Query 000252
Match_columns 1780
No_of_seqs 397 out of 938
Neff 3.7
Searched_HMMs 46136
Date Fri Mar 29 01:23:47 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/000252.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/000252hhsearch_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 8E-131 2E-135 1190.3 50.2 630 108-758 56-808 (1024)
2 COG5164 SPT5 Transcription elo 100.0 2.6E-52 5.6E-57 477.5 30.3 342 375-744 3-437 (607)
3 PRK08559 nusG transcription an 99.9 8.7E-24 1.9E-28 220.8 16.8 131 222-357 3-133 (153)
4 PF03439 Spt5-NGN: Early trans 99.9 4.1E-22 8.8E-27 190.2 6.8 84 226-310 1-84 (84)
5 KOG1999 RNA polymerase II tran 99.8 2.2E-16 4.7E-21 195.9 49.2 201 490-714 406-639 (1024)
6 TIGR00405 L26e_arch ribosomal 99.8 1.6E-19 3.4E-24 186.4 15.6 124 228-356 1-124 (145)
7 COG0250 NusG Transcription ant 99.7 1.3E-17 2.8E-22 179.1 13.1 133 224-356 2-163 (178)
8 PRK05609 nusG transcription an 99.6 1.2E-14 2.6E-19 154.2 15.6 130 224-356 5-166 (181)
9 TIGR01956 NusG_myco NusG famil 99.6 8.5E-15 1.9E-19 164.1 14.4 129 226-357 1-246 (258)
10 TIGR00922 nusG transcription t 99.6 3.5E-14 7.5E-19 150.0 14.3 127 227-356 1-159 (172)
11 PF11942 Spt5_N: Spt5 transcri 99.5 5.2E-15 1.1E-19 145.3 2.0 92 119-220 1-97 (97)
12 COG5164 SPT5 Transcription elo 99.4 2.3E-14 4.9E-19 167.3 2.4 336 213-590 28-388 (607)
13 PRK09014 rfaH transcriptional 99.4 2.4E-12 5.2E-17 135.3 10.4 126 226-355 3-147 (162)
14 TIGR01955 RfaH transcriptional 99.3 5.2E-12 1.1E-16 131.8 10.4 127 227-356 1-147 (159)
15 smart00738 NGN In Spt5p, this 99.2 3.4E-11 7.4E-16 117.2 9.2 83 226-311 1-105 (106)
16 PF02357 NusG: Transcription t 97.9 2.3E-05 5.1E-10 75.4 6.8 76 226-303 2-91 (92)
17 KOG3973 Uncharacterized conser 97.8 8.1E-05 1.8E-09 86.8 9.2 19 1501-1520 442-460 (465)
18 PF00467 KOW: KOW motif; Inte 97.2 0.00039 8.4E-09 56.6 4.3 32 321-352 1-32 (32)
19 KOG0921 Dosage compensation co 97.1 0.0017 3.7E-08 83.3 10.6 10 1158-1167 1091-1100(1282)
20 PF00467 KOW: KOW motif; Inte 97.1 0.00068 1.5E-08 55.2 4.0 32 662-693 1-32 (32)
21 KOG3973 Uncharacterized conser 96.7 0.0048 1E-07 72.7 9.0 9 351-359 139-147 (465)
22 KOG0921 Dosage compensation co 96.1 0.026 5.7E-07 73.1 10.8 11 71-81 92-102 (1282)
23 TIGR00405 L26e_arch ribosomal 95.6 0.017 3.7E-07 60.8 5.5 50 660-709 87-140 (145)
24 smart00739 KOW KOW (Kyprides, 95.4 0.022 4.8E-07 44.0 3.9 27 555-581 1-27 (28)
25 PRK08559 nusG transcription an 95.2 0.039 8.4E-07 59.2 6.4 51 660-710 95-149 (153)
26 smart00739 KOW KOW (Kyprides, 94.5 0.049 1.1E-06 42.1 3.8 26 319-344 2-27 (28)
27 CHL00141 rpl24 ribosomal prote 94.1 0.075 1.6E-06 52.4 4.9 28 555-582 8-35 (83)
28 PRK12281 rplX 50S ribosomal pr 94.0 0.079 1.7E-06 51.5 4.9 28 555-582 6-33 (76)
29 PRK01191 rpl24p 50S ribosomal 93.9 0.12 2.5E-06 54.3 6.2 50 304-355 33-82 (120)
30 TIGR01955 RfaH transcriptional 93.7 0.11 2.5E-06 55.0 5.8 42 660-701 109-151 (159)
31 PRK00004 rplX 50S ribosomal pr 93.6 0.1 2.2E-06 53.4 5.0 29 554-582 3-31 (105)
32 TIGR00922 nusG transcription t 93.4 0.12 2.6E-06 55.6 5.6 47 660-706 120-170 (172)
33 PRK05609 nusG transcription an 92.9 0.16 3.6E-06 54.9 5.6 48 660-707 127-178 (181)
34 CHL00141 rpl24 ribosomal prote 92.7 0.18 3.8E-06 49.9 5.0 39 316-354 6-44 (83)
35 PF00524 PPV_E1_N: E1 Protein, 91.9 0.049 1.1E-06 57.7 0.2 69 116-198 14-86 (130)
36 TIGR01079 rplX_bact ribosomal 91.9 0.24 5.1E-06 50.9 4.9 28 555-582 3-30 (104)
37 PRK09014 rfaH transcriptional 91.8 0.25 5.5E-06 52.9 5.4 47 660-706 110-159 (162)
38 PRK12281 rplX 50S ribosomal pr 91.6 0.27 5.8E-06 48.0 4.8 38 317-354 5-42 (76)
39 PRK01191 rpl24p 50S ribosomal 91.5 0.38 8.2E-06 50.7 6.0 28 555-582 45-72 (120)
40 TIGR01080 rplX_A_E ribosomal p 91.0 0.44 9.6E-06 49.8 5.9 39 316-354 39-77 (114)
41 TIGR01956 NusG_myco NusG famil 90.8 0.37 8.1E-06 56.2 5.7 47 659-705 205-255 (258)
42 COG0250 NusG Transcription ant 90.8 0.37 8E-06 53.5 5.5 43 659-701 123-167 (178)
43 KOG3262 H/ACA small nucleolar 90.5 0.53 1.2E-05 52.5 6.3 21 1491-1512 193-213 (215)
44 PTZ00194 60S ribosomal protein 90.4 0.53 1.2E-05 50.9 6.0 52 304-357 34-85 (143)
45 PRK00004 rplX 50S ribosomal pr 89.9 0.46 1E-05 48.8 4.9 37 318-354 4-40 (105)
46 PTZ00194 60S ribosomal protein 89.7 0.38 8.2E-06 51.9 4.3 28 555-582 46-73 (143)
47 COG0198 RplX Ribosomal protein 89.4 0.46 1E-05 49.0 4.5 30 554-583 3-32 (104)
48 TIGR01080 rplX_A_E ribosomal p 88.3 0.6 1.3E-05 48.8 4.4 37 660-696 42-78 (114)
49 KOG3262 H/ACA small nucleolar 87.9 1 2.2E-05 50.3 6.1 11 1197-1207 5-15 (215)
50 TIGR01079 rplX_bact ribosomal 86.2 1 2.2E-05 46.4 4.7 36 318-353 3-38 (104)
51 COG2933 Predicted SAM-dependen 85.4 1.2 2.6E-05 52.5 5.2 57 229-292 5-61 (358)
52 KOG1708 Mitochondrial/chloropl 84.2 1.1 2.3E-05 50.8 4.0 30 553-582 70-99 (236)
53 PF11623 DUF3252: Protein of u 82.2 4 8.6E-05 37.8 6.0 47 660-706 2-52 (53)
54 PRK11760 putative 23S rRNA C24 79.6 2.7 5.9E-05 51.3 5.5 65 228-299 4-71 (357)
55 COG0198 RplX Ribosomal protein 78.6 2.9 6.3E-05 43.3 4.6 34 317-352 3-36 (104)
56 KOG0262 RNA polymerase I, larg 77.3 6 0.00013 54.1 7.9 70 226-296 1441-1520(1640)
57 PF04931 DNA_pol_phi: DNA poly 76.6 1.5 3.2E-05 58.1 2.4 16 236-251 764-779 (784)
58 smart00652 eIF1a eukaryotic tr 75.2 15 0.00032 36.7 8.2 66 502-582 5-70 (83)
59 PF09444 MRC1: MRC1-like domai 75.0 0.63 1.4E-05 50.4 -1.3 18 113-130 3-20 (145)
60 CHL00010 infA translation init 74.8 22 0.00048 35.0 9.2 65 504-582 9-73 (78)
61 PTZ00415 transmission-blocking 74.5 1.5 3.2E-05 60.7 1.6 17 223-239 312-328 (2849)
62 KOG1832 HIV-1 Vpr-binding prot 74.0 2.7 5.9E-05 55.4 3.6 9 184-192 1469-1477(1516)
63 PTZ00061 DNA-directed RNA poly 73.8 20 0.00044 41.2 9.9 57 270-329 118-190 (205)
64 PHA02774 E1; Provisional 72.8 1.1 2.4E-05 57.6 -0.2 31 298-332 177-207 (613)
65 KOG0415 Predicted peptidyl pro 71.6 8.9 0.00019 46.8 6.7 112 176-303 198-315 (479)
66 COG1588 POP4 RNase P/RNase MRP 70.7 8.1 0.00017 39.7 5.3 47 660-708 14-63 (95)
67 TIGR01622 SF-CC1 splicing fact 70.7 11 0.00023 46.3 7.5 68 238-311 383-455 (457)
68 cd05793 S1_IF1A S1_IF1A: Trans 70.3 20 0.00044 35.3 7.8 64 504-582 2-65 (77)
69 PF14632 SPT6_acidic: Acidic N 70.1 1.5 3.3E-05 44.5 0.2 9 143-151 20-28 (92)
70 PF14851 FAM176: FAM176 family 69.1 6.4 0.00014 43.4 4.5 16 180-195 115-130 (153)
71 PLN00208 translation initiatio 68.6 17 0.00038 39.8 7.6 77 491-582 20-97 (145)
72 PRK04950 ProP expression regul 66.2 9.2 0.0002 44.1 5.2 46 660-707 167-212 (213)
73 KOG0299 U3 snoRNP-associated p 66.1 3.5 7.5E-05 51.4 2.1 19 180-198 98-116 (479)
74 PF03115 Astro_capsid: Astrovi 66.1 2 4.2E-05 57.0 0.0 13 176-188 717-729 (787)
75 cd04456 S1_IF1A_like S1_IF1A_l 64.7 35 0.00075 33.9 8.2 65 503-582 1-66 (78)
76 PRK00276 infA translation init 64.5 35 0.00076 33.0 8.0 63 505-581 10-72 (72)
77 PTZ00329 eukaryotic translatio 64.2 26 0.00055 39.0 7.9 76 492-582 21-97 (155)
78 PRK04333 50S ribosomal protein 63.3 12 0.00025 37.7 4.7 33 318-351 3-35 (84)
79 PRK03879 ribonuclease P protei 61.6 16 0.00035 37.4 5.5 46 660-707 12-60 (96)
80 PRK04012 translation initiatio 60.6 37 0.0008 35.2 7.8 72 495-581 13-85 (100)
81 PF02724 CDC45: CDC45-like pro 60.5 6 0.00013 51.5 2.9 16 280-295 235-250 (622)
82 PLN03111 DNA-directed RNA poly 60.2 57 0.0012 37.8 9.9 54 274-329 122-191 (206)
83 PF11746 DUF3303: Protein of u 59.8 23 0.0005 35.8 6.2 76 228-303 2-83 (91)
84 TIGR00523 eIF-1A eukaryotic/ar 59.3 31 0.00067 35.7 7.0 64 502-582 19-85 (99)
85 PRK14635 hypothetical protein; 58.4 12 0.00027 41.2 4.3 49 660-708 96-155 (162)
86 PRK04333 50S ribosomal protein 58.3 13 0.00029 37.3 4.2 31 660-690 4-35 (84)
87 PF02736 Myosin_N: Myosin N-te 58.3 19 0.00042 31.5 4.7 30 675-705 12-42 (42)
88 TIGR00739 yajC preprotein tran 57.5 24 0.00051 35.4 5.7 44 660-708 38-81 (84)
89 PRK12269 bifunctional cytidyla 56.8 90 0.0019 42.8 12.5 196 300-565 605-809 (863)
90 PRK05585 yajC preprotein trans 56.1 25 0.00054 36.6 5.8 44 661-709 54-97 (106)
91 PF04931 DNA_pol_phi: DNA poly 56.0 9.8 0.00021 50.7 3.7 7 71-77 545-551 (784)
92 TIGR01659 sex-lethal sex-letha 55.5 39 0.00084 41.4 8.3 67 219-294 102-173 (346)
93 smart00361 RRM_1 RNA recogniti 55.3 25 0.00054 32.9 5.3 28 267-294 34-61 (70)
94 PRK12442 translation initiatio 55.0 49 0.0011 33.8 7.4 63 505-581 10-72 (87)
95 PF01176 eIF-1a: Translation i 54.8 43 0.00093 31.8 6.7 62 503-579 4-65 (65)
96 COG1862 YajC Preprotein transl 53.3 24 0.00053 36.4 5.2 46 662-712 46-91 (97)
97 KOG1708 Mitochondrial/chloropl 53.1 13 0.00028 42.6 3.4 41 659-699 72-115 (236)
98 PTZ00065 60S ribosomal protein 52.9 18 0.00039 39.1 4.4 33 318-351 7-39 (130)
99 PTZ00415 transmission-blocking 52.9 6.7 0.00014 55.0 1.5 17 93-109 120-136 (2849)
100 PF02724 CDC45: CDC45-like pro 52.1 12 0.00026 49.0 3.5 13 184-196 199-211 (622)
101 COG3109 ProQ Activator of osmo 52.1 21 0.00045 40.3 4.7 46 660-707 162-207 (208)
102 PTZ00065 60S ribosomal protein 51.3 27 0.00058 37.9 5.3 35 660-695 8-42 (130)
103 PRK14639 hypothetical protein; 50.8 26 0.00057 37.9 5.2 49 660-708 85-133 (140)
104 PRK12288 GTPase RsgA; Reviewed 50.5 82 0.0018 38.7 9.9 86 504-608 40-127 (347)
105 cd05690 S1_RPS1_repeat_ec5 S1_ 49.1 25 0.00054 32.1 4.2 66 260-351 3-68 (69)
106 PRK05886 yajC preprotein trans 48.7 26 0.00056 36.9 4.6 44 661-709 40-83 (109)
107 PRK00092 ribosome maturation p 48.5 28 0.00061 37.9 5.1 49 660-708 95-147 (154)
108 PF01868 UPF0086: Domain of un 46.9 47 0.001 33.5 6.0 48 660-708 11-61 (89)
109 smart00538 POP4 A domain found 46.4 45 0.00099 34.0 5.8 47 660-707 10-59 (92)
110 TIGR02760 TraI_TIGR conjugativ 45.4 84 0.0018 46.6 10.3 91 489-584 1327-1422(1960)
111 TIGR01642 U2AF_lg U2 snRNP aux 45.4 33 0.00071 42.8 5.7 49 240-294 432-488 (509)
112 smart00316 S1 Ribosomal protei 45.3 53 0.0011 29.1 5.5 67 260-353 5-71 (72)
113 cd01734 YlxS_C YxlS is a Bacil 44.7 36 0.00079 33.5 4.7 49 660-708 22-76 (83)
114 PF10446 DUF2457: Protein of u 44.2 12 0.00025 47.1 1.6 7 226-232 123-129 (458)
115 cd05698 S1_Rrp5_repeat_hs6_sc5 42.8 71 0.0015 29.4 6.1 67 260-353 3-69 (70)
116 PRK14637 hypothetical protein; 42.8 43 0.00093 36.8 5.4 46 660-707 95-141 (151)
117 PF02576 DUF150: Uncharacteris 42.5 41 0.00089 36.0 5.1 49 660-708 84-138 (141)
118 PF10574 UPF0552: Uncharacteri 42.1 31 0.00066 40.2 4.3 109 213-341 44-177 (224)
119 PRK14638 hypothetical protein; 41.6 38 0.00082 37.1 4.8 47 660-708 97-143 (150)
120 PF13051 DUF3912: Protein of u 41.3 52 0.0011 31.4 4.8 49 660-710 3-54 (68)
121 KOG4156 Claspin, protein media 41.1 5 0.00011 51.3 -2.1 13 118-130 1052-1064(1329)
122 TIGR03630 arch_S17P archaeal r 40.5 49 0.0011 34.7 5.0 25 543-567 63-87 (102)
123 PRK14643 hypothetical protein; 40.5 41 0.00089 37.5 4.9 49 660-708 101-157 (164)
124 PRK08572 rps17p 30S ribosomal 39.8 51 0.0011 34.8 5.1 25 543-567 65-89 (108)
125 cd01854 YjeQ_engC YjeQ/EngC. 39.8 1.6E+02 0.0035 35.0 9.9 84 506-608 1-85 (287)
126 cd04451 S1_IF1 S1_IF1: Transla 39.6 1.5E+02 0.0033 27.7 7.8 60 505-578 4-63 (64)
127 COG1471 RPS4A Ribosomal protei 39.3 36 0.00078 40.0 4.3 52 554-609 172-229 (241)
128 PRK14634 hypothetical protein; 38.9 42 0.00091 37.0 4.6 47 660-708 97-147 (155)
129 cd04461 S1_Rrp5_repeat_hs8_sc7 38.5 69 0.0015 30.9 5.5 69 258-353 15-83 (83)
130 COG0361 InfA Translation initi 38.4 1.2E+02 0.0026 30.4 7.1 65 504-582 9-73 (75)
131 PF10842 DUF2642: Protein of u 38.2 73 0.0016 31.1 5.5 45 660-707 18-62 (66)
132 TIGR00008 infA translation ini 38.1 1.3E+02 0.0029 29.5 7.2 61 504-578 7-67 (68)
133 PRK14644 hypothetical protein; 37.8 41 0.00088 36.5 4.2 48 660-707 82-135 (136)
134 KOG0107 Alternative splicing f 37.5 40 0.00087 38.3 4.2 34 259-292 36-69 (195)
135 PF10446 DUF2457: Protein of u 37.4 14 0.0003 46.4 0.8 6 560-565 390-395 (458)
136 PF04050 Upf2: Up-frameshift s 37.3 2.1 4.6E-05 47.0 -5.4 13 183-195 66-78 (170)
137 PRK00098 GTPase RsgA; Reviewed 37.0 2E+02 0.0043 34.4 10.1 86 505-608 2-87 (298)
138 KOG3218 RNA polymerase, 25-kDa 36.3 2E+02 0.0044 33.4 9.4 119 188-329 40-173 (208)
139 PRK11634 ATP-dependent RNA hel 36.2 63 0.0014 42.5 6.4 11 301-311 279-289 (629)
140 PLN00036 40S ribosomal protein 35.4 54 0.0012 39.2 5.0 52 554-609 173-229 (261)
141 PRK02749 photosystem I reactio 35.4 61 0.0013 31.9 4.5 63 319-391 3-69 (71)
142 TIGR02760 TraI_TIGR conjugativ 34.4 1.6E+02 0.0036 43.8 10.4 94 490-588 680-784 (1960)
143 PF00575 S1: S1 RNA binding do 34.1 1.4E+02 0.003 27.8 6.7 57 492-565 2-58 (74)
144 PF11515 Cul7: Mouse developme 33.9 66 0.0014 32.4 4.6 31 317-347 16-49 (78)
145 PRK11634 ATP-dependent RNA hel 33.9 78 0.0017 41.7 6.7 9 684-692 525-533 (629)
146 PRK09521 exosome complex RNA-b 33.7 1.8E+02 0.0039 32.7 8.6 90 491-606 61-156 (189)
147 PTZ00118 40S ribosomal protein 33.5 62 0.0013 38.7 5.1 54 554-609 173-229 (262)
148 cd05703 S1_Rrp5_repeat_hs12_sc 33.4 1E+02 0.0023 29.5 5.8 68 260-353 3-71 (73)
149 PRK10486 autoinducer-2 (AI-2) 33.3 2.1E+02 0.0046 28.7 8.2 65 227-292 5-70 (96)
150 PRK13709 conjugal transfer nic 33.1 1.8E+02 0.0039 42.9 10.3 93 489-589 1273-1373(1747)
151 PTZ00223 40S ribosomal protein 32.6 51 0.0011 39.6 4.3 54 554-609 170-226 (273)
152 PRK14640 hypothetical protein; 32.6 68 0.0015 35.2 5.0 46 660-707 94-143 (152)
153 PF02699 YajC: Preprotein tran 32.3 15 0.00033 36.4 0.0 44 660-708 37-80 (82)
154 PF13893 RRM_5: RNA recognitio 32.2 60 0.0013 28.8 3.7 36 259-294 10-45 (56)
155 KOG0130 RNA-binding protein RB 32.1 70 0.0015 35.3 4.8 61 226-292 71-136 (170)
156 COG1818 Predicted RNA-binding 31.5 1.8E+02 0.0039 33.1 8.0 75 227-310 3-82 (175)
157 CHL00125 psaE photosystem I su 31.4 72 0.0016 30.9 4.2 41 319-360 2-46 (64)
158 PRK14630 hypothetical protein; 31.4 87 0.0019 34.2 5.5 45 660-708 94-139 (143)
159 PLN03134 glycine-rich RNA-bind 30.9 1E+02 0.0022 33.3 5.9 60 225-293 35-99 (144)
160 PRK06531 yajC preprotein trans 30.6 60 0.0013 34.5 4.0 47 662-712 39-85 (113)
161 PRK14645 hypothetical protein; 30.6 69 0.0015 35.4 4.6 45 660-707 99-143 (154)
162 COG2139 RPL21A Ribosomal prote 30.5 85 0.0018 32.8 4.8 49 660-708 33-93 (98)
163 cd05708 S1_Rrp5_repeat_sc12 S1 29.7 1.4E+02 0.003 27.7 5.9 70 260-355 5-74 (77)
164 PRK13709 conjugal transfer nic 29.2 2.2E+02 0.0047 42.1 10.1 92 489-588 646-748 (1747)
165 PRK04313 30S ribosomal protein 29.0 61 0.0013 38.3 4.1 52 554-609 170-227 (237)
166 KOG1819 FYVE finger-containing 28.7 33 0.00072 43.3 2.0 28 211-238 528-556 (990)
167 KOG3130 Uncharacterized conser 28.3 64 0.0014 40.4 4.2 8 219-226 358-365 (514)
168 COG0056 AtpA F0F1-type ATP syn 28.3 95 0.0021 39.8 5.7 33 489-521 44-76 (504)
169 PRK14712 conjugal transfer nic 28.1 2.7E+02 0.0059 40.9 10.6 92 489-587 1144-1242(1623)
170 COG0186 RpsQ Ribosomal protein 28.1 84 0.0018 32.2 4.3 23 544-567 45-67 (87)
171 PF05918 API5: Apoptosis inhib 27.9 20 0.00043 46.5 0.0 10 432-441 271-280 (556)
172 PF02427 PSI_PsaE: Photosystem 27.7 1.1E+02 0.0024 29.6 4.6 40 319-359 1-44 (61)
173 PLN00045 photosystem I reactio 27.6 1E+02 0.0022 32.1 4.8 45 315-360 36-85 (101)
174 PRK05610 rpsQ 30S ribosomal pr 27.6 1.1E+02 0.0023 31.1 5.0 24 544-568 43-66 (84)
175 KOG4211 Splicing factor hnRNP- 27.6 1.2E+02 0.0026 39.1 6.4 97 225-333 8-114 (510)
176 cd05697 S1_Rrp5_repeat_hs5 S1_ 27.4 1.5E+02 0.0032 27.5 5.6 68 259-353 2-69 (69)
177 PF06524 NOA36: NOA36 protein; 27.3 91 0.002 37.4 5.0 26 68-93 210-235 (314)
178 PRK14712 conjugal transfer nic 27.3 2.6E+02 0.0056 41.1 10.1 92 490-589 515-617 (1623)
179 KOG2055 WD40 repeat protein [G 27.2 54 0.0012 41.7 3.4 21 176-196 130-150 (514)
180 PRK14636 hypothetical protein; 27.1 85 0.0018 35.4 4.7 48 660-708 95-146 (176)
181 cd05684 S1_DHX8_helicase S1_DH 27.0 3.4E+02 0.0074 25.9 8.1 53 506-565 6-58 (79)
182 PRK12289 GTPase RsgA; Reviewed 26.8 3.3E+02 0.0071 33.8 9.9 75 503-589 8-85 (352)
183 COG1096 Predicted RNA-binding 26.7 2.2E+02 0.0047 32.9 7.6 42 553-607 116-157 (188)
184 PRK14632 hypothetical protein; 26.7 1E+02 0.0022 34.7 5.1 49 660-708 95-156 (172)
185 cd05688 S1_RPS1_repeat_ec3 S1_ 26.6 1.2E+02 0.0026 27.3 4.8 25 317-351 43-67 (68)
186 PRK08059 general stress protei 26.4 3.8E+02 0.0082 28.3 9.0 80 488-594 1-82 (123)
187 cd05705 S1_Rrp5_repeat_hs14 S1 26.3 1.3E+02 0.0029 29.0 5.2 67 259-351 5-73 (74)
188 PRK11642 exoribonuclease R; Pr 26.3 1.8E+02 0.0038 39.9 8.1 81 259-354 645-725 (813)
189 cd04471 S1_RNase_R S1_RNase_R: 26.0 81 0.0018 29.7 3.7 28 317-354 56-83 (83)
190 TIGR03635 S17_bact 30S ribosom 25.9 1.2E+02 0.0026 29.9 4.8 23 544-567 38-60 (71)
191 PF11623 DUF3252: Protein of u 25.7 1.1E+02 0.0024 28.9 4.2 28 319-346 2-31 (53)
192 COG2163 RPL14A Ribosomal prote 25.6 89 0.0019 33.8 4.3 33 318-351 4-36 (125)
193 PRK14633 hypothetical protein; 25.4 1E+02 0.0023 33.8 4.9 48 660-708 91-142 (150)
194 PRK14646 hypothetical protein; 25.4 1E+02 0.0022 34.2 4.7 47 660-708 97-147 (155)
195 cd05687 S1_RPS1_repeat_ec1_hs1 25.3 2.5E+02 0.0055 25.9 6.7 67 260-353 3-69 (70)
196 cd05792 S1_eIF1AD_like S1_eIF1 25.2 3.1E+02 0.0068 27.7 7.5 64 504-582 2-66 (78)
197 PRK12766 50S ribosomal protein 24.8 19 0.00042 42.1 -0.8 15 180-195 99-113 (232)
198 PRK02001 hypothetical protein; 24.6 1.3E+02 0.0028 33.4 5.3 48 660-707 87-146 (152)
199 PRK08582 hypothetical protein; 24.3 2.4E+02 0.0051 30.7 7.2 57 492-565 3-59 (139)
200 PF11424 DUF3195: Protein of u 24.0 72 0.0016 32.5 3.0 43 228-278 2-44 (89)
201 COG1532 Predicted RNA-binding 24.0 44 0.00095 31.6 1.4 31 322-352 24-56 (57)
202 PRK01889 GTPase RsgA; Reviewed 23.9 2.6E+02 0.0057 34.4 8.4 89 504-608 29-119 (356)
203 COG2139 RPL21A Ribosomal prote 23.9 93 0.002 32.5 3.8 49 488-537 29-91 (98)
204 KOG0943 Predicted ubiquitin-pr 23.8 40 0.00087 46.5 1.6 24 268-291 1915-1938(3015)
205 cd05691 S1_RPS1_repeat_ec6 S1_ 23.8 2.1E+02 0.0046 26.3 5.9 67 260-353 3-69 (73)
206 smart00243 GAS2 Growth-Arrest- 23.7 1.7E+02 0.0037 29.3 5.3 50 304-356 5-55 (73)
207 CHL00142 rps17 ribosomal prote 23.7 1.3E+02 0.0028 30.7 4.7 24 544-568 40-63 (84)
208 PRK05807 hypothetical protein; 23.4 2.4E+02 0.0052 30.5 7.0 57 491-565 2-58 (136)
209 PRK14647 hypothetical protein; 22.6 1.2E+02 0.0027 33.5 4.8 48 660-708 96-152 (159)
210 cd05707 S1_Rrp5_repeat_sc11 S1 22.4 2.1E+02 0.0046 26.4 5.6 64 261-351 4-67 (68)
211 PRK06763 F0F1 ATP synthase sub 22.1 1.5E+02 0.0033 34.5 5.4 15 552-566 161-175 (213)
212 PF02187 GAS2: Growth-Arrest-S 21.9 1.4E+02 0.0031 29.8 4.5 48 304-354 5-53 (73)
213 PLN03078 Putative tRNA pseudou 21.7 1.3E+02 0.0028 39.1 5.4 53 271-323 355-409 (513)
214 PF00076 RRM_1: RNA recognitio 21.4 1.1E+02 0.0023 27.2 3.4 28 267-294 36-63 (70)
215 COG0779 Uncharacterized protei 21.3 1.6E+02 0.0034 32.9 5.2 46 660-707 96-145 (153)
216 cd05706 S1_Rrp5_repeat_sc10 S1 21.2 2.9E+02 0.0062 25.8 6.3 68 259-353 5-72 (73)
217 KOG0339 ATP-dependent RNA heli 21.0 81 0.0018 40.8 3.3 18 406-423 372-391 (731)
218 KOG3297 DNA-directed RNA polym 21.0 6.9E+02 0.015 29.2 10.0 84 330-438 78-165 (202)
219 PF14001 YdfZ: YdfZ protein 20.9 1E+02 0.0022 30.1 3.2 32 548-582 2-33 (64)
220 COG5177 Uncharacterized conser 20.7 67 0.0014 41.3 2.5 18 175-192 437-454 (769)
221 KOG4156 Claspin, protein media 20.5 78 0.0017 41.4 3.1 31 176-207 1027-1058(1329)
222 PF03992 ABM: Antibiotic biosy 20.4 6.3E+02 0.014 23.0 8.3 56 227-282 5-61 (78)
223 PRK00321 rdgC recombination as 20.4 2.7E+02 0.0058 34.1 7.3 85 260-360 124-214 (303)
224 COG2163 RPL14A Ribosomal prote 20.3 1.2E+02 0.0025 33.0 3.8 47 660-707 5-51 (125)
225 PRK12766 50S ribosomal protein 20.3 81 0.0017 37.2 2.9 9 123-131 58-66 (232)
226 COG4371 Predicted membrane pro 20.2 1.6E+02 0.0035 35.3 5.2 49 1437-1486 49-105 (334)
No 1
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=100.00 E-value=8.5e-131 Score=1190.34 Aligned_cols=630 Identities=34% Similarity=0.502 Sum_probs=491.4
Q ss_pred ccccccccccCcceeccccCCCCCchhhcCCCcCCC--CCCCCccchhhhhccCccccccccccCCCCCCCccccCCHHH
Q 000252 108 NRKRKNRSVLQFVEDAADVDYDDDDEEEVGNESDNS--GGFADDDFMEELFDAQPKVNNEMGQAHNLPFIPKEEEMDEEE 185 (1780)
Q Consensus 108 ~rKRkRrr~n~FiDdEAEVDDDeEEEDEeeEe~e~~--~~Fi~dD~~~d~~e~~~~~~~d~r~~~~l~~r~~eEd~DaEe 185 (1780)
.+|+|+.+...||+.|||||||+||+|+|+|++|+. ..||. +..+++++++ .++|.|+.++ ++..+ .+|+
T Consensus 56 ~~~~k~~s~~gf~~~e~dvDdeveddd~~~edEed~~~~~~ie-~~e~~~~d~~----~~~R~~~~~~-~~~~~--~~e~ 127 (1024)
T KOG1999|consen 56 DEKDKKESGGGFIDREADVDDEVEDDDDDEEDEEDIELHNDIE-ESEEDLPDER----GDRRLRRYWD-RQLNE--LEEE 127 (1024)
T ss_pred hhhccccccccccccccccccccccccchhccCcchhhcccch-hccccccccc----ccccchhhhh-hhhhH--HHHH
Confidence 355667888899999999999998877666654321 12222 1112222211 1122222222 12222 5777
Q ss_pred HHHHHHHHhccccchhhchhhHHHhhccccccCCCCCCCCcEEEEEeccchhHHHHHHHHHHHHhhccCCCCCcEEEEEE
Q 000252 186 FDKMMEERYKSNKLIRYAEEDYEAKKMLEREYHMPCPEDPTIWKVKCMAGRERQSAFCLMQKFVDLQSLGSKMQIISAFA 265 (1780)
Q Consensus 186 lAe~lkERY~r~s~~~y~~d~~e~~~~VpQq~LLPSVkDPkLWaVKCK~GKEReVV~sLmrK~i~lq~~g~~L~I~SVFv 265 (1780)
+|+.|+|||.... .|.+.+++++++|+||+|||+|+||+||+|||++|+||+||+|||+||++++++..||+|+|||+
T Consensus 128 ~~~r~aee~~~~~--~~~~~~~~~~d~I~Q~~LLPsvkDP~LW~VKC~iG~Er~~a~~LMrK~i~~~~t~~plqI~Sv~a 205 (1024)
T KOG1999|consen 128 LAKRYAEEYIEKY--GFEDGDDEDSDDIPQQALLPSVKDPNLWIVKCKIGREREVAFCLMRKFIELDKTDTPLQIKSVFA 205 (1024)
T ss_pred HHHHHHHhhcccc--cccccchhcccchhHHhhCCCCCCCCeeEEEeccccHHHHHHHHHHHHHhhcccCCCceEEEEEe
Confidence 7777777776432 13323334458899999999999999999999999999999999999999999999999999999
Q ss_pred eCCCCcEEEEEeccchhHHHHhcCCCCEEeceecccCHHHHHHHhhcccccccccCCCEEEEeCCCCCCCcEEEEEEeCC
Q 000252 266 VDHIKGFIFIEADKQCDINEACKGLSGIYYSRLAPVPKNEVSHLLSAQIKRNEVSEGTWAYVKNGKYKGDLAQVVYVNNA 345 (1780)
Q Consensus 266 pd~lKGYIYVEA~kq~dVkeAIkGI~gVy~~K~~pVPIkEM~dLLkvkkk~~~Lk~GdwVRIKrGpYKGDLAQVveVDen 345 (1780)
+++|+|||||||+++.||++||++|++||..+|+||||+||++||+|+++.+.|++|.|||||+|+||+|||||++|+++
T Consensus 206 ~D~lkGyIYIEA~KqshV~~Ai~gv~niy~~~~~lVPikEM~dvLkV~K~~v~L~~gswVRiKrG~YKgDLAqVd~Vd~~ 285 (1024)
T KOG1999|consen 206 KDHLKGYIYIEADKQSHVKEAIEGVRNIYANRILLVPIKEMPDVLKVVKKVVQLSEGSWVRIKRGKYKGDLAQVDDVDEN 285 (1024)
T ss_pred ccccceeEEEEechhHHHHHHHhhhhhheeccEEEEehhHhhhhhhhhhhhhccCccceEEEeccccccceeeeeeeccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCEEEEEEeccCchhhHhhhcCCCcccCCCCCCCCCCCCHhHHHhhCCceeecccCCCCceEEecCCceeecceEEEEEe
Q 000252 346 RKRATVKLIPRIDLQALAAKFGGGVAMKKTDSPAPRLISPSELEEFRPLIQYRRDRDTGKVFENLDGMMLKDGYLYKKVS 425 (1780)
Q Consensus 346 k~eVtVKLVPRIDy~~l~~k~~gg~~kKK~~RPPqRLFn~~Eark~~~~~e~rrd~~tg~~f~i~~G~~YkDGFLyK~fk 425 (1780)
+++|+|||||||||++++.+++ ....+|++||++|||+..|++.++++++.+++..++.+|+++.+++|+||||||.|+
T Consensus 286 ~n~v~lKlIPRIDyq~~~~~~~-~~~~~ka~~p~~R~~~~~~~~~~~ir~~~~~~~~~Gd~l~~~gn~~~~dGFLyK~v~ 364 (1024)
T KOG1999|consen 286 RNRVRLKLIPRIDYQKLLGKLE-ETTDKKAFRPAPRRPNQKEFDEEAIRSEGRRDHSRGDYLEFEGNELFKDGFLYKDVS 364 (1024)
T ss_pred CCEEEEEEeccccHHhhhcccc-ccchhhccCCcccCCCccccchhhhhhccccccccCceEEecCCceeccceeeeeee
Confidence 9999999999999999998887 566778899999999999999999888889999999999888888999999999999
Q ss_pred ccceEeCCCCCCHHHHhhcCCCCCCccccHHHHHHHH-------------------hccc--cccEEEe-----------
Q 000252 426 IDSLSCWGVVPSEEELLKFQPSESNESADLEWLSQLY-------------------GERK--KKRTTIV----------- 473 (1780)
Q Consensus 426 IssL~tedVnPTLEEL~kF~~~~~~e~~DL~~La~i~-------------------ge~k--k~kIi~v----------- 473 (1780)
|++|++++|+|||+||+||++..+ .+||+.++.++ |+++ |+.|..|
T Consensus 365 i~sI~t~gV~PT~dELekF~~~~e--~~Dl~~~st~~~~r~~~~~F~~GD~VeV~~Gel~glkG~ve~vdg~~vti~~~~ 442 (1024)
T KOG1999|consen 365 ISSIITDGVKPTLDELEKFNPSNE--EGDLEWVSTLKSNRKKKHLFSPGDAVEVIVGELKGLKGKVESVDGTIVTIMSKH 442 (1024)
T ss_pred cceeeecCcccCHHHHHhhcCCCc--cccceeeeeeccccccccccCCCCeEEEeeeeeccceeEEEeccCceEEEeecc
Confidence 999999999999999999998744 78888765221 1111 1111111
Q ss_pred --------------------------ecCCCcc-----------------------------------cccCCCCccccc
Q 000252 474 --------------------------GKGGDKG-----------------------------------EGSSGSSLENSF 492 (1780)
Q Consensus 474 --------------------------~kGg~kg-----------------------------------E~ssG~~slG~F 492 (1780)
+.|.+++ |+.++++.+++|
T Consensus 443 e~l~~pl~~~~~eLrKyF~~GDhVKVi~G~~eG~tGlVvrVe~~~vi~~Sd~t~eel~Vf~~dlq~c~ev~~gv~~~ge~ 522 (1024)
T KOG1999|consen 443 EDLKGPLEVPASELRKYFEPGDHVKVIAGRYEGDTGLVVRVEQGDVILLSDLTMEELKVFARDLQLCSEVTLGVEKSGEY 522 (1024)
T ss_pred ccCCCccccchHhhhhhccCCCeEEEEeccccCCcceEEEEeCCeEEEEecCccceeeEEehhcccchheeecccccccc
Confidence 1121221 345567789999
Q ss_pred ccCceEEecCCceEEEEEEecCceEEEccCCCCCCceEEEecccccCCCCCCccccccCCCCcccCCCeEEEecCCCCCc
Q 000252 493 ELYELVCFGRKDFGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVSEGPSKDR 572 (1780)
Q Consensus 493 eLhDLVQLD~~TVGVIVrVEKDEsfkVLdq~gd~pkVvtVkp~eI~~K~~~rR~vA~D~ngn~I~vGD~VKVIdGphkGR 572 (1780)
||||||||+.++|||||++|+ +.|+||++++ +|++|++++|..|+..++++|+|+++|+|+++|+|+||.||+++|
T Consensus 523 e~hdlVqLd~~~vgvI~rle~-e~~~vl~~~g---~v~~i~~~~i~~kk~~r~~~~~D~~~n~I~~kD~Vkvi~Gp~~g~ 598 (1024)
T KOG1999|consen 523 ELHDLVQLDNQNVGVIVRLER-ETFQVLGMNG---KVVTIRKSSITKKKDNRKAVAVDRNGNEIRVKDTVKVIGGPSKGR 598 (1024)
T ss_pred cccceeecCCCcEEEEEEecc-hheeeecCcC---ceEEEeechhhhhhhhhhheeecccCCeecccceEEEecCCCCCc
Confidence 999999999999999999999 5999999885 799999999999988888999999999999999999999999999
Q ss_pred eEEEEEEECCEEEEEeCcceeeccEEEEeCCceeecccccccCCCCCCCCCCCCCC-CCCCCCCCCCCcchhh--hccCc
Q 000252 573 QGIVKKIYRGILFIYDENETENGGYFCSKSQHCEKTKVEACEGKGGGSGASGFEEF-PSSPKSPLSPKRSWQA--REQNT 649 (1780)
Q Consensus 573 qG~V~HIyRs~VFL~Sr~~tENgGIFVvRArnv~tv~~~~~~~Kgg~~~~~~f~dl-~~sP~~~lsp~~p~~~--~~~~~ 649 (1780)
+|.|+||||.+||||+++++||+||||||++||++++.... ....+...++| +|+|.-.++|+.|... ....+
T Consensus 599 ~G~v~~i~r~~~F~h~r~~~En~Gv~vck~k~~~~~g~~~s----t~~~~~~~~~l~~msP~r~~sp~~~~~~~ga~g~~ 674 (1024)
T KOG1999|consen 599 EGEVLHIYRPFVFLHSRKNLENGGVFVCKEKNLILAGGKKS----TNSLAFNKGALAPMSPGRIQSPMGPSGGPGAFGGH 674 (1024)
T ss_pred cCccceeecceeeeeehhhcccCCeEEEecCCceeccccCc----ccchhhcccccCCCCcccccCCcCCCCCCCCcCcC
Confidence 99999999999999999999999999999999998764211 01111111122 3344222344443211 11112
Q ss_pred cCcCCCCCCccccCCEEEEccCCCCCceeEEEEEeCCeEEEEecCcceEEEEecCccccccCC--c--ccc---------
Q 000252 650 EFKRGDRDGMFAVGQTLRIRVGPLKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLAEVRGK--S--FIT--------- 716 (1780)
Q Consensus 650 ~fgRGgRD~d~lIGKTVKIrkGPYKGylGiVKDaTdt~ARVELHSk~KtITVdK~~Ls~v~~k--~--~~~--------- 716 (1780)
..+|++++++.|||+||+|+.||||||+|||||+|+++||||||++|++|+|++.+|.++... . +++
T Consensus 675 gggrGg~rd~~l~GktVrI~~Gp~KG~~GivkD~~~~~arVELhs~~~ti~vd~~~~~~v~~~~~~g~~~sYg~~~~~~g 754 (1024)
T KOG1999|consen 675 GGGRGGNRDDSLLGKTVRIRLGPKKGYLGIVKDVNGDTARVELHSKCVTIKVDRLKRKIVGSTRDGGETSSYGERTPGYG 754 (1024)
T ss_pred ccCccCcCcchhcCcEEEEecCCcccccceeEeccCCeeEEEEEeccEEEEechhhceEEeeccCCCCcccccccccccc
Confidence 224555334689999999999999999999999999999999999999999999999986422 1 111
Q ss_pred ---cccCCCCCCCc-----cCCCC---CCC-CCCCCCCCCCcccCCCCCCCCCC
Q 000252 717 ---STSDDQGSASF-----KPFDP---LGA-GGGSGDWMSAATTSAEGDRWNAG 758 (1780)
Q Consensus 717 ---s~s~d~~s~~~-----~p~~~---~g~-~~~~g~~~~g~gtsa~~~~wn~G 758 (1780)
.+.+++.+.+. +|+-. ++. .++..+++.|++||+++.+|++.
