.-.-
T Consensus 2 ~g~v~~~~~~-~~~v~~~~~---~~~~~~~~g~---~~--------~~~~~~~vGD~V~~~~-~-~~~~g~i~~i~~R~~ 64 (298)
T PRK00098 2 EGLIIKALGG-FYYVESEDG---QVYQCRARGK---FR--------KKTNTPAVGDRVEFSA-E-NNDEGVILEIHERKN 64 (298)
T ss_pred eEEEEEEECC-EEEEEECCC---CEEEEEeccc---cc--------cCCCCcCCCCEEEEEE-C-CCCcEEEEEEeCCCc
Confidence 4899999984 888876432 3566665421 11 0235578999998842 1 235699999998877
Q ss_pred EEEeCcceeeccEEEEeCCceeec
Q 000247 585 FIYDENETENGGYFCSKSQHCEKT 608 (1790)
Q Consensus 585 FL~Sr~~tENgGIFVvRArnv~tv 608 (1790)
+|.-+.. ...-+++.++..|++|
T Consensus 65 ~l~R~~~-~~~q~iaaniD~vllV 87 (298)
T PRK00098 65 LLVRPPI-FKSKLIAANVDQAVLV 87 (298)
T ss_pred eEECCCC-ccccceeecCCEEEEE
Confidence 7766665 2234455555555444
No 141
>KOG4156 consensus Claspin, protein mediating phosphorylation and activation of Chk1 protein kinase in the DNA replication checkpoint response [Cell cycle control, cell division, chromosome partitioning; Signal transduction mechanisms]
Probab=36.04 E-value=8 Score=49.63 Aligned_cols=13 Identities=38% Similarity=0.690 Sum_probs=10.5
Q ss_pred CcceeccccCCCC
Q 000247 118 QFVEDAADVDYDD 130 (1790)
Q Consensus 118 ~FiDdEAEVDDDe 130 (1790)
.+|||||+|.-+|
T Consensus 1052 k~~eDEAevSGsD 1064 (1329)
T KOG4156|consen 1052 KYLEDEAEVSGSD 1064 (1329)
T ss_pred HhhcchhhcccCc
Confidence 5999999997444
No 142
>KOG0130 consensus RNA-binding protein RBM8/Tsunagi (RRM superfamily) [General function prediction only]
Probab=35.94 E-value=56 Score=35.99 Aligned_cols=61 Identities=20% Similarity=0.299 Sum_probs=48.3
Q ss_pred cEEEEEecCchhHHHHHHHHHHHHhhccCCCCCcEEEEEE---e--CCCCcEEEEEeccchhHHHHhcCCCC
Q 000247 226 TIWKVKCMAGRERQSAFCLMQKFVDLQSLGSKMQIISAFA---V--DHIKGFIFIEADKQCDINEACKGLSG 292 (1790)
Q Consensus 226 kLWaVKCK~GkEReVV~~LmrKii~lq~~g~~L~I~SVFv---p--d~lKGYIYVEA~kq~dVkeAIkGI~g 292 (1790)
.=|+|-|..=+|...-..|..+|.++.. |+-|-. + -.+|||-+||-........||..+.+
T Consensus 71 EGwIi~VtgvHeEatEedi~d~F~dyGe------iKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng 136 (170)
T KOG0130|consen 71 EGWIIFVTGVHEEATEEDIHDKFADYGE------IKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNG 136 (170)
T ss_pred eeEEEEEeccCcchhHHHHHHHHhhccc------ccceeeccccccccccceeeeehHhHHHHHHHHHhccc
Confidence 3688999888999999999999998862 222222 1 25899999999999999999988776
No 143
>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=35.88 E-value=90 Score=28.95 Aligned_cols=70 Identities=17% Similarity=0.130 Sum_probs=42.6
Q ss_pred EEEEEEeCCCCcEEEEEeccchhHHHHhcCCCCEEeceeccCCHHHHHHHhhcccccccccCCCEEEEecCcCCCCcEEE
Q 000247 260 IISAFAVDHIKGFIFIEADKQCDINEACKGLSGIYYSRLAPVPKNEVSHLLSAQIKRNEVSEGTWAYVKNGKYKGDLAQV 339 (1790)
Q Consensus 260 I~SVFvpd~lKGYIYVEA~kq~dVkeAIkGI~gVy~sK~~pVPikEM~dLLkvkkks~~Lk~GdwVRIKrGpYKGDLAQV 339 (1790)
|+...+....+-.||||.... ++ ..+||+.||.+-. .......|++|+.|++ +|
T Consensus 5 ~v~g~V~~i~~~g~~v~l~~~--------~~-------~g~i~~~~l~~~~-~~~~~~~~~~Gd~v~v----------~i 58 (77)
T cd05708 5 KIDGTVRRVEDYGVFIDIDGT--------NV-------SGLCHKSEISDNR-VADASKLFRVGDKVRA----------KV 58 (77)
T ss_pred EEEEEEEEEEcceEEEEECCC--------Ce-------EEEEEHHHCCCCc-cCCHhHeecCCCEEEE----------EE
Confidence 455555555677888887430 11 2344455543211 1111235788999987 49
Q ss_pred EEEeCCCCEEEEEEec
Q 000247 340 VYVNNARKRATVKLIP 355 (1790)
Q Consensus 340 ~eVDenk~kVtVKLVP 355 (1790)
..|+++..++.|.|-+
T Consensus 59 ~~vd~~~~~i~ls~k~ 74 (77)
T cd05708 59 LKIDAEKKRISLGLKA 74 (77)
T ss_pred EEEeCCCCEEEEEEEe
Confidence 9999998888888754
No 144
>PF11515 Cul7: Mouse development and cellular proliferation protein Cullin-7; InterPro: IPR021097 The CPH domain is found in the Cullin-7, PARC and HERC2 proteins, which are all components of known or predicted E3-ubiquitin ligases. The CPH domain is a protein-protein interaction module that binds the teramerisation domain of the tumour suppressor protein p53 []. Structurally it forms a beta-barrel fold similar to the SH3, Tudor and KOW and domains. Unlike the SH3 and Tudor domains, which bind to small peptides, the CPH domain appears to bind to an extended surface on p53.; PDB: 2JUF_A 2JNG_A.
Probab=35.84 E-value=56 Score=32.87 Aligned_cols=39 Identities=10% Similarity=0.156 Sum_probs=24.2
Q ss_pred HHHHHHhhcccccccccCCCEEEEec---CcCCCCcEEEEEEeCCCC
Q 000247 304 NEVSHLLSAQIKRNEVSEGTWAYVKN---GKYKGDLAQVVYVNNARK 347 (1790)
Q Consensus 304 kEM~dLLkvkkks~~Lk~GdwVRIKr---GpYKGDLAQV~eVDenk~ 347 (1790)
.|...+++ ..|.||+.||+.+ -..+||+++|..++.++.
T Consensus 8 d~Ya~YVr-----~~i~~GM~VRc~~~yeeV~~GD~G~V~k~~~dg~ 49 (78)
T PF11515_consen 8 DDYAEYVR-----DNIQPGMRVRCCRDYEEVRAGDEGEVFKQDRDGL 49 (78)
T ss_dssp HHHHHHHH-----HH--TT-EEEESS-BTTB-TT-EEE-EEEE-TTS
T ss_pred hHHHHHHH-----HhCCCCcEEEEecccccccccccceeEeeccCCC
Confidence 44445553 3689999999997 479999999999988764
No 145
>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=35.37 E-value=67 Score=30.96 Aligned_cols=40 Identities=13% Similarity=0.319 Sum_probs=27.5
Q ss_pred ccCCCEEEEecC--cCCCCcEEEEEEeCCCCE--EEEEEeccCch
Q 000247 319 VSEGTWAYVKNG--KYKGDLAQVVYVNNARKR--ATVKLIPRIDL 359 (1790)
Q Consensus 319 Lk~GdwVRIKrG--pYKGDLAQV~eVDenk~k--VtVKLVPRIDy 359 (1790)
++.|+.|||+|- -+=.|++.|..||...-+ |+|++ -.++|
T Consensus 1 i~rgskVrIlR~ESYWyn~vGtV~svdqs~i~YPV~VRF-~kvNY 44 (61)
T PF02427_consen 1 IKRGSKVRILRKESYWYNEVGTVASVDQSGIRYPVVVRF-DKVNY 44 (61)
T ss_dssp S-TTSEEEE-SSSSTTTTSEEEEEEETTSSSSSSEEEE--SSS-S
T ss_pred CCCCCEEEEccccceeecccceEEEEccCCccccEEEEE-EEecc
Confidence 467999999996 467999999999998743 55543 34455
No 146
>PLN00045 photosystem I reaction center subunit IV; Provisional
Probab=35.31 E-value=63 Score=33.53 Aligned_cols=45 Identities=13% Similarity=0.195 Sum_probs=33.1
Q ss_pred ccccccCCCEEEEecC--cCCCCcEEEEEEeCC-CC--EEEEEEeccCchh
Q 000247 315 KRNEVSEGTWAYVKNG--KYKGDLAQVVYVNNA-RK--RATVKLIPRIDLQ 360 (1790)
Q Consensus 315 ks~~Lk~GdwVRIKrG--pYKGDLAQV~eVDen-k~--kVtVKLVPRIDy~ 360 (1790)
+.+.++.|+.|||+|- -+=+|++.|+.||.. +- -|+|++ -.++|.
T Consensus 36 p~ig~~RGskVrIlR~ESYWyn~vGtVvsVDq~~girYPVvVRF-~kvNY~ 85 (101)
T PLN00045 36 PPIGPKRGSKVKILRPESYWFNDVGKVVAVDQDPGVRYPVVVRF-EKVNYA 85 (101)
T ss_pred CCcccCCCCEEEEccccceeecCcceEEEEeCCCCcccceEEEe-eeeecc
Confidence 4567899999999996 467899999999987 32 255553 344553
No 147
>PF13893 RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); PDB: 2PE8_A 2PEH_A 2D9O_A 1A9N_D 2DIT_A 3S6E_A 2LQ5_A 1SJQ_A 2AD9_A 1X4D_A ....
Probab=35.26 E-value=50 Score=29.31 Aligned_cols=36 Identities=22% Similarity=0.315 Sum_probs=29.1
Q ss_pred cEEEEEEeCCCCcEEEEEeccchhHHHHhcCCCCEE
Q 000247 259 QIISAFAVDHIKGFIFIEADKQCDINEACKGLSGIY 294 (1790)
Q Consensus 259 ~I~SVFvpd~lKGYIYVEA~kq~dVkeAIkGI~gVy 294 (1790)
.|..|.+.+.-++++|||....++...|++.|.+..
T Consensus 10 ~V~~i~~~~~~~~~a~V~f~~~~~A~~a~~~l~~~~ 45 (56)
T PF13893_consen 10 EVKKIKIFKKKRGFAFVEFASVEDAQKAIEQLNGRQ 45 (56)
T ss_dssp -EEEEEEETTSTTEEEEEESSHHHHHHHHHHHTTSE
T ss_pred cEEEEEEEeCCCCEEEEEECCHHHHHHHHHHhCCCE
Confidence 478888776558999999999999999998776643
No 148
>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=34.84 E-value=1.6e+02 Score=43.85 Aligned_cols=94 Identities=11% Similarity=0.100 Sum_probs=62.0
Q ss_pred cccccCcEEEecC-----CceEEEEEEecCceEEEc-cCCCCCCceEEEecccccCCCCCCcccccccCCCcccCCCeEE
Q 000247 490 NSFELYELVCFGR-----KDFGLIVGMEKDDHYKIL-KEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTAR 563 (1790)
Q Consensus 490 G~FeLgDLVQLD~-----~TVGVIVrVEkDEsfkVL-dq~gD~~~VvtVk~~eI~~K~~~rr~vAtD~~gn~I~vGD~VK 563 (1790)
..|.+||.|+... ...++|+.|++++...+| +.. ++.+++.|.++..+. ..+..--...-+|.+||.|+
T Consensus 680 ~~Yr~Gdvv~~y~~~~~~~~~y~V~~V~~~~n~L~l~~~d---G~~~~~~p~~l~~~~--~~~svy~~~~l~ia~Gdrl~ 754 (1960)
T TIGR02760 680 AHYKQGMVIRFWQKGKIPHDDYVVTNVNKHNNTLTLKDAQ---GKTQKFKPSSLKDLE--RPFSVYRPEQLEVAAGERLQ 754 (1960)
T ss_pred hhcCCCCEEEeecccCccCCcEEEEEEeCCCCEEEEEcCC---CCEEEECHHHhcccc--cceeeeccccccccCCCEEE
Confidence 5899999999742 334799999985444444 433 357889988774321 12333445566888999998
Q ss_pred EecCC-----CCCceEEEEEEECCEEEEEe
Q 000247 564 VSEGP-----SKDRQGIVKKIYRGILFIYD 588 (1790)
Q Consensus 564 VIdGp-----hkGRqG~VlHIyRs~VFL~S 588 (1790)
+..-. ..|...+|..|....+.|..
T Consensus 755 ~trn~~~~gl~ng~~~tV~~i~~~~i~l~~ 784 (1960)
T TIGR02760 755 VTGNHFHSRVRNGELLTVSSINNEGITLIT 784 (1960)
T ss_pred EccCCcccCccCCCEEEEEEEcCCeEEEEe
Confidence 87543 24578888888776555544
No 149
>PTZ00223 40S ribosomal protein S4; Provisional
Probab=34.26 E-value=47 Score=39.90 Aligned_cols=52 Identities=19% Similarity=0.199 Sum_probs=40.0
Q ss_pred CcccCCCeEEEecCCCCCceEEEEEEECC-----EEEEEeCcceeeccEEEEeCCceeecc
Q 000247 554 KVISLNDTARVSEGPSKDRQGIVKKIYRG-----ILFIYDENETENGGYFCSKSQHCEKTK 609 (1790)
Q Consensus 554 n~I~vGD~VKVIdGphkGRqG~VlHIyRs-----~VFL~Sr~~tENgGIFVvRArnv~tv~ 609 (1790)
-.|.+|.+|-|+.|.|.|+.|+|.+|.+. +|.|.+ .++--|-++..+|..++
T Consensus 170 ikfe~G~l~~vtgG~n~GriG~I~~i~~~~~~~~iv~i~d----~~g~~F~T~~~~VfvIG 226 (273)
T PTZ00223 170 IKNRNGKVVMVTGGANRGRIGEIVSIERHPGAFDIARLKD----ASGHEFATRAANIFVIG 226 (273)
T ss_pred EecCCCCEEEEECCeeceeEEEEEEEEecCCCCCEEEEEe----CCCCeEEEEeeeEEEEe
Confidence 35789999999999999999999999543 233332 23336999999999885
No 150
>PLN00036 40S ribosomal protein S4; Provisional
Probab=34.14 E-value=61 Score=38.75 Aligned_cols=52 Identities=17% Similarity=0.302 Sum_probs=40.2
Q ss_pred CcccCCCeEEEecCCCCCceEEEEEEECC-----EEEEEeCcceeeccEEEEeCCceeecc
Q 000247 554 KVISLNDTARVSEGPSKDRQGIVKKIYRG-----ILFIYDENETENGGYFCSKSQHCEKTK 609 (1790)
Q Consensus 554 n~I~vGD~VKVIdGphkGRqG~VlHIyRs-----~VFL~Sr~~tENgGIFVvRArnv~tv~ 609 (1790)
-.|.+|.+|-|+.|.|.||.|+|.+|.+. +|.|.+ .++--|-++..+|..++
T Consensus 173 ikfe~G~l~~vtgG~n~GrvG~I~~i~~~~~~~~iV~i~d----~~g~~F~T~~~~vfvIG 229 (261)
T PLN00036 173 IKFDVGNLVMVTGGRNRGRVGVIKNREKHKGSFEIIHVKD----ATGHEFATRLGNVFVIG 229 (261)
T ss_pred EecCCCCEEEEECCeeceeEEEEEEEEecCCCCCEEEEEe----CCCCeEEEEeeeEEEEc
Confidence 35789999999999999999999999842 233322 23447999999999875
No 151
>COG1471 RPS4A Ribosomal protein S4E [Translation, ribosomal structure and biogenesis]
Probab=34.01 E-value=50 Score=38.88 Aligned_cols=52 Identities=17% Similarity=0.143 Sum_probs=40.0
Q ss_pred CcccCCCeEEEecCCCCCceEEEEEEECC------EEEEEeCcceeeccEEEEeCCceeecc
Q 000247 554 KVISLNDTARVSEGPSKDRQGIVKKIYRG------ILFIYDENETENGGYFCSKSQHCEKTK 609 (1790)
Q Consensus 554 n~I~vGD~VKVIdGphkGRqG~VlHIyRs------~VFL~Sr~~tENgGIFVvRArnv~tv~ 609 (1790)
-.|.+|-.|-|+.|.|.|+.|+|++|... +|.|-+ +++--|.|...+|.+++
T Consensus 172 i~fe~g~~~~vtgG~h~G~~G~I~~I~~~~~~~~~~v~~e~----~~g~~F~T~~~yVfvIG 229 (241)
T COG1471 172 IKFEEGALVYVTGGRHVGRVGTIVEIEIQESSKPNLVTVED----EEGNTFQTIKDYVFVIG 229 (241)
T ss_pred eccCCCcEEEEECCccccceEEEEEEEEecCCCccEEEEec----CCCCceEEeeeEEEEEc
Confidence 35788999999999999999999999754 233322 22336999999999885
No 152
>PF04050 Upf2: Up-frameshift suppressor 2 ; InterPro: IPR007193 This entry represents Up-frameshift suppressor 2 (also known as Nonsense-mediated mRNA decay protein 2). Transcripts harbouring premature signals for translation termination are recognised and rapidly degraded by eukaryotic cells through a pathway known as nonsense-mediated mRNA decay. In Saccharomyces cerevisiae, three trans-acting factors (Upf1 to Upf3) are required for nonsense-mediated mRNA decay [].; PDB: 2WJV_D.
