Query 000294
Match_columns 1711
No_of_seqs 411 out of 941
Neff 3.9
Searched_HMMs 46136
Date Fri Mar 29 03:12:03 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/000294.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/000294hhsearch_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 2E-130 4E-135 1187.6 52.7 631 107-758 55-808 (1024)
2 COG5164 SPT5 Transcription elo 100.0 1.8E-51 4E-56 470.0 29.6 361 375-763 3-459 (607)
3 PRK08559 nusG transcription an 99.9 1.3E-23 2.8E-28 219.5 16.9 131 222-357 3-133 (153)
4 PF03439 Spt5-NGN: Early trans 99.9 2.9E-22 6.3E-27 191.0 6.8 84 226-310 1-84 (84)
5 TIGR00405 L26e_arch ribosomal 99.8 2.9E-19 6.2E-24 184.5 15.7 124 228-356 1-124 (145)
6 KOG1999 RNA polymerase II tran 99.8 1E-15 2.2E-20 190.0 47.4 201 490-714 406-639 (1024)
7 COG0250 NusG Transcription ant 99.7 1.9E-17 4.2E-22 177.6 13.2 133 224-356 2-163 (178)
8 PRK05609 nusG transcription an 99.6 3.2E-14 6.9E-19 151.1 15.8 130 224-356 5-166 (181)
9 TIGR01956 NusG_myco NusG famil 99.6 2.1E-14 4.5E-19 160.9 14.5 129 226-357 1-246 (258)
10 TIGR00922 nusG transcription t 99.5 1E-13 2.2E-18 146.6 14.2 127 227-356 1-159 (172)
11 PF11942 Spt5_N: Spt5 transcri 99.5 5.6E-15 1.2E-19 145.0 1.9 92 119-220 1-97 (97)
12 COG5164 SPT5 Transcription elo 99.5 1.3E-14 2.7E-19 169.2 2.3 337 213-590 28-388 (607)
13 PRK09014 rfaH transcriptional 99.3 6.3E-12 1.4E-16 132.2 10.4 126 226-355 3-147 (162)
14 TIGR01955 RfaH transcriptional 99.3 1.4E-11 3E-16 128.7 10.4 128 227-357 1-148 (159)
15 smart00738 NGN In Spt5p, this 99.2 6E-11 1.3E-15 115.6 9.1 83 226-311 1-105 (106)
16 PF02357 NusG: Transcription t 97.8 2.4E-05 5.1E-10 75.4 5.5 76 226-303 2-91 (92)
17 KOG0921 Dosage compensation co 97.4 0.00059 1.3E-08 87.1 10.6 11 71-81 92-102 (1282)
18 PF00467 KOW: KOW motif; Inte 97.3 0.00034 7.3E-09 56.8 4.2 32 321-352 1-32 (32)
19 PF00467 KOW: KOW motif; Inte 97.1 0.00064 1.4E-08 55.2 4.2 32 662-693 1-32 (32)
20 KOG0921 Dosage compensation co 97.0 0.0029 6.3E-08 81.2 10.6 15 1517-1531 1266-1280(1282)
21 KOG3973 Uncharacterized conser 96.8 0.0037 8.1E-08 73.4 8.9 9 351-359 139-147 (465)
22 TIGR00405 L26e_arch ribosomal 95.6 0.018 3.9E-07 60.6 5.5 50 660-709 87-140 (145)
23 smart00739 KOW KOW (Kyprides, 95.4 0.022 4.7E-07 43.9 3.8 27 555-581 1-27 (28)
24 PRK08559 nusG transcription an 95.1 0.042 9.1E-07 58.9 6.4 51 660-710 95-149 (153)
25 KOG3262 H/ACA small nucleolar 94.6 0.063 1.4E-06 59.3 6.3 17 1207-1223 5-22 (215)
26 smart00739 KOW KOW (Kyprides, 94.5 0.049 1.1E-06 42.0 3.8 27 318-344 1-27 (28)
27 CHL00141 rpl24 ribosomal prote 94.1 0.073 1.6E-06 52.4 4.9 28 555-582 8-35 (83)
28 PRK01191 rpl24p 50S ribosomal 94.1 0.11 2.3E-06 54.4 6.3 50 304-355 33-82 (120)
29 PRK12281 rplX 50S ribosomal pr 94.0 0.077 1.7E-06 51.4 4.8 28 555-582 6-33 (76)
30 TIGR01955 RfaH transcriptional 93.9 0.095 2.1E-06 55.6 5.7 42 660-701 109-151 (159)
31 TIGR00922 nusG transcription t 93.7 0.11 2.3E-06 56.1 5.6 47 660-706 120-170 (172)
32 PRK00004 rplX 50S ribosomal pr 93.7 0.097 2.1E-06 53.5 5.0 29 554-582 3-31 (105)
33 PRK05609 nusG transcription an 93.1 0.14 3.1E-06 55.3 5.6 48 660-707 127-178 (181)
34 CHL00141 rpl24 ribosomal prote 92.5 0.2 4.3E-06 49.4 5.0 39 316-354 6-44 (83)
35 PRK09014 rfaH transcriptional 92.2 0.22 4.7E-06 53.4 5.3 47 660-706 110-159 (162)
36 KOG3262 H/ACA small nucleolar 92.1 0.27 5.7E-06 54.6 5.9 21 1501-1522 193-213 (215)
37 TIGR01079 rplX_bact ribosomal 92.0 0.23 4.9E-06 50.9 4.9 28 555-582 3-30 (104)
38 PF00524 PPV_E1_N: E1 Protein, 91.9 0.046 1E-06 57.7 -0.1 69 116-198 14-86 (130)
39 PRK01191 rpl24p 50S ribosomal 91.6 0.35 7.7E-06 50.7 5.9 28 555-582 45-72 (120)
40 PRK12281 rplX 50S ribosomal pr 91.6 0.28 6.1E-06 47.7 4.8 38 317-354 5-42 (76)
41 TIGR01080 rplX_A_E ribosomal p 91.4 0.39 8.5E-06 50.0 5.9 39 316-354 39-77 (114)
42 TIGR01956 NusG_myco NusG famil 91.2 0.33 7.1E-06 56.5 5.7 43 659-701 205-249 (258)
43 COG0250 NusG Transcription ant 91.1 0.32 7E-06 53.9 5.4 43 659-701 123-167 (178)
44 PTZ00194 60S ribosomal protein 90.9 0.46 9.9E-06 51.2 6.0 52 304-357 34-85 (143)
45 TIGR01080 rplX_A_E ribosomal p 90.1 0.38 8.3E-06 50.1 4.5 28 555-582 41-68 (114)
46 PTZ00194 60S ribosomal protein 90.0 0.35 7.6E-06 52.1 4.3 28 555-582 46-73 (143)
47 COG0198 RplX Ribosomal protein 89.8 0.42 9E-06 49.1 4.5 30 554-583 3-32 (104)
48 PRK00004 rplX 50S ribosomal pr 89.6 0.51 1.1E-05 48.4 4.9 37 318-354 4-40 (105)
49 PF11623 DUF3252: Protein of u 86.0 2.1 4.7E-05 39.2 5.9 47 660-706 2-52 (53)
50 TIGR01079 rplX_bact ribosomal 85.7 1.1 2.5E-05 45.9 4.7 37 318-354 3-39 (104)
51 COG2933 Predicted SAM-dependen 82.8 1.8 3.9E-05 50.9 5.2 64 229-299 5-71 (358)
52 KOG1708 Mitochondrial/chloropl 81.6 1.5 3.1E-05 49.6 3.8 31 552-582 69-99 (236)
53 COG0198 RplX Ribosomal protein 79.4 2.7 5.9E-05 43.4 4.6 34 317-352 3-36 (104)
54 PRK11760 putative 23S rRNA C24 78.3 3.4 7.4E-05 50.3 5.7 65 228-299 4-71 (357)
55 PF09444 MRC1: MRC1-like domai 75.8 0.66 1.4E-05 50.2 -0.9 18 113-130 3-20 (145)
56 PF04931 DNA_pol_phi: DNA poly 73.7 1.9 4.1E-05 57.1 2.3 16 236-251 764-779 (784)
57 COG1588 POP4 RNase P/RNase MRP 73.3 6.5 0.00014 40.1 5.3 47 660-708 14-63 (95)
58 PTZ00415 transmission-blocking 73.1 1.7 3.8E-05 60.0 1.6 17 223-239 312-328 (2849)
59 CHL00010 infA translation init 72.9 26 0.00056 34.4 9.2 65 504-582 9-73 (78)
60 PHA02774 E1; Provisional 72.4 1.1 2.3E-05 57.6 -0.4 31 298-332 177-207 (613)
61 KOG1832 HIV-1 Vpr-binding prot 72.0 3.3 7.1E-05 54.7 3.6 9 184-192 1469-1477(1516)
62 smart00652 eIF1a eukaryotic tr 71.1 21 0.00046 35.5 8.2 65 502-581 5-69 (83)
63 TIGR01622 SF-CC1 splicing fact 70.9 10 0.00022 46.5 7.4 67 238-310 383-454 (457)
64 KOG0415 Predicted peptidyl pro 70.7 9.5 0.00021 46.4 6.7 111 176-302 198-314 (479)
65 PF14632 SPT6_acidic: Acidic N 70.5 1.4 3.1E-05 44.5 0.1 9 143-151 20-28 (92)
66 PF11746 DUF3303: Protein of u 69.4 14 0.00031 37.1 6.7 76 228-303 2-83 (91)
67 KOG0262 RNA polymerase I, larg 69.2 13 0.00029 51.0 8.1 69 227-296 1442-1520(1640)
68 PF14851 FAM176: FAM176 family 68.9 6.4 0.00014 43.2 4.5 17 179-195 114-130 (153)
69 PLN00208 translation initiatio 67.3 19 0.00041 39.4 7.5 77 491-582 20-97 (145)
70 PTZ00061 DNA-directed RNA poly 67.0 34 0.00074 39.4 9.8 57 270-329 118-190 (205)
71 cd05793 S1_IF1A S1_IF1A: Trans 66.6 27 0.00058 34.4 7.8 64 504-582 2-65 (77)
72 PRK04333 50S ribosomal protein 66.6 9.2 0.0002 38.2 4.7 33 318-351 3-35 (84)
73 PRK04950 ProP expression regul 66.1 9.2 0.0002 44.0 5.2 46 660-707 167-212 (213)
74 PF03115 Astro_capsid: Astrovi 63.0 2.4 5.2E-05 56.1 0.0 12 177-188 718-729 (787)
75 PRK03879 ribonuclease P protei 62.9 15 0.00032 37.6 5.5 46 660-707 12-60 (96)
76 PRK00276 infA translation init 62.5 40 0.00087 32.5 8.0 63 505-581 10-72 (72)
77 KOG0299 U3 snoRNP-associated p 62.4 4.3 9.4E-05 50.5 1.9 19 180-198 98-116 (479)
78 PTZ00329 eukaryotic translatio 60.6 33 0.00071 38.0 7.9 76 492-582 21-97 (155)
79 cd04456 S1_IF1A_like S1_IF1A_l 60.6 46 0.00099 32.9 8.1 64 504-582 2-66 (78)
80 PF02736 Myosin_N: Myosin N-te 59.8 17 0.00037 31.7 4.6 30 675-705 12-42 (42)
81 PRK12269 bifunctional cytidyla 59.6 96 0.0021 42.5 13.5 196 300-565 605-809 (863)
82 PRK04333 50S ribosomal protein 58.6 13 0.00028 37.2 4.2 31 660-690 4-35 (84)
83 PF02724 CDC45: CDC45-like pro 58.5 6.9 0.00015 51.0 2.9 30 281-310 236-266 (622)
84 smart00361 RRM_1 RNA recogniti 58.3 22 0.00047 33.2 5.4 28 267-294 34-61 (70)
85 TIGR00739 yajC preprotein tran 57.1 24 0.00052 35.2 5.7 43 661-708 39-81 (84)
86 PRK14635 hypothetical protein; 57.0 13 0.00029 40.8 4.3 49 660-708 96-155 (162)
87 PRK04012 translation initiatio 56.3 48 0.001 34.3 7.8 73 494-581 12-85 (100)
88 PRK12442 translation initiatio 56.2 48 0.001 33.7 7.5 63 505-581 10-72 (87)
89 TIGR00523 eIF-1A eukaryotic/ar 56.1 37 0.00081 35.0 7.0 64 502-582 19-85 (99)
90 PRK05585 yajC preprotein trans 55.5 26 0.00056 36.4 5.8 44 661-709 54-97 (106)
91 PF04931 DNA_pol_phi: DNA poly 54.4 11 0.00024 50.3 3.7 7 71-77 545-551 (784)
92 COG1862 YajC Preprotein transl 54.0 23 0.00051 36.4 5.2 46 662-712 46-91 (97)
93 PTZ00065 60S ribosomal protein 53.7 17 0.00038 39.1 4.4 33 318-351 7-39 (130)
94 KOG1708 Mitochondrial/chloropl 53.5 12 0.00027 42.6 3.4 40 659-698 72-114 (236)
95 PLN03111 DNA-directed RNA poly 53.5 82 0.0018 36.5 9.8 55 273-329 121-191 (206)
96 PTZ00065 60S ribosomal protein 52.4 25 0.00055 37.9 5.3 35 660-695 8-42 (130)
97 PTZ00415 transmission-blocking 52.3 6.9 0.00015 54.8 1.5 17 93-109 120-136 (2849)
98 PRK11634 ATP-dependent RNA hel 51.3 25 0.00055 46.0 6.2 11 301-311 279-289 (629)
99 PF01176 eIF-1a: Translation i 51.1 56 0.0012 30.9 6.8 62 503-579 4-65 (65)
100 COG3109 ProQ Activator of osmo 50.9 22 0.00048 39.9 4.7 46 660-707 162-207 (208)
101 COG4371 Predicted membrane pro 50.4 26 0.00057 41.2 5.4 7 1452-1458 55-61 (334)
102 PF02724 CDC45: CDC45-like pro 50.0 14 0.00029 48.4 3.6 13 184-196 199-211 (622)
103 PRK14639 hypothetical protein; 49.1 28 0.00061 37.6 5.2 49 660-708 85-133 (140)
104 cd05690 S1_RPS1_repeat_ec5 S1_ 48.6 26 0.00057 31.9 4.2 66 260-351 3-68 (69)
105 PF01868 UPF0086: Domain of un 48.5 43 0.00093 33.7 5.9 48 660-708 11-61 (89)
106 TIGR01659 sex-lethal sex-letha 48.0 61 0.0013 39.8 8.3 68 219-295 102-174 (346)
107 smart00538 POP4 A domain found 47.9 42 0.0009 34.1 5.8 47 660-707 10-59 (92)
108 PRK00092 ribosome maturation p 47.2 29 0.00064 37.7 5.0 49 660-708 95-147 (154)
109 TIGR02760 TraI_TIGR conjugativ 47.2 77 0.0017 46.9 10.4 93 489-586 1327-1424(1960)
110 TIGR01642 U2AF_lg U2 snRNP aux 46.8 29 0.00063 43.2 5.6 49 240-294 432-488 (509)
111 PRK05886 yajC preprotein trans 46.3 46 0.00099 35.0 5.9 43 661-708 40-82 (109)
112 PRK02749 photosystem I reactio 46.1 33 0.00072 33.4 4.5 43 319-362 3-49 (71)
113 TIGR03630 arch_S17P archaeal r 45.8 36 0.00078 35.5 5.0 25 543-567 63-87 (102)
114 PRK08572 rps17p 30S ribosomal 45.1 37 0.00081 35.6 5.1 25 543-567 65-89 (108)
115 PF10446 DUF2457: Protein of u 44.4 12 0.00025 47.0 1.6 8 225-232 122-129 (458)
116 smart00316 S1 Ribosomal protei 44.3 53 0.0012 29.0 5.4 67 260-353 5-71 (72)
117 cd01734 YlxS_C YxlS is a Bacil 43.8 38 0.00081 33.3 4.7 49 660-708 22-76 (83)
118 cd05698 S1_Rrp5_repeat_hs6_sc5 43.8 65 0.0014 29.6 6.0 67 260-353 3-69 (70)
119 PF02576 DUF150: Uncharacteris 43.5 36 0.00078 36.3 4.9 49 660-708 84-138 (141)
120 PRK12288 GTPase RsgA; Reviewed 41.7 1.4E+02 0.0031 36.7 10.1 86 504-608 40-127 (347)
121 CHL00125 psaE photosystem I su 41.4 40 0.00087 32.4 4.2 41 319-360 2-46 (64)
122 PRK14637 hypothetical protein; 41.2 46 0.001 36.5 5.3 46 660-707 95-141 (151)
123 PRK14643 hypothetical protein; 41.1 39 0.00084 37.6 4.8 49 660-708 101-157 (164)
124 PRK14638 hypothetical protein; 40.7 39 0.00085 36.9 4.7 47 660-708 97-143 (150)
125 PF13051 DUF3912: Protein of u 40.0 55 0.0012 31.0 4.8 49 660-710 3-54 (68)
126 TIGR00008 infA translation ini 39.9 1.3E+02 0.0028 29.5 7.4 60 505-578 8-67 (68)
127 PRK04313 30S ribosomal protein 39.8 3E+02 0.0065 32.7 11.8 49 661-710 173-227 (237)
128 PRK09521 exosome complex RNA-b 39.7 1.3E+02 0.0028 33.7 8.7 90 491-606 61-156 (189)
129 cd04461 S1_Rrp5_repeat_hs8_sc7 39.7 62 0.0014 31.1 5.4 69 258-353 15-83 (83)
130 PRK14634 hypothetical protein; 38.9 41 0.00089 36.9 4.6 47 660-708 97-147 (155)
131 cd04451 S1_IF1 S1_IF1: Transla 38.6 1.6E+02 0.0034 27.5 7.7 60 505-578 4-63 (64)
132 PF10446 DUF2457: Protein of u 37.9 14 0.0003 46.3 0.9 10 572-581 399-408 (458)
133 PF11623 DUF3252: Protein of u 37.5 53 0.0011 30.7 4.2 29 319-347 2-32 (53)
134 PRK14644 hypothetical protein; 37.2 41 0.0009 36.3 4.2 48 660-707 82-135 (136)
135 PF10842 DUF2642: Protein of u 37.1 76 0.0017 30.8 5.4 45 660-707 18-62 (66)
136 PF02427 PSI_PsaE: Photosystem 37.1 60 0.0013 31.1 4.6 40 319-359 1-44 (61)
137 TIGR02760 TraI_TIGR conjugativ 36.8 1.5E+02 0.0032 44.2 10.5 94 490-588 680-784 (1960)
138 KOG0107 Alternative splicing f 36.5 44 0.00095 37.9 4.3 34 259-292 36-69 (195)
139 PRK11634 ATP-dependent RNA hel 36.3 65 0.0014 42.4 6.6 12 682-693 523-534 (629)
140 COG0361 InfA Translation initi 36.1 1.4E+02 0.003 29.8 7.1 65 504-582 9-73 (75)
141 PF13893 RRM_5: RNA recognitio 35.8 54 0.0012 29.0 4.0 36 259-294 10-45 (56)
142 PLN00036 40S ribosomal protein 35.6 55 0.0012 39.0 5.1 52 554-609 173-229 (261)
143 PF11515 Cul7: Mouse developme 35.6 58 0.0013 32.6 4.5 39 304-347 8-49 (78)
144 KOG4156 Claspin, protein media 35.4 8.6 0.00019 49.2 -1.3 13 118-130 1052-1064(1329)
145 PLN00045 photosystem I reactio 35.4 63 0.0014 33.3 4.8 45 315-360 36-85 (101)
146 cd01854 YjeQ_engC YjeQ/EngC. 35.2 2.1E+02 0.0045 34.0 9.9 84 506-608 1-85 (287)
147 PRK10486 autoinducer-2 (AI-2) 35.2 1.9E+02 0.0041 29.0 8.2 65 227-292 5-70 (96)
148 PRK13709 conjugal transfer nic 34.3 1.7E+02 0.0037 43.1 10.4 93 489-589 1273-1373(1747)
149 COG2139 RPL21A Ribosomal prote 34.3 67 0.0015 33.3 4.8 49 660-708 33-93 (98)
150 PRK05610 rpsQ 30S ribosomal pr 34.0 73 0.0016 32.1 5.0 25 543-568 42-66 (84)
151 PTZ00118 40S ribosomal protein 33.6 63 0.0014 38.5 5.2 54 554-609 173-229 (262)
152 PF05918 API5: Apoptosis inhib 33.3 14 0.00031 47.7 0.0 11 431-441 270-280 (556)
153 PTZ00223 40S ribosomal protein 33.3 50 0.0011 39.5 4.4 54 554-609 170-226 (273)
154 PRK00098 GTPase RsgA; Reviewed 33.1 2.5E+02 0.0055 33.5 10.2 86 505-608 2-87 (298)
155 COG0186 RpsQ Ribosomal protein 33.1 67 0.0014 32.8 4.5 24 543-567 44-67 (87)
156 PF00575 S1: S1 RNA binding do 32.1 1.6E+02 0.0035 27.3 6.7 57 492-565 2-58 (74)
157 PRK14640 hypothetical protein; 32.1 69 0.0015 35.1 4.9 46 660-707 94-143 (152)
158 PRK13709 conjugal transfer nic 32.0 1.9E+02 0.0041 42.7 10.2 92 489-588 646-748 (1747)
159 PF02699 YajC: Preprotein tran 31.7 16 0.00034 36.2 0.0 43 661-708 38-80 (82)
160 cd05703 S1_Rrp5_repeat_hs12_sc 31.4 1.2E+02 0.0025 29.1 5.7 68 260-353 3-71 (73)
161 cd05708 S1_Rrp5_repeat_sc12 S1 31.1 1.1E+02 0.0025 28.2 5.6 70 260-355 5-74 (77)
162 PRK14630 hypothetical protein; 31.1 87 0.0019 34.1 5.4 45 660-708 94-139 (143)
163 COG1096 Predicted RNA-binding 30.6 1.7E+02 0.0036 33.7 7.6 43 552-607 115-157 (188)
164 PRK14712 conjugal transfer nic 30.2 2.2E+02 0.0047 41.8 10.2 92 490-589 515-617 (1623)
165 TIGR03635 S17_bact 30S ribosom 29.9 91 0.002 30.5 4.8 23 544-567 38-60 (71)
166 PRK04313 30S ribosomal protein 29.9 59 0.0013 38.3 4.1 52 554-609 170-227 (237)
167 PRK14645 hypothetical protein; 29.9 71 0.0015 35.3 4.6 45 660-707 99-143 (154)
168 KOG0130 RNA-binding protein RB 29.7 84 0.0018 34.5 4.9 61 226-292 71-136 (170)
169 PRK06531 yajC preprotein trans 29.6 64 0.0014 34.2 3.9 47 662-712 39-85 (113)
170 PRK14712 conjugal transfer nic 29.5 2.5E+02 0.0055 41.1 10.7 92 489-587 1144-1242(1623)
171 PF10574 UPF0552: Uncharacteri 28.8 1.2E+02 0.0025 35.6 6.1 99 226-340 58-176 (224)
172 PRK06958 single-stranded DNA-b 28.2 1.5E+02 0.0032 33.8 6.8 9 1525-1533 168-176 (182)
173 KOG4211 Splicing factor hnRNP- 27.7 1.1E+02 0.0025 39.1 6.2 97 225-333 8-114 (510)
174 PF14001 YdfZ: YdfZ protein 27.6 64 0.0014 31.2 3.2 32 548-582 2-33 (64)
175 KOG3218 RNA polymerase, 25-kDa 27.3 3.4E+02 0.0073 31.6 9.2 56 268-329 118-173 (208)
176 cd05688 S1_RPS1_repeat_ec3 S1_ 27.1 1.2E+02 0.0025 27.3 4.8 64 260-351 4-67 (68)
177 CHL00142 rps17 ribosomal prote 27.0 1.1E+02 0.0024 31.0 4.9 24 544-568 40-63 (84)
178 COG2163 RPL14A Ribosomal prote 26.9 82 0.0018 33.9 4.3 33 318-351 4-36 (125)
179 PRK14636 hypothetical protein; 26.9 84 0.0018 35.4 4.6 48 660-708 95-146 (176)
180 KOG2055 WD40 repeat protein [G 26.7 57 0.0012 41.4 3.5 21 176-196 130-150 (514)
181 KOG1819 FYVE finger-containing 26.7 40 0.00087 42.6 2.2 28 211-238 528-556 (990)
182 cd05697 S1_Rrp5_repeat_hs5 S1_ 26.7 1.5E+02 0.0032 27.4 5.5 68 259-353 2-69 (69)
183 PRK08059 general stress protei 26.5 3.7E+02 0.0081 28.3 8.9 80 488-594 1-82 (123)
184 PRK11642 exoribonuclease R; Pr 26.4 1.8E+02 0.0038 39.8 8.1 81 259-354 645-725 (813)
185 PRK14632 hypothetical protein; 26.4 99 0.0021 34.7 5.0 49 660-708 95-156 (172)
186 COG2139 RPL21A Ribosomal prote 26.3 82 0.0018 32.7 3.9 49 488-537 29-91 (98)
187 PRK12289 GTPase RsgA; Reviewed 25.9 3.5E+02 0.0075 33.6 9.8 76 503-590 8-86 (352)
188 PRK14633 hypothetical protein; 25.3 1E+02 0.0022 33.8 4.8 48 660-708 91-142 (150)
189 PRK14646 hypothetical protein; 25.2 99 0.0021 34.1 4.6 47 660-708 97-147 (155)
190 PF06524 NOA36: NOA36 protein; 24.5 1.1E+02 0.0024 36.6 5.0 6 81-86 206-211 (314)
191 cd05687 S1_RPS1_repeat_ec1_hs1 24.3 2.6E+02 0.0056 25.8 6.6 67 260-353 3-69 (70)
192 cd04471 S1_RNase_R S1_RNase_R: 24.2 94 0.002 29.2 3.8 28 317-354 56-83 (83)
193 COG1471 RPS4A Ribosomal protei 24.0 86 0.0019 36.9 4.1 52 554-609 172-229 (241)
194 PRK02001 hypothetical protein; 24.0 1.3E+02 0.0028 33.3 5.3 48 660-707 87-146 (152)
195 cd05684 S1_DHX8_helicase S1_DH 23.9 4.3E+02 0.0094 25.1 8.2 15 551-565 44-58 (79)
196 COG1532 Predicted RNA-binding 23.9 47 0.001 31.3 1.6 31 322-352 24-56 (57)
197 smart00243 GAS2 Growth-Arrest- 23.7 1.7E+02 0.0037 29.2 5.3 50 304-356 5-55 (73)
198 PRK08582 hypothetical protein; 23.6 2.5E+02 0.0054 30.5 7.2 57 492-565 3-59 (139)
199 PF08595 RXT2_N: RXT2-like, N- 23.6 39 0.00084 37.2 1.2 6 119-124 54-59 (149)
200 PRK05807 hypothetical protein; 23.3 2.4E+02 0.0052 30.4 7.0 57 491-565 2-58 (136)
201 COG2163 RPL14A Ribosomal prote 23.3 95 0.002 33.5 3.9 47 660-707 5-51 (125)
202 KOG0116 RasGAP SH3 binding pro 23.2 1.2E+02 0.0026 38.5 5.4 13 182-194 12-24 (419)
203 PF11424 DUF3195: Protein of u 23.2 79 0.0017 32.1 3.1 43 228-278 2-44 (89)
204 KOG0943 Predicted ubiquitin-pr 23.1 42 0.00091 46.3 1.5 24 268-291 1915-1938(3015)
205 PF03992 ABM: Antibiotic biosy 23.0 5.3E+02 0.011 23.4 8.3 56 227-282 5-61 (78)
206 PLN03134 glycine-rich RNA-bind 22.8 1.5E+02 0.0033 32.0 5.4 59 226-293 36-99 (144)
207 PF01157 Ribosomal_L21e: Ribos 22.8 1.6E+02 0.0034 30.7 5.3 60 546-606 23-96 (99)
208 PRK12766 50S ribosomal protein 22.6 69 0.0015 37.6 3.0 17 270-286 171-187 (232)
209 COG0056 AtpA F0F1-type ATP syn 22.4 1.5E+02 0.0032 38.1 5.8 32 489-520 44-75 (504)
210 PRK12766 50S ribosomal protein 22.3 23 0.00049 41.4 -0.8 15 118-133 54-68 (232)
211 cd05691 S1_RPS1_repeat_ec6 S1_ 22.3 2.3E+02 0.0049 26.0 5.8 26 318-353 44-69 (73)
212 PF05918 API5: Apoptosis inhib 22.1 30 0.00064 44.9 0.0 9 437-445 291-299 (556)
213 PRK14647 hypothetical protein; 21.9 1.3E+02 0.0027 33.3 4.7 48 660-708 96-152 (159)
214 cd05706 S1_Rrp5_repeat_sc10 S1 21.9 2.7E+02 0.0058 25.9 6.2 68 259-353 5-72 (73)
215 cd05705 S1_Rrp5_repeat_hs14 S1 21.6 1.9E+02 0.004 27.9 5.2 67 259-351 5-73 (74)
216 COG0779 Uncharacterized protei 21.5 1.5E+02 0.0033 32.9 5.1 47 660-708 96-146 (153)
217 PF00076 RRM_1: RNA recognitio 21.5 1E+02 0.0022 27.3 3.3 28 267-294 36-63 (70)
218 cd05707 S1_Rrp5_repeat_sc11 S1 21.5 2.2E+02 0.0048 26.2 5.5 65 260-351 3-67 (68)
219 cd05792 S1_eIF1AD_like S1_eIF1 21.3 4.2E+02 0.0091 26.7 7.6 64 504-582 2-66 (78)
220 PF05320 Pox_RNA_Pol_19: Poxvi 21.2 97 0.0021 34.5 3.6 39 187-226 69-108 (167)
221 PLN00036 40S ribosomal protein 21.1 1.7E+02 0.0036 35.1 5.7 29 316-344 172-200 (261)
222 PF15470 DUF4637: Domain of un 21.0 77 0.0017 34.9 2.7 17 116-132 15-31 (173)
223 PF02187 GAS2: Growth-Arrest-S 21.0 1.6E+02 0.0035 29.3 4.6 48 304-354 5-53 (73)
224 KOG0339 ATP-dependent RNA heli 20.9 80 0.0017 40.8 3.2 17 406-422 372-390 (731)
225 PF02211 NHase_beta: Nitrile h 20.9 83 0.0018 36.7 3.2 34 553-586 132-175 (222)
226 PRK00321 rdgC recombination as 20.7 2.7E+02 0.0058 34.0 7.4 69 260-329 124-198 (303)
227 PRK06763 F0F1 ATP synthase sub 20.7 1.8E+02 0.0039 33.8 5.5 15 552-566 161-175 (213)
228 PRK06531 yajC preprotein trans 20.4 2.4E+02 0.0051 30.1 6.0 42 303-355 27-68 (113)
229 COG5177 Uncharacterized conser 20.3 68 0.0015 41.1 2.5 18 175-192 437-454 (769)
No 1
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=100.00 E-value=1.6e-130 Score=1187.64 Aligned_cols=631 Identities=34% Similarity=0.501 Sum_probs=489.6
Q ss_pred CcccccccccccccccccccCCCCCchhhcCCCcCCC--CCCCCccchhhhhccCccccccccccCCCCCCCccccCCHH
Q 000294 107 HNRKRKNRSVLQFVEDAADVDYDDDDEEEVGNESDNS--GGFADDDFMEELFDAQPKVNNEMGQAHNLPFIPKEEEMDEE 184 (1711)
Q Consensus 107 r~rKRkrr~~n~FiDdEAEVDDDeEeEDEeeEe~e~~--~~Fi~dD~~~d~~e~~~~~~~d~r~~~~l~~r~~eed~DaE 184 (1711)
..+|+|+.+...||+.|||||||+||+|+|+|++|+. ..||. +..+++++++ .++|.|+.++ ++..+ .+|
T Consensus 55 ~~~~~k~~s~~gf~~~e~dvDdeveddd~~~edEed~~~~~~ie-~~e~~~~d~~----~~~R~~~~~~-~~~~~--~~e 126 (1024)
T KOG1999|consen 55 PDEKDKKESGGGFIDREADVDDEVEDDDDDEEDEEDIELHNDIE-ESEEDLPDER----GDRRLRRYWD-RQLNE--LEE 126 (1024)
T ss_pred hhhhccccccccccccccccccccccccchhccCcchhhcccch-hccccccccc----ccccchhhhh-hhhhH--HHH
Confidence 3456677888899999999999988776666554321 12221 1111222211 1122222222 12222 677
Q ss_pred HHHHHHHHHhccccchhhchhhHHHhhhcccccCCCCCCCCcEEEEEeccchHHHHHHHHHHHHHhhccCCCCCcEEEEE
Q 000294 185 EFDKMMEERYKSNKLIRYAEEDYEAKKMLEREYHMPCPEDPTIWKVKCMAGRERQSAFCLMQKFVDLQSLGSKMQIISAF 264 (1711)
Q Consensus 185 elAe~lkERY~r~s~~~y~~d~~e~~~~VpQq~LLPSV~DPkLWaVKCk~GkEReVV~~LmrKii~lq~~g~~L~I~SVF 264 (1711)
++|+.|+|||.... .|.+.++++.++|+||+|||+|+||+||+|||++|+||+||+|||+||++++++..||+|+|||
T Consensus 127 ~~~~r~aee~~~~~--~~~~~~~~~~d~I~Q~~LLPsvkDP~LW~VKC~iG~Er~~a~~LMrK~i~~~~t~~plqI~Sv~ 204 (1024)
T KOG1999|consen 127 ELAKRYAEEYIEKY--GFEDGDDEDSDDIPQQALLPSVKDPNLWIVKCKIGREREVAFCLMRKFIELDKTDTPLQIKSVF 204 (1024)
T ss_pred HHHHHHHHhhcccc--cccccchhcccchhHHhhCCCCCCCCeeEEEeccccHHHHHHHHHHHHHhhcccCCCceEEEEE
Confidence 77777777776532 1232333445889999999999999999999999999999999999999999999999999999
Q ss_pred EeCCCCcEEEEEeccchhHHHHhcCCCCeEeccccccCHHHHHHHhhcccccccccCCCEEEEecCcCCCCcEEEEEEeC
Q 000294 265 AVDHIKGFIFIEADKQCDINEACKGLSGIYYSRLAPVPKNEVSHLLSAQIKRNEVSEGTWAYVKNGKYKGDLAQVVYVNN 344 (1711)
Q Consensus 265 vpd~lKGYIYIEA~kq~dVk~AIkGI~gVy~~k~~pVPikEM~dLL~vkkk~~~Lk~GdwVRIKrGpYKGDLAQVveVde 344 (1711)
++++|+|||||||++|.||++||++|++||.++|+||||+||++||+|.++.+.|++|.|||||+|+||||||||++|++
T Consensus 205 a~D~lkGyIYIEA~KqshV~~Ai~gv~niy~~~~~lVPikEM~dvLkV~K~~v~L~~gswVRiKrG~YKgDLAqVd~Vd~ 284 (1024)
T KOG1999|consen 205 AKDHLKGYIYIEADKQSHVKEAIEGVRNIYANRILLVPIKEMPDVLKVVKKVVQLSEGSWVRIKRGKYKGDLAQVDDVDE 284 (1024)
T ss_pred eccccceeEEEEechhHHHHHHHhhhhhheeccEEEEehhHhhhhhhhhhhhhccCccceEEEeccccccceeeeeeecc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCEEEEEEeccCchhhHHhhcCCCcccCCCCCCCCCCCChhhHhhhcCceeecccCCCCceEEecCCceeecceEEEEE
Q 000294 345 ARKRATVKLIPRIDLQALAAKFGGGVAMKKTDSPAPRLISPSELEEFRPLIQYRRDRDTGKVFENLDGMMLKDGYLYKKV 424 (1711)
Q Consensus 345 nk~eVtVKLIPRIDy~~l~~k~~gg~~kKK~~RPPqRLFn~~Eark~~~~~~~rrd~~tg~~f~i~~G~~y~DGFLyK~f 424 (1711)
++++|+|||||||||+++..+++ ....++++||++|||+..|++.++++++.+++..++.+|+++.+++|+||||||.|
T Consensus 285 ~~n~v~lKlIPRIDyq~~~~~~~-~~~~~ka~~p~~R~~~~~~~~~~~ir~~~~~~~~~Gd~l~~~gn~~~~dGFLyK~v 363 (1024)
T KOG1999|consen 285 NRNRVRLKLIPRIDYQKLLGKLE-ETTDKKAFRPAPRRPNQKEFDEEAIRSEGRRDHSRGDYLEFEGNELFKDGFLYKDV 363 (1024)
T ss_pred cCCEEEEEEeccccHHhhhcccc-ccchhhccCCcccCCCccccchhhhhhccccccccCceEEecCCceeccceeeeee
Confidence 99999999999999999998887 56677889999999999999999988888999999999988888899999999999
Q ss_pred eccceEecCCCCCHHHHhhcCCCCCCccccHHHHHHHH-------------------hccc--cccEEEe----------
Q 000294 425 SIDSLSCWGVVPSEEELLKFQPSESNESADLEWLSQLY-------------------GERK--KKRTTIV---------- 473 (1711)
Q Consensus 425 kI~sL~t~dVnPTLEEL~kF~~~~~de~~DL~~La~~~-------------------ge~k--k~kii~v---------- 473 (1711)
+|++|++++|+|||+||+||++..+ .+||+.++.++ |+++ |+.|..|
T Consensus 364 ~i~sI~t~gV~PT~dELekF~~~~e--~~Dl~~~st~~~~r~~~~~F~~GD~VeV~~Gel~glkG~ve~vdg~~vti~~~ 441 (1024)
T KOG1999|consen 364 SISSIITDGVKPTLDELEKFNPSNE--EGDLEWVSTLKSNRKKKHLFSPGDAVEVIVGELKGLKGKVESVDGTIVTIMSK 441 (1024)
T ss_pred ecceeeecCcccCHHHHHhhcCCCc--cccceeeeeeccccccccccCCCCeEEEeeeeeccceeEEEeccCceEEEeec
Confidence 9999999999999999999998744 78888765221 1111 1111111
Q ss_pred ---------------------------ecCCCcc-----------------------------------cccCCCCcCcc
Q 000294 474 ---------------------------GKGGDKG-----------------------------------EGSSGSSLENS 491 (1711)
Q Consensus 474 ---------------------------~kGg~kg-----------------------------------E~ssG~~s~G~ 491 (1711)
+.|.+++ |+.+++..+++
T Consensus 442 ~e~l~~pl~~~~~eLrKyF~~GDhVKVi~G~~eG~tGlVvrVe~~~vi~~Sd~t~eel~Vf~~dlq~c~ev~~gv~~~ge 521 (1024)
T KOG1999|consen 442 HEDLKGPLEVPASELRKYFEPGDHVKVIAGRYEGDTGLVVRVEQGDVILLSDLTMEELKVFARDLQLCSEVTLGVEKSGE 521 (1024)
T ss_pred cccCCCccccchHhhhhhccCCCeEEEEeccccCCcceEEEEeCCeEEEEecCccceeeEEehhcccchheeeccccccc
Confidence 1122222 34566778899
Q ss_pred cccCceEEEcCCceEEEEEEeccceEEEccCCCCCCceEEEecccccCCCCCCcccccccCCCcccCCCeEEEecCCCCC
Q 000294 492 FELYELVCFGRKDFGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVSEGPSKD 571 (1711)
Q Consensus 492 FeLgDLVQLD~~TVGVIVrVEkDe~fkVLd~~gd~~~VvtVk~~~I~~K~~~rr~vAtD~~gk~I~vGD~VKVIdGp~kG 571 (1711)
|||||||||+.++|||||++++ +.|+||++++ .|++|++++|..|+..++++|+|+++|+|+++|+|+||.||+++
T Consensus 522 ~e~hdlVqLd~~~vgvI~rle~-e~~~vl~~~g---~v~~i~~~~i~~kk~~r~~~~~D~~~n~I~~kD~Vkvi~Gp~~g 597 (1024)
T KOG1999|consen 522 YELHDLVQLDNQNVGVIVRLER-ETFQVLGMNG---KVVTIRKSSITKKKDNRKAVAVDRNGNEIRVKDTVKVIGGPSKG 597 (1024)
T ss_pred ccccceeecCCCcEEEEEEecc-hheeeecCcC---ceEEEeechhhhhhhhhhheeecccCCeecccceEEEecCCCCC
Confidence 9999999999999999999999 5999999885 79999999999998888899999999999999999999999999
Q ss_pred ceEEEEEEECCEEEEEeCcceeeccEEEEeCCceeecccccccCCCCCCCCCCCCCC-CCCCCCCCCCCcchhh--hccC
Q 000294 572 RQGIVKKIYRGILFIYDENETENGGYFCSKSQHCEKTKVEACEGKGGGSGASGFEEF-PSSPKSPLSPKRSWQA--REQN 648 (1711)
Q Consensus 572 RqG~VlHIyRs~VFL~Sr~~tENgGIFVvRarnv~tv~~~~~~~Kgg~~~~~~f~dl-~~sp~~~lsp~rp~~~--~~~~ 648 (1711)
|+|.|+||||.+||||+++++||+||||||++||++++.... ..+.+...++| +|+|.-.++|+.|... ....