T Consensus 755 ~~~~~~~~~Gs~tp~~~s~tpl~~~s~tp~~~~~~Tp~~dG~rTP~r~~aW~~~ 808 (1024)
T KOG1999|consen 755 RVTPARYGMGSSTPMYGSNTPLWGGSRTPARDGGATPSHDGSRTPARGRAWNPY 808 (1024)
T ss_pred ccCccccCCCCcCccCCCCCCCCCcccCccccCCCCcCCCCCcCCCCCCCcCCC
Confidence 11122222111 11111 111 24566677899999999999976
No 2
>COG5164 SPT5 Transcription elongation factor [Transcription]
Probab=100.00 E-value=2.6e-52 Score=477.50 Aligned_cols=342 Identities=21% Similarity=0.212 Sum_probs=254.4
Q ss_pred CCCCCCCCCCHhHHHhhCCceeecccCCCCceEEecCCceeecceEEEEEeccceEeCCCCCCHHHHhhcCCCCCCcccc
Q 000252 375 TDSPAPRLISPSELEEFRPLIQYRRDRDTGKVFENLDGMMLKDGYLYKKVSIDSLSCWGVVPSEEELLKFQPSESNESAD 454 (1780)
Q Consensus 375 ~~RPPqRLFn~~Eark~~~~~e~rrd~~tg~~f~i~~G~~YkDGFLyK~fkIssL~tedVnPTLEEL~kF~~~~~~e~~D 454 (1780)
+.|||+|||||.|+.++.+...+.|++. .| .|.++.|+||||||.|+|++++|++|+||+|||.+|...+. .+|
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 35 57799999999999999999999999999999999997654 588
Q ss_pred HHHHHHHH-----------------hcccc---------ccEE---------------------------EeecCCCccc
Q 000252 455 LEWLSQLY-----------------GERKK---------KRTT---------------------------IVGKGGDKGE 481 (1780)
Q Consensus 455 L~~La~i~-----------------ge~kk---------~kIi---------------------------~v~kGg~kgE 481 (1780)
|-.+++.+ |+++. .-|+ .|+.++++.+
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 88777644 22211 0111 0111222221
Q ss_pred cc--------------------------------CCCCcccccccCceEEecCCceEEEEEEecCceEEEccCCCCCCce
Q 000252 482 GS--------------------------------SGSSLENSFELYELVCFGRKDFGLIVGMEKDDHYKILKEGSEGPAV 529 (1780)
Q Consensus 482 ~s--------------------------------sG~~slG~FeLhDLVQLD~~TVGVIVrVEKDEsfkVLdq~gd~pkV 529 (1780)
.. ........|+|||||+|+..+|.||+.|++| .|+|+++.+ +|
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 0011346899999999999999999999995 999999985 69
Q ss_pred EEEecccccCCCCCCcc--ccccCCCCcccCCCeEEEecCCCCCceEEEEEEECCEEEEEeCcceeeccEEEEeCCceee
Q 000252 530 VTVERRTLKNGPFDMKF--TALDQSMKVISLNDTARVSEGPSKDRQGIVKKIYRGILFIYDENETENGGYFCSKSQHCEK 607 (1780)
Q Consensus 530 vtVkp~eI~~K~~~rR~--vA~D~ngn~I~vGD~VKVIdGphkGRqG~V~HIyRs~VFL~Sr~~tENgGIFVvRArnv~t 607 (1780)
.|+.+.+|..|+..+|. +++|+++++|+++|.|+++.| .+++|+|+|||+.|+|++++.+.||.||||++.+||.+
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 99999999999877774 899999999999999999999 67999999999999999999999999999999999998
Q ss_pred cccccccCCCCCCC-CCCCCCCCCCCCCCCC--CCcchhhhccCccCcC--CCCCCccccCCEEEEccCCCCCceeEEEE
Q 000252 608 TKVEACEGKGGGSG-ASGFEEFPSSPKSPLS--PKRSWQAREQNTEFKR--GDRDGMFAVGQTLRIRVGPLKGYLCRVLA 682 (1780)
Q Consensus 608 v~~~~~~~Kgg~~~-~~~f~dl~~sP~~~ls--p~~p~~~~~~~~~fgR--GgRD~d~lIGKTVKIrkGPYKGylGiVKD 682 (1780)
|+ +|+.+.. .-+|.+ |+|++. +..|. -..+.| ++| +.+||+||+||.|+|||++|+|||
T Consensus 311 VA-----tkd~~~s~k~dl~k----mnp~v~~~~~~p~-----~~~l~r~i~gR--d~aigktVrIr~g~yKG~lGVVKd 374 (607)
T COG5164 311 VA-----TKDFTESLKVDLDK----MNPPVTVNLQNPK-----TNELERKIVGR--DPAIGKTVRIRCGEYKGHLGVVKD 374 (607)
T ss_pred EE-----eccchhhhcccHhh----cCchhhcCCCCCc-----chhhhcccccc--ccccCceEEEeecccccccceeee
Confidence 85 3554422 112332 333321 11111 011222 345 489999999999999999999999
Q ss_pred EeCCeEEEEecCcceEEEEecCccccccCCc-ccccccCCCCCCCccCCCCCCCCCCCCCCCC
Q 000252 683 VRYSDVTVKLDSQQKILTVKGEHLAEVRGKS-FITSTSDDQGSASFKPFDPLGAGGGSGDWMS 744 (1780)
Q Consensus 683 aTdt~ARVELHSk~KtITVdK~~Ls~v~~k~-~~~s~s~d~~s~~~~p~~~~g~~~~~g~~~~ 744 (1780)
++++.|||||||+||.|||+|++|.+..-.. .++..---...+...|.++-.+-++.-+.+.
T Consensus 375 v~~~~arVeLhs~nK~VTI~K~~l~y~~reGe~ity~e~vnr~~~~~p~r~s~a~gs~~pn~a 437 (607)
T COG5164 375 VDRNIARVELHSNNKFVTIEKSRLAYLGREGEGITYDELVNRRGLSKPLRYSEAIGSKTPNYA 437 (607)
T ss_pred ccCceEEEEEecCCceEEeehhheEEecccccccchhhhhhhhcCCCcccccccccCCCCCcc
Confidence 9999999999999999999999999853222 1222111233445566665555544444333
No 3
>PRK08559 nusG transcription antitermination protein NusG; Validated
Probab=99.91 E-value=8.7e-24 Score=220.83 Aligned_cols=131 Identities=27% Similarity=0.446 Sum_probs=119.4
Q ss_pred CCCCcEEEEEeccchhHHHHHHHHHHHHhhccCCCCCcEEEEEEeCCCCcEEEEEeccchhHHHHhcCCCCEEeceeccc
Q 000252 222 PEDPTIWKVKCMAGRERQSAFCLMQKFVDLQSLGSKMQIISAFAVDHIKGFIFIEADKQCDINEACKGLSGIYYSRLAPV 301 (1780)
Q Consensus 222 VkDPkLWaVKCK~GKEReVV~sLmrK~i~lq~~g~~L~I~SVFvpd~lKGYIYVEA~kq~dVkeAIkGI~gVy~~K~~pV 301 (1780)
-+||+||+|+|++|+|+.|+.+|++|+... ++.|++||+|+.|||||||||++.++++++|+++++|++....+|
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 000252 302 PKNEVSHLLSAQIKRNEVSEGTWAYVKNGKYKGDLAQVVYVNNARKRATVKLIPRI 357 (1780)
Q Consensus 302 PIkEM~dLLkvkkk~~~Lk~GdwVRIKrGpYKGDLAQVveVDenk~eVtVKLVPRI 357 (1780)
|++||..||...+....|++|++|||++|||+|++|+|++|+.++.+|+|+|+.|-
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 99999999986654567999999999999999999999999999999999999864
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=4.1e-22 Score=190.18 Aligned_cols=84 Identities=43% Similarity=0.727 Sum_probs=71.7
Q ss_pred cEEEEEeccchhHHHHHHHHHHHHhhccCCCCCcEEEEEEeCCCCcEEEEEeccchhHHHHhcCCCCEEeceecccCHHH
Q 000252 226 TIWKVKCMAGRERQSAFCLMQKFVDLQSLGSKMQIISAFAVDHIKGFIFIEADKQCDINEACKGLSGIYYSRLAPVPKNE 305 (1780)
Q Consensus 226 kLWaVKCK~GKEReVV~sLmrK~i~lq~~g~~L~I~SVFvpd~lKGYIYVEA~kq~dVkeAIkGI~gVy~~K~~pVPIkE 305 (1780)
+||+|||++|+|++||++||+|++++..... +.|+|||+|+++||||||||+++++|.+||++|++||...+.+||++|
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 000252 306 VSHLL 310 (1780)
Q Consensus 306 M~dLL 310 (1780)
|++||
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=2.2e-16 Score=195.92 Aligned_cols=201 Identities=18% Similarity=0.224 Sum_probs=137.5
Q ss_pred cccccCceEEec----CCceEEEEEEecCceEEEccCCCCCCceEEEecccccCCCCCCccccccCCCCcccCCCeEEEe
Q 000252 490 NSFELYELVCFG----RKDFGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVS 565 (1780)
Q Consensus 490 G~FeLhDLVQLD----~~TVGVIVrVEKDEsfkVLdq~gd~pkVvtVkp~eI~~K~~~rR~vA~D~ngn~I~vGD~VKVI 565 (1780)
..|+.+|.|+|. .+..|+|++|+.+ .++|+....+++..+.|+.++| .|+|++|||||||
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 359999999984 3577999999984 5444433223334445554443 7999999999999
Q ss_pred cCCCCCceEEEEEEECCEEEEEeCcceeeccEEEEeCCceeecccccccCCCCCCCCCCCCCCCCCCCCC----------
Q 000252 566 EGPSKDRQGIVKKIYRGILFIYDENETENGGYFCSKSQHCEKTKVEACEGKGGGSGASGFEEFPSSPKSP---------- 635 (1780)
Q Consensus 566 dGphkGRqG~V~HIyRs~VFL~Sr~~tENgGIFVvRArnv~tv~~~~~~~Kgg~~~~~~f~dl~~sP~~~---------- 635 (1780)
.|+|+|.+|+|+.|++++|||+++.++|+..|||+....|..|++. ..+.+ ...+.+|.......
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 12223332211000
Q ss_pred ------CCCC----cch--hhhccCccCcC--CCCCCccccCCEEEEccCCCCCceeEEEEEeCCeEEEEecCcce----
Q 000252 636 ------LSPK----RSW--QAREQNTEFKR--GDRDGMFAVGQTLRIRVGPLKGYLCRVLAVRYSDVTVKLDSQQK---- 697 (1780)
Q Consensus 636 ------lsp~----~p~--~~~~~~~~fgR--GgRD~d~lIGKTVKIrkGPYKGylGiVKDaTdt~ARVELHSk~K---- 697 (1780)
|.+. ++. .....+ ++.. -+......|+.+|+++.||.||-.|.|+.+....+. ||+++-
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 0000 000 000001 1100 012234678999999999999999999999999988 888775
Q ss_pred -EEEEecCccccccCCcc
Q 000252 698 -ILTVKGEHLAEVRGKSF 714 (1780)
Q Consensus 698 -tITVdK~~Ls~v~~k~~ 714 (1780)
++.+...+|.++.++.+
T Consensus 622 Gv~vck~k~~~~~g~~~s 639 (1024)
T KOG1999|consen 622 GVFVCKEKNLILAGGKKS 639 (1024)
T ss_pred CeEEEecCCceeccccCc
Confidence 77788888888766543
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=1.6e-19 Score=186.39 Aligned_cols=124 Identities=23% Similarity=0.409 Sum_probs=110.8
Q ss_pred EEEEeccchhHHHHHHHHHHHHhhccCCCCCcEEEEEEeCCCCcEEEEEeccchhHHHHhcCCCCEEeceecccCHHHHH
Q 000252 228 WKVKCMAGRERQSAFCLMQKFVDLQSLGSKMQIISAFAVDHIKGFIFIEADKQCDINEACKGLSGIYYSRLAPVPKNEVS 307 (1780)
Q Consensus 228 WaVKCK~GKEReVV~sLmrK~i~lq~~g~~L~I~SVFvpd~lKGYIYVEA~kq~dVkeAIkGI~gVy~~K~~pVPIkEM~ 307 (1780)
|+|+|++|+|+.|+..|.+|+.. ..+.|+++|+|..||||||||+....+++++|+.+++|......+||.+||.
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 3466999999999999999999999999999999999988655689999999
Q ss_pred HHhhcccccccccCCCEEEEeCCCCCCCcEEEEEEeCCCCEEEEEEecc
Q 000252 308 HLLSAQIKRNEVSEGTWAYVKNGKYKGDLAQVVYVNNARKRATVKLIPR 356 (1780)
Q Consensus 308 dLLkvkkk~~~Lk~GdwVRIKrGpYKGDLAQVveVDenk~eVtVKLVPR 356 (1780)
.||........|++|++|||++|||+|++|+|++++.++..|+|.|+-+
T Consensus 76 ~l~~~~~~~~~~~~Gd~V~I~~GPf~G~~g~v~~~d~~k~~v~v~l~~~ 124 (145)
T TIGR00405 76 RFLTPKKIIESIKKGDIVEIISGPFKGERAKVIRVDESKEEVTLELIEA 124 (145)
T ss_pred HHhcccccccccCCCCEEEEeecCCCCCeEEEEEEcCCCCEEEEEEEEc
Confidence 9997533234589999999999999999999999999999999999874
No 7
>COG0250 NusG Transcription antiterminator [Transcription]
Probab=99.74 E-value=1.3e-17 Score=179.09 Aligned_cols=133 Identities=17% Similarity=0.226 Sum_probs=110.5
Q ss_pred CCcEEEEEeccchhHHHHHHHHHHHHhhccCCCC--------------CcEEEEEEeCCCCcEEEEEeccchhHHHHhcC
Q 000252 224 DPTIWKVKCMAGRERQSAFCLMQKFVDLQSLGSK--------------MQIISAFAVDHIKGFIFIEADKQCDINEACKG 289 (1780)
Q Consensus 224 DPkLWaVKCK~GKEReVV~sLmrK~i~lq~~g~~--------------L~I~SVFvpd~lKGYIYVEA~kq~dVkeAIkG 289 (1780)
.++||+|+|++|+|+.|+..|++++..+.....- ...+.++.++.|||||||||.+.++++++|+.
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 5789999999999999999999999887643110 02344477889999999999999999999999
Q ss_pred CCCEEe------ceecccCHHHHHHHhhcc-------cccccccCCCEEEEeCCCCCCCcEEEEEEeCCCCE--EEEEEe
Q 000252 290 LSGIYY------SRLAPVPKNEVSHLLSAQ-------IKRNEVSEGTWAYVKNGKYKGDLAQVVYVNNARKR--ATVKLI 354 (1780)
Q Consensus 290 I~gVy~------~K~~pVPIkEM~dLLkvk-------kk~~~Lk~GdwVRIKrGpYKGDLAQVveVDenk~e--VtVKLV 354 (1780)
+|+|.+ .+|.||+.+||.++|... +..+.|++|+.|||+.|||+++.|+|.+||.++.+ |.|.++
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 999864 478999999999966532 23578999999999999999999999999999875 555556
Q ss_pred cc
Q 000252 355 PR 356 (1780)
Q Consensus 355 PR 356 (1780)
.|
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=99.60 E-value=1.2e-14 Score=154.25 Aligned_cols=130 Identities=16% Similarity=0.233 Sum_probs=103.3
Q ss_pred CCcEEEEEeccchhHHHHHHHHHHHHhhccCCCCCcEEEEEEe-----------------CCCCcEEEEEeccchhHHHH
Q 000252 224 DPTIWKVKCMAGRERQSAFCLMQKFVDLQSLGSKMQIISAFAV-----------------DHIKGFIFIEADKQCDINEA 286 (1780)
Q Consensus 224 DPkLWaVKCK~GKEReVV~sLmrK~i~lq~~g~~L~I~SVFvp-----------------d~lKGYIYVEA~kq~dVkeA 286 (1780)
+.+||+|+|++|+|+.|+..|.+++.... .+..++.+|+| +.|||||||++.....+...
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------ceecccCHHHHHHHhhc-c------cccccccCCCEEEEeCCCCCCCcEEEEEEeCCCC--EEEE
Q 000252 287 CKGLSGIYY------SRLAPVPKNEVSHLLSA-Q------IKRNEVSEGTWAYVKNGKYKGDLAQVVYVNNARK--RATV 351 (1780)
Q Consensus 287 IkGI~gVy~------~K~~pVPIkEM~dLLkv-k------kk~~~Lk~GdwVRIKrGpYKGDLAQVveVDenk~--eVtV 351 (1780)
|+.+++|.. .+|.+||.+||..|+.. . .....|++|+.|||+.|||+|..|+|++|+..+. .|.|
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 999998742 36889999999999873 1 1235688999999999999999999999997665 4667
Q ss_pred EEecc
Q 000252 352 KLIPR 356 (1780)
Q Consensus 352 KLVPR 356 (1780)
.|+.|
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=99.59 E-value=8.5e-15 Score=164.13 Aligned_cols=129 Identities=13% Similarity=0.213 Sum_probs=104.6
Q ss_pred cEEEEEeccchhHHHHHHHHHHHHhhccCCCCCcEEEEEEe---------------------------------------
Q 000252 226 TIWKVKCMAGRERQSAFCLMQKFVDLQSLGSKMQIISAFAV--------------------------------------- 266 (1780)
Q Consensus 226 kLWaVKCK~GKEReVV~sLmrK~i~lq~~g~~L~I~SVFvp--------------------------------------- 266 (1780)
+||+|+|.+|+|..|+..|++|+..+.. ...|..|++|
T Consensus 1 kWYvv~t~sG~E~kV~~~l~~kv~~~~~---ed~i~~v~Vp~e~~ve~~v~e~k~~~~p~~~k~~~~~~w~~~~~gk~~k 77 (258)
T TIGR01956 1 QWYIATTINGNEDEVIENIKAKVRALGL---ENYISDFKILKEREIEEKVFEPKNGQAPRSMKNTATTKWETLDETKYKK 77 (258)
T ss_pred CeEEEEeeCCcHHHHHHHHHHHHHhCCC---ccEEEEEEEeeeEEEEEEEEEeecCcccccccccccccceeccCCcccc
Confidence 5999999999999999999999987653 2234444433
Q ss_pred ------CCCCcEEEEEeccchhHHHHhcCCCCEEe--------ceecccCHHHH-HHHhhccc-----------------
Q 000252 267 ------DHIKGFIFIEADKQCDINEACKGLSGIYY--------SRLAPVPKNEV-SHLLSAQI----------------- 314 (1780)
Q Consensus 267 ------d~lKGYIYVEA~kq~dVkeAIkGI~gVy~--------~K~~pVPIkEM-~dLLkvkk----------------- 314 (1780)
..|||||||+|.+.++++++|+.+++|.+ .+|+||+.+|+ .+||....
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 46999999999999999999999999863 27999999888 78885211
Q ss_pred --------------------------------------------ccccccCCCEEEEeCCCCCCCcEEEEEEeCCCC--E
Q 000252 315 --------------------------------------------KRNEVSEGTWAYVKNGKYKGDLAQVVYVNNARK--R 348 (1780)
Q Consensus 315 --------------------------------------------k~~~Lk~GdwVRIKrGpYKGDLAQVveVDenk~--e 348 (1780)
..+.|++|+.|||+.|||+|+.|+|++|+.++. .
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 124578999999999999999999999997655 5
Q ss_pred EEEEEeccC
Q 000252 349 ATVKLIPRI 357 (1780)
Q Consensus 349 VtVKLVPRI 357 (1780)
|.|.||.|.
T Consensus 238 VlV~IfGR~ 246 (258)
T TIGR01956 238 VEVEILGKS 246 (258)
T ss_pred EEEEecCCc
Confidence 667777763
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=99.56 E-value=3.5e-14 Score=150.02 Aligned_cols=127 Identities=17% Similarity=0.212 Sum_probs=100.3
Q ss_pred EEEEEeccchhHHHHHHHHHHHHhhccCCCCCcEEEEEEe-----------------CCCCcEEEEEeccchhHHHHhcC
Q 000252 227 IWKVKCMAGRERQSAFCLMQKFVDLQSLGSKMQIISAFAV-----------------DHIKGFIFIEADKQCDINEACKG 289 (1780)
Q Consensus 227 LWaVKCK~GKEReVV~sLmrK~i~lq~~g~~L~I~SVFvp-----------------d~lKGYIYVEA~kq~dVkeAIkG 289 (1780)
||+|+|++|+|+.|+..|.+++..+. .+-.++.+|+| +.|||||||++....+.+..|..
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 89999999999999999998864322 11113344444 68999999999988888999999
Q ss_pred CCCEEe-----ceecccCH-HHHHHHhhccc-------ccccccCCCEEEEeCCCCCCCcEEEEEEeCCCC--EEEEEEe
Q 000252 290 LSGIYY-----SRLAPVPK-NEVSHLLSAQI-------KRNEVSEGTWAYVKNGKYKGDLAQVVYVNNARK--RATVKLI 354 (1780)
Q Consensus 290 I~gVy~-----~K~~pVPI-kEM~dLLkvkk-------k~~~Lk~GdwVRIKrGpYKGDLAQVveVDenk~--eVtVKLV 354 (1780)
+++|.. .+|.+||. +||..|+.... ....|++|+.|||+.|||+|.+|.|++|+..+. .|.|.|+
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 999754 36899999 99999986421 123488999999999999999999999996665 4666777
Q ss_pred cc
Q 000252 355 PR 356 (1780)
Q Consensus 355 PR 356 (1780)
.|
T Consensus 158 g~ 159 (172)
T TIGR00922 158 GR 159 (172)
T ss_pred CC
Confidence 75
No 11
>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=5.2e-15 Score=145.34 Aligned_cols=92 Identities=27% Similarity=0.452 Sum_probs=57.7
Q ss_pred cceeccccCCCCCchhhcCCCcCCCCCCCCcc--chhhhhccCccccccccccCCCCC-CCccccCCHHHHHHHHH--HH
Q 000252 119 FVEDAADVDYDDDDEEEVGNESDNSGGFADDD--FMEELFDAQPKVNNEMGQAHNLPF-IPKEEEMDEEEFDKMME--ER 193 (1780)
Q Consensus 119 FiDdEAEVDDDeEEEDEeeEe~e~~~~Fi~dD--~~~d~~e~~~~~~~d~r~~~~l~~-r~~eEd~DaEelAe~lk--ER 193 (1780)
|||+||+||||+|||||++++. .||... ++++. . ...+.++|+.+++ ++++++|++|+||++|+ +|
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 1112334444544 58889999999999999 99
Q ss_pred hccccchhhchhhHHHhhccccccCCC
Q 000252 194 YKSNKLIRYAEEDYEAKKMLEREYHMP 220 (1780)
Q Consensus 194 Y~r~s~~~y~~d~~e~~~~VpQq~LLP 220 (1780)
|++++...+... .+.+.+||||+|||
T Consensus 72 Y~~~~~~~~~~~-~~~~~~v~q~~LLP 97 (97)
T PF11942_consen 72 YARSSESRYDGD-DEDSDEVPQQLLLP 97 (97)
T ss_pred hccccccccccc-ccccccchHhccCc
Confidence 998641112122 12347899999999
No 12
>COG5164 SPT5 Transcription elongation factor [Transcription]
Probab=99.45 E-value=2.3e-14 Score=167.32 Aligned_cols=336 Identities=20% Similarity=0.234 Sum_probs=202.6
Q ss_pred cccccCCCCCCCCcEEEEEeccchhHHHHHHHHHHHHhhccCCCCCcEEEEEEeCCCCcEEEEEeccchhHH----HHhc
Q 000252 213 LEREYHMPCPEDPTIWKVKCMAGRERQSAFCLMQKFVDLQSLGSKMQIISAFAVDHIKGFIFIEADKQCDIN----EACK 288 (1780)
Q Consensus 213 VpQq~LLPSVkDPkLWaVKCK~GKEReVV~sLmrK~i~lq~~g~~L~I~SVFvpd~lKGYIYVEA~kq~dVk----eAIk 288 (1780)
.+|.+|.|--+-+..|+||++...|+++...+ . +..++.++++.+-+ |+.|.|+|+.+..|+. ++|+
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 DDRHFTYKNEDYIDGFLVKVKRISERETLMRI----P----TNDEKNVFSIICKD-LDLYSYVESFKKQHAVFQPGDALE 98 (607)
T ss_pred CchhccccCcccccceEEEEeeeceeeecccc----c----ccchhhhcCccccc-cchhHHHHHHhhcccccCCCCeee
Confidence 67888999988899999999999999874322 2 23466677777755 9999999999999998 8888
Q ss_pred CCCCEEeceecccC-HHHHHHHhhcccccccccCCCEEEEeCCCCCCCcEEEEEEeCCCCEEEEEEeccCchhhHhhhcC
Q 000252 289 GLSGIYYSRLAPVP-KNEVSHLLSAQIKRNEVSEGTWAYVKNGKYKGDLAQVVYVNNARKRATVKLIPRIDLQALAAKFG 367 (1780)
Q Consensus 289 GI~gVy~~K~~pVP-IkEM~dLLkvkkk~~~Lk~GdwVRIKrGpYKGDLAQVveVDenk~eVtVKLVPRIDy~~l~~k~~ 367 (1780)
=++++-....-.|| .+||...|...- ..-..+-|-||+.+.|+||+++|++= +.++.+.||||||-..
T Consensus 99 vl~Geqrg~~gVV~~~~~~I~tm~~~~--~~rl~~p~~~lRk~f~~gD~vkVI~g---~~~~d~g~V~rI~~~~------ 167 (607)
T COG5164 99 VLRGEQRGRVGVVPRQKEMIETMTYHF--EQRLCGPWGRLRKGFYKGDLVKVIEG---GEMVDIGTVPRIDGEK------ 167 (607)
T ss_pred eecceecccceeecccccceeeeeecc--CceeecchhhhhcccccCCeEEEecc---ccccccceEEEecCce------
Confidence 88877665555566 777776665431 11235678888889999998888864 5678889999998431
Q ss_pred CCcccCCCCCCCCCCCCHhHHHhhCCceeecc---cCCCCceEEecCCceeecceEEEEEeccceEeCCCCCCHHHHhhc
Q 000252 368 GGVAMKKTDSPAPRLISPSELEEFRPLIQYRR---DRDTGKVFENLDGMMLKDGYLYKKVSIDSLSCWGVVPSEEELLKF 444 (1780)
Q Consensus 368 gg~~kKK~~RPPqRLFn~~Eark~~~~~e~rr---d~~tg~~f~i~~G~~YkDGFLyK~fkIssL~tedVnPTLEEL~kF 444 (1780)
.+|+++....- ..+..+. ..++.-+-.+|.-..|+++||.|..-|.+|-. ||.|++|||.+|
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 34665543210 0111111 01122233467778999999999999988865 799999999999
Q ss_pred CCCCCCccccHHHH--HHHH-----hccccccEEEeecCCCcccccCCCCcccccccCceEEe--cCCceEEEEEEecCc
Q 000252 445 QPSESNESADLEWL--SQLY-----GERKKKRTTIVGKGGDKGEGSSGSSLENSFELYELVCF--GRKDFGLIVGMEKDD 515 (1780)
Q Consensus 445 ~~~~~~e~~DL~~L--a~i~-----ge~kk~kIi~v~kGg~kgE~ssG~~slG~FeLhDLVQL--D~~TVGVIVrVEKDE 515 (1780)
.....-...+-... ++++ +.+.+..+.++++.+.+.|+. +++.|.-.|+|+- -...-||+|.++.+.
T Consensus 233 ~t~~~~sI~~kv~~~Rg~~i~~d~ng~eI~igd~VvE~~g~~~egq----~l~i~~~f~f~~t~~i~ennGVfv~~~~nv 308 (607)
T COG5164 233 HTACPISIGDKVRVTRGELIGMDGNGREISIGDAVVESRGGKFEGQ----SLGIVKHFDFGETVSIKENNGVFVKIEGNV 308 (607)
T ss_pred eEecchhhhhhhecccceeEeeccccceEeeceeEEEecCCceeeE----EEEEEEEEeeeeeeeeeccCceEEEecCce
Confidence 75432111111000 0000 011111111223333333332 2333444444332 134568999998853
Q ss_pred eEEEccCCCCCCceEEEeccc----ccCCCCCCccccccC--CCCcccCCCeEEEecCCCCCceEEEEEEECCEE--EEE
Q 000252 516 HYKILKEGSEGPAVVTVERRT----LKNGPFDMKFTALDQ--SMKVISLNDTARVSEGPSKDRQGIVKKIYRGIL--FIY 587 (1780)
Q Consensus 516 sfkVLdq~gd~pkVvtVkp~e----I~~K~~~rR~vA~D~--ngn~I~vGD~VKVIdGphkGRqG~V~HIyRs~V--FL~ 587 (1780)
..+.....-. -+.|.+.. |..++-..+...+-+ -+....+|-+|+|--|+|||.-|+|+.+.++.+ -||
T Consensus 309 ~~VAtkd~~~---s~k~dl~kmnp~v~~~~~~p~~~~l~r~i~gRd~aigktVrIr~g~yKG~lGVVKdv~~~~arVeLh 385 (607)
T COG5164 309 CIVATKDFTE---SLKVDLDKMNPPVTVNLQNPKTNELERKIVGRDPAIGKTVRIRCGEYKGHLGVVKDVDRNIARVELH 385 (607)
T ss_pred eEEEeccchh---hhcccHhhcCchhhcCCCCCcchhhhccccccccccCceEEEeecccccccceeeeccCceEEEEEe
Confidence 3322222211 11112111 111111100000000 245678999999999999999999999999964 555
Q ss_pred eCc
Q 000252 588 DEN 590 (1780)
Q Consensus 588 Sr~ 590 (1780)
+..