Probab=33.99 E-value=2.6 Score=46.43 Aligned_cols=13 Identities=54% Similarity=0.818 Sum_probs=8.1
Q ss_pred HHHHHHHHHHHhc
Q 000247 183 EEEFDKMMEERYK 195 (1790)
Q Consensus 183 aEelAe~LkERY~ 195 (1790)
+.+|+++|.+=|.
T Consensus 66 eref~kmm~eS~~ 78 (170)
T PF04050_consen 66 EREFQKMMAESLE 78 (170)
T ss_dssp HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHH
Confidence 4466667766664
No 153
>PRK14640 hypothetical protein; Provisional
Probab=33.19 E-value=65 Score=35.43 Aligned_cols=46 Identities=17% Similarity=0.122 Sum_probs=35.3
Q ss_pred ccCCCEEEEcc-CC---CCCceeEEEEEeCCeEEEEecCcceEEEEecCccc
Q 000247 660 FAVGQTLRIRV-GP---LKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLA 707 (1790)
Q Consensus 660 ~lIGKTVKIrk-GP---YKGylGiVKDaTdt~ARVELHSk~KtITVdKe~Ls 707 (1790)
.++|+.|+|+- -| .|=+.|++++++++.+++++. .+++.|+.+.|.
T Consensus 94 r~~G~~v~V~l~~~~~~~k~~~G~L~~v~~~~v~l~~~--~~~~~i~~~~I~ 143 (152)
T PRK14640 94 KYVGQEAAVTLRMATNNRRKFKGVIKAVQGDMITLTVD--GKDEVLAFTNIQ 143 (152)
T ss_pred HhCCCeEEEEEecccCCceEEEEEEEEEeCCEEEEEEC--CeEEEEEhHHee
Confidence 47999999974 33 366799999999999998875 556677666665
No 154
>PTZ00118 40S ribosomal protein S4; Provisional
Probab=32.74 E-value=65 Score=38.56 Aligned_cols=52 Identities=12% Similarity=0.218 Sum_probs=39.9
Q ss_pred CcccCCCeEEEecCCCCCceEEEEEEECC-----EEEEEeCcceeeccEEEEeCCceeecc
Q 000247 554 KVISLNDTARVSEGPSKDRQGIVKKIYRG-----ILFIYDENETENGGYFCSKSQHCEKTK 609 (1790)
Q Consensus 554 n~I~vGD~VKVIdGphkGRqG~VlHIyRs-----~VFL~Sr~~tENgGIFVvRArnv~tv~ 609 (1790)
-.|.+|.+|-|+.|.|.|+.|+|+++.+. +|.|.+ .++--|-++..+|..++
T Consensus 173 ikfe~G~l~~vtgG~n~GriG~I~~~~~~~~~~~~V~i~d----~~g~~F~T~~~~vfvIG 229 (262)
T PTZ00118 173 LKFEVGNLVMITGGHNVGRVGTIVSKEKHPGSFDLIHVKD----SRGKTFATRLSNVFVIG 229 (262)
T ss_pred EecCCCCEEEEECCeeceeEEEEEEEEecCCCCcEEEEEe----CCCCeEEEEeeeEEEEc
Confidence 35789999999999999999999997653 232222 23447999999999874
No 155
>KOG3130 consensus Uncharacterized conserved protein [Function unknown]
Probab=32.26 E-value=50 Score=41.30 Aligned_cols=11 Identities=27% Similarity=0.809 Sum_probs=7.6
Q ss_pred CCCCCCCc-EEE
Q 000247 219 MPCPEDPT-IWK 229 (1790)
Q Consensus 219 LPSVkDPk-LWa 229 (1790)
||+|+.|. ||+
T Consensus 358 lp~i~~p~d~y~ 369 (514)
T KOG3130|consen 358 LPTIRTPADIYR 369 (514)
T ss_pred CCccCCcchhhh
Confidence 79988666 443
No 156
>PRK14712 conjugal transfer nickase/helicase TraI; Provisional
Probab=32.05 E-value=2e+02 Score=42.24 Aligned_cols=92 Identities=9% Similarity=0.055 Sum_probs=66.6
Q ss_pred cccccCcEEE-ecCC----ceEEEEEEecCceEEEc-cCCCCCCceEEEecccccCCCCCCcccccccCCCcccCCCeEE
Q 000247 490 NSFELYELVC-FGRK----DFGLIVGMEKDDHYKIL-KEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTAR 563 (1790)
Q Consensus 490 G~FeLgDLVQ-LD~~----TVGVIVrVEkDEsfkVL-dq~gD~~~VvtVk~~eI~~K~~~rr~vAtD~~gn~I~vGD~VK 563 (1790)
..|+.|+.|+ .+.. ..=+|+.|+++.+..+| +.. ++.+++.|+.+. .++.+.....-+|..||.|+
T Consensus 515 ~~Y~~GmVl~~~~r~~k~~~~y~V~~V~~~~n~LtL~~~d---G~~~~~~p~~~~-----~~~~vy~~e~lelA~GDrlr 586 (1623)
T PRK14712 515 DMYRPGMVMEQWNPETRSHDRYVTERVTAQSHSLTLRNAQ---GETQVVRISSLD-----SSWSLFRPEKMPVADGERLR 586 (1623)
T ss_pred hcCCCCCEEEecccCcCcCceEEEEEEcCCCceEEEEcCC---CcEEEechHHcc-----cceeeecccccccCCCCEEE
Confidence 6899999997 6542 22399999986555555 444 357889987653 23556666778999999999
Q ss_pred EecCCC-----CCceEEEEEEECCEEEEEeC
Q 000247 564 VSEGPS-----KDRQGIVKKIYRGILFIYDE 589 (1790)
Q Consensus 564 VIdGph-----kGRqG~VlHIyRs~VFL~Sr 589 (1790)
+....+ .|...+|++|..+.+.|..+
T Consensus 587 ~t~nd~~~~L~ngd~~tV~~i~~~~itl~~~ 617 (1623)
T PRK14712 587 VTGKIPGLRVSGGDRLQVASVSEDAMTVVVP 617 (1623)
T ss_pred EccCCcccCccCCCEEEEEEecCCeEEEEEC
Confidence 987643 45788999999887776654
No 157
>PRK08059 general stress protein 13; Validated
Probab=31.78 E-value=2.7e+02 Score=29.44 Aligned_cols=58 Identities=19% Similarity=0.324 Sum_probs=35.4
Q ss_pred ccccCcEEEecCCceEEEEEEecCceEEEccCCCCCCceEEEecccccCCCCCCcccccccCCCcccCCCeEEEe
Q 000247 491 SFELYELVCFGRKDFGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVS 565 (1790)
Q Consensus 491 ~FeLgDLVQLD~~TVGVIVrVEkDEsfkVLdq~gD~~~VvtVk~~eI~~K~~~rr~vAtD~~gn~I~vGD~VKVI 565 (1790)
.|.+++.|. |+|++|.+.-.|+.|...- .-.|..++|.... + ......|++||+|+|.
T Consensus 4 ~~k~G~iv~------G~V~~i~~~G~fV~i~~~~----~Gli~~sel~~~~-----~--~~~~~~~~vGD~I~vk 61 (123)
T PRK08059 4 QYEVGSVVT------GKVTGIQPYGAFVALDEET----QGLVHISEITHGF-----V--KDIHDFLSVGDEVKVK 61 (123)
T ss_pred cCCCCCEEE------EEEEEEecceEEEEECCCC----EEEEEHHHCCccc-----c--cCHHHcCCCCCEEEEE
Confidence 577888875 8899988865666665331 2233445553321 1 1124578999999984
No 158
>PRK13709 conjugal transfer nickase/helicase TraI; Provisional
Probab=31.61 E-value=1.9e+02 Score=42.63 Aligned_cols=92 Identities=11% Similarity=0.023 Sum_probs=65.1
Q ss_pred ccccccCcEEEecC-----CceEEEEEEecCceEEEc-cCCCCCCceEEEecccccCCCCCCcccccccCCCcccCCCeE
Q 000247 489 ENSFELYELVCFGR-----KDFGLIVGMEKDDHYKIL-KEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTA 562 (1790)
Q Consensus 489 lG~FeLgDLVQLD~-----~TVGVIVrVEkDEsfkVL-dq~gD~~~VvtVk~~eI~~K~~~rr~vAtD~~gn~I~vGD~V 562 (1790)
...|+.||+|+.-. ...-+|+.|+.+....+| +..+ ..++++|..+. .++.+-....-+|.+||.|
T Consensus 646 a~~Y~~G~vi~~~~~~~~~~~~y~V~~v~~~~n~LtL~~~~G---~~~~~~p~~~~-----~~~~vy~~~~ieiA~GDrL 717 (1747)
T PRK13709 646 RDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQG---ETQVVKISSLD-----SSWSLFRPEKMPVADGERL 717 (1747)
T ss_pred hhcCCCCcEEEeeccccccCccEEEEEEcCCCCEEEEEcCCC---CEEEeChHHhc-----ccceeccccccccCCCCEE
Confidence 45899999999732 234599999885444334 4443 57788887653 2244555667899999999
Q ss_pred EEecCC-----CCCceEEEEEEECCEEEEEe
Q 000247 563 RVSEGP-----SKDRQGIVKKIYRGILFIYD 588 (1790)
Q Consensus 563 KVIdGp-----hkGRqG~VlHIyRs~VFL~S 588 (1790)
++.... ..|...+|+.|..+.|.|..
T Consensus 718 r~T~nd~~~~l~Ngd~~tV~~i~~~~i~l~~ 748 (1747)
T PRK13709 718 RVLGKIPGLRLKGGDRLQVTSVSEDGLTVVV 748 (1747)
T ss_pred EEccCCcccCccCCCEEEEEEecCCeEEEEE
Confidence 998654 24678999999998887775
No 159
>PRK14630 hypothetical protein; Provisional
Probab=31.43 E-value=86 Score=34.31 Aligned_cols=45 Identities=13% Similarity=0.169 Sum_probs=35.4
Q ss_pred ccCCCEEEEccC-CCCCceeEEEEEeCCeEEEEecCcceEEEEecCcccc
Q 000247 660 FAVGQTLRIRVG-PLKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLAE 708 (1790)
Q Consensus 660 ~lIGKTVKIrkG-PYKGylGiVKDaTdt~ARVELHSk~KtITVdKe~Ls~ 708 (1790)
.++|+.|+|+-. |. +.|+++++.++.++++++ .+++.|+.+.|.-
T Consensus 94 r~~G~~v~V~l~~~~--~~G~L~~~~d~~i~l~~~--~~~~~i~~~~I~k 139 (143)
T PRK14630 94 IFEGKKIKLMLDNDF--EEGFILEAKADSFIFKTD--SKEVNVLYSDVKK 139 (143)
T ss_pred HhCCCEEEEEEcCcc--eEEEEEEEeCCEEEEEEC--CEEEEEEhHhcce
Confidence 479999999753 33 489999999999998864 5678888777763
No 160
>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=31.17 E-value=1.7e+02 Score=27.12 Aligned_cols=67 Identities=16% Similarity=0.149 Sum_probs=39.7
Q ss_pred EEEEEEeCCCCcEEEEEeccchhHHHHhcCCCCEEeceeccCCHHHHHHHhhcccccccccCCCEEEEecCcCCCCcEEE
Q 000247 260 IISAFAVDHIKGFIFIEADKQCDINEACKGLSGIYYSRLAPVPKNEVSHLLSAQIKRNEVSEGTWAYVKNGKYKGDLAQV 339 (1790)
Q Consensus 260 I~SVFvpd~lKGYIYVEA~kq~dVkeAIkGI~gVy~sK~~pVPikEM~dLLkvkkks~~Lk~GdwVRIKrGpYKGDLAQV 339 (1790)
|+...+....+-++||+.... ....||+.|+..-. +......|++|+.|+++ |
T Consensus 3 iv~g~V~~i~~~~~~v~l~~~----------------~~g~l~~~e~~~~~-~~~~~~~~~~Gd~i~~~----------i 55 (70)
T cd05687 3 IVKGTVVSVDDDEVLVDIGYK----------------SEGIIPISEFSDDP-IENGEDEVKVGDEVEVY----------V 55 (70)
T ss_pred EEEEEEEEEeCCEEEEEeCCC----------------ceEEEEHHHhCccc-cCCHhHcCCCCCEEEEE----------E
Confidence 444445445556888887431 13355666664321 11112347899998865 8
Q ss_pred EEEeCCCCEEEEEE
Q 000247 340 VYVNNARKRATVKL 353 (1790)
Q Consensus 340 ~eVDenk~kVtVKL 353 (1790)
+.+++...++.|.+
T Consensus 56 ~~~~~~~~~i~lS~ 69 (70)
T cd05687 56 LRVEDEEGNVVLSK 69 (70)
T ss_pred EEEECCCCeEEEEe
Confidence 88887777777654
No 161
>PRK14645 hypothetical protein; Provisional
Probab=31.14 E-value=66 Score=35.59 Aligned_cols=45 Identities=18% Similarity=0.124 Sum_probs=36.7
Q ss_pred ccCCCEEEEccCCCCCceeEEEEEeCCeEEEEecCcceEEEEecCccc
Q 000247 660 FAVGQTLRIRVGPLKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLA 707 (1790)
Q Consensus 660 ~lIGKTVKIrkGPYKGylGiVKDaTdt~ARVELHSk~KtITVdKe~Ls 707 (1790)
..+|+.|+|+.+ .|=+.|+++++++..++|++ ..+++.|+.+.|.
T Consensus 99 r~~G~~v~v~~~-~k~~~G~L~~~~d~~i~l~~--~~~~~~i~~~~I~ 143 (154)
T PRK14645 99 RFAGLKAKVRGP-GENFTGRIKAVSGDQVTFDV--GGEDRTLRIGTFQ 143 (154)
T ss_pred HhCCCEEEEEcC-CeEEEEEEEEEeCCEEEEEE--CCeEEEEEHHHhh
Confidence 478999999864 47788999999999999776 4677888877775
No 162
>cd05688 S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 3 (ec3) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=31.04 E-value=88 Score=28.16 Aligned_cols=64 Identities=14% Similarity=0.153 Sum_probs=37.1
Q ss_pred EEEEEEeCCCCcEEEEEeccchhHHHHhcCCCCEEeceeccCCHHHHHHHhhcccccccccCCCEEEEecCcCCCCcEEE
Q 000247 260 IISAFAVDHIKGFIFIEADKQCDINEACKGLSGIYYSRLAPVPKNEVSHLLSAQIKRNEVSEGTWAYVKNGKYKGDLAQV 339 (1790)
Q Consensus 260 I~SVFvpd~lKGYIYVEA~kq~dVkeAIkGI~gVy~sK~~pVPikEM~dLLkvkkks~~Lk~GdwVRIKrGpYKGDLAQV 339 (1790)
|+.+.+-...+..|||+... ++ .+||+.|+.. ..+......|++|+.|++ +|
T Consensus 4 ~~~g~V~~v~~~g~~v~l~~-------~~----------g~l~~~e~~~-~~~~~~~~~~~~Gd~v~v----------~i 55 (68)
T cd05688 4 VVEGTVKSITDFGAFVDLGG-------VD----------GLLHISDMSW-GRVKHPSEVVNVGDEVEV----------KV 55 (68)
T ss_pred EEEEEEEEEEeeeEEEEECC-------eE----------EEEEhHHCCC-ccccCHhHEECCCCEEEE----------EE
Confidence 44444444455678887631 11 2445555541 112222235789999997 48
Q ss_pred EEEeCCCCEEEE
Q 000247 340 VYVNNARKRATV 351 (1790)
Q Consensus 340 ~eVDenk~kVtV 351 (1790)
++|+..+.++.|
T Consensus 56 ~~vd~~~~~i~l 67 (68)
T cd05688 56 LKIDKERKRISL 67 (68)
T ss_pred EEEECCCCEEec
Confidence 899888777764
No 163
>PRK11634 ATP-dependent RNA helicase DeaD; Provisional
Probab=30.89 E-value=77 Score=41.83 Aligned_cols=11 Identities=9% Similarity=0.045 Sum_probs=6.4
Q ss_pred CCHHHHHHHhh
Q 000247 301 VPKNEVSHLLS 311 (1790)
Q Consensus 301 VPikEM~dLLk 311 (1790)
++.++...+|.