T Consensus 598 ~~G~v~~i~r~~~F~h~r~~~En~Gv~vck~k~~~~~g~~~s----t~~~~~~~~~l~~msP~r~~sp~~~~~~~ga~g~ 673 (1024)
T KOG1999|consen 598 REGEVLHIYRPFVFLHSRKNLENGGVFVCKEKNLILAGGKKS----TNSLAFNKGALAPMSPGRIQSPMGPSGGPGAFGG 673 (1024)
T ss_pred ccCccceeecceeeeeehhhcccCCeEEEecCCceeccccCc----ccchhhcccccCCCCcccccCCcCCCCCCCCcCc
Confidence 999999999999999999999999999999999998764211 01111111112 2333212333333211 1111
Q ss_pred ccccCCCCCCccccCCEEEEccCCCCCceeEEEEEeCCeEEEEecCCceEEEEeCCccccccCC--c--cc---------
Q 000294 649 TEFKRGDRDGMFAVGQTLRIRVGPLKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLAEVRGK--S--FI--------- 715 (1711)
Q Consensus 649 ~~~gRGgRd~d~lIGKTVkIrkGPYKGylGiVKDaTdt~ARVELHSk~KtITVdK~~Ls~v~~~--~--~~--------- 715 (1711)
+..+|++++++.|||+||+|+.||||||+|||||+|+++||||||++|++|+|++.+|.++... . ++
T Consensus 674 ~gggrGg~rd~~l~GktVrI~~Gp~KG~~GivkD~~~~~arVELhs~~~ti~vd~~~~~~v~~~~~~g~~~sYg~~~~~~ 753 (1024)
T KOG1999|consen 674 HGGGRGGNRDDSLLGKTVRIRLGPKKGYLGIVKDVNGDTARVELHSKCVTIKVDRLKRKIVGSTRDGGETSSYGERTPGY 753 (1024)
T ss_pred CccCccCcCcchhcCcEEEEecCCcccccceeEeccCCeeEEEEEeccEEEEechhhceEEeeccCCCCccccccccccc
Confidence 2224444333689999999999999999999999999999999999999999999999976422 1 11
Q ss_pred ---ccccCCCCCCCcc-----CCC---CCCC-CCCCCCCCCCcccCCCCCCCCCC
Q 000294 716 ---TSTSDDQGSASFK-----PFD---PLGA-GGGSGDWMSAATTSAEGDRWNAG 758 (1711)
Q Consensus 716 ---~s~~~d~~s~~~~-----p~~---~~g~-~~~~g~~~~g~gt~~~~~~wn~G 758 (1711)
+.+.+++++.+.. |+- +++. .++..+++.|++||+++.+|++.
T Consensus 754 g~~~~~~~~~Gs~tp~~~s~tpl~~~s~tp~~~~~~Tp~~dG~rTP~r~~aW~~~ 808 (1024)
T KOG1999|consen 754 GRVTPARYGMGSSTPMYGSNTPLWGGSRTPARDGGATPSHDGSRTPARGRAWNPY 808 (1024)
T ss_pred cccCccccCCCCcCccCCCCCCCCCcccCccccCCCCcCCCCCcCCCCCCCcCCC
Confidence 1112233332111 111 1111 24555666788888888888865
No 2
>COG5164 SPT5 Transcription elongation factor [Transcription]
Probab=100.00 E-value=1.8e-51 Score=469.97 Aligned_cols=361 Identities=21% Similarity=0.213 Sum_probs=261.1
Q ss_pred CCCCCCCCCChhhHhhhcCceeecccCCCCceEEecCCceeecceEEEEEeccceEecCCCCCHHHHhhcCCCCCCcccc
Q 000294 375 TDSPAPRLISPSELEEFRPLIQYRRDRDTGKVFENLDGMMLKDGYLYKKVSIDSLSCWGVVPSEEELLKFQPSESNESAD 454 (1711)
Q Consensus 375 ~~RPPqRLFn~~Eark~~~~~~~rrd~~tg~~f~i~~G~~y~DGFLyK~fkI~sL~t~dVnPTLEEL~kF~~~~~de~~D 454 (1711)
+.|||+|||||.||.++.+...+.|+.. .| .|.++.|+||||||.|+|++++|++|+||+|||.+|...+. .+|
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 5699999999999999988654555443 35 57799999999999999999999999999999999997654 488
Q ss_pred HHHHHHHH-----------------hcccc---------ccEEE---------------------------eecCCCccc
Q 000294 455 LEWLSQLY-----------------GERKK---------KRTTI---------------------------VGKGGDKGE 481 (1711)
Q Consensus 455 L~~La~~~-----------------ge~kk---------~kii~---------------------------v~kGg~kgE 481 (1711)
|-++++.+ |+++. .-|+. |+.|+++.+
T Consensus 77 l~s~~~s~kk~ha~fqpgD~~Evl~Geqrg~~gVV~~~~~~I~tm~~~~~~rl~~p~~~lRk~f~~gD~vkVI~g~~~~d 156 (607)
T COG5164 77 LYSYVESFKKQHAVFQPGDALEVLRGEQRGRVGVVPRQKEMIETMTYHFEQRLCGPWGRLRKGFYKGDLVKVIEGGEMVD 156 (607)
T ss_pred hhHHHHHHhhcccccCCCCeeeeecceecccceeecccccceeeeeeccCceeecchhhhhcccccCCeEEEeccccccc
Confidence 88887654 22211 00110 011222221
Q ss_pred cc--------------------------------CCCCcCcccccCceEEEcCCceEEEEEEeccceEEEccCCCCCCce
Q 000294 482 GS--------------------------------SGSSLENSFELYELVCFGRKDFGLIVGMEKDDHYKILKEGSEGPAV 529 (1711)
Q Consensus 482 ~s--------------------------------sG~~s~G~FeLgDLVQLD~~TVGVIVrVEkDe~fkVLd~~gd~~~V 529 (1711)
.. ........|+|||||+|+..+|.||+.|++| .|+|+++.+ +|
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 000294 530 VTVERRTLKNGPFDMKF--TALDQSMKVISLNDTARVSEGPSKDRQGIVKKIYRGILFIYDENETENGGYFCSKSQHCEK 607 (1711)
Q Consensus 530 vtVk~~~I~~K~~~rr~--vAtD~~gk~I~vGD~VKVIdGp~kGRqG~VlHIyRs~VFL~Sr~~tENgGIFVvRarnv~t 607 (1711)
.|+.+.+|..|+..+|. +++|+++++|+++|.|+++.| .+++|+|+|||+.|+|++++.+.||.||||++.+||.+
T Consensus 233 ~t~~~~sI~~kv~~~Rg~~i~~d~ng~eI~igd~VvE~~g--~~~egq~l~i~~~f~f~~t~~i~ennGVfv~~~~nv~~ 310 (607)
T COG5164 233 HTACPISIGDKVRVTRGELIGMDGNGREISIGDAVVESRG--GKFEGQSLGIVKHFDFGETVSIKENNGVFVKIEGNVCI 310 (607)
T ss_pred eEecchhhhhhhecccceeEeeccccceEeeceeEEEecC--CceeeEEEEEEEEEeeeeeeeeeccCceEEEecCceeE
Confidence 99999999999877764 899999999999999999999 67999999999999999999999999999999999998
Q ss_pred cccccccCCCCCCC-CCCCCCCCCCCCCCCC--CCcchhhhccCccccC--CCCCCccccCCEEEEccCCCCCceeEEEE
Q 000294 608 TKVEACEGKGGGSG-ASGFEEFPSSPKSPLS--PKRSWQAREQNTEFKR--GDRDGMFAVGQTLRIRVGPLKGYLCRVLA 682 (1711)
Q Consensus 608 v~~~~~~~Kgg~~~-~~~f~dl~~sp~~~ls--p~rp~~~~~~~~~~gR--GgRd~d~lIGKTVkIrkGPYKGylGiVKD 682 (1711)
|+ +|+.+.. .-+|.+| +|++. +..|. -..+.| ++| +.+||+||+||.|+|||++|+|||
T Consensus 311 VA-----tkd~~~s~k~dl~km----np~v~~~~~~p~-----~~~l~r~i~gR--d~aigktVrIr~g~yKG~lGVVKd 374 (607)
T COG5164 311 VA-----TKDFTESLKVDLDKM----NPPVTVNLQNPK-----TNELERKIVGR--DPAIGKTVRIRCGEYKGHLGVVKD 374 (607)
T ss_pred EE-----eccchhhhcccHhhc----CchhhcCCCCCc-----chhhhcccccc--ccccCceEEEeecccccccceeee
Confidence 75 4554422 1123333 33221 11110 011112 245 489999999999999999999999
Q ss_pred EeCCeEEEEecCCceEEEEeCCccccccCCc-ccccccCCCCCCCccCCCCCCCCCCCCCCCCCc---ccCCCCCCCCCC
Q 000294 683 VRYSDVTVKLDSQQKILTVKGEHLAEVRGKS-FITSTSDDQGSASFKPFDPLGAGGGSGDWMSAA---TTSAEGDRWNAG 758 (1711)
Q Consensus 683 aTdt~ARVELHSk~KtITVdK~~Ls~v~~~~-~~~s~~~d~~s~~~~p~~~~g~~~~~g~~~~g~---gt~~~~~~wn~G 758 (1711)
++++.|||||||+||.|||+|++|.+..-.. .++..---.-.+...|.++-.+-+...+.+... ..-+...+|+.|
T Consensus 375 v~~~~arVeLhs~nK~VTI~K~~l~y~~reGe~ity~e~vnr~~~~~p~r~s~a~gs~~pn~atgg~aa~~a~t~s~~sg 454 (607)
T COG5164 375 VDRNIARVELHSNNKFVTIEKSRLAYLGREGEGITYDELVNRRGLSKPLRYSEAIGSKTPNYATGGIAAGAAATSSGLSG 454 (607)
T ss_pred ccCceEEEEEecCCceEEeehhheEEecccccccchhhhhhhhcCCCcccccccccCCCCCccccccccccccccccccC
Confidence 9999999999999999999999999853222 112111123344455666544444333322211 122334456666
Q ss_pred CcCCC
Q 000294 759 GASAG 763 (1711)
Q Consensus 759 g~s~~ 763 (1711)
.++.+
T Consensus 455 ~rTPg 459 (607)
T COG5164 455 YRTPG 459 (607)
T ss_pred CcCcC
Confidence 66555
No 3
>PRK08559 nusG transcription antitermination protein NusG; Validated
Probab=99.91 E-value=1.3e-23 Score=219.49 Aligned_cols=131 Identities=27% Similarity=0.446 Sum_probs=119.3
Q ss_pred CCCCcEEEEEeccchHHHHHHHHHHHHHhhccCCCCCcEEEEEEeCCCCcEEEEEeccchhHHHHhcCCCCeEecccccc
Q 000294 222 PEDPTIWKVKCMAGRERQSAFCLMQKFVDLQSLGSKMQIISAFAVDHIKGFIFIEADKQCDINEACKGLSGIYYSRLAPV 301 (1711)
Q Consensus 222 V~DPkLWaVKCk~GkEReVV~~LmrKii~lq~~g~~L~I~SVFvpd~lKGYIYIEA~kq~dVk~AIkGI~gVy~~k~~pV 301 (1711)
-+||+||+|+|++|+|+.|+.+|++|+... ++.|++||+|+.|||||||||++.++++++|+++++|++.-..+|
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 345999999999999999999999999999999999998655689
Q ss_pred CHHHHHHHhhcccccccccCCCEEEEecCcCCCCcEEEEEEeCCCCEEEEEEeccC
Q 000294 302 PKNEVSHLLSAQIKRNEVSEGTWAYVKNGKYKGDLAQVVYVNNARKRATVKLIPRI 357 (1711)
Q Consensus 302 PikEM~dLL~vkkk~~~Lk~GdwVRIKrGpYKGDLAQVveVdenk~eVtVKLIPRI 357 (1711)
+++||..+|........|.+|++|||++|||+|++|+|++|+.++..|+|+|+.|-
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 99999999986554567999999999999999999999999999999999999874
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=2.9e-22 Score=191.00 Aligned_cols=84 Identities=43% Similarity=0.727 Sum_probs=71.7
Q ss_pred cEEEEEeccchHHHHHHHHHHHHHhhccCCCCCcEEEEEEeCCCCcEEEEEeccchhHHHHhcCCCCeEeccccccCHHH
Q 000294 226 TIWKVKCMAGRERQSAFCLMQKFVDLQSLGSKMQIISAFAVDHIKGFIFIEADKQCDINEACKGLSGIYYSRLAPVPKNE 305 (1711)
Q Consensus 226 kLWaVKCk~GkEReVV~~LmrKii~lq~~g~~L~I~SVFvpd~lKGYIYIEA~kq~dVk~AIkGI~gVy~~k~~pVPikE 305 (1711)
+||+|||++|+|++||++||+|++++...+. +.|+|||+|+++||||||||+++.+|.+||++|++||...+.+||++|
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 899999999999999999999999999999999999999999999999
Q ss_pred HHHHh
Q 000294 306 VSHLL 310 (1711)
Q Consensus 306 M~dLL 310 (1711)
|++||
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
>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=99.81 E-value=2.9e-19 Score=184.52 Aligned_cols=124 Identities=23% Similarity=0.409 Sum_probs=110.6
Q ss_pred EEEEeccchHHHHHHHHHHHHHhhccCCCCCcEEEEEEeCCCCcEEEEEeccchhHHHHhcCCCCeEeccccccCHHHHH
Q 000294 228 WKVKCMAGRERQSAFCLMQKFVDLQSLGSKMQIISAFAVDHIKGFIFIEADKQCDINEACKGLSGIYYSRLAPVPKNEVS 307 (1711)
Q Consensus 228 WaVKCk~GkEReVV~~LmrKii~lq~~g~~L~I~SVFvpd~lKGYIYIEA~kq~dVk~AIkGI~gVy~~k~~pVPikEM~ 307 (1711)
|+|+|++|+|+.|+..|.+|+.. ..+.|+++|+|..||||||||+....+++++|+.+++|...-..+||.+||.
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 3466999999999999999999999999999999999988655679999999
Q ss_pred HHhhcccccccccCCCEEEEecCcCCCCcEEEEEEeCCCCEEEEEEecc
Q 000294 308 HLLSAQIKRNEVSEGTWAYVKNGKYKGDLAQVVYVNNARKRATVKLIPR 356 (1711)
Q Consensus 308 dLL~vkkk~~~Lk~GdwVRIKrGpYKGDLAQVveVdenk~eVtVKLIPR 356 (1711)
.||........|++|++|||++|||+|++|+|++++.++..|+|.|+-+
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 6
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=99.80 E-value=1e-15 Score=190.00 Aligned_cols=201 Identities=18% Similarity=0.211 Sum_probs=134.3
Q ss_pred cccccCceEEEcC----CceEEEEEEeccceEEEccCCCCCCceEEEecccccCCCCCCcccccccCCCcccCCCeEEEe
Q 000294 490 NSFELYELVCFGR----KDFGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVS 565 (1711)
Q Consensus 490 G~FeLgDLVQLD~----~TVGVIVrVEkDe~fkVLd~~gd~~~VvtVk~~~I~~K~~~rr~vAtD~~gk~I~vGD~VKVI 565 (1711)
..|+++|.|+|.. ...|+|++|+.+ .++|+....+++..+.|+ +.. +.|+|++|||||||
T Consensus 406 ~~F~~GD~VeV~~Gel~glkG~ve~vdg~-~vti~~~~e~l~~pl~~~--------------~~e-LrKyF~~GDhVKVi 469 (1024)
T KOG1999|consen 406 HLFSPGDAVEVIVGELKGLKGKVESVDGT-IVTIMSKHEDLKGPLEVP--------------ASE-LRKYFEPGDHVKVI 469 (1024)
T ss_pred cccCCCCeEEEeeeeeccceeEEEeccCc-eEEEeeccccCCCccccc--------------hHh-hhhhccCCCeEEEE
Confidence 4599999999943 467999999874 444443222222223333 222 58999999999999
Q ss_pred cCCCCCceEEEEEEECCEEEEEeCcceeeccEEEEeCCceeecccccccCCCCCCCCCCCCCCCCCCCC-----------
Q 000294 566 EGPSKDRQGIVKKIYRGILFIYDENETENGGYFCSKSQHCEKTKVEACEGKGGGSGASGFEEFPSSPKS----------- 634 (1711)
Q Consensus 566 dGp~kGRqG~VlHIyRs~VFL~Sr~~tENgGIFVvRarnv~tv~~~~~~~Kgg~~~~~~f~dl~~sp~~----------- 634 (1711)
.|+|+|.+|+|+.|++++|||+++.++|+..|||+.-.-|+.|.+. ..+.+ ...+.+|....+.
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 9999999999999999999999999999999999998888766541 11211 1222333221110
Q ss_pred -----CCCCC----cch--hhhccCccccC--CCCCCccccCCEEEEccCCCCCceeEEEEEeCCeEEEEecCCce----
Q 000294 635 -----PLSPK----RSW--QAREQNTEFKR--GDRDGMFAVGQTLRIRVGPLKGYLCRVLAVRYSDVTVKLDSQQK---- 697 (1711)
Q Consensus 635 -----~lsp~----rp~--~~~~~~~~~gR--GgRd~d~lIGKTVkIrkGPYKGylGiVKDaTdt~ARVELHSk~K---- 697 (1711)
.|.+. ++. ...... ++.- -.......|+.+|+++.||.||-.|.|+.+....+. ||+++-
T Consensus 545 ~~~vl~~~g~v~~i~~~~i~~kk~~-r~~~~~D~~~n~I~~kD~Vkvi~Gp~~g~~G~v~~i~r~~~F--~h~r~~~En~ 621 (1024)
T KOG1999|consen 545 TFQVLGMNGKVVTIRKSSITKKKDN-RKAVAVDRNGNEIRVKDTVKVIGGPSKGREGEVLHIYRPFVF--LHSRKNLENG 621 (1024)
T ss_pred heeeecCcCceEEEeechhhhhhhh-hhheeecccCCeecccceEEEecCCCCCccCccceeecceee--eeehhhcccC
Confidence 00000 000 000000 1100 012234678999999999999999999999999988 887775
Q ss_pred -EEEEeCCccccccCCcc
Q 000294 698 -ILTVKGEHLAEVRGKSF 714 (1711)
Q Consensus 698 -tITVdK~~Ls~v~~~~~ 714 (1711)
++.+...+|.++.++.+
T Consensus 622 Gv~vck~k~~~~~g~~~s 639 (1024)
T KOG1999|consen 622 GVFVCKEKNLILAGGKKS 639 (1024)
T ss_pred CeEEEecCCceeccccCc
Confidence 67788888888766543
No 7
>COG0250 NusG Transcription antiterminator [Transcription]
Probab=99.73 E-value=1.9e-17 Score=177.59 Aligned_cols=133 Identities=17% Similarity=0.233 Sum_probs=110.1
Q ss_pred CCcEEEEEeccchHHHHHHHHHHHHHhhccCCC------C-C-------cEEEEEEeCCCCcEEEEEeccchhHHHHhcC
Q 000294 224 DPTIWKVKCMAGRERQSAFCLMQKFVDLQSLGS------K-M-------QIISAFAVDHIKGFIFIEADKQCDINEACKG 289 (1711)
Q Consensus 224 DPkLWaVKCk~GkEReVV~~LmrKii~lq~~g~------~-L-------~I~SVFvpd~lKGYIYIEA~kq~dVk~AIkG 289 (1711)
.++||+|+|++|+|+.|+..|++++..+..... | . ..+.++.++.|||||||||.+.++++++|+.
T Consensus 2 ~~~Wyvv~~~sg~E~~V~~~l~~~~~~~~~~~~~~~v~vp~E~v~e~~~~~~~~~e~~~fpGYVlVem~~~~~~w~~Vr~ 81 (178)
T COG0250 2 MKRWYVVQTYSGQEKKVKENLERKAELLGMEDLIFEVLVPTEEVVEVKGKRKVIVERKLFPGYVLVEMDMTDEAWHLVRN 81 (178)
T ss_pred CceEEEEEeeccHHHHHHHHHHHHHHhcCCccceeeEEeceEEEEEecCceEEEEecccCCcEEEEEEEcCCceEEEEec
Confidence 578999999999999999999999988764311 0 0 2344477889999999999999999999999
Q ss_pred CCCeEe------ccccccCHHHHHHHhhcc-------cccccccCCCEEEEecCcCCCCcEEEEEEeCCCCE--EEEEEe
Q 000294 290 LSGIYY------SRLAPVPKNEVSHLLSAQ-------IKRNEVSEGTWAYVKNGKYKGDLAQVVYVNNARKR--ATVKLI 354 (1711)
Q Consensus 290 I~gVy~------~k~~pVPikEM~dLL~vk-------kk~~~Lk~GdwVRIKrGpYKGDLAQVveVdenk~e--VtVKLI 354 (1711)
+|+|.+ .+|.+|+.+||.++|... +..+.|++|+.|||+.|||+++.|+|.+||.++.+ |.|.++
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 478999999999966522 23578999999999999999999999999999875 555555
Q ss_pred cc
Q 000294 355 PR 356 (1711)
Q Consensus 355 PR 356 (1711)
.|
T Consensus 162 gr 163 (178)
T COG0250 162 GR 163 (178)
T ss_pred CC
Confidence 55
No 8
>PRK05609 nusG transcription antitermination protein NusG; Validated
Probab=99.57 E-value=3.2e-14 Score=151.14 Aligned_cols=130 Identities=16% Similarity=0.233 Sum_probs=102.9
Q ss_pred CCcEEEEEeccchHHHHHHHHHHHHHhhccCCCCCcEEEEEEe-----------------CCCCcEEEEEeccchhHHHH
Q 000294 224 DPTIWKVKCMAGRERQSAFCLMQKFVDLQSLGSKMQIISAFAV-----------------DHIKGFIFIEADKQCDINEA 286 (1711)
Q Consensus 224 DPkLWaVKCk~GkEReVV~~LmrKii~lq~~g~~L~I~SVFvp-----------------d~lKGYIYIEA~kq~dVk~A 286 (1711)
+.+||+|+|++|+|+.|+..|.+++.... -...++.+|+| +.|||||||+++....+...
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 11114455555 46999999999988888889
Q ss_pred hcCCCCeEe------ccccccCHHHHHHHhhc-c------cccccccCCCEEEEecCcCCCCcEEEEEEeCCCC--EEEE
Q 000294 287 CKGLSGIYY------SRLAPVPKNEVSHLLSA-Q------IKRNEVSEGTWAYVKNGKYKGDLAQVVYVNNARK--RATV 351 (1711)
Q Consensus 287 IkGI~gVy~------~k~~pVPikEM~dLL~v-k------kk~~~Lk~GdwVRIKrGpYKGDLAQVveVdenk~--eVtV 351 (1711)
|+.+++|.. .+|.+||.+||..|+.. . .....|++|+.|||+.|||+|..|+|++|+..+. .|.|
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 999988742 36889999999999873 1 1235688999999999999999999999996665 5667
Q ss_pred EEecc
Q 000294 352 KLIPR 356 (1711)
Q Consensus 352 KLIPR 356 (1711)
.|+.|
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=99.57 E-value=2.1e-14 Score=160.87 Aligned_cols=129 Identities=13% Similarity=0.213 Sum_probs=104.2
Q ss_pred cEEEEEeccchHHHHHHHHHHHHHhhccCCCCCcEEEEEEe---------------------------------------
Q 000294 226 TIWKVKCMAGRERQSAFCLMQKFVDLQSLGSKMQIISAFAV--------------------------------------- 266 (1711)
Q Consensus 226 kLWaVKCk~GkEReVV~~LmrKii~lq~~g~~L~I~SVFvp--------------------------------------- 266 (1711)
+||+|+|++|+|..|+..|++|+..+.. ...|+.|++|
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 5999999999999999999999988653 2234444433
Q ss_pred ------CCCCcEEEEEeccchhHHHHhcCCCCeEe--------ccccccCHHHH-HHHhhccc-----------------
Q 000294 267 ------DHIKGFIFIEADKQCDINEACKGLSGIYY--------SRLAPVPKNEV-SHLLSAQI----------------- 314 (1711)
Q Consensus 267 ------d~lKGYIYIEA~kq~dVk~AIkGI~gVy~--------~k~~pVPikEM-~dLL~vkk----------------- 314 (1711)
..|||||||+|.+.++++++|+.+++|.+ .+|+||+.+|+ .+||....
T Consensus 78 ~k~~er~~fPGYI~IkM~m~d~~W~~VRnt~gVTGFvGssg~g~kPiPls~~e~~~~ml~~~~~~~~~~~~~~~~~~~~~ 157 (258)
T TIGR01956 78 TKISEKNKYNGYIYIKMIMTEDAWFLIRNTENVTGLVGSSGKGAKPIPISADADKLKMLKGISENTKKRVLVTNTAIVEM 157 (258)
T ss_pred EEEEEeeecCcEEEEEEEecccHhhheecCCCCCeecCCCCCCCCCcCCCHHHHHHHHhhhhhhcccccccccccccccc
Confidence 46999999999999999999999999864 26999999888 78875211
Q ss_pred --------------------------------------------ccccccCCCEEEEecCcCCCCcEEEEEEeCCCC--E
Q 000294 315 --------------------------------------------KRNEVSEGTWAYVKNGKYKGDLAQVVYVNNARK--R 348 (1711)
Q Consensus 315 --------------------------------------------k~~~Lk~GdwVRIKrGpYKGDLAQVveVdenk~--e 348 (1711)
..+.|++|+.|||+.|||+|..|+|++|+..+. .
T Consensus 158 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~vGd~VrI~dGPF~GfeG~I~eid~~k~Rv~ 237 (258)
T TIGR01956 158 EENKFDEKCQYILKHKQVKPEAIAQVSESGEIIDEIVEEFQLVDNLSKFRVGNFVKIVDGPFKGIVGKIKKIDQEKKKAI 237 (258)
T ss_pred cccccccccccccccccccccccccccccccccccccccccccccccCCCCCCEEEEEecCCCCcEEEEEEEeCCCCEEE
Confidence 124578999999999999999999999996555 5
Q ss_pred EEEEEeccC
Q 000294 349 ATVKLIPRI 357 (1711)
Q Consensus 349 VtVKLIPRI 357 (1711)
|.|.|+.|.
T Consensus 238 VlV~IfGR~ 246 (258)
T TIGR01956 238 VEVEILGKS 246 (258)
T ss_pred EEEEecCCc
Confidence 777777763
No 10
>TIGR00922 nusG transcription termination/antitermination factor NusG. Archaeal proteins once termed NusG share the KOW domain but are actually a ribosomal protein corresponding to L24p in bacterial and L26e in eukaryotes (TIGR00405).
Probab=99.52 E-value=1e-13 Score=146.64 Aligned_cols=127 Identities=17% Similarity=0.212 Sum_probs=99.8
Q ss_pred EEEEEeccchHHHHHHHHHHHHHhhccCCCCCcEEEEEEe-----------------CCCCcEEEEEeccchhHHHHhcC
Q 000294 227 IWKVKCMAGRERQSAFCLMQKFVDLQSLGSKMQIISAFAV-----------------DHIKGFIFIEADKQCDINEACKG 289 (1711)
Q Consensus 227 LWaVKCk~GkEReVV~~LmrKii~lq~~g~~L~I~SVFvp-----------------d~lKGYIYIEA~kq~dVk~AIkG 289 (1711)
||+|+|++|+|+.|+..|.+++..+. -+..++.+|+| +.|||||||++....+....|..
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 58999999999988888888999
Q ss_pred CCCeEe-----ccccccCH-HHHHHHhhccc-------ccccccCCCEEEEecCcCCCCcEEEEEEeCCCC--EEEEEEe
Q 000294 290 LSGIYY-----SRLAPVPK-NEVSHLLSAQI-------KRNEVSEGTWAYVKNGKYKGDLAQVVYVNNARK--RATVKLI 354 (1711)
Q Consensus 290 I~gVy~-----~k~~pVPi-kEM~dLL~vkk-------k~~~Lk~GdwVRIKrGpYKGDLAQVveVdenk~--eVtVKLI 354 (1711)
+++|.. .+|.+||. +||..|+.... ....|++|+.|||+.|||+|..|.|++|+..+. .|.|.|+
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 998754 36899999 99999986421 123488999999999999999999999986555 5666777
Q ss_pred cc
Q 000294 355 PR 356 (1711)
Q Consensus 355 PR 356 (1711)
.|
T Consensus 158 g~ 159 (172)
T TIGR00922 158 GR 159 (172)
T ss_pred CC
Confidence 76
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=99.49 E-value=5.6e-15 Score=144.96 Aligned_cols=92 Identities=27% Similarity=0.452 Sum_probs=57.2
Q ss_pred ccccccccCCCCCchhhcCCCcCCCCCCCCcc--chhhhhccCccccccccccCCCC-CCCccccCCHHHHHHHHH--HH
Q 000294 119 FVEDAADVDYDDDDEEEVGNESDNSGGFADDD--FMEELFDAQPKVNNEMGQAHNLP-FIPKEEEMDEEEFDKMME--ER 193 (1711)
Q Consensus 119 FiDdEAEVDDDeEeEDEeeEe~e~~~~Fi~dD--~~~d~~e~~~~~~~d~r~~~~l~-~r~~eed~DaEelAe~lk--ER 193 (1711)
|||+||+||||+|||||++++. .||... +.++. . ...+.++|+.++ +++++++|++|+||++|+ +|
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 111233344444 458889999999999999 99
Q ss_pred hccccchhhchhhHHHhhhcccccCCC
Q 000294 194 YKSNKLIRYAEEDYEAKKMLEREYHMP 220 (1711)
Q Consensus 194 Y~r~s~~~y~~d~~e~~~~VpQq~LLP 220 (1711)
|++++...+... .+...+||||+|||
T Consensus 72 Y~~~~~~~~~~~-~~~~~~v~q~~LLP 97 (97)
T PF11942_consen 72 YARSSESRYDGD-DEDSDEVPQQLLLP 97 (97)
T ss_pred hccccccccccc-ccccccchHhccCc
Confidence 998641112111 12347899999999
No 12
>COG5164 SPT5 Transcription elongation factor [Transcription]
Probab=99.47 E-value=1.3e-14 Score=169.20 Aligned_cols=337 Identities=21% Similarity=0.261 Sum_probs=204.4
Q ss_pred cccccCCCCCCCCcEEEEEeccchHHHHHHHHHHHHHhhccCCCCCcEEEEEEeCCCCcEEEEEeccchhHH----HHhc
Q 000294 213 LEREYHMPCPEDPTIWKVKCMAGRERQSAFCLMQKFVDLQSLGSKMQIISAFAVDHIKGFIFIEADKQCDIN----EACK 288 (1711)
Q Consensus 213 VpQq~LLPSV~DPkLWaVKCk~GkEReVV~~LmrKii~lq~~g~~L~I~SVFvpd~lKGYIYIEA~kq~dVk----~AIk 288 (1711)
.+|.+|.|.-+-+..|+||++...|+++.+.+ . +..++.++++.+-+ |+.|.|+|+.+..|+. ++|+
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 67888999999999999999999999875432 2 33566777777765 9999999999999999 8888
Q ss_pred CCCCeEeccccccC-HHHHHHHhhcccccccccCCCEEEEecCcCCCCcEEEEEEeCCCCEEEEEEeccCchhhHHhhcC
Q 000294 289 GLSGIYYSRLAPVP-KNEVSHLLSAQIKRNEVSEGTWAYVKNGKYKGDLAQVVYVNNARKRATVKLIPRIDLQALAAKFG 367 (1711)
Q Consensus 289 GI~gVy~~k~~pVP-ikEM~dLL~vkkk~~~Lk~GdwVRIKrGpYKGDLAQVveVdenk~eVtVKLIPRIDy~~l~~k~~ 367 (1711)
=++++-....-.|| .+||...|...- ..-..+-|-||+.+.|+||+++|++= +.++.+.||||||-..
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 88887665555666 677766665431 12235678888889999999888864 5678889999998431
Q ss_pred CCcccCCCCCCCCCCCChhhHhhhcCceeecc---cCCCCceEEecCCceeecceEEEEEeccceEecCCCCCHHHHhhc
Q 000294 368 GGVAMKKTDSPAPRLISPSELEEFRPLIQYRR---DRDTGKVFENLDGMMLKDGYLYKKVSIDSLSCWGVVPSEEELLKF 444 (1711)
Q Consensus 368 gg~~kKK~~RPPqRLFn~~Eark~~~~~~~rr---d~~tg~~f~i~~G~~y~DGFLyK~fkI~sL~t~dVnPTLEEL~kF 444 (1711)
.+|+++....- ..+..+. ..++.-+-++|.-..|+++||.|..-|.+|-. ||.|++|||.+|
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 35666543210 0111111 01122233467778999999999999988865 899999999999
Q ss_pred CCCCCCccccHHHHH--HHH-----hccccccEEEeecCCCcccccCCCCcCcccccCceEEEcCCceEEEEEEeccceE
Q 000294 445 QPSESNESADLEWLS--QLY-----GERKKKRTTIVGKGGDKGEGSSGSSLENSFELYELVCFGRKDFGLIVGMEKDDHY 517 (1711)
Q Consensus 445 ~~~~~de~~DL~~La--~~~-----ge~kk~kii~v~kGg~kgE~ssG~~s~G~FeLgDLVQLD~~TVGVIVrVEkDe~f 517 (1711)
.....-...+-...+ +++ +.+.+..+.++++.+.+.|+.+- -...+|.++-.|.| ...-||+|.++.+ ..
T Consensus 233 ~t~~~~sI~~kv~~~Rg~~i~~d~ng~eI~igd~VvE~~g~~~egq~l-~i~~~f~f~~t~~i-~ennGVfv~~~~n-v~ 309 (607)
T COG5164 233 HTACPISIGDKVRVTRGELIGMDGNGREISIGDAVVESRGGKFEGQSL-GIVKHFDFGETVSI-KENNGVFVKIEGN-VC 309 (607)
T ss_pred eEecchhhhhhhecccceeEeeccccceEeeceeEEEecCCceeeEEE-EEEEEEeeeeeeee-eccCceEEEecCc-ee
Confidence 754221111110000 000 11111111122333333332210 11224444444433 3456899998875 22
Q ss_pred EEcc-CCCCCCceEEEecc----cccCCCCCCccccccc--CCCcccCCCeEEEecCCCCCceEEEEEEECCEE--EEEe
Q 000294 518 KILK-EGSEGPAVVTVERR----TLKNGPFDMKFTALDQ--SMKVISLNDTARVSEGPSKDRQGIVKKIYRGIL--FIYD 588 (1711)
Q Consensus 518 kVLd-~~gd~~~VvtVk~~----~I~~K~~~rr~vAtD~--~gk~I~vGD~VKVIdGp~kGRqG~VlHIyRs~V--FL~S 588 (1711)
.|-. ..-. -+.|.+. .|..++...+...+.+ -+....+|-+|+|-.|+|||.-|+|+.+.++.+ -||+
T Consensus 310 ~VAtkd~~~---s~k~dl~kmnp~v~~~~~~p~~~~l~r~i~gRd~aigktVrIr~g~yKG~lGVVKdv~~~~arVeLhs 386 (607)
T COG5164 310 IVATKDFTE---SLKVDLDKMNPPVTVNLQNPKTNELERKIVGRDPAIGKTVRIRCGEYKGHLGVVKDVDRNIARVELHS 386 (607)
T ss_pred EEEeccchh---hhcccHhhcCchhhcCCCCCcchhhhccccccccccCceEEEeecccccccceeeeccCceEEEEEec
Confidence 2222 2210 1111111 1122221111101110 245568999999999999999999999999964 5555
Q ss_pred Cc
Q 000294 589 EN 590 (1711)
Q Consensus 589 r~ 590 (1711)
..
T Consensus 387 ~n 388 (607)
T COG5164 387 NN 388 (607)
T ss_pred CC
Confidence 44
No 13
>PRK09014 rfaH transcriptional activator RfaH; Provisional
Probab=99.31 E-value=6.3e-12 Score=132.23 Aligned_cols=126 Identities=15% Similarity=0.206 Sum_probs=91.7
Q ss_pred cEEEEEeccchHHHHHHHHHHHHHhhccCCCCC--------cEEEEEEeCCCCcEEEEEeccchhHHHHhcCCCCeEe--
Q 000294 226 TIWKVKCMAGRERQSAFCLMQKFVDLQSLGSKM--------QIISAFAVDHIKGFIFIEADKQCDINEACKGLSGIYY-- 295 (1711)
Q Consensus 226 kLWaVKCk~GkEReVV~~LmrKii~lq~~g~~L--------~I~SVFvpd~lKGYIYIEA~kq~dVk~AIkGI~gVy~-- 295 (1711)
+||+|+|++++|+.++..|.++-++.- .|+ .-......+.|||||||++..+......|+.+++|..