T Consensus 386 s~n 388 (607)
T COG5164 386 SNN 388 (607)
T ss_pred cCC
Confidence 544
No 13
>PRK09014 rfaH transcriptional activator RfaH; Provisional
Probab=99.36 E-value=2.4e-12 Score=135.29 Aligned_cols=126 Identities=15% Similarity=0.204 Sum_probs=92.5
Q ss_pred cEEEEEeccchhHHHHHHHHHHHHhhccCCCCCc--------EEEEEEeCCCCcEEEEEeccchhHHHHhcCCCCEEe--
Q 000252 226 TIWKVKCMAGRERQSAFCLMQKFVDLQSLGSKMQ--------IISAFAVDHIKGFIFIEADKQCDINEACKGLSGIYY-- 295 (1780)
Q Consensus 226 kLWaVKCK~GKEReVV~sLmrK~i~lq~~g~~L~--------I~SVFvpd~lKGYIYVEA~kq~dVkeAIkGI~gVy~-- 295 (1780)
+||+|+|++++|+.|+..|.++-++.- .|+. -......+.|||||||++..+......|+.+++|..
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 799999999999999999877532210 1110 112223368999999999876665666777777642
Q ss_pred ---ceecccCHHHHHHHhhccc----ccccccCCCEEEEeCCCCCCCcEEEEEEeCCCCE--EEEEEec
Q 000252 296 ---SRLAPVPKNEVSHLLSAQI----KRNEVSEGTWAYVKNGKYKGDLAQVVYVNNARKR--ATVKLIP 355 (1780)
Q Consensus 296 ---~K~~pVPIkEM~dLLkvkk----k~~~Lk~GdwVRIKrGpYKGDLAQVveVDenk~e--VtVKLVP 355 (1780)
.+|.+||.+||..|+.... ....+++|+.|||+.|||+|.+|.|++++. +.+ |.|.|+.
T Consensus 80 ~~g~~p~~I~~~ei~~l~~~~~~~~~~~~~~~~G~~V~I~~Gp~~g~eg~v~~~~~-~~r~~v~v~~~g 147 (162)
T PRK09014 80 RFGAQPAIVPSDVIYQLSVYKPEKIVDPETPKPGDKVIITEGAFEGLQAIYTEPDG-EARSILLLNLLN 147 (162)
T ss_pred ccCCCccccCHHHHHHHHhhcccccccccCCCCCCEEEEecCCCCCcEEEEEEeCC-CeEEEEeehhhC
Confidence 4799999999999986422 123578999999999999999999999984 444 4455555
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=99.32 E-value=5.2e-12 Score=131.77 Aligned_cols=127 Identities=17% Similarity=0.247 Sum_probs=93.0
Q ss_pred EEEEEeccchhHHHHHHHHHHHHhhccCCCCC--------cEEEEEEeCCCCcEEEEEeccchhHHHHhcCCCCEEe---
Q 000252 227 IWKVKCMAGRERQSAFCLMQKFVDLQSLGSKM--------QIISAFAVDHIKGFIFIEADKQCDINEACKGLSGIYY--- 295 (1780)
Q Consensus 227 LWaVKCK~GKEReVV~sLmrK~i~lq~~g~~L--------~I~SVFvpd~lKGYIYVEA~kq~dVkeAIkGI~gVy~--- 295 (1780)
||+|+|++++|+.++..|.++-++.- .|+ .-...+..+.|||||||+++...+....|..+++|..
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 89999999999999988877532210 111 0112334479999999999987766666777777643
Q ss_pred --ceecccCHHHHHHHhhccc------ccccccCCCEEEEeCCCCCCCcEEEEEEeCCCC-EEEEEEecc
Q 000252 296 --SRLAPVPKNEVSHLLSAQI------KRNEVSEGTWAYVKNGKYKGDLAQVVYVNNARK-RATVKLIPR 356 (1780)
Q Consensus 296 --~K~~pVPIkEM~dLLkvkk------k~~~Lk~GdwVRIKrGpYKGDLAQVveVDenk~-eVtVKLVPR 356 (1780)
.+|.+||.+||..|+.... ....|++|+.|||+.|||+|.+|.|++++..+. .|.|.|+.|
T Consensus 78 ~~~~p~~I~~~~i~~l~~~~~~~~~~~~~~~~~~G~~V~V~~GPf~g~~g~v~~~~~~~r~~v~l~~~gr 147 (159)
T TIGR01955 78 FGGHPAPVPDDLIHQLRQYEPKDSVPPATTLPYKGDKVRITDGAFAGFEAIFLEPDGEKRSMLLLNMIGK 147 (159)
T ss_pred CCCCcccCCHHHHHHHHhccccccCCccccCCCCCCEEEEeccCCCCcEEEEEEECCCceEEEEEhhhCC
Confidence 4799999999998875421 124588999999999999999999999984432 355566665
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=99.22 E-value=3.4e-11 Score=117.23 Aligned_cols=83 Identities=28% Similarity=0.464 Sum_probs=71.0
Q ss_pred cEEEEEeccchhHHHHHHHHHHHHhhccCCCCCcEEEEEEe-----------------CCCCcEEEEEeccchhHHHHhc
Q 000252 226 TIWKVKCMAGRERQSAFCLMQKFVDLQSLGSKMQIISAFAV-----------------DHIKGFIFIEADKQCDINEACK 288 (1780)
Q Consensus 226 kLWaVKCK~GKEReVV~sLmrK~i~lq~~g~~L~I~SVFvp-----------------d~lKGYIYVEA~kq~dVkeAIk 288 (1780)
+||+|+|++|+|++|+..|++++.++. .+..++.+|+| +.|||||||+++.+.++..+|+
T Consensus 1 ~Wyvv~~~~g~E~~v~~~L~~~~~~~~---~~~~~~~~~~P~~~~~~~~~g~~~~~~~plfpGYvFv~~~~~~~~~~~i~ 77 (106)
T smart00738 1 NWYAVRTTSGQEKRVAENLERKAEALG---LEDKIVSILVPTEEVKEIRRGKKKVVERPLFPGYIFVEADLEDEVWTAIR 77 (106)
T ss_pred CEEEEEEeCCcHHHHHHHHHHHHHhcC---CccccCEEEeeEEEEEEecCCEEEEEEEecCCCEEEEEEEeCCcHHHHHh
Confidence 599999999999999999999986543 23346677777 4689999999999999999999
Q ss_pred CCCCEEe-----ceecccCHHHHHHHhh
Q 000252 289 GLSGIYY-----SRLAPVPKNEVSHLLS 311 (1780)
Q Consensus 289 GI~gVy~-----~K~~pVPIkEM~dLLk 311 (1780)
.+++|+. .+|.+||.+||..||+
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=97.90 E-value=2.3e-05 Score=75.45 Aligned_cols=76 Identities=16% Similarity=0.314 Sum_probs=51.6
Q ss_pred cEEEEEeccchhHHHHHHHHHHHH-hhccC----CC---CC-cEEEEEEeCCCCcEEEEEeccchhHHHHhcCCCCEEe-
Q 000252 226 TIWKVKCMAGRERQSAFCLMQKFV-DLQSL----GS---KM-QIISAFAVDHIKGFIFIEADKQCDINEACKGLSGIYY- 295 (1780)
Q Consensus 226 kLWaVKCK~GKEReVV~sLmrK~i-~lq~~----g~---~L-~I~SVFvpd~lKGYIYVEA~kq~dVkeAIkGI~gVy~- 295 (1780)
+||+|+|++++|..|+..|.++-+ .+-.. .. .- .+.. ...+.|||||||++...+++ ..|+.+++|+.
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 699999999999999999955533 32100 00 11 3444 55679999999999999665 44488888864
Q ss_pred ----ceecccCH
Q 000252 296 ----SRLAPVPK 303 (1780)
Q Consensus 296 ----~K~~pVPI 303 (1780)
.+|++||.
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 36777764
No 17
>KOG3973 consensus Uncharacterized conserved glycine-rich protein [Function unknown]
Probab=97.76 E-value=8.1e-05 Score=86.83 Aligned_cols=19 Identities=53% Similarity=1.071 Sum_probs=10.3
Q ss_pred CCCCCCCCCCCCCCCCCCCC
Q 000252 1501 SDRGGFGGRGRGRRDQGGGW 1520 (1780)
Q Consensus 1501 g~RGg~gGrg~~~~~~~~~~ 1520 (1780)
|+|+| ||||||+++.+||+
T Consensus 442 ggr~g-ggrgrgggggrg~y 460 (465)
T KOG3973|consen 442 GGRDG-GGRGRGGGGGRGGY 460 (465)
T ss_pred CCCCC-CCCCCCCCCCCccc
Confidence 44554 55555555555554
No 18
>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=97.24 E-value=0.00039 Score=56.60 Aligned_cols=32 Identities=28% Similarity=0.532 Sum_probs=29.9
Q ss_pred CCCEEEEeCCCCCCCcEEEEEEeCCCCEEEEE
Q 000252 321 EGTWAYVKNGKYKGDLAQVVYVNNARKRATVK 352 (1780)
Q Consensus 321 ~GdwVRIKrGpYKGDLAQVveVDenk~eVtVK 352 (1780)
+|++|+|++|||+|..|+|++|++++.+|+|+
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 68999999999999999999999999888873
No 19
>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]
Probab=97.15 E-value=0.0017 Score=83.30 Aligned_cols=10 Identities=10% Similarity=0.116 Sum_probs=5.6
Q ss_pred CcchhccCCC
Q 000252 1158 EPDQQHRKNG 1167 (1780)
Q Consensus 1158 ~~~~~~~~~g 1167 (1780)
++++-+.+.|
T Consensus 1091 shEaAAcItg 1100 (1282)
T KOG0921|consen 1091 SHEAAACITG 1100 (1282)
T ss_pred cHHHHHHHhh
Confidence 5555555555
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=97.05 E-value=0.00068 Score=55.20 Aligned_cols=32 Identities=31% Similarity=0.675 Sum_probs=28.7
Q ss_pred cCCEEEEccCCCCCceeEEEEEeCCeEEEEec
Q 000252 662 VGQTLRIRVGPLKGYLCRVLAVRYSDVTVKLD 693 (1780)
Q Consensus 662 IGKTVKIrkGPYKGylGiVKDaTdt~ARVELH 693 (1780)
.|++|+|+.|||||+.|+|+++....+||.++
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=96.74 E-value=0.0048 Score=72.71 Aligned_cols=9 Identities=22% Similarity=0.313 Sum_probs=4.2
Q ss_pred EEEeccCch
Q 000252 351 VKLIPRIDL 359 (1780)
Q Consensus 351 VKLVPRIDy 359 (1780)
++|+|-||-
T Consensus 139 ~ev~q~i~~ 147 (465)
T KOG3973|consen 139 LEVTQLIDS 147 (465)
T ss_pred chHHHHHHH
Confidence 344555553
No 22
>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]
Probab=96.11 E-value=0.026 Score=73.06 Aligned_cols=11 Identities=36% Similarity=0.036 Sum_probs=5.5
Q ss_pred eecCccccccC
Q 000252 71 IVCDPEMATDK 81 (1780)
Q Consensus 71 ~~~~~~~~~~~ 81 (1780)
-..|-|||++-
T Consensus 92 ~l~~~~~a~~~ 102 (1282)
T KOG0921|consen 92 TWQDSETATMF 102 (1282)
T ss_pred ccccccccccc
Confidence 34455555543
No 23
>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=95.63 E-value=0.017 Score=60.80 Aligned_cols=50 Identities=30% Similarity=0.468 Sum_probs=43.9
Q ss_pred cccCCEEEEccCCCCCceeEEEEEe--CCeEEEEecCcceE--EEEecCccccc
Q 000252 660 FAVGQTLRIRVGPLKGYLCRVLAVR--YSDVTVKLDSQQKI--LTVKGEHLAEV 709 (1780)
Q Consensus 660 ~lIGKTVKIrkGPYKGylGiVKDaT--dt~ARVELHSk~Kt--ITVdK~~Ls~v 709 (1780)
+.+|+.|+|+.|||||+.|+|+++. ...|+|+|...... |+|+-+.|..+
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 66899999988888 99998888754
No 24
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=95.35 E-value=0.022 Score=44.01 Aligned_cols=27 Identities=33% Similarity=0.464 Sum_probs=25.0
Q ss_pred cccCCCeEEEecCCCCCceEEEEEEEC
Q 000252 555 VISLNDTARVSEGPSKDRQGIVKKIYR 581 (1780)
Q Consensus 555 ~I~vGD~VKVIdGphkGRqG~V~HIyR 581 (1780)
.|++||.|+|+.|+++|+.|+|++|.+
T Consensus 1 ~~~~G~~V~I~~G~~~g~~g~i~~i~~ 27 (28)
T smart00739 1 KFEVGDTVRVIAGPFKGKVGKVLEVDG 27 (28)
T ss_pred CCCCCCEEEEeECCCCCcEEEEEEEcC
Confidence 378999999999999999999999975
No 25
>PRK08559 nusG transcription antitermination protein NusG; Validated
Probab=95.18 E-value=0.039 Score=59.24 Aligned_cols=51 Identities=31% Similarity=0.494 Sum_probs=43.8
Q ss_pred cccCCEEEEccCCCCCceeEEEEEe--CCeEEEEecCcceE--EEEecCcccccc
Q 000252 660 FAVGQTLRIRVGPLKGYLCRVLAVR--YSDVTVKLDSQQKI--LTVKGEHLAEVR 710 (1780)
Q Consensus 660 ~lIGKTVKIrkGPYKGylGiVKDaT--dt~ARVELHSk~Kt--ITVdK~~Ls~v~ 710 (1780)
+.+|..|+|+.|||+|+.|+|+++. ...|+|+|-.+... |||+-+.|.++.
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 6789999999999999999999995 55688887777766 999999998763
No 26
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=94.53 E-value=0.049 Score=42.12 Aligned_cols=26 Identities=27% Similarity=0.443 Sum_probs=24.5
Q ss_pred ccCCCEEEEeCCCCCCCcEEEEEEeC
Q 000252 319 VSEGTWAYVKNGKYKGDLAQVVYVNN 344 (1780)
Q Consensus 319 Lk~GdwVRIKrGpYKGDLAQVveVDe 344 (1780)
|++|+.|+|+.|+|++..|.|++|+.
T Consensus 2 ~~~G~~V~I~~G~~~g~~g~i~~i~~ 27 (28)
T smart00739 2 FEVGDTVRVIAGPFKGKVGKVLEVDG 27 (28)
T ss_pred CCCCCEEEEeECCCCCcEEEEEEEcC
Confidence 68999999999999999999999975
No 27
>CHL00141 rpl24 ribosomal protein L24; Validated
Probab=94.09 E-value=0.075 Score=52.44 Aligned_cols=28 Identities=29% Similarity=0.487 Sum_probs=26.7
Q ss_pred cccCCCeEEEecCCCCCceEEEEEEECC
Q 000252 555 VISLNDTARVSEGPSKDRQGIVKKIYRG 582 (1780)
Q Consensus 555 ~I~vGD~VKVIdGphkGRqG~V~HIyRs 582 (1780)
.|+.||.|.||.|+++|++|+|++|++.
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 7899999999999999999999999885
No 28
>PRK12281 rplX 50S ribosomal protein L24; Reviewed
Probab=94.01 E-value=0.079 Score=51.53 Aligned_cols=28 Identities=21% Similarity=0.325 Sum_probs=26.4
Q ss_pred cccCCCeEEEecCCCCCceEEEEEEECC
Q 000252 555 VISLNDTARVSEGPSKDRQGIVKKIYRG 582 (1780)
Q Consensus 555 ~I~vGD~VKVIdGphkGRqG~V~HIyRs 582 (1780)
.|+.||.|.||.|+++|++|+|+.|++.
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 29
>PRK01191 rpl24p 50S ribosomal protein L24P; Validated
Probab=93.93 E-value=0.12 Score=54.31 Aligned_cols=50 Identities=26% Similarity=0.326 Sum_probs=40.5
Q ss_pred HHHHHHhhcccccccccCCCEEEEeCCCCCCCcEEEEEEeCCCCEEEEEEec
Q 000252 304 NEVSHLLSAQIKRNEVSEGTWAYVKNGKYKGDLAQVVYVNNARKRATVKLIP 355 (1780)
Q Consensus 304 kEM~dLLkvkkk~~~Lk~GdwVRIKrGpYKGDLAQVveVDenk~eVtVKLVP 355 (1780)
+|+...+.+. ...|+.||.|.|+.|+|||-.|+|+.|++.+.+|+|+=|=
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 4444444333 4689999999999999999999999999999999987543
No 30
>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=93.66 E-value=0.11 Score=55.02 Aligned_cols=42 Identities=21% Similarity=0.236 Sum_probs=34.5
Q ss_pred cccCCEEEEccCCCCCceeEEEEEe-CCeEEEEecCcceEEEE
Q 000252 660 FAVGQTLRIRVGPLKGYLCRVLAVR-YSDVTVKLDSQQKILTV 701 (1780)
Q Consensus 660 ~lIGKTVKIrkGPYKGylGiVKDaT-dt~ARVELHSk~KtITV 701 (1780)
+..|+.|+|+.||++|+.|+|+++. ...|.|+|+--.+.+.|
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 5689999999999999999999996 44677887777765444
No 31
>PRK00004 rplX 50S ribosomal protein L24; Reviewed
Probab=93.56 E-value=0.1 Score=53.38 Aligned_cols=29 Identities=31% Similarity=0.345 Sum_probs=26.8
Q ss_pred CcccCCCeEEEecCCCCCceEEEEEEECC
Q 000252 554 KVISLNDTARVSEGPSKDRQGIVKKIYRG 582 (1780)
Q Consensus 554 n~I~vGD~VKVIdGphkGRqG~V~HIyRs 582 (1780)
-.|+.||.|.||.|+++|++|+|+.|++.
T Consensus 3 ~~i~kGD~V~Vi~G~dKGk~G~V~~V~~~ 31 (105)
T PRK00004 3 MKIKKGDTVIVIAGKDKGKRGKVLKVLPK 31 (105)
T ss_pred CcccCCCEEEEeEcCCCCcEEEEEEEEcC
Confidence 36899999999999999999999999964
No 32
>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=93.44 E-value=0.12 Score=55.65 Aligned_cols=47 Identities=21% Similarity=0.376 Sum_probs=36.2
Q ss_pred cccCCEEEEccCCCCCceeEEEEEe--CCeEEEEecCcce--EEEEecCcc
Q 000252 660 FAVGQTLRIRVGPLKGYLCRVLAVR--YSDVTVKLDSQQK--ILTVKGEHL 706 (1780)
Q Consensus 660 ~lIGKTVKIrkGPYKGylGiVKDaT--dt~ARVELHSk~K--tITVdK~~L 706 (1780)
+.+|+.|+|+.||++|+.|+|+.+. ...|+|+|+--.+ .|+|+-++|
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 3477777666555 566655544
No 33
>PRK05609 nusG transcription antitermination protein NusG; Validated
Probab=92.88 E-value=0.16 Score=54.91 Aligned_cols=48 Identities=21% Similarity=0.317 Sum_probs=36.5
Q ss_pred cccCCEEEEccCCCCCceeEEEEEe--CCeEEEEecCcce--EEEEecCccc
Q 000252 660 FAVGQTLRIRVGPLKGYLCRVLAVR--YSDVTVKLDSQQK--ILTVKGEHLA 707 (1780)
Q Consensus 660 ~lIGKTVKIrkGPYKGylGiVKDaT--dt~ARVELHSk~K--tITVdK~~Ls 707 (1780)
+..|+.|+|+.|||+|+.|+|+.+. ...|+|+|+--.+ .|.|+-+.|.
T Consensus 127 ~~~Gd~VrI~~GPf~G~~g~v~~i~~~~~r~~v~l~~~G~~~~v~l~~~~l~ 178 (181)
T PRK05609 127 FEVGEMVRVIDGPFADFNGTVEEVDYEKSKLKVLVSIFGRETPVELEFSQVE 178 (181)
T ss_pred CCCCCEEEEeccCCCCCEEEEEEEeCCCCEEEEEEEECCCceEEEEchHHEE
Confidence 4579999999999999999999996 3467777666555 4555555553
No 34
>CHL00141 rpl24 ribosomal protein L24; Validated
Probab=92.68 E-value=0.18 Score=49.91 Aligned_cols=39 Identities=23% Similarity=0.315 Sum_probs=35.4
Q ss_pred cccccCCCEEEEeCCCCCCCcEEEEEEeCCCCEEEEEEe
Q 000252 316 RNEVSEGTWAYVKNGKYKGDLAQVVYVNNARKRATVKLI 354 (1780)
Q Consensus 316 ~~~Lk~GdwVRIKrGpYKGDLAQVveVDenk~eVtVKLV 354 (1780)
...|.+||.|.|++|+|||-.+.|..|+..+++|+|+=|
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 35
>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=91.94 E-value=0.049 Score=57.67 Aligned_cols=69 Identities=23% Similarity=0.312 Sum_probs=33.0
Q ss_pred ccCcceeccccCCCC----CchhhcCCCcCCCCCCCCccchhhhhccCccccccccccCCCCCCCccccCCHHHHHHHHH
Q 000252 116 VLQFVEDAADVDYDD----DDEEEVGNESDNSGGFADDDFMEELFDAQPKVNNEMGQAHNLPFIPKEEEMDEEEFDKMME 191 (1780)
Q Consensus 116 ~n~FiDdEAEVDDDe----EEEDEeeEe~e~~~~Fi~dD~~~d~~e~~~~~~~d~r~~~~l~~r~~eEd~DaEelAe~lk 191 (1780)
.+.+|.+|||++||. |.|+..++++ .+.+||++.... +.+. ++.| |.+.+.+.+ ++....||
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 455666799998822 2222222222 235787543321 1010 1111 122233333 45556899
Q ss_pred HHhcccc
Q 000252 192 ERYKSNK 198 (1780)
Q Consensus 192 ERY~r~s 198 (1780)
.+|..++
T Consensus 80 RK~~~SP 86 (130)
T PF00524_consen 80 RKYLGSP 86 (130)
T ss_pred HHHcCCc
Confidence 9998654
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=91.89 E-value=0.24 Score=50.88 Aligned_cols=28 Identities=32% Similarity=0.437 Sum_probs=26.4
Q ss_pred cccCCCeEEEecCCCCCceEEEEEEECC
Q 000252 555 VISLNDTARVSEGPSKDRQGIVKKIYRG 582 (1780)
Q Consensus 555 ~I~vGD~VKVIdGphkGRqG~V~HIyRs 582 (1780)
.|..||.|.||.|+.+|++|+|++|++.
T Consensus 3 ~ikkGD~V~Vi~G~dKGK~G~V~~V~~~ 30 (104)
T TIGR01079 3 KIKKGDTVKVISGKDKGKRGKVLKVLPK 30 (104)
T ss_pred cccCCCEEEEeEcCCCCcEEEEEEEEcC
Confidence 5899999999999999999999999875
No 37
>PRK09014 rfaH transcriptional activator RfaH; Provisional
Probab=91.83 E-value=0.25 Score=52.94 Aligned_cols=47 Identities=15% Similarity=0.139 Sum_probs=36.2
Q ss_pred cccCCEEEEccCCCCCceeEEEEEe-CCeEEEEecCcceE--EEEecCcc
Q 000252 660 FAVGQTLRIRVGPLKGYLCRVLAVR-YSDVTVKLDSQQKI--LTVKGEHL 706 (1780)
Q Consensus 660 ~lIGKTVKIrkGPYKGylGiVKDaT-dt~ARVELHSk~Kt--ITVdK~~L 706 (1780)
+..|++|+|+.||++|+.|+|+++. ...|.|+|+.-.+. |+|+-+.|
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 44667777776664 44554444
No 38
>PRK12281 rplX 50S ribosomal protein L24; Reviewed
Probab=91.63 E-value=0.27 Score=47.97 Aligned_cols=38 Identities=26% Similarity=0.316 Sum_probs=34.8
Q ss_pred ccccCCCEEEEeCCCCCCCcEEEEEEeCCCCEEEEEEe
Q 000252 317 NEVSEGTWAYVKNGKYKGDLAQVVYVNNARKRATVKLI 354 (1780)
Q Consensus 317 ~~Lk~GdwVRIKrGpYKGDLAQVveVDenk~eVtVKLV 354 (1780)
..|.+||.|.|++|++||-.+.|..|+..+++|+|+=|
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 39
>PRK01191 rpl24p 50S ribosomal protein L24P; Validated
Probab=91.45 E-value=0.38 Score=50.65 Aligned_cols=28 Identities=25% Similarity=0.296 Sum_probs=26.6
Q ss_pred cccCCCeEEEecCCCCCceEEEEEEECC
Q 000252 555 VISLNDTARVSEGPSKDRQGIVKKIYRG 582 (1780)
Q Consensus 555 ~I~vGD~VKVIdGphkGRqG~V~HIyRs 582 (1780)
.|+.||.|+||.|+++|++|.|+.|++.
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
>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=91.01 E-value=0.44 Score=49.77 Aligned_cols=39 Identities=26% Similarity=0.307 Sum_probs=34.9
Q ss_pred cccccCCCEEEEeCCCCCCCcEEEEEEeCCCCEEEEEEe
Q 000252 316 RNEVSEGTWAYVKNGKYKGDLAQVVYVNNARKRATVKLI 354 (1780)
Q Consensus 316 ~~~Lk~GdwVRIKrGpYKGDLAQVveVDenk~eVtVKLV 354 (1780)
...|+.||.|+|+.|+|||-.+.|+.|+..+.+|+|+=|
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 458899999999999999999999999998888887643
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=90.83 E-value=0.37 Score=56.21 Aligned_cols=47 Identities=23% Similarity=0.418 Sum_probs=36.8
Q ss_pred ccccCCEEEEccCCCCCceeEEEEEe--CCeEEEEecCcceE--EEEecCc
Q 000252 659 MFAVGQTLRIRVGPLKGYLCRVLAVR--YSDVTVKLDSQQKI--LTVKGEH 705 (1780)
Q Consensus 659 d~lIGKTVKIrkGPYKGylGiVKDaT--dt~ARVELHSk~Kt--ITVdK~~ 705 (1780)
++.+|++|+|+.|||+|+.|+|.++. ...|+|+|+--.+. |.|+-..
T Consensus 205 ~f~vGd~VrI~dGPF~GfeG~I~eid~~k~Rv~VlV~IfGR~TpVeL~~~q 255 (258)
T TIGR01956 205 KFRVGNFVKIVDGPFKGIVGKIKKIDQEKKKAIVEVEILGKSVDVDLNFKH 255 (258)
T ss_pred CCCCCCEEEEEecCCCCcEEEEEEEeCCCCEEEEEEEecCCcEEEEEchHH
Confidence 36789999999999999999999996 67777777766654 4444333
No 42
>COG0250 NusG Transcription antiterminator [Transcription]
Probab=90.77 E-value=0.37 Score=53.48 Aligned_cols=43 Identities=26% Similarity=0.396 Sum_probs=36.4
Q ss_pred ccccCCEEEEccCCCCCceeEEEEEeCC--eEEEEecCcceEEEE
Q 000252 659 MFAVGQTLRIRVGPLKGYLCRVLAVRYS--DVTVKLDSQQKILTV 701 (1780)
Q Consensus 659 d~lIGKTVKIrkGPYKGylGiVKDaTdt--~ARVELHSk~KtITV 701 (1780)
++.+|+.|+|+.|||+|+.|+|.++... .++|+|..-.+.++|
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 43
>KOG3262 consensus H/ACA small nucleolar RNP component GAR1 [Translation, ribosomal structure and biogenesis]
Probab=90.55 E-value=0.53 Score=52.52 Aligned_cols=21 Identities=71% Similarity=1.434 Sum_probs=10.0
Q ss_pred CCCCCCCCCCCCCCCCCCCCCC
Q 000252 1491 DRGGFGGRGSSDRGGFGGRGRG 1512 (1780)
Q Consensus 1491 ~rGgfgG~ggg~RGg~gGrg~~ 1512 (1780)
.|++|.+|+ +.+++|.+++|.
T Consensus 193 ~rGG~~~Rg-g~ggg~rgrgR~ 213 (215)
T KOG3262|consen 193 SRGGFRGRG-GHGGGFRGRGRG 213 (215)
T ss_pred CCCCccccC-CCCCCCCCCCCC
Confidence 344443322 345566555554
No 44
>PTZ00194 60S ribosomal protein L26; Provisional
Probab=90.39 E-value=0.53 Score=50.86 Aligned_cols=52 Identities=19% Similarity=0.169 Sum_probs=42.6
Q ss_pred HHHHHHhhcccccccccCCCEEEEeCCCCCCCcEEEEEEeCCCCEEEEEEeccC
Q 000252 304 NEVSHLLSAQIKRNEVSEGTWAYVKNGKYKGDLAQVVYVNNARKRATVKLIPRI 357 (1780)
Q Consensus 304 kEM~dLLkvkkk~~~Lk~GdwVRIKrGpYKGDLAQVveVDenk~eVtVKLVPRI 357 (1780)
+|+...+.+. ...|+.||.|.|++|.|||-.++|+.|+....+|+|+=|.++
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 4444444433 458999999999999999999999999999999999876654
No 45
>PRK00004 rplX 50S ribosomal protein L24; Reviewed
Probab=89.88 E-value=0.46 Score=48.79 Aligned_cols=37 Identities=24% Similarity=0.338 Sum_probs=34.5
Q ss_pred cccCCCEEEEeCCCCCCCcEEEEEEeCCCCEEEEEEe
Q 000252 318 EVSEGTWAYVKNGKYKGDLAQVVYVNNARKRATVKLI 354 (1780)
Q Consensus 318 ~Lk~GdwVRIKrGpYKGDLAQVveVDenk~eVtVKLV 354 (1780)
.|.+||.|.|++|++||-++.|..|+..+++|+|+=|
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 6889999999999999999999999999999998754
No 46
>PTZ00194 60S ribosomal protein L26; Provisional
Probab=89.69 E-value=0.38 Score=51.93 Aligned_cols=28 Identities=32% Similarity=0.526 Sum_probs=26.7
Q ss_pred cccCCCeEEEecCCCCCceEEEEEEECC
Q 000252 555 VISLNDTARVSEGPSKDRQGIVKKIYRG 582 (1780)
Q Consensus 555 ~I~vGD~VKVIdGphkGRqG~V~HIyRs 582 (1780)
.|+.||+|+||.|.++|++|.|+.|++.
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 47
>COG0198 RplX Ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=89.42 E-value=0.46 Score=48.96 Aligned_cols=30 Identities=27% Similarity=0.359 Sum_probs=27.6
Q ss_pred CcccCCCeEEEecCCCCCceEEEEEEECCE
Q 000252 554 KVISLNDTARVSEGPSKDRQGIVKKIYRGI 583 (1780)
Q Consensus 554 n~I~vGD~VKVIdGphkGRqG~V~HIyRs~ 583 (1780)
..|+.||+|+||.|.++|++|.|+.++...
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 48
>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=88.26 E-value=0.6 Score=48.81 Aligned_cols=37 Identities=22% Similarity=0.294 Sum_probs=29.7
Q ss_pred cccCCEEEEccCCCCCceeEEEEEeCCeEEEEecCcc
Q 000252 660 FAVGQTLRIRVGPLKGYLCRVLAVRYSDVTVKLDSQQ 696 (1780)
Q Consensus 660 ~lIGKTVKIrkGPYKGylGiVKDaTdt~ARVELHSk~ 696 (1780)
...|++|+|+.|+|||..|.|+.|.....+|.++--+
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 3468999999999999999999997665566665544
No 49
>KOG3262 consensus H/ACA small nucleolar RNP component GAR1 [Translation, ribosomal structure and biogenesis]
Probab=87.88 E-value=1 Score=50.35 Aligned_cols=11 Identities=55% Similarity=1.020 Sum_probs=6.2
Q ss_pred CCCCCCCCCcC
Q 000252 1197 DGGRGSGGRWG 1207 (1780)
Q Consensus 1197 ~~~~~~~~~~~ 1207 (1780)
+||.|.+++.|
T Consensus 5 rgggg~~g~~g 15 (215)
T KOG3262|consen 5 RGGGGGGGGGG 15 (215)
T ss_pred cCCCCCCCCCC
Confidence 35556655555
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=86.23 E-value=1 Score=46.38 Aligned_cols=36 Identities=25% Similarity=0.291 Sum_probs=33.5
Q ss_pred cccCCCEEEEeCCCCCCCcEEEEEEeCCCCEEEEEE
Q 000252 318 EVSEGTWAYVKNGKYKGDLAQVVYVNNARKRATVKL 353 (1780)
Q Consensus 318 ~Lk~GdwVRIKrGpYKGDLAQVveVDenk~eVtVKL 353 (1780)
.|..||.|.|++|++||=.+.|..|+..+++|+|+=
T Consensus 3 ~ikkGD~V~Vi~G~dKGK~G~V~~V~~~~~~V~Veg 38 (104)
T TIGR01079 3 KIKKGDTVKVISGKDKGKRGKVLKVLPKTNKVIVEG 38 (104)
T ss_pred cccCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEECC
Confidence 578999999999999999999999999999998863
No 51
>COG2933 Predicted SAM-dependent methyltransferase [General function prediction only]
Probab=85.43 E-value=1.2 Score=52.48 Aligned_cols=57 Identities=21% Similarity=0.306 Sum_probs=48.6
Q ss_pred EEEeccchhHHHHHHHHHHHHhhccCCCCCcEEEEEEeCCCCcEEEEEeccchhHHHHhcCCCC
Q 000252 229 KVKCMAGRERQSAFCLMQKFVDLQSLGSKMQIISAFAVDHIKGFIFIEADKQCDINEACKGLSG 292 (1780)
Q Consensus 229 aVKCK~GKEReVV~sLmrK~i~lq~~g~~L~I~SVFvpd~lKGYIYVEA~kq~dVkeAIkGI~g 292 (1780)
++.|++|.|+|++.-|-.|+..+. |+-..-.+.-.|||..|.+..+++..+|+.|+.
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 678999999999999999987654 554444467889999999999999999999986
No 52
>KOG1708 consensus Mitochondrial/chloroplast ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=84.17 E-value=1.1 Score=50.82 Aligned_cols=30 Identities=30% Similarity=0.324 Sum_probs=27.6
Q ss_pred CCcccCCCeEEEecCCCCCceEEEEEEECC
Q 000252 553 MKVISLNDTARVSEGPSKDRQGIVKKIYRG 582 (1780)
Q Consensus 553 gn~I~vGD~VKVIdGphkGRqG~V~HIyRs 582 (1780)
-=+|.+||+|+|+.|.-+|++|.|+.|++.