T Consensus 279 ~~q~~R~~il~ 289 (629)
T PRK11634 279 MNQALREQTLE 289 (629)
T ss_pred CCHHHHHHHHH
Confidence 45566666664
No 164
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=30.78 E-value=1.6e+02 Score=33.87 Aligned_cols=42 Identities=12% Similarity=0.225 Sum_probs=32.1
Q ss_pred CCcccCCCeEEEecCCCCCceEEEEEEECCEEEEEeCcceeeccEEEEeCCceee
Q 000247 553 MKVISLNDTARVSEGPSKDRQGIVKKIYRGILFIYDENETENGGYFCSKSQHCEK 607 (1790)
Q Consensus 553 gn~I~vGD~VKVIdGphkGRqG~VlHIyRs~VFL~Sr~~tENgGIFVvRArnv~t 607 (1790)
...|++||+|| +.|+.+. ..++|.... ...||+-++|.+|-.
T Consensus 116 ~d~f~~GDivr----------A~Vis~~-~~~~Lst~~--~dlGVI~A~CsrC~~ 157 (188)
T COG1096 116 SDAFRIGDIVR----------ARVISTG-DPIQLSTKG--NDLGVIYARCSRCRA 157 (188)
T ss_pred ccccccccEEE----------EEEEecC-CCeEEEecC--CcceEEEEEccCCCc
Confidence 37899999998 5677777 556666555 567999999888863
No 165
>PRK04313 30S ribosomal protein S4e; Validated
Probab=30.67 E-value=56 Score=38.61 Aligned_cols=52 Identities=17% Similarity=0.135 Sum_probs=39.8
Q ss_pred CcccCCCeEEEecCCCCCceEEEEEEECC------EEEEEeCcceeeccEEEEeCCceeecc
Q 000247 554 KVISLNDTARVSEGPSKDRQGIVKKIYRG------ILFIYDENETENGGYFCSKSQHCEKTK 609 (1790)
Q Consensus 554 n~I~vGD~VKVIdGphkGRqG~VlHIyRs------~VFL~Sr~~tENgGIFVvRArnv~tv~ 609 (1790)
-.|.+|.+|-|+.|.|.||.|+|++|.+. +|.|.+ .++--|-++..+|..++
T Consensus 170 i~fe~G~l~~itgG~n~GriG~I~~i~~~~~~~~~~V~i~d----~~G~~F~T~~~~vfvIG 227 (237)
T PRK04313 170 IPFEEGNLAIITGGKHVGEIGKIKEIEVTKSSKPNIVTLED----KDGEKFETILDYVFVIG 227 (237)
T ss_pred EecCCCCEEEEECCeeeeeEEEEEEEEEccCCCCcEEEEEc----CCCCEEEEEeeeEEEEc
Confidence 35789999999999999999999999643 344431 22334999999999874
No 166
>PRK13709 conjugal transfer nickase/helicase TraI; Provisional
Probab=30.48 E-value=2.1e+02 Score=42.24 Aligned_cols=94 Identities=15% Similarity=0.153 Sum_probs=64.1
Q ss_pred cccccc--CcEEEecCCceEEEEEEecCceEEEccCCCCCCceEEEecccccCCCCCCcccccccCCCcccCCCeEEEec
Q 000247 489 ENSFEL--YELVCFGRKDFGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVSE 566 (1790)
Q Consensus 489 lG~FeL--gDLVQLD~~TVGVIVrVEkDEsfkVLdq~gD~~~VvtVk~~eI~~K~~~rr~vAtD~~gn~I~vGD~VKVId 566 (1790)
...|+. ||+|++. .+.-.|+.|+++....+|.... ++.+.+.|.++. ..++.+-.....+|.+||.|+...
T Consensus 1273 ~~~Y~~~~G~vv~~~-~~y~~V~~vd~~~~~ltl~~~~--G~~~~~~P~~~~----~~~~~vy~~~~~ela~GDrIr~Tr 1345 (1747)
T PRK13709 1273 LSTWEAHRGALALVD-NVYHRIAGIDKDDGLITLRDAE--GNTRLISPREAV----AEGVTLYTPDTIRVGTGDRMRFTK 1345 (1747)
T ss_pred hhhcccCCCcEEEec-CceEEEEEEcCCCCEEEEEcCC--CCEEEeChhhcc----cccccccccccccccCCCEEEEcc
Confidence 457888 8999885 4566789998876655554321 457788886542 223455566678999999999875
Q ss_pred C-----CCCCceEEEEEEECCEEEEEeC
Q 000247 567 G-----PSKDRQGIVKKIYRGILFIYDE 589 (1790)
Q Consensus 567 G-----phkGRqG~VlHIyRs~VFL~Sr 589 (1790)
- -..|..++|+.|..+-|.|.+.
T Consensus 1346 nDk~~G~~Ng~~~tV~~I~~~~I~l~~~ 1373 (1747)
T PRK13709 1346 SDRERGYVANSVWTVTAVSGDSVTLSDG 1373 (1747)
T ss_pred cCcccccccCCEEEEEEEcCCeEEEEcC
Confidence 4 3356778999998776555543
No 167
>PRK11642 exoribonuclease R; Provisional
Probab=30.45 E-value=1.3e+02 Score=41.05 Aligned_cols=81 Identities=16% Similarity=0.105 Sum_probs=46.0
Q ss_pred cEEEEEEeCCCCcEEEEEeccchhHHHHhcCCCCEEeceeccCCHHHHHHHhhcccccccccCCCEEEEecCcCCCCcEE
Q 000247 259 QIISAFAVDHIKGFIFIEADKQCDINEACKGLSGIYYSRLAPVPKNEVSHLLSAQIKRNEVSEGTWAYVKNGKYKGDLAQ 338 (1790)
Q Consensus 259 ~I~SVFvpd~lKGYIYVEA~kq~dVkeAIkGI~gVy~sK~~pVPikEM~dLLkvkkks~~Lk~GdwVRIKrGpYKGDLAQ 338 (1790)
.++...+....+--||||.... .|+|+.+|..-.---....|....|.-......|++|+.|+|+
T Consensus 645 e~f~G~Is~V~~fGifVeL~~~-----~vEGlV~vs~L~~d~y~~d~~~~~L~g~~~~~~~~lGD~V~Vk---------- 709 (813)
T PRK11642 645 NVFKGVISSVTGFGFFVRLDDL-----FIDGLVHVSSLDNDYYRFDQVGQRLIGESSGQTYRLGDRVEVR---------- 709 (813)
T ss_pred cEEEEEEEEeecCceEEEECCC-----CeeeeEEEeecCCcceEecchheEEecccCCcEECCCCEEEEE----------
Confidence 4566666555555588887432 1444444321100000123333334322223468889999974
Q ss_pred EEEEeCCCCEEEEEEe
Q 000247 339 VVYVNNARKRATVKLI 354 (1790)
Q Consensus 339 V~eVDenk~kVtVKLV 354 (1790)
|+.|+..+.+|.+.|+
T Consensus 710 V~~vD~~~rkI~f~l~ 725 (813)
T PRK11642 710 VEAVNMDERKIDFSLI 725 (813)
T ss_pred EEEeecCCCeEEEEEe
Confidence 8999999999999987
No 168
>PRK10486 autoinducer-2 (AI-2) modifying protein LsrG; Provisional
Probab=30.35 E-value=2.5e+02 Score=28.26 Aligned_cols=65 Identities=9% Similarity=-0.056 Sum_probs=42.6
Q ss_pred EEEEEecCchhHHHHHHHHHHHHhhccCCCCCcEEEEEEeCCCCc-EEEEEeccchhHHHHhcCCCC
Q 000247 227 IWKVKCMAGRERQSAFCLMQKFVDLQSLGSKMQIISAFAVDHIKG-FIFIEADKQCDINEACKGLSG 292 (1790)
Q Consensus 227 LWaVKCK~GkEReVV~~LmrKii~lq~~g~~L~I~SVFvpd~lKG-YIYVEA~kq~dVkeAIkGI~g 292 (1790)
|-.+++++|++.+++..|..-+ ..-+....+-.+.++....-|+ |++||.....+..++=...++
T Consensus 5 ia~~~~kpg~~~~~~~~l~~~~-~~sr~EpGcl~y~~~~~~~~p~~~~~~E~w~d~~Al~~H~~tph 70 (96)
T PRK10486 5 LVEINVKEDKVDEFIEVFRQNH-LGSIQEPGNLRFDVLQDPEVPTRFYIYEAYKDEAAVAFHKTTPH 70 (96)
T ss_pred EEEEEECcchHHHHHHHHHHHH-HHHhCCCCceEEEEEeCCCCCCEEEEEEEeCCHHHHHHHhcCHH
Confidence 5567899999888877655444 4333444455667776655565 888899877665555544444
No 169
>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=29.87 E-value=17 Score=35.98 Aligned_cols=44 Identities=16% Similarity=0.212 Sum_probs=0.0
Q ss_pred ccCCCEEEEccCCCCCceeEEEEEeCCeEEEEecCcceEEEEecCcccc
Q 000247 660 FAVGQTLRIRVGPLKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLAE 708 (1790)
Q Consensus 660 ~lIGKTVKIrkGPYKGylGiVKDaTdt~ARVELHSk~KtITVdKe~Ls~ 708 (1790)
--+|+.|....| +.|.|+++.+++|.||+.. .-+|+|.|..+..
T Consensus 37 Lk~Gd~VvT~gG----i~G~V~~i~~~~v~lei~~-g~~i~v~k~aI~~ 80 (82)
T PF02699_consen 37 LKPGDEVVTIGG----IYGTVVEIDDDTVVLEIAP-GVEITVEKSAIAR 80 (82)
T ss_dssp -------------------------------------------------
T ss_pred CCCCCEEEECCc----EEEEEEEEeCCEEEEEECC-CeEEEEEHHHhHh
Confidence 346888877765 7799999999999999988 5678999887763
No 170
>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=29.79 E-value=83 Score=29.62 Aligned_cols=28 Identities=29% Similarity=0.293 Sum_probs=19.8
Q ss_pred ccCCCEEEEecC--cCCCCcEEEEEEeCCC
Q 000247 319 VSEGTWAYVKNG--KYKGDLAQVVYVNNAR 346 (1790)
Q Consensus 319 Lk~GdwVRIKrG--pYKGDLAQV~eVDenk 346 (1790)
|.||+.|||+.. +|-+..++|-.|...+
T Consensus 2 ilPG~~V~V~n~~~~Y~~y~G~VQRvsdgk 31 (53)
T PF11623_consen 2 ILPGSTVRVKNPNDIYYGYEGFVQRVSDGK 31 (53)
T ss_dssp --TT-EEEE--TTSTTTT-EEEEEEEETTE
T ss_pred ccCCCEEEEeCCCCccchheEEEEEeeCCe
Confidence 679999999974 8999999999998864
No 171
>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=28.52 E-value=1.3e+02 Score=27.83 Aligned_cols=68 Identities=18% Similarity=0.181 Sum_probs=0.0
Q ss_pred cEEEEEEeCCCCcEEEEEeccchhHHHHhcCCCCEEeceeccCCHHHHHHHhhcccccccccCCCEEEEecCcCCCCcEE
Q 000247 259 QIISAFAVDHIKGFIFIEADKQCDINEACKGLSGIYYSRLAPVPKNEVSHLLSAQIKRNEVSEGTWAYVKNGKYKGDLAQ 338 (1790)
Q Consensus 259 ~I~SVFvpd~lKGYIYVEA~kq~dVkeAIkGI~gVy~sK~~pVPikEM~dLLkvkkks~~Lk~GdwVRIKrGpYKGDLAQ 338 (1790)
+|+.+.+....+-.||||. ......+||+.+|.+- .+......|++|+.|++ +
T Consensus 2 ~~v~g~V~~v~~~Gv~V~l----------------~~~v~g~i~~~~l~~~-~~~~~~~~~~~Gd~i~~----------~ 54 (69)
T cd05697 2 QVVKGTIRKLRPSGIFVKL----------------SDHIKGLVPPMHLADV-RLKHPEKKFKPGLKVKC----------R 54 (69)
T ss_pred CEEEEEEEEEeccEEEEEe----------------cCCcEEEEEHHHCCCc-cccCHHHcCCCCCEEEE----------E
Q ss_pred EEEEeCCCCEEEEEE
Q 000247 339 VVYVNNARKRATVKL 353 (1790)
Q Consensus 339 V~eVDenk~kVtVKL 353 (1790)
|.+|++.+.++.|.|
T Consensus 55 V~~id~~~~~i~ls~ 69 (69)
T cd05697 55 VLSVEPERKRLVLTL 69 (69)
T ss_pred EEEEECCCCEEEEEC
No 172
>cd05792 S1_eIF1AD_like S1_eIF1AD_like: eukaryotic translation initiation factor 1A domain containing protein (eIF1AD)-like, S1-like RNA-binding domain. eIF1AD is also known as MGC11102 protein. Little is known about the function of eIF1AD. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins, including translation initiation factor IF1A (also referred to as eIF1A in eukaryotes). eIF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors.
Probab=28.34 E-value=2.6e+02 Score=28.19 Aligned_cols=64 Identities=13% Similarity=0.034 Sum_probs=41.5
Q ss_pred ceEEEEEEecCceEEEccCCCCCCceEEEecccccCCCCCCcccccccCCCcccCCCeEEEecCCCCC-ceEEEEEEECC
Q 000247 504 DFGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVSEGPSKD-RQGIVKKIYRG 582 (1790)
Q Consensus 504 TVGVIVrVEkDEsfkVLdq~gD~~~VvtVk~~eI~~K~~~rr~vAtD~~gn~I~vGD~VKVIdGphkG-RqG~VlHIyRs 582 (1790)
.+-.|+++.-+..+.|.+.++ +.+.+.+. .|. +..--|+.||+|.|.--+... ..|.|+|||..
T Consensus 2 ~i~rV~~~~G~n~~~V~~~dG---~~~l~~iP---~Kf---------Rk~iWIkrGd~VlV~p~~~~~kvkgeIv~i~~~ 66 (78)
T cd05792 2 QIVRVLGSKGNNLHEVETPNG---SRYLVSMP---TKF---------RKNIWIKRGDFVLVEPIEEGDKVKAEIVKILTR 66 (78)
T ss_pred eEEEEEEcCCCcEEEEEcCCC---CEEEEEec---hhh---------cccEEEEeCCEEEEEecccCCceEEEEEEEECH
Confidence 455677777766778887664 34444432 221 123468999999997555433 58999999874
No 173
>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]
Probab=28.32 E-value=67 Score=39.89 Aligned_cols=71 Identities=21% Similarity=0.303 Sum_probs=48.8
Q ss_pred ccCCCCCCCCcEEEEEecCchhHHHHHHHHHHHHhhccCCCCCcEEEEEEe---CCCCcEEEEEeccchhHHHHhcCCCC
Q 000247 216 EYHMPCPEDPTIWKVKCMAGRERQSAFCLMQKFVDLQSLGSKMQIISAFAV---DHIKGFIFIEADKQCDINEACKGLSG 292 (1790)
Q Consensus 216 qlLLPSVkDPkLWaVKCK~GkEReVV~~LmrKii~lq~~g~~L~I~SVFvp---d~lKGYIYVEA~kq~dVkeAIkGI~g 292 (1790)
-.+|++..||.+ |-++.=-|-.--..|..-|..+. +|+||-+- +..+|| |||-..+.....||.-+.+
T Consensus 67 ~rim~s~rd~~~--~~i~nl~~~~~~~~~~d~f~~~g------~ilS~kv~~~~~g~kg~-FV~f~~e~~a~~ai~~~ng 137 (369)
T KOG0123|consen 67 IRIMWSQRDPSL--VFIKNLDESIDNKSLYDTFSEFG------NILSCKVATDENGSKGY-FVQFESEESAKKAIEKLNG 137 (369)
T ss_pred EEeehhccCCce--eeecCCCcccCcHHHHHHHHhhc------CeeEEEEEEcCCCceee-EEEeCCHHHHHHHHHHhcC
Confidence 467899999998 44433233333334444444433 47777665 569999 9999999999999998888
Q ss_pred EEe
Q 000247 293 IYY 295 (1790)
Q Consensus 293 Vy~ 295 (1790)
-+.