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 111 0112223368999999999876655566777777632
Q ss_pred ---ccccccCHHHHHHHhhccc----ccccccCCCEEEEecCcCCCCcEEEEEEeCCCCE--EEEEEec
Q 000294 296 ---SRLAPVPKNEVSHLLSAQI----KRNEVSEGTWAYVKNGKYKGDLAQVVYVNNARKR--ATVKLIP 355 (1711)
Q Consensus 296 ---~k~~pVPikEM~dLL~vkk----k~~~Lk~GdwVRIKrGpYKGDLAQVveVdenk~e--VtVKLIP 355 (1711)
.+|.+||.+||..|+.... ....+++|+.|||+.|||+|.+|.|++++. +.+ |.|.|+.
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 5555554
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=99.28 E-value=1.4e-11 Score=128.74 Aligned_cols=128 Identities=17% Similarity=0.241 Sum_probs=92.6
Q ss_pred EEEEEeccchHHHHHHHHHHHHHhhccCCCCC--------cEEEEEEeCCCCcEEEEEeccchhHHHHhcCCCCeEe---
Q 000294 227 IWKVKCMAGRERQSAFCLMQKFVDLQSLGSKM--------QIISAFAVDHIKGFIFIEADKQCDINEACKGLSGIYY--- 295 (1711)
Q Consensus 227 LWaVKCk~GkEReVV~~LmrKii~lq~~g~~L--------~I~SVFvpd~lKGYIYIEA~kq~dVk~AIkGI~gVy~--- 295 (1711)
||+|+|++++|+.++..|.++-++.- .|+ .-...+..+.|||||||+++...+....|..+++|..
T Consensus 1 WYvl~~~~~~E~~v~~~L~~~gi~~~---~P~~~~~~~~~g~~~~~~~plfpgYvFv~~~~~~~~~~~i~~~~gv~~~v~ 77 (159)
T TIGR01955 1 WYLLYCKPRQEQRAQEHLERQAVECY---LPMITVEKIVRGKRQAVSEPLFPNYLFIEFDPEVDSWTTIRSTRGVSRFVR 77 (159)
T ss_pred CEEEEEcCchHHHHHHHHHHCCCEEE---ccCEEEEEEECCcEEEEEEecCCCeEEEEEccCCCceEEEecCCCcCEEEC
Confidence 89999999999999998877532210 111 0112334468999999999877666666666666532
Q ss_pred --ccccccCHHHHHHHhhccc------ccccccCCCEEEEecCcCCCCcEEEEEEeCCCC-EEEEEEeccC
Q 000294 296 --SRLAPVPKNEVSHLLSAQI------KRNEVSEGTWAYVKNGKYKGDLAQVVYVNNARK-RATVKLIPRI 357 (1711)
Q Consensus 296 --~k~~pVPikEM~dLL~vkk------k~~~Lk~GdwVRIKrGpYKGDLAQVveVdenk~-eVtVKLIPRI 357 (1711)
.+|.+||.+||..|+.... ....|++|+.|||+.|||+|..|.|++++..+. .|.|.|+.|.
T Consensus 78 ~~~~p~~I~~~~i~~l~~~~~~~~~~~~~~~~~~G~~V~V~~GPf~g~~g~v~~~~~~~r~~v~l~~~gr~ 148 (159)
T TIGR01955 78 FGGHPAPVPDDLIHQLRQYEPKDSVPPATTLPYKGDKVRITDGAFAGFEAIFLEPDGEKRSMLLLNMIGKQ 148 (159)
T ss_pred CCCCcccCCHHHHHHHHhccccccCCccccCCCCCCEEEEeccCCCCcEEEEEEECCCceEEEEEhhhCCc
Confidence 4799999999998875421 124588999999999999999999999984431 3555666653
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=99.19 E-value=6e-11 Score=115.62 Aligned_cols=83 Identities=28% Similarity=0.464 Sum_probs=71.0
Q ss_pred cEEEEEeccchHHHHHHHHHHHHHhhccCCCCCcEEEEEEe-----------------CCCCcEEEEEeccchhHHHHhc
Q 000294 226 TIWKVKCMAGRERQSAFCLMQKFVDLQSLGSKMQIISAFAV-----------------DHIKGFIFIEADKQCDINEACK 288 (1711)
Q Consensus 226 kLWaVKCk~GkEReVV~~LmrKii~lq~~g~~L~I~SVFvp-----------------d~lKGYIYIEA~kq~dVk~AIk 288 (1711)
+||+|+|++|+|++|+..|++++.++. .+..++++|+| +.|||||||+++...++..+|+
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 4688999999999999999999
Q ss_pred CCCCeEe-----ccccccCHHHHHHHhh
Q 000294 289 GLSGIYY-----SRLAPVPKNEVSHLLS 311 (1711)
Q Consensus 289 GI~gVy~-----~k~~pVPikEM~dLL~ 311 (1711)
.+++|+. .+|.+||.+||.+|++
T Consensus 78 ~~~~v~~~v~~~~~p~~v~~~e~~~l~~ 105 (106)
T smart00738 78 GTPGVRGFVGGGGKPTPVPDDEIEKILK 105 (106)
T ss_pred cCCCccEECCCCCeeeECCHHHHHHHhh
Confidence 9999864 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=97.83 E-value=2.4e-05 Score=75.39 Aligned_cols=76 Identities=16% Similarity=0.319 Sum_probs=51.6
Q ss_pred cEEEEEeccchHHHHHHHHHHH-HHhhccC----CC---CC-cEEEEEEeCCCCcEEEEEeccchhHHHHhcCCCCeEe-
Q 000294 226 TIWKVKCMAGRERQSAFCLMQK-FVDLQSL----GS---KM-QIISAFAVDHIKGFIFIEADKQCDINEACKGLSGIYY- 295 (1711)
Q Consensus 226 kLWaVKCk~GkEReVV~~LmrK-ii~lq~~----g~---~L-~I~SVFvpd~lKGYIYIEA~kq~dVk~AIkGI~gVy~- 295 (1711)
+||+|+|++++|..|+..|.++ +..+-.. .. .- .+.. ...+.|||||||++...+++ ..|+.+++|+.
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 6999999999999999999555 4332200 00 11 3444 45579999999999998665 44488888764
Q ss_pred ----ccccccCH
Q 000294 296 ----SRLAPVPK 303 (1711)
Q Consensus 296 ----~k~~pVPi 303 (1711)
.+|++||.
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 46777774
No 17
>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]
Probab=97.41 E-value=0.00059 Score=87.13 Aligned_cols=11 Identities=36% Similarity=0.036 Sum_probs=5.5
Q ss_pred eecCccccccC
Q 000294 71 IVCDPEMATDK 81 (1711)
Q Consensus 71 ~~~~~~~~~~~ 81 (1711)
-..|-|||++-
T Consensus 92 ~l~~~~~a~~~ 102 (1282)
T KOG0921|consen 92 TWQDSETATMF 102 (1282)
T ss_pred ccccccccccc
Confidence 34455555543
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=97.27 E-value=0.00034 Score=56.75 Aligned_cols=32 Identities=28% Similarity=0.532 Sum_probs=30.0
Q ss_pred CCCEEEEecCcCCCCcEEEEEEeCCCCEEEEE
Q 000294 321 EGTWAYVKNGKYKGDLAQVVYVNNARKRATVK 352 (1711)
Q Consensus 321 ~GdwVRIKrGpYKGDLAQVveVdenk~eVtVK 352 (1711)
+|++|+|++|||+|..|+|++|+.++.+|+|+
T Consensus 1 ~Gd~V~V~~G~~~G~~G~I~~i~~~~~~V~ve 32 (32)
T PF00467_consen 1 VGDTVKVISGPFKGKIGKIVEIDRSKVRVTVE 32 (32)
T ss_dssp TTSEEEESSSTTTTEEEEEEEEETTTTEEEES
T ss_pred CCCEEEEeEcCCCCceEEEEEEECCCCEEEEC
Confidence 69999999999999999999999999888873
No 19
>PF00467 KOW: KOW motif; InterPro: IPR005824 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The KOW (Kyprides, Ouzounis, Woese) motif is found in a variety of ribosomal proteins and the bacterial transcription antitermination proteins NusG []. ; PDB: 3BBO_W 2HGJ_X 2HGQ_X 2HGU_X 1NPP_B 1M1G_D 1NPR_A 2XHC_A 2KVQ_G 2JVV_A ....
Probab=97.10 E-value=0.00064 Score=55.15 Aligned_cols=32 Identities=31% Similarity=0.675 Sum_probs=28.8
Q ss_pred cCCEEEEccCCCCCceeEEEEEeCCeEEEEec
Q 000294 662 VGQTLRIRVGPLKGYLCRVLAVRYSDVTVKLD 693 (1711)
Q Consensus 662 IGKTVkIrkGPYKGylGiVKDaTdt~ARVELH 693 (1711)
.|++|+|+.|||||+.|+|+++....+||.++
T Consensus 1 ~Gd~V~V~~G~~~G~~G~I~~i~~~~~~V~ve 32 (32)
T PF00467_consen 1 VGDTVKVISGPFKGKIGKIVEIDRSKVRVTVE 32 (32)
T ss_dssp TTSEEEESSSTTTTEEEEEEEEETTTTEEEES
T ss_pred CCCEEEEeEcCCCCceEEEEEEECCCCEEEEC
Confidence 37899999999999999999999998887764
No 20
>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]
Probab=97.00 E-value=0.0029 Score=81.20 Aligned_cols=15 Identities=40% Similarity=0.727 Sum_probs=6.4
Q ss_pred CCCCCCCCCCCCCCC
Q 000294 1517 GGRGRGRRDQGGGWN 1531 (1711)
Q Consensus 1517 ggrg~~~~~~~g~~~ 1531 (1711)
++.+.+.++++|+|.
T Consensus 1266 ggGgfg~G~~Gg~~~ 1280 (1282)
T KOG0921|consen 1266 GGGGFGGGGRGGNAS 1280 (1282)
T ss_pred CCCCCCCCCcccccc
Confidence 333334444444444
No 21
>KOG3973 consensus Uncharacterized conserved glycine-rich protein [Function unknown]
Probab=96.83 E-value=0.0037 Score=73.40 Aligned_cols=9 Identities=22% Similarity=0.313 Sum_probs=4.5
Q ss_pred EEEeccCch
Q 000294 351 VKLIPRIDL 359 (1711)
Q Consensus 351 VKLIPRIDy 359 (1711)
++|+|-||-
T Consensus 139 ~ev~q~i~~ 147 (465)
T KOG3973|consen 139 LEVTQLIDS 147 (465)
T ss_pred chHHHHHHH
Confidence 445555553
No 22
>TIGR00405 L26e_arch ribosomal protein L24p/L26e, archaeal. This protein contains a KOW domain, shared by bacterial NusG and the L24p/L26e family of ribosomal proteins. Although called archaeal NusG in several publications, it is the only close homolog of eukaryotic L26e in archaeal genomes, shares an operon with L11 in many genomes, and has been sequenced from purified ribosomes. It is here designated as a ribosomal protein for these reasons.
Probab=95.58 E-value=0.018 Score=60.57 Aligned_cols=50 Identities=30% Similarity=0.468 Sum_probs=43.7
Q ss_pred cccCCEEEEccCCCCCceeEEEEEe--CCeEEEEecCCceE--EEEeCCccccc
Q 000294 660 FAVGQTLRIRVGPLKGYLCRVLAVR--YSDVTVKLDSQQKI--LTVKGEHLAEV 709 (1711)
Q Consensus 660 ~lIGKTVkIrkGPYKGylGiVKDaT--dt~ARVELHSk~Kt--ITVdK~~Ls~v 709 (1711)
..+|+.|+|+.|||||+.|+|+++. ...|+|+|...... |+|+-+.|..+
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 66888998888888 99998888754
No 23
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=95.36 E-value=0.022 Score=43.94 Aligned_cols=27 Identities=33% Similarity=0.464 Sum_probs=25.0
Q ss_pred cccCCCeEEEecCCCCCceEEEEEEEC
Q 000294 555 VISLNDTARVSEGPSKDRQGIVKKIYR 581 (1711)
Q Consensus 555 ~I~vGD~VKVIdGp~kGRqG~VlHIyR 581 (1711)
.|++||.|+|+.|+++|+.|+|++|.+
T Consensus 1 ~~~~G~~V~I~~G~~~g~~g~i~~i~~ 27 (28)
T smart00739 1 KFEVGDTVRVIAGPFKGKVGKVLEVDG 27 (28)
T ss_pred CCCCCCEEEEeECCCCCcEEEEEEEcC
Confidence 378999999999999999999999975
No 24
>PRK08559 nusG transcription antitermination protein NusG; Validated
Probab=95.10 E-value=0.042 Score=58.89 Aligned_cols=51 Identities=31% Similarity=0.494 Sum_probs=43.4
Q ss_pred cccCCEEEEccCCCCCceeEEEEEe--CCeEEEEecCCceE--EEEeCCcccccc
Q 000294 660 FAVGQTLRIRVGPLKGYLCRVLAVR--YSDVTVKLDSQQKI--LTVKGEHLAEVR 710 (1711)
Q Consensus 660 ~lIGKTVkIrkGPYKGylGiVKDaT--dt~ARVELHSk~Kt--ITVdK~~Ls~v~ 710 (1711)
+.+|+.|+|+.|||+|+.|+|+++. ...|+|+|-.+... |||+-+.|.++.
T Consensus 95 ~~~G~~V~I~~Gpf~g~~g~V~~vd~~k~~v~v~ll~~~~~~pv~v~~~~~~~~~ 149 (153)
T PRK08559 95 IKEGDIVELIAGPFKGEKARVVRVDESKEEVTVELLEAAVPIPVTVRGDQVRVVK 149 (153)
T ss_pred CCCCCEEEEeccCCCCceEEEEEEcCCCCEEEEEEECCcceeeEEEeccEEEEec
Confidence 6789999999999999999999996 55677777777755 999999998753
No 25
>KOG3262 consensus H/ACA small nucleolar RNP component GAR1 [Translation, ribosomal structure and biogenesis]
Probab=94.65 E-value=0.063 Score=59.29 Aligned_cols=17 Identities=59% Similarity=1.187 Sum_probs=9.2
Q ss_pred CCCCCCCCCcC-CCCCCC
Q 000294 1207 DGGRGSGGRWG-QGGGQG 1223 (1711)
Q Consensus 1207 ~~~~~~~~~~~-~~~~~~ 1223 (1711)
++|.|.+++.| |+++++
T Consensus 5 rgggg~~g~~gfRgg~gg 22 (215)
T KOG3262|consen 5 RGGGGGGGGGGFRGGGGG 22 (215)
T ss_pred cCCCCCCCCCCcccCCCC
Confidence 35666666666 444333
No 26
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=94.55 E-value=0.049 Score=41.98 Aligned_cols=27 Identities=26% Similarity=0.442 Sum_probs=24.8
Q ss_pred cccCCCEEEEecCcCCCCcEEEEEEeC
Q 000294 318 EVSEGTWAYVKNGKYKGDLAQVVYVNN 344 (1711)
Q Consensus 318 ~Lk~GdwVRIKrGpYKGDLAQVveVde 344 (1711)
.|++|+.|+|+.|+|+|..|.|++|+.
T Consensus 1 ~~~~G~~V~I~~G~~~g~~g~i~~i~~ 27 (28)
T smart00739 1 KFEVGDTVRVIAGPFKGKVGKVLEVDG 27 (28)
T ss_pred CCCCCCEEEEeECCCCCcEEEEEEEcC
Confidence 368999999999999999999999975
No 27
>CHL00141 rpl24 ribosomal protein L24; Validated
Probab=94.12 E-value=0.073 Score=52.38 Aligned_cols=28 Identities=29% Similarity=0.487 Sum_probs=26.7
Q ss_pred cccCCCeEEEecCCCCCceEEEEEEECC
Q 000294 555 VISLNDTARVSEGPSKDRQGIVKKIYRG 582 (1711)
Q Consensus 555 ~I~vGD~VKVIdGp~kGRqG~VlHIyRs 582 (1711)
.|+.||.|.||.|+++|++|+|++|++.
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
>PRK01191 rpl24p 50S ribosomal protein L24P; Validated
Probab=94.08 E-value=0.11 Score=54.44 Aligned_cols=50 Identities=26% Similarity=0.326 Sum_probs=41.1
Q ss_pred HHHHHHhhcccccccccCCCEEEEecCcCCCCcEEEEEEeCCCCEEEEEEec
Q 000294 304 NEVSHLLSAQIKRNEVSEGTWAYVKNGKYKGDLAQVVYVNNARKRATVKLIP 355 (1711)
Q Consensus 304 kEM~dLL~vkkk~~~Lk~GdwVRIKrGpYKGDLAQVveVdenk~eVtVKLIP 355 (1711)
+|+...+.+. ...|+.||.|.|+.|+|||-.|+|+.|+..+.+|+|+=|=
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 4555544443 4689999999999999999999999999999999997543
No 29
>PRK12281 rplX 50S ribosomal protein L24; Reviewed
Probab=94.04 E-value=0.077 Score=51.45 Aligned_cols=28 Identities=21% Similarity=0.325 Sum_probs=26.4
Q ss_pred cccCCCeEEEecCCCCCceEEEEEEECC
Q 000294 555 VISLNDTARVSEGPSKDRQGIVKKIYRG 582 (1711)
Q Consensus 555 ~I~vGD~VKVIdGp~kGRqG~VlHIyRs 582 (1711)
.|+.||.|.||.|+++|++|+|+.|++.
T Consensus 6 ~I~kGD~V~Vi~G~dKGK~G~V~~V~~~ 33 (76)
T PRK12281 6 KVKKGDMVKVIAGDDKGKTGKVLAVLPK 33 (76)
T ss_pred cccCCCEEEEeEcCCCCcEEEEEEEEcC
Confidence 6899999999999999999999999874
No 30
>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=93.91 E-value=0.095 Score=55.57 Aligned_cols=42 Identities=21% Similarity=0.236 Sum_probs=34.9
Q ss_pred cccCCEEEEccCCCCCceeEEEEEe-CCeEEEEecCCceEEEE
Q 000294 660 FAVGQTLRIRVGPLKGYLCRVLAVR-YSDVTVKLDSQQKILTV 701 (1711)
Q Consensus 660 ~lIGKTVkIrkGPYKGylGiVKDaT-dt~ARVELHSk~KtITV 701 (1711)
+..|+.|+|+.||++|+.|+|+++. ...|.|+|+.-.+.+.|
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 5689999999999999999999997 44688888877776444
No 31
>TIGR00922 nusG transcription termination/antitermination factor NusG. Archaeal proteins once termed NusG share the KOW domain but are actually a ribosomal protein corresponding to L24p in bacterial and L26e in eukaryotes (TIGR00405).
Probab=93.66 E-value=0.11 Score=56.09 Aligned_cols=47 Identities=21% Similarity=0.376 Sum_probs=36.5
Q ss_pred cccCCEEEEccCCCCCceeEEEEEe--CCeEEEEecCCce--EEEEeCCcc
Q 000294 660 FAVGQTLRIRVGPLKGYLCRVLAVR--YSDVTVKLDSQQK--ILTVKGEHL 706 (1711)
Q Consensus 660 ~lIGKTVkIrkGPYKGylGiVKDaT--dt~ARVELHSk~K--tITVdK~~L 706 (1711)
..+|+.|+|+.||++|+.|+|+.+. ...|+|+|+.-.+ .|+|+-++|
T Consensus 120 ~~~G~~V~I~~Gpf~G~~g~v~~~~~~~~r~~V~v~~~g~~~~v~v~~~~l 170 (172)
T TIGR00922 120 FEVGEQVRVNDGPFANFTGTVEEVDYEKSKLKVSVSIFGRETPVELEFSQV 170 (172)
T ss_pred CCCCCEEEEeecCCCCcEEEEEEEcCCCCEEEEEEEECCCceEEEEcHHHe
Confidence 4579999999999999999999996 3477777776665 455555444
No 32
>PRK00004 rplX 50S ribosomal protein L24; Reviewed
Probab=93.65 E-value=0.097 Score=53.45 Aligned_cols=29 Identities=31% Similarity=0.345 Sum_probs=26.8
Q ss_pred CcccCCCeEEEecCCCCCceEEEEEEECC
Q 000294 554 KVISLNDTARVSEGPSKDRQGIVKKIYRG 582 (1711)
Q Consensus 554 k~I~vGD~VKVIdGp~kGRqG~VlHIyRs 582 (1711)
-.|+.||.|.||.|+++|++|+|+.|++.
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 33
>PRK05609 nusG transcription antitermination protein NusG; Validated
Probab=93.10 E-value=0.14 Score=55.31 Aligned_cols=48 Identities=21% Similarity=0.317 Sum_probs=36.9
Q ss_pred cccCCEEEEccCCCCCceeEEEEEe--CCeEEEEecCCce--EEEEeCCccc
Q 000294 660 FAVGQTLRIRVGPLKGYLCRVLAVR--YSDVTVKLDSQQK--ILTVKGEHLA 707 (1711)
Q Consensus 660 ~lIGKTVkIrkGPYKGylGiVKDaT--dt~ARVELHSk~K--tITVdK~~Ls 707 (1711)
+..|+.|+|+.|||+|+.|+|+.+. ...|+|+|+--.+ .|.|+-+.|.
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 3467777776665 4555555443
No 34
>CHL00141 rpl24 ribosomal protein L24; Validated
Probab=92.49 E-value=0.2 Score=49.44 Aligned_cols=39 Identities=23% Similarity=0.315 Sum_probs=35.4
Q ss_pred cccccCCCEEEEecCcCCCCcEEEEEEeCCCCEEEEEEe
Q 000294 316 RNEVSEGTWAYVKNGKYKGDLAQVVYVNNARKRATVKLI 354 (1711)
Q Consensus 316 ~~~Lk~GdwVRIKrGpYKGDLAQVveVdenk~eVtVKLI 354 (1711)
...|.+||.|.|++|+|||-.++|..|+..+.+|+|+=|
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
>PRK09014 rfaH transcriptional activator RfaH; Provisional
Probab=92.16 E-value=0.22 Score=53.41 Aligned_cols=47 Identities=15% Similarity=0.139 Sum_probs=36.3
Q ss_pred cccCCEEEEccCCCCCceeEEEEEe-CCeEEEEecCCceE--EEEeCCcc
Q 000294 660 FAVGQTLRIRVGPLKGYLCRVLAVR-YSDVTVKLDSQQKI--LTVKGEHL 706 (1711)
Q Consensus 660 ~lIGKTVkIrkGPYKGylGiVKDaT-dt~ARVELHSk~Kt--ITVdK~~L 706 (1711)
+..|++|+|+.||++|+.|+|+++. ...|.|+|+.-.+. |+|+-+.|
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 44677777776664 44554444
No 36
>KOG3262 consensus H/ACA small nucleolar RNP component GAR1 [Translation, ribosomal structure and biogenesis]
Probab=92.11 E-value=0.27 Score=54.61 Aligned_cols=21 Identities=62% Similarity=1.246 Sum_probs=10.5
Q ss_pred CCCCCCCCCCCCCCCCCCCCCC
Q 000294 1501 DRGGFGGRGSSDRGGFGGRGRG 1522 (1711)
Q Consensus 1501 ~rgg~~g~~~g~rgg~ggrg~~ 1522 (1711)
.||+|.+ +++.+++|++|++.
T Consensus 193 ~rGG~~~-Rgg~ggg~rgrgR~ 213 (215)
T KOG3262|consen 193 SRGGFRG-RGGHGGGFRGRGRG 213 (215)
T ss_pred CCCCccc-cCCCCCCCCCCCCC
Confidence 4455433 23345566666554
No 37
>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=91.96 E-value=0.23 Score=50.86 Aligned_cols=28 Identities=32% Similarity=0.437 Sum_probs=26.4
Q ss_pred cccCCCeEEEecCCCCCceEEEEEEECC
Q 000294 555 VISLNDTARVSEGPSKDRQGIVKKIYRG 582 (1711)
Q Consensus 555 ~I~vGD~VKVIdGp~kGRqG~VlHIyRs 582 (1711)
.|+.||.|.||.|+.+|++|+|++|++.
T Consensus 3 ~ikkGD~V~Vi~G~dKGK~G~V~~V~~~ 30 (104)
T TIGR01079 3 KIKKGDTVKVISGKDKGKRGKVLKVLPK 30 (104)
T ss_pred cccCCCEEEEeEcCCCCcEEEEEEEEcC
Confidence 6899999999999999999999999874
No 38
>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=91.86 E-value=0.046 Score=57.72 Aligned_cols=69 Identities=23% Similarity=0.319 Sum_probs=33.0
Q ss_pred cccccccccccCCCC----CchhhcCCCcCCCCCCCCccchhhhhccCccccccccccCCCCCCCccccCCHHHHHHHHH
Q 000294 116 VLQFVEDAADVDYDD----DDEEEVGNESDNSGGFADDDFMEELFDAQPKVNNEMGQAHNLPFIPKEEEMDEEEFDKMME 191 (1711)
Q Consensus 116 ~n~FiDdEAEVDDDe----EeEDEeeEe~e~~~~Fi~dD~~~d~~e~~~~~~~d~r~~~~l~~r~~eed~DaEelAe~lk 191 (1711)
.+.+|.+|||++||. |.|+..++++ .+.+||++.... +.+ .++.| |..++.+.+ ++....||
T Consensus 14 ~~gw~~vEAec~dd~~s~de~E~~~d~~s-d~~dfIDd~~~~---~qg--------nslaL-f~~Q~~~~d-~~~v~~LK 79 (130)
T PF00524_consen 14 CGGWFIVEAECSDDDISEDEDEDLFDSGS-DISDFIDDSEVS---EQG--------NSLAL-FNQQEAEDD-ERAVQALK 79 (130)
T ss_pred cCcEEEEEEEEcCCCCCCCcccccccCCc-cccccccCCCcc---ccc--------HHHHH-HHHHHHHHH-HHHHHHHH
Confidence 345666799998822 2222222222 235788543321 101 01111 122233333 45556899
Q ss_pred HHhcccc
Q 000294 192 ERYKSNK 198 (1711)
Q Consensus 192 ERY~r~s 198 (1711)
.+|-.++
T Consensus 80 RK~~~SP 86 (130)
T PF00524_consen 80 RKYLGSP 86 (130)
T ss_pred HHHcCCc
Confidence 9998654
No 39
>PRK01191 rpl24p 50S ribosomal protein L24P; Validated
Probab=91.62 E-value=0.35 Score=50.72 Aligned_cols=28 Identities=25% Similarity=0.296 Sum_probs=26.5
Q ss_pred cccCCCeEEEecCCCCCceEEEEEEECC
Q 000294 555 VISLNDTARVSEGPSKDRQGIVKKIYRG 582 (1711)
Q Consensus 555 ~I~vGD~VKVIdGp~kGRqG~VlHIyRs 582 (1711)
.|+.||.|+||.|+++|++|.|+.|.+.
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
>PRK12281 rplX 50S ribosomal protein L24; Reviewed
Probab=91.58 E-value=0.28 Score=47.70 Aligned_cols=38 Identities=26% Similarity=0.316 Sum_probs=34.8
Q ss_pred ccccCCCEEEEecCcCCCCcEEEEEEeCCCCEEEEEEe
Q 000294 317 NEVSEGTWAYVKNGKYKGDLAQVVYVNNARKRATVKLI 354 (1711)
Q Consensus 317 ~~Lk~GdwVRIKrGpYKGDLAQVveVdenk~eVtVKLI 354 (1711)
..|.+||.|.|++|++||-.+.|..|+..+.+|+|+=|
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 41
>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=91.38 E-value=0.39 Score=50.00 Aligned_cols=39 Identities=26% Similarity=0.307 Sum_probs=35.1
Q ss_pred cccccCCCEEEEecCcCCCCcEEEEEEeCCCCEEEEEEe
Q 000294 316 RNEVSEGTWAYVKNGKYKGDLAQVVYVNNARKRATVKLI 354 (1711)
Q Consensus 316 ~~~Lk~GdwVRIKrGpYKGDLAQVveVdenk~eVtVKLI 354 (1711)
...|+.||.|+|+.|+|+|-.|.|+.|+..+..|+|+=|
T Consensus 39 ~~~IkkGD~V~Vi~Gk~KGk~GkV~~V~~~~~~V~Vegv 77 (114)
T TIGR01080 39 ALPVRKGDKVRIMRGDFKGHEGKVSKVDLKRYRIYVEGV 77 (114)
T ss_pred cceeecCCEEEEecCCCCCCEEEEEEEEcCCCEEEEcCe
Confidence 458999999999999999999999999998888888644
No 42
>TIGR01956 NusG_myco NusG family protein. This model represents a family of Mycoplasma proteins orthologous to the bacterial transcription termination/antitermination factor NusG. These sequences from Mycoplasma are notably diverged (long branches in a Neighbor-joining phylogenetic tree) from the bacterial species. And although NusA and ribosomal protein S10 (NusE) appear to be present, NusB may be absent in Mycoplasmas calling into question whether these species have a functional Nus system including this family as a member.
Probab=91.19 E-value=0.33 Score=56.54 Aligned_cols=43 Identities=26% Similarity=0.448 Sum_probs=35.5
Q ss_pred ccccCCEEEEccCCCCCceeEEEEEe--CCeEEEEecCCceEEEE
Q 000294 659 MFAVGQTLRIRVGPLKGYLCRVLAVR--YSDVTVKLDSQQKILTV 701 (1711)
Q Consensus 659 d~lIGKTVkIrkGPYKGylGiVKDaT--dt~ARVELHSk~KtITV 701 (1711)
++.+|++|+|+.|||+|+.|+|.++. ...|+|+|+.-.+.+.|
T Consensus 205 ~f~vGd~VrI~dGPF~GfeG~I~eid~~k~Rv~VlV~IfGR~TpV 249 (258)
T TIGR01956 205 KFRVGNFVKIVDGPFKGIVGKIKKIDQEKKKAIVEVEILGKSVDV 249 (258)
T ss_pred CCCCCCEEEEEecCCCCcEEEEEEEeCCCCEEEEEEEecCCcEEE
Confidence 36689999999999999999999996 67888887776665444
No 43
>COG0250 NusG Transcription antiterminator [Transcription]
Probab=91.15 E-value=0.32 Score=53.86 Aligned_cols=43 Identities=26% Similarity=0.396 Sum_probs=36.5
Q ss_pred ccccCCEEEEccCCCCCceeEEEEEeCC--eEEEEecCCceEEEE
Q 000294 659 MFAVGQTLRIRVGPLKGYLCRVLAVRYS--DVTVKLDSQQKILTV 701 (1711)
Q Consensus 659 d~lIGKTVkIrkGPYKGylGiVKDaTdt--~ARVELHSk~KtITV 701 (1711)
++.+|+.|+|+.|||+|+.|+|.++... .++|+|..-.+.+.|
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 44
>PTZ00194 60S ribosomal protein L26; Provisional
Probab=90.88 E-value=0.46 Score=51.20 Aligned_cols=52 Identities=19% Similarity=0.169 Sum_probs=43.0
Q ss_pred HHHHHHhhcccccccccCCCEEEEecCcCCCCcEEEEEEeCCCCEEEEEEeccC
Q 000294 304 NEVSHLLSAQIKRNEVSEGTWAYVKNGKYKGDLAQVVYVNNARKRATVKLIPRI 357 (1711)
Q Consensus 304 kEM~dLL~vkkk~~~Lk~GdwVRIKrGpYKGDLAQVveVdenk~eVtVKLIPRI 357 (1711)
+|+...+.+. ...|..||.|.|++|.|||-.|+|+.|+....+|+|+=|.++
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 4555555443 458999999999999999999999999999999999877655
No 45
>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=90.06 E-value=0.38 Score=50.06 Aligned_cols=28 Identities=25% Similarity=0.335 Sum_probs=26.4
Q ss_pred cccCCCeEEEecCCCCCceEEEEEEECC
Q 000294 555 VISLNDTARVSEGPSKDRQGIVKKIYRG 582 (1711)
Q Consensus 555 ~I~vGD~VKVIdGp~kGRqG~VlHIyRs 582 (1711)
.|+.||.|+||.|+++|.+|.|+.|.+.
T Consensus 41 ~IkkGD~V~Vi~Gk~KGk~GkV~~V~~~ 68 (114)
T TIGR01080 41 PVRKGDKVRIMRGDFKGHEGKVSKVDLK 68 (114)
T ss_pred eeecCCEEEEecCCCCCCEEEEEEEEcC
Confidence 7999999999999999999999999764
No 46
>PTZ00194 60S ribosomal protein L26; Provisional
Probab=89.99 E-value=0.35 Score=52.05 Aligned_cols=28 Identities=32% Similarity=0.526 Sum_probs=26.6
Q ss_pred cccCCCeEEEecCCCCCceEEEEEEECC
Q 000294 555 VISLNDTARVSEGPSKDRQGIVKKIYRG 582 (1711)
Q Consensus 555 ~I~vGD~VKVIdGp~kGRqG~VlHIyRs 582 (1711)
.|+.||+|+||.|.++|++|.|+.|++.
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=89.81 E-value=0.42 Score=49.14 Aligned_cols=30 Identities=27% Similarity=0.359 Sum_probs=27.5
Q ss_pred CcccCCCeEEEecCCCCCceEEEEEEECCE
Q 000294 554 KVISLNDTARVSEGPSKDRQGIVKKIYRGI 583 (1711)
Q Consensus 554 k~I~vGD~VKVIdGp~kGRqG~VlHIyRs~ 583 (1711)
..|+.||+|+||.|.++|++|.|+.|+...
T Consensus 3 ~~IrkGD~V~Vi~GkdKGk~GkVl~v~~k~ 32 (104)
T COG0198 3 MKVKKGDTVKVIAGKDKGKEGKVLKVLPKK 32 (104)
T ss_pred cceecCCEEEEEecCCCCcceEEEEEecCe
Confidence 468999999999999999999999998764
No 48
>PRK00004 rplX 50S ribosomal protein L24; Reviewed
Probab=89.62 E-value=0.51 Score=48.38 Aligned_cols=37 Identities=24% Similarity=0.338 Sum_probs=34.5
Q ss_pred cccCCCEEEEecCcCCCCcEEEEEEeCCCCEEEEEEe
Q 000294 318 EVSEGTWAYVKNGKYKGDLAQVVYVNNARKRATVKLI 354 (1711)
Q Consensus 318 ~Lk~GdwVRIKrGpYKGDLAQVveVdenk~eVtVKLI 354 (1711)
.|.+||.|.|++|++||-++.|..|+..+.+|+|+=|
T Consensus 4 ~i~kGD~V~Vi~G~dKGk~G~V~~V~~~~~~V~Vegv 40 (105)
T PRK00004 4 KIKKGDTVIVIAGKDKGKRGKVLKVLPKKNKVIVEGV 40 (105)
T ss_pred cccCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEEcCc
Confidence 6889999999999999999999999999999999754
No 49
>PF11623 DUF3252: Protein of unknown function (DUF3252); InterPro: IPR021659 This family of proteins has no known function. Some members are annotated as Ssl0352 however this cannot be confirmed. Currently there is no known function. ; PDB: 3C4S_B 2JZ2_A.
Probab=85.99 E-value=2.1 Score=39.19 Aligned_cols=47 Identities=23% Similarity=0.286 Sum_probs=36.8
Q ss_pred cccCCEEEEccC--CCCCceeEEEEEeCCeEEEEecCCc--eEEEEeCCcc
Q 000294 660 FAVGQTLRIRVG--PLKGYLCRVLAVRYSDVTVKLDSQQ--KILTVKGEHL 706 (1711)
Q Consensus 660 ~lIGKTVkIrkG--PYKGylGiVKDaTdt~ARVELHSk~--KtITVdK~~L 706 (1711)
.|-|-+|+|+.- +|-+|.|+|-.+++..|-|...-.| |.||..-++|
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 355788999877 8999999999999999999999887 8999887766
No 50
>TIGR01079 rplX_bact ribosomal protein L24, bacterial/organelle. This model recognizes bacterial and organellar forms of ribosomal protein L24. It excludes eukaryotic and archaeal forms, designated L26 in eukaryotes.
Probab=85.71 E-value=1.1 Score=45.90 Aligned_cols=37 Identities=24% Similarity=0.311 Sum_probs=33.9
Q ss_pred cccCCCEEEEecCcCCCCcEEEEEEeCCCCEEEEEEe
Q 000294 318 EVSEGTWAYVKNGKYKGDLAQVVYVNNARKRATVKLI 354 (1711)
Q Consensus 318 ~Lk~GdwVRIKrGpYKGDLAQVveVdenk~eVtVKLI 354 (1711)
.|..||.|.|++|++||=.+.|..|+..+.+|+|+=|
T Consensus 3 ~ikkGD~V~Vi~G~dKGK~G~V~~V~~~~~~V~Vegv 39 (104)
T TIGR01079 3 KIKKGDTVKVISGKDKGKRGKVLKVLPKTNKVIVEGV 39 (104)
T ss_pred cccCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEECCc
Confidence 5789999999999999999999999999999998643
No 51
>COG2933 Predicted SAM-dependent methyltransferase [General function prediction only]
Probab=82.83 E-value=1.8 Score=50.90 Aligned_cols=64 Identities=20% Similarity=0.299 Sum_probs=51.4
Q ss_pred EEEeccchHHHHHHHHHHHHHhhccCCCCCcEEEEEEeCCCCcEEEEEeccchhHHHHhcCCCC---eEecccc
Q 000294 229 KVKCMAGRERQSAFCLMQKFVDLQSLGSKMQIISAFAVDHIKGFIFIEADKQCDINEACKGLSG---IYYSRLA 299 (1711)
Q Consensus 229 aVKCk~GkEReVV~~LmrKii~lq~~g~~L~I~SVFvpd~lKGYIYIEA~kq~dVk~AIkGI~g---Vy~~k~~ 299 (1711)
++.|++|-|+|++.-|-.|...+. |+-..-.+.-.|||..|.+..+++..+|+.|+. |+..++.
T Consensus 5 ~lyCRpGFEkE~aAEi~d~Aa~l~-------IfGfarvk~n~gyV~feCyq~d~adrL~r~lpf~~lIFaRQ~~ 71 (358)
T COG2933 5 ALYCRPGFEKECAAEITDKAAQLE-------IFGFARVKENSGYVIFECYQPDDADRLIRELPFRRLIFARQWF 71 (358)
T ss_pred eeeecCCCcHHHHHHHHHhhhhhc-------cccceeecccCceEEEEEcCcccHHHHHHhCcHHHHHHHHHHH
Confidence 578999999999999998886543 554444467889999999999999999999986 4444433
No 52
>KOG1708 consensus Mitochondrial/chloroplast ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=81.59 E-value=1.5 Score=49.62 Aligned_cols=31 Identities=29% Similarity=0.316 Sum_probs=28.2
Q ss_pred CCCcccCCCeEEEecCCCCCceEEEEEEECC
Q 000294 552 SMKVISLNDTARVSEGPSKDRQGIVKKIYRG 582 (1711)
Q Consensus 552 ~gk~I~vGD~VKVIdGp~kGRqG~VlHIyRs 582 (1711)
+-=+|.+||+|+|+.|.-+|++|.|+.|.+.