T Consensus 70 dw~ff~GDtVeVlvGkDkGkqG~Vtqv~r~ 99 (236)
T KOG1708|consen 70 DWHFFFGDTVEVLVGKDKGKQGEVTQVIRH 99 (236)
T ss_pred ceeEecCCEEEEEecccCCccceEEEEeec
Confidence 457899999999999999999999999875
No 53
>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=82.19 E-value=4 Score=37.75 Aligned_cols=47 Identities=23% Similarity=0.286 Sum_probs=36.4
Q ss_pred cccCCEEEEccC--CCCCceeEEEEEeCCeEEEEecCcc--eEEEEecCcc
Q 000252 660 FAVGQTLRIRVG--PLKGYLCRVLAVRYSDVTVKLDSQQ--KILTVKGEHL 706 (1780)
Q Consensus 660 ~lIGKTVKIrkG--PYKGylGiVKDaTdt~ARVELHSk~--KtITVdK~~L 706 (1780)
.|-|-+|+|+.- +|-+|.|+|-.+++..|-|...--| |.||..-++|
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 345778999876 8999999999999999999998887 8999887766
No 54
>PRK11760 putative 23S rRNA C2498 ribose 2'-O-ribose methyltransferase; Provisional
Probab=79.64 E-value=2.7 Score=51.25 Aligned_cols=65 Identities=18% Similarity=0.300 Sum_probs=50.9
Q ss_pred EEEEeccchhHHHHHHHHHHHHhhccCCCCCcEEEEEEeCCCCcEEEEEeccchhHHHHhcCCCC---EEeceec
Q 000252 228 WKVKCMAGRERQSAFCLMQKFVDLQSLGSKMQIISAFAVDHIKGFIFIEADKQCDINEACKGLSG---IYYSRLA 299 (1780)
Q Consensus 228 WaVKCK~GKEReVV~sLmrK~i~lq~~g~~L~I~SVFvpd~lKGYIYVEA~kq~dVkeAIkGI~g---Vy~~K~~ 299 (1780)
+++.|++|.|++++.-|..++.++. |+-..-...-.|||..|.+...+...+++.|+. |+..+++
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 7899999999999999999987654 333333355679999999999999999998885 5554443
No 55
>COG0198 RplX Ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=78.57 E-value=2.9 Score=43.35 Aligned_cols=34 Identities=29% Similarity=0.314 Sum_probs=30.1
Q ss_pred ccccCCCEEEEeCCCCCCCcEEEEEEeCCCCEEEEE
Q 000252 317 NEVSEGTWAYVKNGKYKGDLAQVVYVNNARKRATVK 352 (1780)
Q Consensus 317 ~~Lk~GdwVRIKrGpYKGDLAQVveVDenk~eVtVK 352 (1780)
..|..||.|+|++|++||-.++|++|++.. |+|+
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 357789999999999999999999999976 6665
No 56
>KOG0262 consensus RNA polymerase I, large subunit [Transcription]
Probab=77.28 E-value=6 Score=54.07 Aligned_cols=70 Identities=7% Similarity=0.082 Sum_probs=38.3
Q ss_pred cEEEEEec--cchhHHHHHHHHHHHHhhccCCCCCcEEEEEEeC------CCCcEEEEEeccchhHHHH--hcCCCCEEe
Q 000252 226 TIWKVKCM--AGRERQSAFCLMQKFVDLQSLGSKMQIISAFAVD------HIKGFIFIEADKQCDINEA--CKGLSGIYY 295 (1780)
Q Consensus 226 kLWaVKCK--~GKEReVV~sLmrK~i~lq~~g~~L~I~SVFvpd------~lKGYIYVEA~kq~dVkeA--IkGI~gVy~ 295 (1780)
+|..|+.+ ..+|+..+.+|.+++...-..-.--.|..+++.+ ..+ ++.-|...-.++++. +-.|..||.
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 34444443 4678888888887775432112233577777763 122 555566555555533 334455554
Q ss_pred c
Q 000252 296 S 296 (1780)
Q Consensus 296 ~ 296 (1780)
+
T Consensus 1520 N 1520 (1640)
T KOG0262|consen 1520 N 1520 (1640)
T ss_pred c
Confidence 3
No 57
>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=76.58 E-value=1.5 Score=58.07 Aligned_cols=16 Identities=13% Similarity=0.420 Sum_probs=10.1
Q ss_pred hhHHHHHHHHHHHHhh
Q 000252 236 RERQSAFCLMQKFVDL 251 (1780)
Q Consensus 236 KEReVV~sLmrK~i~l 251 (1780)
.+++.++.+..|++++
T Consensus 764 ~~~~~~~~Fk~RvlDL 779 (784)
T PF04931_consen 764 EAKENVIHFKNRVLDL 779 (784)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 3455566677777765
No 58
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=75.15 E-value=15 Score=36.70 Aligned_cols=66 Identities=11% Similarity=0.014 Sum_probs=47.8
Q ss_pred CCceEEEEEEecCceEEEccCCCCCCceEEEecccccCCCCCCccccccCCCCcccCCCeEEEecCCCCCceEEEEEEEC
Q 000252 502 RKDFGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVSEGPSKDRQGIVKKIYR 581 (1780)
Q Consensus 502 ~~TVGVIVrVEKDEsfkVLdq~gd~pkVvtVkp~eI~~K~~~rR~vA~D~ngn~I~vGD~VKVIdGphkGRqG~V~HIyR 581 (1780)
.+.+|.|+++..+..|.|.+.++ ..+.+.. ..|+. ..--|..||.|.|--=++.-..|.|+|+|.
T Consensus 5 ~q~~g~V~~~lG~~~~~V~~~dG---~~~la~i---pgK~R---------k~iwI~~GD~VlVe~~~~~~~kg~Iv~r~~ 69 (83)
T smart00652 5 GQEIAQVVKMLGNGRLEVMCADG---KERLARI---PGKMR---------KKVWIRRGDIVLVDPWDFQDVKADIIYKYT 69 (83)
T ss_pred CcEEEEEEEEcCCCEEEEEECCC---CEEEEEE---chhhc---------ccEEEcCCCEEEEEecCCCCCEEEEEEEeC
Confidence 35789999999888999998764 2444432 22321 234689999999987777778899999886
Q ss_pred C
Q 000252 582 G 582 (1780)
Q Consensus 582 s 582 (1780)
.
T Consensus 70 ~ 70 (83)
T smart00652 70 K 70 (83)
T ss_pred H
Confidence 3
No 59
>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=74.97 E-value=0.63 Score=50.43 Aligned_cols=18 Identities=28% Similarity=0.479 Sum_probs=14.2
Q ss_pred cccccCcceeccccCCCC
Q 000252 113 NRSVLQFVEDAADVDYDD 130 (1780)
Q Consensus 113 Rrr~n~FiDdEAEVDDDe 130 (1780)
+..+..||+.|||..|||
T Consensus 3 k~~~~~~vE~EAEESeDE 20 (145)
T PF09444_consen 3 KSGASEFVEEEAEESEDE 20 (145)
T ss_pred chhHHHHHHHHHhcchhh
Confidence 345678999999987765
No 60
>CHL00010 infA translation initiation factor 1
Probab=74.78 E-value=22 Score=34.98 Aligned_cols=65 Identities=14% Similarity=0.061 Sum_probs=42.4
Q ss_pred ceEEEEEEecCceEEEccCCCCCCceEEEecccccCCCCCCccccccCCCCcccCCCeEEEecCCCCCceEEEEEEECC
Q 000252 504 DFGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVSEGPSKDRQGIVKKIYRG 582 (1780)
Q Consensus 504 TVGVIVrVEKDEsfkVLdq~gd~pkVvtVkp~eI~~K~~~rR~vA~D~ngn~I~vGD~VKVIdGphkGRqG~V~HIyRs 582 (1780)
..|+|+++-....|.|.+.++ .++.+.+.- |+. .....|.+||+|.|--=++....|.|+|=|++
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 469999998434777765332 356665432 211 11344789999999744555678999998875
No 61
>PTZ00415 transmission-blocking target antigen s230; Provisional
Probab=74.52 E-value=1.5 Score=60.70 Aligned_cols=17 Identities=24% Similarity=0.345 Sum_probs=9.9
Q ss_pred CCCcEEEEEeccchhHH
Q 000252 223 EDPTIWKVKCMAGRERQ 239 (1780)
Q Consensus 223 kDPkLWaVKCK~GKERe 239 (1780)
+-|-+-.|+.+.|.|..
T Consensus 312 kapyv~l~~~~~~~~e~ 328 (2849)
T PTZ00415 312 KAPYVTLTKANEGSEEK 328 (2849)
T ss_pred CCceEEEEccCCcchhh
Confidence 34666666776665443
No 62
>KOG1832 consensus HIV-1 Vpr-binding protein [Cell cycle control, cell division, chromosome partitioning]
Probab=73.96 E-value=2.7 Score=55.44 Aligned_cols=9 Identities=33% Similarity=0.560 Sum_probs=4.8
Q ss_pred HHHHHHHHH
Q 000252 184 EEFDKMMEE 192 (1780)
Q Consensus 184 EelAe~lkE 192 (1780)
+++++.|+|
T Consensus 1469 ~df~~elee 1477 (1516)
T KOG1832|consen 1469 GDFMEELEE 1477 (1516)
T ss_pred hHHHHHHhh
Confidence 455555554
No 63
>PTZ00061 DNA-directed RNA polymerase; Provisional
Probab=73.79 E-value=20 Score=41.24 Aligned_cols=57 Identities=14% Similarity=0.096 Sum_probs=36.0
Q ss_pred CcEEEEEeccchhHHHHhcCCCCEEeceecccCHHHHHHHhhc---cc-------------ccccccCCCEEEEeC
Q 000252 270 KGFIFIEADKQCDINEACKGLSGIYYSRLAPVPKNEVSHLLSA---QI-------------KRNEVSEGTWAYVKN 329 (1780)
Q Consensus 270 KGYIYVEA~kq~dVkeAIkGI~gVy~~K~~pVPIkEM~dLLkv---kk-------------k~~~Lk~GdwVRIKr 329 (1780)
+.| .||.+.++++.-- =+.|+..-+-.+++.+|...||+- +. +...+++|+.|+|+|
T Consensus 118 ~~~-~iE~F~E~eLlvn--it~H~lVPkH~~Ls~eEk~~lL~~y~i~~~qLPrI~~~DPvary~g~k~G~vvkI~R 190 (205)
T PTZ00061 118 PRH-IIENFLETELLVN--ITKHELVPKHIPLTDDEKLNLLQRYKVKESQLPRIQSADPVARYFGLSKGQVVKIIR 190 (205)
T ss_pred CCc-EEEEeeehheEEe--cccceecCCeEEcCHHHHHHHHHHhCCCHHHCCcccccChhhHhcCCCCCCEEEEEE
Confidence 454 4677766554221 122445556677889999999962 11 134678999999987
No 64
>PHA02774 E1; Provisional
Probab=72.81 E-value=1.1 Score=57.57 Aligned_cols=31 Identities=13% Similarity=0.133 Sum_probs=19.4
Q ss_pred ecccCHHHHHHHhhcccccccccCCCEEEEeCCCC
Q 000252 298 LAPVPKNEVSHLLSAQIKRNEVSEGTWAYVKNGKY 332 (1780)
Q Consensus 298 ~~pVPIkEM~dLLkvkkk~~~Lk~GdwVRIKrGpY 332 (1780)
..-|+..|+++.++--|. --.+||-..-|.+
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 455777777777764432 2357888777753
No 65
>KOG0415 consensus Predicted peptidyl prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]
Probab=71.56 E-value=8.9 Score=46.76 Aligned_cols=112 Identities=16% Similarity=0.202 Sum_probs=71.5
Q ss_pred CccccCCHHHHHHHHHHHhccccchhhchhhHHHhhccccccCCCCCCCCcEEEEEeccchhHHHHHHHHHHHHhhccCC
Q 000252 176 PKEEEMDEEEFDKMMEERYKSNKLIRYAEEDYEAKKMLEREYHMPCPEDPTIWKVKCMAGRERQSAFCLMQKFVDLQSLG 255 (1780)
Q Consensus 176 ~~eEd~DaEelAe~lkERY~r~s~~~y~~d~~e~~~~VpQq~LLPSVkDPkLWaVKCK~GKEReVV~sLmrK~i~lq~~g 255 (1780)
+.++.+.||||+++|+||-+...+. .-|+-..+|--.+.|- +--||+.|..|=-+-+=+..|.-+|=
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 4557889999999999998864432 1122234444444442 23488888776555555555555542
Q ss_pred CCCcEEEEEE-eC----CCCcEEEEEeccchhHHHHhcCCCCEEe-ceecccCH
Q 000252 256 SKMQIISAFA-VD----HIKGFIFIEADKQCDINEACKGLSGIYY-SRLAPVPK 303 (1780)
Q Consensus 256 ~~L~I~SVFv-pd----~lKGYIYVEA~kq~dVkeAIkGI~gVy~-~K~~pVPI 303 (1780)
.|.|+-+ ++ ..-=|-|||-+.+..+..|.-.|.+|.. ...+-|.+
T Consensus 265 ---~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHVDF 315 (479)
T KOG0415|consen 265 ---KIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHVDF 315 (479)
T ss_pred ---cceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEeeh
Confidence 2444433 32 2335999999999999999999999875 34445543
No 66
>COG1588 POP4 RNase P/RNase MRP subunit p29 [Translation, ribosomal structure and biogenesis]
Probab=70.75 E-value=8.1 Score=39.66 Aligned_cols=47 Identities=15% Similarity=0.123 Sum_probs=40.0
Q ss_pred cccCCEEEEccCC---CCCceeEEEEEeCCeEEEEecCcceEEEEecCcccc
Q 000252 660 FAVGQTLRIRVGP---LKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLAE 708 (1780)
Q Consensus 660 ~lIGKTVKIrkGP---YKGylGiVKDaTdt~ARVELHSk~KtITVdK~~Ls~ 708 (1780)
.|||..|+|+.=+ |-|..|+|+|-|.++.+|+-.+ +.++|+|+...+
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 7999999999885 5677888999999999987776 788899888764
No 67
>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=70.73 E-value=11 Score=46.33 Aligned_cols=68 Identities=12% Similarity=0.102 Sum_probs=50.5
Q ss_pred HHHHHHHHHHHHhhccCCCCCcEEEEEEe-CCCCcEEEEEeccchhHHHHhcCCCCEEe----ceecccCHHHHHHHhh
Q 000252 238 RQSAFCLMQKFVDLQSLGSKMQIISAFAV-DHIKGFIFIEADKQCDINEACKGLSGIYY----SRLAPVPKNEVSHLLS 311 (1780)
Q Consensus 238 ReVV~sLmrK~i~lq~~g~~L~I~SVFvp-d~lKGYIYVEA~kq~dVkeAIkGI~gVy~----~K~~pVPIkEM~dLLk 311 (1780)
.+|..-|+..|..+. .|.+|++. ....||||||-...++...||+.|.+-+. ..+..+|.+++..++.
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 445555555555443 47788887 67899999999999999999999999653 3566788887776653
No 68
>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=70.30 E-value=20 Score=35.33 Aligned_cols=64 Identities=11% Similarity=0.046 Sum_probs=46.6
Q ss_pred ceEEEEEEecCceEEEccCCCCCCceEEEecccccCCCCCCccccccCCCCcccCCCeEEEecCCCCCceEEEEEEECC
Q 000252 504 DFGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVSEGPSKDRQGIVKKIYRG 582 (1780)
Q Consensus 504 TVGVIVrVEKDEsfkVLdq~gd~pkVvtVkp~eI~~K~~~rR~vA~D~ngn~I~vGD~VKVIdGphkGRqG~V~HIyRs 582 (1780)
..|.|+++-.+..|.|.+.++ ..+.+. |..|+. ..--|.+||.|.|--=||.-..|.|+|+|..
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---KKRLCR---IRGKMR---------KRVWINEGDIVLVAPWDFQDDKADIIYKYTP 65 (77)
T ss_pred EEEEEEEEcCCCEEEEEECCC---CEEEEE---Echhhc---------ccEEEcCCCEEEEEeccccCCEEEEEEEcCH
Confidence 468999998888999998764 233333 223321 2346899999999777888889999999863
No 69
>PF14632 SPT6_acidic: Acidic N-terminal SPT6
Probab=70.06 E-value=1.5 Score=44.46 Aligned_cols=9 Identities=44% Similarity=0.534 Sum_probs=6.6
Q ss_pred CCCCCCccc
Q 000252 143 SGGFADDDF 151 (1780)
Q Consensus 143 ~~~Fi~dD~ 151 (1780)
+.+||.++.
T Consensus 20 ~eGFIvDde 28 (92)
T PF14632_consen 20 REGFIVDDE 28 (92)
T ss_pred hcCCccCCc
Confidence 479998753
No 70
>PF14851 FAM176: FAM176 family
Probab=69.10 E-value=6.4 Score=43.35 Aligned_cols=16 Identities=31% Similarity=0.368 Sum_probs=11.0
Q ss_pred cCCHHHHHHHHHHHhc
Q 000252 180 EMDEEEFDKMMEERYK 195 (1780)
Q Consensus 180 d~DaEelAe~lkERY~ 195 (1780)
...|-|+|+.|+||-+
T Consensus 115 sae~~e~A~rlEeRe~ 130 (153)
T PF14851_consen 115 SAEELERAQRLEERER 130 (153)
T ss_pred cHHHHHHHHHHHHHHH
Confidence 4445578888888865
No 71
>PLN00208 translation initiation factor (eIF); Provisional
Probab=68.60 E-value=17 Score=39.83 Aligned_cols=77 Identities=14% Similarity=0.063 Sum_probs=55.2
Q ss_pred ccccCceEEecC-CceEEEEEEecCceEEEccCCCCCCceEEEecccccCCCCCCccccccCCCCcccCCCeEEEecCCC
Q 000252 491 SFELYELVCFGR-KDFGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVSEGPS 569 (1780)
Q Consensus 491 ~FeLhDLVQLD~-~TVGVIVrVEKDEsfkVLdq~gd~pkVvtVkp~eI~~K~~~rR~vA~D~ngn~I~vGD~VKVIdGph 569 (1780)
.-+..+|+.... +.+|+|+++-.+..|.|.+.++ ..+.+. |.-|+.. .--|.+||+|.|---+|
T Consensus 20 ~~~~~el~~p~egq~~g~V~~~lGn~~~~V~c~dG---~~rLa~---IpGKmRK---------rIWI~~GD~VlVel~~~ 84 (145)
T PLN00208 20 DDEKRELIFKEDGQEYAQVLRMLGNGRCEALCIDG---TKRLCH---IRGKMRK---------KVWIAAGDIILVGLRDY 84 (145)
T ss_pred ccceeecccCCCCcEEEEEEEEcCCCEEEEEECCC---CEEEEE---Eecccee---------eEEecCCCEEEEEccCC
Confidence 345666776644 5789999999888999998764 234433 2233221 24689999999987788
Q ss_pred CCceEEEEEEECC
Q 000252 570 KDRQGIVKKIYRG 582 (1780)
Q Consensus 570 kGRqG~V~HIyRs 582 (1780)
.-..|.|+|+|..
T Consensus 85 d~~KgdIv~ry~~ 97 (145)
T PLN00208 85 QDDKADVILKYMP 97 (145)
T ss_pred CCCEEEEEEEcCH
Confidence 8889999999874
No 72
>PRK04950 ProP expression regulator; Provisional
Probab=66.18 E-value=9.2 Score=44.07 Aligned_cols=46 Identities=35% Similarity=0.590 Sum_probs=38.1
Q ss_pred cccCCEEEEccCCCCCceeEEEEEeCCeEEEEecCcceEEEEecCccc
Q 000252 660 FAVGQTLRIRVGPLKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLA 707 (1780)
Q Consensus 660 ~lIGKTVKIrkGPYKGylGiVKDaTdt~ARVELHSk~KtITVdK~~Ls 707 (1780)
..+|+.|+|.-|. -=.-+.|++|+.+.|||+|.+.+. |.|.-+||.
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 4679999999982 234589999999999999999886 678888875
No 73
>KOG0299 consensus U3 snoRNP-associated protein (contains WD40 repeats) [RNA processing and modification]
Probab=66.12 E-value=3.5 Score=51.38 Aligned_cols=19 Identities=16% Similarity=0.300 Sum_probs=15.2
Q ss_pred cCCHHHHHHHHHHHhcccc
Q 000252 180 EMDEEEFDKMMEERYKSNK 198 (1780)
Q Consensus 180 d~DaEelAe~lkERY~r~s 198 (1780)
++|.|.||+.|+|-|..++
T Consensus 98 ~~~~e~va~rLked~le~~ 116 (479)
T KOG0299|consen 98 DLDDELVASRLKEDVLEQS 116 (479)
T ss_pred hhhHHHHHHHHHHHHHHhc
Confidence 5566889999999998665
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=66.06 E-value=2 Score=56.98 Aligned_cols=13 Identities=15% Similarity=0.189 Sum_probs=0.0
Q ss_pred CccccCCHHHHHH
Q 000252 176 PKEEEMDEEEFDK 188 (1780)
Q Consensus 176 ~~eEd~DaEelAe 188 (1780)
..++-+++|+-++
T Consensus 717 LVNqGi~eerAar 729 (787)
T PF03115_consen 717 LVNQGIPEERAAR 729 (787)
T ss_dssp -------------
T ss_pred HHHcCCCHHHHHh
Confidence 3445555555443
No 75
>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=64.72 E-value=35 Score=33.87 Aligned_cols=65 Identities=11% Similarity=-0.031 Sum_probs=46.3
Q ss_pred CceEEEEEEecCceEEEccCCCCCCceEEEecccccCCCCCCccccccCCCCcccCCCeEEEecCCC-CCceEEEEEEEC
Q 000252 503 KDFGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVSEGPS-KDRQGIVKKIYR 581 (1780)
Q Consensus 503 ~TVGVIVrVEKDEsfkVLdq~gd~pkVvtVkp~eI~~K~~~rR~vA~D~ngn~I~vGD~VKVIdGph-kGRqG~V~HIyR 581 (1780)
+.+|+|+++..+..|.|.+.++ ..+.+.. ..|+. ..--|..||.|.|--=|+ .-..|.|+|+|.
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---QRRLVSI---PGKLR---------KNIWIKRGDFLIVDPIEEGEDVKADIIFVYC 65 (78)
T ss_pred CeEEEEEEECCCCEEEEEECCC---CEEEEEE---chhhc---------cCEEEcCCCEEEEEecccCCCceEEEEEEeC
Confidence 3579999998888899988764 2444432 22321 124689999999987677 567899999987
Q ss_pred C
Q 000252 582 G 582 (1780)
Q Consensus 582 s 582 (1780)
.
T Consensus 66 ~ 66 (78)
T cd04456 66 K 66 (78)
T ss_pred H
Confidence 4
No 76
>PRK00276 infA translation initiation factor IF-1; Validated
Probab=64.49 E-value=35 Score=32.95 Aligned_cols=63 Identities=14% Similarity=0.073 Sum_probs=40.7
Q ss_pred eEEEEEEecCceEEEccCCCCCCceEEEecccccCCCCCCccccccCCCCcccCCCeEEEecCCCCCceEEEEEEEC
Q 000252 505 FGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVSEGPSKDRQGIVKKIYR 581 (1780)
Q Consensus 505 VGVIVrVEKDEsfkVLdq~gd~pkVvtVkp~eI~~K~~~rR~vA~D~ngn~I~vGD~VKVIdGphkGRqG~V~HIyR 581 (1780)
.|+|+++-.+..|.|.+.++ .++.+.+.- |+.. ....|.+||.|.|--=++....|.|+|=||
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 48999988654777765432 355655432 2111 123389999999985555566799998775
No 77
>PTZ00329 eukaryotic translation initiation factor 1A; Provisional
Probab=64.18 E-value=26 Score=38.96 Aligned_cols=76 Identities=16% Similarity=0.051 Sum_probs=53.3
Q ss_pred cccCceEEec-CCceEEEEEEecCceEEEccCCCCCCceEEEecccccCCCCCCccccccCCCCcccCCCeEEEecCCCC
Q 000252 492 FELYELVCFG-RKDFGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVSEGPSK 570 (1780)
Q Consensus 492 FeLhDLVQLD-~~TVGVIVrVEKDEsfkVLdq~gd~pkVvtVkp~eI~~K~~~rR~vA~D~ngn~I~vGD~VKVIdGphk 570 (1780)
-+..+|+.=. .+.+|+|+++-.+..|.|.+.++. .+.+. |.-|+.. .--|.+||+|.|--=+|.
T Consensus 21 ~~~rel~~~eegq~~g~V~~~LGn~~f~V~c~dG~---~rLa~---I~GKmRK---------~IWI~~GD~VlVel~~yd 85 (155)
T PTZ00329 21 GEKRELVFKEEGQEYAQVLRMLGNGRLEAYCFDGV---KRLCH---IRGKMRK---------RVWINIGDIILVSLRDFQ 85 (155)
T ss_pred cceeeeccCCCCcEEEEEEEEcCCCEEEEEECCCC---EEEEE---eecccee---------eEEecCCCEEEEeccCCC
Confidence 3444555433 367899999998889999987642 33333 3333321 246899999999888888
Q ss_pred CceEEEEEEECC
Q 000252 571 DRQGIVKKIYRG 582 (1780)
Q Consensus 571 GRqG~V~HIyRs 582 (1780)
-..|.|+|.|..
T Consensus 86 ~~KgdIi~Ry~~ 97 (155)
T PTZ00329 86 DSKADVILKYTP 97 (155)
T ss_pred CCEEEEEEEcCH
Confidence 889999998874
No 78
>PRK04333 50S ribosomal protein L14e; Validated
Probab=63.27 E-value=12 Score=37.68 Aligned_cols=33 Identities=15% Similarity=0.181 Sum_probs=28.4
Q ss_pred cccCCCEEEEeCCCCCCCcEEEEEEeCCCCEEEE
Q 000252 318 EVSEGTWAYVKNGKYKGDLAQVVYVNNARKRATV 351 (1780)
Q Consensus 318 ~Lk~GdwVRIKrGpYKGDLAQVveVDenk~eVtV 351 (1780)
++++|..|+++.|+|+|-++.|++|.++ ++|.|
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 6789999999999999999999999654 55655
No 79
>PRK03879 ribonuclease P protein component 1; Validated
Probab=61.56 E-value=16 Score=37.45 Aligned_cols=46 Identities=15% Similarity=0.174 Sum_probs=40.3
Q ss_pred cccCCEEEEccCC---CCCceeEEEEEeCCeEEEEecCcceEEEEecCccc
Q 000252 660 FAVGQTLRIRVGP---LKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLA 707 (1780)
Q Consensus 660 ~lIGKTVKIrkGP---YKGylGiVKDaTdt~ARVELHSk~KtITVdK~~Ls 707 (1780)
.|||-.|+|+.=+ |-|..|+|++-|..+..|+ +.++.++|+|++-.
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 77888999999854
No 80
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=60.60 E-value=37 Score=35.24 Aligned_cols=72 Identities=13% Similarity=-0.012 Sum_probs=49.9
Q ss_pred CceEEecC-CceEEEEEEecCceEEEccCCCCCCceEEEecccccCCCCCCccccccCCCCcccCCCeEEEecCCCCCce
Q 000252 495 YELVCFGR-KDFGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVSEGPSKDRQ 573 (1780)
Q Consensus 495 hDLVQLD~-~TVGVIVrVEKDEsfkVLdq~gd~pkVvtVkp~eI~~K~~~rR~vA~D~ngn~I~vGD~VKVIdGphkGRq 573 (1780)
++++.... +..|+|+++..+..|.|.+.++ ..+.+.. .-|+. ..--|.+||.|.|--=+|.-..
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---VERMGRI---PGKMK---------KRMWIREGDVVIVAPWDFQDEK 77 (100)
T ss_pred EEccCCCCCEEEEEEEEEcCCCEEEEEeCCC---CEEEEEE---chhhc---------ccEEecCCCEEEEEecccCCCE
Confidence 44555543 4679999998888999997764 2334332 22321 1346789999999876777778
Q ss_pred EEEEEEEC
Q 000252 574 GIVKKIYR 581 (1780)
Q Consensus 574 G~V~HIyR 581 (1780)
|.|+|+|.
T Consensus 78 g~Iv~r~~ 85 (100)
T PRK04012 78 ADIIWRYT 85 (100)
T ss_pred EEEEEEcC
Confidence 99999986
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=60.52 E-value=6 Score=51.51 Aligned_cols=16 Identities=25% Similarity=0.146 Sum_probs=11.4
Q ss_pred chhHHHHhcCCCCEEe
Q 000252 280 QCDINEACKGLSGIYY 295 (1780)
Q Consensus 280 q~dVkeAIkGI~gVy~ 295 (1780)
.+.++.||=|+...|.
T Consensus 235 ~d~LW~AIvGlT~q~i 250 (622)
T PF02724_consen 235 NDLLWLAIVGLTDQYI 250 (622)
T ss_pred hHHHHHHHHhhhHHhh
Confidence 3567888888877664
No 82
>PLN03111 DNA-directed RNA polymerase II subunit family protein; Provisional
Probab=60.19 E-value=57 Score=37.83 Aligned_cols=54 Identities=11% Similarity=0.101 Sum_probs=34.2
Q ss_pred EEEeccchhHHHHhcCCCCEEeceecccCHHHHHHHhhc---cc-------------ccccccCCCEEEEeC
Q 000252 274 FIEADKQCDINEACKGLSGIYYSRLAPVPKNEVSHLLSA---QI-------------KRNEVSEGTWAYVKN 329 (1780)
Q Consensus 274 YVEA~kq~dVkeAIkGI~gVy~~K~~pVPIkEM~dLLkv---kk-------------k~~~Lk~GdwVRIKr 329 (1780)
.||.+.++++.--| +.|+..-+-.+++.+|...||+. +. +...+++|+.|+|+|
T Consensus 122 ~iE~F~e~eLlvni--t~H~lVPkH~~ls~eEk~~lL~~y~i~~~qLPrI~~~DPvary~g~k~G~vvkI~R 191 (206)
T PLN03111 122 KIEVFQETELLVNI--TKHVLVPKHQVLTDEEKKTLLKRYTVKETQLPRIQVSDPIARYYGLKRGQVVKIIR 191 (206)
T ss_pred eEEEeehhHheecc--ccceecCCeEEcCHHHHHHHHHHcCCCHHHCCcccccChhhHhcCCCCCCEEEEEE
Confidence 46666666543221 22444456677889999999962 11 134678899998876
No 83
>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=59.85 E-value=23 Score=35.76 Aligned_cols=76 Identities=16% Similarity=0.237 Sum_probs=50.0
Q ss_pred EEEEec--cchhHHHHHHHHHHHHhhccCC---CCC-cEEEEEEeCCCCcEEEEEeccchhHHHHhcCCCCEEeceeccc
Q 000252 228 WKVKCM--AGRERQSAFCLMQKFVDLQSLG---SKM-QIISAFAVDHIKGFIFIEADKQCDINEACKGLSGIYYSRLAPV 301 (1780)
Q Consensus 228 WaVKCK--~GKEReVV~sLmrK~i~lq~~g---~~L-~I~SVFvpd~lKGYIYVEA~kq~dVkeAIkGI~gVy~~K~~pV 301 (1780)
|+|.+. ++....-...++.++++..... ..+ .|.+++.|....|||.|||+....+.+.+.--+.+++..+..+
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 666663 5555534445566666543111 112 2558888899999999999999999999888877755444333
Q ss_pred CH
Q 000252 302 PK 303 (1780)
Q Consensus 302 PI 303 (1780)
|+
T Consensus 82 Pv 83 (91)
T PF11746_consen 82 PV 83 (91)
T ss_pred ec
Confidence 43
No 84
>TIGR00523 eIF-1A eukaryotic/archaeal initiation factor 1A. Recommended nomenclature: eIF-1A for eukaryotes, aIF-1A for Archaea. Also called eIF-4C
Probab=59.25 E-value=31 Score=35.70 Aligned_cols=64 Identities=14% Similarity=-0.022 Sum_probs=43.3
Q ss_pred CCceEEEEEEecCceEEEccCCCCCCceEEEecccccCCCCCCccccccCCCCcccCCCeEEEecCCCCC---ceEEEEE
Q 000252 502 RKDFGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVSEGPSKD---RQGIVKK 578 (1780)
Q Consensus 502 ~~TVGVIVrVEKDEsfkVLdq~gd~pkVvtVkp~eI~~K~~~rR~vA~D~ngn~I~vGD~VKVIdGphkG---RqG~V~H 578 (1780)
.+.+|+|+++-.+..|.|.+.++ ..+.+. |..|+. ..--|..||.|.|- |+.- ..|.|+|
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---KTRLGR---IPGKLK---------KRIWIREGDVVIVK--PWEFQGDDKCDIVW 81 (99)
T ss_pred CEEEEEEEEEcCCCEEEEEeCCC---CEEEEE---Echhhc---------ccEEecCCCEEEEE--EccCCCCccEEEEE
Confidence 45789999998888999998664 233333 223321 13468999999993 5432 3699999
Q ss_pred EECC
Q 000252 579 IYRG 582 (1780)
Q Consensus 579 IyRs 582 (1780)
+|..
T Consensus 82 r~~~ 85 (99)
T TIGR00523 82 RYTK 85 (99)
T ss_pred EcCH
Confidence 8863
No 85
>PRK14635 hypothetical protein; Provisional
Probab=58.42 E-value=12 Score=41.18 Aligned_cols=49 Identities=12% Similarity=0.087 Sum_probs=37.8
Q ss_pred cccCCEEEEcc---C--CCCCceeEEEEEeCCeEEEEecCc------ceEEEEecCcccc
Q 000252 660 FAVGQTLRIRV---G--PLKGYLCRVLAVRYSDVTVKLDSQ------QKILTVKGEHLAE 708 (1780)
Q Consensus 660 ~lIGKTVKIrk---G--PYKGylGiVKDaTdt~ARVELHSk------~KtITVdK~~Ls~ 708 (1780)
.++|+.|+|+- + .|+|++|++++++++.+++++..+ .++++|+.+.|.-
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 47889888752 2 567888899999999999988543 5678888877763
No 86
>PRK04333 50S ribosomal protein L14e; Validated
Probab=58.33 E-value=13 Score=37.27 Aligned_cols=31 Identities=23% Similarity=0.310 Sum_probs=25.9
Q ss_pred cccCCEEEEccCCCCCceeEEEEE-eCCeEEE
Q 000252 660 FAVGQTLRIRVGPLKGYLCRVLAV-RYSDVTV 690 (1780)
Q Consensus 660 ~lIGKTVKIrkGPYKGylGiVKDa-Tdt~ARV 690 (1780)
.-+|+-|.|+.|+|+|.+.+|+++ .+.+|-|
T Consensus 4 v~~GrvV~~~~Grd~gk~~vIv~i~d~~~vlV 35 (84)
T PRK04333 4 IEVGRVCVKTAGREAGRKCVIVDIIDKNFVLV 35 (84)
T ss_pred ccccEEEEEeccCCCCCEEEEEEEecCCEEEE
Confidence 347899999999999999999999 4555555
No 87
>PF02736 Myosin_N: Myosin N-terminal SH3-like domain; InterPro: IPR004009 This domain has an SH3-like fold. It is found at the N terminus of many but not all myosins. The function of this domain is unknown.; GO: 0003774 motor activity, 0005524 ATP binding, 0016459 myosin complex; PDB: 2EC6_A 2W4H_M 1O1E_P 1O1D_D 1O18_A 1O1C_P 1O1B_D 1O1F_A 2W4A_M 2W4G_M ....
Probab=58.26 E-value=19 Score=31.52 Aligned_cols=30 Identities=30% Similarity=0.403 Sum_probs=26.4
Q ss_pred Cc-eeEEEEEeCCeEEEEecCcceEEEEecCc
Q 000252 675 GY-LCRVLAVRYSDVTVKLDSQQKILTVKGEH 705 (1780)
Q Consensus 675 Gy-lGiVKDaTdt~ARVELHSk~KtITVdK~~ 705 (1780)
|| +|.|+++.+..|+|+|.. .++++|.+++
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 8899998864
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=57.51 E-value=24 Score=35.35 Aligned_cols=44 Identities=14% Similarity=0.254 Sum_probs=35.7
Q ss_pred cccCCEEEEccCCCCCceeEEEEEeCCeEEEEecCcceEEEEecCcccc
Q 000252 660 FAVGQTLRIRVGPLKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLAE 708 (1780)
Q Consensus 660 ~lIGKTVKIrkGPYKGylGiVKDaTdt~ARVELHSk~KtITVdK~~Ls~ 708 (1780)
-..|+.|....| ..|+|+++.++++.||+. ..-.|+|+|..+..