T Consensus 138 ~ll 140 (369)
T KOG0123|consen 138 MLL 140 (369)
T ss_pred ccc
Confidence 553
No 174
>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=28.26 E-value=3.2e+02 Score=26.09 Aligned_cols=15 Identities=13% Similarity=0.275 Sum_probs=12.3
Q ss_pred cCCCcccCCCeEEEe
Q 000247 551 QSMKVISLNDTARVS 565 (1790)
Q Consensus 551 ~~gn~I~vGD~VKVI 565 (1790)
...+.|++||.|+|.
T Consensus 44 ~~~~~~~~Gd~v~v~ 58 (79)
T cd05684 44 NPSDVVKRGQKVKVK 58 (79)
T ss_pred ChhheeCCCCEEEEE
Confidence 446789999999985
No 175
>COG2139 RPL21A Ribosomal protein L21E [Translation, ribosomal structure and biogenesis]
Probab=28.24 E-value=71 Score=33.32 Aligned_cols=49 Identities=16% Similarity=0.256 Sum_probs=35.1
Q ss_pred cccccccCcEEEec--------------CCceEEEEEEecCceEEEccCCCCCCceEEEecccc
Q 000247 488 LENSFELYELVCFG--------------RKDFGLIVGMEKDDHYKILKEGSEGPAVVTVERRTL 537 (1790)
Q Consensus 488 slG~FeLgDLVQLD--------------~~TVGVIVrVEkDEsfkVLdq~gD~~~VvtVk~~eI 537 (1790)
.+-.|++||+|.|+ ...+|+||.+-.+ +|.|.--.++..+.+-|.|.-|
T Consensus 29 ~l~ey~~Gd~V~I~IdpSv~kGmPh~rf~G~TG~Vvg~~g~-ay~V~v~~G~k~K~liv~peHL 91 (98)
T COG2139 29 YLQEYKVGDKVHIDIDPSVHKGMPHPRFQGKTGTVVGVRGR-AYKVEVYDGNKEKTLIVRPEHL 91 (98)
T ss_pred HHhhccCCCEEEEEeCcccccCCCCccccCcceEEEeccCC-EEEEEEecCCceEEEEeCHHHc
Confidence 46689999999984 2578999999884 7777643444456666666544
No 176
>KOG1819 consensus FYVE finger-containing proteins [General function prediction only]
Probab=28.24 E-value=35 Score=43.16 Aligned_cols=28 Identities=21% Similarity=0.354 Sum_probs=19.6
Q ss_pred hhcccccCCCCC-CCCcEEEEEecCchhH
Q 000247 211 KMLEREYHMPCP-EDPTIWKVKCMAGRER 238 (1790)
Q Consensus 211 ~~VpQqlLLPSV-kDPkLWaVKCK~GkER 238 (1790)
..+-|++-||+. +.|-.=--+||.-+|.
T Consensus 528 s~tlqrlrlpssdneplaep~~~kaseeh 556 (990)
T KOG1819|consen 528 SDTLQRLRLPSSDNEPLAEPKKCKASEEH 556 (990)
T ss_pred HHHHHHhcCCcccCccccCcccccchHHH
Confidence 346799999985 4555556678776664
No 177
>PRK12289 GTPase RsgA; Reviewed
Probab=27.93 E-value=3.1e+02 Score=34.12 Aligned_cols=75 Identities=16% Similarity=0.299 Sum_probs=43.4
Q ss_pred CceEEEEEEecCceEEEccCCCC---CCceEEEecccccCCCCCCcccccccCCCcccCCCeEEEecCCCCCceEEEEEE
Q 000247 503 KDFGLIVGMEKDDHYKILKEGSE---GPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVSEGPSKDRQGIVKKI 579 (1790)
Q Consensus 503 ~TVGVIVrVEkDEsfkVLdq~gD---~~~VvtVk~~eI~~K~~~rr~vAtD~~gn~I~vGD~VKVIdGphkGRqG~VlHI 579 (1790)
...|.||++..+ .+.|+...++ .+.++.+..+.. .+ ..+..+-|||.|.+-.-...+..|+|.+|
T Consensus 8 ~~~g~V~~~~~~-~y~V~~~~~~~~~~~~~~~~~~r~~------lk-----~~~~~~~vGD~V~~~~~~~~~~~~~I~~v 75 (352)
T PRK12289 8 QLLGTVVAVQAN-FYRVQLDEPQNLNPPSLLLCTRRTR------LK-----KIGQQVMVGDRVIVEEPDWQGQRGAIAEV 75 (352)
T ss_pred cccEEEEEEECC-EEEEEECCCcccCcceEEEEEcccc------cc-----cCCCCcccCCEEEEeecCCCCCceEEEEE
Confidence 457999999995 7777653221 112344443211 11 12455899999988532223467999999
Q ss_pred ECCEEEEEeC
Q 000247 580 YRGILFIYDE 589 (1790)
Q Consensus 580 yRs~VFL~Sr 589 (1790)
+.---+|.-.
T Consensus 76 lpR~~~L~R~ 85 (352)
T PRK12289 76 LPRKTELDRP 85 (352)
T ss_pred eccccceech
Confidence 7654344333
No 178
>PRK05807 hypothetical protein; Provisional
Probab=27.90 E-value=1.8e+02 Score=31.50 Aligned_cols=57 Identities=12% Similarity=0.173 Sum_probs=36.2
Q ss_pred ccccCcEEEecCCceEEEEEEecCceEEEccCCCCCCceEEEecccccCCCCCCcccccccCCCcccCCCeEEEe
Q 000247 491 SFELYELVCFGRKDFGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVS 565 (1790)
Q Consensus 491 ~FeLgDLVQLD~~TVGVIVrVEkDEsfkVLdq~gD~~~VvtVk~~eI~~K~~~rr~vAtD~~gn~I~vGD~VKVI 565 (1790)
.|++|+.|. |+|+.|...-.|+.|. + ..-.|..++|.... +. | -...|++||.|+|.
T Consensus 2 ~~~vG~vv~------G~Vt~i~~~GafV~L~-~----~~Glvhiseis~~~-----v~-~-~~~~~kvGd~V~Vk 58 (136)
T PRK05807 2 TLKAGSILE------GTVVNITNFGAFVEVE-G----KTGLVHISEVADTY-----VK-D-IREHLKEQDKVKVK 58 (136)
T ss_pred CccCCCEEE------EEEEEEECCeEEEEEC-C----EEEEEEhhhccccc-----cc-C-ccccCCCCCEEEEE
Confidence 477888886 8888888766777772 2 13445555554321 11 1 13568999999985
No 179
>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=27.90 E-value=70 Score=30.17 Aligned_cols=28 Identities=25% Similarity=0.337 Sum_probs=22.9
Q ss_pred ccccCCCEEEEecCcCCCCcEEEEEEeCCCCEEEEEEe
Q 000247 317 NEVSEGTWAYVKNGKYKGDLAQVVYVNNARKRATVKLI 354 (1790)
Q Consensus 317 ~~Lk~GdwVRIKrGpYKGDLAQV~eVDenk~kVtVKLV 354 (1790)
..|++|+.|+++ |..|+.++.++.++|+
T Consensus 56 ~~~~~gd~v~v~----------v~~vd~~~~~i~~~l~ 83 (83)
T cd04471 56 KVFRLGDKVKVR----------VVRVDLDRRKIDFELV 83 (83)
T ss_pred CEEcCCCEEEEE----------EEEeccccCEEEEEEC
Confidence 467889999984 8999988888888763
No 180
>PRK06531 yajC preprotein translocase subunit YajC; Validated
Probab=27.79 E-value=70 Score=34.05 Aligned_cols=47 Identities=23% Similarity=0.143 Sum_probs=32.1
Q ss_pred CCCEEEEccCCCCCceeEEEEEeCCeEEEEecCcceEEEEecCccccccCC
Q 000247 662 VGQTLRIRVGPLKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLAEVRGK 712 (1790)
Q Consensus 662 IGKTVKIrkGPYKGylGiVKDaTdt~ARVELHSk~KtITVdKe~Ls~v~~k 712 (1790)
.|+.|.-+. |++|+|+++.++..+|+|....-.|+|.|..|..+-.+
T Consensus 39 ~GD~VvT~G----Gi~G~V~~I~~~~~~v~le~~gv~i~v~r~AI~~Vv~~ 85 (113)
T PRK06531 39 KGDEVVTIG----GLYGTVDEVDTEAKTIVLDVDGVYLTFELAAIKRVVPK 85 (113)
T ss_pred CCCEEEECC----CcEEEEEEEecCCCEEEEEECCEEEEEEhhHhhhhcCC
Confidence 456665444 58899999987544444433567899999999865433
No 181
>COG0056 AtpA F0F1-type ATP synthase, alpha subunit [Energy production and conversion]
Probab=27.71 E-value=1e+02 Score=39.63 Aligned_cols=33 Identities=21% Similarity=0.184 Sum_probs=27.4
Q ss_pred ccccccCcEEEecCCceEEEEEEecCceEEEcc
Q 000247 489 ENSFELYELVCFGRKDFGLIVGMEKDDHYKILK 521 (1790)
Q Consensus 489 lG~FeLgDLVQLD~~TVGVIVrVEkDEsfkVLd 521 (1790)
+..|++|.||++...+.|++..+|.|....||.
T Consensus 44 l~~~~~~E~~ef~~~v~G~alnle~d~VG~vi~ 76 (504)
T COG0056 44 LENVMAGELVEFPGGVKGMALNLEEDSVGAVIL 76 (504)
T ss_pred CchhhcCceEEecCCcEEEEEeccccceeEEEe
Confidence 458999999999999999999999975544443
No 182
>PRK14636 hypothetical protein; Provisional
Probab=27.50 E-value=82 Score=35.59 Aligned_cols=48 Identities=17% Similarity=0.153 Sum_probs=35.9
Q ss_pred ccCCCEEEEc-cCCC---CCceeEEEEEeCCeEEEEecCcceEEEEecCcccc
Q 000247 660 FAVGQTLRIR-VGPL---KGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLAE 708 (1790)
Q Consensus 660 ~lIGKTVKIr-kGPY---KGylGiVKDaTdt~ARVELHSk~KtITVdKe~Ls~ 708 (1790)
+++|+.|+|+ ..|+ |=+.|+++++.+..++|++.- .++|+|+.+.|.-
T Consensus 95 r~~G~~V~V~l~~~~~g~k~~~G~L~~v~~~~v~l~~~~-~~~~~i~~~~I~k 146 (176)
T PRK14636 95 DWAGHEARIALSEPLDGRKQFRGELKGIDGDTVTIADNK-AGEVILPFAAIES 146 (176)
T ss_pred HhCCCeEEEEEecccCCeEEEEEEEEEEeCCEEEEEEcC-CcEEEEEhHHcce
Confidence 4799999996 3444 445899999999999988742 3467777777663
No 183
>PF11424 DUF3195: Protein of unknown function (DUF3195); InterPro: IPR021540 This archaeal family of proteins has no known function. ; PDB: 1RKI_B.
Probab=26.76 E-value=60 Score=33.04 Aligned_cols=43 Identities=12% Similarity=0.064 Sum_probs=30.0
Q ss_pred EEEEecCchhHHHHHHHHHHHHhhccCCCCCcEEEEEEeCCCCcEEEEEec
Q 000247 228 WKVKCMAGRERQSAFCLMQKFVDLQSLGSKMQIISAFAVDHIKGFIFIEAD 278 (1790)
Q Consensus 228 WaVKCK~GkEReVV~~LmrKii~lq~~g~~L~I~SVFvpd~lKGYIYVEA~ 278 (1790)
..|++.++||+.|+.-|-.=+.-+. .+|.+.+..||.|||+..
T Consensus 2 iii~TipkKE~~VARDLCDClYyyD--------~~V~C~~i~pg~vYv~t~ 44 (89)
T PF11424_consen 2 IIITTIPKKEAIVARDLCDCLYYYD--------QSVMCEPISPGRVYVYTS 44 (89)
T ss_dssp EEEEE-CCGHHHHHCHHHHHHCCC---------TT-EEEEEETTEEEEEE-
T ss_pred EEEEecCcchhhhHHHhhhhheecC--------ceEEEEEccCcEEEEEEe
Confidence 3689999999999988875543221 136677778999999994
No 184
>PRK08582 hypothetical protein; Provisional
Probab=26.75 E-value=2e+02 Score=31.22 Aligned_cols=57 Identities=18% Similarity=0.205 Sum_probs=35.3
Q ss_pred cccCcEEEecCCceEEEEEEecCceEEEccCCCCCCceEEEecccccCCCCCCcccccccCCCcccCCCeEEEe
Q 000247 492 FELYELVCFGRKDFGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVS 565 (1790)
Q Consensus 492 FeLgDLVQLD~~TVGVIVrVEkDEsfkVLdq~gD~~~VvtVk~~eI~~K~~~rr~vAtD~~gn~I~vGD~VKVI 565 (1790)
|++++.|. |+|+.|..--.|+-|...- .-.|..++|.... + .| ....|++||.|+|.
T Consensus 3 ~kvG~iv~------G~V~~I~~fG~fV~L~~~~----~GlVhiSels~~~-----v-~~-~~~~l~vGD~Vkvk 59 (139)
T PRK08582 3 IEVGSKLQ------GKVTGITNFGAFVELPEGK----TGLVHISEVADNY-----V-KD-INDHLKVGDEVEVK 59 (139)
T ss_pred CcCCCEEE------EEEEEEECCeEEEEECCCC----EEEEEeeccCccc-----c-cc-cccccCCCCEEEEE
Confidence 66777775 8888888765666665431 2344445554321 1 11 23679999999883
No 185
>PRK11634 ATP-dependent RNA helicase DeaD; Provisional
Probab=26.61 E-value=1.2e+02 Score=40.13 Aligned_cols=12 Identities=25% Similarity=0.216 Sum_probs=5.6
Q ss_pred EEeCCeEEEEec
Q 000247 682 AVRYSDVTVKLD 693 (1790)
Q Consensus 682 DaTdt~ARVELH 693 (1790)
++.+++-.|||.
T Consensus 523 ~i~~~~s~v~~~ 534 (629)
T PRK11634 523 KLFASHSTIELP 534 (629)
T ss_pred EEeCCceEEEcC
Confidence 344444444444
No 186
>PRK14632 hypothetical protein; Provisional
Probab=26.56 E-value=1e+02 Score=34.77 Aligned_cols=49 Identities=16% Similarity=0.326 Sum_probs=38.0
Q ss_pred ccCCCEEEEc-cCCC------CCceeEEEEEeCCeEEEEecCc------ceEEEEecCcccc
Q 000247 660 FAVGQTLRIR-VGPL------KGYLCRVLAVRYSDVTVKLDSQ------QKILTVKGEHLAE 708 (1790)
Q Consensus 660 ~lIGKTVKIr-kGPY------KGylGiVKDaTdt~ARVELHSk------~KtITVdKe~Ls~ 708 (1790)
.+||+.|+|+ ..|+ |=+.|+++.++++.++|++..+ ..+|+|+.+.|..