T Consensus 69 ~dw~ff~GDtVeVlvGkDkGkqG~Vtqv~r~ 99 (236)
T KOG1708|consen 69 EDWHFFFGDTVEVLVGKDKGKQGEVTQVIRH 99 (236)
T ss_pred cceeEecCCEEEEEecccCCccceEEEEeec
Confidence 3468999999999999999999999999875
No 53
>COG0198 RplX Ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=79.37 E-value=2.7 Score=43.43 Aligned_cols=34 Identities=29% Similarity=0.314 Sum_probs=30.2
Q ss_pred ccccCCCEEEEecCcCCCCcEEEEEEeCCCCEEEEE
Q 000294 317 NEVSEGTWAYVKNGKYKGDLAQVVYVNNARKRATVK 352 (1711)
Q Consensus 317 ~~Lk~GdwVRIKrGpYKGDLAQVveVdenk~eVtVK 352 (1711)
..|..||.|+|++|++||-.|+|++|++.. |+|+
T Consensus 3 ~~IrkGD~V~Vi~GkdKGk~GkVl~v~~k~--V~VE 36 (104)
T COG0198 3 MKVKKGDTVKVIAGKDKGKEGKVLKVLPKK--VVVE 36 (104)
T ss_pred cceecCCEEEEEecCCCCcceEEEEEecCe--EEEE
Confidence 357889999999999999999999999976 7765
No 54
>PRK11760 putative 23S rRNA C2498 ribose 2'-O-ribose methyltransferase; Provisional
Probab=78.25 E-value=3.4 Score=50.34 Aligned_cols=65 Identities=18% Similarity=0.300 Sum_probs=50.9
Q ss_pred EEEEeccchHHHHHHHHHHHHHhhccCCCCCcEEEEEEeCCCCcEEEEEeccchhHHHHhcCCCC---eEecccc
Q 000294 228 WKVKCMAGRERQSAFCLMQKFVDLQSLGSKMQIISAFAVDHIKGFIFIEADKQCDINEACKGLSG---IYYSRLA 299 (1711)
Q Consensus 228 WaVKCk~GkEReVV~~LmrKii~lq~~g~~L~I~SVFvpd~lKGYIYIEA~kq~dVk~AIkGI~g---Vy~~k~~ 299 (1711)
+++.|++|.|++++.-|..+..++. |+-..-...-.|||..|.+...++..+++.|+- |+..++.
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 6889999999999999999986543 333333355679999999999999999998875 5555543
No 55
>PF09444 MRC1: MRC1-like domain; InterPro: IPR018564 This putative domain is found in the most conserved region in mediator of replication checkpoint protein 1. This protein is a component of the replisome and is required for Rad3-dependent activation of the checkpoint kinase Cds1 in response to replication fork arrest [].
Probab=75.76 E-value=0.66 Score=50.17 Aligned_cols=18 Identities=28% Similarity=0.479 Sum_probs=14.2
Q ss_pred ccccccccccccccCCCC
Q 000294 113 NRSVLQFVEDAADVDYDD 130 (1711)
Q Consensus 113 rr~~n~FiDdEAEVDDDe 130 (1711)
+.....||+.|||..|||
T Consensus 3 k~~~~~~vE~EAEESeDE 20 (145)
T PF09444_consen 3 KSGASEFVEEEAEESEDE 20 (145)
T ss_pred chhHHHHHHHHHhcchhh
Confidence 345678999999987755
No 56
>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=73.74 E-value=1.9 Score=57.11 Aligned_cols=16 Identities=13% Similarity=0.420 Sum_probs=9.7
Q ss_pred hHHHHHHHHHHHHHhh
Q 000294 236 RERQSAFCLMQKFVDL 251 (1711)
Q Consensus 236 kEReVV~~LmrKii~l 251 (1711)
.+++.++.+..|++++
T Consensus 764 ~~~~~~~~Fk~RvlDL 779 (784)
T PF04931_consen 764 EAKENVIHFKNRVLDL 779 (784)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 3455556666777665
No 57
>COG1588 POP4 RNase P/RNase MRP subunit p29 [Translation, ribosomal structure and biogenesis]
Probab=73.30 E-value=6.5 Score=40.14 Aligned_cols=47 Identities=15% Similarity=0.123 Sum_probs=40.1
Q ss_pred cccCCEEEEccCC---CCCceeEEEEEeCCeEEEEecCCceEEEEeCCcccc
Q 000294 660 FAVGQTLRIRVGP---LKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLAE 708 (1711)
Q Consensus 660 ~lIGKTVkIrkGP---YKGylGiVKDaTdt~ARVELHSk~KtITVdK~~Ls~ 708 (1711)
.|||..|+|+.=+ |-|..|+|+|-|.++..|+-.+ +.++|+|+...+
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 7999999999884 5777889999999999977766 888999988764
No 58
>PTZ00415 transmission-blocking target antigen s230; Provisional
Probab=73.05 E-value=1.7 Score=60.02 Aligned_cols=17 Identities=24% Similarity=0.345 Sum_probs=9.7
Q ss_pred CCCcEEEEEeccchHHH
Q 000294 223 EDPTIWKVKCMAGRERQ 239 (1711)
Q Consensus 223 ~DPkLWaVKCk~GkERe 239 (1711)
+-|-+-+|+.+.|.|..
T Consensus 312 kapyv~l~~~~~~~~e~ 328 (2849)
T PTZ00415 312 KAPYVTLTKANEGSEEK 328 (2849)
T ss_pred CCceEEEEccCCcchhh
Confidence 34556666776665443
No 59
>CHL00010 infA translation initiation factor 1
Probab=72.88 E-value=26 Score=34.39 Aligned_cols=65 Identities=14% Similarity=0.061 Sum_probs=41.9
Q ss_pred ceEEEEEEeccceEEEccCCCCCCceEEEecccccCCCCCCcccccccCCCcccCCCeEEEecCCCCCceEEEEEEECC
Q 000294 504 DFGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVSEGPSKDRQGIVKKIYRG 582 (1711)
Q Consensus 504 TVGVIVrVEkDe~fkVLd~~gd~~~VvtVk~~~I~~K~~~rr~vAtD~~gk~I~vGD~VKVIdGp~kGRqG~VlHIyRs 582 (1711)
..|+|+++-....|.|.+.++ .++.+.+.- |+. .....|.+||+|.|--=++....|.|+|=|++
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 459999987434777765432 355555322 211 12344789999999744455678999998875
No 60
>PHA02774 E1; Provisional
Probab=72.37 E-value=1.1 Score=57.59 Aligned_cols=31 Identities=13% Similarity=0.133 Sum_probs=20.5
Q ss_pred ccccCHHHHHHHhhcccccccccCCCEEEEecCcC
Q 000294 298 LAPVPKNEVSHLLSAQIKRNEVSEGTWAYVKNGKY 332 (1711)
Q Consensus 298 ~~pVPikEM~dLL~vkkk~~~Lk~GdwVRIKrGpY 332 (1711)
..-|+..|+++.++-.|. --.+||-..-|.+
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 556778888888765442 2358888877753
No 61
>KOG1832 consensus HIV-1 Vpr-binding protein [Cell cycle control, cell division, chromosome partitioning]
Probab=71.99 E-value=3.3 Score=54.66 Aligned_cols=9 Identities=33% Similarity=0.560 Sum_probs=4.8
Q ss_pred HHHHHHHHH
Q 000294 184 EEFDKMMEE 192 (1711)
Q Consensus 184 EelAe~lkE 192 (1711)
+++++.|+|
T Consensus 1469 ~df~~elee 1477 (1516)
T KOG1832|consen 1469 GDFMEELEE 1477 (1516)
T ss_pred hHHHHHHhh
Confidence 455555554
No 62
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=71.13 E-value=21 Score=35.53 Aligned_cols=65 Identities=11% Similarity=0.043 Sum_probs=46.9
Q ss_pred CCceEEEEEEeccceEEEccCCCCCCceEEEecccccCCCCCCcccccccCCCcccCCCeEEEecCCCCCceEEEEEEEC
Q 000294 502 RKDFGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVSEGPSKDRQGIVKKIYR 581 (1711)
Q Consensus 502 ~~TVGVIVrVEkDe~fkVLd~~gd~~~VvtVk~~~I~~K~~~rr~vAtD~~gk~I~vGD~VKVIdGp~kGRqG~VlHIyR 581 (1711)
.+.+|.|+++..+..|.|.+.++ ..+.+.. ..|+ +..--|+.||.|.|--=++.-..|.|+|+|.
T Consensus 5 ~q~~g~V~~~lG~~~~~V~~~dG---~~~la~i---pgK~---------Rk~iwI~~GD~VlVe~~~~~~~kg~Iv~r~~ 69 (83)
T smart00652 5 GQEIAQVVKMLGNGRLEVMCADG---KERLARI---PGKM---------RKKVWIRRGDIVLVDPWDFQDVKADIIYKYT 69 (83)
T ss_pred CcEEEEEEEEcCCCEEEEEECCC---CEEEEEE---chhh---------cccEEEcCCCEEEEEecCCCCCEEEEEEEeC
Confidence 35689999998888999998764 2344432 2222 1234689999999987777778899999886
No 63
>TIGR01622 SF-CC1 splicing factor, CC1-like family. A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the model.
Probab=70.90 E-value=10 Score=46.52 Aligned_cols=67 Identities=12% Similarity=0.113 Sum_probs=50.1
Q ss_pred HHHHHHHHHHHHhhccCCCCCcEEEEEEe-CCCCcEEEEEeccchhHHHHhcCCCCeEe----ccccccCHHHHHHHh
Q 000294 238 RQSAFCLMQKFVDLQSLGSKMQIISAFAV-DHIKGFIFIEADKQCDINEACKGLSGIYY----SRLAPVPKNEVSHLL 310 (1711)
Q Consensus 238 ReVV~~LmrKii~lq~~g~~L~I~SVFvp-d~lKGYIYIEA~kq~dVk~AIkGI~gVy~----~k~~pVPikEM~dLL 310 (1711)
.+|..-|+..|..+. .|.+|++. ....||||||-...++...||+.|.+-+. ..+..+|.+++..++
T Consensus 383 ~~~~~dv~~e~~k~G------~v~~v~v~~~~~~G~~fV~F~~~e~A~~A~~~lnGr~f~gr~i~~~~~~~~~~~~~~ 454 (457)
T TIGR01622 383 NEILDDVKEECSKYG------GVVHIYVDTKNSAGKIYLKFSSVDAALAAFQALNGRYFGGKMITAAFVVNDVYDMSC 454 (457)
T ss_pred HHHHHHHHHHHHhcC------CeeEEEEeCCCCceeEEEEECCHHHHHHHHHHhcCcccCCeEEEEEEEcHHHHHhhc
Confidence 445555665555443 47888887 67899999999999999999999999653 346677877776655
No 64
>KOG0415 consensus Predicted peptidyl prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]
Probab=70.66 E-value=9.5 Score=46.38 Aligned_cols=111 Identities=16% Similarity=0.208 Sum_probs=70.5
Q ss_pred CccccCCHHHHHHHHHHHhccccchhhchhhHHHhhhcccccCCCCCCCCcEEEEEeccchHHHHHHHHHHHHHhhccCC
Q 000294 176 PKEEEMDEEEFDKMMEERYKSNKLIRYAEEDYEAKKMLEREYHMPCPEDPTIWKVKCMAGRERQSAFCLMQKFVDLQSLG 255 (1711)
Q Consensus 176 ~~eed~DaEelAe~lkERY~r~s~~~y~~d~~e~~~~VpQq~LLPSV~DPkLWaVKCk~GkEReVV~~LmrKii~lq~~g 255 (1711)
..++.+.||||+++|+||-+...+. .-|+-..+|---+.|- +--||++|..|=-+-+=+..|..+|=.
T Consensus 198 d~~~g~saeel~e~~~e~ea~~~A~-----iLEmvGDlpdAd~~PP--eNVLFVCKLNPVTtDeDLeiIFSrFG~----- 265 (479)
T KOG0415|consen 198 DDDEGLSAEELEEVLAEKEAKAQAV-----ILEMVGDLPDADVKPP--ENVLFVCKLNPVTTDEDLEIIFSRFGK----- 265 (479)
T ss_pred ccccccCHHHHHHHHHHHHHHhhHh-----HHHHhcCCcccccCCC--cceEEEEecCCcccccchhhHHhhccc-----
Confidence 4467889999999999998764432 1122233444444442 234888888776666655556556521
Q ss_pred CCCcEEEEE-EeC----CCCcEEEEEeccchhHHHHhcCCCCeEe-ccccccC
Q 000294 256 SKMQIISAF-AVD----HIKGFIFIEADKQCDINEACKGLSGIYY-SRLAPVP 302 (1711)
Q Consensus 256 ~~L~I~SVF-vpd----~lKGYIYIEA~kq~dVk~AIkGI~gVy~-~k~~pVP 302 (1711)
|.|+- +++ ..-=|-|||-+.+..+..|.=.|-+|.. ..-+-|.
T Consensus 266 ----i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHVD 314 (479)
T KOG0415|consen 266 ----IVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHVD 314 (479)
T ss_pred ----ceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEee
Confidence 33332 222 2345999999999999999999999875 3334443
No 65
>PF14632 SPT6_acidic: Acidic N-terminal SPT6
Probab=70.54 E-value=1.4 Score=44.47 Aligned_cols=9 Identities=44% Similarity=0.534 Sum_probs=6.6
Q ss_pred CCCCCCccc
Q 000294 143 SGGFADDDF 151 (1711)
Q Consensus 143 ~~~Fi~dD~ 151 (1711)
+.+||.++.
T Consensus 20 ~eGFIvDde 28 (92)
T PF14632_consen 20 REGFIVDDE 28 (92)
T ss_pred hcCCccCCc
Confidence 479998753
No 66
>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=69.40 E-value=14 Score=37.12 Aligned_cols=76 Identities=16% Similarity=0.240 Sum_probs=50.4
Q ss_pred EEEEec--cchHHHHHHHHHHHHHhhccCC-CC--C-cEEEEEEeCCCCcEEEEEeccchhHHHHhcCCCCeEecccccc
Q 000294 228 WKVKCM--AGRERQSAFCLMQKFVDLQSLG-SK--M-QIISAFAVDHIKGFIFIEADKQCDINEACKGLSGIYYSRLAPV 301 (1711)
Q Consensus 228 WaVKCk--~GkEReVV~~LmrKii~lq~~g-~~--L-~I~SVFvpd~lKGYIYIEA~kq~dVk~AIkGI~gVy~~k~~pV 301 (1711)
|+|.+. ++....-...++.++++..... .+ + .|.+++.|....|||.|||++...+.+.+.--+.+++..+..+
T Consensus 2 flv~w~f~~~~~~~~~~~~~~~~~~~G~~~~~peG~~~l~rw~~~~~g~g~~i~eadd~~~l~~~~~~W~~~fg~~~ei~ 81 (91)
T PF11746_consen 2 FLVIWQFPPGESQQEAYKAFERFMESGAPGDPPEGFKVLGRWHDPGGGRGFAIVEADDAKALFKHFAPWRDLFGMEFEIT 81 (91)
T ss_pred EEEEEEeCCcccchhHHHHHHHHHhcCCCCCCCCCEEEEEEEEecCCCcEEEEEEeCCHHHHHHHHhhhhhccCceEEEE
Confidence 666664 5555534444556666544111 11 2 3668888899999999999999999999888887755444444
Q ss_pred CH
Q 000294 302 PK 303 (1711)
Q Consensus 302 Pi 303 (1711)
|+
T Consensus 82 Pv 83 (91)
T PF11746_consen 82 PV 83 (91)
T ss_pred ec
Confidence 43
No 67
>KOG0262 consensus RNA polymerase I, large subunit [Transcription]
Probab=69.20 E-value=13 Score=50.97 Aligned_cols=69 Identities=7% Similarity=0.103 Sum_probs=37.2
Q ss_pred EEEEEec--cchHHHHHHHHHHHHHhhccCCCCCcEEEEEEeC------CCCcEEEEEeccchhHHHHhc--CCCCeEec
Q 000294 227 IWKVKCM--AGRERQSAFCLMQKFVDLQSLGSKMQIISAFAVD------HIKGFIFIEADKQCDINEACK--GLSGIYYS 296 (1711)
Q Consensus 227 LWaVKCk--~GkEReVV~~LmrKii~lq~~g~~L~I~SVFvpd------~lKGYIYIEA~kq~dVk~AIk--GI~gVy~~ 296 (1711)
|..|+.+ ..+|+..+.+|.+++...--.-+--.|..+++.+ ..+ ++.-|...-.++++..+ .|..||.+
T Consensus 1442 wcev~~~lp~~~~k~~mssiVe~~~~~~vI~q~~gIeRc~~~~~~~~~k~~~-~l~TeGVnl~a~~~~~d~LDv~~lySN 1520 (1640)
T KOG0262|consen 1442 WCEVELKLPLDKEKLDMSSIVESIAPKSVIHQVPGIERCVVSEPQDDVKEKS-VLLTEGVNLPALFDHADILDVNRLYSN 1520 (1640)
T ss_pred EEEEEEEecCCCcchHHHHHHHHHhcceeeeccCCceeeeccCCcccccccc-eehhcCccHHHHHHHHhhhhhhhhccc
Confidence 4444443 4678888888887765432111223566666663 222 66666665555554433 34455543
No 68
>PF14851 FAM176: FAM176 family
Probab=68.89 E-value=6.4 Score=43.19 Aligned_cols=17 Identities=29% Similarity=0.345 Sum_probs=11.5
Q ss_pred ccCCHHHHHHHHHHHhc
Q 000294 179 EEMDEEEFDKMMEERYK 195 (1711)
Q Consensus 179 ed~DaEelAe~lkERY~ 195 (1711)
-...|-|+|+.|+||-+
T Consensus 114 ~sae~~e~A~rlEeRe~ 130 (153)
T PF14851_consen 114 TSAEELERAQRLEERER 130 (153)
T ss_pred ccHHHHHHHHHHHHHHH
Confidence 34445578888888865
No 69
>PLN00208 translation initiation factor (eIF); Provisional
Probab=67.33 E-value=19 Score=39.43 Aligned_cols=77 Identities=14% Similarity=0.061 Sum_probs=54.6
Q ss_pred ccccCceEEEcC-CceEEEEEEeccceEEEccCCCCCCceEEEecccccCCCCCCcccccccCCCcccCCCeEEEecCCC
Q 000294 491 SFELYELVCFGR-KDFGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVSEGPS 569 (1711)
Q Consensus 491 ~FeLgDLVQLD~-~TVGVIVrVEkDe~fkVLd~~gd~~~VvtVk~~~I~~K~~~rr~vAtD~~gk~I~vGD~VKVIdGp~ 569 (1711)
.-+..+|+.... +.+|+|+++-.+..|.|.+.++ ..+.+. |..|+. -.--|.+||+|.|---+|
T Consensus 20 ~~~~~el~~p~egq~~g~V~~~lGn~~~~V~c~dG---~~rLa~---IpGKmR---------KrIWI~~GD~VlVel~~~ 84 (145)
T PLN00208 20 DDEKRELIFKEDGQEYAQVLRMLGNGRCEALCIDG---TKRLCH---IRGKMR---------KKVWIAAGDIILVGLRDY 84 (145)
T ss_pred ccceeecccCCCCcEEEEEEEEcCCCEEEEEECCC---CEEEEE---Eeccce---------eeEEecCCCEEEEEccCC
Confidence 345666766644 5789999998888999998764 234433 223321 124689999999987788
Q ss_pred CCceEEEEEEECC
Q 000294 570 KDRQGIVKKIYRG 582 (1711)
Q Consensus 570 kGRqG~VlHIyRs 582 (1711)
.-..|.|+|+|..
T Consensus 85 d~~KgdIv~ry~~ 97 (145)
T PLN00208 85 QDDKADVILKYMP 97 (145)
T ss_pred CCCEEEEEEEcCH
Confidence 8889999999864
No 70
>PTZ00061 DNA-directed RNA polymerase; Provisional
Probab=66.95 E-value=34 Score=39.38 Aligned_cols=57 Identities=14% Similarity=0.103 Sum_probs=36.2
Q ss_pred CcEEEEEeccchhHHHHhcCCCCeEeccccccCHHHHHHHhhc---cc-------------ccccccCCCEEEEec
Q 000294 270 KGFIFIEADKQCDINEACKGLSGIYYSRLAPVPKNEVSHLLSA---QI-------------KRNEVSEGTWAYVKN 329 (1711)
Q Consensus 270 KGYIYIEA~kq~dVk~AIkGI~gVy~~k~~pVPikEM~dLL~v---kk-------------k~~~Lk~GdwVRIKr 329 (1711)
+.| .||.+.++++.- +=+.++...+-.+++.+|...||+. +. +...+++|+.|+|+|
T Consensus 118 ~~~-~iE~F~E~eLlv--nit~H~lVPkH~~Ls~eEk~~lL~~y~i~~~qLPrI~~~DPvary~g~k~G~vvkI~R 190 (205)
T PTZ00061 118 PRH-IIENFLETELLV--NITKHELVPKHIPLTDDEKLNLLQRYKVKESQLPRIQSADPVARYFGLSKGQVVKIIR 190 (205)
T ss_pred CCc-EEEEeeehheEE--ecccceecCCeEEcCHHHHHHHHHHhCCCHHHCCcccccChhhHhcCCCCCCEEEEEE
Confidence 444 467776655422 1123455566778889999999962 11 134678999999887
No 71
>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=66.59 E-value=27 Score=34.37 Aligned_cols=64 Identities=11% Similarity=0.070 Sum_probs=46.3
Q ss_pred ceEEEEEEeccceEEEccCCCCCCceEEEecccccCCCCCCcccccccCCCcccCCCeEEEecCCCCCceEEEEEEECC
Q 000294 504 DFGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVSEGPSKDRQGIVKKIYRG 582 (1711)
Q Consensus 504 TVGVIVrVEkDe~fkVLd~~gd~~~VvtVk~~~I~~K~~~rr~vAtD~~gk~I~vGD~VKVIdGp~kGRqG~VlHIyRs 582 (1711)
..|.|+++-.+..|.|.+.++ ..+.+. |..|+ +..--|..||.|.|--=||.-..|.|+|+|..
T Consensus 2 ~~g~V~~~~g~~~~~V~~~~g---~~~la~---i~gK~---------rk~iwI~~GD~V~Ve~~~~d~~kg~Iv~r~~~ 65 (77)
T cd05793 2 EYGQVEKMLGNGRLEVRCFDG---KKRLCR---IRGKM---------RKRVWINEGDIVLVAPWDFQDDKADIIYKYTP 65 (77)
T ss_pred EEEEEEEEcCCCEEEEEECCC---CEEEEE---Echhh---------cccEEEcCCCEEEEEeccccCCEEEEEEEcCH
Confidence 468999998888899998764 233333 22232 12356899999999777888889999999863
No 72
>PRK04333 50S ribosomal protein L14e; Validated
Probab=66.59 E-value=9.2 Score=38.22 Aligned_cols=33 Identities=15% Similarity=0.181 Sum_probs=28.4
Q ss_pred cccCCCEEEEecCcCCCCcEEEEEEeCCCCEEEE
Q 000294 318 EVSEGTWAYVKNGKYKGDLAQVVYVNNARKRATV 351 (1711)
Q Consensus 318 ~Lk~GdwVRIKrGpYKGDLAQVveVdenk~eVtV 351 (1711)
++++|..|+++.|+|+|-++.|++|.++ ++|.|
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 45555
No 73
>PRK04950 ProP expression regulator; Provisional
Probab=66.12 E-value=9.2 Score=43.97 Aligned_cols=46 Identities=35% Similarity=0.590 Sum_probs=37.9
Q ss_pred cccCCEEEEccCCCCCceeEEEEEeCCeEEEEecCCceEEEEeCCccc
Q 000294 660 FAVGQTLRIRVGPLKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLA 707 (1711)
Q Consensus 660 ~lIGKTVkIrkGPYKGylGiVKDaTdt~ARVELHSk~KtITVdK~~Ls 707 (1711)
..+|+.|+|.-|. -=.-+.|++|+.+.|||+|.+.+. |.|.-+||.
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 224589999999999999999887 677888875
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=63.02 E-value=2.4 Score=56.11 Aligned_cols=12 Identities=17% Similarity=0.268 Sum_probs=0.0
Q ss_pred ccccCCHHHHHH
Q 000294 177 KEEEMDEEEFDK 188 (1711)
Q Consensus 177 ~eed~DaEelAe 188 (1711)
.++-+++|+-++
T Consensus 718 VNqGi~eerAar 729 (787)
T PF03115_consen 718 VNQGIPEERAAR 729 (787)
T ss_dssp ------------
T ss_pred HHcCCCHHHHHh
Confidence 355555555443
No 75
>PRK03879 ribonuclease P protein component 1; Validated
Probab=62.94 E-value=15 Score=37.61 Aligned_cols=46 Identities=15% Similarity=0.174 Sum_probs=40.4
Q ss_pred cccCCEEEEccCC---CCCceeEEEEEeCCeEEEEecCCceEEEEeCCccc
Q 000294 660 FAVGQTLRIRVGP---LKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLA 707 (1711)
Q Consensus 660 ~lIGKTVkIrkGP---YKGylGiVKDaTdt~ARVELHSk~KtITVdK~~Ls 707 (1711)
.|||-.|+|+.=+ |-|..|+|++-|..+..|+ +.++.++|+|+.-.
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 76
>PRK00276 infA translation initiation factor IF-1; Validated
Probab=62.53 E-value=40 Score=32.47 Aligned_cols=63 Identities=14% Similarity=0.073 Sum_probs=40.1
Q ss_pred eEEEEEEeccceEEEccCCCCCCceEEEecccccCCCCCCcccccccCCCcccCCCeEEEecCCCCCceEEEEEEEC
Q 000294 505 FGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVSEGPSKDRQGIVKKIYR 581 (1711)
Q Consensus 505 VGVIVrVEkDe~fkVLd~~gd~~~VvtVk~~~I~~K~~~rr~vAtD~~gk~I~vGD~VKVIdGp~kGRqG~VlHIyR 581 (1711)
.|+|+++-.+..|.|.+.++ .++.+.+.- |+.. ....|.+||.|.|---++....|.|+|=|+
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 48999987644677765432 355555322 2111 123389999999985455566799998775
No 77
>KOG0299 consensus U3 snoRNP-associated protein (contains WD40 repeats) [RNA processing and modification]
Probab=62.42 E-value=4.3 Score=50.49 Aligned_cols=19 Identities=16% Similarity=0.300 Sum_probs=15.1
Q ss_pred cCCHHHHHHHHHHHhcccc
Q 000294 180 EMDEEEFDKMMEERYKSNK 198 (1711)
Q Consensus 180 d~DaEelAe~lkERY~r~s 198 (1711)
++|.|.||+.|+|-|..++
T Consensus 98 ~~~~e~va~rLked~le~~ 116 (479)
T KOG0299|consen 98 DLDDELVASRLKEDVLEQS 116 (479)
T ss_pred hhhHHHHHHHHHHHHHHhc
Confidence 5566889999999998655
No 78
>PTZ00329 eukaryotic translation initiation factor 1A; Provisional
Probab=60.65 E-value=33 Score=38.04 Aligned_cols=76 Identities=16% Similarity=0.060 Sum_probs=52.8
Q ss_pred cccCceEEEc-CCceEEEEEEeccceEEEccCCCCCCceEEEecccccCCCCCCcccccccCCCcccCCCeEEEecCCCC
Q 000294 492 FELYELVCFG-RKDFGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVSEGPSK 570 (1711)
Q Consensus 492 FeLgDLVQLD-~~TVGVIVrVEkDe~fkVLd~~gd~~~VvtVk~~~I~~K~~~rr~vAtD~~gk~I~vGD~VKVIdGp~k 570 (1711)
.+..+|+.=. .+.+|+|+++-.+..|.|++.++ ..+.+. |.-|+.. .--|.+||+|.|--=+|.
T Consensus 21 ~~~rel~~~eegq~~g~V~~~LGn~~f~V~c~dG---~~rLa~---I~GKmRK---------~IWI~~GD~VlVel~~yd 85 (155)
T PTZ00329 21 GEKRELVFKEEGQEYAQVLRMLGNGRLEAYCFDG---VKRLCH---IRGKMRK---------RVWINIGDIILVSLRDFQ 85 (155)
T ss_pred cceeeeccCCCCcEEEEEEEEcCCCEEEEEECCC---CEEEEE---eecccee---------eEEecCCCEEEEeccCCC
Confidence 3444555433 35789999998888999998764 233333 2233221 246899999999888888
Q ss_pred CceEEEEEEECC
Q 000294 571 DRQGIVKKIYRG 582 (1711)
Q Consensus 571 GRqG~VlHIyRs 582 (1711)
-..|.|+|.|..
T Consensus 86 ~~KgdIi~Ry~~ 97 (155)
T PTZ00329 86 DSKADVILKYTP 97 (155)
T ss_pred CCEEEEEEEcCH
Confidence 889999999864
No 79
>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=60.55 E-value=46 Score=32.93 Aligned_cols=64 Identities=11% Similarity=-0.039 Sum_probs=45.3
Q ss_pred ceEEEEEEeccceEEEccCCCCCCceEEEecccccCCCCCCcccccccCCCcccCCCeEEEecCCC-CCceEEEEEEECC
Q 000294 504 DFGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVSEGPS-KDRQGIVKKIYRG 582 (1711)
Q Consensus 504 TVGVIVrVEkDe~fkVLd~~gd~~~VvtVk~~~I~~K~~~rr~vAtD~~gk~I~vGD~VKVIdGp~-kGRqG~VlHIyRs 582 (1711)
.+|.|+++-.+..|.|.+.++ ..+.+.. ..|+. ..--|+.||.|.|--=++ .-..|.|+|+|..
T Consensus 2 ~i~~V~~~lG~~~~~V~~~dg---~~~l~~i---~gK~R---------k~iwI~~GD~VlV~~~~~~~~~kg~Iv~r~~~ 66 (78)
T cd04456 2 QIVRVLRMLGNNRHEVECADG---QRRLVSI---PGKLR---------KNIWIKRGDFLIVDPIEEGEDVKADIIFVYCK 66 (78)
T ss_pred eEEEEEEECCCCEEEEEECCC---CEEEEEE---chhhc---------cCEEEcCCCEEEEEecccCCCceEEEEEEeCH
Confidence 578999998888899887764 2444432 22221 125689999999987677 5678999999864
No 80
>PF02736 Myosin_N: Myosin N-terminal SH3-like domain; InterPro: IPR004009 This domain has an SH3-like fold. It is found at the N terminus of many but not all myosins. The function of this domain is unknown.; GO: 0003774 motor activity, 0005524 ATP binding, 0016459 myosin complex; PDB: 2EC6_A 2W4H_M 1O1E_P 1O1D_D 1O18_A 1O1C_P 1O1B_D 1O1F_A 2W4A_M 2W4G_M ....
Probab=59.78 E-value=17 Score=31.70 Aligned_cols=30 Identities=30% Similarity=0.403 Sum_probs=26.4
Q ss_pred Cc-eeEEEEEeCCeEEEEecCCceEEEEeCCc
Q 000294 675 GY-LCRVLAVRYSDVTVKLDSQQKILTVKGEH 705 (1711)
Q Consensus 675 Gy-lGiVKDaTdt~ARVELHSk~KtITVdK~~ 705 (1711)
|| +|.|+++.+..|+|+|.. .++++|++++
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 8899998764
No 81
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=59.64 E-value=96 Score=42.50 Aligned_cols=196 Identities=12% Similarity=0.100 Sum_probs=0.0
Q ss_pred ccCHHHHHHHhhcccccccccCCCEEEEecCcCCCCcEEEEEEeCCCCEEEEEEeccCchhhHHhhcCCCcccCCCCCCC
Q 000294 300 PVPKNEVSHLLSAQIKRNEVSEGTWAYVKNGKYKGDLAQVVYVNNARKRATVKLIPRIDLQALAAKFGGGVAMKKTDSPA 379 (1711)
Q Consensus 300 pVPikEM~dLL~vkkk~~~Lk~GdwVRIKrGpYKGDLAQVveVdenk~eVtVKLIPRIDy~~l~~k~~gg~~kKK~~RPP 379 (1711)
+|++.||...-++......|++|+.|++ +|+.||..+.++.|.+ ++....|-
T Consensus 605 LvhiSEls~~~~~~~p~~~~kvGd~V~v----------kVl~iD~e~~rIsLS~------------------K~l~~~Pw 656 (863)
T PRK12269 605 LAHISEFSWVKKTSKPSDMVKIGDEVEC----------MILGYDIQAGRVSLGL------------------KQVTANPW 656 (863)
T ss_pred eeEHHHhcCccccCCHHHcCCCCCEEEE----------EEEEEecccCceEEEe------------------hhcccCch
Q ss_pred CCCCChhhHhhhcCcee--ecccCCCCceEEecCCceeecceEEEEEeccceEecCCCCCHHHHhhcCCCCCCccccHHH
Q 000294 380 PRLISPSELEEFRPLIQ--YRRDRDTGKVFENLDGMMLKDGYLYKKVSIDSLSCWGVVPSEEELLKFQPSESNESADLEW 457 (1711)
Q Consensus 380 qRLFn~~Eark~~~~~~--~rrd~~tg~~f~i~~G~~y~DGFLyK~fkI~sL~t~dVnPTLEEL~kF~~~~~de~~DL~~ 457 (1711)
..| .+....+..++ +..-...|-+..+..| ++|||. ++.|....+...++++ |..+.
T Consensus 657 ~~~---~~~~~vG~~v~G~V~~i~~~G~fV~l~~g---V~GlIh----~sels~~~~~~~~~~~--~kvGq--------- 715 (863)
T PRK12269 657 EEI---EARYPVGARFTRRIVKVTNAGAFIEMEEG---IDGFLH----VDDLSWVKRTRPADHE--LEVGK--------- 715 (863)
T ss_pred HHH---HHhCCCCCEEEEEEEEEecceEEEEeCCC---cEEEEE----hHHhhccccccchhhc--cCCCC---------
Q ss_pred HHHHHhccccccEEEeecCCCcccccCCCCcC-------cccccCceEEEcCCceEEEEEEeccceEEEccCCCCCCceE
Q 000294 458 LSQLYGERKKKRTTIVGKGGDKGEGSSGSSLE-------NSFELYELVCFGRKDFGLIVGMEKDDHYKILKEGSEGPAVV 530 (1711)
Q Consensus 458 La~~~ge~kk~kii~v~kGg~kgE~ssG~~s~-------G~FeLgDLVQLD~~TVGVIVrVEkDe~fkVLd~~gd~~~Vv 530 (1711)
.-+.+|+.+.....+-..+.=.... ..|.+||.|. |.|++|...-.|+-|..+ ..-
T Consensus 716 -------~VkvkVl~ID~e~rrI~LS~K~l~~dpw~~~~~~~~vG~iV~------GkV~~v~~~GvFVeL~~g----VeG 778 (863)
T PRK12269 716 -------EIECMVIECDPQARRIRLGVKQLSDNPWQVFANAYGVGSTVE------GEVSSVTDFGIFVRVPGG----VEG 778 (863)
T ss_pred -------EEEEEEEEEeccCCEEEEEecccccChHHHHHhhCCCCCEEE------EEEEEEecCeEEEEcCCC----eEE
Q ss_pred EEecccccCCCCCCcccccccCCCcccCCCeEEEe
Q 000294 531 TVERRTLKNGPFDMKFTALDQSMKVISLNDTARVS 565 (1711)
Q Consensus 531 tVk~~~I~~K~~~rr~vAtD~~gk~I~vGD~VKVI 565 (1711)
.|..++|....... .....+.|++||.|+++
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 82
>PRK04333 50S ribosomal protein L14e; Validated
Probab=58.59 E-value=13 Score=37.18 Aligned_cols=31 Identities=23% Similarity=0.288 Sum_probs=25.8
Q ss_pred cccCCEEEEccCCCCCceeEEEEEe-CCeEEE
Q 000294 660 FAVGQTLRIRVGPLKGYLCRVLAVR-YSDVTV 690 (1711)
Q Consensus 660 ~lIGKTVkIrkGPYKGylGiVKDaT-dt~ARV 690 (1711)
.-+|+-|.|..|+|+|.+.+|+++- +.+|-|
T Consensus 4 v~~GrvV~~~~Grd~gk~~vIv~i~d~~~vlV 35 (84)
T PRK04333 4 IEVGRVCVKTAGREAGRKCVIVDIIDKNFVLV 35 (84)
T ss_pred ccccEEEEEeccCCCCCEEEEEEEecCCEEEE
Confidence 3478999999999999999999994 545554
No 83
>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=58.55 E-value=6.9 Score=50.99 Aligned_cols=30 Identities=23% Similarity=0.201 Sum_probs=16.2
Q ss_pred hhHHHHhcCCCCeEe-ccccccCHHHHHHHh
Q 000294 281 CDINEACKGLSGIYY-SRLAPVPKNEVSHLL 310 (1711)
Q Consensus 281 ~dVk~AIkGI~gVy~-~k~~pVPikEM~dLL 310 (1711)
+.++.||=|+...|. .++..-....+..+|
T Consensus 236 d~LW~AIvGlT~q~i~~~i~~~~Y~~~~~~L 266 (622)
T PF02724_consen 236 DLLWLAIVGLTDQYIHERISSERYDRYVPLL 266 (622)
T ss_pred HHHHHHHHhhhHHhhhcccchhhHHHHHHHH
Confidence 457888888877654 233333333334444
No 84
>smart00361 RRM_1 RNA recognition motif.
Probab=58.34 E-value=22 Score=33.24 Aligned_cols=28 Identities=29% Similarity=0.540 Sum_probs=24.9
Q ss_pred CCCCcEEEEEeccchhHHHHhcCCCCeE
Q 000294 267 DHIKGFIFIEADKQCDINEACKGLSGIY 294 (1711)
Q Consensus 267 d~lKGYIYIEA~kq~dVk~AIkGI~gVy 294 (1711)
.+.+||+||+-...++...||+.|.+-+
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 85
>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=57.12 E-value=24 Score=35.19 Aligned_cols=43 Identities=14% Similarity=0.244 Sum_probs=35.3
Q ss_pred ccCCEEEEccCCCCCceeEEEEEeCCeEEEEecCCceEEEEeCCcccc
Q 000294 661 AVGQTLRIRVGPLKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLAE 708 (1711)
Q Consensus 661 lIGKTVkIrkGPYKGylGiVKDaTdt~ARVELHSk~KtITVdK~~Ls~ 708 (1711)
..|+.|....| ..|+|+++.++++.||+. ..-.|+|+|..++.