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 346777877665 789999999999999995 55679999998864
No 89
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=56.82 E-value=90 Score=42.79 Aligned_cols=196 Identities=12% Similarity=0.087 Sum_probs=0.0
Q ss_pred ccCHHHHHHHhhcccccccccCCCEEEEeCCCCCCCcEEEEEEeCCCCEEEEEEeccCchhhHhhhcCCCcccCCCCCCC
Q 000252 300 PVPKNEVSHLLSAQIKRNEVSEGTWAYVKNGKYKGDLAQVVYVNNARKRATVKLIPRIDLQALAAKFGGGVAMKKTDSPA 379 (1780)
Q Consensus 300 pVPIkEM~dLLkvkkk~~~Lk~GdwVRIKrGpYKGDLAQVveVDenk~eVtVKLVPRIDy~~l~~k~~gg~~kKK~~RPP 379 (1780)
+|++.||...-++......|++|+.|++ +|+.||.++.++.|.+ ++....|-
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 CCCCCHhHHHhhCCce--eecccCCCCceEEecCCceeecceEEEEEeccceEeCCCCCCHHHHhhcCCCCCCccccHHH
Q 000252 380 PRLISPSELEEFRPLI--QYRRDRDTGKVFENLDGMMLKDGYLYKKVSIDSLSCWGVVPSEEELLKFQPSESNESADLEW 457 (1780)
Q Consensus 380 qRLFn~~Eark~~~~~--e~rrd~~tg~~f~i~~G~~YkDGFLyK~fkIssL~tedVnPTLEEL~kF~~~~~~e~~DL~~ 457 (1780)
..| .+....+..+ .+..-...+-+..+. .-++|||. ++.|....+...++++ |.
T Consensus 657 ~~~---~~~~~vG~~v~G~V~~i~~~G~fV~l~---~gV~GlIh----~sels~~~~~~~~~~~--~k------------ 712 (863)
T PRK12269 657 EEI---EARYPVGARFTRRIVKVTNAGAFIEME---EGIDGFLH----VDDLSWVKRTRPADHE--LE------------ 712 (863)
T ss_pred HHH---HHhCCCCCEEEEEEEEEecceEEEEeC---CCcEEEEE----hHHhhccccccchhhc--cC------------
Q ss_pred HHHHHhccccccEEEeecCCCcccccCCCCcc-------cccccCceEEecCCceEEEEEEecCceEEEccCCCCCCceE
Q 000252 458 LSQLYGERKKKRTTIVGKGGDKGEGSSGSSLE-------NSFELYELVCFGRKDFGLIVGMEKDDHYKILKEGSEGPAVV 530 (1780)
Q Consensus 458 La~i~ge~kk~kIi~v~kGg~kgE~ssG~~sl-------G~FeLhDLVQLD~~TVGVIVrVEKDEsfkVLdq~gd~pkVv 530 (1780)
.|..-+.+|+.+.....+-..+.=.... ..|.++|.|. |.|++|...-.|+-|..+ ..-
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 000252 531 TVERRTLKNGPFDMKFTALDQSMKVISLNDTARVS 565 (1780)
Q Consensus 531 tVkp~eI~~K~~~rR~vA~D~ngn~I~vGD~VKVI 565 (1780)
.|..++|....... .....+.|++||.|+++
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 90
>PRK05585 yajC preprotein translocase subunit YajC; Validated
Probab=56.10 E-value=25 Score=36.64 Aligned_cols=44 Identities=20% Similarity=0.286 Sum_probs=36.4
Q ss_pred ccCCEEEEccCCCCCceeEEEEEeCCeEEEEecCcceEEEEecCccccc
Q 000252 661 AVGQTLRIRVGPLKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLAEV 709 (1780)
Q Consensus 661 lIGKTVKIrkGPYKGylGiVKDaTdt~ARVELHSk~KtITVdK~~Ls~v 709 (1780)
-+|+.|.-..| +.|+|+++.+++|.||+ +..-+|+|+|.-|..+
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 46778877665 78999999999999999 4567899999998854
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=56.03 E-value=9.8 Score=50.70 Aligned_cols=7 Identities=29% Similarity=0.439 Sum_probs=3.0
Q ss_pred eecCccc
Q 000252 71 IVCDPEM 77 (1780)
Q Consensus 71 ~~~~~~~ 77 (1780)
+.|+|+.
T Consensus 545 ~~~~~~~ 551 (784)
T PF04931_consen 545 LYNGPEE 551 (784)
T ss_pred HhcCChH
Confidence 3444443
No 92
>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=55.50 E-value=39 Score=41.42 Aligned_cols=67 Identities=15% Similarity=0.185 Sum_probs=44.1
Q ss_pred CCCCCCCcEEEEEeccchhHHHHHHHHHHHHhhccCCCCCcEEEEEEeC-----CCCcEEEEEeccchhHHHHhcCCCCE
Q 000252 219 MPCPEDPTIWKVKCMAGRERQSAFCLMQKFVDLQSLGSKMQIISAFAVD-----HIKGFIFIEADKQCDINEACKGLSGI 293 (1780)
Q Consensus 219 LPSVkDPkLWaVKCK~GKEReVV~sLmrK~i~lq~~g~~L~I~SVFvpd-----~lKGYIYVEA~kq~dVkeAIkGI~gV 293 (1780)
.+...+-+||+=.+-.--..+.+..|...+ . .|.+|.+.. ..+||-|||...++++..||+.|.++
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 377776642 35699999999999999999988875
Q ss_pred E
Q 000252 294 Y 294 (1780)
Q Consensus 294 y 294 (1780)
.
T Consensus 173 ~ 173 (346)
T TIGR01659 173 T 173 (346)
T ss_pred c
Confidence 4
No 93
>smart00361 RRM_1 RNA recognition motif.
Probab=55.31 E-value=25 Score=32.93 Aligned_cols=28 Identities=29% Similarity=0.540 Sum_probs=24.9
Q ss_pred CCCCcEEEEEeccchhHHHHhcCCCCEE
Q 000252 267 DHIKGFIFIEADKQCDINEACKGLSGIY 294 (1780)
Q Consensus 267 d~lKGYIYVEA~kq~dVkeAIkGI~gVy 294 (1780)
.+.+||+||+....++...||+.|.+-+
T Consensus 34 ~~~rG~~fV~f~~~~dA~~A~~~l~g~~ 61 (70)
T smart00361 34 NHKRGNVYITFERSEDAARAIVDLNGRY 61 (70)
T ss_pred CCCcEEEEEEECCHHHHHHHHHHhCCCE
Confidence 3579999999999999999999988854
No 94
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=54.98 E-value=49 Score=33.83 Aligned_cols=63 Identities=13% Similarity=0.081 Sum_probs=45.5
Q ss_pred eEEEEEEecCceEEEccCCCCCCceEEEecccccCCCCCCccccccCCCCcccCCCeEEEecCCCCCceEEEEEEEC
Q 000252 505 FGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVSEGPSKDRQGIVKKIYR 581 (1780)
Q Consensus 505 VGVIVrVEKDEsfkVLdq~gd~pkVvtVkp~eI~~K~~~rR~vA~D~ngn~I~vGD~VKVIdGphkGRqG~V~HIyR 581 (1780)
.|+|+.+-.+..|+|...++. ++... |.-|+.. +.--|.+||.|+|--=||.-..|.|++=|+
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 599999998889998876642 33332 3334322 234688999999988899888899887775
No 95
>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=54.83 E-value=43 Score=31.80 Aligned_cols=62 Identities=15% Similarity=0.128 Sum_probs=42.7
Q ss_pred CceEEEEEEecCceEEEccCCCCCCceEEEecccccCCCCCCccccccCCCCcccCCCeEEEecCCCCCceEEEEEE
Q 000252 503 KDFGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVSEGPSKDRQGIVKKI 579 (1780)
Q Consensus 503 ~TVGVIVrVEKDEsfkVLdq~gd~pkVvtVkp~eI~~K~~~rR~vA~D~ngn~I~vGD~VKVIdGphkGRqG~V~HI 579 (1780)
+.+|+|+++..+..|.|...++ ..+.+.+. .| + ++.--|+.||.|.|---++.-..|.|+|.
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 4579999999988999998774 34444432 12 1 23446899999999877888889999884
No 96
>COG1862 YajC Preprotein translocase subunit YajC [Intracellular trafficking and secretion]
Probab=53.34 E-value=24 Score=36.41 Aligned_cols=46 Identities=22% Similarity=0.224 Sum_probs=37.9
Q ss_pred cCCEEEEccCCCCCceeEEEEEeCCeEEEEecCcceEEEEecCccccccCC
Q 000252 662 VGQTLRIRVGPLKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLAEVRGK 712 (1780)
Q Consensus 662 IGKTVKIrkGPYKGylGiVKDaTdt~ARVELHSk~KtITVdK~~Ls~v~~k 712 (1780)
-|+.|.... |+.|+|+.+.++++.|||. .+-.|+|.|+.+..+..+
T Consensus 46 kGD~VvT~g----Gi~G~V~~v~d~~v~I~l~-~~~~i~~~k~aI~~v~~~ 91 (97)
T COG1862 46 KGDEVVTIG----GIVGTVTKVGDDTVEIELG-DGTKIKFEKEAIATVLEK 91 (97)
T ss_pred CCCEEEEcC----CeEEEEEEEecCcEEEEEC-CCeEEEEEHHHHHhhccC
Confidence 366776655 4889999999999999999 888899999999865443
No 97
>KOG1708 consensus Mitochondrial/chloroplast ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=53.07 E-value=13 Score=42.65 Aligned_cols=41 Identities=34% Similarity=0.370 Sum_probs=32.3
Q ss_pred ccccCCEEEEccCCCCCceeEEEEEe--CCeEEEE-ecCcceEE
Q 000252 659 MFAVGQTLRIRVGPLKGYLCRVLAVR--YSDVTVK-LDSQQKIL 699 (1780)
Q Consensus 659 d~lIGKTVKIrkGPYKGylGiVKDaT--dt~ARVE-LHSk~KtI 699 (1780)
.++.|+||.|+.|.-||.+|+|.-+. .+.|-|+ ||++-+++
T Consensus 72 ~ff~GDtVeVlvGkDkGkqG~Vtqv~r~~s~VvV~gln~k~r~~ 115 (236)
T KOG1708|consen 72 HFFFGDTVEVLVGKDKGKQGEVTQVIRHRSWVVVKGLNTKYRHM 115 (236)
T ss_pred eEecCCEEEEEecccCCccceEEEEeecCceEEEcccchhhhhh
Confidence 35779999999999999999999986 4466666 77666533
No 98
>PTZ00065 60S ribosomal protein L14; Provisional
Probab=52.94 E-value=18 Score=39.09 Aligned_cols=33 Identities=24% Similarity=0.333 Sum_probs=28.1
Q ss_pred cccCCCEEEEeCCCCCCCcEEEEEEeCCCCEEEE
Q 000252 318 EVSEGTWAYVKNGKYKGDLAQVVYVNNARKRATV 351 (1780)
Q Consensus 318 ~Lk~GdwVRIKrGpYKGDLAQVveVDenk~eVtV 351 (1780)
-+++|=.|.|..|||+|-||.|++|-+. ++|.|
T Consensus 7 fVEiGRVvli~~Gp~~GKL~vIVDIID~-nRvLV 39 (130)
T PTZ00065 7 FVEPGRLCLIQYGPDAGKLCFIVDIVTP-TRVLV 39 (130)
T ss_pred ceeeceEEEEecCCCCCCEEEEEEEEcC-CeEEE
Confidence 4688999999999999999999999764 55555
No 99
>PTZ00415 transmission-blocking target antigen s230; Provisional
Probab=52.88 E-value=6.7 Score=54.98 Aligned_cols=17 Identities=24% Similarity=0.184 Sum_probs=8.2
Q ss_pred CccccCCCCCCCCCCcc
Q 000252 93 GKRKRNDGSSGVKPHNR 109 (1780)
Q Consensus 93 ~~~~~~~~~~~~~~r~r 109 (1780)
||.++.+-+.-+-.|||
T Consensus 120 g~~~~~~~d~~i~~~~~ 136 (2849)
T PTZ00415 120 GKAEIGDLDMIIIKRRR 136 (2849)
T ss_pred chhhcCCcceEEeehHH
Confidence 55555555544443333
No 100
>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=52.13 E-value=12 Score=48.96 Aligned_cols=13 Identities=31% Similarity=0.636 Sum_probs=6.4
Q ss_pred HHHHHHHHHHhcc
Q 000252 184 EEFDKMMEERYKS 196 (1780)
Q Consensus 184 EelAe~lkERY~r 196 (1780)
++..+.|++.|..
T Consensus 199 ~~~~~~i~~yY~~ 211 (622)
T PF02724_consen 199 EEYREEIEKYYSQ 211 (622)
T ss_pred HHHHHHHHHHHhc
Confidence 3444555555543
No 101
>COG3109 ProQ Activator of osmoprotectant transporter ProP [Signal transduction mechanisms]
Probab=52.13 E-value=21 Score=40.28 Aligned_cols=46 Identities=33% Similarity=0.563 Sum_probs=37.9
Q ss_pred cccCCEEEEccCCCCCceeEEEEEeCCeEEEEecCcceEEEEecCccc
Q 000252 660 FAVGQTLRIRVGPLKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLA 707 (1780)
Q Consensus 660 ~lIGKTVKIrkGPYKGylGiVKDaTdt~ARVELHSk~KtITVdK~~Ls 707 (1780)
..||+.|+|..|. --+--+|++|+.+.|||+|.+... ++|..+||.
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 345689999999999999998775 677888874
No 102
>PTZ00065 60S ribosomal protein L14; Provisional
Probab=51.35 E-value=27 Score=37.87 Aligned_cols=35 Identities=26% Similarity=0.424 Sum_probs=28.7
Q ss_pred cccCCEEEEccCCCCCceeEEEEEeCCeEEEEecCc
Q 000252 660 FAVGQTLRIRVGPLKGYLCRVLAVRYSDVTVKLDSQ 695 (1780)
Q Consensus 660 ~lIGKTVKIrkGPYKGylGiVKDaTdt~ARVELHSk 695 (1780)
.-||..|.|..|||+|-++.|+||-|.. ||.++-.
T Consensus 8 VEiGRVvli~~Gp~~GKL~vIVDIID~n-RvLVDGP 42 (130)
T PTZ00065 8 VEPGRLCLIQYGPDAGKLCFIVDIVTPT-RVLVDGA 42 (130)
T ss_pred eeeceEEEEecCCCCCCEEEEEEEEcCC-eEEEeCC
Confidence 3578999999999999999999997543 5566655
No 103
>PRK14639 hypothetical protein; Provisional
Probab=50.81 E-value=26 Score=37.94 Aligned_cols=49 Identities=10% Similarity=0.231 Sum_probs=39.3
Q ss_pred cccCCEEEEccCCCCCceeEEEEEeCCeEEEEecCcceEEEEecCcccc
Q 000252 660 FAVGQTLRIRVGPLKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLAE 708 (1780)
Q Consensus 660 ~lIGKTVKIrkGPYKGylGiVKDaTdt~ARVELHSk~KtITVdK~~Ls~ 708 (1780)
.++|+.|+|+-.--|=+.|++++++++.+++|+-...++++|+.+.|.-
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 4799999998644588899999999999999774345678888877763
No 104
>PRK12288 GTPase RsgA; Reviewed
Probab=50.49 E-value=82 Score=38.68 Aligned_cols=86 Identities=9% Similarity=0.079 Sum_probs=55.9
Q ss_pred ceEEEEEEecCceEEEccCCCCCCceEEEecccccCCCCCCccccccCCCCcccCCCeEEEecCC--CCCceEEEEEEEC
Q 000252 504 DFGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVSEGP--SKDRQGIVKKIYR 581 (1780)
Q Consensus 504 TVGVIVrVEKDEsfkVLdq~gd~pkVvtVkp~eI~~K~~~rR~vA~D~ngn~I~vGD~VKVIdGp--hkGRqG~V~HIyR 581 (1780)
..|.||++.+. .+.|++..+ .++.+.++.. + +.+-|||.|.+-.-. .....|.|.+|+.
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 788876443 3555554321 1 238999999985211 0012499999998
Q ss_pred CEEEEEeCcceeeccEEEEeCCceeec
Q 000252 582 GILFIYDENETENGGYFCSKSQHCEKT 608 (1780)
Q Consensus 582 s~VFL~Sr~~tENgGIFVvRArnv~tv 608 (1780)
-+-.|.-.......-+++++...|++|
T Consensus 101 R~n~L~R~~~~~~~q~iaANvD~vlIV 127 (347)
T PRK12288 101 RTSVLTRPDYYDGVKPIAANIDQIVIV 127 (347)
T ss_pred ccceEECCCcccccceEEEEccEEEEE
Confidence 775555444444447788998888766
No 105
>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=49.15 E-value=25 Score=32.12 Aligned_cols=66 Identities=17% Similarity=0.179 Sum_probs=40.3
Q ss_pred EEEEEEeCCCCcEEEEEeccchhHHHHhcCCCCEEeceecccCHHHHHHHhhcccccccccCCCEEEEeCCCCCCCcEEE
Q 000252 260 IISAFAVDHIKGFIFIEADKQCDINEACKGLSGIYYSRLAPVPKNEVSHLLSAQIKRNEVSEGTWAYVKNGKYKGDLAQV 339 (1780)
Q Consensus 260 I~SVFvpd~lKGYIYVEA~kq~dVkeAIkGI~gVy~~K~~pVPIkEM~dLLkvkkk~~~Lk~GdwVRIKrGpYKGDLAQV 339 (1780)
|+.+.+....+-.||||... ++. -+|++.|+............|++|+.|+++ |
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 44555555555668888743 122 245566665212222223458899999985 8
Q ss_pred EEEeCCCCEEEE
Q 000252 340 VYVNNARKRATV 351 (1780)
Q Consensus 340 veVDenk~eVtV 351 (1780)
++|+.++.++.+
T Consensus 57 ~~id~~~~~i~l 68 (69)
T cd05690 57 LNIDVERERISL 68 (69)
T ss_pred EEEECCcCEEeC
Confidence 999988877754
No 106
>PRK05886 yajC preprotein translocase subunit YajC; Validated
Probab=48.65 E-value=26 Score=36.93 Aligned_cols=44 Identities=9% Similarity=0.159 Sum_probs=35.2
Q ss_pred ccCCEEEEccCCCCCceeEEEEEeCCeEEEEecCcceEEEEecCccccc
Q 000252 661 AVGQTLRIRVGPLKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLAEV 709 (1780)
Q Consensus 661 lIGKTVKIrkGPYKGylGiVKDaTdt~ARVELHSk~KtITVdK~~Ls~v 709 (1780)
-.|+.|.-.. |+.|+|+++++++|.||+. ..-.|+|.|..|..+
T Consensus 40 k~GD~VvT~g----Gi~G~V~~I~d~~v~leia-~gv~i~~~r~AI~~v 83 (109)
T PRK05886 40 QPGDRVHTTS----GLQATIVGITDDTVDLEIA-PGVVTTWMKLAVRDR 83 (109)
T ss_pred CCCCEEEECC----CeEEEEEEEeCCEEEEEEC-CCeEEEEEhhheeee
Confidence 4567776655 5889999999999999995 456799999999843
No 107
>PRK00092 ribosome maturation protein RimP; Reviewed
Probab=48.53 E-value=28 Score=37.90 Aligned_cols=49 Identities=18% Similarity=0.352 Sum_probs=38.3
Q ss_pred cccCCEEEEc----cCCCCCceeEEEEEeCCeEEEEecCcceEEEEecCcccc
Q 000252 660 FAVGQTLRIR----VGPLKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLAE 708 (1780)
Q Consensus 660 ~lIGKTVKIr----kGPYKGylGiVKDaTdt~ARVELHSk~KtITVdK~~Ls~ 708 (1780)
..+|+.|+|+ ...-|=+.|++++++++.+++++..+.++++|+.+.|..
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 244466689999999999998876443489998888764
No 108
>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=46.88 E-value=47 Score=33.51 Aligned_cols=48 Identities=13% Similarity=0.070 Sum_probs=37.6
Q ss_pred cccCCEEEEccCC---CCCceeEEEEEeCCeEEEEecCcceEEEEecCcccc
Q 000252 660 FAVGQTLRIRVGP---LKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLAE 708 (1780)
Q Consensus 660 ~lIGKTVKIrkGP---YKGylGiVKDaTdt~ARVELHSk~KtITVdK~~Ls~ 708 (1780)
.|+|-.|+|+.=+ |-|+.|||++-|..+.+|+- ...++++|+|.+-.+
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 5899999998874 68999999999999999763 344789999998764
No 109
>smart00538 POP4 A domain found in a protein subunit of human RNase MRP and RNase P ribonucleoprotein complexes and archaeal proteins.
Probab=46.43 E-value=45 Score=33.97 Aligned_cols=47 Identities=15% Similarity=0.188 Sum_probs=39.2
Q ss_pred cccCCEEEEccCC---CCCceeEEEEEeCCeEEEEecCcceEEEEecCccc
Q 000252 660 FAVGQTLRIRVGP---LKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLA 707 (1780)
Q Consensus 660 ~lIGKTVKIrkGP---YKGylGiVKDaTdt~ARVELHSk~KtITVdK~~Ls 707 (1780)
.|||-.|+|+.=+ |-|..|||++-|..+..|+... .++.+|+|.+-.
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 477889988844
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=45.42 E-value=84 Score=46.56 Aligned_cols=91 Identities=11% Similarity=0.122 Sum_probs=65.1
Q ss_pred ccccccCceEEecCCceEEEEEEecCceEEEccCCCCCCceEEEecccccCCCCCCccccccCCCCcccCCCeEEEecCC
Q 000252 489 ENSFELYELVCFGRKDFGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVSEGP 568 (1780)
Q Consensus 489 lG~FeLhDLVQLD~~TVGVIVrVEKDEsfkVLdq~gd~pkVvtVkp~eI~~K~~~rR~vA~D~ngn~I~vGD~VKVIdGp 568 (1780)
...|+.+|+|+|.....-.|+.|+++....+|....+ +..+.+.|.++.. ............|..||.|+...-.
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 4689999999999999999999999767666643111 3567788876532 1234556677899999999987432
Q ss_pred -----CCCceEEEEEEECCEE
Q 000252 569 -----SKDRQGIVKKIYRGIL 584 (1780)
Q Consensus 569 -----hkGRqG~V~HIyRs~V 584 (1780)
..+..++|+.|..+.+
T Consensus 1402 ~~~g~~n~~~~~V~~v~~~~~ 1422 (1960)
T TIGR02760 1402 KNRGIKANEVYTVTQVVNGLS 1422 (1960)
T ss_pred cccccccCCeEEEEEEcCCcE
Confidence 2467889999866543
No 111
>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor. Members of this subfamily are found in plants, metazoa and fungi.
Probab=45.35 E-value=33 Score=42.80 Aligned_cols=49 Identities=16% Similarity=0.162 Sum_probs=36.0
Q ss_pred HHHHHHHHHHhhccCCCCCcEEEEEEeCC--------CCcEEEEEeccchhHHHHhcCCCCEE
Q 000252 240 SAFCLMQKFVDLQSLGSKMQIISAFAVDH--------IKGFIFIEADKQCDINEACKGLSGIY 294 (1780)
Q Consensus 240 VV~sLmrK~i~lq~~g~~L~I~SVFvpd~--------lKGYIYVEA~kq~dVkeAIkGI~gVy 294 (1780)
|+..|.+.|..+. .|.+|+++.. -.||||||-...++...||..|.+..
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 112
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=45.27 E-value=53 Score=29.07 Aligned_cols=67 Identities=16% Similarity=0.219 Sum_probs=41.7
Q ss_pred EEEEEEeCCCCcEEEEEeccchhHHHHhcCCCCEEeceecccCHHHHHHHhhcccccccccCCCEEEEeCCCCCCCcEEE
Q 000252 260 IISAFAVDHIKGFIFIEADKQCDINEACKGLSGIYYSRLAPVPKNEVSHLLSAQIKRNEVSEGTWAYVKNGKYKGDLAQV 339 (1780)
Q Consensus 260 I~SVFvpd~lKGYIYVEA~kq~dVkeAIkGI~gVy~~K~~pVPIkEM~dLLkvkkk~~~Lk~GdwVRIKrGpYKGDLAQV 339 (1780)
|+.+++....+.++||+... ++ ...||+.||.+-.. .+....|++|+.|++ +|
T Consensus 5 ~v~g~V~~v~~~g~~v~i~~---------~~-------~g~l~~~~~~~~~~-~~~~~~~~~G~~v~~----------~V 57 (72)
T smart00316 5 VVEGTVTEITPFGAFVDLGN---------GV-------EGLIPISELSDKRV-KDPEEVLKVGDEVKV----------KV 57 (72)
T ss_pred EEEEEEEEEEccEEEEEeCC---------CC-------EEEEEHHHCCcccc-CCHHHeecCCCEEEE----------EE
Confidence 55566656666788887753 11 12445555554321 111235889999986 69
Q ss_pred EEEeCCCCEEEEEE
Q 000252 340 VYVNNARKRATVKL 353 (1780)
Q Consensus 340 veVDenk~eVtVKL 353 (1780)
..|+..+.++.|.+
T Consensus 58 ~~~~~~~~~i~ls~ 71 (72)
T smart00316 58 LSVDEEKGRIILSL 71 (72)
T ss_pred EEEeCCCCEEEEEe
Confidence 99998878877765
No 113
>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=44.67 E-value=36 Score=33.49 Aligned_cols=49 Identities=22% Similarity=0.352 Sum_probs=37.4
Q ss_pred cccCCEEEEcc----CCCCCceeEEEEEeCCeEEEEecCc--ceEEEEecCcccc
Q 000252 660 FAVGQTLRIRV----GPLKGYLCRVLAVRYSDVTVKLDSQ--QKILTVKGEHLAE 708 (1780)
Q Consensus 660 ~lIGKTVKIrk----GPYKGylGiVKDaTdt~ARVELHSk--~KtITVdK~~Ls~ 708 (1780)
..||+.|+|+- +.-|=+.|+++++.++.++|+++.+ .++|+|+.++|..
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 5688888877763
No 114
>PF10446 DUF2457: Protein of unknown function (DUF2457); InterPro: IPR018853 This entry represents a family of uncharacterised proteins.
Probab=44.21 E-value=12 Score=47.06 Aligned_cols=7 Identities=14% Similarity=0.610 Sum_probs=3.0
Q ss_pred cEEEEEe
Q 000252 226 TIWKVKC 232 (1780)
Q Consensus 226 kLWaVKC 232 (1780)
.||+-..
T Consensus 123 ~~WtP~~ 129 (458)
T PF10446_consen 123 EFWTPGA 129 (458)
T ss_pred eeecccc
Confidence 3444443
No 115
>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=42.83 E-value=71 Score=29.43 Aligned_cols=67 Identities=13% Similarity=0.083 Sum_probs=41.9
Q ss_pred EEEEEEeCCCCcEEEEEeccchhHHHHhcCCCCEEeceecccCHHHHHHHhhcccccccccCCCEEEEeCCCCCCCcEEE
Q 000252 260 IISAFAVDHIKGFIFIEADKQCDINEACKGLSGIYYSRLAPVPKNEVSHLLSAQIKRNEVSEGTWAYVKNGKYKGDLAQV 339 (1780)
Q Consensus 260 I~SVFvpd~lKGYIYVEA~kq~dVkeAIkGI~gVy~~K~~pVPIkEM~dLLkvkkk~~~Lk~GdwVRIKrGpYKGDLAQV 339 (1780)
|+.+.+....+.-||||... + ...+||+.||.+=. +......|++|+.|++ +|
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 44555555567778887632 1 13466677764321 1112235788998886 68
Q ss_pred EEEeCCCCEEEEEE
Q 000252 340 VYVNNARKRATVKL 353 (1780)
Q Consensus 340 veVDenk~eVtVKL 353 (1780)
++|++...++.|.+
T Consensus 56 ~~~d~~~~~i~ls~ 69 (70)
T cd05698 56 LSCDPEQQRLLLSC 69 (70)
T ss_pred EEEcCCCCEEEEEe
Confidence 99999888887765
No 116
>PRK14637 hypothetical protein; Provisional
Probab=42.79 E-value=43 Score=36.83 Aligned_cols=46 Identities=9% Similarity=0.114 Sum_probs=35.8
Q ss_pred cccCCEEEEccCCCCCc-eeEEEEEeCCeEEEEecCcceEEEEecCccc
Q 000252 660 FAVGQTLRIRVGPLKGY-LCRVLAVRYSDVTVKLDSQQKILTVKGEHLA 707 (1780)
Q Consensus 660 ~lIGKTVKIrkGPYKGy-lGiVKDaTdt~ARVELHSk~KtITVdK~~Ls 707 (1780)
..+|+.|+|+-..-+-+ .|++++++++.+++++ ..+++.|+.+.|.
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 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=42.50 E-value=41 Score=35.98 Aligned_cols=49 Identities=14% Similarity=0.452 Sum_probs=35.3
Q ss_pred cccCCEEEEcc-CCCCC---ceeEEEEEeCCeEEEEecCc--ceEEEEecCcccc
Q 000252 660 FAVGQTLRIRV-GPLKG---YLCRVLAVRYSDVTVKLDSQ--QKILTVKGEHLAE 708 (1780)
Q Consensus 660 ~lIGKTVKIrk-GPYKG---ylGiVKDaTdt~ARVELHSk--~KtITVdK~~Ls~ 708 (1780)
..||+.|+|+- -|..+ +.|++++++++.++|+++.+ .++++|+.++|.-
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 34544 69999999999999999887 4689999888763
No 118
>PF10574 UPF0552: Uncharacterised protein family UPF0552; InterPro: IPR018889 This family of proteins has no known function.
Probab=42.11 E-value=31 Score=40.18 Aligned_cols=109 Identities=16% Similarity=0.177 Sum_probs=59.3
Q ss_pred cccccCC-CCCCCCcEEEEEeccchhHHHHHHHHHHHHhhccCCCCCcEEEEEEe--C-----CCCcEEEEEec------
Q 000252 213 LEREYHM-PCPEDPTIWKVKCMAGRERQSAFCLMQKFVDLQSLGSKMQIISAFAV--D-----HIKGFIFIEAD------ 278 (1780)
Q Consensus 213 VpQq~LL-PSVkDPkLWaVKCK~GKEReVV~sLmrK~i~lq~~g~~L~I~SVFvp--d-----~lKGYIYVEA~------ 278 (1780)
|.++.+. ++-..-++|+|.|++- ..+.|+| +.. +.+ |-.-|.. + .++-| -|||.
T Consensus 44 ~sRH~I~D~~~~k~Ry~vl~i~~~------~~hrR~f-d~~--G~E--Iepnfs~T~kVntGyL~Ssy-kveAkg~tDrl 111 (224)
T PF10574_consen 44 VSRHSITDASGQKERYYVLYIRPS------RIHRRKF-DAK--GNE--IEPNFSDTTKVNTGYLNSSY-KVEAKGDTDRL 111 (224)
T ss_pred eeEEEEEcCCCCceEEEEEEEeec------hhhhhcc-cCC--CcC--cCCCccceeeeeecccCccc-EEEecCCcccc
Confidence 4444443 3344456999999874 2333443 321 222 2222222 1 23333 68887
Q ss_pred cchhHHHHhcC--CCCEE---e---ceecccCHHHHHHHhhcccccccccCCCEEEEeC---CCCCCCcEEEEE
Q 000252 279 KQCDINEACKG--LSGIY---Y---SRLAPVPKNEVSHLLSAQIKRNEVSEGTWAYVKN---GKYKGDLAQVVY 341 (1780)
Q Consensus 279 kq~dVkeAIkG--I~gVy---~---~K~~pVPIkEM~dLLkvkkk~~~Lk~GdwVRIKr---GpYKGDLAQVve 341 (1780)
.++++..+|.. +..|. . .-.+.+|..||. ..+|++|+-||||. +||-.-||+++.