T Consensus 95 r~iG~~V~V~l~~~~~~~~g~k~~~G~L~~v~~~~i~l~~~~~~~~~~~~~~~~i~~~~I~k 156 (172)
T PRK14632 95 PYVGRQIELTLIDPTPEWPGRRKFRGELLAVEGDTVVLRPEGAPAPEAEEAVLRTSWQGVRK 156 (172)
T ss_pred HhCCCEEEEEEeccccccCCceEEEEEEEEEeCCEEEEEEcCcccccCCceeEEEEhHHccE
Confidence 4799999995 3443 5678999999999999998643 2478888887774
No 187
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=26.49 E-value=95 Score=37.24 Aligned_cols=6 Identities=50% Similarity=0.927 Sum_probs=2.5
Q ss_pred CCceec
Q 000247 81 KGKAVA 86 (1790)
Q Consensus 81 ~~~~~~ 86 (1790)
|+|+++
T Consensus 206 k~k~~P 211 (314)
T PF06524_consen 206 KGKPIP 211 (314)
T ss_pred cCCCCC
Confidence 344443
No 188
>PRK14633 hypothetical protein; Provisional
Probab=26.35 E-value=97 Score=34.10 Aligned_cols=48 Identities=17% Similarity=0.221 Sum_probs=37.0
Q ss_pred ccCCCEEEEcc-CC---CCCceeEEEEEeCCeEEEEecCcceEEEEecCcccc
Q 000247 660 FAVGQTLRIRV-GP---LKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLAE 708 (1790)
Q Consensus 660 ~lIGKTVKIrk-GP---YKGylGiVKDaTdt~ARVELHSk~KtITVdKe~Ls~ 708 (1790)
.+||+.|+|+- .| -|=+.|+++.++++.+++++.- .+++.|+.++|.-
T Consensus 91 r~~G~~v~V~~~~~~~~~~~~~G~L~~v~~~~i~l~~~~-~~~~~i~~~~I~k 142 (150)
T PRK14633 91 ALVGFNVKAVTLAPVGSQTKFKGVLERVEGNNVILNLED-GKEISFDFDELKK 142 (150)
T ss_pred HhCCCeEEEEEecccCCcEEEEEEEEEEeCCEEEEEEcC-CcEEEEEhHHeee
Confidence 47999999964 33 4557899999999999988742 4677888887764
No 189
>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=26.32 E-value=1.3e+02 Score=29.02 Aligned_cols=67 Identities=16% Similarity=0.258 Sum_probs=42.7
Q ss_pred cEEEEEEeCCCCcEEEEEeccchhHHHHhcCCCCEEeceeccCCHHHHHHHh-h-cccccccccCCCEEEEecCcCCCCc
Q 000247 259 QIISAFAVDHIKGFIFIEADKQCDINEACKGLSGIYYSRLAPVPKNEVSHLL-S-AQIKRNEVSEGTWAYVKNGKYKGDL 336 (1790)
Q Consensus 259 ~I~SVFvpd~lKGYIYVEA~kq~dVkeAIkGI~gVy~sK~~pVPikEM~dLL-k-vkkks~~Lk~GdwVRIKrGpYKGDL 336 (1790)
+|...++....+..+||+.. .+ ...+||+.||.+-. + +......|++|+-|++
T Consensus 5 ~~V~g~V~~i~~~G~fV~l~---------~~-------v~G~v~~~~ls~~~~~~~~~~~~~~~~G~~v~~--------- 59 (74)
T cd05705 5 QLLRGYVSSVTKQGVFFRLS---------SS-------IVGRVLFQNVTKYFVSDPSLYNKYLPEGKLLTA--------- 59 (74)
T ss_pred CEEEEEEEEEeCCcEEEEeC---------CC-------CEEEEEHHHccCccccChhhHhcccCCCCEEEE---------
Confidence 46666666666677887741 12 23356777776654 1 1111346789999975
Q ss_pred EEEEEEeCCCCEEEE
Q 000247 337 AQVVYVNNARKRATV 351 (1790)
Q Consensus 337 AQV~eVDenk~kVtV 351 (1790)
+|++|++++.++.|
T Consensus 60 -kVl~id~~~~~i~L 73 (74)
T cd05705 60 -KVLSVNSEKNLVEL 73 (74)
T ss_pred -EEEEEECCCCEEec
Confidence 59999998887665
No 190
>PRK14646 hypothetical protein; Provisional
Probab=26.25 E-value=93 Score=34.44 Aligned_cols=47 Identities=9% Similarity=0.011 Sum_probs=36.4
Q ss_pred ccCCCEEEEcc-CCC---CCceeEEEEEeCCeEEEEecCcceEEEEecCcccc
Q 000247 660 FAVGQTLRIRV-GPL---KGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLAE 708 (1790)
Q Consensus 660 ~lIGKTVKIrk-GPY---KGylGiVKDaTdt~ARVELHSk~KtITVdKe~Ls~ 708 (1790)
.++|+.|+|+- .|+ |=+.|+++++.++.++|++. .+++.|+.+.|.-
T Consensus 97 r~~G~~v~V~l~~~~~~~~~~~G~L~~~~~~~v~l~~~--g~~~~i~~~~I~k 147 (155)
T PRK14646 97 TFKGFPVNVELNQKNSKIKFLNGLLYEKSKDYLAINIK--GKIKKIPFNEVLK 147 (155)
T ss_pred HhCCCEEEEEEecCcCCeEEEEEEEEEEeCCEEEEEEC--CEEEEEEHHHeee
Confidence 47999999973 344 44579999999999998864 6778887777764
No 191
>PF05918 API5: Apoptosis inhibitory protein 5 (API5); InterPro: IPR008383 This family consists of apoptosis inhibitory protein 5 (API5) sequences from several organisms. Apoptosis or programmed cell death is a physiological form of cell death that occurs in embryonic development and organ formation. It is characterised by biochemical and morphological changes such as DNA fragmentation and cell volume shrinkage. API5 is an anti apoptosis gene located in Homo sapiens chromosome 11, whose expression prevents the programmed cell death that occurs upon the deprivation of growth factors [,].; PDB: 3U0R_A 3V6A_A.
Probab=26.21 E-value=22 Score=46.12 Aligned_cols=11 Identities=36% Similarity=0.700 Sum_probs=5.4
Q ss_pred ecCCCCCHHHH
Q 000247 431 CWGVVPSEEEL 441 (1790)
Q Consensus 431 tedVnPTLEEL 441 (1790)
++.|.|.|++|
T Consensus 270 ~~kvlP~l~~l 280 (556)
T PF05918_consen 270 CEKVLPKLSDL 280 (556)
T ss_dssp HHHTCCCTT--
T ss_pred HHHhcCChhhC
Confidence 34566666666
No 192
>PRK14712 conjugal transfer nickase/helicase TraI; Provisional
Probab=26.15 E-value=3.2e+02 Score=40.35 Aligned_cols=93 Identities=13% Similarity=0.121 Sum_probs=67.7
Q ss_pred cccccc-CcEEEecCCceEEEEEEecCceEEEccCCCCCCceEEEecccccCCCCCCcccccccCCCcccCCCeEEEecC
Q 000247 489 ENSFEL-YELVCFGRKDFGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVSEG 567 (1790)
Q Consensus 489 lG~FeL-gDLVQLD~~TVGVIVrVEkDEsfkVLdq~gD~~~VvtVk~~eI~~K~~~rr~vAtD~~gn~I~vGD~VKVIdG 567 (1790)
...|+. +|.|.|.....-.|+.|+++..+.+|.... ++.+.+.|..+. ..++.+-.....+|.+||.|+...-
T Consensus 1144 a~~Y~~~~~~i~l~~~~y~~V~~vd~~~~~vtl~d~~--G~~~~~~P~~~~----~~~~~vy~~~~~ela~GD~Ir~Trn 1217 (1623)
T PRK14712 1144 LSTWENNPDALALVDNVYHRIAGISKDDGLITLQDAE--GNTRLISPREAV----AEGVTLYTPDTIRVGTGDRIRFTKS 1217 (1623)
T ss_pred hhccccCCceeeecCCceEEEEEEcCCCCEEEEEcCC--CCEEEeChhhcc----ccceeeecccccccCCCCEEEEccC
Confidence 457888 678888888888999999876776664321 356778876542 2234556677889999999999754
Q ss_pred -----CCCCceEEEEEEECCEEEEE
Q 000247 568 -----PSKDRQGIVKKIYRGILFIY 587 (1790)
Q Consensus 568 -----phkGRqG~VlHIyRs~VFL~ 587 (1790)
-..+...+|+.|..+.|.|.
T Consensus 1218 D~~~G~~Ng~~~tV~~i~~~~i~l~ 1242 (1623)
T PRK14712 1218 DRERGYVANSVWTVTAVSGDSVTLS 1242 (1623)
T ss_pred CcccccccCceEEEEEEcCCeEEEe
Confidence 33567899999999877776
No 193
>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=26.02 E-value=1.8e+02 Score=26.85 Aligned_cols=67 Identities=9% Similarity=0.106 Sum_probs=38.6
Q ss_pred EEEEEEeCCCCcEEEEEeccchhHHHHhcCCCCEEeceeccCCHHHHHHHhhcccccccccCCCEEEEecCcCCCCcEEE
Q 000247 260 IISAFAVDHIKGFIFIEADKQCDINEACKGLSGIYYSRLAPVPKNEVSHLLSAQIKRNEVSEGTWAYVKNGKYKGDLAQV 339 (1790)
Q Consensus 260 I~SVFvpd~lKGYIYVEA~kq~dVkeAIkGI~gVy~sK~~pVPikEM~dLLkvkkks~~Lk~GdwVRIKrGpYKGDLAQV 339 (1790)
|+.+.+.....-.||||... ++. .+||+.|+.+-. +......|++|+.|++ +|
T Consensus 3 ~v~g~V~~v~~~g~~v~l~~---------~~~-------g~i~~~~~~~~~-~~~~~~~~~~Gd~v~~----------~v 55 (73)
T cd05691 3 IVTGKVTEVDAKGATVKLGD---------GVE-------GFLRAAELSRDR-VEDATERFKVGDEVEA----------KI 55 (73)
T ss_pred EEEEEEEEEECCeEEEEeCC---------CCE-------EEEEHHHCCCcc-ccCHHHccCCCCEEEE----------EE
Confidence 34444545556678887751 122 233444443211 1112234788999987 59
Q ss_pred EEEeCCCCEEEEEE
Q 000247 340 VYVNNARKRATVKL 353 (1790)
Q Consensus 340 ~eVDenk~kVtVKL 353 (1790)
.+++....++.|.+
T Consensus 56 ~~~d~~~~~i~ls~ 69 (73)
T cd05691 56 TNVDRKNRKISLSI 69 (73)
T ss_pred EEEeCCCCEEEEEE
Confidence 99999887777665
No 194
>PLN03134 glycine-rich RNA-binding protein 4; Provisional
Probab=25.91 E-value=1.4e+02 Score=32.34 Aligned_cols=59 Identities=15% Similarity=0.245 Sum_probs=40.1
Q ss_pred cEEEEEecCchhHHHHHHHHHHHHhhccCCCCCcEEEEEEe-----CCCCcEEEEEeccchhHHHHhcCCCCE
Q 000247 226 TIWKVKCMAGRERQSAFCLMQKFVDLQSLGSKMQIISAFAV-----DHIKGFIFIEADKQCDINEACKGLSGI 293 (1790)
Q Consensus 226 kLWaVKCK~GkEReVV~~LmrKii~lq~~g~~L~I~SVFvp-----d~lKGYIYVEA~kq~dVkeAIkGI~gV 293 (1790)
+||+=.+...-..+-+..|..++ . .|.+|.++ ...+||=|||....+++..||+.|.+.
T Consensus 36 ~lfVgnL~~~~te~~L~~~F~~~---G------~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~ 99 (144)
T PLN03134 36 KLFIGGLSWGTDDASLRDAFAHF---G------DVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGK 99 (144)
T ss_pred EEEEeCCCCCCCHHHHHHHHhcC---C------CeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCC
Confidence 57777666555554444444332 1 35555554 246899999999999999999987664
No 195
>COG2163 RPL14A Ribosomal protein L14E/L6E/L27E [Translation, ribosomal structure and biogenesis]
Probab=25.82 E-value=89 Score=33.87 Aligned_cols=33 Identities=15% Similarity=0.300 Sum_probs=28.5
Q ss_pred cccCCCEEEEecCcCCCCcEEEEEEeCCCCEEEE
Q 000247 318 EVSEGTWAYVKNGKYKGDLAQVVYVNNARKRATV 351 (1790)
Q Consensus 318 ~Lk~GdwVRIKrGpYKGDLAQV~eVDenk~kVtV 351 (1790)
.|++|..|-|++|.|+|=.+.|+++-+++ .|+|
T Consensus 4 ~l~~GrVvvv~~GR~aGkk~VIv~~iDd~-~v~i 36 (125)
T COG2163 4 SLEVGRVVVVTAGRFAGKKVVIVKIIDDN-FVLI 36 (125)
T ss_pred cccCCeEEEEecceeCCceEEEEEEccCC-EEEE
Confidence 57899999999999999999999998776 4443
No 196
>KOG0943 consensus Predicted ubiquitin-protein ligase/hyperplastic discs protein, HECT superfamily [Posttranslational modification, protein turnover, chaperones]
Probab=25.53 E-value=35 Score=47.02 Aligned_cols=24 Identities=8% Similarity=0.008 Sum_probs=15.9
Q ss_pred CCCcEEEEEeccchhHHHHhcCCC
Q 000247 268 HIKGFIFIEADKQCDINEACKGLS 291 (1790)
Q Consensus 268 ~lKGYIYVEA~kq~dVkeAIkGI~ 291 (1790)
..+|.+||.-++-..-..+|.+++
T Consensus 1915 S~~~ierf~PyrfssrssflSN~R 1938 (3015)
T KOG0943|consen 1915 SSAGIERFDPYRFSSRSSFLSNLR 1938 (3015)
T ss_pred cCCCeeeeccccccchhhhhhhcc
Confidence 577888888766655555555554
No 197
>COG1818 Predicted RNA-binding protein, contains THUMP domain [General function prediction only]
Probab=25.20 E-value=2.6e+02 Score=31.90 Aligned_cols=76 Identities=16% Similarity=0.097 Sum_probs=48.3
Q ss_pred EEEEEecCchhHHHHHHHHHHHHhhccCCCCCcEEEEEEeCCCCcEEEEEeccc-hhHHHHhcCCCCEEecee----ccC
Q 000247 227 IWKVKCMAGRERQSAFCLMQKFVDLQSLGSKMQIISAFAVDHIKGFIFIEADKQ-CDINEACKGLSGIYYSRL----APV 301 (1790)
Q Consensus 227 LWaVKCK~GkEReVV~~LmrKii~lq~~g~~L~I~SVFvpd~lKGYIYVEA~kq-~dVkeAIkGI~gVy~sK~----~pV 301 (1790)
...|+|.+++|++++..|..-+..+ ..-..|..|+|-+.||...+ ..+...++.++-+-...| ...
T Consensus 3 ~~lv~t~~~~e~~~~~ei~~~~~~~---------~~~~~~~g~~gvliv~~~~d~~~~~~~~~~~~~~~rv~pv~~~~~~ 73 (175)
T COG1818 3 KLLVTTPPGFERQAREEIKEIIGDL---------EAEPRPTGFPGVLIVESELDEEEALEKLKEVPEVERVIPVEIEVET 73 (175)
T ss_pred eEEEeCCCCccHHHHHHHHhhcccc---------cccccccCCceEEEEEccCcHHHHHHHhcCCCceeeEEEEEeeccC
Confidence 4689999999999988877655311 22344568999999999776 334445555555433332 234
Q ss_pred CHHHHHHHhh
Q 000247 302 PKNEVSHLLS 311 (1790)
Q Consensus 302 PikEM~dLLk 311 (1790)
+++||.+...
T Consensus 74 dldeI~~~~~ 83 (175)
T COG1818 74 DLDEIEEAAA 83 (175)
T ss_pred CHHHHHHHHH
Confidence 5566655543
No 198
>COG0186 RpsQ Ribosomal protein S17 [Translation, ribosomal structure and biogenesis]
Probab=25.14 E-value=1.1e+02 Score=31.44 Aligned_cols=23 Identities=26% Similarity=0.394 Sum_probs=19.8
Q ss_pred CcccccccCCCcccCCCeEEEecC
Q 000247 544 MKFTALDQSMKVISLNDTARVSEG 567 (1790)
Q Consensus 544 rr~vAtD~~gn~I~vGD~VKVIdG 567 (1790)
.++.|-| ..+.+++||.|+|.+=
T Consensus 45 kK~~aHd-e~~~~k~GD~V~I~Et 67 (87)
T COG0186 45 KKYHAHD-ECNEAKVGDIVRIAET 67 (87)
T ss_pred eeeEeec-ccccCCCCCEEEEEEc
Confidence 4578999 7899999999999864
No 199
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=24.84 E-value=19 Score=42.12 Aligned_cols=15 Identities=20% Similarity=0.545 Sum_probs=8.8
Q ss_pred cCCHHHHHHHHHHHhc
Q 000247 180 EMDEEEFDKMMEERYK 195 (1790)
Q Consensus 180 d~DaEelAe~LkERY~ 195 (1790)
+|| +|..+.|+.|-.