T Consensus 39 ~~Gd~VvT~gG----i~G~V~~i~d~~v~vei~-~g~~i~~~r~aI~~ 81 (84)
T TIGR00739 39 KKGDKVLTIGG----IIGTVTKIAENTIVIELN-DNTEITFSKNAIVE 81 (84)
T ss_pred CCCCEEEECCC----eEEEEEEEeCCEEEEEEC-CCeEEEEEhHHhhh
Confidence 45778877665 789999999999999985 56779999998763
No 86
>PRK14635 hypothetical protein; Provisional
Probab=56.95 E-value=13 Score=40.84 Aligned_cols=49 Identities=12% Similarity=0.087 Sum_probs=37.8
Q ss_pred cccCCEEEEcc---C--CCCCceeEEEEEeCCeEEEEecCC------ceEEEEeCCcccc
Q 000294 660 FAVGQTLRIRV---G--PLKGYLCRVLAVRYSDVTVKLDSQ------QKILTVKGEHLAE 708 (1711)
Q Consensus 660 ~lIGKTVkIrk---G--PYKGylGiVKDaTdt~ARVELHSk------~KtITVdK~~Ls~ 708 (1711)
+++|+.|+|+- + .|+|++|++++++++.+++++..+ .++++++.+.|.-
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 47899988752 2 567888899999999999988543 5678888877763
No 87
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=56.28 E-value=48 Score=34.30 Aligned_cols=73 Identities=12% Similarity=0.002 Sum_probs=50.1
Q ss_pred cCceEEEcC-CceEEEEEEeccceEEEccCCCCCCceEEEecccccCCCCCCcccccccCCCcccCCCeEEEecCCCCCc
Q 000294 494 LYELVCFGR-KDFGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVSEGPSKDR 572 (1711)
Q Consensus 494 LgDLVQLD~-~TVGVIVrVEkDe~fkVLd~~gd~~~VvtVk~~~I~~K~~~rr~vAtD~~gk~I~vGD~VKVIdGp~kGR 572 (1711)
..+++.... +..|+|+++-.+..|.|.+.++ ..+.+. |..|+. ..--|..||.|.|--=+|.-.
T Consensus 12 ~~~~~~p~e~e~~g~V~~~lG~~~~~V~~~dG---~~~la~---i~GK~R---------k~IwI~~GD~VlVe~~~~~~~ 76 (100)
T PRK04012 12 RVRLPMPEEGEVFGVVEQMLGANRVRVRCMDG---VERMGR---IPGKMK---------KRMWIREGDVVIVAPWDFQDE 76 (100)
T ss_pred eEEccCCCCCEEEEEEEEEcCCCEEEEEeCCC---CEEEEE---Echhhc---------ccEEecCCCEEEEEecccCCC
Confidence 345555544 4679999998888999997764 233433 222321 134678999999986677777
Q ss_pred eEEEEEEEC
Q 000294 573 QGIVKKIYR 581 (1711)
Q Consensus 573 qG~VlHIyR 581 (1711)
.|.|+|+|.
T Consensus 77 kg~Iv~r~~ 85 (100)
T PRK04012 77 KADIIWRYT 85 (100)
T ss_pred EEEEEEEcC
Confidence 899999986
No 88
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=56.16 E-value=48 Score=33.74 Aligned_cols=63 Identities=13% Similarity=0.086 Sum_probs=45.7
Q ss_pred eEEEEEEeccceEEEccCCCCCCceEEEecccccCCCCCCcccccccCCCcccCCCeEEEecCCCCCceEEEEEEEC
Q 000294 505 FGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVSEGPSKDRQGIVKKIYR 581 (1711)
Q Consensus 505 VGVIVrVEkDe~fkVLd~~gd~~~VvtVk~~~I~~K~~~rr~vAtD~~gk~I~vGD~VKVIdGp~kGRqG~VlHIyR 581 (1711)
.|+|+.+-.+..|+|...++. ++... |.-|+. .+.--|.+||.|+|--=||.-..|.|++=|+
T Consensus 10 ~G~V~e~Lp~~~frV~LenG~---~vla~---isGKmR--------~~rIrIl~GD~V~VE~spYDltkGRIiyR~~ 72 (87)
T PRK12442 10 DGIVDEVLPDSRFRVTLENGV---EVGAY---ASGRMR--------KHRIRILAGDRVTLELSPYDLTKGRINFRHK 72 (87)
T ss_pred EEEEEEECCCCEEEEEeCCCC---EEEEE---ecccee--------eeeEEecCCCEEEEEECcccCCceeEEEEec
Confidence 599999988889998877642 33332 333432 1344688999999988899888899988775
No 89
>TIGR00523 eIF-1A eukaryotic/archaeal initiation factor 1A. Recommended nomenclature: eIF-1A for eukaryotes, aIF-1A for Archaea. Also called eIF-4C
Probab=56.10 E-value=37 Score=34.99 Aligned_cols=64 Identities=14% Similarity=-0.022 Sum_probs=43.0
Q ss_pred CCceEEEEEEeccceEEEccCCCCCCceEEEecccccCCCCCCcccccccCCCcccCCCeEEEecCCCCC---ceEEEEE
Q 000294 502 RKDFGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVSEGPSKD---RQGIVKK 578 (1711)
Q Consensus 502 ~~TVGVIVrVEkDe~fkVLd~~gd~~~VvtVk~~~I~~K~~~rr~vAtD~~gk~I~vGD~VKVIdGp~kG---RqG~VlH 578 (1711)
.+.+|.|+++-.+..|.|.+.++ ..+.+. |..|+. ..--|..||.|.|- |+.- ..|.|+|
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 35779999998888899987664 233333 222321 23468999999993 5533 3699999
Q ss_pred EECC
Q 000294 579 IYRG 582 (1711)
Q Consensus 579 IyRs 582 (1711)
+|..
T Consensus 82 r~~~ 85 (99)
T TIGR00523 82 RYTK 85 (99)
T ss_pred EcCH
Confidence 8863
No 90
>PRK05585 yajC preprotein translocase subunit YajC; Validated
Probab=55.52 E-value=26 Score=36.44 Aligned_cols=44 Identities=20% Similarity=0.286 Sum_probs=36.4
Q ss_pred ccCCEEEEccCCCCCceeEEEEEeCCeEEEEecCCceEEEEeCCccccc
Q 000294 661 AVGQTLRIRVGPLKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLAEV 709 (1711)
Q Consensus 661 lIGKTVkIrkGPYKGylGiVKDaTdt~ARVELHSk~KtITVdK~~Ls~v 709 (1711)
-+|+.|.-..| ..|+|+++.+++|.||+ +..-+|+|+|.-|..+
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 45778877665 77999999999999999 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=54.35 E-value=11 Score=50.30 Aligned_cols=7 Identities=29% Similarity=0.439 Sum_probs=3.0
Q ss_pred eecCccc
Q 000294 71 IVCDPEM 77 (1711)
Q Consensus 71 ~~~~~~~ 77 (1711)
+.|+|+.
T Consensus 545 ~~~~~~~ 551 (784)
T PF04931_consen 545 LYNGPEE 551 (784)
T ss_pred HhcCChH
Confidence 3344443
No 92
>COG1862 YajC Preprotein translocase subunit YajC [Intracellular trafficking and secretion]
Probab=54.01 E-value=23 Score=36.41 Aligned_cols=46 Identities=22% Similarity=0.224 Sum_probs=38.0
Q ss_pred cCCEEEEccCCCCCceeEEEEEeCCeEEEEecCCceEEEEeCCccccccCC
Q 000294 662 VGQTLRIRVGPLKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLAEVRGK 712 (1711)
Q Consensus 662 IGKTVkIrkGPYKGylGiVKDaTdt~ARVELHSk~KtITVdK~~Ls~v~~~ 712 (1711)
.|+.|.... |+.|+|..+.++++.|||. .+-.|+|.|+.+..+..+
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 366776665 4889999999999999999 888899999999865443
No 93
>PTZ00065 60S ribosomal protein L14; Provisional
Probab=53.68 E-value=17 Score=39.07 Aligned_cols=33 Identities=24% Similarity=0.333 Sum_probs=28.1
Q ss_pred cccCCCEEEEecCcCCCCcEEEEEEeCCCCEEEE
Q 000294 318 EVSEGTWAYVKNGKYKGDLAQVVYVNNARKRATV 351 (1711)
Q Consensus 318 ~Lk~GdwVRIKrGpYKGDLAQVveVdenk~eVtV 351 (1711)
-+++|=.|.|..|||+|-||.|++|-+. ++|.|
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 94
>KOG1708 consensus Mitochondrial/chloroplast ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=53.53 E-value=12 Score=42.59 Aligned_cols=40 Identities=35% Similarity=0.356 Sum_probs=31.6
Q ss_pred ccccCCEEEEccCCCCCceeEEEEEeC--CeEEEE-ecCCceE
Q 000294 659 MFAVGQTLRIRVGPLKGYLCRVLAVRY--SDVTVK-LDSQQKI 698 (1711)
Q Consensus 659 d~lIGKTVkIrkGPYKGylGiVKDaTd--t~ARVE-LHSk~Kt 698 (1711)
.++.|+||.|+.|.-||.+|+|..+.. +.|-|+ ||++-++
T Consensus 72 ~ff~GDtVeVlvGkDkGkqG~Vtqv~r~~s~VvV~gln~k~r~ 114 (236)
T KOG1708|consen 72 HFFFGDTVEVLVGKDKGKQGEVTQVIRHRSWVVVKGLNTKYRH 114 (236)
T ss_pred eEecCCEEEEEecccCCccceEEEEeecCceEEEcccchhhhh
Confidence 357799999999999999999999864 456665 6666553
No 95
>PLN03111 DNA-directed RNA polymerase II subunit family protein; Provisional
Probab=53.52 E-value=82 Score=36.47 Aligned_cols=55 Identities=11% Similarity=0.085 Sum_probs=34.7
Q ss_pred EEEEeccchhHHHHhcCCCCeEeccccccCHHHHHHHhhc---cc-------------ccccccCCCEEEEec
Q 000294 273 IFIEADKQCDINEACKGLSGIYYSRLAPVPKNEVSHLLSA---QI-------------KRNEVSEGTWAYVKN 329 (1711)
Q Consensus 273 IYIEA~kq~dVk~AIkGI~gVy~~k~~pVPikEM~dLL~v---kk-------------k~~~Lk~GdwVRIKr 329 (1711)
..||.+.+.++.-- =+.++...+-.+++.+|...||+. +. +...+++|+.|+|+|
T Consensus 121 ~~iE~F~e~eLlvn--it~H~lVPkH~~ls~eEk~~lL~~y~i~~~qLPrI~~~DPvary~g~k~G~vvkI~R 191 (206)
T PLN03111 121 FKIEVFQETELLVN--ITKHVLVPKHQVLTDEEKKTLLKRYTVKETQLPRIQVSDPIARYYGLKRGQVVKIIR 191 (206)
T ss_pred ceEEEeehhHheec--cccceecCCeEEcCHHHHHHHHHHcCCCHHHCCcccccChhhHhcCCCCCCEEEEEE
Confidence 34676666554322 122444556677889999999962 11 134678899998876
No 96
>PTZ00065 60S ribosomal protein L14; Provisional
Probab=52.36 E-value=25 Score=37.89 Aligned_cols=35 Identities=26% Similarity=0.424 Sum_probs=28.3
Q ss_pred cccCCEEEEccCCCCCceeEEEEEeCCeEEEEecCC
Q 000294 660 FAVGQTLRIRVGPLKGYLCRVLAVRYSDVTVKLDSQ 695 (1711)
Q Consensus 660 ~lIGKTVkIrkGPYKGylGiVKDaTdt~ARVELHSk 695 (1711)
.-||..|.|..|||+|-|+.|+||-|.. ||.++-.
T Consensus 8 VEiGRVvli~~Gp~~GKL~vIVDIID~n-RvLVDGP 42 (130)
T PTZ00065 8 VEPGRLCLIQYGPDAGKLCFIVDIVTPT-RVLVDGA 42 (130)
T ss_pred eeeceEEEEecCCCCCCEEEEEEEEcCC-eEEEeCC
Confidence 3579999999999999999999997543 5555555
No 97
>PTZ00415 transmission-blocking target antigen s230; Provisional
Probab=52.28 E-value=6.9 Score=54.77 Aligned_cols=17 Identities=24% Similarity=0.184 Sum_probs=8.1
Q ss_pred CccccCCCCCCCCCCcc
Q 000294 93 GKRKRNDGSSGVKPHNR 109 (1711)
Q Consensus 93 ~~~~~~~~~~~~~~r~r 109 (1711)
||.++.+-+.-+-.|||
T Consensus 120 g~~~~~~~d~~i~~~~~ 136 (2849)
T PTZ00415 120 GKAEIGDLDMIIIKRRR 136 (2849)
T ss_pred chhhcCCcceEEeehHH
Confidence 55555555544443333
No 98
>PRK11634 ATP-dependent RNA helicase DeaD; Provisional
Probab=51.35 E-value=25 Score=45.99 Aligned_cols=11 Identities=9% Similarity=0.045 Sum_probs=6.1
Q ss_pred cCHHHHHHHhh
Q 000294 301 VPKNEVSHLLS 311 (1711)
Q Consensus 301 VPikEM~dLL~ 311 (1711)
++.++...+|.
T Consensus 279 ~~q~~R~~il~ 289 (629)
T PRK11634 279 MNQALREQTLE 289 (629)
T ss_pred CCHHHHHHHHH
Confidence 45556555554
No 99
>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=51.06 E-value=56 Score=30.91 Aligned_cols=62 Identities=13% Similarity=0.066 Sum_probs=42.5
Q ss_pred CceEEEEEEeccceEEEccCCCCCCceEEEecccccCCCCCCcccccccCCCcccCCCeEEEecCCCCCceEEEEEE
Q 000294 503 KDFGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVSEGPSKDRQGIVKKI 579 (1711)
Q Consensus 503 ~TVGVIVrVEkDe~fkVLd~~gd~~~VvtVk~~~I~~K~~~rr~vAtD~~gk~I~vGD~VKVIdGp~kGRqG~VlHI 579 (1711)
+.+|+|+++..+..|.|...++ ..+.+.+. .| -++.--|+.||.|.|---++.-..|.|+|.
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---------FRKRIWIKRGDFVLVEPSPYDKVKGRIIYR 65 (65)
T ss_dssp EEEEEEEEEESSSEEEEEETTS---EEEEEEE----HH---------HHTCC---TTEEEEEEESTTCTTEEEEEEE
T ss_pred EEEEEEEEECCCCEEEEEeCCC---CEEEEEec---cc---------eeeeEecCCCCEEEEEecccCCCeEEEEEC
Confidence 3579999999888999988764 34444332 12 124457999999999877888889999884
No 100
>COG3109 ProQ Activator of osmoprotectant transporter ProP [Signal transduction mechanisms]
Probab=50.90 E-value=22 Score=39.91 Aligned_cols=46 Identities=33% Similarity=0.563 Sum_probs=37.8
Q ss_pred cccCCEEEEccCCCCCceeEEEEEeCCeEEEEecCCceEEEEeCCccc
Q 000294 660 FAVGQTLRIRVGPLKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLA 707 (1711)
Q Consensus 660 ~lIGKTVkIrkGPYKGylGiVKDaTdt~ARVELHSk~KtITVdK~~Ls 707 (1711)
-.||+.|+|..|. --.--+|++|+.+.|||+|.+... ++|..+||.
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 345679999999999999998776 667778874
No 101
>COG4371 Predicted membrane protein [Function unknown]
Probab=50.37 E-value=26 Score=41.24 Aligned_cols=7 Identities=43% Similarity=0.914 Sum_probs=3.0
Q ss_pred CCCCCCC
Q 000294 1452 SGNFRGR 1458 (1711)
Q Consensus 1452 g~~~~g~ 1458 (1711)
|++||+.
T Consensus 55 GgSfrap 61 (334)
T COG4371 55 GGSFRAP 61 (334)
T ss_pred CCCCCCC
Confidence 3444443
No 102
>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=50.05 E-value=14 Score=48.38 Aligned_cols=13 Identities=31% Similarity=0.636 Sum_probs=6.6
Q ss_pred HHHHHHHHHHhcc
Q 000294 184 EEFDKMMEERYKS 196 (1711)
Q Consensus 184 EelAe~lkERY~r 196 (1711)
++..+.|++.|..
T Consensus 199 ~~~~~~i~~yY~~ 211 (622)
T PF02724_consen 199 EEYREEIEKYYSQ 211 (622)
T ss_pred HHHHHHHHHHHhc
Confidence 3445555555543
No 103
>PRK14639 hypothetical protein; Provisional
Probab=49.14 E-value=28 Score=37.60 Aligned_cols=49 Identities=10% Similarity=0.231 Sum_probs=39.1
Q ss_pred cccCCEEEEccCCCCCceeEEEEEeCCeEEEEecCCceEEEEeCCcccc
Q 000294 660 FAVGQTLRIRVGPLKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLAE 708 (1711)
Q Consensus 660 ~lIGKTVkIrkGPYKGylGiVKDaTdt~ARVELHSk~KtITVdK~~Ls~ 708 (1711)
+++|+.|+|+-.--|=+.|++++++++.++|++-...++++|+.+.|.-
T Consensus 85 r~~G~~v~v~l~~~~~~~G~L~~~~~~~i~l~~~~~~~~~~i~~~~I~k 133 (140)
T PRK14639 85 KSIGELVKITTNEKEKFEGKIVSVDDENITLENLENKEKTTINFNDIKK 133 (140)
T ss_pred HhCCCEEEEEECCCcEEEEEEEEEeCCEEEEEEccCCcEEEEEhHHeee
Confidence 4799999998644588899999999999999764345678888877763
No 104
>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=48.64 E-value=26 Score=31.92 Aligned_cols=66 Identities=17% Similarity=0.179 Sum_probs=40.2
Q ss_pred EEEEEEeCCCCcEEEEEeccchhHHHHhcCCCCeEeccccccCHHHHHHHhhcccccccccCCCEEEEecCcCCCCcEEE
Q 000294 260 IISAFAVDHIKGFIFIEADKQCDINEACKGLSGIYYSRLAPVPKNEVSHLLSAQIKRNEVSEGTWAYVKNGKYKGDLAQV 339 (1711)
Q Consensus 260 I~SVFvpd~lKGYIYIEA~kq~dVk~AIkGI~gVy~~k~~pVPikEM~dLL~vkkk~~~Lk~GdwVRIKrGpYKGDLAQV 339 (1711)
|+.+.+....+-.||||... ++. .+|++.||............|++|+.|+++ |
T Consensus 3 ~~~g~V~~i~~~G~fv~l~~---------~~~-------Glv~~~~l~~~~~~~~~~~~~~~G~~v~v~----------v 56 (69)
T cd05690 3 VVSGKIKSITDFGIFVGLDG---------GID-------GLVHISDISWTQRVRHPSEIYKKGQEVEAV----------V 56 (69)
T ss_pred EEEEEEEEEEeeeEEEEeCC---------CCE-------EEEEHHHCCCccccCChhhEECCCCEEEEE----------E
Confidence 45555555556668888753 122 245556665212222223458999999985 8
Q ss_pred EEEeCCCCEEEE
Q 000294 340 VYVNNARKRATV 351 (1711)
Q Consensus 340 veVdenk~eVtV 351 (1711)
++|+.++.++.+
T Consensus 57 ~~id~~~~~i~l 68 (69)
T cd05690 57 LNIDVERERISL 68 (69)
T ss_pred EEEECCcCEEeC
Confidence 999988877654
No 105
>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=48.51 E-value=43 Score=33.70 Aligned_cols=48 Identities=13% Similarity=0.079 Sum_probs=37.7
Q ss_pred cccCCEEEEccCC---CCCceeEEEEEeCCeEEEEecCCceEEEEeCCcccc
Q 000294 660 FAVGQTLRIRVGP---LKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLAE 708 (1711)
Q Consensus 660 ~lIGKTVkIrkGP---YKGylGiVKDaTdt~ARVELHSk~KtITVdK~~Ls~ 708 (1711)
.|+|-.|+|+.=+ |-|..|||++-|..+..|+ ....++++|+|.+-.+
T Consensus 11 dl~G~~i~V~~s~~pslvG~~GiVV~ETknt~~I~-t~~~~~~~IpK~~~vF 61 (89)
T PF01868_consen 11 DLIGAKIEVVRSKNPSLVGIEGIVVDETKNTFVIV-TEDGKVKTIPKAGSVF 61 (89)
T ss_dssp --TT-EEEEEEESSCCCTTEEEEEEEEETTEEEEE-ETTEEEEEEESTTEEE
T ss_pred hhcCCEEEEEEcCCCCccCCEEEEEEcccceEEEE-ecCCcEEEEecCCEEE
Confidence 5899999999873 7899999999999999976 3344789999998764
No 106
>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=48.04 E-value=61 Score=39.75 Aligned_cols=68 Identities=15% Similarity=0.177 Sum_probs=44.5
Q ss_pred CCCCCCCcEEEEEeccchHHHHHHHHHHHHHhhccCCCCCcEEEEEEeC-----CCCcEEEEEeccchhHHHHhcCCCCe
Q 000294 219 MPCPEDPTIWKVKCMAGRERQSAFCLMQKFVDLQSLGSKMQIISAFAVD-----HIKGFIFIEADKQCDINEACKGLSGI 293 (1711)
Q Consensus 219 LPSV~DPkLWaVKCk~GkEReVV~~LmrKii~lq~~g~~L~I~SVFvpd-----~lKGYIYIEA~kq~dVk~AIkGI~gV 293 (1711)
.+...+-+||+=.+-.--..+.+..|...+ . .|.+|.+.. ..+||-|||-..++++..||+.|.++
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 377776542 35699999999999999999988875
Q ss_pred Ee
Q 000294 294 YY 295 (1711)
Q Consensus 294 y~ 295 (1711)
..
T Consensus 173 ~l 174 (346)
T TIGR01659 173 TV 174 (346)
T ss_pred cc
Confidence 43
No 107
>smart00538 POP4 A domain found in a protein subunit of human RNase MRP and RNase P ribonucleoprotein complexes and archaeal proteins.
Probab=47.93 E-value=42 Score=34.12 Aligned_cols=47 Identities=15% Similarity=0.188 Sum_probs=39.2
Q ss_pred cccCCEEEEccCC---CCCceeEEEEEeCCeEEEEecCCceEEEEeCCccc
Q 000294 660 FAVGQTLRIRVGP---LKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLA 707 (1711)
Q Consensus 660 ~lIGKTVkIrkGP---YKGylGiVKDaTdt~ARVELHSk~KtITVdK~~Ls 707 (1711)
.|||-.|+|+.=+ |-|..|||++-|..+..|+... +++.+|+|.+-.
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 6789999999999999987654 577889988844
No 108
>PRK00092 ribosome maturation protein RimP; Reviewed
Probab=47.22 E-value=29 Score=37.69 Aligned_cols=49 Identities=18% Similarity=0.352 Sum_probs=38.1
Q ss_pred cccCCEEEEc----cCCCCCceeEEEEEeCCeEEEEecCCceEEEEeCCcccc
Q 000294 660 FAVGQTLRIR----VGPLKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLAE 708 (1711)
Q Consensus 660 ~lIGKTVkIr----kGPYKGylGiVKDaTdt~ARVELHSk~KtITVdK~~Ls~ 708 (1711)
..+|+.|+|+ ...-|=+.|++++++++.+++++..+.++++|+.+.|..
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 233456689999999999998876443488998888764
No 109
>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=47.16 E-value=77 Score=46.90 Aligned_cols=93 Identities=11% Similarity=0.106 Sum_probs=66.1
Q ss_pred CcccccCceEEEcCCceEEEEEEeccceEEEccCCCCCCceEEEecccccCCCCCCcccccccCCCcccCCCeEEEecC-
Q 000294 489 ENSFELYELVCFGRKDFGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVSEG- 567 (1711)
Q Consensus 489 ~G~FeLgDLVQLD~~TVGVIVrVEkDe~fkVLd~~gd~~~VvtVk~~~I~~K~~~rr~vAtD~~gk~I~vGD~VKVIdG- 567 (1711)
...|+.||+|+|.....-.|+.|+++....+|....+ +..+.+.|.++.. ..+........+|..||.|+...-
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 4689999999999999999999998766666644111 3567788876532 123455667789999999998743
Q ss_pred ----CCCCceEEEEEEECCEEEE
Q 000294 568 ----PSKDRQGIVKKIYRGILFI 586 (1711)
Q Consensus 568 ----p~kGRqG~VlHIyRs~VFL 586 (1711)
-..|..++|+.|..+.+.+
T Consensus 1402 ~~~g~~n~~~~~V~~v~~~~~~~ 1424 (1960)
T TIGR02760 1402 KNRGIKANEVYTVTQVVNGLSVQ 1424 (1960)
T ss_pred cccccccCCeEEEEEEcCCcEEE
Confidence 2246788999986654333
No 110
>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor. Members of this subfamily are found in plants, metazoa and fungi.
Probab=46.79 E-value=29 Score=43.25 Aligned_cols=49 Identities=16% Similarity=0.162 Sum_probs=36.1
Q ss_pred HHHHHHHHHHhhccCCCCCcEEEEEEeCC--------CCcEEEEEeccchhHHHHhcCCCCeE
Q 000294 240 SAFCLMQKFVDLQSLGSKMQIISAFAVDH--------IKGFIFIEADKQCDINEACKGLSGIY 294 (1711)
Q Consensus 240 VV~~LmrKii~lq~~g~~L~I~SVFvpd~--------lKGYIYIEA~kq~dVk~AIkGI~gVy 294 (1711)
|+..|.+.|..+. .|.+|+++.. -.||||||-...++...||..|.+..
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 3444555554443 4888888742 25999999999999999999999853
No 111
>PRK05886 yajC preprotein translocase subunit YajC; Validated
Probab=46.30 E-value=46 Score=35.03 Aligned_cols=43 Identities=9% Similarity=0.178 Sum_probs=35.0
Q ss_pred ccCCEEEEccCCCCCceeEEEEEeCCeEEEEecCCceEEEEeCCcccc
Q 000294 661 AVGQTLRIRVGPLKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLAE 708 (1711)
Q Consensus 661 lIGKTVkIrkGPYKGylGiVKDaTdt~ARVELHSk~KtITVdK~~Ls~ 708 (1711)
-.|+.|.-.. |+.|+|+++++++|.||+. ..-.|+|.|..|..
T Consensus 40 k~GD~VvT~g----Gi~G~V~~I~d~~v~leia-~gv~i~~~r~AI~~ 82 (109)
T PRK05886 40 QPGDRVHTTS----GLQATIVGITDDTVDLEIA-PGVVTTWMKLAVRD 82 (109)
T ss_pred CCCCEEEECC----CeEEEEEEEeCCEEEEEEC-CCeEEEEEhhheee
Confidence 3577776655 4889999999999999995 45679999999984
No 112
>PRK02749 photosystem I reaction center subunit IV; Provisional
Probab=46.07 E-value=33 Score=33.44 Aligned_cols=43 Identities=12% Similarity=0.295 Sum_probs=32.0
Q ss_pred ccCCCEEEEecC--cCCCCcEEEEEEeCCCCE--EEEEEeccCchhhH
Q 000294 319 VSEGTWAYVKNG--KYKGDLAQVVYVNNARKR--ATVKLIPRIDLQAL 362 (1711)
Q Consensus 319 Lk~GdwVRIKrG--pYKGDLAQVveVdenk~e--VtVKLIPRIDy~~l 362 (1711)
|+.|+.|||+|. -+=+|++.|+.||...-+ |+|+ |-.++|..+
T Consensus 3 i~rGskVrIlR~ESYWyn~vGtV~svD~sgi~YPV~VR-F~kvNY~g~ 49 (71)
T PRK02749 3 ISRGDKVRILRPESYWYNEVGTVASVDKSGIKYPVIVR-FDKVNYNGF 49 (71)
T ss_pred cccCCEEEEccccceeecCcceEEEEccCCCeeeEEEE-eeeeecccc
Confidence 578999999996 467899999999998643 4444 345566543
No 113
>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=45.81 E-value=36 Score=35.46 Aligned_cols=25 Identities=16% Similarity=0.106 Sum_probs=21.1
Q ss_pred CCcccccccCCCcccCCCeEEEecC
Q 000294 543 DMKFTALDQSMKVISLNDTARVSEG 567 (1711)
Q Consensus 543 ~rr~vAtD~~gk~I~vGD~VKVIdG 567 (1711)
..++.|.|...++.++||+|+|.+-
T Consensus 63 ~kky~aHDe~cn~~kvGD~V~I~E~ 87 (102)
T TIGR03630 63 RSKIHAHNPPCIDVKEGDIVIIGET 87 (102)
T ss_pred eeeEEEECCCCCCCCCCCEEEEEEc
Confidence 3458899977789999999999875
No 114
>PRK08572 rps17p 30S ribosomal protein S17P; Reviewed
Probab=45.12 E-value=37 Score=35.64 Aligned_cols=25 Identities=12% Similarity=0.183 Sum_probs=21.3
Q ss_pred CCcccccccCCCcccCCCeEEEecC
Q 000294 543 DMKFTALDQSMKVISLNDTARVSEG 567 (1711)
Q Consensus 543 ~rr~vAtD~~gk~I~vGD~VKVIdG 567 (1711)
..++.|.|...++.++||.|+|.+-
T Consensus 65 ~kky~aHDe~cn~~kvGD~V~I~E~ 89 (108)
T PRK08572 65 RSRIHAHNPPCIDAKVGDKVKIAEC 89 (108)
T ss_pred eeeEEEECCCCCCCCCCCEEEEEEc
Confidence 3458899977799999999999976
No 115
>PF10446 DUF2457: Protein of unknown function (DUF2457); InterPro: IPR018853 This entry represents a family of uncharacterised proteins.
Probab=44.44 E-value=12 Score=46.97 Aligned_cols=8 Identities=13% Similarity=0.405 Sum_probs=3.5
Q ss_pred CcEEEEEe
Q 000294 225 PTIWKVKC 232 (1711)
Q Consensus 225 PkLWaVKC 232 (1711)
..||+-..
T Consensus 122 ~~~WtP~~ 129 (458)
T PF10446_consen 122 YEFWTPGA 129 (458)
T ss_pred ceeecccc
Confidence 33444443
No 116
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=44.33 E-value=53 Score=29.00 Aligned_cols=67 Identities=16% Similarity=0.234 Sum_probs=41.8
Q ss_pred EEEEEEeCCCCcEEEEEeccchhHHHHhcCCCCeEeccccccCHHHHHHHhhcccccccccCCCEEEEecCcCCCCcEEE
Q 000294 260 IISAFAVDHIKGFIFIEADKQCDINEACKGLSGIYYSRLAPVPKNEVSHLLSAQIKRNEVSEGTWAYVKNGKYKGDLAQV 339 (1711)
Q Consensus 260 I~SVFvpd~lKGYIYIEA~kq~dVk~AIkGI~gVy~~k~~pVPikEM~dLL~vkkk~~~Lk~GdwVRIKrGpYKGDLAQV 339 (1711)
|+.+++....+.++||+... ++. ..||..||.+-.. ......|++|+.|++ +|
T Consensus 5 ~v~g~V~~v~~~g~~v~i~~---------~~~-------g~l~~~~~~~~~~-~~~~~~~~~G~~v~~----------~V 57 (72)
T smart00316 5 VVEGTVTEITPFGAFVDLGN---------GVE-------GLIPISELSDKRV-KDPEEVLKVGDEVKV----------KV 57 (72)
T ss_pred EEEEEEEEEEccEEEEEeCC---------CCE-------EEEEHHHCCcccc-CCHHHeecCCCEEEE----------EE
Confidence 55566666666788887753 111 2445555554321 111235889999986 68
Q ss_pred EEEeCCCCEEEEEE
Q 000294 340 VYVNNARKRATVKL 353 (1711)
Q Consensus 340 veVdenk~eVtVKL 353 (1711)
..|+....++.|.+
T Consensus 58 ~~~~~~~~~i~ls~ 71 (72)
T smart00316 58 LSVDEEKGRIILSL 71 (72)
T ss_pred EEEeCCCCEEEEEe
Confidence 99998877777765
No 117
>cd01734 YlxS_C YxlS is a Bacillus subtilis gene of unknown function with two domains that each have an alpha/beta fold. The N-terminal domain is composed of two alpha-helices and a three-stranded beta-sheet, while the C-terminal domain is composed of one alpha-helix and a five-stranded beta-sheet. This CD represents the C-terminal domain which has a fold similar to the Sm fold of proteins like Sm-D3.
Probab=43.79 E-value=38 Score=33.30 Aligned_cols=49 Identities=24% Similarity=0.407 Sum_probs=37.3
Q ss_pred cccCCEEEEcc-CC---CCCceeEEEEEeCCeEEEEecCC--ceEEEEeCCcccc
Q 000294 660 FAVGQTLRIRV-GP---LKGYLCRVLAVRYSDVTVKLDSQ--QKILTVKGEHLAE 708 (1711)
Q Consensus 660 ~lIGKTVkIrk-GP---YKGylGiVKDaTdt~ARVELHSk--~KtITVdK~~Ls~ 708 (1711)
..||+.|+|+- -| -|-+.|+++++.++.++|+++.+ .++|+|+.++|..
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 33 35579999999999999887643 5688888877764
No 118
>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=43.78 E-value=65 Score=29.62 Aligned_cols=67 Identities=13% Similarity=0.083 Sum_probs=42.1
Q ss_pred EEEEEEeCCCCcEEEEEeccchhHHHHhcCCCCeEeccccccCHHHHHHHhhcccccccccCCCEEEEecCcCCCCcEEE
Q 000294 260 IISAFAVDHIKGFIFIEADKQCDINEACKGLSGIYYSRLAPVPKNEVSHLLSAQIKRNEVSEGTWAYVKNGKYKGDLAQV 339 (1711)
Q Consensus 260 I~SVFvpd~lKGYIYIEA~kq~dVk~AIkGI~gVy~~k~~pVPikEM~dLL~vkkk~~~Lk~GdwVRIKrGpYKGDLAQV 339 (1711)
|+.+.+....+.-||||... + ...+||+.||.+=. +......|++|+.|++ +|
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 44555555567778888742 1 23466666664321 1112235788999887 68
Q ss_pred EEEeCCCCEEEEEE
Q 000294 340 VYVNNARKRATVKL 353 (1711)
Q Consensus 340 veVdenk~eVtVKL 353 (1711)
++|+....++.|.+
T Consensus 56 ~~~d~~~~~i~ls~ 69 (70)
T cd05698 56 LSCDPEQQRLLLSC 69 (70)
T ss_pred EEEcCCCCEEEEEe
Confidence 99998888887765
No 119
>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=43.52 E-value=36 Score=36.31 Aligned_cols=49 Identities=14% Similarity=0.452 Sum_probs=35.2
Q ss_pred cccCCEEEEcc-CCCCC---ceeEEEEEeCCeEEEEecCC--ceEEEEeCCcccc
Q 000294 660 FAVGQTLRIRV-GPLKG---YLCRVLAVRYSDVTVKLDSQ--QKILTVKGEHLAE 708 (1711)
Q Consensus 660 ~lIGKTVkIrk-GPYKG---ylGiVKDaTdt~ARVELHSk--~KtITVdK~~Ls~ 708 (1711)
..||+.|+|+- -|..+ +.|++++++++.++|+++.+ .++++|+.++|.-
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 35554 69999999999999999887 4689998888763
No 120
>PRK12288 GTPase RsgA; Reviewed
Probab=41.74 E-value=1.4e+02 Score=36.69 Aligned_cols=86 Identities=9% Similarity=0.079 Sum_probs=55.2
Q ss_pred ceEEEEEEeccceEEEccCCCCCCceEEEecccccCCCCCCcccccccCCCcccCCCeEEEecCC--CCCceEEEEEEEC
Q 000294 504 DFGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVSEGP--SKDRQGIVKKIYR 581 (1711)
Q Consensus 504 TVGVIVrVEkDe~fkVLd~~gd~~~VvtVk~~~I~~K~~~rr~vAtD~~gk~I~vGD~VKVIdGp--~kGRqG~VlHIyR 581 (1711)
..|.||++.+. .+.|++..+ .++.+.++. ++ +.+-|||.|.+-.-. .....|+|.+|+.
T Consensus 40 ~~g~Vi~~~~~-~~~v~~~~g---~~~~~~~~g---~~------------~~~~vGD~V~~~~~~~~~~~~~~~I~~il~ 100 (347)
T PRK12288 40 QEGIVISRFGQ-HADVEAADG---EVHRCNIRR---TI------------RSLVTGDRVVWRPGKEALEGVSGVVEAVHP 100 (347)
T ss_pred cceEEEEEECC-EEEEEeCCC---cEEEEEecc---cC------------CCCCCCcEEEEEeCCCcccccceEEEEEec
Confidence 45999999984 788876443 355554322 11 238999999985211 0012499999998
Q ss_pred CEEEEEeCcceeeccEEEEeCCceeec
Q 000294 582 GILFIYDENETENGGYFCSKSQHCEKT 608 (1711)
Q Consensus 582 s~VFL~Sr~~tENgGIFVvRarnv~tv 608 (1711)
-+-.|.-.......-+++++...|++|
T Consensus 101 R~n~L~R~~~~~~~q~iaANvD~vlIV 127 (347)
T PRK12288 101 RTSVLTRPDYYDGVKPIAANIDQIVIV 127 (347)
T ss_pred ccceEECCCcccccceEEEEccEEEEE
Confidence 776665444444447788888887765
No 121
>CHL00125 psaE photosystem I subunit IV; Reviewed
Probab=41.42 E-value=40 Score=32.36 Aligned_cols=41 Identities=15% Similarity=0.315 Sum_probs=30.2
Q ss_pred ccCCCEEEEecC--cCCCCcEEEEEEeCCCCE--EEEEEeccCchh
Q 000294 319 VSEGTWAYVKNG--KYKGDLAQVVYVNNARKR--ATVKLIPRIDLQ 360 (1711)
Q Consensus 319 Lk~GdwVRIKrG--pYKGDLAQVveVdenk~e--VtVKLIPRIDy~ 360 (1711)
|+.|+.|||+|. -+=.|++.|+.||..+-+ |+|++ -.++|.
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 567999999996 467899999999998643 55543 345553
No 122
>PRK14637 hypothetical protein; Provisional
Probab=41.24 E-value=46 Score=36.51 Aligned_cols=46 Identities=9% Similarity=0.114 Sum_probs=35.7
Q ss_pred cccCCEEEEccCCCCCc-eeEEEEEeCCeEEEEecCCceEEEEeCCccc
Q 000294 660 FAVGQTLRIRVGPLKGY-LCRVLAVRYSDVTVKLDSQQKILTVKGEHLA 707 (1711)
Q Consensus 660 ~lIGKTVkIrkGPYKGy-lGiVKDaTdt~ARVELHSk~KtITVdK~~Ls 707 (1711)
+.+|+.|+|+-..-+-+ .|++++++++.++++. ..+++.|+.+.|.