T Consensus 112 s~~~L~~~V~k~~ll~lt~~~~~~~~~aFW~~e~~~~--------~~ele~G~~vRlKT~GDspFieSlaKlD~ 177 (224)
T PF10574_consen 112 SPEQLKALVNKPELLALTESHTPDQTFAFWMPEAEME--------KMELELGDEVRLKTRGDSPFIESLAKLDS 177 (224)
T ss_pred CHHHHHHHhCchhhcccccccCCCCeEEEeechhhcc--------ceecccCCeEEEEecCCchhheeeeeecc
Confidence 23445555541 11111 0 124556666665 35799999999995 689888887764
No 119
>PRK14638 hypothetical protein; Provisional
Probab=41.58 E-value=38 Score=37.13 Aligned_cols=47 Identities=11% Similarity=0.142 Sum_probs=37.8
Q ss_pred cccCCEEEEccCCCCCceeEEEEEeCCeEEEEecCcceEEEEecCcccc
Q 000252 660 FAVGQTLRIRVGPLKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLAE 708 (1780)
Q Consensus 660 ~lIGKTVKIrkGPYKGylGiVKDaTdt~ARVELHSk~KtITVdK~~Ls~ 708 (1780)
..+|+.|+|+----|=+.|+++++++..++|++ ..++|.|+.+.|.-
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 46778888877763
No 120
>PF13051 DUF3912: Protein of unknown function (DUF3912)
Probab=41.32 E-value=52 Score=31.42 Aligned_cols=49 Identities=20% Similarity=0.238 Sum_probs=34.3
Q ss_pred cccCCEEEEccCCCCCceeEEEEEe---CCeEEEEecCcceEEEEecCcccccc
Q 000252 660 FAVGQTLRIRVGPLKGYLCRVLAVR---YSDVTVKLDSQQKILTVKGEHLAEVR 710 (1780)
Q Consensus 660 ~lIGKTVKIrkGPYKGylGiVKDaT---dt~ARVELHSk~KtITVdK~~Ls~v~ 710 (1780)
.++||...|..|||.-.+||||.-. +.+..|-+. -+.|.|.-.+|.+|+
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 345666666666543
No 121
>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=41.05 E-value=5 Score=51.30 Aligned_cols=13 Identities=38% Similarity=0.690 Sum_probs=10.4
Q ss_pred CcceeccccCCCC
Q 000252 118 QFVEDAADVDYDD 130 (1780)
Q Consensus 118 ~FiDdEAEVDDDe 130 (1780)
.+|||||+|.-+|
T Consensus 1052 k~~eDEAevSGsD 1064 (1329)
T KOG4156|consen 1052 KYLEDEAEVSGSD 1064 (1329)
T ss_pred HhhcchhhcccCc
Confidence 5999999997444
No 122
>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=40.50 E-value=49 Score=34.68 Aligned_cols=25 Identities=16% Similarity=0.106 Sum_probs=21.2
Q ss_pred CCccccccCCCCcccCCCeEEEecC
Q 000252 543 DMKFTALDQSMKVISLNDTARVSEG 567 (1780)
Q Consensus 543 ~rR~vA~D~ngn~I~vGD~VKVIdG 567 (1780)
..++.|-|.+.++..+||+|+|.+-
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 123
>PRK14643 hypothetical protein; Provisional
Probab=40.48 E-value=41 Score=37.46 Aligned_cols=49 Identities=22% Similarity=0.217 Sum_probs=38.6
Q ss_pred cccCCEEEEcc-CCCCC---ceeEEEEEeCCeEEEEec----CcceEEEEecCcccc
Q 000252 660 FAVGQTLRIRV-GPLKG---YLCRVLAVRYSDVTVKLD----SQQKILTVKGEHLAE 708 (1780)
Q Consensus 660 ~lIGKTVKIrk-GPYKG---ylGiVKDaTdt~ARVELH----Sk~KtITVdK~~Ls~ 708 (1780)
.++|+.|+|+- -|+.| +.|+++++.+..++|+|+ ...++|.|+.+.|.-
T Consensus 101 r~~G~~V~V~l~~~~~g~k~~~G~L~~~~~~~~~l~l~~~~~~~~~~~~ip~~~I~k 157 (164)
T PRK14643 101 KALNQWVYVQLNNEIKKVKEFEGYVTKYNVNTNTFRFTFFIKGQKKKLDVKYEQIKF 157 (164)
T ss_pred HhcCCeEEEEEecccCCceEEEEEEEEEeCCcEEEEEEeeccCcCcEEEEeHHHhhh
Confidence 47999999963 45444 799999999999998864 346789998888774
No 124
>PRK08572 rps17p 30S ribosomal protein S17P; Reviewed
Probab=39.85 E-value=51 Score=34.85 Aligned_cols=25 Identities=12% Similarity=0.183 Sum_probs=21.5
Q ss_pred CCccccccCCCCcccCCCeEEEecC
Q 000252 543 DMKFTALDQSMKVISLNDTARVSEG 567 (1780)
Q Consensus 543 ~rR~vA~D~ngn~I~vGD~VKVIdG 567 (1780)
..++.|-|.+.++.++||.|+|.+-
T Consensus 65 ~kky~aHDe~cn~~kvGD~V~I~E~ 89 (108)
T PRK08572 65 RSRIHAHNPPCIDAKVGDKVKIAEC 89 (108)
T ss_pred eeeEEEECCCCCCCCCCCEEEEEEc
Confidence 3458899988799999999999976
No 125
>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=39.81 E-value=1.6e+02 Score=34.98 Aligned_cols=84 Identities=12% Similarity=0.171 Sum_probs=51.9
Q ss_pred EEEEEEecCceEEEccCCCCCCceEEEecccccCCCCCCccccccCCCCcccCCCeEEEecCCCCCceEEEEEEECC-EE
Q 000252 506 GLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVSEGPSKDRQGIVKKIYRG-IL 584 (1780)
Q Consensus 506 GVIVrVEKDEsfkVLdq~gd~pkVvtVkp~eI~~K~~~rR~vA~D~ngn~I~vGD~VKVIdGphkGRqG~V~HIyRs-~V 584 (1780)
|.||++.+ ..+.|++.+ .++..+++..-. .....+-|||.|.+..- ...++.|.+|+.- -+
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 355555433211 01456899999987532 2467999999954 34
Q ss_pred EEEeCcceeeccEEEEeCCceeec
Q 000252 585 FIYDENETENGGYFCSKSQHCEKT 608 (1780)
Q Consensus 585 FL~Sr~~tENgGIFVvRArnv~tv 608 (1780)
|+.-..... .-+++.++..|++|
T Consensus 63 l~R~~~~~~-~~~i~anvD~vllV 85 (287)
T cd01854 63 LSRPAAGGR-EQVIAANVDQLVIV 85 (287)
T ss_pred EEccCCCCc-ceeEEEeCCEEEEE
Confidence 444332222 56677777666655
No 126
>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=39.65 E-value=1.5e+02 Score=27.71 Aligned_cols=60 Identities=13% Similarity=0.071 Sum_probs=35.5
Q ss_pred eEEEEEEecCceEEEccCCCCCCceEEEecccccCCCCCCccccccCCCCcccCCCeEEEecCCCCCceEEEEE
Q 000252 505 FGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVSEGPSKDRQGIVKK 578 (1780)
Q Consensus 505 VGVIVrVEKDEsfkVLdq~gd~pkVvtVkp~eI~~K~~~rR~vA~D~ngn~I~vGD~VKVIdGphkGRqG~V~H 578 (1780)
.|+|++.-....|.|.+..+ .++++.++. ++.. ....+.+||.|.+---++...+|.|+|
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 47888876323666655332 356666433 2110 234489999998874443445688876
No 127
>COG1471 RPS4A Ribosomal protein S4E [Translation, ribosomal structure and biogenesis]
Probab=39.26 E-value=36 Score=39.95 Aligned_cols=52 Identities=17% Similarity=0.143 Sum_probs=40.1
Q ss_pred CcccCCCeEEEecCCCCCceEEEEEEECC------EEEEEeCcceeeccEEEEeCCceeecc
Q 000252 554 KVISLNDTARVSEGPSKDRQGIVKKIYRG------ILFIYDENETENGGYFCSKSQHCEKTK 609 (1780)
Q Consensus 554 n~I~vGD~VKVIdGphkGRqG~V~HIyRs------~VFL~Sr~~tENgGIFVvRArnv~tv~ 609 (1780)
-.|++|-.|-|+.|.|-|+.|+|++|... +|.|-+ +++--|.|...+|.+++
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 45788999999999999999999999754 222222 22336999999999885
No 128
>PRK14634 hypothetical protein; Provisional
Probab=38.87 E-value=42 Score=36.97 Aligned_cols=47 Identities=6% Similarity=0.064 Sum_probs=37.3
Q ss_pred cccCCEEEEc-cCCC---CCceeEEEEEeCCeEEEEecCcceEEEEecCcccc
Q 000252 660 FAVGQTLRIR-VGPL---KGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLAE 708 (1780)
Q Consensus 660 ~lIGKTVKIr-kGPY---KGylGiVKDaTdt~ARVELHSk~KtITVdK~~Ls~ 708 (1780)
..+|+.|+|+ ..|. |=+.|+++++.++.+++++. .++|+|+.+.|.-
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 4443 66899999999999998874 6778888877764
No 129
>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=38.52 E-value=69 Score=30.86 Aligned_cols=69 Identities=17% Similarity=0.213 Sum_probs=46.0
Q ss_pred CcEEEEEEeCCCCcEEEEEeccchhHHHHhcCCCCEEeceecccCHHHHHHHhhcccccccccCCCEEEEeCCCCCCCcE
Q 000252 258 MQIISAFAVDHIKGFIFIEADKQCDINEACKGLSGIYYSRLAPVPKNEVSHLLSAQIKRNEVSEGTWAYVKNGKYKGDLA 337 (1780)
Q Consensus 258 L~I~SVFvpd~lKGYIYVEA~kq~dVkeAIkGI~gVy~~K~~pVPIkEM~dLLkvkkk~~~Lk~GdwVRIKrGpYKGDLA 337 (1780)
-.|+.+.+....+--|||+... ++. .+||+.|+.+-. +......|++|+.|++
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 3577888877778888888742 222 245566654321 1122345788999987
Q ss_pred EEEEEeCCCCEEEEEE
Q 000252 338 QVVYVNNARKRATVKL 353 (1780)
Q Consensus 338 QVveVDenk~eVtVKL 353 (1780)
+|..++.++.++.|.|
T Consensus 68 kV~~id~~~~~i~lsl 83 (83)
T cd04461 68 KVTSVDEEKQRFLLSL 83 (83)
T ss_pred EEEEEcCCCCEEEEeC
Confidence 6999999888888764
No 130
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=38.41 E-value=1.2e+02 Score=30.40 Aligned_cols=65 Identities=14% Similarity=0.118 Sum_probs=48.0
Q ss_pred ceEEEEEEecCceEEEccCCCCCCceEEEecccccCCCCCCccccccCCCCcccCCCeEEEecCCCCCceEEEEEEECC
Q 000252 504 DFGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVSEGPSKDRQGIVKKIYRG 582 (1780)
Q Consensus 504 TVGVIVrVEKDEsfkVLdq~gd~pkVvtVkp~eI~~K~~~rR~vA~D~ngn~I~vGD~VKVIdGphkGRqG~V~HIyRs 582 (1780)
..|+|+++..+..|+|.+.++ .++.-. |.-|+.. +.--|.+||.|.|--=||.-..|.|++=|+.
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 4444321 2346899999999988998888999887763
No 131
>PF10842 DUF2642: Protein of unknown function (DUF2642); InterPro: IPR020139 This entry contains proteins with no known function.
Probab=38.22 E-value=73 Score=31.11 Aligned_cols=45 Identities=7% Similarity=0.115 Sum_probs=35.1
Q ss_pred cccCCEEEEccCCCCCceeEEEEEeCCeEEEEecCcceEEEEecCccc
Q 000252 660 FAVGQTLRIRVGPLKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLA 707 (1780)
Q Consensus 660 ~lIGKTVKIrkGPYKGylGiVKDaTdt~ARVELHSk~KtITVdK~~Ls 707 (1780)
.+||+.|.|..- .-=+.|+++|+..+++.||-+ .+.+-|.-.+|.
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 132
>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=38.10 E-value=1.3e+02 Score=29.51 Aligned_cols=61 Identities=13% Similarity=0.071 Sum_probs=43.1
Q ss_pred ceEEEEEEecCceEEEccCCCCCCceEEEecccccCCCCCCccccccCCCCcccCCCeEEEecCCCCCceEEEEE
Q 000252 504 DFGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVSEGPSKDRQGIVKK 578 (1780)
Q Consensus 504 TVGVIVrVEKDEsfkVLdq~gd~pkVvtVkp~eI~~K~~~rR~vA~D~ngn~I~vGD~VKVIdGphkGRqG~V~H 578 (1780)
..|+|+++-.+..|+|...++ ..+... |.-|+.. +.--|.+||.|+|--=||.-..|.|+|
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 233332 3334322 244689999999998888877888875
No 133
>PRK14644 hypothetical protein; Provisional
Probab=37.77 E-value=41 Score=36.47 Aligned_cols=48 Identities=13% Similarity=0.190 Sum_probs=36.2
Q ss_pred cccCCEEEEcc-CC---CCCceeEEEEEeCCeEEEEe--cCcceEEEEecCccc
Q 000252 660 FAVGQTLRIRV-GP---LKGYLCRVLAVRYSDVTVKL--DSQQKILTVKGEHLA 707 (1780)
Q Consensus 660 ~lIGKTVKIrk-GP---YKGylGiVKDaTdt~ARVEL--HSk~KtITVdK~~Ls 707 (1780)
..||+.|+|+- -| -|=+.|+++++.+..+++++ ..+.+.|++++++|.
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 36678999999999999964 444467777777764
No 134
>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]
Probab=37.50 E-value=40 Score=38.32 Aligned_cols=34 Identities=26% Similarity=0.478 Sum_probs=31.3
Q ss_pred cEEEEEEeCCCCcEEEEEeccchhHHHHhcCCCC
Q 000252 259 QIISAFAVDHIKGFIFIEADKQCDINEACKGLSG 292 (1780)
Q Consensus 259 ~I~SVFvpd~lKGYIYVEA~kq~dVkeAIkGI~g 292 (1780)
.|.+|.+-...|||-|||-+...|..+||..|-+
T Consensus 36 ~lrsvWvArnPPGfAFVEFed~RDA~DAvr~LDG 69 (195)
T KOG0107|consen 36 PLRSVWVARNPPGFAFVEFEDPRDAEDAVRYLDG 69 (195)
T ss_pred cceeEEEeecCCCceEEeccCcccHHHHHhhcCC
Confidence 4789999889999999999999999999999887
No 135
>PF10446 DUF2457: Protein of unknown function (DUF2457); InterPro: IPR018853 This entry represents a family of uncharacterised proteins.
Probab=37.37 E-value=14 Score=46.45 Aligned_cols=6 Identities=17% Similarity=0.086 Sum_probs=2.5
Q ss_pred CeEEEe
Q 000252 560 DTARVS 565 (1780)
Q Consensus 560 D~VKVI 565 (1780)
|||+=+
T Consensus 390 DIVkGL 395 (458)
T PF10446_consen 390 DIVKGL 395 (458)
T ss_pred cceech
Confidence 444433
No 136
>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=37.29 E-value=2.1 Score=47.02 Aligned_cols=13 Identities=54% Similarity=0.818 Sum_probs=8.0
Q ss_pred HHHHHHHHHHHhc
Q 000252 183 EEEFDKMMEERYK 195 (1780)
Q Consensus 183 aEelAe~lkERY~ 195 (1780)
+.||+++|.+=|.
T Consensus 66 eref~kmm~eS~~ 78 (170)
T PF04050_consen 66 EREFQKMMAESLE 78 (170)
T ss_dssp HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHH
Confidence 4466666666664
No 137
>PRK00098 GTPase RsgA; Reviewed
Probab=36.99 E-value=2e+02 Score=34.44 Aligned_cols=86 Identities=13% Similarity=0.130 Sum_probs=53.4
Q ss_pred eEEEEEEecCceEEEccCCCCCCceEEEecccccCCCCCCccccccCCCCcccCCCeEEEecCCCCCceEEEEEEECCEE
Q 000252 505 FGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVSEGPSKDRQGIVKKIYRGIL 584 (1780)
Q Consensus 505 VGVIVrVEKDEsfkVLdq~gd~pkVvtVkp~eI~~K~~~rR~vA~D~ngn~I~vGD~VKVIdGphkGRqG~V~HIyRs~V 584 (1780)
.|.||++.+. .+.|++..+ .+++++++.. +. .....+-+||.|.|-. + ....|.|++|+.-.-
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 3556654321 11 0235578999998842 1 234699999998877
Q ss_pred EEEeCcceeeccEEEEeCCceeec
Q 000252 585 FIYDENETENGGYFCSKSQHCEKT 608 (1780)
Q Consensus 585 FL~Sr~~tENgGIFVvRArnv~tv 608 (1780)
+|.-+.. ...-+++.++..|++|
T Consensus 65 ~l~R~~~-~~~q~iaaniD~vllV 87 (298)
T PRK00098 65 LLVRPPI-FKSKLIAANVDQAVLV 87 (298)
T ss_pred eEECCCC-ccccceeecCCEEEEE
Confidence 7766665 2334455555555544
No 138
>KOG3218 consensus RNA polymerase, 25-kDa subunit (common to polymerases I, II and III) [Transcription]
Probab=36.29 E-value=2e+02 Score=33.41 Aligned_cols=119 Identities=16% Similarity=0.163 Sum_probs=58.3
Q ss_pred HHHHHHhccccchhhchhhHHHhhccccccCCCCCCCCc--EEEEEeccchhHHHHHHHHHHHHhhccCCCCCcEEEE-E
Q 000252 188 KMMEERYKSNKLIRYAEEDYEAKKMLEREYHMPCPEDPT--IWKVKCMAGRERQSAFCLMQKFVDLQSLGSKMQIISA-F 264 (1780)
Q Consensus 188 e~lkERY~r~s~~~y~~d~~e~~~~VpQq~LLPSVkDPk--LWaVKCK~GKEReVV~sLmrK~i~lq~~g~~L~I~SV-F 264 (1780)
+.|++||....-.+ ++ =+.+.+-.+||. ||++.|...+ .-|..|..-++.++. -.|..+ +
T Consensus 40 e~F~~~yg~~~p~r--~~---------L~~~~~~~~dp~~ki~V~F~~~~k--vgvk~~k~~~~~~~~----~ni~~~Il 102 (208)
T KOG3218|consen 40 EEFKARYGDKMPDR--ED---------LRILAAHRDDPTDKIYVFFPEEPK--VGVKTMKTYVIQMQS----ENIFRAIL 102 (208)
T ss_pred HHHHHHhccCCcch--hh---------EEEEeccCCCCcCcEEEEeCCCCc--ccHHHHHHHHHHHHh----cCceEEEE
Confidence 45788998642100 01 123445567765 9999995432 222222222222221 123322 2
Q ss_pred Ee------------CCCCcEEEEEeccchhHHHHhcCCCCEEeceecccCHHHHHHHhhcccccccccCCCEEEEeC
Q 000252 265 AV------------DHIKGFIFIEADKQCDINEACKGLSGIYYSRLAPVPKNEVSHLLSAQIKRNEVSEGTWAYVKN 329 (1780)
Q Consensus 265 vp------------d~lKGYIYVEA~kq~dVkeAIkGI~gVy~~K~~pVPIkEM~dLLkvkkk~~~Lk~GdwVRIKr 329 (1780)
+. ..|+.-.-||.+..+++.--| ..++...+-..+..+|-..||+. ..|++.+.=||-.
T Consensus 103 V~q~~mt~~A~k~i~~~~p~f~iE~F~e~eLlvNI--T~H~lvPkH~vL~~eEK~~LL~r----y~l~e~qLPRIq~ 173 (208)
T KOG3218|consen 103 VVQNGMTPSALKALSDFTPKFTIEVFLEAELLVNI--TEHELVPKHQVLTDEEKEELLRR----YKLKETQLPRIQK 173 (208)
T ss_pred EecCCCChHHHHHHHhcCCceEEEeeehhhheeec--cceeecCceEEcCHHHHHHHHHH----hcCCcccCCeeec
Confidence 21 245555666666655542211 12334445566778999999963 2344444444443
No 139
>PRK11634 ATP-dependent RNA helicase DeaD; Provisional
Probab=36.16 E-value=63 Score=42.52 Aligned_cols=11 Identities=9% Similarity=0.045 Sum_probs=6.4
Q ss_pred cCHHHHHHHhh
Q 000252 301 VPKNEVSHLLS 311 (1780)
Q Consensus 301 VPIkEM~dLLk 311 (1780)
++.++...+|.
T Consensus 279 ~~q~~R~~il~ 289 (629)
T PRK11634 279 MNQALREQTLE 289 (629)
T ss_pred CCHHHHHHHHH
Confidence 45566666654
No 140
>PLN00036 40S ribosomal protein S4; Provisional
Probab=35.44 E-value=54 Score=39.18 Aligned_cols=52 Identities=17% Similarity=0.302 Sum_probs=40.3
Q ss_pred CcccCCCeEEEecCCCCCceEEEEEEECC-----EEEEEeCcceeeccEEEEeCCceeecc
Q 000252 554 KVISLNDTARVSEGPSKDRQGIVKKIYRG-----ILFIYDENETENGGYFCSKSQHCEKTK 609 (1780)
Q Consensus 554 n~I~vGD~VKVIdGphkGRqG~V~HIyRs-----~VFL~Sr~~tENgGIFVvRArnv~tv~ 609 (1780)
-.|.+|.+|-|+.|.|.||.|+|++|.+. +|.|.+ .++--|-++..+|..++
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 45789999999999999999999999843 233322 23447999999999874
No 141
>PRK02749 photosystem I reaction center subunit IV; Provisional
Probab=35.43 E-value=61 Score=31.91 Aligned_cols=63 Identities=19% Similarity=0.300 Sum_probs=40.2
Q ss_pred ccCCCEEEEeCC--CCCCCcEEEEEEeCCCCE--EEEEEeccCchhhHhhhcCCCcccCCCCCCCCCCCCHhHHHhh
Q 000252 319 VSEGTWAYVKNG--KYKGDLAQVVYVNNARKR--ATVKLIPRIDLQALAAKFGGGVAMKKTDSPAPRLISPSELEEF 391 (1780)
Q Consensus 319 Lk~GdwVRIKrG--pYKGDLAQVveVDenk~e--VtVKLVPRIDy~~l~~k~~gg~~kKK~~RPPqRLFn~~Eark~ 391 (1780)
|+.|+.|||+|- -.=.|++.|..||...-+ |+|+ |-.++|..+.....+-.. --|.++|+++.
T Consensus 3 i~rGskVrIlR~ESYWyn~vGtV~svD~sgi~YPV~VR-F~kvNY~g~sG~~gG~nT---------Nnfa~~El~~v 69 (71)
T PRK02749 3 ISRGDKVRILRPESYWYNEVGTVASVDKSGIKYPVIVR-FDKVNYNGFSGVDGGINT---------NNFAESELEEV 69 (71)
T ss_pred cccCCEEEEccccceeecCcceEEEEccCCCeeeEEEE-eeeeeccccccccCcccc---------ccccHHHHhhh
Confidence 678999999996 467899999999998643 4444 345556543322222111 23777777643
No 142
>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=34.40 E-value=1.6e+02 Score=43.78 Aligned_cols=94 Identities=10% Similarity=0.105 Sum_probs=62.7
Q ss_pred cccccCceEEecC-----CceEEEEEEecCce-EEEccCCCCCCceEEEecccccCCCCCCccccccCCCCcccCCCeEE
Q 000252 490 NSFELYELVCFGR-----KDFGLIVGMEKDDH-YKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTAR 563 (1780)
Q Consensus 490 G~FeLhDLVQLD~-----~TVGVIVrVEKDEs-fkVLdq~gd~pkVvtVkp~eI~~K~~~rR~vA~D~ngn~I~vGD~VK 563 (1780)
..|.+||.|+... ...++|+.|++++. ++|.+.. +..+++.|.++..+. ..+...-...-.|.+||.|+
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 5799999999742 23479999998544 4444434 357889998774321 22344555667889999998
Q ss_pred EecCC-----CCCceEEEEEEECCEEEEEe
Q 000252 564 VSEGP-----SKDRQGIVKKIYRGILFIYD 588 (1780)
Q Consensus 564 VIdGp-----hkGRqG~V~HIyRs~VFL~S 588 (1780)
+..-- ..|...+|..|....+-|..
T Consensus 755 ~trn~~~~gl~ng~~~tV~~i~~~~i~l~~ 784 (1960)
T TIGR02760 755 VTGNHFHSRVRNGELLTVSSINNEGITLIT 784 (1960)
T ss_pred EccCCcccCccCCCEEEEEEEcCCeEEEEe
Confidence 87442 24678888888776555443
No 143
>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=34.11 E-value=1.4e+02 Score=27.76 Aligned_cols=57 Identities=19% Similarity=0.256 Sum_probs=37.0
Q ss_pred cccCceEEecCCceEEEEEEecCceEEEccCCCCCCceEEEecccccCCCCCCccccccCCCCcccCCCeEEEe
Q 000252 492 FELYELVCFGRKDFGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVS 565 (1780)
Q Consensus 492 FeLhDLVQLD~~TVGVIVrVEKDEsfkVLdq~gd~pkVvtVkp~eI~~K~~~rR~vA~D~ngn~I~vGD~VKVI 565 (1780)
|+.+|.|. |.|++|+....|.=|..+ ..--|..++|... ..+.....|.+||.|++.
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 56677765 899999986555555522 2345666666432 234456789999999874
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=33.88 E-value=66 Score=32.39 Aligned_cols=31 Identities=13% Similarity=0.122 Sum_probs=20.4
Q ss_pred ccccCCCEEEEeC---CCCCCCcEEEEEEeCCCC
Q 000252 317 NEVSEGTWAYVKN---GKYKGDLAQVVYVNNARK 347 (1780)
Q Consensus 317 ~~Lk~GdwVRIKr---GpYKGDLAQVveVDenk~ 347 (1780)
..|.||+.||+.+ -..+||+++|..++.+..
T Consensus 16 ~~i~~GM~VRc~~~yeeV~~GD~G~V~k~~~dg~ 49 (78)
T PF11515_consen 16 DNIQPGMRVRCCRDYEEVRAGDEGEVFKQDRDGL 49 (78)
T ss_dssp HH--TT-EEEESS-BTTB-TT-EEE-EEEE-TTS
T ss_pred HhCCCCcEEEEecccccccccccceeEeeccCCC
Confidence 3689999999998 479999999999988764
No 145
>PRK11634 ATP-dependent RNA helicase DeaD; Provisional
Probab=33.88 E-value=78 Score=41.72 Aligned_cols=9 Identities=33% Similarity=0.261 Sum_probs=3.4
Q ss_pred eCCeEEEEe
Q 000252 684 RYSDVTVKL 692 (1780)
Q Consensus 684 Tdt~ARVEL 692 (1780)
.+++-.|||
T Consensus 525 ~~~~s~v~~ 533 (629)
T PRK11634 525 FASHSTIEL 533 (629)
T ss_pred eCCceEEEc
Confidence 333333333
No 146
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=33.75 E-value=1.8e+02 Score=32.66 Aligned_cols=90 Identities=11% Similarity=0.199 Sum_probs=47.8
Q ss_pred ccccCceEEecCCceEEEEEEecCceEEEccCCC------CCCceEEEecccccCCCCCCccccccCCCCcccCCCeEEE
Q 000252 491 SFELYELVCFGRKDFGLIVGMEKDDHYKILKEGS------EGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARV 564 (1780)
Q Consensus 491 ~FeLhDLVQLD~~TVGVIVrVEKDEsfkVLdq~g------d~pkVvtVkp~eI~~K~~~rR~vA~D~ngn~I~vGD~VKV 564 (1780)
.++++|+|. |.|++|..+-.|.-|..-. ..+..-.+..++|... ..+.-...|++||.|++
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 667899985 8899887653333331100 0001112333333211 11223567999999986
Q ss_pred ecCCCCCceEEEEEEECCEEEEEeCcceeeccEEEEeCCcee
Q 000252 565 SEGPSKDRQGIVKKIYRGILFIYDENETENGGYFCSKSQHCE 606 (1780)
Q Consensus 565 IdGphkGRqG~V~HIyRs~VFL~Sr~~tENgGIFVvRArnv~ 606 (1780)
. |+.|. ..+.|..+. +..|++.+++..|-
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 147
>PTZ00118 40S ribosomal protein S4; Provisional
Probab=33.49 E-value=62 Score=38.70 Aligned_cols=54 Identities=11% Similarity=0.149 Sum_probs=40.1
Q ss_pred CcccCCCeEEEecCCCCCceEEEEEEECC---EEEEEeCcceeeccEEEEeCCceeecc
Q 000252 554 KVISLNDTARVSEGPSKDRQGIVKKIYRG---ILFIYDENETENGGYFCSKSQHCEKTK 609 (1780)
Q Consensus 554 n~I~vGD~VKVIdGphkGRqG~V~HIyRs---~VFL~Sr~~tENgGIFVvRArnv~tv~ 609 (1780)
-.|.+|.+|-|+.|.|.||.|+|+++.+. +-.+|-++ .++--|-++..+|..++
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 45789999999999999999999997653 11222222 23447999999999874
No 148
>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=33.40 E-value=1e+02 Score=29.45 Aligned_cols=68 Identities=16% Similarity=0.218 Sum_probs=43.2
Q ss_pred EEEEEEeCCCCcEEEEEeccchhHHHHhcCCCCEEeceecccCHHHHHHHh-hcccccccccCCCEEEEeCCCCCCCcEE
Q 000252 260 IISAFAVDHIKGFIFIEADKQCDINEACKGLSGIYYSRLAPVPKNEVSHLL-SAQIKRNEVSEGTWAYVKNGKYKGDLAQ 338 (1780)
Q Consensus 260 I~SVFvpd~lKGYIYVEA~kq~dVkeAIkGI~gVy~~K~~pVPIkEM~dLL-kvkkk~~~Lk~GdwVRIKrGpYKGDLAQ 338 (1780)
|...++....+..||||... +| .-+||+.|+.+-. .+......|++|+.|+ |+
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 44556666667777777521 11 2355666665431 1222234688999987 56
Q ss_pred EEEEeCCCCEEEEEE
Q 000252 339 VVYVNNARKRATVKL 353 (1780)
Q Consensus 339 VveVDenk~eVtVKL 353 (1780)
|++||++++++.|.+
T Consensus 57 V~~id~~~~~i~Ls~ 71 (73)
T cd05703 57 VVGVDKEHKLLRLSA 71 (73)
T ss_pred EEEEeCCCCEEEEEe
Confidence 999999999988876
No 149
>PRK10486 autoinducer-2 (AI-2) modifying protein LsrG; Provisional
Probab=33.25 E-value=2.1e+02 Score=28.74 Aligned_cols=65 Identities=8% Similarity=-0.076 Sum_probs=42.6
Q ss_pred EEEEEeccchhHHHHHHHHHHHHhhccCCCCCcEEEEEEeCCCCc-EEEEEeccchhHHHHhcCCCC
Q 000252 227 IWKVKCMAGRERQSAFCLMQKFVDLQSLGSKMQIISAFAVDHIKG-FIFIEADKQCDINEACKGLSG 292 (1780)
Q Consensus 227 LWaVKCK~GKEReVV~sLmrK~i~lq~~g~~L~I~SVFvpd~lKG-YIYVEA~kq~dVkeAIkGI~g 292 (1780)
|-.+++++|++.+++..| +.++...+...-+..+.++....-|+ |++||.....+..++=...++
T Consensus 5 ia~~~~kpg~~~~~~~~l-~~~~~~sr~EpGcl~y~~~~~~~~p~~~~~~E~w~d~~Al~~H~~tph 70 (96)
T PRK10486 5 LVEINVKEDKVDEFIEVF-RQNHLGSIQEPGNLRFDVLQDPEVPTRFYIYEAYKDEAAVAFHKTTPH 70 (96)
T ss_pred EEEEEECcchHHHHHHHH-HHHHHHHhCCCCceEEEEEeCCCCCCEEEEEEEeCCHHHHHHHhcCHH
Confidence 556789999988887755 45444444444455666766655566 888899887665555444444
No 150
>PRK13709 conjugal transfer nickase/helicase TraI; Provisional
Probab=33.12 E-value=1.8e+02 Score=42.89 Aligned_cols=93 Identities=16% Similarity=0.162 Sum_probs=64.5
Q ss_pred cccccc--CceEEecCCceEEEEEEecCceEEEcc-CCCCCCceEEEecccccCCCCCCccccccCCCCcccCCCeEEEe
Q 000252 489 ENSFEL--YELVCFGRKDFGLIVGMEKDDHYKILK-EGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVS 565 (1780)
Q Consensus 489 lG~FeL--hDLVQLD~~TVGVIVrVEKDEsfkVLd-q~gd~pkVvtVkp~eI~~K~~~rR~vA~D~ngn~I~vGD~VKVI 565 (1780)
...|+. +|+|++. .+.-.|+.|+++....+|. .. ++.+.+.|.++. ..++.+......+|.+||.|+..
T Consensus 1273 ~~~Y~~~~G~vv~~~-~~y~~V~~vd~~~~~ltl~~~~---G~~~~~~P~~~~----~~~~~vy~~~~~ela~GDrIr~T 1344 (1747)
T PRK13709 1273 LSTWEAHRGALALVD-NVYHRIAGIDKDDGLITLRDAE---GNTRLISPREAV----AEGVTLYTPDTIRVGTGDRMRFT 1344 (1747)
T ss_pred hhhcccCCCcEEEec-CceEEEEEEcCCCCEEEEEcCC---CCEEEeChhhcc----cccccccccccccccCCCEEEEc
Confidence 457888 8888885 4566789998866555553 33 357788886542 22455667778899999999997
Q ss_pred c-----CCCCCceEEEEEEECCEEEEEeC
Q 000252 566 E-----GPSKDRQGIVKKIYRGILFIYDE 589 (1780)
Q Consensus 566 d-----GphkGRqG~V~HIyRs~VFL~Sr 589 (1780)
. |-..|..++|+.|..+-|.|.+.
T Consensus 1345 rnDk~~G~~Ng~~~tV~~I~~~~I~l~~~ 1373 (1747)
T PRK13709 1345 KSDRERGYVANSVWTVTAVSGDSVTLSDG 1373 (1747)
T ss_pred ccCcccccccCCEEEEEEEcCCeEEEEcC
Confidence 4 33456789999998776555543
No 151
>PTZ00223 40S ribosomal protein S4; Provisional
Probab=32.64 E-value=51 Score=39.56 Aligned_cols=54 Identities=15% Similarity=0.129 Sum_probs=40.2
Q ss_pred CcccCCCeEEEecCCCCCceEEEEEEECC---EEEEEeCcceeeccEEEEeCCceeecc
Q 000252 554 KVISLNDTARVSEGPSKDRQGIVKKIYRG---ILFIYDENETENGGYFCSKSQHCEKTK 609 (1780)
Q Consensus 554 n~I~vGD~VKVIdGphkGRqG~V~HIyRs---~VFL~Sr~~tENgGIFVvRArnv~tv~ 609 (1780)
-.|.+|-+|-|+.|.|.||.|+|.+|.+. +-.+|..+ .++--|-++..+|..++
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 45789999999999999999999999543 11222222 23336999999999885
No 152
>PRK14640 hypothetical protein; Provisional
Probab=32.63 E-value=68 Score=35.23 Aligned_cols=46 Identities=17% Similarity=0.122 Sum_probs=35.4
Q ss_pred cccCCEEEEcc-CC---CCCceeEEEEEeCCeEEEEecCcceEEEEecCccc
Q 000252 660 FAVGQTLRIRV-GP---LKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLA 707 (1780)
Q Consensus 660 ~lIGKTVKIrk-GP---YKGylGiVKDaTdt~ARVELHSk~KtITVdK~~Ls 707 (1780)
..+|+.|+|+- -| .|=+.|++++++++.++++++ .+++.|+.+.|.
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 556677766665
No 153
>PF02699 YajC: Preprotein translocase subunit; InterPro: IPR003849 Secretion across the inner membrane in some Gram-negative bacteria occurs via the preprotein translocase pathway. Proteins are produced in the cytoplasm as precursors, and require a chaperone subunit to direct them to the translocase component []. From there, the mature proteins are either targeted to the outer membrane, or remain as periplasmic proteins []. The translocase protein subunits are encoded on the bacterial chromosome. The translocase itself comprises 7 proteins, including a chaperone (SecB), ATPase (SecA), an integral membrane complex (SecY, SecE and SecG), and two additional membrane proteins that promote the release of the mature peptide into the periplasm (SecD and SecF) []. Other cytoplasmic/periplasmic proteins play a part in preprotein translocase activity, namely YidC and YajC []. The latter is bound in a complex to SecD and SecF, and plays a part in stabilising and regulating secretion through the SecYEG integral membrane component via SecA []. Homologues of the YajC gene have been found in a range of pathogenic and commensal microbes. Brucella abortis YajC- and SecD-like proteins were shown to stimulate a Th1 cell-mediated immune response in mice, and conferred protection when challenged with B.abortis []. Therefore, these proteins may have an antigenic role as well as a secretory one in virulent bacteria []. A number of previously uncharacterised "hypothetical" proteins also show similarity to E.coli YajC, suggesting that this family is wider than first thought []. More recently, the precise interactions between the E.coli SecYEG complex, SecD, SecF, YajC and YidC have been studied []. Rather than acting individually, the four proteins form a heterotetrameric complex and associate with the SecYEG heterotrimeric complex []. The SecF and YajC subunits link the complex to the integral membrane translocase. ; PDB: 2RDD_B.
Probab=32.27 E-value=15 Score=36.38 Aligned_cols=44 Identities=16% Similarity=0.212 Sum_probs=0.0
Q ss_pred cccCCEEEEccCCCCCceeEEEEEeCCeEEEEecCcceEEEEecCcccc
Q 000252 660 FAVGQTLRIRVGPLKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLAE 708 (1780)
Q Consensus 660 ~lIGKTVKIrkGPYKGylGiVKDaTdt~ARVELHSk~KtITVdK~~Ls~ 708 (1780)
--.|+.|....| +.|+|+++.+++|.||+.. .-+|+|.|..+..
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 346788877665 7799999999999999988 4678999988763
No 154
>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=32.24 E-value=60 Score=28.79 Aligned_cols=36 Identities=22% Similarity=0.315 Sum_probs=29.0
Q ss_pred cEEEEEEeCCCCcEEEEEeccchhHHHHhcCCCCEE
Q 000252 259 QIISAFAVDHIKGFIFIEADKQCDINEACKGLSGIY 294 (1780)
Q Consensus 259 ~I~SVFvpd~lKGYIYVEA~kq~dVkeAIkGI~gVy 294 (1780)
.|..|.+.+.-++++|||....++...|++.+.+..
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 478888776558999999999999999988776643
No 155
>KOG0130 consensus RNA-binding protein RBM8/Tsunagi (RRM superfamily) [General function prediction only]
Probab=32.14 E-value=70 Score=35.28 Aligned_cols=61 Identities=20% Similarity=0.298 Sum_probs=48.0
Q ss_pred cEEEEEeccchhHHHHHHHHHHHHhhccCCCCCcEEEEEEe-----CCCCcEEEEEeccchhHHHHhcCCCC
Q 000252 226 TIWKVKCMAGRERQSAFCLMQKFVDLQSLGSKMQIISAFAV-----DHIKGFIFIEADKQCDINEACKGLSG 292 (1780)
Q Consensus 226 kLWaVKCK~GKEReVV~sLmrK~i~lq~~g~~L~I~SVFvp-----d~lKGYIYVEA~kq~dVkeAIkGI~g 292 (1780)
.=|+|-|..=+|...-..|..+|.++.. |+-|-.. --+|||-+||-........||..+.+
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 3688888888899899999999998862 3322221 25899999999999999999888776
No 156
>COG1818 Predicted RNA-binding protein, contains THUMP domain [General function prediction only]
Probab=31.51 E-value=1.8e+02 Score=33.10 Aligned_cols=75 Identities=16% Similarity=0.094 Sum_probs=48.3
Q ss_pred EEEEEeccchhHHHHHHHHHHHHhhccCCCCCcEEEEEEeCCCCcEEEEEeccc-hhHHHHhcCCCCEEeceec----cc
Q 000252 227 IWKVKCMAGRERQSAFCLMQKFVDLQSLGSKMQIISAFAVDHIKGFIFIEADKQ-CDINEACKGLSGIYYSRLA----PV 301 (1780)
Q Consensus 227 LWaVKCK~GKEReVV~sLmrK~i~lq~~g~~L~I~SVFvpd~lKGYIYVEA~kq-~dVkeAIkGI~gVy~~K~~----pV 301 (1780)
...|+|.+|+|++++..|..-+..+ ..-..|..|+|-+.||...+ ..+...++.++-+-...|+ ..