T Consensus 99 ~l~-~~~~rll~~r~~ 113 (232)
T PRK12766 99 ELS-DEEARLLTQRRR 113 (232)
T ss_pred CCC-HHHHHHHHHHHh
Confidence 444 356677766663
No 200
>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=24.73 E-value=2.2e+02 Score=26.63 Aligned_cols=68 Identities=9% Similarity=0.112 Sum_probs=0.0
Q ss_pred cEEEEEEeCCCCcEEEEEeccchhHHHHhcCCCCEEeceeccCCHHHHHHHhhcccccccccCCCEEEEecCcCCCCcEE
Q 000247 259 QIISAFAVDHIKGFIFIEADKQCDINEACKGLSGIYYSRLAPVPKNEVSHLLSAQIKRNEVSEGTWAYVKNGKYKGDLAQ 338 (1790)
Q Consensus 259 ~I~SVFvpd~lKGYIYVEA~kq~dVkeAIkGI~gVy~sK~~pVPikEM~dLLkvkkks~~Lk~GdwVRIKrGpYKGDLAQ 338 (1790)
.|+.+.+....+-.|||| +-.....+|++.++.+-. .......|++|+.|++ +
T Consensus 5 ~iv~g~V~~v~~~gi~v~----------------l~~~~~g~v~~s~l~~~~-~~~~~~~~~~Gd~v~~----------~ 57 (73)
T cd05706 5 DILPGRVTKVNDRYVLVQ----------------LGNKVTGPSFITDALDDY-SEALPYKFKKNDIVRA----------C 57 (73)
T ss_pred CEEEEEEEEEeCCeEEEE----------------eCCCcEEEEEhhhccCcc-ccccccccCCCCEEEE----------E
Q ss_pred EEEEeCCCCEEEEEE
Q 000247 339 VVYVNNARKRATVKL 353 (1790)
Q Consensus 339 V~eVDenk~kVtVKL 353 (1790)
|++++..+.++.|.+
T Consensus 58 V~~~d~~~~~i~ls~ 72 (73)
T cd05706 58 VLSVDVPNKKIALSL 72 (73)
T ss_pred EEEEeCCCCEEEEEE
No 201
>KOG2055 consensus WD40 repeat protein [General function prediction only]
Probab=24.72 E-value=61 Score=41.28 Aligned_cols=21 Identities=14% Similarity=0.404 Sum_probs=14.5
Q ss_pred CccccCCHHHHHHHHHHHhcc
Q 000247 176 PKEEEMDEEEFDKMMEERYKS 196 (1790)
Q Consensus 176 ~~eEd~DaEelAe~LkERY~r 196 (1790)
+.|..++--++.++|++++++
T Consensus 130 e~e~~~~~~~Y~~RLr~~F~k 150 (514)
T KOG2055|consen 130 ENEGLLSGKEYKGRLREQFQK 150 (514)
T ss_pred ccccccchHHHHHHHHHHHHH
Confidence 344456777888888887765
No 202
>PF08595 RXT2_N: RXT2-like, N-terminal; InterPro: IPR013904 The entry represents the N-terminal region of RXT2-like proteins. In Saccharomyces cerevisiae (Baker's yeast), RXT2 has been demonstrated to be involved in conjugation with cellular fusion (mating) and invasive growth []. A high throughput localisation study has localised RXT2 to the nucleus [].
Probab=24.56 E-value=36 Score=37.58 Aligned_cols=6 Identities=0% Similarity=0.324 Sum_probs=2.4
Q ss_pred cceecc
Q 000247 119 FVEDAA 124 (1790)
Q Consensus 119 FiDdEA 124 (1790)
.+|.|-
T Consensus 54 ~~d~~~ 59 (149)
T PF08595_consen 54 RIDEEG 59 (149)
T ss_pred ccCccc
Confidence 344333
No 203
>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=24.47 E-value=1.8e+02 Score=26.93 Aligned_cols=65 Identities=15% Similarity=0.218 Sum_probs=38.8
Q ss_pred EEEEEEeCCCCcEEEEEeccchhHHHHhcCCCCEEeceeccCCHHHHHHHhhcccccccccCCCEEEEecCcCCCCcEEE
Q 000247 260 IISAFAVDHIKGFIFIEADKQCDINEACKGLSGIYYSRLAPVPKNEVSHLLSAQIKRNEVSEGTWAYVKNGKYKGDLAQV 339 (1790)
Q Consensus 260 I~SVFvpd~lKGYIYVEA~kq~dVkeAIkGI~gVy~sK~~pVPikEM~dLLkvkkks~~Lk~GdwVRIKrGpYKGDLAQV 339 (1790)
|+...+....+--||||... + ...+||+.||.+-. +......|++|+.|++ +|
T Consensus 3 ~v~g~V~~v~~~Gv~V~l~~---------~-------~~G~v~~s~l~~~~-~~~~~~~~~~Gd~v~~----------~v 55 (68)
T cd05707 3 VVRGFVKNIANNGVFVTLGR---------G-------VDARVRVSELSDSY-LKDWKKRFKVGQLVKG----------KI 55 (68)
T ss_pred EEEEEEEEEECccEEEEeCC---------C-------CEEEEEHHHCCchh-hcCHhhccCCCCEEEE----------EE
Confidence 34444545556668888743 2 23355666664321 1122345788999986 68
Q ss_pred EEEeCCCCEEEE
Q 000247 340 VYVNNARKRATV 351 (1790)
Q Consensus 340 ~eVDenk~kVtV 351 (1790)
..+++...++.|
T Consensus 56 ~~~d~~~~~i~l 67 (68)
T cd05707 56 VSIDPDNGRIEM 67 (68)
T ss_pred EEEeCCCCEEec
Confidence 899888777654
No 204
>PRK02001 hypothetical protein; Validated
Probab=24.43 E-value=1.3e+02 Score=33.46 Aligned_cols=48 Identities=15% Similarity=0.189 Sum_probs=36.8
Q ss_pred ccCCCEEEEccCCCCCceeEEEEEeCCeEEEEecCc------------ceEEEEecCccc
Q 000247 660 FAVGQTLRIRVGPLKGYLCRVLAVRYSDVTVKLDSQ------------QKILTVKGEHLA 707 (1790)
Q Consensus 660 ~lIGKTVKIrkGPYKGylGiVKDaTdt~ARVELHSk------------~KtITVdKe~Ls 707 (1790)
+++|+.|+|+----|=+.|+++++.+..++++++.+ .++++|+.+.|.
T Consensus 87 r~~G~~v~V~l~~~~~~~G~L~~~~~~~i~l~~~~~~~~~~~k~~~~~~~~~~i~~~~I~ 146 (152)
T PRK02001 87 KNIGRELEVLTKNGKKIEGELKSADENDITLEVKAREPKEGGKGKVTVEKEETITYDDIK 146 (152)
T ss_pred HhCCCEEEEEECCCCEEEEEEEEEeCCEEEEEEcccccccccccccccceeEEEEhHhee
Confidence 479999999753347799999999999999998743 235677666654
No 205
>smart00243 GAS2 Growth-Arrest-Specific Protein 2 Domain. GROWTH-ARREST-SPECIFIC PROTEIN 2 Domain
Probab=24.17 E-value=1.6e+02 Score=29.45 Aligned_cols=50 Identities=20% Similarity=0.263 Sum_probs=32.7
Q ss_pred HHHHHHhhcccccccccCCCEEEEecCcCC-CCcEEEEEEeCCCCEEEEEEecc
Q 000247 304 NEVSHLLSAQIKRNEVSEGTWAYVKNGKYK-GDLAQVVYVNNARKRATVKLIPR 356 (1790)
Q Consensus 304 kEM~dLLkvkkks~~Lk~GdwVRIKrGpYK-GDLAQV~eVDenk~kVtVKLVPR 356 (1790)
+|+.+++....=..+| ..+||-.|+|+ ||..++.-|---+..|+|++=.=
T Consensus 5 ~~v~~~~~~C~C~~~f---~i~ri~eGkYr~Gd~~~~~~vRil~~~VMVRVGGG 55 (73)
T smart00243 5 DEVKRIVEDCKCPTKF---QVEKISEGKYRFGDSQILRLVRILRSTVMVRVGGG 55 (73)
T ss_pred HHHHHHHhcCCCCCCc---ceEEecCCceEEcCCceEEEEEEeCCeEEEEECCc
Confidence 3566666543322333 78999999999 87766555555556888887543
No 206
>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]
Probab=24.11 E-value=1.5e+02 Score=38.27 Aligned_cols=97 Identities=11% Similarity=0.079 Sum_probs=61.2
Q ss_pred CcEEEEEec----CchhHHHHHHHHHHHHhhccCCCCCcEEEEEEeC---CCCcEEEEEeccchhHHHHhcCCCCEEec-
Q 000247 225 PTIWKVKCM----AGRERQSAFCLMQKFVDLQSLGSKMQIISAFAVD---HIKGFIFIEADKQCDINEACKGLSGIYYS- 296 (1790)
Q Consensus 225 PkLWaVKCK----~GkEReVV~~LmrKii~lq~~g~~L~I~SVFvpd---~lKGYIYVEA~kq~dVkeAIkGI~gVy~s- 296 (1790)
+.-|.|||+ .--|++|... |. .+.|..++++. .-.|=-|||+..+++|+.||+.-+--+..
T Consensus 8 ~~~~~vr~rGLPwsat~~ei~~F----f~-------~~~I~~~~~~r~~Gr~sGeA~Ve~~seedv~~AlkkdR~~mg~R 76 (510)
T KOG4211|consen 8 STAFEVRLRGLPWSATEKEILDF----FS-------NCGIENLEIPRRNGRPSGEAYVEFTSEEDVEKALKKDRESMGHR 76 (510)
T ss_pred CcceEEEecCCCccccHHHHHHH----Hh-------cCceeEEEEeccCCCcCcceEEEeechHHHHHHHHhhHHHhCCc
Confidence 346778886 4566665332 22 35577766653 36799999999999999999986543332
Q ss_pred --eeccCCHHHHHHHhhcccccccccCCCEEEEecCcCC
Q 000247 297 --RLAPVPKNEVSHLLSAQIKRNEVSEGTWAYVKNGKYK 333 (1790)
Q Consensus 297 --K~~pVPikEM~dLLkvkkks~~Lk~GdwVRIKrGpYK 333 (1790)
....+--+||..+|+....... .+--.|||+-=||.
T Consensus 77 YIEVf~~~~~e~d~~~~~~g~~s~-~~d~vVRLRGLPfs 114 (510)
T KOG4211|consen 77 YIEVFTAGGAEADWVMRPGGPNSS-ANDGVVRLRGLPFS 114 (510)
T ss_pred eEEEEccCCccccccccCCCCCCC-CCCceEEecCCCcc
Confidence 2334455677777764332111 45567777554665
No 207
>PLN03078 Putative tRNA pseudouridine synthase; Provisional
Probab=23.69 E-value=1.1e+02 Score=39.61 Aligned_cols=53 Identities=8% Similarity=0.047 Sum_probs=35.1
Q ss_pred cEEEEEeccchhHHHHhcCCCCEEe-ceeccCCHHHHHHHhhcc-cccccccCCC
Q 000247 271 GFIFIEADKQCDINEACKGLSGIYY-SRLAPVPKNEVSHLLSAQ-IKRNEVSEGT 323 (1790)
Q Consensus 271 GYIYVEA~kq~dVkeAIkGI~gVy~-sK~~pVPikEM~dLLkvk-kks~~Lk~Gd 323 (1790)
-||-|+..=+..+++-|+.|-++.. .....+|.+.|..+|... ...+++.|..
T Consensus 355 ~fv~i~I~GqSFmlhQIRKMIG~~~aV~rg~~~~~~i~~~L~~~~r~~~P~AP~~ 409 (513)
T PLN03078 355 DFVELSIWGESFMLHQIRKMVGTAVAVKRELLPRDIIRLSLTKFSRIVLPLAPSE 409 (513)
T ss_pred eEEEEEEEehhHHHHHHHHHHHHHHHHHhccCCHHHHHHHhccccccccccCCCc
Confidence 4677777778888888888887543 234455888888888642 2234555543
No 208
>PRK05610 rpsQ 30S ribosomal protein S17; Reviewed
Probab=23.63 E-value=1.4e+02 Score=30.29 Aligned_cols=25 Identities=24% Similarity=0.348 Sum_probs=20.5
Q ss_pred CCcccccccCCCcccCCCeEEEecCC
Q 000247 543 DMKFTALDQSMKVISLNDTARVSEGP 568 (1790)
Q Consensus 543 ~rr~vAtD~~gn~I~vGD~VKVIdGp 568 (1790)
..++.|-|. .+..++||+|+|.+..
T Consensus 42 ~kk~~aHD~-~n~~k~GD~V~I~e~r 66 (84)
T PRK05610 42 SKKYHAHDE-NNEAKIGDVVRIMETR 66 (84)
T ss_pred ceEEEEECC-CCCCCCCCEEEEEEcc
Confidence 345789998 4689999999999873
No 209
>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=23.35 E-value=1.7e+02 Score=28.19 Aligned_cols=60 Identities=5% Similarity=-0.008 Sum_probs=37.7
Q ss_pred ccccccCcEEEecCCceEEEEEEecCceEEEccCCCCCCceEEEecccccCCCCCCcccccccCCCcccCCCeEEEe
Q 000247 489 ENSFELYELVCFGRKDFGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVS 565 (1790)
Q Consensus 489 lG~FeLgDLVQLD~~TVGVIVrVEkDEsfkVLdq~gD~~~VvtVk~~eI~~K~~~rr~vAtD~~gn~I~vGD~VKVI 565 (1790)
+..|+.++.|. |+|++|...-.|.-|..+ ..-.|..++|.... . ......|++||.|+|.
T Consensus 9 ~~~~~~G~i~~------g~V~~v~~~G~fv~l~~~----~~g~v~~~el~~~~----~---~~~~~~~~~Gd~v~vk 68 (83)
T cd04461 9 FSDLKPGMVVH------GYVRNITPYGVFVEFLGG----LTGLAPKSYISDEF----V---TDPSFGFKKGQSVTAK 68 (83)
T ss_pred HHhCCCCCEEE------EEEEEEeeceEEEEcCCC----CEEEEEHHHCCccc----c---cCHHHhcCCCCEEEEE
Confidence 34677787774 889998875455555433 23445566664321 1 1235789999999984
No 210
>PRK14647 hypothetical protein; Provisional
Probab=22.60 E-value=1.2e+02 Score=33.56 Aligned_cols=48 Identities=17% Similarity=0.233 Sum_probs=37.0
Q ss_pred ccCCCEEEEcc-CC--------CCCceeEEEEEeCCeEEEEecCcceEEEEecCcccc
Q 000247 660 FAVGQTLRIRV-GP--------LKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLAE 708 (1790)
Q Consensus 660 ~lIGKTVKIrk-GP--------YKGylGiVKDaTdt~ARVELHSk~KtITVdKe~Ls~ 708 (1790)
.++|+.|+|+- -| -|=+.|++++++++.+++++. ..++|+|+.+.|.-
T Consensus 96 r~~G~~v~V~l~~~~~~~~~~~~~~~~G~L~~~~~~~v~l~~~-~~~~~~i~~~~I~k 152 (159)
T PRK14647 96 RYAGRLVKVRTFELLADEAGNKRKTFLGELEGLADGVVTIALK-EGQQARIPLDKIAK 152 (159)
T ss_pred HhCCcEEEEEEeccccccccCCceEEEEEEEeecCCEEEEEEc-CCcEEEEEHHHCCE
Confidence 47999999974 23 467899999999999998874 24567888777763
No 211
>COG1532 Predicted RNA-binding protein [General function prediction only]
Probab=22.55 E-value=50 Score=31.25 Aligned_cols=32 Identities=13% Similarity=0.100 Sum_probs=26.7
Q ss_pred CCCEEEEec--CcCCCCcEEEEEEeCCCCEEEEE
Q 000247 321 EGTWAYVKN--GKYKGDLAQVVYVNNARKRATVK 352 (1790)
Q Consensus 321 ~GdwVRIKr--GpYKGDLAQV~eVDenk~kVtVK 352 (1790)
.++-|+.+. |-||-+.+||.+||-+..++.|+
T Consensus 23 ~~e~V~a~Dilgd~ke~~G~vkriDldehkI~lE 56 (57)
T COG1532 23 TEEGVVARDILGDEKEFEGQVKRIDLDEHKIELE 56 (57)
T ss_pred ecCcEEEEeccCCceEecceEEEEEccccEEEec
Confidence 366777776 99999999999999998888764
No 212
>PRK06763 F0F1 ATP synthase subunit alpha; Validated
Probab=22.52 E-value=1.5e+02 Score=34.47 Aligned_cols=15 Identities=20% Similarity=0.313 Sum_probs=13.2
Q ss_pred CCCcccCCCeEEEec
Q 000247 552 SMKVISLNDTARVSE 566 (1790)
Q Consensus 552 ~gn~I~vGD~VKVId 566 (1790)
++..|.+||.|||-.