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 4677887777665
No 123
>PRK14643 hypothetical protein; Provisional
Probab=41.12 E-value=39 Score=37.55 Aligned_cols=49 Identities=22% Similarity=0.217 Sum_probs=38.6
Q ss_pred cccCCEEEEcc-CCCCC---ceeEEEEEeCCeEEEEec----CCceEEEEeCCcccc
Q 000294 660 FAVGQTLRIRV-GPLKG---YLCRVLAVRYSDVTVKLD----SQQKILTVKGEHLAE 708 (1711)
Q Consensus 660 ~lIGKTVkIrk-GPYKG---ylGiVKDaTdt~ARVELH----Sk~KtITVdK~~Ls~ 708 (1711)
.++|+.|+|+- -|+.| +.|+++++.++.++|+|+ ...++|.|+.+.|.-
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 47999999964 45444 799999999999998864 346789998888764
No 124
>PRK14638 hypothetical protein; Provisional
Probab=40.65 E-value=39 Score=36.93 Aligned_cols=47 Identities=11% Similarity=0.142 Sum_probs=37.6
Q ss_pred cccCCEEEEccCCCCCceeEEEEEeCCeEEEEecCCceEEEEeCCcccc
Q 000294 660 FAVGQTLRIRVGPLKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLAE 708 (1711)
Q Consensus 660 ~lIGKTVkIrkGPYKGylGiVKDaTdt~ARVELHSk~KtITVdK~~Ls~ 708 (1711)
+.+|+.|+|+----|=+.|++++++++.++|++ ..++|.++.+.|.-
T Consensus 97 r~~G~~v~V~~~~~k~~~G~L~~~~~~~i~l~~--~~~~~~i~~~~I~~ 143 (150)
T PRK14638 97 RFTGKLAKIVTKDGKTFIGRIESFVDGTITISD--EKEKYEINIDDVKR 143 (150)
T ss_pred HhCCCEEEEEECCCcEEEEEEEEEeCCEEEEEE--CCcEEEEEhHHcce
Confidence 479999999753347799999999999999874 45778888777764
No 125
>PF13051 DUF3912: Protein of unknown function (DUF3912)
Probab=39.95 E-value=55 Score=31.05 Aligned_cols=49 Identities=20% Similarity=0.238 Sum_probs=34.2
Q ss_pred cccCCEEEEccCCCCCceeEEEEEe---CCeEEEEecCCceEEEEeCCcccccc
Q 000294 660 FAVGQTLRIRVGPLKGYLCRVLAVR---YSDVTVKLDSQQKILTVKGEHLAEVR 710 (1711)
Q Consensus 660 ~lIGKTVkIrkGPYKGylGiVKDaT---dt~ARVELHSk~KtITVdK~~Ls~v~ 710 (1711)
.++||...|..|||.-.+||||.-. +.+..|-+. -+.|.|.-.+|.+|.
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 333333333 345666666666543
No 126
>TIGR00008 infA translation initiation factor IF-1. This family consists of translation initiation factor IF-1 as found in bacteria and chloroplasts. This protein, about 70 residues in length, consists largely of an S1 RNA binding domain (pfam00575).
Probab=39.86 E-value=1.3e+02 Score=29.53 Aligned_cols=60 Identities=13% Similarity=0.088 Sum_probs=42.6
Q ss_pred eEEEEEEeccceEEEccCCCCCCceEEEecccccCCCCCCcccccccCCCcccCCCeEEEecCCCCCceEEEEE
Q 000294 505 FGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVSEGPSKDRQGIVKK 578 (1711)
Q Consensus 505 VGVIVrVEkDe~fkVLd~~gd~~~VvtVk~~~I~~K~~~rr~vAtD~~gk~I~vGD~VKVIdGp~kGRqG~VlH 578 (1711)
.|+|+++-.+..|+|...++ ..+... |.-|+.. +.--|.+||.|+|--=||.-..|.|+|
T Consensus 8 ~G~V~e~L~~~~f~V~l~ng---~~vla~---i~GKmr~--------~rI~I~~GD~V~Ve~spyd~tkgrIi~ 67 (68)
T TIGR00008 8 EGKVTESLPNAMFRVELENG---HEVLAH---ISGKIRM--------HYIRILPGDKVKVELSPYDLTRGRITY 67 (68)
T ss_pred EEEEEEECCCCEEEEEECCC---CEEEEE---ecCcchh--------ccEEECCCCEEEEEECcccCCcEeEEe
Confidence 59999998888999887664 233332 3334321 344689999999998888777788875
No 127
>PRK04313 30S ribosomal protein S4e; Validated
Probab=39.84 E-value=3e+02 Score=32.70 Aligned_cols=49 Identities=14% Similarity=0.122 Sum_probs=35.1
Q ss_pred ccCCEEEEccCCCCCceeEEEEEe------CCeEEEEecCCceEEEEeCCcccccc
Q 000294 661 AVGQTLRIRVGPLKGYLCRVLAVR------YSDVTVKLDSQQKILTVKGEHLAEVR 710 (1711)
Q Consensus 661 lIGKTVkIrkGPYKGylGiVKDaT------dt~ARVELHSk~KtITVdK~~Ls~v~ 710 (1711)
-+|..|.|+.|.+-|.+|+|+.+. .+.|+|| +....++.--.+.+.+++
T Consensus 173 e~G~l~~itgG~n~GriG~I~~i~~~~~~~~~~V~i~-d~~G~~F~T~~~~vfvIG 227 (237)
T PRK04313 173 EEGNLAIITGGKHVGEIGKIKEIEVTKSSKPNIVTLE-DKDGEKFETILDYVFVIG 227 (237)
T ss_pred CCCCEEEEECCeeeeeEEEEEEEEEccCCCCcEEEEE-cCCCCEEEEEeeeEEEEc
Confidence 468889999999999999999884 4677777 444444444445555543
No 128
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=39.67 E-value=1.3e+02 Score=33.72 Aligned_cols=90 Identities=11% Similarity=0.213 Sum_probs=47.3
Q ss_pred ccccCceEEEcCCceEEEEEEeccceEEEccC-CC-----CCCceEEEecccccCCCCCCcccccccCCCcccCCCeEEE
Q 000294 491 SFELYELVCFGRKDFGLIVGMEKDDHYKILKE-GS-----EGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARV 564 (1711)
Q Consensus 491 ~FeLgDLVQLD~~TVGVIVrVEkDe~fkVLd~-~g-----d~~~VvtVk~~~I~~K~~~rr~vAtD~~gk~I~vGD~VKV 564 (1711)
.+++||+|. |.|++|..+-.|.-|.. .+ ..+..-.+..++|... ..+.....|++||.|++
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 567899985 88888876433332211 00 0001112222333211 11224567999999986
Q ss_pred ecCCCCCceEEEEEEECCEEEEEeCcceeeccEEEEeCCcee
Q 000294 565 SEGPSKDRQGIVKKIYRGILFIYDENETENGGYFCSKSQHCE 606 (1711)
Q Consensus 565 IdGp~kGRqG~VlHIyRs~VFL~Sr~~tENgGIFVvRarnv~ 606 (1711)
. |+.|. ..+.|..+. +..|++.+++..|-
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 55788888776554
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=39.67 E-value=62 Score=31.07 Aligned_cols=69 Identities=17% Similarity=0.213 Sum_probs=46.3
Q ss_pred CcEEEEEEeCCCCcEEEEEeccchhHHHHhcCCCCeEeccccccCHHHHHHHhhcccccccccCCCEEEEecCcCCCCcE
Q 000294 258 MQIISAFAVDHIKGFIFIEADKQCDINEACKGLSGIYYSRLAPVPKNEVSHLLSAQIKRNEVSEGTWAYVKNGKYKGDLA 337 (1711)
Q Consensus 258 L~I~SVFvpd~lKGYIYIEA~kq~dVk~AIkGI~gVy~~k~~pVPikEM~dLL~vkkk~~~Lk~GdwVRIKrGpYKGDLA 337 (1711)
-+|+.+.+....+--|||+... ++. .+||+.||..-. +......|.+|+.|++
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 3688888887788888988742 222 245556654321 1122345788999987
Q ss_pred EEEEEeCCCCEEEEEE
Q 000294 338 QVVYVNNARKRATVKL 353 (1711)
Q Consensus 338 QVveVdenk~eVtVKL 353 (1711)
+|+.++.++.++.|.|
T Consensus 68 kV~~id~~~~~i~lsl 83 (83)
T cd04461 68 KVTSVDEEKQRFLLSL 83 (83)
T ss_pred EEEEEcCCCCEEEEeC
Confidence 6999999888888764
No 130
>PRK14634 hypothetical protein; Provisional
Probab=38.90 E-value=41 Score=36.95 Aligned_cols=47 Identities=6% Similarity=0.077 Sum_probs=37.2
Q ss_pred cccCCEEEEc-cCCC---CCceeEEEEEeCCeEEEEecCCceEEEEeCCcccc
Q 000294 660 FAVGQTLRIR-VGPL---KGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLAE 708 (1711)
Q Consensus 660 ~lIGKTVkIr-kGPY---KGylGiVKDaTdt~ARVELHSk~KtITVdK~~Ls~ 708 (1711)
+.+|+.|+|+ ..|. |=+.|+++++.++.+++++ ..++|+|+.+.|.-
T Consensus 97 r~~G~~V~V~l~~~~~~~k~~~G~L~~~~~~~v~l~~--~~~~~~i~~~~I~k 147 (155)
T PRK14634 97 TFRGFPVEVSHRDDDGSEQRLEGLLLERNEDHLQINI--RGRIKRIPRDSVIS 147 (155)
T ss_pred HhCCCeEEEEEecCCCCeEEEEEEEEEEeCCEEEEEE--CCEEEEEEHHHeee
Confidence 4789999996 4443 6689999999999999887 46778888777764
No 131
>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=38.65 E-value=1.6e+02 Score=27.52 Aligned_cols=60 Identities=13% Similarity=0.082 Sum_probs=35.1
Q ss_pred eEEEEEEeccceEEEccCCCCCCceEEEecccccCCCCCCcccccccCCCcccCCCeEEEecCCCCCceEEEEE
Q 000294 505 FGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVSEGPSKDRQGIVKK 578 (1711)
Q Consensus 505 VGVIVrVEkDe~fkVLd~~gd~~~VvtVk~~~I~~K~~~rr~vAtD~~gk~I~vGD~VKVIdGp~kGRqG~VlH 578 (1711)
.|+|++.-....|.|.+..+ .++++.+.. ++. .....+.+||.|.+---++...+|.|+|
T Consensus 4 ~G~Vi~~~~g~~~~V~~~~g---~~~~c~~rG---klr--------~~~~~~~vGD~V~~~~~~~~~~~g~I~~ 63 (64)
T cd04451 4 EGVVTEALPNAMFRVELENG---HEVLAHISG---KMR--------MNYIRILPGDRVKVELSPYDLTKGRIVY 63 (64)
T ss_pred EEEEEEEeCCCEEEEEeCCC---CEEEEEECc---eee--------cCCcccCCCCEEEEEEeecCCCEEEEEE
Confidence 47888876323666655332 356665432 211 0234489999998874443445688876
No 132
>PF10446 DUF2457: Protein of unknown function (DUF2457); InterPro: IPR018853 This entry represents a family of uncharacterised proteins.
Probab=37.92 E-value=14 Score=46.33 Aligned_cols=10 Identities=40% Similarity=0.551 Sum_probs=4.0
Q ss_pred ceEEEEEEEC
Q 000294 572 RQGIVKKIYR 581 (1711)
Q Consensus 572 RqG~VlHIyR 581 (1711)
||-.=...|+
T Consensus 399 RQrRKEKf~r 408 (458)
T PF10446_consen 399 RQRRKEKFWR 408 (458)
T ss_pred hhhhhHHHHH
Confidence 4433333343
No 133
>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=37.50 E-value=53 Score=30.65 Aligned_cols=29 Identities=28% Similarity=0.279 Sum_probs=20.3
Q ss_pred ccCCCEEEEecC--cCCCCcEEEEEEeCCCC
Q 000294 319 VSEGTWAYVKNG--KYKGDLAQVVYVNNARK 347 (1711)
Q Consensus 319 Lk~GdwVRIKrG--pYKGDLAQVveVdenk~ 347 (1711)
|.||+.|||+.. +|-+..++|..|.+.+-
T Consensus 2 ilPG~~V~V~n~~~~Y~~y~G~VQRvsdgka 32 (53)
T PF11623_consen 2 ILPGSTVRVKNPNDIYYGYEGFVQRVSDGKA 32 (53)
T ss_dssp --TT-EEEE--TTSTTTT-EEEEEEEETTEE
T ss_pred ccCCCEEEEeCCCCccchheEEEEEeeCCeE
Confidence 579999999985 89999999999998643
No 134
>PRK14644 hypothetical protein; Provisional
Probab=37.17 E-value=41 Score=36.31 Aligned_cols=48 Identities=13% Similarity=0.202 Sum_probs=36.1
Q ss_pred cccCCEEEEcc-CC---CCCceeEEEEEeCCeEEEEec--CCceEEEEeCCccc
Q 000294 660 FAVGQTLRIRV-GP---LKGYLCRVLAVRYSDVTVKLD--SQQKILTVKGEHLA 707 (1711)
Q Consensus 660 ~lIGKTVkIrk-GP---YKGylGiVKDaTdt~ARVELH--Sk~KtITVdK~~Ls 707 (1711)
..||+.|+|+- -| -|=+.|+++++.++.+++++. .+-+.|++++++|.
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 34 366789999999999999654 44467777777664
No 135
>PF10842 DUF2642: Protein of unknown function (DUF2642); InterPro: IPR020139 This entry contains proteins with no known function.
Probab=37.14 E-value=76 Score=30.84 Aligned_cols=45 Identities=7% Similarity=0.115 Sum_probs=34.7
Q ss_pred cccCCEEEEccCCCCCceeEEEEEeCCeEEEEecCCceEEEEeCCccc
Q 000294 660 FAVGQTLRIRVGPLKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLA 707 (1711)
Q Consensus 660 ~lIGKTVkIrkGPYKGylGiVKDaTdt~ARVELHSk~KtITVdK~~Ls 707 (1711)
.+||+.|.|..- .-=+.|+++|+..+++.||-+ .+.+-|.-.+|.
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 666666655554
No 136
>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=37.08 E-value=60 Score=31.08 Aligned_cols=40 Identities=13% Similarity=0.319 Sum_probs=27.4
Q ss_pred ccCCCEEEEecC--cCCCCcEEEEEEeCCCCE--EEEEEeccCch
Q 000294 319 VSEGTWAYVKNG--KYKGDLAQVVYVNNARKR--ATVKLIPRIDL 359 (1711)
Q Consensus 319 Lk~GdwVRIKrG--pYKGDLAQVveVdenk~e--VtVKLIPRIDy 359 (1711)
++.|+.|||+|. -+=.|++.|+.||...-+ |+|++ ..++|
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 457999999996 467999999999988643 55543 34455
No 137
>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=36.79 E-value=1.5e+02 Score=44.24 Aligned_cols=94 Identities=10% Similarity=0.105 Sum_probs=62.8
Q ss_pred cccccCceEEEcC-----CceEEEEEEeccce-EEEccCCCCCCceEEEecccccCCCCCCcccccccCCCcccCCCeEE
Q 000294 490 NSFELYELVCFGR-----KDFGLIVGMEKDDH-YKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTAR 563 (1711)
Q Consensus 490 G~FeLgDLVQLD~-----~TVGVIVrVEkDe~-fkVLd~~gd~~~VvtVk~~~I~~K~~~rr~vAtD~~gk~I~vGD~VK 563 (1711)
..|.+||.|+... ...++|+.|++++. ++|.+.. +..+++.|.++..+. ..+.......-.|.+||.|+
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 5899999999732 23479999997444 4444433 357889988774321 22344556667889999998
Q ss_pred EecCC-----CCCceEEEEEEECCEEEEEe
Q 000294 564 VSEGP-----SKDRQGIVKKIYRGILFIYD 588 (1711)
Q Consensus 564 VIdGp-----~kGRqG~VlHIyRs~VFL~S 588 (1711)
+..-- ..|...+|..|....+.|..
T Consensus 755 ~trn~~~~gl~ng~~~tV~~i~~~~i~l~~ 784 (1960)
T TIGR02760 755 VTGNHFHSRVRNGELLTVSSINNEGITLIT 784 (1960)
T ss_pred EccCCcccCccCCCEEEEEEEcCCeEEEEe
Confidence 87432 34678888888776555544
No 138
>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]
Probab=36.45 E-value=44 Score=37.90 Aligned_cols=34 Identities=26% Similarity=0.478 Sum_probs=31.1
Q ss_pred cEEEEEEeCCCCcEEEEEeccchhHHHHhcCCCC
Q 000294 259 QIISAFAVDHIKGFIFIEADKQCDINEACKGLSG 292 (1711)
Q Consensus 259 ~I~SVFvpd~lKGYIYIEA~kq~dVk~AIkGI~g 292 (1711)
.|.+|.+--..|||-|||-+...|..+||..|-+
T Consensus 36 ~lrsvWvArnPPGfAFVEFed~RDA~DAvr~LDG 69 (195)
T KOG0107|consen 36 PLRSVWVARNPPGFAFVEFEDPRDAEDAVRYLDG 69 (195)
T ss_pred cceeEEEeecCCCceEEeccCcccHHHHHhhcCC
Confidence 4789998889999999999999999999998877
No 139
>PRK11634 ATP-dependent RNA helicase DeaD; Provisional
Probab=36.35 E-value=65 Score=42.36 Aligned_cols=12 Identities=25% Similarity=0.216 Sum_probs=5.2
Q ss_pred EEeCCeEEEEec
Q 000294 682 AVRYSDVTVKLD 693 (1711)
Q Consensus 682 DaTdt~ARVELH 693 (1711)
++.+++-+|||.
T Consensus 523 ~i~~~~s~v~~~ 534 (629)
T PRK11634 523 KLFASHSTIELP 534 (629)
T ss_pred EEeCCceEEEcC
Confidence 344444444443
No 140
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=36.07 E-value=1.4e+02 Score=29.82 Aligned_cols=65 Identities=14% Similarity=0.118 Sum_probs=47.5
Q ss_pred ceEEEEEEeccceEEEccCCCCCCceEEEecccccCCCCCCcccccccCCCcccCCCeEEEecCCCCCceEEEEEEECC
Q 000294 504 DFGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVSEGPSKDRQGIVKKIYRG 582 (1711)
Q Consensus 504 TVGVIVrVEkDe~fkVLd~~gd~~~VvtVk~~~I~~K~~~rr~vAtD~~gk~I~vGD~VKVIdGp~kGRqG~VlHIyRs 582 (1711)
..|+|+.+-.+..|+|.+.++ .++.-. |..|+.. +.--|.+||.|.|--=||.-..|.|++=|+.
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 459999999888999999875 233332 3344321 2446899999999988888788989887753
No 141
>PF13893 RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); PDB: 2PE8_A 2PEH_A 2D9O_A 1A9N_D 2DIT_A 3S6E_A 2LQ5_A 1SJQ_A 2AD9_A 1X4D_A ....
Probab=35.79 E-value=54 Score=28.99 Aligned_cols=36 Identities=22% Similarity=0.315 Sum_probs=29.2
Q ss_pred cEEEEEEeCCCCcEEEEEeccchhHHHHhcCCCCeE
Q 000294 259 QIISAFAVDHIKGFIFIEADKQCDINEACKGLSGIY 294 (1711)
Q Consensus 259 ~I~SVFvpd~lKGYIYIEA~kq~dVk~AIkGI~gVy 294 (1711)
.|..|...+.-++++|||....++...|++.+.+..
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 488888876558999999999999999998776643
No 142
>PLN00036 40S ribosomal protein S4; Provisional
Probab=35.61 E-value=55 Score=39.02 Aligned_cols=52 Identities=17% Similarity=0.302 Sum_probs=40.2
Q ss_pred CcccCCCeEEEecCCCCCceEEEEEEECC-----EEEEEeCcceeeccEEEEeCCceeecc
Q 000294 554 KVISLNDTARVSEGPSKDRQGIVKKIYRG-----ILFIYDENETENGGYFCSKSQHCEKTK 609 (1711)
Q Consensus 554 k~I~vGD~VKVIdGp~kGRqG~VlHIyRs-----~VFL~Sr~~tENgGIFVvRarnv~tv~ 609 (1711)
-.|.+|-+|-|+.|.|.||.|+|.+|.+. +|.|.+ .++--|-++..+|..++
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 35789999999999999999999999843 233322 23447999999999874
No 143
>PF11515 Cul7: Mouse development and cellular proliferation protein Cullin-7; InterPro: IPR021097 The CPH domain is found in the Cullin-7, PARC and HERC2 proteins, which are all components of known or predicted E3-ubiquitin ligases. The CPH domain is a protein-protein interaction module that binds the teramerisation domain of the tumour suppressor protein p53 []. Structurally it forms a beta-barrel fold similar to the SH3, Tudor and KOW and domains. Unlike the SH3 and Tudor domains, which bind to small peptides, the CPH domain appears to bind to an extended surface on p53.; PDB: 2JUF_A 2JNG_A.
Probab=35.59 E-value=58 Score=32.60 Aligned_cols=39 Identities=10% Similarity=0.156 Sum_probs=24.1
Q ss_pred HHHHHHhhcccccccccCCCEEEEec---CcCCCCcEEEEEEeCCCC
Q 000294 304 NEVSHLLSAQIKRNEVSEGTWAYVKN---GKYKGDLAQVVYVNNARK 347 (1711)
Q Consensus 304 kEM~dLL~vkkk~~~Lk~GdwVRIKr---GpYKGDLAQVveVdenk~ 347 (1711)
.+...+++ ..|.||+.||+.+ -..+||+++|..++.++.
T Consensus 8 d~Ya~YVr-----~~i~~GM~VRc~~~yeeV~~GD~G~V~k~~~dg~ 49 (78)
T PF11515_consen 8 DDYAEYVR-----DNIQPGMRVRCCRDYEEVRAGDEGEVFKQDRDGL 49 (78)
T ss_dssp HHHHHHHH-----HH--TT-EEEESS-BTTB-TT-EEE-EEEE-TTS
T ss_pred hHHHHHHH-----HhCCCCcEEEEecccccccccccceeEeeccCCC
Confidence 44445553 3689999999997 479999999999988764
No 144
>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=35.39 E-value=8.6 Score=49.21 Aligned_cols=13 Identities=38% Similarity=0.690 Sum_probs=10.5
Q ss_pred cccccccccCCCC
Q 000294 118 QFVEDAADVDYDD 130 (1711)
Q Consensus 118 ~FiDdEAEVDDDe 130 (1711)
.+|||||+|.-+|
T Consensus 1052 k~~eDEAevSGsD 1064 (1329)
T KOG4156|consen 1052 KYLEDEAEVSGSD 1064 (1329)
T ss_pred HhhcchhhcccCc
Confidence 5999999997444
No 145
>PLN00045 photosystem I reaction center subunit IV; Provisional
Probab=35.35 E-value=63 Score=33.32 Aligned_cols=45 Identities=13% Similarity=0.195 Sum_probs=33.1
Q ss_pred ccccccCCCEEEEecC--cCCCCcEEEEEEeCC-CC--EEEEEEeccCchh
Q 000294 315 KRNEVSEGTWAYVKNG--KYKGDLAQVVYVNNA-RK--RATVKLIPRIDLQ 360 (1711)
Q Consensus 315 k~~~Lk~GdwVRIKrG--pYKGDLAQVveVden-k~--eVtVKLIPRIDy~ 360 (1711)
..+.++.|+.|||+|- -+=+|++.|+.||.. +- -|+|++ -.++|.
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 3567899999999996 467899999999987 32 255553 345553
No 146
>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=35.25 E-value=2.1e+02 Score=34.01 Aligned_cols=84 Identities=12% Similarity=0.173 Sum_probs=51.0
Q ss_pred EEEEEEeccceEEEccCCCCCCceEEEecccccCCCCCCcccccccCCCcccCCCeEEEecCCCCCceEEEEEEECCE-E
Q 000294 506 GLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVSEGPSKDRQGIVKKIYRGI-L 584 (1711)
Q Consensus 506 GVIVrVEkDe~fkVLd~~gd~~~VvtVk~~~I~~K~~~rr~vAtD~~gk~I~vGD~VKVIdGp~kGRqG~VlHIyRs~-V 584 (1711)
|.||++.+ ..+.|++.+ .++..+++..-. .....+-+||.|.+..- ...+|.|..|+.-. +
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 488887653 355555432111 01456899999987532 24679999999543 4
Q ss_pred EEEeCcceeeccEEEEeCCceeec
Q 000294 585 FIYDENETENGGYFCSKSQHCEKT 608 (1711)
Q Consensus 585 FL~Sr~~tENgGIFVvRarnv~tv 608 (1711)
++.-..... .-+++.++..|++|
T Consensus 63 l~R~~~~~~-~~~i~anvD~vllV 85 (287)
T cd01854 63 LSRPAAGGR-EQVIAANVDQLVIV 85 (287)
T ss_pred EEccCCCCc-ceeEEEeCCEEEEE
Confidence 444332222 55667777665554
No 147
>PRK10486 autoinducer-2 (AI-2) modifying protein LsrG; Provisional
Probab=35.23 E-value=1.9e+02 Score=29.00 Aligned_cols=65 Identities=9% Similarity=-0.056 Sum_probs=43.3
Q ss_pred EEEEEeccchHHHHHHHHHHHHHhhccCCCCCcEEEEEEeCCCCc-EEEEEeccchhHHHHhcCCCC
Q 000294 227 IWKVKCMAGRERQSAFCLMQKFVDLQSLGSKMQIISAFAVDHIKG-FIFIEADKQCDINEACKGLSG 292 (1711)
Q Consensus 227 LWaVKCk~GkEReVV~~LmrKii~lq~~g~~L~I~SVFvpd~lKG-YIYIEA~kq~dVk~AIkGI~g 292 (1711)
|-.+++++|++.+++..|..-+ ...+...-+..+.++....-|+ |++||.....+..++=...++
T Consensus 5 ia~~~~kpg~~~~~~~~l~~~~-~~sr~EpGcl~y~~~~~~~~p~~~~~~E~w~d~~Al~~H~~tph 70 (96)
T PRK10486 5 LVEINVKEDKVDEFIEVFRQNH-LGSIQEPGNLRFDVLQDPEVPTRFYIYEAYKDEAAVAFHKTTPH 70 (96)
T ss_pred EEEEEECcchHHHHHHHHHHHH-HHHhCCCCceEEEEEeCCCCCCEEEEEEEeCCHHHHHHHhcCHH
Confidence 5567899999988887655444 4333444466677777655566 888899887666655555554
No 148
>PRK13709 conjugal transfer nickase/helicase TraI; Provisional
Probab=34.34 E-value=1.7e+02 Score=43.08 Aligned_cols=93 Identities=16% Similarity=0.162 Sum_probs=64.3
Q ss_pred Cccccc--CceEEEcCCceEEEEEEeccceEEEcc-CCCCCCceEEEecccccCCCCCCcccccccCCCcccCCCeEEEe
Q 000294 489 ENSFEL--YELVCFGRKDFGLIVGMEKDDHYKILK-EGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVS 565 (1711)
Q Consensus 489 ~G~FeL--gDLVQLD~~TVGVIVrVEkDe~fkVLd-~~gd~~~VvtVk~~~I~~K~~~rr~vAtD~~gk~I~vGD~VKVI 565 (1711)
...|+. ||+|++. .+.-.|+.|+++....+|. .. ++.+.+.|..+. ..++.+......+|.+||.|+..
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 8999885 4566789998765555553 33 357788876542 22355667778899999999997
Q ss_pred c-----CCCCCceEEEEEEECCEEEEEeC
Q 000294 566 E-----GPSKDRQGIVKKIYRGILFIYDE 589 (1711)
Q Consensus 566 d-----Gp~kGRqG~VlHIyRs~VFL~Sr 589 (1711)
. |-..|..++|+.|..+-|.|.+.
T Consensus 1345 rnDk~~G~~Ng~~~tV~~I~~~~I~l~~~ 1373 (1747)
T PRK13709 1345 KSDRERGYVANSVWTVTAVSGDSVTLSDG 1373 (1747)
T ss_pred ccCcccccccCCEEEEEEEcCCeEEEEcC
Confidence 4 33456788999998776555543
No 149
>COG2139 RPL21A Ribosomal protein L21E [Translation, ribosomal structure and biogenesis]
Probab=34.31 E-value=67 Score=33.30 Aligned_cols=49 Identities=33% Similarity=0.551 Sum_probs=38.5
Q ss_pred cccCCEEEEc------cC-C---CCCceeEEEEEeCCeEEEEe--cCCceEEEEeCCcccc
Q 000294 660 FAVGQTLRIR------VG-P---LKGYLCRVLAVRYSDVTVKL--DSQQKILTVKGEHLAE 708 (1711)
Q Consensus 660 ~lIGKTVkIr------kG-P---YKGylGiVKDaTdt~ARVEL--HSk~KtITVdK~~Ls~ 708 (1711)
+-+|+.|.|. +| | |-|+.|+|+.+++.-.-||+ -.+.|+|.|-.+||.-
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 5578888876 44 3 57899999999999877775 4556789999999874
No 150
>PRK05610 rpsQ 30S ribosomal protein S17; Reviewed
Probab=33.95 E-value=73 Score=32.10 Aligned_cols=25 Identities=24% Similarity=0.348 Sum_probs=20.5
Q ss_pred CCcccccccCCCcccCCCeEEEecCC
Q 000294 543 DMKFTALDQSMKVISLNDTARVSEGP 568 (1711)
Q Consensus 543 ~rr~vAtD~~gk~I~vGD~VKVIdGp 568 (1711)
..++.|.|. .+..++||+|+|.+.+
T Consensus 42 ~kk~~aHD~-~n~~k~GD~V~I~e~r 66 (84)
T PRK05610 42 SKKYHAHDE-NNEAKIGDVVRIMETR 66 (84)
T ss_pred ceEEEEECC-CCCCCCCCEEEEEEcc
Confidence 345789996 5799999999999873
No 151
>PTZ00118 40S ribosomal protein S4; Provisional
Probab=33.62 E-value=63 Score=38.53 Aligned_cols=54 Identities=11% Similarity=0.149 Sum_probs=40.0
Q ss_pred CcccCCCeEEEecCCCCCceEEEEEEECC---EEEEEeCcceeeccEEEEeCCceeecc
Q 000294 554 KVISLNDTARVSEGPSKDRQGIVKKIYRG---ILFIYDENETENGGYFCSKSQHCEKTK 609 (1711)
Q Consensus 554 k~I~vGD~VKVIdGp~kGRqG~VlHIyRs---~VFL~Sr~~tENgGIFVvRarnv~tv~ 609 (1711)
-.|.+|-+|-|+.|.|.||.|+|+++.+. +-.+|-++ .++--|-++..+|..++
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 152
>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=33.30 E-value=14 Score=47.68 Aligned_cols=11 Identities=36% Similarity=0.700 Sum_probs=5.5
Q ss_pred ecCCCCCHHHH
Q 000294 431 CWGVVPSEEEL 441 (1711)
Q Consensus 431 t~dVnPTLEEL 441 (1711)
++.|.|.|++|
T Consensus 270 ~~kvlP~l~~l 280 (556)
T PF05918_consen 270 CEKVLPKLSDL 280 (556)
T ss_dssp HHHTCCCTT--
T ss_pred HHHhcCChhhC
Confidence 34566666666
No 153
>PTZ00223 40S ribosomal protein S4; Provisional
Probab=33.27 E-value=50 Score=39.50 Aligned_cols=54 Identities=15% Similarity=0.129 Sum_probs=40.0
Q ss_pred CcccCCCeEEEecCCCCCceEEEEEEECC---EEEEEeCcceeeccEEEEeCCceeecc
Q 000294 554 KVISLNDTARVSEGPSKDRQGIVKKIYRG---ILFIYDENETENGGYFCSKSQHCEKTK 609 (1711)
Q Consensus 554 k~I~vGD~VKVIdGp~kGRqG~VlHIyRs---~VFL~Sr~~tENgGIFVvRarnv~tv~ 609 (1711)
-.|.+|-+|-|+.|.|.||.|+|.+|.+. +-.++..+ .++--|.++..+|..++
T Consensus 170 ikfe~G~l~~vtgG~n~GriG~I~~i~~~~~~~~iv~i~d--~~g~~F~T~~~~VfvIG 226 (273)
T PTZ00223 170 IKNRNGKVVMVTGGANRGRIGEIVSIERHPGAFDIARLKD--ASGHEFATRAANIFVIG 226 (273)
T ss_pred EecCCCCEEEEECCeeceeEEEEEEEEecCCCCCEEEEEe--CCCCeEEEEeeeEEEEe
Confidence 35789999999999999999999999543 11222222 23336999999999885
No 154
>PRK00098 GTPase RsgA; Reviewed
Probab=33.13 E-value=2.5e+02 Score=33.49 Aligned_cols=86 Identities=13% Similarity=0.130 Sum_probs=52.8
Q ss_pred eEEEEEEeccceEEEccCCCCCCceEEEecccccCCCCCCcccccccCCCcccCCCeEEEecCCCCCceEEEEEEECCEE
Q 000294 505 FGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVSEGPSKDRQGIVKKIYRGIL 584 (1711)
Q Consensus 505 VGVIVrVEkDe~fkVLd~~gd~~~VvtVk~~~I~~K~~~rr~vAtD~~gk~I~vGD~VKVIdGp~kGRqG~VlHIyRs~V 584 (1711)
.|.||++.+. .+.|++..+ .++++.++.. +. .....+-+||.|.|-. + ....|.|.+|+.-.-
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 4899999884 788876432 3556554321 11 0235578999998842 1 234699999998877
Q ss_pred EEEeCcceeeccEEEEeCCceeec
Q 000294 585 FIYDENETENGGYFCSKSQHCEKT 608 (1711)
Q Consensus 585 FL~Sr~~tENgGIFVvRarnv~tv 608 (1711)
+|.-+.. ...-+++.++..|++|
T Consensus 65 ~l~R~~~-~~~q~iaaniD~vllV 87 (298)
T PRK00098 65 LLVRPPI-FKSKLIAANVDQAVLV 87 (298)
T ss_pred eEECCCC-ccccceeecCCEEEEE
Confidence 7766665 2234455555554443
No 155
>COG0186 RpsQ Ribosomal protein S17 [Translation, ribosomal structure and biogenesis]
Probab=33.06 E-value=67 Score=32.77 Aligned_cols=24 Identities=25% Similarity=0.385 Sum_probs=20.2
Q ss_pred CCcccccccCCCcccCCCeEEEecC
Q 000294 543 DMKFTALDQSMKVISLNDTARVSEG 567 (1711)
Q Consensus 543 ~rr~vAtD~~gk~I~vGD~VKVIdG 567 (1711)
..++.|.| ..+.+++||.|+|.+=
T Consensus 44 ~kK~~aHd-e~~~~k~GD~V~I~Et 67 (87)
T COG0186 44 SKKYHAHD-ECNEAKVGDIVRIAET 67 (87)
T ss_pred EeeeEeec-ccccCCCCCEEEEEEc
Confidence 34578999 8899999999999865
No 156
>PF00575 S1: S1 RNA binding domain; InterPro: IPR003029 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The S1 domain was originally identified in ribosomal protein S1 but is found in a large number of RNA-associated proteins. The structure of the S1 RNA-binding domain from the Escherichia coli polynucleotide phosphorylase has been determined using NMR methods and consists of a five-stranded antiparallel beta barrel. Conserved residues on one face of the barrel and adjacent loops form the putative RNA-binding site []. The structure of the S1 domain is very similar to that of cold shock proteins. This suggests that they may both be derived from an ancient nucleic acid-binding protein []. More information about these proteins can be found at Protein of the Month: RNA Exosomes []. This entry does not include translation initiation factor IF-1 S1 domains.; GO: 0003723 RNA binding; PDB: 3L7Z_F 2JE6_I 2JEA_I 2JEB_I 1E3P_A 2Y0S_E 1WI5_A 2BH8_A 2CQO_A 2EQS_A ....
Probab=32.14 E-value=1.6e+02 Score=27.32 Aligned_cols=57 Identities=19% Similarity=0.256 Sum_probs=36.3
Q ss_pred cccCceEEEcCCceEEEEEEeccceEEEccCCCCCCceEEEecccccCCCCCCcccccccCCCcccCCCeEEEe
Q 000294 492 FELYELVCFGRKDFGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVS 565 (1711)
Q Consensus 492 FeLgDLVQLD~~TVGVIVrVEkDe~fkVLd~~gd~~~VvtVk~~~I~~K~~~rr~vAtD~~gk~I~vGD~VKVI 565 (1711)
|+.+|.|. |.|++|+....|.=|..+ ..--|..++|... ..+.....|++||.|++.
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 56677775 899999885444444422 2345566666442 224456789999999874
No 157
>PRK14640 hypothetical protein; Provisional
Probab=32.07 E-value=69 Score=35.09 Aligned_cols=46 Identities=17% Similarity=0.122 Sum_probs=35.2
Q ss_pred cccCCEEEEcc-CC---CCCceeEEEEEeCCeEEEEecCCceEEEEeCCccc
Q 000294 660 FAVGQTLRIRV-GP---LKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLA 707 (1711)
Q Consensus 660 ~lIGKTVkIrk-GP---YKGylGiVKDaTdt~ARVELHSk~KtITVdK~~Ls 707 (1711)
..+|+.|+|+- .| .|=+.|++++++++.++++++ .+++.|+.+.|.
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 366789999999999998875 556677666665
No 158
>PRK13709 conjugal transfer nickase/helicase TraI; Provisional
Probab=32.02 E-value=1.9e+02 Score=42.69 Aligned_cols=92 Identities=10% Similarity=0.021 Sum_probs=65.1
Q ss_pred CcccccCceEEEcC-----CceEEEEEEeccceE-EEccCCCCCCceEEEecccccCCCCCCcccccccCCCcccCCCeE
Q 000294 489 ENSFELYELVCFGR-----KDFGLIVGMEKDDHY-KILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTA 562 (1711)
Q Consensus 489 ~G~FeLgDLVQLD~-----~TVGVIVrVEkDe~f-kVLd~~gd~~~VvtVk~~~I~~K~~~rr~vAtD~~gk~I~vGD~V 562 (1711)
...|+.|++|++-. ...-+|+.|+.+... +|.+..+ ..+++.|..+. .++.+.....-+|.+||.|
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 233589999875443 3334443 56788887653 2344566678899999999
Q ss_pred EEecCC-----CCCceEEEEEEECCEEEEEe
Q 000294 563 RVSEGP-----SKDRQGIVKKIYRGILFIYD 588 (1711)
Q Consensus 563 KVIdGp-----~kGRqG~VlHIyRs~VFL~S 588 (1711)
++.... ..|...+|+.|..+.|.|..