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 4689999999999988877554311 22334568999999999766 3345555666655444333 24
Q ss_pred CHHHHHHHh
Q 000252 302 PKNEVSHLL 310 (1780)
Q Consensus 302 PIkEM~dLL 310 (1780)
+++||.+..
T Consensus 74 dldeI~~~~ 82 (175)
T COG1818 74 DLDEIEEAA 82 (175)
T ss_pred CHHHHHHHH
Confidence 456655544
No 157
>CHL00125 psaE photosystem I subunit IV; Reviewed
Probab=31.37 E-value=72 Score=30.91 Aligned_cols=41 Identities=15% Similarity=0.315 Sum_probs=29.8
Q ss_pred ccCCCEEEEeCC--CCCCCcEEEEEEeCCCCE--EEEEEeccCchh
Q 000252 319 VSEGTWAYVKNG--KYKGDLAQVVYVNNARKR--ATVKLIPRIDLQ 360 (1780)
Q Consensus 319 Lk~GdwVRIKrG--pYKGDLAQVveVDenk~e--VtVKLVPRIDy~ 360 (1780)
|+.|+.|||+|- -.=.|++.|..||..+-+ |+|++ -.++|.
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 466899999999997543 55543 344553
No 158
>PRK14630 hypothetical protein; Provisional
Probab=31.36 E-value=87 Score=34.22 Aligned_cols=45 Identities=13% Similarity=0.169 Sum_probs=35.4
Q ss_pred cccCCEEEEccC-CCCCceeEEEEEeCCeEEEEecCcceEEEEecCcccc
Q 000252 660 FAVGQTLRIRVG-PLKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLAE 708 (1780)
Q Consensus 660 ~lIGKTVKIrkG-PYKGylGiVKDaTdt~ARVELHSk~KtITVdK~~Ls~ 708 (1780)
..+|+.|+|+-. |. +.|+++++.++.++++++ .+++.|+.+.|.-
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 5678888877763
No 159
>PLN03134 glycine-rich RNA-binding protein 4; Provisional
Probab=30.88 E-value=1e+02 Score=33.30 Aligned_cols=60 Identities=17% Similarity=0.283 Sum_probs=41.0
Q ss_pred CcEEEEEeccchhHHHHHHHHHHHHhhccCCCCCcEEEEEEe-----CCCCcEEEEEeccchhHHHHhcCCCCE
Q 000252 225 PTIWKVKCMAGRERQSAFCLMQKFVDLQSLGSKMQIISAFAV-----DHIKGFIFIEADKQCDINEACKGLSGI 293 (1780)
Q Consensus 225 PkLWaVKCK~GKEReVV~sLmrK~i~lq~~g~~L~I~SVFvp-----d~lKGYIYVEA~kq~dVkeAIkGI~gV 293 (1780)
.+||+=.+...-..+-+..|..++ + .|.+|.++ ...+||-|||....+++..||+.|.+.
T Consensus 35 ~~lfVgnL~~~~te~~L~~~F~~~------G---~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~ 99 (144)
T PLN03134 35 TKLFIGGLSWGTDDASLRDAFAHF------G---DVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGK 99 (144)
T ss_pred CEEEEeCCCCCCCHHHHHHHHhcC------C---CeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCC
Confidence 357777766555555444444443 1 35665554 246899999999999999999987664
No 160
>PRK06531 yajC preprotein translocase subunit YajC; Validated
Probab=30.59 E-value=60 Score=34.50 Aligned_cols=47 Identities=26% Similarity=0.213 Sum_probs=31.7
Q ss_pred cCCEEEEccCCCCCceeEEEEEeCCeEEEEecCcceEEEEecCccccccCC
Q 000252 662 VGQTLRIRVGPLKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLAEVRGK 712 (1780)
Q Consensus 662 IGKTVKIrkGPYKGylGiVKDaTdt~ARVELHSk~KtITVdK~~Ls~v~~k 712 (1780)
.|+.|.-. | |++|+|+++.++..+|+|....-.|+|.|..|..+-.+
T Consensus 39 ~GD~VvT~-G---Gi~G~V~~I~~~~~~v~le~~gv~i~v~r~AI~~Vv~~ 85 (113)
T PRK06531 39 KGDEVVTI-G---GLYGTVDEVDTEAKTIVLDVDGVYLTFELAAIKRVVPK 85 (113)
T ss_pred CCCEEEEC-C---CcEEEEEEEecCCCEEEEEECCEEEEEEhhHhhhhcCC
Confidence 35555443 4 68899999987544444433467899999999865433
No 161
>PRK14645 hypothetical protein; Provisional
Probab=30.55 E-value=69 Score=35.41 Aligned_cols=45 Identities=18% Similarity=0.124 Sum_probs=37.0
Q ss_pred cccCCEEEEccCCCCCceeEEEEEeCCeEEEEecCcceEEEEecCccc
Q 000252 660 FAVGQTLRIRVGPLKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLA 707 (1780)
Q Consensus 660 ~lIGKTVKIrkGPYKGylGiVKDaTdt~ARVELHSk~KtITVdK~~Ls 707 (1780)
..+|+.|+|+.+ .|=+.|+++++++..++|++ ..+++.|+.+.|.
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 57788999999999999776 4677888888775
No 162
>COG2139 RPL21A Ribosomal protein L21E [Translation, ribosomal structure and biogenesis]
Probab=30.48 E-value=85 Score=32.76 Aligned_cols=49 Identities=33% Similarity=0.564 Sum_probs=38.3
Q ss_pred cccCCEEEEcc------C-C---CCCceeEEEEEeCCeEEEEec--CcceEEEEecCcccc
Q 000252 660 FAVGQTLRIRV------G-P---LKGYLCRVLAVRYSDVTVKLD--SQQKILTVKGEHLAE 708 (1780)
Q Consensus 660 ~lIGKTVKIrk------G-P---YKGylGiVKDaTdt~ARVELH--Sk~KtITVdK~~Ls~ 708 (1780)
+-+|+.|.|.- | | |-|+.|+|+.+++.-.-||+- .+.|+|.|-.+||.-
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 55788888763 4 2 578899999999998877754 556789999999874
No 163
>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=29.66 E-value=1.4e+02 Score=27.67 Aligned_cols=70 Identities=17% Similarity=0.130 Sum_probs=41.6
Q ss_pred EEEEEEeCCCCcEEEEEeccchhHHHHhcCCCCEEeceecccCHHHHHHHhhcccccccccCCCEEEEeCCCCCCCcEEE
Q 000252 260 IISAFAVDHIKGFIFIEADKQCDINEACKGLSGIYYSRLAPVPKNEVSHLLSAQIKRNEVSEGTWAYVKNGKYKGDLAQV 339 (1780)
Q Consensus 260 I~SVFvpd~lKGYIYVEA~kq~dVkeAIkGI~gVy~~K~~pVPIkEM~dLLkvkkk~~~Lk~GdwVRIKrGpYKGDLAQV 339 (1780)
|+...+....+-.||||.... ++ ..+||+.||.+-. .......|++|+.|++ +|
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 444455555667788877420 11 2244445543211 1111235788999987 49
Q ss_pred EEEeCCCCEEEEEEec
Q 000252 340 VYVNNARKRATVKLIP 355 (1780)
Q Consensus 340 veVDenk~eVtVKLVP 355 (1780)
..|+++..++.|.|-+
T Consensus 59 ~~vd~~~~~i~ls~k~ 74 (77)
T cd05708 59 LKIDAEKKRISLGLKA 74 (77)
T ss_pred EEEeCCCCEEEEEEEe
Confidence 9999998888887654
No 164
>PRK13709 conjugal transfer nickase/helicase TraI; Provisional
Probab=29.18 E-value=2.2e+02 Score=42.11 Aligned_cols=92 Identities=10% Similarity=0.021 Sum_probs=65.4
Q ss_pred ccccccCceEEecC-----CceEEEEEEecCceE-EEccCCCCCCceEEEecccccCCCCCCccccccCCCCcccCCCeE
Q 000252 489 ENSFELYELVCFGR-----KDFGLIVGMEKDDHY-KILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTA 562 (1780)
Q Consensus 489 lG~FeLhDLVQLD~-----~TVGVIVrVEKDEsf-kVLdq~gd~pkVvtVkp~eI~~K~~~rR~vA~D~ngn~I~vGD~V 562 (1780)
...|+.|++|+.-. ...-+|+.|+.+... +|.+..+ ..++++|..+. .++.+.....-+|.+||.|
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 45899999999722 223589999885443 3334443 56788887653 2345566678899999999
Q ss_pred EEecCC-----CCCceEEEEEEECCEEEEEe
Q 000252 563 RVSEGP-----SKDRQGIVKKIYRGILFIYD 588 (1780)
Q Consensus 563 KVIdGp-----hkGRqG~V~HIyRs~VFL~S 588 (1780)
++.... ..|...+|+.|..+.|.|..
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 998553 24688999999998877775
No 165
>PRK04313 30S ribosomal protein S4e; Validated
Probab=28.98 E-value=61 Score=38.27 Aligned_cols=52 Identities=17% Similarity=0.135 Sum_probs=39.9
Q ss_pred CcccCCCeEEEecCCCCCceEEEEEEECC------EEEEEeCcceeeccEEEEeCCceeecc
Q 000252 554 KVISLNDTARVSEGPSKDRQGIVKKIYRG------ILFIYDENETENGGYFCSKSQHCEKTK 609 (1780)
Q Consensus 554 n~I~vGD~VKVIdGphkGRqG~V~HIyRs------~VFL~Sr~~tENgGIFVvRArnv~tv~ 609 (1780)
-.|.+|-+|-|+.|.|.||.|+|++|.+. +|.|.+ .++--|-++..+|..++
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 46789999999999999999999999643 333331 22334999999999874
No 166
>KOG1819 consensus FYVE finger-containing proteins [General function prediction only]
Probab=28.73 E-value=33 Score=43.33 Aligned_cols=28 Identities=21% Similarity=0.369 Sum_probs=19.2
Q ss_pred hccccccCCCCCCC-CcEEEEEeccchhH
Q 000252 211 KMLEREYHMPCPED-PTIWKVKCMAGRER 238 (1780)
Q Consensus 211 ~~VpQq~LLPSVkD-PkLWaVKCK~GKER 238 (1780)
..+-|++-||+.+. |-.=.-+||.-+|.
T Consensus 528 s~tlqrlrlpssdneplaep~~~kaseeh 556 (990)
T KOG1819|consen 528 SDTLQRLRLPSSDNEPLAEPKKCKASEEH 556 (990)
T ss_pred HHHHHHhcCCcccCccccCcccccchHHH
Confidence 34679999999654 55556678776554
No 167
>KOG3130 consensus Uncharacterized conserved protein [Function unknown]
Probab=28.34 E-value=64 Score=40.39 Aligned_cols=8 Identities=25% Similarity=0.663 Sum_probs=6.1
Q ss_pred CCCCCCCc
Q 000252 219 MPCPEDPT 226 (1780)
Q Consensus 219 LPSVkDPk 226 (1780)
||+|+.|.
T Consensus 358 lp~i~~p~ 365 (514)
T KOG3130|consen 358 LPTIRTPA 365 (514)
T ss_pred CCccCCcc
Confidence 79988665
No 168
>COG0056 AtpA F0F1-type ATP synthase, alpha subunit [Energy production and conversion]
Probab=28.26 E-value=95 Score=39.77 Aligned_cols=33 Identities=21% Similarity=0.184 Sum_probs=27.6
Q ss_pred ccccccCceEEecCCceEEEEEEecCceEEEcc
Q 000252 489 ENSFELYELVCFGRKDFGLIVGMEKDDHYKILK 521 (1780)
Q Consensus 489 lG~FeLhDLVQLD~~TVGVIVrVEKDEsfkVLd 521 (1780)
+..|.+|.||++...+.|++.++|.|....||.
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 468999999999999999999999975555443
No 169
>PRK14712 conjugal transfer nickase/helicase TraI; Provisional
Probab=28.12 E-value=2.7e+02 Score=40.90 Aligned_cols=92 Identities=14% Similarity=0.130 Sum_probs=68.1
Q ss_pred cccccc-CceEEecCCceEEEEEEecCceEEEcc-CCCCCCceEEEecccccCCCCCCccccccCCCCcccCCCeEEEec
Q 000252 489 ENSFEL-YELVCFGRKDFGLIVGMEKDDHYKILK-EGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVSE 566 (1780)
Q Consensus 489 lG~FeL-hDLVQLD~~TVGVIVrVEKDEsfkVLd-q~gd~pkVvtVkp~eI~~K~~~rR~vA~D~ngn~I~vGD~VKVId 566 (1780)
...|+. +|.|.|.....-.|+.|+++..+.+|. .. ++.+.+.|.... ..++.+......+|.+||.|+...
T Consensus 1144 a~~Y~~~~~~i~l~~~~y~~V~~vd~~~~~vtl~d~~---G~~~~~~P~~~~----~~~~~vy~~~~~ela~GD~Ir~Tr 1216 (1623)
T PRK14712 1144 LSTWENNPDALALVDNVYHRIAGISKDDGLITLQDAE---GNTRLISPREAV----AEGVTLYTPDTIRVGTGDRIRFTK 1216 (1623)
T ss_pred hhccccCCceeeecCCceEEEEEEcCCCCEEEEEcCC---CCEEEeChhhcc----ccceeeecccccccCCCCEEEEcc
Confidence 457888 678888888888999999866666663 33 356778875542 223556777889999999999974
Q ss_pred -----CCCCCceEEEEEEECCEEEEE
Q 000252 567 -----GPSKDRQGIVKKIYRGILFIY 587 (1780)
Q Consensus 567 -----GphkGRqG~V~HIyRs~VFL~ 587 (1780)
|-..+...+|+.|..+.|.|.
T Consensus 1217 nD~~~G~~Ng~~~tV~~i~~~~i~l~ 1242 (1623)
T PRK14712 1217 SDRERGYVANSVWTVTAVSGDSVTLS 1242 (1623)
T ss_pred CCcccccccCceEEEEEEcCCeEEEe
Confidence 334578999999999877766
No 170
>COG0186 RpsQ Ribosomal protein S17 [Translation, ribosomal structure and biogenesis]
Probab=28.06 E-value=84 Score=32.22 Aligned_cols=23 Identities=26% Similarity=0.394 Sum_probs=19.8
Q ss_pred CccccccCCCCcccCCCeEEEecC
Q 000252 544 MKFTALDQSMKVISLNDTARVSEG 567 (1780)
Q Consensus 544 rR~vA~D~ngn~I~vGD~VKVIdG 567 (1780)
.++.|-| .-+.+++||+|+|.+=
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 7899999999999865
No 171
>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=27.95 E-value=20 Score=46.50 Aligned_cols=10 Identities=30% Similarity=0.388 Sum_probs=4.8
Q ss_pred CCCCCCHHHH
Q 000252 432 WGVVPSEEEL 441 (1780)
Q Consensus 432 edVnPTLEEL 441 (1780)
+.|-|.|++|
T Consensus 271 ~kvlP~l~~l 280 (556)
T PF05918_consen 271 EKVLPKLSDL 280 (556)
T ss_dssp HHTCCCTT--
T ss_pred HHhcCChhhC
Confidence 4466666666
No 172
>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=27.69 E-value=1.1e+02 Score=29.61 Aligned_cols=40 Identities=13% Similarity=0.319 Sum_probs=27.1
Q ss_pred ccCCCEEEEeCC--CCCCCcEEEEEEeCCCCE--EEEEEeccCch
Q 000252 319 VSEGTWAYVKNG--KYKGDLAQVVYVNNARKR--ATVKLIPRIDL 359 (1780)
Q Consensus 319 Lk~GdwVRIKrG--pYKGDLAQVveVDenk~e--VtVKLVPRIDy 359 (1780)
++.|+.|||+|- -.=.|++.|+.||...-+ |+|++ ..++|
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 467999999999988642 55543 34445
No 173
>PLN00045 photosystem I reaction center subunit IV; Provisional
Probab=27.64 E-value=1e+02 Score=32.09 Aligned_cols=45 Identities=13% Similarity=0.195 Sum_probs=32.7
Q ss_pred ccccccCCCEEEEeCC--CCCCCcEEEEEEeCC-CC--EEEEEEeccCchh
Q 000252 315 KRNEVSEGTWAYVKNG--KYKGDLAQVVYVNNA-RK--RATVKLIPRIDLQ 360 (1780)
Q Consensus 315 k~~~Lk~GdwVRIKrG--pYKGDLAQVveVDen-k~--eVtVKLVPRIDy~ 360 (1780)
..+.++.|+.|||+|- -+=+|++.|+.||.. +- -|+|++ -.++|.
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 3567899999999995 467899999999987 32 255543 344553
No 174
>PRK05610 rpsQ 30S ribosomal protein S17; Reviewed
Probab=27.60 E-value=1.1e+02 Score=31.08 Aligned_cols=24 Identities=25% Similarity=0.356 Sum_probs=20.1
Q ss_pred CccccccCCCCcccCCCeEEEecCC
Q 000252 544 MKFTALDQSMKVISLNDTARVSEGP 568 (1780)
Q Consensus 544 rR~vA~D~ngn~I~vGD~VKVIdGp 568 (1780)
.++.|-|. .+..++||+|+|.+..
T Consensus 43 kk~~aHD~-~n~~k~GD~V~I~e~r 66 (84)
T PRK05610 43 KKYHAHDE-NNEAKIGDVVRIMETR 66 (84)
T ss_pred eEEEEECC-CCCCCCCCEEEEEEcc
Confidence 45789998 4689999999999873
No 175
>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]
Probab=27.59 E-value=1.2e+02 Score=39.08 Aligned_cols=97 Identities=11% Similarity=0.085 Sum_probs=62.7
Q ss_pred CcEEEEEec----cchhHHHHHHHHHHHHhhccCCCCCcEEEEEEeC---CCCcEEEEEeccchhHHHHhcCCCCEEec-
Q 000252 225 PTIWKVKCM----AGRERQSAFCLMQKFVDLQSLGSKMQIISAFAVD---HIKGFIFIEADKQCDINEACKGLSGIYYS- 296 (1780)
Q Consensus 225 PkLWaVKCK----~GKEReVV~sLmrK~i~lq~~g~~L~I~SVFvpd---~lKGYIYVEA~kq~dVkeAIkGI~gVy~~- 296 (1780)
+.-|.|||+ .--|++|. .-|. .+.|..++++. .-.|=-|||+..+++|+.||+.-+--+..
T Consensus 8 ~~~~~vr~rGLPwsat~~ei~----~Ff~-------~~~I~~~~~~r~~Gr~sGeA~Ve~~seedv~~AlkkdR~~mg~R 76 (510)
T KOG4211|consen 8 STAFEVRLRGLPWSATEKEIL----DFFS-------NCGIENLEIPRRNGRPSGEAYVEFTSEEDVEKALKKDRESMGHR 76 (510)
T ss_pred CcceEEEecCCCccccHHHHH----HHHh-------cCceeEEEEeccCCCcCcceEEEeechHHHHHHHHhhHHHhCCc
Confidence 446778886 35566553 2222 35577766653 36799999999999999999986654432
Q ss_pred --eecccCHHHHHHHhhcccccccccCCCEEEEeCCCCC
Q 000252 297 --RLAPVPKNEVSHLLSAQIKRNEVSEGTWAYVKNGKYK 333 (1780)
Q Consensus 297 --K~~pVPIkEM~dLLkvkkk~~~Lk~GdwVRIKrGpYK 333 (1780)
....+.-+||..+|+...... -.+.-.|||+-=||.
T Consensus 77 YIEVf~~~~~e~d~~~~~~g~~s-~~~d~vVRLRGLPfs 114 (510)
T KOG4211|consen 77 YIEVFTAGGAEADWVMRPGGPNS-SANDGVVRLRGLPFS 114 (510)
T ss_pred eEEEEccCCccccccccCCCCCC-CCCCceEEecCCCcc
Confidence 334455577787886543211 145677887665775
No 176
>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=27.44 E-value=1.5e+02 Score=27.53 Aligned_cols=68 Identities=18% Similarity=0.181 Sum_probs=0.0
Q ss_pred cEEEEEEeCCCCcEEEEEeccchhHHHHhcCCCCEEeceecccCHHHHHHHhhcccccccccCCCEEEEeCCCCCCCcEE
Q 000252 259 QIISAFAVDHIKGFIFIEADKQCDINEACKGLSGIYYSRLAPVPKNEVSHLLSAQIKRNEVSEGTWAYVKNGKYKGDLAQ 338 (1780)
Q Consensus 259 ~I~SVFvpd~lKGYIYVEA~kq~dVkeAIkGI~gVy~~K~~pVPIkEM~dLLkvkkk~~~Lk~GdwVRIKrGpYKGDLAQ 338 (1780)
+|+.+.+....+-.||||. ......+||+.+|.+. ........|++|+.|++ +
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 000252 339 VVYVNNARKRATVKL 353 (1780)
Q Consensus 339 VveVDenk~eVtVKL 353 (1780)
|.+|++.++++.|.|
T Consensus 55 V~~id~~~~~i~ls~ 69 (69)
T cd05697 55 VLSVEPERKRLVLTL 69 (69)
T ss_pred EEEEECCCCEEEEEC
No 177
>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=27.33 E-value=91 Score=37.38 Aligned_cols=26 Identities=23% Similarity=0.363 Sum_probs=9.9
Q ss_pred CCceecCccccccCCceeccCCcccC
Q 000252 68 PPRIVCDPEMATDKGKAVAVGKDAYG 93 (1780)
Q Consensus 68 ~~~~~~~~~~~~~~~~~~~~~~~~~~ 93 (1780)
||---|--|...-|---|.+-+-.||
T Consensus 210 ~PCPKCg~et~eTkdLSmStR~hkyG 235 (314)
T PF06524_consen 210 IPCPKCGYETQETKDLSMSTRSHKYG 235 (314)
T ss_pred CCCCCCCCcccccccceeeeecchhc
Confidence 33334444444333333333333344
No 178
>PRK14712 conjugal transfer nickase/helicase TraI; Provisional
Probab=27.26 E-value=2.6e+02 Score=41.11 Aligned_cols=92 Identities=9% Similarity=0.055 Sum_probs=66.8
Q ss_pred cccccCceEE-ecCC----ceEEEEEEecCceEEEc-cCCCCCCceEEEecccccCCCCCCccccccCCCCcccCCCeEE
Q 000252 490 NSFELYELVC-FGRK----DFGLIVGMEKDDHYKIL-KEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTAR 563 (1780)
Q Consensus 490 G~FeLhDLVQ-LD~~----TVGVIVrVEKDEsfkVL-dq~gd~pkVvtVkp~eI~~K~~~rR~vA~D~ngn~I~vGD~VK 563 (1780)
..|..|+.|+ .+.. ..=+|+.|+++....+| +.. ++.+++.|+.+. .++.......-+|..||.|+
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 22399999986555544 444 357889987653 24566777788999999999
Q ss_pred EecCCC-----CCceEEEEEEECCEEEEEeC
Q 000252 564 VSEGPS-----KDRQGIVKKIYRGILFIYDE 589 (1780)
Q Consensus 564 VIdGph-----kGRqG~V~HIyRs~VFL~Sr 589 (1780)
+....+ .|...+|++|..+.+.|..+
T Consensus 587 ~t~nd~~~~L~ngd~~tV~~i~~~~itl~~~ 617 (1623)
T PRK14712 587 VTGKIPGLRVSGGDRLQVASVSEDAMTVVVP 617 (1623)
T ss_pred EccCCcccCccCCCEEEEEEecCCeEEEEEC
Confidence 986643 45788999999887766654
No 179
>KOG2055 consensus WD40 repeat protein [General function prediction only]
Probab=27.25 E-value=54 Score=41.67 Aligned_cols=21 Identities=14% Similarity=0.404 Sum_probs=14.3
Q ss_pred CccccCCHHHHHHHHHHHhcc
Q 000252 176 PKEEEMDEEEFDKMMEERYKS 196 (1780)
Q Consensus 176 ~~eEd~DaEelAe~lkERY~r 196 (1780)
+.|...+--++.++|++++++
T Consensus 130 e~e~~~~~~~Y~~RLr~~F~k 150 (514)
T KOG2055|consen 130 ENEGLLSGKEYKGRLREQFQK 150 (514)
T ss_pred ccccccchHHHHHHHHHHHHH
Confidence 344456777788888877765
No 180
>PRK14636 hypothetical protein; Provisional
Probab=27.11 E-value=85 Score=35.44 Aligned_cols=48 Identities=15% Similarity=0.134 Sum_probs=35.9
Q ss_pred cccCCEEEEc-cCCCC---CceeEEEEEeCCeEEEEecCcceEEEEecCcccc
Q 000252 660 FAVGQTLRIR-VGPLK---GYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLAE 708 (1780)
Q Consensus 660 ~lIGKTVKIr-kGPYK---GylGiVKDaTdt~ARVELHSk~KtITVdK~~Ls~ 708 (1780)
+.+|+.|+|+ ..|+. =+.|+++++.+..++|++.- .++|+|+.+.|.-
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 34444 45899999999999988742 3467877777663
No 181
>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=26.97 E-value=3.4e+02 Score=25.86 Aligned_cols=53 Identities=13% Similarity=0.094 Sum_probs=26.9
Q ss_pred EEEEEEecCceEEEccCCCCCCceEEEecccccCCCCCCccccccCCCCcccCCCeEEEe
Q 000252 506 GLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVS 565 (1780)
Q Consensus 506 GVIVrVEKDEsfkVLdq~gd~pkVvtVkp~eI~~K~~~rR~vA~D~ngn~I~vGD~VKVI 565 (1780)
|.|++|..--.|+-|.... .+.--.+..++|... +. .+...+.|++||.|+|.
T Consensus 6 g~V~~v~~~G~fv~l~~~~-~~~~gll~~s~l~~~----~~--~~~~~~~~~~Gd~v~v~ 58 (79)
T cd05684 6 GKVTSIMDFGCFVQLEGLK-GRKEGLVHISQLSFE----GR--VANPSDVVKRGQKVKVK 58 (79)
T ss_pred EEEEEEEeeeEEEEEeCCC-CCcEEEEEhHhccCC----CC--cCChhheeCCCCEEEEE
Confidence 6666666533444443110 001223444555332 11 23446789999999985
No 182
>PRK12289 GTPase RsgA; Reviewed
Probab=26.76 E-value=3.3e+02 Score=33.82 Aligned_cols=75 Identities=16% Similarity=0.299 Sum_probs=43.2
Q ss_pred CceEEEEEEecCceEEEccCCCC---CCceEEEecccccCCCCCCccccccCCCCcccCCCeEEEecCCCCCceEEEEEE
Q 000252 503 KDFGLIVGMEKDDHYKILKEGSE---GPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVSEGPSKDRQGIVKKI 579 (1780)
Q Consensus 503 ~TVGVIVrVEKDEsfkVLdq~gd---~pkVvtVkp~eI~~K~~~rR~vA~D~ngn~I~vGD~VKVIdGphkGRqG~V~HI 579 (1780)
...|.||++..+ .+.|+...++ .+.++.+..... .+ +.+..+-|||.|.+-.-...+..|+|.+|
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 357999999995 7777653221 112344433211 11 12455899999988532223467999999
Q ss_pred ECCEEEEEeC
Q 000252 580 YRGILFIYDE 589 (1780)
Q Consensus 580 yRs~VFL~Sr 589 (1780)
+----+|.-.
T Consensus 76 lpR~~~L~R~ 85 (352)
T PRK12289 76 LPRKTELDRP 85 (352)
T ss_pred eccccceech
Confidence 7754444433
No 183
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=26.75 E-value=2.2e+02 Score=32.93 Aligned_cols=42 Identities=12% Similarity=0.225 Sum_probs=31.8
Q ss_pred CCcccCCCeEEEecCCCCCceEEEEEEECCEEEEEeCcceeeccEEEEeCCceee
Q 000252 553 MKVISLNDTARVSEGPSKDRQGIVKKIYRGILFIYDENETENGGYFCSKSQHCEK 607 (1780)
Q Consensus 553 gn~I~vGD~VKVIdGphkGRqG~V~HIyRs~VFL~Sr~~tENgGIFVvRArnv~t 607 (1780)
...|++||+|| +.|+.+. ..++|.... .+.||+-++|.+|-.
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 667999888888863
No 184
>PRK14632 hypothetical protein; Provisional
Probab=26.70 E-value=1e+02 Score=34.72 Aligned_cols=49 Identities=16% Similarity=0.326 Sum_probs=38.0
Q ss_pred cccCCEEEEc-cCCC------CCceeEEEEEeCCeEEEEecCc------ceEEEEecCcccc
Q 000252 660 FAVGQTLRIR-VGPL------KGYLCRVLAVRYSDVTVKLDSQ------QKILTVKGEHLAE 708 (1780)
Q Consensus 660 ~lIGKTVKIr-kGPY------KGylGiVKDaTdt~ARVELHSk------~KtITVdK~~Ls~ 708 (1780)
.+||+.|+|+ ..|+ |=+.|+++.++++.++|++..+ ..+|.|+.+.|..
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 185
>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=26.58 E-value=1.2e+02 Score=27.25 Aligned_cols=25 Identities=28% Similarity=0.405 Sum_probs=19.6
Q ss_pred ccccCCCEEEEeCCCCCCCcEEEEEEeCCCCEEEE
Q 000252 317 NEVSEGTWAYVKNGKYKGDLAQVVYVNNARKRATV 351 (1780)
Q Consensus 317 ~~Lk~GdwVRIKrGpYKGDLAQVveVDenk~eVtV 351 (1780)
..|++|+.|++ +|++|+..+.++.|
T Consensus 43 ~~~~~Gd~v~v----------~i~~vd~~~~~i~l 67 (68)
T cd05688 43 EVVNVGDEVEV----------KVLKIDKERKRISL 67 (68)
T ss_pred HEECCCCEEEE----------EEEEEECCCCEEec
Confidence 35789999987 48899888777764
No 186
>PRK08059 general stress protein 13; Validated
Probab=26.41 E-value=3.8e+02 Score=28.31 Aligned_cols=80 Identities=18% Similarity=0.242 Sum_probs=0.0
Q ss_pred cccccccCceEEecCCceEEEEEEecCceEEEccCCCCCCceEEEecccccCCCCCCccccccCCCCcccCCCeEEEecC
Q 000252 488 LENSFELYELVCFGRKDFGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVSEG 567 (1780)
Q Consensus 488 slG~FeLhDLVQLD~~TVGVIVrVEKDEsfkVLdq~gd~pkVvtVkp~eI~~K~~~rR~vA~D~ngn~I~vGD~VKVIdG 567 (1780)
....|.+++.|. |+|++|.+.-.|+.|... ..-.+..++|........ ...|++||+|+|
T Consensus 1 ~~~~~k~G~iv~------G~V~~i~~~G~fV~i~~~----~~Gli~~sel~~~~~~~~-------~~~~~vGD~I~v--- 60 (123)
T PRK08059 1 MMSQYEVGSVVT------GKVTGIQPYGAFVALDEE----TQGLVHISEITHGFVKDI-------HDFLSVGDEVKV--- 60 (123)
T ss_pred CcccCCCCCEEE------EEEEEEecceEEEEECCC----CEEEEEHHHCCcccccCH-------HHcCCCCCEEEE---
Q ss_pred CCCCceEEEEEEEC--CEEEEEeCcceee
Q 000252 568 PSKDRQGIVKKIYR--GILFIYDENETEN 594 (1780)
Q Consensus 568 phkGRqG~V~HIyR--s~VFL~Sr~~tEN 594 (1780)
.|+.|.+ ..+.|..+...++
T Consensus 61 -------kI~~id~~~~~i~lslk~~~~~ 82 (123)
T PRK08059 61 -------KVLSVDEEKGKISLSIRATEEA 82 (123)
T ss_pred -------EEEEEECCCCeEEEEEEEcccC
No 187
>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=26.33 E-value=1.3e+02 Score=28.96 Aligned_cols=67 Identities=15% Similarity=0.249 Sum_probs=42.5
Q ss_pred cEEEEEEeCCCCcEEEEEeccchhHHHHhcCCCCEEeceecccCHHHHHHHh--hcccccccccCCCEEEEeCCCCCCCc
Q 000252 259 QIISAFAVDHIKGFIFIEADKQCDINEACKGLSGIYYSRLAPVPKNEVSHLL--SAQIKRNEVSEGTWAYVKNGKYKGDL 336 (1780)
Q Consensus 259 ~I~SVFvpd~lKGYIYVEA~kq~dVkeAIkGI~gVy~~K~~pVPIkEM~dLL--kvkkk~~~Lk~GdwVRIKrGpYKGDL 336 (1780)
.|...++....+..+||+.. .+ ...+||+.||.+-. .+......|++|+-|++
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 45666666666667887741 12 23356777776654 12111346789999875
Q ss_pred EEEEEEeCCCCEEEE
Q 000252 337 AQVVYVNNARKRATV 351 (1780)
Q Consensus 337 AQVveVDenk~eVtV 351 (1780)
+|++|++++.++.|
T Consensus 60 -kVl~id~~~~~i~L 73 (74)
T cd05705 60 -KVLSVNSEKNLVEL 73 (74)
T ss_pred -EEEEEECCCCEEec
Confidence 59999998887654
No 188
>PRK11642 exoribonuclease R; Provisional
Probab=26.26 E-value=1.8e+02 Score=39.90 Aligned_cols=81 Identities=16% Similarity=0.105 Sum_probs=45.1
Q ss_pred cEEEEEEeCCCCcEEEEEeccchhHHHHhcCCCCEEeceecccCHHHHHHHhhcccccccccCCCEEEEeCCCCCCCcEE
Q 000252 259 QIISAFAVDHIKGFIFIEADKQCDINEACKGLSGIYYSRLAPVPKNEVSHLLSAQIKRNEVSEGTWAYVKNGKYKGDLAQ 338 (1780)
Q Consensus 259 ~I~SVFvpd~lKGYIYVEA~kq~dVkeAIkGI~gVy~~K~~pVPIkEM~dLLkvkkk~~~Lk~GdwVRIKrGpYKGDLAQ 338 (1780)
.++...+....+--||||.... .|+|+.+|-....--..+.|....|.-......|++|+.|+|+
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 4555555554444588887431 1444433321100000123333344322223468889999974
Q ss_pred EEEEeCCCCEEEEEEe
Q 000252 339 VVYVNNARKRATVKLI 354 (1780)
Q Consensus 339 VveVDenk~eVtVKLV 354 (1780)
|+.|+..+.+|.+.|+
T Consensus 710 V~~vD~~~rkI~f~l~ 725 (813)
T PRK11642 710 VEAVNMDERKIDFSLI 725 (813)
T ss_pred EEEeecCCCeEEEEEe
Confidence 8999999999999987
No 189
>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=25.96 E-value=81 Score=29.71 Aligned_cols=28 Identities=25% Similarity=0.337 Sum_probs=22.8
Q ss_pred ccccCCCEEEEeCCCCCCCcEEEEEEeCCCCEEEEEEe
Q 000252 317 NEVSEGTWAYVKNGKYKGDLAQVVYVNNARKRATVKLI 354 (1780)
Q Consensus 317 ~~Lk~GdwVRIKrGpYKGDLAQVveVDenk~eVtVKLV 354 (1780)
..|++|+.|+++ |..|+.++.++.++|+
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 190
>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=25.87 E-value=1.2e+02 Score=29.89 Aligned_cols=23 Identities=26% Similarity=0.359 Sum_probs=19.3
Q ss_pred CccccccCCCCcccCCCeEEEecC
Q 000252 544 MKFTALDQSMKVISLNDTARVSEG 567 (1780)
Q Consensus 544 rR~vA~D~ngn~I~vGD~VKVIdG 567 (1780)
.++.|-|. .+..++||+|+|.+-
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 35789998 468999999999875
No 191
>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=25.69 E-value=1.1e+02 Score=28.88 Aligned_cols=28 Identities=29% Similarity=0.293 Sum_probs=19.8
Q ss_pred ccCCCEEEEeCC--CCCCCcEEEEEEeCCC
Q 000252 319 VSEGTWAYVKNG--KYKGDLAQVVYVNNAR 346 (1780)
Q Consensus 319 Lk~GdwVRIKrG--pYKGDLAQVveVDenk 346 (1780)
|.||+.|||+.. +|-+..++|..|.+.+
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 679999999984 8999999999999754
No 192
>COG2163 RPL14A Ribosomal protein L14E/L6E/L27E [Translation, ribosomal structure and biogenesis]
Probab=25.63 E-value=89 Score=33.81 Aligned_cols=33 Identities=15% Similarity=0.300 Sum_probs=28.5
Q ss_pred cccCCCEEEEeCCCCCCCcEEEEEEeCCCCEEEE
Q 000252 318 EVSEGTWAYVKNGKYKGDLAQVVYVNNARKRATV 351 (1780)
Q Consensus 318 ~Lk~GdwVRIKrGpYKGDLAQVveVDenk~eVtV 351 (1780)
.|++|..|-|++|.|+|-.+.|+++-+++ .|+|
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 193
>PRK14633 hypothetical protein; Provisional
Probab=25.45 E-value=1e+02 Score=33.81 Aligned_cols=48 Identities=17% Similarity=0.221 Sum_probs=37.0
Q ss_pred cccCCEEEEcc-CC---CCCceeEEEEEeCCeEEEEecCcceEEEEecCcccc
Q 000252 660 FAVGQTLRIRV-GP---LKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLAE 708 (1780)
Q Consensus 660 ~lIGKTVKIrk-GP---YKGylGiVKDaTdt~ARVELHSk~KtITVdK~~Ls~ 708 (1780)
..||+.|+|+- .| -|=+.|+++.++++.+++++.- .+++.|+.++|.-
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 194
>PRK14646 hypothetical protein; Provisional
Probab=25.37 E-value=1e+02 Score=34.17 Aligned_cols=47 Identities=9% Similarity=0.011 Sum_probs=36.4
Q ss_pred cccCCEEEEcc-CCC---CCceeEEEEEeCCeEEEEecCcceEEEEecCcccc
Q 000252 660 FAVGQTLRIRV-GPL---KGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLAE 708 (1780)
Q Consensus 660 ~lIGKTVKIrk-GPY---KGylGiVKDaTdt~ARVELHSk~KtITVdK~~Ls~ 708 (1780)
.++|+.|+|+- .|+ |=+.|+++++.++.++|++. .+++.|+.+.|.-
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 44579999999999998874 6778887777763
No 195
>cd05687 S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 1 of the Escherichia coli and Homo sapiens RPS1 (ec1 and hs1, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=25.26 E-value=2.5e+02 Score=25.94 Aligned_cols=67 Identities=16% Similarity=0.149 Sum_probs=38.8
Q ss_pred EEEEEEeCCCCcEEEEEeccchhHHHHhcCCCCEEeceecccCHHHHHHHhhcccccccccCCCEEEEeCCCCCCCcEEE
Q 000252 260 IISAFAVDHIKGFIFIEADKQCDINEACKGLSGIYYSRLAPVPKNEVSHLLSAQIKRNEVSEGTWAYVKNGKYKGDLAQV 339 (1780)
Q Consensus 260 I~SVFvpd~lKGYIYVEA~kq~dVkeAIkGI~gVy~~K~~pVPIkEM~dLLkvkkk~~~Lk~GdwVRIKrGpYKGDLAQV 339 (1780)
|+...+....+-++||+.... ....||+.|+..-. +......|++|+.|+++ |
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 344444444556888887431 13355666664321 11112347889988864 8
Q ss_pred EEEeCCCCEEEEEE
Q 000252 340 VYVNNARKRATVKL 353 (1780)
Q Consensus 340 veVDenk~eVtVKL 353 (1780)
+.+++...++.|.+
T Consensus 56 ~~~~~~~~~i~lS~ 69 (70)
T cd05687 56 LRVEDEEGNVVLSK 69 (70)
T ss_pred EEEECCCCeEEEEe
Confidence 88887766776654
No 196
>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=25.16 E-value=3.1e+02 Score=27.65 Aligned_cols=64 Identities=13% Similarity=0.034 Sum_probs=40.6
Q ss_pred ceEEEEEEecCceEEEccCCCCCCceEEEecccccCCCCCCccccccCCCCcccCCCeEEEecCCCCC-ceEEEEEEECC
Q 000252 504 DFGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVSEGPSKD-RQGIVKKIYRG 582 (1780)
Q Consensus 504 TVGVIVrVEKDEsfkVLdq~gd~pkVvtVkp~eI~~K~~~rR~vA~D~ngn~I~vGD~VKVIdGphkG-RqG~V~HIyRs 582 (1780)
.+-.|+++.-+..+.|.+.++ +.+.+... .|. +..-=|+.||+|.|---+... ..|.|+|||..