T Consensus 161 ~GQkFnVGDkVKV~~ 175 (213)
T PRK06763 161 KGQVFHVGDKVKVDM 175 (213)
T ss_pred cCCEEecCCEEEEEe
Confidence 589999999999974
No 213
>COG2163 RPL14A Ribosomal protein L14E/L6E/L27E [Translation, ribosomal structure and biogenesis]
Probab=22.42 E-value=1e+02 Score=33.48 Aligned_cols=46 Identities=15% Similarity=0.302 Sum_probs=33.5
Q ss_pred ccCCCEEEEccCCCCCceeEEEEEeCCeEEEEecCcceEEEEecCcc
Q 000247 660 FAVGQTLRIRVGPLKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHL 706 (1790)
Q Consensus 660 ~lIGKTVKIrkGPYKGylGiVKDaTdt~ARVELHSk~KtITVdKe~L 706 (1790)
.-+|+.|.|+.|.|.|-.+.|+++-|+. +|.....+++--|++..+
T Consensus 5 l~~GrVvvv~~GR~aGkk~VIv~~iDd~-~v~i~gp~~v~gv~r~r~ 50 (125)
T COG2163 5 LEVGRVVVVTAGRFAGKKVVIVKIIDDN-FVLITGPKKVKGVPRRRI 50 (125)
T ss_pred ccCCeEEEEecceeCCceEEEEEEccCC-EEEEeCCccccCCccccc
Confidence 4689999999999999999999998887 555554443333444433
No 214
>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=22.29 E-value=2.8e+02 Score=26.33 Aligned_cols=57 Identities=12% Similarity=0.272 Sum_probs=30.6
Q ss_pred ccCcEEEecCCceEEEEEEecCceEEEccCCCCCCceEEEecccccCCCCCCcccccccCCCcccCCCeEEEe
Q 000247 493 ELYELVCFGRKDFGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVS 565 (1790)
Q Consensus 493 eLgDLVQLD~~TVGVIVrVEkDEsfkVLdq~gD~~~VvtVk~~eI~~K~~~rr~vAtD~~gn~I~vGD~VKVI 565 (1790)
++|+.|+ |+|++|..--.|.=|.... ..-.|..++|... + .++....|++||.|+|.
T Consensus 2 ~~g~~~~------g~V~~i~~fG~fv~l~~~~---~eGlvh~sel~~~----~---~~~~~~~~~~Gd~v~vk 58 (73)
T cd05686 2 ALYQIFK------GEVASVTEYGAFVKIPGCR---KQGLVHKSHMSSC----R---VDDPSEVVDVGEKVWVK 58 (73)
T ss_pred cCCCEEE------EEEEEEEeeeEEEEECCCC---eEEEEEchhhCCC----c---ccCHhhEECCCCEEEEE
Confidence 3455554 6777776533444442210 1233444556442 1 13446679999999984
No 215
>TIGR03635 S17_bact 30S ribosomal protein S17. This model describes the bacterial ribosomal small subunit protein S17, while excluding cytosolic eukaryotic homologs and archaeal homologs. The model finds many, but not, chloroplast and mitochondrial counterparts to bacterial S17.
Probab=22.26 E-value=1.5e+02 Score=29.17 Aligned_cols=23 Identities=26% Similarity=0.359 Sum_probs=19.3
Q ss_pred CcccccccCCCcccCCCeEEEecC
Q 000247 544 MKFTALDQSMKVISLNDTARVSEG 567 (1790)
Q Consensus 544 rr~vAtD~~gn~I~vGD~VKVIdG 567 (1790)
.++.|-|. .+..++||+|+|.+-
T Consensus 38 kk~~aHD~-~~~~k~GD~V~I~ec 60 (71)
T TIGR03635 38 KKYHAHDE-NNECKVGDVVRIIET 60 (71)
T ss_pred EEEEEECC-CCCCCCCCEEEEEEc
Confidence 45789998 468999999999875
No 216
>PF14001 YdfZ: YdfZ protein
Probab=22.25 E-value=94 Score=30.35 Aligned_cols=32 Identities=19% Similarity=0.392 Sum_probs=27.3
Q ss_pred ccccCCCcccCCCeEEEecCCCCCceEEEEEEECC
Q 000247 548 ALDQSMKVISLNDTARVSEGPSKDRQGIVKKIYRG 582 (1790)
Q Consensus 548 AtD~~gn~I~vGD~VKVIdGphkGRqG~VlHIyRs 582 (1790)
+-|+++|.|.+|..|-|- | .|.+|+|+.||-.
T Consensus 2 tYDRnRN~i~~G~rVMia-g--tG~~gvikAih~~ 33 (64)
T PF14001_consen 2 TYDRNRNAITTGSRVMIA-G--TGATGVIKAIHAD 33 (64)
T ss_pred ccccccCcCCCCCEEEEc-C--CCcccEEeeeecC
Confidence 459999999999999875 3 6899999999864
No 217
>PRK00321 rdgC recombination associated protein; Reviewed
Probab=22.25 E-value=2.3e+02 Score=34.60 Aligned_cols=85 Identities=14% Similarity=0.121 Sum_probs=45.9
Q ss_pred EEEEEEeCCCCcEEEEEeccchhHHHHhcCCCCEEe------ceeccCCHHHHHHHhhcccccccccCCCEEEEecCcCC
Q 000247 260 IISAFAVDHIKGFIFIEADKQCDINEACKGLSGIYY------SRLAPVPKNEVSHLLSAQIKRNEVSEGTWAYVKNGKYK 333 (1790)
Q Consensus 260 I~SVFvpd~lKGYIYVEA~kq~dVkeAIkGI~gVy~------sK~~pVPikEM~dLLkvkkks~~Lk~GdwVRIKrGpYK 333 (1790)
++.|++ +.-.|||||.+-......+++.-++..++ ..+..-|...|+.-|.-......|..|+.+
T Consensus 124 ~~~~~i-d~~~g~l~VdasS~k~aE~~l~lLrkslgsLpv~p~~~~~~p~~~mt~WL~~~~~P~~f~l~~~~-------- 194 (303)
T PRK00321 124 QTFAWI-DPVNGLIVVDAASAKKAEDVLALLRKSLGSLPVVPLSTEQSPEATMTEWLASGEAPAGFTLDDEC-------- 194 (303)
T ss_pred eEEEEE-ECCCCEEEEeCCCHHHHHHHHHHHHHhcCCCceeccccCCCHHHHHHHHHccCCCCCCcEeccee--------
Confidence 444443 56789999999876554444433333222 122334566788888543323345555444
Q ss_pred CCcEEEEEEeCCCCEEEEEEeccCchh
Q 000247 334 GDLAQVVYVNNARKRATVKLIPRIDLQ 360 (1790)
Q Consensus 334 GDLAQV~eVDenk~kVtVKLVPRIDy~ 360 (1790)
....+.+.+..|+++ |.|+.
T Consensus 195 ----eL~~~~e~~~~vr~k---~~~L~ 214 (303)
T PRK00321 195 ----ELKSALEDGAVVRCK---RQDLD 214 (303)
T ss_pred ----EEecCCCCccEEEEe---CCCCC
Confidence 444545554445554 55554
No 218
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=22.16 E-value=1.9e+02 Score=26.55 Aligned_cols=48 Identities=19% Similarity=0.177 Sum_probs=0.0
Q ss_pred ccccCcEEEecC--Cce---EEEEEEecCceEEEccCCCCCCceEEEeccccc
Q 000247 491 SFELYELVCFGR--KDF---GLIVGMEKDDHYKILKEGSEGPAVVTVERRTLK 538 (1790)
Q Consensus 491 ~FeLgDLVQLD~--~TV---GVIVrVEkDEsfkVLdq~gD~~~VvtVk~~eI~ 538 (1790)
.|.+||+|++-. ... |+|+++..++.+.|.=.....+...+|...+|.
T Consensus 2 ~~~~G~~Ve~~~~~~~~W~~a~V~~~~~~~~~~V~~~~~~~~~~e~v~~~~LR 54 (61)
T smart00743 2 DFKKGDRVEVFSKEEDSWWEAVVTKVLGDGKYLVRYLTESEPLKETVDWSDLR 54 (61)
T ss_pred CcCCCCEEEEEECCCCEEEEEEEEEECCCCEEEEEECCCCcccEEEEeHHHcc
No 219
>PF02187 GAS2: Growth-Arrest-Specific Protein 2 Domain; InterPro: IPR003108 The growth-arrest-specific protein 2 domain is found associated with the spectrin repeat, calponin homology domain and EF hand in many proteins. It is found among others in the growth arrest-specific protein 2 [].; GO: 0007050 cell cycle arrest; PDB: 1V5R_A.
Probab=21.96 E-value=1.5e+02 Score=29.74 Aligned_cols=48 Identities=25% Similarity=0.403 Sum_probs=30.5
Q ss_pred HHHHHHhhcccccccccCCCEEEEecCcCC-CCcEEEEEEeCCCCEEEEEEe
Q 000247 304 NEVSHLLSAQIKRNEVSEGTWAYVKNGKYK-GDLAQVVYVNNARKRATVKLI 354 (1790)
Q Consensus 304 kEM~dLLkvkkks~~Lk~GdwVRIKrGpYK-GDLAQV~eVDenk~kVtVKLV 354 (1790)
+|+.+++....=...| ..+||-.|+|+ ||.-++.-|.--+..|+|++=
T Consensus 5 ~~V~~iv~~C~C~~~f---~v~rv~~GkYr~g~~~~l~~~ril~~~vMVRVG 53 (73)
T PF02187_consen 5 DEVRRIVNQCSCPNKF---PVERVSEGKYRFGDSKKLFFVRILRSHVMVRVG 53 (73)
T ss_dssp HHHHHHHTS--SSS------EEEEETTEEE-ETTEEEEEEEETTTEEEEEET
T ss_pred HHHHHHHhcCCCCCce---eEEEeCCCceEeCCCceEEEEEEeCCEEEEEeC
Confidence 4566666544322234 35889999999 887776666656678999863
No 220
>COG0779 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.70 E-value=1.5e+02 Score=33.08 Aligned_cols=47 Identities=19% Similarity=0.328 Sum_probs=38.1
Q ss_pred ccCCCEEEEcc----CCCCCceeEEEEEeCCeEEEEecCcceEEEEecCcccc
Q 000247 660 FAVGQTLRIRV----GPLKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLAE 708 (1790)
Q Consensus 660 ~lIGKTVKIrk----GPYKGylGiVKDaTdt~ARVELHSk~KtITVdKe~Ls~ 708 (1790)
.++|+.|+|.- .--|=+.|+|+.+.+++++|++. .|+|.|+...|.-
T Consensus 96 r~~G~~Vkv~l~~~~~~~k~~~G~i~~~d~~~v~~~~~--~k~v~Ip~~~i~k 146 (153)
T COG0779 96 RFIGEKVKVKLRLPIEGRKKFEGKIVAVDGETVTLEVD--GKEVEIPFSDIAK 146 (153)
T ss_pred HhcCcEEEEEEecccCCceEEEEEEEEEcCCeEEEEEC--CEEEEEEcccchh
Confidence 47999999998 44677899999999999998855 5558888777763
No 221
>COG5177 Uncharacterized conserved protein [Function unknown]
Probab=21.59 E-value=62 Score=41.59 Aligned_cols=18 Identities=28% Similarity=0.302 Sum_probs=14.4
Q ss_pred CCccccCCHHHHHHHHHH
Q 000247 175 IPKEEEMDEEEFDKMMEE 192 (1790)
Q Consensus 175 r~~eEd~DaEelAe~LkE 192 (1790)
-+..+++.+||-++.|+|
T Consensus 437 ne~f~els~eee~rq~~e 454 (769)
T COG5177 437 NEGFEELSPEEEERQLRE 454 (769)
T ss_pred cccchhcChHHHHHHHHH
Confidence 456788888988888876
No 222
>PF00076 RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); InterPro: IPR000504 Many eukaryotic proteins containing one or more copies of a putative RNA-binding domain of about 90 amino acids are known to bind single-stranded RNAs [, , ]. The largest group of single strand RNA-binding proteins is the eukaryotic RNA recognition motif (RRM) family that contains an eight amino acid RNP-1 consensus sequence [, ]. RRM proteins have a variety of RNA binding preferences and functions, and include heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing (SR, U2AF, Sxl), protein components of small nuclear ribonucleoproteins (U1 and U2 snRNPs), and proteins that regulate RNA stability and translation (PABP, La, Hu) [, , ]. The RRM in heterodimeric splicing factor U2 snRNP auxiliary factor (U2AF) appears to have two RRM-like domains with specialised features for protein recognition []. The motif also appears in a few single stranded DNA binding proteins. The typical RRM consists of four anti-parallel beta-strands and two alpha-helices arranged in a beta-alpha-beta-beta-alpha-beta fold with side chains that stack with RNA bases. Specificity of RNA binding is determined by multiple contacts with surrounding amino acids. A third helix is present during RNA binding in some cases []. The RRM is reviewed in a number of publications [, , ].; GO: 0003676 nucleic acid binding; PDB: 2RNE_A 2DGO_A 2DO4_A 1YTY_B 2VOO_B 2VOP_A 2VON_B 1ZH5_B 2VOD_A 1S79_A ....
Probab=21.49 E-value=94 Score=27.64 Aligned_cols=28 Identities=29% Similarity=0.483 Sum_probs=24.9
Q ss_pred CCCCcEEEEEeccchhHHHHhcCCCCEE
Q 000247 267 DHIKGFIFIEADKQCDINEACKGLSGIY 294 (1790)
Q Consensus 267 d~lKGYIYVEA~kq~dVkeAIkGI~gVy 294 (1790)
...++|.||+-...+++..||+.+.+..
T Consensus 36 ~~~~~~a~V~F~~~~~a~~a~~~l~g~~ 63 (70)
T PF00076_consen 36 GKSKGYAFVEFESEEDAEKALEELNGKK 63 (70)
T ss_dssp SSEEEEEEEEESSHHHHHHHHHHHTTEE
T ss_pred ccccceEEEEEcCHHHHHHHHHHcCCCE
Confidence 3689999999999999999999888754
No 223
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=21.41 E-value=74 Score=37.53 Aligned_cols=9 Identities=11% Similarity=0.320 Sum_probs=4.2
Q ss_pred ccccCCCCC
Q 000247 123 AADVDYDDD 131 (1790)
Q Consensus 123 EAEVDDDeE 131 (1790)
+.||++|.|
T Consensus 58 ~~~~~~~~~ 66 (232)
T PRK12766 58 GLEVSEETE 66 (232)
T ss_pred ccccccccc
Confidence 455544443
No 224
>PF03992 ABM: Antibiotic biosynthesis monooxygenase; InterPro: IPR007138 This domain is found in monooxygenases involved in the biosynthesis of several antibiotics by Streptomyces species, which can carry out oxygenation without the assistance of any of the prosthetic groups, metal ions or cofactors normally associated with activation of molecular oxygen. The structure of ActVA-Orf6 monooxygenase from Streptomyces coelicolor (Q53908 from SWISSPROT), which is involved in actinorhodin biosynthesis, reveals a dimeric alpha+beta barrel topology []. There is also a conserved histidine that is likely to be an active site residue. In S. coelicolor SCO1909 (Q9X9W3 from SWISSPROT) this domain occurs as a repeat. This domain is also found in protein LsrG, involved in the degradation of quorum-sensing molecule autoinducer-2 [], and in several uncharacterised proteins.; PDB: 1X7V_A 3F44_A 4DN9_B 1N5T_B 1LQ9_A 1N5Q_B 1N5V_A 1N5S_A 2GFF_B 3BM7_A ....
Probab=21.27 E-value=6e+02 Score=23.19 Aligned_cols=56 Identities=11% Similarity=0.041 Sum_probs=32.8
Q ss_pred EEEEEecCchhHHHHHHHHHHHHhhccCCCCCcEEEEEEeCCCCc-EEEEEeccchh
Q 000247 227 IWKVKCMAGRERQSAFCLMQKFVDLQSLGSKMQIISAFAVDHIKG-FIFIEADKQCD 282 (1790)
Q Consensus 227 LWaVKCK~GkEReVV~~LmrKii~lq~~g~~L~I~SVFvpd~lKG-YIYVEA~kq~d 282 (1790)
+-.+++++|++.+++..|..-+.........+--+.++....-++ ||++|--....