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 998543 35678999999998887775
No 159
>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=31.70 E-value=16 Score=36.17 Aligned_cols=43 Identities=16% Similarity=0.202 Sum_probs=0.0
Q ss_pred ccCCEEEEccCCCCCceeEEEEEeCCeEEEEecCCceEEEEeCCcccc
Q 000294 661 AVGQTLRIRVGPLKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLAE 708 (1711)
Q Consensus 661 lIGKTVkIrkGPYKGylGiVKDaTdt~ARVELHSk~KtITVdK~~Ls~ 708 (1711)
-.|+.|....| +.|+|+++.+++|.||+.. .-+|+|.|..+..
T Consensus 38 k~Gd~VvT~gG----i~G~V~~i~~~~v~lei~~-g~~i~v~k~aI~~ 80 (82)
T PF02699_consen 38 KPGDEVVTIGG----IYGTVVEIDDDTVVLEIAP-GVEITVEKSAIAR 80 (82)
T ss_dssp ------------------------------------------------
T ss_pred CCCCEEEECCc----EEEEEEEEeCCEEEEEECC-CeEEEEEHHHhHh
Confidence 46788877665 7799999999999999988 5678999987763
No 160
>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=31.37 E-value=1.2e+02 Score=29.06 Aligned_cols=68 Identities=16% Similarity=0.218 Sum_probs=43.1
Q ss_pred EEEEEEeCCCCcEEEEEeccchhHHHHhcCCCCeEeccccccCHHHHHHHh-hcccccccccCCCEEEEecCcCCCCcEE
Q 000294 260 IISAFAVDHIKGFIFIEADKQCDINEACKGLSGIYYSRLAPVPKNEVSHLL-SAQIKRNEVSEGTWAYVKNGKYKGDLAQ 338 (1711)
Q Consensus 260 I~SVFvpd~lKGYIYIEA~kq~dVk~AIkGI~gVy~~k~~pVPikEM~dLL-~vkkk~~~Lk~GdwVRIKrGpYKGDLAQ 338 (1711)
|...++....+..||||... +| ..+||+.|+.+-. .+......|++|+-|+ |+
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 46
Q ss_pred EEEEeCCCCEEEEEE
Q 000294 339 VVYVNNARKRATVKL 353 (1711)
Q Consensus 339 VveVdenk~eVtVKL 353 (1711)
|++||.+++++.|.+
T Consensus 57 V~~id~~~~~i~Ls~ 71 (73)
T cd05703 57 VVGVDKEHKLLRLSA 71 (73)
T ss_pred EEEEeCCCCEEEEEe
Confidence 999999999988876
No 161
>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=31.13 E-value=1.1e+02 Score=28.18 Aligned_cols=70 Identities=17% Similarity=0.130 Sum_probs=41.9
Q ss_pred EEEEEEeCCCCcEEEEEeccchhHHHHhcCCCCeEeccccccCHHHHHHHhhcccccccccCCCEEEEecCcCCCCcEEE
Q 000294 260 IISAFAVDHIKGFIFIEADKQCDINEACKGLSGIYYSRLAPVPKNEVSHLLSAQIKRNEVSEGTWAYVKNGKYKGDLAQV 339 (1711)
Q Consensus 260 I~SVFvpd~lKGYIYIEA~kq~dVk~AIkGI~gVy~~k~~pVPikEM~dLL~vkkk~~~Lk~GdwVRIKrGpYKGDLAQV 339 (1711)
|+...+....+-.||||.... ++ ..+||+.||.+-. .......|++|+.|++ +|
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 445555555677788887430 11 2234444443211 1111235789999987 49
Q ss_pred EEEeCCCCEEEEEEec
Q 000294 340 VYVNNARKRATVKLIP 355 (1711)
Q Consensus 340 veVdenk~eVtVKLIP 355 (1711)
..|+.+..++.|.|-+
T Consensus 59 ~~vd~~~~~i~ls~k~ 74 (77)
T cd05708 59 LKIDAEKKRISLGLKA 74 (77)
T ss_pred EEEeCCCCEEEEEEEe
Confidence 9999988888888754
No 162
>PRK14630 hypothetical protein; Provisional
Probab=31.06 E-value=87 Score=34.13 Aligned_cols=45 Identities=13% Similarity=0.169 Sum_probs=35.4
Q ss_pred cccCCEEEEccC-CCCCceeEEEEEeCCeEEEEecCCceEEEEeCCcccc
Q 000294 660 FAVGQTLRIRVG-PLKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLAE 708 (1711)
Q Consensus 660 ~lIGKTVkIrkG-PYKGylGiVKDaTdt~ARVELHSk~KtITVdK~~Ls~ 708 (1711)
+.+|+.|+|+-. |. ..|+++++.++.++++++ .+++.|+.+.|.-
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 489999999999998764 5678888777753
No 163
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=30.64 E-value=1.7e+02 Score=33.67 Aligned_cols=43 Identities=12% Similarity=0.203 Sum_probs=32.2
Q ss_pred CCCcccCCCeEEEecCCCCCceEEEEEEECCEEEEEeCcceeeccEEEEeCCceee
Q 000294 552 SMKVISLNDTARVSEGPSKDRQGIVKKIYRGILFIYDENETENGGYFCSKSQHCEK 607 (1711)
Q Consensus 552 ~gk~I~vGD~VKVIdGp~kGRqG~VlHIyRs~VFL~Sr~~tENgGIFVvRarnv~t 607 (1711)
....|++||+|| +.|+.+. ..++|.... ...||+.++|.+|-.
T Consensus 115 ~~d~f~~GDivr----------A~Vis~~-~~~~Lst~~--~dlGVI~A~CsrC~~ 157 (188)
T COG1096 115 LSDAFRIGDIVR----------ARVISTG-DPIQLSTKG--NDLGVIYARCSRCRA 157 (188)
T ss_pred cccccccccEEE----------EEEEecC-CCeEEEecC--CcceEEEEEccCCCc
Confidence 347899999998 5677777 556666555 567999888888864
No 164
>PRK14712 conjugal transfer nickase/helicase TraI; Provisional
Probab=30.20 E-value=2.2e+02 Score=41.76 Aligned_cols=92 Identities=9% Similarity=0.055 Sum_probs=66.4
Q ss_pred cccccCceEE-EcCC----ceEEEEEEeccceEEEc-cCCCCCCceEEEecccccCCCCCCcccccccCCCcccCCCeEE
Q 000294 490 NSFELYELVC-FGRK----DFGLIVGMEKDDHYKIL-KEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTAR 563 (1711)
Q Consensus 490 G~FeLgDLVQ-LD~~----TVGVIVrVEkDe~fkVL-d~~gd~~~VvtVk~~~I~~K~~~rr~vAtD~~gk~I~vGD~VK 563 (1711)
..|..|+.|+ ++.. ..=+|+.|+++....+| +.. ++.+++.|+.+. .++.......-+|..||.|+
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 22399999986555444 444 357889987653 23556677788999999999
Q ss_pred EecCCC-----CCceEEEEEEECCEEEEEeC
Q 000294 564 VSEGPS-----KDRQGIVKKIYRGILFIYDE 589 (1711)
Q Consensus 564 VIdGp~-----kGRqG~VlHIyRs~VFL~Sr 589 (1711)
+....+ .|...+|++|..+.+.|..+
T Consensus 587 ~t~nd~~~~L~ngd~~tV~~i~~~~itl~~~ 617 (1623)
T PRK14712 587 VTGKIPGLRVSGGDRLQVASVSEDAMTVVVP 617 (1623)
T ss_pred EccCCcccCccCCCEEEEEEecCCeEEEEEC
Confidence 986642 45788999999887766654
No 165
>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=29.95 E-value=91 Score=30.50 Aligned_cols=23 Identities=26% Similarity=0.359 Sum_probs=19.3
Q ss_pred CcccccccCCCcccCCCeEEEecC
Q 000294 544 MKFTALDQSMKVISLNDTARVSEG 567 (1711)
Q Consensus 544 rr~vAtD~~gk~I~vGD~VKVIdG 567 (1711)
.++.|.|. .+..++||+|+|.+-
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 45789997 578999999999875
No 166
>PRK04313 30S ribosomal protein S4e; Validated
Probab=29.88 E-value=59 Score=38.28 Aligned_cols=52 Identities=17% Similarity=0.135 Sum_probs=39.8
Q ss_pred CcccCCCeEEEecCCCCCceEEEEEEECC------EEEEEeCcceeeccEEEEeCCceeecc
Q 000294 554 KVISLNDTARVSEGPSKDRQGIVKKIYRG------ILFIYDENETENGGYFCSKSQHCEKTK 609 (1711)
Q Consensus 554 k~I~vGD~VKVIdGp~kGRqG~VlHIyRs------~VFL~Sr~~tENgGIFVvRarnv~tv~ 609 (1711)
-.|.+|-+|-|+.|.|.||.|+|++|.+. +|.|.+ .++--|-++..+|..++
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 45789999999999999999999999643 344331 22334999999998874
No 167
>PRK14645 hypothetical protein; Provisional
Probab=29.87 E-value=71 Score=35.25 Aligned_cols=45 Identities=18% Similarity=0.124 Sum_probs=36.8
Q ss_pred cccCCEEEEccCCCCCceeEEEEEeCCeEEEEecCCceEEEEeCCccc
Q 000294 660 FAVGQTLRIRVGPLKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLA 707 (1711)
Q Consensus 660 ~lIGKTVkIrkGPYKGylGiVKDaTdt~ARVELHSk~KtITVdK~~Ls 707 (1711)
..+|+.|+|+.+ .|=+.|+++++++..++|++ ..+++.|+.+.|.
T Consensus 99 r~~G~~v~v~~~-~k~~~G~L~~~~d~~i~l~~--~~~~~~i~~~~I~ 143 (154)
T PRK14645 99 RFAGLKAKVRGP-GENFTGRIKAVSGDQVTFDV--GGEDRTLRIGTFQ 143 (154)
T ss_pred HhCCCEEEEEcC-CeEEEEEEEEEeCCEEEEEE--CCeEEEEEHHHhh
Confidence 478999999864 47788999999999999776 4677888887775
No 168
>KOG0130 consensus RNA-binding protein RBM8/Tsunagi (RRM superfamily) [General function prediction only]
Probab=29.73 E-value=84 Score=34.53 Aligned_cols=61 Identities=20% Similarity=0.299 Sum_probs=47.2
Q ss_pred cEEEEEeccchHHHHHHHHHHHHHhhccCCCCCcEEEEEE---e--CCCCcEEEEEeccchhHHHHhcCCCC
Q 000294 226 TIWKVKCMAGRERQSAFCLMQKFVDLQSLGSKMQIISAFA---V--DHIKGFIFIEADKQCDINEACKGLSG 292 (1711)
Q Consensus 226 kLWaVKCk~GkEReVV~~LmrKii~lq~~g~~L~I~SVFv---p--d~lKGYIYIEA~kq~dVk~AIkGI~g 292 (1711)
.=|+|-|..=+|...-..|..+|.++.. |+-|-. + --+|||-+||-........||..+.+
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 3588888888888888999999988762 222221 1 25899999999999998888888776
No 169
>PRK06531 yajC preprotein translocase subunit YajC; Validated
Probab=29.55 E-value=64 Score=34.18 Aligned_cols=47 Identities=23% Similarity=0.143 Sum_probs=32.0
Q ss_pred cCCEEEEccCCCCCceeEEEEEeCCeEEEEecCCceEEEEeCCccccccCC
Q 000294 662 VGQTLRIRVGPLKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLAEVRGK 712 (1711)
Q Consensus 662 IGKTVkIrkGPYKGylGiVKDaTdt~ARVELHSk~KtITVdK~~Ls~v~~~ 712 (1711)
.|+.|.-.. |++|+|+++.++..+|+|....-.|+|.|..|..+-.+
T Consensus 39 ~GD~VvT~G----Gi~G~V~~I~~~~~~v~le~~gv~i~v~r~AI~~Vv~~ 85 (113)
T PRK06531 39 KGDEVVTIG----GLYGTVDEVDTEAKTIVLDVDGVYLTFELAAIKRVVPK 85 (113)
T ss_pred CCCEEEECC----CcEEEEEEEecCCCEEEEEECCEEEEEEhhHhhhhcCC
Confidence 355565443 68899999987644444443567899999999865433
No 170
>PRK14712 conjugal transfer nickase/helicase TraI; Provisional
Probab=29.48 E-value=2.5e+02 Score=41.13 Aligned_cols=92 Identities=14% Similarity=0.130 Sum_probs=67.7
Q ss_pred Cccccc-CceEEEcCCceEEEEEEeccceEEEcc-CCCCCCceEEEecccccCCCCCCcccccccCCCcccCCCeEEEec
Q 000294 489 ENSFEL-YELVCFGRKDFGLIVGMEKDDHYKILK-EGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVSE 566 (1711)
Q Consensus 489 ~G~FeL-gDLVQLD~~TVGVIVrVEkDe~fkVLd-~~gd~~~VvtVk~~~I~~K~~~rr~vAtD~~gk~I~vGD~VKVId 566 (1711)
...|+. +|.|.|.....-.|+.|+++..+.+|. .. +..+.+.|.... ..++.+......+|.+||.|+.-.
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 678888888888999999866666664 33 356778875442 223456777889999999999974
Q ss_pred -----CCCCCceEEEEEEECCEEEEE
Q 000294 567 -----GPSKDRQGIVKKIYRGILFIY 587 (1711)
Q Consensus 567 -----Gp~kGRqG~VlHIyRs~VFL~ 587 (1711)
|-..+...+|+.|..+.|.|.
T Consensus 1217 nD~~~G~~Ng~~~tV~~i~~~~i~l~ 1242 (1623)
T PRK14712 1217 SDRERGYVANSVWTVTAVSGDSVTLS 1242 (1623)
T ss_pred CCcccccccCceEEEEEEcCCeEEEe
Confidence 334568999999999877766
No 171
>PF10574 UPF0552: Uncharacterised protein family UPF0552; InterPro: IPR018889 This family of proteins has no known function.
Probab=28.84 E-value=1.2e+02 Score=35.59 Aligned_cols=99 Identities=13% Similarity=0.112 Sum_probs=0.0
Q ss_pred cEEEEEeccchHHHHHHHHHHHHHhhccCCCCCcEEEEEEe---CCCCcEEEEEec------cchhHHHHhc--CCCCeE
Q 000294 226 TIWKVKCMAGRERQSAFCLMQKFVDLQSLGSKMQIISAFAV---DHIKGFIFIEAD------KQCDINEACK--GLSGIY 294 (1711)
Q Consensus 226 kLWaVKCk~GkEReVV~~LmrKii~lq~~g~~L~I~SVFvp---d~lKGYIYIEA~------kq~dVk~AIk--GI~gVy 294 (1711)
++|+|.|++- .|.+|-++..-...+......-.. .+++-| -|||. .++.+..+|. .+..|.
T Consensus 58 Ry~vl~i~~~-------~~hrR~fd~~G~EIepnfs~T~kVntGyL~Ssy-kveAkg~tDrls~~~L~~~V~k~~ll~lt 129 (224)
T PF10574_consen 58 RYYVLYIRPS-------RIHRRKFDAKGNEIEPNFSDTTKVNTGYLNSSY-KVEAKGDTDRLSPEQLKALVNKPELLALT 129 (224)
T ss_pred EEEEEEEeec-------hhhhhcccCCCcCcCCCccceeeeeecccCccc-EEEecCCccccCHHHHHHHhCchhhcccc
Q ss_pred ec------cccccCHHHHHHHhhcccccccccCCCEEEEec---CcCCCCcEEEE
Q 000294 295 YS------RLAPVPKNEVSHLLSAQIKRNEVSEGTWAYVKN---GKYKGDLAQVV 340 (1711)
Q Consensus 295 ~~------k~~pVPikEM~dLL~vkkk~~~Lk~GdwVRIKr---GpYKGDLAQVv 340 (1711)
.. -...+|..||.++ +|++|+-||||. +||-.-||+|+
T Consensus 130 ~~~~~~~~~aFW~~e~~~~~~--------ele~G~~vRlKT~GDspFieSlaKlD 176 (224)
T PF10574_consen 130 ESHTPDQTFAFWMPEAEMEKM--------ELELGDEVRLKTRGDSPFIESLAKLD 176 (224)
T ss_pred cccCCCCeEEEeechhhccce--------ecccCCeEEEEecCCchhheeeeeec
No 172
>PRK06958 single-stranded DNA-binding protein; Provisional
Probab=28.16 E-value=1.5e+02 Score=33.80 Aligned_cols=9 Identities=33% Similarity=0.867 Sum_probs=4.7
Q ss_pred CCCCCCCCC
Q 000294 1525 DQGGGWNNN 1533 (1711)
Q Consensus 1525 ~~~g~~~~~ 1533 (1711)
..++||.+-
T Consensus 168 ~~~~~~~~~ 176 (182)
T PRK06958 168 PAGGGFDEM 176 (182)
T ss_pred CCCCCcccc
Confidence 335666553
No 173
>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]
Probab=27.66 E-value=1.1e+02 Score=39.14 Aligned_cols=97 Identities=11% Similarity=0.069 Sum_probs=61.7
Q ss_pred CcEEEEEec----cchHHHHHHHHHHHHHhhccCCCCCcEEEEEEeC---CCCcEEEEEeccchhHHHHhcCCCCeEec-
Q 000294 225 PTIWKVKCM----AGRERQSAFCLMQKFVDLQSLGSKMQIISAFAVD---HIKGFIFIEADKQCDINEACKGLSGIYYS- 296 (1711)
Q Consensus 225 PkLWaVKCk----~GkEReVV~~LmrKii~lq~~g~~L~I~SVFvpd---~lKGYIYIEA~kq~dVk~AIkGI~gVy~~- 296 (1711)
+.-|.|||+ .--|++|...| ..+.|..++++. .-.|=-|||+..+++|+.||+.-+--...
T Consensus 8 ~~~~~vr~rGLPwsat~~ei~~Ff-----------~~~~I~~~~~~r~~Gr~sGeA~Ve~~seedv~~AlkkdR~~mg~R 76 (510)
T KOG4211|consen 8 STAFEVRLRGLPWSATEKEILDFF-----------SNCGIENLEIPRRNGRPSGEAYVEFTSEEDVEKALKKDRESMGHR 76 (510)
T ss_pred CcceEEEecCCCccccHHHHHHHH-----------hcCceeEEEEeccCCCcCcceEEEeechHHHHHHHHhhHHHhCCc
Confidence 446788887 45666654332 245677766653 36799999999999999999976544332
Q ss_pred --cccccCHHHHHHHhhcccccccccCCCEEEEecCcCC
Q 000294 297 --RLAPVPKNEVSHLLSAQIKRNEVSEGTWAYVKNGKYK 333 (1711)
Q Consensus 297 --k~~pVPikEM~dLL~vkkk~~~Lk~GdwVRIKrGpYK 333 (1711)
....+.-+||..+|+...... -.+.-.|||+-=||.
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 334445567777776432111 145567777655665
No 174
>PF14001 YdfZ: YdfZ protein
Probab=27.61 E-value=64 Score=31.23 Aligned_cols=32 Identities=19% Similarity=0.392 Sum_probs=27.5
Q ss_pred ccccCCCcccCCCeEEEecCCCCCceEEEEEEECC
Q 000294 548 ALDQSMKVISLNDTARVSEGPSKDRQGIVKKIYRG 582 (1711)
Q Consensus 548 AtD~~gk~I~vGD~VKVIdGp~kGRqG~VlHIyRs 582 (1711)
+.|+|+|.|.+|..|-|- | .|.+|+|+-||-.
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 569999999999999875 4 6899999999853
No 175
>KOG3218 consensus RNA polymerase, 25-kDa subunit (common to polymerases I, II and III) [Transcription]
Probab=27.35 E-value=3.4e+02 Score=31.61 Aligned_cols=56 Identities=11% Similarity=0.069 Sum_probs=31.4
Q ss_pred CCCcEEEEEeccchhHHHHhcCCCCeEeccccccCHHHHHHHhhcccccccccCCCEEEEec
Q 000294 268 HIKGFIFIEADKQCDINEACKGLSGIYYSRLAPVPKNEVSHLLSAQIKRNEVSEGTWAYVKN 329 (1711)
Q Consensus 268 ~lKGYIYIEA~kq~dVk~AIkGI~gVy~~k~~pVPikEM~dLL~vkkk~~~Lk~GdwVRIKr 329 (1711)
.|+.-.-||.+..+++.--| ..++...+-..+..+|-..||+. ..|++.+.=||..
T Consensus 118 ~~~p~f~iE~F~e~eLlvNI--T~H~lvPkH~vL~~eEK~~LL~r----y~l~e~qLPRIq~ 173 (208)
T KOG3218|consen 118 DFTPKFTIEVFLEAELLVNI--TEHELVPKHQVLTDEEKEELLRR----YKLKETQLPRIQK 173 (208)
T ss_pred hcCCceEEEeeehhhheeec--cceeecCceEEcCHHHHHHHHHH----hcCCcccCCeeec
Confidence 45555666766655542211 12344455666778999999963 2344445555544
No 176
>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=27.10 E-value=1.2e+02 Score=27.30 Aligned_cols=64 Identities=14% Similarity=0.153 Sum_probs=36.4
Q ss_pred EEEEEEeCCCCcEEEEEeccchhHHHHhcCCCCeEeccccccCHHHHHHHhhcccccccccCCCEEEEecCcCCCCcEEE
Q 000294 260 IISAFAVDHIKGFIFIEADKQCDINEACKGLSGIYYSRLAPVPKNEVSHLLSAQIKRNEVSEGTWAYVKNGKYKGDLAQV 339 (1711)
Q Consensus 260 I~SVFvpd~lKGYIYIEA~kq~dVk~AIkGI~gVy~~k~~pVPikEM~dLL~vkkk~~~Lk~GdwVRIKrGpYKGDLAQV 339 (1711)
|+.+.+-...+..|||+... ++ .+||+.|+.. ..+......|++|+.|++ +|
T Consensus 4 ~~~g~V~~v~~~g~~v~l~~-------~~----------g~l~~~e~~~-~~~~~~~~~~~~Gd~v~v----------~i 55 (68)
T cd05688 4 VVEGTVKSITDFGAFVDLGG-------VD----------GLLHISDMSW-GRVKHPSEVVNVGDEVEV----------KV 55 (68)
T ss_pred EEEEEEEEEEeeeEEEEECC-------eE----------EEEEhHHCCC-ccccCHhHEECCCCEEEE----------EE
Confidence 34444444455678887631 11 2445555541 111122235789999997 48
Q ss_pred EEEeCCCCEEEE
Q 000294 340 VYVNNARKRATV 351 (1711)
Q Consensus 340 veVdenk~eVtV 351 (1711)
++|+..+.++.|
T Consensus 56 ~~vd~~~~~i~l 67 (68)
T cd05688 56 LKIDKERKRISL 67 (68)
T ss_pred EEEECCCCEEec
Confidence 889887777664
No 177
>CHL00142 rps17 ribosomal protein S17; Validated
Probab=26.96 E-value=1.1e+02 Score=30.97 Aligned_cols=24 Identities=17% Similarity=0.225 Sum_probs=19.9
Q ss_pred CcccccccCCCcccCCCeEEEecCC
Q 000294 544 MKFTALDQSMKVISLNDTARVSEGP 568 (1711)
Q Consensus 544 rr~vAtD~~gk~I~vGD~VKVIdGp 568 (1711)
.++.|.| ..++.++||+|+|.+-+
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 4578999 66789999999999763
No 178
>COG2163 RPL14A Ribosomal protein L14E/L6E/L27E [Translation, ribosomal structure and biogenesis]
Probab=26.92 E-value=82 Score=33.95 Aligned_cols=33 Identities=15% Similarity=0.300 Sum_probs=28.4
Q ss_pred cccCCCEEEEecCcCCCCcEEEEEEeCCCCEEEE
Q 000294 318 EVSEGTWAYVKNGKYKGDLAQVVYVNNARKRATV 351 (1711)
Q Consensus 318 ~Lk~GdwVRIKrGpYKGDLAQVveVdenk~eVtV 351 (1711)
.|+||..|-|++|.|+|-.+.|+++-+++ .|+|
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 57899999999999999999999998775 4443
No 179
>PRK14636 hypothetical protein; Provisional
Probab=26.90 E-value=84 Score=35.37 Aligned_cols=48 Identities=15% Similarity=0.134 Sum_probs=35.8
Q ss_pred cccCCEEEEc-cCCCC---CceeEEEEEeCCeEEEEecCCceEEEEeCCcccc
Q 000294 660 FAVGQTLRIR-VGPLK---GYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLAE 708 (1711)
Q Consensus 660 ~lIGKTVkIr-kGPYK---GylGiVKDaTdt~ARVELHSk~KtITVdK~~Ls~ 708 (1711)
+.+|+.|+|+ ..|+. =+.|+++++.+..++|++.- .++|+|+.+.|.-
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 34544 45899999999999988742 3467777777663
No 180
>KOG2055 consensus WD40 repeat protein [General function prediction only]
Probab=26.74 E-value=57 Score=41.37 Aligned_cols=21 Identities=14% Similarity=0.404 Sum_probs=14.4
Q ss_pred CccccCCHHHHHHHHHHHhcc
Q 000294 176 PKEEEMDEEEFDKMMEERYKS 196 (1711)
Q Consensus 176 ~~eed~DaEelAe~lkERY~r 196 (1711)
+.|..++--++.++|++++++
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 181
>KOG1819 consensus FYVE finger-containing proteins [General function prediction only]
Probab=26.70 E-value=40 Score=42.55 Aligned_cols=28 Identities=21% Similarity=0.354 Sum_probs=19.2
Q ss_pred hhcccccCCCCC-CCCcEEEEEeccchHH
Q 000294 211 KMLEREYHMPCP-EDPTIWKVKCMAGRER 238 (1711)
Q Consensus 211 ~~VpQq~LLPSV-~DPkLWaVKCk~GkER 238 (1711)
..+-|++-||+. +.|-.=--+||.-+|.
T Consensus 528 s~tlqrlrlpssdneplaep~~~kaseeh 556 (990)
T KOG1819|consen 528 SDTLQRLRLPSSDNEPLAEPKKCKASEEH 556 (990)
T ss_pred HHHHHHhcCCcccCccccCcccccchHHH
Confidence 347799999995 4455555677776664
No 182
>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=26.68 E-value=1.5e+02 Score=27.42 Aligned_cols=68 Identities=18% Similarity=0.181 Sum_probs=0.0
Q ss_pred cEEEEEEeCCCCcEEEEEeccchhHHHHhcCCCCeEeccccccCHHHHHHHhhcccccccccCCCEEEEecCcCCCCcEE
Q 000294 259 QIISAFAVDHIKGFIFIEADKQCDINEACKGLSGIYYSRLAPVPKNEVSHLLSAQIKRNEVSEGTWAYVKNGKYKGDLAQ 338 (1711)
Q Consensus 259 ~I~SVFvpd~lKGYIYIEA~kq~dVk~AIkGI~gVy~~k~~pVPikEM~dLL~vkkk~~~Lk~GdwVRIKrGpYKGDLAQ 338 (1711)
+|+.+.+....+-.||||. ......+||+.+|.+. .+......|++|+.|++ +
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 000294 339 VVYVNNARKRATVKL 353 (1711)
Q Consensus 339 VveVdenk~eVtVKL 353 (1711)
|.+|+..+.++.|.|
T Consensus 55 V~~id~~~~~i~ls~ 69 (69)
T cd05697 55 VLSVEPERKRLVLTL 69 (69)
T ss_pred EEEEECCCCEEEEEC
No 183
>PRK08059 general stress protein 13; Validated
Probab=26.51 E-value=3.7e+02 Score=28.28 Aligned_cols=80 Identities=18% Similarity=0.266 Sum_probs=0.0
Q ss_pred cCcccccCceEEEcCCceEEEEEEeccceEEEccCCCCCCceEEEecccccCCCCCCcccccccCCCcccCCCeEEEecC
Q 000294 488 LENSFELYELVCFGRKDFGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVSEG 567 (1711)
Q Consensus 488 s~G~FeLgDLVQLD~~TVGVIVrVEkDe~fkVLd~~gd~~~VvtVk~~~I~~K~~~rr~vAtD~~gk~I~vGD~VKVIdG 567 (1711)
.+..|.+++.|. |+|++|.+.-.|+.|... ..-.|..++|.... .......|++||+|+|
T Consensus 1 ~~~~~k~G~iv~------G~V~~i~~~G~fV~i~~~----~~Gli~~sel~~~~-------~~~~~~~~~vGD~I~v--- 60 (123)
T PRK08059 1 MMSQYEVGSVVT------GKVTGIQPYGAFVALDEE----TQGLVHISEITHGF-------VKDIHDFLSVGDEVKV--- 60 (123)
T ss_pred CcccCCCCCEEE------EEEEEEecceEEEEECCC----CEEEEEHHHCCccc-------ccCHHHcCCCCCEEEE---
Q ss_pred CCCCceEEEEEEEC--CEEEEEeCcceee
Q 000294 568 PSKDRQGIVKKIYR--GILFIYDENETEN 594 (1711)
Q Consensus 568 p~kGRqG~VlHIyR--s~VFL~Sr~~tEN 594 (1711)
.|+.|.+ ..+.|-.+...++
T Consensus 61 -------kI~~id~~~~~i~lslk~~~~~ 82 (123)
T PRK08059 61 -------KVLSVDEEKGKISLSIRATEEA 82 (123)
T ss_pred -------EEEEEECCCCeEEEEEEEcccC
No 184
>PRK11642 exoribonuclease R; Provisional
Probab=26.44 E-value=1.8e+02 Score=39.84 Aligned_cols=81 Identities=16% Similarity=0.105 Sum_probs=45.3
Q ss_pred cEEEEEEeCCCCcEEEEEeccchhHHHHhcCCCCeEeccccccCHHHHHHHhhcccccccccCCCEEEEecCcCCCCcEE
Q 000294 259 QIISAFAVDHIKGFIFIEADKQCDINEACKGLSGIYYSRLAPVPKNEVSHLLSAQIKRNEVSEGTWAYVKNGKYKGDLAQ 338 (1711)
Q Consensus 259 ~I~SVFvpd~lKGYIYIEA~kq~dVk~AIkGI~gVy~~k~~pVPikEM~dLL~vkkk~~~Lk~GdwVRIKrGpYKGDLAQ 338 (1711)
.++...+....+--||||.... .|+|+.+|-.-.---....|....|.-......|++|+.|+|+
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 4555555554555588887432 1444443321100000122333333322223468889999974
Q ss_pred EEEEeCCCCEEEEEEe
Q 000294 339 VVYVNNARKRATVKLI 354 (1711)
Q Consensus 339 VveVdenk~eVtVKLI 354 (1711)
|+.|+..+.+|.+.|+
T Consensus 710 V~~vD~~~rkI~f~l~ 725 (813)
T PRK11642 710 VEAVNMDERKIDFSLI 725 (813)
T ss_pred EEEeecCCCeEEEEEe
Confidence 8999999999999987
No 185
>PRK14632 hypothetical protein; Provisional
Probab=26.43 E-value=99 Score=34.66 Aligned_cols=49 Identities=16% Similarity=0.326 Sum_probs=37.9
Q ss_pred cccCCEEEEc-cCCC------CCceeEEEEEeCCeEEEEecCC------ceEEEEeCCcccc
Q 000294 660 FAVGQTLRIR-VGPL------KGYLCRVLAVRYSDVTVKLDSQ------QKILTVKGEHLAE 708 (1711)
Q Consensus 660 ~lIGKTVkIr-kGPY------KGylGiVKDaTdt~ARVELHSk------~KtITVdK~~Ls~ 708 (1711)
.+||+.|+|+ ..|+ |=+.|+++.++++.++|++..+ ..+|+|+.+.|..
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 2468888887764
No 186
>COG2139 RPL21A Ribosomal protein L21E [Translation, ribosomal structure and biogenesis]
Probab=26.32 E-value=82 Score=32.72 Aligned_cols=49 Identities=16% Similarity=0.256 Sum_probs=34.1
Q ss_pred cCcccccCceEEEc--------------CCceEEEEEEeccceEEEccCCCCCCceEEEecccc
Q 000294 488 LENSFELYELVCFG--------------RKDFGLIVGMEKDDHYKILKEGSEGPAVVTVERRTL 537 (1711)
Q Consensus 488 s~G~FeLgDLVQLD--------------~~TVGVIVrVEkDe~fkVLd~~gd~~~VvtVk~~~I 537 (1711)
.+-.|++||+|-|+ ...+|+||.+..+ +|.|.--.++..+.+.|.|.-|
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 45689999999984 2367999999885 6666643334456666666544
No 187
>PRK12289 GTPase RsgA; Reviewed
Probab=25.91 E-value=3.5e+02 Score=33.58 Aligned_cols=76 Identities=16% Similarity=0.300 Sum_probs=43.5
Q ss_pred CceEEEEEEeccceEEEccCCCC---CCceEEEecccccCCCCCCcccccccCCCcccCCCeEEEecCCCCCceEEEEEE
Q 000294 503 KDFGLIVGMEKDDHYKILKEGSE---GPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVSEGPSKDRQGIVKKI 579 (1711)
Q Consensus 503 ~TVGVIVrVEkDe~fkVLd~~gd---~~~VvtVk~~~I~~K~~~rr~vAtD~~gk~I~vGD~VKVIdGp~kGRqG~VlHI 579 (1711)
...|.||++..+ .+.|+...++ .+.++.+.... ..+ ..+..+-|||.|.+-.-...+..|+|.+|
T Consensus 8 ~~~g~V~~~~~~-~y~V~~~~~~~~~~~~~~~~~~r~------~lk-----~~~~~~~vGD~V~~~~~~~~~~~~~I~~v 75 (352)
T PRK12289 8 QLLGTVVAVQAN-FYRVQLDEPQNLNPPSLLLCTRRT------RLK-----KIGQQVMVGDRVIVEEPDWQGQRGAIAEV 75 (352)
T ss_pred cccEEEEEEECC-EEEEEECCCcccCcceEEEEEccc------ccc-----cCCCCcccCCEEEEeecCCCCCceEEEEE
Confidence 356999999995 7777653221 11234443211 111 12355899999988532223467999999
Q ss_pred ECCEEEEEeCc
Q 000294 580 YRGILFIYDEN 590 (1711)
Q Consensus 580 yRs~VFL~Sr~ 590 (1711)
+.---+|.-..
T Consensus 76 lpR~~~L~R~~ 86 (352)
T PRK12289 76 LPRKTELDRPP 86 (352)
T ss_pred eccccceechh
Confidence 87544444333
No 188
>PRK14633 hypothetical protein; Provisional
Probab=25.27 E-value=1e+02 Score=33.76 Aligned_cols=48 Identities=17% Similarity=0.221 Sum_probs=36.9
Q ss_pred cccCCEEEEcc-CC---CCCceeEEEEEeCCeEEEEecCCceEEEEeCCcccc
Q 000294 660 FAVGQTLRIRV-GP---LKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLAE 708 (1711)
Q Consensus 660 ~lIGKTVkIrk-GP---YKGylGiVKDaTdt~ARVELHSk~KtITVdK~~Ls~ 708 (1711)
..||+.|+|+- .| -|=+.|+++.++++.+++++.- .+++.|+.++|.-
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 3557899999999999988742 4677888877764
No 189
>PRK14646 hypothetical protein; Provisional
Probab=25.18 E-value=99 Score=34.11 Aligned_cols=47 Identities=9% Similarity=0.011 Sum_probs=36.3
Q ss_pred cccCCEEEEcc-CCC---CCceeEEEEEeCCeEEEEecCCceEEEEeCCcccc
Q 000294 660 FAVGQTLRIRV-GPL---KGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLAE 708 (1711)
Q Consensus 660 ~lIGKTVkIrk-GPY---KGylGiVKDaTdt~ARVELHSk~KtITVdK~~Ls~ 708 (1711)
+++|+.|+|+- .|+ |=+.|+++.+.++.++|+++ .+++.|+.+.|.-
T Consensus 97 r~~G~~v~V~l~~~~~~~~~~~G~L~~~~~~~v~l~~~--g~~~~i~~~~I~k 147 (155)
T PRK14646 97 TFKGFPVNVELNQKNSKIKFLNGLLYEKSKDYLAINIK--GKIKKIPFNEVLK 147 (155)
T ss_pred HhCCCEEEEEEecCcCCeEEEEEEEEEEeCCEEEEEEC--CEEEEEEHHHeee
Confidence 47999999973 344 44579999999999998864 6677887777764
No 190
>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=24.49 E-value=1.1e+02 Score=36.62 Aligned_cols=6 Identities=50% Similarity=0.927 Sum_probs=2.4
Q ss_pred CCceec
Q 000294 81 KGKAVA 86 (1711)
Q Consensus 81 ~~~~~~ 86 (1711)
|+|+++
T Consensus 206 k~k~~P 211 (314)
T PF06524_consen 206 KGKPIP 211 (314)
T ss_pred cCCCCC
Confidence 344443
No 191
>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=24.31 E-value=2.6e+02 Score=25.79 Aligned_cols=67 Identities=16% Similarity=0.149 Sum_probs=38.8
Q ss_pred EEEEEEeCCCCcEEEEEeccchhHHHHhcCCCCeEeccccccCHHHHHHHhhcccccccccCCCEEEEecCcCCCCcEEE
Q 000294 260 IISAFAVDHIKGFIFIEADKQCDINEACKGLSGIYYSRLAPVPKNEVSHLLSAQIKRNEVSEGTWAYVKNGKYKGDLAQV 339 (1711)
Q Consensus 260 I~SVFvpd~lKGYIYIEA~kq~dVk~AIkGI~gVy~~k~~pVPikEM~dLL~vkkk~~~Lk~GdwVRIKrGpYKGDLAQV 339 (1711)
|+...+....+-++||+.... ....||+.|+..-. +......|++|+.|+++ |
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 13355666664311 11112347889998865 8
Q ss_pred EEEeCCCCEEEEEE
Q 000294 340 VYVNNARKRATVKL 353 (1711)
Q Consensus 340 veVdenk~eVtVKL 353 (1711)
+.+++...++.|.+
T Consensus 56 ~~~~~~~~~i~lS~ 69 (70)
T cd05687 56 LRVEDEEGNVVLSK 69 (70)
T ss_pred EEEECCCCeEEEEe
Confidence 88887766676654
No 192
>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=24.25 E-value=94 Score=29.24 Aligned_cols=28 Identities=25% Similarity=0.337 Sum_probs=22.7
Q ss_pred ccccCCCEEEEecCcCCCCcEEEEEEeCCCCEEEEEEe
Q 000294 317 NEVSEGTWAYVKNGKYKGDLAQVVYVNNARKRATVKLI 354 (1711)
Q Consensus 317 ~~Lk~GdwVRIKrGpYKGDLAQVveVdenk~eVtVKLI 354 (1711)
..|++|+.|+++ |..|+.++.++.++|+
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 8999888888888763
No 193
>COG1471 RPS4A Ribosomal protein S4E [Translation, ribosomal structure and biogenesis]
Probab=24.03 E-value=86 Score=36.91 Aligned_cols=52 Identities=17% Similarity=0.143 Sum_probs=39.7
Q ss_pred CcccCCCeEEEecCCCCCceEEEEEEECC------EEEEEeCcceeeccEEEEeCCceeecc
Q 000294 554 KVISLNDTARVSEGPSKDRQGIVKKIYRG------ILFIYDENETENGGYFCSKSQHCEKTK 609 (1711)
Q Consensus 554 k~I~vGD~VKVIdGp~kGRqG~VlHIyRs------~VFL~Sr~~tENgGIFVvRarnv~tv~ 609 (1711)
-.|..|-.|-|+.|.|-|+.|+|++|... +|.|-+ +++--|.|...+|.+++
T Consensus 172 i~fe~g~~~~vtgG~h~G~~G~I~~I~~~~~~~~~~v~~e~----~~g~~F~T~~~yVfvIG 229 (241)
T COG1471 172 IKFEEGALVYVTGGRHVGRVGTIVEIEIQESSKPNLVTVED----EEGNTFQTIKDYVFVIG 229 (241)
T ss_pred eccCCCcEEEEECCccccceEEEEEEEEecCCCccEEEEec----CCCCceEEeeeEEEEEc
Confidence 35788999999999999999999999754 222222 22336999999999885
No 194
>PRK02001 hypothetical protein; Validated
Probab=23.99 E-value=1.3e+02 Score=33.25 Aligned_cols=48 Identities=15% Similarity=0.189 Sum_probs=36.7
Q ss_pred cccCCEEEEccCCCCCceeEEEEEeCCeEEEEecCC------------ceEEEEeCCccc
Q 000294 660 FAVGQTLRIRVGPLKGYLCRVLAVRYSDVTVKLDSQ------------QKILTVKGEHLA 707 (1711)
Q Consensus 660 ~lIGKTVkIrkGPYKGylGiVKDaTdt~ARVELHSk------------~KtITVdK~~Ls 707 (1711)
+++|+.|+|+----|=+.|+++++.++.++|+++.+ .++++|+.+.|.