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 345677777766777887664 23444321 221 124468999999997544433 58999999874
No 197
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=24.83 E-value=19 Score=42.05 Aligned_cols=15 Identities=20% Similarity=0.545 Sum_probs=8.7
Q ss_pred cCCHHHHHHHHHHHhc
Q 000252 180 EMDEEEFDKMMEERYK 195 (1780)
Q Consensus 180 d~DaEelAe~lkERY~ 195 (1780)
+|| +|..+.|+.|-.
T Consensus 99 ~l~-~~~~rll~~r~~ 113 (232)
T PRK12766 99 ELS-DEEARLLTQRRR 113 (232)
T ss_pred CCC-HHHHHHHHHHHh
Confidence 444 355677766663
No 198
>PRK02001 hypothetical protein; Validated
Probab=24.62 E-value=1.3e+02 Score=33.44 Aligned_cols=48 Identities=15% Similarity=0.189 Sum_probs=36.9
Q ss_pred cccCCEEEEccCCCCCceeEEEEEeCCeEEEEecCc------------ceEEEEecCccc
Q 000252 660 FAVGQTLRIRVGPLKGYLCRVLAVRYSDVTVKLDSQ------------QKILTVKGEHLA 707 (1780)
Q Consensus 660 ~lIGKTVKIrkGPYKGylGiVKDaTdt~ARVELHSk------------~KtITVdK~~Ls 707 (1780)
.+||+.|+|+----|=+.|+++++.+..+.++++.+ .+.++|+.+.|.
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 478999999753347799999999999999998753 235777666654
No 199
>PRK08582 hypothetical protein; Provisional
Probab=24.33 E-value=2.4e+02 Score=30.73 Aligned_cols=57 Identities=18% Similarity=0.202 Sum_probs=35.2
Q ss_pred cccCceEEecCCceEEEEEEecCceEEEccCCCCCCceEEEecccccCCCCCCccccccCCCCcccCCCeEEEe
Q 000252 492 FELYELVCFGRKDFGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVS 565 (1780)
Q Consensus 492 FeLhDLVQLD~~TVGVIVrVEKDEsfkVLdq~gd~pkVvtVkp~eI~~K~~~rR~vA~D~ngn~I~vGD~VKVI 565 (1780)
|++++.|. |+|+.|..--.|+-|... ..-.|..++|.... + .| ....|++||.|+|.
T Consensus 3 ~kvG~iv~------G~V~~I~~fG~fV~L~~~----~~GlVhiSels~~~-----v-~~-~~~~l~vGD~Vkvk 59 (139)
T PRK08582 3 IEVGSKLQ------GKVTGITNFGAFVELPEG----KTGLVHISEVADNY-----V-KD-INDHLKVGDEVEVK 59 (139)
T ss_pred CcCCCEEE------EEEEEEECCeEEEEECCC----CEEEEEeeccCccc-----c-cc-cccccCCCCEEEEE
Confidence 56777765 888888876667666543 12344555664321 1 11 23679999999884
No 200
>PF11424 DUF3195: Protein of unknown function (DUF3195); InterPro: IPR021540 This archaeal family of proteins has no known function. ; PDB: 1RKI_B.
Probab=24.05 E-value=72 Score=32.51 Aligned_cols=43 Identities=12% Similarity=0.074 Sum_probs=29.6
Q ss_pred EEEEeccchhHHHHHHHHHHHHhhccCCCCCcEEEEEEeCCCCcEEEEEec
Q 000252 228 WKVKCMAGRERQSAFCLMQKFVDLQSLGSKMQIISAFAVDHIKGFIFIEAD 278 (1780)
Q Consensus 228 WaVKCK~GKEReVV~sLmrK~i~lq~~g~~L~I~SVFvpd~lKGYIYVEA~ 278 (1780)
..|++.++||+.|++.|-.=+.-+ ++ +|.+.+..||.|||+..
T Consensus 2 iii~TipkKE~~VARDLCDClYyy---D~-----~V~C~~i~pg~vYv~t~ 44 (89)
T PF11424_consen 2 IIITTIPKKEAIVARDLCDCLYYY---DQ-----SVMCEPISPGRVYVYTS 44 (89)
T ss_dssp EEEEE-CCGHHHHHCHHHHHHCCC----T-----T-EEEEEETTEEEEEE-
T ss_pred EEEEecCcchhhhHHHhhhhheec---Cc-----eEEEEEccCcEEEEEEe
Confidence 368999999999998886554322 11 35666678999999994
No 201
>COG1532 Predicted RNA-binding protein [General function prediction only]
Probab=24.05 E-value=44 Score=31.58 Aligned_cols=31 Identities=13% Similarity=0.104 Sum_probs=26.2
Q ss_pred CCEEEEeC--CCCCCCcEEEEEEeCCCCEEEEE
Q 000252 322 GTWAYVKN--GKYKGDLAQVVYVNNARKRATVK 352 (1780)
Q Consensus 322 GdwVRIKr--GpYKGDLAQVveVDenk~eVtVK 352 (1780)
++-|+.+. |-||-..+||.+||.+..++.|+
T Consensus 24 ~e~V~a~Dilgd~ke~~G~vkriDldehkI~lE 56 (57)
T COG1532 24 EEGVVARDILGDEKEFEGQVKRIDLDEHKIELE 56 (57)
T ss_pred cCcEEEEeccCCceEecceEEEEEccccEEEec
Confidence 56677766 89999999999999998888764
No 202
>PRK01889 GTPase RsgA; Reviewed
Probab=23.89 E-value=2.6e+02 Score=34.41 Aligned_cols=89 Identities=9% Similarity=0.082 Sum_probs=52.7
Q ss_pred ceEEEEEEecCceEEEccCCCCCCceEEEecccccCCCCCCccccccCCCCcccCCCeEEEecCCCCCceEEEEEEECCE
Q 000252 504 DFGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVSEGPSKDRQGIVKKIYRGI 583 (1780)
Q Consensus 504 TVGVIVrVEKDEsfkVLdq~gd~pkVvtVkp~eI~~K~~~rR~vA~D~ngn~I~vGD~VKVIdGphkGRqG~V~HIyRs~ 583 (1780)
..|.||++.+. .+.|++.++ .+ ...++ .|+ +... ......+-+||.|.+-. +..|.|.+|+.-.
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 46999999984 888876432 22 22211 111 1111 11235589999998853 3569999998765
Q ss_pred EEEEeCcc--eeeccEEEEeCCceeec
Q 000252 584 LFIYDENE--TENGGYFCSKSQHCEKT 608 (1780)
Q Consensus 584 VFL~Sr~~--tENgGIFVvRArnv~tv 608 (1780)
-+|.-+.. ..-.-+++++.-.|.+|
T Consensus 93 ~~L~R~~~~~~~~~q~iaANvD~vliV 119 (356)
T PRK01889 93 SLFSRKAAGTRSEEQLIAANVDTVFIV 119 (356)
T ss_pred ceEEcCCCCCCccceeEEEeCCEEEEE
Confidence 45544443 23345778887776655
No 203
>COG2139 RPL21A Ribosomal protein L21E [Translation, ribosomal structure and biogenesis]
Probab=23.87 E-value=93 Score=32.49 Aligned_cols=49 Identities=16% Similarity=0.256 Sum_probs=34.7
Q ss_pred cccccccCceEEec--------------CCceEEEEEEecCceEEEccCCCCCCceEEEecccc
Q 000252 488 LENSFELYELVCFG--------------RKDFGLIVGMEKDDHYKILKEGSEGPAVVTVERRTL 537 (1780)
Q Consensus 488 slG~FeLhDLVQLD--------------~~TVGVIVrVEKDEsfkVLdq~gd~pkVvtVkp~eI 537 (1780)
.+-.|+++|+|.|+ ...+|+||.+-.+ +|.|.--.++..+.+.|.|.-|
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 46789999999984 2467999999884 7776643334456666766554
No 204
>KOG0943 consensus Predicted ubiquitin-protein ligase/hyperplastic discs protein, HECT superfamily [Posttranslational modification, protein turnover, chaperones]
Probab=23.80 E-value=40 Score=46.52 Aligned_cols=24 Identities=8% Similarity=0.008 Sum_probs=15.8
Q ss_pred CCCcEEEEEeccchhHHHHhcCCC
Q 000252 268 HIKGFIFIEADKQCDINEACKGLS 291 (1780)
Q Consensus 268 ~lKGYIYVEA~kq~dVkeAIkGI~ 291 (1780)
..+|.+||.-++-..-..+|.+++
T Consensus 1915 S~~~ierf~PyrfssrssflSN~R 1938 (3015)
T KOG0943|consen 1915 SSAGIERFDPYRFSSRSSFLSNLR 1938 (3015)
T ss_pred cCCCeeeeccccccchhhhhhhcc
Confidence 578888888766655555555554
No 205
>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=23.77 E-value=2.1e+02 Score=26.29 Aligned_cols=67 Identities=9% Similarity=0.106 Sum_probs=38.2
Q ss_pred EEEEEEeCCCCcEEEEEeccchhHHHHhcCCCCEEeceecccCHHHHHHHhhcccccccccCCCEEEEeCCCCCCCcEEE
Q 000252 260 IISAFAVDHIKGFIFIEADKQCDINEACKGLSGIYYSRLAPVPKNEVSHLLSAQIKRNEVSEGTWAYVKNGKYKGDLAQV 339 (1780)
Q Consensus 260 I~SVFvpd~lKGYIYVEA~kq~dVkeAIkGI~gVy~~K~~pVPIkEM~dLLkvkkk~~~Lk~GdwVRIKrGpYKGDLAQV 339 (1780)
|+.+.+.....-.||||... ++. .+||+.|+.+-. +......|++|+.|++ +|
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 34444444556677887751 122 233444443211 1111234788999986 59
Q ss_pred EEEeCCCCEEEEEE
Q 000252 340 VYVNNARKRATVKL 353 (1780)
Q Consensus 340 veVDenk~eVtVKL 353 (1780)
.+++....++.|.+
T Consensus 56 ~~~d~~~~~i~ls~ 69 (73)
T cd05691 56 TNVDRKNRKISLSI 69 (73)
T ss_pred EEEeCCCCEEEEEE
Confidence 99999877777665
No 206
>smart00243 GAS2 Growth-Arrest-Specific Protein 2 Domain. GROWTH-ARREST-SPECIFIC PROTEIN 2 Domain
Probab=23.75 E-value=1.7e+02 Score=29.31 Aligned_cols=50 Identities=20% Similarity=0.263 Sum_probs=32.4
Q ss_pred HHHHHHhhcccccccccCCCEEEEeCCCCC-CCcEEEEEEeCCCCEEEEEEecc
Q 000252 304 NEVSHLLSAQIKRNEVSEGTWAYVKNGKYK-GDLAQVVYVNNARKRATVKLIPR 356 (1780)
Q Consensus 304 kEM~dLLkvkkk~~~Lk~GdwVRIKrGpYK-GDLAQVveVDenk~eVtVKLVPR 356 (1780)
+|+.+++..+.=...| ..+||-.|+|+ ||..++.-|.--+..|+|++=.=
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 3556666543322333 77999999999 87766555554556888887543
No 207
>CHL00142 rps17 ribosomal protein S17; Validated
Probab=23.71 E-value=1.3e+02 Score=30.66 Aligned_cols=24 Identities=17% Similarity=0.225 Sum_probs=19.6
Q ss_pred CccccccCCCCcccCCCeEEEecCC
Q 000252 544 MKFTALDQSMKVISLNDTARVSEGP 568 (1780)
Q Consensus 544 rR~vA~D~ngn~I~vGD~VKVIdGp 568 (1780)
.++.|-| ..++.++||+|+|.+-+
T Consensus 40 kk~~aHD-e~n~~~~GD~V~I~e~R 63 (84)
T CHL00142 40 KKYLVHD-EENECNIGDQVLIEETR 63 (84)
T ss_pred EEEEEeC-CCCCCCCCCEEEEEEcC
Confidence 3578999 56689999999999763
No 208
>PRK05807 hypothetical protein; Provisional
Probab=23.42 E-value=2.4e+02 Score=30.54 Aligned_cols=57 Identities=12% Similarity=0.173 Sum_probs=36.1
Q ss_pred ccccCceEEecCCceEEEEEEecCceEEEccCCCCCCceEEEecccccCCCCCCccccccCCCCcccCCCeEEEe
Q 000252 491 SFELYELVCFGRKDFGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVS 565 (1780)
Q Consensus 491 ~FeLhDLVQLD~~TVGVIVrVEKDEsfkVLdq~gd~pkVvtVkp~eI~~K~~~rR~vA~D~ngn~I~vGD~VKVI 565 (1780)
.|++++.|. |+|+.|...-.|+.|+ + ..-.|..++|.... +. + -...|++||.|+|.
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 467788876 8888888766777773 2 13445556664321 11 1 13468999999985
No 209
>PRK14647 hypothetical protein; Provisional
Probab=22.63 E-value=1.2e+02 Score=33.51 Aligned_cols=48 Identities=17% Similarity=0.233 Sum_probs=37.0
Q ss_pred cccCCEEEEcc-CC--------CCCceeEEEEEeCCeEEEEecCcceEEEEecCcccc
Q 000252 660 FAVGQTLRIRV-GP--------LKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLAE 708 (1780)
Q Consensus 660 ~lIGKTVKIrk-GP--------YKGylGiVKDaTdt~ARVELHSk~KtITVdK~~Ls~ 708 (1780)
..+|+.|+|+- -| -|=+.|++++++++.+++++. ..++|+|+.+.|.-
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 47899999973 23 467899999999999998874 24568888777763
No 210
>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=22.40 E-value=2.1e+02 Score=26.42 Aligned_cols=64 Identities=16% Similarity=0.205 Sum_probs=37.6
Q ss_pred EEEEEeCCCCcEEEEEeccchhHHHHhcCCCCEEeceecccCHHHHHHHhhcccccccccCCCEEEEeCCCCCCCcEEEE
Q 000252 261 ISAFAVDHIKGFIFIEADKQCDINEACKGLSGIYYSRLAPVPKNEVSHLLSAQIKRNEVSEGTWAYVKNGKYKGDLAQVV 340 (1780)
Q Consensus 261 ~SVFvpd~lKGYIYVEA~kq~dVkeAIkGI~gVy~~K~~pVPIkEM~dLLkvkkk~~~Lk~GdwVRIKrGpYKGDLAQVv 340 (1780)
+...+....+--||||... + ...+||+.||.+-. +......|++|+.|++ +|+
T Consensus 4 v~g~V~~v~~~Gv~V~l~~---------~-------~~G~v~~s~l~~~~-~~~~~~~~~~Gd~v~~----------~v~ 56 (68)
T cd05707 4 VRGFVKNIANNGVFVTLGR---------G-------VDARVRVSELSDSY-LKDWKKRFKVGQLVKG----------KIV 56 (68)
T ss_pred EEEEEEEEECccEEEEeCC---------C-------CEEEEEHHHCCchh-hcCHhhccCCCCEEEE----------EEE
Confidence 3444444455668888743 2 23355566654321 1112345788999886 688
Q ss_pred EEeCCCCEEEE
Q 000252 341 YVNNARKRATV 351 (1780)
Q Consensus 341 eVDenk~eVtV 351 (1780)
.+++...++.|
T Consensus 57 ~~d~~~~~i~l 67 (68)
T cd05707 57 SIDPDNGRIEM 67 (68)
T ss_pred EEeCCCCEEec
Confidence 99988777654
No 211
>PRK06763 F0F1 ATP synthase subunit alpha; Validated
Probab=22.10 E-value=1.5e+02 Score=34.46 Aligned_cols=15 Identities=20% Similarity=0.313 Sum_probs=13.2
Q ss_pred CCCcccCCCeEEEec
Q 000252 552 SMKVISLNDTARVSE 566 (1780)
Q Consensus 552 ngn~I~vGD~VKVId 566 (1780)
++..|.+||.|||-.
T Consensus 161 ~GQkFnVGDkVKV~~ 175 (213)
T PRK06763 161 KGQVFHVGDKVKVDM 175 (213)
T ss_pred cCCEEecCCEEEEEe
Confidence 589999999999973
No 212
>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=21.90 E-value=1.4e+02 Score=29.77 Aligned_cols=48 Identities=25% Similarity=0.403 Sum_probs=30.3
Q ss_pred HHHHHHhhcccccccccCCCEEEEeCCCCC-CCcEEEEEEeCCCCEEEEEEe
Q 000252 304 NEVSHLLSAQIKRNEVSEGTWAYVKNGKYK-GDLAQVVYVNNARKRATVKLI 354 (1780)
Q Consensus 304 kEM~dLLkvkkk~~~Lk~GdwVRIKrGpYK-GDLAQVveVDenk~eVtVKLV 354 (1780)
+||..++..+.=...| ..+||-.|+|+ ||..++.-|.--+..|+|++=
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 4566666544322334 34889999999 887776666656678999873
No 213
>PLN03078 Putative tRNA pseudouridine synthase; Provisional
Probab=21.73 E-value=1.3e+02 Score=39.07 Aligned_cols=53 Identities=8% Similarity=0.047 Sum_probs=34.1
Q ss_pred cEEEEEeccchhHHHHhcCCCCEEe-ceecccCHHHHHHHhhcc-cccccccCCC
Q 000252 271 GFIFIEADKQCDINEACKGLSGIYY-SRLAPVPKNEVSHLLSAQ-IKRNEVSEGT 323 (1780)
Q Consensus 271 GYIYVEA~kq~dVkeAIkGI~gVy~-~K~~pVPIkEM~dLLkvk-kk~~~Lk~Gd 323 (1780)
-||-|+..=+..+++-|+.|-++.. .....+|.+.|..+|... ...+.+.|..
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 3666777778888888888877543 233455888888888632 2234555543
No 214
>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=21.37 E-value=1.1e+02 Score=27.23 Aligned_cols=28 Identities=29% Similarity=0.483 Sum_probs=24.9
Q ss_pred CCCCcEEEEEeccchhHHHHhcCCCCEE
Q 000252 267 DHIKGFIFIEADKQCDINEACKGLSGIY 294 (1780)
Q Consensus 267 d~lKGYIYVEA~kq~dVkeAIkGI~gVy 294 (1780)
...++|.||+-...+++..||+.+.+..
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 3589999999999999999999888854
No 215
>COG0779 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.30 E-value=1.6e+02 Score=32.93 Aligned_cols=46 Identities=20% Similarity=0.327 Sum_probs=37.9
Q ss_pred cccCCEEEEcc----CCCCCceeEEEEEeCCeEEEEecCcceEEEEecCccc
Q 000252 660 FAVGQTLRIRV----GPLKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLA 707 (1780)
Q Consensus 660 ~lIGKTVKIrk----GPYKGylGiVKDaTdt~ARVELHSk~KtITVdK~~Ls 707 (1780)
.++|+.|+|.- .--|=+.|+|+.+.+++++|++. .|.|.|+...|.
T Consensus 96 r~~G~~Vkv~l~~~~~~~k~~~G~i~~~d~~~v~~~~~--~k~v~Ip~~~i~ 145 (153)
T COG0779 96 RFIGEKVKVKLRLPIEGRKKFEGKIVAVDGETVTLEVD--GKEVEIPFSDIA 145 (153)
T ss_pred HhcCcEEEEEEecccCCceEEEEEEEEEcCCeEEEEEC--CEEEEEEcccch
Confidence 47999999998 44677899999999999998855 555888877776
No 216
>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=21.22 E-value=2.9e+02 Score=25.80 Aligned_cols=68 Identities=9% Similarity=0.112 Sum_probs=0.0
Q ss_pred cEEEEEEeCCCCcEEEEEeccchhHHHHhcCCCCEEeceecccCHHHHHHHhhcccccccccCCCEEEEeCCCCCCCcEE
Q 000252 259 QIISAFAVDHIKGFIFIEADKQCDINEACKGLSGIYYSRLAPVPKNEVSHLLSAQIKRNEVSEGTWAYVKNGKYKGDLAQ 338 (1780)
Q Consensus 259 ~I~SVFvpd~lKGYIYVEA~kq~dVkeAIkGI~gVy~~K~~pVPIkEM~dLLkvkkk~~~Lk~GdwVRIKrGpYKGDLAQ 338 (1780)
.|+.+.+....+-.|||| +-......|++.++.+-. .......|++|+.|++ +
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 000252 339 VVYVNNARKRATVKL 353 (1780)
Q Consensus 339 VveVDenk~eVtVKL 353 (1780)
|++++..+.++.|.+
T Consensus 58 V~~~d~~~~~i~ls~ 72 (73)
T cd05706 58 VLSVDVPNKKIALSL 72 (73)
T ss_pred EEEEeCCCCEEEEEE
No 217
>KOG0339 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=21.03 E-value=81 Score=40.85 Aligned_cols=18 Identities=22% Similarity=0.292 Sum_probs=11.2
Q ss_pred eEEecCCc--eeecceEEEE
Q 000252 406 VFENLDGM--MLKDGYLYKK 423 (1780)
Q Consensus 406 ~f~i~~G~--~YkDGFLyK~ 423 (1780)
.|.+|+-- ||.-||++--
T Consensus 372 S~LV~DEadrmfdmGfe~qV 391 (731)
T KOG0339|consen 372 SYLVLDEADRMFDMGFEPQV 391 (731)
T ss_pred eEEEEechhhhhccccHHHH
Confidence 46666543 6777887643
No 218
>KOG3297 consensus DNA-directed RNA polymerase subunit E' [Transcription]
Probab=20.99 E-value=6.9e+02 Score=29.16 Aligned_cols=84 Identities=17% Similarity=0.235 Sum_probs=49.9
Q ss_pred CCCCCC--cEEEEEEeCCCCEEEEEEeccCchhhHhhhcCCCcccCCCCCCCCCCCCHhHHHhhCCceeeccc--CCCCc
Q 000252 330 GKYKGD--LAQVVYVNNARKRATVKLIPRIDLQALAAKFGGGVAMKKTDSPAPRLISPSELEEFRPLIQYRRD--RDTGK 405 (1780)
Q Consensus 330 GpYKGD--LAQVveVDenk~eVtVKLVPRIDy~~l~~k~~gg~~kKK~~RPPqRLFn~~Eark~~~~~e~rrd--~~tg~ 405 (1780)
-||-|+ +|+|.+-++++.+|+|-+|--|=+.+. .-|+|..|.|+|.-= .-+|... +.+.-
T Consensus 78 rPF~gEVi~gki~~cs~eG~rvtl~FFdDI~IP~~-------------~L~~p~~f~~~e~vW---VWey~~Edg~~~~L 141 (202)
T KOG3297|consen 78 RPFVGEVITGKIKECSEEGLRVTLGFFDDIFIPKE-------------MLPEPCVFEPDEQVW---VWEYEQEDGPGTKL 141 (202)
T ss_pred ecccceEEEEEeecCCccceEEEEEeeeceeechh-------------hCCCCcccccccEEE---EEEecccCCCCcee
Confidence 466666 688999999999999999877765421 235666666663211 1123311 11111
Q ss_pred eEEecCCceeecceEEEEEeccceEeCCCCCCH
Q 000252 406 VFENLDGMMLKDGYLYKKVSIDSLSCWGVVPSE 438 (1780)
Q Consensus 406 ~f~i~~G~~YkDGFLyK~fkIssL~tedVnPTL 438 (1780)
+ |..|=.+ .|++...++.+|.|+-
T Consensus 142 y--------~D~~e~I-RFRV~~e~f~d~~p~~ 165 (202)
T KOG3297|consen 142 Y--------FDVGEEI-RFRVEDESFVDVSPEG 165 (202)
T ss_pred E--------ecCCCeE-EEEEeeecccccCccc
Confidence 1 1222222 3889888889999974
No 219
>PF14001 YdfZ: YdfZ protein
Probab=20.92 E-value=1e+02 Score=30.07 Aligned_cols=32 Identities=19% Similarity=0.392 Sum_probs=27.2
Q ss_pred cccCCCCcccCCCeEEEecCCCCCceEEEEEEECC
Q 000252 548 ALDQSMKVISLNDTARVSEGPSKDRQGIVKKIYRG 582 (1780)
Q Consensus 548 A~D~ngn~I~vGD~VKVIdGphkGRqG~V~HIyRs 582 (1780)
+-|+|+|.|.+|..|-|- | .|.+|+|+-||-.
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 6899999998764
No 220
>COG5177 Uncharacterized conserved protein [Function unknown]
Probab=20.70 E-value=67 Score=41.30 Aligned_cols=18 Identities=28% Similarity=0.302 Sum_probs=14.3
Q ss_pred CCccccCCHHHHHHHHHH
Q 000252 175 IPKEEEMDEEEFDKMMEE 192 (1780)
Q Consensus 175 r~~eEd~DaEelAe~lkE 192 (1780)
-+..+++.+||-++.|+|
T Consensus 437 ne~f~els~eee~rq~~e 454 (769)
T COG5177 437 NEGFEELSPEEEERQLRE 454 (769)
T ss_pred cccchhcChHHHHHHHHH
Confidence 456788888988888876
No 221
>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=20.53 E-value=78 Score=41.38 Aligned_cols=31 Identities=32% Similarity=0.420 Sum_probs=13.5
Q ss_pred CccccCCHHHHHHHHHHHhccccc-hhhchhhH
Q 000252 176 PKEEEMDEEEFDKMMEERYKSNKL-IRYAEEDY 207 (1780)
Q Consensus 176 ~~eEd~DaEelAe~lkERY~r~s~-~~y~~d~~ 207 (1780)
+.+++.+++++-. -.|+|.+... ..|.++..
T Consensus 1027 eD~eDd~e~~~~~-r~ek~Krqmr~Rk~~eDEA 1058 (1329)
T KOG4156|consen 1027 EDHEDDDEEELLK-RSEKLKRQMRLRKYLEDEA 1058 (1329)
T ss_pred ccccchHHHHHHH-HHHHHHHHHHHHHhhcchh
Confidence 3344544444432 2355654432 23555543
No 222
>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=20.43 E-value=6.3e+02 Score=22.99 Aligned_cols=56 Identities=11% Similarity=0.041 Sum_probs=32.5
Q ss_pred EEEEEeccchhHHHHHHHHHHHHhhccCCCCCcEEEEEEeCCCCc-EEEEEeccchh
Q 000252 227 IWKVKCMAGRERQSAFCLMQKFVDLQSLGSKMQIISAFAVDHIKG-FIFIEADKQCD 282 (1780)
Q Consensus 227 LWaVKCK~GKEReVV~sLmrK~i~lq~~g~~L~I~SVFvpd~lKG-YIYVEA~kq~d 282 (1780)
+-.+++++|++.+++..|..-+.........+.-+.++....-|+ ||++|-.....
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 456778999999988876666554521222222233333344555 77777765533
No 223
>PRK00321 rdgC recombination associated protein; Reviewed
Probab=20.36 E-value=2.7e+02 Score=34.07 Aligned_cols=85 Identities=15% Similarity=0.146 Sum_probs=45.8
Q ss_pred EEEEEEeCCCCcEEEEEeccchhHHHHhcCCCCEEe------ceecccCHHHHHHHhhcccccccccCCCEEEEeCCCCC
Q 000252 260 IISAFAVDHIKGFIFIEADKQCDINEACKGLSGIYY------SRLAPVPKNEVSHLLSAQIKRNEVSEGTWAYVKNGKYK 333 (1780)
Q Consensus 260 I~SVFvpd~lKGYIYVEA~kq~dVkeAIkGI~gVy~------~K~~pVPIkEM~dLLkvkkk~~~Lk~GdwVRIKrGpYK 333 (1780)
++.|++ +.-.|||||.+-......+++.-++..++ ..+..-|...|+.-|.-......|..|
T Consensus 124 ~~~~~i-d~~~g~l~VdasS~k~aE~~l~lLrkslgsLpv~p~~~~~~p~~~mt~WL~~~~~P~~f~l~----------- 191 (303)
T PRK00321 124 QTFAWI-DPVNGLIVVDAASAKKAEDVLALLRKSLGSLPVVPLSTEQSPEATMTEWLASGEAPAGFTLD----------- 191 (303)
T ss_pred eEEEEE-ECCCCEEEEeCCCHHHHHHHHHHHHHhcCCCceeccccCCCHHHHHHHHHccCCCCCCcEec-----------
Confidence 444444 56789999999877554444433333222 122334556788888543323344444
Q ss_pred CCcEEEEEEeCCCCEEEEEEeccCchh
Q 000252 334 GDLAQVVYVNNARKRATVKLIPRIDLQ 360 (1780)
Q Consensus 334 GDLAQVveVDenk~eVtVKLVPRIDy~ 360 (1780)
+.|....+.+.+..|+++ |.|+.
T Consensus 192 -~~~eL~~~~e~~~~vr~k---~~~L~ 214 (303)
T PRK00321 192 -DECELKSALEDGAVVRCK---RQDLD 214 (303)
T ss_pred -ceeEEecCCCCccEEEEe---CCCCC
Confidence 445555555554445544 55554
No 224
>COG2163 RPL14A Ribosomal protein L14E/L6E/L27E [Translation, ribosomal structure and biogenesis]
Probab=20.33 E-value=1.2e+02 Score=33.01 Aligned_cols=47 Identities=15% Similarity=0.293 Sum_probs=34.2
Q ss_pred cccCCEEEEccCCCCCceeEEEEEeCCeEEEEecCcceEEEEecCccc
Q 000252 660 FAVGQTLRIRVGPLKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLA 707 (1780)
Q Consensus 660 ~lIGKTVKIrkGPYKGylGiVKDaTdt~ARVELHSk~KtITVdK~~Ls 707 (1780)
.-+|+.|.|+.|.|.|-.+.|+++-|.. +|.....+++--|++..+.
T Consensus 5 l~~GrVvvv~~GR~aGkk~VIv~~iDd~-~v~i~gp~~v~gv~r~r~n 51 (125)
T COG2163 5 LEVGRVVVVTAGRFAGKKVVIVKIIDDN-FVLITGPKKVKGVPRRRIN 51 (125)
T ss_pred ccCCeEEEEecceeCCceEEEEEEccCC-EEEEeCCccccCCcccccc
Confidence 4579999999999999999999998887 5555544443334444433
No 225
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=20.30 E-value=81 Score=37.22 Aligned_cols=9 Identities=11% Similarity=0.320 Sum_probs=4.2
Q ss_pred ccccCCCCC
Q 000252 123 AADVDYDDD 131 (1780)
Q Consensus 123 EAEVDDDeE 131 (1780)
+.||++|.|
T Consensus 58 ~~~~~~~~~ 66 (232)
T PRK12766 58 GLEVSEETE 66 (232)
T ss_pred ccccccccc
Confidence 455544443
No 226
>COG4371 Predicted membrane protein [Function unknown]
Probab=20.16 E-value=1.6e+02 Score=35.26 Aligned_cols=49 Identities=39% Similarity=0.590 Sum_probs=0.0
Q ss_pred CCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-------CCCCCCCCC
Q 000252 1437 FNNR-GSGNFRGRGGFRGRGDSDRGGFGGRGRTNRGGYGGRG-------RFDREGFGG 1486 (1780)
Q Consensus 1437 ~~~~-g~g~~~g~ggf~grg~~~rggfgg~g~g~rgg~gg~g-------~~~rGGfGG 1486 (1780)
.++| |+++||+.+++. |+...++-.||..+++.=++||.+ ++.+|||+|
T Consensus 49 SGGriGGgSfraps~~s-r~YS~~gpsGGgY~gg~Y~GGGfgfPfiip~~G~GGGfgG 105 (334)
T COG4371 49 SGGRIGGGSFRAPSGYS-RGYSGGGPSGGGYSGGGYSGGGFGFPFIIPGGGGGGGFGG 105 (334)
T ss_pred hCCCccCCCCCCCCCCC-CCcCCCCCCCCCCCCCCCCCCCcCcCeEeccCCcCCcccc
Done!