T Consensus 5 ~~~~~v~~~~~~~f~~~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~~~~~~W~s~~ 61 (78)
T PF03992_consen 5 IVKFKVKPGKEEEFLAAFQELAEATLRKEPGCLSYELYRSLDDPNRYVIVERWESEE 61 (78)
T ss_dssp EEEEEEETTGHHHHHHHHHHHHHHHHHTSTTEEEEEEEEESSSTTEEEEEEEESSHH
T ss_pred EEEEEeCcchHHHHHHHHHHHHHHHHhcCCCcEEEEEEEecCCCCEEEEEEEECCHH
Confidence 456778999999998887666554521222232333333344555 88877765533
No 225
>KOG0339 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=21.26 E-value=79 Score=40.96 Aligned_cols=18 Identities=22% Similarity=0.292 Sum_probs=10.9
Q ss_pred eEEecCCc--eeecceEEEE
Q 000247 406 VFENLDGM--MLKDGYLYKK 423 (1790)
Q Consensus 406 ~f~i~~G~--~ykDGFLyK~ 423 (1790)
.|.+|+-- ||.-||++--
T Consensus 372 S~LV~DEadrmfdmGfe~qV 391 (731)
T KOG0339|consen 372 SYLVLDEADRMFDMGFEPQV 391 (731)
T ss_pred eEEEEechhhhhccccHHHH
Confidence 36666543 6777887543
No 226
>PF10781 DSRB: Dextransucrase DSRB; InterPro: IPR019717 DSRB is a novel dextransucrase which produces a dextran different from the typical dextran, as it contains (1-6) and (1-2) linkages, when this strain is grown in the presence of sucrose [].
Probab=21.13 E-value=2.2e+02 Score=27.48 Aligned_cols=34 Identities=21% Similarity=0.528 Sum_probs=23.3
Q ss_pred ccCCCeEEEe-cCCCCCceEEEEEEE---CCEEEEEeCc
Q 000247 556 ISLNDTARVS-EGPSKDRQGIVKKIY---RGILFIYDEN 590 (1790)
Q Consensus 556 I~vGD~VKVI-dGphkGRqG~VlHIy---Rs~VFL~Sr~ 590 (1790)
++++|.|.|. +|. .-|+|+|+.|. .++.||.+-.
T Consensus 1 MkvnD~VtVKTDG~-~rR~G~ilavE~F~EG~MYLvaL~ 38 (62)
T PF10781_consen 1 MKVNDRVTVKTDGG-PRREGVILAVEPFNEGTMYLVALE 38 (62)
T ss_pred CccccEEEEecCCc-ccccceEEEEeeccCcEEEEEEcC
Confidence 3678888886 442 45899999884 3566666544
No 227
>smart00360 RRM RNA recognition motif.
Probab=21.01 E-value=2.7e+02 Score=23.79 Aligned_cols=25 Identities=36% Similarity=0.602 Sum_probs=21.7
Q ss_pred CCcEEEEEeccchhHHHHhcCCCCE
Q 000247 269 IKGFIFIEADKQCDINEACKGLSGI 293 (1790)
Q Consensus 269 lKGYIYVEA~kq~dVkeAIkGI~gV 293 (1790)
.+||.||+....+.+..||+.+.+.
T Consensus 37 ~~~~a~v~f~~~~~a~~a~~~~~~~ 61 (71)
T smart00360 37 SKGFAFVEFESEEDAEKALEALNGK 61 (71)
T ss_pred CCceEEEEeCCHHHHHHHHHHcCCC
Confidence 4799999999999999999888753
No 228
>PRK01889 GTPase RsgA; Reviewed
Probab=21.01 E-value=3.2e+02 Score=33.76 Aligned_cols=89 Identities=9% Similarity=0.082 Sum_probs=52.1
Q ss_pred ceEEEEEEecCceEEEccCCCCCCceEEEecccccCCCCCCcccccccCCCcccCCCeEEEecCCCCCceEEEEEEECCE
Q 000247 504 DFGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVSEGPSKDRQGIVKKIYRGI 583 (1790)
Q Consensus 504 TVGVIVrVEkDEsfkVLdq~gD~~~VvtVk~~eI~~K~~~rr~vAtD~~gn~I~vGD~VKVIdGphkGRqG~VlHIyRs~ 583 (1790)
..|.||++.+. .+.|++.++ .+ ...++ .|+ +.+. ......+-+||.|.+-. +..|.|.+|+.-.
T Consensus 29 ~~g~v~~~~~~-~~~v~~~~~---~~-~~~~~---gk~---~~~~-~~~~~~~~vGD~V~~~~----~~~g~I~~i~pR~ 92 (356)
T PRK01889 29 EPGRVVEEHRS-GYVVATEEG---EV-RAEVS---GKW---RHEA-FPPGDRPAVGDWVLLDN----EKKARIVRLLPRR 92 (356)
T ss_pred ccEEEEEEECC-EEEEEECCc---EE-EEEec---chh---hccc-cccCCCCccCcEEEEec----CCceEEEEEECCC
Confidence 46999999994 888876442 22 22221 111 1111 11235589999998853 3569999998754
Q ss_pred EEEEeCcc--eeeccEEEEeCCceeec
Q 000247 584 LFIYDENE--TENGGYFCSKSQHCEKT 608 (1790)
Q Consensus 584 VFL~Sr~~--tENgGIFVvRArnv~tv 608 (1790)
-+|.-+.. ..-.-+++++.-.|++|
T Consensus 93 ~~L~R~~~~~~~~~q~iaANvD~vliV 119 (356)
T PRK01889 93 SLFSRKAAGTRSEEQLIAANVDTVFIV 119 (356)
T ss_pred ceEEcCCCCCCccceeEEEeCCEEEEE
Confidence 44444443 22335677777766654
No 229
>PF01037 AsnC_trans_reg: AsnC family; InterPro: IPR019887 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One such family is the AsnC/Lrp subfamily []. The Lrp family of transcriptional regulators appears to be widely distributed among bacteria and archaea, as an important regulatory system of the amino acid metabolism and related processes []. Members of the Lrp family are small DNA-binding proteins with molecular masses of around 15 kDa. Target promoters often contain a number of binding sites that typically lack obvious inverted repeat elements, and to which binding is usually co-operative. LrpA from Pyrococcus furiosus is the first Lrp-like protein to date of which a three-dimensional structure has been solved. In the crystal structure LrpA forms an octamer consisting of four dimers. The structure revealed that the N-terminal part of the protein consists of a helix-turn-helix (HTH) domain, a fold generally involved in DNA binding. The C terminus of Lrp-like proteins has a beta-fold, where the two alpha-helices are located at one side of the four-stranded antiparallel beta-sheet. LrpA forms a homodimer mainly through interactions between the beta-strands of this C-terminal domain, and an octamer through further interactions between the second alpha-helix and fourth beta-strand of the motif. Hence, the C-terminal domain of Lrp-like proteins appears to be involved in ligand-response and activation [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2DJW_F 2GQQ_A 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2CG4_B 2DBB_B 1I1G_A ....
Probab=20.87 E-value=5.2e+02 Score=23.76 Aligned_cols=61 Identities=11% Similarity=0.239 Sum_probs=40.4
Q ss_pred EEEecCchhHHHHHHHHHHHHhhccCCCCCcEEEEEEeCCC-CcEEEEEeccchhHHHH----hcCCCCEEece
Q 000247 229 KVKCMAGRERQSAFCLMQKFVDLQSLGSKMQIISAFAVDHI-KGFIFIEADKQCDINEA----CKGLSGIYYSR 297 (1790)
Q Consensus 229 aVKCK~GkEReVV~~LmrKii~lq~~g~~L~I~SVFvpd~l-KGYIYVEA~kq~dVkeA----IkGI~gVy~sK 297 (1790)
.|+|.+++ +....+.+.+.++ ..|..|+..-.- .=.+.|.+....++.++ |..+++|....
T Consensus 2 ~V~~~~~~--~~~~~~~~~l~~~------p~V~~~~~vtG~~d~~~~v~~~d~~~l~~~i~~~l~~~~gV~~~~ 67 (74)
T PF01037_consen 2 LVKVEPGH--DAYDEFAEALAEI------PEVVECYSVTGEYDLILKVRARDMEELEEFIREKLRSIPGVRRTE 67 (74)
T ss_dssp EEEESTTG--THHHHHHHHHHTS------TTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTHHTSTTEEEEE
T ss_pred EEEEcCCC--chHHHHHHHHHcC------CCEEEEEEEeCCCCEEEEEEECCHHHHHHHHHHHhhcCCCEEEEE
Confidence 48898888 3333344444433 258888777543 33456788888888888 88889987654
No 230
>PRK08059 general stress protein 13; Validated
Probab=20.81 E-value=2.2e+02 Score=30.01 Aligned_cols=71 Identities=15% Similarity=0.200 Sum_probs=43.0
Q ss_pred cEEEEEEeCCCCcEEEEEeccchhHHHHhcCCCCEEeceeccCCHHHHHHHhhcccccccccCCCEEEEecCcCCCCcEE
Q 000247 259 QIISAFAVDHIKGFIFIEADKQCDINEACKGLSGIYYSRLAPVPKNEVSHLLSAQIKRNEVSEGTWAYVKNGKYKGDLAQ 338 (1790)
Q Consensus 259 ~I~SVFvpd~lKGYIYVEA~kq~dVkeAIkGI~gVy~sK~~pVPikEM~dLLkvkkks~~Lk~GdwVRIKrGpYKGDLAQ 338 (1790)
.|+.+.+....+--|||+.... +.+ +||+.|+..=. +......|++|+.|++ +
T Consensus 9 ~iv~G~V~~i~~~G~fV~i~~~---------~~G-------li~~sel~~~~-~~~~~~~~~vGD~I~v----------k 61 (123)
T PRK08059 9 SVVTGKVTGIQPYGAFVALDEE---------TQG-------LVHISEITHGF-VKDIHDFLSVGDEVKV----------K 61 (123)
T ss_pred CEEEEEEEEEecceEEEEECCC---------CEE-------EEEHHHCCccc-ccCHHHcCCCCCEEEE----------E
Confidence 4667777777777888887321 222 33334432110 1111235788999987 4
Q ss_pred EEEEeCCCCEEEEEEecc
Q 000247 339 VVYVNNARKRATVKLIPR 356 (1790)
Q Consensus 339 V~eVDenk~kVtVKLVPR 356 (1790)
|++|+....++.|.+.+.
T Consensus 62 I~~id~~~~~i~lslk~~ 79 (123)
T PRK08059 62 VLSVDEEKGKISLSIRAT 79 (123)
T ss_pred EEEEECCCCeEEEEEEEc
Confidence 999998888888876543
No 231
>PTZ00287 6-phosphofructokinase; Provisional
Probab=20.53 E-value=2.2e+02 Score=41.12 Aligned_cols=96 Identities=11% Similarity=-0.000 Sum_probs=56.2
Q ss_pred ecCchhHHHHHHHHHHHHhhccCCCCCcEEEEEEeCCCCcEEEEEe-cc-----------chhHHHHhcCCCCEEe----
Q 000247 232 CMAGRERQSAFCLMQKFVDLQSLGSKMQIISAFAVDHIKGFIFIEA-DK-----------QCDINEACKGLSGIYY---- 295 (1790)
Q Consensus 232 CK~GkEReVV~~LmrKii~lq~~g~~L~I~SVFvpd~lKGYIYVEA-~k-----------q~dVkeAIkGI~gVy~---- 295 (1790)
-....|+-++..+.+++.++...+.++.+.+. +.||.-==| .. ...|.-++.+..+++.
T Consensus 478 s~i~te~lL~~~V~~~L~~~~~~g~~~k~~~h-----~lGYe~RcA~PS~fD~~yay~LG~~Av~l~~~G~tG~Mv~I~n 552 (1419)
T PTZ00287 478 GKIATERLIIVLVESELAKLNDNNLNIQFMAH-----YLGYEGRCAIPSNFDCNYCYALGYNAALLIDHKKTGYMSIIQN 552 (1419)
T ss_pred cccchHHHHHHHHHHHHHHHHhcCCCeeEEEe-----ecCcchhccCCcHHHHHHHHHHHHHHHHHHhcCCCCeEEEEEe
Confidence 46799999999888888877544444444444 444432101 11 1336677788777642
Q ss_pred -------ceeccCCHHHHHHHhhcc-cccccccCCCEEEEecCcC
Q 000247 296 -------SRLAPVPKNEVSHLLSAQ-IKRNEVSEGTWAYVKNGKY 332 (1790)
Q Consensus 296 -------sK~~pVPikEM~dLLkvk-kks~~Lk~GdwVRIKrGpY 332 (1790)
..+..||+.+|..|=+.. .+..++..-..|.+...+|
T Consensus 553 l~~~~~~w~~~~vPl~~~m~~e~~~~g~~~pvi~k~~v~l~g~~f 597 (1419)
T PTZ00287 553 LEDSYANWIPAAIPFLRIMHVNRDNTGKEFPAVKRYLVDLNSPLF 597 (1419)
T ss_pred CCCCcceeEEcccCHHHHhhHHhhccCCCceeEEeeeeCCCCHHH
Confidence 357889999988877643 2223333444555544443
No 232
>PRK06531 yajC preprotein translocase subunit YajC; Validated
Probab=20.45 E-value=2.3e+02 Score=30.27 Aligned_cols=42 Identities=17% Similarity=0.182 Sum_probs=32.4
Q ss_pred HHHHHHHhhcccccccccCCCEEEEecCcCCCCcEEEEEEeCCCCEEEEEEec
Q 000247 303 KNEVSHLLSAQIKRNEVSEGTWAYVKNGKYKGDLAQVVYVNNARKRATVKLIP 355 (1790)
Q Consensus 303 ikEM~dLLkvkkks~~Lk~GdwVRIKrGpYKGDLAQV~eVDenk~kVtVKLVP 355 (1790)
.+|+.+||. .|++|+.|.-.-| ..|.|++|+++...|.|++ |
T Consensus 27 ~Ke~~em~~------sLk~GD~VvT~GG----i~G~V~~I~~~~~~v~le~-~ 68 (113)
T PRK06531 27 AQERQNQLN------AIQKGDEVVTIGG----LYGTVDEVDTEAKTIVLDV-D 68 (113)
T ss_pred HHHHHHHHH------hcCCCCEEEECCC----cEEEEEEEecCCCEEEEEE-C
Confidence 455666663 6788999986655 5689999999888899986 6
No 233
>PRK10708 hypothetical protein; Provisional
Probab=20.23 E-value=2e+02 Score=27.78 Aligned_cols=35 Identities=20% Similarity=0.421 Sum_probs=23.7
Q ss_pred ccCCCeEEEecCCCCCceEEEEEEEC---CEEEEEeCc
Q 000247 556 ISLNDTARVSEGPSKDRQGIVKKIYR---GILFIYDEN 590 (1790)
Q Consensus 556 I~vGD~VKVIdGphkGRqG~VlHIyR---s~VFL~Sr~ 590 (1790)
++++|.|.|..--..-|+|+|+.|.. ++.||.+-.
T Consensus 1 MkvnD~VtVKTDG~~rR~G~iLavE~F~EG~MyLvaL~ 38 (62)
T PRK10708 1 MKVNDRVTVKTDGGPRRPGVVLAVEEFSEGTMYLVSLE 38 (62)
T ss_pred CccccEEEEecCCCccccceEEEEeeccCcEEEEEEcC
Confidence 36788888863222459999999853 566766644
No 234
>PLN00036 40S ribosomal protein S4; Provisional
Probab=20.09 E-value=1.9e+02 Score=34.89 Aligned_cols=29 Identities=14% Similarity=0.249 Sum_probs=26.1
Q ss_pred cccccCCCEEEEecCcCCCCcEEEEEEeC
Q 000247 316 RNEVSEGTWAYVKNGKYKGDLAQVVYVNN 344 (1790)
Q Consensus 316 s~~Lk~GdwVRIKrGpYKGDLAQV~eVDe 344 (1790)
.+.|++|..|.|+.|...|.+|+|+++..
T Consensus 172 ~ikfe~G~l~~vtgG~n~GrvG~I~~i~~ 200 (261)
T PLN00036 172 FIKFDVGNLVMVTGGRNRGRVGVIKNREK 200 (261)
T ss_pred EEecCCCCEEEEECCeeceeEEEEEEEEe
Confidence 45789999999999999999999999873
No 235
>KOG2897 consensus DNA-binding protein YL1 and related proteins [General function prediction only]
Probab=20.08 E-value=65 Score=40.15 Aligned_cols=18 Identities=33% Similarity=0.265 Sum_probs=8.4
Q ss_pred cccCCHHHHHHHHHHHhc
Q 000247 178 EEEMDEEEFDKMMEERYK 195 (1790)
Q Consensus 178 eEd~DaEelAe~LkERY~ 195 (1790)
++|.+++++.=.+++|-.
T Consensus 84 ~~d~~~k~~vl~~~~rkk 101 (390)
T KOG2897|consen 84 EEDEDAKRKVLRTKERKK 101 (390)
T ss_pred ccccccccchhhhHHhhh
Confidence 445555554433444443
Done!