T Consensus 87 r~~G~~v~V~l~~~~~~~G~L~~~~~~~i~l~~~~~~~~~~~k~~~~~~~~~~i~~~~I~ 146 (152)
T PRK02001 87 KNIGRELEVLTKNGKKIEGELKSADENDITLEVKAREPKEGGKGKVTVEKEETITYDDIK 146 (152)
T ss_pred HhCCCEEEEEECCCCEEEEEEEEEeCCEEEEEEcccccccccccccccceeEEEEhHhee
Confidence 479999999753347799999999999999998743 235677666654
No 195
>cd05684 S1_DHX8_helicase S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH (Asp-Glu-Ala-His) box polypeptide. The DEAH-box RNA helicases are thought to play key roles in pre-mRNA splicing and DHX8 facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. DHX8 is also known as HRH1 (human RNA helicase 1) in Homo sapiens and PRP22 in Saccharomyces cerevisiae.
Probab=23.95 E-value=4.3e+02 Score=25.11 Aligned_cols=15 Identities=13% Similarity=0.275 Sum_probs=12.2
Q ss_pred cCCCcccCCCeEEEe
Q 000294 551 QSMKVISLNDTARVS 565 (1711)
Q Consensus 551 ~~gk~I~vGD~VKVI 565 (1711)
...+.|++||.|+|.
T Consensus 44 ~~~~~~~~Gd~v~v~ 58 (79)
T cd05684 44 NPSDVVKRGQKVKVK 58 (79)
T ss_pred ChhheeCCCCEEEEE
Confidence 446789999999985
No 196
>COG1532 Predicted RNA-binding protein [General function prediction only]
Probab=23.92 E-value=47 Score=31.25 Aligned_cols=31 Identities=13% Similarity=0.104 Sum_probs=26.3
Q ss_pred CCEEEEec--CcCCCCcEEEEEEeCCCCEEEEE
Q 000294 322 GTWAYVKN--GKYKGDLAQVVYVNNARKRATVK 352 (1711)
Q Consensus 322 GdwVRIKr--GpYKGDLAQVveVdenk~eVtVK 352 (1711)
++-|+.+. |-||-..+||.+||.+..++.|+
T Consensus 24 ~e~V~a~Dilgd~ke~~G~vkriDldehkI~lE 56 (57)
T COG1532 24 EEGVVARDILGDEKEFEGQVKRIDLDEHKIELE 56 (57)
T ss_pred cCcEEEEeccCCceEecceEEEEEccccEEEec
Confidence 56677765 99999999999999999888764
No 197
>smart00243 GAS2 Growth-Arrest-Specific Protein 2 Domain. GROWTH-ARREST-SPECIFIC PROTEIN 2 Domain
Probab=23.71 E-value=1.7e+02 Score=29.16 Aligned_cols=50 Identities=20% Similarity=0.263 Sum_probs=32.3
Q ss_pred HHHHHHhhcccccccccCCCEEEEecCcCC-CCcEEEEEEeCCCCEEEEEEecc
Q 000294 304 NEVSHLLSAQIKRNEVSEGTWAYVKNGKYK-GDLAQVVYVNNARKRATVKLIPR 356 (1711)
Q Consensus 304 kEM~dLL~vkkk~~~Lk~GdwVRIKrGpYK-GDLAQVveVdenk~eVtVKLIPR 356 (1711)
+|+.+++....=...| ..+||-.|+|+ ||..++.-|.--+..|+|++=.=
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 3455666543322333 78999999999 87766555555556888887543
No 198
>PRK08582 hypothetical protein; Provisional
Probab=23.62 E-value=2.5e+02 Score=30.46 Aligned_cols=57 Identities=18% Similarity=0.205 Sum_probs=34.4
Q ss_pred cccCceEEEcCCceEEEEEEeccceEEEccCCCCCCceEEEecccccCCCCCCcccccccCCCcccCCCeEEEe
Q 000294 492 FELYELVCFGRKDFGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVS 565 (1711)
Q Consensus 492 FeLgDLVQLD~~TVGVIVrVEkDe~fkVLd~~gd~~~VvtVk~~~I~~K~~~rr~vAtD~~gk~I~vGD~VKVI 565 (1711)
|.+++.|. |+|+.|..--.|+-|...- .-.|..++|.... + .| ....|++||.|+|.
T Consensus 3 ~kvG~iv~------G~V~~I~~fG~fV~L~~~~----~GlVhiSels~~~-----v-~~-~~~~l~vGD~Vkvk 59 (139)
T PRK08582 3 IEVGSKLQ------GKVTGITNFGAFVELPEGK----TGLVHISEVADNY-----V-KD-INDHLKVGDEVEVK 59 (139)
T ss_pred CcCCCEEE------EEEEEEECCeEEEEECCCC----EEEEEeeccCccc-----c-cc-cccccCCCCEEEEE
Confidence 66777775 8888887755666665431 2234445554321 1 12 24679999999884
No 199
>PF08595 RXT2_N: RXT2-like, N-terminal; InterPro: IPR013904 The entry represents the N-terminal region of RXT2-like proteins. In Saccharomyces cerevisiae (Baker's yeast), RXT2 has been demonstrated to be involved in conjugation with cellular fusion (mating) and invasive growth []. A high throughput localisation study has localised RXT2 to the nucleus [].
Probab=23.58 E-value=39 Score=37.19 Aligned_cols=6 Identities=0% Similarity=0.324 Sum_probs=2.4
Q ss_pred cccccc
Q 000294 119 FVEDAA 124 (1711)
Q Consensus 119 FiDdEA 124 (1711)
.+|.|-
T Consensus 54 ~~d~~~ 59 (149)
T PF08595_consen 54 RIDEEG 59 (149)
T ss_pred ccCccc
Confidence 344333
No 200
>PRK05807 hypothetical protein; Provisional
Probab=23.34 E-value=2.4e+02 Score=30.41 Aligned_cols=57 Identities=12% Similarity=0.173 Sum_probs=35.4
Q ss_pred ccccCceEEEcCCceEEEEEEeccceEEEccCCCCCCceEEEecccccCCCCCCcccccccCCCcccCCCeEEEe
Q 000294 491 SFELYELVCFGRKDFGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVS 565 (1711)
Q Consensus 491 ~FeLgDLVQLD~~TVGVIVrVEkDe~fkVLd~~gd~~~VvtVk~~~I~~K~~~rr~vAtD~~gk~I~vGD~VKVI 565 (1711)
.|++++.|. |+|+.|...-.|+.|. + ..-.|..++|.... +. + ....|++||.|+|.
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 7888887766677772 2 12344555554321 11 1 23568999999985
No 201
>COG2163 RPL14A Ribosomal protein L14E/L6E/L27E [Translation, ribosomal structure and biogenesis]
Probab=23.27 E-value=95 Score=33.52 Aligned_cols=47 Identities=15% Similarity=0.293 Sum_probs=34.2
Q ss_pred cccCCEEEEccCCCCCceeEEEEEeCCeEEEEecCCceEEEEeCCccc
Q 000294 660 FAVGQTLRIRVGPLKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLA 707 (1711)
Q Consensus 660 ~lIGKTVkIrkGPYKGylGiVKDaTdt~ARVELHSk~KtITVdK~~Ls 707 (1711)
.-+|+.|.|+.|.|.|-.+.|+++-|+. +|....-+++--|++..+.
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 5555544433334444433
No 202
>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]
Probab=23.22 E-value=1.2e+02 Score=38.48 Aligned_cols=13 Identities=8% Similarity=0.176 Sum_probs=5.9
Q ss_pred CHHHHHHHHHHHh
Q 000294 182 DEEEFDKMMEERY 194 (1711)
Q Consensus 182 DaEelAe~lkERY 194 (1711)
+.+.|..+|-+-|
T Consensus 12 ~~~~vg~~Fv~qY 24 (419)
T KOG0116|consen 12 TPQLVGNEFVRQY 24 (419)
T ss_pred CHHHHHHHHHHHH
Confidence 3445555444333
No 203
>PF11424 DUF3195: Protein of unknown function (DUF3195); InterPro: IPR021540 This archaeal family of proteins has no known function. ; PDB: 1RKI_B.
Probab=23.16 E-value=79 Score=32.07 Aligned_cols=43 Identities=12% Similarity=0.074 Sum_probs=29.3
Q ss_pred EEEEeccchHHHHHHHHHHHHHhhccCCCCCcEEEEEEeCCCCcEEEEEec
Q 000294 228 WKVKCMAGRERQSAFCLMQKFVDLQSLGSKMQIISAFAVDHIKGFIFIEAD 278 (1711)
Q Consensus 228 WaVKCk~GkEReVV~~LmrKii~lq~~g~~L~I~SVFvpd~lKGYIYIEA~ 278 (1711)
..|++.++||+.|+..|--=+.-+ .+ +|.+....||.|||+..
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 368999999999998886544321 11 35566678999999994
No 204
>KOG0943 consensus Predicted ubiquitin-protein ligase/hyperplastic discs protein, HECT superfamily [Posttranslational modification, protein turnover, chaperones]
Probab=23.05 E-value=42 Score=46.27 Aligned_cols=24 Identities=8% Similarity=0.008 Sum_probs=14.3
Q ss_pred CCCcEEEEEeccchhHHHHhcCCC
Q 000294 268 HIKGFIFIEADKQCDINEACKGLS 291 (1711)
Q Consensus 268 ~lKGYIYIEA~kq~dVk~AIkGI~ 291 (1711)
..+|.+||.-++-..--.+|.+++
T Consensus 1915 S~~~ierf~PyrfssrssflSN~R 1938 (3015)
T KOG0943|consen 1915 SSAGIERFDPYRFSSRSSFLSNLR 1938 (3015)
T ss_pred cCCCeeeeccccccchhhhhhhcc
Confidence 567888887765544444444443
No 205
>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=23.03 E-value=5.3e+02 Score=23.45 Aligned_cols=56 Identities=11% Similarity=0.041 Sum_probs=33.2
Q ss_pred EEEEEeccchHHHHHHHHHHHHHhhccCCCCCcEEEEEEeCCCCc-EEEEEeccchh
Q 000294 227 IWKVKCMAGRERQSAFCLMQKFVDLQSLGSKMQIISAFAVDHIKG-FIFIEADKQCD 282 (1711)
Q Consensus 227 LWaVKCk~GkEReVV~~LmrKii~lq~~g~~L~I~SVFvpd~lKG-YIYIEA~kq~d 282 (1711)
+-.+++++|++.+++..|..-+........-+.-+.++....-++ ||++|-.....
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 456778999999998887666554521222232333444344555 88888765533
No 206
>PLN03134 glycine-rich RNA-binding protein 4; Provisional
Probab=22.83 E-value=1.5e+02 Score=31.99 Aligned_cols=59 Identities=17% Similarity=0.287 Sum_probs=40.1
Q ss_pred cEEEEEeccchHHHHHHHHHHHHHhhccCCCCCcEEEEEEe-----CCCCcEEEEEeccchhHHHHhcCCCCe
Q 000294 226 TIWKVKCMAGRERQSAFCLMQKFVDLQSLGSKMQIISAFAV-----DHIKGFIFIEADKQCDINEACKGLSGI 293 (1711)
Q Consensus 226 kLWaVKCk~GkEReVV~~LmrKii~lq~~g~~L~I~SVFvp-----d~lKGYIYIEA~kq~dVk~AIkGI~gV 293 (1711)
+||+=.+-..-..+-+..|..++ + .|.+|.++ ...+||=|||....+++..||+.|.+.
T Consensus 36 ~lfVgnL~~~~te~~L~~~F~~~------G---~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~ 99 (144)
T PLN03134 36 KLFIGGLSWGTDDASLRDAFAHF------G---DVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGK 99 (144)
T ss_pred EEEEeCCCCCCCHHHHHHHHhcC------C---CeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCC
Confidence 57777666555554444444433 1 35565554 246899999999999999999987654
No 207
>PF01157 Ribosomal_L21e: Ribosomal protein L21e; InterPro: IPR001147 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. L21E family contains proteins from a number of eukaryotic and archaebacterial organisms which include; mammalian L2, Entamoeba histolytica L21, Caenorhabditis elegans L21 (C14B9.7), Saccharomyces cerevisiae (Baker's yeast) L21E (URP1) and Haloarcula marismortui HL31.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3IZR_U 1S1I_Q 3O58_T 3IZS_U 3O5H_T 1Q82_R 1KQS_P 3CCJ_Q 3CCQ_Q 1VQ5_Q ....
Probab=22.83 E-value=1.6e+02 Score=30.74 Aligned_cols=60 Identities=10% Similarity=0.222 Sum_probs=30.4
Q ss_pred ccccccCCCcccCCCeEEEe-cCC---------CCCceEEEEEEECCE---EEEE-eCcceeeccEEEEeCCcee
Q 000294 546 FTALDQSMKVISLNDTARVS-EGP---------SKDRQGIVKKIYRGI---LFIY-DENETENGGYFCSKSQHCE 606 (1711)
Q Consensus 546 ~vAtD~~gk~I~vGD~VKVI-dGp---------~kGRqG~VlHIyRs~---VFL~-Sr~~tENgGIFVvRarnv~ 606 (1711)
.+.+.....+|++||.|-|+ ++. |-|++|+|..|.+.. +++. -+.-.. .-.++|++.||.
T Consensus 23 ~~~ls~~l~~yk~GD~V~I~id~sv~kGmPh~~yHGkTG~V~~v~~~~~G~~~~~~v~~~~~-~K~i~vr~eHlk 96 (99)
T PF01157_consen 23 MIPLSTYLQEYKVGDKVDIKIDPSVHKGMPHKRYHGKTGRVFNVTKGARGVAYNKQVKDRIK-EKRIIVRPEHLK 96 (99)
T ss_dssp S--CHHHH----TT-EEEE---TTSSSSS--GGGTTEEEEEEEE-SSCEEEEEEEECSSSCE-EEEEEEEGGGEE
T ss_pred CCcHHHHHHHccCCCEEEEEecCccccCCCcceECCCceeEEEeCCCceEEEEEEEecCCcc-cEEEEECHHHcc
Confidence 44555667899999999986 332 357899999998863 2222 122111 123677777765
No 208
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=22.58 E-value=69 Score=37.61 Aligned_cols=17 Identities=18% Similarity=0.323 Sum_probs=9.8
Q ss_pred CcEEEEEeccchhHHHH
Q 000294 270 KGFIFIEADKQCDINEA 286 (1711)
Q Consensus 270 KGYIYIEA~kq~dVk~A 286 (1711)
.||.=|=.....++.-+
T Consensus 171 sG~~~vlV~N~~eLe~l 187 (232)
T PRK12766 171 SGFEEVRVHNTDDLEGV 187 (232)
T ss_pred CCCeeEEecCHHHHhhc
Confidence 46655555566665555
No 209
>COG0056 AtpA F0F1-type ATP synthase, alpha subunit [Energy production and conversion]
Probab=22.37 E-value=1.5e+02 Score=38.14 Aligned_cols=32 Identities=22% Similarity=0.211 Sum_probs=26.7
Q ss_pred CcccccCceEEEcCCceEEEEEEeccceEEEc
Q 000294 489 ENSFELYELVCFGRKDFGLIVGMEKDDHYKIL 520 (1711)
Q Consensus 489 ~G~FeLgDLVQLD~~TVGVIVrVEkDe~fkVL 520 (1711)
+..|..|.||+|...+.|++.++|.|..+.||
T Consensus 44 l~~~~~~E~~ef~~~v~G~alnle~d~VG~vi 75 (504)
T COG0056 44 LENVMAGELVEFPGGVKGMALNLEEDSVGAVI 75 (504)
T ss_pred CchhhcCceEEecCCcEEEEEeccccceeEEE
Confidence 45899999999999999999999987544444
No 210
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=22.34 E-value=23 Score=41.40 Aligned_cols=15 Identities=20% Similarity=0.220 Sum_probs=8.1
Q ss_pred cccccccccCCCCCch
Q 000294 118 QFVEDAADVDYDDDDE 133 (1711)
Q Consensus 118 ~FiDdEAEVDDDeEeE 133 (1711)
.||. +.||++|.|+|
T Consensus 54 e~l~-~~~~~~~~~~~ 68 (232)
T PRK12766 54 ADVG-GLEVSEETEAE 68 (232)
T ss_pred HHhc-cccccccccch
Confidence 4553 66666555443
No 211
>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=22.32 E-value=2.3e+02 Score=26.04 Aligned_cols=26 Identities=8% Similarity=0.236 Sum_probs=20.7
Q ss_pred cccCCCEEEEecCcCCCCcEEEEEEeCCCCEEEEEE
Q 000294 318 EVSEGTWAYVKNGKYKGDLAQVVYVNNARKRATVKL 353 (1711)
Q Consensus 318 ~Lk~GdwVRIKrGpYKGDLAQVveVdenk~eVtVKL 353 (1711)
.|++|+.|++ +|.+++....++.|.|
T Consensus 44 ~~~~Gd~v~~----------~v~~~d~~~~~i~ls~ 69 (73)
T cd05691 44 RFKVGDEVEA----------KITNVDRKNRKISLSI 69 (73)
T ss_pred ccCCCCEEEE----------EEEEEeCCCCEEEEEE
Confidence 4788999986 5999998877777665
No 212
>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=22.10 E-value=30 Score=44.91 Aligned_cols=9 Identities=33% Similarity=0.172 Sum_probs=3.9
Q ss_pred CHHHHhhcC
Q 000294 437 SEEELLKFQ 445 (1711)
Q Consensus 437 TLEEL~kF~ 445 (1711)
.|.||.-|.
T Consensus 291 ~lAE~s~~~ 299 (556)
T PF05918_consen 291 LLAELSPFC 299 (556)
T ss_dssp HHHHHHTT-
T ss_pred HHHHHcCCC
Confidence 344555554
No 213
>PRK14647 hypothetical protein; Provisional
Probab=21.93 E-value=1.3e+02 Score=33.34 Aligned_cols=48 Identities=17% Similarity=0.233 Sum_probs=36.9
Q ss_pred cccCCEEEEcc-CC--------CCCceeEEEEEeCCeEEEEecCCceEEEEeCCcccc
Q 000294 660 FAVGQTLRIRV-GP--------LKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLAE 708 (1711)
Q Consensus 660 ~lIGKTVkIrk-GP--------YKGylGiVKDaTdt~ARVELHSk~KtITVdK~~Ls~ 708 (1711)
..+|+.|+|+- -| -|=+.|++++++++.++|++. ..++|+|+.+.|.-
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 47899999974 23 366899999999999998874 24567888777763
No 214
>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=21.87 E-value=2.7e+02 Score=25.93 Aligned_cols=68 Identities=9% Similarity=0.112 Sum_probs=0.0
Q ss_pred cEEEEEEeCCCCcEEEEEeccchhHHHHhcCCCCeEeccccccCHHHHHHHhhcccccccccCCCEEEEecCcCCCCcEE
Q 000294 259 QIISAFAVDHIKGFIFIEADKQCDINEACKGLSGIYYSRLAPVPKNEVSHLLSAQIKRNEVSEGTWAYVKNGKYKGDLAQ 338 (1711)
Q Consensus 259 ~I~SVFvpd~lKGYIYIEA~kq~dVk~AIkGI~gVy~~k~~pVPikEM~dLL~vkkk~~~Lk~GdwVRIKrGpYKGDLAQ 338 (1711)
.|+.+.+....+-.|||| +-.....+|++.++.+-. .......|++|+.|++ +
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 000294 339 VVYVNNARKRATVKL 353 (1711)
Q Consensus 339 VveVdenk~eVtVKL 353 (1711)
|++++..+.++.|.+
T Consensus 58 V~~~d~~~~~i~ls~ 72 (73)
T cd05706 58 VLSVDVPNKKIALSL 72 (73)
T ss_pred EEEEeCCCCEEEEEE
No 215
>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=21.59 E-value=1.9e+02 Score=27.89 Aligned_cols=67 Identities=16% Similarity=0.258 Sum_probs=42.0
Q ss_pred cEEEEEEeCCCCcEEEEEeccchhHHHHhcCCCCeEeccccccCHHHHHHHh-h-cccccccccCCCEEEEecCcCCCCc
Q 000294 259 QIISAFAVDHIKGFIFIEADKQCDINEACKGLSGIYYSRLAPVPKNEVSHLL-S-AQIKRNEVSEGTWAYVKNGKYKGDL 336 (1711)
Q Consensus 259 ~I~SVFvpd~lKGYIYIEA~kq~dVk~AIkGI~gVy~~k~~pVPikEM~dLL-~-vkkk~~~Lk~GdwVRIKrGpYKGDL 336 (1711)
.|...++....+..+||+.. .+ ...+||+.||.+-. . +......|++|+-|++
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 35566666666666887751 12 23356777776654 1 1111246789999975
Q ss_pred EEEEEEeCCCCEEEE
Q 000294 337 AQVVYVNNARKRATV 351 (1711)
Q Consensus 337 AQVveVdenk~eVtV 351 (1711)
+|++|++++.++.|
T Consensus 60 -kVl~id~~~~~i~L 73 (74)
T cd05705 60 -KVLSVNSEKNLVEL 73 (74)
T ss_pred -EEEEEECCCCEEec
Confidence 59999998887654
No 216
>COG0779 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.49 E-value=1.5e+02 Score=32.94 Aligned_cols=47 Identities=19% Similarity=0.328 Sum_probs=37.9
Q ss_pred cccCCEEEEcc----CCCCCceeEEEEEeCCeEEEEecCCceEEEEeCCcccc
Q 000294 660 FAVGQTLRIRV----GPLKGYLCRVLAVRYSDVTVKLDSQQKILTVKGEHLAE 708 (1711)
Q Consensus 660 ~lIGKTVkIrk----GPYKGylGiVKDaTdt~ARVELHSk~KtITVdK~~Ls~ 708 (1711)
+++|+.|+|.- .--|=+.|+|+.+.+++++|++. .|+|.|+...|.-
T Consensus 96 r~~G~~Vkv~l~~~~~~~k~~~G~i~~~d~~~v~~~~~--~k~v~Ip~~~i~k 146 (153)
T COG0779 96 RFIGEKVKVKLRLPIEGRKKFEGKIVAVDGETVTLEVD--GKEVEIPFSDIAK 146 (153)
T ss_pred HhcCcEEEEEEecccCCceEEEEEEEEEcCCeEEEEEC--CEEEEEEcccchh
Confidence 47999999998 44677899999999999998855 5558887777763
No 217
>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=21.48 E-value=1e+02 Score=27.33 Aligned_cols=28 Identities=29% Similarity=0.483 Sum_probs=24.9
Q ss_pred CCCCcEEEEEeccchhHHHHhcCCCCeE
Q 000294 267 DHIKGFIFIEADKQCDINEACKGLSGIY 294 (1711)
Q Consensus 267 d~lKGYIYIEA~kq~dVk~AIkGI~gVy 294 (1711)
...++|.||+-...+++..||+.+.+..
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 218
>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=21.46 E-value=2.2e+02 Score=26.24 Aligned_cols=65 Identities=15% Similarity=0.218 Sum_probs=38.0
Q ss_pred EEEEEEeCCCCcEEEEEeccchhHHHHhcCCCCeEeccccccCHHHHHHHhhcccccccccCCCEEEEecCcCCCCcEEE
Q 000294 260 IISAFAVDHIKGFIFIEADKQCDINEACKGLSGIYYSRLAPVPKNEVSHLLSAQIKRNEVSEGTWAYVKNGKYKGDLAQV 339 (1711)
Q Consensus 260 I~SVFvpd~lKGYIYIEA~kq~dVk~AIkGI~gVy~~k~~pVPikEM~dLL~vkkk~~~Lk~GdwVRIKrGpYKGDLAQV 339 (1711)
|+...+....+--||||... + ...+||+.||.+-. +......|++|+.|++ +|
T Consensus 3 ~v~g~V~~v~~~Gv~V~l~~---------~-------~~G~v~~s~l~~~~-~~~~~~~~~~Gd~v~~----------~v 55 (68)
T cd05707 3 VVRGFVKNIANNGVFVTLGR---------G-------VDARVRVSELSDSY-LKDWKKRFKVGQLVKG----------KI 55 (68)
T ss_pred EEEEEEEEEECccEEEEeCC---------C-------CEEEEEHHHCCchh-hcCHhhccCCCCEEEE----------EE
Confidence 33444444555668888743 2 23345556654321 1112345788999986 68
Q ss_pred EEEeCCCCEEEE
Q 000294 340 VYVNNARKRATV 351 (1711)
Q Consensus 340 veVdenk~eVtV 351 (1711)
+.+++...++.|
T Consensus 56 ~~~d~~~~~i~l 67 (68)
T cd05707 56 VSIDPDNGRIEM 67 (68)
T ss_pred EEEeCCCCEEec
Confidence 888887777654
No 219
>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=21.27 E-value=4.2e+02 Score=26.67 Aligned_cols=64 Identities=13% Similarity=0.036 Sum_probs=39.3
Q ss_pred ceEEEEEEeccceEEEccCCCCCCceEEEecccccCCCCCCcccccccCCCcccCCCeEEEecCCCCC-ceEEEEEEECC
Q 000294 504 DFGLIVGMEKDDHYKILKEGSEGPAVVTVERRTLKNGPFDMKFTALDQSMKVISLNDTARVSEGPSKD-RQGIVKKIYRG 582 (1711)
Q Consensus 504 TVGVIVrVEkDe~fkVLd~~gd~~~VvtVk~~~I~~K~~~rr~vAtD~~gk~I~vGD~VKVIdGp~kG-RqG~VlHIyRs 582 (1711)
.+..|+++.-+..+.|.+.++ +.+.+.. -.|+ +..--|+.||+|.|---+... ..|.|+|||..
T Consensus 2 ~i~rV~~~~G~n~~~V~~~dG---~~~l~~i---P~Kf---------Rk~iWIkrGd~VlV~p~~~~~kvkgeIv~i~~~ 66 (78)
T cd05792 2 QIVRVLGSKGNNLHEVETPNG---SRYLVSM---PTKF---------RKNIWIKRGDFVLVEPIEEGDKVKAEIVKILTR 66 (78)
T ss_pred eEEEEEEcCCCcEEEEEcCCC---CEEEEEe---chhh---------cccEEEEeCCEEEEEecccCCceEEEEEEEECH
Confidence 345667776655677777654 2333332 1221 134568999999997544432 58999999864
No 220
>PF05320 Pox_RNA_Pol_19: Poxvirus DNA-directed RNA polymerase 19 kDa subunit; InterPro: IPR007984 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. The poxvirus DNA-directed RNA polymerase (2.7.7.6 from EC) catalyses the transcription of DNA into RNA. It consists of at least eight subunits, this is the 19 kDa subunit.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent
Probab=21.19 E-value=97 Score=34.52 Aligned_cols=39 Identities=15% Similarity=0.112 Sum_probs=22.9
Q ss_pred HHHHHHHhccccch-hhchhhHHHhhhcccccCCCCCCCCc
Q 000294 187 DKMMEERYKSNKLI-RYAEEDYEAKKMLEREYHMPCPEDPT 226 (1711)
Q Consensus 187 Ae~lkERY~r~s~~-~y~~d~~e~~~~VpQq~LLPSV~DPk 226 (1711)
...||+||-|+-+. ...+-..| +=..-||--||=|.|..
T Consensus 69 I~~iK~RYTRRiSLfEiTGIiaE-SyNLLqRGRlPLv~dls 108 (167)
T PF05320_consen 69 ISAIKKRYTRRISLFEITGIIAE-SYNLLQRGRLPLVSDLS 108 (167)
T ss_pred HHHHHHHHHhhhhHHHHHHHHHH-HHHHHHccccccccccc
Confidence 35689999875321 11111111 13477999999988764
No 221
>PLN00036 40S ribosomal protein S4; Provisional
Probab=21.14 E-value=1.7e+02 Score=35.14 Aligned_cols=29 Identities=14% Similarity=0.249 Sum_probs=26.1
Q ss_pred cccccCCCEEEEecCcCCCCcEEEEEEeC
Q 000294 316 RNEVSEGTWAYVKNGKYKGDLAQVVYVNN 344 (1711)
Q Consensus 316 ~~~Lk~GdwVRIKrGpYKGDLAQVveVde 344 (1711)
.+.|++|..|-|+.|...|.+|+|+++..
T Consensus 172 ~ikfe~G~l~~vtgG~n~GrvG~I~~i~~ 200 (261)
T PLN00036 172 FIKFDVGNLVMVTGGRNRGRVGVIKNREK 200 (261)
T ss_pred EEecCCCCEEEEECCeeceeEEEEEEEEe
Confidence 45789999999999999999999999873
No 222
>PF15470 DUF4637: Domain of unknown function (DUF4637)
Probab=20.97 E-value=77 Score=34.89 Aligned_cols=17 Identities=6% Similarity=-0.001 Sum_probs=10.4
Q ss_pred cccccccccccCCCCCc
Q 000294 116 VLQFVEDAADVDYDDDD 132 (1711)
Q Consensus 116 ~n~FiDdEAEVDDDeEe 132 (1711)
...|.+-|+|..+++|.
T Consensus 15 ~Ee~~a~E~e~e~~ee~ 31 (173)
T PF15470_consen 15 PEEPRAREAEQEEAEEG 31 (173)
T ss_pred ccccccchhhhhhcccc
Confidence 45677777776554443
No 223
>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=20.96 E-value=1.6e+02 Score=29.34 Aligned_cols=48 Identities=25% Similarity=0.403 Sum_probs=30.2
Q ss_pred HHHHHHhhcccccccccCCCEEEEecCcCC-CCcEEEEEEeCCCCEEEEEEe
Q 000294 304 NEVSHLLSAQIKRNEVSEGTWAYVKNGKYK-GDLAQVVYVNNARKRATVKLI 354 (1711)
Q Consensus 304 kEM~dLL~vkkk~~~Lk~GdwVRIKrGpYK-GDLAQVveVdenk~eVtVKLI 354 (1711)
+|+.+++....=...| ..+||-.|+|+ ||.-++.-|.--+..|+|++=
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 4556666543322334 35889999999 887776666656678999863
No 224
>KOG0339 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=20.90 E-value=80 Score=40.81 Aligned_cols=17 Identities=24% Similarity=0.342 Sum_probs=10.5
Q ss_pred eEEecCCc--eeecceEEE
Q 000294 406 VFENLDGM--MLKDGYLYK 422 (1711)
Q Consensus 406 ~f~i~~G~--~y~DGFLyK 422 (1711)
.|.+|+-- ||.-||++-
T Consensus 372 S~LV~DEadrmfdmGfe~q 390 (731)
T KOG0339|consen 372 SYLVLDEADRMFDMGFEPQ 390 (731)
T ss_pred eEEEEechhhhhccccHHH
Confidence 36666543 677788754
No 225
>PF02211 NHase_beta: Nitrile hydratase beta subunit; InterPro: IPR024690 Nitrile hydratases (EC:4.2.1.84) are unusual metalloenzymes that catalyse the hydration of nitriles to their corresponding amides. They are used as biocatalysts in acrylamide production, one of the few commercial scale bioprocesses, as well as in environmental remediation for the removal of nitriles from waste streams. Nitrile hydratases are composed of two subunits, alpha and beta, and they contain one iron atom per alpha beta unit []. This entry represents the structural domain of nitrile hydratase beta subunit which contains irregular array of helices in the N-terminal extension.; GO: 0018822 nitrile hydratase activity; PDB: 2DXB_H 2DD5_K 2DD4_H 2ZZD_B 2DXC_H 1AHJ_F 2ZPE_B 2ZCF_B 2D0Q_B 2CZ7_B ....
Probab=20.88 E-value=83 Score=36.70 Aligned_cols=34 Identities=18% Similarity=0.403 Sum_probs=19.0
Q ss_pred CCcccCCCeEEEecCC----------CCCceEEEEEEECCEEEE
Q 000294 553 MKVISLNDTARVSEGP----------SKDRQGIVKKIYRGILFI 586 (1711)
Q Consensus 553 gk~I~vGD~VKVIdGp----------~kGRqG~VlHIyRs~VFL 586 (1711)
--.|.+||.|+|.+-. ..|++|+|+.++..|+|-
T Consensus 132 ~~~F~vGd~Vrv~~~~~~~HtR~P~Y~rg~~G~I~~~~g~~~~p 175 (222)
T PF02211_consen 132 PPRFAVGDRVRVRNLPPPGHTRLPRYVRGKTGTIERVHGAFVFP 175 (222)
T ss_dssp S-SS-TT-EEEE-----SS--SS-GGGTT-EEEEEEEEEEE--H
T ss_pred CCCCCCCCEEEECCCCCCCcccccHhhCCCeeEEEEEecCCCCc
Confidence 3568999999998543 168999999888755553
No 226
>PRK00321 rdgC recombination associated protein; Reviewed
Probab=20.71 E-value=2.7e+02 Score=33.97 Aligned_cols=69 Identities=13% Similarity=0.118 Sum_probs=37.8
Q ss_pred EEEEEEeCCCCcEEEEEeccchhHHHHhcCCCCeEe------ccccccCHHHHHHHhhcccccccccCCCEEEEec
Q 000294 260 IISAFAVDHIKGFIFIEADKQCDINEACKGLSGIYY------SRLAPVPKNEVSHLLSAQIKRNEVSEGTWAYVKN 329 (1711)
Q Consensus 260 I~SVFvpd~lKGYIYIEA~kq~dVk~AIkGI~gVy~------~k~~pVPikEM~dLL~vkkk~~~Lk~GdwVRIKr 329 (1711)
++.|++ +.-.|||||.+-......+++.-++..++ ..+..-|...|+.-|.-......|..|+.+.++.
T Consensus 124 ~~~~~i-d~~~g~l~VdasS~k~aE~~l~lLrkslgsLpv~p~~~~~~p~~~mt~WL~~~~~P~~f~l~~~~eL~~ 198 (303)
T PRK00321 124 QTFAWI-DPVNGLIVVDAASAKKAEDVLALLRKSLGSLPVVPLSTEQSPEATMTEWLASGEAPAGFTLDDECELKS 198 (303)
T ss_pred eEEEEE-ECCCCEEEEeCCCHHHHHHHHHHHHHhcCCCceeccccCCCHHHHHHHHHccCCCCCCcEecceeEEec
Confidence 444443 56789999999876554444433332221 1223345567888885433334455555555543
No 227
>PRK06763 F0F1 ATP synthase subunit alpha; Validated
Probab=20.68 E-value=1.8e+02 Score=33.82 Aligned_cols=15 Identities=20% Similarity=0.313 Sum_probs=13.3
Q ss_pred CCCcccCCCeEEEec
Q 000294 552 SMKVISLNDTARVSE 566 (1711)
Q Consensus 552 ~gk~I~vGD~VKVId 566 (1711)
++..|.+||.|||-.
T Consensus 161 ~GQkFnVGDkVKV~~ 175 (213)
T PRK06763 161 KGQVFHVGDKVKVDM 175 (213)
T ss_pred cCCEEecCCEEEEEe
Confidence 689999999999973
No 228
>PRK06531 yajC preprotein translocase subunit YajC; Validated
Probab=20.39 E-value=2.4e+02 Score=30.10 Aligned_cols=42 Identities=17% Similarity=0.182 Sum_probs=32.3
Q ss_pred HHHHHHHhhcccccccccCCCEEEEecCcCCCCcEEEEEEeCCCCEEEEEEec
Q 000294 303 KNEVSHLLSAQIKRNEVSEGTWAYVKNGKYKGDLAQVVYVNNARKRATVKLIP 355 (1711)
Q Consensus 303 ikEM~dLL~vkkk~~~Lk~GdwVRIKrGpYKGDLAQVveVdenk~eVtVKLIP 355 (1711)
.+|+.+||. .|++|+.|.-..| ..|+|++|+++...|.|++ |
T Consensus 27 ~Ke~~em~~------sLk~GD~VvT~GG----i~G~V~~I~~~~~~v~le~-~ 68 (113)
T PRK06531 27 AQERQNQLN------AIQKGDEVVTIGG----LYGTVDEVDTEAKTIVLDV-D 68 (113)
T ss_pred HHHHHHHHH------hcCCCCEEEECCC----cEEEEEEEecCCCEEEEEE-C
Confidence 355566653 6788999987665 4589999999888899986 6
No 229
>COG5177 Uncharacterized conserved protein [Function unknown]
Probab=20.32 E-value=68 Score=41.09 Aligned_cols=18 Identities=28% Similarity=0.302 Sum_probs=14.4
Q ss_pred CCccccCCHHHHHHHHHH
Q 000294 175 IPKEEEMDEEEFDKMMEE 192 (1711)
Q Consensus 175 r~~eed~DaEelAe~lkE 192 (1711)
-+..+++.+||-++.|+|
T Consensus 437 ne~f~els~eee~rq~~e 454 (769)
T COG5177 437 NEGFEELSPEEEERQLRE 454 (769)
T ss_pred cccchhcChHHHHHHHHH
Confidence 456788889998888876
Done!